title: LGESS_5 [5B]

city: Quebec City

first: Deepthi

last: Sudarshan

state: Quebec

address: 9 Rue Mc Mahon

institute: Université Laval

data_processing:
Paired-end reads were trimmed using fastp v0.20.1. Quality check was performed on raw and trimmed data to ensure the quality of the reads using FastQC v0.11.7 and MultiQC v1.5
The quantification was performed with Kallisto v0.46.2 against the human genome (hg38).
Differential expression analysis was also performed using the DESeq2 v1.30.1 package
Genome_build: hg38
Supplementary_files_format_and_content: log2FoldChange
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Uterus

extract_protocol:
RNA from frozen tissue samples were extracted using the miRNEASY micro kit (QIAGEN).
Only samples with RIN above 7 was used for library preparation using the NEBNext Ultra II Directional RNA library + NEBNext Poly(A) mRNA-dual index kit.

tag: disease

value: Normal


title: LGESS_5 [5A]

status: Public on Feb 18 2022

type: SRA

country: Canada

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens


title: IE9MP1_IDO_vehicle_1

city: BUFFALO

first: Eduardo

last: Cortes

state: NY

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

country: USA

institute: ROSWELL PARK CANCER INSTITUTE

description:
VoomCounts_2.csv
Grp1-1

data_processing:
Fastq files generated with CASAVA
fastq files mapped to hg38 with STAR aligner
gene count levels obtained from STAR
Voom normalized counts using limma
Genome_build: Genome_build: hg38
Supplementary_files_format_and_content: voom normalized counts in csv format

organism: Mus musculus

growth_protocol: C57BL/6 mice were challenged intraperitoneally (i.p.) with 1×107 IE9mp1-mIDO1 or IE9mp1-Empty-Vector tumor cells in a final volume of 500ml Dulbecco’s PBS (Corning Cellgro®) and treated by oral gavage with 300mg/kg IDO1 inhibitor INCB023843 (Incyte Corp.) in 200ml 0.5% methylcellulose

extract_protocol:
RNA extraction was performed using Qiagen miRNAeasy mini kit
Total RNA library perp prepared using The KAPA RNA HyperPrep Kit with RiboErase (HMR) with 500ng RNA input.

treatment_protocol: injection 5 days on and two days off from d7-d21, with or without (i) NAMPT inhibitor FK866 (Sigma-Aldrich, 500 μg per mouse i.p.)  once every week for 3 weeks (on day 13, 20, 27); (ii) purinergic receptor A2a or A2b antagonists (Sch 58261 from Sigma-Aldrich or PSB 1115 from Tocris Bioscience, 1mg/kg)

tag: strain

tag: replicate

value: vehicle

tag: treatment


title: wild-type_monoclonal_rep4

city: Freiburg

first: Yong

last: Li

address: Hugstetter Str. 49

department: Institute of Genetic Epidemiology

country: Germany

institute: Medical Center - University of Freiburg

data_processing:
Illumina Casava 1.8 software used for basecalling.
Remove reads containing adapters. Remove reads containing N > 10% (N represents the base cannot be determined). Remove reads containing low quality (Qscore<= 5) base which is over 50% of the total base.
Reads were then aligned to mouse reference genome GRCm38 using STAR 2.7.3a with default parameters.
RSEM v1.3.1 was used to calculate gene expression values.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample.

source_name: mIMCD-3 wild-type cells

growth_protocol: Cells were cultured with DMEM:F12 (LONZA, cat.no. BE12-719F), fetal bovine serum was added to a final concentration of 10% and penicillin/streptomycin (Sigma, P0781) with a final concentration of 1%.  Subculturing of cells was performed twice a week in a 1:10 ratio. Cells were maintained in a humidified incubator at 37°C and 10% CO2.

extract_protocol:
RNA Isolation was performed 4 days after full confluency according to manufacturer’s protocol using the RNeasy Plus Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were harvested using 0.25 % Trypsin-EDTA (Gibco)

tag: cell line

value: monoclonal


title: WT hiPSC GLYR1 ChIPseq rep 4 [glyr1_wt2_ipsc.2]

city: San Francisco

first: Deepak

last: Srivastava

state: CA

address: 1650 Owens St

institute: J David Gladstone Institutes

library_source: genomic

data_processing:
ChIP seq:
Cluster generation, sequencing, and base calling was performed on Illumina NextSeq 500.
Trimming of known adapters and low-quality regions of reads was performed using Fastq-mcf. Sequence quality control was assessed using FastQC.
Alignment to the hg19 reference human genome was performed using Bowtie 2.2.4. Peaks were called BCP for GLYR1.
single cell RNA seq:
Cluster generation, sequencing, and base calling was performed on NovaSeq (Illumina, software v1.5)
6-8 replicate samples (from independent differentiation runs involving either wild-type or P496L mutant cells) were each processed in 3 batches. Reads from each sample were aligned to the hg38 human reference (version 2020-A from 10X Genomics website) using Cell Ranger version 5.0.1. The resulting count matrices for all samples within each batch were aggregated without depth normalization.
Genome_build: hg19 (ChIP-seq); hg38 (RNA-seq)
Supplementary_files_format_and_content: We provide bed ad BigWig files for ChIPseq.
Supplementary_files_format_and_content: We provide the aligned bam files and count matrices in h5 format

molecule: genomic DNA

source_name: WT hiPSC

growth_protocol: Human iPSCs were maintained on tissue culture-treated polystyrene plates (Cat. 430630, Corning) with hESC-qualified LDEV-free matrigel (Cat. 354277, Corning) in Essential 8 medium (E8) (Cat. A1517001, Life Technologies). The medium was changed daily and the hiPSCs were split every 4 – 6 days using Accutase (Cat. 07920, Stem Cell Technologies). The rho kinase (ROCK) inhibitor (Y-27632 2HCl, Cat. S1049, Selleckchem.com) was included in the medium at 5μM final concentration on the day of passaging.

extract_protocol:
For ChIPseq experiments, CPs (30×106 for cTFs and 10×106 for GLYR1 and histone marks) were pelleted and suspended in 10ml DMEM and cross-linked in 1% Formaldehyde solution (Cat. 28906, Thermo Fisher Scientific) by rocking in room temperature for 10 min. Then glycine (final concentration 0.125M) was added to quench the cross-link for 5 min. Samples were centrifuged at 1000 rcf for 5 min. at 4°C. Cells were washed with 10ml of cold 1x PBS supplemented with proteinase inhibitors and phosphatase inhibitors (Cat. 4693132001 Roche and Cat. 4906837001 Sigma-Aldrich) and the pellets were snap frozen in liquid nitrogen. All samples were stored at −80°C until use. When ready, cell pellets were incubated in cell lysis buffer (20 mM Tris-HCl, pH 8, 85 mM KCl, 0.5% NP-40, protease/phosphatase inhibitors) for 10 min. on a rotator at 4°C. Nuclei were isolated by centrifugation (2,500 x g, 5 min., 4°C), resuspended in nuclear lysis buffer (50 mM Tris-HCl, pH 8, 10 mM EDTA, pH 8, 1% SDS, protease/phosphatase inhibitors) and incubated on a rotator for 30 min. at 4°C. Chromatin was sheared using a Covaris S2 sonicator (Covaris Inc) for 15 min. (60 s cycles, 5% duty cycle, 200 cycles/burst, intensity = 6) until DNA was in the 200–700 base pair range. Chromatin was diluted 3-fold in ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2mMEDTA, 16.7mMTris-HCl, pH 8, 167 mM NaCl, protease/phosphatase inhibitors) and incubated with the corresponding primary antibody at 4°C overnight under rotation. Antibody-protein complexes were immunoprecipitated using 50μl of Dynabeads™ Protein A/Protein G (Cat. 10015D, Invitrogen) per sample at 4°C for 2 h under rotation. After incubation, beads were washed five times (2 min./wash under rotation) with cold RIPA buffer [50 mM HEPES-KOH, pH 7.5, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-deoxycholate], followed by one wash in cold final wash buffer [1xTE, 50 mM NaCl]. Immunoprecipitated chromatin was eluted at 65°C with agitation for 30 min. in elution buffer [50mMTris-HCl pH 8.0, 10mMEDTA, 1% SDS]. High-salt buffer [250mM Tris-HCl, pH 7.5, 32.5 mM EDTA, pH 8, 1.25M NaCl] and Proteinase K (Cat. P8107s, New England Biolabs Inc (NEB)) were added and crosslinks were reversed overnight at 65°C. Samples were treated with RNase A, and DNA was purified with AMPure XP beads (Cat. A63881, Beckman Coulter). Primary antibodies used for ChIP were: GATA4 (Cat. sc-1237 X, Santa Cruz), TBX5 (Cat. sc-17866 X, Santa Cruz), H3K36me3 (Cat. ab9050, Abcam), GLYR1 (anti-serum 7; provided by James T. Kadonaga’s laboratory), NKX2-5 (Cat. sc-8697 X, Santa Cruz), MEIS1 (Cat. ab19867, Abcam).
Fragmented ChIP and input DNA were end-repaired, 5’-phosphorylated and dA-tailed with NEBNext Ultra II DNA Library Prep Kit for Illumina (Cat. E7645, New England BioLabs). Samples were ligated to adaptor oligos for multiplex sequencing (Cat. E7335, New England BioLabs), PCR amplified, and sequenced on an Illumina NextSeq 500 at the Gladstone Institutes.

tag: cardiomyocyte differentiation day

value: Day 0:hiPSC

tag: chip antibody

value: GLYR1 anti-sera 7

tag: chip antibody vendor

value: James T. Kadonaga Laboratory

tag: processing batch

tag: comparison analysis

value: Day 6 Cardiac Progenitor versus Day 0 hiPSC stage differential GLYR1 binding


title: WT hiPSC GLYR1 ChIPseq rep 5 [glyr1_wt3_ipsc.3]


title: k56ac-h3x2-wt-alpha-s43

city: Rehovot

first: Naama

last: Barkai

state: --- Select a state ---

address: Herzl St 234

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

data_processing:
demultiplexing with bcl2fastq
paired end alignment to S288_R64 with bowtie2 (-p8 --local --very-sensitive )
readfiltering based on fragment size (keep 100-200 bp)
genome coverage with bedtools (-pc -d)
Genome_build: GCA_000146045.2, for samples ending with X39, S43, S44 and S47c ombined S. cerevisiae (GCA_000146045.2) and C. glabrata (GCF_000002545.3_ASM254v2) genome
Supplementary_files_format_and_content: *.out.txt file contains zipped genome coverage for all 12,157,105 bases in the S. cerevisiae genome (CHr 1-16+mitochondria); or 24,495,413 bases in the combined genome (first S.cerevisae then C. glabrata). The chromosomes are included sequentially in the outfile. If the C. glabrata genome was included it also goes sequentially after the S.cerevisae genome.

organism:
Saccharomyces cerevisiae
Nakaseomyces glabratus

source_name: Sensor-carrying cells

growth_protocol: yeast cells were grown to saturation overnight in YPD and then dilute in fresh,pre-warmed YPD and incubated for at least 6 hours at 30deg before G1 arrest (alpha factor). After 3 hours in alpha factor, cells were released into HU and samples for ChIP taken in 10-20 minute intervals. The number after 'HU' in the sample title indicates the minutes after release into HU.

extract_protocol:
ChIP was carried out as detailed in Gutin et all, Cell reports 2019, with following modifications. Cell pellets (each from 50 ml of cultures at OD600 0.4, 20 ODs total) were thawed on ice and washed in 10 ml 1M sorbitol. After complete liquid removal, pellets were resuspended in 600 ul RIPA buffer (10 mM Tris pH 8.0, 140 mM NaCl, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, EDTA-free protease inhibitor cocktail) and transferred to chilled LoBind Eppendorf microcentrifuge tubes containing ~500 ul of 0.5 mm zirconium oxide beads (Next Advance, ZrOB05). Cells were processed for 3 cycles in a Bullet Blender 24 (Next Advance) at level 8 for 1 min, with 1 minute on ice between cycles. Debris and lysate were transferred by piercing a hole in the bottom of the tube, placing a clean chilled tube under and centrifuging at 600xg for 5 seconds at 4C. The upper tube with the Zirconium beads was discarded and the lysate was hard spun at 17,000xg for 10 minutes at 4C. The supernatant containing cleaved solubilized 8xmyc tags was discarded, and the pellet was thoroughly resuspended in 100 ul NP buffer (10 mM Tris pH 7.4, 1 M sorbitol, 50 mM NaCl, 5 mM MgCl2, 1 mM CaCl2, and 0.075% NP-40, freshly supplemented with 1 mM β-mercaptoethanol, 500 μM spermidine, and EDTA-free protease inhibitor cocktail), and SLIM-ChIP protocol was carried continued as in Gutin et al.  SLIM-Chip, as per Gutin et al, Cell Reports 2019
SLIM-Chip, as per Gutin et al, Cell Reports 2019

tag: genotype

value: MATa his3delta1 leu2delta0 LYS2 met15delta0 ura3delta0 HTB2-GGS-TEV  HHT1-GGS-HA-Fast-MYC HHT2-GGS-HA-Fast-MYC, bar1

tag: sensor

tag: antibody

tag: growth condition

value: alpha

value: wt


title: wild-type_monoclonal_rep3


title: proliferating cells (Y)

city: Taoyuan City

first: chunhao

last: feng

address: No.259, Wenhua 1st Rd., Guishan Dist., Taoyuan City 33302, Taiwan (R.O.C.)

department: Graduate Institute of Natural Product

country: Taiwan

institute: Chang Gung University

data_processing:
Raw reads QC: adapter trimming and quality filtering (trimmomatic PE {input.r1} {input.r2} {output.r1_clean} {output.r1_clean_up} {output.r2_clean} {output.r2_clean_up} ILLUMINACLIP:/adapters/{adapter}.fa:2:30:10:1:true LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:20)
Align against reference genome with reference annotation Aligner: bowtie2 Reference : transcript sequences
Gene expression (RSEM) http://deweylab.github.io/RSEM/
Differential gene expression (EBSeq) https://www.biostat.wisc.edu/~kendzior/EBSEQ/
Pathway enrichment
GO enrichment
Genome_build: hg19/mm10
Supplementary_files_format_and_content: excel file included Expected count (S), Expected count (S-C), Expected count (Y), TPM (S), TPM (S-C), TPM (Y), FPKM (S), FPKM (S-C), FPKM (Y), Fold change (S-C_S), Fold change (S-C_Y), Fold change (S_Y), PPEE (S-C_S), PPEE (S-C_Y), PPEE (S_Y), Description, GO (BP)GO (MF)GO (CC), Pathway (KEGG), EC number

source_name: Bioresource Collection and Research Center, Taiwan

growth_protocol: HUVECs were cultured in M199 supplemented with HEPES, ECGS (Millipore), heparin, NaHCO3, L-glutamine, sodium pyruvate, and FBS (20% final concentration). The cells were grown in an atmosphere of 5% CO2 at 37°C and sub-cultured by trypsinization with trypsin-EDTA (Lonza).

extract_protocol:
RNA was collected from HUVECs and extracted by TRIzol (T9424, Sigma, USA). The extracted RNA samples were sent to Genomics (Taipei, Taiwan) for analysis, and a library was constructed. Briefly, after quality control of raw reads, mRNA was purified using reverse transcriptase and a random primer to synthesize single-strand cDNA, and dUTP was used in place of dTTP to generate double-stranded cDNA. A single ‘A’ nucleotide was added to the 3’ end of ds cDNAs. Then, multiple indexing adapters were ligated to the 5’ and 3’ ends of ds cDNA.
Library was validate on Agilent 2100 Bio-analyzer and Real-Time PCR System.

treatment_protocol: The cells were treated with DNSO or corylin for 24days.

tag: tissue

value: Human umbilical vein

tag: pdl

value: untreated


title: LGESS_3 [3B]

value: Low Grade Endometrial Stromal Sarcoma (LG-ESS)


title: wild-type_monoclonal_rep2


title: WT hiPSC GLYR1 ChIPseq rep 3 [glyr1_wt1_ipsc.1]


title: k56ac-h3x2-wt-HU030-s43


title: AR1547_01

type: RNA

city: Yufu-city

first: Yoshiyuki

last: Tsukamoto

state: Oita

address: hasamacho idaigaoka 1-1

department: Molecular Pathology

country: Japan

institute: Oita university, Faculty of Medicine

hyb_protocol: Gene Expression Hybridization kit was used for hybridization in accordance with the manufacture's instructions (Agilent Technologies).

scan_protocol: Microarray images were obtained by using a laser confocal scanner G2565BA (Agilent Technologies).

data_processing: Data analysis  were carried out by a contract research service at Dragon Genomics Center (Takara Bio, Mie, Japan). The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Processed signal intensities were normalized by the global scaling method. A trimmed mean probe intensity was determined by removing 2% of the lower and the higher end of the probe intensities in order to calculate the scaling factor. Normalized signal intensities were then calculated from the target intensity on each array using the scaling factor, so that the trimmed mean target intensity of each array was arbitrarily set to 2500.

source_name: DMSO, 16h

label_protocol: Experiments were carried out by a contract research service at Dragon Genomics Center (Takara Bio, Mie, Japan). Cy3-labeled cRNA targets were generated by use of Low input Quick Amp labeling Kit according to manufacture's instructions (Agilent Technologies).

extract_protocol: For each probe, the values were expressed as log2(normalized signal/median of normalized signals from DMSO treated samples).

value: ATL cell line


title: k56ac-h3x2-vps75-HU150-s47

value: MATa his3delta1 leu2delta0 LYS2 met15delta0 ura3delta0 HTB2-TEV, HHT1-HA-TEVsite-MYC, HHT2-HA-TEVsite-MYC, bar1, vps75::HYG


title: WT Day 6 GLYR1 ChIPseq rep 5 [glyr1_wt_r1_cpc.1]

source_name: WT hiPSC cardiomyocyte differentiation day 6 (cardiac progenitor stage)

growth_protocol: For human cardiac differentiation into D6 cardiac progenitors, we modified the protocols originally developed by Lian et al. and Tohyama et al. to achieve stage-specific, high yield, high-purity cardiac commitment in vitro (Lian et al. 2013; Tohyama et al. 2013). Briefly hiPSCs were detached from hESC-qualified LDEV-free matrigel (Cat. 354277, Corning) with accutase (Cat. 07920, Stem Cell Technologies) and reseeded on matrigel at 0.6–1.2x105 cells per 12well in Essential 8 medium (E8) (Cat. A1517001, Life Technologies) with 5μM ROCK inhibitor (Y-27632 2HCl, Cat. S1049, Selleckchem.com) (day-3). We optimized each hiPSC clone individually to identify the best cell seeding density that resulted in high levels of cTNT, NKX2-5, TBX5 and GATA4-positive sheet-like beating CMs at day15 of differentiation. On the next two days, media was changed daily with fresh E8 medium without ROCK inhibitor. On the day of cardiac induction (day0), 6μM CHIR99021 (Cat. 4423, Tocris) was added for 24 hr. in 1ml per well of B27-supplemented (without insulin) RPMI1640 media (Cat. 11875-119, Life Technologies). On day1 media was changed for freshly prepared 6μM CHIR99021 in B27-supplemented (without insulin) (Cat. A1895601, Life Technologies) RPMI1640 media. At day 2 and 3 IWP4 (Cat. 5214, Tocris) in B27-supplemented (without insulin) RPMI1640 media was added to activate Wnt signaling at a final concentration of 5μM. At day 4, IWP4 was removed, and 1ml of B27-supplemented (without insulin) RPMI1640 media per was daily added per well (days 4-6). At day day 6 cells were collected.

value: Day 6


title: wild-type_monoclonal_rep1


title: LGESS_1 [1B]


title: WT Day 6 GLYR1 ChIPseq rep 4 [glyr1_wt2_cpc.4]

value: Day 6 Cardiac Progenitor versus Day 0 hiPSC stage differential GLYR1 binding AND P496L GLYR1 mutant versus WT at Day 6 cardiac progenitor stage differential GLYR1 binding


title: k56ac-h3x2-vps75-HU180-s47


title: k56ac-h3x2-vps75-HU130-s47


title: BMM treat-3

city: Xiamen

first: Chen

last: Yongjie

state: Fujian

address: Xiang'an East street

department: Orthopedics Surgery

country: China

institute: Xiang'an Hospital of Xiamen University

data_processing:
Sequenced reads were trimmed for adaptor sequence and low-complexity or low-quality sequence  by Cutadapt (V1.9.1).
Clean data mapped to GRCm38.100 whole genome using Hisat2 (v2.0.1).
In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Genome_build: GRCm38

source_name: bone marrow macrophages

extract_protocol:
Total RNA was extracted from BMMs that had been stimulated with 30 ng/ml RANKL and treated without or with 20 μM mogrol for 5 days using an RNA isolation kit (Vazyme, Nanjing, China) based on the manufacturer’s protocol.
1 μg total RNA was used for following library preparation. Next generation sequencing library preparations were constructed according to the manufacturer’s protocol. The poly(A) mRNA isolation was performed using Poly(A) mRNA Magnetic Isolation Module or rRNA removal Kit. The mRNA fragmentation and priming was performed using First Strand Synthesis Reaction Buffer and Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double-stranded cDNA by beads was then treated with End Prep Enzyme Mix to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using beads, and fragments of ~400 bp (with the approximate insert size of 300 bp) were recovered. Each sample was then amplified by PCR using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR andP5/ P7 primer carrying index allowing for multiplexing. The PCR products were cleaned up using beads, validated using an Qsep100 (Bioptic, Taiwan, China), and quantified by Qubit3.0 Fluorometer (Invitrogen, Carlsbad, CA, USA). Then libraries with different indices were multiplexed and loaded on an Illumina HiSeq/Novaseq instrument according to manufacturer’s instructions (Illumina, San Diego, CA, USA) or a MGI2000 instrument according to manufacturer’s instructions (MGI, Shenzhen, China)

tag: cell type

value: bone marrow macrophages

value: 30 ng/ml RANKL+20 μM mogrol

tag: treat time

value: 5 days


title: LGESS_1 [1A]

tag: disease


title: k56ac-h3x2-vps75-HU110-s47

tag: strain


title: BMM treat-2

tag: treatment


title: BMM treat-1


title: K562, Mock-1

description: mock

data_processing:
Paired-end reads were trimmed using fastp v0.20.1. Quality check was performed on raw and trimmed data to ensure the quality of the reads using FastQC v0.11.7 and MultiQC v1.5
The quantification was performed with Kallisto v0.46.2 against the human genome (hg38).
Differential expression analysis was also performed using the DESeq2 v1.30.1 package
Genome_build: hg38
Supplementary_files_format_and_content: Comma-separated values, tpm values
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
RNA from K562 cell lines was extracted using the Monarch Total RNA purification kit (NEB) according to manufacturer’s instructions
library preparation was done using the NEBNext Ultra II Directional RNA library + NEBNext Poly(A) mRNA-dual index kit.

tag: cell line


title: k56ac-h3x2-wt-HU180-s47


title: BMM control-3

value: 30 ng/ml RANKL


title: k56ac-h3x2-vps75-HU070-s47


title: k56ac-h3x2-vps75-HU090-s47


title: K562, Mock-2

description: mock


title: J15_D24_si_S15

city: Kyoto

first: Yoshinori

last: Yoshida

address: 53, Kawahara-cho, Shogoin, Sakyo-ku

institute: Kyoto University

data_processing:
Illumina bcl2fastq (v2.17.14) were performed for converting fastq files and separation by samples with default setting
Too short (<20base) reads were removed and adapter sequence were trimmed by cutadapt (v1.15) with parameters -m 20 --nextseq-trim=20.
For removing human rRNA tRNA mapped reads, bowtie2 (v2.2.5), with parameters --very-sensitive --score-min L,0,-0.6.
The reads were mapped by STAR  (v2.5.3a)
HTSeq (v0.9.1) were perfomed for counting reads with the GENCODE (version 27) annotation gtf file.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file including count values for each sample.

source_name: hiPSC-EPI at day24+8 downregulating CDH18

growth_protocol: The hiPSC lines 201B7 and 409B2 (retroviral reprogramming by Yamanaka factors) as well as a MYH6-eGFP reporter cell line (MYH6-EIP4) were cultured in ReproCell media containing 4 ng/ml bFGF on irradiated MEF feeder cells. For removal of the feeder layer, the cells were treated with CTK.

extract_protocol:
RNeasy Mini Kit
TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold

treatment_protocol: Epicardial differentiation was started by iPSC dissociation using Accutase and subsequent plated onto a low-attachment HEMA-coated plates (6000-8000/96-well) to form embryoid body (EB). Differentiation media composed of StemPro 34 including   50 μg/ml ascorbic acid, 2 mM L-glutamine, 0.4 μM monothioglycerol and 150 mg/ml transferrin. To initiate differentiation, media was supplemented with 0.5% Matrigel, 10 μM Y-27632 and 2 ng/ml human recombinant BMP4 (hrBMP4. After 24 h EBs were cultured in differentiation media with a final concentration of 10 ng/ml hrBMP4, 2 ng/ml Activin A and 5 ng/ml hrbFGF. 84 h later, EBs were collected, dissociated using Accutase, and plated onto gelatin-coated dishes (0.3 x 105 cells/cm2) in differentiation media containing 3 mM CHIR99021, 30 ng/ml hrBMP4, 5 ng/ml hrVEGF and 10 µM SB431542. From d7 onwards, induced epicardial-like cells were maintained in DMEM containing 10% FBS and 10 µM SB431542. For cell passaging, induced epicardial cells were detached by Accutase and replated as described above.

tag: genotype/variation

value: CDH18-downregulated cells

value: Fetal EPI-like cells


title: J14_D24_si_S14


title: K562, JS-2


title: J16_D24_scr_S16

source_name: hiPSC-EPI at day24+8 control

value: scr-expressing cells (control)


title: k56ac-h3x2-vps75-HU050-s47


title: BMM control-2


title: J11_D12_si_plusSB_S11

source_name: hiPSC-EPI at day12+8 downregulating CDH18

value: PE-like cells


title: k56ac-h3x2-vps75-HU040-s47


title: IE9MP1_IDO_FK866_Incyte_3

description:
VoomCounts_2.csv
Grp4-5

tag: replicate


title: BMM control-1


title: K562-EPC1-PHF1-HA

data_processing:
Library strategy: Cut & Run
the paired-end reads  were trimmed using fastp v0.21.0
Trimmed reads were aligned on the human genome (hg38) using bwa mem v0.7.17 and samtools v1.13
Raw signal tracks and normalized tracks (in reads per million, RPM) were produced from mapped reads using deepTool's v2.17.0 bamCoverage tool and bedtools genomecov tool, respectively
Tracks were converted to the bigwig format using bedGraphToBigWig v2.8
The macs2 v2.2.1 software was used to perform the peak calling.
Genome_build: hg38
Supplementary_files_format_and_content: Tracks were converted to the bigwig format using bedGraphToBigWig v2.8

source_name: K562 from ATCC

growth_protocol: RPMI, 10% FBS, 1ug/ml Puromycin

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
As manufacturer's instruction in NEBNext Ultra II DNA kit

treatment_protocol: No Treatment

value: lymphoblast from chronic myelogenous leukemia (CML)

tag: growth conditions

value: normal growth conditions

tag: chip antibody

value: HA Tag CUTANA CUT&RUN Antibody, Rabbit Polyclonal, Epicypher, 13-2010

value: Insertion of Tag only at the AAVS1 locus by Zinc finger Nuclease,puromycin selection


title: J17_D24_scr_S17


title: k56ac-h3x2-vps75-HU030-s47


title: In Vivo_CT1BA5 2

city: Dallas

first: Huocong

last: Huang

state: TX

address: 6000 Harry Hines Blvd NB8.212

department: Department of Surgery

institute: UT Southwestern Medical Center

data_processing:
Illumina Casava software used for basecalling (performed by Novogene)
Sequencing reads were mapped (performed by Novogene). Reads with adaptor contamination, uncertain nucleotides for more than 10% of either read and low quality nucleotides (base quality < 20) for more than 50% of read were removed.
FPKM values were generated from count values and differential gene expression was performed using DESeq2_1.24.0 using the raw counts matrix (performed by Novogene)
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Mesothelial cells

growth_protocol: The PanMeso cells were cultured in the mesothelial cell media (medium 199, 10% FBS, 1% penicillin/streptomycin, 3.3 nM mouse epidermal growth factor, 400 nM hydrocortisone, 870 nM zinc-free bovine insulin, 20 mM HEPES), maintained at 33°C, washed with PBS three times and cultured in new mesothelial cell media at 37°C three days before any experiments.

extract_protocol:
RNA of parental and sorted PanMeso cells was extracted using RNeasy Mini Kit (Qiagen) following the kit protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: eGFP+ PanMeso cells were injected with pancreatic cancer cells BMFA3 or CT1BA5 orthotopically to form tumors and then subjected to FACS sorting for eGFP+ cells from the tumors.

value: Pancreas-derived eGFP expressing mesothelial cells

value: sorted from CT1BA5 tumors


title: K562, JS-1


title: K562-Mock-HA

value: Insertion of Tag only at the AAVS1 locus by Zinc finger Nuclease, puromycin selection


title: k56ac-h3x2-vps75-HU015-s47

value: MATa his3delta1 leu2delta0 LYS2 met15delta0 ura3delta0 HTB2-TEV, HHT1-HA-TEVsite-MYC, HHT2-HA-TEVsite-MYC, bar1, vps75::HYG


title: In Vivo_CT1BA5 1


title: J04_D24_8_iCF_S4

source_name: Induced Cardiac Fibroblasts (iCF) from hiPSCs

value: hiPSC-EPI cells at d24 treated with bFGF for CF induction

value: iCF cells from hiPSC-EPI


title: In Vivo_BMFA3 2

value: sorted from BMFA3 tumors


title: In Vivo_BMFA3 1


title: k56ac-h3x2-vps75-async-s47

value: async


title: k56ac-h3x2-vps75-HU190-s44


title: J10_D12_si_plusSB_S10


title: Parental 3

value: parental


title: Parental 2


title: ECO2_input

city: hangzhou

first: Li

last: Yang

address: banshan east road

institute: zhejiang cancer hospital

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp.
We used HISAT2 (http://daehwankimlab.github.io/hisat2) to map reads to the reference Homo sapiens (Version: GRCh38).
Mapped reads of IP and input libraries were provided for R package exomePeak (https://bioconductor.org/packages/exomePeak), which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software (http://www.igv.org).  HOMER (http://homer.ucsd.edu/homer/motif) were used for de novo  motif finding followed by localization of the motif with respect to peak summit. Called peaks were annotated by intersection with gene architecture using R package ChIPseeker (https://bioconductor.org/packages/ChIPseeker).
Then StringTie (https://ccb.jhu.edu/software/stringtie) was used to perform expression level for all mRNAs from input libraries by calculating FPKM (total exon fragments /mapped reads (millions) × exon length (kB)).
The differentially expressed mRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and p value < 0.05 by R package edgeR (https://bioconductor.org/packages/edgeR).
Genome_build: GRCh38（hg38）
Supplementary_files_format_and_content: text files include FPKM values and annotation for each Sample
Supplementary_files_format_and_content: text files include peak  information for each group

source_name: endometrioid ovarian cancer

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 50μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification.
Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 86℃ 7min. Then the cleaved RNA fragments were incubated for 2h at 4℃ with m6A-specific antibody (No. 202003, Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630). Then the IP RNA was reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average  size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: endometrioid ovarian cancer


title: OE2_input

source_name: ovarian endometriosis

value: ovarian endometriosis


title: k56ac-h3x2-vps75-HU150-s44


title: ECO3_input


title: isl1_3128.1 ChIPseq rep 1

data_processing:
ChIP seq:
Cluster generation, sequencing, and base calling was performed on Illumina NextSeq 500.
Trimming of known adapters and low-quality regions of reads was performed using Fastq-mcf. Sequence quality control was assessed using FastQC.
Alignment to the hg19 reference human genome was performed using Bowtie 2.2.4. Peaks were called using GEM for transcription factors (GATA4, NKX2-5, TBX5, MEIS1, ISL1) and BCP for GLYR1 and H3K36me3.
Bulk RNA seq:
Cluster generation, sequencing, and base calling was performed on Illumina HiSeq 2500.
Trimming of known adapters and low-quality regions of reads was performed using Fastq-mcf. Sequence quality control was assessed using FastQC.
Reads were mapped to the hg19 reference human genome using STAR (v 2.7.3a) and assigned to Ensembl genes. We quantified gene expression using raw counts and kept the protein coding genes that showed an average FPKM value across the samples >0.5 FPKM. We then performed differential expression gene testing with DESeq25 (v.1.24.0 R package) using default settings.
Genome_build: hg19
Supplementary_files_format_and_content: We provide bed ad BigWig files for ChIPseq.       We provide excel files for differential expression analysis for every gene for Bulk RNAseq experiments.

value: hiPSC cardiomyocyte

value: wild type

tag: cardiomyocyte differentiation day

value: Day 6

tag: type of experiment

value: ChIPseq

value: ISL1 anibody

tag: chip antibody vendor

value: R&D Systems

tag: chip antibody cat. #


title: Parental 1

value: Pancreas-derived eGFP expressing mesothelial cells


title: input_wtc11_meis_171114 ChIPseq rep1


title: k56ac-h3x2-vps75-HU130-s44

tag: genotype

tag: sensor

tag: antibody

tag: growth condition


title: meis1_wtc11.1_171114 ChIPseq rep 1

tag: cell type

value: MEIS1 antibody

value: Abcam


title: J06_D24_8_iSMC_S6

source_name: Induced Smooth Muscle Cells (iSMC) from hiPSCs

value: hiPSC-EPI cells at d24 treated with TGF+bFGF for CF induction

value: iSMC cells from hiPSC-EPI


title: input_wt_180417 ChIPseq rep 2


title: ECO1_input

tag: disease


title: k56ac-h3x2-vps75-HU110-s44

value: MATa his3delta1 leu2delta0 LYS2 met15delta0 ura3delta0 HTB2-TEV, HHT1-HA-TEVsite-MYC, HHT2-HA-TEVsite-MYC, bar1, vps75::HYG

tag: strain


title: OE3_input


title: k56ac-h3x2-vps75-HU090-s44


title: k56ac-h3x2-vps75-alpha-s47

value: alpha


title: OE3_IP

data_processing:
Library strategy: m6A-seq
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp.
We used HISAT2 (http://daehwankimlab.github.io/hisat2) to map reads to the reference Homo sapiens (Version: GRCh38).
Mapped reads of IP and input libraries were provided for R package exomePeak (https://bioconductor.org/packages/exomePeak), which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software (http://www.igv.org).  HOMER (http://homer.ucsd.edu/homer/motif) were used for de novo  motif finding followed by localization of the motif with respect to peak summit. Called peaks were annotated by intersection with gene architecture using R package ChIPseeker (https://bioconductor.org/packages/ChIPseeker).
Then StringTie (https://ccb.jhu.edu/software/stringtie) was used to perform expression level for all mRNAs from input libraries by calculating FPKM (total exon fragments /mapped reads (millions) × exon length (kB)).
The differentially expressed mRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and p value < 0.05 by R package edgeR (https://bioconductor.org/packages/edgeR).
Genome_build: GRCh38（hg38）
Supplementary_files_format_and_content: text files include FPKM values and annotation for each Sample
Supplementary_files_format_and_content: text files include peak  information for each group


title: bulk RNA-seq data on sorted NK cells from the liver of mouse number 6

city: New York

first: Ming

address: 200, East 89th Street

department: Immunology Program

institute: Sloan Kettering Institute

description:
DP_FMSP_NK_DN_RNAseq_counts.csv
NK6

data_processing:
Paired-end reads in fastq format from 15 total samples (4 DP, 4 FMSP, 3 DN, and 4 NK) were quantified at the transcript level using the mm10 reference with Salmon (v1.6) using default parameters, and then aggregated to gene-level counts using tximport (v1.2).  For ATAC-seq analysis, for all replicates in all biological conditions, we first used seqtk to trim 10 bp from either end of raw paired-end ATAC-seq reads. The trimmed fastqs were then aligned to the mm10 reference genome using bowtie2. Duplicates were removed using samtools, and peaks were called using MACS2 with parameters “shift 100 --extsize 200 -p 0.2 -B –SPMR”. To define an atlas of peaks reproducible across replicates within each biological condition, we used the irreproducible discovery rate framework (IDR) at FDR P < 0.1 for each pair of replicates within each condition, followed by merged peak calling across all replicates using MACS2. This defined a final atlas of 51412 peaks for downstream analysis. Peaks were annotated to the closest gene.
Differential expression analyses were conducted using DESeq2 separately for all six pairwise comparisons between the four cell types, and genes were included in the six lists of differentially expressed genes (Table S3) if they met all three of the following criteria: base mean expression > 50, false discovery rate (FDR) P < 0.05, and log2 fold change either > 1 or < -1.  For ATAC-seq analysis, we used DESeq2, and peaks were considered significantly differentially accessible at FDR P < 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: .csv files for gene x sample count matrix for bulk RNA-seq; peaks x sample count matrix for bulk ATAC-seq.

source_name: Mouse 6

extract_protocol:
Briefly, spleen single-cell suspension was obtained by tissue disruption with glass slides. For liver, tissue was manually dissociated using a razor blade and digested with 1 mg/ml Collagenase D (Sigma Aldrich) for 30 minutes at 37°C. For salivary gland, tissue was manually dissociated using a razor blade and digested for 1 hour in 1 mg/ml Collagenase Type III (Worthington) and 4 mg/ml DNase I (Sigma-Aldrich) in HBSS at 37°C with periodic vortex. After collagenase treatment, cells isolated from the liver and salivary gland were filtered through a 70-mM cell strainer, layered in a 44% and 66% Percoll gradient (Sigma-Aldrich), and centrifuged at 1,900 g for 30 minutes without brake.
For bulk ATAC-seq, 50,000 cells were sorted for each sample and frozen in FBS + 10% DMSO. Profiling of chromatin was performed by ATACseq as described previously. Briefly, 50,000 viably frozen cells were washed in cold PBS and lysed. The transposition reaction was incubated at 42°C for 45 minutes. The DNA was cleaned with the MinElute PCR Purification Kit (Qiagen catalog # 28004) and material was amplified for 5 cycles. After evaluation by real-time PCR, 8-10 additional PCR cycles were done. The final product was cleaned by aMPure XP beads (Beckman Coulter catalog # A63882) at a 1X ratio. Libraries were sequenced on a Hiseq 2500 in High Output mode in a PE50 run, using the TruSeq SBS Kit v4 (Illumina). An average of 57 million paired reads were generated per sample. For bulk RNA-seq, all cells in a given population were sorted from one mouse per sample for DP, FMSP, DN and NK cells directly into 750 mL Trizol LS. After sort, total volume was brought up to 1 mL with sterile PBS, and samples were flash frozen. Four DP, four FMSP, three DN and four NK cell samples were processed and sequenced. For RNA extraction, phase separation in cells lysed in 1 mL TRIzol Reagent (ThermoFisher catalog # 15596018) was induced with 200 mL chloroform and RNA was extracted from the aqueous phase using the miRNeasy Micro Kit (Qiagen catalog # 217084) on the QIAcube Connect (Qiagen) according to the manufacturer’s protocol with 350 mL input. Samples were eluted in 15 mL RNase-free water. For transcriptome sequencing, after RiboGreen quantification and quality control by Agilent BioAnalyzer, 282-300 pg total RNA with RNA integrity numbers ranging from 7.8 to 9.4 underwent amplification using the SMART-Seq v4 Ultra Low Input RNA Kit (Clonetech catalog # 63488), with 12 cycles of amplification. Subsequently, 2.1-3 ng of amplified cDNA was used to prepare libraries with the KAPA Hyper Prep Kit (Kapa Biosystems KK8504) using 8 cycles of PCR. Samples were barcoded and run on a NovaSeq 6000 in a PE100 run, using the NovaSeq 6000 S4 Reagent Kit (200 Cycles) (Illumina). An average of 82 million paired reads were generated per sample and the percent of mRNA bases per sample ranged from 67% to 83%.
Bulk RNA seq; bulk ATAC seq

tag: tissue

value: Liver

value: S1pr5eGFP+ NK cells

tag: cell population

value: NK


title: bulk RNA-seq data on sorted NK cells from the liver of mouse number 5

description:
DP_FMSP_NK_DN_RNAseq_counts.csv
NK5

source_name: Mouse 5


title: J03_CF_S3

source_name: Primary cardiac fibroblast (CF)

tag: genotype/variation

value: Primary cells


title: input_3218_isl1 ChIPseq rep1

value: hiPSC cardiomyocyte


title: OE1_input

value: ovarian endometriosis


title: gata4_wt_R3_180417 ChIPseq rep 2

value: wild type

value: Day 6

value: GATA4 (C-20) antibody

value: Santa Cruz

tag: chip antibody lot/batch #


title: OE2_IP


title: k56ac-h3x2-vps75-HU070-s44

source_name: Sensor-carrying cells


title: bulk RNA-seq data on sorted NK cells from the liver of mouse number 4

description:
DP_FMSP_NK_DN_RNAseq_counts.csv
NK4

source_name: Mouse 4


title: bulk RNA-seq data on sorted DP ILC1 cells from the liver of mouse number 6

description:
DP_FMSP_NK_DN_RNAseq_counts.csv
DP6

value: GzmC+GzmcFM+ ILC1 cells

value: DP


title: k56ac-h3x2-vps75-HU050-s44


title: OE1_IP


title: k56ac-h3x2-vps75-HU040-s44


title: ECO3_IP

value: endometrioid ovarian cancer


title: bulk RNA-seq data on sorted DP ILC1 cells from the liver of mouse number 5

description:
DP_FMSP_NK_DN_RNAseq_counts.csv
DP5


title: k56ac-h3x2-vps75-HU030-s44


title: ECO1_IP


title: k56ac-h3x2-vps75-HU015-s44


title: input_wtc11_171214 ChIPseq rep 1

value: ChIPseq


title: nkx2-5_wt.1_180417 ChIPseq rep1

value: NKX2-5 (N19) antibody


title: nkx2-5_wt11.1_171214 ChIPseq rep 1


title: ECO2_IP


title: tbx5_wt.1_180417 ChIPseq rep1

value: TBX5 (C-20) antibody


title: tbx5_wt11.1_171214 ChIPseq rep 1


title: CD8+PD-L1-, rep3

city: Shanghai

first: zheyi

last: chen

address: 1665 Kong Jiang Road

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences and low-quality reads. The clean reads were then aligned to the human genome (GRCh38) using STAR. StringTie was used to obtain gene counts, and the FPKM method was used to determine gene expression.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample.

source_name: T cells

growth_protocol: Fresh blood was obtained from healthy volunteers. PBMCs were isolated from fresh heparinized blood using standard density gradient centrifugation using the commercial solution named Ficoll-Paque Plus (GE Healthcare). CD8+ T cells were isolated from PBMCs by negative selection (Miltenyi) and resuspended in RPMI-1640 medium supplemented with 10% FBS, penicillin (100 U/mL), and streptomycin (100 mg/mL) (Gibco).   Cells were incubated at 37°C (5% CO2) in the complete medium with 0.5 μg/mL soluble anti-human CD28 mAb (BD Bioscience) in 96-well round-bottom plates pre-coated with 1 μg/mL anti-human CD3 mAb (BD Bioscience).

extract_protocol:
After the stimulation, cells were surface stained for CD8, and PD-L1, and CD8+PD-L1+ and CD8+PD-L1- T cells were sorted using a BD FACSAria II cell sorter. The purity of the sorted samples was greater than 95%.
Cells were sorted into tubes containing lysis buffer, and and total RNA were extracted by using the Quick-RNA Microprep Kit (Zymo). Then transcriptome amplifications were performed by using Single Cell Full Length mRNA-Amplification Kit (Vazyme). The amplified cDNA products were purified with DNA beads (KAPA) to eliminate short fragments (less than 500 bp). At this step, the concentration of each sample was quantified with Qubit HsDNA kits (Invitrogen), and libraries were then constructed with the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme). Finally, the libraries were sequenced on an Illumina Nova6000 sequencer (Illumina).

treatment_protocol: CD8 T cells were stimulated with 50 ng/mL IL-27 ((PeproTech)) for 48 hours.

value: blood

value: CD8 T cells

tag: treatment

tag: cell type (sorted)

value: CD8+PD-L1- T cells


title: k56ac-h3x2-vps75-alpha-s44

value: MATa his3delta1 leu2delta0 LYS2 met15delta0 ura3delta0 HTB2-TEV, HHT1-HA-TEVsite-MYC, HHT2-HA-TEVsite-MYC, bar1, vps75::HYG

value: alpha


title: CD8+PD-L1-, rep2


title: bulk RNA-seq data on sorted DP ILC1 cells from the liver of mouse number 4

description:
DP_FMSP_NK_DN_RNAseq_counts.csv
DP4

value: Liver


title: gata4_wt_R2_171214 ChIPseq rep 1

source_name: WT hiPSC cardiomyocyte differentiation day 6 (cardiac progenitor stage)

value: hiPSC

tag: cardiomyocyte differentiation day

tag: chip antibody


title: bulk RNA-seq data on sorted DN ILC1 cells from the liver of mouse number 4

description:
DP_FMSP_NK_DN_RNAseq_counts.csv
DN4

value: GzmC-GzmcFM- ILC1 cells

value: DN


title: bulk RNA-seq data on sorted DN ILC1 cells from the liver of mouse number 6

description:
DP_FMSP_NK_DN_RNAseq_counts.csv
DN6


title: k56ac-h3x2-vps75-async-s44

value: async


title: bulk RNA-seq data on sorted FMSP ILC1 cells from the liver of mouse number 6

description:
DP_FMSP_NK_DN_RNAseq_counts.csv
FMSP6

value: GzmC-GzmcFM+ ILC1 cells

value: FMSP


title: input_ipsc.2 ChIPseq rep 2

description: input_ipsc.2 ChIPseq rep 2

source_name: WT hiPSC

value: wild type

value: Day 6

tag: type of experiment


title: ha-h3x2-wt-HU180spike-x39

value: MATa his3delta1 leu2delta0 LYS2 met15delta0 ura3delta0 HTB2-GGS-TEV  HHT1-GGS-HA-Fast-MYC HHT2-GGS-HA-Fast-MYC, bar1

value: ha

value: wt


title: input_ipsc.1 ChIPseq rep 1

description: input_ipsc.1 ChIPseq rep 1

value: ChIPseq


title: bulk RNA-seq data on sorted FMSP ILC1 cells from the liver of mouse number 4

description:
DP_FMSP_NK_DN_RNAseq_counts.csv
FMSP4


title: CD8+PD-L1+, rep2

value: blood

value: CD8 T cells

value: CD8+PD-L1+ T cells


title: h3k36me3_ipsc.2 ChIPseq rep 2

value: H3K36me3 antibody

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #


title: ha-h3x2-wt-HU150spike-x39

tag: genotype

tag: sensor


title: ha-h3x2-wt-HU130spike-x39

tag: antibody

tag: growth condition


title: bulk RNA-seq data on sorted DP ILC1 cells from the liver of mouse number 3

description:
DP_FMSP_NK_DN_RNAseq_counts.csv
DP3

source_name: Mouse 3

value: Liver

tag: cell type

value: GzmC+GzmcFM+ ILC1 cells

value: DP


title: CD8+PD-L1+, rep3


title: CD8+PD-L1+, rep1


title: ha-h3x2-wt-HU110spike-x39

tag: strain


title: ha-h3x2-wt-HU90spike-x39


title: bulk RNA-seq data on sorted DN ILC1 cells from the liver of mouse number 2

description:
DP_FMSP_NK_DN_RNAseq_counts.csv
DN2

source_name: Mouse 2

tag: tissue

value: GzmC-GzmcFM- ILC1 cells

value: DN


title: bulk RNA-seq data on sorted FMSP ILC1 cells from the liver of mouse number 3

description:
DP_FMSP_NK_DN_RNAseq_counts.csv
FMSP3

value: GzmC-GzmcFM+ ILC1 cells

tag: cell population

value: FMSP


title: glyr1Ab7_ipsc.2 ChIPseq rep 2

value: hiPSC

tag: genotype/variation

value: wild type

value: Day 6

value: GLYR1 anti-sera 7

value: James T. Kadonaga Laboratory


title: glyr1Ab7_ipsc.1 ChIPseq rep 1

value: ChIPseq

tag: chip antibody lot/batch #


title: HS spleen

city: Cambridge

first: Hugo

middle: P.

last: Bastos

address: Jeffrey Cheah Biomedical Centre, Puddicombe Way

department: Haematology

country: United Kingdom

institute: Wellcome - MRC Cambridge Stem Cell Institute

description: data from 2 pooled donors

data_processing:
Library strategy: CITE-seq
Reads (SITTB8 library) processed and aligned to hg19 using CellRanger v6.0.1
Donors/genotype demultiplexed using the Souporcell pipeline
Genome_build: hg19
Supplementary_files_format_and_content: Processed files are a 10x-Genomics-formatted hdf5 file containing the UMI counts for the processed library; tabulated text file with genotype assignments per cell

source_name: spleen

extract_protocol: Libraries were prepared using the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (CG000204 Rev D) (for mRNA library) and TotalSeq™-A Antibodies and Cell Hashing with 10x Single Cell 3' Reagent Kit v3 or v3.1 Protocol (for TotalSeq library)

value: spleen

tag: condition

value: Hereditary spherocytosis


title: ha-h3x2-wt-HU70spike-x39

value: MATa his3delta1 leu2delta0 LYS2 met15delta0 ura3delta0 HTB2-GGS-TEV  HHT1-GGS-HA-Fast-MYC HHT2-GGS-HA-Fast-MYC, bar1

value: ha

value: wt


title: h3k36me3_ipsc.1 ChIPseq rep 1

value: H3K36me3 antibody

value: Abcam


title: CD8+PD-L1-, rep1

value: blood

value: CD8 T cells

tag: treatment

tag: cell type (sorted)

value: CD8+PD-L1- T cells


title: CBS-u2-RH-OE-Catenin-RNA-seq_2

city: Hangzhou

first: Huacheng

last: Luo

state: Zhejiang

address: No. 150, Fucheng Road, Qiantang District

institute: Hangzhou Institute of Medicine (HIM), The Chinese Academy of Sciences

data_processing:
Standard Illumina software base-calling and quality-control filtering was applied Sequences (Paired end)
Paired end ChIRP-seq, HiC-seq and scRNA-seq and scATAC-seq reads from mice were aligned to the mm9 genome assembly using BWA, and NG capture-C-seq, RNA-seq, GRO-seq, ChIP-seq, DRIP-seq and DRIPc-seq reads from human AML cells were aligned to the hg19 genome assembly using BOWTIE2 default parameters.
Peak calling was performed using MACS algorithm (version 2.1.1)
Genome coverage tracks were created using deepTools version 3.0
Genome_build: mm9, hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for RNA-seq, scRNA-seq and scATAC-seq Samples and peaks for DRIP-seq ,GRO-seq, DRIPc-seq,ChIRP-seq, ChIP-seq, NG-capture-C and HIC-seq.

source_name: MOLM13 leukemia cells

growth_protocol: Total bone marrow cells were isolate from WT and Hottip-Tg mice, and sorted with Lin-, Sca1+ and Kit+ markers.  Human MOLM13 leukemia cells were culture at RMPI1640 medium with 10% FBS media.

extract_protocol:
RNA samples extracted with Trizon and treated with Dnase I.  ChIP Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with CTCF, SA1, SA2, RAD21, H3K4me3 and H3K27me3 antibody (antibody: Anti-CTCF, Cell Signaling Technology, Cat# 2899; Anti-SA1, Abcam, Cat# ab4457; Anti-SA2, Abcam, Cat# ab4464;  Anti-RAD21, Abcam, Cat# ab992;  Anti-H3K4me3, Millipore, Cat No. 04-745;   Anti-H3K27me3, Millipore, Cat No. 07-449).  ATAC-seq samples derived according to Nextera Tn5 Transposase kits. DNA:RNA immunoprecipitation sequencing (DRIP-seq) was performed as described previously with s9.6 antibody (Anti-DNA-RNA Hybrid [S9.6] Antibody, Kerafast, Cat# ENH001). ChIRP libraries were prepared using Illumina’s TruSeq ChIP Sample Preparation Kit according to the manufacturer’s instructions. The quality of the library was checked with Agilent Bioanalyzer. NG-Capture-C assay was performed as previously described. Hi-C assay was performed to generate a genome-wide interaction as described previously with Arima-HiC Kit (Cat: A410030) (https://arimagenomics.com/) with minor modifications. Single cells were generated using Chromium Controller (10x Genomics), and scRNA-seq and scATAC-seq libraries were constructed using chromium single cell 3’ reagent kits v2 (10x Genomics, California USA) according to the manufacturer’s recommendations. For GRO-seq, cells were subjected to nuclear run-on at 30°C with BrU labeling. The run-on RNAs were pull down by BrU beads and subjected to library preparation for deep sequencing.
RNA-seq libraries were prepared according to TruSeq Stranded mRNA Library Prep (#20020594). ChIRP libraries were prepared using Illumina’s TruSeq ChIP Sample Preparation Kit according to the manufacturer’s instructions. The quality of the library was checked with Agilent Bioanalyzer.  ChIP-seq libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Library Preparation Kit (#IP-202-1012). ATAC-seq libraries were prepared according to Nextera DNA Library Prep Kit (#FC-121-1030). NG-Capture-C-seq libraries were prepared according to  using the Herculase II PCR kit (Agilent). . Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols. For GRO-seq, cells were subjected to nuclear run-on at 30°C with BrU labeling. The run-on RNAs were pull down by BrU beads and subjected to library preparation for deep sequencing. Briefly, NRO-RNA were used to make GRO-seq library with NEBNext Ultra II Directional RNA Library Prep kit (NEB Cat#E7765).

treatment_protocol: Immediately extract RNA from LK, LSK cells and MOLM13 AML cells without any treatment

tag: cell line

tag: cell types

value: Human-derived acute myeloid leukemia

tag: tissue source

value: peripheral blood


title: bulk RNA-seq data on sorted NK cells from the liver of mouse number 1

description:
DP_FMSP_NK_DN_RNAseq_counts.csv
NK1

source_name: Mouse 1

value: Liver

value: S1pr5eGFP+ NK cells

value: NK


title: ha-h3x2-wt-HU50spike-x39


title: input_cpc.2 ChIPseq rep 2

value: hiPSC cardiomyocyte

value: wild type

tag: cardiomyocyte differentiation day

value: Day 6

tag: type of experiment


title: bulk RNA-seq data on sorted FMSP ILC1 cells from the liver of mouse number 5

description:
DP_FMSP_NK_DN_RNAseq_counts.csv
FMSP5

value: GzmC-GzmcFM+ ILC1 cells

value: FMSP


title: CBS-u2-RH-OE-Catenin-RNA-seq_1


title: ha-h3x2-wt-HU40spike-x39

tag: genotype

value: MATa his3delta1 leu2delta0 LYS2 met15delta0 ura3delta0 HTB2-GGS-TEV  HHT1-GGS-HA-Fast-MYC HHT2-GGS-HA-Fast-MYC, bar1

tag: sensor

value: ha


title: HN mice, PEC3

city: chengdu

first: Qian

last: Ren

state: China

address: 三住7楼

institute: 四川大学华西临床医学院肾内科

data_processing:
Illumina Novaseq™ 6000 platform at the LC-BIO Bio-tech ltd (Hangzhou, China) was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 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: mm9
Supplementary_files_format_and_content: tab-delimited text file includes count and FPKM values for each Sample

source_name: Kidney

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.Approximately 1 μg of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease state

value: Hyperuricemic Nephropathy (HN)

value: Pectolinarigenin

value: Kidney


title: HN mice, PEC2

institute: 四川大学华西临床医学院肾内科


title: LGESS_3 [3A]

data_processing:
Paired-end reads were trimmed using fastp v0.20.1. Quality check was performed on raw and trimmed data to ensure the quality of the reads using FastQC v0.11.7 and MultiQC v1.5
The quantification was performed with Kallisto v0.46.2 against the human genome (hg38).
Differential expression analysis was also performed using the DESeq2 v1.30.1 package
Genome_build: hg38
Supplementary_files_format_and_content: log2FoldChange
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Uterus

extract_protocol:
RNA from frozen tissue samples were extracted using the miRNEASY micro kit (QIAGEN).
Only samples with RIN above 7 was used for library preparation using the NEBNext Ultra II Directional RNA library + NEBNext Poly(A) mRNA-dual index kit.

tag: disease

value: Low Grade Endometrial Stromal Sarcoma (LG-ESS)


title: CBS-u2-RH-RNA-seq_2


title: CBS-u2-RH-RNA-seq_1


title: HN mice, PEC1

institute: 四川大学华西临床医学院肾内科

tag: strain


title: ha-h3x2-wt-HU30spike-x39

data_processing:
demultiplexing with bcl2fastq
paired end alignment to S288_R64 with bowtie2 (-p8 --local --very-sensitive )
readfiltering based on fragment size (keep 100-200 bp)
genome coverage with bedtools (-pc -d)
Genome_build: GCA_000146045.2, for samples ending with X39, S43, S44 and S47c ombined S. cerevisiae (GCA_000146045.2) and C. glabrata (GCF_000002545.3_ASM254v2) genome
Supplementary_files_format_and_content: *.out.txt file contains zipped genome coverage for all 12,157,105 bases in the S. cerevisiae genome (CHr 1-16+mitochondria); or 24,495,413 bases in the combined genome (first S.cerevisae then C. glabrata). The chromosomes are included sequentially in the outfile. If the C. glabrata genome was included it also goes sequentially after the S.cerevisae genome.

tag: antibody

tag: growth condition

value: wt


title: input_cpc.1 ChIPseq rep 1

tag: cell type

tag: genotype/variation

value: ChIPseq


title: h3k36me3_cpc.2 ChIPseq rep 2

tag: chip antibody

value: H3K36me3 antibody

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #


title: Ctrl-RNA-seq_2

tag: cell line

value: Human-derived acute myeloid leukemia

value: peripheral blood

value: Ctrl


title: input_cpc.3 ChIPseq rep 3

value: hiPSC cardiomyocyte

value: wild type


title: HN mice, M12

institute: 四川大学华西临床医学院肾内科

tag: treatment

value: untreated

tag: tissue


title: ha-h3x2-wt-alpha2spike-x39


title: Ctrl-RNA-seq_1

tag: cell types

tag: tissue source


title: HN mice, M8

institute: 四川大学华西临床医学院肾内科


title: ha-h3x2-wt-alpha1spike-x39

tag: genotype


title: h3k36me3_cpc.1 ChIPseq rep 1

tag: cardiomyocyte differentiation day

value: Day 6

tag: type of experiment


title: glyr1Ab7_cpc.3 ChIPseq rep 3

value: GLYR1 anti-sera 7

value: James T. Kadonaga Laboratory


title: HN mice, C5

institute: 四川大学华西临床医学院肾内科

tag: disease state

value: control


title: ha-h3x2-wt-asyncspike-x39

value: MATa his3delta1 leu2delta0 LYS2 met15delta0 ura3delta0 HTB2-GGS-TEV  HHT1-GGS-HA-Fast-MYC HHT2-GGS-HA-Fast-MYC, bar1

tag: sensor

value: ha

value: asyncspike

tag: strain


title: HOTTIP-KO-GRO-seq_1

data_processing:
library strategy: GRO-seq
Standard Illumina software base-calling and quality-control filtering was applied Sequences (Paired end)
Paired end ChIRP-seq, HiC-seq and scRNA-seq and scATAC-seq reads from mice were aligned to the mm9 genome assembly using BWA, and NG capture-C-seq, RNA-seq, GRO-seq, ChIP-seq, DRIP-seq and DRIPc-seq reads from human AML cells were aligned to the hg19 genome assembly using BOWTIE2 default parameters.
Peak calling was performed using MACS algorithm (version 2.1.1)
Genome coverage tracks were created using deepTools version 3.0
Genome_build: mm9, hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for RNA-seq, scRNA-seq and scATAC-seq Samples and peaks for DRIP-seq ,GRO-seq, DRIPc-seq,ChIRP-seq, ChIP-seq, NG-capture-C and HIC-seq.

value: HOTTIP-KO

tag: molecule subtype

value: Nascent RNA


title: HOTTIP-KO-GRO-seq_2


title: HN mice, C4

institute: 四川大学华西临床医学院肾内科

value: Kidney


title: ha-h3x2-wt-HU180-s47

tag: antibody

tag: growth condition

value: wt


title: WT-GRO-seq_2

value: Human-derived acute myeloid leukemia

tag: genotype/variation

value: WT


title: HN mice, C2

institute: 四川大学华西临床医学院肾内科


title: WT-GRO-seq_1

value: peripheral blood


title: ha-h3x2-wt-HU150-s47


title: ha-h3x2-wt-HU15spike-x39


title: ha-h3x2-wt-HU130-s47


title: GLYR1 P496L mutant Day 18 scRNAseq rep 3 [Day18CM_WT_V2_2]

description: Chromium Single Cell 3′ Chip kit v.17

data_processing:
ChIP seq:
Cluster generation, sequencing, and base calling was performed on Illumina NextSeq 500.
Trimming of known adapters and low-quality regions of reads was performed using Fastq-mcf. Sequence quality control was assessed using FastQC.
Alignment to the hg19 reference human genome was performed using Bowtie 2.2.4. Peaks were called BCP for GLYR1.
single cell RNA seq:
Cluster generation, sequencing, and base calling was performed on NovaSeq (Illumina, software v1.5)
6-8 replicate samples (from independent differentiation runs involving either wild-type or P496L mutant cells) were each processed in 3 batches. Reads from each sample were aligned to the hg38 human reference (version 2020-A from 10X Genomics website) using Cell Ranger version 5.0.1. The resulting count matrices for all samples within each batch were aggregated without depth normalization.
Genome_build: hg19 (ChIP-seq); hg38 (RNA-seq)
Supplementary_files_format_and_content: We provide bed ad BigWig files for ChIPseq.
Supplementary_files_format_and_content: We provide the aligned bam files and count matrices in h5 format

source_name: GLYR1 P496L mutant hiPSC cardiomyocyte differentiation day 18

growth_protocol: For human cardiac differentiation into D6 cardiac progenitors or D18 cardiomyocytes, we modified the protocols originally developed by Lian et al. and Tohyama et al. to achieve stage-specific, high yield, high-purity cardiac commitment in vitro (Lian et al. 2013; Tohyama et al. 2013). Briefly hiPSCs were detached from hESC-qualified LDEV-free matrigel (Cat. 354277, Corning) with accutase (Cat. 07920, Stem Cell Technologies) and reseeded on matrigel at 0.6–1.2x105 cells per 12well in Essential 8 medium (E8) (Cat. A1517001, Life Technologies) with 5μM ROCK inhibitor (Y-27632 2HCl, Cat. S1049, Selleckchem.com) (day-3). We optimized each hiPSC clone individually to identify the best cell seeding density that resulted in high levels of cTNT, NKX2-5, TBX5 and GATA4-positive sheet-like beating CMs at day15 of differentiation. On the next two days, media was changed daily with fresh E8 medium without ROCK inhibitor. On the day of cardiac induction (day0), 6μM CHIR99021 (Cat. 4423, Tocris) was added for 24 hr. in 1ml per well of B27-supplemented (without insulin) RPMI1640 media (Cat. 11875-119, Life Technologies). On day1 media was changed for freshly prepared 6μM CHIR99021 in B27-supplemented (without insulin) (Cat. A1895601, Life Technologies) RPMI1640 media. At day 2 and 3 IWP4 (Cat. 5214, Tocris) in B27-supplemented (without insulin) RPMI1640 media was added to activate Wnt signaling at a final concentration of 5μM. At day 4, IWP4 was removed, and 1ml of B27-supplemented (without insulin) RPMI1640 media per was daily added per well (days 4-9) and collected at day 6 cardiac progenitor stage or continue with media changes for cardiomyocyte stage collection. At day 10 the media was changed to regular B27-supplemented (with insulin) (Cat. A1895601, Life Technologies) RPMI1640 hereafter.

extract_protocol:
Cells were wash with PBS and detached with 0.25% Trypsin (CMs) or accutase (hiPSCs and CPs) incubated for 5 minutes. Quenched with 1 mL of PBS + 1% FBS and spin down at 800-1000 rpms for 3 min. Cells were washed twice with PBS + 1% FBS, resuspend in cold PBS + 1% FBS (use 0.5mL PBS per well collected from a 12-well-plate) and put on ice. Cells were filtered to avoid clumps and manually count with hemocytometer. Both live and dead cells were included in the count and cells were diluted to 1e6 cells/ml. A total of 60,000 cells were used to proceed with the scRNASeq library construction protocol.
Single-cell droplet libraries from the hiPSC (1x GLYR1KO, 2x GLYR1WT, 2x GLYR1P496L), CM-differentiation day 6 (3x GLYR1WT, 3x GLYR1P496L) and day 18 (3x GLYR1WT, 3x GLYR1P496L) cell suspension (Figure 7 and S8) were generated in the 10X Genomics Chromium controller according to the manufacturer’s instructions in the Chromium Single Cell 3′ Reagent Kit v.2 User Guide. Additional components used for library preparation include the Chromium Single Cell 3′ Library and Gel Bead Kit v.2 (PN-120237) and the Chromium Single Cell 3′ Chip kit v.2 (PN-120236). Libraries were prepared according to the manufacturer’s instructions using the Chromium Single Cell 3′ Library and Gel Bead Kit v.2 (PN-120237) and Chromium i7 Multiplex Kit (PN-120262). Final libraries were sequenced on the NovaSeq (Illumina, software v1.5). Sequencing parameters were selected according to the Chromium Single Cell v.2 specifications. All libraries were sequenced to a mean read depth of at least 50,000 total aligned reads per cell. Raw sequencing reads were processed using the Cell Ranger v.2.2.0 pipeline from 10X Genomics.

treatment_protocol: For the generation of the GLYR1P496L line, the HDR template (12nM):  CCTCAGATATCCTGCAAGGAAACTTTAAGCTTGATTTCTACCTGAAATACATTCAGAAGGA, was added to the Cas9-RNP complexes, prior to transferring into the nucleofector wells. This was repeated for every Cas9-RNP condition. The nucleofector cassette was placed in the nucleofector instrument (Nucleofector 4D system, Lonza) and cells nucleofector using the preset program DS-138. The nucleofection cassette was brought back to sterile hood and 80μL of Essential 8 medium (E8) (Cat. A1517001, Life Technologies) with 5μM rho kinase (ROCK) inhibitor (Y-27632 2HCl, Cat. S1049, Selleckchem.com) added into each well and incubated for 10 min. at 37°C.  During the incubation time, we removed the hESC-qualified LDEV-free matrigel (Cat. 354277, Corning) from 12 well plates (Corning) pre-coated for 1 hr. at 37°C with 0.5ml per well of matrigel and added 2mL of pre-warmed E8 medium plus 5μM ROCK inhibitor (Y-27632 2HCl) in each well. Then pipetted the nucleofected cells to each of the pre-coted wells with media. After ~3-5 days, wells with surviving clones were expanded to isolate gDNA for screening. A genomic fragment spanning the gRNA target sites was amplified using primers FW 5’ CACCAGTGCACTCTAGCCT 3’ and REV 5’ TGCAGCAAATGAGGTAGGGT 3’ for GLYR1 with Phusion® High-Fidelity PCR Master Mix with GC Buffer (Cat. M0532S, New England BioLabs) and Sanger sequenced (Quintara Biosciences or MCLAB) to identify clones with frame-shift insertions/deletions. Synthego ICE analysis was run to identify clones with highest knock-out efficiency (https://ice.synthego.com/#/), which were subsequently subjected to the colony picking and clone sequencing until monoclonal lines were generated. The top 5 sgRNA predicted off-targets (https://horizondiscovery.com/en/products/tools/crispr-specificity-analysis) were verified to be intact by sanger sequencing in the final monoclonal lines and checked for normal karyotype (Cell Line Genetics).

value: Day 18

tag: processing batch

tag: comparison analysis

value: P496L GLYR1 mutant versus WT hiPSC at day 18  cardiomyocyte stage


title: GLYR1 P496L mutant Day 18 scRNAseq rep 2 [Day18CM_GLYR1_P496L_V2_2]

description: Chromium Single Cell 3′ Chip kit v.16


title: ha-h3x2-wt-HU110-s47


title: MCC-NC

first: Yu

last: Miao

address: Shanghai Jiao Tong University Affiliated Sixth People’s Hospital

data_processing:
Raw data (raw reads) were processed using Trimmomatic software
The reads containing ploy-N and the low-quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference genome using hisat2
Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) of each gene was calculated using Cufflinks, and the read counts of each gene were obtained by HTSeqcount
Genome_build: GRCm38
Supplementary_files_format_and_content: xls files include FPKM values for each Sample

source_name: primary mouse chondrocyte

growth_protocol: The cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM; HyClone) supplemented with 10% FBS (Gibco) and 1% penicillin/streptomycin cocktail and maintained in a humidified incubator containing 5% CO2 at 37 °C.

extract_protocol:
Total RNA from  MCCs were extracted using EZ-press RNA Purification Kit (EZBioscience) in line with the user manual and quantified on a NanoDrop 2000 (Thermo, Waltham, USA).
RNA libraries were prepared for sequencing using VAHTS Stranded mRNA-seq Library Prep Kit for Illumina V2 (Vazyme, Cat#NR612-02) according to the manufacturer’s instructions.

treatment_protocol: treated with lentivirus

tag: cell type

value: primary chondrocyte

value: shNC


title: HN mice, M4

institute: 四川大学华西临床医学院肾内科

value: Hyperuricemic Nephropathy (HN)

tag: treatment

value: untreated


title: ha-h3x2-wt-HU090-s47

extract_protocol:
ChIP was carried out as detailed in Gutin et all, Cell reports 2019, with following modifications. Cell pellets (each from 50 ml of cultures at OD600 0.4, 20 ODs total) were thawed on ice and washed in 10 ml 1M sorbitol. After complete liquid removal, pellets were resuspended in 600 ul RIPA buffer (10 mM Tris pH 8.0, 140 mM NaCl, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, EDTA-free protease inhibitor cocktail) and transferred to chilled LoBind Eppendorf microcentrifuge tubes containing ~500 ul of 0.5 mm zirconium oxide beads (Next Advance, ZrOB05). Cells were processed for 3 cycles in a Bullet Blender 24 (Next Advance) at level 8 for 1 min, with 1 minute on ice between cycles. Debris and lysate were transferred by piercing a hole in the bottom of the tube, placing a clean chilled tube under and centrifuging at 600xg for 5 seconds at 4C. The upper tube with the Zirconium beads was discarded and the lysate was hard spun at 17,000xg for 10 minutes at 4C. The supernatant containing cleaved solubilized 8xmyc tags was discarded, and the pellet was thoroughly resuspended in 100 ul NP buffer (10 mM Tris pH 7.4, 1 M sorbitol, 50 mM NaCl, 5 mM MgCl2, 1 mM CaCl2, and 0.075% NP-40, freshly supplemented with 1 mM β-mercaptoethanol, 500 μM spermidine, and EDTA-free protease inhibitor cocktail), and SLIM-ChIP protocol was carried continued as in Gutin et al.  SLIM-Chip, as per Gutin et al, Cell Reports 2019
SLIM-Chip, as per Gutin et al, Cell Reports 2019


title: GLYR1 P496L mutant Day 18 scRNAseq rep 1 [Day18CM_GLYR1_P496L]

description: Chromium Single Cell 3′ Chip kit v.15


title: ha-h3x2-wt-HU070-s47


title: WT Day 18 scRNAseq rep 3 [Day18CM_WT_V2_1]

description: Chromium Single Cell 3′ Chip kit v.14

source_name: WT hiPSC cardiomyocyte differentiation day 18


title: Tbet-KO Treg-2

city: Charleston

first: Sophie

last: Paczesny

state: South Carolina

address: 86 Jonathan Lucas Street

department: Microbiology & Immunology

institute: Medical University of South Carolina

description: Tbet-KOTreg from malignant bone marrow

data_processing:
QC of the raw sequence data with FASTQC
no trimming required
The sequence reads were mapped to the designated reference geneome using STAR (Spliced Transcripts Alignment to a Reference) (Dobin et al. 2012)
To evaluate the quality of the RNA-seq data, number of reads that fall into different annotated regions (exonic, intronic, splicing junction, intergenic, promoter, UTR, etc.) of the reference genes were determined with bamUtils  (Breese and Liu 2013).
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample; tab-delimited text files include FPKM values for each Sample

source_name: Regulatory T cell

growth_protocol: On Day 14 post leukemic cells challenge, Tregs were sorted from the nonmaligant and malignant bone marrow niches.

extract_protocol:
Lysates were clarified from sonicated nuclei and total RNA were isolated with PureLinkTM RNA Micro Kit (Cat.no. 12183-016)
KAPA Hyperprep Kit, plus QIAseq FastSelect rRNA Removal Kit.
bulk RNA-sequencing

treatment_protocol: Purified Tregs were directly subjected to the total RNA extraction.

tag: tumor stage

value: Tumor Loaded

tag: tissue

value: Mus Bone Marrow

value: Tbet-KO


title: glyr1Ab7_cpc.1 ChIPseq rep 1

extract_protocol:
For ChIPseq experiments, CPs (30×106 for cTFs and 10×106 for GLYR1 and histone marks) were pelleted and suspended in 10ml DMEM and cross-linked in 1% Formaldehyde solution (Cat. 28906, Thermo Fisher Scientific) by rocking in room temperature for 10 min. Then glycine (final concentration 0.125M) was added to quench the cross-link for 5 min. Samples were centrifuged at 1000 rcf for 5 min. at 4°C. Cells were washed with 10ml of cold 1x PBS supplemented with proteinase inhibitors and phosphatase inhibitors (Cat. 4693132001 Roche and Cat. 4906837001 Sigma-Aldrich) and the pellets were snap frozen in liquid nitrogen. All samples were stored at −80°C until use. When ready, cell pellets were incubated in cell lysis buffer (20 mM Tris-HCl, pH 8, 85 mM KCl, 0.5% NP-40, protease/phosphatase inhibitors) for 10 min. on a rotator at 4°C. Nuclei were isolated by centrifugation (2,500 x g, 5 min., 4°C), resuspended in nuclear lysis buffer (50 mM Tris-HCl, pH 8, 10 mM EDTA, pH 8, 1% SDS, protease/phosphatase inhibitors) and incubated on a rotator for 30 min. at 4°C. Chromatin was sheared using a Covaris S2 sonicator (Covaris Inc) for 15 min. (60 s cycles, 5% duty cycle, 200 cycles/burst, intensity = 6) until DNA was in the 200–700 base pair range. Chromatin was diluted 3-fold in ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2mMEDTA, 16.7mMTris-HCl, pH 8, 167 mM NaCl, protease/phosphatase inhibitors) and incubated with the corresponding primary antibody at 4°C overnight under rotation. Antibody-protein complexes were immunoprecipitated using 50μl of Dynabeads™ Protein A/Protein G (Cat. 10015D, Invitrogen) per sample at 4°C for 2 h under rotation. After incubation, beads were washed five times (2 min./wash under rotation) with cold RIPA buffer [50 mM HEPES-KOH, pH 7.5, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-deoxycholate], followed by one wash in cold final wash buffer [1xTE, 50 mM NaCl]. Immunoprecipitated chromatin was eluted at 65°C with agitation for 30 min. in elution buffer [50mMTris-HCl pH 8.0, 10mMEDTA, 1% SDS]. High-salt buffer [250mM Tris-HCl, pH 7.5, 32.5 mM EDTA, pH 8, 1.25M NaCl] and Proteinase K (Cat. P8107s, New England Biolabs Inc (NEB)) were added and crosslinks were reversed overnight at 65°C. Samples were treated with RNase A, and DNA was purified with AMPure XP beads (Cat. A63881, Beckman Coulter). Primary antibodies used for ChIP were: GATA4 (Cat. sc-1237 X, Santa Cruz), TBX5 (Cat. sc-17866 X, Santa Cruz), H3K36me3 (Cat. ab9050, Abcam), GLYR1 (anti-serum 7; provided by James T. Kadonaga’s laboratory), NKX2-5 (Cat. sc-8697 X, Santa Cruz), MEIS1 (Cat. ab19867, Abcam).
Fragmented ChIP and input DNA were end-repaired, 5’-phosphorylated and dA-tailed with NEBNext Ultra II DNA Library Prep Kit for Illumina (Cat. E7645, New England BioLabs). Samples were ligated to adaptor oligos for multiplex sequencing (Cat. E7335, New England BioLabs), PCR amplified, and sequenced on an Illumina NextSeq 500 at the Gladstone Institutes.

value: hiPSC cardiomyocyte

value: wild type

value: Day 6

value: ChIPseq

tag: chip antibody

value: GLYR1 anti-sera 7

tag: chip antibody vendor

value: James T. Kadonaga Laboratory

tag: chip antibody cat. #

tag: chip antibody lot/batch #


title: ha-h3x2-wt-HU040-s47

tag: genotype

value: MATa his3delta1 leu2delta0 LYS2 met15delta0 ura3delta0 HTB2-GGS-TEV  HHT1-GGS-HA-Fast-MYC HHT2-GGS-HA-Fast-MYC, bar1

value: ha

value: wt


title: bulk ATAC-seq data on sorted NK cells from spleen of ATAC mouse replicate 2

description:
ATAC_counts.csv
Spl_cNK_rep2

source_name: Mouse (ATAC-seq) rep 2

value: Spleen

value: S1pr5eGFP+ NK cells

tag: cell population

value: NK cell phenotype


title: bulk ATAC-seq data on sorted NK cells from spleen of ATAC mouse replicate 1

description:
ATAC_counts.csv
Spl_cNK_rep1

source_name: Mouse (ATAC-seq) rep 1


title: bulk ATAC-seq data on sorted ILC1 cells from salivary gland of ATAC mouse replicate 1

description:
ATAC_counts.csv
SG_ILC1_rep1

value: Salivary gland

value: GzmC+GzmcFM+ ILC1 cells

value: ILC1 phenotype


title: WT Day 18 scRNAseq rep 2 [Day18CM_GLYR1_P496L_V2_1]

description: Chromium Single Cell 3′ Chip kit v.13

tag: cardiomyocyte differentiation day

value: Day 18

value: P496L GLYR1 mutant versus WT hiPSC at day 18  cardiomyocyte stage


title: Tbet-KO Treg-3

description: Tbet-KOTreg from malignant bone marrow

tag: strain

value: Tumor Loaded

value: Mus Bone Marrow

value: Tbet-KO


title: bulk ATAC-seq data on sorted ILC1 cells from liver of ATAC mouse replicate 2

description:
ATAC_counts.csv
Liv_ILC1_rep2

value: Liver


title: Tbet-KO Treg-1

description: Tbet-KOTreg from malignant bone marrow


title: MCC-shGpx4

institute: Shanghai Jiao Tong University Affiliated Sixth People’s Hospital

value: primary chondrocyte

value: GPX4 knockdown


title: ha-h3x2-wt-HU015-s47

source_name: Sensor-carrying cells

value: MATa his3delta1 leu2delta0 LYS2 met15delta0 ura3delta0 HTB2-GGS-TEV  HHT1-GGS-HA-Fast-MYC HHT2-GGS-HA-Fast-MYC, bar1

tag: sensor

tag: antibody


title: ha-h3x2-wt-HU030-s47

value: ha

tag: growth condition


title: GLYR1 P496L mutant Day 6 scRNAseq rep 3 [P4_D6CPCSI-GA-G4]

description: Chromium Single Cell 3′ Chip kit v.11

source_name: GLYR1 P496L mutant hiPSC cardiomyocyte differentiation day 6

value: Day 6

tag: processing batch

value: P496L GLYR1 mutant versus WT hiPSC at day 6 cardiac progenitor stage


title: WT Day 18 scRNAseq rep 1 [Day18CM_WT]

description: Chromium Single Cell 3′ Chip kit v.12

tag: comparison analysis


title: GLYR1 P496L mutant Day 6 scRNAseq rep 2 [Day6CPC_GLYR1_P496L_V3]

description: Chromium Single Cell 3′ Chip kit v.10


title: bulk ATAC-seq data on sorted ILC1 cells from salivary gland of ATAC mouse replicate 2

description:
ATAC_counts.csv
SG_ILC1_rep2

tag: cell type


title: glyr1Ab7_cpc.2 ChIPseq rep 2

source_name: WT hiPSC cardiomyocyte differentiation day 6 (cardiac progenitor stage)

value: hiPSC cardiomyocyte

tag: genotype/variation

value: wild type

tag: type of experiment

value: ChIPseq

value: GLYR1 anti-sera 7

value: James T. Kadonaga Laboratory


title: ha-h3x2-wt-HU050-s47

value: wt


title: GLYR1 P496L mutant Day 6 scRNAseq rep 1 [Day6CPC_GLYR1_P496L]

description: Chromium Single Cell 3′ Chip kit v.9


title: ha-h3x2-wt-alpha-s47

value: alpha


title: ST2-KO Treg-3

description: ST2-KO Treg from malignant bone marrow

tag: tumor stage

value: Tumor Loaded

tag: tissue


title: WT Day 6 scRNAseq rep 3 [Day6CPC_WT_V3]

description: Chromium Single Cell 3′ Chip kit v.8

source_name: WT hiPSC cardiomyocyte differentiation day 6


title: WT Treg-3

description: WT Treg from malignant bone marrow

value: Mus Bone Marrow

value: WT


title: bulk ATAC-seq data on sorted NK cells from liver of ATAC mouse replicate 2

description:
ATAC_counts.csv
Liv_cNK_rep2

value: Liver

value: S1pr5eGFP+ NK cells

value: NK cell phenotype


title: bulk ATAC-seq data on sorted NK cells from liver of ATAC mouse replicate 1

description:
ATAC_counts.csv
Liv_cNK_rep1


title: WT Treg-2

description: WT Treg from malignant bone marrow


title: ST2-KO Treg-2

description: ST2-KO Treg from malignant bone marrow


title: WT Day 6 scRNAseq rep 2 [WT_D6CPCSI-GA-G3]

description: Chromium Single Cell 3′ Chip kit v.7


title: No Tumor-3

description: WT Treg from No tumor bone marrow

value: No Tumor


title: SD70-2

city: Wuhan

first: hua

middle: xiao

last: jie

state: Hubei

address: Xinhua Road

department: Tongji Medical College

institute: Huazhong University of Science and Technology

data_processing:
The RNA integrity was verified using Agilent 2100 Bioanalyzer (Agilent Technologies).
Paired-end libraries sequencing20 with Illumina HiSeq2500 were prepared with the mRNA-seq sample prep kit (Illumina) according to the manufacturer’s specifications.
Illumina data analysis pipeline was then used for sequence analysis. All samples were allocated to lanes and processed in blinded fashion to keep bias to a minimum
Genome_build: mm8
Supplementary_files_format_and_content: Analysis description: Calculate the expression read count using the Stringtie-1.3.3b software. Then, the gene and transcript FPKM were calculated. In this process we simply filtered the expression:1）Remove genes or transcripts with length less than 100 bp. ;2）If the FPKM of a gene or transcript is less than 0.0001, it is considered to be expressed as 0. Remove genes with a table of 0 in all samples.

source_name: Mouse lung adenocarcinoma cells

growth_protocol: All the cells were cultured in DMEM medium containing 10% FBS and 100 μg/mL penicillin and streptomycin in 5% CO2 at 37℃.

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2 mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

treatment_protocol: Lewis cells were treated with DMSO or SD70 for 24 hours.

tag: cell lines

value: Lewis

tag: treatment


title: WT Day 6 scRNAseq rep 1 [Day6CPC_WT]

description: Chromium Single Cell 3′ Chip kit v.6

value: Day 6


title: ST2-KO Treg-1

description: ST2-KO Treg from malignant bone marrow


title: ha-h3x2-wt-HU150-s43

value: MATa his3delta1 leu2delta0 LYS2 met15delta0 ura3delta0 HTB2-GGS-TEV  HHT1-GGS-HA-Fast-MYC HHT2-GGS-HA-Fast-MYC, bar1

value: ha


title: GLYR1 knockout mutant hiPSC scRNAseq [hiPSC_GLYR1_KO_11A]

description: Chromium Single Cell 3′ Chip kit v.5

source_name: GLYR1 P496L mutant hiPSC cardiomyocyte differentiation day 0

treatment_protocol: To generate the GLYR1 knockout lines as well as the GLYR1P496L hiPSC lines, WTC11 hiPSCs were dissociated in accutase (Cat. 07920, Stem Cell Technologies), and 250.000 cells were aliquoted per condition and nucleofected with Cas9-ribonucleoprotein complexes (Cas9-RNP) following the Primary Cell Nucleofection P3 Kit manufacturer’s instructions (V4XP-3960, Lonza). For Cas9-RNP complex preparation 180pmol of the synthetic modified sgRNA (Synthego) to target the GLYR1 locus at chr16:4811270-4811248 (ATGTATTTCAGGTAGAAATCAGG) and 20pmol of SpCas9-NLS purified protein (QB3 Macrolab, UCB) were diluted into 20μl of nucleofection buffer prepared as indicated in Primary Cell Nucleofection P3 Kit, mixed and incubated at room temperature for 10 min. After 10 min. of incubation, the aliquoted 250.000 cells were resuspended in 20μL nucleofection buffer containing the corresponding Cas9-RNP complexes, mixed 5-6 times and then transferred to the bottom of a nucleofector well (nucleofector 96 well cassette from the Primary Cell Nucleofection P3 Kit).

value: Day 0:hiPSC

value: GLYR1 knockout versus WT hiPSC at day0 hIPSC stage


title: ha-h3x2-wt-HU130-s43


title: No Tumor-2

description: WT Treg from No tumor bone marrow


title: SD70-3


title: bulk ATAC-seq data on sorted ILC1 cells from liver of ATAC mouse replicate 1

description:
ATAC_counts.csv
Liv_ILC1_rep1

value: GzmC+GzmcFM+ ILC1 cells

value: ILC1 phenotype


title: WT Treg-1

description: WT Treg from malignant bone marrow


title: WT hiPSC scRNAseq [hiPSC_WT]

description: Chromium Single Cell 3′ Chip kit v.4

source_name: WT hiPSC cardiomyocyte differentiation day 0


title: ha-h3x2-wt-HU110-s43

value: wt


title: No Tumor-1

description: WT Treg from No tumor bone marrow


title: DMSO-3

value: DMSO


title: DMSO-2


title: ha-h3x2-wt-async-s47

value: async


title: ha-h3x2-wt-HU180-s43


title: WT hiPSC scRNAseq [WT_iPSCSI-GA-G1]

description: Chromium Single Cell 3′ Chip kit v.2

value: P496L GLYR1 mutant versus WT hiPSC at day0 hIPSC stage


title: ApoE-/- PX-478 2

city: Atlanta

first: Hanjoong

last: Jo

state: GA

address: 1760 Haygood Drive NE

department: Biomedical Engineering

institute: Georgia Tech & Emory University

data_processing:
Reads were aligned to mm10, counted, filtered, and normalized using R packages Rsubread and edgeR as described in Lun et al, Statistical Genomics pp 391-416, 2016
Alignment was performed with the align command and the mapped reads were counted by using the featureCounts function with the set of BAM files as the input.
Genes with low counts across libraries were filtered using the keep function. Genes with count-per-million > 0.5 in at least 2 samples were retained.
The calcNormFactors function was utilized to generate factors for normalization
The makeContrasts and qlmQLFTest functions were used to genearte a porcessed data matrix and test for significant differential expression in each gene.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Liver

extract_protocol:
Following sacrifice, livers were removed, flash frozen using liquid nitrogen, and RNA was harvested using Qiazol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: All ApoE-/- mice were fed Western diet for 3 months. Saline or PX-478 (40 mg/kg) were injected intraperitoneally bi-weekly thorughout the course of the study.

value: liver

tag: age

value: 4 months

value: ApoE-/-

value: PX-478 (40mg/kg) IP bi-weekly + Western Diet 3 months


title: ha-h3x2-wt-HU070-s43

tag: genotype


title: ha-h3x2-wt-HU090-s43


title: ha-h3x2-wt-HU060-s43


title: M0 (HBV+)_3

city: LA

first: Yumei

last: Li

state: CALIFORNIA

address: HMR404, 2011 Zonal avenue

department: MMI

institute: USC

data_processing:
Raw sequencing reads were trimmed based on the quality score (Phred QC>=20, min read length=25 nt)
Trimmed reads were mapped to mouse genome build hg38 using Star 2.73a (Dobin et al. 2013) with default parameter settings and Gencode 34 human transcriptome annotation (Mudge JM and Harrow J 2015)
Gencode 34 was then used to quantify the aligned reads to genes using Partek E/M method
Gene level read counts in all samples were normalized using Upper Quartile normalization (Bullard et al. 2010) and subjected to differential expression analysis using Partek Gene Specific Analysis method (genes with fewer than 10 aligned reads in any sample among a data set were excluded)
Genome_build: hg38
Supplementary_files_format_and_content: raw gene counts in tab deliminated txt file with gene on rows and sample on columns.

source_name: MΦ(HBV+)

growth_protocol: HepAD38 cell seeded at a density of 0.5x10^6 cells per well in a 6-well plate were incubated with 2 ml DMEM containing 10% FBS with or without tetracycline for 18 hours. Cells were rinsed once with PBS and incubated with fresh medium. Subsequently, 2x10^6 of THP-1-derived macrophages were seeded in each insert of the 6-well plate for co-culturing with HepAD38 cells in RPMI. The incubation media were replaced with the 1:1 mixture of DMEM and RPMI on a daily basis for 4 days.

extract_protocol:
Total cellular RNA was isolated from MΦ (M0), MΦ (HBV-), and MΦ (HBV+) cells using AllPrep DNA/RNA Mini Kit (QIAGEN, #80204).
NEBNext Ultra™ II RNA Library Prep Kit for Illumina was used for the preparation of cDNAs.

treatment_protocol: Three groups of cells were studied. They include THP-1 derived macrophages without co-culturing (M0), M0 cells co-cultured with HepAD38 in the presenc e of 0.5 μg/mL tetracycline (HBV-), and M0 cells co-cultured with HepAD38 without tetracycline (HBV+).

value: Peripheral blood

value: THP-1 derived macrophage

value: Co-culturing with HepAD38


title: SD70-1

value: Lewis


title: ApoE-/- PX-478 1


title: M0 (HBV+)_2


title: ApoE-/- Saline 4

value: Saline IP bi-weekly + Western Diet 3 months


title: ApoE-/- Saline 3


title: GLYR1 P496L mutant hiPSC scRNAseq [P4_iPSCSI-GA-G2]

city: San Francisco

first: Deepak

last: Srivastava

address: 1650 Owens St

institute: J David Gladstone Institutes

description: Chromium Single Cell 3′ Chip kit v.3

value: Day 0:hiPSC


title: ha-h3x2-wt-HU040-s43

city: Rehovot

first: Naama

last: Barkai

address: Herzl St 234

institute: Weizmann Institute

value: MATa his3delta1 leu2delta0 LYS2 met15delta0 ura3delta0 HTB2-GGS-TEV  HHT1-GGS-HA-Fast-MYC HHT2-GGS-HA-Fast-MYC, bar1

value: ha


title: VIP-U8

city: Toronto

first: Etienne

last: Sibille

state: Ontario

address: RM,133, 250 college street

department: Neuroscience of Aging and Depression

institute: Center for Addiction and Mental Health

data_processing:
Sequencing performed on Illumina HiSeq 2500 platform. Run mode: High Output (2x125 cycles), 8 lanes. Yield (GBp): 286, Q30: Read 1=90.5%, Read 2=82.9%
Reads were trimmed 9bp on 5' and 21bp on 3' end based on Phred score distribution, and Read 2 was excluded from genomic mapping. Reads were mapped to the mouse genome (build GRCm38-mm10) using HiSat2.
BAM files were processed using SAMTOOLS v1.3
Counts were summarized at the gene level (i.e. meta-analysis of all transcript variants). Count normalization and differential expression was performed using DESeq2 R package. Co-expression analyses were performed using WGCNA R package.
Genome_build: GRCm38-mm10
Supplementary_files_format_and_content: Comma seperated values files include Ensembl gene identifiers (ENSMUSG), HUGO gene symbols, and DESeq2-normalized counts

source_name: Vasoactive intestinal peptide-expressing interneurons isolated from medial prefrontal cortex

extract_protocol:
Mice were sacrificed by cervical dislocation and decapitation. Brains were removed and snap-frozen at -80C. Samples of 130 cells of either pyramidal, somatostatin, parvalbumin, or vasoactive-intestinal-peptide types were collected from 12uM coronal sections of the medial prefronal cortex using RNAscope to visualize (using cell-type specific cDNA probes) and laser-capture microdissection to extract. Extracted cells were collected in PicoPure extraction buffer, incubated at +40C for 30 minutes and frozen on dry ice and stored at -80C until library preparation.
Libraries were prepared using the SMARTer Stranded Total RNA-Seq Pico Input Kit (Clontech) according to the manufacturer's directions.

treatment_protocol: All experiments were performed with male C57Bl/6J mice exposed to UCMS (n=10) or control housing (n=10). Controls were group-housed with littermates whereas UCMS-exposed mice were single-housed. All mice were provided with food and water ad libitum. UCMS consisted of a variable sequence of mild social-environmental stressors occurring 1-4 times daily for 5 weeks , as previously described. Stressors included forced bath, light cycle disruptions, predator odor, wet bedding, tilted cage, and restraint. Behavioural testing occurred during week 4 and 5, during which UCMS was continued with 1-2 daily stressors to attenuate their acute effects on test outcomes. Behavioural tests including elevated plus maze (EPM), open-field (OF), novelty-suppressed feeding (NSF), novelty-induced hypophagia (NIH), sucrose preference test (SPT), phenotyper test (PT), and a general locomotor activity test were used to assess anxiety-like and depressive-like behaviours.

tag: experimental group

value: Control

tag: cell-type

value: VIP neurons

value: brain


title: VIP-U9

tag: strain


title: M0 (HBV+)_1


title: VIP-U7


title: ApoE-/- Saline 2


title: ha-h3x2-wt-HU050-s43

tag: sensor

value: wt


title: ha-h3x2-wt-HU030-s43

tag: antibody


title: M0 (HBV-)_2

source_name: MΦ(HBV-)

value: Co-culturing with HepAD38+Tetracycline


title: ApoE-/- Saline 1

value: liver


title: M0 (HBV-)_3


title: VIP-U610

value: UCMS (5-weeks)


title: DMSO-1

value: DMSO


title: M0 (HBV-)_1


title: VIP-U607


title: ha-h3x2-wt-alpha-s43

tag: growth condition

value: alpha


title: M0 (Mock)_3

value: Peripheral blood


title: VIP-U608


title: ha-h3x2-vps75-HU180-s47

value: MATa his3delta1 leu2delta0 LYS2 met15delta0 ura3delta0 HTB2-TEV, HHT1-HA-TEVsite-MYC, HHT2-HA-TEVsite-MYC, bar1, vps75::HYG


title: M0 (Mock)_2

value: THP-1 derived macrophage


title: ha-h3x2-vps75-HU150-s47


title: ha-h3x2-vps75-HU090-s47


title: VIP-U605


title: M0 (Mock)_1


title: VIP-U604


title: VIP-U602


title: ha-h3x2-vps75-HU130-s47