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| Status |
Public on Mar 14, 2018 |
| Title |
UC_ab41 |
| Sample type |
SRA |
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| Source name |
descending colon pinch biopsy
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| Organism |
Homo sapiens |
| Characteristics |
tissue: colon
condition: UC active
barcode: #6 (ACG)
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| Treatment protocol |
The biopsies were immediately placed in RNAlater® Stabilization Solution (Ambion™, Life Technologies) and kept at 4°C for 24 hours before long term storage at -80 °C
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| Extracted molecule |
total RNA |
| Extraction protocol |
The RNA was extracted using PureLink® RNA Mini Kit (Ambion™, Life Technologies) with freshly made lysis buffer containing 1% 2-mercaptoethanol (Sigma).
CAGE libraries were prepared according to doi:10.1038/nprot.2012.005 with an input of 1500 ng of total RNA as starting material. CAGE libraries were prepared individually, but prior to sequencing four CAGE libraries with different barcodes were pooled and applied to the same sequencing lane. To compensate for the low complexity in the 5’ends of the CAGE libraries, 30% Phi-X spike-ins were added to each sequencing lane, as recommended by Illumina.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
CAGE |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Basecalling was done by CASAVA version 1.8.2. The first 11 nt from 5'-end and the last 13nt from 3'-end are trimmed off resulting in 25 nucleotide reads.
CAGE tags were mapped using the Bowtie4 (version 0.12.7) (to the hg19 assembly using v=2 and otherwise standard settings but allowing for multiple alignments. Subsequently, only uniquely mapping reads were retained. Reads that mapped to unconventional chromosomes or chrM were discarded.
5’ ends of the CAGE tags that mapped close to each other on the same strand were grouped into tag clusters (TCs), To remove cluster tails before subsequent expression analysis a queue based trimming algorithm was applied to all clusters, removing tags from the ends until a maximum of 10 % of the total number of tags has been trimmed away
Expression was calculated as Tags Per Million (TPM), by counting the tags per TSS and normalizing to library size (tags/total tags in library*1e6). Unless otherwise mentioned, only TCs having 1 or more TPM in at least 3 libraries were retained for further analysis. Information on batches can be obtained from supplementay data of the manuscript (to be determined).
Genome_build: hg19
Supplementary_files_format_and_content: ctss bed files for CAGE defined transcription start sites for each fastq file as processed by our pipeline
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| Submission date |
Feb 27, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Morana Vitezic |
| E-mail(s) |
mvitezic@gmail.com
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| Organization name |
University of Copenhagen
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| Department |
Department of Biology
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| Lab |
Sandelin Lab
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| Street address |
Ole Maaloes Vej 5
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| City |
Copenhagen N |
| ZIP/Postal code |
2200 |
| Country |
Denmark |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE95437 |
The transcription start site and enhancer landscape of the descending colon in inflammatory bowel disease |
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| Relations |
| SRA |
SRX2596133 |
| BioSample |
SAMN06467231 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2511602_hg19.CAGE_QHHH_IBD_b41.ctss.bed.gz |
20.5 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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