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| Status |
Public on Jun 07, 2023 |
| Title |
CB_Population3_Donor1_RNAseq_biorep1 |
| Sample type |
SRA |
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| Source name |
Blood
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Blood
cell type: Erythroblast
genotype: WT
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| Treatment protocol |
BM- and CB-derived erythroid progenitor cells were differentiated using the three phase EDM. The differentiation state of the cells was determined by staining the cells with fluorescently conjugated antibodies specific to erythroid surface markers: CD36-FITC (Becton, Dickinson, and Company, 20 µL/test), CD71-APC (Becton, Dickinson, and Company, 20 µL/test) and CD235a-BV421 (Becton, Dickinson, and Company, 5 µL/test). The antibody co-stained cells were subjected to FACS (Sony SH800, Sony Biotechnology) and were gated based on differential expression of CD36, CD71 and CD235a on different days of erythroid differentiation.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was isolated using RNeasy Mini Kit (QIAGEN)
20 ng RNA was used for library prep using the SMARTer UltraLow PolyA library kit for Illumina Sequencing (Clontech Laboratories Inc.).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
cb_and_bm_rnaseq_reads.txt
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| Data processing |
Reads were aligned to the hg19 ensemble transcriptome and gene-level counts computed using the RSEM-1.3.0 algorithm
Reads rounded to the nearest integer obtained from the rsem-calculate-expression function of the RSEM algorithm were used as input to the DESEQ2.0 algorithm for calculating differential expression. These rounded read counts are made available as a processed data file
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| Submission date |
Jun 05, 2023 |
| Last update date |
Jun 07, 2023 |
| Contact name |
Nisha Rajagopal |
| E-mail(s) |
nish.iitg@gmail.com
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| Phone |
6507202183
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| Organization name |
Syros Pharmaceuticals
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| Street address |
1069 Liberty Square Road
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| City |
Boxborough |
| State/province |
MA |
| ZIP/Postal code |
01719 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE234155 |
Chromatin Accessibility Mapping of Primary Erythroid Cell Populations Leads to Identification and Validation of NFIX As a Novel Fetal Hemoglobin Repressor |
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| Relations |
| BioSample |
SAMN35624362 |
| SRA |
SRX20594395 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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