title: PP_12: Postpartum cow 3 d100

source_name: Endometrial tissue in fertile cow_3


title: PP_13: Postpartum cow 4 d10

status: Public on Jan 16 2021

type: RNA

city: Aichi-gun

first: Shuichi

last: Matsuyama

address: 94 Hatajiri, Morowa

country: Japan

institute: Nagoya University

hyb_protocol: For microarray hybridization, 1650 ng of Cy3-labeled cRNA was fragmented and hybridized on a slide of bovine 4 × 44K microarray (Agilent Technologies; 023647) at 65°C for 17 hours.

scan_protocol: Slides were scanned on the Agilent G2505C DNA microarray scanner.

data_processing: Background correction of the Cy3 raw signals was performed using the Agilent Feature Extraction software (version 10.5.1.1). Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

molecule: total RNA

organism: Bos taurus

source_name: Endometrial tissue in fertile cow_4

label_protocol: One-color spike-mix was added to the total RNA prior to the labeling reaction. Labeling was performed using a Quick Amp Labeling Kit, One-Color (Agilent Technologies) in the presence of cyanine-3 (Cy3)-CTP according to the manufacturer's protocol.

extract_protocol: Total RNA was extracted from the endometrial samples using RNeasy Plus Universal Mini kit (Qiagen) according to the manufacturer’s instructions. Total RNA quality and quantity were confirmed using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and a NanoDrop ND-1000 (Thermo Fisher Scientific, Waltham, MA, USA), respectively.

tag: animal no.

tag: days after parturition

tag: tissue

value: endometrium


title: D11_OFF_D7

type: SRA

city: Stanford

first: Evan

middle: W

last: Weber

state: California

address: 265 Campus Drive, SIM1, Room G2105

department: Stanford Cancer Institute

country: USA

institute: Stanford University

description:
Processed_log2TPM_Tuning-CAR-dataset.csv
Donor3047_D11_OFF_D7

library_source: transcriptomic

data_processing:
Expression levels of genes were quantified using Kallisto 0.44.0 , with Gencode v27 reference transcriptome , and hg38 as the reference human genome
TPMs were summed for transcript-level quantification
TPM
Genome_build: hg38
Supplementary_files_format_and_content: TPM

organism: Homo sapiens

source_name: CAR T CELLS

extract_protocol:
Cryopreserved T cells were thawed and activated on day 0 with Human T-Expander αCD3/CD28 Dynabeads (Gibco) at 3:1 bead:cell ratio in T cell media (AIMV supplemented with 5% FBS, 10mM HEPES, 2mM GlutaMAX, 100 U/mL penicillin, and 100ug/mL streptomycin (Gibco). Recombinant human IL-2 (Peprotech) was provided at 100 U/mL. Lentiviral transduction was done on day 1 and retroviral transductions were done on days 2 and 3 post-bead activation. Magnetic beads were removed on day 4, and T cells were fed with fresh culture medium every 2-3 days and normalized to 0.5 x 106 cells/mL. For culture conditions requiring αPD-1, 5ug/mL nivolumab was added on D7 and supplemented every 2-3 days. For culture conditions requiring shield-1 (1uM unless otherwise noted), trimethoprim (1uM unless otherwise noted), dasatinib (1uM), or tazemetostat (1uM), freshly thawed drug was mixed with T cell culture medium and supplemented every 2-3d ays. HA.28ζ.FKBP CAR-T cells were rested via removal of either shield-1 or trimethoprim from the culture medium, whereby cells were washed 2X in PBS (changing conicals in between washes to ensure complete drug washout) and resuspended in fresh T cell culture medium lacking shield-1/trimethoprim. On days 7, 11, and 15 of culture, RNA was isolated using Qiagen mRNEasy kit.
Samples library prep and sequencing was performed by BGI America (Cambridge, MA)

tag: individual

tag: cell type

value: CAR T CELLS

tag: treatment

tag: culture conditions

value: Shield-1 D1-D7 + complete medium

tag: timepoint

value: Day 11


title: polyA RNA from AEC, harvested at 48hpi, SARS-CoV-2 infected, DMSO (solvent) treated, replicate 1

city: Berlin

first: Emanuel

last: Wyler

address: Robert Roessle Str 10

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max Delbrück Center for Molecular Medicine

description:
polyA RNA extracted from whole cells
AEC_SARSCoV2_17AAG_readcounts.tsv.gz
AECII_19_48h_S2_DMSO-1

data_processing:
Sequencing reads were aligned to the human genome (version hg19) using hisat2 (Kim et al., 2015, doi: 10.1038/s41587-019-0201-4), and reads counted using quasR (Gaidatzis et al., 2015, doi: 10.1093/bioinformatics/btu781)
Genome_build: hg19
Supplementary_files_format_and_content: tab separated values; readcounts

molecule: polyA RNA

source_name: AEC

growth_protocol: Airway epithelial cells (AEC) were prepared as described previously (Imai-Matsushima et al., 2018, doi: 10.1016/j.ebiom.2018.05.032)

extract_protocol:
For polyA/total/small RNA-seq, cells were lysed in Trizol and RNA extracted using standard methods.
RNA was extracted using the RNA clean and concentrator kit (Zymo) and subjected to bulk polyA RNA-sequencing using the NebNext Ultra II Directional RNA Library (New England Biolabs).

treatment_protocol: Infections were done by adding the appropriate amount of virus stock solution (produced in Vero E6 cells) at an MOI of 0.5 directly to the cells. For mock infections, supernatant from non-infected Vero E6 cells was used. Two hours after adding the virus, growth mediu was supplemented with DMSO (solvent control) or 17-AAG as indicated.

tag: infection

tag: moi

tag: time point


title: polyA RNA from AEC, harvested at 48hpi, SARS-CoV-2 infected, DMSO (solvent) treated, replicate 3

description:
polyA RNA extracted from whole cells
AEC_SARSCoV2_17AAG_readcounts.tsv.gz
AECII_21_48h_S2_DMSO-3


title: D11_A_ON_Nivo

description:
Processed_log2TPM_Tuning-CAR-dataset.csv
Donor3047_D11_A_ON_Nivo

value: Shield-1 D1-11 + anti-PD-1 D7-11 + complete medium


title: polyA RNA from AEC, harvested at 48hpi, mock infected, 17-AAG (200 nM) treated, replicate 3

description:
polyA RNA extracted from whole cells
AEC_SARSCoV2_17AAG_readcounts.tsv.gz
AECII_18_48h_200nM17AAG-3

value: mock


title: M_MCF10A-sh:p53_3D_rep2

city: Chapel Hill

first: Melissa

middle: A

last: Troester

state: NC

address: 135 Dauer Dr

institute: University of North Carolina

hyb_protocol: Standard Agilent protocol

scan_protocol: Standard Agilent protocol

data_processing: Microarray data were Lowess-normalized, and probes with signal >10 dpi in both channels and data present in at least 80% of samples were selected for further analysis. During data pre-processing, we: 1) eliminated probes without corresponding ENTREZ Gene IDs; 2) collapsed duplicate probes corresponding to the same ENTREZ Gene ID by averaging; and 3) imputed missing data using the k-nearest neighbors’ imputation with k = 10.

source_name: MCF10A-sh:p53 3D mono-culture

label_protocol: Samples were labeled and amplified using the Agilent Low Input Two-Color, QuickAmp Labeling kit (#5190-2306). Cy-5-labeled cDNAs were generated from all experimental samples, and reference RNA (Stratagene Universal Human Reference spiked 1:1000 with MCF-7 RNA and 1:1000 ME16C RNA to increase expression of breast cancer genes) was labeled with Cy-3.

growth_protocol: MCF10 series cells were maintained in Dulbecco’s modified Eagle’s medium/F12 nutrient mix (DMEM/F12, Gibco, Life Technologies, Carlsbad, CA) supplemented with 5% horse serum (Gibco), 20 ng/mL epidermal growth factor (Invitrogen, Life Technologies, Carlsbad, CA), 0.5 μg/mL hydrocortisone (Sigma-Aldrich, St. Louis, MO), 10 μg/mL insulin (Gibco), and 0.1 μg/mL cholera toxin (Millipore Sigma, Burlington, MA). RMFs were maintained in RPMI1640 medium with 10% fetal bovine serum prior to use in co-cultures. All cells were grown in a humidified incubator at 37°C and 5% CO2, and propagated for <6 months (breast cells) or <1 month (RMFs) prior to use in experiments.

extract_protocol: Cultures were rinsed with cold PBS, and technical replicates (2 cultures per independent experiment) were transferred into a single conical tube containing 800 μL of Cell Recovery Solution (#354253; Corning) on ice. Each well was rinsed with additional Cell Recovery Solution to ensure complete sample transfer. Phenol-chloroform RNA extraction was then performed using QIAzol lysis reagent (QIAGEN) according to the manufacturer’s instructions, with modifications: following centrifugal separation of the organic and aqueous phases, the aqueous phase was mixed with 100% ethanol at a ratio of 1:1 v/v and applied to a QIAGEN RNeasy column. RNA concentrations were determined using a NanoDrop 2000 Spectrophotometer (Thermo Fisher Scientific, Waltham, MA). Samples were further purified with the RNA Clean and Concentrator Kit (Zymo Research, Irvine, CA) as needed.

treatment_protocol: Cells were suspended in a biologically derived matrix comprised of 50% phenol red-free Matrigel (#356237; Corning, Corning, NY) and 50% rat-tail collagen I (#354236; Corning) diluted to a final concentration of 1 mg/mL as previously described [8, 9, 22, 23]. Suspended cells were then seeded into tissue culture plates pre-coated with the same matrix, and growth medium was dispensed to the apical side of each culture after 30-60 minutes. Cultures were constructed with the same total starting cell number (30,000 cells/mL for mono-cultures; 15,000 breast cells/mL + 15,000 RMFs/mL for co-cultures), rather than the same starting number of breast cells, to reduce the potential for nutrient deprivation in co-cultures. RMF mono-cultures (30,000 cells/mL) were generated as normalization controls for gene expression microarray analyses (see below). Cultures were refreshed with MCF10 growth medium every 2-3 days, and maintained for 14 days.

tag: cell line

tag: epithelial p53 status

value: p53-deficient (knock-down)

tag: sample type

value: reference


title: D11_A_ON

description:
Processed_log2TPM_Tuning-CAR-dataset.csv
Donor3047_D11_A_ON

value: Shield-1 D1-11 + complete medium


title: polyA RNA from AEC, harvested at 48hpi, mock infected, 17-AAG (200 nM) treated, replicate 2

description:
polyA RNA extracted from whole cells
AEC_SARSCoV2_17AAG_readcounts.tsv.gz
AECII_17_48h_200nM17AAG-2


title: PP_11: Postpartum cow 3 d50


title: D11_A_OFF

description:
Processed_log2TPM_Tuning-CAR-dataset.csv
Donor3047_D11_A_OFF

value: Complete medium


title: PP_10: Postpartum cow 3 d30


title: M_MCF10A-sh:p53_3D_rep1

source_name: Stratagene Universal Human Reference spiked 1:1000 with MCF-7 RNA and 1:1000 ME16C RNA


title: ATAC_Crypt_rep2

city: Piscataway

first: Michael

middle: P

last: Verzi

state: NJ

address: 145 Bevier Road

department: Genetics

institute: Rutgers, the State University of New Jersey

library_source: genomic

data_processing:
HiChIP-seq: Data were processed using the HiC-Pro pipeline, version 2.11.1.
HiChIP-seq: Reads were aligned to the mouse (mm9) genome assembly using bowtie2 (version 2.3.4.3) with mapping quality filter 15. HiC-Pro first performs global alignment using bowtie2 (--very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end –reorder) followed by local alignment (--very-sensitive -L 20 --score-min L,-0.6,-0.2 --end-to-end –reorder). Singleton, multi-mapped, and duplicate reads were removed. Reads were assigned to MboI restriction fragments using min and max size parameters of 100 and 100,000, respectively.
HiChIP-seq: HiC-Pro valid pairs were used as input for hichipper (version 0.7.0) to identify chromatin loops at regions known to contain active intestinal chromatin features, including promoter regions (identified by UCSC transcription start site +/- 2 kb). Active intestinal chromatin regions were defined from our data and public data sources of that empirically defined intestinal active chromatin regions, including ATAC-seq, DNase-seq, H3k4me3, H3K27ac and H3K4me3 ChIP-seq from intestinal stem, crypt, villus or intestinal epithelial cells.
MNase ChIP-seq: raw sequencing reads (fastq) were quality checked using fastQC (v0.11.3) and were further aligned to mouse (mm9) genomes using bowtie2 (v2.2.6) to obtain bam files.
MNase ChIP-seq: Deeptools bamCoverage (v2.4.2, duplicate reads ignored, RPKM normalized and extended reads) was used to generate bigwig files from bam files.
MNase ChIP-seq: Model-based Analysis of ChIP-Seq (MACS 1.4.1) was used for peak calling and to generate bed files from aligned reads.
ATAC-seq: Nextera transpose adapter reverse complement was removed from the 3’ end of the ATAC-seq reads using CutAdapt v1.9.1.
ATAC-seq: The trimmed FASTQ files were aligned to the mouse (mm9) genome using Bowtie2. The SAM files were converted into BAM files using the SAMtoBAM utility included in SAMtools v0.1.19. These BAM files were then sorted using the SortBAM utility included in SAMtools v0.1.19.
ATAC-seq: A BigWig file was generated for each sorted BAM file using the default parameters for the bamCoverage utility included in deeptools v2.4.2.
ATAC-seq:  A BED file was generated from each sorted BAM file using the BAMtoBED utility included in bedtools v2.17.0. The median insert size of each BED file was determined using the CollectInsertSizeMetrics utility included in the Picard v2.18.27 suite. Statistically significant enriched genomic regions (“peaks”) were identified from the BED files using MACS2 v2.1.0 with a 5’ shift of one-half the median insert length for each BED file.
Genome_build: mm9

molecule: genomic DNA

organism: Mus musculus

source_name: WT adult duodenal crypt cells

extract_protocol:
Freshly harvested duodenum was flushed with cold PBS, opened longitudinally, cut into 1 cm pieces, and then rotated in 3 mM EDTA in PBS for 5 mins, 10 mins and 40 mins at 4 °C (refresh EDTA/PBS every time). The tissue was then violently shaken to release the epithelium from underlying muscular tissue. The intestine pieces were discard and the supernatant was collected as whole epithelium fraction. 70-μm cell strainer was used to separate the villi and crypt fractions. Villi were collected from the top of a 70-μm cell strainer, while crypts passed through. Cells were pelleted by centrifugation at 170g at 4 °C, and followed by cold PBS wash. Duodenal villi and crypts were treated with pre-warmed 0.25% Trypsin for 8 mins at 37°C on a vortex station, neutralized with 10% FBS, and passed through a 40-μm cell strainer to obtain single cells for ATAC-seq. 50,000 cells were used for ATAC-seq. Briefly, cells were centrifuged at 500g for 5mins at 4°C, and resuspended in ice-cold lysis buffer (10 mM Tris, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% NP-40), followed by centrifugation at 500 g for 10 minutes at 4°C. The isolated nuclear pellets were incubated with a 50 μl reaction of Nextera Tn5 Transposase (Illumina FC-121-1030) for 30 min at 37°C. The transposed chromatin was purified with QIAquick PCR Purification Kit (QIAGEN) and PCR amplified with high-fidelity 2X PCR Master Mix (New England Biolabs M0541). The optimum number of additional cycles was based on 1/3 of the maximum fluorescent intensity. The PCR amplified libraries were purified, fragment size was selected using Pippin Prep.
NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs)

value: Adult crypt cells

value: jejunal epithelium

tag: genotype

value: WT


title: polyA RNA from AEC, harvested at 48hpi, mock infected, 17-AAG (200 nM) treated, replicate 1

description:
polyA RNA extracted from whole cells
AEC_SARSCoV2_17AAG_readcounts.tsv.gz
AECII_16_48h_200nM17AAG-1


title: M_MCF10A-sh:GFP_3D_rep2

source_name: MCF10A-sh:GFP 3D mono-culture

value: p53-sufficient (wild-type)


title: ATAC_Crypt_rep3


title: PP_09: Postpartum cow 3 d10


title: Blastocyst culture media, conditioned, 17 hours

type: other

city: London

first: Dean

middle: Harvey

last: Betts

state: Ontario

address: 1151 Richmond St.

department: Department of Physiology and Pharmacology

country: Canada

institute: Western University

description: Test

data_processing:
The array data was normalized to the endogenous control (U6) signals on each plate. Caution: Since these arrays were used as a discovery tool to identify new mature microRNAs in conditioned culture media, this typical normalization regime is less meaningful in this context. Notably, the U6 RNA in the blank negative control microdroplets originated from a non-murine origin.
Fold-change matrix reflects the fold change increase in the normalized conditioned sample compared to the normalized blank, calculated when possible.

label: FAM

source_name: Spent blastocyst culture media (KSOM, BSA-free, 0.1% polyvinylacetate) from 25 murine (CD1) blastocysts from 99 h to 116 h post-hCG

label_protocol: A TaqMan MicroRNA Cells-to-Ct Kit was used to lyse and digest the samples. Reverse transcription of microRNA target cDNA was generated using TaqMan MicroRNA Reverse Transcription Kit followed by preamplification using TaqMan Megaplex Preamp Primers (12 cycles). qPCR amplification was performed using a Viia7 instrument equipped with an adapter block for compatibility with TaqMan MicroRNA Rodent v3.0 A + B Cards.

growth_protocol: 3 wk. old female mice were superovulated, mated with male CD1 mice, euthanized and the zygotes collected. Zygotes were collected and cultured (5% O2, 5% CO2, 37C) until 99 hours post-hCG, at which point 25 blastocysts were selected and cultured separately under this atmosphere in an 8 uL microdroplet until 116 hours post-hCG.

extract_protocol: No RNA extraction was performed; instead, a TaqMan 'Cells-to-Ct' kit was used. 6 µL of whole conditioned media was mixed with equal parts 'Lysis Solution' containing 1:100 DNase I, followed by 'Stop Solution' after 8 minutes. RT/qPCR was performed directly on this.

tag: culture

value: CD1 mouse blastocysts

tag: sample

value: Spent murine blastocyst culture media


title: ATAC_Villus_rep3

source_name: WT adult duodenal villus cells

value: Adult villus cells


title: input-IR+Vehicle-vivo

city: Beijing

first: Yulin

last: Lyu

address: No.5 Yiheyuan Road Haidian District

department: School of Life Sciences

country: China

institute: Peking University

data_processing:
ChIP-seq reads were aligned to mouse genome build mm10 using bwa (v0.7.12)
Duplicate PCR reads were removed from the aligned sequences using Picard (version 2.6)
Chromatin profiles were calculated over all RefSeq genes and plotted using ngsplot software
Genome_build: mm10
Supplementary_files_format_and_content: bw files include ChIP signal intensity across genome

source_name: input control

growth_protocol: Crypts were isolated and cultured as previously described.1 Briefly, proximal small intestine sections of approximately 20 cm were harvested, opened longitudinally, cut into 2–4mm pieces, rinsed with cold PBS and incubated in 2mM EDTA at 4 °C for 30 min with gentle shaking. Crypts were released after vigorous shaking in cold PBS and passed through a 70 μM cell strainer (BD Biosciences) for further enrichment. Approximately 500 crypts were embedded in 20 μL Matrigel (growth factor reduced; BD bioscience) and plated in 48-well plates. After Matrigel polymerization, 500 μL culture medium containing Advanced DMEM/F12 (Gibco), 10mM HEPES (Gibco), 1× GlutaMAX (Gibco), 1% penicillin/ streptomycin (Gibco), 1× N2 Supplement (Gibco), 1× B27 Supplement (Gibco), and 1mM N-Acetylcysteine (Sigma-Aldrich) was added. For ENR-organoids, culture medium containing 50 ng/mL murine EGF, 100 ng/mL murine Noggin and 500 ng/mL human R-Spondin 1 was used. For Hyper-organoids, culture medium containing 0.2 μM LDN193189, 0.1 μM GSK-3 Inhibitor XV, 1 μM Pexmetinib, 500 μM VPA, 2 μM EPZ6438, 50 ng/mL murine EGF, 10% R-Spondin 1 Conditioned Medium (Trevigen), and 20 ng/mL  FGF2 was used. The cell culture medium was changed every other day. Hyper-organoids can be generated from either ENRorganoids or primary crypts. For passage, organoids were removed from Matrigel, mechanically dissociated into singlecrypt domains and transferred to fresh Matrigel. Passage was  performed every 7 days with a 1:8 split ratio for ENR-organoids and a 1:30 split ratio for Hyper-organoids. 5% knockout serum replacement (KSR, GIBCO) was recommended to enhance expansion of Hyper-organoids after they were passaged. Six days after passage, the number of colonies containing typical organoid structures and expressing Lgr5-GFP was counted. Directed differentiation of organoid cultures was performed as previously reported.46 In brief, ENR- and Hyper-organoids were cultured under ENR conditions, supplemented with Notch inhibitor DAPT (10 μM) to induce enterocyte (alpi); with Notch inhibitor DAPT (10 μM) and Wnt inhibitor IWP2 (2 μM) to induce PC (lyz1), GC (muc2) and enteroendocrine cell (chga).

extract_protocol: ChIP material was obtained and processed as described previously48 with the following modifications. In brief, for each sample, approximately 5 × 10e6 cells were crosslinked in PBS containing 1% formaldehyde at room temperature for 10 min, after which they were quenched with glycine for 5 min. The fixed cells were washed twice with cold PBS and centrifuged at 500× g for 3 min at 4 °C, followed by removal of the supernatant. The cell pellets were re-suspended, and the resulting homogenates were further lysed. Crosslinked material was sonicated using a Covaris sonicator for 12 min at duty 5%, intensity 3, and bursts 200. The size of the sonicated fragments ranged between 400 and 800 bp.

value: crypt

tag: chip antibody


title: ATAC_Villus_rep2


title: M_RMF_DMEM/F12_3D_rep3

source_name: RMF mono-culture

value: Reduction mammoplasty fibroblast


title: polyA RNA from AEC, harvested at 48hpi, mock infected, DMSO (solvent) treated, replicate 3

description:
polyA RNA extracted from whole cells
AEC_SARSCoV2_17AAG_readcounts.tsv.gz
AECII_15_48h_DMSO-3


title: ATAC_Crypt_rep1


title: M_MCF10A-sh:GFP_3D_rep1


title: input-IR+AB-vivo


title: ATAC_Villus_rep1


title: polyA RNA from AEC, harvested at 48hpi, mock infected, DMSO (solvent) treated, replicate 2

description:
polyA RNA extracted from whole cells
AEC_SARSCoV2_17AAG_readcounts.tsv.gz
AECII_14_48h_DMSO-2


title: IgG-vivo

value: Cy3 AffiniPure Donkey AntiMouse IgG (H+L) (Jackson ImmunoResearch Laboratories, 715-165-150)


title: H3K4me3_HiChIP_Hnf4DKO_Crypt_rep2

description: H3K4me3_HiChIP_Hnf4DKO_Crypt_CombinedReplicates.interactions.all.mango

source_name: Hnf4DKO adult duodenal crypt cells

extract_protocol:
Freshly harvested duodenum was flushed with cold PBS, opened longitudinally, cut into 1 cm pieces, and then rotated in 3 mM EDTA in PBS at 4 °C for 5 min, 10 min and 40 min at 4 °C (refresh EDTA/PBS every time). The EDTA incubation time was adjusted to release all the epithelial cells from underlying muscular tissue, so for the WT and mutant tissues, the last incubation step is 40 min and 20 min, respectively. The tissue was then vigorously shaken to release the epithelium, and the supernatant was collected as the whole epithelium fraction; villi were collected from the top of a 70-μm cell strainer while crypts passed through. Cells were pelleted by centrifugation at 170 g at 4 °C and then washed by cold PBS. Duodenal villus and crypt cells were then cross-linked in 1.5% formaldehyde (Sigma F8775) for 10 min at 4°C and then for 50 min at room temperature. Cells were pelleted (300 g, 4 °C for 5 min) and washed with ice-cold PBS twice. Cells were quick frozen in liquid nitrogen and stored at -80°C for later processing for HiChIP. The HiChIP protocol was performed using an antibody to H3K4me3 (Millipore 05-745R, lot 3158071).
Phusion High-Fidelity PCR Master Mix (New England Biolabs)

treatment_protocol: Mice were treated with tamoxifen (50mg/kg/day) via intraperitoneal injection for 3 consecutive days and were sacrificed 1 day after last injection.

value: duodenal epithelium

value: tamoxifen 50mg/kg/day

tag: antibody


title: polyA RNA from AEC, harvested at 48hpi, mock infected, DMSO (solvent) treated, replicate 1

description:
polyA RNA extracted from whole cells
AEC_SARSCoV2_17AAG_readcounts.tsv.gz
AECII_13_48h_DMSO-1

value: mock


title: PP_08: Postpartum cow 2 d100

source_name: Endometrial tissue in fertile cow_2

tag: animal no.

tag: days after parturition

tag: tissue

value: endometrium


title: H3K27me3-Normal-vivo

source_name: normal crypt

tag: treatment in vivo

value: normal crypt

value: anti-H3K27me3(Abcam, ab6002)


title: PP_07: Postpartum cow 2 d50


title: PP_06: Postpartum cow 2 d30


title: H3K27me3-NC-vitro

source_name: organoid with 8C -VE condition

value: organoid

tag: condition in vitro

value: 8C -VE condition


title: polyA RNA from AEC, harvested at 24hpi, SARS-CoV-2 infected, 17-AAG (200 nM) treated, replicate 2

description:
polyA RNA extracted from whole cells
AEC_SARSCoV2_17AAG_readcounts.tsv.gz
AECII_11_24h_S2_200nM17AAG-2


title: PP_03: Postpartum cow 1 d50

source_name: Endometrial tissue in fertile cow_1


title: PP_05: Postpartum cow 2 d10


title: PP_02: Postpartum cow 1 d30


title: H3K4me3_HiChIP_Hnf4DKO_Crypt_rep1

tag: cell type

value: Adult crypt cells

tag: treatment


title: polyA RNA from AEC, harvested at 24hpi, SARS-CoV-2 infected, 17-AAG (200 nM) treated, replicate 1

description:
polyA RNA extracted from whole cells
AEC_SARSCoV2_17AAG_readcounts.tsv.gz
AECII_10_24h_S2_200nM17AAG-1

tag: infection

tag: moi


title: H3K27me3-IR+Vehicle-vivo

source_name: crypt after irradiation 3 day

value: irradiation 3 day


title: H3K4me3_HiChIP_Hnf4DKO_Villus_rep2

description: H3K4me3_HiChIP_Hnf4DKO_Villus_CombinedReplicates.interactions.all.mango

source_name: Hnf4DKO adult duodenal villus cells


title: H3K4me3_HiChIP_Hnf4DKO_Villus_rep1


title: H3K4me3_HiChIP_WT_Crypt_rep2

description: H3K4me3_HiChIP_WT_Crypt_CombinedReplicates.interactions.all.mango

treatment_protocol: Mice were treated with oil (vehicle for tamoxifen) via intraperitoneal injection for 3 consecutive days and were sacrificed 1 day after last injection.

value: WT

value: oil vehicle


title: PP_04: Postpartum cow 1 d100


title: H3K27me3-IR+AB-vivo

source_name: crypt after irradiation 3 day +VE

value: irradiation 3 day +VE


title: ISO_12: PVP-I treatment cow 3 d14

source_name: Endometrial tissue in fertile cow_3

tag: days after pvp-i administration


title: polyA RNA from AEC, harvested at 24hpi, SARS-CoV-2 infected, DMSO (solvent) treated, replicate 2

description:
polyA RNA extracted from whole cells
AEC_SARSCoV2_17AAG_readcounts.tsv.gz
AECII_08_24h_S2_DMSO-2

source_name: AEC

tag: time point


title: H3K27me3-Hyper-vitro

source_name: organoid with 8C condition

value: 8C condition


title: H3K4me3_HiChIP_WT_Crypt_rep1

source_name: WT adult duodenal crypt cells


title: ISO_11: PVP-I treatment cow 2 d14


title: polyA RNA from AEC, harvested at 24hpi, SARS-CoV-2 infected, 17-AAG (200 nM) treated, replicate 3

description:
polyA RNA extracted from whole cells
AEC_SARSCoV2_17AAG_readcounts.tsv.gz
AECII_12_24h_S2_200nM17AAG-3


title: H3K4me3_HiChIP_WT_Villus_rep2

description: H3K4me3_HiChIP_WT_Villus_CombinedReplicates.interactions.all.mango

value: Adult villus cells


title: PP_01: Postpartum cow 1 d10


title: ISO_10: PVP-I treatment cow 1 d14


title: polyA RNA from AEC, harvested at 24hpi, SARS-CoV-2 infected, DMSO (solvent) treated, replicate 1

description:
polyA RNA extracted from whole cells
AEC_SARSCoV2_17AAG_readcounts.tsv.gz
AECII_07_24h_S2_DMSO-1


title: ISO_09: PVP-I treatment cow 3 d7


title: ISO_08: PVP-I treatment cow 2 d7


title: polyA RNA from AEC, harvested at 24hpi, mock infected, 17-AAG (200 nM) treated, replicate 3

description:
polyA RNA extracted from whole cells
AEC_SARSCoV2_17AAG_readcounts.tsv.gz
AECII_06_24h_200nM17AAG-3


title: H3K4me3_HiChIP_WT_Villus_rep1


title: polyA RNA from AEC, harvested at 24hpi, mock infected, 17-AAG (200 nM) treated, replicate 2

description:
polyA RNA extracted from whole cells
AEC_SARSCoV2_17AAG_readcounts.tsv.gz
AECII_05_24h_200nM17AAG-2


title: polyA RNA from AEC, harvested at 24hpi, SARS-CoV-2 infected, DMSO (solvent) treated, replicate 3

description:
polyA RNA extracted from whole cells
AEC_SARSCoV2_17AAG_readcounts.tsv.gz
AECII_09_24h_S2_DMSO-3


title: polyA RNA from AEC, harvested at 24hpi, mock infected, 17-AAG (200 nM) treated, replicate 1

description:
polyA RNA extracted from whole cells
AEC_SARSCoV2_17AAG_readcounts.tsv.gz
AECII_04_24h_200nM17AAG-1


title: ISO_07: PVP-I treatment cow 1 d7


title: high-REST cells (REST transduced cells) [UW426-REST]

city: Dallas

first: Lin

last: Xu

state: TX

address: H106A,5323 Harry Hines Blvd.

department: Population & Data Sciences

institute: UT Southwestern Medical Center

data_processing:
The quality of sequencing reads were evaluated using NGS QC Toolkit (v2.3.3) and high-quality reads were extracted. The human reference genome sequence and gene annotation data, hg38 were downloaded from Illumina iGenomes. (https://support.illumina.com/sequencing/sequencing_software/igenome.html).
The quality of RNA-sequencing libraries were estimated by mapping the reads onto human transcript and ribosomal RNA sequences (Ensembl release 89) using Bowtie (v2.3.2) . STAR (v2.5.2b) was employed to align the reads onto the human and viral genomes. SAMtools (v1.9) was employed to sort the alignments, and HTSeq Python package was employed to count reads per gene.
DESeq2 R Bioconductor package was used to normalize read counts and identify differentially expressed (DE) genes
KEGG pathway data was downloaded using KEGG API (https://www.kegg.jp/kegg/rest/keggapi.html) and gene ontology (GO) data was downloaded from NCBI FTP (ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2go.gz). The enrichment of DE genes to pathways and GOs were calculated by Fisher's exact test in R statistical package.
Genome_build: hg38
Supplementary_files_format_and_content: txt format, gene read count

source_name: Medulloblastoma cell line

growth_protocol: Cell lines were cultured at 37°C, in 5% CO2, in DMEM supplemented with 10% heat-activated fetal bovine serum (with streptomycin and penicillin).

extract_protocol:
The cell lines were flash frozen on liquid nitrogen, and RNA was harvested using Zymo pure Quick RNA mini prep Kit ( Catalog No. R1055). RNA quality/quantity of each samples was checked using RNA Nano assay using Bioanalyzer 2100 (Agilent Technologies - RNA RIN should be >8) and the RNA sample quantity was measured  using Qubit 2.0 Fluorometer (Thermo Fisher Scientific). Using 1000 ng of RNA from each sample to start library prep using TruSeq Stranded Total RNA Gold (Illumina RS-122-2303).
Sequencing library preparations were performed by Truseq Stranded Total RNA Sample Reference Guide (Illumina).  RNA-seq  library quality/quantity checking was done using  Tape Station 2200 D1000 assay (Agilent Technologies) and QuantStudio 6 Flex Real time PCR System (Applied Biosystem). RNA-seq libraries were sequenced in Hiseq 3000 (Illumina) and the sequence type used was Paired End with 75 cycles.

tag: cell line

tag: disease

value: Medulloblastoma


title: parental cell line [DAOY]

description: DAOY

value: DAOY


title: high-REST cells (REST transduced cells) [DAOY-REST]

description: DAOY-REST


title: D283


title: IP SeV infected RNA2 A549

city: CHICAGO

first: Zijie

last: Zhang

state: IL

department: Chemistry

institute: University of Chicago

data_processing:
library strategy: meRIP-seq
Seequencing reads were aligned to SeV reference genome by Hisat2
m6A peak calling was performed using R package m6Amonster
Genome_build: SeV reference genome
Supplementary_files_format_and_content: m6A peak

organism:
Homo sapiens
Respirovirus muris

growth_protocol: A549 (ATCC CCL-185) cell lines were purchased from the American Type Culture Collection (Manassas, VA) and were grown in Dulbecco's modified Eagle's medium (DMEM; Life Technologies) supplemented with 10% FBS.

extract_protocol:
TRIzol (Invitrogen) + polyT beads (thermo fisher)
SMARTer Stranded Total RNA-Seq Kit v2

treatment_protocol: Confluent A549 cells in 60 mm dishes were mock-infected or infected with SeV at an MOI of 0.1. At 24h after infection, total RNA was isolated from virus-infected cells using the TRIzol reagent (Life Technologies) and dissoved in RNase-free water.

tag: human cell line

value: SeV infected

tag: molecule subtype

value: m6A enriched virus RNA + mRNA


title: IP SeV infected RNA3 A549


title: ISO_06: PVP-I treatment cow 3 d2


title: H3K27me3-ENR-vitro

source_name: organoid with ENR condition

value: ENR condition

tag: chip antibody


title: parental cell line [UW426]


title: polyA RNA from AEC, harvested at 24hpi, mock infected, DMSO (solvent) treated, replicate 2

description:
polyA RNA extracted from whole cells
AEC_SARSCoV2_17AAG_readcounts.tsv.gz
AECII_02_24h_DMSO-2

value: mock


title: polyA RNA from AEC, harvested at 24hpi, mock infected, DMSO (solvent) treated, replicate 3

description:
polyA RNA extracted from whole cells
AEC_SARSCoV2_17AAG_readcounts.tsv.gz
AECII_03_24h_DMSO-3


title: Input SeV infected RNA3 A549

value: virus RNA + mRNA


title: Input SeV infected RNA2 A549


title: polyA RNA from AEC, harvested at 24hpi, mock infected, DMSO (solvent) treated, replicate 1

description:
polyA RNA extracted from whole cells
AEC_SARSCoV2_17AAG_readcounts.tsv.gz
AECII_01_24h_DMSO-1


title: high-REST cells (REST transduced cells) [UW228-REST]


title: Input SeV infected RNA1 A549


title: ISO_03: PVP-I treatment cow 3 d0

value: endometrium


title: ISO_04: PVP-I treatment cow 1 d2


title: IP SeV infected RNA1 A549


title: 29_iCELL8_3pDEUMI_lymphocyte_cell line_mix

status: Public on Jan 15 2021

city: SOUTH SAN FRANCISCO

first: Tracy

last: Yamawaki

address: 1120 VETERANS BLVD.

institute: AMGEN, INC.

description: 1:1:1:1 mixture of Jurkat, TALL104, EL4, IVA12 cells sequenced using the DropSeq method with encapsulation with the iCELL8 cx system using a modified 3'DE protocol processing 1465 wells

data_processing:
fastq files were downsampled using seqtk v1.3-r106
Cell barcode extraction and transcript counting was peformed using the mappa v0.9 pipeline (read counts) or Drop-seq_Tools v2.3.0 and PicardTools v2.18.14 (UMI counts).
Genome_build: Data was aligned to a “cellRanger_1.2.0” referenced composed of hg19 with Ensembl 82 and mm10 with Ensembl 84 using STAR v2.7.0b (read counts) or STAR v2.4.2a (UMI counts).
Supplementary_files_format_and_content: count_genematrix, UMIcount_genematrix

organism:
Homo sapiens
Mus musculus

source_name: lymphocyte cell line mix

extract_protocol:
cell suspensions were processed using the iCELL8 cx system to isolate and identify single cells and perform RT and cDNA amplification.
Libraries were constructed with the Takara iCELL8 3'DE kit

value: Jurkat, TALL104, EL4, IVA12 (1:1:1:1 mixture)


title: 28_iCELL8_3pDE_lymphocyte_cell line_mix

description: 1:1:1:1 mixture of Jurkat, TALL104, EL4, IVA12 cells sequenced using the DropSeq method with encapsulation with the iCELL8 3'DE kit processing 1498 wells


title: 27_iCELL8_3pDE_lymphocyte_cell line_mix

description: 1:1:1:1 mixture of Jurkat, TALL104, EL4, IVA12 cells sequenced using the DropSeq method with encapsulation with the iCELL8 3'DE kit processing 1684 wells


title: 15_ddSEQ_lymphocyte_cell line_mix

description: 1:1:1:1 mixture of Jurkat, TALL104, EL4, IVA12 cells sequenced using the ddSEQ kit using a cell concentration of 2500 cells/ul.

data_processing:
fastq files were downsampled using seqtk v1.3-r106
cell barcodes were extracted using ddSeeker v0.9.0
Transcript counting was peformed using Drop-seq_Tools v2.3.0 and PicardTools v2.18.14.
Genome_build: Data was aligned to a “cellRanger_1.2.0” referenced composed of hg19 with Ensembl 82 and mm10 with Ensembl 84 using STAR v2.4.2a.
Supplementary_files_format_and_content: DigitalExpressionTable.txt

extract_protocol:
cell suspensions were encapsulated in cell lysis buffer with the BioRad ddSEQ.
Libraries were constructed with the SureCell WTA 3′ Library Prep kit.


title: 10_ddSEQ_lymphocyte_cell line_mix

description: 1:1:1:1 mixture of Jurkat, TALL104, EL4, IVA12 cells sequenced using the ddSEQ kit using a cell concentration of 2000 cells/ul.


title: 12_ddSEQ_lymphocyte_cell line_mix


title: 16_ddSEQ_lymphocyte_cell line_mix


title: 13_ddSEQ_lymphocyte_cell line_mix


title: ISO_02: PVP-I treatment cow 2 d0


title: 19_DropSeq_lymphocyte_cell line_mix

description: 1:1:1:1 mixture of Jurkat, TALL104, EL4, IVA12 cells sequenced using the DropSeq method with encapsulation with the Dolomite scRNAseq system using a cell concentration of 150 cells/ul cells/ul.

data_processing:
fastq files were downsampled using seqtk v1.3-r106
Cell barcode extraction and transcript counting was peformed using Drop-seq_Tools v2.3.0 and PicardTools v2.18.14.
Genome_build: Data was aligned to a “cellRanger_1.2.0” referenced composed of hg19 with Ensembl 82 and mm10 with Ensembl 84 using STAR v2.4.2a.
Supplementary_files_format_and_content: DigitalExpressionTable.txt

extract_protocol:
cell suspensions were encapsulated in cell lysis buffer with the Dolomite scRNA-Seq system
Libraries were constructed according to the Drop-seq protocol.


title: 20_DropSeq_lymphocyte_cell line_mix

description: 1:1:1:1 mixture of Jurkat, TALL104, EL4, IVA12 cells sequenced using the DropSeq method with encapsulation with the Dolomite scRNAseq system using a cell concentration of 300 cells/ul cells/ul.


title: ISO_01: PVP-I treatment cow 1 d0


title: ISO_05: PVP-I treatment cow 2 d2


title: 09_ddSEQ_lymphocyte_cell line_mix


title: GS_M7_Cel_SyringicAcid (CS_28)

city: Golden

first: Davinia

last: Salvachua

state: CO

address: 15013 Denver West Parkway

institute: National Renewable Energy Laboratory

data_processing:
Read quality was assessed using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Read-trimming was conducted using bbduk (http://jgi.doe.gov/data-and-tools/bb-tools/) with parameters trimq=10, qtrim="rl", maq=10.
Reads were aligned to the Trametes versicolor and Gelatoporia subvermispora genomes using bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml). using parameters -local, --sensitive-local
Aligned reads were mapped to genes using htseq-count (https://pubmed.ncbi.nlm.nih.gov/25260700/) with parameters -a=1, --mode="union".
Genome_build: Trametes versicolor genome https://www.ncbi.nlm.nih.gov/assembly/GCF_000271585.1/
Genome_build: Gelatoporia subvermispora genome https://www.ncbi.nlm.nih.gov/assembly/GCA_000320605.2/
Supplementary_files_format_and_content: read counts per gene

organism: Gelatoporia subvermispora

source_name: Gelatoporia subvermispora

growth_protocol:
Fungal seed preparation:
To start each experiment with fungal suspensions in an equivalent metabolic state, seed cultures were prepared as follows. An agar square (~0.5 cm2) with fungal mycelia was taken from agar plates maintained at 4°C, deposited on a fresh YMPG-agar plate (mycelia in contact with the agar), and incubated for 7 days at 28°C. Then, 4-5 agar squares (~0.5 cm2) with mycelia from the fungal mat edges were inoculated in 50 mL liquid culture of YMPG (pre-seed cultures) in non-baffled 250 mL flasks and incubated at 220 rpm and 28°C for 7 days. Resulting fungal pellets were homogenized (10 s, speed 6) using an Omni Mixer 115V with a 50 mL SS Chamber PTFE, and 2 mL of the resulting fungal suspension were re-inoculated and cultured in YMPG under the same conditions for 5 days (seed cultures). Fungal pellets were homogenized as described previously and a ratio of 1:12.5 (v:v)  of fungal suspension per media volume was used to inoculate the corresponding cultivations. Glucose content was analyzed in the seed cultures before inoculation in a rapid biochemistry analyzer (2900D YSI) to verify that the cultures had not reached glucose starvation.

extract_protocol:
The total RNA was extracted using Qiagen RNeasy Kits (cat#74104) and RNA samples were assessed using the Agilent 2100 Bioanalyzer.  The RNA with RIN > 7 was chosen to proceed with ribosomal rRNA remover using Ribo-zero yeast (illumina cat#MRZY1306).
cDNA libraries for illumina NextSeq550 platform were generated using TruSeq Stranded Total RNA (cat# 20020596) according to the manufacturer's protocol.

treatment_protocol:
Media preparation:
The media utilized to maintain the strains and initiate seed cultures was adapted YMPG-agar medium. Adapted YMPG medium consisted of 2 g yeast extract, 10 g malt extract, 2 g peptone, 10 g glucose, 2 g KH2PO4, and 1 g MgSO4 x 7H2O per liter in H2O on 1.5 % agar plates. This medium was autoclaved for 30 min at 121°C and plated. The liquid pre-seed and seed cultures consisted of the same media but excluding agar.
For the experimental campaigns, we developed a minimal and defined medium which is an adapted version of Czapek-Dox medium (CDM). CDM consisted of 2 g ammonium tartrate, 0.5 g MgSO4, 1 g KH2PO4, 0.5 g KCl, 1 mL sterile vitamins supplement (ATCC® MD-VS™), and 1 mL trace elements solution per liter in H2O. The trace elements solution contains 0.1 g Na2B4O7 x 10 H2O, 0.07 g ZnSO4 x 7 H2O, 0.01 g CuSO4 x 5 H2O, 0.01 g MnSO4  x 7 H2O, 0.05 g FeSO4 x 7 H2O, and 0.01 (NH4)6MoO2 x 4 H2O per liter in H2O. Trace elements were filter-sterilized through 0.2 µM PES filters (Millipore) and further added to CDM after autoclaving (30 min at 121°C).
Carbon sources and concentrations added to CDM for submerged-state cultivations were specific to each experimental campaign. Specifically, concentrated stocks of cellobiose (100 g/L), aromatic compounds such as 4-HBA (10 g/L), vanillic acid (10 g/L), and syringic acid (10 g/L) were prepared by dissolving the compound in H2O and slowly adjusting the pH to 7 with 4 M NaOH. These compounds were subsequently filter sterilized using 0.22 µm PES Steriflip filter units (Millipore) and added to CDM. Lignin isolated from poplar was resuspended in H2O (in aliquots of 25 mg in 0.5 mL of H2O), UV-sterilized, and added to CDM. When poplar was the substrate, 2 g of milled poplar were autoclaved for 30 min at 121°C in individual flasks containing 8 mL of H2O. Then, CDM without cellobiose was added to the poplar mixture.
Cultivations for multi-omic experiments and sample preparation:
G. subvermispora and T. versicolor cultivations were conducted in 250 mL flasks containing 25 mL of CDM with cellobiose (5 g/L) and incubated at 28°C in static conditions using a humidity-controlled incubator (˃50 % humidity). When the remaining cellobiose was ~50-80% of the initial concentration (12 d and 5 d for G. subvermispora and T. versicolor, respectively), we induced the cultivations with different substrates, 4-HBA (2 mM), syringic acid (2 mM), or lignin (25 mg, see media preparation in Section 2). Poplar was also used as an inducing substrate. However, poplar (2 g) was present since the beginning of the cultivation in CDM without cellobiose (see media preparation in Section 2). Antioxidants (5 mM ascorbic acid and 1 mM α-tocopherol) were added in the media 30 min before the induction, including the media that contained poplar. Cultivations were harvested 48 h after the induction, corresponding to 14 d and 7 d for G. subvermispora and T. versicolor, respectively. Each experimental condition, including controls, was performed in triplicate. In this case the controls were (1) cultivations conducted in CDM and cellobiose as the sole carbon source and (2) non-inoculated media.
Transcriptomic samples were generated by centrifugation at 6,000 x g for 10 min, followed by flash freezing the pellets in liquid nitrogen after discarding the supernatants. Samples were stored at -80°C.

value: 5 g/L cellobiose, 2 mM syringic acid


title: 05_Chromium_5p_v1_lymphocyte_cell line_mix

description: 1:1:1:1 mixture of Jurkat, TALL104, EL4, IVA12 cells sequenced using the 10X Chromium 5' v1 kit targeting a capture of 5000 cells.

data_processing:
fastq files were downsampled using seqtk v1.3-r106
fastq files were processed with cellranger v3.0.2 for cell demultiplexing, read alignment and transcript counting
Genome_build: Data was aligned to a “cellRanger_1.2.0” reference composed of hg19 with Ensembl 82 and mm10 with Ensembl 84.
Supplementary_files_format_and_content: barcodes.tsv, features.tsv, matrix.mtx

extract_protocol:
cell suspensions were encapsulated in cell lysis buffer with the 10X Chromium
Libraries were constructed with the 10X Genomics 3' v2, v3 or 5' v1 kits.


title: GS_M7_Cel_SyringicAcid (CS_30)


title: parental cell line [UW228]


title: 06_Chromium_5p_v1_lymphocyte_cell line_mix

description: 1:1:1:1 mixture of Jurkat, TALL104, EL4, IVA12 cells sequenced using the 10X Chromium 5' v1 kit targeting a capture of 2000 cells.


title: GS_M7_Cel_SyringicAcid (CS_29)


title: polyA RNA from AEC, harvested at 72hpi, mock infected, DMSO (solvent) treated, replicate 3

description:
polyA RNA extracted from whole cells
AEC_SARSCoV2_17AAG_readcounts.tsv.gz
AECII_27_72h_DMSO-3


title: GS_M7_Cel_Lignin (CS_27)

value: 5 g/L cellobiose, 25 mg lignin/25 mL


title: GS_M7_Cel_Lignin (CS_26)


title: 14_ddSEQ_lymphocyte_cell line_mix


title: GS_M7_Cel_Lignin (CS_25)


title: GS_M7_Poplar (CS40)

value: 2 g milled poplar/25 mL


title: GS_M7_Poplar (CS41)


title: 11_ddSEQ_lymphocyte_cell line_mix


title: GS_M7_Poplar (CS42)


title: GS_M7_Cel_4HBA (CS36)

value: 5 g/L cellobiose, 2 mM 4-hydroxybenzoic acid


title: GS_M7_Cel_4HBA (CS35)


title: GS_M7_Cel_4HBA (CS34)


title: TV_M7_Cel_SyringicAcid (TV_22)

organism: Trametes versicolor

source_name: Trametes versicolor


title: GS_M7_Cel (CS28)

value: 5 g/L cellobiose


title: TV_M7_Cel_Lignin (TV_21)


title: TV_M7_Cel_Lignin (TV_19)


title: GS_M7_Cel (CS29)


title: TV_M7_Poplar (TV38)


title: TV_M7_Poplar (TV37)


title: GS_M7_Cel (CS30)


title: TV_M7_Poplar (TV39)


title: TV_M7_Cel_SyringicAcid (TV_23)


title: TV_M7_Cel_4HBA (TV33)


title: TV_M7_Cel_4HBA (TV32)


title: TV_M7_Cel_4HBA (TV31)


title: TV_M7_Cel (TV25)


title: TV_M7_Cel (TV27)


title: TV_M7_Cel (TV26)


title: TV_M7_Cel_Lignin (TV_20)


title: DMDII after SKGM and 7 days in KC rep 3

city: Milan

first: Fabio

last: Marchiano

address: Via Alessandro Manzoni 56

country: Italy

institute: Humanitas

data_processing:
STAR (v2.5.1b) for reads mapping
featureCounts (1.6.2) for reads count
DESeq2 (v 1.22.2) for gene expression analysis
Genome_build: ENSEMBL GRCh38 release 77
Supplementary_files_format_and_content: raw count matrix and excel tables containing the results of the differential expression analysis + normalized counts

source_name: iPSC cell culture

growth_protocol: For wildtype samples, NCRM1 cell line was differentiated into myogenic cultures as described in (Chal et al., 2016) and cells were harvested on day 0, day 8, day 16, day 24 and day 32 of differentiation. For secondary differentiation, 3-week old primary myogenic cultures were enzymatically dissociated and myogenic progenitors were replated at a density of 35-40,000/cm2 onto Matrigel (Corning, 354277) coated dishes in skeletal muscle growth media (SKGM-2, Lonza CC-3245) with 10 μM ROCK inhibitor (R&D Systems, 1254). Samples were collected after two days in SKGM culture. The cultures were further differentiated in three different conditions - KC (DMEM/F12 supplemented with 2% knockout serum replacement (Invitrogen, 10828028), 0.2% Pen/Strep (Life Technologies, 15140122), 1x ITS (Life Technologies, 41400045) and 1 μM CHIR (Tocris, 4423), KCTi (KC supplemented with 10 μM TGFβ inhibitor SB431542 (Tocris,1614)) and KCTiP (KCTi supplemented with 10 μM Prednisolone (Sigma Aldrich, P6004)). For each condition, cells were harvested after 7 and 15 days of differentiation. For each time point samples were collected from three independent experiments.For DMD samples, two isogenic DMD cell lines and parental wildtype line were differentiated into myogenic cultures as described in (Chal et al., 2016). Cells were replated for secondary differentiation in SKGM and were cultured in KC medium for one week. Samples were collected from three independent experiments.

extract_protocol:
RNA was isolated using NucleoSpin RNA kit (Macherey and Nagel, 740955) with on-column DNA digestion following the manufacturer’s protocol.
Libraries were prepared using Roche Kapa mRNA HyperPrep sample preparation kits from 100ng of purified total RNA according to the manufacturer’s protocol. The finished dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and RT-qPCR using the Kapa Biosystems library quantification kit according to manufacturer’s protocols. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on two Illumina NextSeq500 runs with single-end 75bp reads by the Dana-Farber Cancer Institute Molecular Biology Core Facilities.

value: NCRM1 DMDII

tag: age + media

value: DMDII day 7 (KC)


title: secondary differentiation at day 15 (KCTi) rep 3

value: iPSC

value: day 15 (KCTi)


title: DMDI after SKGM and 7 days in KC rep 2

value: NCRM1 DMDI

value: DMDI day 7 (KC)


title: DMDI after SKGM and 7 days in KC rep 3


title: WT after SKGM and 7 days in KC rep 1

value: NCRM1 wildtype

value: WT day 7 (KC)


title: WT after SKGM and 7 days in KC rep 2


title: DMDI after SKGM and 7 days in KC rep 1


title: DMDII after SKGM and 7 days in KC rep 2


title: secondary differentiation at day 15 (KCTi) rep 2


title: DMDII after SKGM and 7 days in KC rep 1


title: secondary differentiation at day 15 (KCTi) rep 1


title: secondary differentiation at day 15 (KC) rep 3

value: day 15 (KC)


title: secondary differentiation at day 15 (KC) rep 2


title: secondary differentiation at day 7 (KCTiP) rep 2

value: day 7 (KCTiP)


title: secondary differentiation at day 15 (KC) rep 1


title: secondary differentiation at day 7 (KCTiP) rep 3


title: secondary differentiation at day 7 (KCTi) rep 3

value: day 7 (KCTi)


title: secondary differentiation at day 7 (KCTiP) rep 1


title: secondary differentiation at day 7 (KC) rep 3

value: day 7 (KC)


title: secondary differentiation at day 7 (KCTi) rep 1


title: secondary differentiation at day 7 (KC) rep 2


title: WT after SKGM and 7 days in KC rep 3


title: secondary differentiation at day 2 (SKGM) rep 3

value: day 2 (SKGM)


title: secondary differentiation at day 7 (KC) rep 1


title: secondary differentiation at day 2 (SKGM) rep 1


title: primary differentiation at day 32 rep 3

value: day 32


title: secondary differentiation at day 7 (KCTi) rep 2


title: primary differentiation at day 24 rep 3

value: day 24


title: primary differentiation at day 0 rep 3

value: day 0


title: primary differentiation at day 16 rep 3

value: day 16


title: primary differentiation at day 8 rep 1

value: day 8


title: primary differentiation at day 0 rep 1


title: primary differentiation at day 32 rep 2


title: primary differentiation at day 8 rep 2


title: primary differentiation at day 0 rep 2


title: primary differentiation at day 32 rep 1


title: primary differentiation at day 8 rep 3


title: primary differentiation at day 16 rep 2


title: TV_M7_Cel_SyringicAcid (TV_24)

value: 5 g/L cellobiose, 2 mM syringic acid


title: primary differentiation at day 16 rep 1

value: iPSC


title: SKOV3_wt_untreated_input_control

city: Herne

first: David

last: Diaz-Carballo

state: NRW

address: Düngelstr. 33

department: Medical clinic of hematology & oncology

institute: Marienhospital Herne, Clinic of Ruhr University Bochum

data_processing:
sequencing depth: averagely generating 54370600 raw reads and 54201400 clean reads; Average read depth was 2700000000; a least 94.9% of the reads were mapped.
Peak calling parameters: Only the alignments within 2 mismatches were considered in Peak calling. MACS (Model-based Analysis for ChIP -Seq, version: MACS-1.4.2)  was used then for Peak calling. Parameters for Peak calling are: macs14 -s 49 -g hs -p 1e-5 -w --space 50 -m 10,30
Data filtering parameters: Clean Parameter: SOAPnuke filter -l 5 -q 0.5 -n 0.1 -Q 2 -c 50
Data filtering includes removing adaptor sequences, contamination and low-quality reads from raw reads. These reads were detected by BGI programs. Low-quality reads include three types, and the read which could be accord with anyone of the three types will be removed:
1) The ratio of N in whole read was over 10%;
2) Remove reads in which unknown bases are more than 10%;
3) The ratio of base whose quality was less than 20 was over 10%.
Software: Data filtering: SOAPnuke; Data alignment: SOAPaligner/SOAP2/BWA; Different peak between samples: MAnorm; Peak calling: MACS
Genome_build: hg38
Supplementary_files_format_and_content: peak text files

source_name: Ovarian cancer cell line

growth_protocol: 2*10^6 SKOV3 wt were seeded in T75 flasks for 24 h

extract_protocol:
Chromatin immunoprecipitation was performed using SimpleChIP® Enzymatic Chromatin IP Kit (Magnetic Beads) #9003 from Cell Signaling.
ChIP-seq libraries were generated by BGI Genomics using Illumina TruSeq ChIP Library Prep Kit following the manufactures’ recommendations. 250-300 bp fragment sizes were obtained with SPRIselect reagent kit. Libraries were then sequenced after 75 cycles using NextSeq500 High Output Kit v2 on an Illumina NextSeq500 machine. Circa 30×10e6 reads were generated per sample

treatment_protocol: Cells were incubated with 1x IC50 of romidepsin or vorinostat 24 h prior to harvesting. Untreated cells were used as control.

value: Ovarian cancer cell line SKOV3

value: untreated

tag: concentration

value: 7.5 ng/µl

tag: volume

value: 20 µl


title: SKOV3_wt_romidepsin_input_control

value: 1xIC50 of romidpesin for 24 h


title: SKOV3_wt_vorinostat_input_control

value: 1xIC50 of vorinostat for 24 h


title: SKOV3_wt_untreated_H3ack9

value: H3acK9, Cell Signaling Technology , Catalog # 9649 , Clone:D1H2 , Lot # 9


title: SKOV3_wt_romidepsin_H3ack9

description: This sample was split into  two by the BGI company, so there are two bed-files.


title: SKOV3_wt_vorinostat_H3ack9


title: sciMAP Human VISp

city: Portland

first: Andrew

last: Adey

state: OR

address: 3181 S.W. Sam Jackson Park Rd, RHH, L103

department: MMG

institute: Oregon Health & Science University

data_processing:
scitools fastq-dump to generate index-matched fastq files
bwa mem to align to respective genome (mm10 for mouse, hg38 for human)
scitools count to generate count matrixes
cistopic v3 for dimensionality reduction
Genome_build: mm10 for mouse, hg38 for human
Supplementary_files_format_and_content: Count matrixes in sparse matrix format with row and column files along with a triplet matrix values file
Supplementary_files_format_and_content: Aggregate metadata is a csv file with additional informaiton on all cells

source_name: Human cortex - cryosectioned

extract_protocol:
Nuclei isolation using sciMAP-ATAC protocols
sci-ATAC-seq protocol
sciMAP-ATAC and sci-ATAC-seq

tag: tissue

value: Human cortex - cryosectioned

tag: region

value: VISp

tag: exposure

tag: strain


title: Purified Amyloid-bodies following 60min heat shock 2

city: Miami

first: Stephen

last: Lee

state: Florida

department: Biochemistry & Molecular Biology

institute: University of Miami

description: adenocarcinoma

data_processing:
Illumina Nextseq 500 uses Reat-Time Analysis (RTA) version 2 for base calling and quality scoring. Bcl2fastq converts output bcl files to fastq files.
RNA-seq data were aligned to GRCh38 with STAR 2.5.0 default parameters
Alignment files (BAM files) were annotated and processed through the Cufflinks 2.2.1 pipeline
Gene FPKM values were obtained with Cuffnorm within Cufflinks 2.2.1
Genome_build: GRCh38 (gencode v27)
Supplementary_files_format_and_content: Excel spreadsheet: gene list with raw FPKM values, fold change (60HS/NT) and average fold change, in triplicate.

source_name: MCF7 mammary gland cell culture

growth_protocol: Cells were either grown at basal conditions or heat shocked for 2 hours.

extract_protocol:
Plates were washed with PBS and cells were harvested in cold Solution 1 (0.5M sucrose, 3mM MgCl2) and sonicated for 6 × 10s using a microtip probe. Samples were then underlaid with cold Solution 2 (1M sucrose, 3mM MgCl2) and centrifuged at 2800 × g for 10 min at 4°C. Pellets were resuspended in PBS and a fraction of each sample was used to determine proper isolation of nucleoli and Amyloid-bodies by microscopic evaluation. Remaining resuspended samples were then used for RNA isolation with Trizol reagent (Invitrogen).
Library construction for mRNA sequencing was performed by the SCCC Onco-Genomics Share Resource using the KAPA Stranded mRNA-Seq Kit (KAPA Biosystems).

tag: treatment

value: mammary gland, breast; derived from metastatic site:pleural effusion

tag: protocol

value: 60min heat shock


title: Purified Amyloid-bodies following 60min heat shock 1

description: adenocarcinoma


title: Purified Amyloid-bodies following 60min heat shock 3

description: adenocarcinoma


title: Total RNA from MCF7 cells, purified nucleoli from cells maintained at basal conditions 3

description: adenocarcinoma

value: basal conditions


title: Total RNA from MCF7 cells, purified nucleoli from cells maintained at basal conditions 1

description: adenocarcinoma


title: cNF3 scRNA-seq

first: Adwait Amod

last: Sathe

state: Texas

address: 5323 Harry Hines Blvd.

department: McDermott Center of Human Growth and Development

data_processing:
BCL files were demultiplexed using cellranger(v3.0.0)
Alignment, barcode counting, UMI counting were performed using cellranger(v3.0.0)
PCA, clustering, and differential expression was performed using Seurat v3
Genome_build: Grch38
Supplementary_files_format_and_content: normalized count matrix in csv format

source_name: skin

extract_protocol: The library was generated according to manufacturer's instructions (10X Genomics).

tag: cell type

value: cutaneous neurofibroma cells


title: primary differentiation at day 24 rep 1

value: day 24


title: secondary differentiation at day 2 (SKGM) rep 2

value: day 2 (SKGM)


title: cNF2 scRNA-seq


title: Total RNA from MCF7 cells, purified nucleoli from cells maintained at basal conditions 2

description: adenocarcinoma


title: Stalk_vasopressin_r3

city: Parkville

first: Sean

last: Wilson

state: Victoria

address: 50 Flemington Road

country: Australia

institute: MCRI

data_processing:
10x library demultiplexing:  CellRanger 3.1.0
Single Cell RNA-Seq:  Quality control, sample integration and analysis was performed in Seurat (v3.1.4)
Bulk RNA-seq:  The raw reads were quality and adapter trimmed using trimmomatic (v0.39)
Bulk RNA-seq:  The trimmed reads were mapped to the human genome (hg38) using the STAR aligner version 2.5.2a in the two pass mapping mode
Bulk RNA-seq:  The mapped reads were quantified at the gene level using featureCounts version 1.5.0-p3 using GENCODE Release 20 comprehensive annotation
Genome_build: GRCh38
Supplementary_files_format_and_content: scRNA-seq samples:  barcode, features and matrix files from CellRanger output, scUE_METADATA.csv table containing the metadata related to single cell dataset (column 1 barcodes are appended with "_#" with being 1 for SH1 and 2 for SH2 barcodes).
bulk RNA-seq samples: counts

source_name: Human iPSC kidney organoid

growth_protocol: Takasato et al, 2015 (PMID: 26444236) kidney organoid protocol, modified to use E6 base media as in Howden et al, 2019 (PMID: 30858339).

extract_protocol:
Bulk RNA-Seq: Samples were dissociated and resuspended in HBBS + 2% FBS (50-100 ml per organoid). Where required, cells were stained for 30 min with Alexa Fluor 488 anti-EpCAM antibody (Biolegend) followed by three washes with HBBS + 2% FBS and resuspension in 2 ml HBBS + 2% prior to being sorted based on mCherry reporter expression and EpCAM-488. Following collection, the cells were pellet by centrifugation (3 min, 300 g) and RNA extracted using the Isolate II RNA Mini/Micro Kit (Bioline)
Bulk RNA-seq: Libraries were prepared using the Illumina TruSeq Stranded Total RNA library Prep Kit. Sequenced using Illumina NextSeq 500

treatment_protocol: Day 25 organoids were dissociated with a 1:1 TrypLE/Accutase solution (~0.2 ml per organoid) at 37˚C for 15–25 min, with occasional agitation (flicking) until large clumps were no longer clearly visible. The cell suspension was then centrifuged (3 min, 300 g) and the dissociation solution removed. Cells  were resuspended in HBBS supplemented with 2% FBS and the mCherry+ fraction was isolated by fluorescent activated cell sorting (FACS) . The purified mCherry+ cells were centrifuged and resuspended in UB medium (TesR-E6 supplemented with 200 ng/ml FGF2, 3 mM CHIR99021, 2 mM ATRA, 10 mM Y-27632 and 100 ng/ml GDNF), counted using a haemocytometer and transferred to 24-well Transwell inserts (5e4–10e4 cells per well). Cells were mounted in a 1:1 Matrigel:UB medium solution (placed on top of the Transwell) and 0.5 ml UB medium was placed in the basolateral subcompartment.  Media was changed every other day. At 14 days the samples were passaged. UB cultures were dissociated by adding 0.5 ml of a 1:1 TrypLE/Accutase above and below the Transwell insert followed by incubation at 37˚C for 15–25 min with occasional agitation by gentle pipetting using a P1000 pipette. The cell suspension was then transferred to a 1.5 ml tube and centrifuged (3 min, 300 g), resuspended in fresh UE medium (2e5–5e5 cells per ml) and 2–5e4 cells plated per well of a new 24-well Transwell plate. For transition to ureteric stalk, UB medium was replaced with stalk medium (TesR-E6 supplemented with 200 ng/ml FGF2, 2 mM ATRA, 10 mM Y-27632) plus 1nM vasopressin four days post-passage, with medium changes every 2 days.

value: Kidney organoid

tag: batch


title: Stalk_vasopressin_r2


title: UE_3wk_r2

treatment_protocol: Day 25 organoids were dissociated with a 1:1 TrypLE/Accutase solution (~0.2 ml per organoid) at 37˚C for 15–25 min, with occasional agitation (flicking) until large clumps were no longer clearly visible. The cell suspension was then centrifuged (3 min, 300 g) and the dissociation solution removed. Cells  were resuspended in HBBS supplemented with 2% FBS and the mCherry+ fraction was isolated by fluorescent activated cell sorting (FACS) . The purified mCherry+ cells were centrifuged and resuspended in UB medium (TesR-E6 supplemented with 200 ng/ml FGF2, 3 mM CHIR99021, 2 mM ATRA, 10 mM Y-27632 and 100 ng/ml GDNF), counted using a haemocytometer and transferred to 24-well Transwell inserts (5e4–10e4 cells per well). Cells were mounted in a 1:1 Matrigel:UB medium solution (placed on top of the Transwell) and 0.5 ml UB medium was placed in the basolateral subcompartment.  Media was changed every other day. At 20 days culture the tissue was harvested for RNA extraction.


title: UE_3wk_r3

treatment_protocol: Day 25 organoids were dissociated with a 1:1 TrypLE/Accutase solution (~0.2 ml per organoid) at 37˚C for 15–25 min, with occasional agitation (flicking) until large clumps were no longer clearly visible. The cell suspension was then centrifuged (3 min, 300 g) and the dissociation solution removed. Cells  were resuspended in HBBS supplemented with 2% FBS and the mCherry+ fraction was isolated by fluorescent activated cell sorting (FACS) . The purified mCherry+ cells were centrifuged and resuspended in UB medium (TesR-E6 supplemented with 200 ng/ml FGF2, 3 mM CHIR99021, 2 mM ATRA, 10 mM Y-27632 and 100 ng/ml GDNF), counted using a haemocytometer and transferred to 24-well Transwell inserts (5e4–10e4 cells per well). Cells were mounted in a 1:1 Matrigel:UB medium solution (placed on top of the Transwell) and 0.5 ml UB medium was placed in the basolateral subcompartment.  Media was changed every other day. At 21 days culture the tissue was harvested for RNA extraction.


title: UE_3wk_r1


title: Stalk_control_r1

treatment_protocol: Day 25 organoids were dissociated with a 1:1 TrypLE/Accutase solution (~0.2 ml per organoid) at 37˚C for 15–25 min, with occasional agitation (flicking) until large clumps were no longer clearly visible. The cell suspension was then centrifuged (3 min, 300 g) and the dissociation solution removed. Cells  were resuspended in HBBS supplemented with 2% FBS and the mCherry+ fraction was isolated by fluorescent activated cell sorting (FACS) . The purified mCherry+ cells were centrifuged and resuspended in UB medium (TesR-E6 supplemented with 200 ng/ml FGF2, 3 mM CHIR99021, 2 mM ATRA, 10 mM Y-27632 and 100 ng/ml GDNF), counted using a haemocytometer and transferred to 24-well Transwell inserts (5e4–10e4 cells per well). Cells were mounted in a 1:1 Matrigel:UB medium solution (placed on top of the Transwell) and 0.5 ml UB medium was placed in the basolateral subcompartment.  Media was changed every other day. At 14 days the samples were passaged. UB cultures were dissociated by adding 0.5 ml of a 1:1 TrypLE/Accutase above and below the Transwell insert followed by incubation at 37˚C for 15–25 min with occasional agitation by gentle pipetting using a P1000 pipette. The cell suspension was then transferred to a 1.5 ml tube and centrifuged (3 min, 300 g), resuspended in fresh UE medium (2e5–5e5 cells per ml) and 2–5e4 cells plated per well of a new 24-well Transwell plate. For transition to ureteric stalk, UB medium was replaced with stalk medium (TesR-E6 supplemented with 200 ng/ml FGF2, 2 mM ATRA, 10 mM Y-27632) four days post-passage, with medium changes every 2 days for 10 days total before being harvested for RNA extraction.


title: Stalk_10d_2wk_r3


title: Stalk_10d_2wk_r2


title: Stalk_vasopressin_r1


title: Stalk_control_r3


title: UE_Pass_Thaw_2wk_r2

treatment_protocol: Day 25 organoids were dissociated with a 1:1 TrypLE/Accutase solution (~0.2 ml per organoid) at 37˚C for 15–25 min, with occasional agitation (flicking) until large clumps were no longer clearly visible. The cell suspension was then centrifuged (3 min, 300 g) and the dissociation solution removed. Cells  were resuspended in HBBS supplemented with 2% FBS and the mCherry+ fraction was isolated by fluorescent activated cell sorting (FACS) . The purified mCherry+ cells were centrifuged and resuspended in UB medium (TesR-E6 supplemented with 200 ng/ml FGF2, 3 mM CHIR99021, 2 mM ATRA, 10 mM Y-27632 and 100 ng/ml GDNF), counted using a haemocytometer and transferred to 24-well Transwell inserts (5e4–10e4 cells per well). Cells were mounted in a 1:1 Matrigel:UB medium solution (placed on top of the Transwell) and 0.5 ml UB medium was placed in the basolateral subcompartment.  Media was changed every other day. At 14 days the samples were cryopreserved. Cryopreserved samples were later thawed and replated as single cells in UB conditions. At 14 days culture post passaging the tissue was harvested for RNA extraction.


title: UE_Pass_Thaw_2wk_r1


title: UE_Pass_Thaw_2wk_r3


title: Stalk_10d_2wk_r1


title: UE_Passaged_2wk_r3

treatment_protocol: Day 25 organoids were dissociated with a 1:1 TrypLE/Accutase solution (~0.2 ml per organoid) at 37˚C for 15–25 min, with occasional agitation (flicking) until large clumps were no longer clearly visible. The cell suspension was then centrifuged (3 min, 300 g) and the dissociation solution removed. Cells  were resuspended in HBBS supplemented with 2% FBS and the mCherry+ fraction was isolated by fluorescent activated cell sorting (FACS) . The purified mCherry+ cells were centrifuged and resuspended in UB medium (TesR-E6 supplemented with 200 ng/ml FGF2, 3 mM CHIR99021, 2 mM ATRA, 10 mM Y-27632 and 100 ng/ml GDNF), counted using a haemocytometer and transferred to 24-well Transwell inserts (5e4–10e4 cells per well). Cells were mounted in a 1:1 Matrigel:UB medium solution (placed on top of the Transwell) and 0.5 ml UB medium was placed in the basolateral subcompartment.  Media was changed every other day. At 14 days the samples were passaged. UB cultures were dissociated by adding 0.5 ml of a 1:1 TrypLE/Accutase above and below the Transwell insert followed by incubation at 37˚C for 15–25 min with occasional agitation by gentle pipetting using a P1000 pipette. The cell suspension was then transferred to a 1.5 ml tube and centrifuged (3 min, 300 g), resuspended in fresh UE medium (2e5–5e5 cells per ml) and 2–5e4 cells plated per well of a new 24-well Transwell plate. At 14 days culture post passaging the tissue was harvested for RNA extraction.


title: primary differentiation at day 24 rep 2

value: iPSC


title: UE_1wk_r1

treatment_protocol: Day 25 organoids were dissociated with a 1:1 TrypLE/Accutase solution (~0.2 ml per organoid) at 37˚C for 15–25 min, with occasional agitation (flicking) until large clumps were no longer clearly visible. The cell suspension was then centrifuged (3 min, 300 g) and the dissociation solution removed. Cells  were resuspended in HBBS supplemented with 2% FBS and the mCherry+ fraction was isolated by fluorescent activated cell sorting (FACS) . The purified mCherry+ cells were centrifuged and resuspended in UB medium (TesR-E6 supplemented with 200 ng/ml FGF2, 3 mM CHIR99021, 2 mM ATRA, 10 mM Y-27632 and 100 ng/ml GDNF), counted using a haemocytometer and transferred to 24-well Transwell inserts (5e4–10e4 cells per well). Cells were mounted in a 1:1 Matrigel:UB medium solution (placed on top of the Transwell) and 0.5 ml UB medium was placed in the basolateral subcompartment.  Media was changed every other day. At 14 days culture the tissue was harvested for RNA extraction.


title: Org_EPCAM_only_r2

treatment_protocol: Day 25 organoids were dissociated with a 1:1 TrypLE/Accutase solution (~0.2 ml per organoid) at 37˚C for 15–25 min, with occasional agitation (flicking) until large clumps were no longer clearly visible. The cell suspension was then centrifuged (3 min, 300 g) and the dissociation solution removed. Cells were resuspended in HBBS supplemented with 2% FBS and incubated with an EPCAM:488 fluorescently tagged antibody for 60 minutes. The mCherry-/EPCAM+ fraction was isolated by fluorescent activated cell sorting (FACS) and collected for RNA extraction


title: Org_mCh_only_r2

treatment_protocol: Day 25 organoids were dissociated with a 1:1 TrypLE/Accutase solution (~0.2 ml per organoid) at 37˚C for 15–25 min, with occasional agitation (flicking) until large clumps were no longer clearly visible. The cell suspension was then centrifuged (3 min, 300 g) and the dissociation solution removed. Cells were resuspended in HBBS supplemented with 2% FBS and incubated with an EPCAM:488 fluorescently tagged antibody for 60 minutes. The mCherry+/EPCAM- fraction was isolated by fluorescent activated cell sorting (FACS) and collected for RNA extraction


title: UE_1wk_r3


title: Org_EPCAM_only_r1


title: UE_1wk_r2


title: cNF1 scRNA-seq


title: Org_EPCAM_only_r3


title: Org_mCh_only_r1


title: Org_mCh_only_r3


title: Stalk_control_r2


title: Org_mCh_EPCAM_r3

treatment_protocol: Day 25 organoids were dissociated with a 1:1 TrypLE/Accutase solution (~0.2 ml per organoid) at 37˚C for 15–25 min, with occasional agitation (flicking) until large clumps were no longer clearly visible. The cell suspension was then centrifuged (3 min, 300 g) and the dissociation solution removed. Cells were resuspended in HBBS supplemented with 2% FBS and incubated with an EPCAM:488 fluorescently tagged antibody for 60 minutes. The mCherry+/EPCAM+ fraction was isolated by fluorescent activated cell sorting (FACS) and collected for RNA extraction


title: UE_Passaged_2wk_r1


title: Org_mCh_EPCAM_r2


title: UE_Passaged_2wk_r2


title: Org_mCh_EPCAM_r1


title: Fat008

city: Baltimore

first: Dong Won

middle: Thomas

last: Kim

state: Maryland

address: 733 N.Broadway, MRB building (Rm 332)

department: Neuroscience

institute: Johns Hopkins University

description: bulk RNA-Seq

data_processing:
Bulk RNA-Seq (mouase): The RNA-seq reads were mapped against the mouse reference genome (build 37) using TopHat2. The aligned reads were assembled into transcripts, and gene expression was calculated using. The expression level of genes was determined based on the value of fragments per kilobase per million (FPKM), which was calculated as the number of fragments mapped to the transcripts of one gene divided by the transcript length and the number of total mapped reads in one sample. The differentially expressed genes were identified using Cufflinks (Fold change>4, FDR<0.01). Principal component analysis was carried out with the web tool ClustVis.
Bulk RNA-Seq (human): Illumina adapters of libraries after sequencing were removed using Cutadapt (v1.18)  with default parameters. Libraries were then aligned to GRCh38 using STAR (v2.42a)  with –twopassMode Basic. RSEM (v1.3.1)  was used for transcript quantification, with rsem-calculate-expression (--forwad-prob 0.5). TPM value from RSEM was used to plot white, beige, or brown adipocytes-enriched markers using ggplot (v3.32).
Genome_build: Mouse: Tophat2 mouse reference genome (build 37)
Genome_build: Human: GRCh38

extract_protocol: Nine-week old CD-1 mice were euthanized and their OF, inguinal, epididymal, and brown fat isolated.  Human orbital fat was obtained using using a protocol approved by the Institutional Review Board. RNA was extracted from each fat depot using Trizol and RNeasy mini kits. RNA sequencing performed using Illumina Nextseq500.

value: Orbital fat

tag: age

value: 58 years old

tag: Sex

value: Male


title: UEculture_r1

tag: cell line


title: UEculture_r3


title: Pol2_0h_H6_BRD2AID_HCT116_rep1

city: Chicago

first: Ali

last: Shilatifard

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

description: Pol2 ChIP-seq

data_processing:
For ChIP-seq and RNA-seq, single-end raw reads were trimmed by Trimmomatic 0.33 (Bolger et al., 2014) and aligned to hg19 using Bowtie (1.1.2) and TopHat (2.1.0)(Langmead et al. 2009; Trapnell et al. 2009), allowing only uniquely mapping reads with up to two mismatches within the 50 bp read. The resulting reads were extended to 150 bp toward the interior of the sequenced fragment, normalized to total reads aligned (reads per million, rpm) and formatted as bigWig-coverage tracks using GenomicRanges.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files with normalized read counts were provided for all samples.

growth_protocol: DLD-1 or HCT116 cells were cultured in DMEM (Corning) supplemented with 10% FBS (Corning), 1X GlutaMAX (Gibco), 100 U/ml Penicillin and 100 µg/ml Streptomycin (Gibco).

extract_protocol:
For ChIP-seq, 20-50 million cells were crosslinked with 1% paraformaldehyde (Electron Microscopy Sciences) in PBS for 10 min at r.t. Chromatin was sonicated with the Covaris E220 for 4 min with 10% duty cycle, 140 peak intensity power, 200 cycles per burst. Immunoprecipitations were carried out with antibodies and Protein A/G-agarose beads (Santa Cruz) or Dynabeads Protein G (Invitrogen).
For RNA-seq, total RNAs were isolated using the RNeasy Mini Kit from Qiagen. mRNAs were isolated using NEBNext Poly(A) mRNA Magnetic Isolation Module.
For ChIP-seq, DNA libraries were prepared by the HTP Library Preparation Kit for Illimina (KAPA) and sequenced on the NextSeq 500 (Illumina).
RNA libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit and sequenced on Illumina NovaSeq 6000.

treatment_protocol:
Cells were treated with 500 µM Auxin (3-indole-acetic acid sodium salt, abcam), 250 nM dBET6 (AOBIOUS), or 20 nM KL-1 (Liang et al. 2018). Heat shock treatment at 42 ˚C for 1 h was carried out as described previously (Mahat et al, 2016)
For RNA-seq, cells were treated with or without auxin for 2 h in 37°C incubator and were directly placed into 42°C incubator for heat shock.

value: Colorectal carcinoma

tag: genotype

value: BRD2-AID OsTIR1

tag: growth temperature

value: Auxin

tag: antibody

value: Rpb1 NTD (D8L4Y)


title: Pol2_24h_H6_BRD2AID_HCT116_rep1

description: Pol2 ChIP-seq


title: RNA-seq, day 7 of EBV infection, donor 2 [d07.2]

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

data_processing:
RNA-Seq data analysis was done with rsem (ver. 1.2.3) and hg19 genome with ensemble transcriptome information
DESeq2 was used for differentail expression analysis
Genome_build: hg19
Supplementary_files_format_and_content: Prosessed files contains the raw counts for each gene

source_name: day 7 of EBV infection

extract_protocol:
Total RNA was isolated from 1.5 x 10^6 cells using the Direct-zol microprep kit following the manufacturer’s protocol (Zymo Research).
Sequencing library preparation was then completed using the QuantSeq 3’-mRNA kit (Lexogen) to generate Illumina-compatible sequencing libraries according to the manufacturer’s instructions

tag: donor id

value: B cells

tag: time point

value: day 7 of EBV infection


title: RNA-seq, day 7 of EBV infection, donor 1 [d07.1]


title: RNA-seq, day 21 of EBV infection, donor 1 [d21.1]

source_name: day 21 of EBV infection

value: day 21 of EBV infection


title: RNA-seq, day 21 of EBV infection, donor 2 [d21.2]


title: RNA-seq, day 2 of EBV infection, donor 1 [d02.1]

source_name: day 2 of EBV infection

value: day 2 of EBV infection


title: RNA-seq, day 2 of EBV infection, donor 2 [d02.2]


title: RNA-seq, day 0 of EBV infection, donor 1 [d00.1]

source_name: day 0 of EBV infection

value: day 0 of EBV infection


title: ATAC-seq, day 21 of EBV infection, donor 2

data_processing:
ATAC-seq data was aligned using bowtie against hg19 version of the human genome and HOMER was used to generate bigwig files and call significant peaks using “-style histone” and “-style factor” option
Genome_build: hg19
Supplementary_files_format_and_content: ATAC-seq signal in bigwig track format

extract_protocol:
5 x 104 cells were washed in 50ul cold PBS, spun down at 500 x g and 4C for 5mins, and resuspended in 50ul cold lysis buffer (10mM Tris pH 7.5, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL CA-630).  Resuspended cells were immediately spun at 500 x g and 4C for 10mins, and the supernatant was removed.  The pellet was then resuspended in a 50ul Tn5 transposase reaction following the manufacturer’s protocol (Nextera Tn5 transposase kit, Illumina) and incubated in a thermomixer at 37C and 300rpm for 30mins.  DNA was purified using a MinElute PCR purification kit (Qiagen) and eluted in 10ul to be used in library amplification
PCR amplification of tagmented DNA was done using the NEBNext HiFi PCR mastermix (New England Bioloabs) with a universal forward and sample-specific reverse oligo for sample barcoding


title: ATAC-seq, day 7 of EBV infection, donor 1


title: ATAC-seq, day 21 of EBV infection, donor 1


title: ATAC-seq, day 2 of EBV infection, donor 2


title: ATAC-seq, day 7 of EBV infection, donor 2


title: ATAC-seq, day 0 of EBV infection, donor 2


title: ATAC-seq, day 2 of EBV infection, donor 1


title: ATAC-seq, day 0 of EBV infection, donor 1


title: Pol2_1h_H6_BRD2AID_HCT116_rep1

description: Pol2 ChIP-seq


title: Pol2_4h_H6_BRD2AID_HCT116_rep1

description: Pol2 ChIP-seq


title: Multiplexed_Subcellular_Samples_File96

city: Frankfurt

first: Julio

middle: David

last: Perez

state: Hessen

department: Synaptic plasticity

institute: Max Planck Institute for Brain Research

data_processing:
bcl2fastq v2.20.0.422 to generate fastq files
Drop-seq tools v2.3.0 and Fastp for removal of adapter sequences and low quality reads
Reads were aligned against the RGSC 6.0/rn6 rat genome using STAR v2.5.4b
Gene assigment, and digital expression quantification per samples as done using Drop-seq tools v2.3.0
Genome_build: Rn6
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Rattus norvegicus

growth_protocol: The hippocampus of P1 rat pups or cortex and hippocampus of P0/P1 mice of either sex was dissected out, dissociated with papain and plated on poly-D- lysine coated coverslips of MatTek glass bottom dishes at a density of 20,000.

extract_protocol:
Dendrites and somata were dissected using LCM and collected in a buffer containing detergent and proteases to lyse the cell and release RNAs. RNAs were reverse transcribed, pre-amplified and prepared for Illumina sequencing.
Nextera XT DNA Library prep kit (Illumina)

value: Sprague Dawley

tag: days in vitro

value: wild type


title: 2hH2O_42C1h_AFF4Protec_AFF4AID_DLD_rep1

description: AFF4 ChIP-seq

data_processing:
For ChIP-seq, single-end raw reads were trimmed by Trimmomatic 0.33 (Bolger et al., 2014) and aligned to hg19 using Bowtie version 1.1.2, allowing only uniquely mapping reads with up to two mismatches within the 50 bp read. The resulting reads were extended to 150 bp toward the interior of the sequenced fragment, normalized to total reads aligned (reads per million, rpm), and formatted as bigWig-coverage tracks using GenomicRanges.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files with normalized read counts were provided for all samples.

growth_protocol: DLD-1 cells were cultured in DMEM (Corning) supplemented with 10% FBS (Corning), 1X GlutaMAX (Gibco), 100 U/ml Penicillin and 100 µg/ml Streptomycin (Gibco).

extract_protocol:
For ChIP-seq, 20-50 million cells were crosslinked with 1% paraformaldehyde (Electron Microscopy Sciences) in PBS for 10 min at r.t. Chromatin was sonicated with the Covaris E220 for 4 min with 10% duty cycle, 140 peak intensity power, 200 cycles per burst. Immunoprecipitations were carried out with antibodies and Protein A/G-agarose beads (Santa Cruz) or Dynabeads Protein G (Invitrogen).
For ChIP-seq, DNA libraries were prepared by the HTP Library Preparation Kit for Illimina (KAPA) and sequenced on the NextSeq 500 or NovaSeq 6000 (Illumina).

treatment_protocol: Cells were treated with 500 µM Auxin (3-indole-acetic acid sodium salt, abcam), 250 nM dBET6 (AOBIOUS), or 20 nM KL-1 (Liang et al. 2018). Heat shock treatment at 42 ˚C for 1 h was carried out as described previously (Mahat et al, 2016)

value: Colorectal adenocarcinoma DLD-1

value: AFF4-AID OsTIR1

value: Heat shock

tag: chip antibody

value: AFF4 Proteintech 14662-1-AP


title: 2hAux_42C1h_AFF4Protec_AFF4AID_DLD_rep1

description: AFF4 ChIP-seq


title: Multiplexed_Subcellular_Samples_File95


title: 2hAux_37C1h_AFF4Protec_AFF4AID_DLD_rep1

description: AFF4 ChIP-seq


title: Multiplexed_Subcellular_Samples_File94


title: RNA-seq, day 0 of EBV infection, donor 2 [d00.2]


title: Multiplexed_Subcellular_Samples_File93


title: 2hH2O_37C1h_AFF4Protec_AFF4AID_DLD_rep1

description: AFF4 ChIP-seq


title: Multiplexed_Subcellular_Samples_File92


title: Fat007

description: bulk RNA-Seq

tag: tissue

value: Orbital fat

value: 76 years old


title: Multiplexed_Subcellular_Samples_File89


title: Multiplexed_Subcellular_Samples_File90


title: 2hH2O_42C1h_AFF1Bethyl_AFF1AID_DLD_rep1

description: AFF1 ChIP-seq

value: AFF1-AID OsTIR1

value: AF4 Bethyl A302-345A


title: Multiplexed_Subcellular_Samples_File91


title: 2hH2O_37C1h_AFF1Bethyl_AFF1AID_DLD_rep1

description: AFF1 ChIP-seq


title: 2hAux_37C1h_AFF1Bethyl_AFF1AID_DLD_rep1

description: AFF1 ChIP-seq

value: Auxin


title: input_2hDMSO_37C1h_BRD4AID_DLD_rep1

description: Input

value: BRD4-AID OsTIR1


title: Multiplexed_Subcellular_Samples_File85


title: Multiplexed_Subcellular_Samples_File86


title: Multiplexed_Subcellular_Samples_File87


title: Multiplexed_Subcellular_Samples_File88


title: 2hAux_37C1h_Pol2CST_AFF4AID_DLD_rep1

description: Pol2 ChIP-seq

value: Rpb1 NTD (D8L4Y)


title: 2hH2O_37C1h_Pol2CST_AFF4AID_DLD_rep1

description: Pol2 ChIP-seq


title: 2hAux_42C1h_Pol2CST_AFF4AID_DLD_rep1

description: Pol2 ChIP-seq


title: Multiplexed_Subcellular_Samples_File84


title: Multiplexed_Subcellular_Samples_File82


title: Multiplexed_Subcellular_Samples_File83


title: 2hH2O_42C1h_Pol2CST_AFF1AID_DLD_rep1

description: Pol2 ChIP-seq


title: 2hAux_37C1h_Pol2CST_AFF1AID_DLD_rep1

description: Pol2 ChIP-seq


title: Multiplexed_Subcellular_Samples_File81


title: input_2hH2O_37C1h_WT_DLD_rep1

description: Input


title: 2hAux_42C1h_AFF1Bethyl_AFF1AID_DLD_rep1

description: AFF1 ChIP-seq


title: UEculture_r2

value: Kidney organoid


title: 2hH2O_37C1h_Pol2CST_AFF1AID_DLD_rep1

description: Pol2 ChIP-seq


title: Multiplexed_Subcellular_Samples_File79


title: 2hH2O_42C1h_Pol2CST_AFF4AID_DLD_rep1

description: Pol2 ChIP-seq


title: 2hH2O_42C1h_Pol2CST_BRD4AID_DLD_rep1

description: Pol2 ChIP-seq


title: Multiplexed_Subcellular_Samples_File78


title: Multiplexed_Subcellular_Samples_File77


title: 2hAux_42C1h_Pol2CST_BRD3AID_DLD_rep1

description: Pol2 ChIP-seq

value: BRD3-AID OsTIR1


title: 2hH2O_42C1h_Pol2CST_BRD3AID_DLD_rep1

description: Pol2 ChIP-seq


title: 2hH2O_42C1h_Pol2CST_BRD2AID_DLD_rep1

description: Pol2 ChIP-seq

value: BRD2-AID OsTIR1


title: Multiplexed_Subcellular_Samples_File73


title: Multiplexed_Subcellular_Samples_File76


title: 2hH2O_37C1h_Pol2CST_WT_DLD_rep1

description: Pol2 ChIP-seq


title: 2hAux_42C1h_Pol2CST_AFF1AID_DLD_rep1

description: Pol2 ChIP-seq


title: Multiplexed_Subcellular_Samples_File75


title: Multiplexed_Subcellular_Samples_File72


title: Multiplexed_Subcellular_Samples_File74


title: 2hH2O_42C1h_Pol2CST_WT_DLD_rep1

description: Pol2 ChIP-seq


title: Multiplexed_Subcellular_Samples_File71


title: 2hdBET6_37C1h_Pol2CST_BRD4AID_DLD_rep1

description: Pol2 ChIP-seq


title: Multiplexed_Subcellular_Samples_File70


title: Multiplexed_Subcellular_Samples_File69


title: 2hH2O_37C1h_Pol2CST_BRD4AID_DLD_rep1

description: Pol2 ChIP-seq


title: Multiplexed_Subcellular_Samples_File68


title: 2hAux_37C1h_Pol2CST_BRD3AID_DLD_rep1

description: Pol2 ChIP-seq


title: 2hH2O_37C1h_Pol2CST_BRD3AID_DLD_rep1

description: Pol2 ChIP-seq


title: Multiplexed_Subcellular_Samples_File80


title: 2hAux_42C1h_Pol2CST_BRD4AID_DLD_rep1

description: Pol2 ChIP-seq


title: Multiplexed_Subcellular_Samples_File67


title: 2hAux_37C1h_Pol2CST_BRD2AID_DLD_rep1

description: Pol2 ChIP-seq


title: 2hAux_42C1h_Pol2CST_BRD2AID_DLD_rep1

description: Pol2 ChIP-seq


title: 2hH2O_37C1h_Pol2CST_BRD2AID_DLD_rep1

description: Pol2 ChIP-seq


title: Multiplexed_Subcellular_Samples_File64


title: Multiplexed_Subcellular_Samples_File66


title: 303negF3_S3

city: Lyon

first: Olivier

last: Diaz

address: Avenue Tony Garnier

department: Centre International de Recherche en Infectiologie (CIRI)

country: France

institute: INSERM U1111 – CNRS UMR5308 Université Lyon 1, ENS de LyonINSERM U1111 – CNRS UMR5308 Université Lyon 1, ENS de Lyon

data_processing:
Bcl2fastq v2.17.1.14 was used to demultiplex using 1 mismatch
Trimming was performed using cutadapt v1.9.1. treshold quality score to 30, minimum rate of undetermined bases ("N"s) was set to 30%. Adapters were trimmed with 3 bases overlap, a maximum error rate of 10%.
Reads were mapped using tophat v2.1.0 with default parameters. Reference genome: homo sapiens, GRCh37/hg19.
pLEX-GCKstop.txt contains the sequence of GCK that is expressed in Huh7-GCK+/HK2- cells
signals were normalized using cufflinks (method described by Trapnell, C et al, Nat.Biotechnol. 2010) v2.1.1. wich use Fragments Per Kilobases of exon per Million mapped reads (FPKM) method
Genome_build: hg19
Supplementary_files_format_and_content: excel file containing FPKM for all sample and FPKM_Tracking files containing individual FPKM for each samples

source_name: hepatocellular carcinoma cells

growth_protocol: Cells were cultured at 37°C and 5% CO2 in Dulbecco’s Modified Eagle’s Medium 25mM Glucose (DMEM; Life Technologies) containing 10% foetal calf serum (FCS; Dominique Dutcher, Brumath, France), penicillin/streptomycin and supplemented with pyruvate, glutamine

extract_protocol:
Cells were washed with PBS before pellets frozen at -80°. The pellets were extracted using Direct-zol RNA purification kit (Zymo Research, cat#R2061).
NextFlex Rapid Directional mRNA-Seq (Bioo-Scientific, cat#NOVA-5138-07) was used with 200ng of total RNA for the construction of sequencing libraries.


title: 303negF4_S1

data_processing:
Bcl2fastq v2.17.1.14 was used to demultiplex using 1 mismatch
Trimming was performed using cutadapt v1.9.1. treshold quality score to 30, minimum rate of undetermined bases ("N"s) was set to 30%. Adapters were trimmed with 3 bases overlap, a maximum error rate of 10%.
Reads were mapped using tophat v2.1.0 with default parameters. Reference genome: homo sapiens, GRCh37/hg19.
signals were normalized using cufflinks (method described by Trapnell, C et al, Nat.Biotechnol. 2010) v2.1.1. wich use Fragments Per Kilobases of exon per Million mapped reads (FPKM) method
pLEX-GCKstop.txt contains the sequence of GCK that is expressed in Huh7-GCK+/HK2- cells
Genome_build: hg19
Supplementary_files_format_and_content: excel file containing FPKM for all sample and FPKM_Tracking files containing individual FPKM for each samples


title: 303negF2_S2


title: Multiplexed_Subcellular_Samples_File63


title: Multiplexed_Subcellular_Samples_File59


title: Multiplexed_Subcellular_Samples_File61


title: Multiplexed_Subcellular_Samples_File62


title: Multiplexed_Subcellular_Samples_File58


title: 2hAux_37C1h_Pol2CST_BRD4AID_DLD_rep1

description: Pol2 ChIP-seq


title: Multiplexed_Subcellular_Samples_File60


title: 76negF2_S8

value: wildtype


title: Multiplexed_Subcellular_Samples_File57

value: Sprague Dawley


title: Multiplexed_Subcellular_Samples_File56

value: wild type


title: 76negF1_S7


title: data_TIR1_UVneg_2_Total

city: Leiden

first: Martijn

middle: S.

last: Luijsterburg

state: zuid-holland

address: Einthovenweg 20

department: Human Genetics

country: Netherlands

institute: LUMC

data_processing:
ChIP-seq: Reads were aligned to the Human Genome 38 (Hg38) using bwa-mem tools (Li, 2013) during which only high-quality reads (> q30) were included in the analyses and duplicates were removed. Bam files were converted into TagDirectories using HOMER tools (Heinz et al., 2010). Binding profiles within selected areas of individual genes (e.g. around TSS or TTS), were defined using the AnnotatePeaks.pl tool of HOMER using the default normalization to 10mln reads. Metagene profiles were defined using the makeMetaGeneProfile.pl tool of HOMER, using default settings. Individual datasets were subsequently processed in R (Team, 2019). BrU-seq: Data was processed as previously described (Paulsen et al., 2014).  Briefly, reads were pre-filtered by alignment to the human ribosomal repeating subunit (GenBank U13369.1) and human mitochondrial genome (chrM) from the hg38 reference genome using bowtie2 v.2.3.3.1. The remaining reads were mapped to the hg38 reference genome using STAR v2.7.0f. Base coverages were used to compute read counts for features, such as genes and bins, which were then normalized to feature length and number of uniquely-mapped reads (RPKM method). Gene selection was based on the following criteria: length as indicated per figure, TSS is at least 10kb apart, expression is at least 0.05 RPKM. The median expression was calculated for each 500 bp bins from 5kb upstream until 100kb downstream of the selected genes for each time-point.
Genome_build: hg38
Supplementary_files_format_and_content: excel tables providing avearged read coverage around the TSS or normalized traverling ratios for the top 3000 genes for each individual sample, and the BrU-seq counts versus distance from the TSS for genes of 25-50Kb, 50-100Kb and >100Kb

source_name: U2OS OsTIR1 control

growth_protocol: DMEM GlutaMAX +10% Fetal Calf Serum + antibiotics

extract_protocol:
ChIP-seq: Cells were plated and grown to ~90% confluency and crosslinked with 0.5 mg/mL disuccinimidyl glutarate (DSG; Thermo Fisher) in PBS for 45 min at room temperature. Cells were washed with PBS and crosslinked with 1 % PFA for 20 min at room temperature. Fixation was stopped by adding 1.25 M Glycin in PBS to a final concentration of 0.1 M for 3 minutes at room temperature. Cells were washed with cold PBS and lysed and collected in a buffer containing 0.25% Triton X-100, 10 mM EDTA (pH 8.0), 0.5 mM EGTA (pH 8.0) and 20 mM Hepes (pH 7.6). Chromatin was pelleted in 5 min at 400 g and incubated in a buffer containing 150 mM NaCl, 1 mM EDTA (pH 8.0), 0.5 mM EGTA (pH 8.0) and 50 mM Hepes (pH 7.6) for 10 minutes at 4°C. Chromatin was again pelleted for 5 min at 400 g and resuspended in ChIP-buffer (0.15 % SDS, 1 % Triton X-100, 150 mM NaCl, 1 mM EDTA (pH 8.0), 0.5 mM EGTA (pH 8.0) and 20 mM Hepes (pH 7.6)) to a final concentration of 15x106 cells/ml. BrU-seq: U2OS osTIR1 or PAF1-AID cells were induced with doxycycline for 24 hrs, and subsequently with auxin for 5 hrs. After this treatment, cells were either mock-treated or irradiated with UV-C light (7 J/m2). Cells were then incubated in conditioned media for different periods of time (0, 3, 8, 24h) before being incubated with 2 mM bromouridine (Bru) at 37°C for a 30 min. The cells were then lysed in TRIzol reagent (Invitrogen) and Bru-containing RNA isolated as previously described (Andrade-Lima et al., 2015).
ChIP-seq: Chromatin was sonicated to approximately 1 nucleosome using a Bioruptor waterbath sonicator (Diagenode). Chromatin of ~5x106 cells was incubated with 3ug antibody (RNAPII, rabbit polyclonal, Bethyl laboratories, A304-405A; PAF1, rabbit polyclonal, Bethyl laboratories, A300-172A) over night at 4°C, followed by a 1.5 hrs protein-chromatin pull-down with a 1:1 mix of protein A and protein G Dynabeads (Thermo Fisher; 10001D and 10003D). ChIP samples were washed extensively, followed by decrosslinking for 4 hrs at 65°C in the presence of proteinase K. DNA was purified using a Qiagen MinElute kit. Sample libraries were prepared using Hifi Kapa sample prep kit and A-T mediated ligation of Nextflex adapters. Samples were sequenced using an Illumina NextSeq500, using paired-end sequencing with 42 bp from each end. BrU-seq: cDNA libraries were made from the Bru-labeled RNA using the Illumina TruSeq library kit and paired-end 151 bp sequenced using the Illumina NovaSeq platform at the University of Michigan DNA Sequencing Core. Only single-end sequencing data was used for downstream analyses

treatment_protocol: DNA damage was induced by irradiating cells with varying doses of UV-C as indicated per sample; samples were assayed at different time-periods after UV treatment as indicated per sample; to deplete PAF1 using the auxin-inducible degron system cells were induced with 2ug/ml doxycycline for 24 hrs and pre-treated with 500uM auxin for 5hours prior to UV-C irradiation or harversting.

tag: genotype/variation

value: OsTIR1 control

tag: uv-c dose

value: no UV

tag: time after uv-c

value: not applicable

tag: chip-antibody

value: RPB1; Bethyl (A304-405A)

tag: pre-treatment

value: 24hrs treatment with 2ug/ml Doxycycline, followed by 500uM auxin for 5-6hrs


title: data_TIR1_UVneg_1Combi_Total

tag: cell type


title: data_TIR1_9J_2_Total

value: 8 hours


title: data_TIR1_9J_1Combi_Total


title: Multiplexed_Subcellular_Samples_File55

tag: strain


title: Multiplexed_Subcellular_Samples_File54


title: Multiplexed_Subcellular_Samples_File65


title: data_TIR1_6J_1Combi_Total


title: data_TIR1_6J_2_Total


title: Multiplexed_Subcellular_Samples_File53


title: data_RNAPIICSBKO_UVneg_2_Total

source_name: U2OS CSB-KO

value: CSB-KO


title: Multiplexed_Subcellular_Samples_File52


title: data_RNAPIICSBKO_UVneg_1_Total


title: Multiplexed_Subcellular_Samples_File50


title: data_RNAPIICSBKO_6J_2_Total


title: Multiplexed_Subcellular_Samples_File51


title: Multiplexed_Subcellular_Samples_File49


title: 76negF3_S9


title: data_RNAPII9J26h_2_Total

source_name: U2OS WT

value: WT

value: 26 hours


title: data_RNAPIICSBKO_6J_1_Total


title: Multiplexed_Subcellular_Samples_File48


title: Multiplexed_Subcellular_Samples_File47


title: data_RNAPII9J26h_1_Total


title: Multiplexed_Subcellular_Samples_File46


title: Multiplexed_Subcellular_Samples_File45


title: data_RNAPII9J_Total


title: Multiplexed_Subcellular_Samples_File44


title: data_RNAPII9J_2_Total


title: data_RNAPII6J_Total


title: data_RNAPII6J26h_2_Total


title: Multiplexed_Subcellular_Samples_File43


title: Multiplexed_Subcellular_Samples_File42


title: data_RNAPII6J26h_1_Total


title: Multiplexed_Subcellular_Samples_File41


title: data_RNAPII6J_3_Total


title: Multiplexed_Subcellular_Samples_File40


title: data_RNAPII6J_2_Total


title: Multiplexed_Subcellular_Samples_File39


title: data_RNAPII_Total


title: data_RNAPII_3_Total


title: Multiplexed_Subcellular_Samples_File38


title: Multiplexed_Subcellular_Samples_File37


title: data_RNAPII20J_1_Total


title: data_RNAPII_2_Total


title: Multiplexed_Subcellular_Samples_File34


title: data_PAFAID_UVneg_2_Total

source_name: U2OS OsTIR1 + PAF-AID14

value: OsTIR1 + PAF-AID14


title: data_PAFAID_9J_2_Total


title: data_PAFAID_UVneg_1Combi_Total


title: Multiplexed_Subcellular_Samples_File33


title: Multiplexed_Subcellular_Samples_File31


title: Multiplexed_Subcellular_Samples_File32


title: Multiplexed_Subcellular_Samples_File30


title: Multiplexed_Subcellular_Samples_File29


title: Multiplexed_Subcellular_Samples_File28


title: data_PAFAID_6J_2_Total


title: data_PAFAID_9J_1Combi_Total


title: data_PAF1CSBKO_9J_1_Total

value: PAF1; Bethyl (A300-172A)


title: Multiplexed_Subcellular_Samples_File26


title: data_PAF1CSBKO_6J_2_Total


title: data_PAFAID_6J_1Combi_Total


title: Multiplexed_Subcellular_Samples_File25


title: data_PAF1CSBKO_UVneg_3_Total


title: data_PAF1CSBKO_UVneg_1_Total


title: Multiplexed_Subcellular_Samples_File27


title: Multiplexed_Subcellular_Samples_File24


title: Multiplexed_Subcellular_Samples_File22


title: data_PAF19J26_1_Total


title: data_PAF19J_Total


title: data_PAF19J_4_Total


title: Multiplexed_Subcellular_Samples_File36


title: Multiplexed_Subcellular_Samples_File35


title: Multiplexed_Subcellular_Samples_File23


title: Multiplexed_Subcellular_Samples_File21


title: data_PAF19J_2_Total


title: Multiplexed_Subcellular_Samples_File20


title: Multiplexed_Subcellular_Samples_File19


title: Multiplexed_Subcellular_Samples_File18


title: data_PAF1_2_Total


title: data_PAF1_3_Total


title: Multiplexed_Subcellular_Samples_File17


title: data_InputOsTIR4_Total (6J8h)


title: Multiplexed_Subcellular_Samples_File14


title: data_InputOsTIR3_Total (noUV)


title: Multiplexed_Subcellular_Samples_File13


title: data_InputOsTIR2_Total (9J8h)


title: data_InputOsTIR_Total (6J8h)


title: data_PAF1_Total


title: data_Input5_Total  (WT noUV)


title: Multiplexed_Subcellular_Samples_File11


title: Multiplexed_Subcellular_Samples_File10


title: data_PAF1CSBKO_9J_2_Total


title: Multiplexed_Subcellular_Samples_File9


title: Multiplexed_Subcellular_Samples_File8


title: data_Input6_Total (WT noUV)


title: Multiplexed_Subcellular_Samples_File7


title: data_Input3_Total  (WT 6J8h)


title: data_PAF16J_Total


title: data_InputOsTIR5_Total (9J8h)


title: data_Input2_Total (CSB-KO noUV)


title: Multiplexed_Subcellular_Samples_File6


title: data_Input_Total (CSB-KO 6J8h)


title: data_InputOsTIR6_Total (noUV)


title: Multiplexed_Subcellular_Samples_File15


title: Multiplexed_Subcellular_Samples_File4


title: Multiplexed_Subcellular_Samples_File12


title: Multiplexed_Subcellular_Samples_File3


title: Multiplexed_Subcellular_Samples_File2


title: Multiplexed_Subcellular_Samples_File1


title: Multiplexed_Subcellular_Samples_File5