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Sample GSM1713290 Query DataSets for GSM1713290
Status Public on Jan 01, 2019
Sample type SRA
Source name hematopoietic progenitor cell derived from iPSC
Organism Homo sapiens
Characteristics cell surface marker: CD34+CD43+
cell type: hematopoietic progenitor cell derived from iPSC
Treatment protocol Wnt inhibitors were added on day 6 of the differentiation protocol. Half of the medium was refreshed every other day with inhibitors until cell harvest
Growth protocol iPSCs (passage 11) and ESCs cultured on MEF feeders in human ESC medium were manually dissociated and plated on 8 days old overgrown OP9 feeders to start differentiation. Cells were co-cultured with the OP9 feeders for 12-14 days in OP9 differentiation medium (Alpha MEM containing 10% FBS, 100 μM monothioglycerol and 50 μg/ml ascorbic acid) as described by Vodyanik, M. A. & Slukvin, II. (Curr Protoc Cell Biol 2007). Differentiated cells were dissociated with collagenase and Accutase (Innovative Cell Technologies) and subjected to cell sorting, RNA isolation and transposition assay. Cord blood CD34+ cells were isolated from donated cord blood units by immnuselection with CD34 magnetic microbeads (Miltenyi biotec).
Extracted molecule genomic DNA
Extraction protocol RNA was extracted with Qiagen RNeasy micro kit. ATAC-seq was carried out according to Buenrostro et al (Nat. Methods, 2013).DNA was purified using Zymo ChIP DNA Clean & Concentrator kit (Zymo Research).
The Agilent TapeStation or Bioanalyzer was used to determine RNA integrity (RIN) numbers prior to library preparation. Stranded mRNA-Seq libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit according to the manufacturer’s instructions (Illumina). Briefly, RNA with polyA tail was isolated using poly-T oligos conjugated to magnetic beads. mRNA was then fragmented and reverse-transcribed into cDNA. dUTPs were incorporated, followed by second strand cDNA synthesis. dUTP-incorporated second strand was not amplified. cDNA was then end-repaired, index adapter-ligated and PCR amplified. Purification of nucleic acids after each enzymatic steps was achieved by using AMPure XP beads (Beckman Coulter).
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2500
Description ATAC-Seq of hematopoietic progenitor cells derived from iPSCs treated with DMSO
Data processing Illumina Casava v1.8.2 software used for basecalling.
For RNA-Seq, paired-end reads were aligned to the human genome (hg19) with STAR (v2.2.0c) with default parameters. For ATAC-Seq, single end reads were aligned to the human genome (hg19) using Bowtie2 (v2.2.5) with default parameters. Only uniquely alignable reads were used for downstream analysis.
For RNA-Seq, Fragments Per Kilobase of exon per milion mapped reads were calculated using HOMER ( across annotated gene exons (RefSeq). ATAC-Seq reads were analyzed for peaks using HOMER by treated the experiments as default ChIP-Seq experiments.
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited text file, Columns: (1) RefSeq acc (2) chr (3) start (4) end (5) strand (6) length (7) copies (8) annotation (9-14) FPKM.
Submission date Jun 16, 2015
Last update date May 15, 2019
Contact name Christopher Benner
Organization name University of California, San Diego (UCSD)
Department Medicine
Street address 9500 Gilman Dr. MC 0640
City La Jolla
State/province California
ZIP/Postal code 92093-0640
Country USA
Platform ID GPL16791
Series (1)
GSE69932 Comparison of the transcriptome and chromatin state between human cord blood HSC and human iPSC derived hematopoietic progenitor using next-generation sequencing
BioSample SAMN03776950
SRA SRX1060088

Supplementary file Size Download File type/resource
GSM1713290_Sample3.ATAC-iPSC-HPC-DMSO.peaks.bed.gz 398.4 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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