title: 133154-hg19: Human snATAC FANS rep 2

extract_protocol:
Three separate pieces of tissue were cut from a single human skeletal muscle sample (weighing 60mg, 50mg and 50mg; quadriceps femoris muscle group). Nuclei were isolated using a modified version of the ENCODE protocol (https://github.com/porchard/muscle-protocols/blob/master/Supplemental_Protocol_S1.pdf) (The ENCODE Project Consortium 2012, 2012), customized from Step 5 onwards to accommodate FANS (Fluorescence assisted nuclei sorting). In step 5, the nuclei were resuspended in 700 µL of Sort buffer (1% BSA, 1mM EDTA in PBS) and filtered through a 30 µm filter. Three different nuclei isolations were performed and the nuclei suspended in sort buffer were mixed, pooled together and divided into two groups, one with FANS and one without FANS. FANS nuclei were sorted according to the previously published FANS protocol using DRAQ7 (Preissl et al. 2018). DRAQ7 (0.3mM from Cell Signaling Technology) was added to the FANS nuclei suspension, at 100 fold dilution to get a final concentration of 3 μM. Nuclei were gently mixed and incubated for 10 minutes on ice. Nuclei were analyzed in the presence of DRAQ7 and sorted for high DRAQ7 positive signal using Beckman Coulter’s Astrios MoFlo. We followed the gating strategy outlined in the FANS protocol (Preissl et al, 2018). The sorted nuclei were collected in a recovery buffer (5% BSA in PBS). The nuclei with and without FANS were spun at 1000g for 15 min at 4°C. The nuclei were resuspended in 100 µL of 1X diluted nuclei buffer and counted in the Countess II FL Automated Cell Counter.
The nuclei were submitted to the Universiy of Michigan Advanced Genomics core for processing on the 10x Genomics Chromium platform. Nuclei were loaded at 15.4K nuclei/well.


title: GC0185 Gastric Cancer

status: Public on Jun 23 2021

type: RNA

city: Kanagawa

first: Satoko

last: Takizawa

address: kamakurashi

country: Japan

institute: Toray industries inc

hyb_protocol: Hybridized for 16 h at 32 ºC with rotary shaker (250 rpm). Hybridization buffer and washing protocol was attached in the 3D-Gene® miRNA oligo chip kit.

scan_protocol: 3D-Gene® Scanner (Toray Industries, Inc.) was used for scanning. Images were quantified using Extraction version 2.0.0.6 (Toray Industries, Inc.).

data_processing: The presence of miRNA was determined based on a corresponding microarray signal of greater than [the mean + 2 × standard deviation] of the negative controls signal, of which the top and bottom ranked ones by signal intensity were removed. Once a miRNA was considered present, the mean signal of the negative controls of which the top and bottom 5% ranked by signal intensity were removed was subtracted from the miRNA signal. When the signal value was negative (or undetected) after background subtraction, the value was replaced by 0.1 on a base 2 logarithm scale.

molecule: total RNA

organism: Homo sapiens

source_name: Serum

label_protocol: miRNA was labeled using 3D-Gene® miRNA Labeling kit in accordance with the manufacturer's instructions.

extract_protocol: Total RNA was extracted each from 300uL serum samples using 3D-Gene® RNA extraction reagent from liquid sample kit (Toray Industries, Inc.).

tag: disease state

value: Gastric Cancer

tag: Sex

value: Female

tag: age

tag: Stage

value: IA

tag: histological subtype

value: undiff


title: GC0175 Gastric Cancer

value: Male


title: GC0176 Gastric Cancer

value: diff


title: GC0173 Gastric Cancer


title: 133153-hg19: Human snATAC no FANS rep 2

type: SRA

city: Ann Arbor

first: Stephen

last: Parker

state: MI

address: 100 Washtenaw Avenue

country: USA

institute: University of Michigan

description: ***Raw data are unavailable due to patient privacy concerns***

library_source: genomic

data_processing:
Adapters were trimmed using cta (v. 0.1.2; https://github.com/ParkerLab/cta)
For single-nucleus experiments, we used a custom python script (available in https://github.com/porchard/snATACseq-NextFlow) for 10x Genomics barcode correction
Reads were mapped using BWA-MEM (-I 200,200,5000 -M; v. 0.7.15-r1140). If the sample contained only human nuclei, we used the hg19 reference genome. If the sample contained human and rat nuclei, we mapped the library twice, once to hg19 and once to rn6
For single-nucleus experiments, we filtered out nuclei corresponding to 10x barcodes with fewer than 1000 alignments in the BAM file
We used Picard MarkDuplicates to mark duplicates, and filtered to high-quality, non-duplicate autosomal read pairs using SAMtools view with flags ‘-f 3 -F 4 -F 8 -F 256 -F 1024 -F 2048 -q 30’
We anonymized the BAM files using anonymizeBAM (--strict; v. 0.4.5)
We generated single-end BED files using bedtools bamtobed
We called peaks and generated bedGraph files using macs2 callpeak -f BED --SPMR --nomodel --shift -100 --extsize 200 -B --broad --keep-dup all
We generated the bigWig file from the bedGraph file using bedGraphToBigWig from the UCSC genome browser
Genome_build: hg19 (human) and rn6 (when rat nuclei were included in the library)
Supplementary_files_format_and_content: ATAC-seq read mapping locations, anonymized (BED files)
Supplementary_files_format_and_content: ATAC-seq signal tracks (bigWig files)
Supplementary_files_format_and_content: ATAC-seq peak calls (broadPeak files)

molecule: genomic DNA

source_name: Skeletal muscle

tag: tissue

value: Skeletal muscle


title: 133151-hg19: Human snATAC no FANS rep 1


title: 133152-hg19: Human snATAC FANS rep 1


title: GC0167 Gastric Cancer


title: GC0169 Gastric Cancer


title: HSM1.bulk.rep1.hg19: Human bulk ATAC, sample HSM1 rep 1

extract_protocol:
2 tissue pieces weighing 99.4 mg and 80.7 mg were cut from one human skeletal muscle sample (HSM1) and 2 pieces weighing 67.6 mg and 103.5 mg were cut from a second human skeletal muscle sample (HSM2). Each of the samples was cut on dry ice using frozen scalpel to prevent thawing. The samples were pulverized using a CP02 cryoPREP automated dry pulverizer (Covaris 500001). For bulk ATAC-seq we followed the nuclei isolation protocol outlined in https://github.com/porchard/muscle-protocols/blob/master/Supplemental_Protocol_S2.pdf, except in the final step the nuclei were resuspended in 250 μL of 1% BSA in PBS.
The nuclei were counted in  Countess II FL Automated Cell Counter, and the appropriate volume of the suspension for 50K nuclei was spun down and used for the downstream transposition reaction (a modified version of the ENCODE protocol; https://github.com/porchard/muscle-protocols/blob/master/Supplemental_Protocol_S3.pdf) (The ENCODE Project Consortium 2012, 2012)


title: GC0171 Gastric Cancer


title: GC0184 Gastric Cancer


title: HSM1.bulk.rep2.hg19: Human bulk ATAC, sample HSM1 rep 2


title: GC0168 Gastric Cancer


title: GC0172 Gastric Cancer

value: II


title: NPC EHMT1_WT CF10 cells

city: North Coogee

first: Denise

last: Anderson

state: WA

address: 71 Caledonia Loop

country: Australia

institute: INSiGENe Pty Ltd

library_source: transcriptomic

data_processing:
Raw sequencing reads were processed using the ENCODE rna-seq pipeline (https://github.com/ENCODE-DCC/rna-seq-pipeline) via the Cromwell wrapper software caper (https://github.com/ENCODE-DCC/caper)
Within the ENCODE pipeline, reads were aligned to GRCh38 using the STAR aligner (v2.5.1b) and known transcripts were quantified using Kallisto (v0.44.0)
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed text files contain transcript-level abundance estimates from Kallisto

source_name: KOLF2 iPSCs_EHMT1_WT_NPC

growth_protocol: CF1-CF6, TeSR-E8 media (STEMCELLL technologies); CF7-CF12, STEMdiff Neural Progenitor Medium (STEMCELL technologies)

extract_protocol:
Rneasy minikit, with DNASE on column treatment, QIAGEN
Sureselect strand-specific library preparation, Illumina

treatment_protocol: STEMdiff SMADi Neural Induction Kit (STEMCELL technologies, #08581)

tag: cell line

value: KOLF2 iPSCs

tag: tissue source

value: skin tissue

tag: crispr variant

tag: differentiation cell type

value: NPC

tag: clone pair


title: NPC EHMT1_WT CF11 cells


title: GC0179 Gastric Cancer


title: NPC EHMT1_SNV CF8 cells

source_name: KOLF2 iPSCs_EHMT1_SNV_NPC


title: GC0174 Gastric Cancer


title: GC0166 Gastric Cancer


title: iPSC EHMT1_WT CF5 cells

source_name: KOLF2 iPSCs_EHMT1_WT_iPSC

value: iPSC


title: iPSC EHMT1_WT CF6 cells


title: MCF-7 cells, KD 1

city: Taipei

first: Liang-Chuan

last: Lai

state: Taiwan

address: 1 Jen-Ai Road, Sec 1

department: Physiology

country: Taiwan

institute: National Taiwan University

description:
SAMPLE 4
replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The probe intensities were normalized by quantile algorithm based on the intensity distribution among all slides.

label: biotin

label_protocol: Biotinylated cRNA were prepared with IlluminaTM TotalPrepTM RNA Amplification Kit (Ambion).

extract_protocol: Total RNA was extracted using NucleoZOL reagent (Machery-Nagel, Düren, Germany) according to the manufacturer’s protocol.

treatment_protocol: MCF-7 cells were transfected with 100 nM siRNA against MTORT1 for 48 hours.

tag: transfection

value: siRNA against MTORT1


title: GC0164 Gastric Cancer


title: iPSC EHMT1_WT CF4 cells


title: GC0165 Gastric Cancer


title: NPC EHMT1_SNV CF9 cells


title: NPC EHMT1_WT CF12 cells


title: NPC EHMT1_SNV CF7 cells


title: GC0163 Gastric Cancer


title: GC0170 Gastric Cancer


title: iPSC EHMT1_SNV CF3 cells

source_name: KOLF2 iPSCs_EHMT1_SNV_iPSC


title: iPSC EHMT1_SNV CF2 cells


title: iPSC EHMT1_SNV CF1 cells


title: GC0161 Gastric Cancer

value: IB


title: GC0160 Gastric Cancer


title: CD14 monocytes [33]

city: SAINT LOUIS

last: Zhang

state: MO

address: 425 S Euclid Ave

department: Pathology and Immunology

institute: Washington University in St. Louis

data_processing:
Illumina’s bcl2fastq software used for basecalling.
RNA-seq reads were then aligned to the Ensembl release 76 top-level assembly of the human genome (GRCh38) along with the SARS-CoV-2 reference genome with STAR version 2.0.4b6 with the parameters --outStd BAM_Unsorted --outMultimapperOrder Random --outSAMtype BAM Unsorted --outSAMunmapped None --outSAMmapqUnique 60 --outFilterScoreMinOverLread 0 --outFilterMatchNmin 20 --outFilterMatchNminOverLread 0 --outFilterMismatchNoverLmax 0.1 --clip3pAdapterSeq AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAG AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA. Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.57 to Ensembl and SARS-CoV-2 gene models. Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected. Differential expression analysis to determine genes that differed with severe disease for each cell type and both male and females was performed using DESeq2 (v1.24)8. Genes without at least 10 read counts across all samples were removed prior to analysis. Gene Set Enrichment Analysis (v4.0.3)9 was performed using the GSEAPreranked tool against the Hallmark gene set (v7.2). Genes were ranked using the sign of the fold change times the -log10(p-value) and otherwise default parameters.
Genome_build: GRCh38
Supplementary_files_format_and_content: .gene_counts.txt: Tab-delimited text files include count, CPM and RPKM values.

source_name: Peripheral blood mononuclear cells

extract_protocol:
Cryopreserved peripheral blood mononuclear cells (PBMCs) from COVID-19 patients were thawed and washed with HBSS with 2mM EDTA and 0.04% LPS-free BSA; then blocked with 5% goat serum and stained on ice with anti-CD14-APC/Cy7, anti-CD16-PE/Cy7, anti-CD15 PerCP/Cy5.5, and anti-CD56-Alexa Fluor 700 for 30 minutes and re-suspended in the aforementioned HBSS buffer. Dead cells were excluded based on positive Helix NPTM Green staining. The cells were then sorted straight into Trizol by FACS Aria II. Total RNA was isolated as per Trizol protocol. RNA of each sample was sequenced at the Genome Technology Access Center of the McDonnell Genome Institute at Washington University in St. Louis.
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation. Library preparation was performed with 10ng of total RNA with a Bioanalyzer RIN score greater than 8.0. ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

tag: diagnosis

value: COVID

tag: covid severity

value: Severe COVID with ICU

tag: cell type

value: CD14 monocytes


title: CD14 monocytes [32]

description: Non-COVID control

value: Non-COVID


title: GC0155 Gastric Cancer

value: Gastric Cancer

value: Female


title: CD14 monocytes [28]

description: Non-COVID control


title: CD14 monocytes [27]

description: Non-COVID control


title: CD14 monocytes [31]

description: Non-COVID control


title: CD14 monocytes [29]

description: Non-COVID control


title: CD14 monocytes [26]

description: Non-COVID control


title: CD14 monocytes [30]

description: Non-COVID control


title: CD14 monocytes [23]

description: Non-COVID control


title: GC0153 Gastric Cancer

value: undiff


title: GC0154 Gastric Cancer

value: Male

value: IA


title: CD14 monocytes [22]

description: Non-COVID control


title: GC0157 Gastric Cancer


title: GC0156 Gastric Cancer


title: GC0158 Gastric Cancer


title: GC0159 Gastric Cancer


title: GC0150 Gastric Cancer


title: GC0149 Gastric Cancer


title: GC0151 Gastric Cancer

value: diff


title: GC0152 Gastric Cancer


title: GC0148 Gastric Cancer


title: GC0146 Gastric Cancer


title: CD14 monocytes [20]


title: CD14 monocytes [25]

description: Non-COVID control


title: GC0145 Gastric Cancer


title: CD14 monocytes [19]

value: Mild COVID without hospitalization


title: CD14 monocytes [17]


title: CD14 monocytes [15]


title: CD14 monocytes [13]


title: CD14 monocytes [16]


title: GC0215 Gastric Cancer


title: GC0142 Gastric Cancer


title: GC0144 Gastric Cancer


title: CD14 monocytes [11]


title: CD14 monocytes [9]


title: GC0147 Gastric Cancer


title: CD14 monocytes [21]


title: GC0141 Gastric Cancer


title: CD14 monocytes [8]


title: age-matched non-carrier wild-type (WT) 2

city: Los Angeles

first: Xia

last: Yang

state: California

address: 610 Charles E. Young Drive East

department: Integrative Biology and Physiology

institute: University of California, Los Angeles

data_processing:
Reads corresponding to low quality barcodes with quality score less than 10 was removed using DropSeq Tools version 1.12. Next, any occurrence of the SMART adapter sequence or polyA tails found in the reads was trimmed
Cleaned reads were converted back to fastq format and were aligned to the mouse reference genome mm10 using STAR-2.5.0c
A percentage of the Chemgenes barcoded beads which contain the UMIs and cell barcodes were anticipated to have synthesis errors, which were assessed using the function DetectBeadSynthesisErrors in DropSeq Tools.
A digital gene expression matrix for each sample was generated using DropEst (Petukhov et al., 2018), where each row is the read count of a gene and each column is a unique single cell.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Mus musculus

source_name: Brainstem

extract_protocol:
Each tissue was finely dissected and incubated in Hibernate A without calcium (BrainBits, Springfield, IL, USA) supplemented with 12 mg papain (Worthington, Lakewood, NJ, USA). This solution is then transferred to a shaker-incubator (set to 30 °C and 60 rpm) for 30 min. After 30 min, using a Pasteur pipette, the solution is triturated three times to release cells from the tissue remnants, and transferred to a new collection tube. The media containing the cells is then gently added to the OptiPrep density gradient (Sigma Aldrich, St. Louis, MO, USA) and centrifuged at 800 g for 15 min at 22 °C. The layers consisting of cells were collected, and this solution was passed through a 40-μm strainer (Fisher Scientific, Hampton, NH, USA). The cells were counted and suspended at a concentration of 100 cells/μl in 0.01% BSA-PBS.
Drop-Seq Laboratory Protocol version 3.1

tag: strain

value: brainstem

tag: genotype

value: wild type


title: age-matched non-carrier wild-type (WT) 1


title: Input_OSKM_48h

city: Edinburgh

first: Abdenour

last: Soufi

address: 5 Little France Drive

department: School of Biological Sciences

country: United Kingdom

institute: University of Edinburgh

description: Input DNA from MEF early reprogramming OSKM48h

data_processing:
The ChIP-seq pair-end reads were mapped to the Mus musculus genome assembly MGSCv37 (mm9) using Bowtie (version 2.3.4.1) and very sensitive parameters
Duplicated reads were then removed using MarkDuplicates from the Picard toolkit
Reads mapping to the backlisted regions as determined by Encyclopaedia of DNA Elements (ENCODE) were discarded.
The sequencing coverage and the insert size distribution were measured from the resulting bam files using Qualimap (version 2.2.1)
The peaks of OCT4 wild-type and mutants as well as SOX2, KLF4 and cMYC showing significant enrichment over input DNA were called using MACS2 (version 2.1.1.20160309), and a fragment size of 200 bp and were controlled to a q-value (minimum FDR) cut-off of 0.01. The peaks that overlapped with the ENCODE blacklist were removed.
Genome_build: mm9
Supplementary_files_format_and_content: The aligned ChIP-seq reads (bam files) were normalised for sequencing coverage to 1x genome depth (reads per genome coverage, RPGC) using the bamCoverage tool from DeepTools and a bin size of 10 bp and extendReads parameters. BAM files from replicates were merged before normalized for coverage

source_name: Mouse Embryonic Fibroblasts

growth_protocol: Early passage (passage 1) mouse embryonic fibroblasts (MEFs) were cultured for 48hr in MEF medium (GMEM medium supplemented with 10% FCS, 1 mM sodium pyruvate, 1 mM glutamine, and 5.7 ml MEM 100X Non-Essential Amino Acids Solution, 50 M 2-mercaptoethanol (Gibco, Thermo Fisher Scientific) at 37C and 5% CO2.

extract_protocol:
Cells were then cross-linked with 1% formaldehyde for 10 min at room temperature. Crosslinking was quenched by adding 120 mM glycine and incubating for 10 min at room temperature. Cells were harvested using a scraper and pelleted by centrifugation at 1350 g for 5 min at 4°C. The crosslinked cell pellet was washed 3 times with 10 ml of ice-cold PBS. Finally, the pellet was flash frozen in liquid nitrogen and stored at -80°C.    Before nuclear extraction, the cell pellet was thawed on ice for 2-3 hr and resuspended in 10 ml filtered, ice-cold lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100 and 1 tablet of Complete Ultra protease inhibitor cocktail (Roche). The suspension was gently mixed on a rotating platform at 4°C for 10 min. The cells were disrupted using a 7 ml glass-Dounce homogeniser (40 strokes) on ice. The nuclei were pelleted by centrifugation (1350 g for 5 min at 4°C) and washed with 10 ml ice-cold wash buffer (10 mM Tris-HCl pH 8, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA and 1 tablet of Complete ultra-protease inhibitor cocktail (Roche) for 10 min at 4°C. The nuclei were collected by centrifugation and resuspended in 4 ml sonication buffer (10mM Tis-HCl pH 8, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine and 1 tablet of Complete ultra-protease inhibitor cocktail (Roche). The resuspended nuclei were split into four aliquots in pre-chilled 1 mL millitubes containing AFA Fibre and sonicated using a Covaris M220 Focused-ultrasonicator™ (Covaris, Woburn, MA). Each millitube was sonicated for 10 min and kept on ice for 30 min per sonication cycle for a total of 7 cycles. Sonicated chromatin was transferred to Protein Lobind tubes (Eppendorf). 100 µL of 10% Triton X-100 was then added to each 1 ml sonicated chromatin to increase solubility. Chromatin samples were then centrifuged (20,000 g at 4°C for 10 min) and the supernatants pooled into fresh tubes. A 50 µL aliquot of each pooled sample was analysed to check the fragment size distribution and quantify the DNA content of the resulting sonicated chromatin using a Nanodrop spectrophotometer. Another 50 µL aliquot was retained to be used as input for ChIP analysis. The sonicated chromatin and the input sample were snap frozen in liquid nitrogen and stored at -80°C.    For each ChIP, 30 µl Dyna Protein G magnetic beads (Thermo Fisher Scientific) were washed three times with 1 ml blocking solution (0.5% w/v BSA in PBS-Tween 20). The beads were saturated with the appropriate antibody by adding 10 µg of either OCT4 (Abcam), SOX2, KLF4 or cMYC (R&D) antibody and incubated on a rotating platform at 4°C for at least 6 hr. Sonicated chromatin (40 µg) was then mixed with the antibody-saturated beads and incubated on a rotating platform at 4°C overnight. The beads were transferred to a fresh tube, washed 5 times with 1 mL wash buffer (50 mM HEPES-KOH pH 7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-deoxycholate) and then washed once more with TE buffer (10 mM Tris-HCl pH 8, 1 mM EDTA) containing 50 mM NaCl. The bound-chromatin was eluted by incubating the beads in 210 µl elution buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, 1% SDS) at 65°C for 30 min. The beads were pelleted by centrifugation at 16000 g for 1 min and 200 µl supernatant containing the soluble chromatin was transferred to fresh tubes. The crosslinking was reversed by incubating the eluted chromatin and input DNA (in elution buffer) at 65°C for 16 hr with shaking. An equal volume of TE (200 µl) was added to the eluted chromatin and input DNA to reduce the concentration of SDS. RNA in the samples were digested by adding 0.2 mg/ml RNase A for 2 hr at 37°C. Proteins were then digested by adding 0.2 mg/ml Proteinase K for 2 hr at 55°C. The ChIP and Input DNA was subsequently purified by phenol-chloroform extraction followed by ethanol precipitation. The ChIP and input DNA pellets were resuspended in EB buffer (100 mM Tris pH 8) and DNA concentrations were measured by Qubit Fluorometric Quantitation (Invitrogen, Thermo Fisher Scientific).
ChIPed DNA from three biological replicates were pooled for each OCT4 variant (WT, del-61, del-72, del-73, del-75 and del-79), SOX2, KLF4, MYC and Input controls. The amount of DNA used in the library preparation ranged from ~ 20 – 80 ng. Input DNA from each sample was pooled in equal amounts for a single library preparation. The DNA libraries were prepared using NEBNext Ultra II DNA Library Prep Kit (New England Biolabs, Ipswich, MA) according to the manufacturer’s instructions. Each library was uniquely barcoded using NEBNext® Multiplex Oligos for Illumina® (Dual Index Primers Set 1) (New England Biolabs). Size selection of the DNA libraries was carried out using SpeedBeads™, which comprise magnetic carboxylate modified particles (Thermo Fisher Scientific). The quality of the DNA libraries was assessed using Agilent HS DNA Screen Tape (Agilent. Santa Clara, CA). The DNA libraries were then pooled by mixing an equal volume of each ChIP DNA library. The concentration of the ChIP DNA library pool was determined to be around 3o nM by Qubit Fluorometric Quantitation. The sequencing of the OCT4-48h ChIP-seq libraires were carried out by Edinburgh Genomics in Illumina NovaSeq and OSKM-48h ChIP-seq sequencing was done by the Beijing Genomics Institute using Illumina HiSeq 4000 system, both using a 50 bp pair-end next generation sequencing (Illumina, San Diego, CA).

treatment_protocol: MEFs were seeded onto 15-cm dishes and cultured for 24hr in MEF medium before being infected with Tet-on-O, -S, -K, -M and rtTA2M2 lentiviruses at a multiplicity of infection (M.O.I) of 5 for each virus. OSKM expression was induced by treating infected cells with 1 g/mL Dox for 48hr.

value: Mouse Embryonic fibroblasts isolated from embryos at E12.5 stage

tag: mouse strain

tag: chip-antibody

value: Input DNA control


title: CD14 monocytes [6]


title: GC0162 Gastric Cancer

tag: disease state

tag: Sex

tag: age


title: human SOD1(G93A) (mutant) 2

tag: tissue


title: CD14 monocytes [5]


title: O-WT-ChIP_SKM_48hr

description: Mock OCT4 ChIP in MEF SKM48h

value: Oct4 (Abcam, AB19857)


title: GC0138 Gastric Cancer

tag: Stage

tag: histological subtype


title: human SOD1(G93A) (mutant) 1


title: GC0139 Gastric Cancer


title: CD14 monocytes [4]


title: GC0143 Gastric Cancer


title: CD14 monocytes [12]


title: CD14 monocytes [3]


title: cMyc-ChIP_OSKM_48hr rep2

description: C-Myc ChIP in MEF early reprogramming OSKM48h


title: CD14 monocytes [10]


title: CD14 monocytes [7]


title: GC0140 Gastric Cancer


title: CD14 monocytes [1]


title: GC0137 Gastric Cancer


title: Klf4-ChIP_OSKM_48hr rep2

description:
Klf4 ChIP in MEF early reprogramming OSKM48h
Klf4_OSKM48h_SeqDepthNorm.bw


title: GC0135 Gastric Cancer


title: cMyc-ChIP_OSKM_48hr rep1

description:
C-Myc ChIP in MEF early reprogramming OSKM48h
cMyc_OSKM48h_SeqDepthNorm.bw


title: DroshaKO_miR-320a_BR1

city: Gainesville

first: Christopher

middle: James

last: Fields

state: Florida

address: 2033 Mowry Road

department: Biochemistry and Molecular Biology

institute: University of Florida

data_processing:
Adapter sequences were removed with Cutadapt.
Trimmed reads were aligned to the genome with Hisat2. Output sam files were converted to sorted bam files using samtools.
Transcripts were assembled using StringTie.
Differential Gene Expression was determined using Ballgown.
processed data files format and content: .txt file containing gene counts
Genome_build: hg38

molecule: polyA RNA

source_name: HCT116 Drosha KO

growth_protocol: HCT116 cells were cultured in McCoy's 5A media supplemented with 10% FBS and 1% penicillin/Streptomycin

extract_protocol:
Total RNA was extracted from cells using TRIzol (Invitrogen) and treated with RQ1 Dnase (Promega).
mRNA is isolated using oligo(dT) beads, fragmented randomly in fragmentation buffer, and reverse-transcribed with mRNA template and random heximer primer. Following second strand synthesis is a series of terminal repair, sequencing adapter ligation, size selection, and PCR enrichment.

tag: cell line

value: Drosha KO


title: DroshaKO_Ctrl_BR2


title: HCT116_DicerKO

data_processing:
Adapter and Quality control: Trimmomatic
Alignment: STAR
Gene Expression Determined by RSEM
processed data files format and content: .txt file containing gene counts
Genome_build: hg38

source_name: HCT116 Dicer KO

value: Dicer KO


title: DroshaKO_miR-320a_BR2


title: DroshaKO_Ctrl_BR1


title: WT_miR-320a_BR1

source_name: HCT116 Wild Type

value: Wild Type


title: WT_Ctrl_BR2


title: Sox2-ChIP_OSKM_48hr rep1

description:
Sox2 ChIP in MEF early reprogramming OSKM48h
Sox2_OSKM48h_SeqDepthNorm.bw


title: WT_miR-320a_BR2


title: CD14 monocytes [2]

value: COVID

value: Severe COVID with ICU

value: CD14 monocytes


title: Sox2-ChIP_OSKM_48hr rep2


title: WT_Ctrl_BR1


title: Klf4-ChIP_OSKM_48hr rep1


title: GC0134 Gastric Cancer

value: Gastric Cancer

value: Female

value: IB


title: DicerKO_miR-320a_BR3

extract_protocol:
Total RNA was extracted from cells using TRIzol (Invitrogen) and treated with RQ1 Dnase (Promega).
Total RNA was poly(A) selected and libraries were generated using the NEBNext Ultra II Direction RNA Library Prep Kit


title: DicerKO_miR-320a_BR2


title: GC0132 Gastric Cancer

value: IA

value: undiff


title: GC0133 Gastric Cancer

value: Male


title: DicerKO_miR-320a_BR1


title: GC0136 Gastric Cancer

value: diff


title: O-Del61-ChIP_OSKM_48hr

description: Oct4 ChIP in MEF early reprogramming OSKM48h


title: O-Del72-ChIP_OSKM_48hr


title: DicerKO_Ctrl_BR3


title: DicerKO_Ctrl_BR2


title: DicerKO_Ctrl_BR1


title: Hepa.RNAseq.H8.Dex.3

city: Philadelphia

first: Chunjie

last: Jiang

state: PA

address: 3400 Civic Center Boulevard

department: Institute for Diabetes, Obesity, and Metabolism

institute: University of Pennsylvania

data_processing:
RNA-seq reads were trimmed using fastp v0.19.5 to remove reads with low quality, too short, or too many N. Trimmed reads were then aligned to human reference genome (hg38) using Hisat2 v2.1 with default parameters. Only unique mapped reads extracted by SAMtools v1.9 were considered for downstream analyses. Quantification of gene annotated in GRCh38 v94 from Ensembl database was estimated using StringTie v1.3.4
ChIP-seq raw reads were trimmed using fastp v0.19.5. Trimmed reads were then aligned to human reference genome (hg38) using Bowtie2 v2.3.0 with default parameters. SAMtools v1.9 was used to extract unique mapped reads and remove duplicated reads. Biological replicates from the same individual were pooled together following by peak calling and de novo motif analyses using HOMER v4.9 with default parameters
ChIA-PET paired-end reads were first removed bridge linker and split into 3 category tags: none-linker containing tags, one-end tags and pair-end tags (PETs). Tags longer than 18 bp were used to mapped to human genome (hg38) by Burrows–Wheeler alignment (BWA) (ref). Duplicated PETs are filtered and uniquely non-redundant PETs were classified into inter-chromosomal PETs, intra-chromosomal PETs (two tags distance >=8 kb) and self-ligated PETs (two tags distance <8 kb). Multiple intra-chromosomal PETs whose respective ends were within 1 kb were then clustered together. PET count of each PET cluster represents the interaction strength. Loops with PETs ≥3 were considered for downstream analysis
Genome_build: hg38
Supplementary_files_format_and_content: Normalized abundance measurement was generated using StringTie.Expression profile were extracted using perl script; bigwig files were generated by Homer

source_name: Hepatocyte

growth_protocol: hiPSCs were induced differentiation with Definitive Endoderm Kit for 4 days at 30-40% confluence 24 hrs post seeding, then were transferred into RPMI-B27 supplemented with BMP-4 and FGF basic in 5% oxygen/5% CO2 for 5 days, and treated with RPMI-B27 supplemented with recombinant human HGF in 5% oxygen/5% CO2 for 5 days, and were treated with HCM Hepatocyte Culture Medium without EGF and hydrocortisone and supplemented with recombinant human oncostatin M for 5 days in ambient oxygen/5% CO2.

extract_protocol:
Total RNA was extracted by using Qiagen RNeasey Mini kit.
DNA was isolated using phenol/chloroform extraction and NaCl/EtOH precipitated with 20 μg glycogen carrier.
The H3K4me3 in-situ ChIA-PET was performed according to the previously described protocol (Li et al., 2017)
RNA libraries were prepared for sequencing by Novogene (CA).
ChIP-seq library was prepared for sequencing according to the amplification protocol from Illumina.

treatment_protocol:
adipocytes were treated with 1uM dexamethasone for 24h beginning at day 24 for RNA-seq, 6h beginning at day 20 for ChIP-seq,
hepatocytes were treated with 1uM dexamethasone for 24h beginning at day 20 for RNA-seq, 6h beginning at day 20 for ChIP-seq, ATAC-seq and ChIA-PET

value: hiPSC-derived HLCs

tag: chip antibody

value: GR


title: Hepa.RNAseq.H11.DMSO.3

description: ExpressionProfile.Hepatocyte.txt

data_processing:
none provided by the submitter
Genome_build: hg38

extract_protocol: none provided by the submitter


title: O-Del73-ChIP_OSKM_48hr

value: Mouse Embryonic fibroblasts isolated from embryos at E12.5 stage


title: GC0130 Gastric Cancer


title: GC0129 Gastric Cancer


title: GC0131 Gastric Cancer


title: GC0128 Gastric Cancer


title: O-WT-ChIP_OSKM_48hr rep2

description:
Oct4 ChIP in MEF early reprogramming OSKM48h
O-WT_OSKM48h_SeqDepthNorm.bw

value: Oct4 (Abcam, AB19857)


title: Hepa.RNAseq.H11.DMSO.1

description: ExpressionProfile.Hepatocyte.txt


title: 3RS4_110

city: Ulm

first: Alexey

last: Ushmorov

address: Albert-Einstein-Allee 11

department: Institute of Physiological Chemistry

country: Germany

institute: Ulm University

description: RS4_110-VS-RS4_11Palbo.DEseq2_Method.GeneDiffExp

data_processing:
SOAPnuke software was used for data filtering (version：v1.5.2, parameters: -l 15 -q 0.2 -n 0.05)
Bowtie2 was used to map clean reads to reference (Version: v2.2.5, Parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant -p 1 -k 200)
RSEM was used to calculate gene expression level (Version: v1.2.12, Parameters: default)
DEseq2 was used to detect DEGs (Parameters: Fold Change >= 2.00 and Adjusted P value <= 0.05)
Genome_build: hg38
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample

source_name: B-ALL cell lines

growth_protocol: B-ALL cells were grown in RPMI1640 medium with addition of 20 % FBS, glutamine and antibiotics at 37 ºC, 5% CO2.

extract_protocol:
Total RNA was isolated with RNeasy mini kit (QIAGEN) according to the manufacturers instruction.
RNA libraries were prepared for sequencing using standard BGI protocols (oligo dT mRNA enrichment)

treatment_protocol: BL cells were transduced with a lentiviral vector expressing scrambled shRNA of shRNA tageting human CCND3 mRNA or treated with 1 µM palbociclib or DMSO as a control. The infected cells were sorted on day 4 after transduction, the palbociclib treated cells were collected after three days.  The experiment was done in duplicates or triplicates.  Total RNA was isolated with RNeasy mini kit (QIAGEN).

tag: treatment

value: DMSO


title: O-WT-ChIP_OSKM_48hr rep1


title: GC0127 Gastric Cancer


title: 3RS4_11shC3

description: RS4_11scr-VS-RS4_11shC3.DEseq2_Method.GeneDiffExp


title: E3.5+10h_p38i_rep2

city: Ceske Budejovice

first: Lenka

last: Gahurova

address: Branisovska 1760

department: Department of molecular biology and genetics

country: Czech Republic

institute: University of South Bohemia

data_processing:
Trimming: Trim Galore! v0.4.1
Mapping: Hisat2 v2.0.5
Genome_build: GRCm38
Supplementary_files_format_and_content: txt format table listing all genes and their expression levels in each dataset (each replicate). Expression levels are shown as log2 RPKM values.

source_name: embryos at E3.5+10 hours

growth_protocol: Superovulation and strain mating regimen to produce experimental embryos were as follows; F1 hybrid (C57Bl6 x CBA/W) females were subject to peritoneal injection with 7.5 IU PMSG (Folligon® MSD Animal Health) and 48 hours later with 7.5 IU hCG (Sigma-Aldrich® cat. # CG10), followed by overnight F1 male mating (successful mating confirmed next morning by presence of vaginal sperm plugs). E1.5 (i.e. 2-cell) stage embryos were isolated from the female oviducts in M2 media (pre-warmed at 37˚C for at least 2-3 hours) and thereafter cultured in KSOM (EmbryoMax® KSOM Mouse Embryo Media; cat. # MR-020P-5F - pre-warmed and equilibrated in 5% CO2 and 37˚C), with amino acid (AA) supplementation. For KSOM+AA condition, Gibco™ MEM Non-Essential Amino Acids Solution (100X) (cat. # 11140035) and Gibco™ MEM Amino Acids Solution (50X) (cat. # 11130036) were used to a working concentration of 0.5X. Embryos were cultured in micro-drops prepared in 35mm tissue culture dishes covered with light mineral oil (Irvine Scientific. cat. # 9305), in 5% CO2 incubators maintained at 37˚C until the appropriate stage. 2-cell (E1.5) stage embryos were cultured in normal KSOM+AA conditions until E3.5 and thereafter 30 embryos each were moved to control or p38-MAPKi conditions and cultured for another 4, 7 or 10 hours.

extract_protocol:
The embryos were then processed for total RNA isolation using the ARCTURUS® PicoPure® RNA Isolation Kit (Applied Biosystems™; KIT0204), following the manufacturer’s protocol. Oligo dT-based mRNA isolation was carried out using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB; E7490)
libraries were prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (NEB; E7760), as directed by the manufacturer

treatment_protocol: Pharmacological manipulations were carried out by addition of chemical agents dissolved in dimethyl sulfoxide (DMSO Sigma-Aldrich® cat. # D4540) to KSOM±AA. p38-MAPK inhibition using 20µM SB220025 (Calbiochem; cat. # 559396) was carried out for 4 hours, 7 hours and 10 hours post E3.5 and the embryos were processed for RNA isolation immediately thereafter. Equivalent volumes of solvent control were used to a final working concentration of 0.2-0.5% by volume. All KSOM based culture media, with or without additional chemicals (AAs, pharmacological agents), were pre-warmed and equilibrated in 5% CO2 and 37˚C for at least 3-4 hours prior to embryo transfer.

tag: timepoint

value: E3.5+10 hours

tag: condition

value: embryos


title: Hepa.RNAseq.H11.Dex.1

description: ExpressionProfile.Hepatocyte.txt


title: 3RS4_11scr

value: scrambled


title: O-Del79-ChIP_OSKM_48hr


title: GC0125 Gastric Cancer


title: GC0126 Gastric Cancer


title: Hepa.RNAseq.H11.DMSO.2

description: ExpressionProfile.Hepatocyte.txt


title: E3.5+10h_p38i_rep1


title: E3.5+10h_DMSO_rep2


title: GC0123 Gastric Cancer


title: Hepa.RNAseq.H10.DMSO.3

description: ExpressionProfile.Hepatocyte.txt


title: 3RS4_11Palbo

value: Palbociclib


title: GC0122 Gastric Cancer


title: GC0124 Gastric Cancer


title: 3Nalm_60

description: Nalm_60-VS-Nalm_6Palbo.DEseq2_Method.GeneDiffExp


title: 3Nalm_6scr

description: Nalm_6scr-VS-Nalm_6shC3.DEseq2_Method.GeneDiffExp


title: Hepa.RNAseq.H10.DMSO.1

description: ExpressionProfile.Hepatocyte.txt


title: E3.5+7h_p38i_rep2

source_name: embryos at E3.5+7 hours

value: E3.5+7 hours


title: Hepa.RNAseq.H11.Dex.2

description: ExpressionProfile.Hepatocyte.txt


title: E3.5+10h_DMSO_rep1


title: GC0121 Gastric Cancer

value: Gastric Cancer


title: 3Nalm_6Palbo


title: Hepa.RNAseq.H10.Dex.3

description: ExpressionProfile.Hepatocyte.txt


title: Hepa.RNAseq.H10.Dex.2

description: ExpressionProfile.Hepatocyte.txt


title: E3.5+7h_DMSO_rep2


title: GC0119 Gastric Cancer


title: 3BV_1730

description: BV_1730-VS-BV_173Palbo.DEseq2_Method.GeneDiffExp.xls

value: BCR-ABL


title: Hepa.RNAseq.H9.DMSO.3

description: ExpressionProfile.Hepatocyte.txt


title: E3.5+7h_DMSO_rep1


title: 3BV_173shC3

description: BV_173scr-VS-BV_173shC3.DEseq2_Method.GeneDiffExp


title: GC0118 Gastric Cancer

value: Female


title: Hepa.RNAseq.H10.Dex.1

description: ExpressionProfile.Hepatocyte.txt


title: Hepa.RNAseq.H10.DMSO.2

description: ExpressionProfile.Hepatocyte.txt


title: E3.5+4h_p38i_rep2

source_name: embryos at E3.5+4 hours

value: E3.5+4 hours


title: 3BV_173scr


title: Hepa.RNAseq.H9.DMSO.2

description: ExpressionProfile.Hepatocyte.txt


title: E3.5+4h_p38i_rep1


title: GC0117 Gastric Cancer

source_name: Serum

value: IA

value: undiff


title: 3BV_173Palbo


title: Hepa.RNAseq.H9.DMSO.1

description: ExpressionProfile.Hepatocyte.txt


title: GC0120 Gastric Cancer

value: Male


title: E3.5+4h_DMSO_rep2


title: E3.5+7h_p38i_rep1


title: Hepa.RNAseq.H11.Dex.3

description: ExpressionProfile.Hepatocyte.txt

value: hiPSC-derived HLCs


title: Hepa.RNAseq.H9.Dex.3

description: ExpressionProfile.Hepatocyte.txt


title: GC0116 Gastric Cancer

value: diff


title: E3.5+4h_DMSO_rep1


title: GC0115 Gastric Cancer


title: GC0114 Gastric Cancer


title: NC3 [lncRNA]

city: 广州

first: Runguang

last: LI

address: 广州大道北沙太南路

country: China

institute: 南方医科大学

data_processing:
Illumina Casava1.8 software used for basecalling.
Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20) were removed.
We aligned reads of samples to the reference genome using TopHat2 package.
The mapped reads of each sample were assembled using StringTie, all transcriptomes were merged to reconstruct a comprehensive transcriptome.
Unmapped reads were still mapped to genome using tophat-fusion. CIRCExplorer2 was used to denovo assemble the mapped reads to circular RNAs at first; Then, back splicing reads were identified in unmapped reads by tophat-fusion and CIRCExplorer2. All samples were generated unique circular RNAs.
Genome_build: Ensembl
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Rattus norvegicus

source_name: control group_BMSCs

growth_protocol: 12 8-week old SD rats were randomly divided into exercise group and control group (n = 6). Exercise group was treated with 8 weeks moderate treadmill running. In the first 3 days, the initial speed, slope and time were set as 10 m/min at 0° slope for 20 min, which increased up to 20 m/min at 5° slope for 60 min after 2 days’ rest. The exercise was carried out once a day, 5 days a week for 8 weeks. Finally, femur and tibia BMSCs were collected for sequencing.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 1000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Sprague-Dawley rats

tag: group

value: control group

value: Bone marrow mesenchymal stem cells (BMSCs)


title: 2RS4_11shC3


title: 2RS4_11scr


title: Hepa.RNAseq.H9.Dex.1

description: ExpressionProfile.Hepatocyte.txt

tag: cell type


title: Hepa.RNAseq.H9.Dex.2

description: ExpressionProfile.Hepatocyte.txt


title: NC1 [lncRNA]

tag: strain


title: 2RS4_11Palbo

tag: genotype


title: 2Nalm_60

value: DMSO


title: Hepa.RNAseq.H8.DMSO.2

description: ExpressionProfile.Hepatocyte.txt


title: NC2 [lncRNA]


title: GC0112 Gastric Cancer


title: GC0113 Gastric Cancer


title: 2Nalm_6shC3


title: treadmill 3 [lncRNA]

source_name: exercise group_BMSCs

value: exercise group


title: Hepa.RNAseq.H8.DMSO.1

description: ExpressionProfile.Hepatocyte.txt


title: Hepa.RNAseq.H8.Dex.2

description: ExpressionProfile.Hepatocyte.txt


title: treadmill 2 [lncRNA]


title: 2Nalm_6scr

value: scrambled


title: GC0110 Gastric Cancer


title: Hepa.RNAseq.H8.Dex.1

description: ExpressionProfile.Hepatocyte.txt


title: 2Nalm_6Palbo

value: Palbociclib


title: Hepa.RNAseq.H7.DMSO.3

description: ExpressionProfile.Hepatocyte.txt


title: treadmill 1 [lncRNA]


title: GC0109 Gastric Cancer


title: 2BV_173shC3


title: GC0107 Gastric Cancer


title: si-FTO-2

city: Changzhou

first: You

last: Zhou

state: Jiangsu

address: Juqian Rd No.185

institute: The Third Affiliated Hospital of Soochow University

data_processing:
Solexa pipeline version 1.8 used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 genome using Hisat2 with default parameters.
Fragments Per Kilobase of gene/transcript model per Million mapped reads (FPKM) were calculated using Ballgown. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: AGS

extract_protocol:
Total RNA was extracted using Trizol reagent. Illumina KAPA Stranded RNA-Seq Library Prep Kit was used with 1 ug of purified RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: AGS

value: Stomach

value: FTO-/-


title: si-FTO-3


title: 2BV_173scr

value: BCR-ABL


title: GC0111 Gastric Cancer

value: Gastric Cancer

value: Female


title: si-FTO-1


title: Hepa.RNAseq.H7.DMSO.2

description: ExpressionProfile.Hepatocyte.txt


title: GC0106 Gastric Cancer

value: IA

value: undiff


title: 2BV_173Palbo


title: Hepa.RNAseq.H7.DMSO.1

description: ExpressionProfile.Hepatocyte.txt

value: hiPSC-derived HLCs


title: si-NC-3

value: wild type


title: 1RS4_110


title: 2RS4_110


title: si-NC-2


title: 1RS4_11shC3


title: Hepa.RNAseq.H7.Dex.2

description: ExpressionProfile.Hepatocyte.txt


title: GC0105 Gastric Cancer


title: Hepa.RNAseq.H7.Dex.1

description: ExpressionProfile.Hepatocyte.txt


title: si-NC-1


title: Hepa.RNAseq.H7.Dex.3

description: ExpressionProfile.Hepatocyte.txt


title: GC0102 Gastric Cancer


title: Hepa.RNAseq.H6.DMSO.3

description: ExpressionProfile.Hepatocyte.txt


title: Caco-2_NAPEPLD-KO C35-2

city: Fuchu-City

first: Miki

last: Igarashi

state: Tokyo

address: 3-5-8 Saiwai

institute: Tokyo University of Agriculture and Technology

data_processing:
Raw data filtering (Clean data)
Remove reads containing adapters
Remove reads containing N > 10% (N represents the base cannot be determined).
Remove reads containing low quality (Qscore<= 5) base which is over 50% of the total base.
Raw sequence data were then mapped to the human hg38 reference genome using a custom MOIRAI pipeline (Hasegawa 2014) with STAR 2.51 (Dobin 2013) for alignment.
Read counts for each transcript were obtained using featureCounts (Liao 2014).
Raw count data were directly analyzed for differential gene expression by using the edgeR 3.20.9 (Robinson 2010).
Genome_build: hg38

source_name: Caco-2 cells

growth_protocol: Cells were cultured in RPMI-1640 containing 2 mg/ml glucose and 10% FBS.

extract_protocol:
mRNA from cells were exracted using Qiagen RNAeasy mini kit
Libraries were prepared according to NEBNext Ultra RNA Library Prep Kit for Illumina. mRNA from eukaryotic organisms is enriched using oligo(dT) beads. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.

treatment_protocol: Cells were cultured  by 18 days of post-confluence in order to differentiate them like intestinal epithelial cells.

value: epithelial colorectal adenocarcinoma cells

value: Day 18 of post-confluence

value: NAPE-PLD deleted


title: 1RS4_11Palbo


title: 1RS4_11scr


title: GC0108 Gastric Cancer


title: Caco-2_NAPEPLD-KO C35-1


title: Hepa.RNAseq.H6.DMSO.2

description: ExpressionProfile.Hepatocyte.txt


title: GC0103 Gastric Cancer

value: Male

value: II


title: GC0101 Gastric Cancer


title: 1Nalm_60

value: DMSO


title: GC0104 Gastric Cancer

value: diff


title: Caco-2_Parent-2


title: 1Nalm_6shC3


title: GC0099 Gastric Cancer


title: Hepa.RNAseq.H6.Dex.3

description: ExpressionProfile.Hepatocyte.txt


title: 1Nalm_6scr

value: scrambled


title: Hepa.RNAseq.H6.Dex.2

description: ExpressionProfile.Hepatocyte.txt


title: GC0098 Gastric Cancer


title: 1Nalm_6Palbo

value: Palbociclib


title: GC0097 Gastric Cancer


title: Caco-2_Parent-1


title: 1BV_1730


title: GC0096 Gastric Cancer


title: Hepa.RNAseq.H6.Dex.1

description: ExpressionProfile.Hepatocyte.txt


title: 1BV_173shC3


title: GC0100 Gastric Cancer


title: 1BV_173scr


title: Hepa.RNAseq.H5.DMSO.3

description: ExpressionProfile.Hepatocyte.txt


title: Hepa.RNAseq.H5.DMSO.1

description: ExpressionProfile.Hepatocyte.txt


title: Hepa.RNAseq.H5.DMSO.2

description: ExpressionProfile.Hepatocyte.txt


title: Hepa.RNAseq.H6.DMSO.1

description: ExpressionProfile.Hepatocyte.txt


title: GC0094 Gastric Cancer


title: 1BV_173Palbo


title: Hepa.RNAseq.H5.Dex.3

description: ExpressionProfile.Hepatocyte.txt


title: ChinMS_Body rep2

city: Davis

first: Joanna

middle: C.

last: Chiu

address: One shield Av

institute: University of California

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Trimmed reads were alinged on TopHat using a reference transcriptome (GSE121104) of C. includens.
RNA-seq reads of head and body transcriptomes were mapped to the built reference transcriptome using TopHat and expression values of transcripts in FPKM were estimated using the mapped reads of head and body tissues on Cufflinks.
Annotation of transcripts with Gene Ontology IDs (GO), which reveals the properties of biological process, molecular function, and cellular component, was accomplished using the following parameters: cutoff of 55 and blast filters with E-value-hit-filter of 1.0E-6.
Supplementary_files_format_and_content: output files (.txt) from Cufflinks and the reference transcriptome (.fasta) already uplouded (GSE121104)

organism: Chrysodeixis includens

source_name: Body of soybean looper larvae

extract_protocol:
Larvae was dissected into head and body and total RNA was harvested using Trizol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: MS

value: body

value: third instar

value: Resistant


title: Hepa.RNAseq.H5.Dex.2

description: ExpressionProfile.Hepatocyte.txt


title: GC0095 Gastric Cancer

data_processing: The presence of miRNA was determined based on a corresponding microarray signal of greater than [the mean + 2 × standard deviation] of the negative controls signal, of which the top and bottom ranked ones by signal intensity were removed. Once a miRNA was considered present, the mean signal of the negative controls of which the top and bottom 5% ranked by signal intensity were removed was subtracted from the miRNA signal. When the signal value was negative (or undetected) after background subtraction, the value was replaced by 0.1 on a base 2 logarithm scale.

extract_protocol: Total RNA was extracted each from 300uL serum samples using 3D-Gene® RNA extraction reagent from liquid sample kit (Toray Industries, Inc.).

value: Gastric Cancer

value: IB


title: ChinMS_Body rep1


title: Hepa.RNAseq.H5.Dex.1

description: ExpressionProfile.Hepatocyte.txt

value: hiPSC-derived HLCs


title: GC0092 Gastric Cancer

value: IA


title: ChinMS_Head rep2

source_name: Head of soybean looper larvae

value: head


title: GC0091 Gastric Cancer


title: Biopsy_BY-T1432_Patient 12

city: Leicester

first: Bin

state: Leicestershire

address: University Road

department: Cardiovascular Sciences

institute: University of Leicester

hyb_protocol: The BeadChip were hybridized at 58°C overnight

scan_protocol: Beadchips were scanned on an Illumina BeadArray Reader

data_processing: Data were processed using Illumina Genome Studio

label: Biotin

source_name: Deceased donor

label_protocol: RNA samples were prepared for microarray analysis using the Illumina TotalPrep RNA amplification kit (AMBION ref# AMIL1791) according to manufacturer's protocole. Briefly, the RNA was reverse transcribed. The second strand cDNA was then synthesized. cDNA was hen purified on column. cRNA was then synthesized using biotin-labelled Nucleotide Triphosphate and purified.

growth_protocol: Not applicable

extract_protocol: RNA samples were exptracted from kidney biospsies using the Qiagen RNeasy® Plus Mini Kit

treatment_protocol: Not applicable

tag: donor

value: Deceased donor - 3 months

tag: time

value: 3 months


title: Hepa.RNAseq.H4.DMSO.3

description: ExpressionProfile.Hepatocyte.txt


title: Biopsy_BY-T1186_Patient 8

value: Deceased donor - 1 months

value: 1 months


title: Biopsy_BY-T1320_Patient 11


title: Biopsy_BY-T1282_Patient 9


title: ChinMS_Head rep1


title: Biopsy_BY-T1175_Patient 7


title: Hepa.RNAseq.H4.DMSO.2

description: ExpressionProfile.Hepatocyte.txt


title: ChinLAB_Body rep2

value: LAB

value: Susceptible


title: GC0088 Gastric Cancer

tag: disease state

value: Male

value: diff


title: Hepa.RNAseq.H4.DMSO.1

description: ExpressionProfile.Hepatocyte.txt


title: ChinLAB_Body rep1


title: GC0087 Gastric Cancer

tag: Sex

value: undiff


title: GC0089 Gastric Cancer

tag: age


title: ChinLAB_Head rep2

tag: tissue


title: GC0090 Gastric Cancer

tag: Stage


title: GC0093 Gastric Cancer

value: Female

tag: histological subtype


title: Biopsy_BY-T1257_Patient 10

value: Deceased donor - 2 months

value: 2 months


title: Hepa.RNAseq.H4.Dex.3

description: ExpressionProfile.Hepatocyte.txt


title: Hepa.RNAseq.H4.Dex.2

description: ExpressionProfile.Hepatocyte.txt


title: Biopsy_BY-T1332_Patient 12

value: Deceased donor - 30 minutes

value: 30 minutes


title: Biopsy_BY-T1199_Patient 10


title: Biopsy_BY-T1253_Patient 11


title: GC0085 Gastric Cancer

value: Gastric Cancer


title: Biopsy_BY-T1178_Patient 9


title: GC0084 Gastric Cancer

value: IA


title: ChinLAB_Head rep1

value: head

value: third instar


title: Biopsy_BY-T1163_Patient 8


title: Hepa.RNAseq.H3.DMSO.2

description: ExpressionProfile.Hepatocyte.txt

value: hiPSC-derived HLCs


title: Biopsy_BY-T1120_Patient 7

value: Deceased donor - 7 days

value: 7 days


title: Hepa.RNAseq.H3.DMSO.3

description: ExpressionProfile.Hepatocyte.txt


title: DicerKO_CLASH_Lo

description: Ago IP RNA

data_processing:
Library strategy: CLASH
Trimmomatic was used to remove adapter sequences and low quality reads.
Forward and Reverse Reads were combined into a single read using PEAR.
Chimeric reads were identified with the Hyb software.
processed data files format and content: .viennad and .hyb files containg chimeric reads
Genome_build: hg38

extract_protocol:
Protein G dynabeads were conjugated with 2A8 anti-Ago. Pellets were resuspended in lysis buffer and incubated with RQ1 Dnase. Lysates were quantitated and added to conjugated beads overnight. Following immunoprecipitation, Ago bound RNAs were biefly treated with RNAseA, vigouraously washed, and phosphorylated before being subjected to high concentration of RNA ligase for intermolecular ligation. After overnight incubation, RNAs were dephosphorylated and the miRCat-33 linker was ligated. Samples were eluted from the beads, seperated on a 10% Bis-Tris PAGE, and transfered to nitrocellulose, before being subjected to proteinase K digestion to release RNA complexes from Ago, and phosphorylated for ligation of the 5' adapter. RNA was reverse transcribed and the resulting cDNA was used for library prep.cDNA containing the miRCat-33 (RA3) and 5-adapter adapter (RA5) was PCR amplified using Illumina TruSeq® Small RNA Sample Prep Kits. The resulting library was seperated with Native-PAGE and DNA from 147bps and 527bps was extracted for Illumina sequencing.
cDNA containing the miRCat-33 and 5-adapter adapter was PCR amplified using Illumina TruSeq® Small RNA Sample Prep Kits. The resulting library was seperated with Native-PAGE and DNA from 147bps and 527bps was extracted for Illumina sequencing.

treatment_protocol: HCT116 cells were grown in 15 cm plates until ~90% confluent. Plates were rinsed two times in PBS and UV-irradiated at 250nm with a total energy of 600J/cm2. Cells were scrapped off the plate and centrifuged at 4°C, the supernatant removed, and stored at -80°C.

tag: cell line

value: Dicer KO

tag: antibody

value: Ago 2A8


title: NoAB_CLASH_Lo

description: Ago IP RNA

value: Wild Type


title: Biopsy_BY-T1344_Patient 5

source_name: Living Donor

value: Living Donor - 3 months

value: 3 months


title: GC0082 Gastric Cancer

value: Male

value: diff


title: GC0083 Gastric Cancer

value: Female

value: undiff


title: Biopsy_BY-T1352_Patient 4


title: GC0081 Gastric Cancer


title: Hepa.RNAseq.H3.DMSO.1

description: ExpressionProfile.Hepatocyte.txt

tag: chip antibody


title: DroshaKO_CLASH_Lo

description: Ago IP RNA

source_name: HCT116 Drosha KO

value: Drosha KO


title: Hepa.RNAseq.H4.Dex.1

description: ExpressionProfile.Hepatocyte.txt


title: Hepa.RNAseq.H3.Dex.3

description: ExpressionProfile.Hepatocyte.txt


title: DicerKO_CLASH_Hi

description: Ago IP RNA

source_name: HCT116 Dicer KO


title: Hepa.RNAseq.H3.Dex.2

description: ExpressionProfile.Hepatocyte.txt


title: Hepa.RNAseq.H3.Dex.1

description: ExpressionProfile.Hepatocyte.txt


title: GC0079 Gastric Cancer

value: Gastric Cancer


title: GC0080 Gastric Cancer

value: IB


title: NoAB_CLASH_Hi

description: Ago IP RNA

source_name: HCT116 Wild Type


title: GC0077 Gastric Cancer

value: IA


title: Biopsy_BY-T1329_Patient 3


title: GC0078 Gastric Cancer


title: Biopsy_BY-T1339_Patient 2

value: Living Donor - 4 months

value: 4 months


title: Hepa.RNAseq.H2.DMSO.2

description: ExpressionProfile.Hepatocyte.txt

source_name: Hepatocyte

value: hiPSC-derived HLCs


title: GC0076 Gastric Cancer


title: Biopsy_BY-T1288_Patient 5

value: Living Donor - 30 minutes

value: 30 minutes


title: Biopsy_BY-T1208_Patient 6


title: Biopsy_BY-T1285_Patient 1


title: WT_miR-320a_qCLASH

description: Ago IP RNA

data_processing:
Library strategy: qCLASH
Trimmomatic was used to remove adapter sequences and low quality reads.
Forward and Reverse Reads were combined into a single read using PEAR.
PCR duplicates were removed using fastx_toolkit.
The UMIs were removed using Cutadapt.
Chimeric reads were identified with the Hyb software.
processed data files format and content: .viennad and .hyb files containg chimeric reads
Genome_build: hg38

extract_protocol:
Protein G dynabeads were conjugated with 2A8 anti-Ago while Protein L beads were conjugated with 4F9 anti-Ago. Pellets were resuspended in lysis buffer and incubated with RQ1 Dnase. Lysates were quantitated and added to conjugated beads overnight. Following immunoprecipitation, Ago bound RNAs were biefly treated with RNAseA, vigouraously washed, and phosphorylated before being subjected to high concentration of RNA ligase for intermolecular ligation. After overnight incubation, RNAs were dephosphorylated and the miRCat-33 linker was ligated. Samples were eluted from the beads, subjected to proteinase K digestion to release RNA complexes from Ago, and phosphorylated for ligation of the 5' adapter. RNA was reverse transcribed and the resulting cDNA was used for library prep.cDNA containing the miRCat-33 (RA3) and 5' adapter (RA5) was PCR amplified using Illumina TruSeq® Small RNA Sample Prep Kits. The resulting library was seperated with Native-PAGE and DNA from 147bps and 527bps was extracted for Illumina sequencing.
cDNA containing the miRCat-33 and 5-adapter adapter was PCR amplified using Illumina TruSeq® Small RNA Sample Prep Kits. The resulting library was seperated with Native-PAGE and DNA from 147bps and 527bps was extracted for Illumina sequencing.

value: Ago 2A8


title: Biopsy_BY-T1153_Patient 6


title: WT_CLASH_Hi

description: Ago IP RNA

value: Wild Type


title: Hepa.RNAseq.H2.DMSO.1

description: ExpressionProfile.Hepatocyte.txt


title: GC0075 Gastric Cancer


title: DroshaKO_CLASH_Hi

description: Ago IP RNA


title: DicerKO_qCLASH_BR4

description: Ago IP RNA

data_processing:
Library strategy: qCLASH
Adapter and Quality control: Trimmomatic
Forward and Reverse Reads were combined using PEAR.
PCR duplicates were removed using fastx_toolkit.
The UMIs were removed using Cutadapt.
Chimeric reads were identified with the Hyb software.
Genome_build: hg38
Supplementary_files_format_and_content: .viennad and .hyb files containg chimeric reads

extract_protocol:
Protein G dynabeads were conjugated with 2A8 anti-Ago while Protein L beads were conjugated with 4F9 anti-Ago. Pellets were resuspended in lysis buffer and incubated with RQ1 Dnase. Lysates were quantitated and added to conjugated beads overnight. Following immunoprecipitation, Ago bound RNAs were biefly treated with RNAseA, vigouraously washed, and phosphorylated before being subjected to high concentration of RNA ligase for intermolecular ligation. After overnight incubation, RNAs were dephosphorylated and the miRCat-33 linker was ligated. Samples were eluted from the beads, subjected to proteinase K digestion to release RNA complexes from Ago, and phosphorylated for ligation of the 5' adapter. RNA was reverse transcribed and the resulting cDNA was used for library prep.
cDNA containing the miRCat-33 and 5-adapter adapter was PCR amplified using Illumina TruSeq® Small RNA Sample Prep Kits. The resulting library was seperated with Native-PAGE and DNA from 147bps and 527bps was extracted for Illumina sequencing.

value: Dicer KO

value: Ago 4F9


title: Hepa.RNAseq.H2.Dex.3

description: ExpressionProfile.Hepatocyte.txt


title: WT_CLASH_Lo

description: Ago IP RNA


title: DicerKO_qCLASH_BR3

description: Ago IP RNA


title: THP1-input_rep2

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

data_processing:
Library strategy: ChIRP-Seq
Reads were aligned to hg19 using Bowtie 1 with "-m 1" option
SAM files were sorted and converted to BAM using Samtools
MACS2 was used to call peaks with P value of 1e-05.
Genome_build: hg19
Supplementary_files_format_and_content: text files with MACS2 peaks

source_name: THP-1 monocytes (ATCC TIB-202)

growth_protocol: RPMI containing 10% fetal bovine serum Pen/Strp, 2 mM glutamine,  5.5 mM glucose and 50 uM beta-mercaptoethanol

extract_protocol:
THP1 cells (80 million) were fixed with glutaraldehyde for 30 min, washed and lysed in ChIRP lysis buffer containing SUPERase•In and protease inhibitors. Lysates were sonicated in Bioruptor to fragment DNA (200-1000 bp) and diluted with hybridization buffer (1:2). Then DRAIR tiling biotinylated oligonucleotides (Stellaris, Novato, CA) were added (10 pg/ml) and incubated overnight at 37 °C. The following day, ChIRP complexes were captured using streptavidin-magnetic beads and washed 5 times with wash buffer, and ChIRP-RNA and ChIRP-DNA were isolated from the beads. ChIRP-DNA was used for DNA-seq on Illumina platform.
Library construction and Data analysis to identify DRAIR chromatin binding sites was performed following published protocols (Chu et el, Molecular cell. 2011;44(4):667-78). Enriched and input DNA samples were converted to Illunina libraries using Kapa DNA library prep kit. Libraries were sequenced with Hiseq 2500 following manufacturer's recommendations.
ChIRP-Seq (Chu et al, Molecular cell. 2011;44(4):667-78)

tag: culture condition

value: Cultured in 5.5 mM glucose medium

value: THP-1 monocytes (ATCC TIB-202)

tag: growth state

value: Suspension

tag: sample type

value: Input


title: DicerKO_qCLASH_BR2

description: Ago IP RNA


title: GC0073 Gastric Cancer

city: Kanagawa

address: kamakurashi

institute: Toray industries inc

value: Male

value: diff


title: GC0072 Gastric Cancer

value: Gastric Cancer


title: Hepa.RNAseq.H2.Dex.2

description: ExpressionProfile.Hepatocyte.txt

tag: cell type


title: Hepa.RNAseq.H2.DMSO.3

description: ExpressionProfile.Hepatocyte.txt


title: Biopsy_BY-T1254_Patient 3


title: Biopsy_BY-T1297_Patient 4


title: Biopsy_BY-T1194_Patient 1


title: Hepa.RNAseq.H2.Dex.1

description: ExpressionProfile.Hepatocyte.txt


title: THP1-input_rep1


title: THP1-DRAIR_rep1

value: ChIRP-Seq


title: Biopsy_BY-T1245_Patient 2


title: DroshaKO_qCLASH_BR4

description: Ago IP RNA

value: Drosha KO


title: THP1-DRAIR_rep2


title: GC0074 Gastric Cancer

value: Female

value: IA

value: undiff


title: Type 2 Diabetic_Rep5

data_processing:
Sequences were aligned to hg19 using Tophat2 with default settings
Gene expression level of Refseq coding genes were quantified using in-house R scripts
Genome_build: hg19
Supplementary_files_format_and_content: raw counts in text format

source_name: Blood

extract_protocol:
Total RNA was isolated from CD14+ monocytes using RNeasy mini kit and on-column DNase I digestion to eliminate genomic DNA (Qiagen).
Libraries were prepared according to instructions accompanying the Illumina® EpiCentre ScriptSeq™ Complete Gold kit. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.
Strand specific RNA-seq

value: Type 2 Diabetic

value: CD14+ monocytes


title: GC0070 Gastric Cancer

value: IB


title: Hepa.RNAseq.H1.DMSO.2

description: ExpressionProfile.Hepatocyte.txt

value: hiPSC-derived HLCs


title: DicerKO_qCLASH_BR1

description: Ago IP RNA

value: Dicer KO

value: Ago 2A8


title: GC0068 Gastric Cancer


title: Hepa.RNAseq.H1.Dex.3

description: ExpressionProfile.Hepatocyte.txt


title: Type 2 Diabetic_Rep4


title: DroshaKO_qCLASH_BR2

description: Ago IP RNA


title: DroshaKO_qCLASH_BR1

description: Ago IP RNA


title: GC0071 Gastric Cancer

value: special


title: Hepa.RNAseq.H1.DMSO.1

description: ExpressionProfile.Hepatocyte.txt


title: DroshaKO_qCLASH_BR3

description: Ago IP RNA

value: Ago 4F9


title: WT_qCLASH_BR5

description: Ago IP RNA

value: Wild Type


title: GC0066 Gastric Cancer

value: Male


title: GC0067 Gastric Cancer


title: Hepa.RNAseq.H1.DMSO.3

description: ExpressionProfile.Hepatocyte.txt


title: WT_qCLASH_BR4

description: Ago IP RNA


title: GC0065 Gastric Cancer


title: GC0064 Gastric Cancer


title: Type 2 Diabetic_Rep1


title: Adip.RNAseq.A8.DMSO.3

description: ExpressionProfile.Adipocyte.txt

data_processing:
RNA-seq reads were trimmed using fastp v0.19.5 to remove reads with low quality, too short, or too many N. Trimmed reads were then aligned to human reference genome (hg38) using Hisat2 v2.1 with default parameters. Only unique mapped reads extracted by SAMtools v1.9 were considered for downstream analyses. Quantification of gene annotated in GRCh38 v94 from Ensembl database was estimated using StringTie v1.3.4
ChIP-seq raw reads were trimmed using fastp v0.19.5. Trimmed reads were then aligned to human reference genome (hg38) using Bowtie2 v2.3.0 with default parameters. SAMtools v1.9 was used to extract unique mapped reads and remove duplicated reads. Biological replicates from the same individual were pooled together following by peak calling and de novo motif analyses using HOMER v4.9 with default parameters
ATAC-seq raw reads were trimmed using fastp v0.19.5. Next, trimmed reads were aligned to human reference genome (hg38) using Bowtie2 v2.3.0 with parameter --very-sensitive. Reads mapped to mitochondria were ignored. SAMtools v1.9 was applied to extract unique mapped reads and remove duplicated reads. Peak calling was performed using Genrich (https://github.com/jsh58/Genrich#contact)
ChIA-PET paired-end reads were first removed bridge linker and split into 3 category tags: none-linker containing tags, one-end tags and pair-end tags (PETs). Tags longer than 18 bp were used to mapped to human genome (hg38) by Burrows–Wheeler alignment (BWA) (ref). Duplicated PETs are filtered and uniquely non-redundant PETs were classified into inter-chromosomal PETs, intra-chromosomal PETs (two tags distance >=8 kb) and self-ligated PETs (two tags distance <8 kb). Multiple intra-chromosomal PETs whose respective ends were within 1 kb were then clustered together. PET count of each PET cluster represents the interaction strength. Loops with PETs ≥3 were considered for downstream analysis
Genome_build: hg38
Supplementary_files_format_and_content: Normalized abundance measurement was generated using StringTie.Expression profile were extracted using perl script; hic files were generated by ChIAPIPE

source_name: Adipocyte

growth_protocol:
hASCs were cultured in DMEM medium. Confluent hASCs were then transferred into adipogenic medium for 14 days. Then, cells were further cultured in maintenance medium another 7 days and 1.5%BSA medium for additional 2 days.
hiPSCs were induced differentiation with Definitive Endoderm Kit for 4 days at 30-40% confluence 24 hrs post seeding, then were transferred into RPMI-B27 supplemented with BMP-4 and FGF basic in 5% oxygen/5% CO2 for 5 days, and treated with RPMI-B27 supplemented with recombinant human HGF in 5% oxygen/5% CO2 for 5 days, and were treated with HCM Hepatocyte Culture Medium without EGF and hydrocortisone and supplemented with recombinant human oncostatin M for 5 days in ambient oxygen/5% CO2.

extract_protocol:
Total RNA was extracted by using Qiagen RNeasey Mini kit.
DNA was isolated using phenol/chloroform extraction and NaCl/EtOH precipitated with 20 μg glycogen carrier.
Transposed DNA was purified using a QIAGEN MinElute Reaction Cleanup kit. Transposed fragments were subjected to library preparation following manufacturer protocol
The H3K4me3 in-situ ChIA-PET was performed according to the previously described protocol (Li et al., 2017)
RNA libraries were prepared for sequencing by Novogene (CA).
ChIP-seq library was prepared for sequencing according to the amplification protocol from Illumina.
ATAC-seq libraries were sequenced using paired-end, dual-index sequencing on a NextSeq 500 instrument
The H3K4me3 in-situ ChIA-PET was performed according to the previously described protocol (Li et al., 2017)

value: hASC-derived adipocytes


title: Normal_rep5

value: control


title: WT_qCLASH_BR3

description: Ago IP RNA


title: WT_qCLASH_BR2

description: Ago IP RNA


title: Adip.RNAseq.A8.DMSO.1

description: ExpressionProfile.Adipocyte.txt


title: GC0063 Gastric Cancer

value: Gastric Cancer


title: Hepa.RNAseq.H1.Dex.2

description: ExpressionProfile.Hepatocyte.txt


title: GC0062 Gastric Cancer


title: Type 2 Diabetic_Rep3


title: GC0061 Gastric Cancer

value: diff


title: Normal_rep3


title: Adip.RNAseq.A8.Dex.3

description: ExpressionProfile.Adipocyte.txt


title: Hepa.RNAseq.H1.Dex.1

description: ExpressionProfile.Hepatocyte.txt


title: Adip.RNAseq.A8.Dex.2

description: ExpressionProfile.Adipocyte.txt


title: a_906_C2

city: College Park

first: Jiqiang

last: Ling

state: MD

address: 2202 Microbiology Bldg., 4062 Campus Dr.

department: Cell Biology and Molecular Genetics

institute: The University of Maryland, College Park

data_processing:
Data Filtering  Raw reads are filtered to remove reads containing adapters or reads of low quality, so that downstream analyses are based on clean reads.  The filtering process is as follows:  (1) Discard reads with adaptor contamination.  (2) Discard reads when uncertain nucleotides constitute more than 10 percents of either read (N > 10%).  (3) Discard reads when low quality nucleotides (base quality less than 20) constitute more than 50 percents of the read.  RNA-seq Adapter sequences (Oligonucleotide sequences of adapters from TruSeqTM RNA and DNA Sample Prep Kits):  RNA 5' Adapter (RA5), part # 15013205:  5'-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3'  RNA 3' Adapter (RA3), part # 15013207:  5'-GATCGGAAGAGCACACGTCTGAACTCCAGTCAC(6-nucleotide index)ATCTCGTATGCCGTCTTCTGCTTG-3'  Figure2.3􀀀Raw Reads Components  Results are shown as percentage of total raw reads.  (1)Adapter related: reads that had adapter contamination.  (2)Containing N: reads in which uncertain nucleotides constituted more than 10 percents of the read.  (3)Low quality: reads in which low quality nucleotides constituted more than 50 percents of the read.  (4)Clean reads: reads that passed quality control.  8 /
Mapping to a Reference Genome  Algorithm for mapping sequences: appropriate software is chosen according to the characteristics of the reference genome. In general, TopHat2 is chosen for animal and plant  genomes, and Bowtie2 is chosen for the genomes of bacteria and other species with a high gene density. The mismatch parameter is set to two, and other parameters are set to default.  Appropriate parameters are also set, such as the longest intron length. Only filtered reads are used to analyze the mapping status of RNA-seq data to the reference genome.

organism: Saccharomyces cerevisiae

source_name: Yeast cells

growth_protocol: Yeast cells were grown overnight at 30 °C and shifted to 37 °C for 1 or 2 hours

extract_protocol:
Total RNA extraction using QiaGen RNAeasy kit according to manufacture's protocol
After the QC procedures, mRNA from eukaryotic organisms is enriched using oligo(dT) beads. For prokaryotic samples, rRNA is removed using a specialized kit that leaves the  mRNA. The mRNA from either eukaryotic or prokaryotic sources is then fragmented randomly in fragmentation buffer, followed by cDNA synthesis using random hexamers and  reverse transcriptase. After first-strand synthesis, a custom second-strand synthesis buffer (Illumina) is added with dNTPs, RNase H and Escherichia coli polymerase I to generate the  second strand by nick-translation. The final cDNA library is ready after a round of purification, terminal repair, A-tailing, ligation of sequencing adapters, size selection and PCR  enrichment.
RNA-Seq by Novogene

tag: strains

value: AlaRS G906D

tag: treatment

value: 2 hour after shifting to 37 °C


title: Type 2 Diabetic_Rep2


title: Normal_rep1


title: WT_qCLASH_BR1

description: Ago IP RNA

tag: genotype


title: GC0058 Gastric Cancer

first: Satoko

last: Takizawa

source_name: Serum

value: IA


title: GC0060 Gastric Cancer

value: undiff


title: Adip.RNAseq.A8.Dex.1

description: ExpressionProfile.Adipocyte.txt


title: Normal_rep2

value: CD14+ monocytes


title: a_906_A2


title: a_906_B2


title: Adip.RNAseq.A8.DMSO.2

description: ExpressionProfile.Adipocyte.txt


title: s_719_C2

value: AlaRS C719A


title: Adip.RNAseq.A7.DMSO.3

description: ExpressionProfile.Adipocyte.txt


title: GC0056 Gastric Cancer


title: Normal_rep4


title: GC0057 Gastric Cancer


title: Adip.RNAseq.A7.DMSO.1

description: ExpressionProfile.Adipocyte.txt


title: GC0055 Gastric Cancer

value: Female


title: WT_C2

value: wild type


title: Adip.RNAseq.A7.Dex.2

description: ExpressionProfile.Adipocyte.txt


title: Adip.RNAseq.A7.Dex.3

description: ExpressionProfile.Adipocyte.txt


title: s_719_A2


title: GC0053 Gastric Cancer


title: WT_B2


title: WT_A2


title: GC0052 Gastric Cancer


title: Adip.RNAseq.A6.DMSO.3

description: ExpressionProfile.Adipocyte.txt


title: Adip.RNAseq.A7.DMSO.2

description: ExpressionProfile.Adipocyte.txt


title: reinal_organoid_wildtype_dd10

city: Kobe

first: Takesi

last: Matsuyama Hoyos

state: Hyogo

address: 2-2-3 Minatojima-minamimachi, Chuou-ku

department: BDR

institute: RIKEN

description:
Gene expression of DD10 wildtype retinal organoids
NCTdd10

hyb_protocol: Hybridization was conducted by Hokkaido System Corporation (Hokkaido, Japan), according to Agilent protocols using the Gene Expression Hybridization Kit (Agilent Technologies)

scan_protocol: Scanning was conducted by Hokkaido System Corporation (Hokkaido, Japan), according to Agilent protocols, using Agilent Technologies Microarray Scanner

data_processing: Data was processed by Hokkaido System Corporation (Hokkaido, Japan) suing Agilent Feature Extraction 12.0.3.1. Data was normalized (75 percentile shift) using GeneSpring GX

source_name: retinal organoids

label_protocol: Labeling was conducted by Hokkaido System Corporation (Hokkaido, Japan), according to Agilent protocols, using the Low Input Quick Amp Labeling Kit (Agilent Technologies)

growth_protocol: Retinal organoid were derived from mouse ES/iPS cell using the modified serum-free floating of embryoid-body-like aggregates with quick reaggregation method (SFEBq) (Eiraku et al., 2011, Assawachananont et al., 2014).

extract_protocol: RNA was prepared using TRIZOL reagent (thermo fisher), following manufacturers instructions. Extracted RNA was purified using QIAGEN RNeasy Micro Kit and quantified using a NanoDrop-1000 spectrophotometer and  the quality of purified RNA was monitored using Agilent 2100 Bioanalyzer.

treatment_protocol: Retinal organoids were harvested (5 per sample), homogenized. TRIZOL reagent was added and stored at -80°C until use.

value: wildtype

tag: time

value: differentiation day dd10

value: retinal organoids


title: s_719_B2


title: reinal_organoid_wildtype_dd16

description:
Gene expression of DD16 wildtype retinal organoids
NCTdd16

value: differentiation day dd16


title: a_906_C1

value: 1 hour after shifting to 37 °C


title: Adip.RNAseq.A6.DMSO.2

description: ExpressionProfile.Adipocyte.txt

value: hASC-derived adipocytes


title: a_906_B1


title: GC0049 Gastric Cancer

tag: disease state

value: Male


title: reinal_organoid_wildtype_dd23

description:
Gene expression of DD23 wildtype retinal organoids
NCTdd23

value: differentiation day dd23


title: Adip.RNAseq.A6.DMSO.1

description: ExpressionProfile.Adipocyte.txt


title: GC0054 Gastric Cancer

value: Gastric Cancer

tag: Sex

value: special


title: reinal_organoid_Islet1KO_dd16

description:
Gene expression of DD16 Islet1 KO retinal organoids
Isl1KO dd16

value: Islet1 KO


title: a_906_A1

value: AlaRS G906D


title: AdML+DNA#2+DNA#6_NMIA_8mM

city: La Jolla

first: Kaushik

last: Saha

address: 9500 Gilman Drive

department: Chemistry and Biochemistry

institute: University of California San Diego

data_processing:
Library strategy: SHAPE-MaP
Basecalls performed with Realtime Analysis (RTA) software launched automatically by MiSeq Control Software
All steps of the processing (including quality control by FastQC, alignment by Bowtie, and mutation counting) were carried out by SHAPEMapper 2.0. Each processed file is generated by counting mutations in DMSO (i.e. untreated), NMIA (i.e. treated), and DC (i.e. denatured control) reads of the corresponding samples.
Supplementary_files_format_and_content: tab-delimited files contain SHAPE reactivity per nucleotide

organism: Human adenovirus 2

source_name: In vitro transcribed from plasmid

extract_protocol:
RNA purification by Monarch RNA cleanup kit (New England Biolabs)
cDNA was PCR amplified using primers containing partial Illumina adapter for 20 cycles and then the library was further amplified for 8 cycles with dual index primers
Selective 2′ hydroxyl acylation followed by primer extension by mutational profiling (SHAPE-MaP)

treatment_protocol: RNAs were treated with 2 mM N-Methylisatoic anhydride (NMIA) for 1 hr at 16 °C or 8 mM NMIA for 30 min at 30 °C or the vehicle (DMSO) under the same conditions

value: annealed fluorescent DNA probe and 8 mM NMIA at 30 °C for 30 min


title: GC0048 Gastric Cancer

tag: age

value: IA

value: diff


title: Adip.RNAseq.A7.Dex.1

description: ExpressionProfile.Adipocyte.txt


title: Adip.RNAseq.A6.Dex.3

description: ExpressionProfile.Adipocyte.txt


title: s_719_C1

value: AlaRS C719A


title: Adip.RNAseq.A6.Dex.2

description: ExpressionProfile.Adipocyte.txt


title: AdML+DNA#2+DNA#6_DMSO

value: wild type

value: annealed fluorescent DNA probe and 6.7% DMSO at 30 °C for 30 min


title: GC0051 Gastric Cancer

value: undiff


title: GC0050 Gastric Cancer


title: GC0047 Gastric Cancer


title: reinal_organoid_Islet1KO_dd10

description:
Gene expression of DD10 Islet1 KO retinal organoids
Isl1KO dd10

value: differentiation day dd10

tag: tissue

value: retinal organoids


title: s_719_B1

value: 1 hour after shifting to 37 °C


title: GC0046 Gastric Cancer

tag: Stage

value: IB


title: AdML+DNA#2+DNA#3_NMIA_8mM


title: reinal_organoid_Islet1KO_dd23

description:
Gene expression of DD23 Islet1 KO retinal organoids
Isl1KO dd23


title: s_719_A1


title: reinal_organoid_Bhlhb4KO_dd23

description:
Gene expression of DD23 Bhlhb4 KO retinal organoids
B4KO dd23

value: Bhlb4 KO


title: GC0045 Gastric Cancer

value: Male

tag: histological subtype


title: reinal_organoid_Bhlhb4KO_dd16

description:
Gene expression of DD16 Bhlhb4 KO retinal organoids
B4KO dd16

value: differentiation day dd16


title: reinal_organoid_Bhlhb4KO_dd10

description:
Gene expression of DD10 Bhlhb4 KO retinal organoids
B4KO dd10


title: AdML+DNA#2+DNA#3_DMSO


title: Adip.RNAseq.A5.DMSO.3

description: ExpressionProfile.Adipocyte.txt

value: hASC-derived adipocytes


title: Adip.RNAseq.A5.DMSO.2

description: ExpressionProfile.Adipocyte.txt


title: AdML+DNA#2+DNA#5_NMIA_8mM


title: GC0044 Gastric Cancer

value: Gastric Cancer

value: Female


title: WT_B1


title: Adip.RNAseq.A5.DMSO.1

description: ExpressionProfile.Adipocyte.txt


title: GC0043 Gastric Cancer


title: AdML+DNA#2+DNA#5_DMSO


title: WT_A1


title: GC0042 Gastric Cancer


title: GC0041 Gastric Cancer


title: a_906_B0

value: AlaRS G906D

value: Before shifting to 37 °C


title: a_906_C0


title: AdML+SRSF1_DMSO_2mM

value: SRSF1 and 1.64% DMSO (vehicle) for 1 hour at 16 °C


title: Adip.RNAseq.A5.Dex.1

description: ExpressionProfile.Adipocyte.txt


title: a_906_A0


title: WT_C1


title: GC0040 Gastric Cancer

value: IA


title: Adip.RNAseq.A5.Dex.2

description: ExpressionProfile.Adipocyte.txt


title: GC0039 Gastric Cancer


title: AdMLΔ3'SSΔESE_DC in_vivo

description: Denatured control with 100 mM NAI

source_name: Transfected into HeLa cells

growth_protocol: HeLa cells grown in monolayer were transfected with U1 snRNA antisense morpholino oligonucleotide, then with the plasmids expressing the AdML variant under CMV promoter

extract_protocol:
RNA was extracted with Trizol
cDNA was PCR amplified using primers containing partial Illumina adapter for 20 cycles and then the library was further amplified for 8 cycles with dual index primers
Selective 2′ hydroxyl acylation followed by primer extension by mutational profiling (SHAPE-MaP)

treatment_protocol: Resuspended cells were treated with 2-methylnicotinic acid imidazolide (NAI) for 15 min at 37 °C followed by quenching with 125 mM DTT

value: 3' SS & ESE mutation (cagCT > accTC, TCA > AAT))

value: Denatured control with 100 mM NAI

tag: cell line

value: HeLa


title: AdMLΔ3'SSΔESE_in_vivo_NAI

description:
100 mM NAI for 15 min at 37 °C
Ad3E_vv_Ad3E

value: 100 mM NAI for 15 min at 37  degreeC


title: s_719_C0

value: AlaRS C719A


title: AdMLΔ3'SSΔESE_in_vivo_DMSO

description: DMSO for 15 min at 37 °C

value: DMSO for 15 min at 37  degreeC


title: GC0036 Gastric Cancer

value: undiff


title: GC0038 Gastric Cancer

value: IB

value: diff


title: s_719_B0


title: Adip.RNAseq.A4.DMSO.1

description: ExpressionProfile.Adipocyte.txt


title: Adip.RNAseq.A4.DMSO.2

description: ExpressionProfile.Adipocyte.txt


title: Adip.RNAseq.A5.Dex.3

description: ExpressionProfile.Adipocyte.txt


title: AdMLΔ3'SS_DC

description: Denatured control with 100 mM NAI

value: 3' splice site mutation (cagCT > accTC)


title: s_719_A0


title: Adip.RNAseq.A4.Dex.3

description: ExpressionProfile.Adipocyte.txt

value: hASC-derived adipocytes


title: AdML+SRSF1_NMIA_2mM

value: wild type

value: SRSF1 and 2 mM NMIA for 1 hour at 16 °C


title: GC0034 Gastric Cancer

value: Gastric Cancer

value: Male


title: GC0033 Gastric Cancer


title: AdMLΔ3'SS_in_vivo_NAI

description:
100 mM NAI for 15 min at 37 °C
Ad3_vv_Ad3


title: WT_C0

value: Before shifting to 37 °C


title: Adip.RNAseq.A4.Dex.2

description: ExpressionProfile.Adipocyte.txt


title: WT_B0


title: Adip.RNAseq.A4.DMSO.3

description: ExpressionProfile.Adipocyte.txt


title: GC0032 Gastric Cancer

value: Female

value: IA


title: Adip.RNAseq.A6.Dex.1

description: ExpressionProfile.Adipocyte.txt


title: WT_A0


title: AdML_DC

description: Denatured control with 100 mM NAI

value: Denatured control with 100 mM NAI


title: GC0031 Gastric Cancer


title: Adip.RNAseq.A3.DMSO.2

description: ExpressionProfile.Adipocyte.txt


title: Adip.RNAseq.A4.Dex.1

description: ExpressionProfile.Adipocyte.txt


title: AdML_in_vivo_NAI

description:
100 mM NAI for 15 min at 37 °C
Ad_vv_Ad

value: HeLa


title: Adip.RNAseq.A3.DMSO.3

description: ExpressionProfile.Adipocyte.txt


title: GC0030 Gastric Cancer


title: AdML_in_vivo_DMSO

description: DMSO for 15 min at 37 °C


title: Adip.RNAseq.A3.DMSO.1

description: ExpressionProfile.Adipocyte.txt


title: GC0029 Gastric Cancer


title: Ad5(GU)_DC_8mM

description: Denatured control 8 mM NMIA

growth_protocol: Not Applicable

value: 5' splice site mutation (gt > cc)

value: Denatured control 8 mM NMIA


title: Ad3(AG)_DC_8mM

description: Denatured control 8 mM NMIA

value: 3' splice site mutation (ag > cc)


title: tKO

city: San Antonio

first: Chu

last: Chen

state: Texas

address: 7703 Floyd Curl Dr

department: Cellular and Integrative Physiology

institute: UT Health San Antonio

data_processing:
CellRanger Mkfatsq/Count Analysis
Seurat R package (v3) was used for analysis. For quality control, cell with mitochondrial content > 30% were removed. And we retained genes with a count of 1 in at least 20 cells and removed cells with < 400 or > 6000 genes per cell.
Supplementary_files_format_and_content: nko-final.rds, ako-final.rds, and wt-final.rds are serialized R objects of the Bioconductor class ExpressionSet that contains the final data used to generate the results. It can be imported into R with `readRDS(“eset-final.rds”)`. It contains the gene counts, sample metadata, and feature metadata for single cells that passed quality control.
Supplementary_files_format_and_content: zip files cantain features, barcodes, and matrix files. These files can be imported in to R with "Read10X()". These files contain the raw cell count matrix exported by Cellranger software.

source_name: Brain

extract_protocol:
The brain tissue was extracted after anesthesia and single cell suspensions were prepared.
The libraries were prepared for sequencing following the manufacturer’s recommendations for the 10x Genomics 3’ Gene Expression v3 chemistry

treatment_protocol: Three mild closed head injury once a day for three days

tag: strain

value: 3 months

value: Brain

value: tKO


title: Ad3_DC_8mM

description: Denatured control 8 mM NMIA

value: 3' splice site mutation (cagCT > accTC)


title: GC0028 Gastric Cancer

value: undiff


title: Adip.RNAseq.A3.Dex.3

description: ExpressionProfile.Adipocyte.txt

value: hASC-derived adipocytes


title: AdMLΔ3'SS_in_vivo_DMSO

description: DMSO for 15 min at 37 °C

value: DMSO for 15 min at 37  degreeC


title: GC0027 Gastric Cancer

value: Gastric Cancer


title: AdBS_DC_8mM

description: Denatured control 8 mM NMIA

value: Branch site mutation (tgctgac > tgccgtt)


title: Adip.RNAseq.A3.Dex.1

description: ExpressionProfile.Adipocyte.txt


title: GC0026 Gastric Cancer

value: Male


title: Adip.RNAseq.A3.Dex.2

description: ExpressionProfile.Adipocyte.txt


title: 1809-AB-12

city: Ann Arbor

first: Scott

middle: John

last: Denstaedt

address: 109 Zina Pitcher Pl

department: Internal Medicine

institute: University of Michigan

description: Sample 12

data_processing:
Raw count data were processed by the University of Michigan Advanced Genomics Core.
Read files were concatenated into a fastq file for each sample. Raw read quality was checked using the program FastQC version v0.11.3 to identify potential quality problems from features of the data (e.g. low quality score, over-expressed sequences, and inappropriate GC content).
Reads were aligned to the reference genome including mRNAs and lncRNAs (ENSEMBL GRCm38) using Trim_Galore (v 0.5.0) to trim reads and aligned with STAR (v 2.6.0).
Mapped reads were collapsed using Lexogen's supplied collapse_UMI_bam binary
Reads were counted using the R package Rsubread and featureCounts function
Raw count data were then used for analysis in DESeq2 (v 1.22.2)
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include count data for each Sample and has been filtered and normalized VST using the R package deseq2 (v 1.22.2)

source_name: Lung

extract_protocol:
RNA was isolated from post-mortem lung tissues using TRIzol following the manufacturer's recommended protocol.
cDNA libraries were prepared using theQuantseq 3' mRNA FWD kit (Lexogen, Vienna, Austria) with the UMI Second strand synthesis Module (Lexogen), RNA libraries were subsequently prepared for sequencing using standard Illumina protocols
Quantseq

value: Lung

value: Unoperated


title: 1809-AB-10

description: Sample 10


title: 1809-AB-9

description: Sample 9


title: 1809-AB-11

description: Sample 11


title: Ad5_DC_8mM

description: Denatured control 8 mM NMIA

value: 5' splice site mutation (GTTGGGgtgag > ATTGGAaccac)


title: GC0025 Gastric Cancer

value: IB


title: 1809-AB-7

description: Sample 7


title: Adip.RNAseq.A2.DMSO.3

description: ExpressionProfile.Adipocyte.txt


title: Adip.RNAseq.A2.DMSO.2

description: ExpressionProfile.Adipocyte.txt


title: GC0024 Gastric Cancer

value: IA

value: diff


title: 1809-AB-6

description: Sample 6

value: CLP


title: Ad_DC_8mM

description: Denatured control 8 mM NMIA

value: wild type

value: Denatured control 8 mM NMIA


title: Adip.RNAseq.A2.DMSO.1

description: ExpressionProfile.Adipocyte.txt


title: 1809-AB-5

description: Sample 5


title: AdMLΔ3'SS(ΔAG)_NMIA_8mM

description:
8 mM NMIA at 30 °C for 30 min
3AG_Ad3AG

value: 3' splice site mutation (ag > cc)

value: 8 mM NMIA at 30 degreeC for 30 min


title: AdMLΔ3'SS(ΔAG)_DMSO

description: 6.7% DMSO at 30 °C for 30 min

value: 6.7percent DMSO at 30 degreeC for 30 min


title: Adip.RNAseq.A2.Dex.3

description: ExpressionProfile.Adipocyte.txt

value: hASC-derived adipocytes


title: GC0023 Gastric Cancer


title: GC0022 Gastric Cancer

value: undiff


title: 1809-AB-4

description: Sample 4


title: Adip.RNAseq.A2.Dex.2

description: ExpressionProfile.Adipocyte.txt


title: AdMLΔ5'SS(ΔGU)_NMIA_8mM

description:
8 mM NMIA at 30 °C for 30 min
5GU_Ad5GU

value: 5' splice site mutation (gt > cc)


title: 1809-AB-3

description: Sample 3


title: 1809-AB-8

description: Sample 8


title: GC0021 Gastric Cancer

value: Gastric Cancer


title: GC0020 Gastric Cancer

value: Female


title: 1809-AB-1

description: Sample 1

value: Lung

value: Male


title: GC0019 Gastric Cancer


title: AdMLΔ3'SS_NMIA_8mM

description:
8 mM NMIA at 30 °C for 30 min
8Ad3_Ad3

value: 3' splice site mutation (cagCT > accTC)


title: Adip.RNAseq.A1.DMSO.3

description: ExpressionProfile.Adipocyte.txt


title: 1809-AB-2

description: Sample 2


title: Adip.RNAseq.A1.DMSO.2

description: ExpressionProfile.Adipocyte.txt


title: AdMLΔ5'SS(ΔGU)_DMSO

description: 6.7% DMSO at 30 °C for 30 min


title: GC0018 Gastric Cancer


title: AdMLΔ3'SS_DMSO

description: 6.7% DMSO at 30 °C for 30 min

value: 6.7 percent DMSO at 30 degreeC for 30 min


title: Adip.RNAseq.A1.DMSO.1

description: ExpressionProfile.Adipocyte.txt


title: GC0017 Gastric Cancer

value: IA


title: O-Del72-ChIP_Oct4_48hr

city: Edinburgh

first: Abdenour

address: 5 Little France Drive

institute: University of Edinburgh

description: Oct4 ChIP in MEF O48h

data_processing:
The ChIP-seq pair-end reads were mapped to the Mus musculus genome assembly MGSCv37 (mm9) using Bowtie (version 2.3.4.1) and very sensitive parameters
Duplicated reads were then removed using MarkDuplicates from the Picard toolkit
Reads mapping to the backlisted regions as determined by Encyclopaedia of DNA Elements (ENCODE) were discarded.
The sequencing coverage and the insert size distribution were measured from the resulting bam files using Qualimap (version 2.2.1)
The peaks of OCT4 wild-type and mutants as well as SOX2, KLF4 and cMYC showing significant enrichment over input DNA were called using MACS2 (version 2.1.1.20160309), and a fragment size of 200 bp and were controlled to a q-value (minimum FDR) cut-off of 0.01. The peaks that overlapped with the ENCODE blacklist were removed.
Genome_build: mm9
Supplementary_files_format_and_content: The aligned ChIP-seq reads (bam files) were normalised for sequencing coverage to 1x genome depth (reads per genome coverage, RPGC) using the bamCoverage tool from DeepTools and a bin size of 10 bp and extendReads parameters. BAM files from replicates were merged before normalized for coverage

source_name: Mouse Embryonic Fibroblasts

extract_protocol:
Cells were then cross-linked with 1% formaldehyde for 10 min at room temperature. Crosslinking was quenched by adding 120 mM glycine and incubating for 10 min at room temperature. Cells were harvested using a scraper and pelleted by centrifugation at 1350 g for 5 min at 4°C. The crosslinked cell pellet was washed 3 times with 10 ml of ice-cold PBS. Finally, the pellet was flash frozen in liquid nitrogen and stored at -80°C.    Before nuclear extraction, the cell pellet was thawed on ice for 2-3 hr and resuspended in 10 ml filtered, ice-cold lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100 and 1 tablet of Complete Ultra protease inhibitor cocktail (Roche). The suspension was gently mixed on a rotating platform at 4°C for 10 min. The cells were disrupted using a 7 ml glass-Dounce homogeniser (40 strokes) on ice. The nuclei were pelleted by centrifugation (1350 g for 5 min at 4°C) and washed with 10 ml ice-cold wash buffer (10 mM Tris-HCl pH 8, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA and 1 tablet of Complete ultra-protease inhibitor cocktail (Roche) for 10 min at 4°C. The nuclei were collected by centrifugation and resuspended in 4 ml sonication buffer (10mM Tis-HCl pH 8, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine and 1 tablet of Complete ultra-protease inhibitor cocktail (Roche). The resuspended nuclei were split into four aliquots in pre-chilled 1 mL millitubes containing AFA Fibre and sonicated using a Covaris M220 Focused-ultrasonicator™ (Covaris, Woburn, MA). Each millitube was sonicated for 10 min and kept on ice for 30 min per sonication cycle for a total of 7 cycles. Sonicated chromatin was transferred to Protein Lobind tubes (Eppendorf). 100 µL of 10% Triton X-100 was then added to each 1 ml sonicated chromatin to increase solubility. Chromatin samples were then centrifuged (20,000 g at 4°C for 10 min) and the supernatants pooled into fresh tubes. A 50 µL aliquot of each pooled sample was analysed to check the fragment size distribution and quantify the DNA content of the resulting sonicated chromatin using a Nanodrop spectrophotometer. Another 50 µL aliquot was retained to be used as input for ChIP analysis. The sonicated chromatin and the input sample were snap frozen in liquid nitrogen and stored at -80°C.    For each ChIP, 30 µl Dyna Protein G magnetic beads (Thermo Fisher Scientific) were washed three times with 1 ml blocking solution (0.5% w/v BSA in PBS-Tween 20). The beads were saturated with the appropriate antibody by adding 10 µg of either OCT4 (Abcam), SOX2, KLF4 or cMYC (R&D) antibody and incubated on a rotating platform at 4°C for at least 6 hr. Sonicated chromatin (40 µg) was then mixed with the antibody-saturated beads and incubated on a rotating platform at 4°C overnight. The beads were transferred to a fresh tube, washed 5 times with 1 mL wash buffer (50 mM HEPES-KOH pH 7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-deoxycholate) and then washed once more with TE buffer (10 mM Tris-HCl pH 8, 1 mM EDTA) containing 50 mM NaCl. The bound-chromatin was eluted by incubating the beads in 210 µl elution buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, 1% SDS) at 65°C for 30 min. The beads were pelleted by centrifugation at 16000 g for 1 min and 200 µl supernatant containing the soluble chromatin was transferred to fresh tubes. The crosslinking was reversed by incubating the eluted chromatin and input DNA (in elution buffer) at 65°C for 16 hr with shaking. An equal volume of TE (200 µl) was added to the eluted chromatin and input DNA to reduce the concentration of SDS. RNA in the samples were digested by adding 0.2 mg/ml RNase A for 2 hr at 37°C. Proteins were then digested by adding 0.2 mg/ml Proteinase K for 2 hr at 55°C. The ChIP and Input DNA was subsequently purified by phenol-chloroform extraction followed by ethanol precipitation. The ChIP and input DNA pellets were resuspended in EB buffer (100 mM Tris pH 8) and DNA concentrations were measured by Qubit Fluorometric Quantitation (Invitrogen, Thermo Fisher Scientific).
ChIPed DNA from three biological replicates were pooled for each OCT4 variant (WT, del-61, del-72, del-73, del-75 and del-79), SOX2, KLF4, MYC and Input controls. The amount of DNA used in the library preparation ranged from ~ 20 – 80 ng. Input DNA from each sample was pooled in equal amounts for a single library preparation. The DNA libraries were prepared using NEBNext Ultra II DNA Library Prep Kit (New England Biolabs, Ipswich, MA) according to the manufacturer’s instructions. Each library was uniquely barcoded using NEBNext® Multiplex Oligos for Illumina® (Dual Index Primers Set 1) (New England Biolabs). Size selection of the DNA libraries was carried out using SpeedBeads™, which comprise magnetic carboxylate modified particles (Thermo Fisher Scientific). The quality of the DNA libraries was assessed using Agilent HS DNA Screen Tape (Agilent. Santa Clara, CA). The DNA libraries were then pooled by mixing an equal volume of each ChIP DNA library. The concentration of the ChIP DNA library pool was determined to be around 3o nM by Qubit Fluorometric Quantitation. The sequencing of the OCT4-48h ChIP-seq libraires were carried out by Edinburgh Genomics in Illumina NovaSeq and OSKM-48h ChIP-seq sequencing was done by the Beijing Genomics Institute using Illumina HiSeq 4000 system, both using a 50 bp pair-end next generation sequencing (Illumina, San Diego, CA).

value: Mouse Embryonic fibroblasts isolated from embryos at E12.5 stage

tag: mouse strain

tag: chip-antibody

value: Oct4 (Abcam, AB19857)


title: Input_Oct4_48h

description: Input DNA from MEF O48h

value: Input DNA control


title: AdMLΔBS_NMIA_8mM

description:
8 mM NMIA at 30 °C for 30 min
8AdBS_AdBS

value: Branch site mutation (tgctgac > tgccgtt)


title: Adip.RNAseq.A1.Dex.3

description: ExpressionProfile.Adipocyte.txt


title: AdMLΔBS_DMSO

description: 6.7% DMSO at 30 °C for 30 min


title: Adip.RNAseq.A1.Dex.2

description: ExpressionProfile.Adipocyte.txt


title: GC0016 Gastric Cancer


title: AdMLΔ5'SS_NMIA_8mM

description:
8 mM NMIA at 30 °C for 30 min
8Ad5_Ad5

value: 5' splice site mutation (GTTGGGgtgag > ATTGGAaccac)


title: Adip.RNAseq.A2.Dex.1

description: ExpressionProfile.Adipocyte.txt


title: O-Del73-ChIP_Oct4_48hr

description: Oct4 ChIP in MEF O48h


title: O-Del79-ChIP_Oct4_48hr

description: Oct4 ChIP in MEF O48h


title: GC0015 Gastric Cancer

value: diff


title: O-WT-ChIP_Oct4_48hr

description: Oct4 ChIP in MEF O48h


title: AdMLΔ5'SS_DMSO

description: 6.7% DMSO at 30 °C for 30 min

value: 6.7percent DMSO at 30 degreeC for 30 min


title: GC0014 Gastric Cancer


title: Adip.RNAseq.A1.Dex.1

description: ExpressionProfile.Adipocyte.txt

value: hASC-derived adipocytes


title: AdML_NMIA_8mM

description:
8 mM NMIA at 30 °C for 30 min
8Ad_AdML

value: wild type

value: 8 mM NMIA at 30 degreeC for 30 min