title: Male NFVCT190 duo

city: Illkirch

first: Gérard

last: Gradwohl

address: 1 rue Laurent Fries

country: France

institute: IGBMC

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq 2.20.0.422.
Reads were preprocessed using cutadapt version 1.10 in order to remove adapter, polyA and low-quality sequences (Phred quality score below 20), reads shorter than 40 bases were discarded for further analysis.
Reads mapping to rRNA were discarded (this mapping was performed using bowtie version 2.2.8).
Reads were mapped onto the mm39 assembly of mouse genome using STAR version 2.5.3a.
Gene expression was quantified using htseq-count version 0.6.1p1 and gene annotations from Ensembl release 104.
Assembly: mm39
Supplementary files format and content: Tabulated text file containing raw read counts in each sample.

source_name: duodenum

growth_protocol: RNA sequencing was carried out on the duodenum and ileum from adult Neurog3f/f; Villin-CreERT2 and control males (n=4/genotype) fed with standard chow diet, collected 18 weeks after tamoxifen administration.

extract_protocol:
NucleoSpin RNA Plus, Mini Kit (Macherey-Nagel)
Total RNA-Seq libraries were generated from total RNA using TruSeq Stranded Total RNA Library Prep Gold kit and TruSeq RNA Single Indexes kits A and B (Illumina, San Diego, USA), according to manufacturer's instructions. Briefly, cytoplasmic and mitochondrial ribosomal RNA (rRNA) was removed using biotinylated, target-specific oligos combined with Ribo-Zero rRNA removal beads. Following purification, the depleted RNA was fragmented into small pieces using divalent cations at 94°C for 8 minutes. Cleaved RNA fragments were then copied into first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP during second strand synthesis. The double stranded cDNA fragments were blunted using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK. A single 'A' nucleotide was added to the 3' ends of the blunt DNA fragments using a Klenow fragment (3' to 5'exo minus) enzyme. The cDNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR amplification (30 sec at 98°C; [10 sec at 98°C, 30 sec at 60°C, 30 sec at 72°C] x 12 cycles; 5 min at 72°C). Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

tag: genetic background

tag: Sex

value: male

value: duodenum

value: Neurog3f/f; Villin-CreERT2

value: standard diet


title: miRNAseq_con_2

status: Public on Mar 01 2023

type: SRA

city: Changzhou City

first: kang

last: wen

state: Jiangsu Province

address: Changzhou University, HUTANG Town, Wujin District

department: Institute of Biomedical Engineering and Health Sciences

country: China

institute: Changzhou University

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw single end reads were trimmed and quality controlled by Fastp (https://github.com/OpenGene/fastp )
Then clean reads were separately aligned to reference genome with orientation mode using bowtie software.
the expression level of each miRNA was calculated according to the fragments per Transcripts Per Million reads (TPM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify miRNA abundances.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

molecule: total RNA

organism: Homo sapiens

growth_protocol: ASMCs were cultured in DMEM supplemented with 10% FBS, 2 mM L-glutamine, 100 units/mL penicillin, and 100 μg/mL streptomycin in an incubator containing 5% CO2 humidified at 37 °C. Prior to the experiment

extract_protocol:
RNA was harvested using RNA isolater Total RNA Extraction Reagent（vazyme）and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >10μg) was used to construct sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: exponential proliferating ASMCs at passage 3-10 were plated on type I collagen-coated Bioflex 6-well plates and were serum-deprived for 24 h. With high stretch treatment, cells grown on Bioflex plates were exposed to a 13% cyclic strain at 0.5 Hz (1 s of deformation alternating with 1 s of relaxation, Flexcell 5000, FlexCell International, Hillsborough, NC, USA) to simulate the strain during MV for 72 h. Without high stretch treatment, cells grown in Bioflex plates were maintained in static conditions for 72 h. The cells without high stretch treatment on Bioflex plates were used as the static group and the cells with high stretch treatment on Bioflex plates were used as the experiment  group. Cells in 6-well plates without high stretch treatment were maintained under static conditions for 72 hours as a control group.

tag: tissue

value: airway

tag: cell type

value: airway smooth muscle cells

tag: treatment

value: without high stretch treatment  on 6-well plates


title: Male NFVCT153 duo

organism: Mus musculus

tag: genotype

tag: diet


title: miRNAseq_con_1


title: CRC1306LMO0A04011001R01000, LMO_BASALE, bio rep 1, QC ok

city: Candiolo

first: Livio

last: Trusolino

state: Turin

address: Strada Provinciale, 142 -KM 3.95

department: Oncology

country: Italy

institute: IRCCS Istituto Candiolo

data_processing:
Align with STAR on hybrid mm/hs genome
Assign counts to genes with FeatureCounts
Consider only human genes to normalize with DESeq2
QC based on evidence of lymphomatous infiltration
https://github.com/molinerisLab/StromaDistiller, https://github.com/vodkatad/RNASeq_biod_metadata
Assembly: GRCh38_GRCm38
Supplementary files format and content: merged_hs_mm.tsv.gz: raw counts for human and murine genes
Supplementary files format and content: vsd.tsv.gz: normalized expression values for human genes

molecule: polyA RNA

source_name: Colorectal Cancer

growth_protocol: Please check the linked publication

extract_protocol:
total RNA extraction
PolyA enriched
Forward Stranded

treatment_protocol: Please check the linked publication

value: Colorectal Cancer

tag: cell line

value: O

value: LM

value: WT


title: JGAmr_630_AD_IR_thymus_irradiated tissues [RNA-seq]

city: Houston

first: Yuan

last: Qi

state: TX

address: 1400 Pressler St

department: Bioinformatics & Computational Biology

country: USA

institute: University of Texas M.D. Anderson Cancer Center

data_processing:
alignment and gene count by STAR (version 2.6.0b)
gene annotation used GENCODE M19 (Ensembl 94)
differential expression analysis carried out in R (3.5.1) using Bioconductor package DESeq2
Assembly: GRCm38
Supplementary files format and content: tab-deliminated data matrix of gene counts

source_name: thymus

extract_protocol:
mice with germline p53 alterations of 4 weeks of age were exposed to irradiation or not, and were sacrificed (4h post-IR) for organ collection
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: background strain

value: thymus

tag: tissue type

value: irradiated tissues


title: CRC1304PRX0A01001TUMR01000, PRX_BASALE, bio rep 1, QC ok

value: X

value: PR


title: JGAmr_631_Het_IR_thymus_irradiated tissues [RNA-seq]


title: MCWR_2019_000365

city: Evanston

first: Brian

last: Wray

state: IL

address: 633 Clark Street

department: Feinberg School of Medicine

institute: Northwestern University

data_processing:
none provided
Assembly: mm10
Supplementary files format and content: tab-delimited text files with htseq counts

source_name: BMDM

growth_protocol: BMDM were generated from bone marrow prepared for in vitro differentiation for 5 days in complete Roswell Park Memorial Institute (RPMI) 1640 Medium (Gibco, # 22400089) supplemented with 10% (v/v) fetal bovine serum, 20 ng/mL recombinant murine MCSF (Preprotech, # 315-02), 100 U/mL Penicilin-Streptomycin and 2 mM L-Glutamine, at 37 oC and 5% CO2 atmosphere.

extract_protocol:
RNA was isolated using RNeasy Mini Kit (QIAGEN, # 74106) with additional DNase treatment using RNase-free DNase Set (QIAGEN, # 1023460).
Sequencing libraries were generated using Illumina Novaseq platform.

treatment_protocol: Cells were treated at time points with 100 ng/mL LPS.

value: BMDM

value: macrophage

value: LPS

tag: time


title: A008_ADT_HTO

city: Hamburg

first: Yu

last: Zhao

address: Falkenried 94

department: Institute of Medical Systems Biology

country: Germany

institute: University Medical Center Hamburg-Eppendorf

library_source: transcriptomic single cell

data_processing:
10x Genomics raw sequencing data were processed using CellRanger software (version 5.0.0, 10x Genomics, Pleasanton, CA) and the human genome GRCh38-2020-A release as the reference (function cellranger count). The matrices of cells and the unique molecular identifier (UMI) count were obtained and further processed by the R package Seurat (version 4.0.1)
To remove potential doublets, cutoff values for number of expressed genes (nGene) were determined for samples following visual inspection of the distribution of nGene and nUMI for each cell. The cells with higher nGene values were excluded. We further removed low-quality cells with high mitochondrial genes of all detected genes
Assembly: GRCh38-2020-A and mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample (linked to the corresponding *_GEX sample records)

source_name: kidney and blood mixded

growth_protocol: For single cell suspension kidneys were dissected and incubated for 40 min at 37°C in RPMI medium (including 0.01 M HEPES; 0.5 mL filtered FBS and 0.4µg/ mL DNase and 8 µg/ mL collagenase D). The samples were homogenized using a gentleMACS (Miltenyi Biotec).

extract_protocol:
Cells were loaded on a 10x Chromium single cell instrument.
All steps were performed according to standard protocol of the Chromium single cell 5’ v2 kit to generate high-quality cDNA libraries.

tag: tissue/cell type

value: kidney and blood mixded

tag: disease

value: ANCA-GN

tag: patient id


title: CRC1288PRX0B02004TUMR01000, PRX_BASALE, bio rep 1, QC failed


title: JGAmr_603_Het_IR_thymus_irradiated tissues [RNA-seq]


title: CRC1285PRX0A02001TUMR01000, PRX_BASALE, bio rep 1, QC failed


title: JGAmr_594_Het_IR_thymus_irradiated tissues [RNA-seq]


title: Male NF32 duo

value: male

value: duodenum

value: standard diet


title: Male NFVCT27 duo

value: Neurog3f/f; Villin-CreERT2


title: JGAmr_595_Het_IR_thymus_irradiated tissues [RNA-seq]


title: CRC1281LMX0A02003TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: Colorectal Cancer


title: CRC1280PRX0B02002TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: Male NF29 duo


title: A007_ADT_HTO


title: Male NF17 duo


title: JGAmr_856_Null_IR_thymus_irradiated tissues [RNA-seq]


title: Male NFVCT38 duo


title: Male NFVCT190

source_name: ileum

value: ileum


title: CRC1279PRX0A02002TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: Male NFVCT153


title: CRC1278LMX0A02001TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: LM


title: JGAmr_593_Null_IR_thymus_irradiated tissues [RNA-seq]


title: JGAmr_604_Null_IR_thymus_irradiated tissues [RNA-seq]


title: JGAmr_1087_Null_pancreas_basal tissues [RNA-seq]

source_name: pancreas

value: pancreas

value: basal tissues


title: A005_ADT_HTO


title: A006_ADT_HTO


title: Male NF152 duo


title: A004_ADT_HTO


title: CRC1277LMX0A02003TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: WT


title: Male NFVCT38


title: Male NFVCT27


title: JGAmr_923_Null_pancreas_basal tissues [RNA-seq]


title: CRC1275PRX0B02002TUMR01000, PRX_BASALE, bio rep 1, QC ok

value: X


title: JGAmr_859_Null_pancreas_basal tissues [RNA-seq]


title: JGAmr_857_Null_IR_thymus_irradiated tissues [RNA-seq]

value: thymus

value: irradiated tissues


title: Male NF32


title: CRC1272LMX0A05007TUMR09000, LMX_cetux_h, bio rep 1, QC ok

value: CET


title: JGAmr_701_AD_pancreas_basal tissues [RNA-seq]


title: JGAmr_700_AD_pancreas_basal tissues [RNA-seq]


title: Male NF29


title: JGAmr_702_AD_pancreas_basal tissues [RNA-seq]


title: A002_ADT_HTO


title: Male NF17


title: JGAmr_1087_Null_liver_basal tissues [RNA-seq]

source_name: liver

value: liver


title: CRC1278LMO0A04008001R01000, LMO_BASALE, bio rep 1, QC ok

value: O


title: Bmal1211, KO, Aged

city: Stanford

first: Sur

last: Herrera Paredes

state: CA

address: 371 Serra Mall,  Gilbert Building Room 109

department: Biology

institute: Stanford University

description:
Gene expression profile of mouse microglia
Bmal1211

data_processing:
Raw mRNA sequencing data was processed with the nf-core/rnaseq pipeline (v3.8.1). Default parameters were used except for the additional –remove_ribo_rna parameter to remove reads derived from ribosomal RNA.
Assembly: GRCm38
Supplementary files format and content: tab-separated text file include counts per gene per sample as estimated from Salmon via the nf-core/rnaseq pipeline

source_name: Microglia

growth_protocol: All animals were housed in an environmentally controlled, pathogen-free barrier facility on a 12-hour light–dark cycle, temperature, and humidity, with food and water available ad libitum. All tissue samples were isolated between ZT2 and ZT4 (zeitgebers time).

extract_protocol:
Microglia where issolated from brain tissue. Brain tissue was homogenized in Dounce buffer, supplemented with RNAase inhibitor and then passed through a 70 um cell strainer. Cells were pelleted at 400 xg for 5 minutes at 4C and resuspended in MACS buffer. Cells were incubated with myelin removal beads at 4C for 15 min and then washed in 2 ml MACS buffer supplemented with RNAase inhibitor. Cells were then run through the Miltenyi LD column placed in the MACS magnet and columns were subsequently rinsed twice with MACS buffer. Cells were pelleted at 300 xg for 5 min at 4C, resuspended in MACS buffer and incubated with CD11b microbeads for 15 min at 4C. Cells were washed in MACS buffer at 300 xg for 10 min at 4C and resuspended in MACS Buffer. Cells were separated by Miltenyi LS columns. Cells were then centrifuged at 300 xg for 10 min at 4C and resuspended in TRIzol LS.
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.  1 ug 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.

value: Microglia

value: CD11b cre;Bmal1 lox/lox

tag: age

value: Aged


title: CRC1272LMO0C05041001R02000, LMO_BASALE, bio rep 2, QC ok


title: CRC1272LMO0C04010001R01000, LMO_BASALE, bio rep 1, QC ok


title: CRC1272LMX0A02004TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: JGAmr_923_Null_liver_basal tissues [RNA-seq]


title: A001_ADT_HTO

value: kidney and blood mixded

value: ANCA-GN


title: Bmal193, KO, Aged

description:
Gene expression profile of mouse microglia
Bmal193


title: Male NF152

value: male

value: standard diet


title: SP_MC3

city: 广州

first: Xiaohong

last: Cen

address: 1838, Guangzhou Avenue North

institute: Southern Medical University

data_processing:
Cutadapt software (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9) was used to remove the reads that contained adaptor contamination,(command line: ~cutadapt -a ADAPT1 -A ADAPT2 -o out1.fastq -p out2.fastq in1.fastq in2.fastq -O 5 -m 100). And After removed the low quality bases and undetermined bases ,we used HISAT2 software (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) to map reads to the genome (for example:Homo sapiens Ensembl v96),(command line: ~hisat2 -1 R1.fastq.gz -2 R1.fastq.gz -S sample_mapped.sam).
Mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d.Linux_x86_64) with default parameters (command line: ~stringtie -p 4 -G genome.gtf -o output.gtf -l sample input.bam).
Transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8.Linux_x86_64).
Final transcriptome was generated, StringTie and ballgown(http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]),(command line: ~stringtie -e -B -p 4 -G merged.gtf -o samples.gtf samples.bam).
Differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and p value < 0.05 by R package edgeR(https://bioconductor.org/packages/release/bioc/html/edgeR.html) or DESeq2(http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html),and then analysis GO enrichment and KEGG enrichment to the differentially expressed mRNAs
Assembly: we aligned reads of all samples to the < research species > reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. HISAT2 allows multiple alignments per read (up to 20 by default) and a maximum of two mismatch when mapping the reads to the reference. HISAT2 build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions. And then by removing sequence-dependent bias and amplification noise using UMI-tools
Supplementary files format and content: The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value. FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)

source_name: PBMC

extract_protocol:
Sodium heparin-treated blood specimens was collected and PBMC were isolated using ficoll density gradient centrifugation. Total RNA from of PBMCs specimens were extracted by Trizol reagent.
The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

tag: strain

value: Chinese

value: blood

tag: disease state

value: severe atherosclerosis


title: CRC1272LMO0C02011002R01000, LMO_cetuxi_h, bio rep 2, QC ok

value: Colorectal Cancer

value: LM

value: WT


title: CRC1273PRX0B01001TUMR01000, PRX_BASALE, bio rep 1, QC ok

value: X

value: PR


title: SP_MC4


title: A003_ADT_HTO


title: Bmal191, KO, Aged

description:
Gene expression profile of mouse microglia
Bmal191


title: JGAmr_701_AD_liver_basal tissues [RNA-seq]

value: liver

value: basal tissues


title: SP_MC2


title: CRC1272LMO0C02011001R01000, LMO_cetuxi_h_NT, bio rep 2, QC ok

value: O

value: NT


title: CRC1272LMX0A05003TUMR05000, LMX_cetux_h_NT, bio rep 1, QC ok


title: JGAmr_700_AD_liver_basal tissues [RNA-seq]


title: CRC1272LMO0C02008003R01000, LMO_cetuxi_h, bio rep 1, QC ok

value: CET


title: Bmal192, KO, Aged

description:
Gene expression profile of mouse microglia
Bmal192

value: Microglia

value: CD11b cre;Bmal1 lox/lox

value: Aged


title: Bmal151, KO, Aged

description:
Gene expression profile of mouse microglia
Bmal151


title: MCWR_2019_000382

value: BMDM

value: macrophage

value: LPS


title: SP_MC1

value: Chinese

value: blood

value: severe atherosclerosis


title: JGAmr_859_Null_liver_basal tissues [RNA-seq]


title: JGAmr_702_AD_liver_basal tissues [RNA-seq]


title: Bmal142, KO, Aged

description:
Gene expression profile of mouse microglia
Bmal142


title: CRC1272LMO0C02008002R01000, LMO_cetuxi_h_NT, bio rep 1, QC ok

value: Colorectal Cancer

value: LM

value: WT


title: HD_MC3

value: healthy


title: JGAmr_1087_Null_intestine_basal tissues [RNA-seq]

source_name: Intestine

value: Intestine

value: basal tissues


title: HD_MC2


title: CRC1266PRX0B01001TUMR01000, PRX_BASALE, bio rep 1, QC failed

value: X

value: PR


title: Bmal171, WT, Aged

description:
Gene expression profile of mouse microglia
Bmal171

value: Microglia

value: CD11b cre


title: Bmal141, KO, Aged

description:
Gene expression profile of mouse microglia
Bmal141

value: CD11b cre;Bmal1 lox/lox

value: Aged


title: CRC1264LMX0A03033TUMR01000, LMX_cetux_6w, bio rep 1, QC ok

value: CET


title: JGAmr_923_Null_intestine_basal tissues [RNA-seq]


title: Bmal133, WT, Aged

description:
Gene expression profile of mouse microglia
Bmal133


title: HD_MC1


title: CRC1264LMX0A03013TUMR01000, LMX_cetux_6w_NT, bio rep 1, QC ok

value: NT


title: JGAmr_859_Null_intestine_basal tissues [RNA-seq]


title: CRC1264LMX0A02003TUMR01000, LMX_BASALE, bio rep 2, QC ok


title: PCCVC-2

city: Guangzhou

first: Lipeng

last: Mao

state: Guangdong

address: No.601, West Huangpu Avenue

department: Department of Microbiology and Immunology

institute: Jinan University

description: Additional sequencing was performed three times, there are four folders, 8 fastq files, and the file prefix starts with J1905004

data_processing:
Data quality control and gene expression quantify
Cell Ranger (http://support.10xgenomics.com/single-cell/software/overview/welcome) uses an   aligner called STAR (https://github.com/alexdobin/STAR), which peforms splicing-aware   alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket   the reads into exonic, intronic, and intergenic, and by whether the reads align (confidently) to the   genome. A read is exonic if at least 50% of it intersects an exon, intronic if it is non-exonic and   intersects an intron, and intergenic otherwise
Cell Ranger takes as input the expected number of recovered cells, N. Let m be a robust estimate of   the maximum total UMI counts, taken as the 99th percentile of the top N barcodes by total UMI   counts. All barcodes whose total UMI counts exceed m/10 are called as cells
When combining data from multiple libraries, we recommend equalizing the read depth between libraries before merging, to reduce the batch effect introduced by sequencing. Subsample reads from higher-depth libraries until they all have an equal number of total reads per cell.
Seurat is a popular R package that can perform QC, analysis, and exploration of scRNA-seq data ,which was originally developed as a clustering tool for scRNA-seq data
Assembly: GRCh38
Supplementary files format and content: cellranger raw  count

source_name: Pericytes of sigmoid colon cancer--PCCVC-2 (liver metastasis)

growth_protocol: TPCs were isolated from primary tumor specimens of CRC patients with non-metastasis or liver metastasis

extract_protocol:
The Single Cell 3’ Protocol upgrades short read sequencers to deliver a scalable microfluidic platform for 3’ digital gene expression profiling of 500–10000 individual cells per sample. The 10x™ GemCode™ Technology samples a pool of ~750000 barcodes to separately index each cell’s transcriptome. It does so by partitioning thousands of cells into nanoliter-scale Gel Bead-In_x0002_EMulsions (GEMs), where all generated cDNA share a common 10x Barcode. Libraries are generated and sequenced from the cDNA and the 10x Barcodes are used to associate individual reads back to the individual partitions. Upon dissolution of the Single Cell 3’ Gel Bead in a GEM, primers containing (i) an Illumina® R1 sequence (read 1 sequencing primer), (ii) a 16 nt 10x Barcode, (iii) a 10 nt Unique Molecular Identifier (UMI), and (iv) a poly-dT primer sequence are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded, full-length cDNA from poly_x0002_adenylated mRNA. After incubation, the GEMs are broken and the pooled fractions are recovered.
R1 (read 1 primer sequence) are added to the molecules during GEM incubation. P5, P7, a sample index, and R2 (read 2 primer sequence) are added during library construction via End Repair, A_x0002_tailing, Adaptor Ligation, and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification
10X single cell mRNA

tag: belong

tag: metastasis

value: liver metastasis


title: CCVC-2

description: Additional sequencing was performed three times, there are four folders, 8 fastq files, and the file prefix starts with J1905003

source_name: Sigmoid Colon Carcinoma Vascular Pericytes--CCVC-2 (Liver Metastasis)

value: Liver Metastasis


title: CRC1264LMX0A02001TUMR01000, LMX_BASALE, bio rep 1, QC ok

tag: tissue


title: JGAmr_700_AD_intestine_basal tissues [RNA-seq]


title: Bmal132, WT, Aged

description:
Gene expression profile of mouse microglia
Bmal132

tag: cell type


title: Bmal131, WT, Aged

description:
Gene expression profile of mouse microglia
Bmal131


title: PRCVC-1

description: Additional sequencing was performed three times, there are four folders, 8 fastq files, and the file prefix starts with J1904222

source_name: Pericytes of rectal cancer--PRCVC-1 (not metastasized)

value: not metastasized


title: Bmal122, WT, Aged

description:
Gene expression profile of mouse microglia
Bmal122


title: JGAmr_702_AD_intestine_basal tissues [RNA-seq]


title: CRC1264LMH0000000000R01000, LMH, bio rep 1, QC ok

value: Colorectal Cancer

value: H

tag: treatment


title: Bmal121, WT, Aged

description:
Gene expression profile of mouse microglia
Bmal121

tag: genotype


title: PPAR-alpha ChIP [JGAc_AD_AD_PPARalpha]

library_source: genomic

data_processing:
aligment by bowtie2 (2.3.4.2)
remove duplicates by PICARD (2.9.0)
peak calling by MACS2 (2.1.2)
differential open region by diffReps.pl (5.28.1)
Assembly: GRCh38
Supplementary files format and content: macs2 called peaks

molecule: genomic DNA

extract_protocol:
mice with germline p53 alterations were sacrificed for thymus collection at 4 weeks of age
Libraries were constructed following standard Illumina protocols for paired end indexing.

tag: source genotype

value: p53 AD/AD

tag: ChIP

value: PPAR-alpha ChIP

value: 4 weeks of age

value: thymus


title: CRC1261LMX0A02002TUMR01000, LMX_BASALE, bio rep 1, QC ok

tag: cell line

value: X

value: LM

value: WT


title: JGAmr_701_AD_intestine_basal tissues [RNA-seq]

tag: background strain

value: Intestine

tag: tissue type

value: basal tissues


title: Bmal1645, WT, Young

description:
Gene expression profile of mouse microglia
Bmal1645

value: Microglia

value: CD11b cre

value: Young


title: RCVC-1

description: Additional sequencing was performed three times, there are four folders, 8 fastq files, and the file prefix starts with J1904221

source_name: Rectal Cancer Vascular Pericytes--RCVC-1 (No Metastasis)

value: No Metastasis


title: PCCVC-1

description: Additional sequencing was performed three times, there are four folders, 8 fastq files, and the file prefix starts with J1904220

source_name: Colon cancer perivascular cells--PCCVC-1 (lymphatic metastasis)

value: lymphatic metastasis


title: CRC1257LMO0A04025001R01000.2, LMO_BASALE, bio rep 2, QC ok

value: O


title: p53 ChIP_2 [JGAc_AD_p53_Rep2]

value: p53 ChIP


title: CCVC-1

description: Additional sequencing was performed three times, there are four folders, 8 fastq files, and the file prefix starts with J1904219

source_name: Colon cancer vascular pericytes--CCVC-1 (lymphatic metastasis)


title: p53 ChIP_1 [JGAc_AD_p53_Rep1]


title: p53AD input [JGAc_AD_Input]

value: input


title: Bmal1642, WT, Young

description:
Gene expression profile of mouse microglia
Bmal1642


title: Bmal1644, WT, Young

description:
Gene expression profile of mouse microglia
Bmal1644


title: Bmal1643, WT, Young

description:
Gene expression profile of mouse microglia
Bmal1643


title: A549-GFP_Exp3

city: Kobe City

first: Michiyo

last: Koyanagi-Aoi

address: Chuo-ku, Kusunoki-cho 7-5-1

country: Japan

institute: Kobe University

data_processing:
Raw sequence files (fastq) were aligned to the human genome build 38 (hg38) reference sequences using the Strand NGS software program with default parameters.
All aligned reads were normalized using Transcripts per million (TPM).
TPM values were log2-transformed with an offset value of 1.0. Baseline transformation was not performed.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include Gene Symbol, Entrez Gene ID and TPM values (log2-transformed with an offset value of 1.0) for each Sample.

source_name: Stable GFP-overexpression

extract_protocol:
Total RNA was isolated by Trizol reagent (Life Technologies) according to the manufacture's instruction.
RNA libraries were prepared for TruSeq Stranded mRNA Sample Preparation Guide (Part#15031047 Rev.3).

value: human lung cancer cancer cell line

tag: genotype/variation

value: Stable GFP-overexpression


title: CRC1257LMH0000000000R01000, LMH, bio rep 1, QC ok

source_name: Colorectal Cancer

value: Colorectal Cancer

value: H


title: CRC1257LMO0A04017001R02000, LMO_BASALE, bio rep 1, QC ok


title: CRC1257LMX0A02001TUMR06000, LMX_BASALE, bio rep 1, QC ok

value: X


title: p53-null thymus [JGAa_1164 ATAC-seq]

data_processing:
cut adapter by trim_galore (0.4.5)
aligment by bowtie2 (2.3.4.2)
remove duplicates by PICARD (2.9.0)
peak calling by MACS2 (2.1.2)
differential open region by csaw (1.16.1)
Assembly: GRCm38
Supplementary files format and content: bed file of peaks called

source_name: thymus

extract_protocol:
mice with germline p53 alterations were sacrificed for thymus collection at 4 weeks of age
Library preparation followed standard Illumina protocols

value: 4 weeks of age

value: thymus


title: A549-TIPARP_Exp2

source_name: Stable TIPARP-overexpression

value: Stable TIPARP-overexpression


title: Bmal1641, WT, Young

description:
Gene expression profile of mouse microglia
Bmal1641


title: A549-GFP_Exp2


title: p53-null thymus [JGAa_923 ATAC-seq]


title: Bmal1634, WT, Young

description:
Gene expression profile of mouse microglia
Bmal1634


title: A549-TIPARP_Exp3


title: CRC1251LMX0A02003TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: LM

value: WT


title: Bmal1633, KO, Young

description:
Gene expression profile of mouse microglia
Bmal1633

value: Microglia

value: CD11b cre;Bmal1 lox/lox


title: CRC1251LMO0A04027001R01000, LMO_BASALE, bio rep 2, QC ok


title: AD thymus [JGAa_1286 ATAC-seq]


title: A549-GFP_Exp1


title: AD thymus [JGAa_1284 ATAC-seq]


title: Bmal1632, KO, Young

description:
Gene expression profile of mouse microglia
Bmal1632

value: Young


title: scRNAseq7_CMO

city: Taichung City

first: thh

last: lab

address: 1650 Taiwan Boulevard Sect. 4, Taichung, Taiwan 40705, ROC

country: Taiwan

institute: TCVGH

description: CMO counts are in processed data files on GEX sample (GSM5954928)

data_processing:
sequence reads were mapped to the human reference genome GRCh38 by CellRanger (version 6.0.1)
cells with unique feature counts over 9000 or less 200 will be filtered and cells with mitochondrial counts over than 10% will be eliminate as noise signals.
SCTransform was applied to the cells in each batch for normalization, then the 5 batches were integrated by using SCTransform integration workflow.
Assembly: GRCh38
Supplementary files format and content: tab delimited text file include raw read counts for each sample

source_name: Bone marrow aspirate from AML patient

extract_protocol: Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index, CG000388, Rev A)

value: Bone marrow aspirate

tag: diagnosis

value: AML

tag: group

value: all non-CR

tag: library

tag: cmo


title: Bmal1631, KO, Young

description:
Gene expression profile of mouse microglia
Bmal1631

tag: age


title: AD thymus [JGAa_701 ATAC-seq]


title: CRC1249PRX0A02002TUMR01000, PRX_BASALE, bio rep 1, QC ok

value: PR


title: CRC1247PRX0B02003TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: MRSA_96h_3

city: Beijing

first: Yue

address: FengTai street

institute: Beijing Institute of Microbiology and Epidemiology

description: infected with MRSA for 96h

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by Removing reads containing sequencing adapter;
Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%.
Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The clean reads were mapped to the reference genome using HISAT2 (v2.0.4).
Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set， then expression level of gene was calculated by RSEM (v1.2.12)
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: lung

growth_protocol: Lung tissue was extracted sterile and placed in animal tissue RNA stable preservation solution (RNALater)

extract_protocol:
extracted from lung tissue using Trizol
The mRNA molecules were purified from total RNA using magnetic beads with Oligo (dT), and after the reaction the mRNA molecules were cleaved into small pieces using lysis reagents, and the first strand cDNA was generated by reverse transcription using random hexamer primers over a period of time at the appropriate temperature, followed by second strand cDNA synthesis.

value: lung


title: CRC1251PRX0B02002TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: MRSA_96h_2

description: infected with MRSA for 96h


title: ScAML-Multiplex1

description: CMO counts are in processed data files on GEX sample (GSM5954926)


title: scRNAseq7


title: Bmal1601, KO, Young

description:
Gene expression profile of mouse microglia
Bmal1601


title: ScAML-GEX1


title: CRC1245LMX0A02001TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: A549-TIPARP_Exp1

value: human lung cancer cancer cell line


title: MRSA_96h_1

description: infected with MRSA for 96h


title: ScAML-Multiplex3

description: CMO counts are in processed data files on GEX sample (GSM5954924)

value: all CR

value: multiplexed sample:CMO309, CMO310


title: CRC1245LMO0A04029001R02000, LMO_BASALE, bio rep 1, QC ok

value: Colorectal Cancer

value: O


title: CRC1251LMO0A03045001R01000, LMO_BASALE, bio rep 1, QC ok


title: ScAML-GEX3


title: CRC1242PRX0A02002TUMR01000, PRX_BASALE, bio rep 1, QC ok

value: X


title: ScAML-Multiplex2

description: CMO counts are in processed data files on GEX sample (GSM5954922)

value: multiplexed sample:CR and non-CR

value: multiplexed sample:CMO301, CMO302, CMO303, CMO304, CMO305, CMO306, CMO307, CMO308, CMO311, CMO312


title: SDS+SpA+Antibiotics SAM24375406

city: South San Francisco

first: Jason

middle: A

last: Hackney

address: 1 DNA Way

department: Department of Bioinformatics and Computational Biology

institute: Genentech, Inc.

description: SDS+SpA+Antibiotics

data_processing:
HTSeqGenie 4.2.1
Reads were aligned to the GRCm38 reference genome using GSNAP (version 2013-11-01)
Aligned reads within exons defined by GENCODE (v27) were counted using the countFeatures method from HTSeqGenie
Assembly: GRCm38
Supplementary files format and content: bam alignment files
Supplementary files format and content: tsv count matrices

source_name: skin

growth_protocol: shaven  backsin of  balbc mice was treated daily  with SDS and Protein A for 7 days

extract_protocol:
FF skin was homogenized in Trizol, and chloroform was added and the aqueous phase was separated. 400ul of the aq phase was combined witth 400ul 70% Ethanol and used  in an RNAeasy mini Kit (Qiagen, 74106) in accordance to standard manufacturer's instructions including Dnase treatment treatment procedure.
Libraries were prepared using the Illumina TruSeq Stranded Total RNA Library Prep Kit.

treatment_protocol: Therapeutic intervention included  inhibitory antibodies (IP) againts KLK5 and KLK7 (500ug and 250ug every other day)  or oral antibiotics (amp., vanco, neo., metron.)

value: skin

value: Balb/c

value: SDS+SpA+Antibiotics


title: SDS+SpA+Antibiotics SAM24375407

description: SDS+SpA+Antibiotics


title: MRSA_48h_2

description: infected with MRSA for 48h


title: Bmal1621, KO, Young

description:
Gene expression profile of mouse microglia
Bmal1621

value: Microglia

value: CD11b cre;Bmal1 lox/lox

value: Young


title: MRSA_48h_1

description: infected with MRSA for 48h


title: ScAML-GEX2

value: Bone marrow aspirate

value: AML


title: Bmal1602, KO, Young

description:
Gene expression profile of mouse microglia
Bmal1602


title: SDS+SpA+Antibiotics SAM24375405

description: SDS+SpA+Antibiotics


title: CRC1241LMX0B03005TUMR05000, LMX_cetux_6w_NT, bio rep 1, QC ok

value: LM

value: WT

value: NT


title: SDS+SpA+Antibiotics SAM24375404

description: SDS+SpA+Antibiotics


title: CRC1246PRX0B02002TUMR01000, PRX_BASALE, bio rep 1, QC ok

value: PR


title: MRSA_24h_3

description: infected with MRSA for 24h

value: lung


title: CRC1241LMX0B03003TUMR05000, LMX_cetux_6w, bio rep 1, QC ok

value: Colorectal Cancer

value: CET


title: CRC1241LMX0A02002TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: X


title: SDS+SpA+Antibiotics SAM24375403

description: SDS+SpA+Antibiotics


title: scAML4-CMO

description: CMO counts are in processed data files on GEX sample (GSM5954920)

value: multiplexed sample:CR and non-CR

value: multiplexed sample:CMO301, CMO302, CMO309, CMO0310, CMO312


title: MRSA_24h_2

description: infected with MRSA for 24h


title: CRC1241LMO0A04018001R01000, LMO_BASALE, bio rep 2, QC ok

value: O


title: scAML4-GEX


title: MRSA_24h_1

description: infected with MRSA for 24h


title: SDS+SpA + anti-KLK5+7 SAM24375401

description: SDS+SpA + anti-KLK5+7

value: skin

value: Balb/c

value: SDS+SpA + anti-KLK5+7


title: MRSA_12h_3

description: infected with MRSA for 12h


title: H1 ES-derived salivary gland epithelial progenitors_rep2

first: Siqi

last: Zhang

address: 22# Zhongguancun South Avenue, Haidian District

department: Department of Oral and Maxillofacial Surgery School and Hospital of Stomatology

institute: Peking University

data_processing:
Illumina Casava1.7 software used for basecalling.
Clean data was generated by quality control and then mapped to the reference genome (GRCh38_release95) using Hisat2.
Quantification of gene expression levels were measured by fragments per kilobase of transcript per million fragments mapped (FPKM) from Florea L,. F1000Res. 2013. In the equation, cDNA Fragments represents the number of PE reads mapped to the specific transcript; Mapped Fragments (Millions) is the number of all mapped reads, which is counted as 10^6; Transcript Length(kb) is the length of transcript in unit of 10^3 b.
Genome_build: GRCh38_release95
Supplementary_files_format_and_content: tab-delimited list files include FPKM values for each Sample

source_name: salivary gland epithelial progenitors

growth_protocol: The SGEP were generated by differentiation of hESCs at day 16. Briefly, the colonies of hPSCs were isolated and cell aggregates were plated in low-cell adhesion plates (day 0). EBs was harvested at day 3 and transferred to tissue-treated cell culture plates to allow cell adherent for 2 additional days without disturbing. Cells were then cultured in differentiation medium plus 10 pM BMP4 from day 5 to day 10. RA was applied to the cultures at day 10 for 2 days at a final concentration of 1 μM, followed by a 4-day treatment of 6 μM CHIR99021.

extract_protocol:
Total RNA was extracted from H1 ES derived SGEP at day 16 using RNeasy mini kit (Qiagen) following the manufacturer’s instructions. RNA concentration and quality were measured by NanoDrop 2000 and the Agilent Bioanalyzer 2100 system.
Sequencing libraries were prepared 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.

treatment_protocol: All samples were untreated.

value: hES-derived salivary gland epithelial progenitors

value: untreated


title: MRSA_48h_3

description: infected with MRSA for 48h


title: SDS+SpA + anti-KLK5+7 SAM24375400

description: SDS+SpA + anti-KLK5+7


title: CRC1241LMO0A03013003R01000, LMO_BASALE, bio rep 1, QC ok


title: H1 ES-derived salivary gland epithelial progenitors_rep1


title: CRC1241LMH0000000000R05000, LMH, bio rep 1, QC ok

value: H


title: MRSA_12h_2

description: infected with MRSA for 12h


title: CRC1240PRX0B02002TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: CRC1240LMX0B02001TUMR05000, LMX_BASALE, bio rep 1, QC ok

value: LM


title: MCF7 cells-NFIC1, rep2

city: Chang Chun

first: Xin

last: Hu

address: 2699 Qianjin road,china

institute: Jilin university

data_processing:
The library preparations were sequenced on Novaseq6000-1.7.5, RTA3 software was used for base-calling, and paired-end reads were generated.
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, GC-content and sequence duplication level of the clean data  were calculated. All the downstream analyses were based on clean  data with high quality
Gene expression levels were calculated by fragments per kilobase of  transcript per million fragments mapped(FPKM)
Differential expression analysis of two groups was  performed using the DESeq R package (1.10.1). The resulting P values were adjusted using the Benjamini  and Hochberg’s approach for controlling the false discovery rate (FDR).  Genes withfold change ≥2 or ≤0.5, false discovery rate (FDR) <0.01 were selected as differentially expressed gene.
Genome_build: ensembl CRCh38
Supplementary_files_format_and_content: FPKMs

source_name: MCF7 cells

growth_protocol: MCF-7 cell line was cultured in DMEM (Gibco) supplemented with 10% FBS and streptomycin/penicillin (100 U/mL) at 37˚C in an atmosphere of 5% CO2.

extract_protocol:
The total RNA was harvested using Trizol reagent. Illumina NEBNext Ultra Directional RNA Library Prep Kit(NEB) 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: MCF7 cells were transiently transfected with pcDNA3.1 (Control) or pcDNA3.1-NFIC1 (NFIC1) for 48 h using Lipofectamine 2000.

value: MCF7 cells

value: Breast cancer cells

value: Transient transfection with pcDNA3.1-NFIC1


title: MCF7 cells-NFIC1, rep3


title: MRSA_12h_1

description: infected with MRSA for 12h

value: lung


title: SDS+SpA + anti-KLK5+7 SAM24375398

description: SDS+SpA + anti-KLK5+7


title: SDS+SpA + anti-KLK5+7 SAM24375399

description: SDS+SpA + anti-KLK5+7


title: SDS+SpA + anti-KLK5+7 SAM24375402

description: SDS+SpA + anti-KLK5+7


title: CTRL_3

description: uninfected


title: SDS+SpA + Isotype SAM24375397

description: SDS+SpA + Isotype

value: SDS+SpA + Isotype


title: CTRL_2

description: uninfected


title: CTRL_1

description: uninfected


title: SDS+SpA + Isotype SAM24375396

description: SDS+SpA + Isotype


title: CRC1239LMO0B04007001R01000, LMO_BASALE, bio rep 1, QC ok

value: Colorectal Cancer

value: WT


title: MCF7 cells-Control, rep2

value: Transient transfection with pcDNA3.1


title: SDS+SpA + Isotype SAM24375395

description: SDS+SpA + Isotype


title: SDS+SpA + Isotype SAM24375394

description: SDS+SpA + Isotype


title: CR Female zt22 replicate 2

city: Cleveland

first: Roman

last: Kondratov

state: OH

address: 2121 Euclid Ave

department: BGES

institute: Cleveland State University

data_processing:
50M reads (150bp, paired end) per sample were generated on Illumina NovaSeq 6000 platform.
RNA-seq reads were mapped to the mouse protein coding genes (Ensembl: Mus_musculus; GRCm38) using Bowtie48 allowing up to 2-mismatches.
The gene expected read counts and Transcripts Per Million (TPM) were estimated by RSEM (v1.2.3)
The TPMs were further normalized by EBSeq50 R package to correct potential batch effect.
Assembly: GRCm38
Supplementary files format and content: text files with matrix of normalized TPMs for every gene and every sample
Supplementary files format and content: text file of the matrix table with expected gene counts for every gene and every sample

source_name: Calorie-restricted liver

growth_protocol: After wean, mice were maintained on 5008 LabDiet (proteins 26.5%, fat 16.9%, carbohydrates 56.5%) with ad-libitum access to food and water

extract_protocol:
At 5 month old mice were sacrificed and livers immediately frozen. Total RNA was isolated from mouse liver tissue using mini spin column QIAGEN RNeasy Mini Kit (Ref #74104, Lot#163035346, Hilden, Germany) according to the manufacturer’s protocol.
non-directional – polyA enrichment library was prepared using NEBNext Ultra™ II RNA Library Prep Kit for Illumina, and 50M reads (150bp, paired end) per sample were generated on Illumina NovaSeq 6000 platform.

treatment_protocol: At 3 months of age calorie-restricted group of mice was subjected to gradual reduction of food amount provided – 1st week – 10%, 2nd week – 20%, 3rd week – 30% from 100% estimated AL intake. Food was provided once a day at zt14 - 2 hours after the light was off. Water access was not restricted. All animals in both AL control and CR groups were maintained on a standard light-dark 12:12 hour cycle.

tag: strain

value: liver

value: 5 month old

value: Wild-type

value: Calorie-restricted diet

tag: time point


title: CR Female zt22 replicate 3

tag: tissue


title: MCF7 cells-Control, rep1

tag: cell type


title: MCF7 cells-NFIC1, rep1

tag: treatment


title: CRC1234PRX0A01001TUMR01000, PRX_BASALE, bio rep 1, QC ok

value: X

value: PR

tag: genotype


title: SDS+SpA + Isotype SAM24375393

description: SDS+SpA + Isotype

value: skin

value: Balb/c


title: NHA_INPUT

city: Boston

first: Julie-Aurore

middle: E

last: Losman

state: MA

address: 450 Brookline Ave MA448

institute: Dana-Farber Cancer Institute

data_processing:
Reads were aligned to the human genome (hg38) or drosophila genome (dm3) using Bowtie2 v2.2.9
Samtools v1.3.1 was used to convert SAM files to BAM format, reads were sorted and filtered for duplicates using Sambamba, and were indexed with  Samtools
Peaks were called using MACS2 v2.1.1.20160309 with the ‘--BAMPE’ option
Sample quality was assessed using CHIPQC
Blacklist removal, drosophila spike-in normalization, differential binding analysis, and tornado plot generation were performed using Diffbind v3.2.5
Genome_build: hg38
Supplementary_files_format_and_content: .narrowPeak files contain peaks called by MACS2, prior to spike-in normalization

source_name: NHA cell line

extract_protocol:
20 x 106 cells (TF-1 and NHA cells) or 1 x 106 cells (MCTS lines) were collected per replicate, cross-linked with 1% formaldehyde for 10 minutes at room temperature on a rocker, and quenched with 140mM glycine for 5 minutes at room temperature. Cells were washed 3 times with PBS and snap frozen. Cell pellets were resuspended in ChIP lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl pH8.1) containing protease inhibitor cocktail (Roche). Chromatin was sonicated using a Sonic Dismembrator Model 100 (Fisher Scientific) with rounds of 10 seconds on, 30 seconds off at 30% power (TF1 cells: 11 rounds, NHA cells: 9 rounds, MCTS lines: 7 rounds). Shearing efficacy was confirmed by agarose gel electrophoresis. Immunoprecipitations were performed with the equivalent of 1 x 106 cells for each sample using the Magna ChIP A/G kit (Millipore) and rabbit monoclonal H3K4me3 antibody (Millipore, 15-10C-E4) or normal rabbit IgG (Millipore, #12-370). Drosophila spike-in chromatin (Active Motif) was added along with Drosophila anti-H2Av (Active Motif) to samples prior to immunoprecipitation. Chromatin was incubated with primary antibodies overnight at 4 °C with constant agitation. Inputs were prepared from sonicated controls for each cell line.
Sequencing libraries were generated from purified IP sample DNA using Swift 2S ligation chemistry

value: immortalized normal human astrocyte

tag: chip antibody


title: MCF7 cells-Control, rep3

value: MCF7 cells


title: CRC1239LMX0A02004TUMR01000, LMX_BASALE, bio rep 1, QC ok

data_processing:
Align with STAR on hybrid mm/hs genome
Assign counts to genes with FeatureCounts
Consider only human genes to normalize with DESeq2
QC based on evidence of lymphomatous infiltration
https://github.com/molinerisLab/StromaDistiller, https://github.com/vodkatad/RNASeq_biod_metadata
Assembly: GRCh38_GRCm38
Supplementary files format and content: merged_hs_mm.tsv.gz: raw counts for human and murine genes
Supplementary files format and content: vsd.tsv.gz: normalized expression values for human genes

extract_protocol:
total RNA extraction
PolyA enriched
Forward Stranded

value: LM


title: CR Female zt22 replicate 1


title: CRC1201PRX0A02002TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: TS603_INPUT

source_name: TS603 MTCS

value: glioma patient derived multicellular tumor spheroid


title: CR Female zt18 replicate 2


title: TS516_INPUT

source_name: TS515 MTCS


title: CR Female zt18 replicate 3


title: naive SAM24375391

description: naive

value: naive


title: naive SAM24375392

description: naive


title: CRC1198LMX0B02002TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: MGG152_INPUT

source_name: MGG152 MTCS


title: naive SAM24375390

description: naive


title: CRC1237PRX0A02003TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: HK308_INPUT

source_name: HK308 MTCS


title: CR Female zt14 replicate 3


title: CR Female zt14 replicate 2


title: HK213_INPUT

source_name: HK213 MTCS


title: CRC1190PRX0B02002TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: naive SAM24375388

description: naive


title: CRC1188PRX0B02004TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: CR Female zt14 replicate 1


title: MPP SYNCRIP-ADAR 3

city: new york

first: Michael

last: Kharas

state: New York

address: 417 68th street

department: Molecular Pharmacology Program

institute: Mamorial Sloan Kettering Cancer Center

data_processing:
The paired-end RNA-seq reads to mouse (mm10) genome using STAR aligner (Dobin et al., 2013)
All mutations (SNP) were identified for each RNA-seq library using the GATK (Van der Auwera et al., 2013) workflow for calling variants in RNA-seq
The mutations were then restricted to annotated mRNA transcripts, as well as restricted to A-to-G mutations in transcripts encoded by the forward strand and T-to-C mutations in transcripts encoded by the reverse strand.
Data were then filtered using mutations found in the dbSNP database since they are most likely DNA-level mutations.
The filtered sets of RNA editing events from all RNA-seq libraries of the same experiment were combined, and counted the number of reads containing reference (A/T) and alternative (G/C) alleles from each library at each site
Assembly: mm10
Supplementary files format and content: "HSC-SYNCRIPADAR-_vs_HSC-MIG-_HSC_snp_counts_dedupped_significance_fpkm.csv" and "MPP-SYNCRIPADAR-_vs_MPP-MIG-_MPP_snp_counts_dedupped_significance_fpkm.csv" files includes also difference frequency (editing frequency of a site in SYNCRIP_ADA sample subtracted to the average of editing frequency of the site in MIG sample), p value, adjusted p value, number of edit sites

source_name: Primary Bone Marrow Cells

growth_protocol: B6 mice were used to harvest bone marrow.HSC and MPP cells were FACS sorted and placed in SFEM media supplemented with cytokines (50 ng/ml SCF, 10 ng/ml IL-3, and 10 ng/ml IL-6, 10ng/ml TPO and 20 ng/ml FLT3L)

extract_protocol:
Sorted cells were harvested and frozen in TRIzol reagent. RNA was extracted using Phenol-Chloroform
After PicoGreen quantification and quality control by Agilent BioAnalyzer, library preparation is performed using  the SMART-Seq v4 Ultra Low Input RNA Kit

treatment_protocol: Cells were infected with virus expressing SYNCRIP-HyperADAR at 1:1 ratio (v/v) and sorted for GFP+ expression 48hrs post transduction.

value: Bone Marrow

value: Multipotent Progenitor

value: Overexpressing SYNCRIP-HyperADAR fusion

value: 48hr after transduction

tag: cell type (sorted)

value: GFP+ MPPs (Lin-, Sca1+, cKit+, all remaining CD150 CD48 cells)


title: CRC1185PRX0B02002TUMR01000, PRX_BASALE, bio rep 1, QC ok

value: Colorectal Cancer

tag: cell line

value: WT


title: MPP SYNCRIP-ADAR 2

description: MPP-SYNCRIPADAR-_vs_MPP-MIG-_MPP_snp_counts_dedupped_significance_fpkm.csv


title: HK157_INPUT


title: CR Female zt10 replicate 3

value: liver

value: 5 month old

value: Wild-type

value: Calorie-restricted diet


title: CRC1200PRX0A01001TUMR01000, PRX_BASALE, bio rep 1, QC ok

value: X

value: PR


title: BT260_INPUT

source_name: BT260 MTCS


title: CRC1182PRX0B02001TUMR01000, PRX_BASALE, bio rep 2, QC ok

source_name: Colorectal Cancer


title: BT054_INPUT

source_name: BT054 MTCS


title: CR Female zt10 replicate 2


title: MPP SYNCRIP-ADAR 1


title: CRC1182PRX0A02001TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: CR Female zt10 replicate 1


title: MPP MIG 2

value: Overexpressing Empty Vector


title: naive SAM24375389

description: naive

value: skin

value: Balb/c


title: CR Female zt18 replicate 1


title: TF1_INPUT

source_name: TF1 cell line

value: growth factor dependent erythroblast


title: CR Female zt6 replicate 3


title: CRC1182PRH0000000000R01000, PRH, bio rep 1, QC ok

value: H


title: CRC1182LMX0B02001TUMR02000, LMX_BASALE, bio rep 2, QC ok

value: LM


title: MPP MIG 1

value: Bone Marrow

value: Multipotent Progenitor


title: NHA-R132H_R2_H3K4me3_ChIPseq

value: immortalized normal human astrocyte

value: IDH1-R132H expression vector


title: CR Female zt6 replicate 2


title: HSC SYNCRIP-ADRA 3

description: HSC-SYNCRIPADAR-_vs_HSC-MIG-_HSC_snp_counts_dedupped_significance_fpkm.csv

value: Hematopoietic Stem Cell

value: Overexpressing SYNCRIP-HyperADAR fusion

value: 48hr after transduction

value: GFP+ HSCs (Lin-, Sca1+, cKit+, CD150+ CD48-)


title: NHA-R132H_R1_H3K4me3_ChIPseq


title: CRC1182LMX0A03007TUMR05000, LMX_cetux_6w, bio rep 1, QC ok

value: Colorectal Cancer

value: WT

value: CET


title: CR Female zt2 replicate 3

value: liver

value: 5 month old

value: Wild-type

value: Calorie-restricted diet


title: HSC SYNCRIP-ADAR 2


title: CR Female zt6 replicate 1


title: NHA-IDH1_R2_H3K4me3_ChIPseq

value: IDH1-WT expression vector


title: MPP MIG 3

value: Overexpressing Empty Vector

value: GFP+ MPPs (Lin-, Sca1+, cKit+, all remaining CD150 CD48 cells)


title: NHA-IDH1_R1_H3K4me3_ChIPseq


title: CR Female zt2 replicate 2


title: CRC1182LMX0A03002TUMR01000, LMX_cetux_6w_NT, bio rep 2, QC ok

value: X

value: LM

value: NT


title: TS603_R2_H3K4me3_ChIPseq

value: glioma patient derived multicellular tumor spheroid


title: CRC1182LMX0A03001TUMR01000, LMX_cetux_6w_NT, bio rep 1, QC ok


title: HSC SYNCRIP-ADAR 1

value: Bone Marrow

value: Hematopoietic Stem Cell

value: Overexpressing SYNCRIP-HyperADAR fusion


title: p53-null thymus [JGAa_1000 ATAC-seq]

source_name: thymus

tag: background strain

value: 4 weeks of age

value: thymus


title: TS603_R1_H3K4me3_ChIPseq


title: AL Female zt22 replicate 2

source_name: Ad-libitum liver

value: Ad-libitum diet


title: HSC MIG 2

value: 48hr after transduction

value: GFP+ HSCs (Lin-, Sca1+, cKit+, CD150+ CD48-)


title: CRC1182LMX0A03009TUMR01000, LMX_cetux_6w, bio rep 2, QC ok

value: Colorectal Cancer

value: WT

value: CET


title: HSC MIG 1

value: Overexpressing Empty Vector


title: TS516_R2_H3K4me3_ChIPseq


title: AL Female zt22 replicate 1

value: liver

value: 5 month old

value: Wild-type


title: CRC1181PRX0A02004TUMR01000, PRX_BASALE, bio rep 1, QC failed

value: X

value: PR


title: TS516_R1_H3K4me3_ChIPseq

value: glioma patient derived multicellular tumor spheroid


title: AL Female zt18 replicate 3


title: MGG152_R2_H3K4me3_ChIPseq


title: CRC1178PRX0A02003TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: CRC1197PRX0B02003TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: HSC MIG 3

value: Bone Marrow

value: Hematopoietic Stem Cell


title: HSC Cre Pos 2

description:
KO_vs_Control.norm.gct
DifferentialExpression_30433.csv

data_processing:
RNA-seq data was processed using analysis pipelines by basepairtech. com.
Reads were aligned reads STAR (illumina) and counted using FeatureCounts.
Differential gene expression analysis was done using DESeq2 - Bioconductor
Assembly: mm10
Supplementary files format and content: Gct file is a tab-delimited text file that contains gene expression data
Supplementary files format and content: csv file is the differential anaysis results that includes log2FoldChange, pvalue, padj values for each genes

growth_protocol: Whole bone marrow from SYNCRIP conditional knockout mice mice were transplanted into recipient congenic CD45.1 mice and remained in vivo for 9 weeks before harvesting.

extract_protocol:
HSCs were FACS sorted  and frozen in TRIzol reagent. RNA was extracted using Phenol-Chloroform.
After PicoGreen quantification and quality control by Agilent BioAnalyzer, library preparation is performed using  the SMART-Seq v4 Ultra Low Input RNA Kit

treatment_protocol: Mice were pIpC injected 3 weeks prior to harvesting HSCs.

value: Hematopoietic Stem Cells

value: Syncrip flox/flox, Mx1 Cre+

value: 9 weeks post transplant in CD45.1 congenic mice

value: 3 weeks post pIpC

value: CD45.2+, Lin-, Sca1+, cKit+, CD150+, CD48- sorted cells


title: MGG152_R1_H3K4me3_ChIPseq


title: CRC1176PRX0A02003TUMR01000, PRX_BASALE, bio rep 1, QC ok

value: Colorectal Cancer


title: HSC Cre Neg 3

value: Syncrip flox/flox, Mx1 Cre-


title: AL Female zt18 replicate 1

value: Ad-libitum diet


title: AL Female zt18 replicate 2


title: AL Female zt14 replicate 3


title: CRC1182LMX0A02001TUMR02000, LMX_BASALE, bio rep 1, QC ok

value: LM

value: WT


title: HSC Cre Neg 2


title: HSC Cre Neg 1


title: CRC1175PRX0A01001TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: HK308_R1_H3K4me3_ChIPseq


title: AL Female zt14 replicate 2

value: liver

value: 5 month old


title: CRC1182LMH0000000000R01000, LMH, bio rep 1, QC ok

value: H


title: HSC Cre Pos 3


title: HK213_R2_H3K4me3_ChIPseq


title: LK cells, Cre_pos-3

data_processing:
Single-cell RNA-seq data was processed and aligned to mouse reference mm10 using CellRanger with default parameters. Normalization, dimensionality reduction and Louvain clustering were performed using Scanpy (v1.4.4(Wolf et al., 2018). Cells with < 200 detected genes or percentage of mitochondrial reads > 15% were filtered. Data were log normalized using a scale factor of 10,000.
Assembly: mm10
Supplementary files format and content: h5

source_name: Bone Marrow

growth_protocol: Whole bone marrow from SYNCRIP conditional knockout mice were transplanted into recipient congenic CD45.1 mice and remained in vivo for 9 weeks before harvesting.

extract_protocol: Lin- cKit+ cells were FACS sorted and frozen in TRIzol reagent. RNA was extracted using Phenol-Chloroform.

value: Lineage- cKit + Bone Marrow Cells


title: CRC1174PRX0A01001TUMR01000, PRX_BASALE, bio rep 1, QC ok

value: X

value: PR


title: AL Female zt14 replicate 1

value: Wild-type


title: CRC1171PRX0A02002TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: HK211_R2_H3K4me3_ChIPseq

source_name: HK211 MTCS

value: glioma patient derived multicellular tumor spheroid


title: LK cells, Cre_pos-2

value: Bone Marrow

value: Syncrip flox/flox, Mx1 Cre+


title: AL Female zt10 replicate 2


title: LK cells, Cre_pos-1

value: 9 weeks post transplant in CD45.1 congenic mice

value: 3 weeks post pIpC


title: CRC1169PRX0B02002TUMR01000, PRX_BASALE, bio rep 1, QC ok

value: Colorectal Cancer


title: CRC1170PRX0A01001TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: CRC1169LMX0A01001TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: LK cells, Cre_neg-3

value: Syncrip flox/flox, Mx1 Cre-


title: AL Female zt10 replicate 1

value: Ad-libitum diet


title: HK211_R1_H3K4me3_ChIPseq


title: HK308_R2_H3K4me3_ChIPseq


title: LK cells, Cre_neg-2


title: AL Female zt6 replicate 3


title: CRC1169LMO0C04008001R01000, LMO_BASALE, bio rep 1, QC ok

value: O

value: LM


title: HK157_R1_H3K4me3_ChIPseq


title: CRC1166LMX0A02002TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: WT


title: AL Female zt6 replicate 2

value: liver

value: 5 month old


title: HK213_R1_H3K4me3_ChIPseq


title: LK cells, Cre_neg-1

value: Lineage- cKit + Bone Marrow Cells


title: CRC1164PRX0A02001TUMR01000, PRX_BASALE, bio rep 1, QC ok

value: X


title: BT260_R2_H3K4me3_ChIPseq


title: AL Female zt10 replicate 3


title: scRNA-seq analysis of Mixed pancreas tumor - Replicate 1

city: La Jolla

last: Hamilton

address: 2880 Torrey Pines Scenic Dr.

institute: UCSD

description: Mixed1 pancreas tumor

data_processing:
Cell Ranger v3.0
Seurat v3.0
Genome_build: mm10
Supplementary_files_format_and_content: h5

source_name: Msi2CreER-MycT58A Mouse

growth_protocol: Not applicable

extract_protocol:
According to 10x genomics instructions
scRNA-seq

treatment_protocol: In vivo tamoxifen induction of mice at 8 weeks of age.  Pre-cancer cells collected 5 weeks after induction.  Pancreas tumor cells collected 12 weeks after induction.

value: Mixed pancreas tumor cells

tag: time

value: 12 weeks post-induction


title: scRNA-seq analysis of Mixed pancreas tumor - Replicate 2

description: Mixed2 pancreas tumor


title: AL Female zt6 replicate 1

value: Wild-type


title: CRC1162LMX0A02003TUMR01000, LMX_BASALE, bio rep 1, QC ok

address: Strada Provinciale, 142 -KM 3.95

institute: IRCCS Istituto Candiolo


title: BT054_R2_H3K4me3_ChIPseq

value: glioma patient derived multicellular tumor spheroid


title: scRNA-seq analysis of ASCP pancreas tumor

description: ASCP pancreas tumor

value: ASCP pancreas tumor cells


title: AL Female zt2 replicate 2


title: AL Female zt2 replicate 3


title: CRC1147LMX0A02002TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: BT054_R1_H3K4me3_ChIPseq


title: BT260_R1_H3K4me3_ChIPseq


title: CR Female zt2 replicate 1

source_name: Calorie-restricted liver

value: Calorie-restricted diet


title: TF1_shTET2_R2_H3K4me3_ChIPseq

value: growth factor dependent erythroblast


title: scRNA-seq analysis of Pre-cancer pancreas cells - Replicate 3

description: Pre-cancer pancreas cells – replicate 3

value: Pre-cancer pancreas cells

value: 5 weeks post-induction


title: AL Female zt2 replicate 1

value: Ad-libitum diet


title: CRC1146LMX0A02001TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: Colorectal Cancer


title: NT, WA1PBS, 3DPC, REP4

city: Memphis

first: Colleen

middle: Beth

last: Jonsson

state: TN

address: 858 Madison Avenue

institute: University of Tennessee Health Science Center

data_processing:
CLC Genomics Workbench v 22.0
Sequence reads were trimmed  and filter using default parameters in CLC Genomic Workbench
Trimmed and filter sequence reads were mapped to GRCm39/SARS-CoV-2 Wuhan-Hu-1 concatinated genome using default parameters in CLC Genomic Workbench
Read count results were collected in  CLC Genomic Workbench
Read count were normalized and fold change calculated using DESeq2
Assembly: GRCM39 concatinated with SARS-CoV-2 Wuhan-Hu-1 reference genome
Supplementary files format and content: tab-delimited text files include total counts for each sample

source_name: Nasal turbinate

extract_protocol:
RNA was extracted from homogenized tissue samples using Magmax mirvana RNA isolation kit on Kingfisher instrument.
Libraries were constructed using NEB NEBNext Ultra II RNA Kits

value: Nasal turbinate

value: Infected with WA1


title: TF1_shTET2_R1_H3K4me3_ChIPseq


title: NT, WA1PBS, 3DPC, REP3


title: CRC1145LMX0A02002TUMR01000, LMX_BASALE, bio rep 1, QC ok

city: Candiolo

first: Livio

last: Trusolino

value: LM

value: WT


title: scRNA-seq analysis of Pre-cancer pancreas cells - Replicate 2

description: Pre-cancer pancreas cells – replicate 2


title: NT, WA1PBS, 3DPC, REP2


title: CRC1144PRX0B02003TUMR01000, PRX_BASALE, bio rep 1, QC ok

value: PR


title: scRNA-seq analysis of Pre-cancer pancreas cells - Replicate 1

description: Pre-cancer pancreas cells – replicate 1


title: TF1_shNT_R2_H3K4me3_ChIPseq

value: shNT


title: scRNA-seq analysis of Msi2-GFP Cells in Normal Mouse Pancreas - Replicate 2

description: GFP2 normal pancreas – replicate 2

source_name: Msi2-GFP Mouse

value: Msi2-GFP Cells in Normal Mouse Pancreas

value: 0 weeks post-induction


title: TF1_shNT_R1_H3K4me3_ChIPseq


title: NT, WA1PBS, 3DPC, REP1


title: scRNA-seq analysis of ACC pancreas tumor

description: ACC pancreas tumor

value: ACC pancreas tumor cells

value: 12 weeks post-induction


title: CRC1144LMX0A02002TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: X


title: Lung, WA1PBS, 3DPC, REP4

source_name: Lung

value: Lung


title: scRNA-seq analysis of Msi2-GFP Cells in Normal Mouse Pancreas - Replicate 1

description: GFP1 normal pancreas – replicate 1


title: TF1_sgACD_R1_H3K4me3_ChIPseq

value: growth factor dependent erythroblast


title: CRC1139LMX0A02001TUMR06000, LMX_BASALE, bio rep 1, QC ok


title: CRC1142PRX0B01001TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: TF1_sg3xNT_R2_H3K4me3_ChIPseq


title: CRC1139LMO0A04007001R01000, LMO_BASALE, bio rep 1, QC ok

value: O


title: Lung, WA1PBS, 3DPC, REP2


title: CRC1137LMX0A02002TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: Lung, WA1PBS, 3DPC, REP1


title: TF1_sg3xNT_R1_H3K4me3_ChIPseq


title: CRC1134PRX0A02003TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: TF1_R2HG_500_R2_H3K4me3_ChIPseq

value: 500 uM R2HG


title: TF1_R2HG_500_R1_H3K4me3_ChIPseq


title: NT, PBS, 3DPI, REP3

value: PBS control


title: TF1_sgACD_R2_H3K4me3_ChIPseq


title: CRC1090LMX0A02001TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: Colorectal Cancer


title: TF1_R2HG_250_R2_H3K4me3_ChIPseq

value: 250 uM R2HG


title: CRC1090LMO0A05021001R01000.2, LMO_BASALE, bio rep 2, QC ok


title: NT, PBS, 3DPI, REP2

value: Nasal turbinate


title: Heart_tissue_normal_rep3

type: RNA

city: Zhengzhou

first: Lin

last: Liu

address: 7 Weiwu Road, Jinshui District

institute: Henan Provincial People’s Hospital

description: Gene expression of heart tissue samples of normal children

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by percentile normalization.

source_name: Heart tissue, normal, replicate 3

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: 5 TOF children with no other intracardiac and extracardiac malformations and 5 normal fetuses.

value: Heart Tissue

tag: gender

value: Male

value: 26 weeks

tag: disease state

value: normal


title: Lung, WA1PBS, 3DPC, REP3

value: Infected with WA1


title: Heart_tissue_patient_rep5

description: Gene expression of tissue samples of the right ventricular outflow tract of  TOF children with no other intracardiac and extracardiac malformations

source_name: Heart tissue, patient, replicate 5

value: Female

value: 17 months

value: Tetralogy of Fallot


title: Heart_tissue_normal_rep1

source_name: Heart tissue, normal, replicate 1

value: 25 weeks


title: TF1_R2HG_250_R1_H3K4me3_ChIPseq


title: Heart_tissue_normal_rep2

source_name: Heart tissue, normal, replicate 2


title: NT, PBS, 3DPI, REP1


title: NT, PBS, 3DPI, REP4


title: CRC1090LMO0A04011001R01000, LMO_BASALE, bio rep 1, QC ok

value: LM

value: WT


title: HK211_INPUT

value: glioma patient derived multicellular tumor spheroid


title: CRC1194PRX0A02003TUMR01000, PRX_BASALE, bio rep 1, QC ok

value: X

value: PR


title: CRC1084LMX0A02003TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: Colorectal Cancer


title: Lung, PBS, 3DPI, REP3

value: Lung

value: PBS control


title: Lung, PBS, 3DPI, REP4


title: TF1_R2HG_0_R2_H3K4me3_ChIPseq

value: growth factor dependent erythroblast

value: DMSO vehicle control


title: TF1_R2HG_0_R1_H3K4me3_ChIPseq


title: Heart_tissue_patient_rep4

source_name: Heart tissue, patient, replicate 4

value: Heart Tissue

value: 22 months


title: TF1_R132H_R2_H3K4me3_ChIPseq

value: IDH1-R132H expression vector


title: KYP:3xFLAG-input

city: New Taipei City

first: FU-YU

last: HUNG

address: Singyi Rd. 17ave. 9s 8th 2F

institute: RIKEN

data_processing:
The raw sequence data were processed using the Illumina sequence data analysis pipeline GAPipeline 1.3.2. MACS2 was then employed to map the reads to the Arabidopsis genome (TAIR10).
To determine the correlation between biological repeats, Pearson correlation was computed using R statistical software on normalized signal intensity for ChIP binding peaks. The alignments were first converted to Wiggle (WIG) files. The data were then imported into the Integrated Genome Viewer (IGV) for visualization.
Genome_build: TAIR 10
Supplementary_files_format_and_content: bigwig files

organism: Arabidopsis thaliana

source_name: 10 days old plants

growth_protocol: The transgenic Arabidopsis seedlings were grown under Long-day conditions at 22°C and harvested after 10 days.

extract_protocol:
2 ng of DNA from ChIP was pooled to ensure that there are enough starting DNA for library construction. Two biological replicates were prepared and sequenced for each ChIP-seq experiment. The ChIP DNA was first tested by qRT-PCR and then used to prepare ChIP-seq libraries.
End repair, adaptor ligation, and amplification were carried out using the NEB Genomic DNA Sample Prep kit according to the manufacturer's protocol.

tag: eco-type

tag: antibody

value: input


title: CRC1083LMX0A02001TUMR02000, LMX_BASALE, bio rep 1, QC ok

source_name: Colorectal Cancer


title: Heart_tissue_patient_rep3

source_name: Heart tissue, patient, replicate 3

value: Female

value: 9 months


title: Lung, PBS, 3DPI, REP2


title: Heart_tissue_normal_rep4

source_name: Heart tissue, normal, replicate 4

value: 28 weeks

value: normal


title: Heart_tissue_patient_rep2

source_name: Heart tissue, patient, replicate 2

value: Male

value: 13 months

value: Tetralogy of Fallot


title: Heart_tissue_patient_rep1

source_name: Heart tissue, patient, replicate 1

value: 6 months


title: CRC1082PRX0A02001TUMR01000, PRX_BASALE, bio rep 1, QC ok

value: Colorectal Cancer

value: X

value: PR

value: WT


title: CRC1078LMX0A02002TUMR02000, LMX_BASALE, bio rep 1, QC ok

value: LM


title: Lung, PBS, 3DPI, REP1

value: Lung

value: PBS control


title: CRC1078LMO0A05022001R01000.2, LMO_BASALE, bio rep 2, QC ok

value: O


title: KYP:3xFLAG-IP-2


title: TF1_R132H_R1_H3K4me3_ChIPseq

source_name: TF1 cell line

value: growth factor dependent erythroblast

value: IDH1-R132H expression vector


title: KYP:3xFLAG-IP-1


title: TF1_IDH1_R2_H3K4me3_ChIPseq

value: IDH1-WT expression vector


title: TF1_IDH1_R1_H3K4me3_ChIPseq


title: NT, WA1PBS, 1DPC, REP4

value: Nasal turbinate

value: Infected with WA1


title: CRC1075LMX0A02002TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: NT, WA1PBS, 1DPC, REP2


title: TF1_50_c70_R1_H3K4me3_ChIPseq

value: 50 nM KDM5c70


title: CRC1072LMX0A02001TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: TF1_50_c70_R2_H3K4me3_ChIPseq


title: CRC1078LMO0A05021001R01000.2, LMO_BASALE, bio rep 1, QC ok


title: NT, WA1PBS, 1DPC, REP1


title: TF1_0_c70_R2_H3K4me3_ChIPseq

value: DMSO vehicle control


title: Lung, WA1PBS, 1DPC, REP4


title: NT, WA1PBS, 1DPC, REP3


title: Lung, WA1PBS, 1DPC, REP3


title: CRC1067LMX0A03011TUMR02000, LMX_cetux_6w_NT, bio rep 1, QC ok

value: NT


title: CRC1067LMX0A03002TUMR02000, LMX_cetux_6w, bio rep 1, QC ok

value: CET


title: TF1_0_c70_R1_H3K4me3_ChIPseq


title: library18

city: London

first: Eleni

last: Maniati

address: John Vane Science Centre, Charterhouse Square

department: Barts Cancer Institute

country: United Kingdom

institute: Queen Mary University of London

data_processing:
Adapter sequences were trimmed using cutadapt version 2.1. Raw reads were mapped to the human genome (hg19, Genome Reference Consortium GRCh37) using HISAT2 version 2.1.0 .
Number of reads aligned to the exonic region of each gene were counted using HTSeq version 0.11.2 based on the Ensembl annotation
Genes that achieved at least one read count per million reads (CPM) in at least 4 samples were kept.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes htseq counts for each sample

source_name: CD34+ hematopoietic stem/progenitor cells (HSPCs)

growth_protocol: Cells were grown in MethoCult™ H4434 Classic from StemCell Technologies, over a period of 2 weeks upon normoxic or hypoxic conditions

extract_protocol:
RNA was extracted using Direct-zol RNA Kits from Zymo Research (R2062)
Library construction was performed using the Takara SMART-Seq Stranded Kit (Cat no 634443)

treatment_protocol: Cells were cultured during two weeks upon normoxic or hypoxic conditions

tag: mutation state

value: healthy

tag: culture

value: Hypoxia

tag: donor

tag: other sample name


title: Lung, WA1PBS, 1DPC, REP2

tag: tissue


title: Control U87 Cell Replicate 3

city: Seoul, Republic of Korea

first: Sunghyouk

last: Park

email: cmg8075@gmail.com, psh@snu.ac.kr

address: 1, Gwanak-ro, Gwanak-gu

country: South Korea

institute: SNU

description: Biological replicate 3 of 3. Control U87 cells, untreated, harvested after several passages.

hyb_protocol: 600ng of each labeled cRNA was fragmented by adding 5 μl 10 x blocking agent and 1 μl of 25 x fragmentation buffer, and then heated at 60°C for 30 min. Finally 25 μl 2 x GE hybridization buffer was added to dilute the labeled cRNA. 40μl of hybridization solution was dispensed into the gasket slide and assembled to the Agilent SurePrint G3 Human GE 8X60K, V2 Microarrays (Agilent®). The slides were incubated for 17 h at 65°C in an Agilent hybridization oven. then washed at room temperature by using the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology, V 6.5, 2010).

scan_protocol: The hybridized array was immediately scanned with an Agilent Microarray Scanner D (Agilent Technologies, Inc.)

data_processing: Microarray results were extracted using Agilent Feature Extraction software v11.0 (Agilent Technologies). The raw data for same gene was then summarized automatically in Agilent feature extraction protocol to generate raw data text file, providing expression data for each gene probed on the array.  Array probes that have Flag A in samples were filtered out. Selected gProcessedSignal value was transformed by logarithm and normalized by quantile method.  Statistical significance of the expression data was determined using fold change and LPE test in which the null hypothesis was that no difference exists among 2 groups.  Hierarchical cluster analysis was performed using complete linkage and Euclidean distance as a measure of similarity.  Gene-Enrichment and Functional Annotation analysis for significant probe list was performed using Gene Ontology (http://geneontology.org) and KEGG (http://kegg.jp).  All data analysis and visualization of differentially expressed genes was conducted using R 3.3.3 (www.r-project.org).

source_name: U87 temozolomide sensitive glioma cell lines

label_protocol: RNA labeling and hybridization were performed by using the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology, V 6.5, 2010). Briefly, 100ng of total RNA from each sample was linearly amplified and labeled with Cy3-dCTP. The labeled cRNAs were purified by RNAeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000(NanoDrop, Wilmington, USA).

growth_protocol: All culture media were supplemented with 10% fetal bovine serum (FBS, Welgene, Gyeongsan-si, Korea), 1% penicillin/streptomycin (Gibco, NY, USA) and incubated at 37°C under 5% of CO2 humidified air.

extract_protocol: following manufacturer's protocol

treatment_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: histopathology

value: glioblastoma


title: library17

tag: cell type

value: CD34+ hematopoietic stem/progenitor cells (HSPCs)


title: CRC1064LMX0B02003TUMR01000, LMX_BASALE, bio rep 1, QC ok

growth_protocol: Please check the linked publication

value: Colorectal Cancer

value: X

value: LM

tag: genotype

value: WT

tag: treatment


title: Control U87 Cell Replicate 2

description: Biological replicate 2 of 3. Control U87 cells, untreated, harvested after several passages.


title: Test U87R Cell Replicate 3

description: Biological replicate 3 of 3. Test temozolomide resistant U87R cells, harvested after several passages.

source_name: U87R temozolomide resistant glioma cell lines


title: Lung, WA1PBS, 1DPC, REP1

value: Lung


title: Control U87 Cell Replicate 1

description: Biological replicate 1 of 3. Control U87 cells, untreated, harvested after several passages.


title: Test U87R Cell Replicate 2

description: Biological replicate 2 of 3. Test temozolomide resistant U87R cells, harvested after several passages.


title: NT, PBS, 1DPI, REP4

source_name: Nasal turbinate

value: PBS control


title: CRC1070PRX0B02001TUMR01000, PRX_BASALE, bio rep 1, QC ok

value: PR


title: Psoriasis, Macro biopsy, MUC20508

city: Freiburg

first: Stefanie

last: Eyerich

address: Breisacher Straße 153

department: Department of Dermatology and Venereology

institute: University of Freiburg

data_processing:
Read mapping mit STAR
Assembly: hg38
Supplementary files format and content: tab-delimited tsv file includes raw values per sample

source_name: lesional skin

extract_protocol:
Skin samples were taken under local anesthesia and fixed in RNAprotect tissue reagent (Qiagen, Germany), incubated for 24-48 h at 4°C and stored at -20°C until RNA isolation. mRNA was isolated using the mRNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
TruSeq Stranded Total RNA Kit

value: lesional skin

tag: condition

value: Psoriasis

tag: biopsy type

value: Macro biopsy

value: untreated


title: library12

value: myelodysplastic syndromes


title: Test U87R Cell Replicate 1

description: Biological replicate 1 of 3. Test temozolomide resistant U87R cells, harvested after several passages.

tag: cell line


title: Psoriasis, Micro biopsy, MUC20710

value: Micro biopsy


title: Psoriasis, Macro biopsy, MUC20721


title: NT, PBS, 1DPI, REP3

value: Nasal turbinate


title: library11

value: Hypoxia


title: HK157_R2_H3K4me3_ChIPseq

value: glioma patient derived multicellular tumor spheroid

tag: chip antibody


title: Psoriasis, Micro biopsy, MUC20509


title: CRC0781LMX0B02004TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: NT, PBS, 1DPI, REP2


title: CRC0778LMX0B02002TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: library10

value: CD34+ hematopoietic stem/progenitor cells (HSPCs)


title: Psoriasis, Macro biopsy, MUC20512


title: library9

value: healthy

value: Normoxia


title: NT, PBS, 1DPI, REP1


title: library16


title: Lung, PBS, 1DPI, REP4

source_name: Lung


title: library8


title: Psoriasis, Micro biopsy, MUC20511


title: CRC0773LMX0A02001TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: Colorectal Cancer

value: X

value: LM


title: Psoriasis, Macro biopsy, MUC20510


title: CRC0772LMX0A02004TUMR02000, LMX_BASALE, bio rep 1, QC ok

value: WT


title: CRC1063PRX0B02002TUMR01000, PRX_BASALE, bio rep 1, QC ok

value: PR


title: Psoriasis, Micro biopsy, MUC20507

value: lesional skin


title: CRC0772LMO0B04014003R01000, LMO_BASALE, bio rep 2, QC ok

value: O


title: CRC0772LMO0B04013004R01000, LMO_BASALE, bio rep 1, QC ok


title: CRC0783LMX0B02001TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: Lung, PBS, 1DPI, REP2

value: Lung

value: PBS control


title: Psoriasis, Macro biopsy, MUC20516

value: Psoriasis

value: Macro biopsy

value: untreated


title: Lung, PBS, 1DPI, REP1


title: library2

value: myelodysplastic syndromes


title: Psoriasis, Micro biopsy, MUC20515

value: Micro biopsy


title: library3

value: CD34+ hematopoietic stem/progenitor cells (HSPCs)


title: library1


title: CRC0772LMH0000000000R01000, LMH, bio rep 1, QC ok

value: H


title: Atopic Eczema, Macro biopsy, MUC20709

value: Atopic Eczema


title: NT, WA1Delta, 3DPC, REP4

value: Nasal turbinate

value: Infected with Delta


title: CRC0771LMX0B03012TUMR05000, LMX_cetux_h, bio rep 1, QC ok

value: Colorectal Cancer

value: X

value: LM

value: CET


title: NT, WA1Delta, 3DPC, REP3


title: Kasumi-1_SMARCA5FKBP12_24hdTAG47_2 [ATAC-seq]

city: Nashville

first: Scott

middle: W

last: Hiebert

address: 512 B Preston Research Building

department: Biochemistry

institute: Vanderbilt University

data_processing:
Adaptor trimming with Trimmomatic-0.32 PE ILLUMINACLIP:atac_adaptor.txt:2:30:7 MINLEN:15
Alignment to hg19+dm3 genome with bowtie2.
High quality reads (F4q10) were filtered using samtools.
Peaks called with MACS2 (narrowPeak, q=0.01).
For ATAC-seq +/-dTAG, differential peaks were identified by Diffbind/DESeq2 using S2 Drosophila spike-in for normalization, using 0h as a negative control.
bigwig files were generated using deepTools.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigwig, MACS2 peak files, differential peak files generated by Diffbind+DESeq2.

source_name: Kasumi-1 cells

growth_protocol: Kasumi-1 cells were grown in RPMI +20% FBS +50 U/ml penicillin, 50 μg/ml streptomycin, and 2mM L-glutamine. CD34+ cells were cultured in IMDM + 20% FBS, 55 μM BME, 50 U/ml penicillin, 50 μg/ml streptomycin, 2mM L-glutamine, and 10 ng/mL SCF, Flt3-L, TPO, IL-3, and IL-6.

extract_protocol:
Followed ATAC-seq protocol, isolated nuclei.
Libraries were constructed using the NEBNext Ultra II DNA Library Prep Kit.

treatment_protocol: Cells were treated with 500 nM dTAG-47 for the indicated timepoints.

tag: genotype/variation

tag: time point


title: Atopic Eczema, Macro biopsy, MUC20522

value: lesional skin


title: NT, WA1Delta, 3DPC, REP2


title: CRC0771LMX0B03005TUMR05000, LMX_cetux_h_NT, bio rep 1, QC ok

value: WT

value: NT


title: Lung, PBS, 1DPI, REP3

value: Lung

value: PBS control


title: library7

value: healthy

tag: disease state

value: Normoxia


title: Kasumi-1_SMARCA5FKBP12_24hdTAG47_1 [ATAC-seq]


title: Kasumi-1_SMARCA5FKBP12_6hdTAG47_2 [ATAC-seq]


title: Atopic Eczema, Micro biopsy, MUC20521

value: Micro biopsy

value: untreated


title: NT, WA1Delta, 3DPC, REP1


title: NT, WA1Alpha, 3DPC, REP4

value: Infected with Alpha


title: CRC0771LMH0000000000R05000, LMH, bio rep 1, QC ok

value: H


title: Kasumi-1_SMARCA5FKBP12_6hdTAG47_1 [ATAC-seq]


title: NT, WA1Alpha, 3DPC, REP3

value: Nasal turbinate


title: Atopic Eczema, Macro biopsy, MUC20526

value: Atopic Eczema

value: Macro biopsy


title: Atopic Eczema, Micro biopsy, MUC20525


title: CRC0753LMX0A02001TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: Colorectal Cancer

value: X


title: Kasumi-1_SMARCA5FKBP12_2hdTAG47_2 [ATAC-seq]


title: CRC0748PRX0A01001TUMR09000, PRX_BASALE, bio rep 1, QC ok

value: PR


title: Kasumi-1_SMARCA5FKBP12_0hdTAG47_2 [ATAC-seq]

value: Untreated


title: CRC0745LMX0B01001TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: LM

value: WT


title: Atopic Eczema, Micro biopsy, MUC20708

value: lesional skin


title: Atopic Eczema, Micro biopsy, MUC20523


title: Atopic Eczema, Macro biopsy, MUC20524


title: NT, WA1Alpha, 3DPC, REP1


title: CRC0771LMX0B02003TUMR01000, LMX_BASALE, bio rep 1, QC failed


title: NT, WA1WA1, 3DPC, REP4

value: Infected with WA1


title: CRC0743LMX0B04007TUMR01000, LMX_cetux_h_NT, bio rep 2, QC ok

value: NT


title: Kasumi-1_SMARCA5FKBP12_0hdTAG47_1 [ATAC-seq]


title: NT, WA1WA1, 3DPC, REP3


title: Atopic Eczema, Macro biopsy, MUC20520


title: NT, WA1WA1, 3DPC, REP2


title: Kasumi-1_parental_1 [ATAC-seq]

value: Parental


title: Atopic Eczema, Micro biopsy, MUC20519

value: Micro biopsy


title: Kasumi-1_parental_2 [ATAC-seq]


title: Treated 4

city: Portland

first: Supender

last: Kaur

state: Oregon

address: 3181 SW Sam Jackson Park Road L220

department: Molecular Microbiology and Immuno

institute: Oregon health and science university

data_processing:
Fq file dataset were uploaded into Galaxy Tool Version 2.11.40.2 that was used for the analyses
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Human reference genome “Genome Reference Consortium Human Build 38 patch release 13” (GRCh38.p13
The  htseq-count were further analyesd for the  differentially expressed features from count tables using DESeq2
Assembly: Human reference genome “Genome Reference Consortium Human Build 38 patch release 13” (GRCh38.p13)
Supplementary files format and content: tabular files include htseq-count/values for each Sample ...

source_name: Blood

growth_protocol: Approximately 10 ml of blood was extracted from epilepsy patients  followed by isolation of PBMCs from control and treated patients with vagus nerve stimulation

extract_protocol:
Total RNA was extracted using the RNeasy Plus Universal Kit (Qiagen, Netherlands). Residual genomic DNA was removed using TURBO DNase (Life Technologies, Carlsbad, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Isolated PBMCs were stored frozen in trizol at -80C till RNAextraction.

value: PBMCs

value: vagus nerve stimulation


title: NT, WA1WA1, 3DPC, REP1


title: Kasumi-1_SMARCA5FKBP12_2hdTAG47_1 [ATAC-seq]


title: Treated 3


title: CRC0743LMX0A02001TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: CRC0743LMX0A06007TUMR01000, LMX_cetux_h_NT, bio rep 1, QC ok


title: Lung, WA1Delta, 3DPC, REP4

value: Lung

value: Infected with Delta


title: Kasumi-1_SMARCA5-FKBP12_24hdTAG_antiCTCF_2 [CUT&RUN]

description:
5176-MB-8
24hr_500nM_dTAG47

data_processing:
Library strategy: CUT&RUN
For Cut&Run: Adaptor trimming with Trimmomatic-0.32.
Alignment to hg19+scer genome with bowtie2.
High quality reads (F4q10) were filtered using samtools.
Peaks called with MACS2 ((anti-flag: narrowPeak, q=0.05),(anti-CTCF: narrowPeak, q=0.001)).
For anti-flag cut&run +/-dTAG, differential peaks were identified by Diffbind/DESeq2 using yeast spike-in for normalization.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigwig files were generated using deepTools.
Supplementary_files_format_and_content: narrowPeak files.
Supplementary_files_format_and_content: 070220_cutandrun_S5_peakinfo_qv0.05.csv: Peak information; comma-separate values.
Supplementary_files_format_and_content: 070220_S5_cutandrun_DESEQ_qv0.05.csv: Differential peaks; comma-separate values.

source_name: Kasumi-1 SMARCA5-FKBP12-1xFLAG cells

growth_protocol: Kasumi-1 cells were grown in RPMI +20% FBS +50 U/ml penicillin, 50 μg/ml streptomycin, and 2mM L-glutamine.

extract_protocol:
For Cut&Run anti-flag, released DNA fragments were extracted using phenol:chloroform:IAA and ethanol precipitation. For Cut&Run anti-CTCF, released DNA fragments were extracted using NEB Monarch Nucleic Acid Purification Kits.
Libraries were constructed using the NEBNext Ultra II DNA Library Prep Kit.

tag: assay

value: Cut&Run

tag: antibody

value: anti-CTCF (Millipore, 07-729)

tag: secondary antibody

value: anti-rabbit (Invitrogen, 31238)


title: Kasumi-1_SMARCA5-FKBP12_24hdTAG_antiCTCF_1 [CUT&RUN]

description:
5176-MB-7
24hr_500nM_dTAG47


title: CRC0743LMX0B04008TUMR01000, LMX_cetux_h, bio rep 2, QC ok

value: Colorectal Cancer

value: X

value: CET


title: Treated 2


title: CRC0743LMO0A07034001R02000, LMO_BASALE, bio rep 2, QC ok

value: O

value: LM


title: Lung, WA1Delta, 3DPC, REP3


title: CRC0743LMO0A05032002R01000, LMO_cetuxi_h, bio rep 2, QC ok

value: WT


title: Treated 1


title: Lung, WA1Delta, 3DPC, REP2


title: Control 4

value: control


title: CRC0743LMX0A06010TUMR01000, LMX_cetux_h, bio rep 1, QC ok


title: Kasumi-1_SMARCA5-FKBP12_6hdTAG_antiCTCF_2 [CUT&RUN]

description:
5176-MB-6
6hr_500nM_dTAG47


title: Kasumi-1_SMARCA5-FKBP12_6hdTAG_antiCTCF_1 [CUT&RUN]

description:
5176-MB-5
6hr_500nM_dTAG47


title: Lung, WA1Delta, 3DPC, REP1


title: Control 3


title: CRC0743LMO0A05028002R01000, LMO_cetuxi_h, bio rep 1, QC ok


title: Kasumi-1_SMARCA5-FKBP12_2hdTAG_antiCTCF_1 [CUT&RUN]

description:
5176-MB-3
2hr_500nM_dTAG47


title: Control 2


title: Kasumi-1_SMARCA5-FKBP12_2hdTAG_antiCTCF_2 [CUT&RUN]

description:
5176-MB-4
2hr_500nM_dTAG47


title: CRC0743LMO0A05028001R01000, LMO_cetuxi_h_NT, bio rep 1, QC ok

value: NT


title: Lung, WA1Alpha, 3DPC, REP3

value: Infected with Alpha


title: CRC0743LMO0A04022001R01000, LMO_BASALE, bio rep 1, QC ok


title: Control 1


title: Lung, WA1Alpha, 3DPC, REP2


title: Kasumi-1_SMARCA5-FKBP12_0hdTAG_antiCTCF_2 [CUT&RUN]

value: Untreated


title: Hashtag library 2 [HHT2]

city: New Haven

first: Hong-Jai

state: CT

address: S510, 300 Cedar Street

department: Internal Medicine

institute: Yale University

data_processing:
Quality Control, Barcod processing, alignment, feature counting and sample aggratation by CellRanger Single Cell Software Suite (v.2.1.1)
Assembly: hg19
Supplementary files format and content: Raw gene-by-cell matrix of gene expression, including barcodes, and expressed genes.

source_name: Human CD4+ T cells

extract_protocol:
Single-cell RNA-seq of human PBMC samples from SARS-CoV-2 mRNA vaccinated healthy subjects. The PBMCs were stimulated with spike, flu, and CMV lysates for overnight. The cells were sorted into OX40-CD137-, OX40+CD137-, OX40-CD137+, and OX40+CD137+ CD4+ T cells from spike-stimulated PBMCs, Flu-stimulated OX40+CD137+ and CMV-stimulated OX40+CD137+ PBMCS. Total 7 subsets were stained with cellhashing antibodies for 30 min and pooled in one vial to generate library.
Multiplexed scRNA-seq; Libraries were prepared using Chromium Single Cell 5' Reagent Kits v2 according to manufacturer's protocol (10X genomics).

value: Human CD4+ T cells

value: Untreated, Spike-treated, Flu lysate-treated, and CMV lysate-treated


title: Lung, WA1Alpha, 3DPC, REP1

value: Lung


title: Kasumi-1_SMARCA5-FKBP12(+)dTAG_antiFlag_2 [CUT&RUN]

description:
4617-MB-8
18htreated_500nM_dTAG48

value: anti-Flag (Sigma, F1804)

value: anti-mouse (Abcam, ab46540)


title: Lung, WA1WA1, 3DPC, REP4

value: Infected with WA1


title: Hashtag library 1 [HHT1]


title: Kasumi-1_SMARCA5-FKBP12_0hdTAG_antiCTCF_1 [CUT&RUN]

value: Cut&Run

value: anti-CTCF (Millipore, 07-729)

value: anti-rabbit (Invitrogen, 31238)


title: CRC0740LMX0A02001TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: Colorectal Cancer

value: X


title: Lung, WA1WA1, 3DPC, REP3


title: Lung, WA1Alpha, 3DPC, REP4


title: Kasumi-1_SMARCA5-FKBP12(+)dTAG_antiFlag_1 [CUT&RUN]

description:
4617-MB-7
18htreated_500nM_dTAG47


title: CRC0743LMO0A05032001R01000, LMO_cetuxi_h_NT, bio rep 2, QC ok

value: O

value: LM


title: CRC1157LMX0A02002TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: WT


title: Kasumi-1_SMARCA5-FKBP12(-)dTAG_antiFlag_2 [CUT&RUN]


title: Lung, WA1WA1, 3DPC, REP2


title: KLK7 +antiKLK5/7 SAM24387831

address: 1 DNA Way

institute: Genentech, Inc.

description: KLK7 +antiKLK5/7

data_processing:
HTSeqGenie 4.2.1
Reads were aligned to the GRCh38 reference genome using GSNAP (version 2013-11-01)
Aligned reads within exons defined by GENCODE (v27) were counted using the countFeatures method from HTSeqGenie
Assembly: GRCh38
Supplementary files format and content: bam alignment files
Supplementary files format and content: tsv count matrices

source_name: skin

growth_protocol: Primary keratinocytes (Thermo Fischer, cat C-020-5C) were cultured in basal medium (Thermo Fischer, cat 17005042)

extract_protocol:
Cells were lysed with RLT buffer and RNA was isolated using RNAeasy mini Kit (Qiagen, 74106) in accordance to standard manufacturer's instructions including DNase treatment procedure.
Libraries were prepared using the Illumina TruSeq Stranded Total RNA Library Prep Kit.

treatment_protocol: Cells were plated at 1.5E5 cells per well in the 24-Well TC plate (Costar, 2524) the day before the experiment. The cells were then treated with recombinant produced human active KLK5 at 6 µg/mL (200 nM of 30 kDa MW), human active KLK7 at 5 µg/mL (208 nM of 24 kDa MW), anti-KLK5/7 bispecific antibody at 180 µg/mL (1200 nM of 150 kDa MW) for 4 h.

value: skin

value: primary

value: neonatal keratinocytes

value: KLK7 +antiKLK5/7


title: CRC0736PRH0000000000R01000, PRH, bio rep 1, QC ok

source_name: Colorectal Cancer

value: H

value: PR


title: Kasumi-1_SMARCA5-FKBP12(-)dTAG_antiFlag_1 [CUT&RUN]

value: Untreated

value: anti-Flag (Sigma, F1804)


title: CRC0735PRX0A01001TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: Lung, WA1WA1, 3DPC, REP1

value: Lung

value: Infected with WA1


title: NT, WA1Alpha, 3DPC, REP2

value: Nasal turbinate

value: Infected with Alpha


title: CRC0740PRH0000000000R01000, PRH, bio rep 1, QC ok

value: Colorectal Cancer


title: KLK5+antiKLK5/7 SAM24387829


title: NT, WA1Delta, 1DPC, REP4

value: Infected with Delta


title: CRC0734LMX0A02002TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: X


title: CRC0731LMX0A02002TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: LM


title: CRC0740LMX0B02001TUMR05000, LMX_BASALE, bio rep 2, QC ok

value: WT


title: NT, WA1Delta, 1DPC, REP3


title: KLK5 SAM24387828

value: skin


title: Kasumi-1_SMARCA5FKBP12_24hdTAG47_1 [RNA-seq]

data_processing:
Adaptors were trimmed using TrimmomaticPE LLUMINACLIP:TruSeq3-PE-2.fa:2:30:7
Trimmed reads were aligned to the human genome (hg19) with TopHat v2.0.11.
Differential gene expression was determined using Cuffdiff v.2.1.1.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Cuffdiff differential gene expression output; tab-delimited text files.

extract_protocol:
Total RNA was extracted by Trizol according to the manufacturer's protocol and precipitated with isopropanol.
Libraries were constructed on polyA selected transcript using standard Illumina protocol.


title: Kasumi-1_SMARCA5FKBP12_6hdTAG47_2 [RNA-seq]


title: KLK5+KLK7 SAM24387832

value: primary


title: NT, WA1Delta, 1DPC, REP2


title: CRC0730LMX0A02002TUMR01000, LMX_BASALE, bio rep 1, QC ok

data_processing:
Align with STAR on hybrid mm/hs genome
Assign counts to genes with FeatureCounts
Consider only human genes to normalize with DESeq2
QC based on evidence of lymphomatous infiltration
https://github.com/molinerisLab/StromaDistiller, https://github.com/vodkatad/RNASeq_biod_metadata
Assembly: GRCh38_GRCm38
Supplementary files format and content: merged_hs_mm.tsv.gz: raw counts for human and murine genes
Supplementary files format and content: vsd.tsv.gz: normalized expression values for human genes

extract_protocol:
total RNA extraction
PolyA enriched
Forward Stranded


title: No treatment SAM24387827

description: No treatment

value: neonatal keratinocytes

value: untreated


title: NT, WA1Delta, 1DPC, REP1


title: KLK5+KLK7 SAM24387826


title: CRC0729LMO0A04023002R01000, LMO_cetuxi_h, bio rep 1, QC ok

value: O

value: CET


title: NT, WA1Alpha, 1DPC, REP4


title: CRC0729LMX0A02001TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: KLK7 +antiKLK5/7 SAM24387825

description: KLK7 +antiKLK5/7

value: KLK7 +antiKLK5/7


title: Kasumi-1_SMARCA5FKBP12_2hdTAG47_1 [RNA-seq]


title: Kasumi-1_SMARCA5FKBP12_6hdTAG47_1 [RNA-seq]


title: Kasumi-1_SMARCA5FKBP12_2hdTAG47_2 [RNA-seq]


title: KLK7 SAM24387824


title: KLK7 SAM24387830


title: Kasumi-1_SMARCA5FKBP12_0hdTAG47_2 [RNA-seq]

value: Untreated


title: KLK5+antiKLK5/7 SAM24387823


title: CRC0729LMO0A04023001R01000, LMO_cetuxi_h_NT, bio rep 1, QC ok

value: NT


title: CRC0729LMO0A04021002R01000, LMO_BASALE, bio rep 2, QC ok


title: NT, WA1Alpha, 1DPC, REP3


title: Kasumi-1_SMARCA5FKBP12_24hdTAG47_2 [RNA-seq]


title: Kasumi-1_SMARCA5FKBP12_0hdTAG47_1 [RNA-seq]


title: NT, WA1Alpha, 1DPC, REP2


title: CRC0729LMO0A04008001R01000, LMO_BASALE, bio rep 1, QC ok


title: CRC0721LMX0A02001TUMR01000, LMX_BASALE, bio rep 1, QC ok