Lab Resource - Elsevier



GENERAL INFORMATION

Lab Resource: Stem Cell Line is a peer-reviewed article type detailing the establishment of new pluripotent stem cell lines derived from embryos, generated by SCNT and reprogramming or the establishment of genetically modified stem cell sub-lines.

This template should be used to describe more than one single cell line at the time.

To facilitate a quick turnaround, please do NOT to change the format of the paper and/or the tables. Do not remove any rows from the table. If any field is not relevant, please state: N/A. All information requested in the tables is mandatory except that which is stated as optional.

Further information on submission and FAQs are available at .

Formatting pre-submission checklist

| |Unique cell line identifier generated for all lines by using |

| |Resource table is fully completed |

| |Ethical committee approval number or equivalent proof of ethical approval/consent |

| |Words limits indicated in the template |

| |Only 1 main multi-panel figure provided |

| |No figure legend. Reference to images included in Resource details section |

| |Max 5 references |

| |Table 1,2 and 3 have been filled in and added at the end of the manuscript or as separate Word files |

| |All instruction text formatted in grey and italics has been deleted from the main manuscript (i.e. Resource utility (Max 50 words) |

| |Please explain the rationale for generating this resource and resource utility.) |

Lab Resource: Multiple Stem Cell Lines - template

Title: Brief title, should contain number of lines generated and common feature of cell lines (e.g. Generation of X lines from Parkinson patients; Generation of 6 clones from…; Generation of control and genetically modified line from…)

Authors:

Affiliations:

Abstract: (Maximum 100 words) 2-3 sentence description of resource

Resource Table: Please fill in right-hand column of the table below. All information requested in the table is MANDATORY, except where otherwise indicated. Manuscripts with incomplete or incorrect information will be sent back to author

|Unique stem cell lines identifier |Set up an account at |

| |The system generates and guarantees a unique name based on: researcher’s institution; |

| |type of cell line type (iPSC/hESC); additional clone from patient or subclone of a |

| |line already present in the database. |

| |Include all the unique cell lines name generated HERE. For example: |

| |Unique cell line name 1 |

| |Unique cell line name 2 |

| |Unique cell line name 3 etc. |

|Alternative names of stem cell lines |[Optional] Names commonly used by the researcher |

| |Optional name from cell line 1 (Unique cell line 1 name) |

| |Optional name from cell line 2 (Unique cell line 2 name) |

| |Optional name from cell line 3 (Unique cell line 3 name) etc. |

|Institution |Institution where the cell line was generated |

|Contact information of distributor |Name of contact person and email to request more information on the cell line |

|Type of cell lines |ESC , iPSC, SNT (Somatic Transfer lines) |

|Origin |Species, e.g. human, mouse, rat, monkey, pig, etc. |

| |For human, also include |

|Cell Source |[MANDATORY for iPSC] Original cell type induced: e.g. fibroblasts, blood, etc. |

|Clonality |[MANDATORY] Clonal or mixed |

|Method of reprogramming |[MANDATORY for iPSC] e.g. Transgene free, lentivirus, piggyBAC |

|Multiline rationale |e.g. isogenic clones, same disease non-isogenic cell lines, control and disease pair, |

| |gene corrected clones, etc. |

|Gene modification |YES/NO |

|Type of modification |e.g. Spontaneous mutation, Induced mutation, Gene Correction, Transgene expression |

| |(resistance, reported), etc. |

|Associated disease |For patient derived lines please indicate the name of disease |

|Gene/locus |If applicable, use appropriate standard nomenclature |

| |of locus/gene of mutation/insertion |

|Method of modification |e.g. Zn fingers, TALENS, CRISPR etc |

|Name of transgene or resistance |if applicable , transgene or Resistance gene inserted |

|Inducible/constitutive system |e.g. TET , ROSA, AAV |

|Date archived/stock date |Date cell line archived or deposited in repository |

|Cell line repository/bank |If line has been registered in a repository and/or physically deposited in a stem cell|

| |bank, include the name of the public or commercial repository/bank and the accession |

| |number or direct URL to the database record |

|Ethical approval |[MANDATORY for human ESC and iPSC lines] Please list Ethical committee name and |

| |approval number. |

| |If original line (e.g. fibroblast, blood cells etc.) has been obtained by a commercial|

| |provider, please provide license detail of provider ethical license/patient consent. |

Resource utility (Max 50 words)

Please explain the rationale for generating these resources and resources utility.

Resource Details (Maximum 500 words)

Fill Table 1 with summary/abbreviations of lines generated. Describe summary of lines generation and characteristics, link statements to the specific images/panels shown in the Figure 1 and to the key relevant data presented in Table 2.

Materials and Methods (Maximum 500 words)

Brief summary of culture conditions, methodology used for cell line generation, genetic modification, and analyses performed. Describe in detail any new methodology used, summarise established protocols. Please include details of antibodies and primers separately in Table 3.

References (Max 5 references)

Include only references of direct relevance for the description of the cell lines or where the cell lines have already been used or studied. Do not include references to general protocols for iPSC derivation or analysis or to other Lab Resource articles submitted or previously published in Stem Cell Research if not directly relevant for the description of the current cell lines (e.g. reference to specific data or method).

Additional files:

Figure 1 (Maximum 1 multi-panel figure)

Lab Resource articles should include 1 figure maximum. Collate all images (e.g. karyotype, pluripotency, differentiation) in a multi-panel figure. Upload figure as pdf, .tiff or .jpeg file with a resolution of at least 300 dpi and print size of minimum 148x210mm, 5.83”x8.27” (A5 size) and maximum 210x297mm, 8.27”x11.7” (A4 size).

Main figure 1 should always show images of pluripotency and differentiation for all lines side-by-side. Optionally, karyotype and additional images can be submitted as Supplementary image 1. No more than 1 supplementary image will be accepted for publication.

For immunohistochemistry/immunofluorescence, make sure that nuclear vs cytosolic staining is clearly identifiable. IMPORTANT: include scale bars into all microscopy images.

Do not include a figure legend. The Resource Details section should be used to describe the figure and should include references to all image panels shown in the figure.

Table 1, 2 and 3

Tables are mandatory, please fill in the tables and include them at the end of your manuscript or as separate Word files at submission. The tables will be automatically incorporated into the text at proof stage. Template for both tables is included at the end of this file.

STR analysis

STR analysis (as summary table or full analysis) should be uploaded under the file type “STR analysis”– this file is mandatory for validation of each cell line, it will be archived but will not be published alongside the article to protect identity of human subjects

Supplementary files

Supplementary files can be uploaded at submission, but should be limited to the following:

• Supplementary figure 1: karyotype, additional images that could not fit into main image, excluding pluripotency and differentiation analysis

• Analysis certificates (mycotest, etc)

Table 1: Summary of lines

|iPSC line names |Abbreviation in figures |Gender |Age |

|Morphology |Photography |Visual record of the line: e.g. normal/|e.g. not shown but available with |

| |[mandatory] |abnormal |author |

|Phenotype |Qualitative analysis (i.e. |Assess staining/expression of |e.g. Figure 1 panel A |

| |Immunocytochemistry) |pluripotency markers: Oct4, Nanog, Sox2| |

| |[mandatory] | | |

| |Quantitative analysis (i.e. |Assess % of positive cells or |e.g. Figure 1 panel B |

| |Immunocytochemistry counting, Flow |transcripts for antigen & cell surface| |

| |cytometry, RT-qPCR) |markers e.g. Oct3/4: 97%Tra 1-60: | |

| |[mandatory] |98%SSEA-4: 99%SSEA-1: 6% | |

|Genotype |Karyotype (G-banding) and resolution| E.g. 46XX, |e.g Figure 1 panel C |

| |[mandatory] |Resolution 450-500 | |

|Identity |Microsatellite PCR (mPCR) OR |DNA Profiling e.g. Performed/not |e.g. supplementary file 2 |

|  |STR analysis |performed | |

| |[mandatory] | | |

| | |e.g. specific how many sites tested, |e.g. submitted in archive with |

| | |and if matched or not |journal |

|Mutation analysis (IF APPLICABLE) |Sequencing |e.g. state if heterozygous/homozygous, |e.g. Figure 1 panel D |

|  | |type of mutation | |

| |Southern Blot OR WGS |e.g. number of insertions in genome, | e.g. sequencing deposited at |

| | |off-target effects |DATABASE : recordID |

|Microbiology and virology |Mycoplasma |E.g. Mycoplasma testing by RT-PCR or |e.g. figure 1/supplementary |

| |[mandatory] |luminescence. Negative/Positive | |

|Differentiation potential |e.g. Embryoid body formation OR |Describe expression of genes in |e.g Figure 1 panel D and E |

| |Teratoma formation OR Scorecard OR |embryod bodies: e.g. muscle actin, | |

| |Directed differentiation |β-tubulin and α-feto protein. OR proof | |

| |[mandatory] |of three germlayers formation | |

|Donor screening (OPTIONAL) |HIV 1 + 2 Hepatitis B, Hepatitis C |Negative/Positive | e.g. not shown but available with |

| | | |author |

|Genotype additional info (OPTIONAL) |Blood group genotyping |DNA analysis e.g. AA | e.g. not shown but available with |

| | | |author |

| |HLA tissue typing |HLA typed Class I and Class II | e.g. not shown but available with |

| | | |author |

Table 3: Reagents details

RRID Requirement for antibodies: use to retrieve RRID for antibodies and include ID in table as shown in examples.

|Antibodies used for immunocytochemistry/flow-citometry |

|  |Antibody |Dilution |Company Cat # and RRID |

|e.g. Pluripotency Markers |e.g. Rabbit anti-OCT4 |e.g. 1:300 |e.g. Cell Signaling Technology Cat# 9656, |

| | | |RRID:AB_1658242 |

|e.g. Differentiation Markers |e.g. Mouse anti-PAX6 |e.g. 1:100 |e.g. DSHB Cat# pax6, RRID:AB_528427 |

|e.g. Secondary antibodies |e.g. CF488A Goat Anti-Mouse IgG |e.g. 1:1000 |e.g. Biotium inc Cat# 20010, RRID:AB_10559812 |

|  | |  | |

| | | | |

|Primers |

| |Target |Forward/Reverse primer (5′-3′) |

|e.g. Episomal Plasmids (qPCR) |e.g. OCT4 Plasmid |e.g. CATTCAAACTGAGGTAAGGG/ TAGCGTAAAAGGAGCAACATAG |

|e.g. Pluripotency Markers (qPCR) |e.g. NANOG, etc | |

|e.g. House-Keeping Genes (qPCR) |e.g. HSP90AB1, etc | |

|e.g. Genotyping | | |

|e.g. Targeted mutation | | |

|analysis/sequencing | | |

| | | |

| | | |

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