title: S004537

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: overall survival years

tag: overall survival event


title: S005181

status: Public on May 09 2022

type: SRA

city: Lund

first: Lao

middle: H

last: Saal

address: Scheelevägen 2, MV404B2

department: Department of Oncology and Pathology

country: Sweden

institute: Lund University

description: ER/PgR/HER2/Ki67: 0 negative/normal/low, 1 positive/amplified/high

library_source: transcriptomic

data_processing:
Base-calling using manufacturer's on-instrument software.
Demultiplexing was done with Picard versions 1.120 or 1.128. IlluminaBasecallsToFastq parameters used were ADAPTERS_TO_CHECK=INDEXED, ADAPTERS_TO_CHECK=PAIRED_END, INCLUDE_NON_PF_READS=false
Filtering to remove reads that align (using Bowtie 2 with default parameters except -k 1 --phred33 --local) to ribosomal RNA/DNA (GenBank loci NR_023363.1, NR_003285.2, NR_003286.2, NR_003287.2, X12811.1, U13369.1), phiX174 Illumina control (NC_001422.1), and sequences contained in the UCSC RepeatMasker track (downloaded March 14, 2011).
Fragment size distribution (mean and width) for the alignment step was estimated for each sample using bowtie2 2.2.3 and 2.2.5. Parameter set during estimation were -fr, -k 1, --phred33, --local, and -u 100000, using human genome assembly GRCh38.
Remaining reads were aligned using HISAT2 v 2.1.0 to the human genome reference GRCh38/hg38 together with 104,133 transcript annotations from the UCSC knownGenes table (downloaded September 22, 2014) using the GENCODE release 27 transcriptome model, with default parameters except --no-unal --non-deterministic --novel-splicesite-outfile ${SPLICEFILE}  --rna-strandness RF. HISAT2 indexes were created using the --snp parameter and dbSNP build 150.
Gene expression data in FPKM ( fragments per kilobase of transcript per million mapped reads) were generated using StringTie v1.3.3b (default parameters including --rf -e) using protein coding transcripts from GENCODE release 27 as transcriptome model. Novel transcripts were discarded. An FPKM gene expression matrix was generated from .ctab files using tximport and subsequently transformed to TPM values adding to each expression measurement 0.1, followed by log2 transformation.
PAM50 subtyping was performed using an implementation of the Parker method (Parker et al., J.Clin Oncol 2009). In short, to avoid context dependency when assigning PAM50 subtype by nearest-centroid, a fixed reference was selected to match the original cohort used by Parker et al. with respect to available clinical characteristics. Before subtyping tumors in this study, gene expression of the PAM50 genes for each tumor was centered to the reference set separately using custom R scripts.
Spearman rank correlation was used to determine correlations between expression of ESR1 and ESR2. Kruskal-Wallis non-parametric test and Wilcoxon rank sum test were used to compare and plot expression of the ESR1 and ESR2 genes in various clinical groups such as PAM50 subtype and age groups in the SCAN-B cohort. Transformed ESR2 expression data was divided into tertiles, with the first tertile defined as ESR2-high, and the bottom two tertiles at ESR2-low. Mann Whitney U test and Fisher’s exact test were used to evaluate significant differences in the clinicopathological variables for the ESR2-high and ESR2-low groups. Survival analysis was performed by Kaplan-Meier and Cox regression survival analyses. All analysis was performed for a cohort of 3207 samples from patients enrolled in the SCAN-B study.
Assembly: Human genome reference GRCh38/hg38.
Supplementary files format and content: Gene expression in TPM in CSV format.

molecule: polyA RNA

organism: Homo sapiens

source_name: Primary breast tumor

extract_protocol:
QIAGEN AllPrep
Poly(A) mRNA is isolated from the total RNA in up to 96-well microtiter plate format by two rounds of purification with Dynabeads Oligo (dT)25 (Invitrogen) using a KingFisher Flex magnetic particle processor (ThermoScientific). Zinc-mediated fragmentation (Ambion) is performed and the fragmented mRNA retrieved using column purification (Zymo-Spin I-96 plates; Zymo). The sequencing library generation protocol is a modification of the dUTP method, which importantly retains the directionality (stranded-ness) of the sequenced RNA molecules. First strand cDNA synthesis is performed using random hexamers and standard dNTP mix followed by cleanup using Sephadex gel filtration (Illustra AutoScreen-96A plates; GE Healthcare), and second strand cDNA synthesis is performed using dUTP in place of dTTP in the dNTP-mix and cleanup using Zymo-Spin I-96 plates. The cDNA is end-repaired and A-tailed, and diluted TruSeq adapters with barcodes are ligated using a modified protocol (Illumina). Adapter-ligated cDNA is then size-selected to remove short oligonucleotides using carboxylic acid (CA) paramagnetic beads (Invitrogen) and polyethylene glycol (PEG), similar to the previously described methods, and automated on the KingFisher Flex. The second cDNA strand is digested using uracil-DNA glycosylase and the product is enriched by 12 PCR cycles (Illumina). The PCR product undergoes two cycles of size selection using CA-beads and varying concentrations of PEG, first to exclude DNA fragments >700 bp and then to exclude fragments <200 bp. Quality control is performed on control libraries using Qubit fluorometric measurement (Life Technologies) and Caliper LabChip XT microcapillary gel electrophoresis. Typically, 10-24 barcoded libraries are included in a pool and each pool is sequenced in at least one lane across dual flowcells. Paired-end sequencing of 50 bp read-length is performed on an Illumina HiSeq 2000 or NextSeq 500 instrument.

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

value: NodeNegative

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

value: High

tag: nhg

value: Basal

value: TNBC

value: Ductal

tag: overall survival days

tag: relapse free interval days

tag: relapse free interval years

tag: relapse free interval event

tag: esr1 expression

tag: esr2 expression


title: S004475

tag: pam50 subtype

value: LumA

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: overall survival years

tag: overall survival event


title: S004677

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: er status

tag: pgr status


title: S004522

tag: her2 status

tag: ki67 status

value: Low

tag: nhg

value: Lobular

tag: overall survival days

tag: relapse free interval days

tag: relapse free interval years

tag: relapse free interval event


title: S004631

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: esr1 expression

tag: esr2 expression


title: S005124

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

value: LumB

tag: overall survival years

tag: overall survival event


title: S004536

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: overall survival days

tag: relapse free interval days


title: S004461

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: relapse free interval years

tag: relapse free interval event


title: S004412

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

value: Other

tag: esr1 expression

tag: esr2 expression


title: S004411

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: overall survival years

tag: overall survival event


title: S004307

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: overall survival days

tag: relapse free interval days


title: S004273

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: relapse free interval years

tag: relapse free interval event


title: S005096

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: esr1 expression

tag: esr2 expression


title: S004234

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: overall survival years

tag: overall survival event


title: S004208

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: overall survival days

tag: relapse free interval days


title: S004056

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: relapse free interval years

tag: relapse free interval event


title: S004105

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: esr1 expression

tag: esr2 expression


title: S004047

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: overall survival years

tag: overall survival event


title: S004027

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

value: Normal

tag: overall survival days

tag: relapse free interval days


title: S003996

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: relapse free interval years

tag: relapse free interval event


title: S004646

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: esr1 expression

tag: esr2 expression


title: S004733

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: overall survival years

tag: overall survival event


title: S004021

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: overall survival days

tag: relapse free interval days


title: S003994

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: relapse free interval years

tag: relapse free interval event


title: S003833

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: esr1 expression

tag: esr2 expression


title: S003993

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: overall survival years

tag: overall survival event


title: S003640

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: overall survival days

tag: relapse free interval days


title: S003630

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: relapse free interval years

tag: relapse free interval event


title: S003763

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: esr1 expression

tag: esr2 expression


title: S003613

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: overall survival years

tag: overall survival event


title: S003935

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: overall survival days

tag: relapse free interval days


title: S003938

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: relapse free interval years

tag: relapse free interval event


title: S004036

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: esr1 expression

tag: esr2 expression


title: S003563

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: overall survival years

tag: overall survival event


title: S003626

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: overall survival days

tag: relapse free interval days


title: S003524

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: relapse free interval years

tag: relapse free interval event


title: S003562

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: esr1 expression

tag: esr2 expression


title: S003564

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: overall survival years

tag: overall survival event


title: S003500

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: overall survival days

tag: relapse free interval days


title: S003953

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: relapse free interval years

tag: relapse free interval event


title: S003954

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: esr1 expression

tag: esr2 expression


title: S003545

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: overall survival years

tag: overall survival event


title: S003499

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: overall survival days

tag: relapse free interval days


title: S003483

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: relapse free interval years

tag: relapse free interval event


title: S003581

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

value: Unclassified

tag: esr1 expression

tag: esr2 expression


title: S003498

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: overall survival years

tag: overall survival event


title: S003496

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: overall survival days

tag: relapse free interval days


title: S003550

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: relapse free interval years

tag: relapse free interval event


title: S003479

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: esr1 expression

tag: esr2 expression


title: S003302

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: overall survival years

tag: overall survival event


title: S003417

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: overall survival days

tag: relapse free interval days


title: S003421

value: SubMicroMet

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: relapse free interval years

tag: relapse free interval event


title: S003384

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: esr1 expression

tag: esr2 expression


title: S003215

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: overall survival years

tag: overall survival event


title: S003704

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: overall survival days

tag: relapse free interval days


title: S003014

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: relapse free interval years

tag: relapse free interval event


title: S003243

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: esr1 expression

tag: esr2 expression


title: S003121

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: overall survival years

tag: overall survival event


title: S003473

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: overall survival days

tag: relapse free interval days


title: S003230

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: relapse free interval years

tag: relapse free interval event


title: S003216

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: esr1 expression

tag: esr2 expression


title: S002987

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: overall survival years

tag: overall survival event


title: S003240

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: overall survival days

tag: relapse free interval days


title: S003173

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: relapse free interval years

tag: relapse free interval event


title: S002668

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: esr1 expression

tag: esr2 expression


title: S002917

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: overall survival years

tag: overall survival event


title: S003061

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: overall survival days

tag: relapse free interval days


title: S002851

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: relapse free interval years

tag: relapse free interval event


title: S002595

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: esr1 expression

tag: esr2 expression


title: S002534

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: overall survival years

tag: overall survival event


title: S002577

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: overall survival days

tag: relapse free interval days


title: S002171

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: relapse free interval years

tag: relapse free interval event


title: S002499

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: esr1 expression

tag: esr2 expression


title: S002453

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: overall survival years

tag: overall survival event


title: S002102

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: overall survival days

tag: relapse free interval days


title: S003291

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: relapse free interval years

tag: relapse free interval event


title: S002099

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: esr1 expression

tag: esr2 expression


title: S001625

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: overall survival years

tag: overall survival event


title: S003003

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: overall survival days

tag: relapse free interval days


title: S001207

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: relapse free interval years

tag: relapse free interval event


title: S001089

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: esr1 expression

tag: esr2 expression


title: S002905

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: overall survival years

tag: overall survival event


title: S002493

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: overall survival days

tag: relapse free interval days


title: S002180

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: relapse free interval years

tag: relapse free interval event


title: S002536

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: esr1 expression

tag: esr2 expression


title: S001395

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: overall survival years

tag: overall survival event


title: S001066

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: overall survival days

tag: relapse free interval days


title: S002089

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: relapse free interval years

tag: relapse free interval event


title: S001422

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: esr1 expression

tag: esr2 expression


title: S001074

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: overall survival years

tag: overall survival event


title: S002526

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: overall survival days

tag: relapse free interval days


title: S000953

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: relapse free interval years

tag: relapse free interval event


title: S002202

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: esr1 expression

tag: esr2 expression


title: S001053

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: overall survival years

tag: overall survival event


title: S000909

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: overall survival days

tag: relapse free interval days


title: S000882

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: relapse free interval years

tag: relapse free interval event


title: S000883

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: esr1 expression

tag: esr2 expression


title: S000886

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: overall survival years

tag: overall survival event


title: S000872

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: overall survival days

tag: relapse free interval days


title: S000798

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: relapse free interval years

tag: relapse free interval event


title: S000811

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: esr1 expression

tag: esr2 expression


title: S001088

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: overall survival years

tag: overall survival event


title: S000860

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: overall survival days

tag: relapse free interval days


title: S000742

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: relapse free interval years

tag: relapse free interval event


title: S000891

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: esr1 expression

tag: esr2 expression


title: S002473

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: overall survival years

tag: overall survival event


title: S000709

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: overall survival days

tag: relapse free interval days


title: S000794

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: relapse free interval years

tag: relapse free interval event


title: S000871

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: esr1 expression

tag: esr2 expression


title: S000650

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: overall survival years

tag: overall survival event


title: S000853

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: overall survival days

tag: relapse free interval days


title: S000637

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: relapse free interval years

tag: relapse free interval event


title: S000590

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: esr1 expression

tag: esr2 expression


title: S000605

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: overall survival years

tag: overall survival event


title: S000507

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: overall survival days

tag: relapse free interval days


title: S000552

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: relapse free interval years

tag: relapse free interval event


title: S000486

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: esr1 expression

tag: esr2 expression


title: S000630

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: overall survival years

tag: overall survival event


title: S000466

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: overall survival days

tag: relapse free interval days


title: S000555

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: relapse free interval years

tag: relapse free interval event


title: S000565

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: esr1 expression

tag: esr2 expression


title: S000430

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: overall survival years

tag: overall survival event


title: S000415

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: overall survival days

tag: relapse free interval days


title: S000431

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: relapse free interval years

tag: relapse free interval event


title: S000719

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: esr1 expression

tag: esr2 expression


title: S000492

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: overall survival years

tag: overall survival event


title: S000341

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: overall survival days

tag: relapse free interval days


title: Fibro_patient_2 [Fibro-5_S13]

city: Greenwood

first: Sneha

last: Mokashi

state: South Carolina

address: 113 Gregor Mendel Circle

country: USA

institute: Greenwood Genetic Center

data_processing:
Custom pipeline- Mokashi et al, 2021, biorXiv; Johnstun et al, 2021, Molecular Biol Evolution
Assembly: human reference genome (GRCh38)
Supplementary files format and content: counts file; txt

molecule: total RNA

source_name: fibroblasts

extract_protocol:
Direct zol RNA mini kit (Zymo research)
Universal Plus Total RNA Seq kit with Human AnyDeplete (Tecan, Männedorf, Switzerland)

tag: cell type

value: fibroblasts

tag: genotype

value: Patient


title: Fibro_patient_1 [Fibro-4_S12]


title: S000524

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: relapse free interval years

tag: relapse free interval event

tag: esr1 expression

tag: esr2 expression


title: S000305

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: er status

tag: pgr status

tag: overall survival years

tag: overall survival event


title: Fibro_patient_3 [Fibro-6_S14]

tag: cell type

tag: genotype


title: Fibro_control_2 [Fibro-2_S10]

value: Control


title: S000696

tag: her2 status

tag: ki67 status

tag: nhg

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: overall survival days

tag: relapse free interval days


title: S000346

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: chemo treated

tag: relapse free interval years

tag: relapse free interval event

tag: esr1 expression

tag: esr2 expression


title: S000404

tag: lymph node status

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: overall survival years

tag: overall survival event


title: S000241

tag: nhg

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: overall survival days

tag: relapse free interval days


title: S000243

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: chemo treated

tag: relapse free interval years

tag: relapse free interval event


title: S000240

tag: lymph node status

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: esr1 expression

tag: esr2 expression


title: S000391

tag: nhg

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: overall survival years

tag: overall survival event


title: S000380

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: chemo treated

tag: overall survival days

tag: relapse free interval days


title: S000255

tag: lymph node status

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: relapse free interval years

tag: relapse free interval event


title: S000741

tag: nhg

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: esr1 expression

tag: esr2 expression


title: S000451

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: chemo treated

tag: overall survival years

tag: overall survival event


title: Fibro_control_3 [Fibro-3_S11]

tag: cell type

tag: genotype


title: S000234

tag: lymph node status

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: overall survival days

tag: relapse free interval days

tag: relapse free interval years

tag: relapse free interval event


title: S000212

tag: scanb external id

tag: age at diagnosis

tag: nhg

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: esr1 expression

tag: esr2 expression


title: S000209

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: er status

tag: chemo treated

tag: overall survival years

tag: overall survival event


title: Mono-cultured PDX1 tumor cells 2 , 24hour

city: Guangzhou

first: Dandan

last: Liu

state: Guangdong province

address: Xinzao, Panyu District,

department: Guangdong Provincial Key Laboratory of Protein Modification and Degradation

country: China

institute: Guangzhou Medical University

data_processing:
Illumina Novaseq 6000 reads were trimmed and clipped for quality control in Trimmomatic v0.27
Read quality was checked for each sample using Fastp v0.19.5.
High-quality reads were then imported into TopHat v2.1.1 for alignment into BAM files.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: GCB-DLBCL Tumor

growth_protocol: DMEM, 10% fetal bovine serum,  1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 μg of total RNA was enriched for the Poly-A mRNA and reverse transcribed to double-stranded cDNA. The cDNA was end repaired, adenylated, and ligated with Illumina indexes prior to 15 cycles of PCR. Sequencing was performed using 12pM hybridization to a 2x150 paired end flow cell.
RNA libraries for RNA-seq were prepared using Illumina TruseqTM RNA sample prep Kit following manufacturer's protocols.

treatment_protocol: PDX1 tumor cells mono-cultured and cocultured with stromal cells for 24 hours, were FACS sorted with CD105- and CD20+ tumor cells for RNA-seq.

tag: tissue

value: GCB-DLBCL Tumor

tag: treatment

value: Mono-cultured for 24hours


title: S000199

tag: scanb external id

tag: age at diagnosis

tag: pgr status

tag: her2 status

tag: ki67 status

tag: overall survival days

tag: relapse free interval days

tag: relapse free interval years

tag: relapse free interval event


title: S000195

tag: tumor size

tag: lymph node group

tag: nhg

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: esr1 expression

tag: esr2 expression


title: S000246

tag: scanb external id

tag: age at diagnosis

tag: lymph node status

tag: er status

tag: chemo treated

tag: overall survival years

tag: overall survival event


title: DKD_Scr-1

city: Omaha

first: Samikshan

last: Dutta

state: NE

address: 42 and Emile

department: BMB

institute: univ of nebraska medical center

data_processing:
Sequencing was performed on a Illumina NovaSeq 6000 instrument producing 50 bp pairedend reads running Control Software 1.7.0
The sequenced reads were controlled for quality of sequencing with FastQC and trimmed using Trim_Galore.
Trimmed reads were aligned to the reference genome using the STAR aligner version 2.7.0f
RNA abundance was estimated with featureCounts from the Subread package version 1.6.3
Normalization of counts and differential expression analysis were performed with the DESEQ2 R package version 1.26.0
Assembly: GRCh38/hg38
Supplementary files format and content: raw counts

source_name: Human prostate cancer cell line

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
Library preparation has been done with 770 ng of input RNA using: NEBNext® rRNA Depletion Kit (Human/Mouse/Rat) (NEB #E6310)) followed by NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760) and NEBNext® Multiplex Oligos for Illumina® Index Primers Set 1 (NEB# E6440)

tag: tissue

value: Human prostate cancer cell line

tag: cell line

value: DKD

tag: cell type

value: Neuroendocrine like

tag: genotype

value: RB1/TP53 Depleted

tag: treatment

value: Non silencing siRNA


title: DKD_siNRP2-1


title: Mono-cultured PDX1 tumor cells 1 , 24hour


title: DKD_Scr-3


title: Co-cultured PDX1 tumor cells 1 , 24hour

value: Co-cultured with stromal cells for 24hours


title: S000207

tag: tumor size

tag: lymph node group

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: pam50 subtype

tag: clinical groups

value: Ductal

tag: overall survival days

tag: relapse free interval days

tag: relapse free interval years

tag: relapse free interval event


title: DKD_siNRP2-2

tag: tissue


title: Fibro_control_1 [Fibro-1_S9]


title: DKD_3

tag: cell line


title: S000193

tag: scanb external id

tag: age at diagnosis

tag: lymph node status

tag: er status

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: overall survival years

tag: overall survival event

tag: esr1 expression

tag: esr2 expression


title: DKD_Scr-2

tag: cell type

tag: genotype

tag: treatment


title: S000171

tag: tumor size

tag: lymph node group

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: pam50 subtype

value: LumB

tag: clinical groups

value: Lobular

tag: overall survival days

tag: relapse free interval days

tag: relapse free interval years

tag: relapse free interval event


title: S000170

tag: scanb external id

tag: age at diagnosis

tag: lymph node status

value: NodeNegative

tag: er status

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: overall survival years

tag: overall survival event

tag: esr1 expression


title: S000169

tag: tumor size

tag: lymph node group

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

value: LumA

tag: esr2 expression


title: C4-2_3

tag: tissue

tag: cell line

tag: cell type

value: Adenocarcinoma

tag: genotype

value: Wild type


title: S000165

tag: scanb external id

tag: age at diagnosis

tag: lymph node status

tag: er status

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: overall survival days

tag: relapse free interval days

tag: relapse free interval years

tag: relapse free interval event


title: DKD_1


title: C4-2_2


title: S000189

tag: tumor size

tag: lymph node group

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: endocrine treated

tag: chemo treated

tag: overall survival years

tag: overall survival event

tag: esr1 expression


title: Co-cultured PDX1 tumor cells 2 , 24hour

tag: tissue

tag: treatment


title: DKD_2

tag: cell line

tag: cell type

tag: genotype


title: S000186

tag: scanb external id

tag: age at diagnosis

tag: lymph node status

tag: er status

tag: pam50 subtype

value: Basal

tag: clinical groups

value: TNBC

tag: histopathological type

tag: overall survival days

tag: relapse free interval days

tag: relapse free interval years

tag: relapse free interval event

tag: esr2 expression


title: S000143

tag: tumor size

tag: lymph node group

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: endocrine treated

tag: chemo treated

tag: overall survival years

tag: overall survival event

tag: esr1 expression


title: S000184

tag: scanb external id

tag: age at diagnosis

tag: lymph node status

tag: er status

tag: pam50 subtype

value: Normal

tag: clinical groups

tag: histopathological type


title: S000115

tag: tumor size

tag: lymph node group

tag: overall survival days

tag: relapse free interval days

tag: relapse free interval years

tag: relapse free interval event

tag: esr2 expression


title: C4-2_1

tag: tissue

tag: cell line

tag: cell type

tag: genotype


title: HEK293T, T18

city: Shenzhen

first: Qiang

last: Su

state: None Selected

address: 1066 Xueyuan Street

institute: Shenzheng Uni

data_processing:
Raw sequence reads were checked by FastQC (v0.11.8) for base-calling quality overview
Cutadapt (v2.10; parameter- default) finds and removes adapter sequence from raw sequencing read
The adapter-removed reads were trimmed from 3' end until the final base by trimmomatic (v0.39; parameter- PE, LEADING:30 TRAILING:30 SLIDINGWINDOW:4:15 AVGQUAL:20 MINLEN:20)
The trimmed reads were aligned to the GRCH37(hg19) genome using HISAT2 (v2.2.1; parameter- default). Samtools was used for further processing.
RseQC (v4.0.0) package processes the aligned data to calculate RNA coverage over gene body, FPM, read distribution, read GC, read NVC, and so on.
Assembly: hg19
Supplementary files format and content: *trim_output.geneBodyCoverage.txt is a processing data from the trimmed raw data by the geneBody_coverage.py in the RSeQC package (http://rseqc.sourceforge.net/). The geneBody_coverage.py aims to calculate the RNA-seq reads coverage over each transcript body. This *trim_output.geneBodyCoverage.txt contains the mapping coverage of 59100 transcripts.
Supplementary files format and content: *_cutadapt_trim_1P_polyT.txt is a processing data from the trimmed raw data by the poly(T) base-calling code. The poly(T)-profiling code is written by me and will be published as a part of the manuscript. The read count against the sorted poly(T) length is listed in *_cutadapt_trim_1P_polyT.txt.

source_name: Kidney; Embryo

growth_protocol: HEK293T cells were cultured in DMEM high glucose supplemented with 10% FBS. A549 cells are cultured in F-12K supplemented with 10% FBS

extract_protocol:
The total RNAs were extracted from cells following the worksheet in TRIzol. Total RNA was checked on 2100 Bioanalyzer RNA picochip. A 400 ng total RNA was subjected in CLT-seq.
500 ng of total RNA was subjected to 5 μl RT reaction with 0.5 μL of 1 μM oligo(dT) primer at 37℃ for 30 min. Subsequently, 1 μL of 20 U/μl of Exonuclease I was added and incubated for 30 min at 37°C and 20 min at 80°C. The resulting 1st cDNA was mixed with 1 μL of 10 μM splint-second adaptor at 16°C for 2 hours. The final mix was then amplified by PCR with HIFI KAPA master mix (2X).

value: Kidney; Embryo

value: Human embryonic kidney

value: WT


title: S000145

tag: scanb external id

tag: age at diagnosis

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: endocrine treated

tag: chemo treated

tag: overall survival years

tag: overall survival event

tag: esr1 expression


title: HEK293T, T12, bio rep 1


title: DKD_siNRP2-3

value: Human prostate cancer cell line

value: DKD

value: Neuroendocrine like

tag: treatment


title: S000131

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: er status

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: overall survival days

tag: relapse free interval days

tag: relapse free interval years

tag: relapse free interval event

tag: esr2 expression


title: S000141

tag: scanb external id

tag: age at diagnosis

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: endocrine treated

tag: chemo treated


title: S000150

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: er status

tag: overall survival years

tag: overall survival event

tag: esr1 expression


title: HEK293T, T18VNN

tag: tissue

tag: cell line

tag: cell type

tag: genotype


title: S000128

tag: scanb external id

tag: age at diagnosis

tag: pgr status

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: overall survival days

tag: relapse free interval days

tag: relapse free interval years

tag: relapse free interval event

tag: esr2 expression


title: HCT116 (MCM2-mAID+ S108D MCM2) NS-seq rep2

city: Bethesda

first: Christophe

middle: E

last: Redon

state: MD

address: 37 Convent Drive

institute: NIH

description: HCT116 Nascent strand DNA (activated origins)

library_source: genomic

data_processing:
Library strategy: NS-seq
For ChIP-Seq, peaks were called using the  MACS algorithms againt input. Default parameters were used for sample calling.
For nascent strand peak calling the MACS was used. Nascent strand reads were called by comparison to genomic DNA.  Peaks were filtered using the “peak-score” MACS2 metric in R (version 3.5.1) by accepting regions above the inflection-point threshold of “peak-scores” from the raw output.
Single read  75bp (NextSeq for ChipSeq) or Pair End 101, 125 and 150 bp (HiSeq or NovaSeq) for NGS sequencing
Genome_build: hg19
Supplementary_files_format_and_content: Bed file format of replication initiation peaks and ChipSeq

molecule: genomic DNA

source_name: Colon carcinoma

growth_protocol: Cancer cells were grown in RPMI medium, 10% FBS

extract_protocol:
DNA from cell cultures was isolated, size fractionated and subject to exunuclease digestion as described in Aladjem et al., Science 281, 1005, 1998. and Wang et al., Molecular and Cellular Biology 24:3373-86, 2004. For ChipSeq, DNA molecules were enriched using antibodies against proteins of interest.
Enriched ChIPed DNA molecules were sequenced by Illumina NextSeq 75 cycle High Output kit with single ennd of 75bp. For nascent  DNA, re-replicated DNA, paired-end libraries of genomic DNA (gDNA) were prepared using Illumina TruSeq Nano DNA Library Prep kits. Control genomic DNA was fragmented to ~ 400 bp insert size on the Covaris which generates dsDNA fragments with 3' or 5' overhangs. The sheared DNA was blunt-ended and library size selection was done using sample purification beads. A single 'A' nucleotide was added to the 3' ends of the blunt fragments to prevent them from ligating to each other during the adapter ligation reaction. A corresponding single 'T' nucleotide on the 3' end of the adapter provided a complementary overhang for ligating the adapter to the fragment. The indexed adapters were ligated to the ends of the DNA fragments and then PCR-amplified to enrich for fragments that have adapters on both ends. The final purified product was then quantitated by qPCR before cluster generation and sequencing.

treatment_protocol: All cells were treated with trichostatin A (5nM) for 24hr prior to collection to block HDAC class I and II activity. For aphidicolin treatment, cells were treated with 0.8µM aphidicolin for 24hr.

value: Cultured cancer cell line

value: MCM2-mAID+ S108D MCM2

tag: chip antibody

tag: molecule subtype

value: Nascent DNA


title: S000085

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: er status

tag: her2 status

tag: ki67 status

tag: nhg

value: Ductal

tag: endocrine treated

tag: chemo treated

tag: overall survival years

tag: overall survival event

tag: esr1 expression


title: S000108

tag: scanb external id

tag: age at diagnosis

value: NodeNegative

tag: pgr status

tag: pam50 subtype

value: LumB

tag: clinical groups

tag: histopathological type

tag: overall survival days

tag: relapse free interval days

tag: relapse free interval years


title: S000104

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: er status

tag: her2 status

value: LumA

tag: relapse free interval event

tag: esr2 expression


title: HEK293T, T12, bio rep 2

tag: tissue

tag: cell line

tag: cell type

tag: genotype


title: HEK293T, T30


title: S000109

tag: scanb external id

tag: age at diagnosis

tag: pgr status

tag: ki67 status

tag: nhg

tag: pam50 subtype

tag: endocrine treated

tag: chemo treated

tag: overall survival years

tag: overall survival event

tag: esr1 expression


title: A549, T12, bio rep 2

source_name: Lung

value: Lung

value: Epithelial cell


title: HCT116 (MCM2-mAID+ S108A MCM2) NS-seq rep1

value: MCM2-mAID+ S108A MCM2

tag: chip antibody

tag: molecule subtype


title: HEK293T, T18VN

tag: tissue


title: HCT116 (MCM2-mAID+ S108D MCM2) NS-seq rep1

tag: cell line


title: A549, T12, bio rep 1

tag: cell type


title: HEK293T, T18V

tag: genotype


title: HCT116 (MCM2-mAID+ S139D MCM2) NS-seq rep2

value: MCM2-mAID+ S139D MCM2


title: S000080

tag: scanb external id

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: er status

tag: her2 status

value: Normal

tag: clinical groups

tag: histopathological type

tag: overall survival days

tag: relapse free interval days

tag: relapse free interval years

tag: relapse free interval event

tag: esr2 expression


title: HCT116 (MCM2-mAID+ S139D MCM2) NS-seq rep1

tag: chip antibody

tag: molecule subtype


title: S000075

tag: age at diagnosis

tag: pgr status

tag: ki67 status

tag: nhg

tag: pam50 subtype

tag: endocrine treated

tag: chemo treated

tag: overall survival years

tag: overall survival event

tag: esr1 expression


title: S000047

tag: scanb external id

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: er status

tag: her2 status

tag: clinical groups

tag: histopathological type

value: Lobular

tag: overall survival days


title: HCT116 (MCM2-mAID) NS-seq rep2

tag: cell line

tag: cell type

tag: genotype

tag: chip antibody

tag: molecule subtype


title: HCT116 (MCM2-mAID+ S108A MCM2) NS-seq rep2


title: HCT116 (MCM2-mAID) NS-seq rep1


title: S000105

tag: age at diagnosis

tag: pgr status

tag: ki67 status

tag: nhg

tag: pam50 subtype

tag: endocrine treated

tag: chemo treated

tag: overall survival years

tag: relapse free interval days

tag: relapse free interval years

tag: relapse free interval event

tag: esr2 expression


title: S000028

tag: scanb external id

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: er status

tag: her2 status

tag: clinical groups

tag: histopathological type

tag: overall survival days

tag: overall survival event

tag: esr1 expression


title: S000090

tag: age at diagnosis

tag: pgr status

tag: ki67 status

tag: nhg

tag: pam50 subtype

tag: endocrine treated

tag: chemo treated


title: S000008

tag: scanb external id

tag: tumor size

tag: overall survival years

tag: relapse free interval days

tag: relapse free interval years

tag: relapse free interval event

tag: esr2 expression


title: HCT116 (MCM2-mAID+ WT_MCM2) NS-seq rep1

tag: cell line

tag: cell type

tag: genotype

value: MCM2-mAID+ WT_MCM2

tag: chip antibody

tag: molecule subtype


title: HCT116 (MCM2-mAID+ S139A MCM2) NS-seq rep2

value: MCM2-mAID+ S139A MCM2


title: S000032

tag: age at diagnosis

tag: lymph node group

tag: lymph node status

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: clinical groups

tag: histopathological type

value: Other

tag: overall survival days

tag: overall survival event

tag: esr1 expression


title: HCT116 (MCM2-mAID+ S108A MCM2) input control

description: HCT116 G1/S synchronised cells using double-thymidine block  cells ChipSeq

data_processing:
For ChIP-Seq, peaks were called using the  MACS algorithms againt input. Default parameters were used for sample calling.
For nascent strand peak calling the MACS was used. Nascent strand reads were called by comparison to genomic DNA.  Peaks were filtered using the “peak-score” MACS2 metric in R (version 3.5.1) by accepting regions above the inflection-point threshold of “peak-scores” from the raw output.
Single read  75bp (NextSeq for ChipSeq) or Pair End 101, 125 and 150 bp (HiSeq or NovaSeq) for NGS sequencing
Genome_build: hg19
Supplementary_files_format_and_content: Bed file format of replication initiation peaks and ChipSeq

tag: cell line

value: ChipSeq DNA


title: HCT116 genomic (MCM2-mAID+ WT_MCM2) control

tag: cell type

value: Cultured cancer cell line

value: MCM2-mAID+ WT MCM2


title: S000019

tag: scanb external id

tag: tumor size

tag: nhg

tag: pam50 subtype

tag: endocrine treated

tag: chemo treated

tag: overall survival years

tag: relapse free interval days

tag: relapse free interval years

tag: relapse free interval event

tag: esr2 expression


title: HCT116 (MCM2-mAID+ WT_MCM2) input control

tag: genotype

tag: chip antibody

tag: molecule subtype


title: HCT116 (MCM2-mAID+ WT_MCM2) NS-seq rep2

value: Nascent DNA


title: HCT116 (MCM2-mAID+ S139A MCM2) NS-seq rep1


title: HCT116 genomic (MCM2-mAID+ S108D MCM2) control

value: MCM2-mAID+ S108D MCM2


title: HCT116 genomic (MCM2-mAID+ S139D MCM2) control


title: HCT116 with Rnase treatment followed by lambda exonuclease treatment to low m.w. DNA control for Nascent strands

data_processing:
Library strategy: NS-seq
For ChIP-Seq, peaks were called using the  MACS algorithms againt input. Default parameters were used for sample calling.
For nascent strand peak calling the MACS was used. Nascent strand reads were called by comparison to genomic DNA.  Peaks were filtered using the “peak-score” MACS2 metric in R (version 3.5.1) by accepting regions above the inflection-point threshold of “peak-scores” from the raw output.
Single read  75bp (NextSeq for ChipSeq) or Pair End 101, 125 and 150 bp (HiSeq or NovaSeq) for NGS sequencing
Assembly: hg19
Supplementary files format and content: Bed file format of replication initiation peaks and ChipSeq

tag: chip antobody

value: HCT116 Nascent strand DNA (activated origins)


title: HCT116 with lambda exonuclease treatment to high m.w. DNA (control for Nascent strands)

tag: cell line


title: HCT116 with Rnase treatment followed by lambda exonuclease treatment to high m.w. DNA control for Nascent strands

tag: cell type


title: HCT116 shared genomic DNA (genomic control)


title: HCT116 (MCM2-mAID+ S108A MCM2) pS139-MCM2 rep2

value: pS139 MCM2 antibody (Cell Signaling, 12958)


title: HCT116 with WT_SIRT1 (genomic control) replicate 1

description: HCT116 genomic DNA control

value: WT

value: Genomic DNA


title: HCT116 (MCM2-mAID+ WT_MCM2) pS139-MCM2 rep2


title: HCT116 WT G1/S synchronised cells input DNA

description: HCT116 G1/S synchronised cells using double-thymidine block input control for ChIP-seq

value: input DNA


title: HCT116 (MCM2-mAID+ WT_MCM2) pS139-MCM2 rep1


title: HCT116 genomic (MCM2-mAID+ S108A MCM2) control

value: MCM2-mAID+ S108A MCM2


title: HCT116 with WT_SIRT1 (genomic control) replicate 2

description: HCT116 genomic DNA control


title: HCT116 with H363Y_SIRT1 (genomic control)

description: HCT116 genomic DNA control

value: SIRT1 H363Y


title: HCT116 genomic (MCM2-mAID+ S139A MCM2) control


title: HCT116 with lambda exonuclease treatment to low m.w. DNA (Nascent strands)


title: HCT116 with H363Y_SIRT1 (Nascent strands) replicate 2


title: HCT116 with H363Y_SIRT1 (Nascent strands) replicate 1


title: HCT116 WT asynchronous cells input DNA

description: HCT116 asynchronous cells input control for ChIP-seq


title: HCT116 H363Y SIRT1 cells input DNA


title: HCT116 with KO_SIRT1 (genomic control)

description: HCT116 genomic DNA control

value: SIRT1 KO


title: HCT116 with KO_SIRT1 (Nascent strands) replicate 2


title: HCT116 with WT_SIRT1 + Aphidicolin treatment (Nascent strands) replicate 1


title: HCT116 H363Y pS40/41-MCM2 ChIP-seq

value: pS40/41 MCM2 antibody (Bethyl Labs, A300788A)


title: HCT116 with WT_SIRT1 (Nascent strands) replicate 2


title: I13_IFN_H3K27ac

city: Milan

first: Chiara

last: Balestrieri

address: Via Olgettina 58

department: Center for Omics Sciences

country: Italy

institute: IRCCS San Raffaele Scientific Institute

description: Chromatin IP against H3K27ac

data_processing:
After the pre‐processing steps (quality trimming, and adapter clipping), paired-ended reads with a minimum of 30 bp were aligned to human genome build GRCh38/hg38 using Bowtie2 with parameter “-‐very‐sensitive”. Only reads mapped in proper pairs were retained and were then further processed to filter problematic regions of the genome using ENCODE blacklist v2 (https://github.com/Boyle-Lab/Blacklist), to reomve duplicates and reads aligned to the mitochondrial genome.
Peak counts were estimated using countOverlaps() function of GenomicRanges R package with "any" mode. Normalization was against a set of invariant genes across samples, defined as those with differences in read counts within 1σ from the mean difference (μdiff), assuming a quasi-normal distribution of gene read counts. Tracks were linearly re‐normalized according to the scaling factor.
Genome_build: GRCh38/hg38

source_name: Pancreatic Ductal Adenocarcinoma (PDAC) cell line

growth_protocol: See additional columns of the SAMPLES section

extract_protocol: ChIP lysates were generated from 50x10^6 cells. Cells were fixed in 1% formaldehyde for 10min. Lysate was immunoprecipitated with 10ug of antibody. Antibodies were pre-bound overnight to 100ul of G protein-coupled paramagnetic beads in PBS/BSA 0.5%. Beads were then added to lysates (the preclearing step was omitted) and incubation was let to proceed overnight. Beads were washed 6 times in a modified RIPA buffer (50mM Hepes pH 7.6, 500mM LiCl, 1mM EDTA, 1% NP-40, 0.7% Na-deoxycholate) and once in TE containing 50mM NaCl. DNA was eluted in TE containing 2% SDS and crosslinks reversed by incubation overnight at 65ºC. DNA was then purified by AMPure XP SPRI (Beckman Coulter) and quantified using Quantifluor (Promega). ChIP DNA was prepared for HiSeq2000 or NextSeq500 Illumina sequencing using a standard protocol consisting in blunting, addition of dA overhangs, ligation of Illumina adapters, PCR with index primers and purification. A mixture of T4 DNA polymerase, DNA polymerase I and T4 kinase was used according to manufacturer’s instruction. Library preparation is carried out on SPRIworks Fragment Library System.

value: CFPAC1 clonal cell line

tag: growth protocol

value: IMDM supplemented with 10% Fetal Bovine Serum, 2mM L-Glutamine and 1% Pen/Strep

tag: antibody

value: Anti H3K27ac (Abcam, ab4729)

tag: treatment

value: Isolation of clonal cell line by dilution of CFPAC1 cells infected with lentiCRIPSv2 plasmid (Addgene #52961) carring the expression of wt Cas9 and a guide RNA targeting IRF1 gene, treated with hIFNb for 2 hours


title: HCT116 with KO_SIRT1 (Nascent strands) replicate 1

value: Cultured cancer cell line


title: HCT116 KO pS40/41-MCM2 ChIP-seq

value: ChipSeq DNA


title: HCT116 with WT_SIRT1 + Aphidicolin treatment (Nascent strands) replicate 2

value: Nascent DNA


title: HCT116 (MCM2-mAID+ S108A MCM2) pS139-MCM2 rep1


title: I11_IFN_H3K27ac

description: Chromatin IP against H3K27ac

treatment_protocol: See additional columns of the SAMPLES section


title: HCT116 with WT_SIRT1 (Nascent strands) replicate 1


title: HCT116 KO pS53-MCM2 ChIP-seq

value: pS53 MCM2 antibody (Bethyl labs, A300756A)


title: HCT116 KO pS108-MCM2 ChIP-seq rep2

value: pS108 MCM2 antibody (Bethyl Labs, A300094A)


title: HCT116 H363Y pS108-MCM2 ChIP-seq rep1


title: I11_UT_H3K27ac

description: Chromatin IP against H3K27ac

value: Isolation of clonal cell line by dilution of CFPAC1 cells infected with lentiCRIPSv2 plasmid (Addgene #52961) carring the expression of wt Cas9 and a guide RNA targeting IRF1 gene, UT


title: I13_UT_H3K27ac

description: Chromatin IP against H3K27ac


title: L4_IFN_H3K27ac

description: Chromatin IP against H3K27ac

value: Isolation of clonal cell line by dilution of CFPAC1 cells infected with lentiCRIPSv2 plasmid (Addgene #52961), treated with hIFNb for 2 hours


title: HCT116 WT pS108-MCM2 ChIP-seq rep2

value: WT


title: HCT116 H363Y pS52-MCM2 ChIP-seq


title: HCT116 H363Y pS108-MCM2  ChIP-seq rep2


title: L1_IFN_H3K27ac

description: Chromatin IP against H3K27ac


title: L4_UT_H3K27ac

description: Chromatin IP against H3K27ac

value: Isolation of clonal cell line by dilution of CFPAC1 cells infected with lentiCRIPSv2 plasmid (Addgene #52961), UT


title: HCT116 WT pS108-MCM2 ChIP-seq rep1


title: HCT116 KO pS139-MCM2 ChIP-seq rep2

value: pS139 MCM2 antibody (Cell Signaling, 12958)


title: HCT116 H363Y pS139-MCM2 ChIP-seq rep2

value: SIRT1 H363Y


title: HCT116 KO pS108-MCM2 ChIP-seq rep1

value: SIRT1 KO


title: HCT116 WT pS139-MCM2 ChIP-seqrep2


title: L1_UT_H3K27ac

description: Chromatin IP against H3K27ac


title: HCT116 WT pS40/41-MCM2 ChIP-seq

value: pS40/41 MCM2 antibody (Bethyl Labs, A300788A)


title: HCT116 WT input DNA

value: input DNA


title: HCT116 KO pS139-MCM2 ChIP-seq rep1


title: HCT116 H363Y pS139-MCM2 ChIP-seq rep1


title: HCT116 WT pS139-MCM2 ChIP-seq rep1


title: HCT116 KO pT530-SIRT1 ChIP-seq rep1 (negative control)

description: HCT116 asynchronous cells ChipSeq

value: pT530 SIRT1 antibody (abcam, ab156585)


title: HCT116 WT pT530-SIRT1 ChIP-seq rep1

description: HCT116 asynchronous cells ChipSeq


title: HCT116 H363Y input DNA


title: HCT116 KO input DNA


title: HCT116 H363Y pT530-SIRT1 ChIP-seq rep1

description: HCT116 asynchronous cells ChipSeq


title: dMII-3 [dMII_S25]

city: Fukuoka

first: Kei

last: Miyamoto

address: 744 Moto-oka, Nishi-ku

department: Faculty of Agriculture

country: Japan

institute: Kyushu University

description:
dMII_S25_R1_val_1-pw1_10-cN10-pq20w10m20
Single oocyte was subjected to cDNA synthesis

data_processing:
Fastq files from Illumina sequencing were filtered for low quality reads by sliding window trimming (window size 10, <QV20), and low quality bases were trimmed from the ends of the reads (<QV20) using Trimmomatic. Reads less than 20 bases and unpaired reads were removed. Furthermore, adaptor, polyA, polyT and polyG sequences were removed using trim_galore and cutadapt.
The sequencing reads were then mapped to the human genome (hg19) using STAR. Reads on annotated genes were counted using featureCounts. FPKM values were calculated from mapped reads by normalizing to total counts and transcript.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: Human oocyte at the MII stage that is collected a day after the initial oocyte collection

growth_protocol: After aspirating follicles with a fine needle under the ovarian echo, the cumulus oocyte complexes (COCs) were picked up under a stereomicroscope. COCs from infertile patients were scheduled for intracytoplasmic sperm injection, and surrounding cumulus cells were removed with recombinant human-derived hyaluronidase (Kitazato) in multipurpose handling medium (MHM; Fujifilm Irvine).  After denudation, oocyte morphology was examined and an oocyte at the MII stage was used for infertility treatment. Oocytes other than the MII stage were subjected to in vitro maturation as described in the treatment protocol.

extract_protocol:
Collected surplus oocytes were subjected to micromanipulation to remove their sibling polar bodies, and then zona pellucida was enzymatically removed. After the removal of zona pellucida, embryos were washed with PBS containing 0.1% BSA, and then transferred to a 0.2 ml tube containing 9.5 μl of reaction buffer to make a final volume of 10.5 μl. After cell lysis in the buffer, 1 μl of the solution was removed and, instead, 1 μl of the diluted ERCC RNA Spike-In Mix was added (Thermo Fisher Scientific, 4456740). The lysed RNA solution with the spike-in RNA were subjected to reverse transcription.
The produced cDNA was amplified by PCR with 16 cycles. The amplified cDNA was purified using AMPure XP beads (BECKMAN COULTER, A63882). The purified cDNA was measured on the Bioanalyzer (Agilent) using High Sensitivity DNA Kit (5067-4626) and the normalized volume of DNA was subjected to library preparation using Nextera XT DNA Library Preparation Kit (Illumina, FC-131-1024) by following the vendor’s instruction. The obtained library was quality-checked by Bioanalyzer and quantified using Qubit (Thermo Scientific).
Paired end sequencing (50 bp + 25 bp) was carried out using the Illumina NextSeq system.

treatment_protocol: The collected and denuded oocytes were incubated in the Sydney IVF fertilization medium (Cook medical) at 37°C under 5% CO2 and 5% O2 in air for in vitro maturation, and oocytes that had matured to the MII stage by 16:00 on the same day of oocyte collection were used for the treatment of in vitro fertilization. The remaining oocytes that had not reached the MII stage by 16:00 were normally discarded, but further cultured for this study. A few hours after the incubation, some oocytes were matured to MII oocytes, and such matured oocytes were subjected to sampling for RNA-seq analyses. At that time, GV and MI oocytes were also sampled. Some remaining oocytes were further cultured in in the Sydney IVF fertilization medium for in vitro maturation overnight and collected one day after for RNA-seq analyses.

tag: developmental stage

value: oocyte at the MII stage


title: dMII-2 [dMII_S21]

description:
dMII_S21_R1_val_1-pw1_10-cN10-pq20w10m20
Single oocyte was subjected to cDNA synthesis


title: HCT116 H363Y pT530-SIRT1 ChIP-seq rep2

description: HCT116 asynchronous cells ChipSeq


title: MII-1 [MII_S18]

description:
MII_S18_R1_val_1-pw1_10-cN10-pq20w10m20
Single oocyte was subjected to cDNA synthesis

source_name: Human oocyte at the MII stage


title: HCT116 WT pT530-SIRT1 ChIP-seq rep2

description: HCT116 asynchronous cells ChipSeq


title: dMII-1 [dMII_S08]

description:
dMII_S08_R1_val_1-pw1_10-cN10-pq20w10m20
Single oocyte was subjected to cDNA synthesis


title: MII-2 [MII_S27]

description:
MII_S27_R1_val_1-pw1_10-cN10-pq20w10m20
Single oocyte was subjected to cDNA synthesis


title: dMI-2 [dMI_S11]

description:
dMI_S11_R1_val_1-pw1_10-cN10-pq20w10m20
Single oocyte was subjected to cDNA synthesis

source_name: Human oocyte at the MI stage that is collected a day after the initial oocyte collection

value: oocyte at the MI stage


title: mitfa:GFP+/crestin:mCherry+/double+ cells, DMSO

city: Edinburgh

first: Eleanor

middle: Elizabeth

last: Patton

address: MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Western General Hospital, Crewe Road

country: United Kingdom

institute: MRC Human Genetics Unit, Institute of Genes and Cancer, University of Edinburgh

description:
DMSO_CVT_combined.csv
DMSO_CVT_combined_filtered.csv

data_processing:
Illumina  software used for basecalling.
Reads from each library were aligned to the zebrafish genome (GRCz11) using the CellRanger pipeline (v.2.1.1)
Libraries were aggregated using the CellRanger pipeline (v.3.1.0, CellRanger aggregate)
The gene-cell aggregated matrix  was subjected standard quality control with the Scater package (v.1.18.6). Only cells with total features >1000, log10 total counts > 3.0, and mitochondrial gene counts (%) < 20 were considered as high quality and kept
Genome_build: Zebrafish GRCz11
Supplementary_files_format_and_content: DMSO_CVT_combined.csv (Gene-cell aggregated matrix BEFORE filtering;comma separated (csv) file of raw counts at gene level for each cell)
Supplementary_files_format_and_content: DMSO_CVT_combined_filtered.csv (Gene-cell aggregated matrix AFTER filtering; comma separated (csv) file of raw counts at gene level for each cell)
Supplementary_files_format_and_content: The DMSO barcodes are followed with -1 and the CVT barcodes by -2.

organism: Danio rerio

source_name: mitfa:GFP+/crestin:mCherry+/double+ cells sorted from DMSO-treated 72hpf embryos 8 hours post MoTP washout

extract_protocol:
scRNA-seq, paired end reads
library prepared with 10x genomics Chromium Single Cell 3’ Library Kit v3

tag: strain

value: MoTP+DMSO


title: dMI-1 [dMI_S07]

description:
dMI_S07_R1_val_1-pw1_10-cN10-pq20w10m20
Single oocyte was subjected to cDNA synthesis


title: dMI-3 [dMI_S16]

description:
dMI_S16_R1_val_1-pw1_10-cN10-pq20w10m20
Single oocyte was subjected to cDNA synthesis


title: HCT116 KO pT530-SIRT1 ChIP-seq rep2 (negative control)

description: HCT116 asynchronous cells ChipSeq

value: Cultured cancer cell line

value: ChipSeq DNA


title: MI-2 [MI_S17]

description:
MI_S17_R1_val_1-pw1_10-cN10-pq20w10m20
Single oocyte was subjected to cDNA synthesis

source_name: Human oocyte at the MI stage


title: mitfa:GFP+/crestin:mCherry+/double+ cells, CVT

source_name: mitfa:GFP+/crestin:mCherry+/double+ cells sorted from CVT-10216-treated 72hpf embryos 8 hours post MoTP washout


title: MII-3 [MII_S32]

description:
MII_S32_R1_val_1-pw1_10-cN10-pq20w10m20
Single oocyte was subjected to cDNA synthesis


title: HCT116 WT pS53-MCM2 ChIP-seq

value: pS53 MCM2 antibody (Bethyl labs, A300756A)


title: dGV-3 [dGV_S23]

description:
dGV_S23_R1_val_1-pw1_10-cN10-pq20w10m20
Single oocyte was subjected to cDNA synthesis

source_name: Human oocyte at the GV stage that is collected a day after the initial oocyte collection

value: oocyte at the GV stage


title: clk856, ZT14, R1

city: Waltham

first: Matthias

last: Schlichting

state: MA

address: 450 South St. MS 008

institute: Brandeis University

data_processing:
bcl2fastq v2.20 was used to convert the raw sequencing files into fastq files
Alignment: Reads were aligned to the dm6 version of the Drosophila genome using STAR alignment
PCR duplicate removal: PCR duplicates were removed using picardtools
DE analysis: Differential expression analysis was performed using edgeR
Assembly: dm6
Supplementary files format and content: txt, summary of normalized and raw reads

organism: Drosophila melanogaster

source_name: clock neuron

growth_protocol: All flies were grown at 25°C on standard cornmeal food under 12:12 LD conditions

extract_protocol:
We used the Gal4-UAS system to label with GFP either clock neurons (CLK856-Gal4) or all neurons (nsyb-Gal4) and then purified them using fluorescence activated cell sorting (FACS). Neurons of both types were collected at two circadian time points - ZT02 and ZT14 in duplicates.
cDNA was generated using SMARTseq2 protocol, which was then used to make sequencing libraries using the Illumina Nextera XT Library Prep Kit

treatment_protocol: There was no treatment performed; only cells were collected at the specified circadian timepoint

value: clock neuron

tag: time


title: clk856, ZT2, R2


title: clk856, ZT2, R1


title: nSyb, ZT14, R1

source_name: neuron

value: neuron

value: nSyb>EGFP


title: nSyb, ZT14, R2


title: clk856, ZT14, R2


title: nSyb, ZT2, R2


title: MI-1 [MI_S03]

description:
MI_S03_R1_val_1-pw1_10-cN10-pq20w10m20
Single oocyte was subjected to cDNA synthesis


title: MI-3 [MI_S33]

description:
MI_S33_R1_val_1-pw1_10-cN10-pq20w10m20
Single oocyte was subjected to cDNA synthesis


title: ACHN-Dp 18h-rep1

type: RNA

city: Copenhagen N

first: Thomas

last: Litman

state: Outside the US or Canada

address: Blegdamsvej 3C

department: ISIM

country: Denmark

institute: University of Copenhagen

description: Cells were treated for 6h with romidepsin, followed by 12h incubation with drug free medium

hyb_protocol: Hybridization according to Affymetrix protocol, performed at the NCI-Frederick LMT Microarray Center (Frederick, MD)

scan_protocol: GeneArray scanner, according to Affymetrix protocol, performed at the NCI-Frederick LMT Microarray Center (Frederick, MD)

data_processing: MAS5.0 normalization method, according to Affymetrix protocol. All intensity values were log2 transformed before further analysis.

label: biotin

source_name: ACHN-Dp 18h-rep1

label_protocol: Biotin labeling according to Affymetrix protocol, performed at the NCI-Frederick LMT Microarray Center (Frederick, MD)

growth_protocol: Cells were cultured in appropriate cell culture medium (Gibco Laboratories) supplemented with 10% fetal bovine serum (Gibco Laboratories), 100-units/L penicillin-streptomycin and 2mM glutamine (Gibco Laboratories).

extract_protocol: Total RNA was isolated from all seven cell lines using RNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions.

treatment_protocol: Cell lines were treated with 46 nM (25 ng/ml) of romidepsin for 6h or 6h followed by 12h incubation with drug free medium. Controls were treated with DMSO.

value: ACHN

value: Romidepsin

tag: time (h)


title: MiaPaca2-Dp 6h-rep3

description: Cells were treated for 6h with romidepsin

source_name: MiaPaca2-Dp 6h-rep3


title: ACHN-Dp 18h-rep3

source_name: ACHN-Dp 18h-rep3


title: MiaPaca2-Dp 6h-rep1

source_name: MiaPaca2-Dp 6h-rep1


title: MiaPaca2-Dp 6h-rep2

source_name: MiaPaca2-Dp 6h-rep2


title: MiaPaca2-Dp 18h-rep2

source_name: MiaPaca2-Dp 18h-rep2


title: dGV-2 [dGV_S20]

description:
dGV_S20_R1_val_1-pw1_10-cN10-pq20w10m20
Single oocyte was subjected to cDNA synthesis


title: ACHN-Dp 18h-rep2

source_name: ACHN-Dp 18h-rep2


title: MiaPaca2-Dp 18h-rep1

source_name: MiaPaca2-Dp 18h-rep1


title: EC-OVA-2

city: Boston

first: Manuel

last: Leyva-Castillo

address: 300 Longwood Ave

institute: Boston Children's Hospital

data_processing:
The raw sequencing data were preprocessed to generate the read count per gene per cell matrices using CellRanger (10x Genomics, version 3.1.0), including BCL to FASTQ file conversion, data multiplexing according to cell barcodes, genome alignment to mouse genome mm10 with STAR, and reads counting per gene per cell into matrices
Genome_build: mm10
Supplementary_files_format_and_content: Single cell RNAseq barcodes, features, matrix

organism: Mus musculus

source_name: EC-OVA

extract_protocol:
Balb/c mice were epicutaneously sensitized for 10 days. 2 days later the mouse skin was collected and enzymatically digested to generate a sjingle cell suspension. Barcoding and library preparation were done using  the 10x Genomics Chromium platform, with the Chromium Single Cell 3′ Library & Gel Bead Kit v2 and Chromium Single Cell 3′ Chip kit v2 according to the manufacturer’s instructions.
For single-cell RNA-seq we used 10X protocol.

value: Balb/c

tag: tissue

value: epicutaneously sensitized skin

value: OVA-sensitized


title: EC-OVA-1


title: GV-4 [GV_S14]

description:
GV_S14_R1_val_1-pw1_10-cN10-pq20w10m20
Single oocyte was subjected to cDNA synthesis

source_name: Human oocyte at the GV stage


title: MiaPaca2-ctl-rep1

description: Control cells were treated with DMSO

value: control


title: A549-Dp 18h-rep3


title: GV-2 [GV_S02]

description:
GV_S02_R1_val_1-pw1_10-cN10-pq20w10m20
Single oocyte was subjected to cDNA synthesis


title: dGV-1 [dGV_S10]

description:
dGV_S10_R1_val_1-pw1_10-cN10-pq20w10m20
Single oocyte was subjected to cDNA synthesis


title: PANC1_IFN2h_rep_1

description: 10^6 cells are lysed and processed according to SMART-Seq2 protocol. Briefly, 5 ng of poly-A containing mRNA molecules are copied into first strand cDNA by reverse transcription and template-switching using oligo(dt) primers and LNA-containing template-switching oligo (TSO). cDNA is pre-amplified using limited number of cycles, purified and tagmented with Tn5 transposase. cDNA fragments generated after tagmentation are gap-repaired, enriched by PCR and purified to create the final cDNA library for Illumina sequencing.

data_processing:
Reads were pre-processed (quality trimming and adapter clipping) using Trim Galore v0.6.5, then reads with a minimum of 30 bp were aligned to human genome build GRCh38/hg38 using TopHat2 v2.1.1 with parameter “–b2‐very‐sensitive”. Only uniquely mapped reads were retained.
At the gene level, the expression counts were estimated using summarizeOverlaps() function of GenomicRanges R-package v1.38 with "IntersectionStrict" mode.
Differential expression analysis in biological duplicates or more was performed using the DESeq2 R-package v1.26.
Genome_build: GRCh38/hg38

source_name: Pancreatic Ductal Adenocarcinoma (PDAC) cell line

value: Bulk population of PANC1 cell line

value: DMEM supplemented with 10% Fetal Bovine Serum, 2mM L-Glutamine and 1% Pen/Strep

value: Bulk population treated with 1000 U/ml human IFNbeta for 2 hours


title: MiaPaca2-ctl-rep2

description: Control cells were treated with DMSO


title: EC-OVA-3


title: EC-SAL-3

source_name: EC-SAL


title: GV-3 [GV_S06]

description:
GV_S06_R1_val_1-pw1_10-cN10-pq20w10m20
Single oocyte was subjected to cDNA synthesis


title: EC-SAL-1


title: PANC1_IFN2h_rep_3

extract_protocol: 10^6 cells are lysed and processed according to SMART-Seq2 protocol. Briefly, 5 ng of poly-A containing mRNA molecules are copied into first strand cDNA by reverse transcription and template-switching using oligo(dt) primers and LNA-containing template-switching oligo (TSO). cDNA is pre-amplified using limited number of cycles, purified and tagmented with Tn5 transposase. cDNA fragments generated after tagmentation are gap-repaired, enriched by PCR and purified to create the final cDNA library for Illumina sequencing.


title: MiaPaca2-Dp 18h-rep3

source_name: MiaPaca2-Dp 18h-rep3


title: A549-Dp 18h-rep2


title: MiaPaca2-ctl-rep3

description: Control cells were treated with DMSO


title: nSyb, ZT2, R1


title: MiaPaCa2_IFN2h_rep_3

value: Bulk population of MiaPaCa2 cell line


title: GV-1 [GV_S01]

description:
GV_S01_R1_val_2-pw1_10-cN10-pq20w10m20
Single oocyte was subjected to cDNA synthesis


title: A549-Dp 18h-rep1


title: PANC1_UT_rep_3

value: Untreated bulk population


title: MiaPaCa2_IFN2h_rep_2


title: EC-SAL-2


title: PANC1_UT_rep_2


title: FACS endothelial cells Aged Sham 4

city: Rochester

first: Aditya

last: Bhagwate

state: MN

address: 200 1st Street SW

institute: Mayo Clinic

data_processing:
Sequencing Reads were aligned to mm10 build of the mouse genome using Burrows-Wheeler Alignment (BWA)
Peaks were called using MACS2 software.
TDF files for visualization were generated using in-house scripts
Genome_build: mm10
Supplementary_files_format_and_content: BED and TDF files

source_name: Lung endothelial cells

extract_protocol:
Lungs were perfused, harvested and processed for FACS. Freshly isolated lung endothelial cells were sorted diretly in tubes containing 500 ul of a specific ATAC-seq buffer and transferred for the analysis
The size of library DNA was determined from the amplified and purified library by a Fragment Analyzer, and the enrichment of accessible regions was determined by the fold difference between positive and negative genomic loci using real-time PCR.

value: FVB

value: PBS

tag: age

value: 18 months


title: MiaPaCa2_UT_rep_2


title: C1

city: Taian

first: Victoria

middle: Anthony

last: Uyanga

state: Please select

address: 61 Daizong Street, China

department: Animal Nutrition and Feed Science

institute: Shandong Agricultural University

data_processing:
The raw data provided by the sequencing platform (Fastq files) were filtered for quality check.
The filtered reads were aligned to the chicken reference genome (assembly Gallus gallus_4.0) and annotated transcripts of the Ensembl gene annotation using an upgraded version of hisat2 with tophat
The htseq statistics (https://htseq.readthedocs.io/en/release_0.9.1/) was applied to compare the read count value of each gene as the original expression of the gene
RSeQC was used to analyze the expression saturation of the sequencing results and calculated the expression levels of all genes
The DE-Seq R package (http://www.bioconductor.org/packages/release/bioc/html/DESeq.html) was used to analyze and screen the differential expression of genes among groups
Assembly: Gallus_gallus.GRCg6a.dna.toplevel.fa
Supplementary files format and content: tab-delimited text files include FPKM values for each sample
Supplementary files format and content: excel table with raw gene counts for every gene and every sample

organism: Gallus gallus

source_name: Brain

growth_protocol: The chicks were reared at 32oC for the first 3 days and the temperature was reduced by 2oC at 3 days interval until 24oC. Each chamber had three battery cages with double-tiers and a total of 8 cages per battery cage. The cage dimension was 38 × 47 × 35 cm and three birds were housed per cage.

extract_protocol:
The hypothalamic samples (n =6/group) were lysed using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) for RNA extraction in accordance to the manufacturer's protocol. The concentration and purity were detected and the quality of the library was tested by Agilent 2100 Bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Birds were fed two dietary treatments; basal diets or 1% L-Citrulline supplemented diets. At 28 days old. Birds were allocated to thermoneutral (TNZ- 24oC, 60% RH) or high temperature (HS-35oC, 60% RH) environments. The study had four (4) treatments comprising of CON (TNZ + basal diet); A (TNZ + L-Cit diet); B (HS + basal diet); C (HS+ L-Cit diet). Each treatment had 6 replicates of 12 chickens each.

value: Ros 308

value: Hypothalamus

value: Posthatch day 42

value: L-Citrulline diet +  35oC


title: C6


title: C3


title: PANC1_IFN2h_rep_2


title: PANC1_UT_rep_1


title: C5


title: MiaPaCa2_UT_rep_1


title: Paciente, P6

city: Campinas

first: Estela

middle: Maria

last: Bruxel

state: São Paulo

address: Tessália Vieira de Camargo, 126

department: Translational Medicine

country: Brazil

institute: UNICAMP

hyb_protocol: Hybridization of cRNA with the plate. We assessed the quality of hybridized chips by following the Affymetrix guidelines based on the average background, scaling factor, number of genes called present, and 3' to 5' ratios for endogenous control genes.

scan_protocol: Scanning of image output files using the GeneChip Scanner 3000 (Affymetrix)

data_processing:
We processed in the R environment using the computer packages “affy” and “limma” from Bioconductor.
We considered genes to be significantly differentially expressed when the log2 fold change (log2FC) was ≥1.0 or ≤ -1.0 and the false discovery rate (FDR)-adjusted P-value was ≤ 0.05

source_name: Hippocampus from Sporadic MTLE

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: hippocampus

tag: disease state

value: Sporadic MTLE


title: Paciente, P11


title: C4


title: Paciente, 16A

source_name: Hippocampus from Familial MTLE

value: Familial MTLE


title: Paciente, P13


title: Paciente, P10


title: Paciente, P4


title: CAPAN1_IFN2h_rep_3

value: Bulk population of CAPAN1 cell line

value: RPMI supplemented with 20% Fetal Bovine Serum, 2mM L-Glutamine and 1% Pen/Strep


title: C2


title: MiaPaCa2_IFN2h_rep_1


title: MiaPaCa2_UT_rep_3


title: FACS endothelial cells Young Sham 1

value: 2 months


title: B3

value: Basal diet +  35oC


title: CAPAN1_IFN2h_rep_1

value: Bulk population treated with 1000 U/ml human IFNbeta for 2 hours


title: FACS endothelial cells Young Bleo 4

value: Bleomycin


title: B1


title: B2


title: FACS endothelial cells Young Sham 5


title: CAPAN1_UT_rep_2

value: Untreated bulk population


title: FACS endothelial cells Young Bleo 2

value: FVB


title: B5


title: Paciente, 17A


title: FACS endothelial cells Young Sham 4

value: PBS


title: FACS endothelial cells Young Sham 3


title: FACS endothelial cells Aged Sham 3

value: 18 months


title: CAPAN1_UT_rep_3


title: FACS endothelial cells Young Sham 2


title: CAPAN1_UT_rep_1


title: CAPAN1_IFN2h_rep_2


title: B4

value: Ros 308


title: CFPAC1_IFN2h_rep_3

value: Bulk population of CFPAC1 cell line

value: IMDM supplemented with 10% Fetal Bovine Serum, 2mM L-Glutamine and 1% Pen/Strep


title: A4

value: Hypothalamus

value: Posthatch day 42

value: L-Citrulline diet +  24oC


title: Paciente, 14A

value: hippocampus

value: Familial MTLE


title: A2


title: FACS endothelial cells Young Bleo 3


title: A6


title: CFPAC1_UT_rep_3


title: A1


title: A5


title: FACS endothelial cells Young Bleo 1


title: A3


title: CFPAC1_UT_rep_1


title: FACS endothelial cells Aged Bleo 5


title: CFPAC1_IFN2h_rep_2


title: CFPAC1_UT_rep_2


title: FACS endothelial cells Aged Bleo 3


title: FACS endothelial cells Aged Bleo 4


title: CON  5

value: Basal diet +  24oC


title: FACS endothelial cells Aged Sham 1


title: FACS endothelial cells Aged Sham 2


title: H3K27ac_CFPAC1_WT_clone_2

description: Chromatin IP against H3K27ac

data_processing:
Reads were pre-processing (filtering, quality trimming and adapter clipping) using Trimmomatic (version 0.38),  then reads were aligned to human genome build GRCh38/hg38 using Bowtie2 v2.2.6 with “–very-sensitive” preset of parameters. Reads that did not align to nuclear genome or aligned to mitocondrial genome were removed. PCR duplicates were removed using samtools.
Peak calling was performed using MACS2 (version 2.1.0.20150731) with the “--nomodel”, “--extsize 200” and “--qvalue 0.05” flags and arguments. Each IP was compared to input DNA.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: *.narrowPeak, list of the peaks called by MACS2

value: CFPAC1 clonal cell line

value: Anti H3K27ac (Abcam, ab4729)

value: Isolation of clonal cell line by dilution of CFPAC1 cells infected with lentiCRIPSv2 plasmid (Addgene #52961)


title: CON  4


title: FACS endothelial cells Aged Bleo 1

value: Bleomycin


title: CON  6


title: CFPAC1_IFN2h_rep_1

value: Bulk population treated with 1000 U/ml human IFNbeta for 2 hours


title: CON  3


title: FACS endothelial cells Aged Bleo 2

value: FVB


title: H3K27ac_CFPAC1_WT_clone_1

description: Chromatin IP against H3K27ac


title: CON  2


title: C2C12-S-input,2

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

institute: Medical Institute of Bioregulation

description: H3K27ac-S.norm.bw, H3K4me1-S.norm.bw

data_processing:
For RNA-seq, the raw sequence reads (fastq file) were mapped to the GRCm38 reference genome using HISAT2 (D. Kim et al., 2015, M. Pertea et al., 2016, D. Kim et al., 2019) (version 2.1.0), and BAM files were created using SAMtools (H. Li, 2009, H. Li, 2011)  (version 1.6).
Mapped reads were counted using featureCounts (Liao Y et al., 2014) (version 1.5.0) and a count matrix was created.
The downstream analysis was carried out with R (version 4.0.1).
For ChIP-seq analysis, Bowtie2 (B. Langmead et al., 2012) (version 2.3.0) was used to map the raw sequence reads (fastq) to the mouse mm10 reference genome, and BAM files were created using SAMtools.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: ChIP-seq signal tracks (bigWig) were created using deepTools (Ramírez et al., 2016) (version 3.5.0). The bin size was 200 bp and window size was 10 kbp, except for H3K27me3 where the bin size was 200 bp and window size was 10 kbp.
Supplementary_files_format_and_content: *.csv file include comma-delimited RNA-seq read count matrix.

source_name: C2C12 cell line

growth_protocol: The mouse myoblast C2C12 cell line was maintained in Dulbecco’s modified Eagle’s medium (DMEM) with 1 g/L glucose (Gibco™, Thermo Fisher Scientific) containing 20% fetal bovine serum (FBS), 2 mM L-glutamine, and 1% penicillin-streptomycin.

extract_protocol:
Total RNA was obtained from the C2C12 cells using Sepasol-RNA I Super G (Nacalai Tesque Inc.) and ethanol precipitation.
Sequencing was performed in an Illumina Illumina HiSeq1500 system with 101 cycles for both read 1 and read 2 using HiSeq PE Rapid Cluster Kit v2 and  HiSeq Rapid SBS Kit v2 (200 Cycles) for RNA-seq, and with 51 cycles for read 1 using TruSeq SBS Kit v3-HS (50 Cycles) and TruSeq SR Cluster Kit v3-cBot-HS for ChIP-seq.
C2C12 cells were sorted into three groups on the basis of the cell cycle (G1, S, and G2-M phases) and used for RNA-seq analysis. The C2C12 cells in the three groups (G1, S, and G2-M phases) were used for the ChIP-seq analysis.

treatment_protocol: C2C12 cells in the growing state were treated with trypsin and centrifuged for 5 min. The pelleted cells were resuspended and stained with 1× PBS containing Hoechst 33342 (Nacalai Tesque Inc.) for 15 min. The suspension was analyzed using a cell sorter (SONY, SH800).

value: growing state, S phase

tag: chil antibody

value: Input


title: CON 1

value: Ros 308


title: H3K27Ac_MiaPaCa2_IFN_1

description: Chromatin IP against H3K27ac

value: MiaPaCa2 cell line

value: DMEM supplemented with 10% Fetal Bovine Serum, 2mM L-Glutamine and 1% Pen/Strep

value: Bulk cell line, treated with 1000 U/ml of human IFNbeta for 2 hours


title: YJZYT3

city: changsha，CHINA

first: Hai-ping

last: HUANG

address: 300 Xuesheng Road, Hanpu Science and Education Park, Yuelu District, Changsha, Hunan province, China

institute: Hunan University of Chinese Medicine

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.

organism: Rattus norvegicus

source_name: Bone

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: Bone

value: Sprague-Dawley

tag: condition

value: YJZYT

tag: Sex

value: female

value: ovariectomized


title: YJZYT2


title: H3K27Ac_MiaPaCa2_IFN_2

description: Chromatin IP against H3K27ac


title: H3K27ac_CFPAC1_IRF1KO_clone_1

description: Chromatin IP against H3K27ac

value: CFPAC1 clonal cell line

value: IMDM supplemented with 10% Fetal Bovine Serum, 2mM L-Glutamine and 1% Pen/Strep

value: Isolation of clonal cell line by dilution of CFPAC1 cells infected with lentiCRIPSv2 plasmid (Addgene #52961) carring the expression of wt Cas9 and a guide RNA targeting IRF1 gene


title: YJZYT1


title: YJT3

value: YJT


title: H3K27Ac_MiaPaCa2_UT_2

description: Chromatin IP against H3K27ac

value: Anti H3K27ac (Abcam, ab4729)

value: Bulk cell line, untreated


title: C2C12-S-H3K4me1

value: growing state, S phase

value: mouse anti-H3K4me1 CMA302  [PMID 18227620]


title: H3K27Ac_MiaPaCa2_UT_1

description: Chromatin IP against H3K27ac


title: C2C12-G2M-input, 2

description: H3K27ac-G2M.norm.bw, H3K4me1-G2M.norm.bw

value: growing state, G2-M phase

value: Input


title: C2C12-S-H3K27ac

value: mouse anti-H3K27ac CMA309 [PMID 18227620]


title: H3K27Ac_CFPAC1_IFN_1

description: Chromatin IP against H3K27ac

value: CFPAC1 cell line

value: Bulk cell line, treated with 1000 U/ml of human IFNbeta for 2 hours


title: C2C12-G2M-H3K4me1


title: H3K27Ac_CFPAC1_IFN_2

description: Chromatin IP against H3K27ac


title: SYT3

value: Bone

value: Sprague-Dawley

value: SYT


title: YJT1

value: female

value: ovariectomized


title: H3K27Ac_CFPAC1_UT_2

description: Chromatin IP against H3K27ac

value: IMDM supplemented with 10% Fetal Bovine Serum, 2mM L-Glutamine and 1% Pen/Strep


title: C2C12-G1-input, 2

description: H3K27ac-G1.norm.bw, H3K4me1-G1.norm.bw

value: growing state, G1 phase


title: SYT2


title: H3K27Ac_CFPAC1_UT_1

description: Chromatin IP against H3K27ac


title: C2C12-G2M-H3K27ac


title: STAT1_MiaPaCa2_IFN_2

description: Chromatin IP against STAT1

value: MiaPaCa2 cell line

value: DMEM supplemented with 10% Fetal Bovine Serum, 2mM L-Glutamine and 1% Pen/Strep

value: Anti-STAT1 (Santa Cruz, sc-345)


title: C2C12-G1-H3K4me1


title: Model2

value: Osteoporosis


title: C2C12-G1-H3K27ac


title: Model3


title: STAT1_MiaPaCa2_UT_2

description: Chromatin IP against STAT1

value: Bulk cell line, untreated


title: Model1


title: STAT1_MiaPaCa2_IFN_1

description: Chromatin IP against STAT1


title: YJT2

value: YJT


title: C2C12-S-input

value: growing state, S phase

value: Input


title: STAT1_MiaPaCa2_UT_1

description: Chromatin IP against STAT1


title: STAT1_CFPAC1_IFN_2

description: Chromatin IP against STAT1

value: CFPAC1 cell line


title: C2C12-G2M-input

value: growing state, G2-M phase


title: Blank2

value: Bone

value: Blank


title: C2C12-S-H3K4me2

value: mouse anti-H3K4me2 CMA303  [PMID 18227620]


title: C2C12-G2M-H3K4me2


title: SYT1

value: Sprague-Dawley

value: SYT

value: female


title: Blank1


title: STAT1_CFPAC1_IFN_1

description: Chromatin IP against STAT1

value: IMDM supplemented with 10% Fetal Bovine Serum, 2mM L-Glutamine and 1% Pen/Strep

value: Bulk cell line, treated with 1000 U/ml of human IFNbeta for 2 hours


title: STAT1_CFPAC1_UT_1

description: Chromatin IP against STAT1


title: CFPAC1_ATAC_rep2

data_processing:
Reads were pre-processing (filtering, quality trimming and adapter clipping) using Trimmomatic (version 0.38) (PMID:24695404),  then single-end with min 36-bp reads length were aligned to human genome build GRCh38/hg38 using Bowtie2 v2.2.6 (PMID: 22388286) with “–very-sensitive” preset of parameters. Reads that did not align to nuclear genome or aligned to mitocondrial genome were removed. PCR duplicates were removed using samtools. Then read positions were corrected for transposon insertion offset as described in (PMID:24097267).
Peak calling was performed using MACS2 with the “--nomodel”, “--extsize 146”,  “--qvalue 0.05”, "--nolambda" and "--keep-dup all" flags and arguments
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: *.narrowPeak, list of the peaks called by MACS2

extract_protocol: 50000 cells were pelleted by centrifugation and re-suspended in 50 µl of cold lysis buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% NP40, 0.1% Tween-20 and 0.01% Digitonin). After incubation on ice for three minutes, lysis was washed out by adding 1 mL of lysis buffer without NP40 and digitonin. Nuclei were pelleted by centrifugation for 10 min at 500g, 4 ºC.  The supernatant was discarded and nuclei were re-suspended in 50 µl of reaction buffer containing 1 µl of Tn5 transposase (made in house),  10 ul of 5x transposase buffer (50mM Tris-HCl, pH 8.4 and 25mM MgCl2), 16.5 µl PBS, 0.5 µl of 1% digitonin, 0.5 µl of 10% Tween-20. The reaction was incubated at 37ºC for 30 minutes with 600 RPM mixing. Then 5 µl of clean up buffer (900mM NaCl, 300mM EDTA), 2ul of 5% SDS and 2 µl of Proteinase K (20 µg/µl) (New England Biolabs) were added and incubated for 30 min at 40 ºC. Tagmented DNA was isolated using SPRI beads (2x) and amplified by PCR. Fragments smaller than 600 bp were isolated using SPRI cleanup and libraries where sequenced on an Illumina NextSeq500 platform.

value: CFPAC1 wild-type cell line


title: CFPAC1_ATAC_rep1


title: Blank3


title: C2C12-G1-input

value: growing state, G1 phase


title: input-S


title: C2C12-G1-H3K4me2


title: STAT1_CFPAC1_UT_2

description: Chromatin IP against STAT1

value: Anti-STAT1 (Santa Cruz, sc-345)


title: input-G2M