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| Status |
Public on Feb 29, 2024 |
| Title |
HA_NGFR_1 |
| Sample type |
SRA |
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| Source name |
HA CD8 CAR-T
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| Organism |
Homo sapiens |
| Characteristics |
tissue: HA CD8 CAR-T
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| Treatment protocol |
All cells in this sample were treated the same, the only difference between the cells is which virus they were transduced with (CAR, transcription factor)
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| Growth protocol |
Primary human T cells were grown in AIM-V media supplemented with 5% FBS, 10mM HEPES, 1x Penicillin-Streptomycin-Glutamate, and 100U/mL recombinant human IL-2. T cells were activated with anti-CD3/CD28 beads immediately after thawing from liquid nitrogen, then at 48 and 72 hours post-activation were transduced with retroviruses containing CARs and transcription factors of interest. 96 hours post-activation, beads were removed; subsequently, T cells were resuspended at a concentration of 0.5e6 cells/mL every 2-3 days in the above described media. For experiments requiring magnetic sorting, isolations were performed using Miltenyi MACS or StemCell EasySep magnetic sorting systems. 150,000 T cells were slow-frozen in BamBanker cell preservation media prior to ATAC-seq specific preparation.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei were isolated with ChIP lysis buffer (1% Triton x-100, 0.1% SDS, 150 mM NaCl, 1mM EDTA, and 20 mM Tris, pH 8.0).
DNA was quantified by Qubit and 10 ng DNA was used for sequencing library construction with the Ovation Ultralow Library System V2 (Tecan) using 12 PCR cycles.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Reads were trimmed for quality and adapter sequences using fastQC.
Trimmed reads were aligned to the mm10 reference genome using bowtie2.
Aligned reads were deduplicated using Picard.
Peakswere called using MACS2 from the paired endbed file (bedpe) using a false discovery thresh-old of 0.05 (-q 0.05).
Normalized bigwig files were created by normalizing the coverage track of the bedpe file by reads in peaks.
Assembly: hg38
Supplementary files format and content: Normalized bigwig files.
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| Submission date |
Feb 08, 2024 |
| Last update date |
Feb 29, 2024 |
| Contact name |
Katherine Paige Mueller |
| E-mail(s) |
[email protected]
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| Phone |
3037758187
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| Organization name |
Children's Hospital of Philadelphia
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| Department |
Pediatrics
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| Lab |
Weber Lab
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| Street address |
3501 Civic Center Blvd
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| City |
Philadelphia |
| State/province |
Pennsylvania |
| ZIP/Postal code |
19104-3820 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE255415 |
FOXO1 is a master regulator of CAR T memory programming [ATAC_FOXO1_OE] |
| GSE255416 |
FOXO1 is a master regulator of CAR T memory programming |
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| Relations |
| BioSample |
SAMN39893866 |
| SRA |
SRX23579600 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8072205_HA.28z_NGFR_1_TileSize-5_NormMethod-ReadsInTSS.bw |
100.4 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
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