title: U87 control  replicate 2

value: empty vector (neomycin)


title: LPS_JQ1_2 [ATAC-seq]

status: Public on Mar 20 2022

type: SRA

city: Chapel Hill

first: Shehzad

middle: Z

last: Sheikh

state: North Carolina

address: 111 Mason Farm Road

department: Center of Gastrointestinal Biology and Disease

country: USA

institute: University of North Carolina at Chapel Hill

library_source: genomic

data_processing:
processed PEPATAC v0.9.0
uniquely mapped reads aligned using bowtie2
peaks called using MACS2
post-processing using ChIPSeeker
Genome_build: mm9
Supplementary_files_format_and_content: counts.peaks

molecule: genomic DNA

organism: Mus musculus

source_name: BMDMs_LPS Stimulated_(+)-JQ1

growth_protocol: Bone marrow was harvested from Il10-/- mice (C57BL/6J background; n=3) and cultured for 6 days in RPMI 1640 media supplemented with 10% FBS and 10% L929 conditioned media.

extract_protocol:
Prepared according to Buenrostro et. al. Cells were pelleted and washed with cold PBS followed by lysis using cold lysis buffer (10mM Tris-HCl, 10mM NaCl, 3 mM MgCl2, and 0.1% NP-40). Pelleted nuclei underwent transposition using the Nextera DNA Library Prep Kit (Illumina #FC-121-1030). Samples were resuspended in the transposition reaction (12.5µL 2x TD buffer, 2 µL transposase, and 10.5 µL nuclease-free water) and incubated at 37C for 1 hour at 1000 RPM. Transposed DNA samples were purified using the Qiagen MinElute Kit (#28204).
Prepared according to Buenrostro et. al. Amplified using 1x PCR master mix (NEB #M0541S) and 25µM Ad1_noMX and Ad2.* indexing primer for 10-14 cycles. Libraries were purified and size selected by magnetic separation using Agencourt AMPure XP magnetic beads (Beckman Coulter #A63880)

treatment_protocol: Mature BMDMs were re-seeded at a density of 5x10^5 cells/well and treated for 12 hours with 500nM (+)-JQ1, 10ng/mL IL-10 or remained untreated, followed by the addition of LPS (50ng/mL) or PBS for an additonal 4 hours. Cells were collected in TRIzol at the end of 16 hours.

tag: strain background

tag: genotype

tag: cell type

value: Bone Marrow Derived Macrophages (BMDMs)

tag: stimulation

value: LPS Stimulated

tag: treatment


title: Unstimulated_JQ1_1 [ATAC-seq]

value: Unstimulated


title: Unstimulated_Untreated_3 [ATAC-seq]

value: Untreated


title: 1KO-5mC_G2

city: Toyonaka

first: Takamasa

last: Ito

state: Osaka

address: 1-1 Machikaneyama

department: Biological Science

country: Japan

institute: Osaka University

data_processing:
Raw sequence reads were trimmed using Trim Galore!, then mapped using Bowtie2 to mm10 genome.
The Sam file was converted to a bam file using the Samtools.
DIP-seq data were normalized and generated wig files using MEDIPS .
Wig files were then converted to bigwig files using WigToBigWig (UCSC).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig (.bw) files containing normalized value using MEDIPS software

source_name: mouse embryonic stem cells

growth_protocol: 1KO ESCs were cultured on mitomycin C-treated mouse embryonic fibroblasts (MEFs) in ESC medium [D-MEM/Ham’s F12 (Wako, Osaka, Japan), 10% fetal bovine serum (Corning, NY, USA), 1× penicillin-streptomycin and 2 mM L-glutamate (Gibco®, Thermo Fisher Scientific), 0.1 mM β-mercaptoethanol (Signa-Aldrich), and 10^3 U/ml ESGRO® LIF (Merck, Kenilworth, NJ, USA)] and grown under 5% CO2 at 37˚C. The medium was changed daily.

extract_protocol:
One μg of genomic DNA sheared to 200-500 bp using the LE220 Focused-ultrasonicator (Covaris) was end-repaired and A-tailed. The Illumina PE adapter-ligated DNA was heat-denatured and applied to MeDIP overnight with a monoclonal antibody for 5mC (AnaSpec, Inc.). hMeDIP was performed using a rat monoclonal antibody (Diagenode) for 5hmC. The IP material was recovered with a secondary antibody of rabbit and rat anti-mouse IgG, respectively (Jackson ImmunoResearch) along with protein A/G (Thermo Fisher Scientific), followed by digestion with 20 mg/ml Proteinase K (Invitrogen) for 2 hours.
IP DNA was purified using the MinElute PCR Purification Kit (Qiagen). Confirmation of concentration of 5mC and 5hmC DNA was evaluated by qPCR using positive and negative control primers. The final library amplification was performed using Phusion® hot start II DNA polymerase and 5× Phusion® GC Buffer (Thermo Fisher Scientific) with Illumina paired-end index primers. The PCR-amplified library was size-selected for 220–450-bp fragments on an 8% PAGE gel. The library was normalized based on molarity and pooled for sequencing using v4 ready-to-load reagents for HiSeq 2500 System (Illumina) at 75-bp paired-end reads.

tag: cell line

value: mouse embryonic stem cells

tag: cell cycle

tag: antibody


title: ExVivoBlood_stroke_rep4

type: RNA

city: Guangzhou

first: Wen

last: Jiang

state: Guangdong

address: 111 Dade Road

department: Department of Second Institute of Clinical Medicine

country: China

institute: Guangzhou University of Traditional Chinese Medicine

description: Gene expression in stroke human blood

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity > 9.0 pmol Cy3 per μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions.On completion of the fragmentation reaction, 250 ml of 2x GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Hybridization Chamber(Agilent p/n G2534A) for 17 hours at 65 °C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with Gene Expression Wash Buffer 1 (Agilent) and 1 minute with 37 °C Gene Expression Wash Buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately to minimize the impact of environmental oxidants on signal intensities by Agilent Microarray Scanner (Agilent p/n G2565BA)(Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent).Add the images (.tif) to be extracted to the FE Project.Set FE Project Properties.Check the Extraction Set Configuration.Save the FE Project (.fep) by selecting File > Save As and browse for desired location. Select Project > Start Extracting and export data to txt.

molecule: total RNA

organism: Homo sapiens

source_name: Peripheral Blood

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1ug RNA using the Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442) according to the manufacturer's instructions, followed by RNeasy Mini Kit (Qiagen p/n 74104).   Take 1.5 μl of each sample to determine the yield and specific activity by using the NanoDrop ND-1000.

extract_protocol: RNA isolation was performed by using Trizol (Invitrogen, USA), added into every cryopreserved serum supernatant sample according to the manufacturer’s protocol.The protocol includes homogenization,phase separation,RNA Precipitation and Wash,redissolving the RNA. RNasey Mini Kit(Qiagen p/n 74104) was used to clean up total RNA.Total RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: Blood collection was done once from each participant,and then it was snap frozen and stored at -80℃ until use.

tag: tissue

value: whole blood

tag: condition

value: stroke


title: Mm, J12NSC_1

city: Uppsala

first: Xingqi

last: Chen

address: Husargata

department: Immunology, Genetics and Pathology

country: Sweden

institute: uppsala university

data_processing:
adaptors were trimmed.
ATAC-seq reads were aligned to hg19 using bowtie2 with the following parameters --very-sensitive
duplicate reads were marked and removed with picard tools version 1.119
Reads mapped to repeated regions and chromosomal M were removed.
the rest of reads were shifted +4/-5bp depending on the strand of the read around Tn5 cleavage position and were then extended to 50bp centered by the cleavage position
Peak calling was performed using MACS2 with options  -f BED, -g hs, -q 0.01, --nomodel, --shift 0
Genome_build: hg19 and mm9
Supplementary_files_format_and_content: bigwig

source_name: mouse xenograft glioblastoma stem cell

growth_protocol: Mouse GBM cells (mGCs) were explanted and established as cultures in mouse cancer stem cell media without addition of EGF and FGF2 as described previously.  Surgical samples from GBM patients were obtained and human glioblastoma cell cultures (HGCC) were established from these samples as explained previously (Maturi et al., 2019; Xie et al., 2015). A total of 65 HGCC were used in this paper, among which 59 HGCC were established and sustained in serum-free medium. Whereas 4 HGCC were established and sustained in serum containing medium and 2 HGCC were switched and maintained as serum-free culture from serum containing medium (U3096MG and U3112MG).

extract_protocol:
All the libraries are ATAC protocol, DNA was purified with MiniElution kit
The ATAC library construction was done with standard ATAC-seq protocol.

treatment_protocol: no treatment for the cells

value: brain

value: mouse xenograft glioblastoma stem cells

tag: growth protocol

value: Explanted and established as cultures  in mouse cancer stem cell media


title: Mm, J12NSC_2


title: ExVivoBlood_stroke_rep2

description: Gene expression in stroke human blood


title: Mm, I5NSC_2


title: ExVivoBlood_stroke_rep3

description: Gene expression in stroke human blood


title: Mm, I5NSC_1


title: U87 control  replicate 1

city: Bloomington

first: Heather

middle: Ann

last: Hundley

state: IN

address: 1001 E 3rd St

department: Medical Sciences

institute: Indiana University Bloomington

library_source: transcriptomic

data_processing:
Reads were trimmed using fastp (version 0.20.1)
Reads were aligned to reference genome GRCh38 using STAR (version 2.7.9a)
Read counts for each gene were created using featureCounts from the Subread package (version 2.0.2) and ENSEMBL release 103 as the annotation
Differential expression analysis was performed using the DESeq2 package (version 1.30.1) in R/Bioconductor (R version 4.0.4)
Assembly: GRCh38
Supplementary files format and content: .xlsx files from featurecounts with raw read counts
Supplementary files format and content: .xlsx files from DESeq2 analysis with normalized read counts

molecule: polyA RNA

source_name: U87 cells

growth_protocol: U87 cells were maintained in  Dulbecco’s modified Eagle’s medium (DMEM)  (Mediatech) supplemented with 10% fetal bovine  serum (FBS) (Sigma), 200ug/ml G418, 100ug/ml penicillin and 100  units/ml streptomycin (MediaTech).

extract_protocol:
RNA was isolated using Trizol (Invitrogen), purified by treatment with TURBO DNAase (Ambion) and isolated using the RNeasy Extraction Kit (Qiagen).
Poly-A selected mRNA library preparation was done using KAPPA stranded library preparation kit

treatment_protocol: All cells were incubated at 37°C in 5% CO2 and grown to 80-90% under optimum conditions

tag: expression plasmid

tag: rna source

value: RNA from whole cell lysate


title: Mm, SC112_1


title: ExVivoBlood_control_rep5

description: Gene expression in non-stroke human blood

value: control


title: 1KO-5mC_G1


title: ExVivoBlood_control_rep4


title: 1KO-5hmC_G1

data_processing:
library strategy: hmeDIP-seq
Raw sequence reads were trimmed using Trim Galore!, then mapped using Bowtie2 to mm10 genome.
The Sam file was converted to a bam file using the Samtools.
DIP-seq data were normalized and generated wig files using MEDIPS .
Wig files were then converted to bigwig files using WigToBigWig (UCSC).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig (.bw) files containing normalized value using MEDIPS software


title: U87 ADAR3 replicate 3

value: 3X-FLAG ADAR3 (neomycin)


title: ExVivoBlood_control_rep3


title: 1KO-5hmC_G2


title: ExVivoBlood_control_rep2


title: Leukemia stem cell (LSC)-ILC1 treated 3

status: Public on Mar 19 2022

city: Duarte

first: Zhenlong

last: Li

address: 1500 East Duarte Road

institute: City of hope

data_processing:
Illumina bcl2fastq v2.18.0.12 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using STAR 2.6.0.a with default parameters
The HTSeq software (v.0.6.0) was applied to generate the count matrix, with default parameters. Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using EdgeR 3.28.1.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Spleen

growth_protocol: LSCs were cultured in Iscove's Modified Dulbecco's Media (Thermo Fisher Scientific, USA) with 10% fetal bovine serum (FBS), penicillin (100 U/mL), streptomycin (100 mg/mL), SCF (20 ng/ml), TPO (20 ng/ml), Flt3-L (20 ng/ml), IL-3 (10 ng/ml), and IL-6 (10 ng/ml).

extract_protocol:
The LSCs were re-sorted using BD FACSAriaTM Fusion. Total RNA was isolated from ILC1s or LSCs using a miRNeasy mini kit (QIAGEN).
SMART-Seq® Ultra Low Input RNA Kit for Sequencing–v4 (Takara Bio) was used for getting double-strand cDNA from each sample with 2 ng of input total RNA. The resulting cDNA was sheared using a Covaris LE220 sonicator. The sheared DNA was used for to prepare a sequencing library, using a KAPA HyperPrep Kit. The final libraries were quantified using the Qubit Assay Kit (Thermo Fisher Scientific) and Bioanalyzer (Agilent). Sequencing was performed using the single-read mode of 51 cycles of read1 and 7 cycles of index read with V4 reagents on a Hiseq 2500 system (Illumina). Real-time analysis (RTA) 2.2.38 software was used to process the image analysis and base calling.
polyA RNA-seq without strand information

treatment_protocol: mouse LSCs sorted from MllPTD/WT: Flt3ITD/ITD mice with AML were co-cultured with ILC1s or treated with 10 ng/ml IFN-γ for 3 days

tag: strain

value: Spleen

tag: agent

tag: time point

value: treatment for 3 days


title: Leukemia stem cell (LSC)-ILC1 treated 1


title: ExVivoBlood_stroke_rep1

description: Gene expression in stroke human blood


title: Leukemia stem cell (LSC)-IFN-gamma treated 3

value: IFN-gamma


title: Leukemia stem cell (LSC)-IFN-gamma treated 1


title: Leukemia stem cell (LSC)-untreated 3


title: U87 control  replicate 3

value: empty vector (neomycin)


title: Mm, B8NSC_2


title: Leukemia stem cell (LSC)-untreated 1


title: Leukemia stem cell (LSC)-ILC1 treated 2


title: Leukemia stem cell (LSC)-IFN-gamma treated 2


title: Unstimulated_Untreated_2 [ATAC-seq]

value: Bone Marrow Derived Macrophages (BMDMs)


title: Leukemia stem cell (LSC)-untreated 2


title: ILC1 isolated from AML mice liver 3

source_name: Liver

extract_protocol:
Total RNA was isolated from ILC1s  using a miRNeasy mini kit (QIAGEN).
SMART-Seq® Ultra Low Input RNA Kit for Sequencing–v4 (Takara Bio) was used for getting double-strand cDNA from each sample with 2 ng of input total RNA. The resulting cDNA was sheared using a Covaris LE220 sonicator. The sheared DNA was used for to prepare a sequencing library, using a KAPA HyperPrep Kit. The final libraries were quantified using the Qubit Assay Kit (Thermo Fisher Scientific) and Bioanalyzer (Agilent). Sequencing was performed using the single-read mode of 51 cycles of read1 and 7 cycles of index read with V4 reagents on a Hiseq 2500 system (Illumina). Real-time analysis (RTA) 2.2.38 software was used to process the image analysis and base calling.
polyA RNA-seq without strand information

treatment_protocol: C57BL/6 mice were i.v. injected with or without 1 million C1498 cells. Two weeks later, ILC1s were isolated from the liver of normal mice or AML mice.

value: Liver

tag: disease

value: AML

tag: age

value: post tumor day 14


title: ILC1 isolated from AML mice liver 2


title: ILC1 isolated from AML mice liver 1


title: ILC1 isolated from healthy mice liver 3

value: healthy


title: ILC1 isolated from healthy mice liver 2


title: Rspo WT vs KI 2m infected

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

description: polarity(+)

hyb_protocol: Whole mouse genome 4x44k and 8x60k microarrays were done according to the supplier’s protocol (Agilent Technologies).

scan_protocol: Scanning of microarrays was performed with 5 µm  and extended range (XDR) for 4x44K microarrays and 3µm for 8x60K microarrays using a DNA microarray laser scanner (Agilent Technologies)

data_processing: Raw microarray image data were analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.11.5.1.1, Agilent). The extracted MAGE-ML files were analyzed with the Rosetta Resolver Biosoftware (Rosetta Biosoftware). Intra-array data were normalized with the GE2_1105_Oct12 for 4x44K microarrays and GE2_1200_Dec17 for 8x60K microarrays extraction protocol by the mean of trimmed positive non-flagged/non-control reporters.

source_name: Rspo WT 2m infected

label_protocol: RNA labeling was performed with the Quick-Amp Labeling Kit  (Agilent Technologies) according supplier's instructions.

growth_protocol: All animals were maintained in autoclaved microisolator cages and provided with sterile drinking water and chow ad libitum. Male, 6- to 8-week-old mice were used for this study.

extract_protocol: Total RNA was isolated by the Trizol (Invitrogen) method according the manufacturer´s protocol.

treatment_protocol: Mouse glands from H. pylori infected Rspo3 WT and KI animals were treated with tamoxifen 2 month before euthanasia. Cells  were isolated from the corpus  as previously described.

value: 2 months infected

tag: genotype

value: wildtype

value: corpus

source_name: Rspo KI 2m infected

value: RSPO3 knock-in (KI) mutant


title: ExVivoBlood_control_rep1

value: whole blood


title: GFP+ hiPS

city: Philadelphia

first: Connie

middle: Lan

state: Pennsylvania

address: 415 Curie Boulevard, Room number 415

institute: University of Pennsylvania

description:
10X single cell RNA sequencing
hiPS

data_processing:
Base calling and preliminary quality scoring done in real time on NextSeq500 with RTA 2.0.
Upon downloading our NextSeq sequencing run(s) for single cell RNA-sequencing analysis we mapped reads to the original transcripts and cells using the cellranger pipeline v4.0.0 by 10X Genomics. We began by using cellranger mkfastq with default parameters to demultiplex raw base call files into library-specific FASTQ files. To align FASTQ files to the GRCh38p13 human reference genome and extract gene expression counts matrices, we used cellranger count based on Gencode v32 annotation, filtering and correcting cell identifiers and unique molecular identifiers (UMI) with default settings.
Assembly: GRCh38p13
Supplementary files format and content: *.matrix.mtx: Sparse gene expression matrix: rows are features/genes, columns are cell-associated 10X barcodes (what we call "cellID").
Supplementary files format and content: *.barcodes.tsv: Barcodes
Supplementary files format and content: *.features.tsv: Features/genes

source_name: hiPS cells

growth_protocol: PENN123i-SV20 hiPS cell line was generated as previously described (W. Yang et al. 2015), thawed, and maintained in feeder-free conditions on Geltrex (ThermoFisher, cat. A1413301)-coated dishes in StemMACS iPS Brew-XF medium (Miltenyi, cat. 130-104-368) supplemented with 1% penicillin/streptomycin (Invitrogen, cat. 15140-122). We performed all hiPS culture incubations at 37°C, 5% CO2, 5% O2 and changed the medium every 48 hours. For maintenance, we split cells every 4-5 days at a 1:10 ratio using StemMACS Passaging Solution XF (Miltenyi, cat. 130-104-688).

extract_protocol:
On the day of collection, we used 0.25% trypsin-EDTA (Gibco, cat. 25200-056) to lift cells. To quench trypsinization we used RPMI 1640 +20% FBS following which we used pipetting to generate a single cell suspension. After a 1xDPBS (Invitrogen, cat. 14190-136) wash, we pelleted then resuspended cells in fluorescence-activated cell sorting (FACS) buffer consisting of 1% BSA + 2mM EDTA (from 0.5M EDTA (Life Technologies, cat. 15575-020)) in 1xDPBS, supplemented with 2µM Thiazovivin and 1x Antibiotic-antimycotic (Gibco, cat. 15240-062). Cells were sorted on a MoFlo Astrios machine (Beckman Coulter). In preparation for single cell RNA-sequencing, after gating for live cells and singlets, we collected 15,000 events from each of two GFP positive populations and 300,000 events from each of two GFP negative populations. We spun down and resuspended both sorted GFP positive populations in their entirety according to the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 manufacturer directions (10X Genomics) targeting 10,000 cells for recovery. To match these numbers, we counted 15,000 cells from one of the GFP negative populations and resuspended them in the same way. We generated gel beads-in-emulsion (GEMs) using the 10X Chromium system (10X Genomics, Pleasanton, CA). From these GEMs we extracted barcoded cDNA according to the post-GEM RT-cleanup instructions and amplified cDNA for 11 cycles.
Single-cell RNA sequencing libraries were prepared according to the 10X Genomics single-cell RNA-seq kit v3 protocol. With 10µl of the amplified cDNA we proceeded with fragmentation, end-repair, poly A-tailing, adapter ligation, and 10X sample indexing per the manufacturer’s protocol. We quantified libraries using the Qubit Fluorometer (Thermo Fisher) and Bioanalyzer (Agilent) analysis prior to sequencing on a NextSeq 500 machine (Illumina) using 28 cycles for read 1, 55 cycles for read 2, and 8 cycles for each index.

treatment_protocol: We grew undifferentiated hiPS cells in feeder-free conditions for 4-5 days until they reached ~75% confluency. The day prior to transduction, we used a 4 minute incubation with Accutase (Sigma, cat. A6964) to detach hiPS cells and subsequently counted and seeded cells onto Geltrex-coated 6-well plates at a density of 1x10^5 cells per well in iPS-Brew + 2µM Thiazovivin (Sigma, cat. SML1045-5MG). The next day, to transduce hiPS cells, we added freshly thawed (on ice) virus-laden media (diluted 1:100 in iPS-Brew for all volumes < 10 µl) and polybrene (final concentration, 6 µg/mL) to the cells that had been seeded the day prior, aiming for an MOI of 0.04. We incubated the cells with virus for 6-8 hours and then removed the media, washed the cells with 1x DPBS and added 3 mL of iPS-Brew to each well. After 3 additional days, we again used Accutase to detach the cells and split each infected 6-well well to seed 12-well wells at a density in the range of 3-7x10^5 cells per well in iPS-Brew + 2µM Thiazovivin (Sigma, cat. SML1045-5MG) and moved plates to incubators set to 37°C, 5% CO2, and ambient O2. After 24 hours, we changed the culture medium to iPS-Brew + 1µM Chiron 99021 (Cayman Chemical, cat. 13122) and incubated cells for another 24 hours. On Day 0 to induce cardiac differentiation, we replaced the medium with RPMI/B27-insulin (RPMI 1640 (Invitrogen, cat. 11875085) with 2% B-27 Supplement Minus Insulin (Life Technologies, cat. 17504-044)) medium supplemented with 100ng/mL recombinant human/mouse/rat activin A (R&D systems, cat. 338-AC- 010) and incubated cells for 18 hours. On Day 1, we changed the medium to RPMI/B27-insulin supplemented with 10ng/ml BMP4 (Peprotech, cat. AF-120-05ET) + 1uM Chiron 99021 and incubated cells for 48 hours. On Day 3, we changed the medium to RPMI/B27-insulin supplemented with 1uM Xav 939 (Tocris Bioscience, cat. 3748), and incubated cells for another 48 hours. During this incubation, substantial cell death was typically observed, as noted in the protocol. On Day 5, we replaced the medium with RPMI/B27-insulin without supplementary cytokines for 72 hours. For every 2 days after, we replaced the medium with RPMI/B27+insulin (2% B-27 Supplement Minus Insulin (Invitrogen, cat. 17504044)) + 0.5% penicillin/streptomycin + 1% L-glutamine (Invitrogen, 25030-081). We typically observed spontaneously beating activity beginning between Days 8 and 12.

tag: initial cell line

tag: differentiation protocol

tag: gfp

value: GFP positive


title: Unstimulated_Untreated_1 [ATAC-seq]

tag: strain background

tag: cell type

tag: stimulation

value: Unstimulated

tag: treatment

value: Untreated


title: Rspo KI vs WT 2m infected

description: polarity(-)

tag: tissue


title: OE19_BI-4142_100nM_24h_rep2_J28826

city: Vienna

first: Daniel

last: Gerlach

address: Dr.-Boehringer-Gasse 5-11

department: Global Computational Biology and Digital Sciences

country: Austria

institute: Boehringer Ingelheim RCV GmbH & Co KG

data_processing:
Multiplexed samples were sequenced on an Illumina NextSeq 500 system. Base-calling was performed using the Real-Time Analysis (RTA) software version 2.4.11. Conversion of the raw bcl2 output files to gzipped FASTQ files was performed using the bcl2fastq2 software version 2.20.0 provided by Illumina.
Single-end sequencing reads from grafted samples were filtered into human and mouse reads using Disambiguate (v1.0.0). The filtered reads were then processed with a pipeline building upon the implementation of the ENCODE "Long RNA-seq" pipeline: Reads were mapped against the Homo sapiens (human) genome hg38/GRCh38 (source 1000 Genomes Project - GRCh38_full_analysis_set_plus_decoy_hla.fa,  excluding alternate contigs, chromosome mapping via grch38_ucsc2ensembl.txt) using the STAR (v2.5.2b) aligner allowing for soft clipping of adapter sequences. For quantification, transcript annotation files from Ensembl version 86 were used. Samples were quantified with the above annotations using featureCount (v1.5.1). Quality controls were implemented using FastQC (v0.11.5), picardmetrics (v0.2.4), and dupRadar (v1.0.0) at the respective steps. For human cancer cell lines, the same procedure was applied, omitting the Disambiguate mouse-read-filtering step. Finally, differential expression analysis was performed on the counts derived from featureCount using limma/voom.
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed data files contain sample-wise results produced by FeaturesCounts and include raw count values for each gene.

source_name: OE19 cancer cell line

growth_protocol: The cell lines were cultured with the media DMEM with 10% FCS at 37 degrees Celsius incubators with 5% CO2. Samples from the PDX model were retrieved from tissue biopsies.

extract_protocol:
Cells were lysed in TRI lysis reagent (Qiagen, #79306) according to the manufacturer's instructions. Total RNA was isolated with RNAeasy Mini Kit (Qiagen, #73404).
Quant-seq libraries were prepares using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina from Lexogene (#015.96) according to manufacturer's instructions.

tag: cellline

value: esophagus carcinoma

tag: replicate

tag: ID


title: day 14 GFP+ split B

description:
10X single cell RNA sequencing
10kbarsiblingB

source_name: cardiac differentiated hiPS cells (day 14)

value: cardiac-directed


title: day 14 GFP- split B

description:
10X single cell RNA sequencing
10kbarsilingBneg

value: GFP negative


title: day 14 GFP+ split A

description:
10X single cell RNA sequencing
10kbarsiblingA


title: OE19_Poziotinib_10nM_24h_rep3_J28830


title: OE19_Poziotinib_10nM_24h_rep2_J28829


title: OE19_BI-4142_100nM_24h_rep1_J28825


title: Mm, B8NSC_1

value: brain

value: mouse xenograft glioblastoma stem cells

tag: growth protocol

value: Explanted and established as cultures  in mouse cancer stem cell media


title: OE19_BI-4142_100nM_6h_rep2_J28817


title: OE19_Poziotinib_10nM_24h_rep1_J28828


title: OE19_BI-4142_100nM_6h_rep3_J28818


title: OE19_Poziotinib_10nM_6h_rep2_J28820


title: OE19_Poziotinib_10nM_6h_rep1_J28819


title: OE19_DMSO_6h_rep3_J28824


title: OE19_Poziotinib_10nM_6h_rep3_J28821


title: OE19_BI-4142_100nM_6h_rep1_J28816


title: OE19_DMSO_6h_rep1_J28822


title: OE19_DMSO_6h_rep2_J28823


title: NCI-H1781_BI-4142_300nM_24h_rep2_J28952

source_name: NCI-H1781 cancer cell line

value: NSCLC


title: NCI-H1781_BI-4142_300nM_24h_rep1_J28951


title: NCI-H1781_Poziotinib_30nM_24h_rep2_J28955


title: NCI-H1781_Poziotinib_30nM_24h_rep1_J28954


title: NCI-H1781_BI-4142_300nM_6h_rep2_J28943


title: NCI-H1781_BI-4142_300nM_6h_rep3_J28944


title: NCI-H1781_Poziotinib_30nM_6h_rep3_J28947


title: NCI-H1781_BI-4142_300nM_6h_rep1_J28942


title: ILC1 isolated from healthy mice liver 1

tag: strain

value: Liver

value: post tumor day 14


title: NCI-H1781_DMSO_6h_rep3_J28950


title: NCI-H1781_Poziotinib_30nM_6h_rep1_J28945


title: NCI-H1781_DMSO_6h_rep2_J28949


title: AU565_BI-4142_70nM_24h_rep3_J28809

source_name: AU565 cancer cell line

value: breast carcinoma


title: AU565_BI-4142_70nM_24h_rep2_J28808


title: AU565_BI-4142_70nM_24h_rep1_J28807


title: AU565_Poziotinib_10nM_24h_rep2_J28811


title: AU565_Poziotinib_10nM_24h_rep3_J28812


title: AU565_Poziotinib_10nM_24h_rep1_J28810


title: AU565_BI-4142_70nM_6h_rep2_J28799


title: AU565_BI-4142_70nM_6h_rep3_J28800


title: AU565_DMSO_6h_rep3_J28806


title: AU565_BI-4142_70nM_6h_rep1_J28798


title: AU565_Poziotinib_10nM_6h_rep2_J28802


title: AU565_Poziotinib_10nM_6h_rep3_J28803


title: AU565_DMSO_6h_rep2_J28805


title: AU565_Poziotinib_10nM_6h_rep1_J28801


title: AU565_DMSO_6h_rep1_J28804


title: NCI-H2170-YVMA_BI-1622_120nM_16h_rep3_J19948

source_name: NCI-H2170-YVMA CRISPR/Cas9 engineered cell line


title: NCI-H1781_BI-4142_300nM_24h_rep3_J28953


title: NCI-H2170-YVMA_BI-1622_120nM_16h_rep2_J19816


title: NCI-H2170-YVMA_BI-1622_120nM_16h_rep1_J20141


title: NCI-H2170-YVMA_Poziotinib_28nM_16h_rep2_J20043


title: NCI-H2170-YVMA_Poziotinib_28nM_16h_rep3_J19947


title: NCI-H2170-YVMA_BI-1622_120nM_2h_rep1_J20138


title: NCI-H2170-YVMA_Poziotinib_28nM_16h_rep1_J20139


title: NCI-H2170-YVMA_BI-1622_120nM_2h_rep2_J19813


title: NCI-H1781_Poziotinib_30nM_24h_rep3_J28956


title: NCI-H2170-YVMA_Poziotinib_28nM_2h_rep3_J19944


title: NCI-H2170-YVMA_Poziotinib_28nM_2h_rep1_J20136


title: NCI-H1781_Poziotinib_30nM_6h_rep2_J28946


title: NCI-H2170-YVMA_BI-1622_120nM_0.5h_rep3_J19942


title: NCI-H2170-YVMA_BI-1622_120nM_0.5h_rep2_J19810


title: NCI-H2170-YVMA_BI-1622_120nM_0.5h_rep1_J20135


title: NCI-H2170-YVMA_Poziotinib_28nM_0.5h_rep3_J19941


title: NCI-H2170-YVMA_DMSO_0h_rep3_J19940


title: NCI-H2170-YVMA_DMSO_0h_rep2_J19808


title: NCI-H2170-YVMA_Poziotinib_28nM_0.5h_rep2_J20037


title: NCI-H2170-YVMA_DMSO_0h_rep1_J20036


title: CTG-2534_BI-4142_100mgkg_24h_rep5_J29104

source_name: CTG-2534 PDX model

value: lung


title: NCI-H1781_DMSO_6h_rep1_J28948


title: CTG-2534_BI-4142_100mgkg_24h_rep3_J29102


title: CTG-2534_BI-4142_100mgkg_24h_rep4_J29103


title: NCI-H2170-YVMA_Poziotinib_28nM_0.5h_rep1_J20133


title: CTG-2534_BI-4142_100mgkg_24h_rep2_J29101


title: M2, rep 3

city: Shanghai

first: Chuandong

last: Wang

address: NO.1665 Kongjiang Road

institute: Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
The known miRNA sequences of species were obtained from miRBase database, and the known miRNA was identified by mirdeep2 software.
The counts of mature miRNA were quantified and normalized to CPM (reads count per million) by mirdeep2 software.
Assembly: mm9
Supplementary files format and content: Table with CPM values for every miRNA

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

tag: cell line

value: Macrophage

value: IL-4 and IL-10

tag: cell subtype

value: WT


title: M2, rep 1


title: M1, rep 3

value: LPS and IFN-γ


title: CTG-2534_BI-4142_100mgkg_6h_rep7_J29099

tag: disease


title: CTG-2534_BI-4142_100mgkg_24h_rep1_J29100


title: M1, rep 1

tag: genotype


title: M1, rep 2


title: M0, rep 3

value: untreated


title: CTG-2534_BI-4142_100mgkg_6h_rep5_J29097


title: CTG-2534_BI-4142_100mgkg_6h_rep4_J29096


title: CTG-2534_BI-4142_100mgkg_6h_rep3_J29095


title: M0, rep 1


title: M0, rep 2


title: NCI-H2170-YVMA_Poziotinib_28nM_2h_rep2_J20040


title: CTG-2534_BI-4142_100mgkg_6h_rep2_J29094


title: CTG-2534_Natrosol_6h_rep7_J29092


title: CTG-2534_BI-4142_100mgkg_6h_rep1_J29093


title: CTG-2534_Natrosol_6h_rep6_J29091


title: CTG-2534_Natrosol_6h_rep5_J29090


title: CTG-2534_Natrosol_6h_rep4_J29089


title: Stimulated KO CD8 bulk RNA-seq rep5 [K82_S23]

city: Washington

first: Rong

state: DC

address: 2300 I Street

department: Biochemistry and Molecular Medicine

institute: The George Washington University

description:
K82_S23
processed data file: RNA_seq_stimulated.txt

data_processing:
For RNA-seq, basecalls performed using Illuminal CASAVA software; Reads were aligned to mm10 genome assembly using Tophat; Differentially expressed genes were detected by DESeq2.
For ChIP-seq, fastq files were generated with Bcl2fastq2.
For ATAC-seq, peaks were identified using the MACS 2.1.0 algorithm.
For scRNA-seq, sequencing data were demultiplexed and processed by Cell Ranger (version 3.1.0). STAR was used to map reads to the mouse reference genome refdata-cellranger-mm10-3.0.0. The outputs of individual samples were loaded into the Seurat R package (version 3.1.5).
Genome_build: mm9
Supplementary_files_format_and_content: For RNA-seq, tab-delimited text files include reads counts for each sample. For ChIP-seq and ATAC-seq, bigwig files containing peaks. For scRNA-seq, processed files includes barcodes, features and matrix containing gene expression for individual cells.

source_name: Stimulated KO CD8 bulk RNA-seq

extract_protocol:
For RNA-seq, RNA was harvested using Trizol reagent. For ChIP-seq, lysates were clarified from sonicated nuclei and Protein-DNA complexes were isolated with antibody. For ATAC-seq, cell nuclei were isolated to perform Tn5 tagmentation to make libraries. For scRNA-seq, cells were loaded onto a Chromium Next GEM Chip G (10x Genomics, PN-1000127) and processed with the Chromium Controller (10x Genomics).
RNA libraries were prepared following the Illumina TruSeq stranded mRNA-seq sample preparation guide. ChIP-seq lirabries were prepared using SwiftBiosciences Accel-NGS 2S Plus DNA Library Kit (SwiftBiosciences, 21024). ATAC-seq libraries were prepared by PCR amplification and DNA purification. scRNA-seq libraries were prepared by Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 (10x Genomics, PN-1000128).

value: Nelfb-/-

value: treated with anti-CD3/CD28 for 2 days and then IL2 for 6 days

value: Spleen

value: total CD8


title: CTG-2534_Natrosol_6h_rep3_J29088


title: Stimulated KO CD8 bulk RNA-seq rep4 [K81_S22]

description:
K81_S22
processed data file: RNA_seq_stimulated.txt


title: Stimulated WT CD8 bulk RNA-seq rep2 [W82_S20]

description:
W82_S20
processed data file: RNA_seq_stimulated.txt

source_name: Stimulated WT CD8 bulk RNA-seq

value: wild type


title: Stimulated WT CD8 bulk RNA-seq rep3 [W83_S21]

description:
W83_S21
processed data file: RNA_seq_stimulated.txt


title: Unstimulated KO CD8 bulk RNA-seq rep3 [K03_S6]

description:
K03_S6
processed data file: RNA_seq_unstimulated.txt

source_name: Unstimulated KO CD8 bulk RNA-seq


title: Unstimulated KO CD8 bulk RNA-seq rep2 [K02_S5]

description:
K02_S5
processed data file: RNA_seq_unstimulated.txt


title: CTG-2534_Natrosol_6h_rep1_J29086


title: CTG-2534_Natrosol_6h_rep2_J29087


title: Stimulated WT CD8 bulk RNA-seq rep1 [W81_S19]

description:
W81_S19
processed data file: RNA_seq_stimulated.txt


title: Unstimulated KO CD8 bulk RNA-seq rep1 [K01_S4]

description:
K01_S4
processed data file: RNA_seq_unstimulated.txt


title: mRNA_GastricCancer_rep59

city: Koto

first: Akihisa

last: Takahara

state: Tokyo

institute: Japanese Foundation For Cancer Research

data_processing:
Data was processed with using Bowtie 2 and RSEM softwares.
Genome_build: hg19
Supplementary_files_format_and_content: rsem files were generated using RSEM; Scores represent Transcripts Per Million and Fragments Per Kilobase Million.

source_name: Gastric Cancer tissue.

extract_protocol:
Total RNA was extracted using QIAGEN RNeasy mini kit following manufacturer's instruction.
ilumina True Seq RNA Access sample Preparation Kit

tag: Sex

value: male

tag: age range

value: gastric cancer tumor


title: M2, rep 2


title: CTG-2534_BI-4142_100mgkg_6h_rep6_J29098

value: NSCLC


title: Unstimulated WT CD8 bulk RNA-seq rep3 [W03_S3]

description:
W03_S3
processed data file: RNA_seq_unstimulated.txt

source_name: Unstimulated WT CD8 bulk RNA-seq


title: KO CD8 Pol II ChIP-seq rep2

source_name: KO CD8 Pol II ChIP-seq

value: naive CD8


title: mRNA_GastricCancer_rep60

value: female


title: Unstimulated WT CD8 bulk RNA-seq rep2 [W02_S2]

description:
W02_S2
processed data file: RNA_seq_unstimulated.txt


title: Unstimulated WT CD8 bulk RNA-seq rep1 [W01_S1]

description:
W01_S1
processed data file: RNA_seq_unstimulated.txt


title: mRNA_GastricCancer_rep58


title: KO CD8 Pol II ChIP-seq rep1


title: Stimulated KO CD8 bulk RNA-seq rep6 [K83_S24]

description:
K83_S24
processed data file: RNA_seq_stimulated.txt


title: WT CD8 Pol II ChIP-seq rep2

source_name: WT CD8 Pol II ChIP-seq


title: WT CD8 Pol II ChIP-seq rep1


title: CD8 NELFB ChIP-seq rep2

source_name: CD8 NELFB ChIP-seq


title: mRNA_GastricCancer_rep57


title: mRNA_GastricCancer_rep56


title: Tes45BPA

city: Fayetteville

first: Yongjie

state: Arkansas

address: 400 N Coral Canyon Loop, Apt 402

institute: University of Arkansas

data_processing:
Illumina Casava1.8 software used for basecalling.
HISAT 2.0.4 software used for aignment with reference genome.
HTSeq v0.6.1 software used for gene expression level analysis.
DEGSeq 1.12.0 software used for gene differential expression analysis(|log2foldchang|>1 && qvalue<0.005).
GOSeq Release2.12 software was used for gene GO enrichment analysis(Corrected P-Value<0.05).KOBAS v2.0 software was used for gene KEGG enrichment analysis(Corrected P-Value<0.05).
Assembly: mm10
Supplementary files format and content: Excel file with Gene ID and P value

source_name: testis

extract_protocol:
After the testis was collected , flash frozen on dry ice, and RNA was harvested using Trizol reagent.Then 1 ug of total RNA for the construction of sequencing libraries.
Use magnetic beads with Oligo (dT) to enrich RNA, add fragmentation buffer to convert RNA into short fragments, then use random hexamers to synthesize single-stranded cDNA, use DNA polymerase I to synthesize double-stranded cDNA, and then use AMPure XP beads to purify double-stranded cDNA. The purified double-stranded cDNA is then subjected to end repair, A tail is added, and a sequencing adapter is connected. Then, AMPure XP beads are used for fragment size selection, and finally PCR enrichment is performed to obtain the final cDNA library.

value: balb/c

value: testis

tag: age

value: post natal day 45

value: BPA exposure


title: Tes45


title: SAMPLE 84_205689120174_R05C01

type: genomic

city: Chicago

first: Lucas

last: Santana-Santos

state: IL

address: 710 N. Fairbanks Court, Olson 2-459

department: Pathology

institute: Northwestern University

hyb_protocol: MethylationEPIC beadarray was performed according to the Infinium HD Methylation Assay Protocol, as previously described with minor changes. Eight µl of restored FFPE bs-DNA was used for each sample and 28 µl of hybridization volume was used when loading the microarray microarray.

scan_protocol: Samples were scanned using Illumina's iScan according to manufacturer's recommendations for infinuim arrays

data_processing:
Bioconductor (Version 3.3) package minifi (Version 1.18) using function 'preprocessIllumina'  Average beta
matrix_signal_intensities.tsv: Unmethylated and methylated signal intensities
matrix_processed.tsv: average beta

label: biotin/DNP

source_name: Brain Tumor

label_protocol: Bisulfite conversion: Samples ranging from 50 ng to 500 ng of FFPE DNA was pipetted into strip tubes and processed using the EZ-96 DNA Methylation kit (Zymo Research Corp., CA, USA) following the manufacturer's recommendations for Infinium assays.

extract_protocol: Samples included in the study were all from human brain sample, which was formalin-fixed for 8 hours followed by paraffin-embedding (FFPE) and stored at room temperature. All samples were extracted using either Covaris (FFPE DNA Kit, Covaris, Inc., MA, USA) or Purigen Biosystems (FFPE DNA Kit, Purigen Biosystems, CA, USA) following the manufacturer’s instructions.

value: Brain Tumor

tag: sample type

value: FFPE

tag: tumor type/grade

value: Atypical teratoid/rhabdoid tumor


title: SAMPLE 83_205689120174_R04C01

value: Glioblastoma with giant cell features, WHO grade 4


title: SAMPLE 82_205689120174_R03C01

value: Ganglioglioma, WHO grade I


title: SAMPLE 81_205689120174_R01C01

value: Pituitary adenoma


title: mRNA_GastricCancer_rep55


title: WT CD8 scRNA-seq

source_name: WT CD8 scRNA-seq

value: untreated

value: Spleen

tag: cell type

value: total CD8


title: mRNA_GastricCancer_rep54

value: male

value: gastric cancer tumor


title: KO CD8 scRNA-seq

source_name: KO CD8 scRNA-seq

value: Nelfb-/-

tag: treatment


title: SAMPLE 78_205689120172_R05C01

tag: tissue

value: Atypical meningioma, WHO grade 2


title: SAMPLE 80_205689120172_R07C01

value: Diffuse large B cell lymphoma


title: mRNA_GastricCancer_rep50


title: SAMPLE 79_205689120172_R06C01

value: High grade astrocytoma, IDH-wildtype (IHC), at least WHO grade 3


title: mRNA_GastricCancer_rep51


title: mRNA_GastricCancer_rep52


title: SAMPLE 77_205689120172_R04C01

value: astrocytoma, IDH-mutant, WHO grade 3


title: SAMPLE 76_205689120172_R03C01

value: Ependymoma, WHO grade 2


title: SAMPLE 75_205689120172_R02C01

value: Brain Tumor


title: SAMPLE 74_205689120172_R01C01

value: FFPE

value: Solitary fibrous tumor


title: SAMPLE 73_205689120169_R07C01

value: Schwannoma, WHO grade 1


title: mRNA_GastricCancer_rep49


title: 17_AF2

city: Amherst

first: Soonkyu

last: Chung

state: MA

address: 100 Holdsworth Way Chenoweth Buld Rm211

department: Nutrition

institute: University of Massachusetts

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm9
Supplementary files format and content: Output of STAR pipelines and consist of the number of reads mapped to each gene

source_name: adult brown fat fish oil rep3

extract_protocol:
Interscapular brown fats were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: C57BL/6 female mice were fed either control or fis oil diet during pregnancy and lactation

tag: diet

value: maternal fish oil diet + high fat

tag: sample collection time

value: Adult (15weeks)


title: 18_AF3


title: SAMPLE 72_205689120169_R06C01

value: Hemangioblastoma, WHO grade 1


title: CD8 NELFB ChIP-seq rep1

value: wild type

value: treated with anti-CD3/CD28 for 24 hr

value: Spleen

value: naive CD8


title: mRNA_GastricCancer_rep48

value: male

value: gastric cancer tumor


title: SAMPLE 71_205689120169_R05C01

value: Recurrent/residual glioblastoma, IDH-wildtype (IHC), WHO grade 4


title: 16_AF1

source_name: adult brown fat fish oil rep1


title: SAMPLE 70_205689120169_R04C01

value: Papillary tumor of pineal region


title: 15_AC3

source_name: adult brown fat control rep3

value: maternal control diet + high fat


title: mRNA_GastricCancer_rep47


title: mRNA_GastricCancer_rep46


title: SAMPLE 69_205689120169_R03C01

value: Recurrent anaplastic ependymoma, WHO grade 3


title: SAMPLE 67_205689120169_R01C01

value: Brain Tumor

value: Recurrent/residual glioblastoma, IDH-wildtype, WHO grade 4


title: SAMPLE 66_205460720115_R08C01

value: FFPE

value: Diffuse large B cell lymphoma


title: mRNA_GastricCancer_rep53


title: SAMPLE 65_205460720115_R07C01

value: Ependymoma, WHO grade 2


title: mRNA_GastricCancer_rep45

value: female


title: mRNA_GastricCancer_rep44


title: SAMPLE 63_205460720115_R05C01

value: Astrocytoma, IDH-mutant (IHC), at least WHO grade 3


title: 13_AC1

source_name: adult brown fat control rep1

value: Adult (15weeks)


title: 12_WF3

source_name: weaned brown fat  fish oil rep3

value: maternal fish oil diet

value: weaning (3weeks)


title: 14_AC2

source_name: adult brown fat control rep2


title: SAMPLE 64_205460720115_R06C01

value: High grade astrocytoma, IDH-wildtype (IHC), at least WHO grade 3


title: 11_WF2

source_name: weaned brown fat  fish oil rep2


title: SAMPLE 62_205460720115_R04C01

value: Recurrent/residual anaplastic oligodendroglioma, IDH-mutant (IHC), WHO grade 3


title: 10_WF1

source_name: weaned brown fat fish oil rep1


title: mRNA_GastricCancer_rep43

source_name: Gastric Cancer tissue.

value: gastric cancer tumor


title: SAMPLE 61_205460720115_R03C01

value: Recurrent/residual glioblastoma, IDH-wildtype (IHC), WHO grade 4


title: SAMPLE 60_205460720115_R02C01

value: Metastatic adenocarcinoma, consistent with lung primary


title: SAMPLE 59_205460720115_R01C01

value: Atypical meningioma, WHO grade 2


title: mRNA_GastricCancer_rep41


title: mRNA_GastricCancer_rep42

value: male


title: 9_WC3

source_name: weaned brown fat control rep3

value: maternal control diet


title: SAMPLE 58_205460720104_R08C01

value: Brain Tumor

value: Ganglioglioma, WHO grade I


title: 8_WC2

source_name: weaned brown fat  control rep2


title: SAMPLE 56_205460720104_R06C01

value: FFPE

value: Metastatic melanoma


title: SAMPLE 68_205689120169_R02C01

value: pilocytic astrocytoma, WHO grade 1


title: SAMPLE 54_205460720104_R04C01

value: Pilocytic astrocytoma, WHO grade 1


title: mRNA_GastricCancer_rep39


title: SAMPLE 53_205460720104_R03C01

value: Recurrent glioblastoma, IDH wild type (pyrosequencing), WHO grade 4


title: 7_WC1

source_name: weaned brown fat  control rep1


title: mRNA_GastricCancer_rep38


title: SAMPLE 51_205460720104_R01C01


title: 6_FF3

source_name: fetal brown fat fish oil rep3

value: maternal fish oil diet

value: fetus


title: SAMPLE 50_205460720092_R08C01

value: Metastatic poorly differentiated adenocarcinoma


title: 5_FF2

source_name: fetal brown fat  fish oil rep2


title: mRNA_GastricCancer_rep37


title: SAMPLE 49_205460720092_R07C01

source_name: Brain Tumor

value: Glioblastoma, IDH-wildtype (IHC), WHO grade 4


title: 4_FF1

source_name: fetal brown fat fish oil rep1


title: SAMPLE 47_205460720092_R05C01

value: High grade malignancy favor glioblastoma, IDH-wildtype (IHC), WHO grade IV


title: SAMPLE 48_205460720092_R06C01

value: Subependymoma, WHO grade 1


title: mRNA_GastricCancer_rep36

value: gastric cancer tumor


title: 3_FC3

source_name: fetal brown fat control rep3


title: SAMPLE 44_205460720092_R02C01

value: Solitary fibrous tumor


title: SAMPLE 57_205460720104_R07C01

value: Residual/recurrent astrocytoma, IDH-mutant (R132G per previous molecular testing), at least WHO grade 3


title: SAMPLE 45_205460720092_R03C01

value: Schwannoma, WHO grade 1


title: mRNA_GastricCancer_rep34

value: male


title: SAMPLE 43_205460720092_R01C01

value: Brain Tumor

value: Craniopharyngioma, adamantinomatous type, WHO grade 1


title: mRNA_GastricCancer_rep35

value: female


title: mRNA_GastricCancer_rep40


title: 1_FC1

source_name: fetal brown fat control rep1

value: maternal control diet


title: SAMPLE 55_205460720104_R05C01

value: FFPE

value: Diffuse large B cell lymphoma


title: mRNA_GastricCancer_rep33


title: W5-Alum (2)

city: Paris

first: Olivia

last: Bonduelle

address: 91 bd de l'Hopital

country: France

institute: INSERM U1135

description:
A1-3 to H12-3 (94 single-cells)
SAMPLE 8

data_processing: Data were analysed with Singular Analysis Toolset Software v3.6 from Fluidigm and R 3.3.3. As a result of the lognormal distribution described by Bengtsson et al. (2005) and others, it is useful to view single-cell data as expression level above detection limit on a log scale. For qPCR data, it is convenient and appropriate to do this in Log2 by defining the term Log2Ex: Log2Ex = LoD Ct – Ct [Gene]. If the value is negative, Log2Ex = 0. For more information on this value, see K.J. Livak et al., Methods (2012),http://dx.doi.org/10.1016/j.ymeth.2012.10.004.

label: EvaGreen

source_name: draining lymph node B cells

label_protocol: We use D3 assay design of Fluidigm to design 96 probes.

extract_protocol: Single-cell RT-PCR were performed by using "Two-step single-cell gene expression using EvaGreen Supermix on the BioMark and BioMark HD Systems protocole C" (Fluidigm). This protocol includes a separate reverse transcription step and a specific target amplification step.

treatment_protocol: W614A-3S-specific single B cells were sorted by Facs Aria (BD Biosciences) in 96 well plate directly in reverse transcription Mix solution. Each well contained one cell, except G12 with 10 cells and H12 without cell. Each kinetic and adjuvant conditions was replicated (1 and 2)

value: W614A-3S-specific B cells

tag: adjuvant immunization

value: Alum condition

value: Balb/C


title: SAMPLE 52_205460720104_R02C01

value: Focal cortical dysplasia, type IIa


title: SAMPLE 40_204674440099_R03C01

value: Medulloblastoma


title: SAMPLE 39_204674440099_R02C01


title: SAMPLE 38_204674440099_R01C01


title: SAMPLE 37_204674440040_R06C01

value: meningioma, WHO grade 1


title: W5-Alum (1)

description:
A1-2 to H12-2 (94 single-cells)
SAMPLE 7


title: SAMPLE 46_205460720092_R04C01

value: astrocytoma, IDH-mutant, WHO grade 3


title: W5-SQE (2)

description:
A1-4 to H12-4 (94 single-cells)
SAMPLE 6

value: SQE condition


title: SAMPLE 35_204674440040_R04C01

value: glioblastoma, IDH-wildtype, WHO grade 4


title: 2_FC2

source_name: fetal brown fat control rep2

value: fetus


title: mRNA_GastricCancer_rep30

description:
GC1012
The raw data were produced either on an Illumina HiSeq 2000 or Illumina HiSeq 2500 instrument.

value: gastric cancer tumor


title: mRNA_GastricCancer_rep32

description:
GC1052
The raw data were produced either on an Illumina HiSeq 2000 or Illumina HiSeq 2500 instrument.


title: mRNA_GastricCancer_rep31

description:
GC1042
The raw data were produced either on an Illumina HiSeq 2000 or Illumina HiSeq 2500 instrument.


title: SAMPLE 34_204674440040_R03C01

value: Brain Tumor

value: Atypical meningioma, WHO Grade 2


title: W3-Alum (2)

description:
A1-9 to H12-9 (94 single-cells)
SAMPLE 4


title: W5-SQE (1)

description:
A1-1 to H12-1 (94 single-cells)
SAMPLE 5


title: SAMPLE 33_204674440040_R02C01


title: SAMPLE 32_204674440040_R01C01

value: pituitary adenoma


title: W3-Alum (1)

description:
A1-7 to H12-7 (94 single-cells)
SAMPLE 3


title: mRNA_GastricCancer_rep28

description:
GC962
The raw data were produced either on an Illumina HiSeq 2000 or Illumina HiSeq 2500 instrument.

value: male


title: SAMPLE 42_205460720075_R02C01

value: FFPE

value: classic medulloblastoma with focal anaplasia, WHO grade 4, non-WNT/non-SHH


title: SAMPLE 31_204674440035_R08C01

value: Diffuse large B cell lymphoma


title: SAMPLE 30_204674440035_R07C01


title: mRNA_GastricCancer_rep27

description:
GC942
The raw data were produced either on an Illumina HiSeq 2000 or Illumina HiSeq 2500 instrument.


title: SAMPLE 41_205460720075_R01C01

value: Large cell/anaplastic medulloblastoma, WHO grade 4, SHH


title: W3-SQE (2)

description:
A1-8 to H12-8 (94 single-cells)
SAMPLE 2

value: W614A-3S-specific B cells

value: Balb/C


title: SAMPLE 29_204674440035_R06C01

value: Pituitary adenoma


title: SAMPLE 28_204674440035_R05C01

value: Anaplastic oligodendroglioma, IDH-mutant (IHC), WHO grade 3


title: SAMPLE 27_204674440035_R04C01

value: Meningioma, WHO grade 1


title: SAMPLE 25_204674440035_R02C01

value: pineal parenchymal tumor of intermediate differentiation (PPTID), WHO grade 3


title: SAMPLE 26_204674440035_R03C01

value: metastatic lung adenocarcinoma


title: mRNA_GastricCancer_rep26

description:
GCMK355T1
The raw data were produced either on an Illumina HiSeq 2000 or Illumina HiSeq 2500 instrument.


title: W3-SQE (1)

description:
A1-6 to H12-6 (91 single-cells)
SAMPLE 1

value: SQE condition


title: sc-RNA seq batch 19-2

city: Beijing

first: Xi-Yin

last: Zhang

address: College Road

department: Neuroscience Research Institute

institute: Peking University

data_processing:
Illumina Casava1.7 software used for basecalling.
Extract Barcode and UMI: umi_tools extract.
Trim TSO and PolyA: trim_TSO_polyA.pl, seqtk trimfq.
Mapping With STAR, add feature using featureCounts of subread
Sort and index bam file using Samtools
Assembly: Rnor_6.0.102
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell-id

organism: Rattus norvegicus

source_name: Dorsal root ganglia neurons

growth_protocol: Specific pathogen-free (SPF) male Sprague-Dawley (SD) rats weighing 200 g were supplied by the Animal Center of Peking University Health Science Center. The animals were housed in an SPF laboratory in ventilated cages (IVC) (3-5 rats per cage) on a 12-hour light-dark cycle (lights on at 8:00 AM) with free access to food and water. All experiments were performed according to the guidelines of the Animal Care and Use Committee of Peking University, and efforts were made to minimize the discomfort of the animals.

extract_protocol:
A modified Smart-seq2 protocol developed by the Tang laboratory was used for single-cell RNA-seq. Briefly, acutely dissociated DRG neurons were plated on dishes as described previously. After 15 min, the DMEM was replaced with PBS, and a mouth pipette was then used to place each individual fluorescently labeled single DRG neuron into a volume of lysis buffer under a fluorescence microscope. Harvesting of the single DRG neurons from one rat was completed in 4 h, and the L4-5 DRG of at least 5 rats were harvested at each time point.
The reverse transcription reaction was performed with a TSO primer added at the 5’ end and with 25 nt oligo (dT) primer anchored with an 8 nt cell-specific barcode and 8 nt unique molecular identifiers (UMIs) added at the 3’ end. After reverse transcription, cDNAs were amplified by 15 cycles of PCR, during which the IS primer and the 3’P2 primer were added to the 5’ and 3’ ends of the cDNAs, respectively. The amplified cDNAs from single cells were pooled, purified using a DNA Clean & concentration-5 kit (Zymo Research, D4014) and AMPure XP beads (Beckman Coulter, A63882), and quantified using a Qubit dsDNA HS Assay Kit (Invitrogen, Q32854). To add biotin tags to the 3’ ends of the amplified cDNAs, biotinylated preindexed primers and IS primer were used to further amplify the PCR product through an additional 4 cycles of PCR. The biotinylated cDNAs were then sheared to approximately 300 bp using Covaris S2, and the 3’ termini of the cDNAs were captured using C1 beads (Dynabeads® Myone™ Streptavidin C1, Invitrogen, 65001). The RNA-seq library was constructed using a Kapa Hyper Prep Kit (KAPA Biosystems, KK8505), and short universal primers and QP2 primers were used in the last amplification. Finally, the genome and transcriptome libraries were subjected to 150 bp paired-end sequencing on an Illumina HiSeq 4000 platform (sequenced by Novogene).

treatment_protocol: During the surgery, the rats were anesthetized using isoflurane, and a 2 cm incision was made on the skin at the mid-thigh level of the left thigh to expose the left sciatic nerve. The three branches of the nerve were carefully separated using a glass dissecting needle, and the tibial and common peroneal nerves were crushed for 30 s using 3 clicks of an ultrafine microscope forceps (WA2030, JingZhong, Shanghai, China), leaving the remaining sural nerve intact. The muscle and skin were then closed in two layers, and penicillin was applied to the wound. For the sham surgery, the sciatic nerve was exposed but left uninjured. Animals with marked weight loss or severe immobility at 7 days postsurgery were excluded from the study. For the medial plantar sensory recovery (pinprick and light touch sensitivity) test and skin biopsy, we exposed the saphenous nerve above the knee region and ligated and transected it after SNC, making the medial plantar epidermis innervated only by regenerated sciatic nerve axons.

value: Dorsal root ganglia neurons

value: SD

tag: post-surgical time point

value: SNC 7 d

tag: numbers of indirectly injured/ directly injured cells


title: mRNA_GastricCancer_rep29

description:
GC1002
The raw data were produced either on an Illumina HiSeq 2000 or Illumina HiSeq 2500 instrument.

value: female

value: gastric cancer tumor


title: SAMPLE 36_204674440040_R05C01

value: Brain Tumor

value: FFPE

value: Hemangioblastoma, WHO grade 1


title: SAMPLE 24_204674440035_R01C01

value: pleomorphic xanthoastrocytoma


title: mRNA_GastricCancer_rep24

description:
GC892
The raw data were produced either on an Illumina HiSeq 2000 or Illumina HiSeq 2500 instrument.


title: sc-RNA seq batch 19-1

tag: strain


title: SAMPLE 22_204674430101_R07C01

value: dysembryoplastic neuroepithelial tumor, WHO grade 1


title: SAMPLE 23_204674430101_R08C01

value: pilocytic astrocytoma, WHO grade 1


title: SAMPLE 20_204674430101_R05C01

value: Pituitary adenoma


title: sc-RNA seq batch 18

value: Sham


title: mRNA_GastricCancer_rep23

description:
GC682
The raw data were produced either on an Illumina HiSeq 2000 or Illumina HiSeq 2500 instrument.

value: male


title: mRNA_GastricCancer_rep21

description:
GCMK269T1
The raw data were produced either on an Illumina HiSeq 2000 or Illumina HiSeq 2500 instrument.


title: mRNA_GastricCancer_rep22

description:
GC603
The raw data were produced either on an Illumina HiSeq 2000 or Illumina HiSeq 2500 instrument.


title: SAMPLE 19_204674430101_R04C01

value: astrocytoma, IDH-mutant, WHO grade 3


title: sc-RNA seq batch 17-2

value: SNC 1 d


title: sc-RNA seq batch 17-3

value: SNC 3 d


title: SAMPLE 17_204674430101_R02C01

value: Residual pleomorphic xanthoastrocytoma


title: SAMPLE 16_204674430101_R01C01

value: Glial neoplasm


title: mRNA_GastricCancer_rep20

description:
GCMK248T1
The raw data were produced either on an Illumina HiSeq 2000 or Illumina HiSeq 2500 instrument.


title: SAMPLE 15_204674430074_R08C01

value: Choroid plexus papilloma, WHO grade 1


title: sc-RNA seq batch 17-1

value: Dorsal root ganglia neurons

value: SD


title: SAMPLE 14_204674430074_R07C01

value: Brain Tumor

value: classic medulloblastoma with focal anaplasia, WHO grade 4, non-WNT/non-SHH


title: mRNA_GastricCancer_rep19

description:
GCMK241T1
The raw data were produced either on an Illumina HiSeq 2000 or Illumina HiSeq 2500 instrument.

value: gastric cancer tumor


title: mRNA_GastricCancer_rep25

description:
GCMK324T1
The raw data were produced either on an Illumina HiSeq 2000 or Illumina HiSeq 2500 instrument.


title: SAMPLE 13_204674430074_R06C01

value: FFPE


title: sc-RNA seq batch 16


title: EB_KO_2

city: Tianjin

first: Ni

last: Peiling

address: Weijin Road

institute: nankai university

description: embryoid bodies

data_processing:
Basecalls performed using the software Zebra call
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using Bowtie2.
Fragments Per Kilobase per Million is calculated to represent the gene expression level
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited FPKM files include FPKM values for each Sample ...

source_name: mouse embryonic stem cell

extract_protocol:
Total RNA is extracted from cells using RNeasy Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Hbxip-/-


title: mRNA_GastricCancer_rep18

description:
GCMK112T1
The raw data were produced either on an Illumina HiSeq 2000 or Illumina HiSeq 2500 instrument.


title: SAMPLE 12_204674430074_R05C01

value: dysembryoplastic neuroepithelial tumor, WHO grade 1


title: SAMPLE 21_204674430101_R06C01

value: Large cell/anaplastic medulloblastoma, WHO grade 4, SHH


title: EB_KO_1

description: embryoid bodies


title: mRNA_GastricCancer_rep17

description:
GCMK013T1
The raw data were produced either on an Illumina HiSeq 2000 or Illumina HiSeq 2500 instrument.

value: female


title: EB_WT

description: embryoid bodies

value: wild type


title: sc-RNA seq batch 15


title: SAMPLE 11_204674430074_R04C01


title: SAMPLE 18_204674430101_R03C01

value: pineal parenchymal tumor of intermediate differentiation (PPTID), WHO grade 3


title: sc-RNA seq batch 14


title: D4_KO_2

description: LIF withdrawal for 96h


title: mRNA_GastricCancer_rep16

description:
GC392
The raw data were produced either on an Illumina HiSeq 2000 or Illumina HiSeq 2500 instrument.


title: sc-RNA seq batch 13

value: SNC 1 d


title: mRNA_GastricCancer_rep14

description:
GC312
The raw data were produced either on an Illumina HiSeq 2000 or Illumina HiSeq 2500 instrument.

value: male


title: sc-RNA seq batch 10

value: Sham


title: sc-RNA seq batch 9

value: SNC 7 d


title: SAMPLE 10_204674430074_R03C01

value: Pituitary adenoma


title: SAMPLE 9_204674430074_R02C01

value: astrocytoma, IDH-mutant, WHO grade 3


title: mRNA_GastricCancer_rep15

description:
GC332
The raw data were produced either on an Illumina HiSeq 2000 or Illumina HiSeq 2500 instrument.


title: D4_WT

description: LIF withdrawal for 96h


title: SAMPLE 8_204674430074_R01C01


title: KO_2

description: ESCs cultured  in pluripotent condition


title: mRNA_GastricCancer_rep13

description:
GC262
The raw data were produced either on an Illumina HiSeq 2000 or Illumina HiSeq 2500 instrument.


title: SAMPLE 7_204674430040_R08C01

value: Choroid plexus papilloma, WHO grade 1


title: mRNA_GastricCancer_rep12

description:
GC242
The raw data were produced either on an Illumina HiSeq 2000 or Illumina HiSeq 2500 instrument.


title: KO_1

description: ESCs cultured  in pluripotent condition


title: sc-RNA seq batch 4

value: Dorsal root ganglia neurons

value: SD


title: SAMPLE 6_204674430040_R06C01

value: Brain Tumor

value: meningioma, WHO grade 1


title: mRNA_GastricCancer_rep11

description:
GC202
The raw data were produced either on an Illumina HiSeq 2000 or Illumina HiSeq 2500 instrument.

value: gastric cancer tumor


title: sc-RNA seq batch S-3


title: WT

description: ESCs cultured  in pluripotent condition


title: F_5d_3

city: Kunming

first: Qianqian

last: Liu

state: Yunnan Province

address: No. 2, Cuihu North Road, Wuhua District, Kunming

department: School of Life Sciences

institute: Yunnan University

data_processing:
The data from high-throughput sequencing were analyzed using the OmicShare tools, a free online platform for data analysis (www.majorbio.com).
Genome_build: https://www.ncbi.nlm.nih.gov/assembly/GCF_000225545.1
Supplementary_files_format_and_content: Expression analysis table include TPM values for each sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Orbilia oligospora

source_name: Fungal hyphae

growth_protocol: The WT, ΔAopex1 and ΔAopex6 mutant strains  were cultured in PDA medium at 28°C for  5 d.

extract_protocol:
The WT, ΔAopex1 and ΔAopex6 mutant strains were cultured in PD shaking at 28 °C, 180 rpm for 3 and 5 days.
The libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Mycelium was collected and washed three times with 0.1 Mphosphate buffer saline (PBS) (pH 6.8-7.2).

tag: time point


title: mRNA_GastricCancer_rep10

description:
GC132
The raw data were produced either on an Illumina HiSeq 2000 or Illumina HiSeq 2500 instrument.


title: SAMPLE 5_204674430040_R05C01

value: FFPE

value: Hemangioblastoma, WHO grade 1


title: mRNA_GastricCancer_rep9

description:
GC072
The raw data were produced either on an Illumina HiSeq 2000 or Illumina HiSeq 2500 instrument.


title: sc-RNA seq batch S-2


title: SAMPLE 3_204674430040_R03C01

value: atypical meningioma, WHO Grade 2


title: D4_KO_1

description: LIF withdrawal for 96h

value: Hbxip-/-


title: sc-RNA seq batch Xin


title: SAMPLE 2_204674430040_R02C01


title: F_5d_1


title: F_5d_2


title: F_3d_3


title: mRNA_GastricCancer_rep8

description:
GC522
The raw data were produced either on an Illumina HiSeq 2000 or Illumina HiSeq 2500 instrument.

value: female


title: mRNA_GastricCancer_rep7

description:
GC552
The raw data were produced either on an Illumina HiSeq 2000 or Illumina HiSeq 2500 instrument.


title: sc-RNA seq batch 8


title: SAMPLE 1_204674430040_R01C01

value: pituitary adenoma


title: mRNA_GastricCancer_rep6

description:
GC502
The raw data were produced either on an Illumina HiSeq 2000 or Illumina HiSeq 2500 instrument.

value: male


title: Pigmented 15 months Male [120]

city: Fort Collins

first: Devin

last: Wahl

state: Colorado

address: 1582 Campus Delivery, Moby Reception

institute: Colorado State University

data_processing:
Adapters trimmed & file QC by Fastp
Reads aligned with STAR and counting with LiBiNorm
Differential expression analyzed with DESeq2
Assembly: cavPor3
Supplementary files format and content: raw counts

organism: Cavia porcellus

source_name: Pigmented 15 months Male

extract_protocol:
RNA for polyA RNA-seq extracted using Trizol and Zymo spin columns.
PolyA libraries were prepared according to manufacturer's instructions using the Illumina TruSeq kit

value: Pigmented

value: Male

value: Cortex


title: F_3d_2


title: Pigmented 15 months Male [119]


title: mRNA_GastricCancer_rep5

description:
GC492
The raw data were produced either on an Illumina HiSeq 2000 or Illumina HiSeq 2500 instrument.


title: F_3d_1


title: Pigmented 15 months Male [118]


title: mRNA_GastricCancer_rep4

description:
GC463
The raw data were produced either on an Illumina HiSeq 2000 or Illumina HiSeq 2500 instrument.


title: Patient_5536_ib [S15]

city: Bethesda

first: Mehdi

last: Pirooznia

state: MD

address: 12 SOUTH DR

institute: National Institutes of Health

data_processing:
trimmomatic (v0.39): Illumina adapters were trimmed, and reads were required to have a minimum length of 36, and an average quality of 15 across a sliding window of 4 bases
hisat2 (v2.2.1): Quality metrics were generated and viewed with FastQC (v0.11.9) and MultiQC (v1.10). Reads were aligned to human reference genome (build GRCh38 with Ensembl release version 102) with hisat2 (v2.2.1)
samtools (v1.12): bam files were generated for each sample via samtools (v1.12).
Subread package (v2.0.2) : Reads were quantified with the featureCounts program in the Subread package (v2.0.2) and merged to create a counts matrix
biomaRt (v2.46.3): Ensembl Gene IDs were mapped to gene symbols using biomaRt (v2.46.3). Genes with low expression were filtered out according to the following requirements for inclusion: Transcripts Per Million (TPM) > 0.5 in ≥ 20% of the samples; raw counts > 2 in ≥ 20% of the samples; Counts Per Million (CPM) > 1 in ≥ 50% of the samples
Assembly: build GRCh38 with Ensembl release version 102

source_name: Patient PBMCs

growth_protocol: Culture medium is RPMI1640 with 10% heat inactivated FBS, 1% Penstrep. CLL Cells were cultured at 37℃ in humidified incubator with 5% CO2. Before treatment, seed cells to 24-well plate at the concentration of 3x106 cells/0.5 mL/well. Add reagents to wells and keep culture until cell harvest.

extract_protocol:
Using RNeasy Mini Kit (QIAGEN, CAT NO 74104) to extract and prepare RNA for RNAseq. The extraction process followed protocol of product.
The sequencing libraries were constructed from 100 ng – 500 ng of total RNA using the Illumina’s TruSeq Stranded Total RNA kit with Ribo-Zero (Cat# 20040529) following the manufacturer instruction. The fragment size of RNAseq libraries was verified using the Agilent 2100 Bioanalyzer (Agilent) and the concentrations were determined using Qubit instrument (LifeTech). The libraries were loaded onto Illumina Novaseq 6000 for 2x50 bp paired end read sequencing. The fastq files were generated using the bcl2fastq software for further analysis.

treatment_protocol: Add 0.5 μL hook stock, 0.5 μL ibrutinib stock, and NRX0492 stock to wells to make the final concentration as 2 nM, 1 0.5 μM, and 2 nM respectively. DMSO treatment was set as control. Treat cells with mentioned reagents for 24 hours followed by stimulating cells by 20 0.5 μg/mL anti-IgM for 6 hours. Harvest cells for RNA extraction.

tag: patient id

tag: disease state

value: Chronic lymphocytic leukemia (CLL)

value: IGHV unmutated, deletion 13q

value: blood

value: ib


title: E_5d_3

tag: genotype


title: SAMPLE 4_204674430040_R04C01

value: Brain Tumor

value: glioblastoma, IDH-wildtype, WHO grade 4


title: Patient_5536_hook [S14]

value: hook


title: E_5d_2


title: Pigmented 15 months Female [293]

source_name: Pigmented 15 months Female

tag: Sex

value: Female


title: Pigmented 15 months Female [292]


title: E_5d_1


title: Patient_5536_DMSO [S13]

tag: age

value: DMSO


title: mRNA_GastricCancer_rep2

description:
GC422
The raw data were produced either on an Illumina HiSeq 2000 or Illumina HiSeq 2500 instrument.

source_name: Gastric Cancer tissue.

tag: age range

value: gastric cancer tumor


title: Pigmented 15 months Male [121]


title: Pigmented 15 months Female [291]


title: mRNA_GastricCancer_rep1

description:
GC292
The raw data were produced either on an Illumina HiSeq 2000 or Illumina HiSeq 2500 instrument.

source_name: Gastric Cancer tissue


title: Patient_5514_NRX [S12]

value: IGHV unmutated, deletion 17p

value: NRX


title: Pigmented 15 months Female [290]


title: E_3d_2


title: Patient_5514_ib [S11]


title: Pigmented 5 months Male [256]

source_name: Pigmented 5 months Male


title: E_3d_3


title: Patient_5514_hook [S10]


title: Pigmented 5 months Male [255 A]


title: E_3d_1


title: Patient_5514_DMSO [S9]


title: A_5d_3

value: WT


title: Patient_5536_NRX [S16]


title: Pigmented 5 months Male [254]


title: Patient_4296_NRX [S8]


title: mRNA_GastricCancer_rep3

description:
GC452
The raw data were produced either on an Illumina HiSeq 2000 or Illumina HiSeq 2500 instrument.

value: female


title: A_5d_1


title: A_3d_3


title: A_5d_2


title: Pigmented 5 months Male [253]

value: Pigmented


title: Patient_4296_ib [S7]


title: Pigmented 5 months Female [809]

source_name: Pigmented 5 months Female


title: A_3d_2


title: Pigmented 5 months Female [608]


title: Pigmented 5 months Female [607]


title: 12_r4_TFAM_IR8,Li15948

city: Calgary

first: Savraj

last: Grewal

state: Alberta

address: 3330 Hospital Drive

country: Canada

institute: University of Calgary

data_processing:
1.Using Fast QC for reads quality control. The reads number per sample is around 20 million, and average reads length is 51 bp. All samples passed reads quality control.
2. Map the reads to Drosophila_melanogaster reference version: GCF_000001215.4_Release_6_plus_ISO1_MT_rna
3. QC for reads mapping quality:  at least 90% of reads pseudo aligned to reference.
4. PCA plot for experiments QC, didn’t see obvious experimental problem, for example, uneven rRNA depletion.
5. Apply Wald-test from software sleuth do differential expression analysis, both on transcript level and gene level.

organism: Drosophila melanogaster

source_name: Larval fat bodies

extract_protocol:
Drosophila larval fat bodies were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using the Ultra II Directional RNA library kit (New England BioLabs) according the manufacturer's instructions

value: 96 hr AEL larval fat body

value: r4-Gal4>TFAM RNAi


title: Patient_3058_hook [S2]

value: Chronic lymphocytic leukemia (CLL)


title: A_3d_1


title: Patient_4296_DMSO [S5]


title: Patient_3058_NRX [S4]

value: IGHV unmutated, deletion 13q


title: Hartley 15 months Male [698]

source_name: Hartley 15 months Male

value: Dunkin Hartley

value: Male

value: Cortex


title: Hartley 15 months Male [693]


title: 11_r4_TFAM_IR7,Li15947


title: 10_r4_TFAM_IR6,Li15946


title: Patient_3058_ib [S3]

value: blood

value: ib


title: BC-A ST

city: Wuhan

first: Si-Qing

address: No.9 Zhang Zhidong Road

institute: Wuhan university

description: one sample from human primary breast cancer

data_processing:
Read alignment and count summarization were performed using CellRanger v3.0.2 using the Illumina BCL files as input.
Genome_build: GRCh38
Assembly: mm10
Supplementary files format and content: matrix.mtx files contain genewise read counts for all cells in the space-efficient matrix market format. The supplementary file features.tsv.gz contains the corresponding Ensembl IDs and gene symbols as tab-delimited text. The barcode.tsv files contain the 10X barcodes used to identify cells. Each matrix market file can be read into R, together with features.tsv.gz, using the read10X function of the Seurat software package.

source_name: Mammary Tumor

extract_protocol:
single nucleus and ST transcriptomes were collected using the 10X Genomics platform v3 (adult) chemistry (10× Genomics, Pleasanton, CA) and sequenced on Illumina NovaSeq 6000.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: gender

value: Primary Breast Tumor

value: untreated


title: BC-B snRNAseq


title: Hartley 15 months Female [684]

source_name: Hartley 15 months Female

value: Female


title: Hartley 15 months Female [685]


title: 8_r4_TFAM_IR4,Li15944


title: 9_r4_TFAM_IR5,Li15945


title: Hartley 15 months Male [661]


title: 7_r4_TFAM_IR3,Li15943


title: Patient_4296_hook [S6]

value: IGHV unmutated, deletion 17p

value: hook


title: BC-A snRNAseq


title: Hartley 15 months Female [678]


title: KO CD8 ATAC-seq rep2

source_name: KO CD8 ATAC-seq

value: Nelfb-/-

value: Spleen

tag: cell type

value: naive CD8


title: 6_r4_W8,Li15942

value: 96 hr AEL larval fat body


title: EHT 2 THC + Genistein

city: Aurora

first: Edward

last: Lau

state: CO

address: 12700 E19th Av RCII Rm 8004

department: Medicine/Cardiology

institute: University of Colorado

data_processing:
Alignment to GRCh38 using STAR v.2.7.6a --sjdbGTFfile gencode.v38.annotation.gff3 --sjdbOverhang 149 --outSAMtype BAM SortedByCoordinate --readFilesCommand gunzup -c
Transcript assembly and quantification using StringTie v.2.1.1 -e
Import to R using PrepDE.py
Differential expression analysis using DESeq2
Assembly: GRCh38
Supplementary files format and content: csv file containing transcript counts

source_name: In Vitro iPSC Engineered Heart Tissue

extract_protocol:
RNA was extracted from EHT using Trizol (Qiazol)
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

tag: treatment

value: THC + Genistein


title: Pigmented 5 months Female [606]

value: Pigmented

tag: tissue


title: Hartley 5 months Male [244]

source_name: Hartley 5 months Male


title: 5_r4_W7,Li15941


title: EHT 2 THC

value: THC


title: Hartley 5 months Male [197]

value: Dunkin Hartley


title: KO CD8 ATAC-seq rep1


title: WT CD8 ATAC-seq rep2

source_name: WT CD8 ATAC-seq

value: wild type


title: 4_r4_W6,Li15940


title: EHT 1 THC + Genistein


title: 3_r4_W5,Li15939


title: Patient_3058_DMSO [S1]

value: Chronic lymphocytic leukemia (CLL)

value: IGHV unmutated, deletion 13q

value: DMSO


title: WT CD8 ATAC-seq rep1


title: Non-recurred lesion HL1

city: Seodaemun-gu, Seoul

first: Won Seok

last: Roh

address: 50-1, Yonsei-ro

country: South Korea

institute: severance hospital

data_processing:
Illumina Casava1.9 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to GRCh38 whole genome using Cell ranger v3.1.0.
Read count extraction and normalization were performed using Seurat v4.0.4.
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Skin

extract_protocol:
Skin fresh tissue was achieved. After enzymatic dissociation using 1.6mg/mL of Collagenase IV (Worthington, Ohio, US), viable cells were enriched using flow cytometry then were captured using Chromium GEM Single Cell 5' Kit v1 (10x Genomics, CA, USA)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The patient was treated with anti-IL-17A antibody ixekizumab for 6 times at 2-week interval and suspended from the treatment for 30 weeks

value: psoriasis

value: skin from non-recurred psoriatic lesion


title: Hartley 5 months Female [258]

source_name: Hartley 5 months Female

value: Female

value: Cortex


title: EHT 1 THC


title: 2_r4_W3,Li15938


title: Hartley 5 months Female [255 B]


title: EHT 1 Control

value: Control


title: 1_r4_W2,Li15937


title: Recurred lesion PL1

value: skin from recurred psoriatic lesion


title: Hartley 5 months Female [204]


title: 23-2015-0609-SUB

status: Public on Mar 18 2022

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

institute: IBENS

data_processing:
Illumina Casava 1.8.2 software used for basecalling.
RNA-Seq data analysis was done using the Eoulsan software version 2.0-alpha6 (Jourdren et al, 2012). Before mapping, poly N read tails were trimmed, and reads with less than 40 bases or mean quality of less than 30 were removed using the Java version of samtools (Li et al, 2009). Reads were aligned against the hg19 genome from Ensembl 81 using STAR, v2.4.0k (Dobin et al, 2013) and Ensembl annotation version 81. Transcript expression was computed with reference to the hg19 GFF3 genome annotation of Ensembl 81. All overlapping regions between alignments and referenced exons, or genes, were counted with HTSeq-count (v0.5.3, Anders et al 2014). Sample counts were normalized with DESeq2 (v1.8.1; Love, Huber & Anders, 2014)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include gene counting for each Sample

source_name: Subiculum – Patient 12

extract_protocol:
Total RNA was extracted using the Nucleospin kit (Machery-Nagel)
Libraries were prepared using the strand specific RNA-Seq library preparation TruSeq Stranded mRNA kit (Illumina) from 300ng of total RNA

value: Subiculum

tag: patient


title: 22-2015-0609-DG

source_name: Dentate Gyrus – Patient 12

value: Dentate Gyrus


title: 24-2015-0512 -SUB

source_name: Subiculum – Patient 13


title: 21-2015-0609-CA3

source_name: CA3 – Patient 12


title: 18-2015-0519-DG

source_name: Dentate Gyrus – Patient 11


title: 12-2014-0211-DG

source_name: Dentate Gyrus – Patient 10


title: 13-2014-0211-SUB

source_name: Subiculum – Patient 10


title: 17-2015-0519-CA3

source_name: CA3 – Patient 11


title: 10-2014-021-1CA1

source_name: CA1 – Patient 10


title: Hartley 5 months Male [243]

value: Male


title: 15-2015-0417-CA3

source_name: CA3 – Patient 9


title: 11-2014-0211-CA3

source_name: CA3 – Patient 10


title: 16-2015-0417-DG

source_name: Dentate Gyrus – Patient 9


title: EHT 2 Control

source_name: In Vitro iPSC Engineered Heart Tissue


title: 14-2015-0417-CA1

source_name: CA1 – Patient 9


title: 9-2013-0702-CA1

source_name: CA1 – Patient 8


title: 8-2013-0618-SUB

source_name: Subiculum – Patient 7


title: 7-2013-0618-DG

source_name: Dentate Gyrus – Patient 7


title: 6-2013-0618-CA3

source_name: CA3 – Patient 7


title: 5-2013-0618-CA1

source_name: CA1 – Patient 7


title: 2-2013-0204-CA3

source_name: CA3 – Patient 6


title: 1-2013-0204-CA1

source_name: CA1 – Patient 6


title: 4-2013-0204 -SUB

source_name: Subiculum – Patient 6


title: 83_22-7-14 - Sub

source_name: Subiculum – Patient 5


title: 82_22-7-14 - GD

source_name: Dentate Gyrus – Patient 5


title: 81_22-7-14 - CA3

source_name: CA3 – Patient 5


title: 73_8-7-14 GD

source_name: Dentate Gyrus – Patient 4


title: 19-2015-0519-SUB

source_name: Subiculum – Patient 11


title: 20-2015-0609-CA1

source_name: CA1 – Patient 12


title: 71_7-14 CA1

source_name: CA1 – Patient 4


title: 80_22-7-14 - CA1

source_name: CA1 – Patient 5


title: 74_8-7-14 Sub 1

source_name: Subiculum – Patient 4


title: 72_8-7-14 CA3

source_name: CA3 – Patient 4


title: 66_2014-0617 CA1

source_name: CA1 – Patient 3


title: 68_2014-0617 DG

source_name: Dentate Gyrus – Patient 3


title: 67_2014-0617 CA3

source_name: CA3 – Patient 3


title: 65_10-6-14 - Sub

source_name: Subiculum – Patient 2


title: 70_2014-0617 Sub2

source_name: Subiculum – Patient 3


title: 63_10-6-14 CA3

source_name: CA3 – Patient 2


title: 62_10-6-14 - CA1

source_name: CA1 – Patient 2


title: 64_10-6-14 - DG

source_name: Dentate Gyrus – Patient 2


title: 19_16-4-13-DG

source_name: Dentate Gyrus – Patient 1


title: 22_16-4-13-Sub

source_name: Subiculum – Patient 1


title: 21_16-4-13-CA1

source_name: CA1 – Patient 1


title: STIM_24h_CAR_MiSeq

first: Javed

last: Khan

address: 37 Convent Dr.

department: Genetics Branch

institute: NCI, NIH

data_processing:
CITE-seq including cell surfae protein and gene expression
fastq generation: Illumina bcl2fastq 2.20
sample demultiplexing: popscle demuxlet (https://github.com/statgen/popscle)
mapping, CellRanger 3.1.0 (10x Genomics)
secondary analysis: Seurat 3.1.0 or 4.0.0 (R package)
Genome_build: GRCh38-3.0.0
CAR detection
Whitelist generation: Umi-tools  was used to create a whitelist from the scRNA-seq combined read1 fastq file with parameters --set-cell-number=5000 and --set-cell-number=15000 for cell hashed triplicates in addition to --error-correct-threshold=1.
UMI and barcodes extraction: umi-tools extract function, for PacBio the 26 bp preceding the Template Switch Oligo (TSO) sequence, for MiSeq and Illumina-Seq first 26 bp in read1.
mapping: blastn
A custom script was written to deal with multimapping by selecting best hit for each read if read maps to more than one CAR with same accuracy level it gets disregarded.
Supplementary_files_format_and_content: 14 CAR sequences

source_name: Peripheral Blood Mononuclear Cells(PBMCs)

extract_protocol: Eight anti-GPC2 and six anti-CD276 CAR T- cells were first thawed separately and recover for overnight. Then they were pooled the same way according to its counterpart experiment co-cultured with tumor cells using an E:T ratio of 1:1 for individual anti-GPC2 CAR T- cells expect G27; and 1:4 for each anti-CD276 and G27 CAR T- cells. Pooled CAR T-cells were evenly divided into seven fractions for multimodal single cell assay. One of the 7 fractions were taken as CTRL_0h and remaining 6 fractions were split into two groups: one group of 3 fractions cultured without target tumor cells for 24 hours (CTRL_24h) and other group of 3 fractions co-cultured with target tumor cells for 24 hours (STIM_24h). To improve the cell viability to >85%, dead cells were removed by magnetic negative selection (Dead Cell Removal Kit, Miltenyi Biotec, Cat# 130-090-101). For 2 groups of pooled CAR T-cells at 24 hours, Totalseq-C human ‘hashtag’ antibodies were used for each of CAR T-cell triplicates in 2 groups allowing identification of different samples in the analysis, and then triplicates in each group were combined. Next, three CAR T- cell pools (CTRL_0h, CTRL_24h, and STIM_24h) were stained with a cocktail of TotalSeq-C human lyophilized panel (BioLegend) of 31 surface proteins. After washed three times, CAR-T cells were resuspended in PBS, and counted before proceeding immediately to the single cell immune profiling using a 10X Genomics Chromium system (10x Genomics, Pleasanton, CA). Briefly, CAR T-cells were mixed with the reverse transcription (RT) mix and partitioned into single cell Gel-Bead in Emulsion (GEM) using 10x 5’ Chromium Single Cell Immune Profiling Next GEM v1.1 chemistry. For detection of 14 CAR binders, a fraction of amplified full-length cDNA was used for PCR with CAR binder specific reverse primers. Half of PCR products without size selection were used for sequencing on a MiSeq (MiSeq Reagent Kit v3 (600-cycle)) for those CAR binders shorter than full length.

value: PBMCs transduced individually with 14 different CAR constructs

value: 14 pooled CAR T-cells exposured to target neuroblastoma cells for 24 hours

tag: molecule

value: mRNA


title: 20_16-4-13-CA3

source_name: CA3 – Patient 1


title: 3-2013-0204-DG

source_name: Dentate Gyrus – Patient 6


title: CTRL_24h_CAR_MiSeq

value: 14 pooled CAR T-cells without exposure to target neuroblastoma cells at 24 hours


title: CTRL_0h_CAR_MiSeq

value: 14 pooled CAR T-cells without exposure to target neuroblastoma cells at time 0


title: NSL3_KO_293T_1

city: Changchun

first: hong

middle: sen

last: liu

address: qianjin

institute: jilin university

data_processing:
Sequenced reads were aligned to the GRCh38 genome assembly using HISAT2 (v2.1.0).
Counts of gene fragments were generated using R package summarizeOverlaps. Differential expression analysis was determined using DESeq2.
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: human embryonic kidneys cells

growth_protocol: HEK293T cells were maintained at 37℃ in Dulbecco’s modified Eagle’s medium (DMEM, Gibco, Life Technologies, Waltham, MA, USA), and cultured with 10% fetal bovine serum (FBS, Kang Yuan Biology, Beijing, China) and 1% penicillin-streptomycin mixture (P/S, Thermo Fisher Scientific, Waltham, MA, USA).

extract_protocol:
RNA was extracted using the RNAiso Plus (9109; Takara, Tokyo, Japan). Libraries were generated for sequencing using the VAHTS mRNA-seq V3 Library Prep Kit for Illumina (NR611-02, Vazyme Biotech Co., Ltd, Jiangsu, China).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The second exon sequences of NSL3 region were used for single-guide RNA (sgRNA) targets screening. Designed sequence was ligated into pX459 vector which expresses Cas9 behind CMV promoter. 293T cells were transfected with the pX549-NSL3-KO plasmid for 48 h and clones were selected with 2 μg/ml puromycin. Individual colonies were isolated into the wells of a 96-well plate and the efficiency of the NSL3-KO was measured by western blotting and sequencing genomic DNA.

value: NSL3 KO

tag: cell line

value: human embryonic kidneys cells


title: NSL3_KO_293T_3


title: 293T_WT_4

value: wild type

value: untreated


title: Healthy

city: Tokyo

first: Kyaw Min

last: Soe

department: Orthognathics

institute: TMDU

hyb_protocol: 3D gene Toray

scan_protocol: 3D gene Toray

data_processing: Log2 global normalization test/reference found in the Series supplementary file section

source_name: Healthy PDl cells extracted from apical root of healthy normal patient

label_protocol: Samples were applied to microarrays encased in Agilent SureHyb-enabled hybridization chambers, along with oligoarray control targets and hybridization buffer

growth_protocol: Extracted PDL cells were grown in MEM (Wako, Osaka, Japan) supplemented with 10% fetal bovine serum (Gibco, Life Technologies, Paisley, UK) and penicillin-streptomycin (Gibco). The cultures were maintained in a humidified 5% CO2 atmosphere at 37°C.

extract_protocol: Total RNA was extracted from the cultured PDL cells of  healthy normal patients in 60 mm dishes by using the QiagenRNeasy® Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instruction.The concentration and purity of extracted RNA were assessed by using a DS-11 Spectrophotometer from DeNovix Inc). A260/A280 > 1.8 and an RNA integrity number (RIN) > 7.0 were considered pure and suitable for further analysis.

treatment_protocol: Both cells are extracted at same passage

value: PDL cells

tag: disease

value: healthy

value: female


title: 293T_WT_3


title: NSL3KO 293T cells - pol II

data_processing:
ChIP-seq reads were aligned to the the human assembly GRCh38 using Bowtie2.
peak calling was carried out by using MACS2 (Feng et al., 2012)
Assembly: GRCh38
Supplementary files format and content: bigWig files were generated using deepTools

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA/subunit-DNA complexes were isolated with antibody.
ChIP-Seq libraries were prepared using NEBNext Ultra DNA Library Prep Kit (E7370, NEB, USA) according to manufacturer’s manual and were purified with AMPure XP beads (A63881, Beckman, USA).

tag: chip antibody

value: pol II (Active Motif, 39097)


title: OFCD

source_name: Mutant PDL cells extracted from apical root of OFCD syndrome patient

value: OFCD (Occulofciocardiodental)


title: NSL3KO 293T cells - Input


title: NSL3KO 293T cells - H3K4me3

value: H3K4me3 (Abcam, ab8580)


title: NSL3KO 293T cells - MYST

value: MYST (bacterially expressed proteins)


title: NSL3KO 293T cells - H3K27me3

value: H3K27me3 (Abcam, ab4729)


title: NSL3KO 293T cells - H3K27ac

value: H3K27ac (Abcam, ab6002)


title: NSL3KO 293T cells - H4K5ac

value: H4K5ac (Millipore, 07-327)


title: NSL3KO 293T cells - MOF

value: MOF (Bethyl Laboratories, Inc., A300-992A)


title: NSL3KO 293T cells - NSL3

value: NSL3 (bacterially expressed proteins)


title: NSL3KO 293T cells - H3K4me2

value: H3K4me2 (Millipore, 07-030)


title: NSL3KO 293T cells - H3K4me1

value: NSL3 KO

value: H3K4me1 (Abcam, ab8895)


title: WT 293T cells - MOF

value: wild type

value: human embryonic kidneys cells


title: WT 293T cells - H3K27ac


title: WT 293T cells - MYST


title: NSL3KO 293T cells - H4K16ac

value: H4K16ac (Millipore, 07-329)


title: WT 293T cells - NSL3


title: WT 293T cells - Input


title: WT 293T cells - H3K4me3


title: WT 293T cells - pol II


title: WT 293T cells - H3K27me3


title: NSL3_KO_293T_2


title: WT 293T cells - H3K4me2


title: WT 293T cells - H4K8ac

value: H4K8ac (Millipore, 07-328)


title: WT 293T cells - H4K5ac


title: HC9

first: Wenjie

last: Zheng

address: No1 ShuaiFuYuan，Dong Cheng District ，Beijing, Beijing, CN

institute: Peking Union Medical College Hospital

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.  We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: hg38
Supplementary files format and content: combined csv file of matrix table with raw gene counts for every gene and every sample

source_name: human PBMC

extract_protocol:
RNA was harvested using Trizol reagent.A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: PBMCs were isolated from blood by density gradient centrifugation and then resuspended in PBS

tag: condition

value: healthy control

value: male


title: HC8


title: HC7


title: HC10


title: NSL3KO 293T cells - H4K8ac


title: WT 293T cells - H4K16ac


title: HC5


title: HC4


title: HC1


title: HC6


title: BDU3

value: BD patients


title: HC3


title: BDV4


title: HC2


title: BDV2


title: BDV5


title: BDU2


title: BDV1


title: BDU1


title: WT 293T cells - H3K4me1


title: Alexander1_wt rep2

city: Parma

first: Marco

last: Morselli

state: Parma

address: Parco Area delle Scienze, 23/A

country: Italy

institute: University of Parma

data_processing:
data demultiplexing using Illumina's bcl2fastq
adapter trimming with fastp (v0.23.1) with the following parameters: --adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -l 30
alignment to GRCh38 with STAR (v2.7.4.a) with --quantMode GeneCounts
bigwig files were produced with STAR --outWigType bedGraph --outWigStrand Stranded
Genome_build: GRCh38
Supplementary_files_format_and_content: bigwig files (two per sample. One for each strand:str1 str2)

source_name: human epithelial cell line (HCC)

growth_protocol: cells were cultured at 37 ° C in 5% CO2 atmosphere in DMEM (Dulbecco's Modified Eagle Medium), supplemented with 10% fetal bovine serum, 1% glutamine, and penicillin/streptomycin. The cells were seeded to maintain a cell density between 20%-60% and experiments were performed when cells reached a confluence of 70-80%.

extract_protocol:
Total RNA was isolated with the RNAeasy Plus kit (QIAGEN) from 500-900 x 10^3 cells.
Libraries were constructed with the KAPA mRNA HyperPrep kit (Roche Sequencing, cat# KK8580/ 08098115702) with unique dual-indexed adapters according to the manufacturer's protocol.

treatment_protocol: Retroviral VSVG transfection of Addgene plasmid #24928 and hygromycin B clonal selection

value: Alexander1 cell line (ATCC CRL-8024)

value: wt (Axin1 -)


title: Alexander1_wt rep4


title: Alexander1_Axin1+ rep4

value: Axin1 + (Addgene plasmid #24928)


title: BDV3


title: Alexander1_Axin1+ rep2


title: Alexander1_Axin1+ rep1


title: S9

data_processing:
data demultiplexing using Illumina's bcl2fastq
adapter removal using cutadapt (v2.10)
alignment using BSBolt Align (v1.3.0)
PCR duplicate removal using samtools markdup (samtools v. 1.9)
CpG methylation calling using BSBolt CallMethylation
CGmatrix creation with BSBolt AggreagateMatrix (CpG sites covered by at least 20 reads)
Genome_build: GRCh38
Supplementary_files_format_and_content: CGmap for each sample: text file containing CpG position and methylation values. Please refer to https://doi.org/10.1093/gigascience/giab033 for additional information.
Supplementary_files_format_and_content: CGmatrix: matrix of  sites common to all the samples. Common position and methylation levels for each sample

source_name: peripheral blood

extract_protocol:
Genomic DNA was isolated from the individuals by standard phenol-chloroform extraction method (Guha et al. 2018). 500 ng of extracted DNA were used for Targeted BS-seq library preparation as described in Chang et al., with minor modifications (Chang et al. 2021).
500 ng of extracted DNA were used for TBS-seq library preparation as described in Chang et al., with minor modifications (Chang et al. 2021). Briefly, fragmented DNA was subject to end repair, dA-tailing and adapter ligation using the NEBNext Ultra II Library prep kit using custom pre-methylated adapters (IDT) (Morselli et al. 2020). Purified libraries were hybridized to the biotinylated probes according to the manufacturer’s protocol. Captured DNA was treated with bisulfite prior to PCR amplification using KAPA HiFi Uracil+ with the following conditions: 2 min at 98°C; 14 cycles of (98°C for 20 sec; 60°C for 30 sec; 72°C for 30 sec); 72°C for 5 minutes; hold at 4°C. Library QC was performed using the High-Sensitivity D1000 Assay on a 2200 Agilent TapeStation. Libraries were sequenced on a NovaSeq6000 (S1 lane) as paired-end 150 bases.
Custom protocol based off the NEBNext Ultra II library prep kit, IDT xGen Hybridization Capture, Zymo Lightning bisulfite conversion kit
Illumina NovaSeq 6000 (S1 flowcell)

value: peripheral blood

tag: pcr positivity

value: PCRpos


title: S97

value: ATYPICALpneumonia

value: PCRneg


title: S98


title: Alexander1_wt rep1


title: S96


title: S95


title: S91


title: S94


title: S92


title: S90


title: S89


title: S87


title: S81


title: S85


title: S7


title: S86


title: S83


title: Alexander1_wt rep3


title: Alexander1_Axin1+ rep3


title: S79

value: BRONCHOpneumonia


title: BDV6


title: S78


title: S88


title: S76


title: S84


title: S80


title: S77


title: S74


title: S72


title: S73


title: S71


title: S70


title: S6


title: S68


title: S66


title: S8


title: S82


title: S64


title: S60


title: S57


title: S56


title: S63


title: S60R


title: S65


title: S55


title: S52


title: S62


title: S50


title: S5


title: S58


title: S53


title: S59


title: S56R


title: S75


title: S4


title: S49


title: 293T_WT_5

value: untreated


title: S48


title: S67


title: S69


title: Astrocyte MCM LPS 3

city: Indianapolis

first: Cristian

last: Lasagna-Reeves

address: 320 West 15th Street

department: Anatomy & Cell Biology

institute: Indiana University School of Medicine

hyb_protocol: NanoString Technologies protocol

scan_protocol: NanoString Technologies protocol

data_processing: Counts for target genes were normalized to the best fitting house-keeping genes as determined by nSolver software to account for variability in RNA content. Background signal was calculated as a mean value of the negative hybridization control probes.

source_name: Primary Astrocyte

growth_protocol: Cells were plated at a density of 1x10^6 and incubated until 90% confluent, changing media every 2 days.

extract_protocol: Total RNA was isolated from primary cultures with Rneasy Plus Universal Mini Kit

treatment_protocol: Cells were treated with 50ug of total protein from conditioned media

value: Brain

value: Primary Astrocyte

tag: medium

value: MCM

value: LPS


title: Astrocyte MCM LPS 2


title: S46

tag: disease state


title: Astrocyte MCM LPS 1


title: S45


title: S61


title: S42


title: S43


title: S54


title: S40


title: S41


title: S44


title: S3


title: S39


title: Astrocyte MCM PBS 3

value: PBS


title: Astrocyte MCM PBS 2


title: S38


title: Astrocyte ECM PBS 1

value: ECM


title: Astrocyte ECM LPS 2


title: Astrocyte ECM PBS 2