title: mouse - EP48H_4

city: Kaifeng

first: Haigang

last: wu

state: Henan province

address: dongjing Road

institute: Henan University

data_processing:
Illumina Casava1.7 software used for basecalling
Sequenced reads were trimed for adaptor sequence, and masked for low-complexity or low quality sequence, then mapped to the mm8 hole genome using bowtie v0.12.2 with parameters set as defaults.
Reads for kilobased of exon per megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Assembly: mm8

source_name: BALB/c mouse brain tissue

growth_protocol: The mouse was cultured in the SPF level environment

extract_protocol:
Brain tissue samples were lyzed and harvested using Trizol reagent. THe purification of RNA was performed using protocol provided by extracting kits (Total RNA Extraction Kit, Cat. R1200, Solarbio life science, China).
RNA library were prepared for sequencnig using standard illumina protocols

treatment_protocol: The mouse was received the 5-ALA injection (dosage 20 mg/kg) and further circulating in blood for 30 min. Then, the mouse received the 635 nm laser radiation (doage 20 J/cm, respectively) and continued to be cultured for 1.5,12 h and 48 h. The brain tissues of mouse brain was obtained after downern injection and prefusion using 0.9% NaCl solution.

value: BALB/c mouse brain tissue

tag: strain

value: 48 h post treated with PDT with 20 J/cm2


title: C2

status: Public on Apr 22 2022

type: SRA

city: Beijing

first: Yingmei

last: Feng

address: No. 8 Xi-Tou-Tiao

country: China

institute: Beijing Youan Hospital, Capital Medical University

description: Raw file not provided due to patient privacy concerns

library_source: transcriptomic

data_processing:
Raw data of sequencing result of all patients were processed using Cell Ranger (v3.1.0), taking Human GRCh38 annotation file provided by 10X Genomics as reference.
To reduce chemistry associated batch effect, data was then processed using ‘cellranger aggr’.
Cell quality control and gene quality control was subsequently performed in Seurat R package.
Genome_build: GRCh38
Supplementary_files_format_and_content: Text file containes single-cell expression matrix of each sample. Each column represents one single cell, each row represents a gene symbol, value in matrix is corresponding raw count.

molecule: total RNA

organism: Homo sapiens

source_name: PBMC

extract_protocol:
PBMCs were isolated from EDTA venous blood samples (20 ml per patients) by Ficoll-Hypaque density solution following a standard density gradient centrifugation.
Cells were proceeded GEMs preparation and reverse transcription to barcoded scRNA-seq libraries according to the instruction provided by 10X Genomics.

tag: tissue

value: blood

tag: cell type

value: PBMC

tag: disease state

value: COVID-19 infection

tag: disease stage

value: critical

tag: disease outcome

value: death


title: pxb_inf2

city: Foster City

first: Ricardo

last: Ramirez

state: CA

address: 333 Lakeside Drive

country: USA

institute: Gilead Sciences

description: Human liver-chimeric uPA/SCID mice

data_processing:
fastpv0.19.4 was used to removed low quality reads, homopolymers, and adaapter sequences
trimmed reads were aligned to a combined reference sequence of hg38 and mm10 major contigs using STAR version 2.7.3a
read counts were generated using featureCounts with option --primary only for annotations related to human genome/transcript alignments
Assembly: hg38 and mm10
Supplementary files format and content: gene count matrix

organism: Mus musculus

source_name: liver

extract_protocol:
Qiagen RNeasy
Illumina TruSeq Stranded mRNA sample preparation kit (Illumina # RS-122-2103).

value: liver

tag: model

value: uPA/SCID

tag: cohort

value: HBV+


title: pxb_inf4

description: Human liver-chimeric uPA/SCID mice


title: 10_16h_SKMEL28_siDUSP4_Tram_1

city: Basel

first: Daniel

last: Marbach

address: Grenzacherstrasse 124

department: pRED Pharmaceutical Sciences

country: Switzerland

institute: F. Hoffmann - La Roche Ltd

data_processing:
Base calling was performed with BCL to FASTQ file converter bcl2fastq:2.19 from Illumina
Paired-end RNASeq reads were mapped to the human genome (hg38) with STAR aligner (v2.5.2a) using default mapping parameters
Numbers of mapped reads for all RefSeq transcript variants of a gene (counts) were combined into a single value by using SAMTOOLS software
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: polyA RNA

source_name: melanoma cells

extract_protocol:
RNA was extracted using the Qiagen RNeasy Mini Kit, following manufacturer’s instructions except that lysates were loaded on a QIAshredder column before loading on a spin column. Sequencing libraries were generated from 100ng input RNA using the Illumina TruSeq Stranded mRNA LT Sample Preparation Kit as per manufacturer’s instruction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 3x105 cells were seeded in a 6 well plate. In parallel, either 0.25nM Trametinib or vehicle (DMSO) were added in both siDUSP4 and siNT transfected cells. After 16 hours, cells were harvested and frozen at -80 oC.

tag: cell line

tag: tissue source

value: melanoma

tag: genotype

value: BRAF V600E

tag: treatment

value: siDUSP4+ Trametinib


title: mouse - EP48H_1

department: School of Life Sciences


title: 12_16h_SKMEL28_siDUSP4_Tram_3


title: TRPV1+ neurons CFA  contralateral biological replicate 3

type: RNA

city: Calgary

first: Christophe

last: Altier

address: 3300 Hospital Drive NW

country: Canada

institute: University of Calgary

description: TRPV1-eGFP+ neurons CFA D3 contralateral biological replicate 3

hyb_protocol: Samples were prepared using Affymetrix WT Pico Kit(6C).  • Hybridize 16 hours at 45° • Fluidics washing is FS450_0002

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing: Expression console

label: Biotin

source_name: TRPV1-pHluorin, DRG, TRPV1+ sorted neurons

label_protocol: Biotin Allonamide Triphosphate

extract_protocol: After FACS sorting, RNA was extracted separately from GFP positive and GFP negative cells using a RNeasy Mini kit (Qiagen)

treatment_protocol: DRG extracted at 3 days from CFA-treated TRPV1-pHluorin mice

value: DRG contralateral

tag: cells

value: TRPV1+ sorted cells

value: Complete Freund Adjuvant

tag: time

value: Day 3


title: pxb_inf5

description: Human liver-chimeric uPA/SCID mice


title: C3


title: S8

value: severe

value: recovery


title: TRPV1+ neurons CFA ipsilateral biological replicate 3

description: TRPV1-eGFP+ neurons CFA D3 ipsilateral biological replicate 3

value: DRG ipsilateral


title: C1

value: blood

value: PBMC


title: TRPV1+ neurons CFA  contralateral biological replicate 2

description: TRPV1-eGFP+ neurons CFA D3  contralateral biological replicate 2


title: S11

value: COVID-19 infection


title: 4_16h_SKMEL28_SCR_Tram_1

value: siNT+ Trametinib


title: TRPV1+ neurons CFA ipsilateral biological replicate 2

description: TRPV1-eGFP+ neurons CFA D3 ipsilateral biological replicate 2


title: mouse - EP48H_3

value: BALB/c mouse brain tissue

value: 48 h post treated with PDT with 20 J/cm2


title: S12

value: death


title: mouse - EP12H_1

value: 12 h post treated with PDT with 20 J/cm2


title: 6_16h_SKMEL28_SCR_Tram_3

value: melanoma

value: BRAF V600E


title: S10


title: TRPV1+ neurons CFA  contralateral biological replicate 1

description: TRPV1-eGFP+ neurons CFA D3 contralateral biological replicate 1

value: DRG contralateral


title: TRPV1+ neurons CFA ipsilateral biological replicate 1

description: TRPV1-eGFP+ neurons CFA D3 ipsilateral biological replicate 1

value: TRPV1+ sorted cells


title: 7_16h_SKMEL28_siDUSP4_1

value: siDUSP4+ DMSO


title: 6 KGN PS100uM(24h)

city: Kurashiki

first: Takayuki

last: Tsujioka

address: Matsushima 577

department: Department of Laboratory medicine

country: Japan

institute: Kawasaki Medical School

description: Gene expression data from KGN treated with 100 nM of PS for 24 hr

hyb_protocol: The fragmentation, the labeling and the hybridization of cDNA were treated with GeneChip Hybridization, Wash, and Stain Kit (Affymetrix).

scan_protocol: Chips were scanned with a GeneChip Scanner 3000 7G System (Affymetrix).

data_processing: Data acquisition and normalization (RMA) were used Affymetrix® Expression Console™ Software.

label: biotin

source_name: 6KGN treated with PS

label_protocol: Total RNA converted to cDNA and amplified with GeneChip WT Terminal Labeling and Controls Kit (Affymetrix, Santa Clara, CA, USA).

growth_protocol: Granulosa cell tumor (GCT) cell lines, KGN was maintained in DMEM/Ham’s F12 medium supplemented with 10% fetal bovine serum.

extract_protocol: Total RNA was extracted with RNeasy Mini Kit (Qiagen,Germantown, MD, USA).

treatment_protocol: We cultured KGN cells with or without 100 nM of PS for 24 hr.

value: granulosa cell tumor

value: KGN

value: panobinostat (PS)


title: S6

value: severe

value: recovery


title: 2_16h_SKMEL28_SCR_2

value: siNT+ DMSO


title: mouse - EP12H_3


title: mouse - EP15H_3

value: 1.5 h post treated with PDT with 20 J/cm2


title: S9

value: blood

value: PBMC

value: COVID-19 infection


title: mouse - EP15H_2

value: BALB/c mouse brain tissue


title: 8_16h_SKMEL28_siDUSP4_2


title: 5_16h_SKMEL28_SCR_Tram_2

value: siNT+ Trametinib


title: mouse - EP15H_1


title: mouse - EP12H_2

value: 12 h post treated with PDT with 20 J/cm2


title: S7


title: 5 KGN DMSO(24h)

description: Gene expression data from KGN treated with DMSO for 24 hr

source_name: 5KGN treated with DMSO

value: control


title: miR-con-3

city: WUHAN

first: heng

middle: zhi

last: du

address: 1095 Jiefang Dadao, Wuhan City, Hubei Province, China

institute: Wuhan Tongji Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Cutadapt (Version 1.2.1) (Martin M, 2011) was used to remove 3' end joints, at least 10 bp Overlap (AGATCGGAAG), and 20% base error rate was allowed.
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.
Assembly: Ensembl 38.85
Supplementary files format and content: RPKM.xlsx: Excel file includes counts and RPKM values for each Sample.

source_name: AC16 cells

growth_protocol: AC16 cells (ScienCell research laboratories, Carlsbad, CA) were from a single fetal donor, not pooled, and were maintained in medium (ScienCell research laboratories, Cat. #6201), according to the instruction manual. Medium consists of basal medium, foetal bovine serum (FBS), AC16 cells growth supplement, and penicillin/streptomycin solution.

extract_protocol:
RNA was harvested using Trizol reagent following the instructions.
All of our RNA-seq projects used strand specific kits to construct the libraries. By using next-generation sequencing (NGS) technology, paired-end (PE) sequencing of these libraries was performed based on Illumina HiSeq sequencing platform.

tag: transfection

value: miR-con

tag: antibody


title: miR-con-2


title: 1_16h_SKMEL28_SCR_1

value: melanoma

value: BRAF V600E


title: mouse - PBS_4

value: untreated


title: S2


title: 3_16h_SKMEL28_SCR_3


title: S5


title: S1


title: S4


title: 3 KGN DMSO(24h)

source_name: 3KGN treated with DMSO

value: granulosa cell tumor

value: KGN


title: 4 KGN PS100nM(24h)

source_name: 4KGN treated with PS

value: panobinostat (PS)


title: WGBS_LOS_#1

city: Columbia

first: Rocío

middle: Melissa

last: Rivera

state: MO

address: 920 East Campus Drive

department: Division of Animal Sciences

institute: University of Missouri, Columbia

library_source: genomic

data_processing:
Duplicated reads generated during PCR and sequencing were removed from raw sequencing reads using the clumpify function of BBMap (version 38.90). The remaining raw reads were trimmed for adapter sequences and low quality bases using trimmomatic (version 0.39) with parameters ‘ILLUMINACLIP:adapter_seq:2:30:10:1:true LEADING:20 TRAILING:20 AVGQUAL:20 MAXINFO:0:0.5’. Trimmed reads were aligned to the bovine genome using bismark (version 0.23.0) with parameters ‘-X 900 --unmapped --ambiguous --non_bs_mm’. Trimmed reads were also aligned to lambda phage genome to determine bisulfite conversion rates. Samtools (version 1.13) was used to convert, sort, filter, and index bam files. MarkDuplicates function of picard (version 2.25.5) was used to further remove duplicated reads after alignment. Read groups were added for each samples using AddOrReplaceReadGroups function of picard. Variants identified in bull semen genomic sequencing data and variants in bovine acquired from the 1000 bull genome project, namely ARS1.2PlusY_BQSR_v3.vcf.gz, served as known variants to identify genomic variants in WGBS data. Indel realignment was performed using RealignerTargetCreator and IndelRealigner functions of BisSNP (version 1.0.1). Base quality recalibration was carried out using BisulfiteCountCovariates and BisulfiteTableRecalibration functions of BisSNP (version 0.82.2) since these functions are missing in version 1.0.0 and 1.0.1. Parameters used for BisulfiteCountCovariates were ‘-cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -baqGOP 30’. Genomic variants were identified using BisSNP (version 1.0.1) with default setting expect that ‘-bsRate’ was changed to bisulfite conversion rate observed from lambda phage genome alignment for each sample. BisSNP identified variants were filtered by its VCFpostprocess function with parameter ‘-windSizeForSNPfilter 0’. Additionally, genomic variants were identified using BS-SNPer (version 1.0) with parameters ‘-minhetfreq 0.1 --minhomfreq 0.85 --minquali 15 --mincover 5 --maxcover 1000 --minread2 2 --errorate 0.02 --mapvalue 20’. M-bias plots were generated using bismark and the first 3 bases of R1 reads and the first 4 bases of R2 reads showed biased CpG methylation level, thus these bases were excluded from downstream analyses. CpG methylation information were extracted from the bam files using bismark_methylation_extractor function of bismark with parameters ‘-p --ignore 3 --ignore_r2 4 --comprehensive --no_header –gzip --bedGraph --buffer_size 50% --cytosine_report’. Statistical analyses were conducted using R package hummingbird (version 1.2.0) with parameter ‘minCpGs = 10, minLength = 100, maxGap = 300’ to identify differentially methylated regions (DMRs) between LOS and Control groups. DMRs with at least 15% difference in methylation level (both gain and loss of methylation) and at least 2 mean read coverage at CpG sites were reported. The sex chromosomes were not analyzed to circumvent confounding created by X chromosome inactivation associated DNA methylation.
Genome_build: ARS-UCD1.2
Supplementary_files_format_and_content: Read coverage and DNA methylation percentage for CpG sites in BEDGRAPH format.

molecule: genomic DNA

organism: Bos indicus x Bos taurus

source_name: Day 105 fetal skin fibroblast primary cell

growth_protocol: Day 105 Bos taurus indicus (B. t. indicus; Brahman breed) x Bos taurus taurus (B. t. taurus; Angus breed) F1 hybrid fetuses were generated by our laboratory following the protocol previous described (PMID: 23751783) and used as tissue donors. Fetal skins were collected to establish fibroblast primary cell line using protocol adapted from a publication (PMID: 24198123). Fibroblast cells were cultured in bovine embryonic fibroblast medium (89% (v/v) DMEM (Gibco, 11885084), 10% (v/v) fetal bovine serum (Atlanta Biologicalsa, S11150H), and 1% (v/v) Antibiotic-antimycotic (Gibco, 15240062)) at 38.5°C with 5% CO2.

extract_protocol:
Fibroblasts were lysed in lysis buffer (0.05 M Tris-HCl (pH 8.0), 0.1 M EDTA, and 0.5% (w/v) SDS) with proteinase K (Fisher BioReagents, BP1700) at 55°C for four hours. Genomic DNA was extracted with Phenol:Chloroform:Isoamyl Alcohol (SIGMA, P3803) following the manufacturer’s instructions. The concentration of DNA was measured by using a NanoDrop® ND-1000 Spectrophotometer (Thermo Fisher Scientific) and DNA integrity was confirmed by electrophoresis on a 0.7% agarose gel. Genomic DNA samples were stored at -20°C.
This WGBS was conducted by CD Genomics (Shirley, NY, USA). Information on library preparation and sequencing obtained from the company is as follows: For WGBS library preparation, 1 ug of genomic DNA was fragmented by sonication to a mean size of approximately 200-400 bp. Fragmented DNA was end-repaired, 5'-phosphorylated, 3'-dA-tailed and then ligated to methylated adapters. The methylated adapter-ligated DNAs were purified using 0.8× Agencourt AMPure XP magnetic beads and subjected to bisulfite conversion by ZYMO EZ DNA Methylation-Gold Kit (zymo). The converted DNAs were then amplified using 25 μl KAPA HiFi HotStart Uracil+ ReadyMix (2X) and 8-bp index primers with a final concentration of 1 μM each. The constructed WGBS libraries were then analyzed by Agilent 2100 Bioanalyzer and quantified by a Qubit fluorometer with Quant-iT dsDNA HS Assay Kit (Invitrogen), and finally sequenced on Illumina Hiseq X ten sequencer. 0.1-1% lambda DNA were added during the library preparation to monitor bisulfite conversion rate.

treatment_protocol: For bovine fetuses, artificial insemination was used to generate the control group and assisted reproductive technologies (ART) were used to generate the ART group following the protocol previous described (PMID: 23751783). The large offspring syndrome (LOS) group was defined as individuals from the ART group with body weight greater than 97th centile of controls.

tag: conception method

value: Assisted reproductive technology

tag: developmental stage

value: D105 fetus

tag: disease status

value: LOS

value: fibroblast


title: 1 KGN DMSO(24h)

source_name: 1KGN treated with DMSO

tag: tissue


title: M3

value: blood

tag: cell type

value: PBMC

tag: disease state

value: moderate

value: recurrence


title: kshv-miR-K12-1-5p-2

value: kshv-miR-K12-1-5p mimic


title: WGBS_LOS_#4


title: mouse - PBS_2

value: BALB/c mouse brain tissue

tag: strain


title: WGBS_Control_#4

value: Artificial insemination

value: Healthy


title: WGBS_LOS_#2


title: miR-con-1

value: miR-con


title: S3

value: COVID-19 infection

tag: disease stage

value: severe

tag: disease outcome

value: recovery


title: kshv-miR-K12-1-5p-3

tag: cell line


title: 10x_Liver_iNKT_Treated_Rep1

city: Barcelona

first: Pere

last: Santamaria

address: C/Rosselló 149-153

country: Spain

institute: IDIBAPS

description:
Liver iNKT cells from treated NOD.c3c4 mice
10x library
Treat_L3_S3_L001

data_processing:
CellRanger counts
CellRanger aggr
Downstream analysis in  Seurat (normalization, scaling and differential expression analysis)
mm10
One folder containing the aggregated files from CellRanger aggr (3 files: matrix, features and barcodes)

source_name: Liver

extract_protocol:
Partition of cell suspensions into Gel-Bead-In-Emulsions
10X Single-cell mRNA kit

treatment_protocol: Treated samples are obtained from NOD.c3c4 mice that have received intravenously 10 doses of aGalCer/CD1d-NPs.

value: iNKT cells

value: Treated


title: 10x_Liver_iNKT_Treated_Rep2

description:
Liver iNKT cells from treated NOD.c3c4 mice
10x library
Treat_L4_S4_L001


title: WGBS_Control_#3

value: D105 fetus


title: 10x_Liver_iNKT_Untreated_Rep2

description:
Liver iNKT cells from untreated NOD.c3c4 mice
10x library
Con_L2_S2_L001

value: Untreated


title: 2 KGN PS100nM(24h)

source_name: 2KGN treated with PS

value: granulosa cell tumor

value: KGN

value: panobinostat (PS)


title: mouse - PBS_1

value: untreated


title: WGBS_LOS_#3

value: Assisted reproductive technology

value: LOS

value: fibroblast


title: 10x_Liver_iNKT_Untreated_Rep1

description:
Liver iNKT cells from untreated NOD.c3c4 mice
10x library
Con_L1_S1_L001


title: Non-cancer derived breast cell prophylactic [GUMC-533]

city: Cheonan

first: Keunsoo

last: Kang

address: 119 Dandae-ro

country: South Korea

institute: Dankook University

data_processing:
Sequencing quality was checked using FastQC (version 0.11.9; https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Contaminated adaptor and/or row quality portions of sequenced reads were trimmed using Trim Galore (version 0.6.5; https://github.com/FelixKrueger/TrimGalore).
Trimmed reads were aligned to the genome, concatenating the human (hg38) and mouse (mm10) genome sequences, using STAR (version 2.7.9a) (Dobin et al. Bioinformatics 2013).
Batch effect was normalized using RUVSeq (version 1.26.0) with the RUVg method (Risso et al. Nat Biotech. 2014).
Normalized expression levels were estimated by means of transcripts per million (TPM) using RSEM (version 1.3.1) (Li and Dewey, BMC Bioinformatics 2011): TPM_gene_expression_hg38_matrix.txt
Normalized expression levels of mouse genes due to contamination were also estimated by means of TPM using RSEM: TPM_gene_expression_mm10contam_matrix.txt
Genome_build: hg38 + mm10
Supplementary_files_format_and_content: Text file that includes TPM values for each sample

extract_protocol:
Primary cells cultured in CRC were pelleted and total RNA extracted (Rneasy Mini Kit, Qiagen) and quality analyzed (Nanodrop, Bioanalyzer 2100, Agilent Technologies
RNA libraries were prepared for sequencing using the Illumina TruSeq Stranded mRNA Library Preparation Kit (polyA cDNA synthesis

tag: cancer vs. non-cancer derived

value: Non-cancer derived

value: CRC-isolated Breast epithelial cell

tag: brca mutation reported

value: BRCA mutation (non-specified)


title: M2

value: blood

value: PBMC

value: COVID-19 infection

value: moderate


title: KPC-org

city: Shanghai

first: Wei

last: Zuo

state: Shanghai

address: No. 500 Zhennan Road, Putuo District, Shanghai

institute: University

data_processing:
We use FastQC to perform basic statistics on the quality of the raw reads. Generally, cellranger count support FASTQ files from raw base call (BCL) files generated by Illumina sequencers as input file.
Raw reads were demultiplexed and mapped to the reference genome by 10X Genomics Cell Ranger pipeline using default parameters. In brief, for each gene and each cell barcode (filtered by CellRanger), unique molecule identifiers were counted to construct digital expression matrices.
Secondary filtration by Seurat : A gene with expression in more than 3 cells was considered as expressed, and each cell was required to have at least 200 expressed genes. And filter out some of the foreign cells.
Genome_build: GRCh38-1.2.0
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each single cell

source_name: 3D differentiated renel epithelial cells

extract_protocol:
The cell suspension was loaded into Chromium microfluidic chips with 3’ v3 chemistry and barcoded with a 10× Chromium Controller (10X Genomics). RNA from the barcoded cells was subsequently reverse-transcribed.
Sequencing libraries were constructed with reagents from a Chromium Single Cell 3’ v3 reagent kit (10X Genomics) according to the manufacturer’s instructions.

value: renal epithelial cells

value: kidney


title: kshv-miR-K12-1-5p-1

value: kshv-miR-K12-1-5p mimic


title: WGBS_Control_#2

value: Artificial insemination

value: D105 fetus

value: Healthy


title: BMDMs, BP/OL-CM+DMXAA, biol rep 1 [QW_017]

status: Public on Apr 21 2022

city: Boston

first: Qiwei

last: Wang

state: MA

address: 450 Brookline Avenue

institute: Dana-Farber Cancer Institute

data_processing:
Data processing Used the ampliSeqRNA plugin v5.12.0.1 available inside the Ion Torrent suite 5.12 for Ion torrent sequencing platform default settings for all steps
Assembly: WG00278_Reference
Supplementary files format and content: Tab-separated values and matrix file

source_name: bone marrow

growth_protocol: BMDMs were cultured in DMEM growth medium (DMEM + 10% FBS + 100 μg/mL penicillin–streptomycin) supplemented with 10 ng/mL mouse M-CSF.

extract_protocol:
Total RNA was extracted using RNeasy Plus Mini Kit (QIAGEN, # 74134).
RNA libraries were prepared using Ampliseq Library Prep Kit following manufacturer's protocols for targeted amplicon amplification
Library strategy: Ion AmpliSeq Panels Mouse 46K genes

treatment_protocol: Mouse BMDMs were subjected to transcriptome analysis after treatment for 24 hours with DMSO vehicle control, olaparib (OL, 5 μM), DMXAA (0.05 mg/mL), 50% BRCA1-deficient mouse mammary tumor cells (BP)-CM with or without DMXAA, or 50% olaparib-treated BP cells (BP/OL)-CM with or without DMXAA.

value: bone marrow

value: primary BMDMs

value: macrophages

tag: genotype

value: Wild-type

tag: treatment

value: 24 hours with CM from olaparib-treated BP tumor cells and DMXAA


title: BMDMs, BP/OL-CM+DMXAA, biol rep 2 [QW_018]


title: WGBS_Control_#1

value: fibroblast


title: BMDMs, BP-CM, biol rep 2 [QW_010]

value: 24 hours with BP tumor cell-CM


title: BMDMs, DMXAA, biol rep 1 [QW_005]

value: 24 hours with DMXAA (0.05 mg/mL)


title: BMDMs, BP-CM+DMXAA, biol rep 1 [QW_011]

value: 24 hours with BP tumor cell-CM and DMXAA


title: BMDMs, BP/OL-CM, biol rep 2 [QW_016]

value: 24 hours with CM from olaparib-treated BP tumor cells


title: BMDMs, DMXAA, biol rep 2 [QW_006]


title: BMDMs, olaparib (OL), biol rep 2 [QW_004]

value: 24 hours with olaparib (0.005mM)


title: BMDMs, BP/OL-CM, biol rep 1 [QW_015]


title: BMDMs, olaparib (OL), biol rep 1 [QW_003]


title: BMDMs, control medium, biol rep 2 [QW_002]

value: 24 hours with control medium containing DMSO vehicle control


title: M1

value: blood

value: PBMC

value: COVID-19 infection

value: moderate

value: recovery


title: BMDMs, BP-CM, biol rep 1 [QW_009]

value: bone marrow


title: BMDMs, BP-CM+DMXAA, biol rep 2 [QW_012]

value: primary BMDMs


title: Non-cancer derived breast cell ipsilateral [GUMC-549]

value: Non-cancer derived

value: CRC-isolated Breast epithelial cell

value: BRCA mutation (non-specified)


title: WR3

city: Lan zhou

first: Pan

middle: Yu

last: Cai

state: Gansu

address: Yin Tan Road Street, An Ning District

department: College of Animal Science and Technology

institute: Gansu Agricultural University

data_processing:
Similar to RNA-seq, quality control was conducted by removing dirty reads, including low quality reads, reads with 5’ adaptor contaminants or without 3’ adaptors, ployA in small RNA fragment and reads shorter than 18 nt.
Then, rRNA, scRNA, sonRNA, snRNA and tRNA were removed by blasting against GeneBank database (Release 209.0) and Rfam database (Release 11.0). Finally, the remaining reads were searched against miRBase database (Release 22) to identify conserved and novel miRNAs.
Genome_build: Oncorhynchus mykiss Omyk_1.0
Supplementary_files_format_and_content: tab-delimited text file includes miRNAs TPM values for each Sample

organism: Oncorhynchus mykiss

source_name: dorsal skin

extract_protocol:
The samples were collected immediately, then flash-frozen in liquid nitrogen,and total RNA was extracted using Trizol reagent.
Total RNA of the six libraries from dorsal skin was extracted using Trizol reagen kit (Invitrogen, Carlsbad, CA, USA), then purified RNA were ligated with 3’ and 5’ adapters.
small RNA libraries were prepared for sequencing using standard Illumina protocols
cDNA library were generated after the ligation products were reverse transcribed by PCR amplification and sequenced using Illumina HiSeq Xten by Gene Denovo Biotechnology Co. (Guangzhou, China).

value: wild-type

tag: phenotype

value: black skin (WR)

value: dorsal skin

tag: age

value: 45 days


title: WR1


title: BMDMs, control medium, biol rep 1 [QW_001]

value: macrophages

value: Wild-type


title: YR1

value: yellow mutant

value: yellow skin (YR)


title: YR2


title: glioma stem cells

city: clermont ferrand

first: yoan

last: renaud

address: place henri dunand

country: France

institute: igred

data_processing:
consensus sequence establishment using the Iso-seq3 CCS algorithm
selection of the full-length cDNA sequences including the SMARter IIA adapter at both their 3’ and 5’ ends using the Iso-seq3 LIMA tool
trimming of the polyT tail at the 3’end of each sequence (corresponding to the polyU tail added initially)
alignment of the obtained sequences to the hg19 reference human genome using the minimap2 aligner
Only good quality (MapQ ≥30) aligned reads were retained in a SAM file (specifying chromosome, start and end genomic coordinates, transcription strand, MapQ value)
The genomic coordinates of PacBio read alignments were extracted using the bamtobed tools from the bedtools suite V2.30.0 and the SAM file
Genome_build: Hg19
Supplementary_files_format_and_content: bed file

source_name: glioma stem cells

extract_protocol: To sequence full-length polyA and non-polyA LCT transcripts, a modified Iso-seq protocol (PacBio) was used. For each sample, total RNA was poly-uridinylated using a polyU polymerase (New England Biolabs) following the manufacturer’s recommendations. PolyU RNAwere then reverse transcribed using the SMARTer Kit (Takara) in which the oligodT(30) 3’ SMART CDS Primer II A was replaced by the oligodA(30) 3’ SMART CDS Primer II A. The obtained full-length cDNAs were then amplified by PCR (14 cycles) using GXL PrimeSTAR DNA polymerase (Takara). cDNA size fractionation was then performed on 0.75% agarose gels (without ethidium bromide) to individualize three cDNA fractions: [0.3 - 2 kb], [2 – 5 kb], and [> 5 kb]. Dedicated biotinylated riboprobes, designed against the 5’ 400 bp sequences of the 8,744 recent L1 (myBaits, Arbor Biosciences), were used to perform three independent captures of each cDNA fraction according to the supplier's recommendations (except for the addition of Block C solution = human Cot-1 DNA). Captured cDNAs were then amplified by PCR using Prime StarGXL DNA polymerase (Takara) with 10, 12 and 14 cycles respectively for the  <2 kb, 2-5 kb and >5 kb cDNA fractions. PCR products were pooled and purified using 0.55X AMPurePB beads (PacBio). Finaly, the three samples were pooled together and handled for SMRTbell template preparation and sequencing (Sequel II, Gentyane platform).

value: brain

value: adult


title: YR3


title: WR2


title: sample.0314.t1

city: Montreal

first: Marc

last: Parisien

state: Quebec

address: 740 Dr. Penfield Avenue

department: Dentistry

institute: McGill University

data_processing:
Deep-sequencing reads were aligned on the human genome version hg19/GRCh37 using STAR aligner version 2.5.1b. Gene-level counting was performed using featureCounts version 1.6.0, using RefSeq gene boundaries.
Genome_build: GRCh37 / hg19
Supplementary_files_format_and_content: The file lbp_featurecounts.txt.gz is tab-delimited, contains 27936 lines including a header line, and contains 202 columns. Columns 1-6 are: (1) gene ID from HUGO, (2) gene's chromosome, (3) gene's locus start, (4) end, (5) strand, as well as (6) length. Columns 7-202 are the 98 individuals at two time points = 196 samples.

source_name: Whole peripheral blood

extract_protocol:
Whole peripheral blood was collected at both visits, t0 and t1, at the Pain Service of University Hospital of Parma. Tempus blood RNA tubes were used (Applied Biosystems, n. 4342792, Beverly, MA, USA), shaken vigorously for 10–15 sec immediately after collection for RNA stabilization, and stored at -20 C. Total RNA was isolated using Maxwell® 16 LEV simplyRNA Blood Kit (Promega, Madison, WI, USA) according to the manufacturer’s instructions. After, total RNA was quantified using the NanoDrop ND-1000 (Thermo Scientific, Waltham, MA, USA), and optical purity of RNA was defined according to the 260/280 ratio not less than 1.8 and 260/230 ratio between 1.8–2.2 of the isolated RNA. Then, the RNA integrity was assessed with the Agilent 4200 TapeStation (Agilent Technologies, Santa Clara, CA, USA) using the RNA Screen Tape assay (Agilent Technologies, n. 5067-5576). An average of 8 µg of total RNA was recovered from frozen whole blood, displaying RIN values between 6.5–8.4. Purified RNA was stored at -80 °C in 25-µl aliquots.
All RNA-sequencing was performed by the Genome Quebec Innovation Centre (McGill University, Montreal, Canada). Transcriptome libraries were generated from 1 μg of total RNA using the Kapa RNA-stranded Sample Prep Kit (KK8400, KAPABiosystems, Wilmington, MA, USA) following the manufacturer’s protocols. Briefly, poly-A mRNA was purified using poly-T oligo-attached magnetic beads using two rounds of purification. During the second elution of the poly-A RNA, the RNA was fragmented and primed for cDNA synthesis. During cDNA synthesis, dUTP was incorporated in the second-strand synthesis, and subsequently the dUTP-containing strand was selectively degraded. Adenylation of the 3’ ends and ligation of adapters were done following the manufacturer’s protocol. Enrichment of DNA fragments with adapter molecules on both ends was performed using 10 cycles of PCR amplification using the KAPA PCR mix and Illumina-adapted primers cocktail. Paired-end 2x100 nucleotides sequencing was performed using the Illumina HiSeq2000 machine running TruSeq v3 chemistry at Genome Québec.

tag: individual

tag: Sex

value: Male

tag: smoking

value: Yes

tag: paingroup

value: Persistent

tag: timepoint


title: sample.0314.t0


title: sample.0299.t0


title: sample.0309.t0

value: No


title: sample.0297.t1

value: Female


title: sample.0297.t0


title: sample.0298.t0


title: sample.0299.t1


title: sample.0294.t1


title: sample.0294.t0


title: sample.0289.t1

value: Resolved


title: sample.0286.t1


title: sample.0289.t0


title: adipocyte_ctrl_P8

city: Guelph

first: David

middle: M

last: Mutch

state: Ontario

address: 50 Stone Road East

department: Human Health & Nutritional Sciences

institute: University of Guelph

hyb_protocol: Following fragmentation, 2.3 ug of fragmented and labelled ss-DNA were hybridized for 16 hr at 45C on Clariom_S_Mouse GeneChips. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Applied Biosystems GeneChip Scanner 3000

data_processing: Data were processed using R software. Probe intensities were background corrected, quantile normalized, and log2 transformed via RMA algorithm from R package ‘oligo’.

source_name: differentiated 3T3-L1 adipocyte cells, control, passage number 8

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip WT Plus Reagent Kit User Guide, Publication #: MAN0018137).

growth_protocol: Murine 3T3-L1 pre-adipocytes maintained on growth medium containing high glucose (4.5 mg/mL) Dulbecco's Modified Eagle Medium with 10% heat-inactivated fetal bovine serum and 1% penicillin-streptomycin. Two days after cells reached 100% confluence (day 0), differentiation was initiated with standard differentiation cocktail concurrent with fatty acid/D6D inhibitor treatment. After two days, differentiation media was replaced with maintenance media (growth medium supplemented with 5 μg/ml human insulin) and replaced every 2 days until experiment concluded after 8 days.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen). RNA concentration and purity were determined using a NanoDrop 2000 Spectrophotometer and Agilent BioAnalyzer. All samples had a RNA integrity number (RIN) > 8.9.

treatment_protocol: Fatty acid and D6D inhibitor treatments: ALA stock solution diluted to concentration of 50 μM in culture media containing 2% fatty acid free bovine serum albumin, D6D inhibitor solution diluted in culture media to concentration of 5 μM. Cell treatments of ALA, ALA and D6D inhibitor, D6D inhibitor, and control (ethanol and DMSO) were added throughout differentiation process from day 0 to day 8.

tag: tissue

value: adipocyte

value: ethanol and DMSO

value: RNA extracted from Day 8 differentiated cells

tag: passage number


title: adipocyte_ALA_d6d_P8

source_name: differentiated 3T3-L1 adipocyte cells, ALA and d6d inhibitor, passage number 8

value: alpha-linolenic acid and d6d inhibitor


title: sample.0286.t0


title: adipocyte_ALA_P8

source_name: differentiated 3T3-L1 adipocyte cells, ALA, passage number 8

value: alpha-linolenic acid


title: adipocyte_ctrl_P6

source_name: differentiated 3T3-L1 adipocyte cells, control, passage number 6


title: adipocyte_d6d_P6

source_name: differentiated 3T3-L1 adipocyte cells, d6d inhibitor, passage number 6

value: d6d inhibitor


title: adipocyte_ALA_P7

source_name: differentiated 3T3-L1 adipocyte cells, ALA, passage number 7


title: adipocyte_ALA_d6d_P7

source_name: differentiated 3T3-L1 adipocyte cells, ALA and d6d inhibitor, passage number 7


title: sample.0308.t1


title: sample.0298.t1


title: adipocyte_d6d_P8

source_name: differentiated 3T3-L1 adipocyte cells, d6d inhibitor, passage number 8


title: adipocyte_d6d_P7

source_name: differentiated 3T3-L1 adipocyte cells, d6d inhibitor, passage number 7


title: sample.0308.t0


title: adipocyte_ctrl_P7

source_name: differentiated 3T3-L1 adipocyte cells, control, passage number 7


title: sample.0309.t1


title: sample.0283.t1


title: sample.0281.t0


title: adipocyte_ALA_d6d_P6

source_name: differentiated 3T3-L1 adipocyte cells, ALA and d6d inhibitor, passage number 6


title: sample.0278.t1


title: adipocyte_ALA_P6

source_name: differentiated 3T3-L1 adipocyte cells, ALA, passage number 6


title: sample.0283.t0


title: sample.0273.t1


title: sample.0273.t0


title: sample.0271.t0


title: sample.0279.t0


title: sample.0277.t1


title: sample.0250.t1


title: sample.0243.t1


title: sample.0237.t1


title: sample.0239.t0


title: sample.0240.t0


title: sample.0281.t1


title: sample.0236.t1


title: sample.0239.t1


title: sample.0271.t1


title: sample.0233.t1


title: sample.0279.t1


title: sample.0236.t0


title: sample.0235.t0


title: sample.0243.t0


title: sample.0277.t0


title: sample.0240.t1


title: sample.0237.t0


title: sample.0227.t1


title: sample.0225.t1


title: sample.0278.t0


title: sample.0226.t0


title: sample.0233.t0


title: sample.0228.t1


title: sample.0220.t1


title: sample.0221.t0


title: sample.0232.t0


title: sample.0228.t0


title: sample.0232.t1


title: sample.0220.t0


title: sample.0211.t0


title: sample.0212.t1


title: sample.0225.t0


title: sample.0250.t0


title: sample.0224.t1


title: sample.0210.t0


title: sample.0227.t0


title: sample.0226.t1


title: sample.0224.t0


title: sample.0235.t1


title: sample.0219.t1


title: sample.0223.t0


title: sample.0223.t1


title: sample.0208.t1


title: sample.0212.t0


title: sample.0221.t1


title: sample.0210.t1


title: sample.0211.t1


title: sample.0206.t0


title: sample.0204.t0


title: sample.0204.t1


title: sample.0203.t0


title: sample.0202.t0


title: sample.0208.t0


title: sample.0207.t1


title: sample.0200.t0


title: sample.0209.t1


title: sample.0219.t0


title: sample.0200.t1


title: sample.0202.t1


title: sample.0196.t0


title: sample.0206.t1


title: sample.0195.t1


title: sample.0207.t0


title: sample.0203.t1


title: sample.0190.t1


title: sample.0193.t0


title: sample.0205.t1


title: sample.0190.t0


title: sample.0201.t1


title: sample.0201.t0


title: sample.0197.t1


title: sample.0196.t1


title: sample.0193.t1


title: sample.0197.t0


title: sample.0185.t0


title: sample.0186.t1


title: sample.0188.t1


title: sample.0179.t1


title: sample.0195.t0


title: sample.0182.t1


title: sample.0187.t1


title: sample.0177.t1


title: sample.0187.t0


title: sample.0182.t0


title: sample.0205.t0


title: sample.0185.t1


title: sample.0186.t0


title: sample.0175.t1


title: sample.0188.t0


title: sample.0172.t0


title: sample.0171.t1


title: sample.0178.t0


title: sample.0174.t0


title: sample.0174.t1


title: sample.0179.t0


title: sample.0178.t1


title: sample.0175.t0


title: sample.0165.t1


title: sample.0165.t0


title: sample.0169.t1


title: sample.0166.t1


title: sample.0169.t0


title: sample.0171.t0


title: sample.0172.t1


title: sample.0162.t1


title: sample.0166.t0


title: sample.0164.t1


title: sample.0164.t0


title: sample.0161.t0


title: sample.0177.t0


title: sample.0162.t0


title: sample.0160.t0


title: sample.0160.t1


title: sample.0161.t1


title: sample.0157.t1


title: sample.0154.t1


title: sample.0153.t0


title: sample.0146.t1


title: sample.0145.t1


title: sample.0156.t0


title: sample.0154.t0


title: sample.0145.t0


title: sample.0144.t1


title: sample.0144.t0


title: sample.0146.t0


title: sample.0156.t1


title: sample.0141.t1


title: sample.0139.t1


title: sample.0141.t0


title: sample.0140.t0


title: sample.0140.t1


title: sample.0133.t0


title: sample.0133.t1


title: sample.0143.t1


title: sample.0131.t1


title: sample.0157.t0


title: sample.0131.t0


title: sample.0130.t0


title: T_4_miRNA

city: Harbin

first: He

last: Shengyuan

state: Heilongjiang

address: Baojian Road 157

institute: Harbin Medical University

data_processing:
For miRNAs, trimmed data were mapped to the human reference genome (GRCh38) using bowtie.
Annotation of known miRNAs and prediction of novel miRNAs according to miRBase and expression quantification were performed by miRDeep2.
Expression levels of all miRNAs were quantified as counts per million reads (CPM).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include CPM values for each sample
Supplementary files format and content: Matrix table with CPM for every miRNA and every sample

source_name: torn supraspinatus muscles

extract_protocol:
The torn supraspinatus and intact subscapularis were confirmed by irrigation and debridement in intraarticular and subacromial space, then a small piece of muscle belly from each muscle was carefully collected by a grasper. After that, the supraspinatus tear was repaired using suture anchors. A total of 10 samples from 5 patients were stored in liquid nitrogen for further analysis.
Following the protocol of the NEB Multiplex Small RNA Library Prep Set for Illumina, the total RNA of each sample was used to prepare the miRNA sequencing (miRNA-seq) library which included the following steps: 1) 3’-adaptor ligation; 2) 5’-adaptor ligation; 3) the cDNA synthesis; 4) PCR amplification; and 5) size selection of 135-155 bp PCR-amplified fragments (corresponding to ~15-35 nt small RNAs). The libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters, and finally sequenced for 51 cycles on Illumina NextSeq 500 platform according to the manufacturer’s protocol.

value: torn supraspinatus muscles

tag: gender

value: female


title: T_5_miRNA


title: sample.0153.t1


title: T_3_miRNA


title: T_2_miRNA


title: sample.0143.t0


title: T_1_miRNA


title: sample.0128.t1


title: sample.0128.t0


title: sample.0120.t1


title: sample.0117.t1


title: P_5_miRNA

source_name: unharmed subscapularis muscles

value: unharmed subscapularis muscles


title: sample.0117.t0


title: sample.0123.t1


title: sample.0120.t0


title: sample.0114.t1


title: P_2_miRNA


title: P_1_miRNA


title: T_5_circRNA

data_processing:
For circRNAs, trimmed data were mapped to the human reference genome (GRCh37) using STAR.
Then back-splice junction reads were identified with CIRCexplorer2 and annotated to circBase.
In addition, we also identified novel circRNAs and named them according to their position in the reference genome.
Expression levels of all circRNAs were quantified as counts per million reads (CPM).
Assembly: GRCh37
Supplementary files format and content: tab-delimited text files include FPKM/CPM values for each sample
Supplementary files format and content: Matrix table with FPKM for every mRNA/lncRNA and every sample; Matrix table with CPM for every circRNA and every sample

extract_protocol:
The torn supraspinatus and intact subscapularis were confirmed by irrigation and debridement in intraarticular and subacromial space, then a small piece of muscle belly from each muscle was carefully collected by a grasper. After that, the supraspinatus tear was repaired using suture anchors. A total of 10 samples from 5 patients were stored in liquid nitrogen for further analysis.
For RNA sequencing, the total RNA concentration and quality were determined using the NanoDrop ND-1000. 1~2 µg RNA per sample was used in the construction of libraries. The enrichment of mRNA was performed according to standard procedures of NEB Next® Poly(A) mRNA Magnetic Isolation Module. Ribo-Zero Magnetic Gold Kit was used to deplete ribosomal RNA (rRNA) from total RNA, followed by library preparation using the KAPA Stranded RNA-Seq Library Prep Kit (Illumina). After the library was constructed, the quality and concentration of the sequencing library were assessed by Agilent 2100 Bioanalyzer and then the libraries were sequenced on Illumina NovaSeq 6000 platform according to the manufacturer’s instructions.


title: T_4_circRNA


title: P_4_miRNA


title: P_3_miRNA


title: sample.0130.t1


title: sample.0113.t1


title: T_3_circRNA


title: sample.0115.t1


title: P_5_circRNA


title: T_1_circRNA


title: sample.0123.t0


title: sample.0114.t0


title: sample.0110.t1


title: P_4_circRNA


title: P_3_circRNA


title: sample.0108.t1


title: T_5_mRNA-lncRNA

data_processing:
For mRNAs and lncRNAs, trimmed data were mapped to the human reference genome (GRCh37) using Hisat2 software.
Assembly, annotation and the prediction of novel transcripts were performed by StringTie with the GENCODE transcriptome.
Protein-coding abilities of the novel transcripts were predicted by CPAT (Coding Potential Assessing Tool).
RNA abundance was quantified as fragments per kilobase of exon per million reads (FPKM) by Ballgown.
Assembly: GRCh37
Supplementary files format and content: tab-delimited text files include FPKM/CPM values for each sample
Supplementary files format and content: Matrix table with FPKM for every mRNA/lncRNA and every sample; Matrix table with CPM for every circRNA and every sample


title: P_2_circRNA


title: sample.0105.t0


title: sample.0115.t0


title: T_3_mRNA-lncRNA


title: sample.0108.t0


title: sample.0102.t1


title: T_2_mRNA-lncRNA


title: sample.0113.t0


title: T_4_mRNA-lncRNA


title: T_2_circRNA


title: T_1_mRNA-lncRNA


title: P_5_mRNA-lncRNA


title: sample.0105.t1


title: sample.0101.t0


title: sample.0101.t1


title: sample.0102.t0


title: Uninf_4

city: Lansing

first: Kayla

middle: N

last: Conner

state: Michigan

address: 4125 Beaumont Rd

institute: Michigan State University

data_processing:
Quality Control - FASTQC
Trimming - Trimmomatic
Alignment to GRCm39 - Bowtie2
Read Counts - FeatureCounts
Differential Gene Expression - DESeq2
Assembly: GRCm39
Supplementary files format and content: DESeq2 Output - Gene identifiers, Average Read counts, Log2Fold Change, Standard Error, Wald Statistic, p value, adjusted p value
Supplementary files format and content: Normalized read counts for each gene/sample

source_name: Placenta

extract_protocol:
RNA was extracted from homogenized placental tissues using the Qiagen RNeasy kit
RNAseq analysis by SeqMatic Inc., Mountain View, CA. Single-read sequencing on libraries was performed using the Illumina Genome Analyzer IIx.

treatment_protocol: Mice were injected with 2x10^5 CFU LOG-phase L. monocytogenes strain Xen32 on gestation day 14 (E14)

value: Placenta

tag: strain

value: Uninfected Control


title: P_3_mRNA-lncRNA


title: sample.0110.t0


title: P_2_mRNA-lncRNA


title: P_1_circRNA


title: P_4_mRNA-lncRNA


title: P_1_mRNA-lncRNA


title: sample.0098.t0

value: Male


title: sample.0209.t0


title: Inf_19

value: L. monocytogenes


title: Uninf_1


title: SC2100311_GT21-18745-L2

city: Farmington

first: Marina

last: Yurieva

state: Connecticut

address: 10 Discovery dr

department: Computational Sciences

institute: Jackson Laboratory

description: HTOs for SC2100310 Submerged 2

data_processing:
Illumina base call files for all libraries were converted to FASTQs using bcl2fastq v2.20.0.422 (Illumina)
FASTQ files associated with the gene expression libraries were aligned to the GRCh38.93 reference genome (10x Genomics GRCh38 reference 3.0.0 [including all transcribed unitary pseudogenes]) using the version 3.1.0 Cell Ranger count pipeline (10x Genomics).
FASTQ files representing the hashtag libraries were processed into hashtag-count matrices using CITE-Seq-Count (version 1.4.3)
The Illumina single-cell RNA sequencing base call files of each of the two libraries were demultiplexed by cellranger mkfastq that generated the raw fastq file which was processed with the standard cellranger-3.1.1 pipeline.
The reads were aligned to the Ensembl human genome GRCh38 (https://uswest.ensembl.org/Homo_sapiens/Info/Index) with STAR for each of the 6,794,880 Gel bead-in Emulsions (GEMs).
The hashtag demultiplexing of the six pooled HTO-distinct ALI samples per library and the three HTOs in the submerged sample was performed with Seurat’s HTODemux pipeline(52).
Scrublet and DoubletFinder to predict potential doublets
DecondX to estimate and remove the ambient RNA contamination in individual cells
The singlet expression profiles of each donor were SCT-normalized using log-transform and vst variance stabilization. Data clustering with the Leiden method
Differential expression with Seurat's Likelihood Ratio test
Cell annotation with markers and cellID
Genome_build: hg38
Supplementary_files_format_and_content: ALIdata.rds contains the raw and the normalized counts, the metadata, the cell annotation and the UMAP coordinates for the ALI samples
Supplementary_files_format_and_content: SUBMERGEDdata.rds contains the raw and the normalized counts, the metadata, the cell annotation and the UMAP coordinates for the Submerged samples
Supplementary_files_format_and_content: DE_Table_Submerged.xlsx contains the differential expression analysis for the Submerged data
Supplementary_files_format_and_content: DE_Table_ALI.xlsx contains the differential expression analysis for the ALI data

molecule: other

source_name: HTOs for donor ID 34, 27 and 54

growth_protocol: HBECs were expanded and differentiated according to manufacturer protocols [PneumaCult™-ALI, Stem Cell Technologies; #05001]. Briefly, 1x106 HBECs were seeded into T-25 flasks containing 5ml of ROCK-inhibitor supplemented PneumaCult™-ALI Complete Base Medium. When 80% confluence was achieved cells were harvested and seeded [50,000 cells per 24-well insert] into the apical chamber of inserts [pre-coated with collagen solution 30μg/ml] in 100 μl of ROCK-inhibitor supplemented PneumaCult™-ALI Complete base Medium; the basal chambers of the inserts were cell free and immersed in 500 μl of medium. After 3 days, the medium from the apical and basal chambers were removed and 500 μl PneumaCult™-ALI Complete Maintenance Medium was added to the basal chamber only (air-lift). Upon airlifting, medium was replaced every other day with 500 μl PneumaCult™-ALI Complete Maintenance Medium only to the basal chamber until the cultures reached full differentiation [day 25].

extract_protocol:
Single cell capture, barcoding and library preparation were performed using the 10X Chromium platform (50) version 3.1 chemistry and according to the manufacturer’s protocol (#CG00052) with modifications for generating the hashtag library(51). cDNA and libraries were checked for quality on Agilent 4200 Tapestation, quantified by KAPA qPCR, and pooled using a ratio of 95% gene expression library and 5% hashtag library before sequencing; each gene expression-hashtag library pair was sequenced at 50% of lan Illumina NovaSeq 6000 S2 flow cell lane, targeting 20,000 barcoded cells with an average sequencing depth of 50,000 reads per cell.
Illumina base call files for all libraries were converted to FASTQs using bcl2fastq v2.20.0.422 (Illumina) and FASTQ files associated with the gene expression libraries were aligned to the GRCh38.93 reference genome (10x Genomics GRCh38 reference 3.0.0 [including all transcribed unitary pseudogenes]) using the version 3.1.0 Cell Ranger count pipeline (10x Genomics). FASTQ files representing the hashtag libraries were processed into hashtag-count matrices using CITE-Seq-Count (version 1.4.3) (https://zenodo.org/badge/latestdoi/99617772).

treatment_protocol: On Day 25, we supplemented the basal chambers of fully differentiated ALI cultures with 1X of StemXVivo EMT Inducing Media [R&D; CCM017]. Medium was replaced every other day with 500 μl complete medium containing 1X of StemXVivo EMT Inducing Media only to basal chambers. After EMT treatment, samples were collected at Day 0, Day1 and Day 5. The ALI cultures were harvested using 0.05% trypsin/EDTA (Fisher Scientific # 25-300-054), washed, and pelleted [250g, 5 minutes, RT]. The pelleted cells were suspended in 3-4 mL dispase I/DNase I solution (38 U dispase I, 20mL 1X PBS, and 20μL DNase I [100 mg/mL]) for 15 minutes at 37°C. The cell suspension was then filtered using MACS SmartStrainers [Miltenyi #130-098-458] to obtain single cell suspension. 1-2 million single cells were suspended in 100 μl staining buffer (2%BSA/0.01%Tween, PBS) and blocked with 10 μl Fc Blocking reagent (FcX, BioLegend) for 10 mins at 4C. Later, 0.5ug of a unique cell Hashing antibody was added and incubated for 20 mins at 4C. The cells were then washed 3X with 1 ml staining buffer and pelleted at 4 ̊C for 5 minutes at 350g. The pellet was resuspended in 1x PBS + 0.04% BSA and cell viability was calculated using Countess™ (ThermoFisher). Cell suspensions from each [ALI culture] were labeled with cell hashing antibodies (BioLegend TotalSeq-A anti-human Hashtag A0251-A0256) according to the manufacturer’s protocol (BioLegend protocol https://dx.doi.org/10.17504/protocols.io.8aahsae). Cells were washed and suspended in PBS containing 0.04% BSA and immediately processed as follows. Cell viability was assessed on a Countess II automated cell counter (ThermoFisher), and up to 40,000 cells (~3,500 cells from each hashtagged sample) were loaded onto one lane of a 10X Chromium Controller.

tag: cell type

value: Hashtag oligos

tag: source

value: HTOs for donor ID 34, 27 and 54


title: Uninf_3


title: Inf_18


title: SC2100311_GT21-18745-L1

description: HTOs for SC2100310 Submerged 1


title: Uninf_2


title: sample.0098.t1

source_name: Whole peripheral blood

value: No


title: AW21002_GT21-01793

description: HTOs for AW21001 ALI

source_name: HTOs for donor IDs 27 and 54

value: HTOs for donor IDs 27 and 54


title: Inf_16


title: Inf_20


title: AW21001_GT21-01792_SI

description: AW21001 ALI

source_name: combined data of donor IDs 27 (60 years old black male) and 54 (19 years old black female)

value: primary bronchial epithelial cells


title: Inf_14


title: AW20004_GT20-13865

description: HTOs for AW20003 ALI

source_name: HTOs for donor ID 34

value: HTOs for donor ID 34


title: SC2100310_GT21-18744-L2

description: SC2100310 Submerged 2

source_name: combined data of donor ID 34 (11 years old Caucasian male), donor IDs 27 (60 years old black male) and 54 (19 years old black female)


title: AW20003_GT20-13864_SI

description: AW20003 ALI

source_name: donor ID 34 (11 years old Caucasian male)


title: E2_1

city: Chengdu

first: Xiaomeng

last: Li

address: Renmin South Road, 16#

institute: Sichuan University

data_processing:
A cDNA library constructed by technology from the pooled RNA from brain samples of homo sapiens was sequenced run with Illumina sequence platform.Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon paired-end reads of bp length. This yielded gigabases (Gb) of sequence. Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20) were removed .After that, a total of G bp of cleaned ,paired-end reads were produced.
We aligned reads of samples  to the UCSC (http://genome.ucsc.edu/) homo sapiens reference genome using HISAT package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. HISAT allows multiple alignments pe read (up to 20 by default) and a maximum of two mismatchs when mapping the reads to the reference.HISAT build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions. And then by removing sequence-dependent bias and amplification noise using UMI-tools
The mapped reads of each sample were assembled using StringTie. Then, all transcriptomes from Samples were merged to reconstruct a comprehensive transcriptome using perl scripts. After the final transcriptome was generated, StringTie and edgeR was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM. The differentially expressed mRNAs and genes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package – edgeR
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: human normal ovarian epithelial cells (IOSE80)

extract_protocol:
After 28-day exposure, total RNA was extracted using Trizol reagent (Invitrogen, USA, 15596026). Then the Nano Drop (Nano Drop, USA, ND-1000) was used to quantify the amount and purity of RNA.
Sequencing was carried out on an Illumina Novaseq 6000. RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: cell line

value: immortalized cells

value: treated with E2 for 28 days


title: E2_3


title: sample.0139.t0

value: Yes

value: Persistent


title: Inf_17


title: BPA2_3

value: treated with 2500 nM BPA for 28 days


title: Inf_13


title: SC2100310_GT21-18744-L1

description: SC2100310 Submerged 1

value: combined data of donor ID 34 (11 years old Caucasian male), donor IDs 27 (60 years old black male) and 54 (19 years old black female)


title: Inf_11


title: SiOGT replicate 3

city: Milwaukee

first: Stephanie

last: Olivier Van-Stichelen

state: WI

address: 8701 Watertown Plank Road

institute: Medical College of Wisconsin

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted and given in the counts.txt file.
Assembly: GRCh38

source_name: BeWo

growth_protocol: Bewo cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) containing either 4.5 g/L (Standard, Std), 10% (v/v) fetal bovine serum (FBS), and 1% penicillin/streptomycin at 37°C in a 5% (v/v) CO2-enriched humidified atmosphere.

extract_protocol:
mRNA was isolated with the PureLink RNA Mini Kit (#12183018A, Thermo Fisher Scientific) following the kit instruction.
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA).
Briefly, mRNAs were first enriched with Oligo(dT) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by limited-cycle PCR.

treatment_protocol: MISSION esiRNA against targeting Human OGT were ordered at sigma (#EHU082301). Silencer™ Negative Control No. 1 siRNA (cat# AM4611 Thermofisher Scientific) was used as a control. siRNAs were transfected using the Lipofectamine RNAiMax (thermofisher scientific).

value: BeWo

value: Chorionic carcinoma

value: OGT siRNA


title: Inf_12

value: Placenta


title: Inf_15

value: L. monocytogenes


title: E2_2


title: BPA2_2


title: SiOGT replicate 2


title: SiCtrl replicate 3

value: Scramble negative SiRNA


title: BPA1_2

value: treated with 0.25 nM BPA for 28 days


title: BPA2_1


title: SiCtrl replicate 2


title: Inf_10


title: BPA1_3


title: Inf_9


title: Con_3

value: treated with 0.1% DMSO for 28 days


title: Con_2


title: SiCtrl replicate 1


title: Inf_8


title: SiOGT replicate 1


title: DKO_PTGC_E173

city: la jolla

first: Siting

last: Zhu

state: california

address: 9500 Gilman Drive, University of California San Diego

department: Medicine

institute: UCSD

data_processing:
The sequencing reads longer than 36nt are kept are downstream analysis.
Then, the reads were mapped to assembly of the mouse genome (mm10) using STAR (2.5.3a).
The differential expressed genes were identified by using DESeq2 (v1.12.4)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

molecule: nuclear RNA

source_name: Ptpmt1 cardiomyocytes-specific Knockout and Gcn2 nockout mouse line

extract_protocol: RNA libraries for RNA-seq were prepared using  KAPA RNA Hyper+RiboErase HMR Library Prep Kit following manufacturer's protocols.

value: cardiomyocytes

value: Ptpmt1 cardiomyocytes-specific Knockout and Gcn2 Knockout


title: Con_1


title: DKO_PTGC_E164


title: RNAPII ChIP-seq in rex1 RNAi hESCs replicate 2 (IP-H9-sirex1-polyii-2)

city: guangzhou

first: chengguo

last: yao

address: No. 74 zhongshan 2rd road

department: school of medicine

institute: sysu

data_processing:
Adapters were trimmed with Cutadapt in paired-end mode
Obtained sequences were mapped to the human hg19 reference genome with Bowtie2.
Properly paired and mapped reads were filtered with SAMtools. PCR duplicates were removed with Picard MarkDuplicates tool. FPKM normalized bigwig files were generated for each bam files with Deeptools2 bamCoverage tool (-bs 10 –p max –normalizeUsing RPKM –e).
Metagene profiles of genes scaled to the same length were then generated with Deeptools2 computeMatrix tool with a bin size of 10 bp and the plotting data obtained with plotProfile –outFileNameData tool.
Peak calling was performed using MACS2 and differential binding events were identified using DiffBind package with standard parameters.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM normalized bigwig files were generated for each sample bam files (two replicates bam files were combined together)

source_name: H9 cell line

growth_protocol: control and rex1 RNAi hESCs were grown in mTeSR medium

extract_protocol:
Crosslinked DNA-proteins were fragmented with ChIP-IT® Express Enzymatic Shearing Kit (Active Motif),cell lysates were further subject to IP with antibodies targeting specific protein. Iped DNA-protein were de-crosslinked, DNA was purified and subjected to library preparation.
ChIP-seq library preparation kit (Vazyme, catalog: ND607-01) was used for preparation of ChIP-seq libraries.
Libraries were sequenced with Novaseq PE150

treatment_protocol: no treatment

value: human embryonic stem cell line H9

tag: chip antibody

value: Active Motif  catalog. 39497


title: RNAPII ChIP-seq in rex1 RNAi hESCs replicate 1 (IP-H9-sirex1-polyii-1)


title: RNAPII ChIP-seq in control hESCs replicate 1 (IP-H9-siNC-polyii-1)

value: control


title: Inf_7


title: Inf_6


title: RNAPII ChIP-seq in control hESCs replicate 2 (IP-H9-siNC-polyii-2)


title: ChIP-seq input for rex1 RNAi hESCs (input-H9-siRex1)


title: BPA1_1

value: immortalized cells


title: ChIP-seq for CFIm25 in CFIm25 KO hESCs (CFIm25 KO H9-2)

growth_protocol: control and CFIm25 KO hESCs were grown in mTeSR medium

extract_protocol:
Cells were washed with PBS, and ChIP-seq libraries were prepared using CUT&TagHyperactive In-Situ ChIP Library Prep Kit for Illumina（pG-Tn5）(TD901-01, vazyme) and the indicated antibodies.
ChIP-seq libraries were prepared using VAHTSTM Universal DNA Library Prep Kit for Illumina® V3 (vazyme, ND607-01)
Libraries were sequenced with Novaseq PE150

value: human embroynic stem cell line H9

value: 10322-1-AP-50ul, Proteintech

tag: genotype

value: CFIm25 KO


title: ChIP-seq input for control hESCs (input-H9-siNC)

tag: treatment


title: Inf_5


title: WT_PTGC_E174

value: Control


title: DKO_PTGC_E163


title: ChIP-seq for CFIm25 in CFIm25 KO hESCs (CFIm25 KO H9-1)


title: ChIP-seq for CFIm25 in control hESCs (Control H9-2)


title: Inf_4


title: WT_PTGC_E165


title: Inf_3


title: ChIP-seq for CFIm25 in control hESCs (Control H9-1)


title: CFIm68 ChIP-seq in CFIm25 KO hESCs replicate 2 (CFIm68-KO8-2)

description: DNA fragments

extract_protocol:
Crosslinked DNA-proteins were fragmented with ChIP-IT® Express Enzymatic Shearing Kit (Active Motif),cell lysates were further subject to IP with antibodies targeting specific protein. Iped DNA-protein were de-crosslinked, DNA was purified and subjected to library preparation.
ChIP-seq library preparation kit (Vazyme, catlog: ND607-01) was used for preparation of ChIP-seq libraries.
Libraries were sequenced with Novaseq PE150

value: Bethyl, A301-358A


title: CFIm68 ChIP-seq in control hESCs replicate 2 (CFIm68-H9-2)

description: DNA fragments


title: Inf_1


title: DKO_FST_E162

source_name: Ptpmt1 cardiomyocytes-specific Knockout and Eif2a mutant mouse line


title: CFIm59 ChIP-seq in CFIm25 KO hESCs replicate 1 (CFIm59-KO8-1)

description: DNA fragments

value: Bethyl, A301-359A


title: CFIm68 ChIP-seq in control hESCs replicate 1 (CFIm68-H9-1)

description: DNA fragments


title: CFIm68 ChIP-seq in CFIm25 KO hESCs replicate 1 (CFIm68-KO8-1)

description: DNA fragments


title: CFIm59 ChIP-seq in control hESCs replicate 1 (CFIm59-H9-1)

description: DNA fragments


title: DKO_FST_E145

value: Ptpmt1 cardiomyocytes-specific Knockout and Eif2a mutant


title: DKO_FST_E135


title: BMDC, Fucoidan, 24h, rep3

city: Daejeon

first: Suyoung

last: Choi

address: 266, Munhwa-ro, Jung-gu

department: Department of Medical Science

institute: Chungnam National University

description: Fucoidan treted BMDC

data_processing:
Raw fastq files were quality-checked with FastQC (v0.11.9), and subjected to trimming with ‘Trim galore!’(v0.6.4) of the Python tool (FastQC score Q30 over) to remove adapters and low-quality reads.
Sequences were then aligned to the mouse reference genome (mm10) with STAR (v2.7.3a).
For the mapped data, low read counts and duplicate reads(≤10) were removed and the total read count, counts per million (cpm) and log FC were obtained using R program.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files have read count data for each sample of data.

source_name: Bone marrow

growth_protocol: BMDC cells were maintained in RPMI1640 media containing 10% FBS, 1% penicillin/streptomycin, 50 μM 2-Mercaptoethanol, and 20 ng/ml GM-CSF in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was isolated using the Trizol reagent (Thermo) and RNeasy kit (Qiagen) and the purified mRNAs were used to synthesize double-stranded cDNAs using SuperScript Double-Stranded cDNA Synthesis Kit (Thermo Fisher Scientific).
Sequencing libraries were constructed using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) and sequenced on the Illumina HiSeq 2500.

treatment_protocol:
Bone marrow cells were obtained from the femur of 6- to 10-week old female C57BL/6 mice and cultured in RPMI medium containing 10% FBS, 1% penicillin/streptomycin, 50 μM 2-Mercaptoethanol, and 20 ng/ml GM-CSF for 3 days. The media was replaced with fresh supplemented media and cultured for an additional 3 days.
BMDCs were harvested on day 6, treated with 200 μg /ml fucoidan (F8190, Sigma-Aldrich) or vehicle (0.04% DMSO) in complete media for 24 hours.

value: Bone marrow

value: BMDC

value: Wild type

value: Fucoidan (400ug/ml)

value: female

tag: time point

value: 24h after treatment


title: CFIm59 ChIP-seq in control hESCs replicate 2 (CFIm59-H9-2)

description: DNA fragments


title: BMDC, Fucoidan, 24h, rep2

description: Fucoidan treted BMDC


title: LEO1 ChIP-seq in CFIm25 KO hESCs replicate 2 (LEO1-KO8-2)

description: DNA fragments


title: WT_PTGC_E166

value: cardiomyocytes


title: PKO_FST_E190

value: Ptpmt1 cardiomyocytes-specific Knockout only


title: BMDC, Fucoidan, 24h, rep1

description: Fucoidan treted BMDC


title: CFIm59 ChIP-seq in CFIm25 KO hESCs replicate 2 (CFIm59-KO8-2)

description: DNA fragments


title: BMDC, DMSO control, 24h, rep3

description: DMSO treted BMDC


title: LEO1 ChIP-seq in control hESCs replicate 1 (LEO1-H9-1)

description: DNA fragments

value: control


title: BMDC, DMSO control, 24h, rep2

description: DMSO treted BMDC


title: Ser2 ChIP-seq in CFIm25 KO hESCs replicate 2 (Ser2-KO8-2)

description: DNA fragments

value: Active Motif, 61984


title: PKO_FST_E150


title: LEO1 ChIP-seq in CFIm25 KO hESCs replicate 1 (LEO1-KO8-1)

description: DNA fragments

value: human embroynic stem cell line H9


title: MM_FST_E336

value: Eif2alpha mutant only


title: Inf_2

value: Placenta

value: L. monocytogenes


title: Ser2 ChIP-seq in control hESCs replicate 1 (Ser2-H9-1)

description: DNA fragments


title: BMDC, DMSO control, 24h, rep1

description: DMSO treted BMDC


title: Ser2 ChIP-seq in CFIm25 KO hESCs replicate 1 (Ser2-KO8-1)

description: DNA fragments

value: CFIm25 KO


title: MM_FST_E113


title: shJMJD3 3h Ldlrad4 enh 4C-seq R2

first: Marta

last: Vicioso Mantis

address: Carrer Baldiri Reixac, 15

institute: IBMB-CSIC

data_processing:
Library strategy: 4C-seq
Read quality check was performed using FASTQC (Andrews S. (2010). FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Reads were processed using pipe4C (Krijger P.H.L. et al. (2020). 4C-seq from beginning to end: A detailed protocol for sample preparation and data analysis. https://doi.org/10.1016/j.ymeth.2019.07.014) using default parameters except for trimLength that was set to 36 base pairs in the configuration file. All coordinates refer to the Mus musculus genome version mm10.
Genome_build: mm10
Supplementary_files_format_and_content: wiggle

source_name: Mouse NSCs  dissected from cerebral cortices of fetal brains (E12.5)

growth_protocol: NSCs were cultured in a poly-D-lysine (5 mg/ml, 2 hours at 37°C) and laminin (5 mg/ml, 4 hours at 37°C) pre-coated dishes growing with a media comprising equal parts DMEM F12 (without Phenol Red, Gibco) and Neural Basal Media (Gibco) containing penicillin/streptomycin and Glutamax (1%), N2 and B27 supplements (Gibco), non essential amino acids (0.1 mM), sodium pyruvate (1 mM), Hepes (5 mM), heparin (2 mg/l), bovine serum albumin (25 mg/l) and β-mercaptoethanol (0.01 mM). We added fresh recombinant human EGF (R&D Systems) and FGF (Invitrogen) to 20 ng/ml and 10 ng/ml final, respectively.

extract_protocol:
The 4C-seq experimental protocol was based on (Splinter et al., 2012; Stadhouders et al., 2013), using 1% formaldehyde and NlaIII and DpnII as restriction enzymes.
DNA libraries were prepared during Hi-C protocol according to experimental procedures described in (Splinter et al., 2012; Stadhouders et al., 2013)

treatment_protocol: NSCs were infected with lentivirus expressing shRNA control (shC) or shRNA specific for JMJD3 (shJMJD3). Then cells were treated with 5ng/mL TGFβ for 3 hours.

value: 3h TGFb treatment

value: NSC

tag: restriction enzyme

value: NlaIII (first digestion) and DpnII (second digestion)


title: shc 3h Ldlrad4 enh 4C-seq R2

value: shControl


title: Ser5 ChIP-seq in control hESCs replicate 2 (Ser5-H9-2)

description: DNA fragments

value: Active Motif, 61986


title: hnRNPL ChIP-seq in CFIm25 KO hESCs replicate 1 (hnRNPL-KO8-1)

description: DNA fragments

value: Proteintech, 18354-1-AP


title: hnRNPL ChIP-seq in control hESCs replicate 1 (hnRNPL-H9-1)

description: DNA fragments


title: WT_FST_E111

value: Control


title: shJMJD3 3h Ldlrad4 enh 4C-seq R1


title: Ser2 ChIP-seq in control hESCs replicate 2 (Ser2-H9-2)

description: DNA fragments


title: LEO1 ChIP-seq in control hESCs replicate 2 (LEO1-H9-2)

description: DNA fragments


title: hnRNPL ChIP-seq in CFIm25 KO hESCs replicate 2 (hnRNPL-KO8-2)

description: DNA fragments


title: WT_FST_E108


title: MM_FST_E335


title: shc 3h Ldlrad4 enh 4C-seq R1


title: TBP ChIP-seq in CFIm25 KO hESCs replicate 2 (TBP-KO8-2)

description: DNA fragments


title: PKO_FST_E149


title: TBP ChIP-seq in CFIm25 KO hESCs replicate 1 (TBP-KO8-1)

description: DNA fragments


title: hnRNPL ChIP-seq in control hESCs replicate 2 (hnRNPL-H9-2)

description: DNA fragments


title: Ser5 ChIP-seq in CFIm25 KO hESCs replicate 2 (Ser5-KO8-2)

description: DNA fragments


title: WT_FST_E197


title: shc 0h Ldlrad4 enh 4C-seq R2

value: No TGFb treatment


title: CUT&RUN H3K9me3  Ly49G2 both alleles NK cells

city: Berkeley

first: Djem

middle: Ulian

last: Kissiov

address: 485 Weill Hall

department: MCB

institute: UC Berkeley

data_processing:
Library strategy: CUT&RUN
Raw data were assessed using FastQC
fastq files were aligned to the mm10 reference genome using bowtie2 with the --sensitive parameter
Mitochondrial reads were removed using samtools
PCR duplicate reads were revoed using Picard
Reads mapping to blacklisted regions (ENCODE mm10 database) were removed using bedtools.
Data were normalized to signal per million reads (SPRM) when calling narrow peaks with macs2.
The resulting bedgraph files were converted to bigwigs using the bedGraphToBigWig program from UCSC.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig
SNPs between the C57BL/6 and BALB/c genomes were sourced from the Wellcome Sanger Institute Mouse Genomes Project dbSNP (v142)
Delineation of allele-informative reads
SNPs annotated by the database were replaced by an ‘N’ in the mm10 reference genome using SNPsplit (Babraham Institute)
ATAC-seq datasets were aligned to the N-masked reference genome.
Allele-informative reads were flagged with SNPsplit, and processed and normalized as the rest of the files
Genome_build: mm10/N-masked
Supplementary_files_format_and_content: bigwig

source_name: IL-2 expanded NK cells

growth_protocol: Primary fresh splenic NK cells were isolated from single cell splenocyte suspensions by FACS sorting the indicated NK cell populations. CUT&RUN experiments were performed using splenocyte cultures in 1000U/mL IL-2 + 5% FCS RPMI-1640 cultures. Crude splenocytes were cultured in IL-2 containing medium for 48 hours, then the indicated NK cell populations were FACS sorted and further cultured in IL-2 containing medium for 7-10 days. IL-2 cultures were maintained at a density of ~1 million cells per mL.

extract_protocol:
The ATAC-seq Tn5 transposase reaction was performed on a crude Igepal CA-630 nuclear prep from ~50,000 NK cells. CUT&RUN experiments were performed on ConA-bead immobilized cells permeabilized with a 0.05% Digitonin solution.
ATAC-seq libraries were constructed using Nextera compatible primers. CUT&RUN libraries were constructed using the New England Biolabs Ultra II DNA library prep kit for Illumina

value: IL-2 expanded NK cells

value: (B6 x BALB/c)F1 hybrid

tag: allelic expression status

value: Ly49G2 both alleles

tag: genome alig

tag: antibody

value: anti-H3K9me3 (ab8898)


title: YBX1 ChIP-seq in CFIm25 KO hESCs replicate 1 (YBX1-KO8-1)

description: DNA fragments

value: human embroynic stem cell line H9

value: Proteintech, 20339-1-AP


title: Ser5 ChIP-seq in control hESCs replicate 1 (Ser5-H9-1)

description: DNA fragments

value: control


title: CUT&RUN H3K27me3  Ly49G2 negative NK cells

value: Ly49G2 negative


title: ChIP-seq input for control hESCs (input_H9)

description: DNA fragments


title: shc 3h Aopep enh 4C-seq R2

city: Barcelona


title: shc 0h Ldlrad4 enh 4C-seq R1


title: RNAPII ChIP-seq in CFIm25 KO hESCs replicate 2

extract_protocol:
Crosslinked DNA-proteins were fragmented with ChIP-IT® Express Enzymatic Shearing Kit (Active Motif),cell lysates were further subject to IP with antibodies targeting specific protein. Iped DNA-protein were de-crosslinked, DNA was purified and subjected to library preparation.
ChIP-seq library preparation kit (Vazyme, catlog: ND607-01) was used for preparation of ChIP-seq libraries.

value: H9 cell line

value: human embryonic stem cells

value: Active Motif  catlog. 39497

value: CFIm25 KO


title: TBP ChIP-seq in control hESCs replicate 1 (TBP-H9-1)

description: DNA fragments


title: Ser5 ChIP-seq in CFIm25 KO hESCs replicate 1 (Ser5-KO8-1)

description: DNA fragments


title: RNAPII ChIP-seq in CFIm25 KO hESCs replicate 1


title: CUT&RUN H3K9me3  Ly49G2 negative NK cells


title: YBX1 ChIP-seq in control hESCs replicate 2 (YBX1-H9-2)

description: DNA fragments


title: RNAPII ChIP-seq in control hESCs replicate 1


title: YBX1 ChIP-seq in CFIm25 KO hESCs replicate 2 (YBX1-KO8-2)

description: DNA fragments


title: TBP ChIP-seq in control hESCs replicate 2 (TBP-H9-2)

description: DNA fragments


title: CUT&RUN H2AK119ub1  Ly49G2 both alleles NK cells

value: anti-H2AUb1 (D27C4)


title: CUT&RUN H3K4me3 Ly49G2 both alleles NK cells

value: anti-H3K4me3 (ab8580)


title: shJMJD3 3h Aopep enh 4C-seq R2

value: 3h TGFb treatment

value: NSC

value: NlaIII (first digestion) and DpnII (second digestion)


title: ChIP-seq input for CFIm25 KO hESCs (input-KO8)

description: DNA fragments


title: YBX1 ChIP-seq in control hESCs replicate 1 (YBX1-H9-1)

description: DNA fragments


title: shc 0h Aopep enh 4C-seq R2

value: No TGFb treatment

value: shControl


title: ChIP-seq input for CFIm25 KO hESCs


title: shc 0h Aopep enh 4C-seq R1


title: shJMJD3 3h Aopep enh 4C-seq R1


title: CUT&RUN H3K4me2 Ly49G2 both alleles NK cells

value: IL-2 expanded NK cells

value: (B6 x BALB/c)F1 hybrid

value: Ly49G2 both alleles

value: anti-H3K4me2 (ab7766)


title: shc 3h Aopep enh 4C-seq R1


title: RNAPII ChIP-seq in control hESCs replicate 2

value: control


title: CUT&RUN H3K27ac Ly49G2 both alleles NK cells

value: anti-H3K27ac (ab4729)


title: ChIP-seq input for control hESCs

value: H9 cell line


title: 3'-seq profiling in CFIm25 KO human embryonic stem cells (H9 cell line)-replicate 3

description:
CFIm25 KO 3
ko-3

data_processing:
adaptor related reads, unknown reads,low quality reads (more than half of  the nucleotides whose Qphred<=20), were removed
read 1 sequence was reverse complemented, 3' polyA was trimmed, and mapped to human genome (hg19), allowing up to two mismatches using Bowtie2 with the settings ‘bowtie2 -p 28 -N 1 -k 1′. A poly(A) junction is where the 3′ end of the read maps.Internal priming reads were removed.
For the analysis, we first mapped and clustered the reads to Ensembl genes (GRCh37.75). Next we used Fisher's exact test to compare the ratio of the read counts of one PAS to the total read counts the same gene between two samples. PASes with an adjusted P-value <0.01 (adjusted by Benjamini–Hochberg method) were considered as differentially used.To create mRNA alternative polyadenylation (APA) profiling, we selected two PASes with the smallest P-values for each gene with multiple PASes. The PAS closer to the transcript start site is designated as the proximal PAS and the other as distal. We then calculated the corresponding proximal/distal ratio. PAS pairs with an adjusted P-value <0.01 and |log2(control/CFIm25 KO-proximal/distal ratio)| > 0.5 are highlighted.
Genome_build: hg19
Supplementary_files_format_and_content: The processed data file includes all clustered PASs, fold change, P value, and gene annotation. It is presented as xls file.

source_name: human embryonic stem cells

extract_protocol:
Total RNAs were extracted with Trizol reagent (Thermo fisher); cellular poly(A+) RNAs.
library preparation follows lexogen kit manual (cat. 016.24)
PCR product was sequenced with Novaseq PE150 strategy.

value: human embryonic stem cell line H9

tag: technique

value: CRISPR-Cas9 mediated KO


title: shJMJD3 + JMJD3 3h Chst8 enh 4C-seq R2


title: CUT&RUN H3K27ac Ly49G2 negative NK cells

value: Ly49G2 negative


title: CUT&RUN H3K4me1 Ly49G2 both alleles NK cells

value: anti-H3K4me1 (ab8895)


title: 3'-seq profiling in control human embryonic stem cells (H9 cell line)-replicate 2

description:
control KO 2
h9-2

value: control KO


title: CUT&RUN H3K4me3 Ly49G2 negative NK cells

value: anti-H3K4me3 (ab8580)


title: 3'-seq profiling in CFIm25 KO human embryonic stem cells (H9 cell line)-replicate 2

description:
CFIm25 KO 2
ko-2

value: CFIm25 KO


title: CFIm25 KO+ 3Flag-CFIm25 overexpression-H9-rep1

data_processing:
adaptor related reads, unknown reads,low quality reads (more than half of  the nucleotides whose Qphred<=20), were removed
clean reads were aligned with hg38 genome using HISAT2 software
gene expression quantification was performed with featureCounts tools in subread software
DESeq2 software was used to identify genes showing differential expression in control and CFIm25 KO cells
Genome_build: hg38
Supplementary_files_format_and_content: DESeq2 software was used to identify genes showing differential expression in control and CFIm25 KO cells. The processed data file includes gene ID, RPM value for each sample, fold change, P value, and gene annotation. It is presented as xls file.

growth_protocol: control and CFIm25 KO+ 3Flag-CFIm25 overexpression-H9 were grown in mTeSR medium

extract_protocol:
Total RNAs were extracted with Trizol reagent (Thermo fisher)
poly(A+) RNAs were enriched with oligod(T) beads, fragmented with NEB fragmentation buffer, and further reverse transcribed. After second strand synthesis,double strand products were ligated to adaptors. The ligated product was used for further PCR library amplification.
PCR product was sequenced with Novaseq PE150 strategy.

value: human embryonic stem cells

value: CFIm25 KO+ 3Flag-CFIm25 overexpression


title: CFIm25 KO+ 3Flag-CFIm25 overexpression-H9-rep2


title: shJMJD3 + JMJD3 3h Chst8 enh 4C-seq R1

value: 3h TGFb treatment

value: NSC

value: NlaIII (first digestion) and DpnII (second digestion)


title: control H9-rep2


title: 3'-seq profiling in control human embryonic stem cells (H9 cell line)-replicate 1

description:
control KO 1
h9-1


title: poly(A+)-seq profiling in CFIm25 KO human embroynic stem cells (H9 cell line)-replicate 2


title: shc 0h Chst8 enh 4C-seq R2

value: No TGFb treatment

value: shControl


title: shJMJD3 3h Chst8 enh 4C-seq R2


title: CUT&RUN H3K4me2 Ly49G2 negative NK cells

value: IL-2 expanded NK cells

value: (B6 x BALB/c)F1 hybrid

value: anti-H3K4me2 (ab7766)


title: CUT&RUN H3K4me1 Ly49G2 negative NK cells


title: poly(A+)-seq profiling in CFIm25 KO human embroynic stem cells (H9 cell line)-replicate 1


title: poly(A+)-seq profiling in control human embroynic stem cells (H9 cell line)-replicate 1


title: control H9-rep1

value: H9 cell line

value: control


title: shc 3h Chst8 enh 4C-seq R2


title: shc 3h Chst8 enh 4C-seq R1


title: shJMJD3 3h Chst8 enh 4C-seq R1


title: SUPM2_ZFP91_R2_ChIPseq

city: Guangzhou

first: Wenchao

last: Wu

state: Guangdong

address: 651 Dongfeng Road East, Yuexiu District,

institute: Sun Yat-sen University Cancer Center

description: SUPM2 ZFP91 ChIPseq replicate 2

data_processing:
Illumina Casava1.8 software used for basecalling.
ChIP-seq reads were aligned to human reference genome using BWA (v0.7.12).
Peak detection was performed with MACS2 (v2.1.0)
Genome_build: hg38
Supplementary_files_format_and_content: Bigwig files for each sample

growth_protocol: Chromatin immunoprecipitation (ChIP) was performed on SU-DHL-1 parental, SU-DHL-1 lenalidomide-regrown cells, SU-DHL-1 cells with JUN-KO, Karpas 299, SMZ-1, and SUP-M2 cells (2x10^7).

extract_protocol:
The crosslinking was reversed overnight at 65 °C. Input and ChIPed DNA was cleaned up and submitted to Novogene (Sacramento, CA) for libraries construction and sequencing.
Immunoprecipitated DNA sample quality was assessed by DNA Tapestation (Agilent Technologies Inc., California, USA) and quantified by Qubit 2.0 DNA HS assay (ThermoFisher, Massachusetts, USA). The KAPA HyperPrep kit (Roche, Indianapolis, USA) was used for library preparation and indexing was performed using Illumina 8-nt dual-indices. Final libraries were quantified by Qubit 2.0 (ThermoFisher, Massachusetts, USA) and run on TapeStation D1000 ScreenTape (Agilent Technologies Inc., California, USA) to evaluate the quality of the purified libraries. Final library size was approximately 300 bp. Equimolar pooling of libraries was performed based on QC values and sequenced on an Illumina NovaSeq S4 (Illumina, California, USA) with a read length configuration of 150 PE for 80M PE reads per sample (40M in each direction).

treatment_protocol: The ChIP assay was performed with EZ-ChIP kit (Cell Signaling Technology, #9003) following the manufacturer’s instruction. Briefly, cells were fixed in 1% formaldehyde at room temperature for 10 min, quenched with 0.125 M glycine for 5 min at room temperature, washed with ice-cold PBS. The cells were lysed in ice-cold 1 x Buffer A + DTT + Protease Inhibitor Cocktail (PIC) for 10 min and resuspend in 2 ml 1 x Buffer B + DTT. The chromatin was digested by 2 µl of Micrococcal Nuclease for 20 min at 37°C with frequent mixing. The digestion was stopped by adding 20 µl 0.5M EDTA. Nuclei were lysed by sonication (Qsonica) in 1 x ChIP Buffer + PIC with 3 sets of 20% power of pulses for 15 sec and pause for 15 sec in between. The lysates were then centrifuged for 10 min at 4 °C, supernatants collected and diluted with 4 volume of 1 x ChIP Buffer + PIC. A small portion (2%) of the digested chromatin was set aside as input sample and stored at -20°C. For immunoprecipitation (IP) reaction, 10 µg of ChIP-Grade antibody was added to IP samples and incubate end over end overnight at 4°C. The following day, ChIP-Grade Protein G Magnetic Beads were added to IP reaction and incubated end over end at 4°C for 2 h. Beads were washed with low-salt buffer, high-salt buffer, and LiCl buffer. DNA was then eluted in elution buffer.

value: Cerebrospinal fluid

value: ALK+ ALCL

value: Anti-ZFP91, Bethyl Laboratories, A303-245A


title: poly(A+)-seq profiling in CFIm25 KO human embroynic stem cells (H9 cell line)-replicate 3

value: CRISPR-Cas9 mediated KO


title: CUT&RUN control mouse IgG2a k_rep1

value: Biolegend mouse IgG2a k (MOPC-173)


title: 3'-seq profiling in CFIm25 KO human embryonic stem cells (H9 cell line)-replicate 1

description:
CFIm25 KO 1
ko-1

value: human embryonic stem cell line H9

value: CFIm25 KO


title: shc 0h Chst8 enh 4C-seq R1


title: SUPM2_H3K27ac_ChIPseq

description: SUPM2 H3K27ac ChIPseq

value: Anti-H3K27ac, Cell Signaling Technology, #8173


title: poly(A+)-seq profiling in control human embroynic stem cells (H9 cell line)-replicate 2

value: control KO


title: CUT&RUN control mouse IgG2a k_rep2


title: ATAC-seq NKG2D positive NK cells

data_processing:
Raw data were assessed using FastQC
fastq files were aligned to the mm10 reference genome using bowtie2 with the --sensitive parameter
Mitochondrial reads were removed using samtools
PCR duplicate reads were revoed using Picard
Reads mapping to blacklisted regions (ENCODE mm10 database) were removed using bedtools.
Data were normalized to signal per million reads (SPRM) when calling narrow peaks with macs2.
The resulting bedgraph files were converted to bigwigs using the bedGraphToBigWig program from UCSC.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig
SNPs between the C57BL/6 and BALB/c genomes were sourced from the Wellcome Sanger Institute Mouse Genomes Project dbSNP (v142)
Delineation of allele-informative reads
SNPs annotated by the database were replaced by an ‘N’ in the mm10 reference genome using SNPsplit (Babraham Institute)
ATAC-seq datasets were aligned to the N-masked reference genome.
Allele-informative reads were flagged with SNPsplit, and processed and normalized as the rest of the files
Genome_build: mm10/N-masked
Supplementary_files_format_and_content: bigwig

source_name: Primary splenic NK cells

value: Primary splenic NK cells

value: B6-NKG2D^5'E Deletion

value: NKG2D positive


title: ATAC-seq NKG2D negative NK cells

value: NKG2D negative


title: SUPM2_ZFP91_R1_ChIPseq

description: SUPM2 ZFP91 ChIPseq replicate 1


title: SMZ1_ZFP91_R1_ChIPseq

description: SMZ1 ZFP91 ChIPseq replicate 1

value: Ascites

value: PTCL-NOS


title: SMZ1_ZFP91_R2_ChIPseq

description: SMZ1 ZFP91 ChIPseq replicate 2


title: SUPM2_Input_ChIPseq

description: SUPM2 Input for ChIPseq


title: ATAC-seq NKG2A both alleles NK cells

description:
processed data file (B6 genome-aligned): NKG2A-DP_genome1.final.bw
processed data file (BALB genome-aligned): NKG2A-DP_genome2.final.bw

value: (B6 x BALB/c)F1 hybrid

value: NKG2A both alleles


title: SUPM2_H3K4me3_ChIPseq

description: SUPM2 H3K4me3 ChIPseq

value: Cerebrospinal fluid

value: Anti-H3K4me3, Cell Signaling Technology, #9751


title: ATAC-seq NKG2A BALB allele only NK cells

description:
processed data file (B6 genome-aligned): NKG2A-BALB_genome1.final.bw
processed data file (BALB genome-aligned): NKG2A-BALB_genome2.final.bw

value: NKG2A BALB allele only


title: ATAC-seq NKG2A B6 allele only NK cells

description:
processed data file (B6 genome-aligned): NKG2A-B6_genome1.final.bw
processed data file (BALB genome-aligned): NKG2A-B6_genome2.final.bw

value: NKG2A B6 allele only


title: ATAC-seq NKG2A negative NK cells

description:
processed data file (B6 genome-aligned): NKG2A-DN_genome1.final.bw
processed data file (BALB genome-aligned): NKG2A-DN_genome2.final.bw

value: NKG2A negative


title: F11r KO + WD + α4β7 mAb 3

city: Pittsburgh

first: Reben

last: Raeman

state: PA

address: 200 Lothrop St, S408 South BST

department: Pathology

institute: University of Pittsburgh

data_processing:
Reads were mapped to the mouse genome build mm10 using HISAT (Kim et al. 2015), and gene expression was normalized and quantified using HTSEQ default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: wig files were generated using Python

source_name: Liver

extract_protocol:
Total RNA was isolated from mouse liver with miRNeasy Mini Kit (Qiagen) followed by manufacturer’s instructions.
RNA samples were sequenced using 3'-Tag-RNA-Seq library prep protocol at the UC Davis Genome Center using the Illumina HiSeq 4000 platform.

treatment_protocol: α4β7 mAb (250 µg/mouse; DATK32; Bioxcell, West Lebanon, NH) was administered twice weekly for four weeks starting at week four after the initiation of WD.

value: α4β7 mAb

value: Liver

value: Male

value: F11r KO

value: C57BL/6n background

tag: age

value: 15-16 weeks at sacrifice


title: F11r KO + WD + α4β7 mAb 2

tag: tissue


title: Karpas299_ZFP91_R1_ChIPseq

description: Karpas299 ZFP91 ChIPseq replicate 1

value: peripheral blood

value: ALK+ ALCL

value: Anti-ZFP91, Bethyl Laboratories, A303-245A


title: SMZ1_H3K4me3_ChIPseq

description: SMZ1 H3K4me3 ChIPseq

value: Ascites

value: PTCL-NOS


title: F11r KO + WD + α4β7 mAb 4


title: Karpas299_H3K4me3_ChIPseq

description: Karpas299 H3K4me3 ChIPseq


title: SUDHL1_JUN_KO_Input_ChIPseq

description: SUDHL1 JUN-KO cells Input for ChIPseq

value: lymph node


title: SMZ1_Input_ChIPseq

description: SMZ1 Input for ChIPseq


title: SUDHL1_JUN_WT_ZFP91_ChIPseq

description: SUDHL1 JUN-WT cells ZFP91 ChIPseq


title: SMZ1_H3K27ac_ChIPseq

description: SMZ1 H3K27ac ChIPseq

value: Anti-H3K27ac, Cell Signaling Technology, #8173


title: Karpas299_Input_ChIPseq

description: Karpas299 Input for ChIPseq


title: SUDHL1_JUN_WT_Input_ChIPseq

description: SUDHL1 JUN-WT cells Input for ChIPseq


title: F11r KO + WD + α4β7 mAb 1


title: Karpas299_H3K27ac_ChIPseq

description: Karpas299 H3K27ac ChIPseq


title: SUDHL1_RG3_ZFP91_ChIPseq

description: Len-regrown3 ZFP91 ChIPseq


title: SUDHL1_JUN_KO_ZFP91_ChIPseq

description: SUDHL1 JUN-KO cells ZFP91 ChIPseq


title: SUDHL1_P_IKZF1_ChIPseq

description: SUDHL1 parental IKZF1 ChIPseq

value: Anti-IKZF1, Abcam, Ab229275


title: HD Neuruloid day 4

city: Neew York City

first: Ji-Dung

last: Luo

state: NY

address: 1230 York Avenue

department: Bioinformatics Resource Center

institute: The Rockefeller University

description: humnan embryonic stem cells were obtained from patient with 56-CAG variation\ in HTT locus. Neuruloid differenciation was induced by BMP4 treatment. The neuruloid were harvested on day 4 after treatmeent and was under going single-cell analysis. Library contruction was made by using Chromium™ Single Cell 3’ Library and Gel Bead Kit (V3) then sequenced by Illumina NextSeq 500. The following analysis, including fastq file generation, alingnment to hg19, and counting,  was performed with Cellranger (version 6).

data_processing:
The fastq files were generated with mkfastq fiunction of Cellranger (V6)
The fastq files were aligned to hg19 and followed by counting with count function of Cellranger (V6). The raw count matrix and cell barcodes are listed in the processed data files.
Genome_build: hg19
Supplementary_files_format_and_content: raw count matrix for each sample was in gziped matrix file (matrix.mtx.gz).
Supplementary_files_format_and_content: cell barcodes for eahc sample was listed in gzipped tsv file (barcode.tsv.gz)
Supplementary_files_format_and_content: gene features detected for eahc sample was listed in gzipped tsv file (features.tsv.gz)

source_name: differentiated hESC

growth_protocol: All hESC lines were grown in HUESM medium that was conditioned with mouse embryonic fibroblasts and supplemented with 20 ng/mL bFGF (MEF-CM; Deglincerti et al., 2016). Cells were grown on tissue culture dishes coated with Geltrex solution (Life Technologies) and tested for mycoplasma at two-month intervals.

extract_protocol:
No actual RNA extration in this study. The cell separation and library construction was folowing th user manual of Chromium™ Single Cell 3’ Library and Gel Bead Kit (V3)
The single-cell library contruction for each sample was contracuted with following the manual of Chromium™ Single Cell 3’ Library and Gel Bead Kit (V3)

treatment_protocol: Micropatterned glass coverslips with neuruloids 500 μm in diameter were grown in  3 ng/mL BMP4 from RUES2 hESCs and the isogenic 56CAG HD line. The cells were harvested on day 4 after treatment.

tag: disease status

value: HD

value: differentiated hESC


title: Wt Neuruloid day 4

description: humnan embryonic stem cells were obtained from heatly countrol with wild-type in HTT locus. Neuruloid differenciation was induced by BMP4 treatment. The neuruloid were harvested on day 4 after treatmeent and was under going single-cell analysis. Library contruction was made by using Chromium™ Single Cell 3’ Library and Gel Bead Kit (V3) then sequenced by Illumina NextSeq 500. The following analysis, including fastq file generation, alingnment to hg19, and counting,  was performed with Cellranger (version 6).

value: wild-type


title: F11r KO + WD + IgG 3

value: IgG

tag: gender


title: SUDHL1_RG2_ZFP91_ChIPseq

description: Len-regrown2 ZFP91 ChIPseq


title: Karpas299_ZFP91_R2_ChIPseq

description: Karpas299 ZFP91 ChIPseq replicate 2


title: SUDHL1_RG1_ZFP91_ChIPseq

description: Len-regrown1 ZFP91 ChIPseq


title: F11r KO + WD + IgG 2

value: Liver

tag: strain


title: SUDHL1_P2_ZFP91_ChIPseq

description: SUDHL1 parental ZFP91 ChIPseq replicate 2

tag: cell type


title: HeLa-TFEB-Flag-siRNA-FACT-9

city: Bethesda

first: Jose

last: Martina

state: Maryland

address: 50 South Dr., Building 50, Room 3533

department: NHLBI, CDBC

institute: NIH

description: 9_4427NIH_HeLa-siRNA-FACT-9_RNASeq_hs_i23

data_processing:
Basecalling was performed using Real Time Analysis version 2 (RTA2) software.
RTA2 software was used for basecalling and STAR algorithm version 2.5.2b with default settings was used to align the data to the human GRCh38/hg38 genome assembly to generate BAM files.
Differential gene expression analysis was performed using DESeq2 software version v1.14.1.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for all samples.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Excel file containing DESeq2-normalized gene counts and the results of the performed differential analyses

source_name: HeLa-TFEB-Flag

growth_protocol: HeLa cells stably expressing TFEB-Flag were grown in DMEM, high glucose, GlutaMAX, sodium pyruvate (Gibco, 10569044) supplemented with 10% fetal bovine serum (Invitrogen, 21041-025), 100 U/ml penicillin and 100 μg/ml streptomycin (Gibco, 2114).

extract_protocol:
Total RNA was isolated from cells using the Qiagen RNeasy Mini Kit (Qiagen, cat# 74104). For each sample, 0.5 μg of total RNA was then used in Illumina’s TruSeq Stranded mRNA Library kit (Cat# 20020594) for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with 100 nM of either siRNA-Control or siRNA-FACT for 72h. Then, cells were incubated with 50 μM sodium arsenite for additional 6h.

tag: cell line background

value: HeLa

value: Epithelial cells

tag: disease

value: Adenocarcinoma

value: Treated with 50 μM sodium arsenite for 6h

tag: sirna treatment

value: Treated with 100 nM siRNA-FACT for 72h


title: SUDHL1_P3_ZFP91_ChIPseq

description: SUDHL1 parental ZFP91 ChIPseq replicate 3

value: ALK+ ALCL

tag: cell line

tag: chip antibody


title: F11r KO + WD + IgG 1

tag: treatment

value: Male

tag: genotype

value: F11r KO

value: C57BL/6n background

value: 15-16 weeks at sacrifice


title: SUDHL1_RG3_H3K27ac_ChIPseq

description: Len-regrown3 H3K27ac ChIPseq

value: lymph node

value: Anti-H3K27ac, Cell Signaling Technology, #8173


title: HeLa-TFEB-Flag-siRNA-FACT-7

description: 7_4427NIH_HeLa-siRNA-FACT-7_RNASeq_hs_i21


title: HeLa-TFEB-Flag-siRNA-FACT-8

description: 8_4427NIH_HeLa-siRNA-FACT-8_RNASeq_hs_i22


title: SUDHL1_P1_ZFP91_ChIPseq

description: SUDHL1 parental ZFP91 ChIPseq replicate 1

value: Anti-ZFP91, Bethyl Laboratories, A303-245A


title: SUDHL1_P_H3K27ac_ChIPseq

description: SUDHL1 parental H3K27ac ChIPseq


title: SUDHL1_RG1_H3K27ac_ChIPseq

description: Len-regrown1 H3K27ac ChIPseq


title: HeLa-TFEB-Flag-siRNA-Control-2

description: 2_4427NIH_HeLa-siRNA-Control-2_RNASeq_hs_i15

value: Treated with 100 nM siRNA-Control for 72h


title: SUDHL1_RG3_H3K4me3_ChIPseq

description: Len-regrown3 H3K4me3 ChIPseq

value: Anti-H3K4me3, Cell Signaling Technology, #9751


title: HeLa-TFEB-Flag-siRNA-Control-1

description: 1_4427NIH_HeLa-siRNA-Control-1_RNASeq_hs_i14