title: MDA231_UNC_rep2

city: Brisbane

first: Francesco

last: Casciello

state: Queensland

address: 300 Herston road

country: Australia

institute: QIMR Berghofer Medical Research Institute

data_processing:
Base calling oerformed with Illumina 1.8 basecaller
Sequence reads were trimmed for adapter sequences using Cutadapt (version 1.9) and aligned using STAR (version 2.5.2a) to the GRCh37 assembly with the gene, transcript, and exon features of Ensembl (release 70) gene model. Quality control metrics were computed using RNA-SeQC (version 1.1.8) and transcript quantification was performed using RSEM v1.2.30
Expression was estimated using RSEM (version 1.2.30)
Genome_build: GRCh37
Supplementary_files_format_and_content: Tab-delimited tsv files include raw counts for each sample as well as differential expression analysis of each treatment vs the vehicle (DMSO).

source_name: Breast cancer

growth_protocol: Cells were grown in full media (MDA-MB-231 and CAOV3 in DMEM and D12 in RPMI) containing 10%FBS and 1%P/S.

extract_protocol:
RNA was extracted using the TRIZOL (Invitrogen) protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with Vehicle (DMSO), UNC0642 (5 µM), GSK126 (10 µM) for 8 hours.

tag: cell line

tag: cell type

value: Breast cancer cell line

tag: treatment

value: Treated_G9a inhibitor

tag: disease state

value: Cancer


title: AI007_P5_POST

status: Public on Feb 20 2022

type: SRA

city: Chicago

first: Swati

last: Kulkarni

state: Illinois

address: 600 N. Lake Shore Drive, Apt 3602

department: Surgery

country: USA

institute: Northwestern University

description: KAPA HyperPrep

library_source: transcriptomic

data_processing:
RNA sequencing data analysis was performed using Artificial Intelligene’s (AI, www.artificialintelligene.com) RNAseq analysis platform. Briefly, short reads were aligned to the hg19 human genome using STAR. Subsequently cufflinks packages were used to perform transcript assemblies. Downstream differential gene expression calling on the reference and experimental groups of interest was performed using DESeq2. To perform clustering analyses on a group of samples, a union of all the genes and their expression RPKM values within that group was generated to build a read count matrix for the group of interest. Various unsupervised and other machine learning techniques were applied to this composite read count matrix of interest. The sample-sample correlation heatmaps represent the correlation observed between any two samples. The sample-feature heatmaps represent the signal intensity of a feature for any given sample. ggplot2, heatmap.2 and Pheatmap packages in R were used to build various heatmaps. Functional analysis was performed using gene set enrichment analyses.
Genome_build: HG19
Supplementary_files_format_and_content: counts

molecule: total RNA

organism: Homo sapiens

source_name: Breast tissue

extract_protocol:
Tissue frozen in RNAlater was homogenized and RNA isolated by Qiagen RNEasy Plus Kit. RNA sample was treated with DNASeq I.
Libraries were prepared using KAPA mRNA HyperPrep Kit (KK8580). 100ng RNA was used for each library

treatment_protocol: Bariatric surgery

value: post

tag: patientid

tag: race

value: White

tag: age

tag: childhood obesity

value: No known history

tag: menopause

value: Postmenopausal

tag: hypertension

tag: diabetes

tag: metabolic syndrome

tag: dislipidemia hypercholesterolemia

tag: age of menarche

value: Unknown

tag: depression

value: No

tag: pre weight

tag: pre height

tag: pre bmi

tag: pre waist to hip ratio

tag: post weight

tag: post height

tag: post bmi

tag: post waist to hip ratio

tag: percent ebw loss

tag: type of surgery

value: Roux-En-Y Gastric Bypass

tag: pre or post surgery

value: post 25% EBW loss


title: screen_1:B6:nrd1

city: Jerusalem

first: Alon

last: Chappleboim

address: Givat Ram

department: Biological chemistry

country: Israel

institute: Hebrew University of Jerusalem

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|B6

data_processing:
bcl2fastq (v2.20) for splitting libraries with "-l WARNING --minimum-trimmed-read-length 5 --no-lane-splitting --mask-short-adapter-reads 5 -p 8 -o <output_dir>"
Splitting internal barcodes with a python script (perfect matches only)
R1 were aligned using bowtie2 (2.3.4.3) to the S.cer genome (SacCer3-R64), K.lac genome (build 2515-2), and to K.lac genome were any 18-mer found in the S.cer genome was removed. This alignment was only used to count aligned reads.
R1 were ACG-converted with an awk script and aligned using bowtie2 (2.3.4.3) to a version of the S.cer genome (SacCer3-R64) and the K.lac genome (build 2515-2) that were also converted to an ACG-only alphabet. This alignment was only used to count aligned reads.
R1 were ACG-converted with an awk script and aligned using bowtie2 (2.3.4.3) to a version of the S.cer genome (SacCer3-R64) that was also converted to an ACG-only alphabet. Multiple alignments were allowed. Following alignment an awk script was used to count and mark all deviations of the original observed sequence from the reference genome.
Read filteration and dedupping; Reads in all sequencing runs had lengths between 44-46, and we discarded reads with more than 30 observed Ts (binomial probability < 4e-7, observed fraction ~ 4e-3). For typical analyses of mRNA, we only considered reads that were aligned less than five times with at most 3 errors excluding T→C conversions. Out of these alignments, only the best one was reported. Reads were de-duplicated by grouping according to  (chromosome, strand, position, and UMI), and in each such group, the read with least amount of deviations from the reference was selected.
Filtered and deduplicated alignments were assigned to transcripts by their intersection with a window of 300 bp upstream and 100 bp downstream of previously reported transcription termination site annotations. Read statistics were then collected on individual transcripts, groups of transcripts, or the whole transcriptome in the form of a table with the number of reads for each combination of observed Ts and observed T→C vonersions.
Binomial mixture model was applied to read statistics to estimate conversion/nascent parameters. K. lac proportion of each sample was used to estaimte the relative amount of mRNA between sampels in the same experiment.
Genome_build: SacCer3-R64 (GCA_000146045.2)
Supplementary_files_format_and_content: features.csv.gz - each row is a genomic feature used in analysis (corresponds to "acc" in processed tables)
Supplementary_files_format_and_content: genotypes.csv - each row is a strain and its genotype description
Supplementary_files_format_and_content: samples.csv - each row is a sample with its metadata  (corresponds to "sample" in processed tables)
Supplementary_files_format_and_content: tc_data.csv.gz - gzipped table in which each row is the number of reads with observed Ts and T-C conversions in a specific transcript and a specific sample.
Supplementary_files_format_and_content: reads.csv.gz - gzipped table containing the number of reads (and spike-in-scaled reads) observed in each transcript in each sample
Supplementary_files_format_and_content: pnew.csv.gz - gzipped table containing the estimated proportion of nascent molecules in each transcript in each sample

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: midlog yeast

growth_protocol: Cells were grown overnight in YPD 2% Glucose at 30C. 1-2 hours prior to experiments, cells are distributed to a deep well plate, grown at 25C, and (robotically) pipette-mixed every 10-15 minutes.

extract_protocol:
MetOH is washed twice with ddw. Cells are subjected to proteinaseK treatment, followed by potassium-acetate precipiation. Supernatanant is passed through nucleic-acid binding column, washed multuple time in 60% EtOH and eluted in 10 mM TRIS  pH 7.5. Up to this point DTT is added to maintain reducing conditions. Finally, RNA is roughly quantified and subjected to an alkylation reaction (4tU->C), followed by another binding-washing-elution step.
polyT primers with barcode and UMI are added to each sample and reverse transcription is performed. Samples are pooled, and subjected to a tn5 reaction. Finally an elongation step to extend transposase adapters and a PCR is performed to enrich tagged cDNA. In this protocol R2 starts with a 7bp sample barcode, followed by a 8 bp UMI followed by putative polyT. R1 immediately starts by reading the sense strand, enriched to the 3' of polyA mRNA. I2 is added in PCR and denotes a specific library/experiment. I1 is a constant sequence - ATCTCGTA.

treatment_protocol: At indiicated timepoints auxin (1-2.5 mM, per exp) was added to each sample. 6-10 minutes prior to harvesting 5 mM 4tU is added to samples. Finally cells are harvested by transferring 500 ul to 600 ul of pre-frozen MetOH (-80) that included a constant spike-in of K. lactis cells, and frozen (-80) until further processing.


title: C14

type: RNA

city: Louisville

first: Norman

middle: L

last: Lehman

state: Kentucky

address: CTRB Room 307, 505 South Hancock St.

institute: The University of Louisville

hyb_protocol: Per manufacturer's instructions.

scan_protocol: Per manufacturer's instructions.

data_processing: Nsolver 2.1

source_name: tumor

label_protocol: Per manufacturer's instructions.

extract_protocol: Total RNA was extracted from three 30μm scrolls cut from FFPE tissue blocks containing minimally 90% tumor using the RecoverAll total nucleic acid isolation kit (Ambion/Thermo Fisher Scientific, Waltham, MA) per the manufacturer’s instructions. RNA was then passed through concentration and clean-up columns (Norgen Biotek, Thorold, ON) and quantified using a Nanodrop spectrophotometer (Thermo Fisher Scientific, Waltham, MA).

tag: histology

value: astroblastoma


title: MDA231_UNC_GSK_rep1

tag: cell line

tag: cell type

tag: treatment

tag: disease state


title: MDA231_UNC_GSK_rep2


title: MDA231_GSK_rep1

value: Treated_EZH2 inhibitor


title: MDA231_UNC_rep1


title: MDA231_GSK_rep2


title: C11


title: AI007_P58_POST

description: KAPA HyperPrep

tag: patientid

tag: race

tag: age

tag: childhood obesity

tag: menopause

value: Premenopausal

tag: hypertension

tag: diabetes

tag: metabolic syndrome

tag: dislipidemia hypercholesterolemia

tag: age of menarche

tag: depression

value: Yes

value: Sleeve Gastrectomy


title: screen_1:B9:nab3

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|B9


title: screen_1:B4:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|B4


title: 0425-1iN RNA-Seq

city: Thousand Oaks

first: Xianglong

last: Zhang

state: CA

address: One Amgen Center Dr.

department: Department of Cardiometabolic Disorders

institute: Amgen Inc.

data_processing:
RNA-Seq data: Cutadapt (Version 1.8.1) was used to trim Illumina TruSeq adapters and low-quality ends from the raw reads. Bowtie2 (Version 2.3.1) was used to align the trimmed reads to the RefSeq transcriptome (GRCh38.p10) and RSEM (Version 1.2.30) was used to quantify gene expression in a strand-specific manner by setting parameter “--forward-prob 0”. DESeq2 (Version 1.12.4) was used to perform differential expression analysis between cell types as well as between patients and controls within each cell type.
Methylation data: Cutadapt (Version 1.8.1) was used to trim Illumina adapters and low-quality ends from the raw reads. The trimmed reads were mapped to human RefSeq genome (GRCh38.p10) using Bismark (Version 0.16.3). Duplicates were removed by the deduplicate_bismark script in Bismark. Only one copy of the overlapping parts in the middle of paired-end reads was retained after clipping the read with the lower average quality in the overlap region by the “clipOverlap” tool in bamUtil (Version 1.0.14). Methylation ratio for each CpG was extracted by the bismark_methylation_extractor script in Bismark. Differentially methylated regions (DMRs) were identified between cell types as well as between patients and controls within each cell type by metilene (Version 0.2-6) with >= 3 CpGs and a mean methylation difference between the two compared groups of >= 0.2. DMRs with FDR corrected p-value < 0.05 were considered significant.
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: RNA-Seq data — gene name, transcript id, length, effective_length, expected count, TPM, FPKM
Supplementary_files_format_and_content: Methylation data — chromosome, CpG position, CpG methylation ratio

source_name: induced neuron

growth_protocol: In order to generate induced neurons (iNs), iPSCs cells were maintained under feeder-free conditions in mTeSR1 media ( STEMCELL Technologies). Media was changed daily.  Once cell density reached 75%-80% confluence, clones were dissociated and plated onto 6 well plates.  On day 1, cells were infected with lentivirus ( RTTa, GFP and Ngn2) in mTESR1 media.  Day 2, media was replace with N2 media and doxycycline.  From days 3-6, puromycin selection continued with N2 media changes every day.

extract_protocol:
Genomic DNA was extracted from fibroblast and iPSC’s using Blood & Cell Culture DNA mini kit (Qiagen) and iN’s using Quick –DNA Miniprep Plus Kit (Zymo Research).  Total RNA was extracted from fibroblast, iPSC’s and iN’s using the RNeasy mini kit and RNeasy micro kit (Qiagen).
Libraries were prepared according to KAPA biosystems instructions accompanying KAPA library Preparation Kit Illumina platforms. In brief, genomic DNA was sonicated (Covaris) to generate fragments 180-220 bp in size. Following fragmentation, DNA was used to construct library. After library construction, DNA libraries were bisulfite converted and purified using the EZ DNA Methylation Lightning Kit (Zymo Research). Bisulfite converted samples libraries were amplified using LM-PCR. Amplified bisulfite converted samples and SeqCap Epi probes were hybridized for 64-72 h. Captured DNA samples were washed and recovered, followed by amplification of the capture DNA samples using LM-PCR. Amplified samples were purified using Agencourt AMPure XP Beads (Beckman Coulter). Bisulfite converted libraries captured by SeqCap Epi CpGiant Probes kit sequenced on Illumina HiSeq 4000 platform by 2x150 paired-end.   For RNA-seq, library construction was performed using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs) following manufacturer’s instructions. Briefly, total RNA was converted to mRNA using polyA purification. The mRNA was then fragmented and primed for cDNA synthesis. The cDNA was adenylated and adapters were ligated onto the cDNA. Samples were amplified using PCR, amplified library was then purified using Agencount AMPure XP beads (Beckman Coulter). Final libraries were checked for quality on a Bioanalyzer DNA High Sensitivity chip (Agilent). Stand-specific RNA libraries of all the samples were sequenced on Illumina NextSeq 550 platform using 2x150 paired-end sequencing.

tag: individual

tag: phenotype

value: wild type

value: induced neuron


title: C12

tag: histology


title: C13


title: C16


title: AI007_P1_POST

description: KAPA HyperPrep

value: African American

value: Yes and currently active.

value: yes

tag: pre weight

tag: pre height

tag: pre bmi

tag: pre waist to hip ratio

tag: post weight

tag: post height

tag: post bmi

tag: post waist to hip ratio

tag: percent ebw loss

tag: type of surgery

tag: pre or post surgery


title: AI007_P15_POST

description: KAPA HyperPrep

tag: treatment

value: post

tag: patientid

tag: race

value: White

tag: age

tag: childhood obesity

tag: menopause

tag: hypertension

tag: diabetes

tag: metabolic syndrome

tag: dislipidemia hypercholesterolemia


title: screen_1:B1:pap2

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|B1


title: screen_1:B2:not1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|B2


title: MDA231_DMSO_rep2

tag: cell line

tag: cell type

value: Breast cancer cell line

value: Untreated

tag: disease state

value: Cancer


title: C8

tag: histology


title: C9


title: CAOV3_UNC_GSK_rep2

source_name: Ovarian cancer

value: Ovarian cancer cell line


title: CAOV3_UNC_GSK_rep1


title: C10r


title: AI007_P19_POST

description: KAPA HyperPrep

value: No known history

tag: age of menarche

tag: depression

value: No

tag: pre weight

tag: pre height

tag: pre bmi

tag: pre waist to hip ratio

tag: post weight

tag: post height

tag: post bmi

tag: post waist to hip ratio

tag: percent ebw loss

value: Roux-En-Y Gastric Bypass

value: post 25% EBW loss


title: screen_1:B3:pop2

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|B3


title: screen_1:A12:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|A12


title: AI007_P8_POST

description: KAPA HyperPrep

tag: treatment

tag: patientid

tag: race

tag: age

tag: childhood obesity

tag: menopause

value: Postmenopausal

tag: hypertension

tag: diabetes

tag: metabolic syndrome

value: Yes

tag: type of surgery

value: Biliopancreatic Diversion with Duodenal Switch

tag: pre or post surgery


title: screen_1:A11:fcp1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|A11


title: C4

tag: histology

value: astroblastoma


title: CAOV3_GSK_rep2

tag: cell line

tag: cell type

value: Treated_EZH2 inhibitor

tag: disease state


title: C6


title: AI007_P69_POST

description: KAPA HyperPrep

tag: dislipidemia hypercholesterolemia

tag: age of menarche

tag: depression

tag: pre weight

tag: pre height

tag: pre bmi

tag: pre waist to hip ratio

tag: post weight

tag: post height

tag: post bmi

tag: post waist to hip ratio

value: Roux-en-Y Gastric Bypass


title: screen_1:A10:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|A10


title: AI007_P2_POST

description: KAPA HyperPrep

tag: treatment

tag: patientid

tag: race

tag: age

tag: childhood obesity

tag: menopause

tag: hypertension

value: yes

tag: diabetes

tag: metabolic syndrome

tag: percent ebw loss

tag: type of surgery

value: Sleeve Gastrectomy


title: MDA231_DMSO_rep1

tag: cell line

tag: cell type

tag: disease state


title: CAOV3_GSK_rep1


title: screen_1:A9:nab3

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|A9


title: C3

tag: histology


title: AI007_P17_POST

description: KAPA HyperPrep

value: post

value: African American

value: Premenopausal

tag: dislipidemia hypercholesterolemia

tag: age of menarche

tag: depression

tag: pre weight

tag: pre height

tag: pre bmi

tag: pre waist to hip ratio

tag: post weight

tag: post height

tag: post bmi

tag: pre or post surgery


title: screen_1:A8:sen1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|A8


title: CAOV3_UNC_rep2

tag: treatment

value: Treated_G9a inhibitor

value: Cancer


title: AI007_P29_POST

description: KAPA HyperPrep

tag: patientid

tag: race

tag: age

tag: childhood obesity

value: No known history

tag: menopause

tag: hypertension

tag: diabetes

tag: metabolic syndrome

tag: post waist to hip ratio

tag: percent ebw loss

tag: type of surgery


title: C2

tag: histology


title: screen_1:A7:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|A7


title: CAOV3_UNC_rep1

tag: cell line

tag: cell type

value: Ovarian cancer cell line

tag: disease state


title: C1


title: MSKPCa3_siYAP_Rep2

city: New York

first: Yu

last: Chen

state: NY

address: 1275 York Ave, Box 20

department: Human Oncology and Pathogenesis Program

institute: Memorial Sloan Kettering Cancer Center

data_processing:
RNA sequencing reads were 3’ trimmed for base quality 15 and adapter sequences using version 0.4.5 of TrimGalore, and then aligned to human assembly hg19 with STAR v2.6 using default parameters to generate BAM alignment files.
feature counts were calculated using featureCounts from Subread package
Genome_build: GRCh37.p13
Supplementary_files_format_and_content: tab delimited text file containing counts of genes

source_name: prostate cancer organoid

growth_protocol: MSK-PCa3 prostate cancer organoid cells were maintained in human organoid media as described previously (PMID: 25201529, 26797458).

extract_protocol:
RNA extraction was performed using TRIzol according to manufacture's instuction (Thermo Fisher Scientific #15596018).
RNA-Seq libraries were prepared using the Illumina TruSeq Stranded mRNA kit, with 8 cycles of PCR amplification, starting from 500 ng of total RNA, at the Integrative Genomics Operation (IGO) at MSKCC.

treatment_protocol: MSK-PCa3 cells were transfected with a pooled ON-TARGETplus siRNAs targeting FOSL1, YAP, TAZ, or YAP/TAZ (Dharmacon) using RNAiMAX (Thermo Fisher Scientific #13778075) for 48 hours prior to RNA extraction.

tag: primary site

value: Prostate

tag: knockdown

value: YAP

tag: replicate


title: screen_1:A6:nrd1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|A6


title: CAOV3_DMSO_rep2

tag: treatment

value: Untreated


title: AI007_P25_POST

description: KAPA HyperPrep

tag: patientid

tag: race

tag: age

value: Postmenopausal

tag: dislipidemia hypercholesterolemia

tag: age of menarche

tag: depression

value: No

tag: pre weight

tag: pre height

tag: pre bmi

tag: pre waist to hip ratio

tag: post weight

tag: post height

tag: post bmi

tag: pre or post surgery

value: post 25% EBW loss


title: CAOV3_DMSO_rep1

tag: cell line

tag: cell type

tag: disease state


title: MSKPCa3_siYAPTAZ_Rep2

tag: primary site

tag: knockdown

value: YAP and TAZ

tag: replicate


title: D14_UNC_GSK_rep2

source_name: Melanoma

value: Melanoma cell line

tag: treatment


title: AI007_P20_POST

description: KAPA HyperPrep

tag: patientid

tag: race

value: White

tag: age

tag: childhood obesity

value: Yes and currently active.

tag: menopause

tag: hypertension

value: yes

tag: diabetes

tag: metabolic syndrome

tag: dislipidemia hypercholesterolemia

tag: age of menarche

tag: post waist to hip ratio

tag: percent ebw loss

tag: type of surgery

value: Roux-En-Y Gastric Bypass


title: screen_1:A4:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|A4


title: screen_1:A5:nrd1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|A5


title: AI007_P33_POST

description: KAPA HyperPrep

value: post

value: Yes but currently inactive.

value: Premenopausal

tag: depression

tag: pre weight

tag: pre height

tag: pre bmi

tag: pre waist to hip ratio

tag: post weight

tag: post height

tag: post bmi

value: Biliopancreatic Diversion with Duodenial Switch

tag: pre or post surgery


title: MSKPCa3_siTAZ_Rep2

tag: primary site

tag: knockdown

value: TAZ

tag: replicate


title: screen_1:A2:not1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|A2


title: D14_GSK_rep2

tag: cell line

tag: cell type

tag: treatment

value: Treated_EZH2 inhibitor

tag: disease state

value: Cancer


title: AI007_P59_POST

description: KAPA HyperPrep

tag: patientid

tag: race

value: African American

tag: age

tag: childhood obesity

value: No known history

tag: menopause

tag: hypertension

tag: diabetes

tag: metabolic syndrome

tag: dislipidemia hypercholesterolemia

tag: age of menarche

tag: post waist to hip ratio

tag: percent ebw loss

tag: type of surgery

value: Sleeve Gastrectomy


title: AI007_P30_POST

description: KAPA HyperPrep

tag: depression

value: No

tag: pre weight

tag: pre height

tag: pre bmi

tag: pre waist to hip ratio

tag: post weight

tag: post height

tag: post bmi

tag: pre or post surgery

value: post 25% EBW loss


title: screen_1:A3:pop2

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|A3


title: MSKPCa3_siTAZ_Rep1

tag: primary site

value: Prostate

tag: knockdown

tag: replicate


title: MSKPCa3_siFOSL1_Rep2


title: AI007_P56_POST

description: KAPA HyperPrep

tag: treatment

tag: patientid

tag: race

value: White

tag: age

tag: childhood obesity

tag: menopause

value: Postmenopausal

tag: hypertension

tag: diabetes

tag: metabolic syndrome

tag: dislipidemia hypercholesterolemia

value: Yes


title: D14_UNC_GSK_rep1

tag: cell line

tag: cell type

value: Melanoma cell line

tag: disease state


title: D14_UNC_rep2

value: Treated_G9a inhibitor


title: MSKPCa3_siFOSL1_Rep1


title: AI007_P54_POST

description: KAPA HyperPrep

value: post

tag: age of menarche

tag: depression

tag: pre weight

tag: pre height

tag: pre bmi

tag: pre waist to hip ratio

tag: post weight

tag: post height

tag: post bmi

tag: post waist to hip ratio

tag: percent ebw loss

tag: type of surgery

tag: pre or post surgery


title: AI007_P26_POST

description: KAPA HyperPrep

tag: treatment

tag: patientid

tag: race

tag: age

tag: childhood obesity

value: Yes and currently active.

tag: menopause

tag: hypertension

tag: diabetes

tag: metabolic syndrome

tag: dislipidemia hypercholesterolemia

value: Roux-En-Y Gastric Bypass


title: screen_1:A1:pap2

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|A1


title: MSKPCa3_siYAP_Rep1

tag: primary site

tag: knockdown

value: YAP

tag: replicate


title: D14_GSK_rep1

tag: cell line

tag: cell type

value: Treated_EZH2 inhibitor

tag: disease state


title: MSKPCa3_siCtrl_Rep2

value: Scrambled


title: D14_UNC_rep1

value: Cancer


title: AI007_P39_POST

description: KAPA HyperPrep

value: African American

value: Premenopausal

value: No known history

tag: age of menarche

tag: depression

tag: pre weight

tag: pre height

tag: pre bmi

tag: pre waist to hip ratio

tag: post weight

tag: post height

tag: post bmi

tag: post waist to hip ratio

tag: percent ebw loss

tag: type of surgery

value: Biliopancreatic Diversion with Duodenal Switch

tag: pre or post surgery


title: MSKPCa3_siYAPTAZ_Rep1

tag: primary site

value: Prostate

tag: knockdown

value: YAP and TAZ

tag: replicate


title: D14_DMSO_rep2

tag: cell line

tag: cell type

tag: treatment

value: Untreated

tag: disease state


title: AI007_P64_POST

description: KAPA HyperPrep

tag: patientid

tag: race

value: White

tag: age

tag: childhood obesity

tag: menopause

tag: hypertension

value: yes

tag: diabetes

tag: metabolic syndrome

tag: dislipidemia hypercholesterolemia

tag: age of menarche

tag: depression

value: No

tag: pre weight

tag: pre height

value: Sleeve Gastrectomy

value: post 25% EBW loss


title: AI007_P62_POST

description: KAPA HyperPrep

value: post

tag: pre bmi

tag: pre waist to hip ratio

tag: post weight

tag: post height

tag: post bmi

tag: post waist to hip ratio

tag: percent ebw loss

tag: type of surgery

tag: pre or post surgery


title: D14_DMSO_rep1

tag: cell line

tag: cell type

value: Melanoma cell line

tag: treatment

tag: disease state


title: LNCaP_YAP-FOSL1-Rep1

description: featureCountOut_LNCaP_oe_rnaSeqAll_wRep.txt

source_name: prostate cancer cell line

growth_protocol: LNCaP prostate cancer cells (ATCC CRL-1740) were maintained in RPMI medium supplemented with 10% fetal bovine serum and 1% pen/strep.

treatment_protocol: LNCaP cells were transduced with retroviruses to stably express FOSL1, YAP, YAP/FOSL1, TAZ, or TAZ/FOSL1.

tag: primary site

tag: overexpressed gene

value: YAP and FOSL1

tag: replicate


title: AI007_P43_POST

description: KAPA HyperPrep

tag: patientid

tag: race

tag: age

tag: childhood obesity

tag: menopause

tag: hypertension

tag: diabetes

tag: metabolic syndrome

tag: dislipidemia hypercholesterolemia

tag: age of menarche

tag: depression

tag: pre weight

tag: pre height


title: smFISH:D12:spt6

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
fish1|D12

tag: rep

value: A

tag: treat

value: IAA


title: smFISH:H12:spt6

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
fish1|H12

value: B


title: LNCaP_YAP-Rep2

tag: primary site

tag: overexpressed gene

value: YAP


title: AI007_P40_POST

description: KAPA HyperPrep

tag: treatment

tag: patientid

value: African American

value: No known history

value: Premenopausal

tag: pre bmi

tag: pre waist to hip ratio

tag: post weight

tag: post height

tag: post bmi

tag: post waist to hip ratio

tag: percent ebw loss

tag: type of surgery

tag: pre or post surgery


title: LNCaP_YAP-Rep1

value: Prostate

tag: replicate


title: smFISH:B12:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
fish1|B12


title: smFISH:A12:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
fish1|A12

value: mock


title: AI007_P44_POST

description: KAPA HyperPrep

tag: race

value: White

tag: age

tag: childhood obesity

tag: menopause

tag: hypertension

tag: diabetes

tag: metabolic syndrome

tag: dislipidemia hypercholesterolemia

tag: age of menarche

tag: depression

value: Yes

tag: pre weight

tag: pre height


title: smFISH:G12:spt6

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
fish1|G12

tag: rep

tag: treat


title: LNCaP_TAZ-FOSL1-Rep2

tag: primary site

tag: overexpressed gene

value: TAZ and FOSL1


title: Col-0 rep4

city: Blacksburg

first: Brenda

last: Winkel

state: VA

address: 1015 Life Science Circle

department: Biological Sciences

institute: Virginia Tech

description: wild type

data_processing:
Following sequencing, data were trimmed for both adaptor and quality using a combination of ea-utils and Btrim (Aronesty, e-utils, 2011; Kong, Genomics, 2011).
Sequencing reads were then be aligned to the genome using Tophat2/HiSat2 (Kim et al., Nature Methods, 2015) and counted via HTSeq (Anders et al., Bioinformatics, 2014.
QC summary statistics were examined to identify any problematic samples (e.g. total read counts, quality and base composition profiles (+/- trimming)), raw fastq formatted data files, aligned files (bam and text file containing sample alignment statistics), and count files (HTSeq text files).
Following successful alignment, miRNA and mRNA differential expression were determined using contrasts of and tested for significance using the Benjamini-Hochberg corrected Wald Test in the R-package DESeq2 (Love et al., Genome Biology, 2014).
One of the tt4-11 libraries was eliminated from the final analysis based on quality control outcomes.
Data were normalized such that the total expression within each sample was identical; the sample with the least total expression was used to reduce the others to the same total count.
Supplementary_files_format_and_content: File contains counts and base mean for each gene/transcript, log2fold change, pvalue, padj, gene names, and annotations from Arabidopsis.org (downloaded 06-09-2021).

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: Seeds were sown on 1X MS medium, pH 5.7, 2% sucrose, 0.8% agar as described previously (Kubasek et al., 1992), in 15 mm Petri dishes; following stratification at 4°C in darkness for 3-5 days, seedlings were grown at 22°C in continuous light (~100 µE).

extract_protocol:
RNA was extracted using the Qiagen RNeasy Plant Maxi or Mini Kit with DNase on-column digestion (Qiagen, Germantown, MD)
Libraries (four wild-type and four tt4-11) were prepared at the Virginia Tech Genomics Core Sequencing Laboratory using the TruSeq Stranded mRNA HT Sample Prep Kit (Illumina), which uses polyA enrichment.  These were sequenced on a HiSeq 2500 (Illumina) using Rapid Run 1x100 single read cycle clustering and sequencing.

treatment_protocol: At 5 days following germination, whole seedlings were harvested in 100 mg aliquots, flash frozen in liquid nitrogen, and stored at -80°C prior to processing

tag: light

value: 5 days post germination

tag: genotype


title: tt4-11 rep2

description: chalcone synthase null line

tag: age


title: tt4-11 rep4

description: chalcone synthase null line


title: tt4-11 rep3

description: chalcone synthase null line


title: smFISH:F12:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
fish1|F12


title: AI007_P41_POST

description: KAPA HyperPrep

tag: treatment

tag: patientid

tag: race

tag: childhood obesity

value: Postmenopausal

value: yes

value: No

tag: pre bmi

tag: pre waist to hip ratio

tag: post weight

tag: post height

tag: post bmi

tag: post waist to hip ratio

tag: percent ebw loss

tag: type of surgery

value: Roux-En-Y Gastric Bypass

tag: pre or post surgery

value: post 25% EBW loss


title: Col-0 rep3

description: wild type


title: LNCaP_TAZ-FOSL1-Rep1

tag: primary site

tag: overexpressed gene

tag: replicate


title: MSKPCa3_siCtrl_Rep1

tag: knockdown

value: Scrambled


title: smFISH:E12:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
fish1|E12

tag: rep

value: B

tag: treat


title: LNCaP_YAP-FOSL1-Rep2

value: YAP and FOSL1


title: AI007_P42_POST

description: KAPA HyperPrep

tag: treatment

value: post

tag: patientid

tag: race

tag: age

tag: menopause

tag: hypertension

tag: diabetes

tag: metabolic syndrome

tag: dislipidemia hypercholesterolemia

tag: age of menarche

tag: depression

tag: pre weight

tag: pre height


title: thio_4tU_test:F9:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
calib|F9

tag: add

value: dmso

tag: control

value: no

tag: time


title: thio_4tU_test:F4:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
calib|F4

tag: rep

value: A


title: smFISH:C12:spt6

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
fish1|C12

tag: treat

value: mock


title: AI007_P45_POST

description: KAPA HyperPrep

tag: treatment

tag: patientid

value: White

tag: childhood obesity

value: No known history

value: Premenopausal

tag: pre bmi

tag: pre waist to hip ratio

tag: post weight

tag: post height

tag: post bmi

tag: post waist to hip ratio

tag: percent ebw loss

tag: type of surgery

tag: pre or post surgery


title: Col-0 rep1

description: wild type

tag: light

tag: age

value: 5 days post germination

tag: genotype


title: LNCaP_TAZ-Rep1

tag: primary site

value: Prostate

tag: overexpressed gene

value: TAZ

tag: replicate


title: thio_4tU_test:E9:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
calib|E9

tag: rep

tag: add

value: thio

tag: control

tag: time


title: dChaf1b rep2 (RNA-seq)

city: Riverside

first: Sihem

last: Cheloufi

state: California

address: 3401 Watkins Dr.

department: Biochemistry

institute: University fo California Riverside

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, then mapped to reference genome mm9 using STAR
Transcript abundance was calculated using Htseq
Genome_build: mm9
Supplementary_files_format_and_content: abundance measurements

organism: Mus musculus

source_name: HSPCs

growth_protocol: CD117+ Hematopoietic Stem and Progenitor cells were grown in Stemspan SFEMII supplemented with 50 ng/mL SCF, 20 ng/mL IL6, 10 ng/mL IL3, 1:200 LDL

extract_protocol:
RNA was extracted from HSPCs lysed in TRI, and collected on Direct-Zol miniprep columns with on-column DNAse digestion.
For HSPCs, RNA-sequencing libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with  Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 ¬µg  of total RNA was used as starting material. Libraries were validated using the Agilent DNA  1000 Kit

treatment_protocol: To induce deletion, HSPCs were spinfected with MIGR1-Cre (or MIGR1-empty for control). eGFP positive cells were sorted two days after spinfection

tag: strain

tag: cell type

value: CD117+ hematopoietic stem and progenitors (HSPCs)

tag: treatment

value: spinfected with MIGR1-Cre for 48 hours


title: thio_4tU_test:E4:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
calib|E4


title: LNCaP_FOSL1-Rep2


title: dChaf1b rep1 (RNA-seq)


title: xrn1_ko:H5:hygŒ¥xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
e6tc1|H5

tag: repeat

value: ko


title: LNCaP_EV-Rep2

value: Empty Vector


title: LNCaP_FOSL1-Rep1


title: xrn1_ko:H4:natŒ¥xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
e6tc1|H4

value: B


title: MIGR1 rep2 (RNA-seq)

value: Chaf1b (fl/fl)

value: spinfected with MIGR1 for 48 hours


title: xrn1_ko:H2:natŒ¥xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
e6tc1|H2


title: xrn1_ko:H3:hygŒ¥xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
e6tc1|H3


title: Col-0 rep2

description: wild type


title: LNCaP_TAZ-Rep2

description: featureCountOut_LNCaP_oe_rnaSeqAll_wRep.txt


title: LNCaP_EV-Rep1


title: Hoxa9 OFF 24hrs rep2 (RNA-seq)

source_name: Lys-GFP-ER-HoxA9 cells

growth_protocol: Granulocyte-macrophage progenitor cells containing Hoxa9::ER were cultured in RPMI-1640 supplemented with 10% FBS, 100U ml-1 penicillin, 100 µg ml−1 streptomycin, 2mM L-alanyl-L-glutamine dipeptide and stem cell factor (SCF). The source of SCF was conditioned media generated from a Chinese hamster ovary (CHO) cell line that stably secretes SCF. Conditioned medium was added at a final concentration of 1 - 2 % depending on the batch. β-Estradiol (abbreviated E2) was added to a final concentration of 150 ng/ml from a 3 mg/ml stock dissolved in 100% ethanol.

extract_protocol:
Qiagen RNeasy mini kit.
NEB RNA-seq kit

treatment_protocol: For CAF-1 suppression, IPTG was added at a concentration of 500 µM to express IPTG-inducible Chaf1b shRNA. For Hoxa9 inactivation, cells were washed with PBS twice and then cultured in media without Estradiol.

value: Lys-GFP-ER-HoxA9 cells

value: Culture out of beta-estradiol for 24 hours for HOXA9 inactivation


title: xrn1_ko:G11:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
e6tc1|G11

value: wt


title: Si-CREB3L1 rep2

city: Shanghai

first: Guohe

last: Song

state: Shanghai

address: 180, fenglin road

country: China

institute: Fudan university

data_processing:
The original image data file obtained by Illumina Hiseq recognition was transformed into the  original sequencing sequence (Sequenced Reads) base on the CASAVA(latest version) base recognition  (Base Calling) analysis
In order to guarantee the data quality which was used to analysis, the  useful Perl script was used to filter the original data (Raw Data). The steps are:  1)Trim Smart-seq2 public primer sequence from the Reads (If the length of trimmed  Reads is lower than 30bp, reads should be discarded. If it is PE sequence, both  of the reads must be removed );  2)Remove the contaminated reads for adapters (The contaminated reads for  adapters was defined that the Read Bases contained more than 5bp of adapter  sequences. If either one of the PE Reads was polluted, we will remove both ends  of the reads);  3)Remove the low quality reads (The low quality reads was defined that the number  of Reads Bases whose phred Quality value was less than or equal to 19  accounted for more than 15% . If either one of the PE Reads defined as low  quality, we will remove both ends of the reads);  4)Remove the reads whose N base more than 5% for total bases (If either one of  the PE Reads had high Ns bases, we will remove both ends of the reads);
The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html). Clean Data was then aligned to the reference genome using HISAT2 v2.1.0.
Reads Count for each gene in each sample was counted by featurecount, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.Genes with q≤0.05 and |log2_ratio|≥1 are identified as differentially expressed genes  (DEGs) by using DESeq2-a R package.
Genome_build: GRCH38

source_name: HuCCT1 cells

growth_protocol: HuCCT1 cells were grown in RPMI medium 1640 supplemented with 10% FBS.

extract_protocol:
Total RNAs of bone marrow derived macrophages (BMDMs) (~1x106) were extracted by the manual of TRIzol (TaKaRa).
Preparation of library by using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® and sequencing of transcriptome were implemented with Illumina HiSeq 2500 system

treatment_protocol: RNA interference to knockdown CREB3L1 expression was performed with lentiviral transduction. The knockdown efficiency were validated by RT-PCR and Western blotting.

value: Human cholangiocarcinoma cells


title: Si-CREB3L1 rep3


title: Hoxa9 OFF 24hrs rep1 (RNA-seq)


title: xrn1_ko:G2:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
e6tc1|G2

value: A


title: IPTG treated control 24hrs Rep2 (RNA-seq)

value: Culture with IPTG for 24 hours to serve as a control


title: Si-CREB3L1 rep1


title: IPTG treated control 24hrs Rep1 (RNA-seq)


title: Si-Ctrl rep3

value: Si-Ctrl


title: MIGR1 rep1 (RNA-seq)


title: Si-Ctrl rep2


title: spikin_calib:D11:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
calib|D11

tag: klac


title: spikin_calib:D10:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
calib|D10


title: CAF-1 OFF 24hrs rep2 (RNA-seq)

value: Culture with IPTG for 24 hours for CAF-1 suppression


title: CAF-1 OFF 24hrs rep1 (RNA-seq)


title: RA-FLS_sample 4_control

city: Kobe

first: Koji

last: Fukuda

address: 7-5-1 Kusunoki, Chuo

department: Department of Orthopaedic Surgery

country: Japan

institute: Kobe University Graduate School of Medicine

description: Gene expression data from non-stimulated RA-FLS sample4

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 with Hybridization, Wash and Stain Kit.

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000 scanner.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was set to 500.

label: biotin

source_name: Fibroblast like synoviocytes from patient with rheumatoid arthritis, sample4

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250ng total RNA (3' IVT Express Kit User Manual, 2008, Affymetrix).

growth_protocol: RA-FLS were cultured in DMEM supplemented with 10% fetal bovine serum (FBS; BioWhittaker, Walkersville, MD, USA) and 100 units/ml of penicillin/streptomycin at 37°C with 5% CO2.

extract_protocol: Total RNA was extracted using the QIAshredder and RNeasy Mini kit (Qiagen, Hilden, Germany) according to the manufacture’s protocol.

treatment_protocol: RA-FLS were incubated with either 1.0 μg/ml recombinant human LIGHT protein (LIGHT; R&D Systems, Minneapolis, MN, USA) or phosphate buffered saline (PBS) diluted with serum-free Opti-MEM medium as non-stimulated control for 12 hours at 37°C with 5% CO2.

value: Fibroblast like synoviocytes

tag: patient diagnosis

value: rheumatoid arthritis

tag: stimulation

value: control


title: spikin_calib:D9:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
calib|D9


title: spikin_calib:D8:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
calib|D8


title: RA-FLS_sample 4_LIGHT-stimulated

description: Gene expression data from LIGHT-stimulated RA-FLS sample4

source_name: Fibroblast like synoviocytes from patient with rheumatoid arthritis, sample4, LIGHT-stimulated

value: LIGHT-stimulated


title: Hoxa9 OFF 24hrs rep2 (ATAC-seq)

library_source: genomic

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, then mapped to reference genome mm9 using BWA
Normalized genome coverage bigWig files were generated by Deeptools
Genome_build: mm9
Supplementary_files_format_and_content: bigWig

molecule: genomic DNA

extract_protocol:
Cells were washed in PBS twice, counted and nuclei were isolated from 100,000 cells using 100 μl hypotonic buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40) to generate two independent transposition reactions. Nuclei were split in half and treated with 2.5 μl Illumina Tn5 Transposase for 30 min at 37 °C. DNA were isolated from transposed nuclei.
The libraries were constructed by PCR using barcoded Illumina Nextera primers.


title: Si-Ctrl rep1


title: M14 STAG2-KD_SMC1A 2

city: Bad Nauheim

first: Lei

last: Gu

state: MASSACHUSETTS

address: parkstreet 1

country: Germany

institute: Max Planck Institute for heart and lung research

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg19 genome assembly using bwa
Data were filtered using the samtools and picard
peaks were called using macs2
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated using deeptools
Supplementary_files_format_and_content: peak text files

source_name: melanoma cell line

extract_protocol:
Cell was extracted and protein-DNA complex was immunoprecipited as described before (Hu et al, Gene Dev 2016). Briefly,  Cells were fixed in 1% of fresh formaldehyde for 10 minutes at room temperature, quenched  with glycine and washed twice with ice-cold PBS. Cells were re-suspended in lysis buffer 1 (50 mM HEPESKOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100) for 10 minutesat 4C, pelleted, and then re-suspended in lysis buffer 2 (200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 10 mM Tris pH8) for 5 minutes at 4 ºC. Cells were finally re-suspended in RIPA buffer (50mM Hepes pH 7.9, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 0.2% SDS, 0.5 mM PMSF, and 1x  Protease inhibitor cocktail (Roche)) to a final concentration of 5x107 cells/ml. Chromatin was sonicated to an  average size of 350bp with a Branson sonifier 450 equipped with a micro probe. Chromatin was cleared by  centrifugation at 20,000xg for 10 minutes, and then incubated with 5-10μg of antibodies pre-bound to  Dynabeads protein G (Life technologies), and rotated overnight at 4C.After extensive washing on beads, bound chromatin was eluted and de-crosslinked in 300μl of elution buffer (50 mM Tris pH8, 10 mM EDTA, 1% SDS, 0.3M NaCl) overnight at 650C. Proteinases K was added to a final concentration of 200 μg/ml and incubated at 45C for 2 hours. DNA was ethanol precipitated, re-suspended in TE and purified using the DNA Clean & Concentrator-5 kit (Zymo Research).
Libraries were prepared as described before (Hu et al, Genes Dev, 2016). Briefly, 2.5 to 40ng DNA was end repaired, end adenylated, and then ligated with Illumina Truseq indexed adaptors. The ligated DNA was purified with AMPure XP beads(Beckman Coulter), and then amplified with KAPA HiFi DNA Polymerase (KAPA Biosystems) for 8 to 13 cycles. After amplification, the library DNA was separated on a 2% agarose gel, and DNA fragments in the 200-500 bp range were purified with a gel DNA recovery kit (Zymo Research). The purified DNA was diluted to 10 nM, and multiplexed for sequencing in a HiSeq2000 sequencer following the manufacturer's protocols.

tag: cell line

tag: antibody

value: SMC1A (Bethyl, A300-055A, lot:5)

tag: genotype/variation


title: M14 STAG2-KD_input 2


title: Hoxa9 OFF 24hrs rep1 (ATAC-seq)


title: M14 WT_input 2

value: wild type


title: Acute Coronary Syndrome (ACS)

first: Takuo

last: Emoto

state: Hyogo

address: 7-5-1 Kusunoki-cho, Chuo-ku

department: Division of Cardiovascular Medicine, Department of Internal Medicine

data_processing:
Cell Ranger Single Cell Software (v 6.0.1) by 10X Genomics against the GRCh38 human reference genome with default parameter
Genome_build: GRCh38
Supplementary_files_format_and_content: Cell Ranger output mtx, barcodes, and features

source_name: Coronary Atherosclerotic Plaques

extract_protocol:
Generation of single cell sequencing libraries were prepared as outlined in the 10x Genomics Single Cell 3′ Reagent Kits v3.1 user guide.
Each sequencing library was generated with a unique sample index. Libraries were sequenced on the Illumina NovaSeq 6000 system.

tag: disease

value: Coronary Atherosclerotic Plaques


title: Control vs. luteolin

city: Nagoya

first: Aya

last: Naiki-Ito

address: 1-Kawasumi, Mizuho-cho, Mizuho-ku

department: Department of Experimental Pathology and Tumor Biology

institute: Nagoya City University Graduate School of Medical Sciences

hyb_protocol: 1 µg of labeled probe was used for hybridization with TaKaRa Hybridization Chamber at 37°C for 16 hours. After hybridization, slides were washed sequential

scan_protocol: Scanned on 3D-gene Scanner 3000 (TORAY)

data_processing: LOWESS normalized, background subtracted data obtained.

source_name: Control

label_protocol: １ µg of total RNA were amplified with Ambion Amino Allyl aRNA kit, then 10 µg of amlified RNA labelded with Amersham Cy5 or Cy3 Mono-Reactive Dye.

growth_protocol: 22Rv1 cells were cultured in RPMI1640 medium.

extract_protocol: Total RNA was extracted from 22Rv1using ISOGEN (Nippon Gene) following manufacturer's instructions

treatment_protocol: 22Rv1 cells were treated  25 μM luteolin for 48 hours.

value: Human prostate cancer cell line

source_name: treatment


title: Stable Angina Pectoris (SAP)


title: RA-FLS_sample 3_LIGHT-stimulated

description: Gene expression data from LIGHT-stimulated RA-FLS sample3

source_name: Fibroblast like synoviocytes from patient with rheumatoid arthritis, sample3, LIGHT-stimulated


title: RA-FLS_sample 2_control

description: Gene expression data from non-stimulated RA-FLS sample2

source_name: Fibroblast like synoviocytes from patient with rheumatoid arthritis, sample2


title: spikin_calib:D7:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
calib|D7

source_name: midlog yeast

value: B


title: RA-FLS_sample 1_control

description: Gene expression data from non-stimulated RA-FLS sample1

source_name: Fibroblast like synoviocytes from patient with rheumatoid arthritis, sample1


title: RA-FLS_sample 1_LIGHT-stimulated

description: Gene expression data from LIGHT-stimulated RA-FLS sample1

source_name: Fibroblast like synoviocytes from patient with rheumatoid arthritis, sample1, LIGHT-stimulated


title: RA-FLS_sample 3_control

description: Gene expression data from non-stimulated RA-FLS sample3

source_name: Fibroblast like synoviocytes from patient with rheumatoid arthritis, sample3


title: spikin_calib:C11:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
calib|C11


title: RA-FLS_sample 2_LIGHT-stimulated

description: Gene expression data from LIGHT-stimulated RA-FLS sample2

source_name: Fibroblast like synoviocytes from patient with rheumatoid arthritis, sample2, LIGHT-stimulated


title: IPTG treated control 24hrs Rep2 (ATAC-seq)

value: Lys-GFP-ER-HoxA9 cells


title: IPTG treated control 24hrs Rep1 (ATAC-seq)


title: M14 STAG2-KD_CTCF 2

value: CTCF (Cell Signaling, 2899s, lot:2)


title: M14 WT_CTCF 2


title: spikin_calib:C10:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
calib|C10


title: spikin_calib:C9:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
calib|C9


title: CAF-1 OFF 24hrs rep1 (ATAC-seq)


title: spikin_calib:C8:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
calib|C8


title: M14 STAG2-KD_STAG2 2


title: P. oryzae mycelia - H3K27me3_sin3_rep2_input

city: Hangzhou

first: Chuyu

last: Lin

state: Zhejiang

address: 866#, Yuhangtang Road

department: College of Agriculture and Biotechnology

institute: Zhejiang University

data_processing:
High-throughput sequencing was carried out using Illumina Hiseq-PE150 by Novogene Corporation (Beijing, China) for Illumina (Langmead et al., 2009).
The clean read pairs were mapped to the reference genome with Bowtie2 (Version 2.3.5) (Langmead and Salzberg, 2012)
Enriched peaks were called by HOMER (Version 4.9.1) with default parameters (Heinz, 2010).
Genome_build: MG8
Supplementary_files_format_and_content: peak text files; bedGraph

organism: Pyricularia oryzae

source_name: mycelia

growth_protocol: The Pyricularia oryzae strains were grown on CM medium at 28℃ in the dark for 2 days, followed by growth under continuous lights for 5 days. Then taking 10-12 pieces of mycelia and culture them in liquid CM medium for 2 days.The mycelia were harvested by 2-3 layers of Miracloth.

extract_protocol:
The ChIP experiments with mycelia cultured in liquid CM for 2 days were conducted as previous reports with minor modification (He et al., 2018; Tao et al., 2017). Briefly, 1.0 g mycelia were crosslinked with 1% formaldehyde for 20 mins and stopped with 125 mM glycine for 5 mins at room temperature. Samples were ground with liquid nitrogen and resuspended in nuclei isolating buffer. Subsequently the precipitated nuclei were used to total chromatin extraction with 1mL lysis buffer. The lysis chromatin was sonicated into DNA fragments between 200-500 bp using Diagenode Bioruptor. 20μL chromatin was used to input DNA extraction and the remainder was pre-cleared with 10μL protein A Dynabeads (Thermofisher, 10001D) for 1 hour. Subsequently the chromatin was incubated with anti-H3K27me3 (Abcam, ab6002) overnight at 4°C. Another 20μL protein A Dynabeads was used capture protein-DNA mixture and followed by three washing. Protein-DNA mixture was reverse-crosslinked, and DNA was recovered with phenol-chloroform extraction. The recovery DNA was used as template for followed ChIP-qPCR and ChIP-seq. Two biological repeats were conducted.
The purified DNA was used as libraries construction with the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645L).

treatment_protocol: The mycelia were crosslinked with 1% formaldehyde for 20 mins and stopped with 125 mM glycine for 5 mins at room temperature.

tag: isolate

value: mutant Mosin3

value: complete medium

tag: tissue

value: mycelia

value: input


title: P. oryzae mycelia - H3K27me3_sin3_rep2_IP

description: sin3_vs_background_H3K27me3_DE_Peaks.txt

value: anti-H3K27me3 (Abcam, ab6002)


title: P. oryzae mycelia - H3K27me3_sin3_rep1_input


title: M14 WT_STAG2 2


title: P. oryzae mycelia - H3K27me3_p55_rep2_IP

value: mutant Mop55


title: spikin_calib:C7:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
calib|C7

tag: rep

value: A


title: P. oryzae mycelia - H3K27me3_sin3_rep1_IP


title: M14 WT_STAG1 2


title: P. oryzae mycelia - H3K27me3_p55_rep1_IP


title: ATAC-Seq Hoxa9 OFF 48hrs rep2

description:
Hoxa9 OFF 48hrs rep2
Culture out of beta-estradiol for 48 hours for HOXA9 inactivation


title: 4tU_timecourse_calib:B12:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
calib|B12


title: KD

data_processing:
Basecalls performed using CASAVA version 1.4
Hi-C paired-end reads were aligned to hg19 using Hi-C Pro pipeline
Data were filtered using HOMER
TADs were identified by using findTADsAndLoops.pl and TADbit
Genome_build: hg19
Supplementary_files_format_and_content: peak text files

extract_protocol:
STAG2 Knockdown or control cells were fixed in 1% of fresh formaldehyde for 10 minutes at room temperature, quenched with glycine and washed twice with ice-cold PBS. In situ Hi-C was then performed following the protocol by Rao et al (cell 2014). Briefly, nuclei were permeabilized, and DNA was digested overnight with 100 U MboI (New England BioLabs). The ends of the restriction fragments were labeled using biotin-14-dATP (Life Technologies) and then ligated in 1.2 mL final volume. After reversal of crosslinks, ligated DNA was purified and sheared to a length of ~400 bp with a Covaris E220 evolution instrument (Covaris, Woburn, MA). Ligation junctions were then pulled down with streptavidin beads.
HiC libraries were constructed as described before (Rao et al, cell, 2014). Briefly,  DNA fragments were end-repaired, dA-tailed and Illumina adapters ligated. Libraries were produced by 8 cycles of PCR amplification with KAPA Hifi DNA polymerase (Roche). The HiC libraries were size selected with AMPure XP beads and sequenced at Quick Biology Inc. (Pasadena, CA)

tag: tag

value: STAG2 KD


title: ATAC-Seq Hoxa9 OFF 48hrs rep1

description:
Hoxa9 OFF 48hrs rep1
Culture out of beta-estradiol for 48 hours for HOXA9 inactivation


title: P. oryzae mycelia - H3K27me3_p55_rep2_input


title: 4tU_timecourse_calib:B11:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
calib|B11


title: ATAC-Seq IPTG treated control 48hrs Rep2

description:
IPTG treated control 48hrs Rep2
Culture with IPTG for 48 hours to serve as a control


title: 4tU_timecourse_calib:B10:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
calib|B10


title: ATAC-Seq IPTG treated control 48hrs Rep1

description:
IPTG treated control 48hrs Rep1
Culture with IPTG for 48 hours to serve as a control


title: CAF-1 OFF 24hrs rep2 (ATAC-seq)

value: Culture with IPTG for 24 hours for CAF-1 suppression


title: ATAC-Seq CAF-1 OFF 48hrs rep2

description:
CAF-1 OFF 48hrs rep2
Culture with IPTG for 48 hours for CAF-1 suppression


title: 4tU_timecourse_calib:B9:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
calib|B9


title: P. oryzae mycelia - H3K27me3_kmt6_rep2_IP

description: kmt6_vs_background_H3K27me3_DE_Peaks.txt

value: mutant Mokmt6


title: M14 STAG2-KD H3K27ac HiChIP rep2

data_processing:
mapping using hicpro with hg19
loop calling using FitHiChIP
differential loop calling using diffloop
Genome_build: hg19
Supplementary_files_format_and_content: bed for loop information

growth_protocol: M14 expressing doxy-inducible STAG2 shRNA was maintained in RPMI supplemented with 10% FBS, 1% penicillin- streptomycin- glutamine (PSG) and 1ug/ml puromycin.

extract_protocol:
HiChIP assays were performed according to the previously published protocol (PMID:27643841) Briefly, Briefly, ~10 million cells were crosslinked with 1% Formaldehyde for 10 mins at room temperature and lysed with Hi-C lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.2% NP40) supplemented with protease inhibitors for 30 mins at 4C. Chromatin was digested by the MboI restriction enzyme for two hours at 37C. The sticky ends of the digested DNA were filled with dCTP, dGTP, dTTP and biotin-labeled dATP by DNA Polymerase I, Large Klenow Fragment, and then ligated by T4 DNA ligase for 4 hours at room temperature. Chromatin was sonicated in Nuclear Lysis buffer (50 mM Tris-HCl pH 7.5, 10 mM EDTA, 1% SDS), 1:5 diluted in ChIP Dilution buffer (16.7 mM Tris-HCl pH 7.5, 1.2 mM EDTA, 1.1% Triton X-100, 167 mM NaCl, 0.01% SDS), and then processed with regular chromatin immunoprecipitation using the H3K27ac antibody (7.5ug each sample, Abcam, ab4729). The H3K27ac-associated Biotin-labeled DNA fragments were then enriched by Streptavidin C1 magnetic beads (8ul each sample) and processed for library preparation.
Libraries were prepared for sequencing according to Illumina Nextera DNA library preparation protocol.

treatment_protocol: Cells were cultured with (STAG2-KD) or without (WT) doxycycline for 5 d before they were collected for crosslinking.

value: Human melanoma cell line

tag: chip antibody

value: H3K27ac antibody (Abcam, ab4729)


title: M14 STAG2-KD_STAG1 2


title: ATAC-Seq CAF-1 OFF 48hrs rep1

description:
CAF-1 OFF 48hrs rep1
Culture with IPTG for 48 hours for CAF-1 suppression


title: P. oryzae mycelia - H3K27me3_kmt6_rep2_input


title: M14 WT_SMC1A 2

value: SMC1A (Bethyl, A300-055A, lot:5)

value: wild type


title: 4tU_timecourse_calib:B7:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
calib|B7


title: P. oryzae mycelia - H3K27me3_kmt6_rep1_IP


title: M14 STAG2-KD H3K27ac HiChIP rep1

source_name: M14 expressing doxy-inducible STAG2 shRNA


title: ATAC-Seq t0 rep2

description:
t0 rep2
Culture with beta-estradiol to serve as a 0hrs control

source_name: Lys-GFP-ER-HoxA9 cells


title: 4tU_timecourse_calib:B8:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
calib|B8


title: M14 WT H3K27ac HiChIP rep2


title: P. oryzae mycelia - H3K27me3_p55_rep1_input


title: ATAC-Seq t0 rep1

description:
t0 rep1
Culture with beta-estradiol to serve as a 0hrs control


title: 4tU_timecourse_calib:B5:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
calib|B5


title: M14 WT H3K27ac HiChIP rep1


title: P. oryzae mycelia - H3K27me3_kmt6_rep1_input


title: P. oryzae mycelia - H3K27me3_WT_rep2_IP


title: P. oryzae mycelia - H3K27me3_WT_rep2_input


title: WT


title: RNA-Seq Hoxa9 OFF 48hrs rep2

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, then mapped to reference genome mm9 using STAR
Transcript abundance was calculated using Htseq
Genome_build: mm9


title: 4tU_timecourse_calib:B6:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
calib|B6


title: 4tU_timecourse_calib:B4:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
calib|B4


title: RNA-Seq Hoxa9 OFF 48hrs rep1


title: 4tU_timecourse_calib:B3:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
calib|B3


title: M14 WT_input

data_processing:
mapping using bowtie2 with hg19
peak calling using macs2
Genome_build: hg19
Supplementary_files_format_and_content: fastq for raw datat and bed for peak data

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Purified ChIP DNA was end repaired, end adenylated, and then ligated with Illumina Truseq indexed adaptors. The ligated DNA was purified with AMPure XP beads (Beckman Coulter) and then amplified with KAPA HiFi DNA Polymerase (KAPA Biosystems) for 8 to 13 cycles. After amplification, the library DNA was size selected with AMPurex XP beads to 200-600 bp range.


title: RNA-Seq IPTG treated control 48hrs Rep2


title: M14 STAG2-KD_SMC1A


title: RNA-Seq IPTG treated control 48hrs Rep1


title: P. oryzae mycelia - H3K27me3_WT_rep1_input


title: P. oryzae mycelia - H3K27me3_WT_rep1_IP


title: 4tU_timecourse_calib:B2:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
calib|B2

data_processing:
bcl2fastq (v2.20) for splitting libraries with "-l WARNING --minimum-trimmed-read-length 5 --no-lane-splitting --mask-short-adapter-reads 5 -p 8 -o <output_dir>"
Splitting internal barcodes with a python script (perfect matches only)
R1 were aligned using bowtie2 (2.3.4.3) to the S.cer genome (SacCer3-R64), K.lac genome (build 2515-2), and to K.lac genome were any 18-mer found in the S.cer genome was removed. This alignment was only used to count aligned reads.
R1 were ACG-converted with an awk script and aligned using bowtie2 (2.3.4.3) to a version of the S.cer genome (SacCer3-R64) and the K.lac genome (build 2515-2) that were also converted to an ACG-only alphabet. This alignment was only used to count aligned reads.
R1 were ACG-converted with an awk script and aligned using bowtie2 (2.3.4.3) to a version of the S.cer genome (SacCer3-R64) that was also converted to an ACG-only alphabet. Multiple alignments were allowed. Following alignment an awk script was used to count and mark all deviations of the original observed sequence from the reference genome.
Read filteration and dedupping; Reads in all sequencing runs had lengths between 44-46, and we discarded reads with more than 30 observed Ts (binomial probability < 4e-7, observed fraction ~ 4e-3). For typical analyses of mRNA, we only considered reads that were aligned less than five times with at most 3 errors excluding T→C conversions. Out of these alignments, only the best one was reported. Reads were de-duplicated by grouping according to  (chromosome, strand, position, and UMI), and in each such group, the read with least amount of deviations from the reference was selected.
Filtered and deduplicated alignments were assigned to transcripts by their intersection with a window of 300 bp upstream and 100 bp downstream of previously reported transcription termination site annotations. Read statistics were then collected on individual transcripts, groups of transcripts, or the whole transcriptome in the form of a table with the number of reads for each combination of observed Ts and observed T→C vonersions.
Binomial mixture model was applied to read statistics to estimate conversion/nascent parameters. K. lac proportion of each sample was used to estaimte the relative amount of mRNA between sampels in the same experiment.
Genome_build: SacCer3-R64 (GCA_000146045.2)
Supplementary_files_format_and_content: features.csv.gz - each row is a genomic feature used in analysis (corresponds to "acc" in processed tables)
Supplementary_files_format_and_content: genotypes.csv - each row is a strain and its genotype description
Supplementary_files_format_and_content: samples.csv - each row is a sample with its metadata  (corresponds to "sample" in processed tables)
Supplementary_files_format_and_content: tc_data.csv.gz - gzipped table in which each row is the number of reads with observed Ts and T-C conversions in a specific transcript and a specific sample.
Supplementary_files_format_and_content: reads.csv.gz - gzipped table containing the number of reads (and spike-in-scaled reads) observed in each transcript in each sample
Supplementary_files_format_and_content: pnew.csv.gz - gzipped table containing the estimated proportion of nascent molecules in each transcript in each sample

extract_protocol:
MetOH is washed twice with ddw. Cells are subjected to proteinaseK treatment, followed by potassium-acetate precipiation. Supernatanant is passed through nucleic-acid binding column, washed multuple time in 60% EtOH and eluted in 10 mM TRIS  pH 7.5. Up to this point DTT is added to maintain reducing conditions. Finally, RNA is roughly quantified and subjected to an alkylation reaction (4tU->C), followed by another binding-washing-elution step.
polyT primers with barcode and UMI are added to each sample and reverse transcription is performed. Samples are pooled, and subjected to a tn5 reaction. Finally an elongation step to extend transposase adapters and a PCR is performed to enrich tagged cDNA. In this protocol R2 starts with a 7bp sample barcode, followed by a 8 bp UMI followed by putative polyT. R1 immediately starts by reading the sense strand, enriched to the 3' of polyA mRNA. I2 is added in PCR and denotes a specific library/experiment. I1 is a constant sequence - ATCTCGTA.


title: M14 WT_SMC1A


title: RNA-Seq CAF-1 OFF 48hrs rep1


title: 4tU_timecourse_calib:B1:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
calib|B1


title: M14 STAG2-KD_CTCF


title: M14 STAG2-KD_input


title: M14 WT_CTCF


title: Mock vaccinated animal 4, lung sample used for scRNAseq

city: Berlin

first: Dylan

last: Postmus

state: Berlin

address: Charitépl. 1

department: Institute of Virology

institute: Charité – Universitätsmedizin Berlin

data_processing:
Data were analysed using CellRanger v5.0 (10X Genomics) using hamster and SARS-CoV-2 genome scaffolds
Sequencing reads were aligned to the MesAur 1.0 version of the Mesocricetus auratus genome using standard parameter, using the Refseq gtf file described in GEO accession number GSE162208
R packages Seurat v4.0 and DoRothEA v3.12  were used for cell clustering, annotation, and transcription factor activity analysis.
Genome_build: MesAur 1.0
Genome_build: SARS-CoV-2 MN908947
Supplementary_files_format_and_content: Seurat R object
Supplementary_files_format_and_content: h5 matrix

organism: Mesocricetus auratus

source_name: Lung

growth_protocol:
Six to 12-weeks old Syrian hamsters (Envigo RMS, Venray, Netherlands) were randomized for age- and sex-matched groups. Male and female hamsters were used in a 1:1 ratio to ensure transferability of results to both sexes.
Animals were vaccinated intraperitonally (i.p.) in a prime-boost schedule (Days 0 and 21) with 5x105 TCID50 of recombinant MeV-derived vaccine virus in 200 l volume or subcutaneously (s.c.) with 10 g recombinant SARS-CoV-2 S protein (Sino Biological Europe, Eschborn, Germany) adjuvanted with 500 g aluminum hydroxide (Allhydrogel adjuvant 2%, vac-alu-250, InvivoGen, San Diego, CA, USA) in 100 l volume.

extract_protocol:
The right caudal lope of the lung was removed from the body and transferred on ice in PBS containing 1% BSA (w/v) and 2 mg/ml Actinomycin D (Sigma-Aldrich) for further processing. Lung tissue was incubated in 2 mL Dispase (Corning, Bedford, MA, USA) containing 2 mg DNAse (AppliChem, Darmstadt, Germany), 4.6 mg Collagenase B (Roche, Basel, Switzerland) and 2 mg/ml Actinomycin D (Sigma-Aldrich) and at 37 °C for 30 min. Digest was stopped by the addition of cold PBS containing 0.5% (w/v) BSA and Actinomycin D. The tissue was disrupted by pipetting in a repeated pumping motion. Cell suspension was collected and filtered through 70 mm-filter to obtain a single-cell suspension. Red Blood cell were lysed by incubation with RBC lysis buffer (Santa Cruz Biotechnology, Dallas, Texas, USA) for 4 min at room-temperature. Lysis reaction as stopped by the addition of PBS containing 0.04% BSA, the supernatant was removed by centrifugation (1,200 rpm, 6 min, 4 °C) and cells were resuspended in PBS containing 0.04% BSA.
Barcoding of single cells and RNA Isolation was performed using the Chromium controller and Chromium Next Gem Chip G Single Cell Kit and Chromium Next Gem Single cell 3’ GEM, Library & Gel Bead Kit v3.1 (10x Genomics B.V., Leiden, The Netherlands) according to the manufactures instructions.
After enzymatic fragmentation and size selection, resulting double-stranded cDNA amplicons optimized for library construction were subjected to adaptor ligation and sample index PCRs needed for Illumina bridge amplification and sequencing according to the manufacturer’s instruction (10x genomics).
Single cell libraries were quantified using Qubit (Thermo Fisher) and quality-controlled using the Bioanalyzer System (Agilent). Sequencing was performed on a Novaseq 6000 (Illumina), aiming for 200 Million reads per library (read1: 28, read2: 150 nucleotides).

value: Mock vaccinated


title: RNA-Seq t0 rep2


title: 4tU_timecourse_calib:A11:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
calib|A11


title: 4tU_timecourse_calib:A12:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
calib|A12


title: Mock vaccinated animal 2, lung sample used for scRNAseq


title: RNA-Seq t0 rep1


title: M14 STAG2-KD_STAG2


title: 4tU_timecourse_calib:A10:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
calib|A10


title: Mock vaccinated animal 1, lung sample used for scRNAseq

value: Vaccination with TH1 MeV-S vaccine


title: M14 STAG2-KD_STAG1


title: M14 WT_STAG2


title: 4tU_timecourse_calib:A9:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
calib|A9


title: MeV-S vaccinated animal 4, lung sample used for scRNAseq


title: M14 WT_STAG1


title: AI011_MCF10A_Octanoate_rep3

first: Seema

middle: Ahsan

last: Khan

state: IL

address: 303 E. Superior Street, 4-111

description: LiMe genes

data_processing:
RNA sequencing data analysis was performed using Artificial Intelligene’s (AI, www.artificialintelligene.com) RNAseq analysis platform. Briefly, short reads were aligned to the hg19 human genome using STAR. Subsequently cufflinks packages were used to perform transcript assemblies. Downstream differential gene expression calling on the reference and experimental groups of interest was performed using DESeq2. To perform clustering analyses on a group of samples, a union of all the genes and their expression RPKM values within that group was generated to build a read count matrix for the group of interest. Various unsupervised and other machine learning techniques were applied to this composite read count matrix of interest. The sample-sample correlation heatmaps represent the correlation observed between any two samples. The sample-feature heatmaps represent the signal intensity of a feature for any given sample. ggplot2, heatmap.2 and Pheatmap packages in R were used to build various heatmaps. Functional analysis was performed using gene set enrichment analyses.
Genome_build: HG19
Supplementary_files_format_and_content: counts

source_name: MCF-10A cell line

extract_protocol:
RNA extracted from MCF-10A cell lines
Total RNA was first evaluated for its quantity, and quality, using Agilent Bioanalyzer 2100. A RIN (RNA Integrity Number) of five or higher was required to pass the quality control. One to two nanograms of total RNA per sample were used for library preparation. cDNA was first synthesized using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Clontech Laboratories, Inc.). Dual indexed cDNA library was then prepared using Nextera XT DNA Library Prep Kit (Illumina, Inc.). Each library was quantified and its quality accessed by Qubit and Agilent Bioanalyzer, and multiple libraries were pooled in equal molarity. Average size of library insert was about 150b. Five microliters of 2 nM pooled libraries per lane were then denatured, neutralized and applied to the cBot for flow cell deposition and cluster amplification, before loading on to HiSeq 4000 for 75b paired-end sequencing (Illumina, Inc.). Each lane generated approximately 300-350 million reads. A Phred quality score (Q score) was used to measure the quality of sequencing. More than 90% of the sequencing reads reached Q30 (99.9% base call accuracy).

treatment_protocol: cell lines treated with C8 (8 carbon long fatty acid)

value: Treated

tag: technical replicates


title: RNA-Seq CAF-1 OFF 48hrs rep2

description:
CAF-1 OFF 48hrs rep2
Culture with IPTG for 48 hours for CAF-1 suppression

tag: strain


title: AI011_MCF10A_Octanoate_rep2

description: LiMe genes


title: MeV-S vaccinated animal 2, lung sample used for scRNAseq


title: AI011_MCF10A_Octanoate_rep1

description: LiMe genes


title: MeV-S vaccinated animal 3, lung sample used for scRNAseq


title: M14 STAG2-KD RNA-seq rep3 [kd-3]

data_processing:
mapping using STAR with hg19
DE analysis is performed by rsem
Genome_build: hg19
Supplementary_files_format_and_content: gene expression matrix

extract_protocol:
Total RNA was extracted from cells using the RNeasy Mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol
Library construction was completed using the New England BioLabs NEBNext PolyA mRNA Magnetic Isolation Module [Cat#: E7490S] & NEBNext Ultra Directional RNA Library Prep Kit for Illumina [Cat#: E7420S].

treatment_protocol: Cells were cultured with (STAG2-KD) or without (WT) doxycycline for 5 d before they were collected for RNA extraction.

tag: cell type


title: M14 STAG2-KD RNA-seq rep2 [kd-2]


title: 4tU_timecourse_calib:A6:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
calib|A6


title: M14 STAG2-KD RNA-seq rep1 [kd-1]


title: AI011_MCF10A_Control_rep3

description: LiMe genes

tag: treatment

value: Control


title: 4tU_timecourse_calib:A5:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
calib|A5


title: 4tU_timecourse_calib:A7:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
calib|A7


title: Alum-S vaccinated animal 4, lung sample used for scRNAseq

value: Vaccination with TH2 Alum-S vaccine


title: AI011_MCF10A_Control_rep2

description: LiMe genes


title: AI011_MCF10A_Control_rep1

description: LiMe genes


title: 4tU_timecourse_calib:A8:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
calib|A8


title: 4tU_timecourse_calib:A4:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
calib|A4


title: 4tU_timecourse_calib:A3:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
calib|A3


title: Alum-S vaccinated animal 3, lung sample used for scRNAseq


title: M14 WT RNA-seq rep3 [control-3]


title: 4tU_timecourse_calib:A2:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
calib|A2


title: M14 WT RNA-seq rep2 [control-2]


title: Mock vaccinated animal 3, lung sample used for scRNAseq


title: MeV-S vaccinated animal 1, lung sample used for scRNAseq


title: Alum-S vaccinated animal 1, lung sample used for scRNAseq


title: M14 WT RNA-seq rep1 [control-1]


title: SETMAR(R371A)_ChIPseq

city: Indianapolis

first: Millie

middle: M

last: Georgiadis

state: IN

address: 635 Barnhill Dr. MS4032

department: Biochemistry and Molecular Biology

institute: Indiana University School of Medicine

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie2-2.2.6.
Data were filtered using MQ10
peaks were called using MACS software (version 2.1.1.20160309) with a cutoff of P = 5e-5
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak

growth_protocol: HEK293T cells were seeded into four 10-cm dishes, each dish with 2.5 million cells. At 70-80% confluency, two dishes cells were transfected pFLAG-CMV4-SETMAR (wt) and the other two dishes for pFLAG-CMV4-SETMAR (R371A) at the amount of 20 ug per dish using the PEI transfection protocol. After 16-20 h, the transfected cells were harvested for ChIP experiment.

extract_protocol:
Cross-linked chromatin DNA was sonicated to an average length of 150 bp. Protein SETMAR-DNA complexes were immunoprecipitated using anti-FLAG M2 affinity agarose beads. After reversing crosslinks and digesting protein, ChIP DNA samples were purified by using a PCR purification kit (QIAGEN).
ChIP DNA samples from SETMAR(wt) and SETMAR(R371A) groups were sent to the Center for Medical Genomics at Indiana University School of Medicine. The DNA libraries were prepared following to Illumina's instructions and sequenced on Illumina NextSeq500.

tag: chip resin

value: Anti-FLAG M2 affinity agarose (Sigma-Aldrich, cat. A2220).

value: FLAG-tagged SETMAR(R371A)


title: SETMAR(wt)_ChIPseq

value: FLAG-tagged SETMAR(wt)


title: Injured_7dpa_zebrafish heart cells

status: Public on Feb 19 2022

city: Los Angeles

first: subir

last: kapuria

address: 4650 Sunset Blvd.

department: Cardiothoracic surgery

institute: Children's Hospital Los Angeles

description: single cell transcriptome

data_processing:
There are generally 3 fastq files ( l1 for sample barcodes, R1 for 10Xbarcodes+UMI (unique moleular identifier sequence), R2 for cDNA fragment sequences, for each sample. The fastq files for each samples are combined and aligned with the zebrafish reference genome (assembly GRCz11) from the Ensembl database and the digital expression matrix was generated using the Cell Ranger pipeline (10x Genomics).
For further processing of the data R based Seurat package was used.
Genome_build: GRCz11
Supplementary_files_format_and_content: Cell Ranger output files

organism: Danio rerio

source_name: pdgfrb:EGFP cells from adult heart ventricle

growth_protocol: The hearts are isolated from young adult (around 6 months old) and adult (~ 18 months old) zebrafish. The fish were grown in the zebrafish husbandry facility at Children's Hospital Los Angeles following institute's IACUC protocol which follows standard practice.

extract_protocol:
After dissecting out the heart ventricles, they were digested by an enzyme cocktail containing collagenase and elastase at suboptimal temperature with continuous mechanical movement. Except digestion step the cells were kept on ice all the time and FACS sorted to isolate pdgfrb:EGFP+ cells.
The libraries are constructed using the 10X Genomics 3’ Gene expression kit v3.1 following manufacture’s protocol.
single cell RNA-seq.

treatment_protocol: pdgfrb mutant fish were grown following the same protocol for wild type fish. For injured hearts, apical part of the adult heart ventricles were amputated following the aseptic techniques and the injured fishes were rared in the system for 7 days following normal zebrafish husbandry protocols. By 7 days when regeneration was happening in them,  the injured hearts were collected to dissociate into single cell uspension.

tag: age

value: 18 months

value: AB

tag: genotype

value: Tg(pdgfrb:EGFP; cxcl12b:Citrine)

value: heart ventricle

value: Injured

value: Tg(pdgfrb:EGFP) reporter expressing cell


title: pdgfrb mutant young adult zebrafish heart cells

description: single cell transcriptome

value: 6 months

value: Tg(pdgfrb:EGFP; cxcl12b:Citrine; fli1a:DsRed); pdgfrb-/- (um148 allele)


title: wildtype young adult zebrafish heart cells

description: single cell transcriptome


title: Alum-S vaccinated animal 2, lung sample used for scRNAseq


title: 4tU_timecourse_calib:A1:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
calib|A1


title: Uninjured adult zebrafish heart cells

description: single cell transcriptome

value: Uninjured


title: ID060: fireXnitrogenXwaterXheatXco2_rep2

type: genomic

city: Beijing

first: yang

last: sihang

address: Haidian district Shuangqing road #30

institute: Tsinghua University

description:
raw data file:
2_JRGCE128_SNR4p81p7_2bg_GeoChip_rawdata_fire_64.txt

hyb_protocol: Then DNA was dried in a SpeedVac (ThermoSavant, Milford, MA, USA) at 45°C for 45 minutes. The hybridization was carried out at 42°C for 16 hours on a MAUI hybridization station (BioMicro, Salt Lake City, UT, USA).

scan_protocol: After purification, GeoChip microarrays were scanned by a NimbleGen MS200 scanner (Roche, Madison, WI, USA) at 633 nm using a laser power and photomultiplier tube (PMT) gain of 100% and 75%, respectively.

data_processing: Signal intensities were quantified and processed using the data analysis pipeline as previously described (He et al 2010). Then processed GeoChip data were analyzed using the following steps: (i) remove the poor quality spots, which were flagged as 1 or 3 by ImaGene or with a signal to noise ratio (SNR) of less than 2.0; (ii) normalize the signal intensity of each spot by dividing the signal intensity by the total intensity of the microarray followed by multiplying by a constant; (iii) transform the data to the natural logarithmic form; and (iv) remove genes detected in only one out of three samples from the same elevation.

organism: soil metagenome

source_name: Soil microbes at JRGCE

label_protocol: As previously described (Yang et al 2013), DNA samples were labeled with the fluorescent dye Cy-3 using a random priming method and purified using the QIA quick purification kit (Qiagen, Valencia, CA, USA).

extract_protocol: DNA was extracted from 5 g of soil samples with a freeze-grinding mechanical lysis method (Zhou, Bruns, & Tiedje, 1996). DNA was purified by gel electrophoresis with a 0.5% low-melting-point agarose, then extracted with phenol and chloroform and finally precipitated with butanol. DNA quality was assessed by ratios of light absorbance at A260/A280 (>1.8) and A260/A230 (>1.7), using a Nanodrop (NanoDrop Technologies Inv., Wilmington, DE, USA). The final DNA concentration was quantified using a PicoGreen® method using a FLUOstar Optima microplate reader (BMG Labtech, Jena, Germany) (S. Liu et al., 2015).

treatment_protocol: This experiment was initiated in October 1998 at the Jasper Ridge Global Change Experiment (JRGCE) site located in centraloastal California, USA (37o24’N, 122o13’W). This annual grassland ecosystem experiences a Mediterranean-type climate, in which the growing season is cool and wet from November to May, and the rest of the year is hot and dry. The plant community comprises of non-native annual grasses, perennial native grasses, native annual forbs and non-native forbs (Henry et al., 2005). Soils mainly consists of weathered alluvium, which is a fine and mixed Typic Haploxeralf. Initially, the JRGCE experiment was designed to assess grassland ecosystem responses to single and multiple components of global changes, including elevated CO2, warming, N deposition, and enhanced precipitation. To this end, each 2 m-diameter circular plot at the JRGCE was equally divided into four quadrants (i.e.,or subplots) of 0.78 m2. N deposition and enhanced precipitation treatments were arranged at the quadrant level, and the elevated CO2 and warming treatments were arranged at the plot level in a full factorial design. In the summer of 2003, an accidental wildfire burned two of the eight blocks of the experiment (i.e. 32 of the 128 subplots). In the summer of 2011, a controlled fire was applied to four of the eight blocks (i.e. 64 of the 128 subplots including the subplots that were already burned in 2003).

tag: treatments


title: ID059: fireXnitrogenXco2Xheat_rep2


title: ID045: fireXnitrogenXco2Xheat_rep1


title: ID048: fireXwaterXheatXco2_rep1


title: ID116: fireXwaterXheatXco2_rep4


title: ID052: fireXwaterXco2_rep3


title: ID113: fireXheatXco2_rep4


title: ID056: fireXnitrogenXwaterXheatXco2_rep3


title: ID071: fireXwaterXco2_rep2


title: ID055: fireXwaterXheatXco2_rep3


title: ID057: fireXheatXco2_rep2


title: ID051: fireXnitrogenXwaterXco2_rep3


title: ID047: fireXheatXco2_rep1


title: ID054: fireXnitrogenXco2Xheat_rep3


title: ID110: fireXwaterXco2_rep4


title: ID046: fireXnitrogenXwaterXheatXco2_rep1


title: ID072: fireXnitrogenXwaterXco2_rep2


title: ID069: fireXnitrogenXco2_rep2


title: ID114: fireXnitrogenXwaterXheatXco2_rep4


title: ID025: fireXnitrogenXwaterXco2_rep1


title: ID111: fireXnitrogenXco2_rep4


title: ID115: fireXnitrogenXco2Xheat_rep4


title: ID050: fireXco2_rep3


title: ID053: fireXheatXco2_rep3


title: ID026: fireXnitrogenXco2_rep1


title: ID027: fireXwaterXco2_rep1


title: ID049: fireXnitrogenXco2_rep3


title: ID058: fireXwaterXheatXco2_rep2


title: ID109: fireXco2_rep4


title: ID112: fireXnitrogenXwaterXco2_rep4


title: ID033: fireXwaterXheatXnitrogen_rep1

value: fireXwaterXheatXnitrogen


title: ID118: fireXwaterXheatXnitrogen_rep4


title: HEK293T transfected with H150A [THTD3-1]

city: Wuhan

first: Peng

last: Xu

state: Hubei

address: No.1, Shizishan Street, Hongshan District

department: College of Life Science and Technology

institute: Huazhong Agricultural University

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, then mapped to Homo sapiens whole genome using bowtie2 v2-2.0.5
Fragments per kilobase of exon per million fragments mapped(FPKM). 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: Homo sapiens
Supplementary_files_format_and_content: gene_expression.xls file includes counts and FPKM values for each Sample ...

extract_protocol:
RNA was harvested using Trizol reagent. RNeasy Mini Kit （250） Qiagen#74106 was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

tag: transfection

value: transfected with H150A


title: HEK293T transfected with H150A [THTD2-1]


title: ID070: fireXco2_rep2


title: ID061: fireXnitrogenXheat_rep2

value: fireXnitrogenXheat


title: ID062: fireXwaterXheatXnitrogen_rep2


title: ID117: fireXheatXwater_rep4

value: fireXheatXwater


title: ID120: fireXheat_rep4

value: fireXheat


title: ID101: fireXwaterXheatXnitrogen_rep3


title: ID067: fireXnitrogenXwater_rep2

value: fireXnitrogenXwater


title: ID063: fireXheat_rep2


title: ID104: fireXnitrogenXheat_rep3


title: ID034: fireXheat_rep1


title: ID035: fireXnitrogenXheat_rep1


title: ID028: fireXco2_rep1


title: ID064: fireXheatXwater_rep2


title: ID119: fireXnitrogenXheat_rep4


title: ID065: fireXwater_rep2

value: fireXwater


title: ID102: fireXheatXwater_rep3


title: ID126: fireXnitrogenXwater_rep3


title: ID029: fireXwater_rep1


title: ID108: fireXwater_rep4


title: ID105: fireXnitrogen_rep4

value: fireXnitrogen


title: ID103: fireXheat_rep3


title: ID106: fireXnitrogenXwater_rep4


title: ID036: fireXheatXwater_rep1


title: HEK293T transfected with H150A [THTD1-1]


title: HEK293T transfected with CdhM [THTC3-1]

value: transfected with CdhM


title: HEK293T transfected with CdhM [THTC2-1]


title: ID031: fireXnitrogenXwater_rep1


title: HEK293T transfected with CdhM [THTC1-1]


title: HEK293T transfected with vector [THTB2-1]

value: transfected with vector


title: HEK293T transfected with vector [THTB3-1]


title: untransfected HEK293T [THTA3-1]


title: untransfected HEK293T [THTA2-1]


title: untransfected HEK293T [THTA1-1]


title: HEK293T transfected with vector [THTB1-1]


title: A_16_SF_neg

city: Heidelberg

first: Ricardo

last: Grieshaber-Bouyer

address: Im Neuenheimer Feld 410

department: Division of Rheumatology

institute: Heidelberg University Hospital

data_processing:
Short sequence reads were aligned to the reference genome (GRCh38) and Ensembl transcriptome using STAR aligner.
The uniquely aligned reads were used to quantify gene expression levels for all Ensembl genes.
Genes with low expression (less than 10 reads in at least three samples in at least one group) were removed.
Data was analyzed in limma using voom normalization and the expression of each gene was modeled as a combination of donor- and group-specific effects.
Genome_build: GRCh38
Supplementary_files_format_and_content: Two data files are presented and contain log2 normalized, library size normalized counts per million. First, CD177neg and CD177pos neutrophils separately and second CD177neg and CD177pos data averaged for each individual donor/patient.

source_name: synovial fluid

extract_protocol:
RNA was extracted from lysed neutrophils using the Qiagen RNeasy micro kit following manufacturer instructions. RNA sequencing was performed at the Broad Institute under the Smartseq2 protocol. Samples were sequenced on an Illumina NextSeq500 with 25bp paired-end reads and an average sequencing depth of 6 x 106 reads per sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: group

value: arthritis

value: neg


title: A_16_PB_pos

source_name: blood

value: pos


title: A_16_SF_pos


title: A_15_SF_pos


title: A_16_PB_neg


title: A_15_SF_neg


title: AI001_69_pre

city: Chicago

institute: Northwestern University

description: Generating RNA-seq data from primary tumors.

data_processing:
RNA sequencing data analysis was performed using Artificial Intelligene’s (AI, www.artificialintelligene.com) RNAseq analysis platform. Briefly, short reads were aligned to the hg19 human genome using STAR. Subsequently cufflinks packages were used to perform transcript assemblies. Downstream differential gene expression calling on the reference and experimental groups of interest was performed using DESeq2. To perform clustering analyses on a group of samples, a union of all the genes and their expression RPKM values within that group was generated to build a read count matrix for the group of interest. Various unsupervised and other machine learning techniques were applied to this composite read count matrix of interest. The sample-sample correlation heatmaps represent the correlation observed between any two samples. The sample-feature heatmaps represent the signal intensity of a feature for any given sample. ggplot2, heatmap.2 and Pheatmap packages in R were used to build various heatmaps. Functional analysis was performed using gene set enrichment analyses.
Genome_build: HG19
Supplementary_files_format_and_content: AI001_ReadCounts.csv

source_name: breast

extract_protocol:
Roche high pure FFPET kit (Cat # 0665077500)
RNA libraries were prepared using TruSeq RNA Access Library Prep Guide, RS-301-9001DOC, Part# 15049525 Rev. B (Illumina, Inc.)
paired end RNA-seq

value: tumor containing tissue

tag: specimen type

value: core needle biospy

tag: age at diagnois

tag: characteristics

value: menopausal status:postmenopausal

tag: tumor type

value: ILC

tag: er status

value: high positive

tag: pr status

tag: treatment group

value: TPA

tag: ki67 response

value: Yes


title: AI001_70_pre

tag: tissue

value: IDC

value: placebo

value: No


title: AI001_69_post

value: surgical specimen


title: ID128: fireXnitrogen_rep3

value: fireXnitrogen


title: AI001_70_post


title: A_15_PB_neg


title: AI001_68_post

value: menopausal status:premenopausal


title: A_14_SF_pos


title: ID032: fireXnitrogen_rep1


title: ID066: fire_rep2

value: fire


title: AI001_67_post


title: ID125: fire_rep3


title: ID030: fire_rep1


title: ID068: fireXnitrogen_rep2


title: AI001_68_pre


title: ID107: fire_rep4


title: A_15_PB_pos

value: arthritis


title: A_14_SF_neg

value: neg


title: A_14_PB_pos

value: pos


title: A_13_SF_pos


title: A_14_PB_neg


title: AI001_67_pre

value: tumor containing tissue


title: AI001_66_post


title: A_13_SF_neg


title: AI001_66_pre

value: core needle biospy


title: AI001_65_post


title: AI001_65_pre


title: A_13_PB_pos


title: AI001_64_post


title: AI001_63_pre


title: AI001_63_post


title: A_12_SF_pos


title: A_13_PB_neg


title: A_12_PB_pos


title: A_12_SF_neg


title: AI001_62_pre

value: low positive


title: A_12_PB_neg


title: A_11_SF_neg


title: A_11_SF_pos


title: A_11_PB_neg


title: AI001_62_post


title: A_11_PB_pos


title: AI001_61_post

value: menopausal status:postmenopausal


title: AI001_60_post

value: high positive


title: A_10_SF_pos


title: A_10_SF_neg


title: A_10_PB_neg


title: A_10_PB_pos


title: AI001_58_post

value: TPA


title: AI001_59_pre

value: Yes


title: AI001_58_pre

value: IDC


title: AI001_64_pre


title: A_9_SF_pos


title: A_9_SF_neg


title: AI001_57_post

value: placebo


title: A_9_PB_neg


title: AI001_57_pre


title: AI001_61_pre

value: No


title: A_8_SF_pos


title: AI001_55_post

value: surgical specimen


title: AI001_56_pre

value: DCIS


title: AI001_54_post

value: menopausal status:premenopausal


title: A_8_PB_neg


title: A_9_PB_pos


title: AI001_54_pre


title: AI001_60_pre


title: A_8_PB_pos


title: A_7_SF_neg


title: AI001_56_post


title: AI001_59_post


title: AI001_53_pre


title: H_15_PB_pos

value: healthy


title: AI001_52_post


title: AI001_52_pre


title: AI001_51_post


title: H_15_PB_neg


title: H_14_PB_pos


title: A_8_SF_neg

value: arthritis


title: H_14_PB_neg

value: neg


title: A_7_SF_pos

value: pos


title: AI001_50_post

value: tumor containing tissue


title: AI001_53_post


title: H_13_PB_pos


title: AI001_55_pre

value: core needle biospy


title: AI001_50_pre


title: AI001_48_post


title: H_13_PB_neg


title: H_12_PB_neg


title: AI001_47_pre


title: A_7_PB_pos


title: AI001_46_pre


title: A_7_PB_neg


title: AI001_46_post


title: H_10_PB_pos


title: H_12_PB_high


title: AI001_45_post


title: H_10_PB_neg


title: H_11_PB_neg


title: AI001_45_pre


title: AI001_51_pre


title: H_9_PB_pos


title: H_9_PB_neg


title: AI001_43_pre


title: AI001_43_post


title: H_8_PB_pos


title: AI001_48_pre


title: AI001_47_post


title: H_7_PB_pos


title: AI001_41_pre


title: H_11_PB_high


title: AI001_41_post


title: AI001_39_pre

value: ILC

value: low positive

value: negative


title: H_8_PB_neg


title: AI001_39_post


title: H_6_PB_pos


title: H_7_PB_neg


title: AI001_38_post

value: high positive


title: H_6_PB_neg


title: E14Tg2a_ctcfAIDplusIAA_120m_rep2

city: paris

first: Pablo

last: Navarro

address: 25 rue du Docteur Roux

country: France

institute: Institut Pasteur

data_processing:
Gencode (vM12) gtf was used after adding a pre-mRNA isoform for each annotated gene, spanning the longest isoform of all available mRNA isoforms
Reads were aligned using STAR
Quantifications were made by RSEM and counts transformed into Transcripts per Million
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample

source_name: Embryonic Stem cells

growth_protocol: ES cells were cultured on standard serum and LIF conditions and passaged 1:10 every 2-3 days. To obtain mitotic ES cells a double synchronisation method (4h in the presence of 10 μM of RO-3306 (Sigma, SML0569), followed by 4h with 50 ng/ml nocodazole (Sigma, M1404), and shake-off.

extract_protocol:
RNA was extracted with 500 μl TRIzol (ThermoFisher, 15596026), according to the manufacturer’s protocol, and treated with DNAse I (Qiagen,) for 20min at 37°C. Following phenol:chloroform purification, RNAs were resuspended in Ultrapure DNAse/RNase Free Distilled Water (Thermo, 10977035)
Ribo-depleted, stranded and paired-end RNA-seq libraries were prepared and sequenced by Novogene Co Ltd

treatment_protocol: CTCF depletion in CTCF-AID cells was achieved with 0.5 mM auxin (IAA Sigma, I5148) for 2h, starting after 2h of nocodazole treatment. IAA was maintained throughout the whole release procedure.

tag: cell type

value: E14Tg2a cells engineered for auxin-induced degradation of CTCF

tag: strain

tag: time point

value: 120min post-release

tag: treatment

value: IAA (auxin)


title: E14Tg2a_ctcfAIDplusIAA_asy_rep2

value: asynchronous


title: E14Tg2a_ctcfAIDplusIAA_asy_rep1


title: H_5_PB_pos


title: E14Tg2a_ctcfAIDplusIAA_60m_rep2

value: 60min post-release


title: E14Tg2a_ctcfAIDplusIAA_asy_rep3


title: AI001_38_pre

value: IDC

value: placebo

value: Yes


title: E14Tg2a_ctcfAIDplusIAA_90m_rep3

value: 90min post-release


title: E14Tg2a_ctcfAIDplusIAA_60m_rep1


title: E14Tg2a_ctcfAIDplusIAA_90m_rep1


title: H_5_PB_neg

value: healthy

value: neg


title: AI001_37_post

value: tumor containing tissue

value: surgical specimen

value: menopausal status:premenopausal

value: TPA

value: No


title: E14Tg2a_ctcfAIDplusIAA_50m_rep3

value: 50min post-release


title: AI001_37_pre

value: core needle biospy

value: high positive


title: ID127: fireXwater_rep3

tag: treatments

value: fireXwater


title: E14Tg2a_ctcfAIDplusIAA_50m_rep1

value: E14Tg2a cells engineered for auxin-induced degradation of CTCF

value: IAA (auxin)


title: H_4_PB_pos

value: pos


title: E14Tg2a_ctcfAIDplusIAA_40m_rep2

value: 40min post-release


title: AI001_36_post

value: IDC


title: H_4_PB_neg


title: E14Tg2a_ctcfAIDplusIAA_40m_rep1


title: AI001_36_pre


title: E14Tg2a_ctcfAIDplusIAA_120m_rep1

value: 120min post-release


title: E14Tg2a_ctcfAIDplusIAA_20m_rep2

value: 20min post-release


title: AI001_35_post

value: ILC

value: placebo


title: H_3_PB_pos

value: healthy


title: E14Tg2a_ctcfAIDplusIAA_20m_rep1


title: H1299 cells, Melatonin, rep2

first: Yixian

last: Fan

address: Hangkong Road 13, Wuhan

institute: Huazhong University of Science and Technology

data_processing:
The sequencing data was filtered with SOAPnuke.
Trimmed reads were then mapped to human genome (GRCh38) using STAR aligner (v2.7.9a) with standard ENCODE RNA-seq pipeline options, and gene level counts were obtained by setting --quantMode parameter to “GeneCounts”.
Read counts for annotated genes were subsequently normalized to transcripts per million (TPM).
Genome_build: hg38
Supplementary_files_format_and_content: raw counts

extract_protocol:
Total RNA was isolated using Trizol reagent (Invitrogen).
Double stranded PCR products were heated denatured and circularized by the splint oligo sequence to get the library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and pair end 150 bases reads were generated on BGIseq500 platform.

tag: cell line

value: 0.1 mM Melatonin


title: H1299 cells, Melatonin, rep3


title: H1299 cells, Melatonin, rep1


title: AI001_35_pre

value: tumor containing tissue

value: menopausal status:premenopausal


title: H_2_PB_pos_1


title: H_3_PB_neg

value: neg


title: H1299 cells, siCLOCK, rep3

value: siCLOCK


title: H_2_PB_neg_1


title: H1299 cells, siCLOCK, rep2


title: AI001_34_pre

value: core needle biospy

value: high positive

value: No