title: NmuMG, PBRM1, rep1, ChIP

city: Seville

first: Jose

middle: Antonio

last: Guerrero-Martinez

state: Seville

address: Av. Americo Vespucio, N 24

department: Genome Biology

country: Spain

institute: CABIMER

data_processing:
ChIP-seq data were primarily filtered using the FASTQ Toolkit v1.0.0 program
ChIP-seq data were primarily filtered using the FASTQ Toolkit program. Data were aligned using align function from Rsubread package, to map reads to the mm9 mouse reference genome using type = 1, TH1=2 and unique=TRUE parameters. The downstream analysis was performed on bamfiles with duplicates removed using the samtools rmdup command
BamCoverage from Deeptools suite was used to create bigWig files using RPKM normalization
Assembly: mm9
Supplementary files format and content: bigWig

source_name: NmuMG

growth_protocol: Normal murine mammary gland NMuMG epithelial cells were cultured in Dulbecco's modified Eagle's medium containing 10% serum and 10 μg/ml insulin, until reaching 70–80% confluency

extract_protocol:
Cells were crosslinked in 1% formaldehyde for 10 min at room temperature followed by addition of glycine (125 mM final concentration) for 5 min. Nuclei were isolated using lysis buffer 1 (5 mM Pipes pH 8, 85 mM KCl, 0.5% NP40, and complete protease inhibitor cocktail (Roche)) and were lysed using lysis buffer 2 (1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH 8.1, and complete protease inhibitor cocktail (Roche)). Chromatin was sheared into an average size of 500 bp by 8 s pulses (30 s pause between pulses) at 4 °C in the water bath sonicator Bioruptor (Diagenode, Liège, Belgium). Thirty micrograms of chromatin were incubated overnight at 4 °C in rotation, diluted 1:10 in IP buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH 8.1, and 167 mM NaCl, 1% sodium deoxycholate) and with 3 µg of anti-H3K27me3 (39055, Active Motif). Immunoprecipitations were incubated for 2 h at 4 °C in rotation with protein A Dynabeads (Invitrogen) and then washed with wash buffer 1 (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, and 150 mM NaCl, 1% sodium deoxycholate), wash buffer 2 (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, and 500 mM NaCl, 1% sodium deoxycholate), wash buffer 3 (0.25 M LiCl, 1% NP40, 1% sodium deoxycholate, 1 mM EDTA, and 10 mM Tris-HCl pH 8.1), and twice with TE buffer (10 mM Tris-HCl pH 8.0 and 1 mM EDTA). The complexes were eluted from the beads with elution buffer (1% SDS in TE buffer) by incubating twice 10 min at 65 °C. The eluates and the inputs were incubated overnight at 65 °C for de-crosslinking and chipped DNA was purified with phenol:chloroform extraction followed by ethanol precipitation and resuspended in miliQ water
Libraries were prepared with the ThruPLEX DNA-Seq Kit (Takara Bio Europe)

treatment_protocol: Cells where treated with DMSO or BRM014 at indicated times

value: NmuMG

value: normal murine mammary gland epithelial cells

tag: chip antibody

value: PBRM1 (Active motif, #61381)


title: S-27B_536APm

status: Public on Mar 08 2024

type: SRA

city: Munich

first: Hans

middle: Carlo

last: Maurer

state: Bavaria

address: Ismaninger Str. 22

department: II. Medizinische Klinik

country: Germany

institute: Klinikum rechts der Isar

description:
R1 fastq file: cDNA; R2 fastq file: barcode/UMI
536APm_mouse_counts.txt

library_source: transcriptomic

data_processing:
Dropseq (v1.0) – see Macosko et al., PMID: 26000488.
Assembly: Mouse GRCm38 and Human GRCh38, respectively.
Supplementary files format and content: Tab-delimited files contain raw counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: Murine PDAC Cells

extract_protocol:
Qiagen RNeasy Plus Micro Kit (Nr. 74034)
RT and template switch with primers containing Barcode, UMI and adapter. Full length amplification of the cDNA. Fragmentation and Adapter ligation with NEB Ultra II FS kit and final amplification of the 3’-end with Illumina overhangs. Sequencing of cDNA in Read1 and sequencing of Barcode and UMI in Read2.

tag: cell type

value: Murine PDAC Cells

tag: cell line_id

tag: morphology

value: star-like

tag: batch

tag: replicate

tag: genotype

value: KC

tag: dimension

tag: day

tag: environment

value: collagen

tag: treatment

value: untreated


title: NmuMG, PBRM1, rep2, ChIP

library_source: genomic

molecule: genomic DNA

tag: cell line


title: S-27A_536APm


title: NmuMG, rep2, input


title: S-26C_536APm

value: Saracatinib treated


title: Male, kidney, BPA 500mg/kg/day, rep 2

city: Daejeon

first: Soontag

last: Jung

address: 141 Gajeong-ro, Yuseong-gu

department: Developmental and reproductive toxicology

country: South Korea

institute: Korea Institute of Toxicology

data_processing:
The RNA-seq reads were trimmed using BBDuk tool and quality checked with FastQC
Clean reads were mapped to the reference genome using Bowtie2.
The raw read counts were calculated from unique and multiple alignments using Bedtools.
The raw read count data were normalized by trimmed mean of M-values (TMM) method  using edgeR
Assembly: rn6
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Rattus norvegicus

source_name: kidney

extract_protocol:
Total RNA was extracted from all tissues using TRIzol
RNA libraries for RNA-seq were prepared using the QuantSeq 3’ mRNA-Seq Library Prep Kit following manufactuer's protocols

tag: tissue

value: kidney

tag: strain

value: Sprague-Dawley rat

tag: Sex

value: Male

tag: age

value: PND 63


title: S-26B_536APm


title: Gel, cultured, 24h, rep3

city: Beijing

first: sa

last: du

country: China

institute: Peking University School of Stomatology

description:
three dimensional culture
PBS-3

data_processing:
The llumina Novaseq 6000 platform was used to sequence the libraries.
Fastp1 was used to manipulate the raw reads in fastq format, removing low quality reads to obtain clean reads.
HISAT22 was applied to map the clean reads to the reference genome.
Calculate FPKM3 for each gene and obtain read counts for each gene using HTSeq-count4.
Assembly: HISAT22
Supplementary files format and content: Calculate FPKM3 for each gene and obtain read counts for each gene using HTSeq-count4.

growth_protocol: RAW264.7 were cultured at 37 °C in Dulbecco’s modified Eagle’s medium (DMEM, Gibco) supplemented with 10% fetal bovine serum (FBS, Gibco), 100 mg/mL penicillin, and 100 mg/mL streptomycin (Gibco) in a 5% CO2 atmosphere.

extract_protocol:
The hydrogel containing macrophages was frozen in liquid nitrogen. After adding the TRIzol solution (Invitrogen), the samples were thoroughly ground with a glass grinder.
The libraries were then built using the VAHTS Universal V6 RNA-seq Library Preparation Kit according to the manufacturer’s instructions.

treatment_protocol: Cells were suspended in PVA solution (7 wt% PVA in DMEM solution) at a final density of 2 million cells/mL. P1 solution (8 wt% P1 in DMEM solution) for solubilizing flavonoids was prepared. Equal volumes of these two solutions were mixed at room temperature to obtain Gel-Fla. Subsequently, they were transferred to a humidified incubator under standard cultivation conditions (37 °C, 5% CO2).

value: Gel

value: macrophage cells

value: WT


title: Male, liver, vehicle control, rep 1

source_name: liver

value: liver


title: NmuMG, rep1, input

value: NmuMG


title: Male, kidney, BPA 500mg/kg/day, rep 1


title: NmuMG, DMSO-6h, rep2, input

value: normal murine mammary gland epithelial cells


title: S-25C_536APm

value: Poziotinib treated


title: S-25B_536APm

value: Murine PDAC Cells


title: S-25A_536APm

value: star-like


title: Male, kidney, Mix (BPA, BPS, and BPF) 500mg/kg/day, rep 1


title: Male, kidney, vehicle control, rep 3


title: NmuMG, DMSO-6h, rep1, input


title: NmuMG, DMSO-30h, rep2, input


title: Male, kidney, vehicle control, rep 2


title: S-24A_536APm

value: KC

value: Birinapant treated


title: Male, kidney, vehicle control, rep 1


title: NmuMG, DMSO-30h, rep1, input


title: S-24C_536APm

value: collagen


title: S-24B_536APm


title: S-22C_536APm

value: firework

value: Saracatinib treated


title: S-22A_536APm


title: Trehalose_t10_rep3

city: Solna

first: Vicent

last: Pelechano

address: Nobels väg 16

department: MTC

country: Sweden

institute: ScilifeLab - Karolinska Institutet

data_processing:
Base-calling was done using bcl2fastq v2.20.0.422  and for demultiplex, we allowed one mismatch in index1 and one mismatch in index2
For HT-5Pseq data, HT-5Pseq reads were trimmed 3’-sequecing adapter using cutadapt V1.16.  The 8-nt random barcodes on the 5’ ends of reads were extracted and added to the header of fastq file as the UMI using UMItools (v0.5.4). Reads were mapped to the reference genome (SGD R64-1-1 for S. cerevisiae genome by star/2.7.9a  with the parameter --alignEndsType Extend5pOfRead1 to exclude soft-clipped bases on the 5’ end. Duplicated 5’ends of read introduced by PCR during library preparation were removed based on random barcodes sequences using UMItools (v0.5.4).
For The distribution of nucleotide position of 5’ends were performed using Fivepseq package (PMID: 33575643), including relative to start, stop codon and codon specific pausing. Specifically, the unique 5’mRNA reads in biological samples were summed up and normalized to reads per million (rpm). Then the relative position of 5’mRNA reads to all codons of all ORF were summed at each position. The metagene plot was showed as the sum value versus the relative distance from respective codon.
Assembly: Saccharomyces cerevisiae R64-1-1
Supplementary files format and content: Bedgraph files for UMI collapsed reads for positive and negative strand. Reads were collapsed to the first 5´nucleotide.
Library strategy: 5PSeq

organism: Saccharomyces cerevisiae

source_name: respiring yeast

growth_protocol: S. cerevisiae were grown in trehalose-grown medium at 30°C. Trehalose-containing medium includes 20 g/l trehalose (Sigma), 6.7 g/l YNB + (NH4)2SO4 (yeast nitrogen base without amino acids; Difco), amino-acid supplements at a final concentration of 100 mg/l. The medium was buffered at pH 4.8 by adding 14.6 g/l succinic acid and 6 g/l NaOH. Pre-cultures were grown overnight in 250 mL flasks and agitated at 150 rpm. The next day, pre-cultures were diluted to OD600 = 0.05 and grown until an OD600 of ~0.5 was reached.

extract_protocol:
Total RNA was isolated by the standard phenol chloroform method and DNA was removed by DNase I treatment, as described in Zhang & Pelechano, 2021 (PMID:33870233 ) :   The amount of RNA was quantified using  a Nanodrop 2000 Spectrophotometer (Thermo Scientific) and RNA integrity was checked by agarose gel electrophoresis.
For HT5Pseq libraries construction, we used 6 μg of DNA-free total RNA. Samples were directly subjected to RNA ligation. The treated RNA samples were incubated with 100 μM RNA/RNA rP5_RND oligo (final 10 μM) 2h at 25°C with 10 Units of T4 RNA ligase 1 (NEB). Ligated RNA was purified with RNAClean XP (Beckman Coulter), according to the manufacturer’s instructions. RNA was reverse transcribed with Superscript II (Life Technologies) and primed with Illumina PE2 compatible oligos containing random hexamers (20 μM) and oligo-dT (0.05 μM). Reverse transcription reaction was incubated for 10 min at 25°C, 50 min at 42°C and heat inactivation for 15 min at 70°C. To deplete RNA in RNA/cDNA hybrid after reverse transcription, we used sodium hydroxide (40 mM) for incubation 20 min at 65°C and then neutralized with Tris-HCl, pH =7.0 (40 mM). For DSN (Duplex-specific nuclease) based rRNA depletion, we used a mixture of probes targeted the 18S rDNA, 25S rDNA and 5.8S rDNA. The probes were designed to occupy the whole ribosomal RNA regions with consecutive 25-30nt long unmodified DNA oligos. The hybridization of probes (2 μM each) with cDNAs were incubated at 68 °C for 2 minutes before adding pre-warmed DSN buffer mix with 1 Units of DSN enzyme (Evrogen). The reaction then performed at 68 °C for 20 minutes. To inactive DSN enzyme, we added 2X DSN stop solution and incubate 10 min at 68 °C. The final PCR amplification was used 2X Phusion High-Fidelity PCR Master Mix with HF Buffer (NEB) and final 0.1 μM of PE1.0 and corresponding multiplex PE2.0_MTX . The program followed this: 30s 98°C; 15 cycles (20s 98°C; 30s 65°C; 30s 72°C); 7min 72°C. Libraries were size selected using 0.7x-0.9x (v/v) AMpure XP beads (Beckman Coulter) to final 200-500 bp and sequenced by NextSeq 2000 using 55 sequencing cycles for Read 1.  5PSeq methods was performed as previously described (PMID: 26820793). 6µg of total RNA was used as input. In brief a RNA oligo (rP5_RND) containing an Illumina adaptor and unique molecular identifiers (UMI) was ligated to the intermediates of mRNA co-translation degradation (5’P). Ribosomal RNA was depleted using Ribo-Zero Magnetic Gold Kit (Illumina).Libraries were PCR amplified (15 cycles). Ampure beads size selected libraries with an average length of 400 nt were sent for sequencing (llumina NextSeq 2000 instrument).

treatment_protocol: For Antimycin A treatment, Antimycin A was added to a final 2 ug/ml to the medium and incubate for 0, 2 ,5, and 10 min. Cells were fast spined down for 15 seconds at 13,000 g in a tabletop microcentrifudge and flash-frozen in liquid nitrogen.

value: respiring yeast

value: BY4741(MATa his3[delta]1 leu2[delta]0 met15[delta]0 ura3[delta]0)

value: 10 min before Antimycin A (final 2 ug/ml)  treatment


title: S-22B_536APm


title: S-21C_536APm


title: NmuMG, BRM014-6h, rep2, input


title: Male, kidney, BPA 500mg/kg/day, rep 3

value: kidney

value: Sprague-Dawley rat

value: Male

value: PND 63


title: NmuMG, BRM014-6h, rep1, input

value: NmuMG


title: S-21A_536APm


title: NmuMG, BRM014-30h, rep2, input

value: normal murine mammary gland epithelial cells


title: S-26A_536APm


title: Trehalose_t5_rep3

value: 5 min before Antimycin A  (final 2 ug/ml)  treatment


title: S-20C_536APm

value: Murine PDAC Cells


title: NmuMG, BRM014-30h, rep1, input


title: S-20A_536APm


title: Trehalose_t10_rep1


title: S-16C_536APm

value: branched mesenchymal


title: Trehalose_t5_rep2

value: 5 min before Antimycin A (final 2 ug/ml)  treatment


title: NmuMG, H3K27ac, DMSO-6h, rep2, ChIP

value: H3K27ac (Abcam, #ab4729)


title: NmuMG, H3K27ac, DMSO-6h, rep1, ChIP


title: Trehalose_t5_rep1


title: S-16A_536APm

value: KC

value: collagen

value: Birinapant treated


title: S-16B_536APm


title: S-14C_536APm

value: Saracatinib treated


title: S-13C_536APm

value: Poziotinib treated


title: S-14B_536APm


title: Trehalose_t10_rep2

value: respiring yeast

value: BY4741(MATa his3[delta]1 leu2[delta]0 met15[delta]0 ura3[delta]0)

value: 10 min before Antimycin A (final 2 ug/ml)  treatment


title: NmuMG, H3K27ac, DMSO-30h, rep2, ChIP


title: Trehalose_t2_rep3

value: 2 min before Antimycin A (final 2 ug/ml)  treatment


title: S-13B_536APm


title: S-14A_536APm


title: NmuMG, H3K27ac, DMSO-30h, rep1, ChIP


title: Trehalose_t2_rep2


title: S-12C_536APm


title: Trehalose_t2_rep1


title: NmuMG, H3K27ac, BRM014-6h, rep2, ChIP


title: S-12B_536APm


title: S-20B_536APm

value: firework


title: Trehalose_t0_rep3

value: 0 min before Antimycin A (final 2 ug/ml) treatment


title: NmuMG, H3K27ac, BRM014-6h, rep1, ChIP

value: NmuMG

value: normal murine mammary gland epithelial cells


title: S-12A_536APm

value: Murine PDAC Cells


title: Trehalose_t0_rep2


title: S54B_432AP

description:
R1 fastq file: cDNA; R2 fastq file: barcode/UMI
432AP_mouse_counts.txt

value: star-like


title: S54C_432AP


title: S54A_432AP


title: NmuMG, H3K27ac, BRM014-30h, rep2, ChIP


title: NmuMG, H3K27ac, BRM014-30h, rep1, ChIP


title: Trehalose_t0_rep1

value: 0 min before Antimycin A (final 2 ug/ml)  treatment


title: S52C_432AP


title: S52A_432AP


title: S52B_432AP


title: S-13A_536APm


title: S50C_432AP

value: branched mesenchymal


title: S50B_432AP

value: KC


title: Trehalose_t-5_rep2

value: 5 min before Antimycin A  (final 2 ug/ml) treatment


title: S48C_432AP

value: bulk population

value: collagen


title: S50A_432AP


title: NmuMG, DPF2, rep2, ChIP


title: NmuMG, BRD9, rep2, ChIP

value: BRD9 (Active motif, #91413)


title: Trehalose_t-5_rep1

value: respiring yeast

value: 5 min before Antimycin A (final 2 ug/ml) treatment


title: NmuMG, DPF2, rep1, ChIP


title: NmuMG, BRD9, rep1, ChIP


title: S46C_432AP

value: tree-like


title: ParasymN_2

city: Athens GA

first: Nadja

last: Zeltner

state: GA

address: 325 Riverbend road

country: USA

institute: University of Georgia

library_source: transcriptomic single cell

data_processing:
FASTQ files were processed and mapped to reference genome GRCh38-2022.04 and single cells clustered using the PIPseeker v02.01.04 package from Fluentbio.
Assembly: GRCh38-2022.04
Supplementary files format and content: Filtered matrix files (matrix.mtx, barcodes.tsv, features.tsv).

organism: Homo sapiens

growth_protocol: On day 16, SCP spheroids were dissociated using accutase and replated on PO (Sigma, P3655)/LM (R&D Systems, 3400-010-01)/FN (VWR/Corning, 47743-654)-coated plates at 100x10^3 cells/cm2 in parasymN differentiation medium that contains Neurobasal medium, B27, L-Glutamine, 1% FBS (Atlanta Biologicals, S11150), 25 ng/ml GDNF (PeproTech, 450), 25 ng/ml BDNF (R&D Systems, 248-BD), 25 ng/ml CNTF (R&D Systems, 257-NT), 200 μM ascorbic acid (Sigma, A8960), 0.2 mM dbcAMP (Sigma, D0627) and 0.125 μM retinoic acid (Sigma, R2625, add freshly every feeding).

extract_protocol:
Day 30 parasymNs were dissociated using 0.25% Trypsin-EDTA (Gibco, 25200056) and 1mg/ml collagenase NB4 (Nordmark, S17454) for 40 minutes at 4 °C.
Single-cell RNA-seq library was prepared using the PIPseqTM T20 3’ Single Cell RNA Kit v4.0 from Fluentbio. A total of 40,000 cells were loaded for each PIP (Particle-templated instant partition) reaction.

value: hPSC-derived parasympathetic neurons

value: WT

tag: time point

value: day 30


title: ParasymN_1


title: S46B_432AP


title: S46A_432AP


title: LM_snRNA_seq

city: NY

first: Doron

last: Haviv

state: NY

address: 1275 York Avenue

institute: Memorial Sloan Kettering Cancer Center

data_processing:
The demultiplexing, barcoded processing, alignment, and count matrix generation was done using the CellRanger software.
Removing lowly expressed genes
Removing cells with low library wize
Removing doublets
Library size normalization
Assembly: mm10
Supplementary files format and content: h5ad

molecule: nuclear RNA

source_name: Brain

extract_protocol:
FFPE samples were preprocessed on a prototype Singulator™ system. The sample was automatically processed in a NIC+™ cartridge (S2 Genomics #100-215-389) by three 10 min deparaffinization steps (CitriSolv, VWR), rehydrated by successive 1 mL washes of 100%, 100%, 70%, 50%, and 30% ethanol, followed by 2 washes of PBS. The sample was then spun at 1,000g for 3 min and resuspended in 0.5 mL Nuclei Isolation Reagent (NIR, S2 Genomics, #100-063-396) with 0.1 u/mL RNase inhibitor (Protector™, Millipore Sigma, #3335399001); all subsequent solutions had RNase inhibitor. The sample was dissociated to single nuclei in a second NIC+ cartridge with 2 mL of NIR for 10 min followed by a 2 mL wash with Nuclei Storage Reagent (NSR, S2 Genomics, #100-063-405). The single nuclei suspension was spun 500g for 5 min, resuspended in NSR, and counted.
Single-nuclei RNA-Seq of FFPE-isolated nuclei suspensions was performed on Chromium instrument (10X genomics) following the user guide manual for Chromium Fixed RNA Kit, Mouse Transcriptome (SinglePlex)
Illumina NovaSeq S4 platform (R1 – 28 cycles, i7 – 8 cycles, R2 – 90 cycles)

value: Brain


title: GN_E7KI-3 (RNA-seq rep-2)

city: LOS ANGELES

first: Chia-ho

last: Lin

state: CA

address: 6577 MRL. 675 CHARLES E YOUNG DR. SOUTH

institute: UCLA

data_processing:
Reads were aligned to mm10 using STAR (STAR-2.5.4b --alignEndsType EndToEnd --outFilterMultimapNmax 1 --outFilterMismatchNmax 4. TPM was generated using Kallisto. FeatureCounts was used to generate read counts. Differential gene expression analysis were performed using R package Deseq2.
Assembly: mm10
Supplementary files format and content: txt. gene expression

molecule: polyA RNA

source_name: HBG3 ES cell line-derived GN

extract_protocol: not provided

value: HBG3 ES cell line-derived GN

value: Glutamatergic neuron (GN)

value: Dpf2 E7-KI

value: Differentiation to GN


title: Trehalose_t-5_rep3

value: BY4741(MATa his3[delta]1 leu2[delta]0 met15[delta]0 ura3[delta]0)


title: S44C_432AP

value: Murine PDAC Cells

value: thick branched

value: KC


title: S-21B_536APm

value: firework

value: collagen

value: Poziotinib treated


title: GN_E7KI-2 (RNA-seq rep-1)


title: S44B_432AP


title: S44A_432AP


title: GN_E7KO-3 (RNA-seq rep-2)

value: Dpf2 E7-KO


title: GN_E7KO-1 (RNA-seq rep-1)


title: GN_WT-1 (RNA-seq rep-1)


title: S42B_432AP

value: cystic branched


title: S48B_432AP

value: bulk population


title: S42A_432AP


title: GN_WT-3 (RNA-seq rep-2)

value: WT


title: S42C_432AP


title: S48A_432AP


title: 786-O-sgEPAS1-rep1

city: South Bend

first: XUECHUN

last: WANG

state: Indiana

address: university of notre dame

institute: University of Notre Dame

data_processing:
Illumina Casava used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Trimmed seqence reads then were mapped to hg19 whole genome using STAR alinger
Reads counts were extracted and normalized for differential gene expression anlaysis.
Assembly: hg19
Supplementary files format and content: tab-delimited txt file with raw gene counts for every gene and every sample in comparions of 786-O-Ctrl with 786-O-sgEPAS1
Supplementary files format and content: tab-delimited txt file with raw gene counts for every gene and every sample in comparions of with and without -doxycycline induced TNFSF10 knocking down in 786-O.

growth_protocol: All cells lines were  cultured in RPMI1640 supplemented with 10% FBS and 1% penicillin/streptomycin

extract_protocol:
RNA was harvested using Quick-RNA Miniprep Kit (Zymo Research #R1054) .
Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cell lines with Inducible shRNA against TNFSF10 were treated with doxcycline for 48hours to induce the TNFSF10 knocking down.

value: primary clear cell adenocarcinoma

value: HIF2alpha knocking out


title: 786-O-dishTRAIL-Dox-off-rep1

value: inducible TRAIL knocking down


title: 786-O-dishTRAIL-Dox-on-rep1

value: Doxcycline induction for 48 hours


title: 786-O-Ctrl-rep1


title: 786-O-sgEPAS1-rep2


title: 786-O-Ctrl-rep2


title: NPC_E7KI-3 (RNA-seq rep-2)

source_name: HBG3 ES cell line-derived NPC

value: HBG3 ES cell line-derived NPC

value: Neural  Progenitor Cell (NPC)

value: Dpf2 E7-KI

value: Differentiation to NPC


title: S40C_432AP

value: Murine PDAC Cells

value: TEBBO


title: NPC_E7KI-2 (RNA-seq rep-1)


title: 786-O-dishTRAIL-Dox-on-rep2


title: S40B_432AP

value: KC


title: NANA-067-3DIL

city: San Francisco

first: Prescott

last: Woodruff

address: 513 Parnassus

department: DOM

institute: University of California San Francisco

data_processing:
Fastq reads aligned to Ensembl Genome build and annotation GRCh38.95
Read counts per gene output by STAR  --quantMode GeneCounts
STAR parameters: --outFilterType BySJout --outFilterMismatchNoverLmax 0.04 --outFilterMismatchNmax 999 --alignSJDBoverhangMin 1 --outFilterMultimapNmax 1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000  --limitBAMsortRAM 96000000000 --outSAMtype BAM Unsorted
Supplementary files format and content: ACE_longRNAseq_gene_counts_file.csv.gz

extract_protocol:
Tecan Universal mRNA plus
mRNA sequencing, poly A selection

value: airway epithelium

tag: gender

value: F

tag: diagnosis

value: NANA

tag: interval


title: 786-O-dishTRAIL-Dox-off-rep2

tag: cell type


title: S40A_432AP

tag: cell line_id

tag: morphology

tag: batch

value: collagen


title: NANA-067-3AC

tag: allergen

value: Cat


title: NPC_E7KO-1 (RNA-seq rep-1)

tag: genotype

value: Dpf2 E7-KO


title: S30-16992-bulk3D-10C_332AP

description:
R1 fastq file: cDNA; R2 fastq file: barcode/UMI
332AP_mouse_counts.txt

tag: replicate

tag: dimension

tag: day

tag: environment


title: NPC_WT-3 (RNA-seq rep-2)

tag: cell line

value: WT

tag: treatment


title: S29-16992-bulk3D-10B_332AP


title: NANA-067-2BL

tag: tissue

tag: age


title: NANA-042-3DIL

tag: gender

value: M


title: S27-16992-2D-9C_332AP


title: 4C_dTAG_6H_rep2.Zfp111

city: Amsterdam

first: Mikhail

last: Magnitov

address: Plesmanlaan 121

country: Netherlands

institute: The Netherlands Cancer Institute

description: 4c_viewpoints.txt ,4c_normalised_counts_per_fragment.tsv.gz

data_processing:
ChIP-seq: ZFP143 ChIP-seq reads were mapped to the mm10 mouse reference genome assembly using bwa mem. Calibrated CTCF ChIP-seq reads were mapped to the mm10 mouse and hg38 human reference genome assemblies using bwa mem. Uniquely mapped reads with MAPQ > 10 mapped in proper read pairs were selected using SAMtools. Duplicate reads were filtered out using the Picard “MarkDuplicates” function. Scaling factors for calibrated CTCF ChIP-seq normalisation were calculated as described previously (Greulich et al., 2021). The bigwig coverage tracks were generated using the “bamCoverage” and "bamCompare" functions from the deepTools. TT-seq: TT-seq reads were mapped to the mm10 mouse reference genome assembly using STAR with GENCODE vM25 gene annotation. Uniquely mapped reads with MAPQ > 10 were selected using SAMtools. Duplicate reads were filtered out using the Picard “MarkDuplicates” function. The reads were split by strand using SAMtools as described previously (Gregersen et al., 2020). Gene counts were obtained using the ”htseq-count” function from HTSeq. Bigwig coverage tracks were generated separately for forward and reverse strands using the "bamCoverage" function from deepTools. Hi-C: Hi-C reads were mapped to the mm10 mouse reference genome assembly using bwa mem with the Open2C distiller-nf pipeline. Mapped reads were parsed using pairtools with the “walks-policy” parameter set to “mask” and the “max_mismatch_bp” parameter set to 1. Read pairs were then binned into Hi-C contact matrices. Iterative correction of the matrices and removal of low coverage bins was performed using the "balance" function from cooler. 4C-seq: 4C-seq reads were processed as previously described (Haarhuis et al., 2017; van de Werken et al., 2012) using custom R scripts. The sequencing data were demultiplexed per viewpoint and mapped to the mm10 mouse reference genome assembly using the bwa aln and bwa samse. To generate the read counts per RE fragment, for each fragment we counted the number of mapped reads that have the same start or end coordinates as the fragment. To obtain 4C contact profiles, the counts were normalised to the total number of overlaps detected per million reads. ATAC-seq: ATAC-seq reads were mapped to the mm10 mouse reference genome assembly bwa mem. Uniquely mapped reads that were not mapped to mitochondrial DNA and had MAPQ > 10 were selected using SAMtools. Duplicate reads were filtered out using the Picard “MarkDuplicates” function. RNA-seq: RNA-seq reads were mapped to the mm10 mouse reference genome assembly using STAR with GENCODE vM25 gene annotation. Read counts per gene were obtained using the "quantMode" parameter in STAR.
Assembly: mm10
Supplementary files format and content: ChIP-seq: normalized signal tracks in bigWig format; peaks in BED format. TT-seq: normalized signal tracks in bigWig format; read counts per gene in TXT format. Hi-C: contact matrices in MCOOL and HIC formats. 4C-seq: viewpoint coordinates in TXT format; normalized coverage per fragment in TSV format. RNA-seq: read counts per gene in TXT format.
Library strategy: 4C

growth_protocol: Mouse Embryonic Stem Cells E14Tg2A (129/Ola) cell lines were cultured on 0.1% gelatin-coated plates in serum-free DMEM/F12 (Gibco) and Neurobasal (Gibco) medium (1:1) supplemented with N-2 (Gibco), B-27 (Gibco), BSA (0.05%, Gibco), 10 × 4 U of Leukaemia Inhibitory Factor (LIF) (Millipore), MEK inhibitor PD0325901 (1 μM, Selleckchem), GSK3-β inhibitor CHIR99021 (3 μM, Cayman Chemical) and 1-Thioglycerol (1.5 × 10−4 M, Sigma-Aldrich). The cell lines were passaged every 2 days in daily culture.

extract_protocol:
ChIP-seq: Chromatin was cross-linked using 1% FA final concentration. Chromatin was sheared on a Bioruptor Plus sonication instrument and immunoprecipitated by different antibodies. DNA was purified using the MiniElute PCR purification kit from Qiagen. TT-seq: Libraries for TTchem-seq were prepared following a published protocol (Gregersen et al., 2020). Cells were labelled with 2 mM of the uridine analog 4-thiouridine (4sU) for 10 min. Total RNA was isolated and fragmented. The 4sU-biotin labelled RNA was enriched using µMacs Streptavidin Kit (Miltenyi). Hi-C: Hi-C data were generated using as a previous published protocol (Rao et al., 2014) with minor modifications (Haarhuis et al., 2017). Cells were harvested and crosslinked using 2% formaldehyde. Crosslinked DNA was digested in nucleus using MboI (NEB), and biotinylated nucleotides were incorporated at the restriction overhangs and joined by blunt-end ligation. The ligated DNA was enriched in a streptavidin pull-down 4C-seq: 4C-seq was performed as previously described (Geeven et al., 2018; van de Werken et al., 2012) using a two-step PCR method for indexing described first in (Haarhuis et al., 2017). MboI (NEB) was used as the first restriction enzyme and Csp6I (NEB) as the second restriction enzyme. ATAC-seq: Cells were washed in cold PBS and subjected to lysis using a 2x lysis buffer. Subsequently, the cells were centrifuged, and the resulting pellet was treated with 2xTD buffer and 2 uL of transposon mix. RNA-seq: RNA was first isolated using standard RNA isolation procedure from Qiagen RNeasy Mini Kit (Qiagen), including a DNaseI treatment.
ChIP-seq: Libraries were prepared following the KAPA HTP Library Preparation Kit (Roche). TT-seq: Libraries were prepared using KAPA RNA HyperPrep and KAPA Dual-Indexed Adapter kits (Roche) using dual indexing adapters. Hi-C: Hi-C libraries were prepared using a standard end-repair and A-tailing method. 4C-seq: 4C-seq libraries were prepared using a two-step PCR method for indexing described first in (Haarhuis et al., 2017). ATAC-seq: PCR amplification was conducted using KAPA HiFi HotStart ReadyMix (Roche). Fragments ranging from 200 to 700 bp were purified utilising AMPure XP beads (Beckman Coulter). RNA-seq: Libraries were prepared following the TruSeq Stranded mRNA kit (Illumina) with TruSeq RNA Single Indexes set A (Illumina).

treatment_protocol: For the knock-in of the FKBP sequence at the genes of interest, cells were transfected with the plasmids containing the gRNA sequence and the donor plasmid designed to include the FKBP-2xHA-P2A-GFP in between two homology arms for the gene of interest. To induce ZFP143 degradation, the cells were treated with 500 nM dTAG-V1 or DMSO as a control.

value: Embryonic Stem Cell

tag: time

tag: viewpoint


title: S28-16992-bulk3D-10A_332AP

tag: cell type


title: ESC_E7KI-3 (RNA-seq rep-2)

source_name: HBG3 ES cell line

value: HBG3 ES cell line

value: Embryonic stem cell (ESC)

value: Stem cell maintenance


title: NANA-042-2BL

tag: diagnosis

tag: interval


title: ESC_E7KI-2 (RNA-seq rep-1)

value: Dpf2 E7-KI


title: ESC_E7KO-3 (RNA-seq rep-2)


title: NPC_E7KO-3 (RNA-seq rep-2)

value: HBG3 ES cell line-derived NPC

value: Neural  Progenitor Cell (NPC)

value: Differentiation to NPC


title: S25-16992-2D-9A_332AP

value: Murine PDAC Cells

tag: cell line_id

tag: batch

value: KC


title: ESC_E7KO-1 (RNA-seq rep-1)

tag: genotype


title: 4C_dTAG_6H_rep2.Sik1


title: 4C_dTAG_6H_rep2.Rbm41


title: NANA-007-2BL

value: airway epithelium


title: S26-16992-2D-9B_332AP

tag: replicate


title: NANA-007-3DIL

value: NANA


title: ESC_WT-3 (RNA-seq rep-2)


title: 4C_dTAG_6H_rep2.Prmt6


title: S24-8028-3D-8C_332AP

tag: dimension

value: collagen


title: ANA-015-3DIL

value: ANA


title: S23-8028-3D-8B_332AP

tag: day


title: ESC_WT-1 (RNA-seq rep-1)


title: 4C_dTAG_6H_rep2.Cpox

value: Cpox


title: ANA-015-3AC

tag: allergen

value: HDMdp


title: BRM014 treated cells during 30h, biological rep2 (RNA-seq)

data_processing:
RNA-Seq data were primarily filtered using the FASTQ Toolkit v1.0.0 program
Data were aligned using subjunc function from Rsubread package, to map reads to the mm9 mouse reference genome using TH1=2 and unique=TRUE parameters. The downstream analysis was performed on bamfiles with duplicates removed using the samtools (v0.1.19) rmdup command
FeatureCounts() function from Rsubread package was used to assign reads to UCSC mm9 KnownGenes (miRNAs were discarded from the analysis) using GTF.featureType=“exon”, GTF.attrType=“gene_id” and strandSpecific = 2 parameters on duplicate removed bamfiles.
Assembly: mm9
Supplementary files format and content: raw counts, tab delimited file

source_name: Mammary Gland

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen)
The libraries were prepared with the TruSeq Stranded TOTAL RNA kit (Illumina, San Diego, CA, USA) and the sequencing was performed with the NovaSeq 6000 1x50bp length

value: Mammary Gland

tag: cell line

value: NMuMG

value: normal murine mammary gland epithelial cells

value: WT


title: NANA-042-3AC

value: M

value: Cat


title: 4C_dTAG_6H_rep2.Cldn1

value: Embryonic Stem Cell

tag: treatment


title: NPC_WT-1 (RNA-seq rep-1)

value: HBG3 ES cell line-derived NPC

value: Neural  Progenitor Cell (NPC)


title: ANA-015-2BL

tag: tissue


title: NANA-007-3AC

tag: age


title: BRM014 treated cells during 30h, biological rep1 (RNA-seq)


title: ANA-003-3DIL

tag: gender

value: F


title: 4C_dTAG_6H_rep1.Zfp111

tag: time


title: S20-8028-2D-7B_332AP

value: Murine PDAC Cells

value: KC


title: 4C_dTAG_6H_rep2.Zfp108

tag: viewpoint


title: 4C_dTAG_6H_rep1.Zfp108

tag: cell type


title: S19-8028-2D-7A_332AP


title: BRM014 treated cells during 6h, biological rep2 (RNA-seq)


title: 4C_dTAG_6H_rep1.Sik1


title: BRM014 treated cells during 6h, biological rep1 (RNA-seq)


title: ANA-003-3AC

value: airway epithelium

tag: diagnosis


title: ANA-003-2BL

tag: interval


title: DMSO treated cells during 30h, biological rep2 (RNA-seq)

value: DMSO


title: 4C_dTAG_6H_rep1.Rbm41


title: AA-075-3DIL

value: AA


title: S18-53631-3D-6C_332AP

tag: cell line_id

tag: environment

value: collagen


title: S22-8028-3D-8A_332AP

tag: batch

tag: genotype


title: S17-53631-3D-6B_332AP

tag: replicate

tag: dimension


title: DMSO treated cells during 30h, biological rep1 (RNA-seq)


title: 4C_dTAG_6H_rep1.Cpox

value: Cpox


title: AA-075-3AC

tag: allergen

value: HDMdp


title: AA-075-2BL


title: DMSO treated cells during 6h, biological rep2 (RNA-seq)

value: Mammary Gland

tag: cell line

value: NMuMG


title: S15-53631-2D-5C_332AP


title: DMSO treated cells during 6h, biological rep1 (RNA-seq)

value: normal murine mammary gland epithelial cells

value: WT

tag: treatment


title: S21-8028-2D-7C_332AP


title: 4C_dTAG_6H_rep1.Cldn1


title: 4C_DMSO_rep2.Zfp111


title: AA-073-3DIL

tag: tissue

value: M


title: S14-53631-2D-5B_332AP


title: S13-53631-2D-5A_332AP


title: BRM014 treated cells during 30h, without crosslinking (MNase-seq)

data_processing:
Mnase-seq data were primarily filtered using the FASTQ Toolkit v1.0.0 program
Mnase-seq  data for each condition were aligned using align function from Rsubread package, to map reads to the mm9 mouse reference genome using type = 1, TH1=2 and unique=TRUE parameters. The downstream analysis was performed on bamfiles with duplicates removed using the samtools rmdup command
BamCoverage from Deeptools suite was used to create bigWig files using RPKM normalization
Assembly: mm9
Supplementary files format and content: BigWig fragment density signal file

extract_protocol:
1-2 x 10e6 cells plated in 100-mm plates and were treated with  DMSO or BRM014 for 6 or 30 hours. After that, proteins were crosslinked to DNA by adding formaldehyde to a final concentration of 1%, and incubating for 10 min at 37ºC. Then the crosslinking reaction was stopped by adding Glycine to a final concentration of 0.1M and incubating for 5 min at room temperature and cells were harvested. The pellet of cells was dissolved in buffer A (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.3 M sucrose and complete protease inhibitor cocktail (Roche)) plus 0.2% of NP40 and incubated for 10 min at 4ºC. Nuclei were obtained after centrifugation and digested with 1 unit of MNase for 5-15 min at room temperature in 200 μl of buffer A plus 3 mM CaCl2. The MNAse digestion was stopped by adding 5 mM EGTA and 10 mM EDTA. Samples were incubated for 1 hour at room temperature with RNaseA, then incubated overnight at 65°C with 0.01% SDS and proteinase K (Promega). DNA was purified by phenol/chloroform extraction and was processed in a 1% agarose gel and visualized with ethidium bromide. The band corresponding to mononucleosome size (~150 bp) was excised from the gel and DNA purified through FavorPrep™ Gel/PCR Purification Kit (Favorgen) column. DNA was again purified using MinElute PCR Purification Kit (Quiagen).
Libraries were prepared with the ThruPLEX DNA-Seq Kit (Takara Bio Europe)

tag: crosslinking

value: no


title: 4C_DMSO_rep2.Zfp108

value: Embryonic Stem Cell


title: BRM014 treated cells during 30h, biological rep2 (MNase-seq)

value: yes


title: AA-073-3AC

tag: gender

tag: age


title: 4C_DMSO_rep2.Sik1

tag: viewpoint


title: S12-8442-3D-4C_332AP

tag: cell type

tag: day


title: AA-073-2BL

tag: diagnosis

tag: interval


title: AA-071-3DIL


title: 4C_dTAG_6H_rep1.Prmt6

tag: time


title: BRM014 treated cells during 6h, without crosslinking (MNase-seq)


title: AA-071-3AC


title: S11-8442-3D-4B_332AP

tag: cell line_id

tag: batch

tag: environment


title: 4C_DMSO_rep2.Rbm41

tag: genotype


title: S10-8442-3D-4A_332AP

tag: replicate

tag: dimension


title: 4C_DMSO_rep2.Prmt6

tag: cell line

tag: treatment


title: AA-071-2BL

tag: tissue


title: BRM014 treated cells during 6h, biological rep2 (MNase-seq)

tag: crosslinking


title: S09-8442-2D-3C_332AP


title: 4C_DMSO_rep2.Cpox


title: BRM014 treated cells during 6h, biological rep1 (MNase-seq)


title: S08-8442-2D-3B_332AP


title: DMSO treated cells, without crosslinking (MNase-seq)


title: AA-062-2BL

tag: gender

value: F

tag: age


title: 4C_DMSO_rep2.Cldn1

tag: cell type

tag: viewpoint


title: DMSO treated cells, biological rep2 (MNase-seq)


title: S07-8442-2D-3A_332AP

value: Murine PDAC Cells


title: AA-057-3DIL

tag: diagnosis


title: BRM014 treated cells during 30h, biological rep1 (MNase-seq)


title: 4C_DMSO_rep1.Zfp108


title: 4C_DMSO_rep1.Sik1


title: AA-057-3AC

tag: allergen

value: Cat

tag: interval


title: BRM014 treated cells during 30h, biological rep2 (Cut&Tag)

data_processing:
Cut&Tag data were primarily filtered using the FASTQ Toolkit v1.0.0 program
Two biological replicates of the Cut&Tag data for each condition and for histone modification H3K27me3 were primarily filtered using the FASTQ Toolkit program. Data were aligned using align function from Rsubread package, to map reads to the mm9 mouse reference genome using type = 1, TH1=2 and unique=TRUE parameters. The downstream analysis was performed on bamfiles with duplicates removed using the samtools rmdup command
BamCoverage from Deeptools suite was used to create bigWig files using RPKM normalization
Assembly: mm9
Supplementary files format and content: BigWig fragment density files
Library strategy: Cut&Tag

extract_protocol:
CUT&Tag (poner ref del paper) was performed using CUT&Tag-IT™ Assay Kit (Active motif, 53160) following manufacturer’s protocol. Briefly, 5x10e5 cells were harvested using Enzyme Free Cell Dissociation Solution Hank's Based (1X) (Sigma-Aldrich, Cat#S-004-C). After binding with Concanavalin A beads, cells were incubated with primary antibody targeting H3K27me3 (Active motif, 39157) overnight at 4°C. Samples were then incubated with Guinea Pig anti-Rabbit antibody, followed by CUT&Tag-IT Assembled pA-Tn5 Transposomes. After tagmentation in tagmentation buffer at 37°C for 1 hour, released DNA was extracted by DNA purification column for library preparation and SPRI Beads clean-up.
DNA libraries for ATAC-seq were prepared using NextEra Library Prep Kit following manufacturer's protocols.

treatment_protocol: Cells were treated with DMSO or BRM014 at 30 hours

tag: chip antibody

value: anti-H3K27me3 (39055, Active Motif)


title: DMSO treated cells, biological rep1 (MNase-seq)

value: DMSO


title: S05-9091-3D-2B_332AP

tag: cell line_id

tag: batch

value: KC

tag: day


title: 4C_DMSO_rep1.Zfp111

tag: genotype


title: S06-9091-3D-2C_332AP

tag: replicate

tag: dimension

tag: environment

value: collagen


title: AA-049-3DIL

tag: tissue

value: airway epithelium

value: AA


title: S04-9091-3D-2A_332AP


title: 4C_DMSO_rep1.Rbm41

tag: cell line

tag: treatment


title: DMSO treated cells, biological rep2 (Cut&Tag)

value: Mammary Gland


title: 4C_DMSO_rep1.Prmt6


title: AA-049-2BL

tag: gender

tag: age


title: S03-9091-2D-1C_332AP

tag: cell type


title: S02-9091-2D-1B_332AP


title: AA-044-3DIL

tag: diagnosis


title: BRM014 treated cells during 30h, biological rep1 (Cut&Tag)

value: NMuMG


title: 4C_DMSO_rep1.Cpox

tag: viewpoint

value: Cpox


title: AA-049-3AC

tag: allergen

value: HDMdp

tag: interval


title: BRM014 treated cells during 30h, biological rep2 (ChRNA-seq)

data_processing:
RNA-Seq data were primarily filtered using the FASTQ Toolkit v1.0.0 program
Data were aligned using subjunc function from Rsubread package, to map reads to the mm9 mouse reference genome using TH1=2 and unique=TRUE parameters. The downstream analysis was performed on bamfiles with duplicates removed using the samtools (v0.1.19) rmdup command
BamCoverage from Deeptools suite was used to create bigWig files using RPKM normalization
Assembly: mm9
Supplementary files format and content: bigWig read density files
Library strategy: ChRNA-seq

extract_protocol:
Cells were resuspended in 400 μl cold cytoplasmic lysis buffer (0.15% NP-40, 10 mM Tris pH 7.5, 150 mM NaCl) and incubated on ice for 5 min. The lysates were layered onto 1 ml cold sucrose buffer (10 mM Tris pH7.5, 150 mM NaCl, 24% sucrose w/v), and centrifuged in microfuge tubes at 3500 g for 10 minutes. The nuclear pellets were gently resuspended into 250 μl cold glycerol buffer (20 mM Tris pH 7.9, 75 mM NaCl, 0.5 mM EDTA, 50% glycerol). An additional 250 μl of cold nuclei lysis buffer (20 mM HEPES pH 7.6, 7.5 mM MgCl2, 0.2 mM EDTA, 0.3 M NaCl, 1 M urea, 1% NP-40, 1 mM DTT) was added to the samples, followed by a pulsed vortexing and incubation on ice for 2 minutes. Samples were then spun in microfuge tubes for 2 min at 13000 g. 50 μl of cold PBS was added to the remaining chromatin pellet, and gently pipetted up and down over the pellet, followed by a brief vortex. Then RNA was extracted using TRIZOL and treated with TURBO DNA-free kit (AM1907, Invitrogen) for DNA removal according to manufacturer's instructions
The libraries were prepared with the TruSeq Stranded TOTAL RNA kit (Illumina, San Diego, CA, USA) and the sequencing was performed with the NovaSeq 6000 1x50bp length

value: normal murine mammary gland epithelial cells

value: WT


title: 4C_DMSO_rep1.Cldn1

value: Embryonic Stem Cell


title: AA-044-3AC

value: M


title: S56C_432AP (re-analysis)

description:
re-analysis of GSM6030851
432AP_mouse_counts.txt

tag: cell line_id

value: KPC


title: BRM014 treated cells during 30h, biological rep1 (ChRNA-seq)


title: AA-057-2BL

value: F


title: TTseq_dTAG_24H_rep2

description:
ttseq_ZFP143_depletion_time_course.gene_counts.txt
TTseq_dTAG_24H_forward.bw
TTseq_dTAG_24H_reverse.bw

data_processing:
ChIP-seq: ZFP143 ChIP-seq reads were mapped to the mm10 mouse reference genome assembly using bwa mem. Calibrated CTCF ChIP-seq reads were mapped to the mm10 mouse and hg38 human reference genome assemblies using bwa mem. Uniquely mapped reads with MAPQ > 10 mapped in proper read pairs were selected using SAMtools. Duplicate reads were filtered out using the Picard “MarkDuplicates” function. Scaling factors for calibrated CTCF ChIP-seq normalisation were calculated as described previously (Greulich et al., 2021). The bigwig coverage tracks were generated using the “bamCoverage” and "bamCompare" functions from the deepTools. TT-seq: TT-seq reads were mapped to the mm10 mouse reference genome assembly using STAR with GENCODE vM25 gene annotation. Uniquely mapped reads with MAPQ > 10 were selected using SAMtools. Duplicate reads were filtered out using the Picard “MarkDuplicates” function. The reads were split by strand using SAMtools as described previously (Gregersen et al., 2020). Gene counts were obtained using the ”htseq-count” function from HTSeq. Bigwig coverage tracks were generated separately for forward and reverse strands using the "bamCoverage" function from deepTools. Hi-C: Hi-C reads were mapped to the mm10 mouse reference genome assembly using bwa mem with the Open2C distiller-nf pipeline. Mapped reads were parsed using pairtools with the “walks-policy” parameter set to “mask” and the “max_mismatch_bp” parameter set to 1. Read pairs were then binned into Hi-C contact matrices. Iterative correction of the matrices and removal of low coverage bins was performed using the "balance" function from cooler. 4C-seq: 4C-seq reads were processed as previously described (Haarhuis et al., 2017; van de Werken et al., 2012) using custom R scripts. The sequencing data were demultiplexed per viewpoint and mapped to the mm10 mouse reference genome assembly using the bwa aln and bwa samse. To generate the read counts per RE fragment, for each fragment we counted the number of mapped reads that have the same start or end coordinates as the fragment. To obtain 4C contact profiles, the counts were normalised to the total number of overlaps detected per million reads. ATAC-seq: ATAC-seq reads were mapped to the mm10 mouse reference genome assembly bwa mem. Uniquely mapped reads that were not mapped to mitochondrial DNA and had MAPQ > 10 were selected using SAMtools. Duplicate reads were filtered out using the Picard “MarkDuplicates” function. RNA-seq: RNA-seq reads were mapped to the mm10 mouse reference genome assembly using STAR with GENCODE vM25 gene annotation. Read counts per gene were obtained using the "quantMode" parameter in STAR.
Assembly: mm10
Supplementary files format and content: ChIP-seq: normalized signal tracks in bigWig format; peaks in BED format. TT-seq: normalized signal tracks in bigWig format; read counts per gene in TXT format. Hi-C: contact matrices in MCOOL and HIC formats. 4C-seq: viewpoint coordinates in TXT format; normalized coverage per fragment in TSV format. RNA-seq: read counts per gene in TXT format.
Library strategy: TT-seq

tag: time


title: TTseq_dTAG_24H_rep1


title: AA-043-3DIL


title: S56B_432AP (re-analysis)

description:
re-analysis of GSM6030850
432AP_mouse_counts.txt

value: Murine PDAC Cells

tag: batch

tag: day


title: BRM014 treated cells during 6h, biological rep2 (ChRNA-seq)

tag: genotype


title: S01-9091-2D-1A_332AP

tag: replicate

tag: dimension


title: S56A_432AP (re-analysis)

description:
re-analysis of GSM6030849
432AP_mouse_counts.txt

tag: environment


title: TTseq_dTAG_6H_rep2

description:
ttseq_ZFP143_depletion_time_course.gene_counts.txt
TTseq_dTAG_6H_forward.bw
TTseq_dTAG_6H_reverse.bw

tag: cell line


title: AA-044-2BL

tag: tissue


title: S38C_432AP (re-analysis)

description:
re-analysis of GSM6030848
432AP_mouse_counts.txt


title: DMSO treated cells during 30h, biological rep2 (ChRNA-seq)

tag: treatment


title: AA-043-3AC

tag: gender

tag: age


title: TTseq_dTAG_6H_rep1

tag: cell type


title: AA-043-2BL

tag: diagnosis


title: DMSO treated cells, biological rep1 (Cut&Tag)

tag: chip antibody

value: anti-H3K27me3 (39055, Active Motif)


title: DMSO treated cells during 30h, biological rep1 (ChRNA-seq)

value: DMSO


title: AA-037-3DIL

tag: interval


title: S38B_432AP (re-analysis)

description:
re-analysis of GSM6030847
432AP_mouse_counts.txt

tag: cell line_id

value: KC


title: S38A_432AP (re-analysis)

description:
re-analysis of GSM6030846
432AP_mouse_counts.txt

value: collagen


title: DMSO treated cells during 6h, biological rep2 (ChRNA-seq)


title: AA-037-3AC

value: airway epithelium

tag: allergen


title: TTseq_DMSO_rep2

description:
ttseq_ZFP143_depletion_time_course.gene_counts.txt
TTseq_DMSO_forward.bw
TTseq_DMSO_reverse.bw


title: S56-9591-bulk3D13D-17E_332AP (re-analysis)

description:
re-analysis of GSM6030845
332AP_mouse_counts.txt

tag: batch


title: AA-037-2BL

value: AA


title: S55-9591-bulk3D13D-17D_332AP (re-analysis)

description:
re-analysis of GSM6030844
332AP_mouse_counts.txt

tag: day


title: BRM014 treated cells during 6h, biological rep1 (ChRNA-seq)

value: Mammary Gland

tag: genotype


title: AA-036-3DIL


title: TTseq_DMSO_rep1


title: AA-036-3AC


title: ChIPseq_ZFP143_dTAG_2H

data_processing:
ChIP-seq: ZFP143 ChIP-seq reads were mapped to the mm10 mouse reference genome assembly using bwa mem. Calibrated CTCF ChIP-seq reads were mapped to the mm10 mouse and hg38 human reference genome assemblies using bwa mem. Uniquely mapped reads with MAPQ > 10 mapped in proper read pairs were selected using SAMtools. Duplicate reads were filtered out using the Picard “MarkDuplicates” function. Scaling factors for calibrated CTCF ChIP-seq normalisation were calculated as described previously (Greulich et al., 2021). The bigwig coverage tracks were generated using the “bamCoverage” and "bamCompare" functions from the deepTools. TT-seq: TT-seq reads were mapped to the mm10 mouse reference genome assembly using STAR with GENCODE vM25 gene annotation. Uniquely mapped reads with MAPQ > 10 were selected using SAMtools. Duplicate reads were filtered out using the Picard “MarkDuplicates” function. The reads were split by strand using SAMtools as described previously (Gregersen et al., 2020). Gene counts were obtained using the ”htseq-count” function from HTSeq. Bigwig coverage tracks were generated separately for forward and reverse strands using the "bamCoverage" function from deepTools. Hi-C: Hi-C reads were mapped to the mm10 mouse reference genome assembly using bwa mem with the Open2C distiller-nf pipeline. Mapped reads were parsed using pairtools with the “walks-policy” parameter set to “mask” and the “max_mismatch_bp” parameter set to 1. Read pairs were then binned into Hi-C contact matrices. Iterative correction of the matrices and removal of low coverage bins was performed using the "balance" function from cooler. 4C-seq: 4C-seq reads were processed as previously described (Haarhuis et al., 2017; van de Werken et al., 2012) using custom R scripts. The sequencing data were demultiplexed per viewpoint and mapped to the mm10 mouse reference genome assembly using the bwa aln and bwa samse. To generate the read counts per RE fragment, for each fragment we counted the number of mapped reads that have the same start or end coordinates as the fragment. To obtain 4C contact profiles, the counts were normalised to the total number of overlaps detected per million reads. ATAC-seq: ATAC-seq reads were mapped to the mm10 mouse reference genome assembly bwa mem. Uniquely mapped reads that were not mapped to mitochondrial DNA and had MAPQ > 10 were selected using SAMtools. Duplicate reads were filtered out using the Picard “MarkDuplicates” function. RNA-seq: RNA-seq reads were mapped to the mm10 mouse reference genome assembly using STAR with GENCODE vM25 gene annotation. Read counts per gene were obtained using the "quantMode" parameter in STAR.
Assembly: mm10
Supplementary files format and content: ChIP-seq: normalized signal tracks in bigWig format; peaks in BED format. TT-seq: normalized signal tracks in bigWig format; read counts per gene in TXT format. Hi-C: contact matrices in MCOOL and HIC formats. 4C-seq: viewpoint coordinates in TXT format; normalized coverage per fragment in TSV format. RNA-seq: read counts per gene in TXT format.

tag: time

tag: antibody

value: HA (ab9110, Abcam)


title: H3K27me3 ChIP (ChIP-seq)

data_processing:
ChIP-seq data were primarily filtered using the FASTQ Toolkit v1.0.0 program
ChIP-seq data were primarily filtered using the FASTQ Toolkit program. Data were aligned using align function from Rsubread package, to map reads to the mm9 mouse reference genome using type = 1, TH1=2 and unique=TRUE parameters. The downstream analysis was performed on bamfiles with duplicates removed using the samtools rmdup command
BamCoverage from Deeptools suite was used to create bigWig files using RPKM normalization
Assembly: mm9
Supplementary files format and content: BigWig read density files

treatment_protocol: No treatment

value: NMuMG

value: No


title: S53-9591-bulk3D13D-17B_332AP (re-analysis)

description:
re-analysis of GSM6030842
332AP_mouse_counts.txt

data_processing:
Dropseq (v1.0) – see Macosko et al., PMID: 26000488.
Assembly: Mouse GRCm38 and Human GRCh38, respectively.
Supplementary files format and content: Tab-delimited files contain raw counts for each sample

tag: replicate

tag: dimension

tag: environment


title: S54-9591-bulk3D13D-17C_332AP (re-analysis)

description:
re-analysis of GSM6030843
332AP_mouse_counts.txt


title: BRM014 treated cells during 30h, biological rep2 (ATAC-seq)

data_processing:
Two independent biological replicates of ATAC-seq data were processed (trimmed, aligned, filtered, and quality controlled) for each condition independently using the ATAC-seq pipeline from the Kundaje lab (https://github.com/ENCODE-DCC/atac-seq-pipeline).
The model-based analysis of ChIP-seq macs2 (v2.1.2) was used to identify the peak regions with options -B, -q 0.01–nomodel, -f BAM, -g mm9. The Irreproducible Discovery Rate (IDR) method was used to identify reproducible peaks between two biological replicates. Only peaks reproducible between the two biological replicates (with IDR ≤ 0.05) were retained for downstream analyses
Assembly: mm9
Supplementary files format and content: narrowPeak, region file

extract_protocol:
The ATAC experiments were performed as described (Buenrostro et al., 2013). NMuMG cells were either vehicle or TGFβ-treated for 2 or 12h, and then collected and treated with transposase Tn5 (Nextera DNA Library Preparation Kit, Illumina). DNA was purified using MinElute PCR Purification Kit (Qiagen). All samples were then amplified by PCR using NEBNextHigh-Fidelity 2× PCR Master Mix (New Englands Labs) with primers containing a barcode to generate libraries. DNA was again purified using AMPure Beads.
DNA libraries for ATAC-seq were prepared using NextEra Library Prep Kit following manufacturer's protocols.

tag: tissue

tag: cell line

value: normal murine mammary gland epithelial cells

tag: treatment


title: ChIPseq_ZFP143_DMSO

tag: cell type


title: S16-53631-3D-6A_332AP


title: S52-9591-bulk3D13D-17A_332AP (re-analysis)

description:
re-analysis of GSM6030841
332AP_mouse_counts.txt


title: BRM014 treated cells during 30h, biological rep1 (ATAC-seq)

value: WT


title: AA-034-3DIL

tag: gender

tag: age

tag: diagnosis


title: TTseq_dTAG_2H_rep1

description:
ttseq_ZFP143_depletion_time_course.gene_counts.txt
TTseq_dTAG_2H_forward.bw
TTseq_dTAG_2H_reverse.bw

value: Embryonic Stem Cell


title: S51-9591-bulk3D7D-16C_332AP (re-analysis)

description:
re-analysis of GSM6030840
332AP_mouse_counts.txt

tag: cell line_id


title: BRM014 treated cells during 6h, biological rep2 (ATAC-seq)


title: TTseq_dTAG_2H_rep2


title: ChIPseq_CTCF_dTAG_6H

value: CTCF (07-729, Merck Millipore)


title: S50-9591-bulk3D7D-16B_332AP (re-analysis)

description:
re-analysis of GSM6030839
332AP_mouse_counts.txt


title: BRM014 treated cells during 6h, biological rep1 (ATAC-seq)


title: DMSO treated cells during 6h, biological rep1 (ChRNA-seq)


title: ChIPseq_Input_ZFP143


title: ChIPseq_CTCF_DMSO


title: AA-034-2BL

tag: interval


title: input Chromatin (ChIP-seq)

tag: chip antibody


title: AA-034-3AC

tag: allergen

value: HDMdp


title: S49-9591-bulk3D7D-16A_332AP (re-analysis)

description:
re-analysis of GSM6030838
332AP_mouse_counts.txt

tag: batch

tag: genotype

tag: day


title: ChIPseq_Input_CTCF


title: DMSO treated cells, biological rep2 (ATAC-seq)


title: AA-036-2BL

value: F


title: DMSO treated cells, biological rep1 (ATAC-seq)


title: AA-033-3DIL


title: AA-033-3AC

value: Cat


title: Third pharyngeal region cells, S1224, scRNAseq

city: Bethesda

first: Michael

middle: C

last: Kelly

state: MD

address: 41 Center Drive

department: Center for Cancer Research

institute: NCI

description:
10x Genomics
SCAF1315_S1224

data_processing:
The demultiplexing, barcoded processing, gene counting were made using the Cell Ranger software v6.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: filtered scRNA-seq expression matrices in hdf5 format

source_name: Third pharyngeal region cells

extract_protocol:
Single cell suspensions were generated from target tissues from specific genotype mice. For venus-positive or venus-negative cell populations, cells were sorted by FACs into collection tubes. Cell suspensions were stored on ice, counted and viabilities checked prior to be loaded on the 10x Genomics chromium platform for single cell partitioning, lysis, and reverse transciption of mRNA into cDNA libraries.
Library constructionwas performed according to the manufacter’s instructions (Single Cell 3’ v3 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscribed to cDNA, which contains a partial Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Third pharyngeal region cells


title: S47-9591-matrigel3D-15B_332AP (re-analysis)

description:
re-analysis of GSM6030836
332AP_mouse_counts.txt

value: Murine PDAC Cells

tag: replicate

value: matrigel


title: Third pharyngeal region cells, S1119, scRNAseq

description:
10x Genomics
SCAF1213_S1119


title: S48-9591-matrigel3D-15C_332AP (re-analysis)

description:
re-analysis of GSM6030837
332AP_mouse_counts.txt

value: KC

tag: dimension


title: Cut&Run NFAT2_SA_rep3

city: Nanjing

first: Xi

last: Wang

address: Longmian Avenue 101, Jiangning District

institute: Nanjing Medical University

data_processing:
Illumina HCS 1.2.0 and RTA 3.7.17 software used for sequencing and basecalling.
scRNA-seq: 10x Genomics Cell Ranger v6.0.1 used for sequencing read alignment and UMI counting.
ATAC-seq: adapter trimming and low-quality read filtering by flexbar (v2.5), read mapping by Bowtie2 (v2.4.2), duplicate read removal by Picard (v 2.17.3), peak calling by macs2 (v 2.2.7.1).
Cut&Run: adapter trimming and low-quality read filtering by flexbar (v2.5), read mapping by Bowtie2 (v 2.4.2), duplicate read removal by Picard (v 2.17.3), peak calling by macs2 (v 2.2.7.1), heatmap by deeptoools (v3.5.0)
Assembly: mm10
Supplementary files format and content: scRNA-seq: 10x Genomics output h5 files
Supplementary files format and content: ATAC-seq and Cut&Run: bigWig
Library strategy: CUT&RUN

source_name: splenocytes

growth_protocol: FoxP3YFP × OT-II splenocytes were cultured for 2-3 days with OVA323-339 peptide (1 μg/ml), IL-2 (10 ng/ml), and TGFβ (5 ng/ml)

extract_protocol:
FoxP3 YFP+ CD4+ T cells were FACS-purified
Cut&Run: Cells were permeabilized using digitonin and incubated with anti-c-Fos, anti-c-Jun, or anti-NFAT2. MNase was activated to cleave and liberate the chromatin fragments bound by c-Fos, c-Jun, or NFAT2. Chromatin fragments were purified and amplified to generate libraries.

treatment_protocol: FoxP3YFP × OT-II splenocytes were cultured in the presence of 5 μM sphinganine or DMSO vehicle control

tag: strain

value: FoxP3YFP X OT-II

value: splenocytes

value: SA

value: replicate #3


title: AA-028-3DIL

tag: tissue

value: airway epithelium

value: M

value: AA


title: ATAC-seq Treg_SA rep3

data_processing:
Illumina HCS 1.2.0 and RTA 3.7.17 software used for sequencing and basecalling.
scRNA-seq: 10x Genomics Cell Ranger v6.0.1 used for sequencing read alignment and UMI counting.
ATAC-seq: adapter trimming and low-quality read filtering by flexbar (v2.5), read mapping by Bowtie2 (v2.4.2), duplicate read removal by Picard (v 2.17.3), peak calling by macs2 (v 2.2.7.1).
Cut&Run: adapter trimming and low-quality read filtering by flexbar (v2.5), read mapping by Bowtie2 (v 2.4.2), duplicate read removal by Picard (v 2.17.3), peak calling by macs2 (v 2.2.7.1), heatmap by deeptoools (v3.5.0)
Assembly: mm10
Supplementary files format and content: scRNA-seq: 10x Genomics output h5 files
Supplementary files format and content: ATAC-seq and Cut&Run: bigWig

extract_protocol:
FoxP3 YFP+ CD4+ T cells were FACS-purified
ATAC-seq: Nuclei were extracted using the ATAC-Seq Kit (Active Motif). Tagmented DNA was then column-purified and immediately used for PCR amplification and library generation.


title: S45-9591-2D-14F_332AP (re-analysis)

description:
re-analysis of GSM6030834
332AP_mouse_counts.txt

extract_protocol:
Qiagen RNeasy Plus Micro Kit (Nr. 74034)
RT and template switch with primers containing Barcode, UMI and adapter. Full length amplification of the cDNA. Fragmentation and Adapter ligation with NEB Ultra II FS kit and final amplification of the 3’-end with Illumina overhangs. Sequencing of cDNA in Read1 and sequencing of Barcode and UMI in Read2.


title: ATAC-seq Treg_SA rep1

value: replicate #1


title: ATAC-seq Treg_SA rep2

value: replicate #2


title: Cut&Run NFAT2_SA_rep2


title: S46-9591-matrigel3D-15A_332AP (re-analysis)

description:
re-analysis of GSM6030835
332AP_mouse_counts.txt

tag: environment


title: AA-028-3AC


title: S44-9591-2D-14E_332AP (re-analysis)

description:
re-analysis of GSM6030833
332AP_mouse_counts.txt


title: ATAC-seq Treg_DMSO rep3

tag: treatment

value: DMSO


title: AA-028-2BL


title: S43-9591-2D-14D_332AP (re-analysis)

description:
re-analysis of GSM6030832
332AP_mouse_counts.txt

tag: cell type


title: Cut&Run NFAT2_SA_rep1


title: Cut&Run NFAT2_DMSO_rep3


title: AA-019-3DIL

tag: gender


title: ATAC-seq Treg_DMSO rep1


title: AA-019-3AC

tag: age


title: S42-9591-2D-14C_332AP (re-analysis)

description:
re-analysis of GSM6030831
332AP_mouse_counts.txt


title: AA-033-2BL

tag: diagnosis


title: Cut&Run NFAT2_DMSO_rep2


title: S41-9591-2D-14B_332AP (re-analysis)

description:
re-analysis of GSM6030830
332AP_mouse_counts.txt

tag: cell line_id


title: Cut&Run NFAT2_DMSO_rep1


title: S40-9591-2D-14A_332AP (re-analysis)

description:
re-analysis of GSM6030829
332AP_mouse_counts.txt


title: Cut&Run Input_SA_rep3

value: none (Input)


title: AA-014-3DIL

value: F

tag: interval


title: Cut&Run Input_SA_rep2

tag: chip antibody


title: AA-019-2BL


title: Cebp_WT

city: Bethesda, MD

first: Frank

last: Gonzalez

address: Bldg. 37 National Institutes of Health

institute: National Institutes of Health, National Cancer Institute

data_processing:
Base calling was performed using RTA 3.10.30, demultiplexing was performed using cellranger v7.1.0 (Bcl2fastq 2.20.0), and alignment was performed using cellranger v7.1.0 (STAR 2.7.2a). Sequenced reads were aligned to the 10x Genomics provided mouse reference sequence (refdata-gex-mm10-2020-A).
Assembly: refdata-gex-mm10-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
The fresh livers were collected after performing the insitu perfusion-digestion. The dissociated cells were purified based on 35% percol centrifugation.
The cellular samples were loaded in the lanes according to the 10X Genomics 3’ v3.1 Single Cell User Guide with a single capture lane per sample targeting recovery of up to 6,000 cells per lane. Cell partitioning completed successfully with uniform emulsion consistency for all samples. Reverse transcription PCR was run overnight. All subsequent steps GEM recovery, cDNA generation, and quality control were performed as described in the 10X Genomics 3’ v3.1 Single Cell User Guide. Libraries were prepared using the 10X validated automation platform, Chromium Connect.

value: liver

value: Cebp WT

value: mice fed a NASH-promoting 40% HFCFD for 2 weeks


title: AB/Tub larvae, 0.0405 uM Ralox, Rep 5

city: Saskatoon

first: Morgan

last: Kirzinger

state: SK

address: 110 Gymnasium Place

country: Canada

institute: National Research Council

data_processing:
raw sequence fiels were trimmed for adapter sequence/low quality sequences using cutadapt
trimmed reads were aligned to the GRCz11 reference genome using STAR (default parameters)
raw read per gene counts from STAR were formatted into a matrix and imported into DESeq2 for differential gene expression analysis and pair wise comparison - results were filtered for visualization using an adjusted p-value = 0.05
corrected, normalized DEseq2 data tables were input directly into BMDexpress
Assembly: GRCz11
Supplementary files format and content: BMDExpress_ready_Raloxifene.tsv
Supplementary files format and content: BMDExpress_ready_Resorcinol.tsv

organism: Danio rerio

source_name: 20 Whole larvae

growth_protocol: Prior to treatment, larvae were stored in nursery baskets on a recirculating system.

extract_protocol:
Total RNA was extracted from each sample of 20 larvae using the Norgen BioTek Corp Total RNA Purification kit (Norgen Cat#17200, Thorold, ON, Canada) with the optional RNase-Free DNase I kit (Norgen Cat#25710, Thorold, ON, Canada).
Sequencing libraries were prepared using the Illumina Truseq Stranded mRNA kit using 1ug of total RNA.

treatment_protocol: At 72 hpf larvae were placed in 96-well plates in HEPES buffered E3 medium and 10X concentrations of test substnce were added. Plates were sealed and incubated at 28 degrees C until 120 hpf, were they were removed and flash frozen prior to RNA extraction.

value: 20 Whole larvae

value: 0.0405 uM Ralox

value: AB/Tub

tag: time

value: 72-120 hours post-fertilization


title: Cebp_KO

value: Cebp KO


title: Cut&Run Input_SA_rep1

value: FoxP3YFP X OT-II

value: splenocytes

value: SA


title: AB/Tub larvae, 0.0405 uM Ralox, Rep 4


title: Venus-negative TECs, rep3, scRNAseq

description:
10x Genomics
SCAF805_P6

source_name: Venus-negative TECs

value: Venus-negative TECs


title: AA-014-2BL

value: airway epithelium

value: AA


title: AA-014-3AC

tag: allergen

value: HDMdp


title: Cut&Run Input_DMSO_rep3

value: DMSO

value: replicate #3

value: none (Input)


title: ATAC-seq Treg_DMSO rep2

value: replicate #2


title: Venus-positive TECs, rep3, scRNAseq

description:
10x Genomics
SCAF804_P5

source_name: Venus-positive TECs

value: Venus-positive TECs

tag: genotype


title: AA-013-3DIL

value: F


title: AB/Tub larvae, 0.0405 uM Ralox, Rep 2

value: 20 Whole larvae

value: 0.0405 uM Ralox


title: Venus-negative TECs, rep2, scRNAseq

description:
10x Genomics
SCAF696_P6


title: AA-013-3AC


title: AB/Tub larvae, 0.0405 uM Ralox, Rep 1

value: AB/Tub

value: 72-120 hours post-fertilization


title: scRNA-seq Treg_SA

extract_protocol:
FoxP3 YFP+ CD4+ T cells were FACS-purified
scRNA-seq: Cells were loaded onto the Chromium Controller (10x Genomics) and the scRNA-seq libraries were prepared using the Chromium Next GEM Single Cell 3ʹ Reagent Kits (v3.1).

value: FoxP3YFP X OT-II

value: replicate #1


title: AA-013-2BL


title: scRNA-seq Treg_DMSO

value: splenocytes


title: AB/Tub larvae, 0.405 uM Ralox, Rep 5

value: 0.405 uM Ralox


title: Cut&Run cJun_SA_rep3

value: SA

value: c-Jun


title: Venus-negative TECs, rep1, scRNAseq

description:
10x Genomics
SCAF622_P6

value: Venus-negative TECs


title: Venus-positive TECs, rep2, scRNAseq

description:
10x Genomics
SCAF695_P5


title: AA-004-3DIL

value: airway epithelium

value: AA


title: AB/Tub larvae, 0.405 uM Ralox, Rep 3


title: Cut&Run cJun_SA_rep2


title: AB/Tub larvae, 0.0405 uM Ralox, Rep 3


title: AA-004-2BL


title: AA-002-3DIL


title: Cut&Run cJun_DMSO_rep3

value: DMSO

value: replicate #3


title: PR+/+ (heterozygous non-inducible), mouse 2 [IAO265]

city: Madrid

first: Orlando

last: Domínguez

address: Melchor F. Almagro 3

institute: CNIO

data_processing:
Raw images generated by the sequencer are submitted to analysis, per-cycle basecalling and quality score assignment with Illumina's RTA (Real Time Analysis) integrated primary analysis software. Conversion of BCL (base calls) binary files to FASTQ format was subsequently performed with BuildFASTQ from Local Run Manager GenerateFASTQ Analysis Module (Illumina).
Sequencing read alignment and quantification and differential gene expression analysis was performed in the Bluebee Genomics Platform, a cloud-based service provider (www.bluebee.com) employing the following steps.
Reads were first trimmed with bbduk from BBTools (Bushnell B., BBMap, https://sourceforge.net/projects/bbmap/) to remove adapter sequences and polyA tails.  Trimmed reads were aligned with STAR v 2.5 (Dobin A et al. Bioinformatics 29:15, 2013.) Read counting was performed with HTSeq (Anders S et al. Bioinformatics 31:166, 2015.)
Differential gene expression analysis was performed with DESeq2 (Love MI et al. Genome Biol 15:550, 2014)
Assembly: GRCm38/mm10
Supplementary files format and content: Normalized counts and results tables from DESeq2 counts() and results() functions, respectively, in a single MS Excel sheet.

extract_protocol:
Total RNA was extracted from liver tissue using TRIzol reagent (Invitrogen), according to the manufacturer’s protocols. A portion of the RNA was purified a second time with the RNA Clean & Concentrator-5 kit (Zymo Research), according to manufacturer’s instructions, and submitted to standard quality controls.
3'-end RNA-seq; RNA Quality scores were 7.2 on average (range 7.0-7.4). Sequencing libraries were prepared from 300ng total RNA samples with the "QuantSeq 3‘ mRNA-Seq Library Prep Kit (FWD) for Illumina" (Lexogen, Cat.No. 015) by following manufacturer instructions. {This kit generates directional libraries stranded in the sense orientation (the read1 (the only read in single read format) has the sense orientation (--library-type fr-secondstrand in TopHat, --stranded=yes in HTSeq).}

value: liver


title: AB/Tub larvae, 0.405 uM Ralox, Rep 2


title: Cut&Run cJun_SA_rep1


title: AA-002-3AC

data_processing:
Fastq reads aligned to Ensembl Genome build and annotation GRCh38.95
Read counts per gene output by STAR  --quantMode GeneCounts
STAR parameters: --outFilterType BySJout --outFilterMismatchNoverLmax 0.04 --outFilterMismatchNmax 999 --alignSJDBoverhangMin 1 --outFilterMultimapNmax 1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000  --limitBAMsortRAM 96000000000 --outSAMtype BAM Unsorted
Supplementary files format and content: ACE_longRNAseq_gene_counts_file.csv.gz

value: F

value: Cat


title: PR+/+ (heterozygous non-inducible), mouse 1 [IAO264]


title: Cut&Run Input_DMSO_rep2

value: replicate #2

value: none (Input)


title: AB/Tub larvae, 0.405 uM Ralox, Rep 1

value: 20 Whole larvae

value: AB/Tub

value: 72-120 hours post-fertilization


title: Cut&Run cJun_DMSO_rep2

value: FoxP3YFP X OT-II

value: splenocytes


title: Cut&Run cJun_DMSO_rep1

value: replicate #1


title: PR+/KI (heterozygous inducible), mouse 1 [IAO238]

value: Col1A1PR97/+ Rosa26+/rtTA


title: AA-002-2BL


title: human Colon line 118, HNF4A OE virus infected

city: New York

first: Sanlan

last: Li

address: 1300 York Avenue

institute: Weill Cornell Medicine

description:
HCO118OE
raw_counts.txt

data_processing:
Briefly, reads alignment was performed by STAR package,the raw count tables were generated by featureCounts
Assembly: hg38
Supplementary files format and content: tab-delimited txt file containing clean counts for each sample

source_name: colon organoid

growth_protocol: Human colon orgnoid lines were cultured and maintained in human colon 3D medium contraining 70% condition medium and appropriate small molecules in Advanced DMEM/F12 base medium at 37 degree incubator with 5% CO2.

extract_protocol:
We used and followed ZYMO micro RNA extraction kit protocol to extract the RNA
The library construction strategy was non-directional eukaryotic mRNA library by using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina.

treatment_protocol: 72h after infected with control virus or HNF4A virus, the human colon organoids were selected by puromycin (1ug/mL) for 4 days and differentiated in human colon differentiation medium for 4 days before harvesting samples for RNA extraction.

value: colon organoid

tag: cell line

value: colon epithelial cells

value: HNF4A OE

value: Infected with HNF4A OE virus


title: AB/Tub larvae, 4.05 uM Ralox, Rep 4

value: 4.05 uM Ralox


title: AB/Tub larvae, 4.05 uM Ralox, Rep 5


title: Cut&Run Input_DMSO_rep1

value: DMSO

tag: replicate


title: Cut&Run cFOS_SA_rep3

value: SA

value: replicate #3

value: c-Fos


title: AB/Tub larvae, 0.405 uM Ralox, Rep 4

value: 0.405 uM Ralox


title: human Colon line 118,  Control virus infected

description:
HCO118C
raw_counts.txt

value: Control

value: Infected with control virus expressing mCherry


title: AB/Tub larvae, 4.05 uM Ralox, Rep 3

value: 20 Whole larvae

value: AB/Tub

value: 72-120 hours post-fertilization


title: KCs_treated3

city: Calgary

first: Paul

last: Gordon

state: AB

address: 3330 Hospital Drive NW

institute: University of Calgary

description: KCs isolated from CCl4 treated mouse

data_processing:
Transcriptome pseudomapping of raw reads using Kallisto v0.42.4
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include Transcripts Per Million values for each Sample

source_name: liver fibrosis

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina following manufacturer's protocols.

treatment_protocol: mice were treated with 0.75 mL/kg carbon tetrachloride (Sigma-Aldrich) dissolved in corn oil (Sigma-Aldrich) 3 times a week for 8 weeks.

value: liver fibrosis

value: liver resident macrophage (Kupffer cells)

value: Wild-type


title: Cut&Run cFOS_SA_rep2

value: FoxP3YFP X OT-II

value: splenocytes

value: replicate #2


title: Venus-positive TECs, rep1, scRNAseq

description:
10x Genomics
SCAF621_P5

value: Venus-positive TECs


title: AB/Tub larvae, 4.05 uM Ralox, Rep 2

value: 4.05 uM Ralox


title: human Colon line 80, HNF4A OE virus infected

description:
HCO80OE
raw_counts.txt

value: colon organoid

value: colon epithelial cells

value: HNF4A OE

value: Infected with HNF4A OE virus


title: Cut&Run cFOS_SA_rep1

value: SA

value: replicate #1

value: c-Fos


title: KCs_treated1

description: KCs isolated from CCl4 treated mouse


title: human Colon line 80, Control virus infected

description:
HCO80C
raw_counts.txt

value: Control

value: Infected with control virus expressing mCherry


title: KCs_treated2-4

description: KCs isolated from CCl4 treated mouse

value: liver fibrosis


title: AB/Tub larvae, 40.5 uM Ralox, Rep 5

value: 20 Whole larvae

value: 40.5 uM Ralox

value: AB/Tub

value: 72-120 hours post-fertilization


title: Cut&Run cFOS_DMSO_rep2

value: FoxP3YFP X OT-II

value: splenocytes

value: DMSO

value: replicate #2


title: human Colon line 83, HNF4A OE virus infected

description:
HCO83OE
raw_counts.txt

value: colon organoid

value: colon epithelial cells


title: human Colon line 83, Control virus infected

description:
HCO83C
raw_counts.txt


title: Cut&Run cFOS_DMSO_rep3

value: replicate #3


title: PR+/KI (heterozygous inducible), mouse 2 [IAO240]

value: liver

value: Col1A1PR97/+ Rosa26+/rtTA


title: KCs_control5

description: KCs isolated from naïve mouse

value: liver resident macrophage (Kupffer cells)

value: Wild-type

value: control untreated


title: Cut&Run cFOS_DMSO_rep1

value: replicate #1

value: c-Fos


title: KCs_control3

description: KCs isolated from naïve mouse


title: AB/Tub larvae, 40.5 uM Ralox, Rep 3

value: 20 Whole larvae

value: 40.5 uM Ralox


title: human Colon line 89, HNF4A OE virus infected

description:
HCO89OE
raw_counts.txt

value: HNF4A OE

value: Infected with HNF4A OE virus


title: siS100A16-3

city: Luohe

first: Yafei

last: Shen

state: Henan

address: 56 Renmin East Road

institute: Luohe Central Hospital

data_processing:
HISAT2 software (version 2.1.0) and DESeq2 software (version 1.14.1) were used to identify differentially expressed genes (DEGs) between each sample using the following filter criteria: P value <0.05 and the absolute value of log2FC >1.
Assembly: mm10
Supplementary files format and content: Excel file includes FPKM for each file

source_name: Bone

growth_protocol: All rats were sacrificed via cervical dislocation and then the whole rats were immersed in 75% ethanol for 15 min for sterilization. Bone marrow cells were isolated from Collum femoris with DMEM and cultured at a temperature of 37°C in the presence of 5% CO2. After three passages, BMSCs were characterized via flow cytometry to detect hematopoietic markers (i.e., CD11b and CD45) and BMSC markers (i.e., CD90 and CD44). The antibodies used were as follows: PE-conjugated mouse anti-CD11b antibody (Santa Cruz Biotechnology Inc., sc-53086 PE), PE-conjugated mouse anti-CD45 antibody (BioLegend Inc., 202207), PE-conjugated mouse anti-CD90 antibody (BioLegend, 202523), and PE-conjugated mouse anti-CD44 antibody (Santa Cruz, sc-7297 PE). All in vitro experiments were performed using cells from passages 3–5.

extract_protocol:
The total RNA of each cell lysate sample was extracted from siRNA interference or scramble groups using RNeasy Mini Kit (QIAGEN) following the manufacturer's instruction.
Sequencing libraries were generated using Unicellular RNAseq Library Prep Kit (Hangzhou Kaitai Biotech Co., Ltd., Hangzhou, China).

value: Bone

value: Mesenchymal stem cells

value: S100A16 silenced

value: Osteogenic differentiation


title: siS100A16-2


title: KCs_control4

description: KCs isolated from naïve mouse


title: human Colon line 88, HNF4A OE virus infected

description:
HCO88OE
raw_counts.txt

value: colon organoid

value: colon epithelial cells


title: siS100A16-1


title: AB/Tub larvae, 40.5 uM Ralox, Rep 2

value: AB/Tub

value: 72-120 hours post-fertilization


title: KCs_control2

description: KCs isolated from naïve mouse

value: liver

value: liver resident macrophage (Kupffer cells)


title: AB/Tub larvae, 40.5 uM Ralox, Rep 1


title: AB/Tub larvae, 40.5 uM Ralox, Rep 4


title: AB/Tub larvae, 405 uM Ralox, Rep 5

value: 405 uM Ralox


title: siNC-3

value: Control


title: T1_3, biological replicate 3, WGS

city: Little Rock

first: Stephanie

middle: D

last: Byrum

state: Arkansas

address: 501 Jack Stephens Dr, Jackson T. Stephens Bldg 4th floor

institute: University of Arkansas for Medical Sciences

data_processing:
DNA sequencing files were processed using the nf-core/sarek pipeline (v3.0.1)
Assembly: GRCh38
Supplementary files format and content: processed data are provided in vcf files which include the unfiltered variants in each of the cell lines compared to the control cell line (A10).

source_name: cell line

extract_protocol:
DNA was prepared via the novel ProMTag Multiomics workflow described in the manuscript. The DNA was treated with RNase A before being sent to Novogene for WGS.
Genomic DNA was sheared into 350 bp fragments and libraries were constructed using the NEBNext DNA Library Prep Kit, followed by end repair, dA-tailing, and ligation with NEBNext adapter. Fragments (300-500 bp) were PCR enriched by p5 and indexed P7 oligos.

value: cell line


title: AB/Tub larvae, 405 uM Ralox, Rep 4

value: 20 Whole larvae


title: PMH, OE2

first: Tingting

last: Yan

state: Maryland

address: Building 37, Room 3106, Mail Stop 4255

institute: National Institutes of Health

data_processing:
For RNA-seq data analysis, reads of the samples were trimmed for adapters and low-quality bases using Trimmomatic 0.36 software before alignment with the reference genome (Mouse-mm10) and the annotated transcripts using STAR 2.5.1.
The mapping statistics were calculated using Picard 1.84 software.
Library complexity was measured in terms of unique fragments in the mapped reads using Picard’s MarkDuplicate utility.
The gene expression quantification analysis was performed for all samples using STAR/RSEM 1.2.22 tools.
Differential gene expression was assessed with DESeq2 with the parameters P-adj 0.05 and log2 fold 1 (for 2-fold differentially expressed genes).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM and FPKM values for each Sample

source_name: Primary Hepatocyte

extract_protocol:
Using Rneasy Plus Mini Kit (#74136, Qiagen)
Illumina TruSeq Stranded mRNA Library Prep (#20020596, Illumina)

value: Primary Hepatocyte

value: Ad-m-Cebpa (Overexpression)

value: biol rep 2


title: AB/Tub larvae, 4.05 uM Ralox, Rep 1

value: 4.05 uM Ralox


title: siNC-2

value: Bone

value: Mesenchymal stem cells


title: PMH, OE1

value: biol rep 1


title: AB/Tub larvae, 405 uM Ralox, Rep 3


title: siNC-1

value: Osteogenic differentiation


title: PMH, GFP3

value: Ad-GFP

value: biol rep 3


title: T1_2, biological replicate 2, WGS


title: T1_1, biological replicate 1, WGS


title: AB/Tub larvae, 405 uM Ralox, Rep 2

value: AB/Tub

value: 72-120 hours post-fertilization


title: human Colon line 89, Control virus infected

description:
HCO89C
raw_counts.txt

value: colon organoid

value: colon epithelial cells

value: Infected with control virus expressing mCherry


title: PMH, GFP2


title: AB/Tub larvae, 405 uM Ralox, Rep 1

value: 405 uM Ralox


title: human Colon line 88, Control virus infected

description:
HCO88C
raw_counts.txt

value: Control


title: NeoT_3, biological replicate 3, WGS

value: cell line


title: PMH, OE3

value: Primary Hepatocyte

value: Ad-m-Cebpa (Overexpression)


title: AB/Tub larvae, Carrier Control 1% Resor, Rep 4

value: 20 Whole larvae

value: Carrier Control 1% Resor


title: CA1_3, biological replicate 3, WGS


title: KCs_control1

description: KCs isolated from naïve mouse

source_name: liver

value: liver

value: liver resident macrophage (Kupffer cells)

value: Wild-type

value: control untreated


title: AB/Tub larvae, Carrier Control 1% Resor, Rep 5


title: NeoT_2, biological replicate 2, WGS


title: PMH, KO3

value: Cebpa{delta}Alb

value: biol rep 3


title: AB/Tub larvae, Carrier Control 1% Resor, Rep 3

value: AB/Tub

value: 72-120 hours post-fertilization


title: NeoT_1, biological replicate 1, WGS


title: PMH, GFP1

value: Ad-GFP

value: biol rep 1


title: CA1_2, biological replicate 2, WGS


title: PMH, WT3

value: Cebpafl/fl


title: AB/Tub larvae, Carrier Control 1% Resor, Rep 1


title: PMH, KO1


title: CA1_1, biological replicate 1, WGS


title: AB/Tub larvae, 0.00201 uM Ralox, Rep 5

value: 0.00201 uM Ralox


title: PMH, WT2

value: biol rep 2


title: A10_2, biological replicate 2, WGS

value: cell line


title: PMH, WT1

value: Primary Hepatocyte


title: AB/Tub larvae, 0.00201 uM Ralox, Rep 3

value: 20 Whole larvae


title: AlbCBHFD2W_KO6

source_name: Liver

value: Liver

value: Cre+

value: biol rep 6


title: A10_1, biological replicate 1, WGS


title: PMH, KO2


title: T1_3, biological replicate 3, RNA-Seq

data_processing:
RNAseq data was analyzed using the nf-core/rnaseq pipeline (v3.4). The human genome GRCh38 was used as the reference genome. Counts obtained using the ‘--aligner_star_salmon’ option were transformed to log2 counts per million (CPM). Low expressed genes were filtered out and libraries normalized by trimmed mean of M-values. Differential expression was performed using limma voom with quality weights and p-values were corrected for multiple testing using the Benjamini-Hochberg procedure. Genes with a false discovery rate (FDR) p-value < 0.05 and fold change > 2 were considered significant
Assembly: GRCh38
Supplementary files format and content: processed data are provided in a single tsv file which includes gene counts.

extract_protocol:
RNA was prepared via the novel ProMTag Multiomics workflow described in the manuscript. The RNA was treated with DNase I before being sent to Novogene for RNA sequencing.
1 µg RNA per sample was used to generate sequencing libraries using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations.


title: AB/Tub larvae, 0.00201 uM Ralox, Rep 1


title: AlbCBHFD2W_KO5

value: biol rep 5


title: AlbCBHFD2W_KO3


title: AB/Tub larvae, 0.00201 uM Ralox, Rep 2


title: T1_2, biological replicate 2, RNA-Seq


title: AlbCBHFD2W_KO2


title: AB/Tub larvae, Carrier Control 1% Resor, Rep 2

value: Carrier Control 1% Resor


title: T1_1, biological replicate 1, RNA-Seq


title: AB/Tub larvae, 0.0201 uM Ralox, Rep 5

value: 0.0201 uM Ralox


title: NeoT_3, biological replicate 3, RNA-Seq


title: A10_3, biological replicate 3, WGS


title: AlbCBHFD2W_KO4

value: biol rep 4


title: NeoT_2, biological replicate 2, RNA-Seq


title: RBM5/10-deficient +RBM10-Flag rep 4

data_processing:
Sequencing reads were mapped to hg19 using star (--alignEndsType EndToEnd --outFilterMultimapNmax 1 --outFilterMismatchNmax 2)
splicing analysis were done by using rMATS4.0.2
Assembly: hg19
Supplementary files format and content: excel files include significant dofferential alternative splicing events in each tabs

growth_protocol: Cells were trypsinized and transferred in 5-cm plates at 7.5E+5 cells per plate and grown overnight in 5 mL DMEM + 10% FBS at 37°C, 5%CO2.

extract_protocol:
Total RNA from freshly harvested cells was obtained with TRIzol reagent (Thermo Fisher Scientific), contaminating DNA was removed by treatment with TURBO DNase (Thermo Fisher Scientific).
Sequencing libraries were prepared from 200 ng total RNA with TruSeq Stranded mRNA library kit (Illumina).

treatment_protocol: The medium was replaced on the next day with fresh medium, supplemented with indicated amount of Doxycycline. The cells were then grown of 72 hours, and harvested in PBS, and split into aliquots for protein and RNA analyses.

value: immortalized human embryonic kidney cells

value: 0.06 ug/µL Doxycycline, 72 hours


title: AlbCBHFD2W_WT5

value: Cre-


title: AB/Tub larvae, 0.0201 uM Ralox, Rep 3

value: AB/Tub

value: 72-120 hours post-fertilization


title: RBM5/10-deficient +RBM10-Flag rep 3


title: NeoT_1, biological replicate 1, RNA-Seq


title: RBM5/10-deficient +RBM10-Flag rep 2


title: AB/Tub larvae, 0.0201 uM Ralox, Rep 2


title: AB/Tub larvae, 0.00201 uM Ralox, Rep 4

value: 0.00201 uM Ralox


title: AlbCBHFD2W_WT4


title: CA1_3, biological replicate 3, RNA-Seq


title: AB/Tub larvae, 0.201 uM Ralox, Rep 5

value: 0.201 uM Ralox


title: AlbCBHFD2W_WT2

value: biol rep 2


title: CA1_2, biological replicate 2, RNA-Seq

value: cell line


title: AB/Tub larvae, 0.0201 uM Ralox, Rep 1

value: 20 Whole larvae


title: RBM5/10-deficient +RBM10-Flag rep 1


title: RBM5/10-deficient +RBM5-Flag rep 4

value: 0.6 ug/µL Doxycycline, 72 hours


title: CA1_1, biological replicate 1, RNA-Seq


title: RBM5/10-deficient +RBM5-Flag rep 3


title: AlbCBHFD2W_WT1

value: Liver

value: biol rep 1


title: AB/Tub larvae, 0.201 uM Ralox, Rep 3


title: AB/Tub larvae, 0.0201 uM Ralox, Rep 4


title: RBM5/10-deficient +RBM5-Flag rep 2


title: AB/Tub larvae, 0.201 uM Ralox, Rep 4


title: HFD12WT10W_WT5

value: biol rep 5


title: A10_1, biological replicate 1, RNA-Seq


title: A10_2, biological replicate 2, RNA-Seq


title: AB/Tub larvae, 0.201 uM Ralox, Rep 2


title: HFD12WT10W_KO5

value: Cre+


title: RBM5/10-deficient +RBM5-Flag rep 1


title: RBM5/10-deficient rep 4


title: AlbCBHFD2W_WT3

value: biol rep 3


title: AB/Tub larvae, 2.01 uM Ralox, Rep 5

value: 2.01 uM Ralox


title: W3

city: Milan

first: Paolo

last: Gandellini

state: Milan

address: Via celoria 26

department: Bioscience

country: Italy

institute: University of Milan

description: non-edited clone

data_processing:
RNA-seq reads were aligned to NCBI RefSeq GRCh38/hg38 genome using STAR.
Gene intensities were computed using RSEM-1.3.1 software.
Assembly: hg38
Supplementary files format and content: tab-delimited genes.results files include raw counts for each sample.
Supplementary files format and content: tab-delimited genes.results files include TPM values for each sample.

source_name: lung

growth_protocol: H520 cells were maintained in RPMI 1640 with stable L-Glutamine (Euroclone S.p.A., Pero, Italy) culture medium supplemented with 10% fetavl bovine serum and 25 mM Hepes (Euroclone S.p.A., Pero, Italy), and cultured at 37°C and 98% relative humidity in a 5% CO2 atmosphere.

extract_protocol:
H520 cells at 48 hours after Gapmer antisense oligonucleotide transfection and CRISPR edited and non-edited clones were washed with PBS Dulbecco’s Phosphate Buffered Saline (Euroclone S.p.A., Pero, Italy) and incubated with Trypsin/EDTA 1X in Phosphate Buffered Saline (Euroclone S.p.A., Pero, Italy) at 37°C for 5 min. Cells were collected and pelleted. Total RNA was isolated from cellular pellets using QIAzol Lysis Reagent and miRNeasy Mini Kit (QIAGEN, Hilden, Germany) with DNase I digestion (QIAGEN, Hilden, Germany) according to the manufacturer’s instructions. RNA integrity was checked through agarose gel electrophoresis. RNA yield and A260/A280 ratio were monitored with Nabi - UV/VIS Nano Spectrophotometer MicroDigital (TWIN HELIX SRL, Rho, Italy). For gene-expression profiling studies, RNA integrity numbers were also measured using 4200 TapeStation System (Agilent Technologies, Santa Clara, CA, USA).
Total RNA was purified through oligo-dT-based RNA capturing, randomly fragmented and transformed into cDNA with NEB library preparation protocol. Library preparation was performed by Novogene, UK.

value: lung

value: lung squamous carcinoma cells

value: WT


title: HFD12WT10W_WT3

value: Cre-


title: W2

description: non-edited clone


title: RBM5/10-deficient rep 3

value: immortalized human embryonic kidney cells


title: AB/Tub larvae, 0.201 uM Ralox, Rep 1

value: AB/Tub

value: 72-120 hours post-fertilization


title: A10_3, biological replicate 3, RNA-Seq


title: AB/Tub larvae, 2.01 uM Ralox, Rep 3


title: AB/Tub larvae, 2.01 uM Ralox, Rep 4


title: RBM5/10-deficient rep 2


title: RBM5/10-deficient rep 1


title: W1

description: non-edited clone


title: AB/Tub larvae, 2.01 uM Ralox, Rep 2


title: HFD12WT10W_WT2

value: biol rep 2


title: E5

description: edited clone

value: NFYC-AS1 knockout


title: HFD12WT10W_WT1


title: E4

description: edited clone


title: AB/Tub larvae, 2.01 uM Ralox, Rep 1

value: 20 Whole larvae


title: HFD12WT10W_KO3


title: HFD12WT10W_KO4

value: biol rep 4


title: PGE2-5

city: Lausanne

first: Nicolas

last: Rayroux

address: Rue du Bugnon 25A

department: Oncology

country: Switzerland

institute: Centre Hospitalier Universitaire Vaudois

data_processing:
STAR Aligner, 2.6.0, Reads were aligned on GRCh37
samtools, 1.8
FastQC, 0.11.7
Htseq, 0.9.1,  read count extraction
Assembly: GRCh37
Supplementary files format and content: tab-delimited text files includes raw counts for each sample

source_name: Exhausted human peripheral CD8+ T-cells + PGE2 (1uM)

growth_protocol: Cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS), at 37°C in 5% CO2 atmosphere and 60 IU of IL-2. CD3/CD28 beads at ratio 1:1 were used for exhausted T-cells

extract_protocol:
CD8+ sorted T-cells. Total RNA was extracted using an RNeasy Mini Kit (Qiagen)
RNA quality was assessed using the Fragment Analyzer. RNA sequencing libraries were prepared using the Illumina TruSeq Stranded according to the protocol supplied by the manufacturer and using 500ng of total RNA and sequenced using HiSeq 4000 SR

treatment_protocol: PGE2 1uM (Sigma) was added for 24hours. CD8+ T-cells were then enriched using available commercial kits (Miltenyi)

value: blood

value: peripheral blood lymphocytes

value: IL-2 (60IU) + Prostaglandin E2 (1UM)

tag: treatment source

value: IL-2 (aldesleukin, novartis) + PGE2 (P5640 Sigma)


title: E2

description: edited clone


title: PGE2-1


title: HFD12WT10W_KO2

value: Liver

value: Cre+


title: AB/Tub larvae, 20.1 uM Ralox, Rep 5

value: 20.1 uM Ralox


title: HFD12WT10W_WT4


title: E1

description: edited clone

value: lung

value: lung squamous carcinoma cells


title: AB/Tub larvae, 20.1 uM Ralox, Rep 4


title: PGE2-3


title: Ctrl-5

source_name: Exhausted human peripheral CD8+ T-cells

value: IL-2 (aldesleukin, novartis)


title: HFD12WT10W_KO1

value: biol rep 1


title: HFD8WT10D_WT5

value: Cre-

value: HFCFD8W+Tamoxfen 10D

value: biol rep 5


title: R4D

description: bulk

value: NFYC-AS1 knockdown


title: Ctrl-3


title: AB/Tub larvae, 20.1 uM Ralox, Rep 3

value: 20 Whole larvae

value: AB/Tub

value: 72-120 hours post-fertilization


title: HFD8WT10D_KO5


title: AB/Tub larvae, 20.1 uM Ralox, Rep 2


title: R4B

description: bulk


title: HFD8WT10D_KO4

value: biol rep 4


title: AB/Tub larvae, 20.1 uM Ralox, Rep 1


title: N6

source_name: unstimulated human peripheral CD8+ T-cells + PGE2

value: blood

value: peripheral blood lymphocytes

value: IL-2 (60IU) + Prostaglandin E2 (1UM)


title: AB/Tub larvae, Carrier Control 0.5% Ralox, Rep 5

value: Carrier Control 0.5% Ralox


title: N5

value: IL-2 (aldesleukin, novartis) + PGE2 (P5640 Sigma)


title: HFD8WT10D_WT4

value: Liver


title: R3D

description: bulk

value: lung

value: lung squamous carcinoma cells


title: N4


title: R4A

description: bulk


title: HFD8WT10D_KO3

value: Cre+

value: biol rep 3


title: R3C

description: bulk


title: AB/Tub larvae, Carrier Control 0.5% Ralox, Rep 3


title: AB/Tub larvae, Carrier Control 0.5% Ralox, Rep 4


title: AB/Tub larvae, Carrier Control 0.5% Ralox, Rep 2


title: N2

source_name: unstimulated human peripheral CD8+ T-cells

value: IL-2 (aldesleukin, novartis)


title: HFD8WT10D_WT2

value: Cre-

value: HFCFD8W+Tamoxfen 10D

value: biol rep 2


title: R4C

description: bulk

value: NFYC-AS1 knockdown


title: N3


title: HFD8WT10D_KO2


title: HFD8WT10D_WT3


title: R3B

description: bulk


title: R3A

description: bulk


title: AB/Tub larvae, Carrier Control 0.5% Ralox, Rep 1

value: 20 Whole larvae

value: AB/Tub

value: 72-120 hours post-fertilization


title: N1

value: blood

value: peripheral blood lymphocytes


title: R2D

description: bulk


title: Ctrl-1


title: MCF-7 PIN1-KO cells biol rep 2

city: boston

first: Shizhong

last: Ke

state: Massachusetts

address: 3 BLACKFAN CIRCLE, CLS0428D

institute: Beth Israel Deaconess Medical Center (BIDMC)

data_processing:
Quality Control (QC) of Raw Data: The first step is to check the quality of the raw sequence data.
Sequence reads were trimmed for adaptor sequence/low-quality sequence
Trimmed sequence reads were mapped to human_hg38
raw counts of sequencing reads extraction and normalization were performed
Assembly: human_hg38
Supplementary files format and content: tab-delimited text files include raw counts of sequencing reads for each sample

growth_protocol: breast cancer cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). Total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Human breast cancer


title: 0768 mutant s4

city: MILWAUKEE

first: CHRIS

last: KRISTICH

state: WI

address: 8701 WATERTOWN PLANK RD

institute: MCW

data_processing:
Illumina Casava 1.7 software used for basecalling.
TrimGalore v. 0.6.6 used to quality filter and trim reads
Bowtie 2 v. 2.3.4.3 used to align trimmed reads to reference (OG1RF: NC_017316.1)
Samtools v. 1.11 used to convert SAM to BAM and sort alignments
featureCounts was used to count reads; stranded set to reverse (-s 2), -t gene -g gene_id
DESeq2 was used for differential expression testing.
Assembly: NC_017316.1
Supplementary files format and content: tab-delimited file containing raw counts (output of featureCounts) of all samples

organism: Enterococcus faecalis

source_name: bacterial culture

growth_protocol: Exponentially growing bacterial cultures in Mueller-Hinton broth in shaking flasks at 37 C

extract_protocol:
Total RNA was purified from cells, then subjected to rRNA depletion
TruSeq stranded libraries were prepared using standard Illumina protocols

treatment_protocol: No treatment applied

tag: strain

value: 768 mutant


title: R2C

description: bulk

tag: tissue


title: HFD8WT10D_KO1

value: Liver

value: biol rep 1


title: MCF-7 PIN1-KO cells biol rep 1


title: 0768 mutant s3


title: R2B

description: bulk

value: lung

value: lung squamous carcinoma cells


title: 22 month rep3

city: Hefei

first: Ding

middle: feng

address: Huang shan road 443

institute: USTC

data_processing:
Sequencing quality was examined by FastQC
Trimmed reads pass Illumina quality filter, trimmed 3¡¯-adaptor bases by cutadapt
Trimmed reads were aligned to mature-tRNA and pre-tRNA sequences from GtRNAdb using NovoAlign software
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited txt files include normalized tsRNA expression for each group

source_name: brain

extract_protocol:
Total RNA was extracted by Trizol. Total amount of 2 ug RNA per sample was used as input material for the RNA sample preparations. For standard small RNA sequencing on Illumina NextSeq instrument, the sequencing type is 50-bp single-read at 10M reads.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: brain

value: 22 months


title: 0768 mutant s2

value: 0768 mutant


title: MCF-7 WT cells biol rep 2

value: WT


title: 22 month rep2


title: MCF-7 WT cells biol rep 1


title: R2A

description: bulk


title: 0768 mutant s1


title: RND

description: bulk


title: MDA-MB-468 PIN1-KO cells biol rep 2


title: RNC

description: bulk


title: RNB

description: bulk


title: 3 month rep3

value: 3 months


title: 3 month rep2


title: MDA-MB-468 PIN1-KO cells biol rep 1


title: HFD8WT10D_WT1

value: Cre-

value: HFCFD8W+Tamoxfen 10D