title: RNA-seq on RUES2 differentiated to endothelial cell - 4DNEXMH7P7QL

description:
lab: Chuck Murry, UW
award: 1U54DK107979-01
4DN accession: 4DNEXMH7P7QL
strandedness: reverse
submitted_by: Kris Alavattam
experiment_type: RNA-seq
contributing_labs: William Noble, UW
biosample_quantity: 1.0 ug
url: https://data.4dnucleome.org/experiments-seq/4DNEXMH7P7QL/

data_processing:
https://data.4dnucleome.org/resources/data-analysis/rnaseq-processing-pipeline
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/f2094826-54b6-4f8a-a646-1257837f00cf/
genome_assembly: GRCh38
derived_from: 4DNFI3FCGSW2.starIndex.tgz, 4DNFIZJB62D1.chrom.sizes, 4DNFIHJRV2WP.fastq.gz, 4DNFIZ5WFN8T.fastq.gz, 4DNFIHBJI984.tsv, 4DNFIB4HV398.rsemindex.tgz
description: Output file from RNA seq pipeline
file_type: read counts (plus)
file_format: bw
file name: 4DNFIB8LAXWR.bw
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/f2094826-54b6-4f8a-a646-1257837f00cf/
genome_assembly: GRCh38
derived_from: 4DNFI3FCGSW2.starIndex.tgz, 4DNFIZJB62D1.chrom.sizes, 4DNFIHJRV2WP.fastq.gz, 4DNFIZ5WFN8T.fastq.gz, 4DNFIHBJI984.tsv, 4DNFIB4HV398.rsemindex.tgz
description: Output file from RNA seq pipeline
file_type: read counts (minus)
file_format: bw
file name: 4DNFICTGL4Q9.bw
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/f2094826-54b6-4f8a-a646-1257837f00cf/
genome_assembly: GRCh38
derived_from: 4DNFI3FCGSW2.starIndex.tgz, 4DNFIZJB62D1.chrom.sizes, 4DNFIHJRV2WP.fastq.gz, 4DNFIZ5WFN8T.fastq.gz, 4DNFIHBJI984.tsv, 4DNFIB4HV398.rsemindex.tgz
description: Output file from RNA seq pipeline
file_type: gene expression
file_format: tsv
file name: 4DNFIXY383IQ.tsv
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/f2094826-54b6-4f8a-a646-1257837f00cf/
genome_assembly: GRCh38
derived_from: 4DNFI3FCGSW2.starIndex.tgz, 4DNFIZJB62D1.chrom.sizes, 4DNFIHJRV2WP.fastq.gz, 4DNFIZ5WFN8T.fastq.gz, 4DNFIHBJI984.tsv, 4DNFIB4HV398.rsemindex.tgz
description: Output file from RNA seq pipeline
file_type: isoform expression
file_format: tsv
file name: 4DNFITY9WXBC.tsv


title: RNA-seq on RUES2 differentiated to mesoderm - 4DNEXNQUX8R8

status: Public on Jan 18 2023

type: SRA

city: Boston

last: DCIC

state: MA

address: 10 Shattuck St

country: USA

institute: 4D Nucleome - Data Coordination and Integration Center

description:
lab: Chuck Murry, UW
award: 1U54DK107979-01
4DN accession: 4DNEXNQUX8R8
strandedness: reverse
submitted_by: Kris Alavattam
experiment_type: RNA-seq
contributing_labs: William Noble, UW
biosample_quantity: 1.0 ug
url: https://data.4dnucleome.org/experiments-seq/4DNEXNQUX8R8/

library_source: transcriptomic

data_processing:
https://data.4dnucleome.org/resources/data-analysis/rnaseq-processing-pipeline
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/ddef7671-9438-4d3b-a6cd-1bd0ed78707d/
genome_assembly: GRCh38
derived_from: 4DNFI3FCGSW2.starIndex.tgz, 4DNFIZJB62D1.chrom.sizes, 4DNFIJ3139I1.fastq.gz, 4DNFIL1LRCRE.fastq.gz, 4DNFIHBJI984.tsv, 4DNFIB4HV398.rsemindex.tgz
description: Output file from RNA seq pipeline
file_type: read counts (plus)
file_format: bw
file name: 4DNFIH7CRDBK.bw
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/ddef7671-9438-4d3b-a6cd-1bd0ed78707d/
genome_assembly: GRCh38
derived_from: 4DNFI3FCGSW2.starIndex.tgz, 4DNFIZJB62D1.chrom.sizes, 4DNFIJ3139I1.fastq.gz, 4DNFIL1LRCRE.fastq.gz, 4DNFIHBJI984.tsv, 4DNFIB4HV398.rsemindex.tgz
description: Output file from RNA seq pipeline
file_type: read counts (minus)
file_format: bw
file name: 4DNFI49KRAJJ.bw
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/ddef7671-9438-4d3b-a6cd-1bd0ed78707d/
genome_assembly: GRCh38
derived_from: 4DNFI3FCGSW2.starIndex.tgz, 4DNFIZJB62D1.chrom.sizes, 4DNFIJ3139I1.fastq.gz, 4DNFIL1LRCRE.fastq.gz, 4DNFIHBJI984.tsv, 4DNFIB4HV398.rsemindex.tgz
description: Output file from RNA seq pipeline
file_type: gene expression
file_format: tsv
file name: 4DNFIKGVXB8P.tsv
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/ddef7671-9438-4d3b-a6cd-1bd0ed78707d/
genome_assembly: GRCh38
derived_from: 4DNFI3FCGSW2.starIndex.tgz, 4DNFIZJB62D1.chrom.sizes, 4DNFIJ3139I1.fastq.gz, 4DNFIL1LRCRE.fastq.gz, 4DNFIHBJI984.tsv, 4DNFIB4HV398.rsemindex.tgz
description: Output file from RNA seq pipeline
file_type: isoform expression
file_format: tsv
file name: 4DNFIKY881XC.tsv

molecule: total RNA

organism: Homo sapiens

source_name: biosource_summary: RUES2 differentiated to mesoderm

extract_protocol:
description: Protocol for Illumina TruSeq Stranded Total RNA Human/Mouse/Rat
download: https://data.4dnucleome.org/protocols/bd3a9473-196d-4191-8e89-c49e05618907/@@download/attachment/truseq-stranded-total-rna-sample-prep-guide-15031048-e.pdf

treatment_protocol:
description: Protocol for passaging hPSCs and differentiating them to endothelial cells
download: https://data.4dnucleome.org/protocols/5390905f-7a27-4c82-816f-5a848c1ae21d/@@download/attachment/Alavattam-Mitzelfelt_endothelial-cells_protocol_passaging-differentiation.pdf

tag: tissue

value: mesoderm

tag: Sex

value: female

value: in vitro differentiated cells

tag: url

value: embryonic


title: CDK9_RBBP5FKBP_0h

city: Beijing

first: Hua

last: Wang

address: 38 Xueyuan Rd

country: China

institute: Peking University

description: RBBP5-FKBP degron

library_source: genomic

data_processing:
Illumina bcl2fastq2 Conversion Software v2.20 used for basecalling.
FASTQ reads were mapped to the GRCm38 (mm10) genome using Bowtie2 (v2.4.1) using the standard settings.
DeepTools (v3.3.0) was used to generate occupancy heat maps, and the resulting normalized occupancy matrix was used as input for custom R scripts to generate average profile plots and to calculate processivity indices.
Genome_build: mm10
Supplementary_files_format_and_content: All other processed data is made available as supplementary files to the manuscript

molecule: genomic DNA

organism: Mus musculus

source_name: mESCs

growth_protocol: E14 ESCs (129/Ola background) were maintained on 0.2% gelatin-coated plates in Glasgow Minimum Essential Medium (GMEM, Sigma-Aldrich, G5154) containing 15% fetal bovine serum (Gibco, 26140079), supplemented with 1× Pen-Strep (Thermofisher Scientific, 15140122), 2 mM Glutamax (Thermofisher Scientific, 35050061), 50 µM β-mercaptoethanol (Thermofisher Scientific, 21985023), 0.1 mM nonessential amino acids (Thermofisher Scientific, 11140050), 1 mM sodium pyruvate (Thermofisher Scientific, 11360070), and Leukemia Inhibitory Factor (LIF, 1000U/mL, Millipore).

extract_protocol:
ES cells were cross-linked by the addition of 1% formaldehyde (Sigma-Aldrich, 252549-1L) in the dish for 10 minutes at RT before quenching with 0.125 M glycine. The fixed cells were washed with PBS and resuspended in SDS buffer (100 mM NaCl, 50 mM Tris-HCl pH 8.0, 5 mM EDTA, 0.5% SDS, 1x protease inhibitor cocktail from Roche). The resulting nuclei were spin down, resuspended in the immunoprecipitation buffer at 1 mL per 16 million cells (SDS buffer and Triton Dilution buffer (100 mM NaCl, 100 mM Tris-HCl pH 8.0, 5 mM EDTA, 5% Triton X-100) mixed in 2:1 ratio with the addition of 1x protease inhibitor cocktail from Roche) and processed on a Bioruptor Plus Sonicator (Diagenode) to achieve an average fragment length of 200-300 bps.
Libraries were constructed using NEBNext Ultra II DNA Library prep kit (NEB, E7645L).

treatment_protocol: Auxin or dTAG-13 was added at the indicated time point.

tag: cell type

value: mESCs

tag: strain

tag: genotype

value: RBBP5-FKBP degron

tag: time

tag: antibody


title: CDK9_RBBP5FKBP_8h

description: RBBP5-FKBP degron


title: DNase Hi-C on RUES2 differentiated to endothelial progenitor cell with DNaseI - 4DNEXMBTNXDO

description:
lab: Chuck Murry, UW
award: 1U54DK107979-01
4DN accession: 4DNEXMBTNXDO
pcr_cycles: 10
submitted_by: Kris Alavattam
ligation_time: 960
biotin_removed: No
digestion_time: 7
tagging_method: Biotin dTTP
experiment_type: DNase Hi-C
ligation_volume: 1.1
digestion_enzyme: DNaseI
library_prep_kit: Kapa HiFi ReadyStart Master Mix (Roche, KK2602) with barcode-containing primers
contributing_labs: William Noble, UW
crosslinking_time: 10
biosample_quantity: 2000000 cells
crosslinking_method: 2% Formaldehyde
fragmentation_method: none
ligation_temperature: 16
digestion_temperature: 20
crosslinking_temperature: 20
fragment_size_selection_method: SPRI beads
url: https://data.4dnucleome.org/experiments-hi-c/4DNEXMBTNXDO/

data_processing:
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/ce89da32-4762-45f8-9823-7219bd64bbde/
genome_assembly: GRCh38
derived_from: 4DNFI823LSII.chrom.sizes, 4DNFI3KCPRZ1.bam, 4DNFI43WWPHD.bam, 4DNFIZMCMNRE.bam
description: This is an output file of the Hi-C processing pipeline
file_type: contact list-replicate
file_format: pairs
https://data.4dnucleome.org/resources/data-analysis/hi_c-processing-pipeline

source_name: biosource_summary: RUES2 differentiated to endothelial progenitor cell

extract_protocol:
description: The Official 4DN Standard in situ DNase Hi-C Protocol adapted from Ramani et al. PMID: 27685100 and approved by SC 01-16-2018
download: https://data.4dnucleome.org/protocols/1f97bb2b-180f-4a6d-b4ea-4e96c90eecdc/@@download/attachment/4DN_DNase_Hi-C_protocol_20180108.pdf

value: endothelial progenitor cell


title: saliva from 23205000

type: genomic

city: Bethesda

first: Paul

last: Meltzer

address: 9100 Rockville Pike

institute: NCI/NIH

description: saliva from 23205000

hyb_protocol: Illumina protocol

scan_protocol: Illumina protocol

data_processing:
Illumina protocol
For the data set, both the beta values as well as the intensity values were generated by using methylumi R package against the raw idat data files, and no normalization method is applied for the beta values.
Average Beta and Unmethylated and methylated signal intensities files are linked to the Series record.

label: Cy5 and Cy3

label_protocol: Illumina protocol

extract_protocol:
Illumina protocol
Bisulfite conversion

treatment_protocol: Saliva collection

value: saliva

tag: kindred

tag: mother or child

value: MOM

tag: gender

value: FEMALE

tag: study

value: Taicang-main


title: saliva from 23205001

description: saliva from 23205001

value: KID

value: MALE


title: H3K4me1_RBBP5FKBP_0h

description: RBBP5-FKBP degron


title: CDK9_DPY30mAID_8h

description: DPY30-mAID degron

value: DPY30-mAID degron


title: saliva from 23204831

description: saliva from 23204831


title: saliva from 23204830

description: saliva from 23204830


title: RNA-seq on RUES2 differentiated to endothelial progenitor cell - 4DNEXI4ZEEMG

description:
lab: Chuck Murry, UW
award: 1U54DK107979-01
4DN accession: 4DNEXI4ZEEMG
strandedness: reverse
submitted_by: Kris Alavattam
experiment_type: RNA-seq
contributing_labs: William Noble, UW
biosample_quantity: 1.0 ug
url: https://data.4dnucleome.org/experiments-seq/4DNEXI4ZEEMG/

data_processing:
https://data.4dnucleome.org/resources/data-analysis/rnaseq-processing-pipeline
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/2fc6cccb-d6d9-461a-8555-5b87e4795728/
genome_assembly: GRCh38
derived_from: 4DNFI3FCGSW2.starIndex.tgz, 4DNFIZJB62D1.chrom.sizes, 4DNFIN4TVOKA.fastq.gz, 4DNFIOOK94FS.fastq.gz, 4DNFIHBJI984.tsv, 4DNFIB4HV398.rsemindex.tgz
description: Output file from RNA seq pipeline
file_type: read counts (plus)
file_format: bw
file name: 4DNFIP18FKER.bw
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/2fc6cccb-d6d9-461a-8555-5b87e4795728/
genome_assembly: GRCh38
derived_from: 4DNFI3FCGSW2.starIndex.tgz, 4DNFIZJB62D1.chrom.sizes, 4DNFIN4TVOKA.fastq.gz, 4DNFIOOK94FS.fastq.gz, 4DNFIHBJI984.tsv, 4DNFIB4HV398.rsemindex.tgz
description: Output file from RNA seq pipeline
file_type: read counts (minus)
file_format: bw
file name: 4DNFI1AHW4D5.bw
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/2fc6cccb-d6d9-461a-8555-5b87e4795728/
genome_assembly: GRCh38
derived_from: 4DNFI3FCGSW2.starIndex.tgz, 4DNFIZJB62D1.chrom.sizes, 4DNFIN4TVOKA.fastq.gz, 4DNFIOOK94FS.fastq.gz, 4DNFIHBJI984.tsv, 4DNFIB4HV398.rsemindex.tgz
description: Output file from RNA seq pipeline
file_type: gene expression
file_format: tsv
file name: 4DNFIY5EPU2L.tsv
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/2fc6cccb-d6d9-461a-8555-5b87e4795728/
genome_assembly: GRCh38
derived_from: 4DNFI3FCGSW2.starIndex.tgz, 4DNFIZJB62D1.chrom.sizes, 4DNFIN4TVOKA.fastq.gz, 4DNFIOOK94FS.fastq.gz, 4DNFIHBJI984.tsv, 4DNFIB4HV398.rsemindex.tgz
description: Output file from RNA seq pipeline
file_type: isoform expression
file_format: tsv
file name: 4DNFIGKZNKBN.tsv


title: CDK9_DPY30mAID_0h

description: DPY30-mAID degron


title: DNase Hi-C on RUES2 with DNaseI - 4DNEXGWVDZL5

description:
lab: Chuck Murry, UW
award: 1U54DK107979-01
4DN accession: 4DNEXGWVDZL5
pcr_cycles: 10
submitted_by: Kris Alavattam
ligation_time: 960
biotin_removed: No
digestion_time: 7
tagging_method: Biotin dTTP
experiment_type: DNase Hi-C
ligation_volume: 1.1
digestion_enzyme: DNaseI
library_prep_kit: Kapa HiFi ReadyStart Master Mix (Roche, KK2602) with barcode-containing primers
contributing_labs: William Noble, UW
crosslinking_time: 10
biosample_quantity: 2000000 cells
crosslinking_method: 2% Formaldehyde
fragmentation_method: none
ligation_temperature: 16
digestion_temperature: 20
crosslinking_temperature: 20
fragment_size_selection_method: SPRI beads
url: https://data.4dnucleome.org/experiments-hi-c/4DNEXGWVDZL5/

data_processing:
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/bf74a63a-b2bf-455f-b38b-9b65bfc0b2a4/
genome_assembly: GRCh38
derived_from: 4DNFI823LSII.chrom.sizes, 4DNFI2Z3E7QJ.bam, 4DNFILWRXCD8.bam, 4DNFIZMXID7X.bam
description: This is an output file of the Hi-C processing pipeline
file_type: contact list-replicate
file_format: pairs
https://data.4dnucleome.org/resources/data-analysis/hi_c-processing-pipeline

source_name: biosource_summary: RUES2

value: stem cell

value: stem cells


title: BRD4_abcam_RBBP5FKBP_8h

description: RBBP5-FKBP degron


title: saliva from 23201121

description: saliva from 23201121


title: saliva from 23203010

description: saliva from 23203010

value: Taicang-substudy


title: DNase Hi-C on RUES2 differentiated to endothelial cell with DNaseI - 4DNEXCJ14SGJ

description:
lab: Chuck Murry, UW
award: 1U54DK107979-01
4DN accession: 4DNEXCJ14SGJ
pcr_cycles: 10
submitted_by: Kris Alavattam
ligation_time: 960
biotin_removed: No
digestion_time: 7
tagging_method: Biotin dTTP
experiment_type: DNase Hi-C
ligation_volume: 1.1
digestion_enzyme: DNaseI
library_prep_kit: Kapa HiFi ReadyStart Master Mix (Roche, KK2602) with barcode-containing primers
contributing_labs: William Noble, UW
crosslinking_time: 10
biosample_quantity: 2000000 cells
crosslinking_method: 2% Formaldehyde
fragmentation_method: none
ligation_temperature: 16
digestion_temperature: 20
crosslinking_temperature: 20
fragment_size_selection_method: SPRI beads
url: https://data.4dnucleome.org/experiments-hi-c/4DNEXCJ14SGJ/

data_processing:
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/fc5a5faa-a164-443f-94db-49953a68792b/
genome_assembly: GRCh38
derived_from: 4DNFI823LSII.chrom.sizes, 4DNFIUI3AQAK.bam, 4DNFIP6U2FGC.bam, 4DNFIKCWZIP9.bam
description: This is an output file of the Hi-C processing pipeline
file_type: contact list-replicate
file_format: pairs
https://data.4dnucleome.org/resources/data-analysis/hi_c-processing-pipeline

source_name: biosource_summary: RUES2 differentiated to endothelial cell

value: endothelial cell


title: saliva from 23203011

description: saliva from 23203011


title: saliva from 23201751

description: saliva from 23201751


title: BRD4_abcam_RBBP5FKBP_0h

description: RBBP5-FKBP degron


title: RNA-seq on RUES2 differentiated to endothelial cell - 4DNEXCBSYZBN

description:
lab: Chuck Murry, UW
award: 1U54DK107979-01
4DN accession: 4DNEXCBSYZBN
strandedness: reverse
submitted_by: Kris Alavattam
experiment_type: RNA-seq
contributing_labs: William Noble, UW
biosample_quantity: 1.0 ug
url: https://data.4dnucleome.org/experiments-seq/4DNEXCBSYZBN/

data_processing:
https://data.4dnucleome.org/resources/data-analysis/rnaseq-processing-pipeline
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/f79bbd70-a073-49f6-80fd-0b730c982380/
genome_assembly: GRCh38
derived_from: 4DNFI3FCGSW2.starIndex.tgz, 4DNFIZJB62D1.chrom.sizes, 4DNFID8RHY88.fastq.gz, 4DNFIG4RKE3Y.fastq.gz, 4DNFIHBJI984.tsv, 4DNFIB4HV398.rsemindex.tgz
description: Output file from RNA seq pipeline
file_type: read counts (plus)
file_format: bw
file name: 4DNFIIPRAF2M.bw
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/f79bbd70-a073-49f6-80fd-0b730c982380/
genome_assembly: GRCh38
derived_from: 4DNFI3FCGSW2.starIndex.tgz, 4DNFIZJB62D1.chrom.sizes, 4DNFID8RHY88.fastq.gz, 4DNFIG4RKE3Y.fastq.gz, 4DNFIHBJI984.tsv, 4DNFIB4HV398.rsemindex.tgz
description: Output file from RNA seq pipeline
file_type: read counts (minus)
file_format: bw
file name: 4DNFI5CUHG1Z.bw
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/f79bbd70-a073-49f6-80fd-0b730c982380/
genome_assembly: GRCh38
derived_from: 4DNFI3FCGSW2.starIndex.tgz, 4DNFIZJB62D1.chrom.sizes, 4DNFID8RHY88.fastq.gz, 4DNFIG4RKE3Y.fastq.gz, 4DNFIHBJI984.tsv, 4DNFIB4HV398.rsemindex.tgz
description: Output file from RNA seq pipeline
file_type: gene expression
file_format: tsv
file name: 4DNFIQFCADXR.tsv
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/f79bbd70-a073-49f6-80fd-0b730c982380/
genome_assembly: GRCh38
derived_from: 4DNFI3FCGSW2.starIndex.tgz, 4DNFIZJB62D1.chrom.sizes, 4DNFID8RHY88.fastq.gz, 4DNFIG4RKE3Y.fastq.gz, 4DNFIHBJI984.tsv, 4DNFIB4HV398.rsemindex.tgz
description: Output file from RNA seq pipeline
file_type: isoform expression
file_format: tsv
file name: 4DNFIN9U7VXN.tsv

value: female


title: saliva from 23208160

description: saliva from 23208160


title: saliva from 23194691

description: saliva from 23194691


title: saliva from 23193661

description: saliva from 23193661


title: BRD4_abcam_DPY30mAID_8h

description: DPY30-mAID degron


title: saliva from 23192751

description: saliva from 23192751


title: DNase Hi-C on RUES2 differentiated to mesoderm with DNaseI - 4DNEXAIR7YJB

description:
lab: Chuck Murry, UW
award: 1U54DK107979-01
4DN accession: 4DNEXAIR7YJB
pcr_cycles: 10
submitted_by: Kris Alavattam
ligation_time: 960
biotin_removed: No
digestion_time: 7
tagging_method: Biotin dTTP
experiment_type: DNase Hi-C
ligation_volume: 1.1
digestion_enzyme: DNaseI
library_prep_kit: Kapa HiFi ReadyStart Master Mix (Roche, KK2602) with barcode-containing primers
contributing_labs: William Noble, UW
crosslinking_time: 10
biosample_quantity: 2000000 cells
crosslinking_method: 2% Formaldehyde
fragmentation_method: none
ligation_temperature: 16
digestion_temperature: 20
crosslinking_temperature: 20
fragment_size_selection_method: SPRI beads
url: https://data.4dnucleome.org/experiments-hi-c/4DNEXAIR7YJB/

data_processing:
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/a09e8b29-1713-44ea-8b09-a65105a692d6/
genome_assembly: GRCh38
derived_from: 4DNFI823LSII.chrom.sizes, 4DNFI8U2VCWX.bam, 4DNFIQBENVT8.bam, 4DNFIWYHWKRH.bam
description: This is an output file of the Hi-C processing pipeline
file_type: contact list-replicate
file_format: pairs
https://data.4dnucleome.org/resources/data-analysis/hi_c-processing-pipeline

value: mesoderm

value: in vitro differentiated cells


title: saliva from 23192201

description: saliva from 23192201


title: RNA-seq on RUES2 - 4DNEX9TQ4UM5

description:
lab: Chuck Murry, UW
award: 1U54DK107979-01
4DN accession: 4DNEX9TQ4UM5
strandedness: reverse
submitted_by: Kris Alavattam
experiment_type: RNA-seq
contributing_labs: William Noble, UW
biosample_quantity: 1.0 ug
url: https://data.4dnucleome.org/experiments-seq/4DNEX9TQ4UM5/

data_processing:
https://data.4dnucleome.org/resources/data-analysis/rnaseq-processing-pipeline
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/8e72c7de-5c91-42e3-8536-2822d5ca4e70/
genome_assembly: GRCh38
derived_from: 4DNFI3FCGSW2.starIndex.tgz, 4DNFIZJB62D1.chrom.sizes, 4DNFI6PKP24T.fastq.gz, 4DNFIDLR37BK.fastq.gz, 4DNFIHBJI984.tsv, 4DNFIB4HV398.rsemindex.tgz
description: Output file from RNA seq pipeline
file_type: read counts (plus)
file_format: bw
file name: 4DNFIJGJ1QP8.bw
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/8e72c7de-5c91-42e3-8536-2822d5ca4e70/
genome_assembly: GRCh38
derived_from: 4DNFI3FCGSW2.starIndex.tgz, 4DNFIZJB62D1.chrom.sizes, 4DNFI6PKP24T.fastq.gz, 4DNFIDLR37BK.fastq.gz, 4DNFIHBJI984.tsv, 4DNFIB4HV398.rsemindex.tgz
description: Output file from RNA seq pipeline
file_type: read counts (minus)
file_format: bw
file name: 4DNFI9JPZ1CW.bw
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/8e72c7de-5c91-42e3-8536-2822d5ca4e70/
genome_assembly: GRCh38
derived_from: 4DNFI3FCGSW2.starIndex.tgz, 4DNFIZJB62D1.chrom.sizes, 4DNFI6PKP24T.fastq.gz, 4DNFIDLR37BK.fastq.gz, 4DNFIHBJI984.tsv, 4DNFIB4HV398.rsemindex.tgz
description: Output file from RNA seq pipeline
file_type: gene expression
file_format: tsv
file name: 4DNFI16BGQOW.tsv
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/8e72c7de-5c91-42e3-8536-2822d5ca4e70/
genome_assembly: GRCh38
derived_from: 4DNFI3FCGSW2.starIndex.tgz, 4DNFIZJB62D1.chrom.sizes, 4DNFI6PKP24T.fastq.gz, 4DNFIDLR37BK.fastq.gz, 4DNFIHBJI984.tsv, 4DNFIB4HV398.rsemindex.tgz
description: Output file from RNA seq pipeline
file_type: isoform expression
file_format: tsv
file name: 4DNFIULKCTNZ.tsv

value: embryonic


title: BRD4_abcam_DPY30mAID_0h

description: DPY30-mAID degron

value: mESCs


title: AFF4_DSG_RBBP5FKBP_0h

description: RBBP5-FKBP degron

value: RBBP5-FKBP degron


title: RNA-seq on RUES2 differentiated to endothelial progenitor cell - 4DNEX58A4SPS

description:
lab: Chuck Murry, UW
award: 1U54DK107979-01
4DN accession: 4DNEX58A4SPS
strandedness: reverse
submitted_by: Kris Alavattam
experiment_type: RNA-seq
contributing_labs: William Noble, UW
biosample_quantity: 1.0 ug
url: https://data.4dnucleome.org/experiments-seq/4DNEX58A4SPS/

data_processing:
https://data.4dnucleome.org/resources/data-analysis/rnaseq-processing-pipeline
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/baa89d97-1ac3-4836-8c30-47858bfcc649/
genome_assembly: GRCh38
derived_from: 4DNFI3FCGSW2.starIndex.tgz, 4DNFIZJB62D1.chrom.sizes, 4DNFISD3SWO1.fastq.gz, 4DNFIPR1CBNT.fastq.gz, 4DNFIHBJI984.tsv, 4DNFIB4HV398.rsemindex.tgz
description: Output file from RNA seq pipeline
file_type: read counts (plus)
file_format: bw
file name: 4DNFIV1OV2NY.bw
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/baa89d97-1ac3-4836-8c30-47858bfcc649/
genome_assembly: GRCh38
derived_from: 4DNFI3FCGSW2.starIndex.tgz, 4DNFIZJB62D1.chrom.sizes, 4DNFISD3SWO1.fastq.gz, 4DNFIPR1CBNT.fastq.gz, 4DNFIHBJI984.tsv, 4DNFIB4HV398.rsemindex.tgz
description: Output file from RNA seq pipeline
file_type: read counts (minus)
file_format: bw
file name: 4DNFI5YNFV86.bw
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/baa89d97-1ac3-4836-8c30-47858bfcc649/
genome_assembly: GRCh38
derived_from: 4DNFI3FCGSW2.starIndex.tgz, 4DNFIZJB62D1.chrom.sizes, 4DNFISD3SWO1.fastq.gz, 4DNFIPR1CBNT.fastq.gz, 4DNFIHBJI984.tsv, 4DNFIB4HV398.rsemindex.tgz
description: Output file from RNA seq pipeline
file_type: gene expression
file_format: tsv
file name: 4DNFIAD8UX3B.tsv
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/baa89d97-1ac3-4836-8c30-47858bfcc649/
genome_assembly: GRCh38
derived_from: 4DNFI3FCGSW2.starIndex.tgz, 4DNFIZJB62D1.chrom.sizes, 4DNFISD3SWO1.fastq.gz, 4DNFIPR1CBNT.fastq.gz, 4DNFIHBJI984.tsv, 4DNFIB4HV398.rsemindex.tgz
description: Output file from RNA seq pipeline
file_type: isoform expression
file_format: tsv
file name: 4DNFIQYT6AAX.tsv

value: endothelial progenitor cell


title: saliva from 23191031

description: saliva from 23191031

value: saliva


title: saliva from 23188681

description: saliva from 23188681

value: FEMALE


title: saliva from 23188071

description: saliva from 23188071

value: Taicang-main


title: saliva from 23189951

description: saliva from 23189951

value: KID


title: saliva from 23187901

description: saliva from 23187901

value: MALE


title: AFF4_DSG_DPY30mAID_8h

description: DPY30-mAID degron

value: DPY30-mAID degron


title: saliva from 23187900

description: saliva from 23187900

value: MOM


title: RNA-seq on RUES2 - 4DNEX2Y8O58V

description:
lab: Chuck Murry, UW
award: 1U54DK107979-01
4DN accession: 4DNEX2Y8O58V
strandedness: reverse
submitted_by: Kris Alavattam
experiment_type: RNA-seq
contributing_labs: William Noble, UW
biosample_quantity: 1.0 ug
url: https://data.4dnucleome.org/experiments-seq/4DNEX2Y8O58V/

data_processing:
https://data.4dnucleome.org/resources/data-analysis/rnaseq-processing-pipeline
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/888eb1d5-7c87-4264-9bfa-625bff89c014/
genome_assembly: GRCh38
derived_from: 4DNFI3FCGSW2.starIndex.tgz, 4DNFIZJB62D1.chrom.sizes, 4DNFIBI4ZOH4.fastq.gz, 4DNFIJT1NWFG.fastq.gz, 4DNFIHBJI984.tsv, 4DNFIB4HV398.rsemindex.tgz
description: Output file from RNA seq pipeline
file_type: read counts (plus)
file_format: bw
file name: 4DNFI2WUB1RH.bw
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/888eb1d5-7c87-4264-9bfa-625bff89c014/
genome_assembly: GRCh38
derived_from: 4DNFI3FCGSW2.starIndex.tgz, 4DNFIZJB62D1.chrom.sizes, 4DNFIBI4ZOH4.fastq.gz, 4DNFIJT1NWFG.fastq.gz, 4DNFIHBJI984.tsv, 4DNFIB4HV398.rsemindex.tgz
description: Output file from RNA seq pipeline
file_type: read counts (minus)
file_format: bw
file name: 4DNFISSA8YO4.bw
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/888eb1d5-7c87-4264-9bfa-625bff89c014/
genome_assembly: GRCh38
derived_from: 4DNFI3FCGSW2.starIndex.tgz, 4DNFIZJB62D1.chrom.sizes, 4DNFIBI4ZOH4.fastq.gz, 4DNFIJT1NWFG.fastq.gz, 4DNFIHBJI984.tsv, 4DNFIB4HV398.rsemindex.tgz
description: Output file from RNA seq pipeline
file_type: gene expression
file_format: tsv
file name: 4DNFI2M1FK6T.tsv
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/888eb1d5-7c87-4264-9bfa-625bff89c014/
genome_assembly: GRCh38
derived_from: 4DNFI3FCGSW2.starIndex.tgz, 4DNFIZJB62D1.chrom.sizes, 4DNFIBI4ZOH4.fastq.gz, 4DNFIJT1NWFG.fastq.gz, 4DNFIHBJI984.tsv, 4DNFIB4HV398.rsemindex.tgz
description: Output file from RNA seq pipeline
file_type: isoform expression
file_format: tsv
file name: 4DNFIAMNA6YD.tsv

value: stem cell

value: stem cells


title: saliva from 23187890

description: saliva from 23187890

value: Taicang-substudy


title: saliva from 23188680

description: saliva from 23188680


title: DNase Hi-C on RUES2 differentiated to endothelial progenitor cell with DNaseI - 4DNEX1G8JPA2

description:
lab: Chuck Murry, UW
award: 1U54DK107979-01
4DN accession: 4DNEX1G8JPA2
pcr_cycles: 10
submitted_by: Kris Alavattam
ligation_time: 960
biotin_removed: No
digestion_time: 7
tagging_method: Biotin dTTP
experiment_type: DNase Hi-C
ligation_volume: 1.1
digestion_enzyme: DNaseI
library_prep_kit: Kapa HiFi ReadyStart Master Mix (Roche, KK2602) with barcode-containing primers
contributing_labs: William Noble, UW
crosslinking_time: 10
biosample_quantity: 2000000 cells
crosslinking_method: 2% Formaldehyde
fragmentation_method: none
ligation_temperature: 16
digestion_temperature: 20
crosslinking_temperature: 20
fragment_size_selection_method: SPRI beads
url: https://data.4dnucleome.org/experiments-hi-c/4DNEX1G8JPA2/

data_processing:
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/a918b580-3715-4a99-b0cb-3036b4292210/
genome_assembly: GRCh38
derived_from: 4DNFI823LSII.chrom.sizes, 4DNFILK7FOID.bam, 4DNFISKML3UE.bam, 4DNFIE3TTZ7E.bam
description: This is an output file of the Hi-C processing pipeline
file_type: contact list-replicate
file_format: pairs
https://data.4dnucleome.org/resources/data-analysis/hi_c-processing-pipeline

value: female


title: DNase Hi-C on RUES2 with DNaseI - 4DNEX561P4FA

description:
lab: Chuck Murry, UW
award: 1U54DK107979-01
4DN accession: 4DNEX561P4FA
pcr_cycles: 10
submitted_by: Kris Alavattam
ligation_time: 960
biotin_removed: No
digestion_time: 7
tagging_method: Biotin dTTP
experiment_type: DNase Hi-C
ligation_volume: 1.1
digestion_enzyme: DNaseI
library_prep_kit: Kapa HiFi ReadyStart Master Mix (Roche, KK2602) with barcode-containing primers
contributing_labs: William Noble, UW
crosslinking_time: 10
biosample_quantity: 2000000 cells
crosslinking_method: 2% Formaldehyde
fragmentation_method: none
ligation_temperature: 16
digestion_temperature: 20
crosslinking_temperature: 20
fragment_size_selection_method: SPRI beads
url: https://data.4dnucleome.org/experiments-hi-c/4DNEX561P4FA/

data_processing:
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/9ab3f706-a3e0-4e51-9a87-7c69478206bb/
genome_assembly: GRCh38
derived_from: 4DNFI823LSII.chrom.sizes, 4DNFIIUMOSSK.bam, 4DNFISDNQN8Q.bam, 4DNFIL988Y1F.bam
description: This is an output file of the Hi-C processing pipeline
file_type: contact list-replicate
file_format: pairs
https://data.4dnucleome.org/resources/data-analysis/hi_c-processing-pipeline


title: saliva from 23187071

description: saliva from 23187071


title: saliva from 23193660

description: saliva from 23193660


title: saliva from 23187891

description: saliva from 23187891


title: AFF4_DSG_DPY30mAID_0h

description: DPY30-mAID degron


title: saliva from 23186271

description: saliva from 23186271


title: saliva from 23185070

description: saliva from 23185070


title: RBBP5FKBP_8h_TT_seq_Rep1

data_processing:
Library strategy: TT-seq
Illumina bcl2fastq2 Conversion Software v2.20 used for basecalling.
Paired-end reads were demultiplexed by bcl2fastq. Raw reads were aligned to the mouse mm10 genome assembly using STAR.
Further data processing was carried out using the R/Bioconductor environment.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

extract_protocol:
Following the specified treatment, we supplemented the treatment medium with 1 mM 4-thiouridine (4sU) and metabolically labeled the cells for 10 min. The cells were lysed in QIAzol (Qiagen, 79306) and total RNA was isolated according to the manufacturer’s instructions before the addition of 100 ng RNA spike-in mix together with QIAzol.
Libraries were constructed using TruSeq Stranded Total RNA kit (Illumina, 20020596).

treatment_protocol: For DRB/TTchem-seq, cells were incubated in 100 µM DRB (Sigma-Aldrich, D1916) for 3.5 h. The cells were then washed twice in PBS, and the pre-warmed fresh DRB-free medium was added to restart transcription. The RNA was labeled in vivo with 1 mM 4sU for 10 min before the addition of QIAzol, which was used to stop the reaction at the desired time point.

tag: time poin


title: saliva from 23185071

description: saliva from 23185071


title: RBBP5FKBP_24h_TT_seq_Rep2


title: RBBP5FKBP_8h_TT_seq_Rep2


title: saliva from 23184691

description: saliva from 23184691


title: saliva from 23184690

description: saliva from 23184690


title: AFF4_DSG_RBBP5FKBP_8h

description: RBBP5-FKBP degron


title: RBBP5FKBP_24h_TT_seq_Rep1


title: A19-2617, Dry AMD, snRNAseq

city: New Haven

first: Marcello

last: DiStasio

state: CT

address: 300 George St. Rm 353D

department: Pathology

institute: Yale School of Medicine

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0, 10X Genomics. (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38-3.0.0
Supplementary files format and content: The data.mtx, genes.csv, and sample_annotations.csv are processed data in aggregate, from all samples, whereas the *_barcodes.tsv.gz, *_features.tsv.gz,  *_matrix.mtx.gz files are for individual samples.

molecule: nuclear RNA

source_name: Retina

extract_protocol:
Globes were placed in RNAlater (ThermoFisher) and transported on ice. Trephine punches (6 mm diameter) were used to isolate samples from the macula in the central retina, located away from the optic disc and major arterioles. For each punch of tissue, the retina was mechanically separated from the underlying retinal pigment epithelium-choroid, snap-frozen on dry ice and stored at -80C. Nuclei were isolated and purified using the Nuclei EZ Prep Nuclei Isolation Kit (Sigma), following the manufacturer’s protocol, with some modification. All procedures were carried out on ice or at 4C. Briefly, frozen retinal tissue was subjected to dounce homogenization (25 times with pestle A followed by 25 times with tight pestle B) using the KIMBLE Dounce Tissue Grinder Set (Sigma) in 2ml EZ Lysis buffer. The sample was transferred to a 15ml tube with an additional 2ml EZ lysis buffer and incubated on ice for 5min. Following incubation, the sample was centrifuged at 500xg, 5min at 4C. Supernatants were discarded, and the isolated nuclei were resuspended in 4ml EZ lysis buffer, incubated for 5min on ice and centrifuged at 500xg for 5min at 4C. Next, the nuclei were washed with 4ml ice-cold Nuclei Suspension Buffer (1X PBS containing 0.01% BSA and 0.1% RNase inhibitor), resuspended in 1ml Nuclei EZ Storage buffer and passed through a 40μM nylon cell strainer. The nuclei suspensions were counted with trypan blue prior to loading on the microfluidics platform.
Isolated nuclei from each macular sample were processed through microfluidics-based single nuclear RNA-seq. Single-cell libraries were prepared using the Chromium 3' v2 and v3 platforms (10X Genomics) following the manufacturer’s protocol. Briefly, single nuclei were partitioned into Gel beads in Emulsion in the 10X Chromium Controller instrument followed by lysis and barcoded reverse transcription of RNA, amplification, shearing and 5' adapter and sample index attachment. On average, ~7000 nuclei were loaded on each channel that resulted in the recovery of ~4000 nuclei.
snRNA-seq

tag: disease state

value: Dry AMD

value: All neurosensory retina cells

value: Retina

tag: age


title: saliva from 23183860

description: saliva from 23183860


title: saliva from 23183200

description: saliva from 23183200


title: saliva from 23183861

description: saliva from 23183861


title: saliva from 23183201

description: saliva from 23183201


title: G1850, Dry AMD, snRNAseq

description: 10x Genomics


title: A20-1232, Wet AMD, snRNAseq

description: 10x Genomics

value: Wet AMD


title: saliva from 23182571

description: saliva from 23182571


title: RBBP5FKBP_0h_TT_seq_Rep2

value: mESCs


title: saliva from 23182570

description: saliva from 23182570


title: A19-2161, Wet AMD, snRNAseq

description: 10x Genomics


title: saliva from 23181741

description: saliva from 23181741


title: DPY30mAID_DMSO_DRB_20min

tag: agent


title: A1547, Wet AMD, snRNAseq

description: 10x Genomics


title: DPY30mAID_DMSO_DRB_30min


title: saliva from 23179980

description: saliva from 23179980


title: A1435, Wet AMD, snRNAseq

description: 10x Genomics


title: DPY30mAID_DMSO_DRB_10min


title: saliva from 23178291

description: saliva from 23178291


title: saliva from 23184531

description: saliva from 23184531


title: DPY30mAID_DMSO_DRB_0min


title: saliva from 23179981

description: saliva from 23179981


title: A1098, Wet AMD, snRNAseq

description: 10x Genomics


title: saliva from 23177900

description: saliva from 23177900


title: DPY30mAID_Auxin_DRB_30min


title: saliva from 23177901

description: saliva from 23177901


title: saliva from 23184530

description: saliva from 23184530


title: A0233, Wet AMD, snRNAseq

description: 10x Genomics


title: RBBP5FKBP_0h_TT_seq_Rep1


title: saliva from 23177771

description: saliva from 23177771


title: saliva from 23176651

description: saliva from 23176651


title: saliva from 23176650

description: saliva from 23176650


title: saliva from 23177731

description: saliva from 23177731


title: DPY30mAID_Auxin_DRB_0min


title: A19-0065, Healthy Control, snRNAseq

description: 10x Genomics

value: Healthy Control


title: 1941W, Healthy Control, snRNAseq

description: 10x Genomics


title: DPY30mAID_Auxin_DRB_20min


title: DPY30mAID_Auxin_DRB_10min


title: saliva from 23180941

description: saliva from 23180941

value: saliva


title: saliva from 23175591

description: saliva from 23175591


title: saliva from 23175990

description: saliva from 23175990

value: FEMALE


title: saliva from 23173461

description: saliva from 23173461

value: Taicang-main


title: saliva from 23175991

description: saliva from 23175991

value: KID


title: HC2016, Healthy Control, snRNAseq

description: 10x Genomics


title: DPY30mAID_8h_TT_seq_Rep1


title: DPY30mAID_8h_TT_seq_Rep2


title: HC2003, Healthy Control, snRNAseq

description: 10x Genomics


title: saliva from 23172441

description: saliva from 23172441


title: DPY30mAID_24h_TT_seq_Rep2


title: saliva from 23172440

description: saliva from 23172440


title: DPY30mAID_24h_TT_seq_Rep1


title: saliva from 23171481

description: saliva from 23171481

value: MALE


title: HC1969, Healthy Control, snRNAseq

description: 10x Genomics


title: saliva from 23170851

description: saliva from 23170851


title: saliva from 23170620

description: saliva from 23170620


title: saliva from 23168851

description: saliva from 23168851


title: HC2229, Healthy Control, snRNAseq

description: 10x Genomics


title: FL_nan_atac_rep2

city: New York

first: Kaustav

last: Mukherjee

state: NY

address: 1 Gustave Levy Place

department: Cell, Developmental and Regenerative Biology

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were aligned to the UCSC mm10 genome using Bowtie 2.1 after trimming 25 nucleotides from the 3' end and in the sensitive-local mode.
Samtools v1.1 was used to convert sam files to sorted bam files
Deeptools v3.5 bamCompare function was used to convert individual bam files from each ChIP experiment to input-normalized bigwig files using the rpkm method
kentUtils v302.1 bigWigMerge was used to merge the input-normalized bigwig files into one bedgraph, sort the bedgraph file, and then convert the bedgraph to an input-normalized bigwig file using bedGraphToBigWig
Homer was used to generate tag directories from bam files of each ChIP-experiment and peaks were called using the region parameter with 125bp window size and maximum peak size of about 250bp. Peaks were filtered based on 4-fold enrichment above input with a q-value threshold of 0.01. Peaks were converted to bed files using the pos2bed.pl Homer script
Assembly: UCSC mouse mm10
Supplementary files format and content: bigwig for ChIP and ATAC, bam for ChIP input, bed for EKLF peaks determined by Homer

source_name: embryonic day E13.5 fetal liver

extract_protocol:
Fetal livers were dissected from E13.5 mouse embryos and mechanically dispersed into single cells by gentle pipetting and straining through a 70µM filter into ice-cold PBS containing 2% FBS. Primary fetal liver cells were crosslinked in 1% formaldehyde and cell pellets were stored at -80ºC. Frozen cells were thawed and resuspended in MNase lysis buffer (0.2% NP-40, 10mM NaCl, 10mM Tris pH 8.0) and kept on ice for 15 mins. Cells were pelleted and resuspended in MNase lysis buffer with 1mM CaCl2, 40 units Micrococcal nuclease (MNase) and incubated at 37ºC for 15 minutes. The MNase reaction was stopped by adding EDTA to a final concentration of 2mM and nuclei were pelleted by centrifugation. The pellet was resuspended in 1X RIPA buffer with 1X Protease Inhibitor Cocktail and sonicated using a cup-horn sonicator (Ultrasonic VC505) at 80 Amplitude for 50 cycles with pulses of 40s on and 50s off. The lysed and fragmented chromatin was cleared by centrifugation and 5%v/v was stored at -80ºC as input. 5-10µg of antibody (depending on the titer) was added to the lysate along with a control IgG (for enrichment estimation) and antibody-lysate mixture was incubated at 4ºC for 16h (overnight). The lysate-antibody mixture was then incubated with Protein-A or Protein-G Dynabeads, depending on the antibody serotype, for 2h at 4ºC. Immunoprecipitated complexes on Dynabeads were then washed three times in 1X RIPA with protease inhibitors, and three times in wash buffer containing 0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris pH 8.0, 500mM NaCl, and protease inhibitors. This was followed by three washes in wash buffer containing 1% NP-40, 1% sodium deoxycholate, 1mM EDTA, 10mM Tris pH 8.0, and 250 mM LiCl. Finally, beads were washed three times in 1X TE buffer containing 10mM Tris pH 8.0 and 1mM EDTA. Elution was performed by adding elution buffer containing 10mM Tris pH 8.0, 1mM EDTA, 200mM NaCl and 1% SDS and incubating at 65ºC in a Thermomixer (Eppendorf Cat# 5382000023) with gentle mixing for 20 mins. Eluate containing ChIP DNA and input chromatin was removed and incubated at 65ºC with gentle mixing overnight for reverse crosslinking. DNA was treated with 0.1µg/µl Proteinase K for 1h at 55ºC followed by purification using Phenol:chloroform extraction and ethanol precipitation. ATAC-Seq was performed exactly as in (Buenrostro et al., 2013; Buenrostro et al., 2015).
ChIP-Seq libraries were made using a Neb Next DNA Ultra II DNA library preparation kit following manufacturer’s instructions. Libraries were quantified using Qubit fluorometer (Invitrogen) and library quality was assessed using a high-sensitivity DNA kit on Agilent Bioanalyzer, followed by Illumina next generation sequencing with single-end 100bp reads

value: embryonic day E13.5 fetal liver

tag: cell line

value: Klf1 / Klf1-Nan

value: primary erythroid

value: Nan/+

tag: chip antibody


title: saliva from 23168850

description: saliva from 23168850

tag: tissue

value: MOM


title: saliva from 23173460

description: saliva from 23173460

value: Taicang-substudy


title: saliva from 23167591

description: saliva from 23167591


title: DPY30mAID_0h_TT_seq_Rep1


title: FL_wt_atac_rep2

value: Nan strain WT


title: FL_wt_atac_rep1


title: saliva from 23167590

description: saliva from 23167590


title: saliva from 23166531

description: saliva from 23166531


title: saliva from 23172971

description: saliva from 23172971


title: saliva from 23172970

description: saliva from 23172970


title: SLAM_seq_RBBP5FKBP_8h_rep3

data_processing:
Illumina bcl2fastq2 Conversion Software v2.20 used for basecalling.
Gene and 3' UTR annotations were obtained from the UCSC table browser (https://genome.ucsc.edu/cgi-bin/hgTables, mm10 vM14 3' UTR). Adapters were trimmed from raw reads using cutadapt through the trim_galore wrapper tool with adapter overlaps set to 3bp for trimming.
SLAM-seq analysis was done similar to previously described by SlamDunk package.
For Quant-seq, concatenated fastq files were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using trim_galore, then mapped to mm10 whole genome using HISAT 2.2.1 with default parameters. The number of reads mapped to the 3' UTR of genes was determined with featureCounts. Raw reads were normalized to counts per million (CPM).
Genome_build: mm10
Supplementary_files_format_and_content: raw counts

extract_protocol:
RNA (1 μg) was treated with 10 mM iodoacetamide in a 50-μl reaction volume at 50 °C for 15 min with 50 mM NaPO4 (pH 8.0), and 50% (v/v) DMSO followed by addition of 1 μl of 1 M DTT to stop the reaction. RNA was precipitated at -80 °C for 60 min with 1 μl of GlycoBlue (Thermofisher Scientific, AM9515), 5 μl of 3 M NaOAc (pH 5.2), and 180 μl of 100% ethanol. RNA was pelleted at 4 °C (12,000g, 30 min), washed with 1 mL of 80% ethanol, and centrifuged at 4 °C (12,000g, 30 min). The RNA pellet was dried at room temperature for 10 min and resuspended in 20 μl of nuclease-free H2O. RNA yield and quality were assessed using the 2200 TapeStation (Agilent).
Libraries were constructed using QuantSeq 3′-mRNA Seq Library Prep Kit FWD for Illumina (Lexogen, SKU: 015.96).

treatment_protocol: For SLAM-seq experiments, cells were incubated with 100 μM 4-thiouridine (4sU; Biosynth, NT06186) for 60 min before RNA isolation.

tag: agemt

tag: time point


title: SLAM_seq_RBBP5FKBP_8h_rep2

tag: cell type

tag: strain


title: saliva from 23164210

description: saliva from 23164210


title: saliva from 23162401

description: saliva from 23162401


title: SLAM_seq_RBBP5FKBP_8h_rep1


title: FL_wt_pol2_input_rep1

tag: genotype


title: FL_nan_pol2S2_chip_rep2

value: anti-Ser2p Pol2, Abcam


title: DPY30mAID_0h_TT_seq_Rep2


title: saliva from 23159181

description: saliva from 23159181


title: saliva from 23162400

description: saliva from 23162400


title: FL_nan_pol2S2_chip_rep1


title: SLAM_seq_RBBP5FKBP_2h_rep2


title: saliva from 23158121

description: saliva from 23158121


title: saliva from 23156351

description: saliva from 23156351


title: saliva from 23157181

description: saliva from 23157181


title: SLAM_seq_RBBP5FKBP_2h_rep1


title: FL_nan_atac_rep1


title: saliva from 23164211

description: saliva from 23164211


title: saliva from 23154980

description: saliva from 23154980

value: Laoting Main


title: saliva from 23156141

description: saliva from 23156141


title: FL_wt_pol2S2_chip_rep1


title: saliva from 23154981

description: saliva from 23154981


title: SLAM_seq_RBBP5FKBP_2h_rep3


title: FL_nan_pol2S5_chip_rep1

value: anti-Ser5p Pol2, Abcam


title: saliva from 23154171

description: saliva from 23154171


title: saliva from 23170621

description: saliva from 23170621


title: FL_nan_pol2S5_chip_rep2


title: SLAM_seq_RBBP5FKBP_24h_rep2

value: mESCs


title: SLAM_seq_RBBP5FKBP_24h_rep1


title: FL_wt_pol2S5_chip_rep2


title: saliva from 23156140

description: saliva from 23156140


title: SLAM_seq_RBBP5FKBP_24h_rep3


title: saliva from 23154170

description: saliva from 23154170


title: saliva from 23153370

description: saliva from 23153370

value: Laoting-substudy


title: saliva from 23152381

description: saliva from 23152381

value: saliva


title: saliva from 23153371

description: saliva from 23153371


title: SLAM_seq_RBBP5FKBP_0h_rep3


title: FL_wt_pol2S5_chip_rep1


title: saliva from 23152380

description: saliva from 23152380

value: FEMALE


title: LKOHFD5

city: Duarte

first: Haiqing

last: Li

state: CA

address: 1500 E Durate Rd

department: Shared Resources Department

institute: City of Hope National Medical Center

data_processing:
HISAT2 v2.0.4
Sequence reads were mapped to referene sequene (mm10) with default setting
Read count extraction were performed using Partek GS ver6.3 with Refseq ver95 annoation database.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include gene symbol and normalized gene count RPKM(read per kilobase per million read)

source_name: liver

growth_protocol: All studies involving animals were performed according to the Institutional Animal Care and Use Committee (IACUC)-approved protocols at the University of California, Irvine. We have complied with the relevant ethical considerations for animal research overseen by this committee. FF mice were generated by inGenious Targeting Laboratory. LKO mice were generated by breeding FF mice with C57BL/6Alb-Cre mice obtained from the Jackson Laboratory.

extract_protocol:
Total RNA was extracted using Trizol reagent. All libraries were prepared using the Illumina TruSeq Small RNA protocol with minor modification following the manufacturer’s instructions with 12 cycles of PCR amplification after ligation of the 3′ and 5′ adapters. Individual libraries were prepared using a unique index primer in order to allow for pooling of multiple samples prior to sequencing.
Standard RNA-seq proocol

treatment_protocol: The following diets were used: Control diet (10 kcal% fat, D12450B, Research Diet Inc.); High Fat Diet (32.5 kcal% fat, D12266, Research Diet Inc.). All mice were housed on a 12-hour light/12-hour dark cycle with free access to water and diet.

value: liver

value: LKOHFD

tag: treatment

value: High fat diet


title: FL_wt_pol2S2_chip_rep2

value: embryonic day E13.5 fetal liver


title: saliva from 23151141

description: saliva from 23151141

tag: kindred

value: KID

value: MALE


title: saliva from 23150131

description: saliva from 23150131

tag: mother or child


title: saliva from 19249571

description: saliva from 19249571

tag: gender


title: SLAM_seq_RBBP5FKBP_0h_rep1


title: SLAM_seq_DPY30mAID_Kdm5dKO_8h_rep2


title: LKOHFD3


title: saliva from 19249151

description: saliva from 19249151

tag: study


title: saliva from 19249570

description: saliva from 19249570


title: LKOHFD4


title: LKOHFD2


title: SLAM_seq_DPY30mAID_Kdm5dKO_8h_rep1


title: SLAM_seq_DPY30mAID_Kdm5dKO_4h_rep2


title: saliva from 19249150

description: saliva from 19249150


title: saliva from 19229981

description: saliva from 19229981


title: saliva from 19238021

description: saliva from 19238021


title: LKOHFD1


title: SLAM_seq_DPY30mAID_Kdm5dKO_4h_rep1


title: saliva from 19218791

description: saliva from 19218791


title: SLAM_seq_RBBP5FKBP_0h_rep2


title: saliva from 19219711

description: saliva from 19219711


title: SLAM_seq_DPY30mAID_Kdm5dKO_48h_rep2


title: saliva from 19221011

description: saliva from 19221011


title: FFHFD4

value: FFHFD


title: saliva from 19218351

description: saliva from 19218351


title: saliva from 19218350

description: saliva from 19218350

value: MOM


title: saliva from 19218130

description: saliva from 19218130


title: FFHFD3


title: saliva from 19218131

description: saliva from 19218131


title: SLAM_seq_DPY30mAID_Kdm5dKO_48h_rep1


title: SLAM_seq_DPY30mAID_Kdm5dKO_2h_rep2


title: saliva from 19207541

description: saliva from 19207541


title: FFHFD2


title: saliva from 19207540

description: saliva from 19207540


title: saliva from 19207471

description: saliva from 19207471


title: FFHFD1


title: SLAM_seq_DPY30mAID_Kdm5dKO_2h_rep1


title: saliva from 19201781

description: saliva from 19201781


title: saliva from 19200491

description: saliva from 19200491


title: LKOCD4

value: LKO

value: Control diet


title: saliva from 19206271

description: saliva from 19206271


title: FFHFD5


title: SLAM_seq_DPY30mAID_Kdm5dKO_24h_rep2


title: saliva from 19200391

description: saliva from 19200391


title: SLAM_seq_DPY30mAID_Kdm5dKO_24h_rep1


title: saliva from 19195401

description: saliva from 19195401


title: SLAM_seq_DPY30mAID_Kdm5dKO_0h_rep2


title: saliva from 19192461

description: saliva from 19192461


title: saliva from 19197731

description: saliva from 19197731


title: LKOCD2


title: SLAM_seq_DPY30mAID_Kdm5dKO_0h_rep1


title: saliva from 19192221

description: saliva from 19192221


title: FFCD4

value: FF


title: LKOCD1


title: SLAM_seq_DPY30mAID_8h_rep3


title: saliva from 19191781

description: saliva from 19191781

value: Laoting Main


title: saliva from 19191891

description: saliva from 19191891


title: saliva from 19191780

description: saliva from 19191780


title: SLAM_seq_DPY30mAID_8h_rep2


title: FFCD3


title: SLAM_seq_DPY30mAID_8h_rep1


title: saliva from 19185301

description: saliva from 19185301


title: saliva from 19186301

description: saliva from 19186301


title: saliva from 19200481

description: saliva from 19200481


title: saliva from 19175861

description: saliva from 19175861


title: saliva from 19175860

description: saliva from 19175860


title: saliva from 19182281

description: saliva from 19182281


title: LKOCD3


title: FFCD1


title: FFCD2


title: SLAM_seq_DPY30mAID_2h_rep3


title: saliva from 19175640

description: saliva from 19175640


title: SLAM_seq_DPY30mAID_2h_rep2


title: saliva from 19175551

description: saliva from 19175551


title: SLAM_seq_DPY30mAID_2h_rep1


title: T16_BBN11

city: paris

first: Elodie

last: chapeaublanc

address: 26 rue d'ulm

department: UMR 144

country: France

institute: Institut Curie

description: BBN-induced urothelial lesion from sample mouse BBN11 at time T16 (16 weeks after treatment initiation T0).

data_processing:
Sequencer: HiSeq2500 (Illumina)
Rapid Run mode
Paired-end 100 bp read length
Aligner: STAR_2.5.0
Reads were counted with the featureCounts function from Rsubreads (version 1.24.2).
Resulting count table was normalized using DESeq2 method and log2-transformed for downstream analyses.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Mouse_BBN_tablecounts_raw.txt: Tab-delimited matrix table with raw gene counts for every gene and every sample.
Supplementary_files_format_and_content: Mouse_BBN_tablecounts_Deseq2.txt: Tab-delimited matrix table includes DESeq2 values for all samples (sample as column).

extract_protocol:
RNeasy FFPE kit (Qiagen).
Ovation SoLo (NuGEN).

treatment_protocol: 8-week-old C57BL/6 mice were treated with 0.05% N-butyl-N-(4-hydroxybutyl)-nitrosamine (BBN) in drinking water ad libitum for a maximum of 14 weeks, and sacrificed at different timepoints.

tag: Sex

value: Male

value: Urothelial lesion

tag: tumor stage

value: pTa

tag: histological differentiation

value: Squamous

tag: bbn treatment (yes/no)

value: yes

tag: time after treatment initiation t0 (in week)

tag: mouse


title: saliva from 19175641

description: saliva from 19175641

data_processing:
Illumina protocol
For the data set, both the beta values as well as the intensity values were generated by using methylumi R package against the raw idat data files, and no normalization method is applied for the beta values.
Average Beta and Unmethylated and methylated signal intensities files are linked to the Series record.

tag: tissue

value: saliva


title: SLAM_seq_DPY30mAID_24h_rep3

value: mESCs

tag: agemt


title: T12_BBN10

description: BBN-induced urothelial lesion from sample mouse BBN10 at time T12 (12 weeks after treatment initiation T0).


title: saliva from 19175510

description: saliva from 19175510

value: FEMALE


title: saliva from 19175461

description: saliva from 19175461


title: saliva from 19175460

description: saliva from 19175460

value: Laoting-substudy


title: T16_BBN5

description: BBN-induced urothelial lesion from sample mouse BBN5 at time T16 (16 weeks after treatment initiation T0).

value: CIS


title: SLAM_seq_DPY30mAID_24h_rep2

tag: time point


title: saliva from 19173791

description: saliva from 19173791

value: KID


title: T08_BBN5

description: BBN-induced urothelial lesion from sample mouse BBN5 at time T08 (8 weeks after treatment initiation T0).


title: saliva from 19175681

description: saliva from 19175681


title: saliva from 19172621

description: saliva from 19172621

value: MALE


title: T16_BBN9

description: BBN-induced urothelial lesion from sample mouse BBN9 at time T16 (16 weeks after treatment initiation T0).

value: Dysplasia


title: SLAM_seq_DPY30mAID_0h_rep2

tag: cell type


title: SLAM_seq_DPY30mAID_0h_rep3

tag: strain


title: saliva from 19163281

description: saliva from 19163281


title: saliva from 19173551

description: saliva from 19173551


title: SLAM_seq_DPY30mAID_0h_rep1


title: saliva from 19168671

description: saliva from 19168671


title: T16_BBN8

description: BBN-induced urothelial lesion from sample mouse BBN8 at time T16 (16 weeks after treatment initiation T0).


title: T12_BBN12

description: BBN-induced urothelial lesion from sample mouse BBN12 at time T12 (12 weeks after treatment initiation T0).

value: Urothelial


title: saliva from 19163280

description: saliva from 19163280

value: MOM


title: T12_BBN4_D2

description: BBN-induced urothelial lesion D2 from sample mouse BBN4 at time T12 (12 weeks after treatment initiation T0).


title: saliva from 19175511

description: saliva from 19175511


title: saliva from 19162651

description: saliva from 19162651


title: saliva from 19161321

description: saliva from 19161321


title: Quant_seq_DPY30mAID_DMSO_RA_day6_rep2


title: Quant_seq_DPY30mAID_DMSO_RA_day6_rep1


title: saliva from 19161320

description: saliva from 19161320


title: T08_BBN2_H

description: BBN-induced urothelial lesion from sample mouse BBN2 at time T8 (8 weeks after treatment initiation T0).

value: Hyperplasia


title: SLAM_seq_DPY30mAID_24h_rep1


title: Quant_seq_DPY30mAID_DMSO_RA_day4_rep2


title: T08_BBN1_H

description: BBN-induced urothelial lesion from sample mouse BBN1 at time T08 (8 weeks after treatment initiation T0).


title: saliva from 19173790

description: saliva from 19173790


title: saliva from 19160561

description: saliva from 19160561


title: saliva from 19154041

description: saliva from 19154041

value: Laoting Main


title: Quant_seq_DPY30mAID_DMSO_RA_day4_rep1


title: saliva from 19168670

description: saliva from 19168670


title: saliva from 19149481

description: saliva from 19149481


title: T02_BBN2_H

description: BBN-induced urothelial lesion from sample mouse BBN2 at time T02 (2 weeks after treatment initiation T0).

value: Male


title: saliva from 19149480

description: saliva from 19149480


title: saliva from 19162921

description: saliva from 19162921


title: T08_BBN2_N

description: Normal BBN-treated urothelium from sample mouse BBN2 at time T08 (8 weeks after treatment initiation T0).

value: Normal urothelium


title: saliva from 19148821

description: saliva from 19148821


title: Quant_seq_DPY30mAID_DMSO_RA_day2_rep1


title: Quant_seq_DPY30mAID_DMSO_RA_day2_rep2


title: T02_BBN1_N

description: Normal BBN-treated urothelium from sample mouse BBN1 at time T02 (2 weeks after treatment initiation T0).


title: saliva from 19147940

description: saliva from 19147940


title: saliva from 19147941

description: saliva from 19147941


title: saliva from 19147681

description: saliva from 19147681


title: T02_BBN2_N

description: Normal BBN-treated urothelium from sample mouse BBN2 at time T02 (2 weeks after treatment initiation T0).


title: saliva from 19144931

description: saliva from 19144931


title: Quant_seq_DPY30mAID_DMSO_RA_day1_rep2


title: T12_BBN4_D1

description: BBN-induced urothelial lesion D1 from sample mouse BBN4 at time T12 (12 weeks after treatment initiation T0).

value: Urothelial lesion


title: Quant_seq_DPY30mAID_DMSO_RA_day1_rep1


title: T24_BBN4

description: BBN-induced urothelial lesion from sample mouse BBN4 at time T24 (24 weeks after treatment initiation T0).

value: MIBC

value: Squamous


title: Quant_seq_DPY30mAID_DMSO_RA_8h_rep2


title: saliva from 19144370

description: saliva from 19144370

value: saliva


title: saliva from 19144371

description: saliva from 19144371


title: saliva from 19144930

description: saliva from 19144930


title: saliva from 19143281

description: saliva from 19143281


title: T24_BBN2

description: BBN-induced urothelial lesion from sample mouse BBN2 at time T24 (24 weeks after treatment initiation T0).

value: yes


title: saliva from 19143280

description: saliva from 19143280

value: FEMALE


title: Quant_seq_DPY30mAID_DMSO_RA_8h_rep1

value: mESCs


title: saliva from 19141731

description: saliva from 19141731

value: Laoting-substudy


title: T20_BBN3

description: BBN-induced urothelial lesion from sample mouse BBN3 at time T20 (20 weeks after treatment initiation T0).


title: saliva from 19141381

description: saliva from 19141381

value: KID


title: Quant_seq_DPY30mAID_DMSO_RA_0h_rep2


title: T16_BBN1

description: BBN-induced urothelial lesion from sample mouse BBN1 at time T16 (16 weeks after treatment initiation T0).


title: T24_BBN5

description: BBN-induced urothelial lesion from sample mouse BBN5 at time T24 (24 weeks after treatment initiation T0).


title: saliva from 19139201

description: saliva from 19139201


title: Quant_seq_DPY30mAID_DMSO_RA_0h_rep1


title: saliva from 19145911

description: saliva from 19145911


title: saliva from 19139191

description: saliva from 19139191

value: MALE


title: saliva from 19138440

description: saliva from 19138440


title: saliva from 19139200

description: saliva from 19139200


title: saliva from 19138441

description: saliva from 19138441


title: saliva from 19138580

description: saliva from 19138580


title: T24_BBN3

description: BBN-induced urothelial lesion from sample mouse BBN3 at time T24 (24 weeks after treatment initiation T0).

value: Sarcomatoid


title: Quant_seq_DPY30mAID_Auxin_RA_day6_rep1


title: T20_BBN5

description: BBN-induced urothelial lesion from sample mouse BBN5 at time T20 (20 weeks after treatment initiation T0).


title: Quant_seq_DPY30mAID_Auxin_RA_day6_rep2


title: T16_BBN4

description: BBN-induced urothelial lesion from sample mouse BBN4 at time T16 (16 weeks after treatment initiation T0).


title: saliva from 19136651

description: saliva from 19136651


title: saliva from 19136650

description: saliva from 19136650


title: T16_BBN2_T3

description: BBN-induced urothelial lesion from tumor T3 of sample mouse BBN2 at time T16 (16 weeks after treatment initiation T0).


title: saliva from 19139021

description: saliva from 19139021


title: T16_BBN2_T2

description: BBN-induced urothelial lesion from tumor T2 of sample mouse BBN2 at time T16 (16 weeks after treatment initiation T0).


title: Quant_seq_DPY30mAID_Auxin_RA_day4_rep2


title: saliva from 19138201

description: saliva from 19138201


title: Quant_seq_DPY30mAID_Auxin_RA_day4_rep1


title: Quant_seq_DPY30mAID_Auxin_RA_day2_rep2


title: saliva from 19136581

description: saliva from 19136581


title: Quant_seq_DPY30mAID_Auxin_RA_day2_rep1


title: saliva from 19135961

description: saliva from 19135961


title: T16_BBN2_T1

description: BBN-induced urothelial lesion from tumor T1 of sample mouse BBN2 at time T16 (16 weeks after treatment initiation T0).


title: saliva from 19138581

description: saliva from 19138581


title: saliva from 19135921

description: saliva from 19135921


title: saliva from 19134521

description: saliva from 19134521


title: Quant_seq_DPY30mAID_Auxin_RA_day1_rep2


title: T12_BBN11

description: BBN-induced urothelial lesion from sample mouse BBN11 at time T12 (12 weeks after treatment initiation T0).


title: saliva from 19134401

description: saliva from 19134401


title: Quant_seq_DPY30mAID_Auxin_RA_day1_rep1


title: saliva from 19138200

description: saliva from 19138200


title: saliva from 19129781

description: saliva from 19129781


title: T12_BBN1

description: BBN-induced urothelial lesion from sample mouse BBN1 at time T12 (12 weeks after treatment initiation T0).

value: pTa


title: T12_BBN9

description: BBN-induced urothelial lesion from sample mouse BBN9 at time T12 (12 weeks after treatment initiation T0).


title: saliva from 19129351

description: saliva from 19129351


title: Quant_seq_DPY30mAID_Auxin_RA_8h_rep2


title: saliva from 19129711

description: saliva from 19129711


title: saliva from 19129010

description: saliva from 19129010

value: MOM


title: T16_BBN10

description: BBN-induced urothelial lesion from sample mouse BBN10 at time T16 (16 weeks after treatment initiation T0).

value: Dysplasia

value: Urothelial


title: saliva from 19129151

description: saliva from 19129151


title: saliva from 19129350

description: saliva from 19129350

value: Laoting Main


title: saliva from 19129011

description: saliva from 19129011


title: saliva from 19125511

description: saliva from 19125511


title: Quant_seq_DPY30mAID_Auxin_RA_8h_rep1


title: mNET_seq_DMSO4h_Trip_5min_rep2

data_processing:
Library strategy: mNET-seq
Illumina bcl2fastq2 Conversion Software v2.20 used for basecalling.
Reads were demultiplexed, trimmed for adapter content with cutadapt and mapped with STAR to the GRCm38 (mm10) genome assembly.
Further data processing was carried out using the R/Bioconductor environment.
Genome_build: mm10
Supplementary_files_format_and_content: All processed data is made available as supplementary files to the manuscript

extract_protocol:
Cells were seeded the day before the experiment to get 100 million cells per sample the following day. We randomly assigned flasks for each treatment and treated cells with DMSO only or Auxin ligand, before extracting the chromatin-bound RNA Pol II. The cells were first washed with ice-cold DPBS, resuspended in 4 mL ice-cold HLB+N buffer (10 mM Tris-HCl (pH 7.5), 10 mM NaCl, 2.5 mM MgCl2, 0.5% (vol/vol) NP-40 and 1× proteinase inhibitor) and incubated on ice for 5 minutes, then cells were scrapped to a 15-mL centrifugate tube.
Libraries were constructed using NEBNext Multiplex Small RNA Library Prep kit (NEB, NC0477293).

treatment_protocol: For promoter-proximal Pol II half-life experiments by mNET-seq, the pre-warmed fresh medium with 1 µM Triptolide (Sigma-Aldrich, T3652) was added to the dish to block transcription initiation. The sample was collected before the addition of QIAzol (Qiagen), which was used to stop the reaction at the desired time point.

tag: auxin treatment

value: DMSO

tag: triptolide treatment

value: 5 min


title: mNET_seq_DMSO4h_Trip_5min_rep1


title: mNET_seq_DMSO4h_Trip_40min_rep2

value: 40 min


title: T02_BBN1

description: BBN-induced urothelial lesion from sample mouse BBN1 at time T02 (2 weeks after treatment initiation T0).

value: Male

value: Urothelial lesion

value: Hyperplasia


title: saliva from 19125510

description: saliva from 19125510

value: saliva

tag: kindred

value: FEMALE


title: T24_CTRL

description: Normal untreated urothelium (control). from sample mouse CTRL at time T24 (24 weeks after treatment initiation T0).

value: Control urothelium

value: no


title: saliva from 19129780

description: saliva from 19129780

tag: mother or child


title: mNET_seq_DMSO4h_Trip_40min_rep1

value: mESCs


title: saliva from 19122941

description: saliva from 19122941

value: KID

tag: gender

value: MALE

value: Laoting-substudy


title: T20_CTRL

description: Normal untreated urothelium (control). from sample mouse CTRL at time T20 (20 weeks after T0 strat treatment).


title: saliva from 19134180

description: saliva from 19134180

value: MOM

tag: study


title: saliva from 19125501

description: saliva from 19125501


title: mNET_seq_DMSO4h_Trip_20min_rep2

value: 20 min


title: saliva from 19120221

description: saliva from 19120221

value: Laoting Main


title: saliva from 19120220

description: saliva from 19120220


title: T16_BBN12

description: BBN-induced urothelial lesion from sample mouse BBN12 at time T16 (16 weeks after treatment initiation T0).

tag: Sex

value: CIS

value: Squamous

value: yes


title: T16_CTRL

description: Normal untreated urothelium (control). from sample mouse CTRL at time T16 (16 weeks after treatment initiation T0).

value: Male

tag: tumor stage

value: Urothelial


title: mNET_seq_DMSO4h_Trip_20min_rep1

value: DMSO


title: T12_CTRL

description: Normal untreated urothelium (control). from sample mouse CTRL at time T12 (12 weeks after treatment initiation T0).

tag: histological differentiation


title: saliva from 19120091

description: saliva from 19120091

value: saliva


title: mNET_seq_DMSO4h_Trip_10min_rep2

value: 10 min


title: saliva from 19119231

description: saliva from 19119231

value: FEMALE


title: saliva from 19119230

description: saliva from 19119230


title: T08_CTRL

description: Normal untreated urothelium (control). from sample mouse CTRL at time T08 (8 weeks after treatment initiation T0).

value: Control urothelium

tag: bbn treatment (yes/no)

value: no


title: saliva from 19117461

description: saliva from 19117461

value: KID


title: saliva from 19117861

description: saliva from 19117861


title: saliva from 19116911

description: saliva from 19116911


title: mNET_seq_DMSO4h_Trip_0min_rep1

value: mESCs

value: 0 min


title: First psychotic episode, hospital arrival, rep13

city: Santiago de Compostela

first: Roberto Carlos

middle: Agís

last: Balboa

state: Coruña

address: Travesía da Choupana s/n

department: Movement Disorders Group (AC22)

country: Spain

institute: Health Research Institute of Santiago de Compostela (IDIS)

data_processing:
myBrain-Seq v0.1.0 (https://github.com/sing-group/my-brain-seq)
Sequence reads were trimmed for adaptor sequence using myBrain-Seq
Trimmed sequences were aligned to GRCh38 using myBrain-Seq.
Quantification and annotation of the aligned sequences to miRBase v.22 was performed using myBrain-Seq.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file include miRNA quantification values for each sample.

extract_protocol:
PAXgene ® Blood microRNA Kit from Qiagen (PreAnalytiX GmbH, Hombrechtikon, Switzerland).
NEBNext Multiplex Small RNA Sample Prep Set for illumina (New England biolabs, Ipswich, MA, USA)

value: Peripheral blood

value: M

tag: age

tag: disease state

value: P

tag: alcohol

tag: tobacco

tag: illegal drugs

tag: medication group

value: Antipsychotics

tag: medication subgroup

value: Other antipsychotics


title: saliva from 19116180

description: saliva from 19116180

tag: tissue

value: MOM

value: Laoting Main


title: First psychotic episode, hospital discharge, rep15


title: First psychotic episode, hospital discharge, rep12

value: yes


title: mice high dose TA rep2

city: Nanning

first: xing

last: lin

address: Shuangyong Road

institute: Guangxi medical university

data_processing:
We applied DEGSeq2 algorithm to filter the differentially expressed genes, after the significant analysis under the following criteria: i) |log2FC|>1;ii) Pvalue<0.05.
Assembly: mm9
Supplementary files format and content: DEGSeq2 output

growth_protocol: Model group and TA group were metabolic-associated fatty liver disease induced by MCD-diet, normal group were given same dose of normal saline

extract_protocol:
Total RNA was extracted from liver tissues with Trizol reagent
NEBNext Ultra TM RNA Library Prep Kit (NEB #E7490), AMPure XP system

treatment_protocol: TA group were treated with TA

value: liver

tag: strain

tag: sample group

value: high dose Tormentic Acid (TA)


title: mice high dose TA rep3


title: mice high dose TA rep1


title: First psychotic episode, hospital arrival, rep14


title: saliva from 19115410

description: saliva from 19115410

value: saliva

tag: kindred

tag: mother or child


title: mNET_seq_Auxin4h_Trip_5min_rep1

tag: cell type

tag: auxin treatment

value: auxin

tag: triptolide treatment

value: 5 min


title: mNET_seq_Auxin4h_Trip_5min_rep2


title: mice model rep3

description:
read_count.N_vs_M.DESeq.DE_results
read_count.M_vs_T.DESeq.DE_results

value: metabolic-associated fatty liver disease (MAFLD) model


title: First psychotic episode, hospital arrival, rep12

tag: Sex


title: mNET_seq_Auxin4h_Trip_40min_rep2

value: 40 min


title: saliva from 19114561

description: saliva from 19114561

value: KID

tag: gender

value: MALE

tag: study

value: Laoting-substudy


title: First psychotic episode, hospital discharge, rep11

value: Peripheral blood

value: M

tag: age

tag: disease state

value: no


title: mice model rep2


title: mNET_seq_Auxin4h_Trip_40min_rep1

value: mESCs


title: mNET_seq_DMSO4h_Trip_10min_rep1

value: DMSO

value: 10 min


title: First psychotic episode, hospital arrival, rep11

value: P

tag: alcohol

tag: tobacco

value: yes


title: saliva from 19116181

description: saliva from 19116181

value: FEMALE

value: Laoting Main


title: mice model rep1

value: liver


title: saliva from 19112501

description: saliva from 19112501

value: saliva


title: saliva from 19122611

description: saliva from 19122611


title: mNET_seq_DMSO4h_Trip_0min_rep2

value: 0 min


title: saliva from 19111951

description: saliva from 19111951


title: First psychotic episode, hospital discharge, rep10

tag: illegal drugs

tag: medication group

value: Antipsychotics

value: Other antipsychotics


title: mNET_seq_Auxin4h_Trip_20min_rep2

value: auxin

value: 20 min


title: mice wt rep3

tag: tissue

value: WT; normal


title: saliva from 19115411

description: saliva from 19115411

value: KID

value: MALE


title: saliva from 19111950

description: saliva from 19111950

value: MOM


title: mice wt rep2

tag: strain


title: mNET_seq_Auxin4h_Trip_20min_rep1

value: mESCs


title: saliva from 19111121

description: saliva from 19111121


title: saliva from 19111120

description: saliva from 19111120


title: mNET_seq_Auxin4h_Trip_10min_rep2

value: 10 min


title: First psychotic episode, hospital discharge, rep9

value: Peripheral blood

value: F

value: P

tag: medication subgroup


title: First psychotic episode, hospital arrival, rep9

value: yes


title: saliva from 19110751

description: saliva from 19110751

tag: kindred

value: FEMALE

value: Laoting-substudy


title: Multiplexed sorted BM Lin-CD127+ cells

city: Ann Arbor

first: Chang

last: Kim

address: 109 Zina Pitcher

institute: University of Michigan

data_processing:
The raw FASTQ data were processed by the Seven Bridge Platform (https://www.sevenbridges.com/) for sample demultiplexing and the generation of expression matrix files.
The scRNA-Seq data were further analyzed with SeqGeq genomic tool Version 9.0 (FlowJo, LLC) and to export the processed CSV files.
Genome_build: Grcm38
Supplementary_files_format_and_content: Single cell matrix files

source_name: Bone marrow progenitors

extract_protocol:
For BM sinusoid cell labeling, WT or Plzf-GFP mice were injected i.v. with anti-CD45.2- AmCyan antibody (1 µg, clone 104, BioLegend). Mice were sacrificed 2 minutes after the injection and BM cells were stained for flow cytometry to determine cell numbers of indicated ILC progenitor populations.
cDNA synthesis was performed using the BD Rhapsody Express Single-Cell Analysis System, and gene expression libraries were prepared using Whole Transcriptome Analysis Amplification Kit (all from BD Biosciences).
Whole Transcriptome Analysis Amplification Kit (all from BD Biosciences).

value: Bone marrow ILC progenitors

tag: genotype

value: mixed sample (non-demultiplexed)


title: mNET_seq_Auxin4h_Trip_0min_rep2

tag: cell type

value: 0 min


title: mice wt rep1

value: liver

tag: sample group


title: First psychotic episode, hospital arrival, rep8

value: no

value: Antipsychotics

value: Other antipsychotics


title: First psychotic episode, hospital discharge, rep8


title: saliva from 19107081

description: saliva from 19107081

value: saliva

tag: mother or child

value: KID

value: Laoting Main


title: CCR6 Tregs from thymic of WT mice - replicate 2

city: Nantes

first: Matthieu

last: Giraud

address: 30 bd Jean Monnet

department: CRTI

institute: INSERM _ Université de Nantes

data_processing:
Illumina HiSeq 2000 machine
single-end 50bp reads
Alignment to the mm10 genome was done using Tophat 2
Read count and gene expression quantification was done using Cufflinks or Cuffdiff
Genome_build: mm10
Supplementary_files_format_and_content: text files with FPKM values

source_name: recirculating thymic Tregs

extract_protocol:
Total RNA was extracted using the RNeasy Micro Kit (Qiagen) and treated with DNase I
RNA-seq libraries were prepared using the TruSeq Stranded mRNA kit (Illumina)

treatment_protocol: Thymic Treg cells were pre-enriched by depleting CD8+ and CD19+ cells using biotinylated anti-CD8α (clone 53.6.7; BD Bioscience) and anti-CD19 (clone 1D3; BD Bioscience) antibodies with anti-biotin microbeads by AutoMACS using the Deplete program (Miltenyi Biotech). Thymic recirculating Treg were sorted as CCR6+CD4+CD8-CD25+ cells using a FACSAria III cell sorter (BD).

value: thymus

tag: type

value: WT


title: CCR6 Tregs from thymic of WT mice - replicate 1


title: First psychotic episode, hospital discharge, rep7

value: Peripheral blood

tag: Sex

value: M

value: Diazepines, oxazepines, thiazepines and oxepines


title: CCR6 Tregs from thymic of Aire-KO mice - replicate 2

value: Aire KO


title: saliva from 19107080

description: saliva from 19107080

value: MOM

tag: gender

value: FEMALE

tag: study


title: CCR6 Tregs from thymic of Aire-KO mice - replicate 1


title: saliva from 19106101

description: saliva from 19106101


title: First psychotic episode, hospital arrival, rep10

tag: age

tag: disease state

value: P

value: yes


title: mNET_seq_Auxin4h_Trip_10min_rep1

value: mESCs

tag: auxin treatment

value: auxin

tag: triptolide treatment

value: 10 min


title: First psychotic episode, hospital discharge, rep6

tag: alcohol

value: no

tag: tobacco

tag: illegal drugs

tag: medication group

value: Antipsychotics


title: saliva from 19106100

description: saliva from 19106100

tag: tissue

value: saliva

tag: kindred


title: saliva from 19109441

description: saliva from 19109441

value: KID

value: Laoting-substudy


title: First psychotic episode, hospital arrival, rep6

tag: medication subgroup


title: saliva from 19105721

description: saliva from 19105721


title: First psychotic episode, hospital discharge, rep5


title: mNET_seq_Auxin4h_Trip_0min_rep1

tag: cell type

tag: strain

value: 0 min


title: HCT116_si-circSTK3_rep3

type: RNA

city: Harbin

first: boyang

last: fan

address: 246 Xuefu Road, Nangang District

department: Department of Colorectal Cancer Surgery

institute: The Second Affiliated Hospital of Harbin Medical University

description: Gene expression data from normal tissue

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, genes that at least 1 out of 6 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes with statistiAgilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, genes that at least 1 out of 6 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes with statistical significance between the two groups were identified through Volcano Plot filtering. Differentially expressed genes between the two samples were identified through Fold Change filtering. Hierarchical Clustering was performed using the R scripts. GO analysis and Pathway analysis were performed in the standard enrichment computation method.

source_name: HCT116 cells transduced with si-circSTK3

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Briefly, total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The Labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: HCT116 cells were cultured in a McCoy's 5a medium containing 10% fetal bovine serum in a humidified atmosphere with 5% CO2 at 37 ºC.

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

treatment_protocol: Three pairs of HCT116 cells were transduced with si-NC and si-circSTK3.

tag: metastasis potential

value: Low-Metastasis cells

tag: circstk3 expression

value: Low


title: First psychotic episode, hospital arrival, rep5

value: Peripheral blood

tag: Sex

value: M

value: Diazepines, oxazepines, thiazepines and oxepines


title: PAB14_5

city: Shanghai

first: Debao

address: No. 1678 Dongfang Road, Tangqiao Street

institute: Shanghai Children's Medical Center

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Reference genome and gene model annotation files were downloaded from  genome website directly. Index of the reference genome was built using Hisat2 v2.0.5  and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b)  (Mihaela Pertea.et al. 2015) in a reference-based approach.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each  gene. And then FPKM of each gene was calculated based on the length of the gene  and reads count mapped to this gene.
Differential expression analysis of two  conditions/groups (two biological replicates per condition) was performed using the  DESeq2 R package (1.20.0).
Gene Ontology (GO) enrichment analysis of differentially expressed genes was  implemented by the clusterProfiler R package, in which gene length bias  wascorrected.We used clusterProfiler R package to test the  statistical enrichment of differential expression genes in KEGG pathways.
GATK2 (v3.7) software was used to perform SNP calling. Raw vcf files were  filtered with GATK standard filter method and other parameters (cluster:3;  WindowSize:35; QD < 2.0 o; FS > 30.0; DP < 10 and SnpEff software was used to  annotation for the Variablesite).
Assembly: GCA_000001895.4
Supplementary files format and content: FPKM

organism: Rattus norvegicus

source_name: RNAseq analyses of the upper lobe of the right lung tissue

growth_protocol: The suckling rats were breastfed by the mother rats and were housed in groups of 8-10 per cage, fed under the same conditions with free access to food and water, maintained in the 12h: 12h day: night cycle.

extract_protocol:
Lung tissue from the upper lobe of the right  lung was rapidly removed from executed rat and flash frozen in -80℃ refrigerator , RNA was harvested using Trizol reagent.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Newborn rats were anesthetized by brief hypothermia on crushed ice for approximately 3 minutes and then transferred to an ice bed to maintain anesthesia during the surgery. The operation was performed under the stereomicroscope in the supine position, including sternum clipping, thoracic cavity opening, pericardium incising, pulmonary artery quantitative constriction, thoracic cavity closing, etc. The constriction procedure which was only performed in the PAB group. After the surgery was completed, the rats were removed from the ice bed and placed on a heat plate of 37℃ to warm and wake up. The pups were not put back to their moms until they were absolutely conscious (around 3h after surgery).

value: SD

value: lung

tag: treatment method

value: pulmonary artery banding (PAB)

tag: treatment  age

value: postnatal day 1

tag: test age

value: postnatal day 14


title: saliva from 19104300

description: saliva from 19104300

tag: mother or child

value: MOM

tag: gender

value: FEMALE

tag: study

value: Laoting Main


title: First psychotic episode, hospital arrival, rep7

tag: age

tag: disease state

value: P

tag: alcohol

value: no

tag: tobacco

value: Antipsychotics


title: First psychotic episode, hospital discharge, rep4

tag: tissue

value: yes

tag: illegal drugs

tag: medication group


title: saliva from 19104041

description: saliva from 19104041

value: saliva

tag: kindred

value: KID


title: PAB14_4

tag: strain


title: First psychotic episode, hospital arrival, rep4

value: Peripheral blood

tag: medication subgroup


title: HCT116_si-circSTK3_rep2

description: Gene expression data from normal tissue

tag: metastasis potential

value: Low-Metastasis cells

tag: circstk3 expression

value: Low


title: HCT116_si-circSTK3_rep1

description: Gene expression data from normal tissue


title: saliva from 19104040

description: saliva from 19104040


title: First psychotic episode, hospital discharge, rep3

tag: Sex

value: F

value: Other antipsychotics


title: saliva from 19101731

description: saliva from 19101731

value: MALE


title: First psychotic episode, hospital arrival, rep3


title: saliva from 19104301

description: saliva from 19104301


title: First psychotic episode, hospital discharge, rep2


title: saliva from 19101730

description: saliva from 19101730


title: PAB14_1

value: SD

value: lung

tag: treatment method

value: pulmonary artery banding (PAB)

tag: treatment  age

value: postnatal day 1

tag: test age


title: saliva from 19101421

description: saliva from 19101421

tag: mother or child

tag: gender

value: FEMALE

tag: study

value: Laoting-substudy


title: Sham14_4

value: sham-operated

value: postnatal day 14


title: saliva from 19100261

description: saliva from 19100261

value: Laoting Main


title: HCT116_si-NC_rep2

description: Gene expression data from normal tissue

source_name: HCT116 cells transduced with si-NC

value: High-Metastasis cells

value: High


title: First psychotic episode, hospital discharge, rep1

value: Peripheral blood

value: M

tag: age

tag: disease state

value: P

tag: alcohol

value: yes

value: Antipsychotics


title: PAB14_2

tag: tissue


title: HCT116_si-NC_rep3

description: Gene expression data from normal tissue


title: Sham14_3


title: First psychotic episode, hospital arrival, rep2

value: F

value: no

tag: tobacco

tag: illegal drugs

tag: medication group

value: Other antipsychotics


title: PAB14_3

tag: strain

value: SD

value: lung

value: pulmonary artery banding (PAB)


title: saliva from 19100260

description: saliva from 19100260

value: saliva

tag: kindred

value: MOM

value: FEMALE


title: Sham14_2

value: sham-operated

value: postnatal day 1

value: postnatal day 14


title: First psychotic episode, hospital arrival, rep1

value: Peripheral blood

tag: medication subgroup


title: HCT116_si-NC_rep1

description: Gene expression data from normal tissue

tag: metastasis potential

value: High-Metastasis cells

tag: circstk3 expression

value: High


title: Sham14_5

tag: treatment method

tag: treatment  age


title: Multiple psychotic episodes, responder, hospital discharge, rep19

tag: Sex

value: M

value: MR

value: yes


title: Sham14_1

tag: test age


title: Multiple psychotic episodes, responder, hospital arrival, rep19

value: no


title: Soma_F_UNCcontrol_BRC2233

city: Cambridge

first: Walfred

last: Tang

address: Tennis Court Road

department: Gurdon Institute

country: United Kingdom

institute: University of Cambridge

data_processing:
The adaptor sequences were removed by Flexbar (3.5.0) as specified by NEB (https://github.com/nebiolabs/nebnext-single-cell-rna-seq) with additional options (“--qtrim TAIL  --qtrim-format i1.8 -qt 20”) to remove low quality reads.
Reads were mapped to the human reference genome (UCSC GRCh38/hg38) using STAR(2.7.1a) (parameters: ‘--outFilterMismatchNoverLmax 0.05 --outFilterMultimapNmax 50 --outMultimapperOrder Random’) guided by the Gencode Human Release 30 comprehensive gene annotation.
Raw read counts per gene were extracted by the featureCounts function of the Subread package(1.6.2) using the default parameters. Normalized read counts and differentially expressed genes were obtained using DEseq2(1.26.0) in R(3.6.2)/Bioconductor(3.10.1).
Assembly: hg38
Supplementary files format and content: Excel table with mRNA expression level [log2(normalised counts +1)]

source_name: Gonad

extract_protocol:
RNA was extracted using the PicoPure RNA Isolation Kit including an on-column DNase 1 digest (Qiagen 79254) following the manufacturer’s instruction.
RNA-seq libraries were generated from 2 to 5 ng of total RNA using NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina (NEB, E6420) and NEBNext®Multiplex Oligos for Illumina (NEB, E7335S). Library quality was accessed by TapeStation 2200 (Agilent) with High Sensitivity D1000 ScreenTape (Agilent), quantified and multiplexed.

value: Gonad

tag: cell type

value: Gonadal somatic cells

value: Female

tag: treatment

value: DMSO


title: Multiple psychotic episodes, responder, hospital arrival, rep18

tag: age

tag: disease state

value: Antipsychotics

value: Diazepines, oxazepines, thiazepines and oxepines


title: Soma_F_UNCcontrol_BRC2197

tag: tissue


title: Soma_F_UNC1999_BRC2233


title: Multiple psychotic episodes, responder, hospital discharge, rep18

tag: alcohol

tag: tobacco


title: Multiple psychotic episodes, responder, hospital discharge, rep17

tag: illegal drugs

tag: medication group

value: Other antipsychotics


title: Multiple psychotic episodes, responder, hospital arrival, rep17


title: Melanoma_brainmet_P12 [P12_B]

city: Dresden

first: Michael

last: Seifert

address: Fetscherstr. 74

country: Germany

institute: TU Dresden

hyb_protocol: Bisulfite conversion was executed with the Zymo EZ Methylation Kit following purification with Zymo DNA Clean Kit (Zymo Research, Irvine, USA). DNA was finally treated with the Infinium HD FFPE Restore kit before hybridization to the Illumina Infinium MethylationEPIC (850K) beadchip (both Illumina, San Diego, USA).

scan_protocol: The bead chips were scanned by iScan (Illumina, San Diego, USA).

data_processing:
Normalization was done by the R function preprocessFunnorm of the R package minfi utilizing the gender of patients. The CpGs were further filtered to exclude polymorphic and off-target probes based on data from McCartney et al. 2016 (PMID: 27330998). Beta values were computed for each CpG in each sample.
MelanomaMetastases_MatrixProcessed.txt: Beta values
MelanomaMetastases_MatrixSignal.txt: unmethylated and methylated signal intensities

label: Cy3 and Cy5

source_name: Melanoma brain metastasis

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from a 2 mm punch biopsy of the selected tumor area of the FFPE sample using the Maxwell16 FFPE Plus LEV DNA purification kit on a Maxwell 16 extractor (Promega, Madison, USA). DNA concentration was determined by a Qubit dsDNA BR Assay Kit (Thermo Scientific, Waltham, USA) and 500 ng DNA was used for further analysis.

tag: gender

value: female

tag: tissue type

value: Melanoma brain metastasis


title: Melanoma_brainmet_P24 [P24_B]


title: Multiple psychotic episodes, responder, hospital discharge, rep16

tag: medication subgroup


title: hPGC_F_UNCcontrol_BRC2233

value: Primordial germ cells


title: Soma_F_UNC1999_BRC2197


title: hPGC_F_UNCcontrol_BRC2197


title: Blood_rtAML_2

city: Gliwice

first: Agnieszka

last: Cecotka

address: Kozielska, 9/8

department: Department of Data Science and Engineering

country: Poland

institute: Politechnika Śląska

hyb_protocol: standard Illumina protocol

scan_protocol: 750ng DNA at a concentration of at least 20ng/ul was sent to NXT-DX (Ghent, Belgium) and run on the Human Methylation 450K BeadChip array for DNA methylation analysis. Samples were first sent for analysis using the 450K array, but due to discontinuation, some patient samples were repeated on the Infinium Human Methylation EPIC BeadChip array. 500ng DNA at a concentration of at least 20ng/ul was sent to NXT-DX and run on the EPIC array for DNA methylation analysis

data_processing: Filtering and BMIQ normalization with ChAMP

source_name: Blood, radiotherapy-related AML

label_protocol: standard Illumina protocol

extract_protocol: DNA was extracted from human bone marrow aspirate samples using the DNeasy® Blood & Tissue kit (Qiagen, Manchester, UK) according to the manufacturer's instructions. DNA quantity was measured by Quant-iT™ PicoGreen™ dsDNA Assay Kits (Thermo Fisher Scientific, Paisley, U.K.) and quality assessed by agarose gel electrophoresis using 1.3% agarose gel.


title: Melanoma_brainmet_P34 [P34_B]

value: male


title: Multiple psychotic episodes, responder, hospital arrival, rep16

value: Peripheral blood


title: hPGC_F_UNC1999_BRC2233


title: Melanoma_lungmet_P16 [P16_Lun]

source_name: Melanoma lung metastasis

value: Melanoma lung metastasis


title: hPGC_F_UNC1999_BRC2197


title: Multiple psychotic episodes, responder, hospital discharge, rep15

value: M

value: Butyrophenone derivatives


title: Blood_dnAML_5

source_name: Blood, de novo AML


title: Blood_ctAML_3

source_name: Blood, chemotherapy-related AML


title: Blood_ctAML_4_450K


title: Blood_rtAML_1_450K


title: Blood_rtAML_3_450K


title: Melanoma_brainmet_P16 [P16_B]


title: Multiple psychotic episodes, responder, hospital discharge, rep14

value: MR

value: yes


title: Melanoma_lungmet_P64 [P64_Lun]


title: Blood_rtAML_1


title: Blood_dnAML_2

value: missing


title: Blood_rtAML_2_450K


title: Blood_ctAML_3_450K


title: Blood_dnAML_5_450K


title: Input_Soma_wk8_F_r2

data_processing:
Paired-end ChIP-seq reads were quality- and adaptor-trimmed by Trim Galore (v0.4.1) using default parameters.
Trimmed reads were mapped to the human reference genome (UCSC GRCh38/hg38) and 680 drosophila (UCSC dm6) by Bowtie 2 (v2.3.4.1) with options ‘--local -X 2000 --no-mixed --no-discordant’, hence retaining properly paired reads with a maximum fragment length of 2000 bp.
Unmapped reads, non-primary reads, supplementary alignment and QC-failed reads were removed using samtools view with option ‘-F 2828’. Duplicated reads were marked and removed by the MarkDuplicates function in Picard Tools (Broad Institute). Subsequently, fragments mapped to hg38 blacklisted regions (http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/hg38-human/hg38.blacklist.bed.gz), non-canonical hg38 contigs and mitochondrial DNA (chrM) were removed.
Prior to peak calling, libraries were subsampled using Picard DownSampleSam so that each library contains approximately the same number of paired-end reads.
Peaks were called following the Encode replicated peak calling guidelines (https://www.encodeproject.org/pipelines/ENCPL272XAE/) with modifications to accommodate for paired-end libraries. To obtain high resolution of peaks, narrow peak call was used for all marks. Histone peaks were called using the input reads as background. Peaks were initially called for each biological replicate (downsampled to similar read depth), for the pooled replicates, and for the pooled pseudoreplicates of each biological replicate using MACS2 with a relaxed p-value threshold of 0.05 (options: ‘-g 3e9 --keep-dup all -p 0.05’). Each pseudoreplicate consists of half the reads of each biological replicate, chosen at random without replacement. Narrow peaks from the pooled replicate set were retained if they overlapped peaks from both biological replicates or peaks from both pooled pseudoreplicates. The thresholds of overlap were set at 30% by peak length for histone peaks. This peak calling strategy allows for the retention of marginal peaks in one replicate to be rescued by a strong biological replicate. To obtain a final high confidence peak set, the reproducible peaks were further filtered using the MACS2 q-value (false discovery rate <0.001).
Assembly: hg38
Supplementary files format and content: Reproducible peaks of the two biological replicates in macs2 narrowPeak format

extract_protocol:
Cells were thawed on ice, incubated with 2 µl of 1 % Triton X-100, 1 % Sodium deoxycholate and digested with Micrococcal Nuclease (MNase) (NEB). MNase activity was blocked by addition of 11 µl 100 mM EDTA and cell lysate was incubated for 1 h in 400 µl of IP buffer at 4 °C followed by 2 h incubation in the presence of 5 µl blocked protein A/G beads (blocking buffer: 100 µg/ml yeast tRNA, 0.1 % BSA in IP buffer). After the removal of the protein A/G beads, the pre-cleared cell lysate was added to the antibody bead complex (antibody was incubated with 5 µl blocked protein A/G beads for 3 h on 4 °C) overnight at 4 °C. Unbound chromatin was removed, and beads were sequentially washed for 4 min for 1.) two times with low salt wash buffer, 2.) two times with high salt buffer, and 3.) two times with LiCl wash buffer (20 mM Tris-HCl pH 8.0, 2 mM EDTA, 250 mM LiCl, 1 % NP-40, 1 % Sodium deoxycholate). To elute the bound DNA, beads were incubated in Proteinase K digestion buffer (20 mM HEPES pH 8.0, 1 mM EDTA, 0.5 % SDS, 1 mg/ml RNase, 0.4 mg/ml Proteinase K) for 15 min at 55 °C and 1 h at 65 °C. The DNA was purified from the eluate through AMPure XP beads following the manufacturer’s instructions and eluted in 20 µl EB buffer (MinElute Reaction Cleanup Kit; Qiagen).
ULI-NChIP-seq libraries were generated by the KAPA Hyper Prep Kit (KAPA Biosystems) according to manufacturer’s protocol. To minimize adaptor dimer formation, the NEBNext Adaptor and NEBNext Index PCR Primers from the NEBNext® Multiplex Oligos for Illumina (Index Primers Set 1) (NEB, E7335S) were used. After library amplification, libraries were purified by AMPure XP beads with double-sided size selection. The libraries were subjected to paired-end sequencing on HiSeq 4000 sequencing system (Illumina)

value: Gonad

value: Gonadal somatic cells

tag: chip antibody


title: Input_Soma_wk8_M_r2

value: Male


title: Blood_tAML

source_name: Blood, therapy-related AML


title: Blood_dnAML_4


title: Blood_ctAML_2_450K


title: Blood_ctAML_1


title: Blood_control_5

source_name: Blood, healthy control


title: Multiple psychotic episodes, responder, hospital arrival, rep14

value: no

value: Antipsychotics


title: Blood_ctAML_1_450K


title: Melanoma_brainmet_P64 [P64_B]


title: Input_hPGC_wk8_M_r2


title: Blood_control_4


title: Blood_dnAML_4_450K


title: Blood_ctAML_2


title: Multiple psychotic episodes, responder, hospital discharge, rep13

value: Other antipsychotics


title: Blood_control_2


title: Melanoma_lungmet_P67-area2 [P67_Lun-2]

value: female


title: Blood_control_3


title: Multiple psychotic episodes, responder, hospital arrival, rep13


title: Melanoma_lungmet_P67-area1 [P67_Lun-1]


title: Melanoma_brainmet_P45 [P45_B]

value: Melanoma brain metastasis


title: H3K9me3_Soma_wk9_F_r2

description: H3K9me3_Soma_wk9_F_pool_final_q3.narrowPeak

value: Female


title: Melanoma_brainmet_P67-area2 [P67_B-2]


title: Blood_control_1

value: male