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| Status |
Public on Jun 30, 2022 |
| Title |
F-HDAC-4.F04 |
| Sample type |
SRA |
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| Source name |
Dermal fibroblasts, neonatal
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| Organism |
Homo sapiens |
| Characteristics |
treatment: TSA
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| Treatment protocol |
Three treatment groups were made, with 1) untreated, 2) 1 uM TSA for 6 hours, and 3) 1 mM VPA for 6 hours.
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| Growth protocol |
Cells were cultured in DMEM high glucose medium supplemented with 10% inactivated fetal bovine serum, 100 U/mL penicillin, 100 ug/mL streptomycin, and 1 mM sodium pyruvate.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Single cell RNA extraction and cDNA amplification were performed according to the C1 CAGE procedure deposited in Fluidigm’s Script Hub (https://www.fluidigm.com/c1openapp/scripthub/script/2015-07/c1-cage-1436761405138-3). For bulk CAGE, total RNA was extracted using RNeasy Mini Kit.
For C1 CAGE, the library was constructed following the same C1 CAGE procedure outlined in the above link. For bulk CAGE, libraries were constructed using the published nAnT-iCAGE protocol.
The prepared libraries were sequenced on Illumina HiSeq 2500 (50 nt single read).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
CAGE |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
C1 CAGE
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| Data processing |
Remove low quality and rDNA reads
Map to the human genome (hg38) using BWA version 0.5.9 (r16) with default parameters, except: : (1) maximum long deletion (-d) = 10 for bwa_aln and (2) maximum number of alignments (-n) = 100 for bwa_samse
Convert mapped reads to CAGE Transcription Start Sites (CTSS) and read in using CAGEfightR package in R (4.0.3). For C1 CAGE, keep only those that are expressed in at least 3 samples. Merge reads within 20bp of one another.
Map processed reads to GENCODE v31 annotation to the nearest 1kbp up/100 bp down, and remove those overlapping known axons
Annotate enhancers using our custom enhancer set, and quantify raw expression counts by summing the overlapping reads
Assembly: hg38
Supplementary files format and content: *_CTSS.tar.gz: CAGE CTSS files (CAGE_Transcription Start Sites in BED format)
Supplementary files format and content: *_annotations.tar.gz: sample and CAGE tag cluster annotation tables
Supplementary files format and content: *_expression_tables.tar.gz: raw and normalized expression tables for CAGE tag clusters
Supplementary files format and content: gold_enhancers.bed.gz: BED file of the curated gold enhancer set
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| Submission date |
Apr 05, 2022 |
| Last update date |
Jun 30, 2022 |
| Contact name |
Andrew Tae-Jun Kwon |
| Organization name |
RIKEN
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| Department |
IMS
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| Lab |
LARGNA
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| Street address |
1-7-22 Suehiro-cho, Tsurumi-ku
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| City |
Yokohama |
| State/province |
Kanagawa |
| ZIP/Postal code |
230-0045 |
| Country |
Japan |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE200186 |
Bulk and single cell profiling of the transcriptional response to Trichostatin A and Valproic Acid using CAGE |
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| Relations |
| BioSample |
SAMN27307238 |
| SRA |
SRX14744932 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6020911_FIB_3.F-HDAC-4-F04.ctss.bed.gz |
123.9 Kb |
(ftp)(http) |
BED |
| GSM6020911_FIB_4.F-HDAC-4-F04.ctss.bed.gz |
122.1 Kb |
(ftp)(http) |
BED |
| GSM6020911_FIB_5.F-HDAC-4-F04.ctss.bed.gz |
126.3 Kb |
(ftp)(http) |
BED |
| GSM6020911_FIB_6.F-HDAC-4-F04.ctss.bed.gz |
122.2 Kb |
(ftp)(http) |
BED |
| GSM6020911_FIB_7.F-HDAC-4-F04.ctss.bed.gz |
118.7 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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