|
| Status |
Public on Jul 30, 2021 |
| Title |
STAG2(fl/fl)_#3 [RNA-seq] |
| Sample type |
SRA |
| |
|
| Source name |
Thymus
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl/6
genotype: Foxn1-cre(-/-) STAG2(fl/fl)
tissue: Thymus
cell type: mTECs
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were isolated by tissue digestion and fluorescence activated cell sorting for viable CD45-Ly51loMHCIIhi as mTECs.
1,000 mTECs were sorted directly into lysis buffer (TCL with 1% 2-Mercaptoethanol) and Smart-seq2 libraries were prepared by the Broad Technology Labs, and were sequenced using the Broad Genomics Platform. Total RNA was captured on RNAClean XP beads followed by selection of mRNA using an anchored oligo(dT) primer. RNA was converted into cDNA via reverse transcription and first-strand cDNA was subjected to limited PCR amplification followed by transposon-based fragmentation using the Nextera XT DNA Library Preparation Kit. Samples were amplified and barcoded with PCR followed by sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
000008573069_B09
|
| Data processing |
Reads were mapped to the mouse reference genome (mm10) with STAR 2.5.4
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM16)
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts
|
| |
|
| Submission date |
Jul 27, 2021 |
| Last update date |
Jul 30, 2021 |
| Contact name |
CBDM Lab |
| E-mail(s) |
cbdm@hms.harvard.edu
|
| Phone |
617-432-7747
|
| Organization name |
Harvard Medical School
|
| Department |
Microbiology and Immunobiology
|
| Lab |
CBDM
|
| Street address |
77 Avenue Louis Pasteur
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE180935 |
Aire regulates chromatin looping by evicting CTCF from domain boundaries and favoring accumulation of cohesin on super-enhancers [RNA-seq] |
| GSE180937 |
Aire regulates chromatin looping by evicting CTCF from domain boundaries and favoring accumulation of cohesin on super-enhancers |
|
| Relations |
| BioSample |
SAMN20436982 |
| SRA |
SRX11570218 |
