title: Pimasertib_2

first: Jason

last: Rodencal

state: CA

address: 327 Campus Drive, Room 420

data_processing:
Basecalls performed using CASAVA.
Reads were filtered using the following criteria (from NovoGene manual): (1) Remove reads containing adaptors; (2) Remove reads containing N > 10% (N represents base that could not be determined); (3) The Qscore (Quality value) of over 50% bases of the read is <= 5.
RNA-seq Adapter information: NEBNext® Ultra TM RNA Library Prep Kit, RNA 5' Adapter (5'Adaptor): 5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, RNA 3' Adapter (3'Adaptor, 6bp bases is Index): 5' GATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG
Paired-end reads were mapped to the genome using STAR v2.5.
Quantification of gene expression level (from NovoGene manual): "HTSeq v0.6.1 was used to count the read numbers mapped of each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene."
Differential expression of genes was calculated using DESeq2 R package (2_1.6.3).
Genome_build: Homo sapiens hg19 (GRCh37)
Supplementary_files_format_and_content: The processed .txt files contain the readcounts and FPKM of each gene for the conditions. Differential expression was calculated using DESeq2, and associated p-values are reported. Corrected p-values were calculated using the Benjamini-Hochberg method, and are reported in the processed files.

source_name: HT-1080 fibrosarcoma cells

growth_protocol: HT-1080 cells were grown in DMEM (+ pen/strep and 10% FBS) supplemented with nonessential amino acids. Cells were split every other day and typically seeded at 700,000 cells in a T75 flask.

extract_protocol:
Cells were scraped into 0.5 mL of PBS, spun down, and then RNA was extracted using the Qiagen RNeasy (cat. 74134) kit as per manufacturer's instructions.
As per Novogene manual: "Then first strand cDNA is synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis is subsequently performed using DNA Polymerase I and RNase H. Double-stranded cDNA is purified using AMPure XP beads. Remaining overhangs of the purified double-stranded cDNA are converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3' ends of DNA fragments, NEBNext Adaptor with hairpin loop structure is ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments are purified with AMPure XP system (Beckman Coulter, Beverly, USA). Finally, the final library is gotten by PCR amplification and purification of PCR products by AMPure XP beads."

treatment_protocol: Cells were treated with DMSO vehicle control, palbociclib (2 micromolar), or pimasertib (500 nanomolar) for 48 hours.

tag: cell line

value: cancer derived cell line

value: Pimasertib


title: DRIP-Seq, EcTopoI 14-kDa CTD overexpression, replicate 1

status: Public on Jan 01 2022

type: SRA

city: Seattle

first: Dmitry

last: Sutormin

state: WA

address: 401 Terry Ave N

country: USA

institute: Institute for Systems Biology

description: Exponentially growing culture was cultivated until reaching OD600~0.2. Then, IPTG was added to final concentration 1 mM to induce EcTopoI 14-kDa CTD overexpression form the pCA25 CTD plasmid and the cultivation proceeded for 1 h when the culture was harvested by centrifugation (4500 g, 5min, 4°C). Total nucleic acids were purified from cells pellet using GeneJET Genomic DNA purification kit (ThermoFisher) according to the manufacturer's protocol but omitting the RNAse A treatment step. Sample was sonicated using Covaris ultrasonicator to get median fragment size 150 bp. 10 µg of S9.6 antibodies (Kerafast, ENH001) were incubated with 20 µL of protein-G Sepharose (Bialexa) pre-equilibrated with PBS in 70 µL of IP-buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 0.1% sodium deoxycholate, 1% Triton X-100, 140 mM NaCl) for 2 h at 4C with gentle shaking. After the pre-incubation, an aliquot (containing 6 µg of sheared DNA, concentrations measured using Qubit 1X dsDNA HS Assay) was added and the immunoprecipitation was continued for 4 h. Then, the resin was washed with 1 mL of IP-buffer, 1 mL of IPS-buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 0.1% sodium deoxycholate, 1% Triton X-100, 500 mM NaCl) and twice with 1 mL of Wash-buffer (10 mM Tris-HCl pH 8, 1 mM EDTA, 0.5% sodium deoxycholate, 1% Triton X-100, 250 mM NaCl). TES-buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 250 mM NaCl) was mixed with the washed resin to get 200 µL of slurry and proteinase K (ThermoFisher) was added to a final concentration 0.5 mg/mL. Proteolysis was performed at 55C for 1 h. After that, the resin was spun down by centrifugation and nucleic acids were purified from the supernatant using AMPure XP magnetic beads (Beckman Coulter). NGS libraries were prepared using strand-specific Accel NGS 1S kit (Swift Bioscience) suitable for single-stranded DNA. Sequencing was performed with Illumina NextSeq with 75+75 bp paired-end reads protocol. Biological replicate 1.

library_source: genomic

data_processing:
Library strategy: DRIP-Seq
Raw reads were trimmed and filtered using Trimmomatic (ILLUMINACLIP:2:30:10 LEADING:0 TRAILING:0 SLIDINGWINDOW:4:0 MINLEN:30).
Processed reads were aligned to the E. coli w3110 MuSGS genome with BWA MEM (default settings).
Strand-specific coverage for forward and reverse strands were obtained based on read alignments stored in SAM files using custom script (see https://github.com/sutormin94/E_coli_DRIP-Seq_analysis).
Genome_build: NC_007779.1_w3110_Mu (custom build, fasta and genome annotation are provided as supplementary files)
Supplementary_files_format_and_content: wig files with strand-specific sequencing coverage depth.

molecule: genomic DNA

organism: Escherichia coli

source_name: Escherichia coli DY330 topA-SPA pCA25 CTD

growth_protocol: For starter culture, a single colony of E. coli DY330 topA-SPA was inoculated in 5 mL of LB supplemented with 50 mkg/ml kanamycin and 0.5% glucose. The starter was grown overnight at 37C with shaking 180 rpm. 0.5 mL of the starter culture was inoculated in 50 mL of fresh LB supplemented with 0.5% glucose, and the culture was cultivated at 37C with shaking 180 rpm until reaching OD600=0.6. For cells expressing EcTopoI 14-kDa CTD cultivation was performed similarly but with E. coli DY330 topA-SPA harboring pCA24 14kDa CTD plasmid. Cultures were grown in LB supplemented with chloramphenicol 34 µg/ml and 0.5% glucose (for catabolyte repression).

extract_protocol:
Total nucleic acids were purified from cells pellet using GeneJET Genomic DNA purification kit (ThermoFisher) according to the manufacturer's protocol but omitting the RNAse A treatment step. To shear nucleic acids, sample was sonicated using Covaris ultrasonicator to get median fragment size 150 bp. 10 µg of S9.6 antibodies (Kerafast, ENH001) were incubated with 20 µL of protein-G Sepharose (Bialexa) pre-equilibrated with PBS in 70 µL of IP-buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 0.1% sodium deoxycholate, 1% Triton X-100, 140 mM NaCl) for 2 h at 4C with gentle shaking. After the pre-incubation, an aliquot (containing 6 µg of sheared DNA, concentrations measured using Qubit 1X dsDNA HS Assay) was added and the immunoprecipitation was continued for 4 h. Then, the resin was washed with 1 mL of IP-buffer, 1 mL of IPS-buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 0.1% sodium deoxycholate, 1% Triton X-100, 500 mM NaCl) and twice with 1 mL of Wash-buffer (10 mM Tris-HCl pH 8, 1 mM EDTA, 0.5% sodium deoxycholate, 1% Triton X-100, 250 mM NaCl). TES-buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 250 mM NaCl) was mixed with the washed resin to get 200 µL of slurry and proteinase K (ThermoFisher) was added to a final concentration 0.5 mg/mL. Proteolysis was performed at 55C for 1 h. After that, the resin was spun down by centrifugation and nucleic acids were purified from the supernatant using AMPure XP magnetic beads (Beckman Coulter). As a control, an aliquot of sonicated nucleic acids (containing 6 µg of sheared DNA, concentrations measured using Qubit 1X dsDNA HS Assay) was treated with 5U of RNAse HI (NEB) in RNAse HI buffer for 30 min at 37oC and then nucleic acids were purified with GeneJET Gel Extraction and DNA cleanup micro kit (General cleanup protocol, ThermoFisher). IP for treated aliquot using S9.6 antibodies and nucleic acid purification were performed as described for the untreated aliquot.
NGS libraries were prepared using strand-specific Accel NGS 1S kit (Swift Bioscience) suitable for single-stranded DNA. DNA sequencing was performed using Illumina NextSeq with 75+75 bp paired-end protocol. Libraries preparation and sequencing were performed at Skoltech Sequencing Core Facilities. DRIP-Seq was performed in triplicate.

treatment_protocol: For the untreated sample, when OD600 reached 0.6, cells were harvested by centrifugation (4500 g, 5min, 4°C). For Rif sample, cell culture was pretreated with 100 µg/ml rifampicin for 20 minutes before cells harvesting. For CTD sample, a culture was cultivated until reaching OD600~0.2. Then, IPTG was added to final concentration 1 mM to induce EcTopoI 14-kDa CTD overexpression and the cultivation proceeded for 1 h before the culture harvesting (OD600~0.6). For CTD/Rif sample, CTD overexpression was induced with 1mM IPTG at OD600~0.2 and the culture was cultivated for 1 h. Then, the culture was treated with 100 µg/ml rifampicin for 20 minutes before cells harvesting.

tag: strain

value: DY330 topA-SPA

tag: plasmid

value: pCA24 14kDa CTD

tag: growth phase

value: Exponential phase

tag: optical density at 600 nm

tag: treatment

value: Overexpression of EcTopoI 14-kDa CTD was induced for 1 h with 1 mM IPTG (CTD)

tag: ip or control

value: IP


title: Cauda sperm DNA - H3K9me2_rep1

city: College Station

first: MICHAEL

middle: C.

last: GOLDING

state: Texas

address: 4466 TAMU

department: Physiology

institute: Texas A&M UNiversity

data_processing:
Basecalls performed using Sanger/Illumina version 1.9
ChIP-seq reads were trimmed for adaptors and quality and aligned to the mm10 genome assembly using BWA-MEM
BAM alignments were filtered on read mapping quality >=20
Peaks were called using MACS2 version 2.1.1.20160309.6 with an extension size of 150 and FDR 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: wig files were generated using the Wig/BedGraph-to-bigWig converter tool

organism: Mus musculus

source_name: Cauda spermatozoa

growth_protocol: We obtained postnatal day 90 adult C57BL/6N (RRID:IMSR_JAX:005304) males from the Texas A&M Institute for Genomic Medicine. We maintained males on a standard diet (catalog# 2019, Teklad Diets, Madison, WI, USA) and 12-hour light/dark cycle.

extract_protocol:
Sperm histone ChIP was carried out using a previously published protocol (Hisano et al., 2013). Briefly, for each individual biological rep, sperm collected from the Caputs and Cauda of 10-15 mice were pooled, purified and pre-treated with 50μM DTT for 2h at RT to open sperm chromatin. Cell suspensions were split into roughly 15-20 million sperm aliquots per IP and treated with 90 U of MNase (New England Biolabs, #M0247S) for 5 min at 37C. MNase-digested chromatin was then pre-cleared with blocked A/G Sepharose beads for 1h at 4C. For IP, 5 μg of antibody (H3K27ac or H3K9me2) was added to the pre-cleared chromatin overnight followed by 50 μL of blocked beads for 4 h at 4C. Beads were washed and DNA was then eluted in elution buffer. Following RNase A and proteinase K treatment, DNA was purified using phenol/chloroform isolation and ethanol precipitation and resuspended in 40 μL ultrapure water.
Library preparation using 10ng of DNA and 75 bp paired-end sequencing with at least 50 million reads per samples was carried out at the UT Health Cancer Genomics Center, Houston.

tag: region

value: Cauda

tag: cell type

value: spermatozoa

tag: chip antibody

value: H3K9me2 (Active Motif, 39240)

value: untreated


title: Control treated with RNAse HI, EcTopoI 14-kDa CTD overexpression, replicate 1

description: Exponentially growing culture was cultivated until reaching OD600~0.2. Then, IPTG was added to final concentration 1 mM to induce EcTopoI 14-kDa CTD overexpression form the pCA25 CTD plasmid and the cultivation proceeded for 1 h when the culture was harvested by centrifugation (4500 g, 5min, 4°C). Total nucleic acids were purified from cells pellet using GeneJET Genomic DNA purification kit (ThermoFisher) according to the manufacturer's protocol but omitting the RNAse A treatment step. Sample was sonicated using Covaris ultrasonicator to get median fragment size 150 bp. An aliquot of sonicated nucleic acids (containing 6 µg of sheared DNA, concentrations measured using Qubit 1X dsDNA HS Assay) was treated with 5U of RNAse HI (NEB) in RNAse HI buffer for 30 min at 37C and then nucleic acids were purified with GeneJET Gel Extraction and DNA cleanup micro kit (General cleanup protocol, ThermoFisher). IP for treated aliquot using S9.6 antibodies and nucleic acid purification were performed as described for the untreated aliquot. NGS libraries were prepared using strand-specific Accel NGS 1S kit (Swift Bioscience) suitable for single-stranded DNA. Sequencing was performed with Illumina NextSeq with 75+75 bp paired-end reads protocol. Biological replicate 1.

value: Control treated with RNAse HI


title: Pimasertib_1

city: Stanford

institute: Stanford University

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens


title: WT_5

city: Gainesville

first: Eric

middle: T

last: Wang

state: FL

address: 2033 Mowry Rd

institute: University of Florida

data_processing:
Illumina bcl2fastq2 Conversion Software v2.20 for basecalling and demultiplexing
Pseudoalignment and Transcripts per Million (TPM) were calculated with Kallisto v0.44.0 to mm10 with parameters quant -b 100
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file including TPM values for each Sample

source_name: WT mouse heart

extract_protocol:
Heart tissues were homogenized in Tri-reagent and RNA was precipitated using isopropanol. RNA pellets were washed with 75% ethanol and then dissolved in RNA storage solution.
Strand-specific paired-end RNA sequencing of total RNA was performed using the NEBNext Ultra II Directional Library Prep Kit.

tag: genotype/variation

value: WT

tag: tissue

value: heart


title: MC.IL2.PC#1

city: Boston

first: Liang

last: Yang

state: MA

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.7.3a
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM25)
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts

source_name: Mast Cell

extract_protocol:
1,000 Cells were double-sorted by FACS Aria 561 into 5ul Buffer TCL (Qiagen) with 1% 2-Mercaptoethanol (Sigma).Total RNA was captured and purified on RNAClean XP beads (Beckman Coulter)
total RNA was captured and purified on RNAClean XP beads (Beckman Coulter). Polyadenylated mRNA was then selected using an anchored oligo(dT) primer (5′–AAGCAGTGGTATCAACGCAGAGTACT30VN-3) and converted to cDNA via reverse transcription. First-strand cDNA was subjected to limited PCR amplification followed by Tn5 transposon-based fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina). Samples were then PCR amplified for 18 cycles using barcoded primers such that each sample carried a specific combination of eight-base Illumina P5 and P7 barcodes and were pooled together prior to Smart sequencing. Smart-seq paired-end sequencing was performed on an Illumina NextSeq500 using 2 x 38bp reads with no further trimming.

treatment_protocol: 5-8 week old C57Bl/6J mice shipped from the Jackson Laboratory, Bar Harbor. Mice were injected retro-orbitally with either a free cytokine or a cytokine-antibody complex with a 2 hour acute readout. Further, mice were injected with 10ug mIL2/110uL PBS,5 μg IL-4 with 25 μg 11B11 in 110 uL PBS, 0.75ug mIL-7 to 15ug anti-m/h IL-7 M25 mAb  in 110uL PBS, 5ug mIL9 in 110uL PBS, 2.5ug mIL-15 to 15ug mIL15Ra-Fc in 110uL PBS, or 20ug mIL-21 in 110uL PBS.

value: Peritoneal Cavity

value: Mast Cell


title: Palbociclib_1

value: Palbociclib


title: WT_4


title: Control treated with RNAse HI, no treatment, replicate 1

description: Exponentially growing culture (OD600=0.6) in LB was harvested by centrifugation (4500 g, 5min, 4°C). Total nucleic acids were purified from cells pellet using GeneJET Genomic DNA purification kit (ThermoFisher) according to the manufacturer's protocol but omitting the RNAse A treatment step. Sample was sonicated using Covaris ultrasonicator to get median fragment size 150 bp. An aliquot of sonicated nucleic acids (containing 6 µg of sheared DNA, concentrations measured using Qubit 1X dsDNA HS Assay) was treated with 5U of RNAse HI (NEB) in RNAse HI buffer for 30 min at 37C and then nucleic acids were purified with GeneJET Gel Extraction and DNA cleanup micro kit (General cleanup protocol, ThermoFisher). IP for treated aliquot using S9.6 antibodies and nucleic acid purification were performed as described for the untreated aliquot. NGS libraries were prepared using strand-specific Accel NGS 1S kit (Swift Bioscience) suitable for single-stranded DNA. Sequencing was performed with Illumina NextSeq with 75+75 bp paired-end reads protocol. Biological replicate 1.

source_name: Escherichia coli DY330 topA-SPA

value: no treatment


title: MC.IL15.PC#3


title: Control treated with RNAse HI, no treatment, replicate 2

description: Exponentially growing culture (OD600=0.6) in LB was harvested by centrifugation (4500 g, 5min, 4°C). Total nucleic acids were purified from cells pellet using GeneJET Genomic DNA purification kit (ThermoFisher) according to the manufacturer's protocol but omitting the RNAse A treatment step. Sample was sonicated using Covaris ultrasonicator to get median fragment size 150 bp. An aliquot of sonicated nucleic acids (containing 6 µg of sheared DNA, concentrations measured using Qubit 1X dsDNA HS Assay) was treated with 5U of RNAse HI (NEB) in RNAse HI buffer for 30 min at 37C and then nucleic acids were purified with GeneJET Gel Extraction and DNA cleanup micro kit (General cleanup protocol, ThermoFisher). IP for treated aliquot using S9.6 antibodies and nucleic acid purification were performed as described for the untreated aliquot. NGS libraries were prepared using strand-specific Accel NGS 1S kit (Swift Bioscience) suitable for single-stranded DNA. Sequencing was performed with Illumina NextSeq with 75+75 bp paired-end reads protocol. Biological replicate 2.


title: MC.IL15.PC#2


title: MC.IL2.PC#3


title: DMSO_2

value: cancer derived cell line

value: DMSO


title: MC.IL15.PC#1


title: DRIP-Seq, no treatment, replicate 3

description: Exponentially growing culture (OD600=0.6) in LB was harvested by centrifugation (4500 g, 5min, 4°C). Total nucleic acids were purified from cells pellet using GeneJET Genomic DNA purification kit (ThermoFisher) according to the manufacturer's protocol but omitting the RNAse A treatment step. Sample was sonicated using Covaris ultrasonicator to get median fragment size 150 bp. 10 µg of S9.6 antibodies (Kerafast, ENH001) were incubated with 20 µL of protein-G Sepharose (Bialexa) pre-equilibrated with PBS in 70 µL of IP-buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 0.1% sodium deoxycholate, 1% Triton X-100, 140 mM NaCl) for 2 h at 4C with gentle shaking. After the pre-incubation, an aliquot (containing 6 µg of sheared DNA, concentrations measured using Qubit 1X dsDNA HS Assay) was added and the immunoprecipitation was continued for 4 h. Then, the resin was washed with 1 mL of IP-buffer, 1 mL of IPS-buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 0.1% sodium deoxycholate, 1% Triton X-100, 500 mM NaCl) and twice with 1 mL of Wash-buffer (10 mM Tris-HCl pH 8, 1 mM EDTA, 0.5% sodium deoxycholate, 1% Triton X-100, 250 mM NaCl). TES-buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 250 mM NaCl) was mixed with the washed resin to get 200 µL of slurry and proteinase K (ThermoFisher) was added to a final concentration 0.5 mg/mL. Proteolysis was performed at 55C for 1 h. After that, the resin was spun down by centrifugation and nucleic acids were purified from the supernatant using AMPure XP magnetic beads (Beckman Coulter). NGS libraries were prepared using strand-specific Accel NGS 1S kit (Swift Bioscience) suitable for single-stranded DNA. Sequencing was performed with Illumina NextSeq with 75+75 bp paired-end reads protocol. Biological replicate 3.

value: DY330 topA-SPA


title: DRIP-Seq, no treatment, replicate 2

description: Exponentially growing culture (OD600=0.6) in LB was harvested by centrifugation (4500 g, 5min, 4°C). Total nucleic acids were purified from cells pellet using GeneJET Genomic DNA purification kit (ThermoFisher) according to the manufacturer's protocol but omitting the RNAse A treatment step. Sample was sonicated using Covaris ultrasonicator to get median fragment size 150 bp. 10 µg of S9.6 antibodies (Kerafast, ENH001) were incubated with 20 µL of protein-G Sepharose (Bialexa) pre-equilibrated with PBS in 70 µL of IP-buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 0.1% sodium deoxycholate, 1% Triton X-100, 140 mM NaCl) for 2 h at 4C with gentle shaking. After the pre-incubation, an aliquot (containing 6 µg of sheared DNA, concentrations measured using Qubit 1X dsDNA HS Assay) was added and the immunoprecipitation was continued for 4 h. Then, the resin was washed with 1 mL of IP-buffer, 1 mL of IPS-buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 0.1% sodium deoxycholate, 1% Triton X-100, 500 mM NaCl) and twice with 1 mL of Wash-buffer (10 mM Tris-HCl pH 8, 1 mM EDTA, 0.5% sodium deoxycholate, 1% Triton X-100, 250 mM NaCl). TES-buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 250 mM NaCl) was mixed with the washed resin to get 200 µL of slurry and proteinase K (ThermoFisher) was added to a final concentration 0.5 mg/mL. Proteolysis was performed at 55C for 1 h. After that, the resin was spun down by centrifugation and nucleic acids were purified from the supernatant using AMPure XP magnetic beads (Beckman Coulter). NGS libraries were prepared using strand-specific Accel NGS 1S kit (Swift Bioscience) suitable for single-stranded DNA. Sequencing was performed with Illumina NextSeq with 75+75 bp paired-end reads protocol. Biological replicate 2.

value: Exponential phase


title: MC.IL7.PC#3


title: DMSO_1


title: Root col + SA190 rep3

city: Jeddah

first: Sabiha

last: Parween

address: Thuwal

department: Hirt lab

country: Saudi Arabia

institute: KAUST

data_processing:
Sequenced reads were trimmed using Trimmomatic 0.36 to remove all low quality reads / base pairs.
Trimmed reads were aligned to the TAIR10 genome using Tohat V2.1.1
Count-based Normalization using DESEq2
Differential expression between two samples / condition is calculated using DESEQ2
Outputs were visualized using cummerbund, Venny etc.,
Genome_build: TAIR10
Supplementary_files_format_and_content: Excel, Count-based values

organism: Arabidopsis thaliana

source_name: 16 days old seedlings under normal conditions (1/2 MS)

growth_protocol: Sterilized seeds (Col-0) were scattered on half strength MS (½  MS) medium supplemented with 100 µl of Luria Broth (LB) medium (Mock) or a fresh culture of SA190 grown in LB to an optical density of 0.21. Plants were stratified in the dark for 2 days at 4 °C and then transferred in a Percival growth chamber set to 22 °C with a long-day photoperiod (16 h light/8 h dark) for 5 days.

extract_protocol:
Total RNA extractions were performed using the NucleoSpin RNA kit (Macherey-Nagel) following the manufacturer's recommendations
using a Ribo-Zero Magnetic Kit

treatment_protocol: The germinated seedlings (∼1.0–1.5 cm in root length) were then transferred to ½  MS as a normal condition or to ½ MS infiltrated with 25% Polyethylene-glycol (PEG) 8000 (Fisher Scientific, Belgium) to induce drought stress for 16 days.

tag: ecotype

value: Root


title: Mock DNA, EcTopoI 14-kDa CTD overexpression and Rif 100 mkg/ml for 20 min, replicate 2

description:
Mock_CTD_Rif_2
Biological replicate 2

data_processing:
Raw reads were trimmed and filtered using Trimmomatic (ILLUMINACLIP:2:30:10 LEADING:0 TRAILING:0 SLIDINGWINDOW:4:0 MINLEN:30).
Processed reads were aligned to the E. coli w3110 MuSGS genome with BWA MEM (default settings).
Resulting sam files were converted to bam and sorted using samtools.
Sequencing coverage depth was calculated from bam file using samtools and converted to wig format using custom script.
Peaks were identified using MACS2 with the following parameters: nomodel, Q-value<0.001.
Genome_build: NC_007779.1_w3110_Mu (custom build, fasta and genome annotation are provided as supplementary files)
Supplementary_files_format_and_content: wig files with sequencing coverage depth.

growth_protocol: For starter culture a single colony of E. coli DY330 topA-SPA pCA25 CTD was inoculated in 5 mL of LB supplemented with 50 mkg/ml kanamycin, 34 mkg/ml chloramphenicol, and 0.5% glucose (for catabolite repression). The starter was grown overnight at 37C with shaking 180 rpm. 0.4 mL of the starter culture was inoculated in 40 mL of fresh LB supplemented with glucose and antibiotics, and the culture was cultivated at 37C with shaking 180 rpm until reaching OD600=0.2.

extract_protocol: 100 µL of clarified lysate were de-crosslinked and deproteinized by incubation with proteinase K (Thermo-Fisher Scientific) for 4 h at 55°C, and DNA was purified using DNA clean-up kit (Thermo Fisher Scientific). Sequencing libraries were prepared using TruSeq kit (Illumina). Sequencing was performed with Illumina NextSeq with 75+75 bp paired-end reads protocol. Libraries preparation and sequencing were performed at Skoltech Sequencing Core Facilities.

treatment_protocol: A culture was cultivated until reaching OD600~0.2. Then, IPTG was added to final concentration 1 mM to induce EcTopoI 14-kDa CTD overexpression and the cultivation proceeded for 1 h. After that, the culture was treated with 100 µg/ml rifampicin for 20 minutes before crosslinking with fresh 1% formaldehyde in PBS for 20 min at room temperature and agitation. Formaldehyde was quenched by incubation with 0.125 M glycine for 10 min at room temperature. Cells were harvested by centrifugation at 4500 g, 5min, 4°C. Cell pellets were washed three times with 10 mL ice-cold PBS and finally resuspended in 1mL of FA lysis buffer (50 mM HEPES-NaOH pH 7.5, 1 mM EDTA, 0.1% Deoxycholate, 0.1 % SDS, 1% Triton X-100, 150 mM NaCl), followed by 10 min incubation on ice. Then, protease inhibitors cocktail (cOmplete ULTRA, Sigma-Aldrich) and RNase A (0.1 mg/ml, Thermo Scientific) were added. To disrupt cells and shear DNA, cells were sonicated in a 1.5 mL Eppendorf tube in an ice-water bath to achieve 100-1000 bp fragments range. Lysates were clarified by centrifugation at 10000 g for 5 min at 4°C, and the resulting supernatant was used for further analysis.

value: Overexpression of EcTopoI 14-kDa CTD was induced for 1 h with 1 mM IPTG and then treated with 100 mkg/ml rifampicin for 20 min before crosslinking (CTD/Rif)

tag: immunoprecipitation reagent

value: none (Mock DNA)


title: Palbociclib_2


title: MC.IL7.PC#1


title: Mock DNA, EcTopoI 14-kDa CTD overexpression and Rif 100 mkg/ml for 20 min, replicate 1

description:
Mock_CTD_Rif_1
Biological replicate 1


title: HSC-3-8GY_1

city: Chiba City

first: Takafumi

last: Nobuchi

state: Chiba Prefecture

address: 1-8-1 Inohana, Chuo-ku, Chiba,, Japan

department: Department of Oral Science

country: Japan

institute: Graduate School of Medicine, Chiba University

data_processing:
Samples were sequenced using Illumina Novaseq 6000 with paired-end 2 x 150-bp cycle
Quality check for sequence reads using FastQC version 0.11.7 and ATACseqQC version 1.8.5
Pre-processing of sequence reads using Skewer version 0.2.2
Mapping of sequence reads using Bowtie2 version 2.3.4.2
Reads mapped to blacklisted regions and duplicated reads were remoned using samtools version 1.9
Generating bigwigs using deeptools bamCoverage
Peak calling of sequence reads using MACS2 version 2.2.6
Genome_build: hg19

source_name: OSCC

growth_protocol: All OSCC-derived cells were grown in Dulbecco’s modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 50 units/ml penicillin and streptomycin. The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: not provided

treatment_protocol: HSC-3 and KOSC-2 were incubated for 24hours after 0 or 8 Gy radiation, cell fast frozen.

value: Oral squamous cell carcinoma (OSCC)

tag: radiosensitivity

value: radioresistant


title: HSC-3-8GY_2


title: MC.IL7.PC#2


title: EcTopoI ChIP-Seq, EcTopoI 14-kDa CTD overexpression and Rif 100 mkg/ml for 20 min, replicate 2

description:
EcTopoI_IP_CTD_Rif_2
Biological replicate 2

data_processing:
Raw reads were trimmed and filtered using Trimmomatic (ILLUMINACLIP:2:30:10 LEADING:0 TRAILING:0 SLIDINGWINDOW:4:0 MINLEN:30).
Processed reads were aligned to the E. coli w3110 MuSGS genome with BWA MEM (default settings).
Resulting sam files were converted to bam and sorted using samtools.
Sequencing coverage depth was calculated from bam file using samtools and converted to wig format using custom script.
Peaks were identified using MACS2 with the following parameters: nomodel, Q-value<0.001.
Genome_build: NC_007779.1_w3110_Mu (custom build, fasta and genome annotation are provided as supplementary files)
Supplementary_files_format_and_content: wig files with sequencing coverage depth.
Supplementary_files_format_and_content: tab-delimited files with enrichment peaks coordinates.

extract_protocol: 900 µL of the clarified lysate were diluted with 1ml of TES buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 250 mM NaCl) and mixed with 80 µL of ANTI-FLAG® M2 affinity gel (Sigma-Aldrich). Immunoprecipitation was performed at room temperature on a rotator for 1.5 h. Then affinity resin was washed consecutively with 1 mL of the following solutions: TES buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 250 mM NaCl); twice with TESS buffer (10 mM Tris-HCl pH 7.5, 250 mM NaCl, 1 mM EDTA, 0.1% Tween-20, 0.05% SDS); and TE buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA). For proteolysis and de-crosslinking after the washing procedure, affinity resin was diluted with 200 µL of TES buffer, proteinase K (Sigma-Aldrich) was added up to 0.5 mg/mL and samples were incubated at 55°C for 4 h. Supernatant was collected by centrifugation (2000 g, 2 min, 25°C) and IP-DNA was finally purified from it using AMPure XP magnetic beads (Beckman Coulter). Sequencing libraries were prepared using TruSeq kit (Illumina). Sequencing was performed with Illumina NextSeq with 75+75 bp paired-end reads protocol. Libraries preparation and sequencing were performed at Skoltech Sequencing Core Facilities.

value: ANTI-FLAG M2 affinity gel (Sigma-Aldrich)


title: shoot col + SA190 rep3

value: Shoot


title: DRIP-Seq, no treatment, replicate 1

description: Exponentially growing culture (OD600=0.6) in LB was harvested by centrifugation (4500 g, 5min, 4°C). Total nucleic acids were purified from cells pellet using GeneJET Genomic DNA purification kit (ThermoFisher) according to the manufacturer's protocol but omitting the RNAse A treatment step. Sample was sonicated using Covaris ultrasonicator to get median fragment size 150 bp. 10 µg of S9.6 antibodies (Kerafast, ENH001) were incubated with 20 µL of protein-G Sepharose (Bialexa) pre-equilibrated with PBS in 70 µL of IP-buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 0.1% sodium deoxycholate, 1% Triton X-100, 140 mM NaCl) for 2 h at 4C with gentle shaking. After the pre-incubation, an aliquot (containing 6 µg of sheared DNA, concentrations measured using Qubit 1X dsDNA HS Assay) was added and the immunoprecipitation was continued for 4 h. Then, the resin was washed with 1 mL of IP-buffer, 1 mL of IPS-buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 0.1% sodium deoxycholate, 1% Triton X-100, 500 mM NaCl) and twice with 1 mL of Wash-buffer (10 mM Tris-HCl pH 8, 1 mM EDTA, 0.5% sodium deoxycholate, 1% Triton X-100, 250 mM NaCl). TES-buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 250 mM NaCl) was mixed with the washed resin to get 200 µL of slurry and proteinase K (ThermoFisher) was added to a final concentration 0.5 mg/mL. Proteolysis was performed at 55C for 1 h. After that, the resin was spun down by centrifugation and nucleic acids were purified from the supernatant using AMPure XP magnetic beads (Beckman Coulter). NGS libraries were prepared using strand-specific Accel NGS 1S kit (Swift Bioscience) suitable for single-stranded DNA. Sequencing was performed with Illumina NextSeq with 75+75 bp paired-end reads protocol. Biological replicate 1.

value: IP


title: A172 cells, MED12knockdown Rep 2

type: RNA

city: New Delhi

first: Dr. Ritu

last: Kulshreshtha

state: New Delhi

address: Room 134, Block I

department: Dept of Biochemical Engineering and Biotechnology

country: India

institute: Indian Institute of Technology

description: Gene expression data

hyb_protocol: Following fragmentation, 2.3 ug of cRNA were hybridized for 16 hr at 45C on  GeneChip Clariom S Human Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Genechip Scanner 3000 7G.

data_processing: The data were analyzed with  Affymetrix Expression Analysis Console and Transcriptome Analysis Console (TAC) using Affymetrix default analysis settings for analysis type - Expression (Gene) and RMA as normalization method.

label: biotin

source_name: A172 cells with MED12 specific siRNA.

label_protocol: Samples were labelled as per and using the WT PLUS reagent kit. Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA.

growth_protocol: A172 cells grown in 6 well plates

extract_protocol: Total RNA prepared using RNA isolation kit according to manufacturer's instructions.

treatment_protocol: Tranfected with MED12 specific siRNA and control siRNA

value: A172 glioblastoma cell line

value: MED12-specific siRNA

tag: genotype

value: MED12 Knockdown


title: A172 cells, MED12knockdown Rep 1

description: Gene expression data


title: shoot col + SA190 rep2


title: HSC-3-0GY_1


title: EcTopoI ChIP-Seq, EcTopoI 14-kDa CTD overexpression and Rif 100 mkg/ml for 20 min, replicate 1

description:
EcTopoI_IP_CTD_Rif_1
Biological replicate 1


title: Mock DNA, Rif 100 mkg/ml for 20 min, replicate 3

description:
Mock_Rif_3
Biological replicate 3

growth_protocol: For starter culture a single colony of E. coli DY330 topA-SPA pCA25 CTD was inoculated in 5 mL of LB supplemented with 50 mkg/ml kanamycin, 34 mkg/ml chloramphenicol, and 0.5% glucose (for catabolite repression). The starter was grown overnight at 37C with shaking 180 rpm. 0.4 mL of the starter culture was inoculated in 40 mL of fresh LB supplemented with glucose and antibiotics, and the culture was cultivated at 37C with shaking 180 rpm until reaching OD600=0.6.

treatment_protocol: An exponentially growing culture (OD600=0.6) was pretreated with 100 µg/ml rifampicin for 20 minutes before crosslinking with fresh 1% formaldehyde in PBS for 20 min at room temperature and agitation. Formaldehyde was quenched by incubation with 0.125 M glycine for 10 min at room temperature. Cells were harvested by centrifugation at 4500 g, 5min, 4°C. Cell pellets were washed three times with 10 mL ice-cold PBS and finally resuspended in 1mL of FA lysis buffer (50 mM HEPES-NaOH pH 7.5, 1 mM EDTA, 0.1% Deoxycholate, 0.1 % SDS, 1% Triton X-100, 150 mM NaCl), followed by 10 min incubation on ice. Then, protease inhibitors cocktail (cOmplete ULTRA, Sigma-Aldrich) and RNase A (0.1 mg/ml, Thermo Scientific) were added. To disrupt cells and shear DNA, cells were sonicated in a 1.5 mL Eppendorf tube in an ice-water bath to achieve 100-1000 bp fragments range. Lysates were clarified by centrifugation at 10000 g for 5 min at 4°C, and the resulting supernatant was used for further analysis.

value: Treated with 100 mkg/ml rifampicin for 20 min before crosslinking (Rif)


title: Root col + SA190 rep1


title: DRIP-Seq, EcTopoI 14-kDa CTD overexpression, replicate 2

description: Exponentially growing culture was cultivated until reaching OD600~0.2. Then, IPTG was added to final concentration 1 mM to induce EcTopoI 14-kDa CTD overexpression form the pCA25 CTD plasmid and the cultivation proceeded for 1 h when the culture was harvested by centrifugation (4500 g, 5min, 4°C). Total nucleic acids were purified from cells pellet using GeneJET Genomic DNA purification kit (ThermoFisher) according to the manufacturer's protocol but omitting the RNAse A treatment step. Sample was sonicated using Covaris ultrasonicator to get median fragment size 150 bp. 10 µg of S9.6 antibodies (Kerafast, ENH001) were incubated with 20 µL of protein-G Sepharose (Bialexa) pre-equilibrated with PBS in 70 µL of IP-buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 0.1% sodium deoxycholate, 1% Triton X-100, 140 mM NaCl) for 2 h at 4C with gentle shaking. After the pre-incubation, an aliquot (containing 6 µg of sheared DNA, concentrations measured using Qubit 1X dsDNA HS Assay) was added and the immunoprecipitation was continued for 4 h. Then, the resin was washed with 1 mL of IP-buffer, 1 mL of IPS-buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 0.1% sodium deoxycholate, 1% Triton X-100, 500 mM NaCl) and twice with 1 mL of Wash-buffer (10 mM Tris-HCl pH 8, 1 mM EDTA, 0.5% sodium deoxycholate, 1% Triton X-100, 250 mM NaCl). TES-buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 250 mM NaCl) was mixed with the washed resin to get 200 µL of slurry and proteinase K (ThermoFisher) was added to a final concentration 0.5 mg/mL. Proteolysis was performed at 55C for 1 h. After that, the resin was spun down by centrifugation and nucleic acids were purified from the supernatant using AMPure XP magnetic beads (Beckman Coulter). NGS libraries were prepared using strand-specific Accel NGS 1S kit (Swift Bioscience) suitable for single-stranded DNA. Sequencing was performed with Illumina NextSeq with 75+75 bp paired-end reads protocol. Biological replicate 2.

value: pCA24 14kDa CTD

value: Overexpression of EcTopoI 14-kDa CTD was induced for 1 h with 1 mM IPTG (CTD)


title: DC.8+.PBS.Sp#15

source_name: Dendritic Cell

value: Spleen

value: Dendritic Cell


title: DC.8+.PBS.Sp#12


title: DC.8+.PBS.Sp#14


title: A172 cells, control Rep 2

description: Gene expression data

source_name: A172 cells with control siRNA.

value: control siRNA

value: control


title: KOSC2-8GY_2

value: radiosensitive


title: A172 cells, control Rep 1

description: Gene expression data


title: HSC-3-0GY_2


title: DC.8+.PBS.Sp#13


title: shoot col + SA190 rep1


title: Mock DNA, Rif 100 mkg/ml for 20 min, replicate 1

description:
Mock_Rif_1
Biological replicate 1

value: DY330 topA-SPA

value: Exponential phase

value: none (Mock DNA)


title: KOSC2-8GY_1

value: Oral squamous cell carcinoma (OSCC)


title: Mock DNA, Rif 100 mkg/ml for 20 min, replicate 2

description:
Mock_Rif_2
Biological replicate 2


title: KOSC2-0GY_2


title: Root col rep3

value: Root

value: Mock


title: Root col + SA190 rep2


title: DC.8+.PBS.Sp#10


title: DC.8+.PBS.Sp#11


title: EcTopoI ChIP-Seq, Rif 100 mkg/ml for 20 min, replicate 3

description:
EcTopoI_IP_Rif_3
Biological replicate 3

value: ANTI-FLAG M2 affinity gel (Sigma-Aldrich)


title: DC.8+.PBS.Sp#9


title: EcTopoI ChIP-Seq, Rif 100 mkg/ml for 20 min, replicate 2

description:
EcTopoI_IP_Rif_2
Biological replicate 2


title: KOSC2-0GY_1


title: Endo_day 14_rep_2

first: Haiqing

last: Bai

address: 5th floor, Center for Life Science, 3 Blackfan Circle

institute: Wyss Institute

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2 followed by differential expression analysis using DESeq2.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Human Alveolus Chip

growth_protocol: Primary human lung alveolar epithelial cells (Cell Biologics, H-6053) was seeded on 0.1% gelatin-coated 12-well plate according to manufacturer’s instruction; Alveolar Chip culture method is descirbed in associated manuscript

extract_protocol:
For RNA extraction, chips were removed from pods. An empty 200 µL filtered tip was inserted to top channel outlet and washed with 100 µL DPBS (+/+) into the top channel inlet to wash the apical channel. After collecting top channel washes, a new empty 200 µL filtered tip was inserted to top channel outlet and 100 ul RNase easy lysis buffer (Qiagen, #74034) was used to lyse epithelial cells by quickly pressing and releasing the micropipette plunger 3 times. Lysates were collected in a clean labelled 1.5 ml tube and stored at -80˚C for RNA-seq analysis.
RNA libraries were prepared for sequencing using standard Illumina HiSeq with 150-bp pair-ended reads

treatment_protocol: Human Alveolus Chips were transfected with plasmid DNA using the TransIT-X2 reagent (Mirus Bio). 3 ug of plasmid DNA and 6 ul TransIT-X2 reagent were constituted in 300 ul OPT-MEM before added to 3 ml chip flow medium. Then 1.5 ml of the solution was added to apical and basal inlet reservoirs and flew at 60 ul/h for 24 hours. Then apical channel was empties to reestablish ALI; basal channel was changed to normal flow medium for additional 24 hours before qPCR analysis.

value: primary microvascuular endothelial cells

tag: time points

value: day 14

tag: % mechanical strain

tag: infection

value: No


title: Root col rep2


title: DC.8+.PBS.Sp#8

tag: strain


title: Endo_day 14_rep_1


title: Mock DNA, EcTopoI 14-kDa CTD overexpression, replicate 3

description:
Mock_CTD_3
Biological replicate 3

treatment_protocol: A culture was cultivated until reaching OD600~0.2. Then, IPTG was added to final concentration 1 mM to induce EcTopoI 14-kDa CTD overexpression and the cultivation proceeded for 1 h before the culture was crosslinked with fresh 1% formaldehyde in PBS for 20 min at room temperature and agitation (OD600~0.6). Formaldehyde was quenched by incubation with 0.125 M glycine for 10 min at room temperature. Cells were harvested by centrifugation at 4500 g, 5min, 4°C. Cell pellets were washed three times with 10 mL ice-cold PBS and finally resuspended in 1mL of FA lysis buffer (50 mM HEPES-NaOH pH 7.5, 1 mM EDTA, 0.1% Deoxycholate, 0.1 % SDS, 1% Triton X-100, 150 mM NaCl), followed by 10 min incubation on ice. Then, protease inhibitors cocktail (cOmplete ULTRA, Sigma-Aldrich) and RNase A (0.1 mg/ml, Thermo Scientific) were added. To disrupt cells and shear DNA, cells were sonicated in a 1.5 mL Eppendorf tube in an ice-water bath to achieve 100-1000 bp fragments range. Lysates were clarified by centrifugation at 10000 g for 5 min at 4°C, and the resulting supernatant was used for further analysis.

tag: growth phase


title: EcTopoI ChIP-Seq, Rif 100 mkg/ml for 20 min, replicate 1

description:
EcTopoI_IP_Rif_1
Biological replicate 1

tag: optical density at 600 nm

value: Treated with 100 mkg/ml rifampicin for 20 min before crosslinking (Rif)


title: Root col rep1

tag: treatment


title: DC.8+.PBS.Sp#6


title: DC.8+.PBS.Sp#7


title: shoot col rep1

value: Shoot


title: Endo_day 8_rep_2

value: day 8


title: shoot col rep2


title: DC.8+.PBS.Sp#5

value: Spleen

value: Dendritic Cell


title: Mock DNA, EcTopoI 14-kDa CTD overexpression, replicate 1

description:
Mock_CTD_1
Biological replicate 1

value: Overexpression of EcTopoI 14-kDa CTD was induced for 1 h with 1 mM IPTG (CTD)


title: Root col + SA190 (PEG) rep3

source_name: 16 days old seedlings under drought stress (PEG)


title: Endo_day 8_rep_1


title: Endo_day 0_rep_2

value: day 0


title: EcTopoI ChIP-Seq, EcTopoI 14-kDa CTD overexpression, replicate 3

description:
EcTopoI_IP_CTD_3
Biological replicate 3

treatment_protocol: A culture was cultivated until reaching OD600~0.2. Then, IPTG was added to final concentration 1 mM to induce EcTopoI 14-kDa CTD overexpression and the cultivation proceeded for 1 h before the culture was crosslinked with formaldehyde (OD600~0.6). Formaldehyde was quenched by incubation with 0.125 M glycine for 10 min at room temperature. Cells were harvested by centrifugation at 4500 g, 5min, 4°C. Cell pellets were washed three times with 10 mL ice-cold PBS and finally resuspended in 1mL of FA lysis buffer (50 mM HEPES-NaOH pH 7.5, 1 mM EDTA, 0.1% Deoxycholate, 0.1 % SDS, 1% Triton X-100, 150 mM NaCl), followed by 10 min incubation on ice. Then, protease inhibitors cocktail (cOmplete ULTRA, Sigma-Aldrich) and RNase A (0.1 mg/ml, Thermo Scientific) were added. To disrupt cells and shear DNA, cells were sonicated in a 1.5 mL Eppendorf tube in an ice-water bath to achieve 100-1000 bp fragments range. Lysates were clarified by centrifugation at 10000 g for 5 min at 4°C, and the resulting supernatant was used for further analysis.

value: DY330 topA-SPA


title: Endo_day 0_rep_1


title: DC.8+.PBS.Sp#4


title: shoot col + SA190 (PEG) rep2


title: shoot col rep3


title: EcTopoI ChIP-Seq, EcTopoI 14-kDa CTD overexpression, replicate 2

description:
EcTopoI_IP_CTD_2
Biological replicate 2

value: Exponential phase


title: Epi_transwell_day 14_rep_3

source_name: Human Alveolus Transwell

value: primary alveolar epithelial cells


title: DC.8+.PBS.Sp#3


title: Root col + SA190 (PEG) rep2


title: EcTopoI ChIP-Seq, EcTopoI 14-kDa CTD overexpression, replicate 1

description:
EcTopoI_IP_CTD_1
Biological replicate 1


title: DC.8+.PBS.Sp#2


title: Root col + SA190 (PEG) rep1


title: DC.8+.PBS.Sp#1


title: Epi_transwell_day 14_rep_2


title: Epi_transwell_day 14_rep_1


title: Mock DNA, EcTopoI 14-kDa CTD overexpression, replicate 2

description:
Mock_CTD_2
Biological replicate 2

value: none (Mock DNA)


title: DC.8+.IL9.Sp#2


title: Mock DNA, no treatment, replicate 2

description:
Mock_2
Biological replicate 2

treatment_protocol: An exponentially growing culture (OD600=0.6) was crosslinked with fresh 1% formaldehyde in PBS for 20 min at room temperature and agitation. Formaldehyde was quenched by incubation with 0.125 M glycine for 10 min at room temperature. Cells were harvested by centrifugation at 4500 g, 5min, 4°C. Cell pellets were washed three times with 10 mL ice-cold PBS and finally resuspended in 1mL of FA lysis buffer (50 mM HEPES-NaOH pH 7.5, 1 mM EDTA, 0.1% Deoxycholate, 0.1 % SDS, 1% Triton X-100, 150 mM NaCl), followed by 10 min incubation on ice. Then, protease inhibitors cocktail (cOmplete ULTRA, Sigma-Aldrich) and RNase A (0.1 mg/ml, Thermo Scientific) were added. To disrupt cells and shear DNA, cells were sonicated in a 1.5 mL Eppendorf tube in an ice-water bath to achieve 100-1000 bp fragments range. Lysates were clarified by centrifugation at 10000 g for 5 min at 4°C, and the resulting supernatant was used for further analysis.

value: no treatment


title: Root col (PEG) rep3

value: Root

value: PEG


title: Mock DNA, no treatment, replicate 1

description:
Mock_1
Biological replicate 1


title: DC.8+.IL7.Sp#3


title: Epi_day 14_rep_2


title: shoot col (PEG) rep3


title: DC.8+.IL7.Sp#1


title: shoot col (PEG) rep2


title: Epi_day 8_rep_3


title: EcTopoI ChIP-Seq, no treatment, replicate 1

description:
EcTopoI_IP_1
Biological replicate 1

value: ANTI-FLAG M2 affinity gel (Sigma-Aldrich)


title: DC.8+.IL4.Sp#3


title: EcTopoI ChIP-Seq, no treatment, replicate 2

description:
EcTopoI_IP_2
Biological replicate 2


title: Mock DNA, no treatment, replicate 3

description:
Mock_3
Biological replicate 3


title: Root col (PEG) rep1


title: ∆ino80 MNase Replicate 2

city: San Francisco

first: Vijay

last: Ramani

state: California

department: Biochemistry & Biophysics

institute: UCSF

description: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 ino80::LEU2

data_processing:
.fq files were aligned to reference .fa genome with bwa mem algorithm
.sam files were converted to .bam files and reads were sorted based on genome position using samtools 1.7
duplicate reads were removed using samtools
reads were indexed for python analysis
Supplementary_files_format_and_content: .bam, sorted, deduped, indexed reads (paired end)

organism: Saccharomyces cerevisiae

source_name: log cells

growth_protocol: Cells were grown to log phase in YPD.

extract_protocol:
Cells were harvested spheroplasted with zymolyase, and chromatin was subjected to MNase digestion. The digested chromatin was treated with Proteinase K and the DNA was subsequently phenol chloroform extracted and ethanol precipitated. The samples were treated with RNaseA and hosphatase, then purified using a Qiagen PCR purification kit.
Libraries were prepared using the manufacturer's protocol for the Nugen Ovation Ultralow System V2 kit

treatment_protocol: Cells were fixed with 1% formaldehyde and quenched with 125mM glycine.

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 ino80::LEU2


title: Epi_day 8_rep_2

value: No


title: Epi_day 8_rep_1


title: ∆ino80 MNase Replicate 1


title: DC.8+.IL4.Sp#2


title: shoot col + SA190 (PEG) rep1


title: Epi_day 0_rep_3


title: Epi_day 14_rep_3

value: day 14


title: DC.8+.IL4.Sp#1


title: EcTopoI ChIP-Seq, no treatment, replicate 3

description:
EcTopoI_IP_3
Biological replicate 3


title: Mouse embryo fibroblast cell Ahi1-KO 3

city: Suzhou

first: Hongguang

last: Zhang

address: Renai load 199

country: China

institute: Soochow University

data_processing:
DNBSEQ-500 software used for basecalling
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads  containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base  quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown  base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored  in FASTQ format. The clean reads were mapped to the reference genome using HISAT2  (v2.0.4). Bowtie2 (v2.2.5)  was applied to align the clean reads to the reference  coding gene set, then expression level of gene was calculated by RSEM (v1.2.12)
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Mouse embryo fibroblast cell

extract_protocol:
Mouse MEFs were prepared from the mouse embryos at day 13.5 and were cultured in Dulbecco’s modified Eagle′s medium (DMEM) supplemented with 10% FBS, and RNA was harvested using Trizol reagent. A-Tailing Mix was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard DNBSEQ protocols

value: Mouse embryo fibroblast cell


title: WT MNase Replicate 2

description: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0

value: WT

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0


title: DC.8+.IL7.Sp#2

value: Spleen

value: Dendritic Cell


title: Root col (PEG) rep2


title: WT MNase Replicate 1

description: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0


title: Mouse embryo fibroblast cell Ahi1-KO 2


title: Epi_day 0_rep_2

value: day 0


title: DC.8+.IL21.Sp#3


title: Epi_day 14_rep_1


title: Epi_day 0_rep_1


title: DC.8+.IL21.Sp#2


title: Mouse embryo fibroblast cell Ahi1-KO 1


title: Solvent2

city: Nanjing

first: Lufeng

last: Zheng

state: Jiangsu

address: Tongjia Xiang 24

department: School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention

institute: China Pharmaceutical University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample …

source_name: breast cancer cells

growth_protocol: Cells were cultured in L-15 medium (Gibco, Grand Island, NY, USA) at 37 °C under a humidified atmosphere with 5% CO2, and supplemented with 10% FBS (Gibco), 80 U/ml penicillin, and 0.08 mg/ml streptomycin.

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

treatment_protocol: MDA-MB-231 cells were treated with TSA (20 μM) for 48 h, and subjected to  deep sequencing.

tag: cell line


title: DC.8+.IL21.Sp#1


title: Mouse embryo fibroblast cell WT 3

value: WT type


title: shoot col (PEG) rep1

value: Shoot


title: healthy human rep5

city: fuzhou

first: weixuan

last: hong

address: fuzhougulou

institute: 900TH Hospital of Joint Logistics Support Force

data_processing:
Paired-end reads were harvested from Illumina Novaseq 6000  sequencer, and were quality controlled by Q30.
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). The high quality trimmed reads were used to analyse LncRNAs and mRNAs.
LncRNA & mRNA: The high quality reads were aligned to the human reference genome (UCSC hg19) with hisat2 software (v2.0.4). Then, HTSeq software (v0.9.1) was used to get the gene level (mRNA) and transcript level (lncRNA) raw count as the expression profiling, and edgeR (v3.16.5) was used to perform normalization and differentially expressed mRNAs were identified by p-value and fold change. GO and Pathway enrichment analysis were also performed based on the differentially expressed mRNAs. LncRNA target genes were predicted by the locations to nearby genes. And GO and Pathway analysis were performed on these target genes.
Genome_build: hg19
Supplementary_files_format_and_content: excel format
Supplementary_files_format_and_content: Number of raw junction read

source_name: exosome

extract_protocol:
The blood sample was centrifuged, plasma was extracted, and RNA was harvested using Trizol reagent. Briefly, total RNA was used for removing the rRNAs with NEBNext rRNA Depletion Kit (New England Biolabs, Inc., Massachusetts, USA) following the manufacturer's instructions.
RNA libraries were constructed by using NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Inc., Massachusetts, USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an illumina Novaseq 6000 instrument with 150bp paired end reads.

value: plasma

tag: age

value: untreated

tag: patient diagnosis

value: healthy


title: Mouse embryo fibroblast cell WT 2


title: healthy human rep4


title: TSA2

value: TSA (20 μM) for 48 h


title: Mouse embryo fibroblast cell WT 1


title: DC.8+.IL2.Sp#2

tag: cell type


title: healthy human rep3


title: Solvent1


title: DC.8+.IL2.Sp#3


title: TSA1


title: DC.8+.IL15.Sp#2


title: TmPAC 5

city: Frederiksberg C

first: Andrew

last: Williams

state: --- Select One ---

address: Dyrlægevej 100

country: Denmark

institute: University of Copenhagen

data_processing:
BGI internal software used to remove adpators and low quality reads.
Mapped to Mus Musculus (mm10) using HISAT
DEG assessed using DeSeq2
Genome_build: mm10
Supplementary_files_format_and_content: count data and FPKM for each sample.

source_name: PAC + Tm_Intestinal tissue

growth_protocol: Female mice were 8 weeks of age, and were gavaged with water or PAC (300mg/kg, derived from grape extract) every 2nd day over a period of 49 days. Where mentioned mice were infected with 20 Tm larvae, 3 times at days 14, 21 and 28 after PAC treatment commenced.

extract_protocol:
Tissue was collected at euthanasia. Total RNA was extracted using miRNAeasy kits (Qiagen).
Standard BGI protocol.

value: PAC + Tm

value: Intestinal tissue


title: healthy human rep1


title: TmPAC 4


title: DC.8+.IL15.Sp#3


title: 18_MSMEG_ΔmadR_C_SDS

first: Eliza

last: Peterson

data_processing:
Illumina RiboZero bacteria kit was used for rRNA depletion. Samples were sequenced on the NextSeq sequencing instrumetn in mid output 150 v2 flow cell. Paired-end 75 bp reads were checked for technical artifacts using FastQC following Illumina default quality filtering steps. Raw FASTQ read data were processed using the R package DuffyNGS.
Genome_build: Mycobacterium smegmatis mc2155 ASM1500v1
Supplementary_files_format_and_content: tab-delimited text file includes RPKM, TPM, and read counts for each sample

organism: Mycolicibacterium smegmatis

source_name: bacterial culture

extract_protocol:
The resuspended cells were transferred to a tube containing Lysing Matrix B (MP Biomedicals, Santa Ana, CA) and vigorously shaken at max speed for 30 s in a FastPrep 120 homogenizer (MP Biomedicals) three times. Tubes were centrifuged for 1 min (max speed), then 66 μL of 3 M sodium acetate pH 5.2 added and mixed well. Acid phenol (pH 4.2) was added at 726 μL and tubes were inverted to mix well (~60 times). Samples were incubated at 65° C for 5 min, inverting tubes to mix samples every 30 s. Then, centrifuged at 14000 rpm for 5 min and upper aqueous phase was transferred to a new tube. 3M sodium acetate (pH 5.2) was added at 1/10th volume along with 3x volumes of 100% ethanol. Sample was mixed well and incubated at -20° C for 1 hr or overnight. Following incubation, samples were centrifuged at 14000 rpm for 30 min at 4° C, ethanol was discarded and 500 μL of 70% ethanol was added. Samples were centrifuged again at 14000 rpm for 10 min at 4° C, supernatant discarded, and any residual ethanol removed using pipet. Pellet was allowed to air dry, resuspended in 30-40 μL of RNase free water and quantified by Nanodrop (Thermo Scientific). This was followed by in solution genomic DNA digestion using RQ1 Dnase (Promega) following manufacturer’s recommendation.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Strains were cultured to mid log phase (OD600 = 0.5) in Middlebrook 7H9 supplemented with 10% OADC, 0.2% glycerol and 0.05% tween-80 at 37°C. Cultures were left untreated or treated with 0.025% SDS for 90 minutes 37°C harvested and snap frozen in liquid nitrogen before RNA isolation.

value: complemented madR deletion

tag: treatment time

value: 90 min


title: PDAC patients rep5

tag: tissue

value: PDAC


title: DC.8+.IL15.Sp#1


title: TmPAC 3


title: 17_MSMEG_ΔmadR_C_SDS


title: healthy human rep2


title: 16_MSMEG_ΔmadR_C_SDS


title: TmPAC 2


title: 15_MSMEG_ΔmadR_C


title: B.fo.PBS.Sp#9

source_name: B Follicular Cell

value: B Follicular Cell


title: PDAC patients rep3


title: 14_MSMEG_ΔmadR_C


title: TmPAC 1


title: B.fo.PBS.Sp#8


title: B.fo.PBS.Sp#7


title: PDAC patients rep2


title: Tm 7

source_name: Water + Tm_Intestinal tissue

value: Water + Tm


title: DC.8+.IL2.Sp#1


title: Tm 8


title: 12_MSMEG_ΔmadR_SDS

value: madR deletion


title: PDAC patients rep4


title: PDAC patients rep1


title: 13_MSMEG_ΔmadR_C


title: B.fo.PBS.Sp#6

value: Spleen


title: B.fo.PBS.Sp#5


title: 11_MSMEG_ΔmadR_SDS


title: Tm 4


title: HNSCC_Tum_ADT_2

city: Paris

first: Floriane

last: Noël

address: 1 avenue Claude Vellefaux

country: France

institute: INSERM

description: antibodies

data_processing:
FASTQ files were processed using the CellRanger pipeline (10X Genomics; V3 for HNSCC samples and V2 for Breast cancer sample), and reads were aligned to the human genome hg38. True cells are distinguished from empty droplets in the Cell Ranger pipeline; additionally, they were also excluded by Dropletutils R package: the intersection of both was used. Cells with a high fraction of mitochondrial genes were filtered (> 10% HNSCC:  > 20% Breast); and potential doublets cells were excluded by filtering cells with too high library complexity were filtered (cells that expressed more than 4000 genes (HNSCC) or 5000 genes (Breast): this threshold was based on the distribution of the number of cells per gene expression).
CITE-seq features were detected using CITE-seq Count (Roelli et al., 2019)
Genome_build: GRCh38
Supplementary_files_format_and_content: output files from CellRanger (filtered gene matrices :barcodes, features and matrix) for each scRNA-seq sample. output files from CITE-seq Count (barcodes, features and matrix) for each ADT sample.

molecule: polyA RNA

source_name: HNSCC tumor-infiltrating cells - Patient 2

extract_protocol:
For HNSCC patient 1 (Pt1), there was single-cell suspensions from a juxtatumor sample and from a tumor sample. The 2 samples were stained with antibodies for cell sorting for 15 min at 4°C (Table 30). The samples were washed, and DAPI was added just before sorting. After sort, the different cell populations sorted were merged in defined proportions as detailed below for each of the 2 samples. The samples were stained with CITEseq antibodies (Table 30) at 4°C for 30min according to manufacturer’s recommendations (Biolegend). Cells were washed, and the tumor sample was split in 2. In one of the samples, the primer specific for ADT was not added, to avoid the expansion by PCR of ADTs. This separation of the tumor sample in two was done to allow for comparison of tumor samples with or without ADT, because this was a new technology. We did not find any relevant difference between the samples with and without ADT, validating the absence of bias induced by this technological approach. Samples were then processed as recommended in 10X Genomics protocols.  For HNSCC patient 2 (Pt2), there was only one tumor sample available. Staining with antibodies for sort and with CITEseq antibodies were done simultaneously for 30 min at 4°C, before wash, DAPI staining and sorting. Sorting was performed using the purity and low-pressure mode, and a 100-μm nozzle on a BD FACS Aria III flow sorter for all samples.  The gating strategy is displayed in Fig S8. We excluded debris and doublets by FSC, SSC gating; dead cells by DAPI gating; red blood cells by CD235a staining (Pt2 only). All remaining cells were sorted in one of the 5 final population groups. Group 1 included CD45+CD3+ T cells; Group 2 included non-immune CD45- cells; Group 3 included MMAC and CD14+DC gated as CD45+CD3-CD19-CD56-CD11c+HLA-DR+CD14+; Group 4 included cDC1 and cDC2 gated as CD45+CD3-CD19-CD56-CD11c+HLA-DR+CD14- and was merged with pDC gated as CD45+CD3-CD19-CD56-CD11c-HLA-DR+CD123+; Group 5 included all remaining cells: CD45+CD3-CD19+ and/or CD56+, CD45+CD3-CD19-CD56-CD11c-HLA-DR+CD123-, and CD45+CD3-CD19-CD56-HLA-DR-.  The count provided by the flow sorter was used for subsequent processing. The population with the highest number of cells was also counted by trypan blue to ensure accuracy of the flow sorter counts. The final sample used for chip loading ScRNAseq contained 18000 (Pt1) or 16000 (Pt2) cells obtained by combining 3600 (Pt1) or 3200 (Pt2) cells from each of the 5 groups. The only exception was for the juxtatumor sample of Pt1, in which only 857 cells were available for the Group 4 of cells.   For the luminal breast cancer sample, the single-cell suspension from the tumor sample was stained with antibodies for cell sorting for 15 min at 4°C (Table 30). The sample was washed, and DAPI was added just before sorting. The gating strategy for DC included the following steps: (i) exclusion of debris and doublets by FSC, SSC gating; (ii) exclusion of dead cells by DAPI gating; (iii) selection of cells positive in CD45 BV570; (iv) exclusion of T cells, identified as CD3+ APC and CD19- Alexa700 and CD56- Alexa700; (v) exclusion of CD19+ Alexa700 and CD56+ Alexa700 cells; (vi) selection of CD11c- PECy5 cells, among which cells CD123+ BV650 and HLA-DR+ eFluor760 double positive were sorted as pDC; besides, selection of CD11c+ PECy5 and HLA-DR+ eFluor760 double positive cells, among which cells were classified according to CD1C PE and CD14 FITC: MMAC defined as CD1C- and CD14+ were excluded and all the other cells were sorted as cDC. Eventually, the DC sample used for ScRNA-seq included the pDC and the cDC. The CD45- cells, CD3+ cells, the MMAC and a mixed group of CD45+CD3- cells were also sorted independently but were not analyzed in the present study.
Single-cell sequencing of final samples was performed using Single Cell 3’ kit V1 (Breast cancer sample), v2 (HNSCC Pt1) and v3 (HNSCC Pt2) (10X Genomics), according to the manufacturer protocol (10X Genomics), including the CITE-seq libraries (HNSCC samples). Sample quality was checked with Bioanalyzer Agilent 2100 using a HighSensitivity DNA chip (Agilent Genomics). Samples were sequenced on an Illumina HiSeq (Breast cancer sample) and Novaseq (HNSCC samples) with a depth of sequencing of 50000 reads/cells (Breast cancer) and 100000 reads/cells (HNSCC samples).

value: Head and neck tumor

tag: donor

value: HNSCC Patient 2

tag: hpv status

value: Negative

tag: molecule subtype

value: ADT


title: Tm 5


title: HNSCC_Juxta_ADT_1

description: antibodies

source_name: HNSCC juxtatumor-infiltrating cells - Patient 1

value: Head and neck juxtatumor

value: HNSCC Patient 1


title: 10_MSMEG_ΔmadR_SDS

tag: genotype


title: HNSCC_Tum_Cite_2

description: gene expression

value: cDNA


title: B.fo.PBS.Sp#3


title: 09_MSMEG_ΔmadR


title: Tm 3


title: 08_MSMEG_ΔmadR


title: Tm 2


title: B.fo.PBS.Sp#1


title: 07_MSMEG_ΔmadR


title: HNSCC_Tum_Cite_1

description: gene expression

source_name: HNSCC tumor-infiltrating cells - Patient 1


title: Tm 1


title: 06_MSMEG_wt_SDS

value: wildtype


title: Tm 6


title: HNSCC_Tum_Norm_1

description: gene expression


title: B.fo.PBS.Sp#4


title: B.fo.IL9.Sp#2


title: PAC 7

source_name: PAC_Intestinal tissue

value: PAC


title: B.fo.IL9.Sp#1


title: EE-3

city: Hefei

first: Jinghe

state: Anhui

address: Huangshan Road 443

institute: University of Science and Technology of China

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using cutadapt v1.18, then mapped to hg38 (Annotation: gencode.v30.annotation.gtf) whole genome using hisat2 v2.1.0 with default parameters.
Read counting were calculated using featureCounts v1.6.4 with parameters: "-T 24 -p --extraAttributes gene_type,gene_name"
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file includes raw geneccounts for each Sample

source_name: endometrium

extract_protocol:
The endometrial tissue was immobilized by formalin and the total RNA was obtained by TRIZOL.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ectopic endometrium

tag: disease state

value: endometriosis


title: EE-2


title: 05_MSMEG_wt_SDS

value: 90 min


title: HNSCC_Juxta_Cite_1

description: gene expression


title: B.fo.IL7.Sp#3


title: PAC 6

value: Intestinal tissue


title: B.fo.PBS.Sp#2

value: B Follicular Cell


title: PAC 5


title: 04_MSMEG_wt_SDS


title: 03_MSMEG_wt


title: B.fo.IL7.Sp#1


title: 02_MSMEG_wt


title: HNSCC_Tum_ADT_1

description: antibodies


title: EE-1


title: B.fo.IL7.Sp#2


title: PAC 4


title: NE-3

value: normal endometrium

value: uterine leiomyoma


title: 01_MSMEG_wt


title: B.fo.IL4.Sp#3

value: Spleen


title: PAC 3


title: PAC 8


title: NE-2


title: NE-1


title: PAC 2


title: ThymusTOT_WT

city: Marseille

first: Delphine

last: Potier

address: 27 boulevard Lei Roure

institute: CRCM

data_processing:
Reads from each sample library were mapped to mm10 GRCh38/mm10 mouse and human composit transcripts and cells using CellRanger software (v5.0.1), giving barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz files for each sample.
Data was loaded using R (v3.6.3) in a Seurat (v3.1.5) object for further processing
Genome_build: GRCh38/mm10 mouse and human composite genome
Supplementary_files_format_and_content: tsv and mtx files

source_name: Thymocyte

extract_protocol: 10x Genomics Chromium Single-Cell 3’ protocol v3

treatment_protocol: DN_WT sample were depleted from CD4+,CD8+ and CD4+CD8 cells with magnetic beads Dynabeads mouse CD4 (11445D, Lifetechnologies) and Dynabeads mouse CD8 (11447D, Lifetechnologies)

value: WT

tag: spike-in cells

value: 5000 Human PBMC

tag: sample type

value: whole thymus


title: WT9-12_pCREB_CUTRUN

city: Tianjin

first: Zhiheng

last: Liu

state: Tianjin

address: No.22 Qixiangtai Road

department: Tianjin Research Center for Basic Medical Science

institute: Tianjin Medical University

data_processing:
Library strategy: CUT&RUN
Bowtie2 (version 2.3.4.1) was used to align paired-end 150 bp sequence reads to human (hg38) genome
HOMER (version 4.10) findPeaks command was used to call peak
BamCoverage within deeptools (version 3.3.0) were used to generate bigwig files from bam files.
Genome_build: hg38 or mm10
Supplementary_files_format_and_content: Bigwig

source_name: WT 9-12 cell

extract_protocol:
For ChIP-seq. Cells were cross-linked with 1% formaldehyde in 1 mL PBS for 10 min at RT. The crosslink was quenched by adding 67 μL of 2.5 M glycine(150 mM final). Cells were washed with PBS and harvested using ChIP lysis buffer. Cells were then sonicated to obtain fragments (200-500 bp) with Sonicator. Immunoprecipitation was performed with indicated antibodies. After elution and reversal cross-linking, DNA was purified for library preparation. For CUT&RUN. Cells were permeabilized with digitonin. DNA were cleaved in situ using a protein A-micrococcal nuclease fusion recruited by an antibody to chromatin associated protein. Then DNA was purified for library preparation.
Library construction were performed using VAHTS Universal DNA Library Prep Kit (Vazyme, ND607-02) and VATHS DNA Adapters set2 for Illumina (Vazyme Biotech, Cat.N802-01)

tag: chip antibody

value: Cell Signaling Technology, #9198


title: B.fo.IL4.Sp#1

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.7.3a
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM25)
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts

extract_protocol:
1,000 Cells were double-sorted by FACS Aria 561 into 5ul Buffer TCL (Qiagen) with 1% 2-Mercaptoethanol (Sigma).Total RNA was captured and purified on RNAClean XP beads (Beckman Coulter)
total RNA was captured and purified on RNAClean XP beads (Beckman Coulter). Polyadenylated mRNA was then selected using an anchored oligo(dT) primer (5′–AAGCAGTGGTATCAACGCAGAGTACT30VN-3) and converted to cDNA via reverse transcription. First-strand cDNA was subjected to limited PCR amplification followed by Tn5 transposon-based fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina). Samples were then PCR amplified for 18 cycles using barcoded primers such that each sample carried a specific combination of eight-base Illumina P5 and P7 barcodes and were pooled together prior to Smart sequencing. Smart-seq paired-end sequencing was performed on an Illumina NextSeq500 using 2 x 38bp reads with no further trimming.

tag: strain


title: PAC 1


title: DN3 gdint

data_processing:
Reads from each sample library were mapped to mm10 (containing the Trdc-H2BEGFP edited version of the Trdc gene) transcripts and cells using CellRanger software (v5.0.1), giving barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz files for each sample.
Data was loaded using R (v3.6.3) in a Seurat (v3.1.5) object for further processing
Genome_build: mm10 mouse genome containing the Trdc-H2BEGFP edited version of the Trdc gene
Supplementary_files_format_and_content: tsv and mtx files

treatment_protocol: WT samples were depleted from CD4+,CD8+ and CD4+CD8 cells with magnetic beads Dynabeads mouse CD4 (11445D, Lifetechnologies) and Dynabeads mouse CD8 (11447D, Lifetechnologies)

value: 500 B lymphocytes


title: ThymusDN_WT

value: double negative (DN) cells (from thymus after a CD8+, CD4+ and CD8+CD4+ cells depletion)


title: B.fo.IL21.Sp#3


title: WT9-12_pCREB_ChIP

data_processing:
Bowtie2 (version 2.3.4.1) was used to align paired-end 150 bp sequence reads to human (hg38) genome
HOMER (version 4.10) findPeaks command was used to call peak
BamCoverage within deeptools (version 3.3.0) were used to generate bigwig files from bam files.
Genome_build: hg38 or mm10
Supplementary_files_format_and_content: Bigwig


title: Water Control 8

source_name: Water_Intestinal tissue

value: Water


title: B.fo.IL21.Sp#2


title: B.fo.IL21.Sp#1


title: Patient 005_HS196 positive cells

city: Durham

first: Erika

last: Crosby

state: NC

address: 203 Research Dr. MSRBI Room 407

institute: DUKE UNIVERSITY MEDICAL CENTER

description: Gene expression library

data_processing:
Fastq files for paired-end reads and the index file for each samples was processed using 10X cellranger v 2.1.0 count program to generate an expression count matrix for each sample.
Fastq files for paired-end reads and the index file for each samples was processed using Partek® Genomics Suite® software (version 9.0.20, Copyright ©; 2018 Partek Inc)
GEX files had tags trimmed and sequences were aligned to the hg19 reference genome (STAR aligner 2.7.3a) and UMI counts were deduplicated and filtered to include only barcodes that corresponded to a cell.
Transcripts were quantified and single cell counts were filtered to include cells with total reads between 700-25,000; expressed genes 15-5,000; and a maximum of 25% mitochondrial reads.
Counts were normalized to counts per million and log(2) transformed. Genes with 0 expression were removed prior to performing PCA and graph-based clusters were assigned using the top 13 principle components.
Genome_build: hg19
Supplementary_files_format_and_content: GEX-HSP01-005Negative_S8.txt and GEX-HSP01-005Positive_S9.txt contains the following in columns: Feature, Sample name, Expressed genes, Graph-based, Mitochondrial reads percent, Total count, UMAP classifications

source_name: tumor

extract_protocol:
Tumors were processed into single cell suspensions as described in manuscript, and top 2% HS196+ and bottom 25% HS196- cells were sorted.
10X Genomics gene expression and TCR libraries were generated using Chromium Single Cell 5’ Library Construction Kit (V1.1). A targeted cell recovery of 7,000 cells were used for each sample.
scRNA seq (10X Genomics), Single Cell 5' Gene Expression Libraries, 26x8x98 single i7 index. GEX sequenced on NovaSeq 6000 (500M PE-reads/sample)

treatment_protocol: Surgicially resected tumor was collected from treated patient

value: Surgically resected tumor

tag: tumor type

value: colon


title: DN4 gd+


title: Water Control 7

tag: treatment


title: DN3 gd-


title: B.fo.IL2.Sp#3


title: Patient 005_HS196 negative cells

description: Gene expression library

value: Colon


title: B.fo.IL2.Sp#2


title: Water Control 6


title: day49 sample for kidney organoid differentiation in suspension culture system bulkRNA-seq

city: BOSTON

first: Takuya

last: Matsumoto

state: Massachusetts

address: 1335 BOYLSTON ST

institute: Massachusetts General Hospital

data_processing:
STAR
Htseq
Cufflink
DESeq2/edgeR
Genome_build: STAR
Supplementary_files_format_and_content: xls

source_name: kidney organoid derived from H9

growth_protocol: hPSCs were differentiated into metanephric mesenchyme cells which include nephron progenitor cells, with approximately 80-90% efficiency, by a 3-step directed differentiation protocol. Metanephric mesenchyme cells, arising on day 8 of differentiation, were transferred into suspension culture in 96-well ultra-low adhesion plates (Corning) and further differentiated into kidney organoids through intermediate stages of pretubular aggregates (day 11) and renal vesicles (day 14).  Kidney organoids were maintained in 200 μl of Advanced RPMI (ARPMI, Thermo Fisher) supplemented with GlutaMAX (Thermo Fisher) in 96-well plates following induction of renal vesicles at day 14 of differentiation. Media changes were conducted three times weekly (Monday, Wednesday, and Friday), with removal of 90 μl and addition of 100 μl of fresh ARPMI. Media changes were conducted in such manner until initiating treatment with supplemented factors at day 49, with ARPMI + GlutaMAX only serving as controls. For suspension culture, Cells were seeded at a density of 2, 4, and 8 × 105 (H9) cells/ml onto 5 ml vessel  (Reprocell, #ABBWVS05A) in StemFit® Basic02 supplemented with the ROCK inhibitor Y27632 (10 µM) and FGF2 (10 ng/ml). The medium was replaced every day. After 96 hours, cells were briefly washed in PBS and then cultured in the basic differentiation medium consisting of aRPMI 1640 and 1X L-GlutaMAX, supplemented with CHIR99021 (3, 5, 7, and 9 µM) for 4 days. Cells were then cultured in the basic differentiation medium supplemented with activin (10 ng/mL) for 3 days. For induction of nephron progenitor cells, the media were then changed to the basic differentiation medium supplemented with FGF9 (10 ng/ml) for a day. NPCs were further differentiated with CHIR (3 µM) and FGF9 (10 ng/mL) for 2 days. The medium was then changed to the basic differentiation medium supplemented with FGF9 10ng/mL and cultured for 3 more days. After that, the organoids were cultured in basic differentiation medium with no additional factors for 7–35 days (a total of 21–49 days). The medium was replaced every 2 or 3 days.

extract_protocol:
RNAs were isolated from kidney organoid samples using TRIzolTM (Thermo Fischer Scientific, 15596018) according to manufacturer’s protocol. A minimum of 5 organoids are used per sample.
NEBNext Ultra RNA Library Prep Kit for Illumina　(New England Biolabs, USA)) according to manufacturer’s recommendations

value: kidney organoid derived from H9

tag: culture time

tag: culture system

value: suspension


title: Water Control 5

value: Intestinal tissue


title: DN3b gd+


title: Water Control 4


title: B.fo.IL4.Sp#2

first: Liang

value: B Follicular Cell


title: DN4 gd-


title: B.fo.IL2.Sp#1


title: DN3b gd-


title: day35 sample for kidney organoid differentiation in suspension culture system bulkRNA-seq


title: Water Control 3


title: B.fo.IL15.Sp#3


title: DN3a


title: day49 sample for kidney organoid differentiation bulkRNA-seq

value: static


title: day21 sample for kidney organoid differentiation in suspension culture system bulkRNA-seq


title: day35 sample for kidney organoid differentiation bulkRNA-seq


title: B.fo.IL15.Sp#2


title: B.fo.IL15.Sp#1


title: MC38_Control_scRNA-seq

first: Dijun

last: Chen

address: Xianlin

department: Life Sciences

institute: Nanjing University

data_processing:
Sample demultiplexing, barcode processing, and single cell 3’ gene counting were performed by the Cell Ranger pipelines (v3.1.0,10X Genomics).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: TSV files with genes and barcode sequences corresponding to row and column indices, respectively.
Supplementary_files_format_and_content: matrix.mtx: Filtered gene-barcode matrix file (demultiplexed)

source_name: MC38 xenograft

growth_protocol: C57BL/6 mice were inoculated with 1 × 106 MC38 cells into the right flank. 5 days after the injection, the MC38 tumor-bearing mice (an average size of 100 mm3) were distributed into 2 groups (n=6 in each group)

extract_protocol:
Solid tumors from mice were excised and mechanically dissociated into single cells using Tumor Dissociation Kit (Miltenyi Biotec, Cat # 130-096-730).
Single cells were captured in the 10×Genomics Chromium Single Cell 3′ Solution, and RNA-seq libraries were prepared following the manufacturer’s protocol (10×Genomics). The libraries were subjected to high-throughput sequencing on an Illumina Hiseq X Ten PE150 platform, and 150-bp paired-end reads were generated.

treatment_protocol: Mice were treated with PBS, SHP099 hydrochloride (5 mg/kg, i.g, every day) for an additional 14 days.

tag: tumor model

value: MC38 xenograft model

value: Untreated


title: MC38_SHP099_scRNA-seq

value: Treated with 5 mg/kg SHP099


title: YAP_Lsd1ko_3

city: Dallas

first: Hongde

last: Li

address: 6001 Forest Park Road, Department of Physiology, ND13-510

institute: UT Southwestern Medical Center

data_processing:
Demultiplexing performed with bcl2fastq
Quality control assessed by FastQC
Sequencing reads mapped using STAR
Count data generated using featureCounts
EdgeR used for differential expression analysis
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text files with raw counts
Supplementary_files_format_and_content: The column names are as follows:
Supplementary_files_format_and_content: 1.  Contig name
Supplementary_files_format_and_content: 2.  First base of the splice junction (1-based)
Supplementary_files_format_and_content: 3.  Last base of the splice junction (1-based)
Supplementary_files_format_and_content: 4.  Strand (0:undefined, 1:+, 2:-)
Supplementary_files_format_and_content: 5.  Intron motif: 0: noncanonical, 1:GT/AG, 2:CT/AC, 3:GC/AG, 4:CT/GC, 5: AT/AC, 6:GT/AT
Supplementary_files_format_and_content: 6.  0:unannotated, 1:annotated
Supplementary_files_format_and_content: 7.  Number of uniquely mapping reads spanning the splice junction
Supplementary_files_format_and_content: 8.  Number of multimapping reads spanning the splice junction
Supplementary_files_format_and_content: 9.  Maximum spliced alignment overhang

source_name: YAP;Lsd1 KO mouse liver

growth_protocol: Mice were raised under normal condition.

extract_protocol:
Total RNA from mouse livers was isolated using TRIzol™ Plus RNA Purification Kit (Cat# 12183555, Thermo Fisher) and DNA was removed by treatment with TURBO DNA-free™ Kit (Cat# AM1907, Thermo Fisher).
The quality of samples was determined on the Agilent Tapestation 4200, and only high quality RNA is used (RIN Score 8 or higher). The Qubit® 4.0 Fluorimeter from ThermoFisher was used to determine the concentration prior to staring library preparation. One microgram of total DNAse treated RNA was then prepared with the TruSeq Stranded Total RNA LT Sample Prep Kit from Illumina. Total RNA was depleted of its rRNA and fragmented before strand specific cDNA synthesis. cDNAs were then a-tailed and indexed adapters were ligated. After adapter ligation, samples were PCR amplified and purified with AmpureXP beads, then validated again on the Agilent Tapestation 4200.

treatment_protocol: All mice were injected with AAV8-ApoE/ATT1-Cre via i.p.. Inducible YAP expression in liver was achieved by addition of 30 mg/L doxycycline in drink water for 14 days.

value: Liver

value: YAP; Lsd1 KO


title: HpPAC4

data_processing:
BGI internal software used to remove adpators and low quality reads.
Mapped to Mus Musculus (mm10) using HISAT
DEG assessed using DeSeq2 and NOIseq
Genome_build: mm10
Supplementary_files_format_and_content: excel file with count data and FPKM for each sample.

source_name: Intestinal tissue

growth_protocol: Female mice were 8 weeks of age, and were gavaged with water or PAC (200mg/kg, derived from grape extract) every 2nd day over a period of 28 days. Where mentioned mice were infected with 200 Hp larvae, 14 days after PAC treatment commenced.

value: PAC + Hp


title: YAP_Lsd1ko_2


title: ST3D ZIKV replicate 4

city: Madison

first: Thaddeus

last: Golos

state: Wisconsin

address: 1223 Capitol Court

department: WNPRC

institute: UW Madison

data_processing:
For EV poly(A)seq data, sequences were filtered and adaptors removed with Cutadapt.
Salmon was used to obtain transcripts estimates. Since only eight samples were sequenceable, EVs released by control TSCs and ST3Ds (five total samples) were combined and compared to EV data obtained from ZIKV exposed TSCs and ST3Ds (three total samples).
Due to limited sample size, differential expression analysis was not performed.
Genome_build: GCF_003339765.1_Mmul _10
Supplementary_files_format_and_content: The NCBI gene ID; the length of the target transcript (nt); the effective length; the estimated transcripts per million (TPM) and the nestimated number of reads (numreads) are provided

organism: Macaca mulatta

source_name: extracellular vesicles

growth_protocol: After cells were cultured with or without virus, the conditioned media was collected and frozen back. To isolate EVs, 20 ml of medium was placed onto a concentration column (Vivaspin 20; Sartorius, Swedesboro, NJ, USA, Cat # 1208L91) and spun for 60 mins at 3,000 x g at room temperature (RT). For EVT EV samples, due to a high density of Matrigel in the conditioned media, the media were first filtered using a 0.22 um filter (Millipore Sigma, Cat # SLGP033RS) and then spun for 60 - 90 mins. The concentrated sample was passed through a size exclusion column (Izon, Medford, MA, USA, Cat # SP5, serial #1000788) according to the manufacturer’s protocol and the 1.5 ml flow through was collected. The sample was then concentrated using an Amicon concentration column (Millipore Sigma, Cat # UFC801024) for 45-60 min at 3,000 x g at RT.

extract_protocol:
Each EV sample was diluted in 5 volumes Qiazol and incubated for 5 mins at RT prior to freezing at -80°C until RNA extraction. The miRNeasy serum/plasma kit (Qiagen, Cat #217184) was used to isolate total RNA from EVs following the manufacturer’s protocol with minor adaptations. The Qiazol with Chloroform was overlaid onto phase maker tubes (ThermoFisher, Cat #A33248) and then spun at 4°C at 16,000 x g for 15 mins. In addition, two RPE washes of 500 µl were applied prior to RNA elution. All samples were eluted in 30 µl RNAse free water and the initial elution was placed back on the column and reeluted to increase RNA concentration. Sample concentration and purity was determined with the NanoDrop One (ThermoFisher, Cat # ND-ONE-W).
The poly(A) RNA cDNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol.

treatment_protocol: cells were either left as uninfected controls or exposed to Zika virus

value: EVs

tag: evs released by

value: ZIKV


title: day21 sample for kidney organoid differentiation bulkRNA-seq


title: HpPAC3


title: Water Control 1

value: Water


title: TSC ZIKV replicate 1

value: TSC


title: HpPAC5


title: ST3D control replicate 4

value: control


title: ST3D ZIKV replicate 3


title: 3 times cisplatin treatment of kidney organoid snRNA-seq

data_processing:
cell ranger
cloupe
Supplementary_files_format_and_content: cloupe file

growth_protocol: hPSCs were differentiated into metanephric mesenchyme cells which include nephron progenitor cells, with approximately 80-90% efficiency, by a 3-step directed differentiation protocol. Metanephric mesenchyme cells, arising on day 8 of differentiation, were transferred into suspension culture in 96-well ultra-low adhesion plates (Corning) and further differentiated into kidney organoids through intermediate stages of pretubular aggregates (day 11) and renal vesicles (day 14).  Kidney organoids were maintained in 200 μl of Advanced RPMI (ARPMI, Thermo Fisher) supplemented with GlutaMAX (Thermo Fisher) in 96-well plates following induction of renal vesicles at day 14 of differentiation. Media changes were conducted three times weekly (Monday, Wednesday, and Friday), with removal of 90 μl and addition of 100 μl of fresh ARPMI. Media changes were conducted in such manner until initiating treatment with supplemented factors at day 49, with ARPMI + GlutaMAX only serving as controls.

extract_protocol:
Nuclei were isolated with Nuclei EZ Lysis buffer (NUC-101; Sigma-Aldrich) supplemented with protease inhibitor (5892791001; Roche) and RNase inhibitor (N2615; Promega and AM2696; Life Technologies). Organoids were homogenized using a Dounce homogenizer (885302–0002; Kimble Chase) in 2 ml of ice-cold Nuclei EZ Lysis buffer, and they were incubated on ice for 5 minutes with an additional 2 ml of lysis buffer. The homogenate was filtered through a 30 mm cell strainer (43– 50030–03; pluriSelect) and then centrifuged at 500g for 5 minutes at 4°C. The pellet was resuspended and washed with 4 ml of the buffer, and then, it was incubated on ice for 5 minutes. After another centrifugation, the pellet was resuspended in Nuclei Suspension Buffer (13 PBS, 0.04 % BSA, and 0.1% RNase inhibitor), filtered through a 5 mm cell strainer (43–50005–03; pluriSelect), and counted.
RNA from single nucleus was encapsulated, barcoded and reversed transcribed on a 10× Chromium Single Cell Platform (10× Genomics).

treatment_protocol: Cisplatin (Sigma-Aldrich) was supplemented in ARPMI at a concentration of 5 μM and full media exchanges of 200 μl were conducted beginning on day 49 of differentiation. Corresponding controls underwent full media exchange with 200 μl of fresh ARPMI. After 24 hours, full media exchanges were conducted in both cisplatin treated samples and control samples on day 50. Similar twice weekly, 24-hour cisplatin treatments were conducted on day 52-53, day 56-57, day 59-60, and day 63-64, for a total of five cisplatin treatments.

tag: cisplatin treatment

value: 3 times


title: YAP_Lsd1ko_1

tag: tissue


title: YAP_3

source_name: YAP transgenic mouse liver

value: YAP transgenic


title: day8 sample for kidney organoid differentiation bulkRNA-seq

value: kidney organoid derived from H9

value: NPC


title: 5 times cisplatin treatment of kidney organoid snRNA-seq

value: 5 times


title: HpPAC2

value: Intestinal tissue


title: HpPAC1


title: day0 sample for kidney organoid differentiation bulkRNA-seq

value: PSC


title: Water Control 2


title: ST3D control replicate 3


title: day 63 kidney organoid snRNA-seq

value: 0 times


title: Hp5

value: Water + Hp


title: YAP_2

value: Liver


title: TSC control replicate 4


title: HCC siL1-5

city: Baton Rouge

first: Sonika

last: Patial

address: Baton Rouge, LA 70803

institute: Louisiana State University

description: individual  -5 knockdown of gene zfp36 L1,  tissue type liver

data_processing:
Illumina Novaseq 6000 used for sequencing
Sequenced reads were trimmed for adaptor sequence by fastp, and masked for low-complexity or low-quality sequence, then mapped to huaman whole genome using STAR 2.6.1d
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated from mapped read by featureCounts V1.5
Differeantial expression analysis with DEseq2
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample, and differential expressed gene for each comparasion

source_name: liver

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

tag: cell type

value: hepatocellular carcinoma

tag: genotype/variation

value: Zfp36l1 knockdown


title: Hp4


title: WT_3

source_name: Wild type mouse liver

value: Wild type


title: TSC control replicate 3

value: EVs


title: Hp3


title: HCC siNC-5

description: individual  -5 knockdown of nontarget control,  tissue type liver


title: HCC siL1-4

description: individual  -4 knockdown of gene zfp36 L1,  tissue type liver


title: Hp2


title: TSC control replicate 1

value: TSC


title: Control5

value: Water


title: WT_1


title: HCC siNC-2

description: individual  -2 knockdown of nontarget control,  tissue type liver

value: control


title: Hp1


title: Control4


title: HCC siL1-1

description: individual  -1 knockdown of gene zfp36 L1,  tissue type liver


title: HCC siL1-2

description: individual  -2 knockdown of gene zfp36 L1,  tissue type liver


title: HSC_healthy

city: Rochester

first: Mrunal

middle: Kishor

last: Dehankar

state: MN

address: 200 First St. SW

department: Computational genomics

institute: Mayo Clinic

data_processing:
10X Genomics Cell Ranger count (v3.0.2) was used for alignment, filtering, and to quantify barcodes and unique molecular identifiers
Genome_build: mm10
Supplementary_files_format_and_content: Filtered hd5 files, BAM files

source_name: Hepatic stellate cells

growth_protocol: C57Bl/6 wild-type mice were used.

extract_protocol:
Hepatic stellate cells were isolated from the livers utilizing the protocol from Mederacke et al. "High-yield and high-purity isolation of hepatic stellate cells from normal and fibrotic mouse livers." Nat Protoc. 2015
single cell RNA sequencing

treatment_protocol: Mice in the control group were healthy. Mice in the disease model group were treated with CCl4 (1μL/g of body weight) twice a week for 6 weeks.

value: wild-type

tag: organ

value: Healthy

value: Hepatic stellate cells


title: HCC siNC-1

description: individual  -1 knockdown of nontarget control,  tissue type liver


title: HSC_CCl4

tag: genotype

value: CCl4-induced liver fibrosis


title: Control3

value: Intestinal tissue


title: YAP_1

value: YAP transgenic


title: Control1


title: MDA-MB-231-PRM75-DOX12-IP

city: xi'an

first: Wu

last: Ying

state: Shaan'xi

address: Changle west road

institute: Fourth Military Medical University

data_processing:
Library strategy: m6A-seq
reads aligned to human genome hg38 using the STAR (version 2.4.2a) with reference annotation GENCODE version 25
top 5,000 peakschosen for motif analysis with MEME
Peaks annotated by the function of annotatePeak of ChIPseeker
GO analysis  performed to facilitate elucidating the biological implications of unique genes in the significant or representative profiles of the gene in the experiment.
Pathway analysis used to find out the significant pathway of the genes according to KEGG database.
Genome_build: human genome hg38
Supplementary_files_format_and_content: wig files were generated

source_name: breast cancer cells

growth_protocol: The MDA-MB-231 cell line was  grown in L-15 medium supplemented with 10% fetal bovine serum (FBS), and 1% penicillin–streptomycin.

extract_protocol:
Total RNAs from breast cancer cells were extracted with TRIzol
The amount of 2 μl of 14 μl eluted RNA was reverse transcribed with High-Capacity cDNA Reverse Transcription Kit (Thermo Fisher Scientific, USA). Once successfully immunoprecipitated methylated RNA was confirmed, further transcriptome-wide interrogation was pursued by deep sequencing using SMARTer Stranded Total RNA-Seq Kit version 2 (Pico Input Mammalian; 634413; Takara/Clontech, Japan) according to the manufacturer's protocol. A purified library was quantified using a Qubit Fluorometer (Thermo Fisher Scientific, USA), and the size distribution was checked using the Bioanalyzer 2100 system (Agilent Technologies, USA). The library preparations were sequenced on an Illumina Novaseq 6000 platform and 150 bp paired-end reads were generated.

treatment_protocol: MDA-MB-231 cells with or without PRMT5 overexpression were treated with or without 0.4 μg/ml doxorubicin for 24 hours.

tag: cell line

value: breast cancer cells

value: parental cells overexpressed with PRMT6 under DOX treatment

tag: reference genome

value: human genome hg38


title: YAP-H3K4me2-r1

data_processing:
Data was analyzed using the encode chipseq pipeline (https://github.com/ENCODE-DCC/chip-seq-pipeline2)
Reads were trimmed using Trimmomatic (v0.39)
Fastq file were aligned to reference using bwa (samse) (v0.7.17-r1188)
Post-alignment filtering was done using SAMtools (v1.7), MarkDuplicates (Picard-v1.126) and bedtools (v2.26.0)
Bam were converted to tagAlign using bedtools (v2.26.0), gawk and shuf.
Cross-correlation QC scores were calculated using phantompeakqualtools (v1.2.1)
Jensen-Shannon distance were calculated using deeptools (v3.3.0) plotFingerprint
GC bias was calculated using CollectGcBiasMetrics (Picard, v1.126) and python packages: pandas, matplotlib
Peaks were called on replicates, self-pseudoreplicates, pooled data and pooled-pseudoreplicates using SPP (v1.14) in phantompeakqualtool (https://github.com/kundajelab/phantompeakqualtools)
IDR analysis was run on all pairs of replicates, self-pseudoreplicates and pooled pseudoreplicates using IDR (https://github.com/kundajelab/idr v2.0.4)
Fraction of Reads in Peaks was calculated using (bedtools v2.26.0)
Signal Tracks were created using MACSv2 (https://github.com/taoliu/MACS/)
Genome_build: mm10
Supplementary_files_format_and_content: bed file per group

extract_protocol:
Chromatin immunoprecipitations were performed with the SimpleChIP® Plus Enzymatic Chromatin IP Kit (Cat# 9005, Cell Signaling Technology) according to the provided protocol. Micrococcal nuclease was used to digest DNA to 150-900 bp fragments.
Libraries were prepared using KAPA HTP Library Preparation Kit from Roche. The ChIP DNA was quantified on the Qubit® 4.0 Fluorimeter from ThermoFisher. Samples were then end repaired, 3' ends adenylated and barcoded with multiplex adapters. Samples were amplified with 15 cycles of PCR and then size selected with Ampure XP beads.

treatment_protocol: Inducible YAP expression in liver was achieved by addition of 50 mg/L doxycycline in drink water for 10 days.

value: Liver

value: H3K4me2 (Abcam, Cat# ab7766)


title: YAP-LSD1-r1

value: LSD1 (Cell signaling technology, Cat# 2184)


title: MDA-MB-231-PRM75-DOX12-input


title: WT_2

value: Wild type