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| Status |
Public on Oct 01, 2015 |
| Title |
4F-iTSC#1 |
| Sample type |
SRA |
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| Source name |
induced trophoblast stem cells
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6 x 129
passages: 20-25
cell type: induced trophoblast stem cells
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| Growth protocol |
TSCs and iTSCs were cultured under TX medium condition as decribed in PMID:24527396. mESCs were cultured in 2i medium and MEFs with DMEM supplemenated with 10% FBS medium
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were homogenized and RNA was harvested using the RNeasy kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Illumina bcl2fastq, v2.15.0.4, was used for transforming basecalls to fastq files.
Sequenced reads were quality trimmed at both ends with PHRED score threshold of 32, trimmed for adaptor sequence with Trim Galore, v0.3.7, and filtered for low-quality reads with the FASTX package, v0.0.13. Reads were then mapped to GRCm38 (mouse) using TopHat v2.0.11 with parameters -N 3 --read-gap-length 5 --read-edit-dist 8 --segment-length 18 --read-realign-edit-dist 5 --b2-i S,1,0.75 --b2-mp 3,1 --b2-score-min L,-0.5,-0.5.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using the Cufflinks package v2.2.1 with the programs cuffquant and cuffnorm, using parameters -b, -u and a masking file with all IG, TR, rRNA, tRNA, miRNA, snRNA, snoRNA and pseudo entries of the mouse GTF file.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include normalized counts and FPKM values at gene level for each sample. Fields are Ensembl_Gene_ID, Ensembl_Transcript_ID, Gene_Full_Name, Gene_Symbol, Gene_Biotype, EntrezGene_ID, RefSeq_mRNA, UCSC_ID, First_replicate_count, Second_replicate_count, First_replicate_fpkm, Second_replicate_fpkm. Multiple data is separated by semicolon. Missing data is represented by a question mark.
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| Submission date |
Jan 05, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Yossi buganim |
| E-mail(s) |
[email protected]
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| Organization name |
The Hebrew University of Jerusalem
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| Department |
Developmental Biology and Cancer Research
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| Lab |
Buganim
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| Street address |
Ein Karem 91120
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| City |
Jerusalem |
| ZIP/Postal code |
91120 |
| Country |
Israel |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE64684 |
Extensive Nuclear Reprogramming Underlies Lineage Conversion into Functional Trophoblast Stem-like Cells |
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| Relations |
| BioSample |
SAMN03275635 |
| SRA |
SRX836149 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1576851_S4_4F-iTSC_1.tsv.gz |
1.7 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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