title: DSP-1001660003872-E-G04


title: OX_536_A1D1_028_E2

status: Public on May 12 2022

type: SRA

city: Oxford

first: Lars

last: Fugger

address: The MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headley Way

department: Nuffield Department of Clinical Neurosciences

country: United Kingdom

institute: University of Oxford

library_source: transcriptomic

data_processing:
ST pipeline v1.5.1 available from https://github.com/SpatialTranscriptomicsResearch/st_pipeline
Genome_build: GRCh38
Supplementary_files_format_and_content: Count data was saved as sparse matrix in the Market Exchange Format (MEX)
Supplementary_files_format_and_content: Tissue coordinates for each spot transcriptome were derived using ST Spot Detector v 2.0.2 available from https://github.com/SpatialTranscriptomicsResearch/st_spot_detector and are provided together with spatial annotations as csv file
Supplementary_files_format_and_content: Microscopy images of HE stained brain tissue linked to spot transcriptomes are provided as png files

molecule: polyA RNA

organism: Homo sapiens

source_name: MS brain 11

extract_protocol:
Fresh-frozen brain tissues from SPMS patients and non-MS controls used in this study were provided by the UK Multiple Sclerosis Society Tissue Bank at Imperial College London
Spatial transcriptomics as previously described by Stahl et al. 2016

tag: tissue

value: brain cortex

tag: disease state

value: MS

tag: ChIP

tag: well


title: RNA-Seq: ESCs-K5aSE-WT-Rep3

city: Tianjin

first: Niannian

last: Li

state: Tianjin

address: No. 94 Weijin Road, Nankai District, Tianjin

department: college of Life Sciences

country: China

institute: Nankai University

description: RNA-Seq of Mus musculus: ESCs-K5aSE-WT-Rep3

data_processing:
Clean reads of RNA-seq were mapped to mm10 using HISAT2(2.2.1)
Expression levels of all genes were counted and expression profile matrix was constructed with featureCounts (2.0.3)
Differential expression analysis was calculated in R using DESeq2(1.18.1), with q value < 0.05 and fold change > 2 or < 1/2
Clean reads of 4C-seq were mapped to mm10 with Bowtie2(2.4.4). Then we obtained the interaction regions by R package FourCSeq
Assembly: mm10
Supplementary files format and content: Text files include genes counts values and bedGraph files include 4C interaction regions

molecule: total RNA

organism: Mus musculus

source_name: Embryonic stem cell

growth_protocol: Mouse ESCs (E14) were grown in culture dishes coated with 0.1% gelatin in DMEM supplemented with 15% FBS, 100 nM NEAA, 200 mM L-Glutamate, 1% Penicillin-streptomycin, 50 μM β-mercaptoethanol, 10 ng/mL LIF, 1 μM PD0325901 and 3 μM CHIR99021. The medium was replaced every 1 - 2 days. All cells are maintained at 37 °C in a 5% CO2 incubator.

extract_protocol:
1. For RNA-seq: cells were lysed with Trizol reagent (Life Technologies) and RNA was extracted according to the manufacturer's instructions.
2. For 4C-seq：Briefly, 10^7 ESCs were trypsinised into single cells and resuspended in 9.5 ml of DMEM/15% FBS. Cells were then cross-linked by adding 0.6 ml of 16% formaldehyde for 10 min. After centrifugation at 4 degrees (2000 g), cells were lysed in 5 ml of lysis buffer (10 mM Tris-HCl [pH 7.5]; 10 mM NaCl; 5 mM MgCl2; 0.1 mM EGTA; 1 x protease inhibitor) for 10 min (placed ice with constant light shaking) and centrifuged to remove the supernatant. The nuclei were then digested with DpnII at 37°C. After inactivation with 1.6% SDS for 20 minutes at 65°C, samples were diluted in 6.125 ml of 1.15× ligation buffer and 100 U T4 ligase and incubated for 4 hours at 16°C, followed by 30 minutes at 25°C. The ligated chromatin was digested by proteinase K, purified by phenol-chloroform extraction and the DNA was precipitated by ethanol. The purified product was further digested with NlaIII and then cyclised with T4 ligase. After purification, PCR reactions containing 100 ng DNA were performed using the bait-primers. PCR products were purified by Agencourt AMPure XP paramagnetic beads and the purified products were sequenced at Novogene (Tianjin city, China).
1. RNA-seq Library. Total RNA 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. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system. Then 3 µl USER Enzyme (NEB, USA) was used with size selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq 6000 platform and 150 bp paired-end reads were generated.
2. 4C-seq Library. After the DNA samples were tested and passed, the DNA fragments specifically enriched by the 4C technique were subjected to end repair, addition of A-tails, addition of sequencing connectors, purification and PCR amplification to complete the entire library preparation. After library construction, initial quantification was performed using Qubit 2.0 to dilute the library, followed by detection of the insert fragment using Agilent 2100. After the insert fragment size met the expectation, the effective concentration of the library was accurately quantified using Q-PCR method to ensure the quality of the library. After the libraries passed the assay, the different libraries were pooled into flowcell according to the effective concentration and the target downstream data volume. cBOT was clustered and sequenced using Illumina high-throughput sequencing platform NovaSeq 6000.

treatment_protocol: RNA-seq was performed using undifferentiated and EB-differentiated （5d) WT and KO ESCs. Undifferentiated ESCs (WT) were used for 4C-seq.

value: blastocyst

tag: cell line

tag: cell type

value: ESC

tag: genotype

value: WT


title: OX_536_A1D1_028_D1


title: DSP-1001660003872-E-G08

city: Cambridge

first: Karthik

last: Jagadeesh

state: MA

address: 415 Main St

department: Human Cell Atlas

country: USA

institute: Broad Institute

data_processing:
Library strategy: NanoString whole-transcriptome digital spatial profiling
Process FASTQ sequencing files (from Illumina NGS run) to DCC digital count files using Nanostring GeoMx NGS Pipeline v1.0
Generate raw and normalized count matrices using Nanostring azorius and hydra scripts, as described in associated manuscript
Assembly: Nanostring GeoMx human whole transcriptome atlas; found in geomx_ngs_data_second_acquisition_WTA_Hs_R_NGS_WTA_v1.0.pkc
Supplementary files format and content: Txt file of uncollapsed raw counts matrix; found in hPDAC_WTA_20210222T2101_TargetCountMatrix.txt
Supplementary files format and content: Txt file of bioprobe QC counts matrix; found in hPDAC_WTA_20210222T2101_BioProbeCountMatrix.txt
Supplementary files format and content: Txt file of negative probe normalized counts matrix; found in hPDAC_WTA_20210222T2101_NegNorm_TargetCountMatrix.txt
Supplementary files format and content: Txt file of q3 normalized counts matrix; found in hPDAC_WTA_20210222T2101_Q3Norm_TargetCountMatrix.txt

source_name: Pancreas

extract_protocol:
In brief, we sectioned clinical FFPE blocks at 5 um onto SuperFrost Plus microscopy slides and then followed the manufacturer instructions for RNA (NanoString) with minor modifications as noted in the associated manuscript.
Libraries were constructed according to manufacturer protocols (NanoString) for sequencing on a NovoSeq S2 (Illumina) with the following paired end read configuration: read 1, 27 nt; read 2, 27 nt; index 1, 8 nt; index 2, 8 nt.

treatment_protocol: 14 specimens received no treatment prior to resection; 7 specimens received neoadjuvant chemotherapy, radiotherapy, losartan, and/or nivolumab prior to resection

value: Pancreas

tag: treatment / other annotation

value: Untreated


title: RNA-Seq: ESCs-K5aSE-KO-Rep3

description: RNA-Seq of Mus musculus: ESCs-K5aSE-KO-Rep3


title: ChIPseq_MCF7_p300_E2

city: Changsha

first: Jiankang

last: Wang

state: Hunan

address: Lushan

institute: School of biology

library_source: genomic

data_processing:
Sequencing reads were aligned to human reference genome (hg38) using Bowtie version 1.2.2 with “-n2 -m1” parameters
Peak calling was performed using MACS2 version 2.2.6 with default settings
Htseq version 0.11.3 was then utilized with default parameters to generate a count table
Genome_build: hg38
Supplementary_files_format_and_content: bed files of ChIP-seq peak; gene count table of RNA-seq

molecule: genomic DNA

source_name: MCF7 cell line

growth_protocol: RPE cells and MCF-7 cells (JCRB Cell Bank) were cultured in DMEM containing 10% FBS and 1% Penicillin/Streptomycin.

extract_protocol:
Chromatin immunoprecipitation was performed as previously described (Komata, M., et al., Chromatin immunoprecipitation protocol for mammalian cells. Methods Mol Biol, 2014. 1164: p. 33-8.).  Total RNA was extracted using TRIzol (Life Technologies) and Nucleospin RNA (Macherey-Nagel) following the manufacturers' instructions.
ChIP-seq libraries were prepared using NEBNext ChIP-seq Library Prep Master Mix Set for Illumina (New England BioLabs).

treatment_protocol: RPE cells were cultured in serum-free medium for 48 hours and then incubated in DMEM containing 10% FBS for 30 min. MCF-7 cells were maintained in phenol red-free medium containing charcoal-dextran stripped FBS (Life Technologies) at 70-80% confluency for 2 days before treatment with 50nM E2 ligand (SIGMA) for the indicated times.

value: MCF7 cell line

tag: antibody

tag: treatment

value: Estrogen +


title: DSP-1001660003872-E-H01


title: OX_536_A1D1_028_C2


title: RNA-Seq: ESCs-K5aSE-WT-Rep1

description: RNA-Seq of Mus musculus: ESCs-K5aSE-WT-Rep1


title: ChIPseq_MCF7_Mau2_KD_Ctrl

value: Estrogen -

tag: sirna


title: OX_438_P6C3_026_D2

source_name: MS brain 4


title: RNA-Seq: ESCs-K5aSE-KO-Rep2

description: RNA-Seq of Mus musculus: ESCs-K5aSE-KO-Rep2


title: OX_438_P6C3_026_C2


title: ChIPseq_MCF7_Input_E2_45min

value: Input

value: Estrogen + 45min


title: RNA-Seq: ESCs-K5aSE-KO-Rep1

description: RNA-Seq of Mus musculus: ESCs-K5aSE-KO-Rep1


title: DSP-1001660003872-E-G11


title: bl6-gm15551_wt_7

city: Odense

first: Jan

middle: Wilhelm

last: Kornfeld

address: Campusbej 50

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

data_processing:
barcode and adapter removal using bcl2fastq2
quality trimming using cutadapt
quantification of transcripts by salmon (GENCODE M22)
normalisation and differential gene expression analysis using DESeq2
Assembly: GRCm38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: interscapular brown adipose tissue

extract_protocol:
Frozen tissue samples were homogenised and lysed in TRIsure (Bioline). Total RNA was isolated using EconoSpin All-In-One Mini Spin Columns (EconoSpin 1920-250).
Paired end libraries were constructed using the NEBNext Ultra II RNA Library Prep Kit for Illumina following the manufacturer’s protocol.

treatment_protocol: Mice were singly housed at 4°C for 24 h prior to dissection.

tag: strain

value: wt

tag: mouseid


title: DSP-1001660003872-E-F10


title: OX_438_P6C3_026_E1


title: RNA-Seq: EBd5-K5aSE-WT-Rep1

description: RNA-Seq of Mus musculus: EBd5-K5aSE-WT-Rep1

value: EBs-day 5


title: ChIPseq_MCF7_TAF1_Ctrl


title: bl6-gm15551_wt_5


title: OX_407_P4C6_023_E2

source_name: MS brain 3


title: ChIPseq_MCF7_Input_E2_30min

value: Estrogen + 30min


title: DSP-1001660003872-E-G10


title: ChIPseq_MCF7_Input_Ctrl


title: ChIPseq_MCF7_Rad21_E2_30min


title: OX_438_P6C3_026_D1


title: DSP-1001660003872-E-G01


title: bl6-gm15551_wt_3


title: ChIPseq_MCF7_p300_Ctrl


title: OX_407_P4C6_023_D2


title: DSP-1001660003872-E-G03


title: ChIPseq_MCF7_TAF1_E2


title: bl6-gm15551_wt_6


title: OX_438_P6C3_026_C1


title: DSP-1001660003872-E-G09


title: bl6-gm15551_ko_5

value: ko


title: ChIPseq_MCF7_Rad21_E2_45min


title: DSP-1001660003872-E-G05


title: OX_407_P4C6_023_C2


title: bl6-gm15551_ko_7


title: RNA-Seq: ESCs-K5aSE-WT-Rep2

description: RNA-Seq of Mus musculus: ESCs-K5aSE-WT-Rep2


title: DSP-1001660003872-E-G02


title: OX_407_P4C6_023_E1


title: ChIPseq_MCF7_Pol2ser2_Ctrl

value: RNA Pol2ser2


title: OX_407_P4C6_023_C1

value: brain cortex


title: ChIPseq_MCF7_Rad21_Ctrl


title: DSP-1001660003872-E-F09


title: DSP-1001660003872-E-G07


title: bl6-gm15551_wt_2


title: OX_407_P4D5_022_E1

value: MS


title: OX_407_P4C6_023_D1


title: ChIPseq_MCF7_Pol2ser2_E2


title: bl6-gm15551_ko_2


title: bl6-gm15551_ko_4


title: ChIPseq_MCF7_Pol2_E2_30min

value: RNA Pol2


title: DSP-1001660003872-E-E10

value: Excluded from analysis due to technical error


title: ChIPseq_MCF7_Pol2_E2_45min


title: DSP-1001660003872-E-F05


title: bl6-gm15551_ko_1


title: OX_407_P4D5_022_D2


title: OX_407_P4D5_022_D1


title: DSP-1001660003872-E-E03


title: bl6-gm15551_eWAT_ko_3

source_name: epididymal white adipose tissue


title: DSP-1001660003872-E-F08


title: DSP-1001660003872-E-E12


title: OX_407_P4D5_022_C2


title: ChIPseq_MCF7_Mau2_E2


title: bl6-gm15551_eWAT_wt_3


title: OX_407_P4D5_022_C1


title: DSP-1001660003872-E-E07


title: ChIPseq_MCF7_Mau2_Ctrl


title: bl6-gm15551_eWAT_ko_2


title: DSP-1001660003872-E-F06


title: bl6-gm15551_eWAT_wt_2


title: ChIPseq_MCF7_CTCF_E2

value: CTCF


title: OX_536_A1B7_021_E2


title: bl6-gm15551_eWAT_ko_1


title: DSP-1001660003872-E-F01

value: Pancreas


title: DSP-1001660003872-E-F04

value: Untreated


title: ChIPseq_MCF7_Pol2_Ctrl

value: MCF7 cell line


title: OX_536_A1B7_021_E1


title: bl6-gm15551_eWAT_wt_1


title: DSP-1001660003872-E-E04


title: ChIPseq_MCF7_AFF4_Ctrl


title: bl6-gm15551_iWAT_ko_3

source_name: inguinal white adipose tissue


title: OX_536_A1B7_021_D1


title: ChIPseq_MCF7_CBP_E2

value: CBP

value: Estrogen +


title: OX_536_A1B7_021_D2


title: bl6-gm15551_iWAT_wt_3


title: OX_536_A1B7_021_C2


title: DSP-1001660003872-E-E06


title: DSP-1001660003872-E-E01


title: ChIPseq_MCF7_CTCF_Ctrl

value: Estrogen -


title: MTP _rep2A

city: BENGALURU

first: TAPAS

middle: K

last: KUNDU

state: KARNATAKA

address: JAKKUR

department: MBGU

country: India

institute: JNCASR

data_processing:
Adapter sequences were trimmed from the raw ATAC-seq reads with CutAdapt v1.121 (Martin, M., 2011).
Trimmed reads of each sample were mapped to the reference human genome build GRCh37/hg19 by using Bowtie2 v2.3.2 with default settings (Langmead, B. & Salzberg, S. L,2012).
Picard tools (http://broadinstitute.github.io/picard/) v1.126 was used to remove PCR duplicated reads and for insert size distribution analysis. Reads mapping to mitochondrial DNA and the Y chromosome were filtered and only uniquely mapping paired reads with a quality score≥30 were kept for subsequent analysis.
The read start sites were adjusted to represent the center of the transposon binding event (5bp on forward strand and 4bp on reverse strand) as described (Buenrostro, J. D et al., 2013). Phantompeakqualtools v2.0 was used to calculate the strand cross-correlation and deepTools v2.0.1 was used to calculate correlation between samples (Landt, S. G. et al., 2012, Ramirez, F. et al., 2016).
MACS2 v2.1.0 was used for peak calling with parameters “--nomodel--nolambda-keep-dup all--call-summits-g hs-B”, and peaks were filtered based on default settings and false discovery rate (FDR) < 0.1 (Zhang, Y. et al., 2008). Peaks in regions known to show artificially high signal were filtered using the hg19 blacklist file from ENCODE. BEDTools v2.26.07 was used for various analyses based on peak locations.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: library-normalized bigWig files of processed ATAC-seq reads

source_name: HEK293 cells

growth_protocol: The HEK293 cells were grown in the DMEM media (Thermo) with 10% FBS and Penicillin-Streptomycin.

extract_protocol:
Library for ATAC-seq was prepared according to a published protocol (Buenrostro J D.et al., 2013) using 50,000 intact cells as input. The cells were spun at 500g for 5 min followed by a wash using 50 μL of cold 1× PBS and centrifugation at 500g for 5 min. Cells were lysed using cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630) and spun at 500g for 10 min using a refrigerated centrifuge generating the nuclei prep.
The nuclei prep was then resuspended in the transposase reaction mix (25 μL 2× TD buffer, 2.5 μL transposase (Illumina) and 22.5 μL nuclease-free water) 30 min at 37 °C. Tn5 transposase tagmentation simultaneously fragments the genome and tags the resulting DNA with Illumina sequencing adapters. DNA fragments were PCR ampliﬁed and subsequently puriﬁed using Qiagen MinElute PCR Puriﬁcation Kit (Qiagen, Hilgen, Germany). Final library quality and quantity were analyzed and measured by Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara,CA, USA) and Life Technologies Qubit3.0 Fluorometer (Life Technologies), respectively.

treatment_protocol: PC4 KD cells generated through lentiviral transduction and sorted for GFP-posiyive cells, PC4, PM-PC4 and MTP5 stably transfected in PC4 KD cells and maintained under neomycin selection

tag: genotype/variation

value: pGIPZ PC4 KD

tag: passages

tag: transfection

value: Flag MTP5


title: ChIPseq_MCF7_CBP_Ctrl


title: bl6-gm15551_iWAT_wt_2

value: wt


title: OX_536_A1B7_021_C1


title: OX_585_P6B6_020_E2

source_name: MS brain 12


title: MTP _rep1A


title: PM _rep2A

value: Flag PM-PC4


title: OX_585_P6B6_020_E1


title: DSP-1001660003872-E-E05


title: DSP-1001660003872-E-D06


title: ChIPseq_MCF7_AFF4_E2


title: PM _rep1A


title: DSP-1001660003872-E-E09


title: bl6-gm15551_iWAT_wt_1


title: DSP-1001660003872-E-D04


title: bl6-gm15551_iBAT_ko_3

value: ko


title: OX_585_P6B6_020_D1


title: FP_ rep2A

value: Flag PC4


title: OX_585_P6B6_020_C1

value: brain cortex


title: bl6-gm15551_iWAT_ko_2


title: OX_585_P6B6_020_C2

value: MS


title: bl6-gm15551_iBAT_wt_3


title: DSP-1001660003872-E-D01


title: DSP-1001660003872-E-E08


title: FP _rep1A


title: bl6-gm15551_iBAT_ko_2


title: DSP-1001660003872-E-D03


title: KD_ rep2A


title: DSP-1001660003872-E-D10


title: bl6-gm15551_iWAT_ko_1


title: OX_585_A2C4_019_E2


title: bl6-gm15551_iBAT_wt_2


title: bl6-gm15551_iBAT_wt_1


title: OX_585_P6B6_020_D2


title: bl6-gm15551_iBAT_ko_1


title: OX_585_A2C4_019_E1


title: Control_rep2A

value: pGIPZ control

value: pGIPZ non-silencing


title: DSP-1001660003872-E-D05


title: DSP-1001660003872-E-E02

value: Excluded from analysis due to technical error


title: wt1-SAM_oe_rep6_pSgRNA-MS2-2+7_iso

source_name: Brown adipocytes

growth_protocol: wt1-SAM brown preadipocytes were grown in high glucose DMEM supplemented with 10 % FBS and 1 % penicillin-streptomycin. After reaching confluency, differentiation was induced by 0.5 μ M rosiglitazone, 1 n M T3, 1 μ M Dexamethasone, 850 n M insulin, 125 μ M indomethacine and 500 μ M IBMX. Two days later, medium was exchanged for medium supplemented with 0.5 μ M rosiglitazone and 850 n M insulin. Afterwards, medium was changed for medium containing 0.5 μ M rosiglitazone every second day.

extract_protocol:
Cells were homogenised and lysed in TRIsure (Bioline). Total RNA was isolated using EconoSpin All-In-One Mini Spin Columns (EconoSpin 1920-250).
Paired end libraries were constructed using the NEBNext Ultra II RNA Library Prep Kit for Illumina following the manufacturer’s protocol.

treatment_protocol: 3 μl TransIT and 250 ng plasmid DNA  in 100 μl Opti-MEM I were pipetted into a well of a 24 well plate. After 15 min, 500 000 cells resuspended in 500 μl Opti-MEM were added. 24 h later, medium was changed for regular differentiation medium. Cells were stimulated using 1 μM isoproterenol for 24 h before harvest.

value: iso

tag: sgrna

tag: replicate


title: Control_rep1A


title: DSP-1001660003872-E-D11

tag: tissue

value: Pancreas

value: Untreated


title: OX_585_A2C4_019_D1

tag: disease state

tag: ChIP


title: wt1-SAM_oe_rep6_pSgRNA-MS2-2+7_ctrl

tag: cell line

value: ctrl


title: OX_585_A2C4_019_C2

tag: well


title: wt1-SAM_oe_rep6_empty_ctrl

value: empty


title: DSP-1001660003872-E-D02


title: DSP-1001660003872-E-D12


title: wt1-SAM_oe_rep6_empty_iso


title: KD_ rep1A


title: wt1-SAM_oe_rep5_pSgRNA-MS2-2+7_iso


title: DSP-1001660003872-E-C05


title: OX_585_A2C4_019_D2


title: RPE Bmal1 KO-ZT19-rep3

city: Atlanta

first: Gianluca

last: Tosini

state: GA

address: 720 Westview Drive

institute: Morehouse School of Medicine

data_processing:
Base calling: RTA2 (Real-Time Analysis)
Alignment: bowtie2 (version 2.3.4) using default parameters
Count generation: htseq-count (version 0.9.1) using default parameters
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table in xlsx file format with raw counts for all genes common in all samples

source_name: RPE Bmal1 KO

growth_protocol: 12:12 light:dark cycle, ad libitum access to food and water

extract_protocol:
Retinal pigment epithelial cell isolation protocol was followed as previously reported (DeVera and Tosini, 2020). Briefly, eyes were enucleated under room light or dim red-light conditions (< 1 lux) and removal of the anterior segment along with the neural retina was dissected from the posterior segment that contains the RPE, choroid, and sclera. Each dissected posterior segment was placed in 50 μL of RNAlater (Qiagen, 76,104). Removal and isolation of RPE cells was done via brief sonication (Fisher, F60) on ice (< 2 s at 10% max power) and was done in ambient light conditions. Two RPE samples from one mouse were pooled into one tube. The isolated RPE cells were processed for RNA isolation with TRIzol (Ambion, 15596018) following the manufacturer's instructions.
The Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus (Illumina, 200050529) was used for library preparation and done according to the manufacturer’s instructions

treatment_protocol: doxycycline food feeding at p60-p74 for two weeks

tag: age

value: 12-16 weeks

tag: genotype

value: Bmal1 KO

value: retinal pigment epithelium


title: RPE Bmal1 KO-ZT19-rep2


title: RPE Bmal1 KO-ZT13-rep3


title: RPE Bmal1 KO-ZT19-rep1


title: OX_535_A1D5_018_E1

source_name: MS brain 10


title: DSP-1001660003872-E-D09

tag: treatment / other annotation


title: RPE Bmal1 KO-ZT13-rep1


title: OX_535_A1D5_018_D1


title: wt1-SAM_oe_rep5_pSgRNA-MS2-2+7_ctrl

tag: treatment


title: DSP-1001660003872-E-C10


title: RPE Bmal1 KO-ZT13-rep2


title: wt1-SAM_oe_rep5_empty_iso


title: DSP-1001660003872-E-D08


title: RPE Bmal1 KO-ZT7-rep3


title: OX_535_A1D5_018_E2


title: OX_535_A1D5_018_C2


title: OX_585_A2C4_019_C1


title: OX_535_A1D5_018_C1


title: DSP-1001660003872-E-C12


title: OX_438_P6B6_017_E2


title: RPE Bmal1 KO-ZT7-rep1


title: wt1-SAM_oe_rep4_pSgRNA-MS2-2+7_ctrl


title: DSP-1001660003872-E-D07


title: DSP-1001660003872-E-B10


title: OX_438_P6B6_017_E1


title: RPE Bmal1 KO-ZT1-rep3


title: OX_438_P6B6_017_C2


title: wt1-SAM_oe_rep4_empty_iso


title: RPE Bmal1 KO-ZT1-rep2


title: DSP-1001660003872-E-C06


title: DSP-1001660003872-E-C03


title: OX_438_P6B6_017_D1


title: OX_438_P6B6_017_C1


title: wt1-SAM_oe_rep4_empty_ctrl


title: wt1-SAM_oe_rep3_pSgRNA-MS2-2+7_iso


title: DSP-1001660003872-E-B11


title: wt1-SAM_oe_rep3_pSgRNA-MS2-2+7_ctrl


title: wt1-SAM_oe_rep4_pSgRNA-MS2-2+7_iso


title: OX_438_P4B4_016_E1


title: RPE Bmal1 WT-ZT19-rep1

source_name: RPE Bmal1 WT

value: Bmal1 WT


title: RPE Bmal1 KO-ZT7-rep2


title: RPE Bmal1 WT-ZT19-rep2


title: wt1-SAM_oe_rep3_empty_iso


title: wt1-SAM_oe_rep5_empty_ctrl


title: DSP-1001660003872-E-B08


title: OX_438_P4B4_016_E2


title: DSP-1001660003872-E-C09


title: RPE Bmal1 WT-ZT13-rep3


title: DSP-1001660003872-E-B04


title: wt1-SAM_oe_rep3_empty_ctrl


title: DSP-1001660003872-E-C11


title: OX_438_P4B4_016_D1


title: OX_438_P4B4_016_C1


title: DSP-1001660003872-E-C01


title: wt1-SAM_kd_rep4_LNA2_ctrl

treatment_protocol: 3 μl TransIT and 1.4 μl (10 μ M ) LNA  in 100 μl Opti-MEM I were pipetted into a well of a 24 well plate. After 15 min, 500 000 cells resuspended in 500 μl Opti-MEM were added. 24 h later, medium was changed for regular differentiation medium. Cells were stimulated using 1 μM isoproterenol for 24 h before harvest.

tag: lna


title: RPE Bmal1 KO-ZT1-rep1

tag: strain


title: DSP-1001660003872-E-C08


title: RPE Bmal1 WT-ZT13-rep2


title: wt1-SAM_kd_rep4_LNA1_ctrl


title: RPE Bmal1 WT-ZT7-rep3


title: wt1-SAM_kd_rep4_LNA1_iso


title: RPE Bmal1 WT-ZT13-rep1


title: RPE Bmal1 WT-ZT19-rep3


title: wt1-SAM_kd_rep4_ctrlA_ctrl

value: ctrlA


title: DSP-1001660003872-E-B12


title: OX_407_P4B7_015_E1


title: wt1-SAM_kd_rep4_LNA2_iso


title: OX_438_P4B4_016_D2


title: OX_407_P4B7_015_E2


title: wt1-SAM_kd_rep3_LNA2_iso


title: DSP-1001660003872-E-C07


title: RPE Bmal1 WT-ZT1-rep3


title: RPE Bmal1 WT-ZT7-rep2


title: wt1-SAM_kd_rep4_ctrlA_iso


title: DSP-1001660003872-E-C02


title: RPE Bmal1 WT-ZT1-rep2


title: OX_407_P4B7_015_C2


title: OX_407_P4B7_015_D2


title: wt1-SAM_kd_rep3_LNA2_ctrl


title: DSP-1001660003872-E-C04


title: DSP-1001660003872-E-B09


title: OX_407_P4B7_015_D1


title: wt1-SAM_kd_rep3_LNA1_iso


title: RPE Bmal1 WT-ZT1-rep1


title: OX_407_P4B7_015_C1


title: ARF17.2_p19-/-+VPA

city: Illkirch-Grafenstaden

first: Bill

last: Keyes

address: 1, rue Laurent Fries

department: Development and Stem Cells

country: France

institute: IGBMC

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Alignment: Reads were mapped onto mm10 assembly of mouse genome using STAR 2.5.3a.
Quantification: Gene expression was quantified using HTSeq v0.6.1p1 (union mode) and Ensembl release 101 annotations.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-separated values file containing raw read counts in each sample.

source_name: RNA collected from mouse embryonic brain

extract_protocol: Full length cDNA were generated from 10 ng of total RNA using Clontech SMART-Seq v4 Ultra Low Input RNA kit for Sequencing (Takara Bio Europe, Saint Germain en Laye, France) according to manufacturer's instructions with 8 cycles of PCR for cDNA amplification by Seq-Amp polymerase. Six hundreds pg of pre-amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit (96 samples) (Illumina, San Diego, CA) followed by 12 cycles of library amplification. Following purification with Agencourt AMPure XP beads (Beckman-Coulter, Villepinte, France), the size and concentration of libraries were assessed by capillary electrophoreris.

tag: genotype and treatment

tag: Stage

value: Forebrain/midbrain


title: wt1-SAM_kd_rep3_LNA1_ctrl


title: OX_342_P5C2_008_E1

source_name: MS brain 1


title: DSP-1001660003872-E-A08


title: DSP-1001660003872-E-B07


title: DSP-1001660003872-E-B05


title: OX_342_P5C2_008_D2


title: ARF16.2_p19-/-+VPA


title: RPE Bmal1 WT-ZT7-rep1


title: ARF9.3_p19-/-+VPA


title: wt1-SAM_kd_rep3_ctrlA_iso


title: OX_438_P4B4_016_C2


title: wt1-SAM_kd_rep3_ctrlA_ctrl


title: OX_342_P5C2_008_D1


title: DSP-1001660003872-E-A04


title: ARF8B.3_p19-/-+VPA


title: wt1-SAM_kd_rep2_LNA2_iso


title: DSP-1001660003684-A-H09


title: OX_342_P5C2_008_C2


title: ARF18.1_p19-/-


title: DSP-1001660003872-E-A06


title: wt1-SAM_kd_rep2_LNA1_iso


title: wt1-SAM_kd_rep2_LNA2_ctrl


title: ARF7.1_p19-/-


title: OX_342_P5D5_007_E2


title: ARF19.3_p19-/-


title: OX_342_P5D5_007_D2


title: ARF6.2_p19-/-


title: DSP-1001660003872-E-B06


title: wt1-SAM_kd_rep2_LNA1_ctrl


title: wt1-SAM_kd_rep2_ctrlA_iso


title: DSP-1001660003872-E-B01


title: OX_342_P5D5_007_D1


title: DSP-1001660003684-A-H11


title: wt1-SAM_kd_rep2_ctrlA_ctrl


title: B6J15.4_WT+VPA

value: WT+VPA


title: OX_342_P5D5_007_C2

value: brain cortex


title: B6J15.3_WT+VPA


title: RAW264.7 HDAC3KO-Input-3

city: Hang Zhou

first: Liping

last: Yang

address: 88 Jiefang Road

institute: The Second Affiliated Hospital, Zhejiang University School of Medicine

data_processing:
Quality control was performed in Linux by fastqc and multiqc software
Data trimming was performed in Linux by trim_galore
ChIP-seq reads were aligned to the mm10 genome assembly using bowtie2
Bam files were generated from sam files using Samtools.
Peaks were called using macs2
Assembly: mm10
Supplementary files format and content: BW files were generated from bam files using bamCoverage
Supplementary files format and content: peak text files (bed)

source_name: macrophage line RAW264.7

extract_protocol:
Lysates were clarified from sonicated nuclei and H3K27ac-DNA complexes or IgG-DNA complexes were isolated with antibody.
Library preparation for ChIP-seq was using KAPA HyperPlus Kit (KAPA Biosystems, #KK8514) according to manufacturer’s protocol. Briefly, 50 μl sample was proceed to End Repair and A-tailing at 65 ℃ for 30 min. Different adapter was added into each sample and incubated at 20 ℃ for 15 min. After ligation, DNA was bound to the beads and washed by 80% ethanol for 3 times, followed by 7-8 cycles PCR. The DNA was performed 1x bead-based cleanup again and the product was ready for sequencing which was done by company (Novogene).

value: BALB/c

tag: cell type

value: macrophage cell line RAW264.7

tag: chip antibody


title: OX_342_P5D5_007_C1

value: MS


title: DSP-1001660003872-E-A12


title: OX_342_P5C2_008_C1


title: OX_528_P2B2_006_E1

source_name: MS brain 5


title: DSP-1001660003872-E-B03

source_name: Pancreas


title: DSP-1001660003872-E-B02


title: B6J15.1_WT+VPA


title: OX_528_P2B2_006_D2


title: RAW264.7 HDAC3KO-Input-1


title: DSP-1001660003872-E-A09


title: DSP-1001660003872-E-A10


title: B6J12.1_WT

value: WT


title: RAW264.7 HDAC3KO-IgG-2

value: IgG


title: OX_528_P2B2_006_D1


title: B6J10.3_WT


title: DSP-1001660003684-A-G04

value: Pancreas


title: OX_528_P2B2_006_C2


title: B6J10.4_WT


title: DSP-1001660003872-E-A11

value: Untreated


title: OX_528_P2B2_006_C1


title: RAW264.7 HDAC3KO-Ace-3


title: RAW264.7 HDAC3KO-Input-2


title: Medio-Basal Hypohtalamus - Ile-de-France/Luteal phase - 5th replicate

city: Nouzilly

first: Hugues

last: Dardente

address: INRA

department: INRAE - Centre Val de Loire

institute: INRAE

data_processing:
Image analyses and base calling were performed using the HiSeq Control Software and Real-Time Analysis component (Illumina). Demultiplexing was performed using Illumina's conversion software (bcl2fastq 2.20). The quality of the raw data was assessed using FastQC from the Babraham Institute and the Illumina software SAV (Sequencing Analysis Viewer).
A splice junction mapper, TopHat 2.1.1 (using Bowtie 2.3.5.1), was used to align the RNA-Seq reads to the Ovis aries genome (NCBI, Oar Rambouillet v1.0) with a set of gene model annotations (genes.gtf downloaded from NCBI on May 25 2020 ; release 103).
Final read alignments having more than 6 mismatches were discarded. Samtools (v1.9) was used to sort the alignment files. Then, the counting was performed with Featurecounts 2.0.0. As the data is from a strand-specific assay, the read has to be mapped to the opposite strand of the gene (-s 2 option).
Assembly: Oar Rambouillet v1.0
Supplementary files format and content: tab-delimited text files include raw gene counts for every gene and every sample

organism: Ovis aries

source_name: Brain - Hypothalamus

extract_protocol:
TriReagent
Libraries were constructed using the Truseq stranded mRNA sample prep kit (Illumina, San Diego, CA,USA) according to the manufacturer instructions.

tag: breed

value: Ile-de-France

value: adult ewe

tag: time point

value: Luteal phase

value: Brain - Hypothalamus


title: OX_PDC29_P3B2_005_E1

source_name: Contr. brain 4

tag: tissue

value: HI


title: DSP-1001660003684-A-G11


title: B6J15.2_WT+VPA


title: OX_PDC29_P3B2_005_D2

tag: disease state


title: DSP-1001660003872-E-A02


title: Medio-Basal Hypohtalamus - Ile-de-France/Luteal phase - 4th replicate


title: B6J11.1_WT


title: OX_PDC29_P3B2_005_D1

tag: ChIP


title: RAW264.7 HDAC3KO-Ace-2


title: RAW264.7 HDAC3KO-Ace-1


title: RAW264.7 HDAC3KO-IgG-3


title: DSP-1001660003872-E-A07


title: Medio-Basal Hypohtalamus - Ile-de-France/Luteal phase - 3rd replicate


title: RAW264.7 Vector-Input-3


title: DSP-1001660003684-A-H10


title: RAW264.7 HDAC3KO-IgG-1


title: RAW264.7 Vector-Input-2


title: OX_PDC29_P3B2_005_C1


title: OX_PDC29_P3B2_005_C2


title: Medio-Basal Hypohtalamus - Ile-de-France/Luteal phase - 2nd replicate


title: Medio-Basal Hypohtalamus - Ile-de-France/Luteal phase - 1st replicate


title: RAW264.7 Vector-Input-1


title: OX_C45_P2C4_003_E2

source_name: Contr. brain 1


title: DSP-1001660003684-A-G05


title: Medio-Basal Hypohtalamus - Ile-de-France/Follicular phase - 5th replicate

value: Follicular phase


title: DSP-1001660003684-A-H12


title: OX_C45_P2C4_003_E1


title: DSP-1001660003872-E-A05


title: RAW264.7 Vector-IgG-3


title: Medio-Basal Hypohtalamus - Ile-de-France/Follicular phase - 4th replicate


title: OX_C45_P2C4_003_D1


title: Medio-Basal Hypohtalamus - Ile-de-France/Follicular phase - 2nd replicate


title: Medio-Basal Hypohtalamus - Ile-de-France/Follicular phase - 3rd replicate


title: DSP-1001660003684-A-H08


title: DSP-1001660003872-E-A03


title: OX_C45_P2C4_003_D2


title: RAW264.7 Vector-IgG-2


title: OX_C45_P2C4_003_C2


title: RAW264.7 Vector-IgG-1


title: DSP-1001660003684-A-H02


title: Medio-Basal Hypohtalamus - Ile-de-France/Follicular phase - 1st replicate


title: RAW264.7 Vector-Ace-2


title: OX_C45_P2C4_003_C1


title: DSP-1001660003872-E-A01

value: No Template Control


title: RAW264.7 Vector-Ace-1


title: RAW264.7 Vector-Ace-3


title: DSP-1001660003684-A-H06


title: OX_C25_P2C3_001_E2

source_name: Contr. brain 3


title: HDAC3KO_3

description: basal expression

data_processing:
Quality control, data trimming, mapping was done by CLC Genomics Workbench software
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using CLC Genomics Workbench software.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: Macrophage line RAW264.7

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (QIAGEN, cat#74104). ProtoScript II Reverse Transcriptase (New England BioLabs, cat#E7420L) was used with 0.6 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line


title: DSP-1001660003684-A-H07


title: OX_C25_P2C3_001_E1

tag: well


title: OX_C25_P2C3_001_D2


title: Mediobasal hypothalamus - Well Fed Group - 4th replicate

data_processing:
Image analyses and base calling were performed using the HiSeq Control Software and Real-Time Analysis component (Illumina). Demultiplexing was performed using Illumina's conversion software (bcl2fastq 2.20). The quality of the raw data was assessed using FastQC from the Babraham Institute and the Illumina software SAV (Sequencing Analysis Viewer).
A splice junction mapper, TopHat 2.1.1 (using Bowtie 2.3.5.1), was used to align the RNA-Seq reads to the Ovis aries genome (NCBI, Oar_rambouillet v1.0) with a set of gene model annotations (genes.gtf downloaded from NCBI on May 25 2020 ; release 103).
Final read alignments having more than 6 mismatches were discarded. Samtools (v1.9) was used to sort the alignment files. Then, the counting was performed with Featurecounts 2.0.0. As the data is from a strand-specific assay, the read has to be mapped to the opposite strand of the gene (-s 2 option).
Assembly: Oar_rambouillet v1.0
Supplementary files format and content: tab-delimited text files include raw gene counts for every gene and every sample

tag: age

value: adult ewes


title: Mediobasal hypothalamus - Well Fed Group - 1st replicate


title: Mediobasal hypothalamus - Well Fed Group - 2nd replicate


title: OX_C25_P2C3_001_D1


title: Mediobasal hypothalamus - Well Fed Group - 3rd replicate


title: DSP-1001660003684-A-H03


title: DSP-1001660003684-A-G08


title: Mediobasal hypothalamus - Food-Restricted Group - 3rd replicate


title: Vector_3

description: basal expression

tag: genotype

value: wild type


title: DSP-1001660003684-A-G09

tag: treatment / other annotation


title: Vector_2

description: basal expression


title: OX_C25_P2C3_001_C2

value: brain cortex


title: Mediobasal hypothalamus - Food-Restricted Group - 4th replicate


title: OX_C25_P2C3_001_C1


title: Mediobasal hypothalamus - Food-Restricted Group - 1st replicate


title: DSP-1001660003684-A-G12


title: Mediobasal hypothalamus - Food-Restricted Group - 2nd replicate


title: RRBS_tumor_MCR_LWB-4-95

city: chapel hill

first: michael

middle: francis

last: coleman

state: North Carolina

address: 235 dauer drive

institute: UNC

data_processing:
Sequence reads were mapped to the mouse genome (mm10) using Bismark Bisulfite Read Mapper.
Assembly: mm10
Supplementary files format and content: raw fastq file (paired end)
Supplementary files format and content: processed data:  normalized read counts in .txt format

source_name: Contralateral normal mammary tissue

growth_protocol: C57BL/6Nmice were randomized to receive a control diet D12450J, or a 60% high fat diet (D12492) to promote diet induced obesity. Once obese, mice were randomized to either remain obese or undergo weight loss via one of 4 diets; 1) nonrestricted LFD; 2) low-fat, 30% calorie-restricted (LFCR); 3) Mediterranean-style, 30% calorie-restricted (MCR); or 4) intermittent calorie-restricted (ICR)

extract_protocol:
DNA was isolated by TRIzol
Genomic DNA (1 mg) was digested with MspI, and enrichment for CpG sites in CG-dense and CpG islands was achieved by selective collection and PCR amplification of MspI fragments with sizes of 40-170 bp

treatment_protocol: 25 weeks after initial randomization mice were orthotopically injected with E0771 cells into the 4th mammary fat pad and tumors were allowed to grow till endpoint. At endpoint the contralateral (9th) mammary fat pad was removed and used for nucleic acid extraction.

value: Contralateral normal mammary tissue

value: mouse mammary cancer

value: wt

tag: treatment

value: MCR


title: Vector_1

description: basal expression

value: BALB/c


title: Control_ovary_2

city: RTP

first: Humphrey

last: Yao

state: NC

address: 111 TW Alexander Dr.

department: DIR

institute: NIEHS

data_processing:
Sequences were aligned with CellRanger
Data were filtered, clustered, visualized, and analyzed with Seurat V4.0
Data were analyzed with Seurat for dKO male, male control and female control (combined)
To analyze changes in gene expression, data was extracted from Seurat and processed with base R.
Genome_build: mm10
Supplementary_files_format_and_content: unswapped filtered_feature_bc_matrix files (barcode, feature, and matrix) files exported from CellRanger.

source_name: Embryonic ovary

extract_protocol:
Cell were disassociated with a 1.2 U/mL Dispase II, 1mgl/mL Collangenase IV, and 5U/mL DNAaseI cocktail. Cell suspension was cryopreserved in liquid nitrogen. For library construccion cells were thawed at 37C, washed and resuspended in PBS+0.04% BSA.
10x Genomics
Single cell RNAseq

value: gonad

tag: developmental stage

value: Amh; Inhbb

value: Amh+/+; Inhbb+/+ (Control)


title: HDAC3KO_2

description: basal expression

tag: strain


title: RRBS_tumor_MCR_LWB-4-85


title: DSP-1001660003684-A-H05

value: Pancreas

value: Untreated


title: Control_ovary_1


title: DSP-1001660003684-A-E10


title: HDAC3KO_1

description: basal expression


title: LNCaP vehicle

city: New York

first: Marcin

last: Imielinski

state: NY

address: 413 E 69th Street

department: Pathology and Laboratory Medicine

institute: Weill Cornell Medicine

data_processing:
Basecalling was done using Guppy base caller version 3.4.0rc3 run in hac mode
Pore-C reads were aligned using bwa bwasw with parameters -b 5 -q 2 -r 1 -T 15 -z 10. Further processing done by custom Pore-C pipeline found here https://github.com/nanoporetech/pore-c
CpG methylation was called using f5c (https://github.com/hasindu2008/f5c), an optimized and gpu-compatible re-implementation of the call-methylation module in Nanopolish (https://github.com/jts/nanopolish}. Per-read calls were aggregated into per-locus calls using f5c meth-freq -s with the default log-likelihood ratio threshold.
Pair wise contacts using pore_c to-matrix in the pore-c pipelines with default settings
mcool files were made using cooler zoomify with default parameters
Genome_build: GRCh38
Supplementary_files_format_and_content: .csv Pore-C multi-way contacts files where each row is a Pore-C monomer and metadata related to them including the concatemer they blong to.
Supplementary_files_format_and_content: .csv Pore-C pair-wise contacts files where each row is a pair-wise contact
Supplementary_files_format_and_content: .mcool Pore-C pair-wise cooler contacts files
Supplementary_files_format_and_content: .csv Pore-C phased methylation file, phased in two haplotypes with aggregated methylation

source_name: Prostate

growth_protocol: LNCaP cells were purchased from the American Type Culture Collection [ATCC CRL-1740), grown on poly-L-lysine coated plates in 5\% Fetal Bovine Serum (FBS) containing RPMI-1640, and incubated at 37C and 5\% CO2. Cells were passaged twice weekly or once cultures reached 80\% confluency. LNCaP cells were starved of hormone for 72 hours then stimulated with vehicle or 1nM DHT for the indicated time points (0 or 18 hours) before fixing with 1\% formaldehyde.

extract_protocol:
To reverse cross-link, samples were treated with 100 μL 20 mg/mL Proteinase K [Thermo Fisher Scientific cat no. 25530049], 100 μL 10% SDS [Thermo Fisher Scientific cat no. 15553027] and 500 μL 20% v/v Tween-20 [Sigma Aldrich cat no. P9416] in a total volume of 2000 μL with nuclease-free water. Samples were incubated in a thermomixer at 56°C for 18 hours with < 1000 rpm rotation (< 30 sec every 15 min) to prevent condensation inside the lid. In order to purify DNA, the sample was transferred to a 5 mL centrifuge tube. The original tube was rinsed with a further 200 μL of nuclease-free H2O to collect any residual sample, bringing the total sample volume to 2.2 mL. DNA was then purified from the sample using a standard phenol chloroform extraction and ethanol precipitation.
Purified DNA was SPRI size selected for fragments >1.5 kb, then prepared for sequencing using Oxford Nanopore Technologies SQK-LSK109, and sequenced on ONT's MinION, GridIONor PromethION platforms.

treatment_protocol: Cross Linking: 10 million cells were washed three times in chilled 1X phosphate buffered saline (PBS) in a 50 mL centrifuge tube, and pelleted by centrifugation at 500 xg for 5 min. at 4°C between each wash. Cells were re-suspended in 10 mL room temperature 1X PBS 1% formaladehyde [EMD Millipore cat no. 818708] by gently pipetting with a wide-bore tip, then incubated at room temperature for 10 min. To quench the cross-linking reaction, 527 μL of 2.5 M glycine was added to achieve a final concentration of 1% w/v or 125 mM in 10.5 mL. Cells were incubated for 5 min. at room temperature followed by 10 min. on ice. The cross-linked cells were pelleted by centrifugation at 500 xg for 5 min. at 4°C. Restriction enzyme digest: Each cell pellet was resuspended in a mixture of 50 μL of protease inhibitor cocktail [Sigma Aldrich cat no. P8340] in 500 μL of cold permeabilization buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% IGEPAL CA-630) and placed on ice for 15 min. Cells were centrifuged at 500 xg for 10 min. at 4°C after which the supernatant was aspirated and replaced with 200 μL of chilled 1.5X digestion reaction buffer [NEB ] compatible with the restriction enzyme used. Cells were centrifuged again at 500 xg for 10 min. at 4°C, then aspirated and re-suspended in 300 μL of chilled 1.5X digestion reaction buffer. To denature the chromatin, 33.5 μL of 1% w/v SDS [Thermo Fisher Scientific cat no. 15553027] was added to each cell suspension and incubated for exactly 10 min. at 65°C with gentle agitation, and then placed on ice immediately afterwards. To quench the SDS, 37.5 μL of 10% v/v Triton X-100 [Sigma Aldrich cat no. 93443] was added for a final concentration of 1%, followed by incubation for 10 min. on ice. Permeablized cells were then digested with a final concentration of 1 U/μL of either DpnII, NlaIII or HindIII [NEB] brought to volume with nuclease-free water to achieve a final 1X digestion reaction buffer in 450 μL. Cells were then mixed by gentle inversion. Cell suspensions were incubated in a thermomixer at 37°C for 18 hours with periodic < 1000 rpm rotation (< 30 sec every 15 min.) to prevent condensation inside the lid. Proximity ligation and reverse cross-linking: DpnII and NlaIII restriction digests were heat inactivated at 65°C for 20 min. with 300 rpm rotation. HindIII digests were chemically inactivated with a final concentration of 0.1% w/v SDS at 65°C for 20 min. with 300 rpm rotation, then quenched with a final concentration of 1% v/v Triton X-100 [Sigma Aldrich cat no. 93443].Proximity ligation was set up at room temperature with the addition of the following reagents: 100 μL of 10X T4 DNA ligase buffer [NEB], 10 μL of 10 mg/mL BSA and 50 μL of T4 Ligase [NEB M0202L] in a total volume of 1000 μL with nuclease-free water. The ligation was cooled to 16°C and incubated for 6 hours with gentle rotation.

value: Prostate cancer cell line

value: DHT starved


title: RRBS_tumor_LFCR_LWB-4-72

value: LFCR


title: Control_testis 2

source_name: Embryonic testis


title: DSP-1001660003684-A-H04


title: RRBS_tumor_LFCR_LWB-4-69


title: RRBS_tumor_MCR_LWB-4-96


title: DSP-1001660003684-A-H01


title: RRBS_tumor_LFCR_LWB-4-67


title: DSP-1001660003684-A-F11


title: dKO_testis_1

value: Amh -/-; Inhbb -/- (dKO)


title: Donor2 78pmols of RNP CD5-HA ssCTS 100 pmol [RNP-CTS-Ratio-VV-F7_S56]

city: San Francisco

first: Vivasvan

last: Vykunta

state: CA

address: 513 Parnassus Avenue HSW901

institute: Gladstone-UCSF Institute of Genomic Immunology

data_processing:
library strategy: amplicon sequencing
Data was processed to calculate insertions/deletions at the CD5 target site with Crispresso2 version 2.2.7 (Clement et al., 2019) with the following options "--skip_failed", "--default_min_aln_score 60", "--min_average_read_quality 30", " --exclude_bp_from_left 40", " --exclude_bp_from_right 40", "--annotate_wildtype_allele CD5_WT", " --min_frequency_alleles_around_cut_to_plot 0.05", "--expected_hdr_amplicon_seq GGAGAAGGGAGAGAGTGGGAGGTTTCACTTCCTGACCCTCCTCTCTTCTTTCTGCAGTCGCTTCCTGCCTCGGAtacccatacgatgtgcctgattacgcaggatcaCGGCTCAGCTGGTATGACCCAGGTAAGGAAGAGCCACATGGAGAAAGGCCTGGGGCAGGGGGAGAGTGGGGCTGTGGTTTCATCAGGCCATCG", " --coding_seq GCTTCCTGCCTCGGACGGCTCAGCTGGTATGACCCA", and " --ignore_substitutions".
Assembly: hg38

source_name: primary Bulk T human cells

growth_protocol: Cells were activated at 1e6  cells per mL  for 2 days in complete XVivo15 medium (Lonza) (5% fetal bovine serum, 50 µM 2-mercaptoethanol, 10 mM N-acetyl L-cysteine) supplemented with anti-human CD3/CD28 magnetic Dynabeads (CTS, ThermoFisher) in a 1:1 ratio with cells, 500 U mL-1  of IL-2 (UCSF Pharmacy), and 5 ng mL-1  of IL-7 and IL-15 (R&D Systems).

extract_protocol:
5 days after electroporations, genomic DNA was isolated from each sample using DNA QuickExtract (Lucigen, Cat#QE09050) based on manufacturer protocols.
Primers were designed around the guideRNA target site and included adapter sequences. Amplicons were generated by adding 0.5 µL each of forward and reverse primer at 100 µM to 10 µL of QuickExtract, 50 µL of KAPA HiFi HotStart Ready Mix PCR kit (Roche, Cat# 07958935001), and H2O to a total of 100 uL reaction volume. The following PCR thermocycler conditions were followed: 95°C for 3 minutes, 30 cycles of 98°C for 30 seconds followed by 68°C for 30 seconds and 72°C for 30 seconds, and a final 3 minute extension at 72°C. Amplicons were submitted to the Innovative Genomics Institute (IGI) Next Generation Sequencing Core for second PCR reactions and sequencing.

treatment_protocol: GuideRNA/Cas9 ribonucleoprotein complexes (50 pmols unless stated otherwise) targeting CD5 were electroporated into primary Bulk T human cells with indicated dose of a homology directed repair template.

value: primary Bulk T human cells

value: 78pmols of RNP CD5-HA ssCTS 100 pmol


title: Donor2 64pmols of RNP CD5-HA ssCTS 100 pmol [RNP-CTS-Ratio-VV-F8_S64]

value: 64pmols of RNP CD5-HA ssCTS 100 pmol


title: Donor2 50pmols of RNP CD5-HA ssCTS 100 pmol [RNP-CTS-Ratio-VV-F9_S72]

value: 50pmols of RNP CD5-HA ssCTS 100 pmol


title: DSP-1001660003684-A-G01


title: RRBS_tumor_LFCR_LWB-4-63

value: Contralateral normal mammary tissue

value: mouse mammary cancer


title: RRBS_tumor_LFD_LWB-4-48

value: wt

value: LFD


title: Donor1 7pmols of RNP CD5-HA ssCTS 100 pmol [RNP-CTS-Ratio-VV-F6_S48]

value: 7pmols of RNP CD5-HA ssCTS 100 pmol


title: INPUT-rep3

data_processing:
Quality control was performed in Linux by fastqc and multiqc software
Data trimming was performed in Linux by trim_galore
ChIP-seq reads were aligned to the mm10 genome assembly using bowtie2
Bam files were generated from sam files using Samtools.
Peaks were called using macs2
Genome_build: mm10
Supplementary_files_format_and_content: BW files were generated from bam files using bamCoverage
Supplementary_files_format_and_content: peak text files (bed)

extract_protocol:
Lysates were clarified from sonicated nuclei and HDAC3-DNA complexes,FOXK1-DNA complexes or IgG-DNA complexes were isolated with antibody.
Library preparation for ChIP-seq was using KAPA HyperPlus Kit (KAPA Biosystems, #KK8514) according to manufacturer’s protocol. Briefly, 50 μl sample was proceed to End Repair and A-tailing at 65 ℃ for 30 min. Different adapter was added into each sample and incubated at 20 ℃ for 15 min. After ligation, DNA was bound to the beads and washed by 80% ethanol for 3 times, followed by 7-8 cycles PCR. The DNA was performed 1x bead-based cleanup again and the product was ready for sequencing which was done by company (Novogene).

tag: background strain

value: BALB/c


title: DSP-1001660003684-A-E12


title: RRBS_tumor_LFD_LWB-4-47


title: Donor1 21pmols of RNP CD5-HA ssCTS 100 pmol [RNP-CTS-Ratio-VV-F5_S40]

value: 21pmols of RNP CD5-HA ssCTS 100 pmol


title: LNCaP DHT

value: DHT exposed


title: IGG-rep3

value: IgG


title: FOXK1-rep3


title: RRBS_tumor_LFD_LWB-4-46


title: Control_testis 1

value: gonad

value: Amh; Inhbb

value: Amh+/+; Inhbb+/+ (Control)


title: Donor1 35pmols of RNP CD5-HA ssCTS 100 pmol [RNP-CTS-Ratio-VV-F4_S32]

value: 35pmols of RNP CD5-HA ssCTS 100 pmol


title: DSP-1001660003684-A-G07

value: Pancreas

value: Untreated


title: HDAC3-rep3


title: RRBS_tumor_LFD_LWB-4-42


title: Donor1 50pmols of RNP CD5-HA ssCTS 100 pmol [RNP-CTS-Ratio-VV-F3_S24]

value: primary Bulk T human cells


title: DSP-1001660003684-A-E09


title: INPUT-rep2


title: RRBS_tumor_Obese_LWB-4-40

value: Obese


title: IGG-rep2


title: RRBS_tumor_Obese_LWB-4-28

value: Contralateral normal mammary tissue


title: DSP-1001660003684-A-F12


title: FOXK1-rep2


title: Donor2 7pmols of RNP CD5-HA ssCTS 100 pmol [RNP-CTS-Ratio-VV-F12_S96]


title: Donor1 64pmols of RNP CD5-HA ssCTS 100 pmol [RNP-CTS-Ratio-VV-F2_S16]

value: 64pmols of RNP CD5-HA ssCTS 100 pmol


title: DSP-1001660003684-A-G06


title: RRBS_tumor_Obese_LWB-4-27

value: mouse mammary cancer

value: wt


title: HDAC3-rep2


title: Donor2 21pmols of RNP CD5-HA ssCTS 100 pmol [RNP-CTS-Ratio-VV-F11_S88]


title: HG002

data_processing:
Library strategy: Pore-C
Basecalling was done using Guppy base caller version 3.4.0rc3 run in hac mode
Pore-C reads were aligned using bwa bwasw with parameters -b 5 -q 2 -r 1 -T 15 -z 10. Further processing done by custom Pore-C pipeline found here https://github.com/nanoporetech/pore-c
CpG methylation was called using f5c (https://github.com/hasindu2008/f5c), an optimized and gpu-compatible re-implementation of the call-methylation module in Nanopolish (https://github.com/jts/nanopolish}. Per-read calls were aggregated into per-locus calls using f5c meth-freq -s with the default log-likelihood ratio threshold.
Pair wise contacts using pore_c to-matrix in the pore-c pipelines with default settings
mcool files were made using cooler zoomify with default parameters
Genome_build: GRCh38
Supplementary_files_format_and_content: .csv Pore-C multi-way contacts files where each row is a Pore-C monomer and metadata related to them including the concatemer they blong to.
Supplementary_files_format_and_content: .csv Pore-C pair-wise contacts files where each row is a pair-wise contact
Supplementary_files_format_and_content: .mcool Pore-C pair-wise cooler contacts files
Supplementary_files_format_and_content: .csv Pore-C phased methylation file, phased in two haplotypes with aggregated methylation

source_name: Blood

growth_protocol: Human B lymphocytes (GM12878) [Coriell Institute] and HG002 cells [Coriell Institute] were each maintained in suspension at a concentration greater than 200,000 cells/mL in RPMI-1640 [ATCC 30-2001] supplemented with 15% fetal bovine serum (FBS) and 1% penicillin/streptomycin. HCC1954 [ATCC CRL-2388] human breast cancer cells were maintained using a subculture ratio of 1:4 every three days in RPMI-1640 (ATCC 30-2001) supplemented with 10% FBS and 1% penicillin/streptomycin.

value: EBV transformed lymphoblastoid cell line


title: Donor2 35pmols of RNP CD5-HA ssCTS 100 pmol [RNP-CTS-Ratio-VV-F10_S80]


title: INPUT-rep1

value: BALB/c


title: DSP-1001660003684-A-F03


title: Donor1 78pmols of RNP CD5-HA ssCTS 100 pmol [RNP-CTS-ratio-VV-F1_S8]

value: 78pmols of RNP CD5-HA ssCTS 100 pmol


title: IGG-rep1


title: DSP-1001660003684-A-F10


title: dKO_testis_2

value: Amh -/-; Inhbb -/- (dKO)


title: Donor2 50pmols of RNP CD5-HA ssDNA 100 pmol [RNP-CTS-Ratio-VV-C9_S71]

value: 50pmols of RNP CD5-HA ssDNA 100 pmol


title: DSP-1001660003684-A-G10


title: RRBS_tumor_ICR_LWB-4-112

value: ICR


title: RRBS_tumor_ICR_LWB-4-106


title: DSP-1001660003684-A-G03


title: FOXK1-rep1


title: Donor2 78pmols of RNP CD5-HA ssDNA 100 pmol [RNP-CTS-Ratio-VV-C7_S55]

value: 78pmols of RNP CD5-HA ssDNA 100 pmol


title: RRBS_tumor_ICR_LWB-4-105


title: Donor1 7pmols of RNP CD5-HA ssDNA 100 pmol [RNP-CTS-Ratio-VV-C6_S47]

value: 7pmols of RNP CD5-HA ssDNA 100 pmol


title: RRBS_tumor_Control_LWB-4-13

value: Control


title: RRBS_tumor_Obese_LWB-4-22


title: DSP-1001660003684-A-G02

value: Pancreas


title: DSP-1001660003684-A-F07

value: Untreated


title: RRBS_tumor_ICR_LWB-4-102


title: RRBS_tumor_ICR_LWB-4-103


title: FOXK1KO_VSV-1

treatment_protocol: RAW264.7 cells were stimulated with  vesicular stomatitis virus for 8h

value: 8h after vesicular stomatitis virus infection


title: RRBS_tumor_Control_LWB-4-10


title: DSP-1001660003684-A-F01


title: FOXK1KO_VSV-2


title: FOXK1KO_VSV-3


title: Donor1 21pmols of RNP CD5-HA ssDNA 100 pmol [RNP-CTS-Ratio-VV-C5_S39]

value: primary Bulk T human cells

value: 21pmols of RNP CD5-HA ssDNA 100 pmol


title: DSP-1001660003684-A-F08


title: DSP-1001660003684-A-F05


title: DSP-1001660003684-A-E06


title: Donor2 64pmols of RNP CD5-HA ssDNA 100 pmol [RNP-CTS-Ratio-VV-C8_S63]

value: 64pmols of RNP CD5-HA ssDNA 100 pmol


title: DSP-1001660003684-A-E11


title: RRBS_tumor_Control_LWB-4-05

value: Contralateral normal mammary tissue

value: mouse mammary cancer


title: HDAC3KO_VSV-3


title: HDAC3-rep1


title: Donor1 64pmols of RNP CD5-HA ssDNA 100 pmol [RNP-CTS-Ratio-VV-C2_S15]


title: Donor1 35pmols of RNP CD5-HA ssDNA 100 pmol [RNP-CTS-Ratio-VV-C4_S31]

value: 35pmols of RNP CD5-HA ssDNA 100 pmol


title: HDAC3KO_VSV-1

value: BALB/c


title: DSP-1001660003684-A-D11


title: RRBS_tumor_Control_LWB-4-01

value: wt


title: HDAC3KO_VSV-2


title: DSP-1001660003684-A-E07


title: DSP-1001660003684-A-F06


title: Donor2 7pmols of RNP CD5-HA ssDNA 100 pmol [RNP-CTS-Ratio-VV-C12_S95]


title: tumor_MCR_LWB-4-96

data_processing:
The reads were mapped to mouse genome (mm10) by TopHat (version 2.0.7).
The aligned reads were counted using HTSeq-count from HTSeq package (version 0.5.3p9).
Differential expression was performed using DESeq2
Assembly: mm10
Supplementary files format and content: raw fastq file (paired end)
Supplementary files format and content: processed data: DESeq2 normalized read counts in .txt format

extract_protocol:
total RNA was extracted using TRIzol reagent, and quality measured using Agilend 2100 Bioanalyzer
Illumina TruSeq Stranded Total RNA Library Preparation Kit, sequenced using a 2x76 bases paired-end protocol on the Illumina HiSeq 2000 instrument

value: MCR


title: tumor_MCR_LWB-4-95


title: Donor2 21pmols of RNP CD5-HA ssDNA 100 pmol [RNP-CTS-Ratio-VV-C11_S87]


title: WT_VSV-3

value: wild type


title: WT_VSV-2


title: Donor1 78pmols of RNP CD5-HA ssDNA 100 pmol [RNP-CTS-ratio-VV-C1_S7]


title: Donor1 50pmols of RNP CD5-HA ssDNA 100 pmol [RNP-CTS-Ratio-VV-C3_S23]

value: 50pmols of RNP CD5-HA ssDNA 100 pmol


title: Donor2 35pmols of RNP CD5-HA ssDNA 100 pmol [RNP-CTS-Ratio-VV-C10_S79]


title: DSP-1001660003684-A-F04

data_processing:
Library strategy: NanoString whole-transcriptome digital spatial profiling
Process FASTQ sequencing files (from Illumina NGS run) to DCC digital count files using Nanostring GeoMx NGS Pipeline v1.0
Generate raw and normalized count matrices using Nanostring azorius and hydra scripts, as described in associated manuscript
Assembly: Nanostring GeoMx human whole transcriptome atlas; found in geomx_ngs_data_second_acquisition_WTA_Hs_R_NGS_WTA_v1.0.pkc
Supplementary files format and content: Txt file of uncollapsed raw counts matrix; found in hPDAC_WTA_20210222T2101_TargetCountMatrix.txt
Supplementary files format and content: Txt file of bioprobe QC counts matrix; found in hPDAC_WTA_20210222T2101_BioProbeCountMatrix.txt
Supplementary files format and content: Txt file of negative probe normalized counts matrix; found in hPDAC_WTA_20210222T2101_NegNorm_TargetCountMatrix.txt
Supplementary files format and content: Txt file of q3 normalized counts matrix; found in hPDAC_WTA_20210222T2101_Q3Norm_TargetCountMatrix.txt


title: Ecoli DIP - PCR

city: Houston

first: Tao

middle: P.

last: Wu

state: TX

address: One Baylor Plaza, MS BCM225

department: Molecular and Human Genetics

institute: Baylor College of Medicine

data_processing:
Library strategy: DIP-seq
Raw reads were first trimmed using cutadapt (1.18) for illumina TruSeq adatper
Trimmed reads were aligned to the reference genome using bowtie2 (v2.3.5.1) with default parameters
6mA peaks were identified using MACS3 (3.0.0a6) using input as control
Supplementary_files_format_and_content: peak text files

organism: Escherichia coli

source_name: E. coli

extract_protocol:
Genomic DNA was extrated using DNeasy Blood and Tissue Kit according to the manufacturer's instructions (Qiagen, 69506)
Genomic DNA was fragmentized to 100-300 bp using Covaris S220 Focused-ultrasonicator. Fragmented gDNA was ligated to TruSeq adaptor using NEBNext Ultra™ II DNA Library Prep Kit for Illumina (NEB, E7645S). 6mA DIP enrichemnt was performed using anti-6mA antibody (CST, D9D9W). Unmodified control DNA was made by amplifying DIP enriched DNA using Q5 DNA polymerase (NEB, M0492S). Nitrite treatment was performed with both native and amplified DNA. Indexed librarier were constructed using NEB ultra ii library prep kit.

value: wild-type

tag: dip antibody

value: 6mA (CST D9D9W)


title: RRBS_tumor_Control_LWB-4-02

tag: cell type

value: Control


title: tumor_MCR_LWB-4-90


title: DSP-1001660003684-A-D07

extract_protocol:
In brief, we sectioned clinical FFPE blocks at 5 um onto SuperFrost Plus microscopy slides and then followed the manufacturer instructions for RNA (NanoString) with minor modifications as noted in the associated manuscript.
Libraries were constructed according to manufacturer protocols (NanoString) for sequencing on a NovoSeq S2 (Illumina) with the following paired end read configuration: read 1, 27 nt; read 2, 27 nt; index 1, 8 nt; index 2, 8 nt.

value: Pancreas


title: DSP-1001660003684-A-F02

value: Untreated


title: Donor2 50pmols of RNP - - [RNP-CTS-Ratio-VV-B9_S167]

value: 50pmols of RNP - -


title: DSP-1001660003684-A-E05


title: tumor_LFCR_LWB-4-72

value: LFCR


title: Ecoli dam/dcm Mut  - PCR

data_processing:
Library strategy: NT-seq
sequencing reads were trimmed using cutadapt (v1.18) to remove adaptors. Duplicated reads were removed using BBMAP (v38.84)34 clumpify package.
Fastq reads and fasta reference were converted to AT-only format (convert all purine to A and all thymine to T). Converted fastq reads were aligned to reference using bowtie2 (v2.3.5.1)
AT only sam files were converted back to sam files with original reads using custom python scripts. NM and MD tags were recalculated using samtools (1.9) calmd. The alignments in sam files were filtered by recreated MD tag to keep allowed base mutation (A to G and C to T)
Base count at each genomic location was generated by igvtools (v2.5.3)
Genome_build: NC_000913.3
Supplementary_files_format_and_content: Comma-separated values

extract_protocol:
Genomic DNA was extrated using DNeasy Blood and Tissue Kit according to the manufacturer's instructions (Qiagen, 69506)
Genomic DNA was fragmentized to 100-300 bp using Covaris S220 Focused-ultrasonicator. Fragmented gDNA was ligated to TruSeq adaptor using NEBNext Ultra™ II DNA Library Prep Kit for Illumina (NEB, E7645S). Unmodified control DNA was made by amplifying adaptor-ligated DNA using Q5 DNA polymerase (NEB, M0492S). Nitrite treatment was performed in both native and amplified DNA. Indexed libraries were constructed using NEB ultra ii library prep kit.

value: dam/dcm mutant


title: Donor2 64pmols of RNP - - [RNP-CTS-Ratio-VV-B8_S159]

value: primary Bulk T human cells

value: 64pmols of RNP - -


title: Ecoli dam/dcm Mut - native


title: DSP-1001660003684-A-D10


title: Donor2 78pmols of RNP - - [RNP-CTS-Ratio-VV-B7_S151]

value: 78pmols of RNP - -


title: DSP-1001660003684-A-E08


title: WT_VSV-1

value: 8h after vesicular stomatitis virus infection


title: Donor1 21pmols of RNP - - [RNP-CTS-Ratio-VV-B5_S135]

value: 21pmols of RNP - -


title: Ecoli hsdM KO - PCR

value: hsdM KO


title: Donor1 7pmols of RNP - - [RNP-CTS-Ratio-VV-B6_S143]

value: 7pmols of RNP - -


title: Ecoli hsdM KO - native


title: tumor_LFCR_LWB-4-67

value: Contralateral normal mammary tissue

value: mouse mammary cancer

value: wt


title: tumor_LFD_LWB-4-57

value: LFD


title: Ecoli DIP - native

value: wild-type

value: 6mA (CST D9D9W)


title: tumor_MCR_LWB-4-85

value: MCR


title: DSP-1001660003684-A-C09

value: Pancreas

value: Untreated


title: tumor_LFCR_LWB-4-66

value: LFCR


title: tumor_LFCR_LWB-4-63


title: Donor1 35pmols of RNP - - [RNP-CTS-Ratio-VV-B4_S127]

value: primary Bulk T human cells

value: 35pmols of RNP - -


title: Ecoli - native


title: DSP-1001660003684-A-D08


title: Ecoli - PCR


title: tumor_LFD_LWB-4-48


title: DSP-1001660003684-A-E03


title: tumor_LFD_LWB-4-47


title: DSP-1001660003684-A-E04


title: Donor1 64pmols of RNP - - [RNP-CTS-Ratio-VV-B2_S111]

value: 64pmols of RNP - -


title: DSP-1001660003684-A-E01


title: Ecoli Input - PCR


title: tumor_LFCR_LWB-4-69


title: Donor2 7pmols of RNP - - [RNP-CTS-Ratio-VV-B12_S184]


title: Ecoli Input - native


title: tumor_LFD_LWB-4-46


title: DSP-1001660003684-A-D09


title: tumor_LFD_LWB-4-42


title: Medio-Basal Hypohtalamus - May/Anestrus - 1st replicate

data_processing:
Image analyses and base calling were performed using the HiSeq Control Software and Real-Time Analysis component (Illumina). Demultiplexing was performed using Illumina's conversion software (bcl2fastq 2.20). The quality of the raw data was assessed using FastQC from the Babraham Institute and the Illumina software SAV (Sequencing Analysis Viewer).
A splice junction mapper, TopHat 2.1.1 (using Bowtie 2.3.5.1), was used to align the RNA-Seq reads to the Capra hircus genome (NCBI, Capra hircus ARS1) with a set of gene model annotations (genes.gtf downloaded from NCBI on May 25 2020 ; release 103).
Final read alignments having more than 6 mismatches were discarded. Samtools (v1.9) was used to sort the alignment files. Then, the counting was performed with Featurecounts 2.0.0. As the data is from a strand-specific assay, the read has to be mapped to the opposite strand of the gene (-s 2 option).
Assembly: Capra hircus ARS1
Supplementary files format and content: tab-delimited text files include raw gene counts for every gene and every sample

organism: Capra hircus

value: Alpine

value: adult goat

value: May/Anestrus

value: Brain - Hypothalamus


title: Donor1 50pmols of RNP - - [RNP-CTS-Ratio-VV-B3_S119]

value: 50pmols of RNP - -


title: Donor1 78pmols of RNP - - [RNP-CTS-Ratio-VV-B1_S103]

value: 78pmols of RNP - -


title: DSP-1001660003684-A-C05


title: Donor2 no electro 0pmols of RNP - - [RNP-CTS-Ratio-VV-A7_S120]

value: no electro 0pmols of RNP - -


title: DSP-1001660003684-A-D04


title: Medio-Basal Hypohtalamus - May/Anestrus - 2nd replicate


title: DSP-1001660003684-A-E02


title: tumor_Obese_LWB-4-28

value: Contralateral normal mammary tissue

value: mouse mammary cancer

value: wt

value: Obese


title: Medio-Basal Hypohtalamus - January/Luteal phase - 2nd replicate

value: January/Luteal phase


title: DSP-1001660003684-A-D05

value: Pancreas

value: Untreated


title: Donor1 electro only 0pmols of RNP - - [RNP-CTS-Ratio-VV-A4_S112]

value: primary Bulk T human cells

value: electro only 0pmols of RNP - -


title: Donor2 21pmols of RNP - - [RNP-CTS-Ratio-VV-B11_S183]

value: 21pmols of RNP - -


title: DSP-1001660003684-A-D12


title: tumor_Obese_LWB-4-27


title: Medio-Basal Hypohtalamus - January/Luteal phase - 1st replicate

value: Alpine


title: tumor_Obese_LWB-4-22


title: tumor_Obese_LWB-4-26


title: Medio-Basal Hypohtalamus - January/Follicular phase - 1st replicate

value: adult goat

value: January/Follicular phase


title: Donor1 no electro 0pmols of RNP - - [RNP-CTS-Ratio-VV-A1_S104]


title: Donor2 electro only 0pmols of RNP - - [RNP-CTS-Ratio-VV-A10_S128]


title: DSP-1001660003684-A-D03


title: tumor_Control_LWB-4-13

value: Control


title: tumor_Obese_LWB-4-40


title: Donor2 G472 CD5-HA ssDNA CTS 4 pmol [CD5-NGS-revision-VVPlate-2F12_S176]

value: G472 CD5-HA ssDNA CTS 4 pmol


title: Donor2 35pmols of RNP - - [RNP-CTS-Ratio-VV-B10_S175]

value: 35pmols of RNP - -


title: 16D LTenza shRb1_shTp53 2

city: Los Angeles

first: Andrew

middle: Scott

last: Goldstein

address: 610 Charles E Young Dr East

department: Urology

institute: University of California, Los Angeles

data_processing:
The Partek flow was used for the data analysis. The alignment was performed using STAR and RSEM with assembly as hg38 and the aligner index as whole genome. The hg38 – Ensembl GRch38 was used for gene feature annotation. For normalization of transcripts counts, the normalization method, TPM, was used.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

growth_protocol: 16D cells were maintained in RPMI + 10% FBS + 1% Penn/Strep

extract_protocol:
The RNA was isolated by RNeasy Mini Kit from Qiagen. The integrity of total RNA was examined by the Agilent 4200 TapeStation System.
Libraries for RNA-Seq were constructed with Nugen Universal plus mRNA-Seq Kit to generate strand-specific RNA-seq libraries. The workflow consists of poly(A) RNA selection, RNA fragmentation and double-stranded cDNA generation using a mixture of random and oligo(dT) priming, followed by end repair to generate blunt ends, adaptor ligation, strand selection, and PCR amplification to produce the final libraries. Amplified libraries were quantified by Qubit dsDNA HS (High Sensitivity) Assay Kit, and quality-checked by the Agilent 4200 TapeStation System. Different index adaptors were used for multiplexing samples in one sequencing lane. Sequencing was performed with HiSeq3000 sequencer to produce 50 base-pair single-end reads (1 x 50 bp).

value: Prostate cancer

value: WT

value: LTenza  shRb1_shTp53


title: tumor_ICR_LWB-4-112

value: Contralateral normal mammary tissue

value: mouse mammary cancer

value: wt

value: ICR


title: Donor2 G472 CD5-HA ssDNA 4 pmol [CD5-NGS-revision-VVPlate-2F11_S182]

value: G472 CD5-HA ssDNA 4 pmol


title: Medio-Basal Hypohtalamus - January/Follicular phase - 2nd replicate

value: Brain - Hypothalamus


title: 16D LTenza shRb1_shTp53 1


title: DSP-1001660003684-A-C06

value: Pancreas

value: Untreated


title: DSP-1001660003684-A-D01


title: Donor2 G472 CD5-HA dsDNA CTS 4 pmol [CD5-NGS-revision-VVPlate-2F10_S174]

value: primary Bulk T human cells

value: G472 CD5-HA dsDNA CTS 4 pmol


title: 16D LTenza shTp53 2

value: LTenza  shTp53


title: 16D LTenza shRb1_shTp53 3


title: DSP-1001660003684-A-D06


title: DSP-1001660003684-A-C11


title: 16D LTenza shTp53 1


title: DSP-1001660003684-A-D02


title: 16D LTenza shTp53 3


title: tumor_ICR_LWB-4-106


title: tumor_ICR_LWB-4-105


title: Donor1 G472 CD5-HA ssDNA CTS 4 pmol [CD5-NGS-revision-VVPlate-2F06_S142]


title: tumor_ICR_LWB-4-102


title: tumor_Control_LWB-4-05

value: Control


title: Donor2 G472 CD5-HA dsDNA 4 pmol [CD5-NGS-revision-VVPlate-2F09_S166]

value: G472 CD5-HA dsDNA 4 pmol


title: tumor_ICR_LWB-4-103


title: Donor2 G472 RNP only - [CD5-NGS-revision-VVPlate-2F08_S158]

value: G472 RNP only -


title: DSP-1001660003684-A-B11


title: 16D LTenza shRb1 3

value: Prostate cancer

value: LTenza  shRb1


title: tumor_Control_LWB-4-10


title: DSP-1001660003684-A-B10


title: 16D LTenza shRb1 2

value: WT


title: 16D LTenza shScr 3

value: LTenza  shScr


title: Donor2 no electro No HDRT - [CD5-NGS-revision-VVPlate-2F07_S150]

value: no electro No HDRT -


title: 16D LTenza shRb1 1


title: Mouse_Fibroblast_rep6

city: Lausanne

first: Jerome

last: Feige

address: EPFL Innovation Park, Building H

department: Musculo-Skeletal Health

country: Switzerland

institute: Nestle Institute Of Health Sciences

description: Murine growth arrested embryonic fibroblasts - GAeFib (Fibro)

data_processing:
Sequencing raw data (bcl) were demultiplexed and transformed in fastq files using cassava v1.8.2.
The fastq files were aligned against the reference genome by RNAstar v2.5.3a.
The raw sequencing counts per gene were generated using htseq_count v2.16.2 using gencode.v25.annotation.exon.tls1.tlsNA-nopseudogene.gff3 or  Mus_musculus.GRCm38.93_proteinCoding_lincRNA.gtf.
To eliminate reads that were mapped on genomes from both human and mouse species we used picard tools.  Readnames from mouse mapped bam were filtered out of human mapped bam using picard FilterSamReads tools as well as  readnames from human mapped bam were filtered out of mouse mapped bam.
Assembly: hs_GRCh38.p2
Assembly: GRCm38
Supplementary files format and content: Comma separated value file including counts per gene (row)  for each sample (column)

source_name: Fibro

growth_protocol: hiPSCs alone or in combination with support cell types were prepared for 3D-aggregation by adding a total of 5.5×106 cells per-well in Corning Costar ultra-low attachment 6-well plates (CLS3471, Sigma Aldrich) in STEMdiff APEL2 medium (05270, STEMCELL Technologies) supplemented with 10 μM ROCK inhibitor (Y-27632, 1254, Tocris Bioscience) with constant shaking (Orbi-Shaker CO2, Benchmark Scientific) at 95 rpm at 37 °C and 8% CO2 overnight.

extract_protocol:
RNA was extracted using RNAdvance Tissue Kit (Beckman Coulter). Quality control was performed with Fragment Analyzer (Advanced Analytical).
Libraries were quantified using Quant-iT Picogreen (Invitrogen, Carlsbad, California, USA) on a Spectramax M2 (Molecular Devices, Sunnyvale, California, USA). Size pattern was controlled using a Fragment Analyzer-96 with the DNF-474-0500 High Sensitivity NGS Fragment Analysis Kit (Agilent Technologies, Santa Clara, California, USA).
Libraries (Average size: 295 bp) were pooled at an equimolar ratio and clustered at a concentration of 9 pM on a single read sequencing flow cell.

treatment_protocol: For Wnt/FGF pathway stimulation, the medium was then replaced with STEMdiff APEL2 medium (05270, STEMCELL Technologies), supplemented with 2.5 μM of GSK3-inhibitor CHIR99021 (Tocris Bioscience) for 6 days.

tag: time

value: Fibroblast

tag: group

value: NoTreat


title: DSP-1001660003684-A-A11


title: 16D LTenza shScr 2


title: Donor1 G472 CD5-HA dsDNA CTS 4 pmol [CD5-NGS-revision-VVPlate-2F04_S126]


title: DSP-1001660003684-A-C01


title: DSP-1001660003684-A-C10


title: DSP-1001660003684-A-C12


title: Donor1 G472 CD5-HA ssDNA 4 pmol [CD5-NGS-revision-VVPlate-2F05_S134]

value: G472 CD5-HA ssDNA 4 pmol


title: Donor1 G472 RNP only - [CD5-NGS-revision-VVPlate-2F02_S110]


title: tumor_Control_LWB-4-02

value: Contralateral normal mammary tissue

value: mouse mammary cancer

value: wt


title: tumor_Control_LWB-4-01


title: 16D LTenza cMyc 2

value: LTenza  cMyc


title: Mouse_Fibroblast_rep5


title: DSP-1001660003684-A-C08

value: Pancreas

value: Untreated


title: Donor1 G472 CD5-HA dsDNA 4 pmol [CD5-NGS-revision-VVPlate-2F03_S118]

value: primary Bulk T human cells


title: 16D LTenza shScr 1


title: Donor1 no electro No HDRT - [CD5-NGS-revision-VVPlate-2F01_S102]


title: DSP-1001660003684-A-C03


title: Donor2 G472 CD5-HA ssDNA CTS 20 pmol [CD5-NGS-revision-VVPlate-2E12_S168]

value: G472 CD5-HA ssDNA CTS 20 pmol


title: Mouse_Fibroblast_rep3


title: Mouse_Fibroblast_rep4


title: DSP-1001660003684-A-C07


title: Donor2 G472 CD5-HA dsDNA CTS 20 pmol [CD5-NGS-revision-VVPlate-2E10_S173]

value: G472 CD5-HA dsDNA CTS 20 pmol


title: DSP-1001660003684-A-B09


title: Mouse_Fibroblast_rep1

description: Murine embryonic endothelial cells - eEC (Endo)


title: Donor2 G472 CD5-HA ssDNA 20 pmol [CD5-NGS-revision-VVPlate-2E11_S181]

value: G472 CD5-HA ssDNA 20 pmol


title: 16D LTenza FUCRW 3

value: Prostate cancer

value: LTenza FUCRW


title: Donor2 no electro No HDRT - [CD5-NGS-revision-VVPlate-2E07_S149]


title: Mouse_Endothelial_rep6

source_name: Endo

value: Enothelial


title: 16D LTenza FUCRW 1

value: WT


title: Donor1 G472 CD5-HA ssDNA CTS 20 pmol [CD5-NGS-revision-VVPlate-2E06_S141]


title: DSP-1001660003684-A-B02


title: Mouse_Endothelial_rep4


title: 16D LTenza cMyc 1


title: DSP-1001660003684-A-B06


title: Mouse_Fibroblast_rep2

value: Fibroblast


title: DSP-1001660003684-A-B05


title: Donor2 G472 CD5-HA dsDNA 20 pmol [CD5-NGS-revision-VVPlate-2E09_S165]

value: G472 CD5-HA dsDNA 20 pmol


title: DSP-1001660003684-A-C02


title: 16D Naïve 3

value: Naive


title: Mouse_Endothelial_rep1

value: NoTreat


title: 16D Naïve 2


title: DSP-1001660003684-A-A03


title: Mouse_Endothelial_rep5


title: Donor1 G472 CD5-HA ssDNA 20 pmol [CD5-NGS-revision-VVPlate-2E05_S133]


title: DSP-1001660003684-A-C04


title: DSP-1001660003684-A-B03


title: Mouse_Endothelial_rep3


title: 16D LTenza cMyc 3


title: 11_cold_hfd_H3K4me3

data_processing:
barcode and adapter removal using flexbar 3.4.0
quality trimming using cutadapt
alignment to genome using bowtie2
Assembly: GRCm38
Supplementary files format and content: peaks were called using macs2
Supplementary files format and content: bw files were generated using "bamCoverage --extendReads=200 -bs 10 --effectiveGenomeSize 2652783500  –normalizeUsing BPM"

source_name: iBAT

extract_protocol:
Prior to ChIP, BAT was dissociated using a gentleMACSTM Dissociator (Miltenyi biotec, Germany). The cell suspension was cross linked with 1 % formaldehyde for 10 min at RT and the reaction was quenched with 0.125 M glycine for 5 min to 10 min at RT. Cells were washed twice with cold PBS and PMSF and snap-frozen in liquid nitrogen before storing at −80°C. Frozen pellets were thawed on ice for 30 min to 60 min. Pellets were resuspended in 5 ml lysis buffer 1 (50 m M Hepes, 140 m M NaCl, 1 m M EDTA, 10 % glycerol, 0.5 % NP-40, 0.25 % Triton X-100) by pipetting and then rotated vertically at 4°C for 10 min. Pellets were resuspended in 5 ml lysis buffer 2 (10 m M Tris, 200 m M NaCl, 1 m M EDTA, 0.5 m M EGTA) and incubated at vertical rotation and at room temperature for 10 min. Samples were centrifuged for 5 min at 1350 g at 4°C and supernatant was carefully aspirated. Then, samples were resuspended in 3 ml lysis buffer 3 (10 m M Tris, 100 m M NaCl, 1 m M EDTA, 0.5 m M EGTA, 0.1 % Na-deoxycholate, 0.5 % N-lauroylsarcosine) and were separated into 2 times 1.5 ml in 15 ml polypropylene tubes, in which they were sonicated with the following settings by Bioruptorő Plus sonication: power = high, on interval = 30 s, off interval = 45 s, total time = 10 min (18 cycles of on/off). Sonicated samples were transferred to a 1.5 ml microfuge tube and were centrifuged for 10 min at 16 000 g at 4°C to pellet cellular debris. 10 % of sample solution were stored to be used as input control, while the rest was used for ChIP. To capture different histone modifications, 5 μg to 10 μg of the respective antibodies (Tab S5) were added to the sonicated ChIP reaction and rotated vertically at 4°C overnight. 100 μl Dynabeads (Protein A or Protein G) for each ChIP sample were prepared according to the manufacturer’s instructions, mixed with 1 ml of antibody-bound chromatin and rotated vertically at 4°C for at least 2 h to 4 h. Bound beads were washed at least five times in 1 ml cold RIPA (50 m M Hepes, 500 m M LiCl, 433 1 mM EDTA, 1 % NP-40, 0.7 % Na-deoxycholate) and once in 1 ml cold TE buffer containing 50 mM NaCl. Samples were eluted for 15 min with elution buffer (50 m M Tris, 10 m M EDTA, 1 % SDS) at 65°C and continuously shaken at 700 min −1 . Beads were separated using a magnet and 200 μl supernatant were transferred to fresh microfuge tubes. Input samples were thawed and mixed with 300 μl elution buffer. ChIP/input samples were incubated at 65°C in a water bath overnight to reverse the cross linking reaction. TE buffer was added at room temperature to dilute SDS in both ChIP and input samples. For digestion of RNA and protein contamination, RNase A was added to the samples and incubated in a 37°C water bath for 2 h; then proteinase K was added to a final concentration of 0.2 mg ml −1 and incubated in a 55°C water bath for 2 h. Finally, DNA was extracted using a standard phenol-chloroform extraction method at room temperature and DNA concentrations were measured using a NanoDrop ND-1000 spectrophotometer or Qubit dsDNA HS Assay Kit and stored at −80°C until sequencing.
Total RNA libraries were constructed using a modified protocol of the Illumina TruSeq kit.

treatment_protocol: Wild type C57BL/6N mice were fed chow diet (Ssniff V1554) up to the age of 8 weeks, where the respective cohorts were put on HFD (Ssniff D12492 (I) mod.) for 12 weeks and kept at 4°C for 24 h.

value: iBAT

tag: chip antibody

value: H3K4me3 (Active Motif 39159)

tag: diet

value: highFatDiet

value: cold

tag: mouseid


title: Donor2 G472 RNP only - [CD5-NGS-revision-VVPlate-2E08_S157]

value: G472 RNP only -


title: 16D LTenza FUCRW 2


title: Donor1 no electro No HDRT - [CD5-NGS-revision-VVPlate-2E01_S101]

value: primary Bulk T human cells

value: no electro No HDRT -


title: Enza long term 1 [since_7_30-1_S16]

source_name: 16D CRPC

growth_protocol: 16D CRPC cells were maintained in RPMI + 10% FBS + 1% Penn/Strep

treatment_protocol: For the indicated time (24/48/96/144 hours or long-term), media was supplemented with 10 micromolar enzalutamide.

value: 16D CRPC

value: enzalutamide (long-term)


title: 16D Naïve 1

value: Prostate cancer


title: 11_cold_hfd_H3K4me1

tag: tissue

value: H3K4me1 (Active Motif 39297)


title: Enza long term 3 [since_7_30-3_S18]

tag: cell line


title: DSP-1001660003684-A-B12

source_name: Pancreas

value: Pancreas

value: Untreated


title: Donor1 G472 CD5-HA dsDNA 20 pmol [CD5-NGS-revision-VVPlate-2E03_S117]


title: Mouse_Endothelial_rep2

value: Enothelial


title: Enza long term 2 [since_7_30-2_S17]

value: WT


title: DSP-1001660003683-G-H07


title: Donor1 G472 CD5-HA dsDNA CTS 20 pmol [CD5-NGS-revision-VVPlate-2E04_S125]

value: G472 CD5-HA dsDNA CTS 20 pmol


title: Enza 144 hours 3 [144_hr-3_S15]

value: enzalutamide (144 hours)


title: DSP-1001660003684-A-B07


title: Enza 96 hours 3 [96_hr-3_S12]

value: enzalutamide (96 hours)


title: DSP-1001660003684-A-B08


title: Donor2 G472 CD5-HA dsDNA CTS 100 pmol [CD5-NGS-revision-VVPlate-2D10_S172]

value: G472 CD5-HA dsDNA CTS 100 pmol


title: Donor2 G472 CD5-HA ssDNA CTS 100 pmol [CD5-NGS-revision-VVPlate-2D12_S160]

value: G472 CD5-HA ssDNA CTS 100 pmol


title: 11_cold_hfd_H3K27me3

value: iBAT

value: H3K27me3 (Active Motif 39155)

value: highFatDiet

value: cold


title: Donor2 G472 CD5-HA ssDNA 100 pmol [CD5-NGS-revision-VVPlate-2D11_S180]

value: primary Bulk T human cells

value: G472 CD5-HA ssDNA 100 pmol


title: DSP-1001660003684-A-B01


title: Donor2 G472 CD5-HA dsDNA 100 pmol [CD5-NGS-revision-VVPlate-2D09_S164]

value: G472 CD5-HA dsDNA 100 pmol


title: Enza 96 hours 1 [96_hr-1_S10]

value: 16D CRPC

value: Prostate cancer


title: Donor2 G472 RNP only - [CD5-NGS-revision-VVPlate-2D08_S156]

value: G472 RNP only -


title: Enza 96 hours 2 [96_hr-2_S11]


title: Enza 144 hours 2 [144_hr-2_S14]


title: Donor1 G472 RNP only - [CD5-NGS-revision-VVPlate-2E02_S109]


title: DSP-1001660003683-G-G09

value: Pancreas

value: Untreated


title: Enza 144 hours 1 [144_hr-1_S13]

value: WT


title: DSP-1001660003684-A-A04


title: 10_cold_hfd_H3K27ac

value: H3K27ac (Active Motif 39133)


title: 10_cold_hfd_H3K4me3

value: H3K4me3 (Active Motif 39159)


title: 11_cold_hfd_input


title: Enza 48 hours 2 [48_hr-2_S8]

value: enzalutamide (48 hours)


title: 11_cold_hfd_H3K27ac


title: Enza 48 hours 1 [48_hr-1_S7]


title: Enza 48 hours 3 [48_hr-3_S9]


title: Enza 24 hours 3 [24_hr-3_S6]

value: enzalutamide (24 hours)


title: Donor2 no electro No HDRT - [CD5-NGS-revision-VVPlate-2D07_S148]

value: no electro No HDRT -


title: 10_cold_hfd_H3K27me3

value: iBAT

value: H3K27me3 (Active Motif 39155)


title: DSP-1001660003684-A-A12


title: Donor1 G472 CD5-HA ssDNA CTS 100 pmol [CD5-NGS-revision-VVPlate-2D06_S140]

value: G472 CD5-HA ssDNA CTS 100 pmol


title: Donor1 G472 RNP only - [CD5-NGS-revision-VVPlate-2D02_S108]

value: primary Bulk T human cells


title: DSP-1001660003684-A-A08


title: DSP-1001660003684-A-A09


title: Donor1 G472 CD5-HA ssDNA 100 pmol [CD5-NGS-revision-VVPlate-2D05_S132]

value: G472 CD5-HA ssDNA 100 pmol


title: DSP-1001660003684-A-B04


title: Donor1 G472 CD5-HA dsDNA CTS 100 pmol [CD5-NGS-revision-VVPlate-2D04_S124]

value: G472 CD5-HA dsDNA CTS 100 pmol


title: DSP-1001660003683-G-H12


title: 8_warm_hfd_H3K4me3

value: highFatDiet

value: warm


title: 8_warm_hfd_input


title: 10_cold_hfd_H3K4me1

value: H3K4me1 (Active Motif 39297)

value: cold


title: 8_warm_hfd_H3K27ac


title: Donor1 G472 CD5-HA dsDNA 100 pmol [CD5-NGS-revision-VVPlate-2D03_S116]

value: G472 CD5-HA dsDNA 100 pmol


title: 8_warm_hfd_H3K27me3


title: Donor1 no electro No HDRT - MTX [CD5-NGS-revision-VVPlate-2D01_S100]

value: no electro No HDRT - MTX


title: Enza 24 hours 1 [24_hr-1_S4]

value: 16D CRPC

value: Prostate cancer

value: WT


title: DMSO control 2 [DMSO-2_S2]

value: control


title: 8_warm_hfd_H3K4me1


title: DSP-1001660003683-G-H11

value: Pancreas

value: Untreated


title: Enza 24 hours 2 [24_hr-2_S5]

value: enzalutamide (24 hours)


title: 7_warm_hfd_H3K4me3

value: iBAT

value: H3K4me3 (Active Motif 39159)


title: 10_cold_hfd_input


title: DSP-1001660003683-G-G07


title: DSP-1001660003683-G-H04


title: 7_warm_hfd_H3K4me1


title: Donor2 G472 CD5-HA dsDNA 4 pmol [CD5-NGS-revision-VVPlate-2C09_S163]

value: primary Bulk T human cells

value: G472 CD5-HA dsDNA 4 pmol


title: DSP-1001660003684-A-A10


title: DMSO control 3 [DMSO-3_S3]


title: 7_warm_hfd_H3K27me3

value: H3K27me3 (Active Motif 39155)

value: highFatDiet


title: 7_warm_hfd_H3K27ac

value: H3K27ac (Active Motif 39133)

value: warm


title: Donor2 no electro No HDRT - [CD5-NGS-revision-VVPlate-2C07_S147]

value: no electro No HDRT -


title: Donor2 G472 CD5-HA ssDNA 4 pmol [CD5-NGS-revision-VVPlate-2C11_S179]

value: G472 CD5-HA ssDNA 4 pmol


title: LNCaP, CSS castration + enzalutamide3

source_name: LNCaP

growth_protocol: LNCaP cells were maintained in RPMI + 10% FBS + 1% Penn/Strep

treatment_protocol: For 72 hours of the experiment, cells were grown in RPMI + 10% charcoal stripped serum (CSS) to model castration. Addition of 0.5 nanomolar DHT was used for the control. Addition of 10 micromolar enzalutamide was used to model AR inhibition in the presence of CSS + DHT. The combined castration + enzalutamide group contained 10% CSS + 10 micromolar enzalutamide (no DHT).

value: LNCaP

value: castration + enzalutamide


title: DSP-1001660003684-A-A05


title: DMSO control 1 [DMSO-1_S1]

value: 16D CRPC

value: Prostate cancer

value: WT


title: LNCaP, CSS castration + enzalutamide 1


title: LNCaP, CSS + DHT + enzalutamide 3

value: enzalutamide


title: Donor2 G472 RNP only - [CD5-NGS-revision-VVPlate-2C08_S155]

value: G472 RNP only -


title: Donor2 G472 CD5-HA ssDNA CTS 4 pmol [CD5-NGS-revision-VVPlate-2C12_S152]

value: G472 CD5-HA ssDNA CTS 4 pmol


title: 7_warm_hfd_input

value: iBAT


title: DSP-1001660003684-A-A07

value: Pancreas

value: Untreated


title: LNCaP, CSS castration + enzalutamide 2


title: 5_cold_ncd_H3K4me3

value: H3K4me3 (Active Motif 39159)

value: chow

value: cold


title: DSP-1001660003684-A-A06


title: LNCaP, CSS + DHT + enzalutamide 2


title: Donor1 G472 CD5-HA ssDNA 4 pmol [CD5-NGS-revision-VVPlate-2C05_S131]

value: primary Bulk T human cells


title: Donor1 G472 CD5-HA ssDNA CTS 4 pmol [CD5-NGS-revision-VVPlate-2C06_S139]


title: DSP-1001660003684-A-A02


title: Donor1 G472 CD5-HA dsDNA CTS 4 pmol [CD5-NGS-revision-VVPlate-2C04_S123]

value: G472 CD5-HA dsDNA CTS 4 pmol


title: LNCaP, CSS + DHT + enzalutamide 1


title: DSP-1001660003684-A-A01

value: No Template Control


title: DSP-1001660003683-G-H08


title: 5_cold_ncd_H3K27me3

value: H3K27me3 (Active Motif 39155)


title: LNCaP, CSS castration 3

value: LNCaP

value: castration


title: DSP-1001660003683-G-H10


title: Donor1 G472 RNP only - [CD5-NGS-revision-VVPlate-2C02_S107]


title: 5_cold_ncd_H3K27ac

value: H3K27ac (Active Motif 39133)


title: LNCaP, CSS castration 2

value: Prostate cancer

value: WT


title: 5_cold_ncd_input


title: Donor1 G472 CD5-HA dsDNA 4 pmol [CD5-NGS-revision-VVPlate-2C03_S115]

value: G472 CD5-HA dsDNA 4 pmol


title: Donor1 no electro No HDRT - [CD5-NGS-revision-VVPlate-2C01_S99]

value: no electro No HDRT -


title: 5_cold_ncd_H3K4me1

value: iBAT

value: H3K4me1 (Active Motif 39297)


title: DSP-1001660003683-G-H09

value: Pancreas

value: Untreated


title: DSP-1001660003683-G-H02


title: LNCaP, CSS castration 1


title: Donor2 G472 CD5-HA ssDNA 20 pmol [CD5-NGS-revision-VVPlate-2B11_S178]

value: G472 CD5-HA ssDNA 20 pmol


title: 4_cold_ncd_H3K4me3

value: H3K4me3 (Active Motif 39159)

value: chow

value: cold


title: Donor2 G472 CD5-HA ssDNA CTS 20 pmol [CD5-NGS-revision-VVPlate-2B12_S144]

value: primary Bulk T human cells

value: G472 CD5-HA ssDNA CTS 20 pmol


title: LNCaP, CSS + DHT control 3

value: LNCaP

value: control


title: DSP-1001660003683-G-H06


title: 4_cold_ncd_H3K27me3

value: H3K27me3 (Active Motif 39155)


title: DSP-1001660003683-G-H05


title: LNCaP, CSS + DHT control 1

value: Prostate cancer


title: Donor2 G472 CD5-HA dsDNA CTS 20 pmol [CD5-NGS-revision-VVPlate-2B10_S170]

value: G472 CD5-HA dsDNA CTS 20 pmol


title: 4_cold_ncd_H3K4me1


title: 4_cold_ncd_H3K27ac

value: H3K27ac (Active Motif 39133)


title: DSP-1001660003683-G-G06


title: 4_cold_ncd_input


title: Donor2 G472 CD5-HA dsDNA 20 pmol [CD5-NGS-revision-VVPlate-2B09_S162]

value: G472 CD5-HA dsDNA 20 pmol


title: DSP-1001660003683-G-H01


title: Donor2 no electro No HDRT - [CD5-NGS-revision-VVPlate-2B07_S146]

value: no electro No HDRT -


title: LNCaP, CSS + DHT control 2

value: WT


title: 2_warm_ncd_H3K4me1

value: iBAT

value: H3K4me1 (Active Motif 39297)

value: warm


title: DSP-1001660003683-G-H03

value: Pancreas

value: Untreated


title: 2_warm_ncd_H3K4me3

value: H3K4me3 (Active Motif 39159)

value: chow


title: 2_warm_ncd_H3K27me3


title: Donor1 G472 CD5-HA ssDNA 20 pmol [CD5-NGS-revision-VVPlate-2B05_S130]

value: primary Bulk T human cells

value: G472 CD5-HA ssDNA 20 pmol


title: DSP-1001660003683-G-G10


title: DSP-1001660003683-G-F12


title: DSP-1001660003683-G-E09


title: DSP-1001660003683-G-G11


title: Donor1 G472 CD5-HA ssDNA CTS 20 pmol [CD5-NGS-revision-VVPlate-2B06_S138]

value: G472 CD5-HA ssDNA CTS 20 pmol


title: Donor2 G472 RNP only - [CD5-NGS-revision-VVPlate-2B08_S154]

value: G472 RNP only -


title: Donor1 G472 CD5-HA dsDNA 20 pmol [CD5-NGS-revision-VVPlate-2B03_S114]


title: 2_warm_ncd_input


title: DSP-1001660003683-G-G12


title: D3614-1

type: RNA

city: Freiburg

first: Marcus

last: Ziemann

state: Baden württemberg

address: Schänzlestraße 1

country: Germany

institute: Albert-Ludwigs-Universität Freiburg

description: Gene expression in deletion strain

hyb_protocol: The labelled RNA was fragmented and hybridized as described by the manufacturer's instructions for Agilent one color microarrays

scan_protocol: Arrays were scanned on the Agilent Technologies Scanner G2505C US90900275, using Agilent Feature Extraction Software 10.7.3.1 and the protocols GE1_107_Sep09 for Cy3 labelled arrays

data_processing: Raw data were processed with the R package Limma. Median signal intensities were normexp background substracted (offset=50) and quantile normalized.

organism: Nostoc sp. PCC 7120 = FACHB-418

source_name: PCC7120, DelAlr3614,replicate 1

label_protocol: DNase-treated RNA was labeled directly, without cDNA synthesis in 2 µg aliquots with the Kreatech “ULS labeling kit for Agilent gene expression arrays” with Cy3 according to the manufacturers protocol. Further details of the labeling and hybridization protocol were published in:  Voß,B. and Hess,W.R. (2014) The identification of bacterial non-coding RNAs through complementary approaches. In Handbook of RNA Biochemistry. WILEY-VCH, Weinheim, Germany, Vol. 2, pp. 787–800.

growth_protocol: Liquid culture in BG11 medium under standard illumination at 30 centigrades.

extract_protocol: RNA was prepared using a hot phenol-based protocol. RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: The protein expression was induced by addition of 1.25 µM CuSO4 for 24 hours to the expression strain and the deletion strain.

value: delta alr3614


title: D3614-2

description: Gene expression in deletion strain

source_name: PCC7120, DelAlr3614,replicate 2


title: Donor1 G472 CD5-HA dsDNA CTS 20 pmol [CD5-NGS-revision-VVPlate-2B04_S122]

value: G472 CD5-HA dsDNA CTS 20 pmol


title: 2_warm_ncd_H3K27ac

value: H3K27ac (Active Motif 39133)


title: DSP-1001660003683-G-G08


title: C3614-2

description: Gene expression in complementary strain

source_name: PCC7120, ComAlr3614,replicate 2

value: Com alr3614


title: DSP-1001660003683-G-G01


title: Patient48

first: Department of Pathology

last: NYU Langone Health

address: 240 East 38th Street

department: Department of Pathology

institute: NYU Langone Health Ambulatory Care Center

description:
16-275
Gene expression of the nCounter PanCancer IO 360 panel for the tumor, microenvironment and immune response.

hyb_protocol: Quality metrics for extracted RNA included both quantitative and qualitative parameters. RNA quantification was performed with the Qubit 2.0 Fluorometer (Life Technologies).

scan_protocol: Qualitative RNA integrity was performed with the Agilent 2100 Bioanalyzer System (Agilent software, Santa Clara, CA, USA) and corresponding RNA kits. Electropherograms showing fragment distribution were reviewed; only cases with an RNA integrity number of >3 were selected.

data_processing: RCC files for tumor samples are direct outputs from NanoString runs. We then extract raw counts for each gene in a sample in R.

source_name: Melanoma

extract_protocol:
Tumor samples were dissected and de-paraffinized using the same methods described in the DNA analysis.
RNA was isolated using the Qiagen RNeasy DSP FFPE Kit, and melanotic samples were purified as the DNA samples were.

value: Melanoma

tag: nf1 status

value: MUT


title: Patient52

description:
17-231
Gene expression of the nCounter PanCancer IO 360 panel for the tumor, microenvironment and immune response.


title: Patient51

description:
17-123
Gene expression of the nCounter PanCancer IO 360 panel for the tumor, microenvironment and immune response.

value: WT


title: 1_warm_ncd_H3K27ac

value: iBAT


title: DSP-1001660003683-G-E12

first: Karthik

last: Jagadeesh

address: 415 Main St

institute: Broad Institute


title: Donor1 G472 RNP only - [CD5-NGS-revision-VVPlate-2B02_S106]


title: Patient50

description:
16-363
Gene expression of the nCounter PanCancer IO 360 panel for the tumor, microenvironment and immune response.


title: C3614-1

description: Gene expression in complementary strain

source_name: PCC7120, ComAlr3614,replicate 1


title: 1_warm_ncd_H3K4me3

value: warm


title: DSP-1001660003683-G-G05

value: Pancreas


title: Patient47

description:
16-095
Gene expression of the nCounter PanCancer IO 360 panel for the tumor, microenvironment and immune response.


title: 1_warm_ncd_H3K4me1

value: H3K4me1 (Active Motif 39297)


title: Patient46

description:
12-148
Gene expression of the nCounter PanCancer IO 360 panel for the tumor, microenvironment and immune response.


title: Donor1 no electro No HDRT - [CD5-NGS-revision-VVPlate-2B01_S98]

value: no electro No HDRT -


title: DSP-1001660003683-G-F10

value: Untreated


title: BL6_iBAT_hfd_cold_3

data_processing:
barcode and adapter removal using flexbar 3.4.0
quality trimming using cutadapt
quantification of transcripts (combination of GENCODE M22 and RNAcentral 5) by salmon
normalisation and differential gene expression analysis using DESeq2
Assembly: GRCm38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
All tissues were dissected, washed with PBS and weighed. They were snap-frozen in liquid nitrogen and stored at -80C. Total RNA was isolated using peqGOLD TriFast (PEQLAB Biotechnologie).
genomic DNA was eliminated following the instructions of the TURBO DNA-freeTM Kit. Total RNA libraries were constructed using the Illumina TruSeq kit following the manufacturer's protocol.

treatment_protocol: Wild type C57BL/6N mice were fed chow diet (Ssniff V1554) up to the age of 8 weeks, where the respective cohorts were put on HFD (Ssniff D12492 (I) mod.) for 12 weeks and kept at 4◦ C for 24 h.

value: hfd

value: cold

tag: batch


title: 1_warm_ncd_input

value: chow


title: Patient49

description:
16-304
Gene expression of the nCounter PanCancer IO 360 panel for the tumor, microenvironment and immune response.


title: Donor2 G472 CD5-HA ssDNA CTS 100 pmol [CD5-NGS-revision-VVPlate-2A12_S136]

value: primary Bulk T human cells

value: G472 CD5-HA ssDNA CTS 100 pmol


title: 1_warm_ncd_H3K27me3

value: H3K27me3 (Active Motif 39155)


title: Donor2 G472 CD5-HA dsDNA 100 pmol [CD5-NGS-revision-VVPlate-2A09_S161]

value: G472 CD5-HA dsDNA 100 pmol


title: Donor2 G472 CD5-HA ssDNA 100 pmol [CD5-NGS-revision-VVPlate-2A11_S177]

value: G472 CD5-HA ssDNA 100 pmol


title: Patient45

description:
11-086
Gene expression of the nCounter PanCancer IO 360 panel for the tumor, microenvironment and immune response.

value: Melanoma


title: Donor2 G472 CD5-HA dsDNA CTS 100 pmol [CD5-NGS-revision-VVPlate-2A10_S169]

value: G472 CD5-HA dsDNA CTS 100 pmol


title: BL6_iBAT_ncd_cold_3

value: ncd


title: DSP-1001660003683-G-F03

treatment_protocol: 14 specimens received no treatment prior to resection; 7 specimens received neoadjuvant chemotherapy, radiotherapy, losartan, and/or nivolumab prior to resection


title: Patient44

description:
11-042
Gene expression of the nCounter PanCancer IO 360 panel for the tumor, microenvironment and immune response.

value: MUT


title: Donor2 G472 RNP only - [CD5-NGS-revision-VVPlate-2A08_S153]

value: G472 RNP only -


title: Patient43

description:
10-230
Gene expression of the nCounter PanCancer IO 360 panel for the tumor, microenvironment and immune response.

value: WT


title: DSP-1001660003683-G-G04

value: Pancreas


title: DSP-1001660003683-G-F09


title: DSP-1001660003683-G-F02


title: Donor1 G472 CD5-HA ssDNA CTS 100 pmol [CD5-NGS-revision-VVPlate-2A06_S137]


title: BL6_iBAT_ncd_rt_3

value: iBAT

value: rt


title: DSP-1001660003683-G-E08

value: Untreated


title: Donor1 G472 CD5-HA ssDNA 100 pmol [CD5-NGS-revision-VVPlate-2A05_S129]


title: Donor1 G472 CD5-HA dsDNA CTS 100 pmol [CD5-NGS-revision-VVPlate-2A04_S121]


title: DSP-1001660003683-G-G03


title: BL6_iBAT_hfd_cold_1

value: hfd

value: cold


title: DSP-1001660003683-G-G02


title: Patient40

description:
16-064
Gene expression of the nCounter PanCancer IO 360 panel for the tumor, microenvironment and immune response.


title: Donor1 G472 CD5-HA dsDNA 100 pmol [CD5-NGS-revision-VVPlate-2A03_S113]

value: primary Bulk T human cells


title: Patient39

description:
15-389
Gene expression of the nCounter PanCancer IO 360 panel for the tumor, microenvironment and immune response.


title: BL6_iBAT_hfd_rt_3


title: Donor2 no electro No HDRT - [CD5-NGS-revision-VVPlate-2A07_S145]

value: no electro No HDRT -


title: BL6_iBAT_ncd_cold_1


title: BL6_iBAT_ncd_cold_2


title: DSP-1001660003683-G-F07


title: Donor1 no electro No HDRT - MT [CD5-NGS-revision-VVPlate-2A01_S97]

value: no electro No HDRT - MT


title: Patient38

description:
15-182
Gene expression of the nCounter PanCancer IO 360 panel for the tumor, microenvironment and immune response.