EXPERIMENT_TITLE: GSM4700363: RT112 shNT; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: 20 million cells per condition were crosslinked with 1% formaldehyde for 10 min at room temperature. Nuclei were permeabilized. DNA was digested with MboI, the ends of the restriction fragments were labelled with biotinylated nucleotides, and then ligated. After revearsal of crosslinks, DNA was purified. Purified DNA was fragmented to obtain fragments of an average size of 300–400 bp using a Bioruptor Pico (Diagenode; 8 cycles; 20 sec ON/60 sec OFF). 3 µg of DNA per condition were used for library preparation. Biotinylated DNA was pulled down with Dynabeads MyOne T1 streptavidin beads. End-repair, A-tailing and the Illumina adaptors ligation were performed on beads. Libraries were amplified by 10 cycles of PCR and purified using AMPure XP beads. The concentration and size distribution of the Hi-C library after PCR amplification were determined using a Qbit fluorometer and visual exploration in an agarose gel. Hi-C libraries were then paired-end sequenced on an Illumina NextSeq500 (200M reads per library).
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Cohesin exists in two variants, containing either STAG1 or STAG2. STAG2 is one of the most commonly mutated genes in human cancer, and a major bladder cancer tumor suppressor. Little is known about how its inactivation contributes to tumor development. Here, we analyze the genomic distribution of STAG1 and STAG2 and perform STAG2 loss-of-function experiments using RT112 bladder cancer cells; we then analyze the resulting genomic effects by integrating gene expression and chromatin interaction data.  Overall design: One control and two STAG2-silenced conditions were evaluated.
SAMPLE_TITLE: RT112 shNT
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "Bladder cancer cell line"}, {"TAG": "shRNA", "VALUE": "control"}]
Pool_Member_@attributes_sample_title: RT112 shNT
RUN_SET_RUN_Pool_Member_@attributes_sample_title: RT112 shNT
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR12344686.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-22/SRR012/12344/SRR12344686/SRR12344686.lite.1", "size": "9051152351", "date": "2022-07-18 11:36:28", "md5": "8dff40b5a7d66f6d9fc177d8dcb6a928", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR12344686", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12344686/SRR12344686", "size": "15889182235", "date": "2020-07-29 15:43:57", "md5": "0678e2df56225fd8228ed83710cdec32", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "RT112_shNT_read2.fastq.gz", "size": "12304162701", "date": "2020-07-29 15:30:59", "md5": "a3fd5958c42aee34e6a06e2f5ce5cd29", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "RT112_shNT_read1.fastq.gz", "size": "11302075638", "date": "2020-07-29 15:25:41", "md5": "56dde97ba249a69308ecaf33f4fb2e83", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]