title: WT_LSECs_3

city: Daejeon

first: Eun Bok

last: Baek

address: 99 Daehak-ro

country: South Korea

institute: Chungnam National University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: LSEC

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

value: WT

value: LSEC


title: sample1, m, bone marrow, WT

status: Public on Jan 10 2024

type: SRA

city: Hamburg

first: Marco

last: Er Lukowiak

address: Bernhard-Nocht-Straße 74

country: Germany

institute: Bernhard-Nocht-Institute for tropical medicine

description: bonemarrow.csv

library_source: transcriptomic

data_processing:
Nextflow RNAseq v3.8 pipeline
using star_salmon
Star results are further processed using DESeq2
Assembly: GRCm38
Supplementary files format and content: VST transformed data matrix

molecule: total RNA

organism: Mus musculus

source_name: bone marrow

extract_protocol:
Neutrophil granulocytes from bone marrow were isolated using a Neutrophil Isolation Kit, blood neutrophils were isolated by FACS-sorting
Library preparation was performed by using a QIAseq FX DNA Library Kit

tag: tissue

value: bone marrow

tag: Sex

value: m

tag: treatment


title: Line#2, Tam-inducible, Day0, RNA rep2

city: Brookline

first: Ramesh

middle: A

last: Shivdasani

state: Massachusetts

address: SM1052, Smith10, 450 Brookline Ave

department: Medical Oncology

country: USA

institute: DFCI

data_processing:
sequence reads were mapped to hg19 using STAR aligner
Read count extraction were performed using STAR aligner v2.6.0c
Assembly: hg19
Supplementary files format and content: tab-delimited text files include STAR raw counts for each Sample

organism: Homo sapiens

growth_protocol: DMEM, 20% F12K, 20% FBS, 10% R-Spondin-2 conditioned medium, 10 mM nicotinamide, 100µg/ml Primocin, 1 μM A8301, 5 μg/ml  insulin, 10 μM Y-27632, 1 μM DMH1, 50 ng/ml EGF and 2 μM T3. Cells were cultured at 37oC at 7.5% CO2.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 2µg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared by Novogene Corporation Inc.

treatment_protocol:
Enteroendocrine differentiation was induced by transient treatment of ISCs (designated day 0, D0) for 48 h with 1µM tamoxifen or 1µg/ml doxycycline.
After 2 days diffrentiated cells were then cultured  with culture media deprived of EGF

tag: cell line

tag: cell type

value: Neurog3 Tam-inducible Ileal intestinal stem cells

tag: genotype

value: No treatment

tag: time

value: Day 0


title: Line#2, D6 scrambled, tam-inducible, Multiome-seq, RNA, rep1

description: 3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

library_source: transcriptomic single cell

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression and ATAC barcode counts) was performed using the 10x genomics Cell Ranger ARC pipeline aligning to the hg19 genome build.
Assembly: hg19
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

molecule: polyA RNA

source_name: Ileum

growth_protocol: DMEM, 20 % F12K, 20% FBS, 10% R-Spondin-2 conditioned medium, 10 mM nicotinamide, 100µg/ml Primocin, 1 μM A8301, 5 μg/ml  insulin, 10 μM Y-27632, 1 μM DMH1, 50 ng/ml EGF and 2 μM T3. Cells were cultured at 37oC at 7.5% CO2.

extract_protocol:
Stem cells / Differentiated EECs were dissociated using 1x TrypLE Exprress at 37 °C for 10 min. Cells were washed and re-suspended in PBS and stained with a Viability Dye, washed and resuspended in FACS buffer (HBSS without Ca+2, Mg+2 and phenol red, 0.9% Glucose, 10 mM HEPES, 500 ppm N-acetyl L-cystein, 10µM Y27632,  2% FBS). Alive cells were sorted using a FACS (BD Aria) according to the presence or absence of mCherry signal. Cells were washed and resuspended in PBS. Nuclei were extracted and resuspended in PBS supplemented with 0.04% w/v BSA.
Library was prepared using Chromium Next GEM Single Cell Multiome ATAC + Gene Expression protocol (10x Genomics). Cellular mRNA and ATAC sites were reverse-transcribed and indexed with a shared cellular barcode. Indexed cDNAs were then pooled and amplified by PCR according to the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression protocol (10x Genomics) and with specific primers amplifying the ATAC sites. SPRI bead size selection was performed in order to separate both the mRNA-derived cDNA (>300bp) and the ATAC sites (>180bp). For the mRNA derived cDNA and ATAC library preparation, we further proceeded according to the manufacturer’s instructions for Next GEM Single Cell Multiome ATAC + Gene Expression protocol (10x Genomics).

value: Ileum

value: D6 scrambled, tam-inducible

tag: library type

value: mRNA


title: WT_LSECs_2


title: TB_6809_Pre-BALF IgA

type: protein

city: Bronx

first: Jacqueline

middle: M.

last: Achkar

state: NY

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

description: IgA

hyb_protocol: Slides with 16 arrays on each were blocked SuperBlock (Thermo Fisher Scientific), then incubated with BALF (1:35) or plasma (1:100) diluted in phosphate buffered saline with 5% skim milk and 0.2% tween 20 (PBST) for 16 hrs at 4°C. After washing with 5% skim milk and 0.2% tween 20 (PBST) (3 x 5 min), slides were incubated with Cy3 Goat Anti-Human Serum IgA (Jackson ImmunoResearch Labs Cat# 109-165-011, RRID:AB_2337721) and Alexa 647 Goat Anti-Human IgG (Jackson ImmunoResearch Labs Cat# 109-605-008, RRID:AB_2337882; diluted at 1:200 in 5% skim milk and 0.2% tween 20 (PBST)) for 2 hrs at 4°C

scan_protocol: Slides were scanned at 635 nm and 535 nm with a Tecan PowerScanner, and images were quantified with the ArrayPro Analyzer Software (Media Cybernetics, Inc.).

data_processing: Spots were considered reactive if the ratio of the median fluorescent intensity (MFI) of the gene was greater than 1.4 x the median of negative control genes

label: Cy3 Goat Anti-Human Serum IgA

molecule: protein

organism: Macaca fascicularis

source_name: Pre-BALF

label_protocol: Cy3 Goat Anti-Human Serum IgA (Jackson ImmunoResearch Labs Cat# 109-165-011, RRID:AB 2337721)

extract_protocol: Plasma was obtained from peripheral blood samples and the BAL procedure was performed as previously described via direct visualization of the airway and lavage of ~ 40 ml normal saline (0.9%). Animal protocols and procedures were approved by the University of Pittsburgh’s Institutional Animal Care and Use Committee before the collection of samples.

tag: infection states

value: Symptomatic uncontrolled Mtb infection/TB disease


title: TB_7009_2mo-BALF IgA

description: IgA


title: TB_7009_2mo-Plasma IgA

description: IgA


title: TB_6809_Pre-Plasma IgA

description: IgA

source_name: Pre-Plasma


title: TB_7009_6mo-BALF IgA

description: IgA


title: TB_6809_2mo-Plasma IgA

description: IgA


title: Line#2, D3 scrambled, tam-inducible, Multiome-seq, RNA, rep2

value: D3 scrambled, tam-inducible


title: sample2, m, bone marrow, WT

description: bonemarrow.csv


title: Line#2, D3 scrambled, tam-inducible, Multiome-seq, RNA, rep1


title: TXNIP-/-_LSECs_3

value: TXNIP-/-


title: TB_4508_2mo-Plasma IgA

description: IgA


title: TXNIP-/-_LSECs_2


title: TB_6809_2mo-BALF IgA

description: IgA


title: TB_4508_Pre-BALF IgA

description: IgA


title: Line#1, Dox-inducible, Day4, ATAC rep2

library_source: genomic

data_processing:
Sequence reads were trimmed for adaptor sequence using cutadapt verion 1.14
Trimmed sequence reads were mapped to hg19 using Bowtie2 2.3.5
bigwig files were quantile normalized over 50bp windows using Haystack Hotspots
Assembly: hg19
Supplementary files format and content: bigwig

molecule: genomic DNA

extract_protocol:
Nuclei were harvested at specified time points and transposed using Tn5, and Nextera DNA library kit was used for the construction of sequencing libraries.
ATAC libraries were prepared by NEBNext High Fidelity 2X PCR Master mix

value: Neurog3 Dox-inducible Ileal intestinal stem cells

value: TetO-Neurog; PGK-rtTA-BlastR

value: 1µg/ml Dox for initial 48 h

value: Day 4


title: Line#1, Dox-inducible, Day4, ATAC rep1


title: Line#1, Dox-inducible, Day8, ATAC rep2

value: Day 8


title: Line#1, Dox-inducible, Day8, ATAC rep1


title: Line#1, Dox-inducible, Day0, ATAC rep1


title: Line#1, Dox-inducible, Day1, ATAC rep1

value: 1µg/ml Dox for initial 24 h

value: Day 1


title: Line#1, Dox-inducible, Day1, ATAC rep2


title: Line#2, Tam-inducible, Day8, ATAC rep3

value: 1µM Tam for initial 48 h


title: TXNIP-/-_LSECs_1

value: LSEC


title: TB_4508_2mo-BALF IgA

description: IgA


title: TB_4108_Pre-BALF IgA

description: IgA


title: Line#2, Tam-inducible, Day8, ATAC rep2

value: Neurog3 Tam-inducible Ileal intestinal stem cells


title: VGA_rep4

city: New York

first: Christopher

last: Roman

address: 450 Clarkson Avenue, Brooklyn

department: Department of Cell Biology

institute: SUNY-Downstate Health Sciences University

data_processing:
Kallisto used for transcriptome alignment followed by Sleuth for differential gene expression analysis
Assembly: GRCm38
Supplementary files format and content: Transcriptome abundance count file and bootstrap from Kallisto

source_name: B cell

extract_protocol:
Highly enriched ex-vivo B cells cells were stored in dry ice and total RNA was extracted using Trizol reagent. The high quality RNA with RIN score above 8  used for construction of cDNA library.
For cDNA library construction the NEBNext Ultra Directional RNA Library Prep Kit for Illumina used according to manufacture recommendation.

value: B cell


title: Line#2, Tam-inducible, Day8, ATAC rep1


title: VGA_rep3


title: VGA_rep2


title: Line#2, Tam-inducible, Day4, ATAC rep1


title: Line#2, Tam-inducible, Day4, ATAC rep2


title: TB_4108_2mo-BALF IgA

description: IgA


title: TB_4108_2mo-Plasma IgA

description: IgA


title: TB_3808_Pre-Plasma IgA

description: IgA


title: VGA_rep1


title: Line#2, D5, tam-inducible, Multiome-seq, RNA

value: Ileum

value: D5, tam-inducible


title: TB_3808_Pre-BALF IgA

description: IgA


title: Line#2, D3, tam-inducible, Multiome-seq, RNA

value: D3, tam-inducible

value: mRNA


title: Line#2, Tam-inducible, Day3, ATAC rep3

value: Day 3


title: HET_rep3


title: Line#2, Tam-inducible, Day3, ATAC rep2


title: HET_rep2


title: Line#2, D1, tam-inducible, Multiome-seq, RNA

value: D1, tam-inducible


title: Line#2, Tam-inducible, Day2, ATAC rep2

value: Day 2


title: Line#2, D6, tam-inducible, scRNAseq, rep2

description: 10x Genomics

data_processing:
The barcoded processing and gene counting were done using the Cell Ranger software v3.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg19
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

extract_protocol:
Stem cells / Differentiated EECs were dissociated using 1x TrypLE Exprress at 37 °C for 10 min. Cells were washed and re-suspended in PBS and stained with a Viability Dye, washed and resuspended in FACS buffer (HBSS without Ca+2, Mg+2 and phenol red, 0.9% Glucose, 10 mM HEPES, 500 ppm N-acetyl L-cystein, 10µM Y27632,  2% FBS). Alive cells were sorted using a FACS (BD Aria) according to the presence or absence of mCherry signal. Cells were washed and resuspended in PBS supplemented with 0.04% w/v BSA.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

tag: strain


title: TB_3808_2mo-Plasma IgA

description: IgA

value: Symptomatic uncontrolled Mtb infection/TB disease


title: Line#2, Tam-inducible, Day3, ATAC rep1


title: TDNBT_rep4

value: TDN-BT


title: HET_rep1


title: Line#2, D6, tam-inducible, scRNAseq, rep1

description: 10x Genomics


title: Line#2, D6, tam-inducible, Multiome-seq, RNA

value: D6, tam-inducible


title: TDNBT_rep3


title: Line#2, D5, tam-inducible, scRNAseq

description: 10x Genomics


title: TB_23210_Pre-BALF IgA

description: IgA


title: Line#2, D4, tam-inducible, scRNAseq

description: 10x Genomics


title: Line#2, D3, tam-inducible, scRNAseq

description: 10x Genomics


title: TDNBT_rep1


title: TDNBT_rep2


title: TB_23210_2mo-Plasma IgA

description: IgA


title: Line#2, D1, tam-inducible, scRNAseq

description: 10x Genomics


title: TDNB_rep3

value: TDN-B


title: TB_3808_2mo-BALF IgA

description: IgA


title: C22orf46 knockout cells - replicate 3

city: Dresden

first: Maciej

last: Paszkowski-Rogacz

address: Tatzberg 47/49

department: UCC / Medical Faculty and University Hospital Carl Gustav Carus

institute: Technische Universität Dresden

data_processing:
Expression levels of individual transcripts were estimated by kallisto (ver. 0.46.1) using human Ensembl transcriptome (release 104) as a reference.
Assembly: hg38
Supplementary files format and content: Abundance files report transcript expression levels, as reported by kallisto.

source_name: Lung

growth_protocol: Cells were cultured in RPMI medium supplemented with 10% fetal bovine serum and antibiotics streptomycin and penicillin at 37 degrees celsius and 5% CO2

extract_protocol:
Total RNA isolated from 1 million cells using Rneasy Kit (Qiagen)
RNA libraries were prepared for sequencing from 500 ng total RNA, using Ultra II Directional RNA library preparation kit with NEB adaptor (0.6µM) and 12 PCR cycles. mRNA enrichment was performed by poly-dT pull down.

value: Lung

tag: tumor type

value: Adenocarcinoma; NSCLC


title: WT_LSECs_1

value: WT


title: TB_23210_2mo-BALF IgA

description: IgA


title: TB_23210_Pre-Plasma IgA

description: IgA


title: C22orf46 knockout cells - replicate 2


title: TB_23110_Pre-BALF IgA

description: IgA


title: TDNB_rep1


title: C22orf46 knockout cells - replicate 1


title: Control cells - replicate 3


title: Control cells - replicate 2


title: WT_rep1


title: TDNB_rep2


title: Control cells - replicate 1


title: PC4

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

institute: University Medical Center Freiburg

data_processing:
Raw sequencing data were processed and aligned to the human genome (hg38) using the CellRanger pipeline (10x Genomics version 3.1, SCR_017344). Raw count data for all three samples was obtained as h5Seurat format 3.1.5.9900
Filtered raw-count matrices were further analysed using the Seurat (v4.1.0) R package (3) for data integration and unbiased clustering of single cell transcriptomes
Low-quality single cell libraries with less than 50% mitochondrial counts were excluded in whole tumour samples.
In addition, low-quality clusters with low numbers of detected genes and high percentages of mitochondrial genes and / or nearly exclusive ribosomal gene expression that lacked expression of biologically relevant cell type markers were removed after clustering.
Datasets from different localisations were integrated using the IntegrateData function in Seurat. Data was centred and scales using the ScaleData function. Principal component analysis (PCA) was used for dimensionality reduction and the K-nearest neighbor (KNN) graph was constructed using the first 30 principal components (PCs). Cells were clustered using the Louvain algorithm and embedded in two- dimensional space (30 PCs) using Uniform Manifold Approximation and Projection (UMAP).
Differentially expressed genes between clusters were identified using Wilcoxon Rank Sum test and clusters were assigned to cell types according to expressed marker genes and their similarity to known cell types.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file containing variance stabilized transformed expression values

source_name: Whole-tumour primary peritoneal carcinomatosis

growth_protocol: Anonymized human CRC, LM and PC biopsies obtained via laparoscopy at the Department of Visceral Surgery, University Medical Center Freiburg. Tumour tissues of patients with primary colorectal cancer and peritoneal carcinomatosis were obtained from surgical tumour resections and enzymatically digested with the Human Tumour Dissociation Kit (Miltenyi) according to the manufacturer’s instructions. All patients gave written informed consent.

extract_protocol:
Following cell viability analysis, tissue samples from CRC, LM and PC were processed for single-cell suspension, RNA isolation, library preparation, single cell RNA sequencing and count data generation by Singleron Biotechnologies (Cologne, Germany) via established protocols.
Single cell capture, reverse transcription, and library preparation were carried out on the Chromium platform (10X Genomics) with the single-cell 3’ reagent v2 protocol according to the manufacturer’s recommendations using 50,000 cells as input per reaction well. The final libraries [PT, LM, PC] were pooled and sequenced on two Illumina NovaSeq SP lanes (paired-end 26 bp + 96 bp).


title: T171_SARS-CoV-2plusIL-13

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

data_processing:
Base calls were processed to FASTQs on BaseSpace (Illumina), and a base call quality-trimming step was applied to remove low-confidence base calls from the ends of reads. The FASTQs were aligned to the University of California Santa Cruz (UCSC) Human genome assembly version 38.91, using STAR v.2.4.2a. Duplicate filtering, QC and metrics analysis was performed using the Picard 1.134 family of tools[ref]. For quality control, samples were kept that had human aligned counts > 1 million mapped reads and median coefficient of variation (CV) coverage < 0.9. Genes were filtered to include those that had a trimmed mean of M values (TMM) normalization count of at least 1.20.8 in at least 23 samples and further filtered for only protein coding genes. Normalized counts were transformed to log2 counts per million mapped reads along with observations level weights using voomWithQualityWeights from the limma R package version 3.5.1.(Ritchie ME et al. Nucleic Acids Res. 2015;20;43(7):e47) Sequencing was performed in 3 sample batches and a batch correction was done using limma removeBatcheffects.
Assembly: GRCm38.91
Supplementary files format and content: csv file voom normalized counts

source_name: Bronchial AECs

extract_protocol:
Total RNA was used to construct libraries by using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara, San Jose, Calif), with reverse transcription followed by PCR amplification to generate full-length amplified cDNA. Sequencing libraries were constructed by using the NexteraXT DNA sample preparation kit with unique dual indexes (Illumina, San Diego, Calif) to generate Illumina-compatible barcoded libraries. Libraries were pooled and quantified using a Qubit Fluorometer (Thermo Fisher Scientific, Waltham, Mass). Sequencing of pooled libraries was carried out on a NextSeq 2000 sequencer (Illumina) with paired-end 53-base reads, using NextSeq P2 and NextSeq P3 sequencing kits (Illumina) with a target depth of 5 million reads per sample. Base calls were processed to FASTQs on BaseSpace (Illumina), and a base call quality-trimming step was applied to remove low-confidence base calls from the ends of reads
Sequencing libraries were constructed from total RNA using SMART-Seq v4 Ultra Low Input RNA Kit (Takara) and clustered onto a flowcell using a cBOT amplification system with a HiSeq SR v4 Cluster Kit (Illumina)

tag: participantid

value: Female

tag: infection status

value: Live

tag: batch

tag: mappedreads

tag: median cv

value: Bronchial AECs


title: T171_SARS-CoV-2


title: TB_22910_2mo-BALF IgA

description: IgA


title: TB_22010_Pre-Plasma IgA

description: IgA


title: WT_rep3

value: B cell


title: TB_22910_Pre-BALF IgA

description: IgA


title: TB_22910_2mo-Plasma IgA

description: IgA


title: TB_23110_2mo-BALF IgA

description: IgA


title: TB_23110_Pre-Plasma IgA

description: IgA


title: TB_23110_2mo-Plasma IgA

description: IgA


title: TB_22910_Pre-Plasma IgA

description: IgA


title: DU145 cells, SAHA, rep3

city: Guangzhou

first: Xiong

last: Li

address: 19 Nonglinxia Road

country: China

institute: Guangdong Pharmaceutical University

data_processing:
Trimmomatic v 0.36
RseQC v 2.6.4
Sequence reads were trimmed using Trimmomatic (parameters - LEADING:3 TRAILING:3 ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10:8:true SLIDINGWINDOW:4:15 MINLEN:50) and RseQC (parameters- default).
Trimmed sequence reads were mapped to GRCh38 using HISAT2 (parameters--rna-strandness rf --fr)
FPKM of each gene was calculated using Cufflinks, and the read counts of each gene were obtained by HTSeqcount.
Assembly: NCBI_GRCh38.p13
Supplementary files format and content: An Excel file including RPKM values for each sample

growth_protocol: DU145 prostate cancer cells were maintained in 1640 medium supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using TRIzol reagent.RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific).RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies).
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina) following manufacturer's protocols.

treatment_protocol: Cells were maintained in 1640 medium supplemented with 10% FBS and 20μm H93 (DMSO dissolved), 500 nm SAHA (DMSO dissolved) or DMSO only for 6 days. The medium were changed everyday.

value: prostate cancer cells

value: SAHA 500nm

value: Day 6


title: WT_rep2


title: PC3

value: Whole-tumour primary peritoneal carcinomatosis


title: DU145 cells, SAHA, rep2


title: Line#2, Tam-inducible, Day1, ATAC rep2

value: Neurog3 Tam-inducible Ileal intestinal stem cells

value: 1µM Tam for initial 24 h

value: Day 1


title: TB_22010_Pre-BALF IgA

description: IgA

value: Symptomatic uncontrolled Mtb infection/TB disease


title: Line#2, Tam-inducible, Day0, ATAC rep2

value: No treatment

value: Day 0


title: Line#2, Tam-inducible, Day1, ATAC rep4


title: Line#2, Tam-inducible, Day1.5, ATAC rep1

value: 1µM Tam for initial 36 h

value: Day 1.5


title: Line#2, Tam-inducible, Day0.5, ATAC rep1

value: Day 0.5


title: Line#2, Tam-inducible, Day2, ATAC rep1

value: 1µM Tam for initial 48 h

value: Day 2


title: Line#2, Tam-inducible, Day0,5, ATAC rep2


title: Line#2, Tam-inducible, Day1.5, ATAC rep2


title: PC2


title: Line#2, Tam-inducible, Day1, ATAC rep3


title: T188_SARS-CoV-2plusIL-13

value: Male

value: Live

value: Bronchial AECs


title: T171_Untr_Ctl

value: Female


title: Line#2, Tam-inducible, Day0, ATAC rep1


title: Line#2, Tam-inducible, Day1, ATAC rep1


title: DU145 cells, SAHA, rep1

value: prostate cancer cells

value: WT

value: SAHA 500nm

value: Day 6


title: TB_22010_6mo-Plasma IgA

description: IgA


title: PC1

value: Whole-tumour primary peritoneal carcinomatosis


title: T188_SARS-CoV-2


title: T188_Untr_Ctl


title: LM28

source_name: Whole-tumour primary liver metastasis

value: Whole-tumour primary liver metastasis


title: DU145 cells, H93, rep3

value: H93 20microM


title: T190_SARS-CoV-2plusIL-13


title: LM21


title: DU145 cells, H93, rep1


title: LM17


title: T190_SARS-CoV-2


title: LM16


title: DU145 cells, DMSO, rep2

value: DMSO


title: DU145 cells, DMSO, rep3


title: LM2


title: LM9


title: CRC4

source_name: Whole-tumour primary CRC

value: Whole-tumour primary CRC


title: T190_Untr_Ctl


title: T189_SARS-CoV-2


title: T189_Untr_Ctl


title: T189_SARS-CoV-2plusIL-13


title: DU145 cells, H93, rep2


title: CRC3


title: CRC2


title: T170_SARS-CoV-2


title: DU145 cells, DMSO, rep1


title: T170_Untr_Ctl


title: T170_SARS-CoV-2plusIL-13


title: RA_KO_COMB_2

city: Utrecht

first: Frank

middle: van

last: Leeuwen

address: Heidelberglaan 25

country: Netherlands

institute: Princess Maxima Center

data_processing:
Raw data (raw reads) of FASTQ format were processed through fastp
alignment to reference genome (hg38) using the HISAT2 v2.0.5 algorithm program
FeatureCounts v1.5.0-p3 was used to count the read numbers mapped of each gene.
FPKM of each gene was calculated
Assembly: Homo Sapiens(GRCh38/hg38)
Supplementary files format and content: Excel file including FPKM values for each Sample

source_name: RCH-ACV

growth_protocol: Cells were grown in RPMI (Invitrogen, Thermo Fisher Scientific, Breda, the Netherlands), supplemented with 10% fetal bovine serum (FBS, Greiner Bio-One, Essen, Germany) and 1% penicillin/streptomycin solution (P/S) (Invitrogen) at a cell density between 0.25 and 3x106 cells per milliliter.

extract_protocol:
mRNA was purified from cell cultures using a NucleoSpin RNA isolation kit (740955, Machery-Nagel).
RNA sequencing and data analysis was performed by NovoGene (Cambridge, UK)

treatment_protocol: Cells were either left untreated or treated for 16 h 2 nM romidepsin, 200 nM Cytarabine or a combination of both drugs

value: RCH-ACV

value: BCP-ALL

value: p53 KO

value: Combination


title: RA_KO_COMB_3


title: T183_SARS-CoV-2plusIL-13

value: Male


title: T183_SARS-CoV-2

value: Live


title: RA_KO_COMB_1


title: Sample_6_KO

city: Maebashi

first: Jun

last: Shirakawa

address: 3-39-15 Showa-machi

department: Institute for Molecular and Cellular Regulation

country: Japan

institute: Gunma University

data_processing:
FactQC (ver. 0.11.9) was used to quality check, and we removed adapter sequences with trimmomatic (ver. 0.39).
Trimmed sequence reads were mapped to mm10 using STAR (ver. 2.7.10b).
Read count extraction was performed using featureCounts (ver. 2.0.3)
Assembly: mm10
Supplementary files format and content: excel files include raw count

source_name: pancreatic islets

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen).
Libraries were prepared from 500 ng of total RNA by means of SureSelect Strand-Specific RNA Library Prep for Illumina Multiplexed Sequencing.

value: pancreatic islets

value: KO

tag: strain background


title: T183_Untr_Ctl

value: Bronchial AECs


title: RA_KO_ROM_3

value: Cytarabine


title: Maize ATAC-seq gDNA rep2

city: Taipei

first: Pao-Yang

last: Chen

address: 128 Sec. 2, Academia Rd, Nankang

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

data_processing:
Cleaned ATAC-seq reads were mapped to the B73 maize genome (AGPv4) using Bowtie 2 version 2.3.5.1
The abundance was calculated by using ATACgraph
Assembly: AGPv4
Supplementary files format and content: Coverage track is bigWig format

organism: Zea mays

source_name: seedlings

growth_protocol: Maize seeds of the inbred line B73 were germinated with potting mix and grown in a growth chamber at 25 °C. Fresh aboveground tissue of 10-day-old plants after germination was collected immediately before the nuclear extraction procedure.

extract_protocol:
Seeding maize was finely chopped using a double-edged razor blade, and the slurry underwent initial filtration through Miracloth, followed by two filtrations through a 20 µm nylon mesh to eliminate large debris. After centrifugation, the pelleted nuclei, chloroplasts, and starch grains were resuspended in the ORB buffer where chloroplasts to burst. The nuclei suspension was then filtered twice through a 10 µm mesh. Approximately 400 µl of the green-coloured nucleus suspension was loaded onto the top of the Percoll-Sucrose gradient and centrifuged. Nuclei fractionation occurred at the interface between the ORB and SCB layers, and the isolated nuclei were transferred and pelleted in NEB buffer.
The freshly isolated nuclei and extracted genomic DNA underwent fragmentation and tagging by Tn5. Following cleanup, the first PCR was conducted to amplify DNA fragments and add barcodes. Subsequently, the number of cycles for the secondary PCR was determined through qPCR. The quality of the constructed library was assessed using Qubit and Bioanalyzer. Sequencing was carried out using the Illumina NovaSeq 6000.

tag: tissue

value: seedlings

tag: line

tag: age

value: wild type


title: Maize ATAC-seq 2500 nuclei rep2


title: Maize ATAC-seq 5000 nuclei rep1


title: Maize ATAC-seq 5000 nuclei rep2


title: Maize ATAC-seq gDNA rep1


title: T175_SARS-CoV-2plusIL-13

tag: Sex

value: Female

tag: treatment


title: RA_KO_ROM_2

tag: cell line

tag: cell type

tag: genotype


title: RA_KO_ROM_1


title: Maize ATAC-seq 2500 nuclei rep1


title: T175_SARS-CoV-2


title: Sample_5_KO


title: Sample_3_WT

value: WT


title: RA_KO_ARA_3

value: Romidepsin


title: RA_KO_ARA_2


title: Sample_2_WT


title: T184_SARS-CoV-2plusIL-13


title: Sample_4_KO


title: T175_Untr_Ctl


title: Sample_1_WT


title: T184_Untr_Ctl


title: RA_KO_CTRL_4

value: Untreated


title: T184_SARS-CoV-2


title: CbWT6

first: Robyn

middle: D

last: Moir

department: Biochemistry

data_processing:
5′ adapter and 3’ CCA and adapter sequences were removed from reads using cutadapt
Reads were mapped with bowtie2 to a mouse tRNA reference generated from GtRNAdb mm10 high-confidence mature tRNA fasta file
Read count tables for each tRNA were produced with Rsubread package’s featureCounts function in R
tRNA reads were summed to generate decoder tables
Differential tRNA expression analysis was performed with DESeq2 in R using default settings and p value adjustment (Benjamin–Hochberg correction).
Assembly: mm10
Supplementary files format and content: Csv files of DESeq2 results for Ca and Cb tRNAs
Supplementary files format and content: Csv files of DESeq2 results for Ca and Cb decoders

source_name: cerebellum

growth_protocol: ad libitum fed

extract_protocol:
Trizol extraction as per protocol, plus NaOAc precipitation
quantM tRNA library preparation
Quant M tRNA-seq

treatment_protocol: tamoxifen-induced recombination at P28, flash freeze tissue at P42

value: cerebellum

tag: time

value: M

value: Wildtype

value: tamoxifen


title: CbWT5

value: F

tag: strain


title: RA_KO_CTRL_2

value: RCH-ACV

value: BCP-ALL

value: p53 KO


title: T187_SARS-CoV-2plusIL-13

value: Male

value: Live


title: RA_KO_CTRL_3


title: CbWT4


title: RA_KO_CTRL_1


title: RA_WT_COMB_3

value: p53 WT

value: Combination


title: T187_Untr_Ctl

value: Bronchial AECs


title: CbWT3


title: CbWT2


title: T187_SARS-CoV-2


title: RA_WT_COMB_2


title: A549 cells,shikonin3

city: xi'an

first: wu

last: dan

address: xinsilu

institute: tangdu

description:
A549_Shk_Ctrl_diffresult_up.csv
A549_Shk_Ctrl_diffresult_down.csv

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: cancer cell

growth_protocol: A549 cells were maintained in 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using chloroform、isopropanol and washed with ethanol
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: A549 Cells were treated with 3μm shikonin for 24 hours,then collected cells and dissolved in trizol

value: cancer cell

value: lung carcinoma cell

value: shikonin


title: CbWT1


title: RA_WT_COMB_1


title: A549 cells,shikonin2

value: WT


title: CbKI5

value: cerebellum

value: Polr3a mutant


title: A549 cells,shikonin1


title: CbKI4


title: RA_WT_ARA_3

value: Cytarabine


title: RA_WT_ARA_2


title: CbKI3

value: M

value: tamoxifen


title: RA_WT_ARA_1

value: RCH-ACV


title: TB_17106_6mo-BALF IgA

description: IgA

tag: infection states

value: Symptomatic uncontrolled Mtb infection/TB disease


title: TB_17106_2mo-BALF IgA

description: IgA


title: TB_17106_6mo-Plasma IgA

description: IgA


title: TB_17406_2mo-BALF IgA

description: IgA


title: TB_20708_5mo-Plasma IgA

description: IgA


title: TB_22010_6mo-BALF IgA

description: IgA


title: TB_20708_Pre-Plasma IgA

description: IgA


title: TB_17106_2mo-Plasma IgA

description: IgA


title: TB_17406_2mo-Plasma IgA

description: IgA


title: TB_17406_6mo-BALF IgA

description: IgA


title: TB_17406_6mo-Plasma IgA

description: IgA


title: TB_18106_2mo-BALF IgA

description: IgA


title: TB_18106_6mo-Plasma IgA

description: IgA


title: TB_18106_6mo-BALF IgA

description: IgA


title: TB_18106_2mo-Plasma IgA

description: IgA


title: TB_20708_2mo-Plasma IgA

description: IgA


title: TB_20708_5mo-BALF IgA

description: IgA


title: TB_20708_2mo-BALF IgA

description: IgA


title: TB_20708_Pre-BALF IgA

description: IgA


title: TB_21410_2mo-BALF IgA

description: IgA


title: TB_21310_2mo-BALF IgA

description: IgA


title: TB_21310_2mo-Plasma IgA

description: IgA


title: TB_21310_Pre-BALF IgA

description: IgA


title: TB_21310_Pre-Plasma IgA

description: IgA


title: TB_21410_Pre-BALF IgA

description: IgA


title: TB_21410_Pre-Plasma IgA

description: IgA


title: TB_21410_2mo-Plasma IgA

description: IgA


title: A549 cells, Control3


title: A549 cells, Control2


title: CbKI2

value: F


title: RA_WT_ROM_3

value: BCP-ALL

value: Romidepsin


title: TB_10908_Pre-Plasma IgA

description: IgA


title: A549 cells, Control1


title: RA_WT_ROM_2

value: p53 WT


title: RA_WT_CTRL_3

value: Untreated


title: CaWT6

source_name: cerebrum

value: cerebrum

value: Wildtype


title: TB_10908_6mo-Plasma IgA

description: IgA


title: RA_WT_CTRL_2


title: HeLa cells, control siRNA, rep2

city: Houston,

first: Hari Krishna

last: Yalamanchili

state: TX

address: 1250 Moursund St #1125,

institute: Baylor College of Medicine

data_processing:
Sequencing quality and adapter contamination were assessed using FastQC v0.10.1
Adapter sequences were trimmed using fastp v0.20.0
Trimmed reads were aligned to human reference genome GRCh38 using HISAT2
Coordinate sorted binary format (BAM) files were generated using SAMtools
Gene counts were computed using featureCounts
Assembly: GRCh38
Supplementary files format and content: Text files with raw gene counts

source_name: HeLa

growth_protocol: HeLa cells were cultured in Dulbecco's modified Eagle's medium with 10% fetal bovine serum (Wisent 080-150) and maintained at 37°C in a humidified incubator containing 5% CO2

extract_protocol:
RNA was extracted using Trizol Reagent and then was further purified using Qiagen RNA clean up kit
The Centre for Applied Genomic (TCAG) prepared RNA libraries from the total rRNA depletion RNA

treatment_protocol: HeLa cells were transfected with 1 µg of negative control siRNA #2 or 1 µg of MATR3 siRNA using Lipofectamine 3000 Transfection Reagent

value: HeLa

value: Cervical cancer cells

value: negative control siRNA #2


title: CaWT5


title: CaT4


title: HeLa cells, MATR3 siRNA, rep1

value: MATR3 KD

value: MATR3 siRNA


title: N6_KO_COMB_1

value: p53 KO

value: Combination


title: HeLa cells, MATR3 siRNA, rep2


title: N6_KO_COMB_3


title: TB_10908_Pre-BALF IgA

description: IgA


title: Medulloblastoma 952

city: Ribeirão Preto

first: Carlos

middle: Alberto

last: Scrideli

state: São Paulo

address: Avenida Bandeirantes 3900

department: Pediatrics

country: Brazil

institute: Ribeirao Preto Medicine School - University of Sao Paulo

data_processing:
Sequencing and base calling: RNA-seq libraries were sequenced on an Illumina HiSeq 2500 equipment (Illumina, San Diego, CA, USA) with base calling by CASAVA software (version 1.8.2, Illumina, San Diego, CA, USA).
Sequenced reads were subjected to quality control using FastQC (Andrews, 2010) and MultiQC (Ewels et al., 2016) tools and trimmed for adaptor sequence and/or low quality reads using TrimGalore. After trimming, the reads were again processed by FastQC/MultiQC and aligned to a reference genome (Genome Reference Consortium Human GRCh38) using STAR (Dobin and Gingeras, 2015). Alignment performance was assessed with Picard and Qualimap tools. DESeq2 (Love et al., 2014) was used to estimate the change in feature expression between conditions.
Reads are in .fastq format and contain the raw base calls from sequencing. Alignment files are in .bam format and contain mapped reads.
Genome_build: GRCh38
Supplementary_files_format_and_content: Normalized abundance measurements are in .txt format as the output from DESeq2.

source_name: Medulloblastoma tumor

extract_protocol:
Total RNA was extracted using AllPrep DNA/RNA/Protein Mini kit (QIAGEN, Hilden, Germany) and RNA integrity was evaluated by Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, USA) following manufacturer’s specifications.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Medulloblastoma tumor

tag: subgroup

value: WNT

tag: metastasis

value: present

tag: recurrence

tag: outcome

value: alive


title: TB_10908_6mo-BALF IgA

description: IgA

value: Symptomatic uncontrolled Mtb infection/TB disease


title: TB_10908_2mo-Plasma IgA

description: IgA


title: Medulloblastoma 1062

value: absent

value: dead


title: CaWT2

value: M

value: tamoxifen


title: CaWT3

value: cerebrum

value: F

value: Wildtype


title: TB_10908_2mo-BALF IgA

description: IgA


title: HeLa cells, control siRNA, rep1

value: HeLa

value: Cervical cancer cells

value: WT

value: negative control siRNA #2


title: N6_KO_ROM_3

value: BCP-ALL

value: p53 KO

value: Cytarabine


title: Medulloblastoma 1001

value: Medulloblastoma tumor

value: WNT


title: N6_KO_COMB_2

value: Combination


title: TB_10808_6mo-Plasma IgA

description: IgA

value: Symptomatic uncontrolled Mtb infection/TB disease


title: TB_10808_6mo-BALF IgA

description: IgA


title: TB_10808_2mo-Plasma IgA

description: IgA


title: CbKI1

value: cerebellum

value: Polr3a mutant


title: CaWT1

value: M

value: tamoxifen


title: N6_KO_ARA_3

value: Romidepsin


title: Medulloblastoma 1078

value: SHH

value: absent

value: dead


title: CaKI2

value: cerebrum

value: F


title: N6_KO_ROM_2

value: BCP-ALL


title: Reactive+JSH23_D_IgG

city: Cleveland

first: Benjamin

last: Clayton

state: OH

address: 2109 Adelbert Rd BRB739A

department: Genetics and Genome Sciences

institute: Case Western Reserve University

data_processing:
Sequencing data was processed and analyzed using CUT&RUNTools2.0
For peak calling, reads were quality and adaptor trimmed using Trimmomatic Version 0.36.
Trimmed reads were aligned to mm10 and the spike in genome with Bowtie2 version 2.3.217.
Duplicate reads (potential artifacts of PCR in library preparation) were removed using Picard MarkDuplicates.
For RelA/p65 samples, deduplicated files were filtered for fragments less than 120bp using SAMtools.
Peaks were called with MACS version 2.1.118 with an FDR threshold of 0.01 for H3K27ac and 0.001 for RelA/p65
Peaks were compared and contrasted using bedtools implemented in the R software environment using the BedtoolsR package (http://phanstiel-lab.med.unc.edu/bedtoolsr.html) and peaks were assigned to the nearest gene using the R packages ChIPSeeker60, ChIPpeakanno61, and GenomicRanges62
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak (for RelA/p65), broadPeak (for H3K27ac)
Library strategy: CUT&RUN

source_name: astrocyte

extract_protocol:
CUT&RUN was performed on fresh or frozen nuclei isolated using the CUTANA ChIC/CUT&RUN kit (EpiCypher Cat#: 14-1048) according to manufacturer’s instructions. Briefly, 500,000 nuclei per sample were bound to activated ConA Beads followed by overnight incubation with primary antibody (1:100 RelA/p65 Cell Signaling Cat #: 8242, 0.5ug IgG EpiCypher Cat#: 14-1048, and 0.5ug either H3K27ac EpiCypher Cat #: 13-0045 or H3K27ac Abcam Cat #: AB4729). Nuclei were then permeabilized followed by addition of pAG-MNase. The reaction was then terminated and E. coli SpikeIn DNA added.
Libraries were prepared for Illumina Sequencing using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (NEB Cat # E7645) according to manufacturer’s instructions, with modifications recommended by Epicypher CUT&RUN Kit Manual Version 2.

value: astrocyte

value: pooled male and female

value: wild-type

tag: condition

value: reactive (treated with TNFa, IL1a, C1q)

value: 5uM JSH-23


title: N6_KO_ARA_1

value: p53 KO


title: Medulloblastoma 155

value: Medulloblastoma tumor

value: WNT

value: alive


title: TB_10808_2mo-BALF IgA

description: IgA

value: Symptomatic uncontrolled Mtb infection/TB disease


title: Medulloblastoma 883


title: N6_KO_ARA_2

value: Romidepsin


title: Medulloblastoma 586-08

value: SHH

value: present


title: CaKI1

value: M

value: Polr3a mutant

value: tamoxifen


title: TB_10208_Pre-BALF IgA

description: IgA

source_name: Pre-BALF


title: N6_KO_ROM_1

value: BCP-ALL

value: Cytarabine


title: Medulloblastoma 670

value: absent

value: dead


title: N6_KO_CTRL_3

value: Untreated


title: Reactive+JSH23_C_IgG

value: astrocyte

value: pooled male and female

value: wild-type

value: reactive (treated with TNFa, IL1a, C1q)

value: 5uM JSH-23


title: Medulloblastoma 310-10

value: Medulloblastoma tumor


title: Reactive+JSH23_B_IgG


title: TB_10208_3mo-Plasma IgA

description: IgA

value: Symptomatic uncontrolled Mtb infection/TB disease


title: Medulloblastoma 926


title: N6_KO_CTRL_2

value: p53 KO


title: Reactive+RGFP966_D_IgG

value: 5uM RGFP966


title: TB_10208_6mo-BALF IgA

description: IgA


title: TB_10208_3mo-BALF IgA

description: IgA


title: TB_10208_Pre-Plasma IgA

description: IgA

source_name: Pre-Plasma


title: N6_KO_CTRL_1


title: CaKI4

value: cerebrum

value: F


title: CaKI3

value: M

value: Polr3a mutant

value: tamoxifen


title: Medulloblastoma 909

value: absent


title: N6_WT_COMB_3

value: BCP-ALL

value: p53 WT

value: Combination


title: Medulloblastoma 222-11

value: present

value: alive


title: Reactive+RGFP966_C_IgG

value: astrocyte

value: pooled male and female

value: wild-type

value: reactive (treated with TNFa, IL1a, C1q)


title: Medulloblastoma 44-07

value: Medulloblastoma tumor

value: dead


title: LTBI_9911_Pre-Plasma IgA

description: IgA

value: Asymptomatic controlled Mtb infection


title: N6_WT_COMB_2


title: Medulloblastoma 168


title: Reactive_C_IgG

value: DMSO


title: N6_WT_ARA_3

value: Cytarabine


title: Reactive_D_IgG


title: Reactive+RGFP966_B_IgG

value: 5uM RGFP966


title: Reactive_B_IgG


title: N6_WT_COMB_1


title: N6_WT_ROM_3

value: Romidepsin


title: N6_WT_ARA_2


title: Resting_D_IgG

value: resting


title: Medulloblastoma 46


title: N6_WT_ROM_2

value: BCP-ALL


title: Resting_C_IgG


title: H4K12bu_CUTnTag_but2

city: Palo Alto

first: Michael

last: Nshanian

state: CA

institute: Stanford University

description: high fat, high sucrose + 5 % aranbinoxyan

data_processing:
Basecalls were performed using bcl2fastq2 (v2.17.1) for HiSeq and Novaseq output.
CUTnTag reads were trimmed from 3' end using cutadapt (v 1.9.1) until the final base had a quality score > 30.
CUTnTag reads were aligned to the UCSC hg38 or mm10 genomes using Bowtie2 (v 2.3.1). Only uniquely mapped reads were retained with at most two mismatches.
To create CUTnTag coverage plots, the locations of the mapped reads were enormalized to reads per million and reformatted to .bigWig file format.
Peaks were called using MACS2 (2.1.0) with the significance cut-off q-value (FDR) <= 0.01.
Assembly: hg38, mm10
Supplementary files format and content: bam, narrowPeak

source_name: Large intestine; colon, epithelial

growth_protocol: EMEM media containing 10 % fetal bovine serum (FBS)/1 % Pen/Strep (PS). All cell lines were maintained at 37C in a humidified atmosphere containing 5 % CO2

extract_protocol:
CUT&Tag was performed using CUT&Tag-ITTM assay kits (Active Motif # 53160, 53170). ~500,000 viable nuclei (30 mg tissue) were used per reaction. Tissue samples were Dounced 20 times with a loose pestle and 10 times with a tight pestle. 5 μg of undiluted primary antibody was added to each sample for an overnight incubation at 4C with orbital mixing. 100 μL of 1:100 of Guinea Pig Anti-Rabbit secondary antibody was then added to each reaction and the samples were incubated on an orbital rotator for 60 min at RT. Assembled pA-Tn5 Transposomes were added to each sample and reactions were incubated on an orbital rotator for 60 min at RT. 125 μL of Tagmentation Buffer (5 mL Dig-300 buffer and 50 µL 1 M MgCl2) was added to each sample and reactions were incubated at 37C for 1 h. Nextera i5 and i7 indexing primers were used and final PCR reactions were purified using Zymo DNA Clean and Concentrator-5 Kit (cat # D4013).
Final PCR reactions were purified using Zymo DNA Clean and Concentrator-5 Kit (cat # D4013)
CUT&Tag-ITTM assay kits (Active Motif # 53160, 53170) and Hatice S. Kaya-Okur et al., (Nat Comm 2019)

treatment_protocol: Cells were treated with 1 mM Na Butyrate (NaBu) for 12-16 hrs followed by counting.

value: Large intestine; colon, epithelial


title: LTBI_9911_3mo-Plasma IgA

description: IgA

data_processing: Spots were considered reactive if the ratio of the median fluorescent intensity (MFI) of the gene was greater than 1.4 x the median of negative control genes

extract_protocol: Plasma was obtained from peripheral blood samples and the BAL procedure was performed as previously described via direct visualization of the airway and lavage of ~ 40 ml normal saline (0.9%). Animal protocols and procedures were approved by the University of Pittsburgh’s Institutional Animal Care and Use Committee before the collection of samples.


title: LTBI_9911_3mo-BALF IgA

description: IgA


title: LTBI_9911_6mo-BALF IgA

description: IgA


title: LTBI_9911_Pre-BALF IgA

description: IgA


title: LTBI_9911_6mo-Plasma IgA

description: IgA


title: LTBI_9811_Pre-Plasma IgA

description: IgA


title: Resting_B_IgG


title: Medulloblastoma 1357

value: absent


title: H4K12bu_CUTnTag_but1


title: N6_WT_ROM_1

value: p53 WT


title: Reactive+JSH23_D_H3K27ac

value: 5uM JSH-23


title: H3K18bu_CUTnTag_but2


title: H3K18bu_CUTnTag_but1


title: N6_WT_CTRL_3

value: Untreated


title: Medulloblastoma 58


title: N6_WT_CTRL_1


title: N6_WT_CTRL_2


title: Reactive+RGFP966_D_H3K27ac

value: astrocyte

value: pooled male and female


title: H4K12ac_CUTnTag_cnt2

description: high fat, high sucrose (HFHS)


title: Reactive+JSH23_C_H3K27ac

value: wild-type

value: reactive (treated with TNFa, IL1a, C1q)


title: Reactive+RGFP966_C_H3K27ac


title: LTBI_9811_Pre-BALF IgA

description: IgA


title: C

first: Zhan

last: Wang

state: Guangdong

address: No.1023,South Shatai Road, Baiyun District

department: Nanfang   Hospital, Southern Medical University/The First School of Clinical Medicine,   Southern Medical University

institute: Southern Medical University

data_processing:
Raw reads of fastq format were firstly processed using fastp  and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2 .
FPKM  of each gene was calculated and the read counts of each gene were obtained by HTSeq-count .
PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples.
Differential expression analysis was performed using the DESeq2 .
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.

source_name: Hair follicle stem cells are treated with a blank group.

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA).
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: hair follicle

value: blank group


title: H4K12ac_CUTnTag_cnt1

description: high fat, high sucrose (HFHS)


title: ra-0.5nm

source_name: Hair follicle stem cells are treated with rapamycin.

value: rapamycin


title: Reactive_D_H3K27ac

value: DMSO


title: H3K18ac_CUTnTag_cnt2

description: high fat, high sucrose (HFHS)


title: Reactive_C_H3K27ac


title: LTBI_9808_Pre-BALF IgA

description: IgA

value: Asymptomatic controlled Mtb infection


title: LTBI_9811_3mo-Plasma IgA

description: IgA


title: LTBI_9811_6mo-BALF IgA

description: IgA


title: LTBI_9811_6mo-Plasma IgA

description: IgA


title: LTBI_9811_3mo-BALF IgA

description: IgA


title: Resting_D_H3K27ac


title: H3K18ac_CUTnTag_cnt1

description: high fat, high sucrose (HFHS)


title: LTBI_9808_6mo-Plasma IgA

description: IgA


title: ChIP-seq of H3K27Ac in Homo sapiens: U251-H3K27ac-Rep2

city: Tianjin

first: Niannian

state: Tianjin

address: No. 94 Weijin Road, Nankai District, Tianjin

department: college of Life Sciences

institute: Nankai University

data_processing:
Clean reads of RNA-seq were mapped to hg19 using HISAT2(2.1.0)
Expression levels of all genes were count.txted and expression profile matrix was constructed with HTSeq (0.9.1)
Differential expression analysis was calculated in R using DESeq2(1.18.1), with p value < 0.05 and fold change > 2 or < 1/2
Clean reads of Capture-C were cut into two pieces in the DpnII sites
All the reads were mapped to mm10 with Bowtie2(2.3.1)
Report all the reads that contains the Bait sequence
Clean reads of ChIP-seq were mapped to mm10 using Bowtie2(2.3.1)
Peak calling using MACS2(2.2.7.1)
Assembly: hg19
Supplementary files format and content: table of genes counts,wig file of  CaptureC signal and bigwig file of ChIPSeq signal

source_name: brain

growth_protocol: U251 and U87 cells were cultured in Dulbecco's Modified Eagle's medium (DMEM, Gibco) containing 10% fetal bovine serum (FBS, Bioind) and 1% penicillin/streptomycin (Gibco) at 37°C, in 90% humidity and 5% CO2.

extract_protocol:
1. For RNA-seq: cells were lysed with Trizol reagent (Life Technologies) and RNA was extracted according to the manufacturer's instructions.     2. For Chip-seq: 10 M cells were crosslinked 10 min with 1% formaldehyde (Thermo Fisher Scientific) at room temperature and the reaction was terminated by a 5 min incubation with a solution containing glycine (0.125 M) (Solarbio). After centrifugation at 4° C, cells were washed twice with ice-cold PBS. Nuclear DNA precipitates were harvested in Farnham lysis buffer [50 mM (pH 7.5) tris-HCl, 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1% Triton X-100，1 mM phenylmethylsulfonyl fluoride and 1× protease inhibitor cocktail]. Nuclear DNA was then sonicated as a nuclear lysate (50 mM Tris-HCL,10 mM EDTA,1% SDS,1× protease inhibitor cocktail) to shear chromatin and obtain 200-500-bp DNA fragments. Sonicated lysates were immunoprecipitated at 4°C with H3K27ac antibody (Abcam) and protein A/G agarose beads (Thermo Fisher Scientific) to enrich H3K27ac-bound DNA fragments. Purified ChIP DNA was used to prepare Illumina sequencing libraries and sequenced using an Illumina HiSeq 4000 system.  3. For Capture-C：In brief, U251 glioma cells (10 M) were harvested and used to generate a standard 3C library with DpnII (New England BioLabs). Then 3C library DNA was sheared to 200-300-bp fragments by sonication. Pre-capture DNA libraries were prepared using the NEBNext DNA Library Kit (New England BioLabs) according to the manufacturer’s instructions. Biotinylated “bait” probes and streptavidin beads (Invitrogen) were used to enrich the “bait” and linked chromatin loci. Barcoded Capture-C libraries were sequenced as 150-bp paired-end reads using the Illumina HiSeq 4000 platform.
RNA-seq, ChIP-seq and Capture-C libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: TMZ-treated groups were 1mM TMZ treated for 72h,and DMSO-treated groups were control groups for the same conditions

value: Glioblastoma cells

value: brain

value: untreated


title: LTBI_9808_6mo-BALF IgA

first: Jacqueline

description: IgA


title: CT26_but4

data_processing:
Basecalls were performed using bcl2fastq2 (v2.17.1) for HiSeq and Novaseq output.
ATAC-seq reads were trimmed from 3' end using cutadapt (v 1.9.1) until the final base had a quality score > 30.
ATAC-seq reads were aligned to the UCSC hg38 or mm10 genomes using Bowtie2 (v 2.3.1). Only uniquely mapped reads were retained with at most two mismatches.
To create ATAC-seq coverage plots, the locations of the mapped reads were enormalized to reads per million and reformatted to .bigWig file format.
Peaks were called using MACS2 (2.1.0) with the significance cut-off q-value (FDR) <= 0.01.
Assembly: hg38, mm10
Supplementary files format and content: narrowPeak

growth_protocol: EMEM media (or RPMI for CT26) containing 10 % fetal bovine serum (FBS)/1 % Pen/Strep (PS). All cell lines were maintained at 37C in a humidified atmosphere containing 5 % CO2

extract_protocol:
ATAC-seq was performed using Omni-ATAC as described in Corces et al. (Nat. Methods 2017). 50,000 viable cells were pelleted and resuspended in ATAC-Resuspension Buffer. Cells were resuspended in transposition mix containing TD buffer and transposase (Illumina Tagmented DNA enzyme and buffer kit, Ref 20034210)
Final PCR reactions were purified using Zymo DNA Clean and Concentrator-5 Kit (cat # D4013)
Corces et al. (Nat. Methods 2017)

treatment_protocol: Cells were treated with 10 mM Na Propionate (NaPr) or 1 mM Na Butyrate (NaBu) for 12-16 hrs followed by counting.

value: Large intestine; colon, epithelial

value: 1 mM NaBu


title: ChIP-seq of H3K27Ac in Homo sapiens: U251-H3K27ac-Rep1


title: CT26_but3


title: Reactive+JSH23_C_RelA/p65


title: CT26_but2


title: LTBI_9808_2mo-Plasma IgA

description: IgA


title: CT26_but1


title: LTBI_9411_Pre-Plasma IgA

description: IgA


title: RNA-Seq of Homo sapiens: U251-LINC02454-OE-Rep2


title: CT26_cnt4

value: 0 mM NaBu


title: LTBI_9411_Pre-BALF IgA

description: IgA


title: Reactive+RGFP966_C_RelA/p65

value: 5uM RGFP966


title: ChIP-seq of H3K27Ac in Homo sapiens: U251-H3K27ac-Input


title: LTBI_9808_2mo-BALF IgA

description: IgA


title: Reactive+RGFP966_B_RelA/p65


title: LTBI_9411_6mo-Plasma IgA

description: IgA


title: RNA-Seq of Homo sapiens: U251-LINC02454-OE-Rep1


title: Reactive_C_RelA/p65


title: RNA-Seq of Homo sapiens: U251-Ctrl-LINC02454-OE-Rep2


title: LTBI_9411_6mo-BALF IgA

description: IgA


title: CT26_cnt3


title: CT26_cnt2


title: Reactive_B_RelA/p65


title: Resting_C_H3K27ac

value: resting


title: Resting_C_RelA/p65

value: astrocyte


title: RNA-Seq of Homo sapiens: U251-Ctrl-LINC02454-OE-Rep1


title: RNA-Seq of Homo sapiens: U251-LINC02454-KD-Rep2


title: Capture-c of LINC02454 SE in Homo sapiens: U251-LINC02454-SE-Capture-C-Rep2

data_processing:
library strategy: Capture-C
Clean reads of RNA-seq were mapped to hg19 using HISAT2(2.1.0)
Expression levels of all genes were count.txted and expression profile matrix was constructed with HTSeq (0.9.1)
Differential expression analysis was calculated in R using DESeq2(1.18.1), with p value < 0.05 and fold change > 2 or < 1/2
Clean reads of Capture-C were cut into two pieces in the DpnII sites
All the reads were mapped to mm10 with Bowtie2(2.3.1)
Report all the reads that contains the Bait sequence
Clean reads of ChIP-seq were mapped to mm10 using Bowtie2(2.3.1)
Peak calling using MACS2(2.2.7.1)
Assembly: hg19
Supplementary files format and content: table of genes counts,wig file of  CaptureC signal and bigwig file of ChIPSeq signal


title: Capture-c of LINC02454 SE in Homo sapiens: U251-LINC02454-SE-Capture-C-Rep1


title: Reactive+JSH23_B_RelA/p65

value: pooled male and female

value: 5uM JSH-23


title: LTBI_9411_2mo-BALF IgA

description: IgA


title: Resting_B_RelA/p65

value: wild-type


title: RNA-Seq of Homo sapiens: U251-LINC02454-KD-Rep1


title: RNA-Seq of Homo sapiens: U251-Ctrl-LINC02454-KD-Rep2


title: HP1cTKO ESCs clone 20 H4K20me3 ChIP

city: Berlin

first: Andrew

last: Newman

address: Charitéplatz 1

department: Institute for Cell and Neurobiology

institute: Charité Universitätsmedizin Berlin

description: For conditional KO, 4-OH Tamoxifen (SIGMA, #H7904; (Z)-4-Hydroxytamoxifen, ≥98% Z isomer, dissolved in ethanol) was added to medium to a final concentration of 800 nM.

data_processing:
RNAseq reads aligned using STAR with --outFilderMultimapNmax 100 --winAnchorMultimapNmax 100 --outSAmstrandField intronMotif and the gencode.vM16.basic.annotation.gtf. Count table across all samples was generated using TETranscripts
ChIPseq reads were trimmed using trimmomatic SE with LEADING:5, TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:30.  Trimmed reads were aligned using bowtie2 using default parameters. Bigwig files were created using deeptools' bamCoverage with --normalizeUsing RPGC --effectiveGenomeSize 2652783500 --extendReads 125
RRBS reads were trimmed using trim_galore --rrbs and aligned to the bisulfite genome using bismark with --bowtie1 -n 1 -l 45
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: RNAseq counts, bigwig for ChIP-seq, coverage files for RRBS

source_name: murine embryonic stem cells

growth_protocol: ESCs were cultured in D-MEM (Kohjin-bio, #16003550) with 20% fetal bovine serum (Sigma-Aldrich, #172012), MEM nonessential amino acids (GIBCO, #11140-050), L-glutamine (GIBCO, #25030-081), 2-mercaptoethanol (Sigma-Aldrich, #M1753), and LIF (in-house preparation) on mitomycin C-treated (Sigma-Aldrich, #M4287) primary MEF feeder layers

extract_protocol:
RNA was isolated using the Relia-prep RNA mini kit (Promega), for ChIP, lysates were clarified from sonicated nuclei and precipitated with an antibody. Genomic DNA for RRBS was isolated using the Allprep DNA/RNA mini kit (QIAGEN #80204) Bisulfite conversion was done by the EZ DNA Methylation Gold kit (Zymo Research, #D5005) with 50ng of DNA per sample.
RNAseq libraries were prepared with NEBNext Ultra RNA library prep kit for Illumina using 1ug of RNA per sample. ChIP multiplex libraries were prepared by NEBNext Ultra DNA library Prep kit for Illumina.

value: murine embryonic stem cells

tag: chip antibody

value: Anti-Histone H4K20me3 (trimethyl Lys20), Mouse(GT9009), GTX60364

value: 4-OHT tamoxifen treatment for 6 days


title: MYO-NT, Day 2, Biol Rep 2

city: Cambridge

first: Ming-Hsuan

last: Wen

address: Tennis Court Road

country: United Kingdom

institute: Wellcome/Cancer Research UK Gurdon Institute, University of Cambridge

data_processing:
Fasta files from M. musculus (mm10) and X. laevis (xla9.1) were concatenated one after the other in order to create a hybrid large mouse-Xenopus genome.
To distinguish the X. laevis chromosomes in the fasta file, they were renamed as ‘xla_chr’ instead of just ‘chr’.
Similarly, the gtf files containing the annotation of all transcripts from Mouse (mm10) and of all primary transcript from X. laevis (xla9.1) have been concatenated.
FastQ files were processed with cutadatp (version 1.9.1, options -q 10 -O 3) for adapter trimming.
Filtered reads were then aligned to the hybrid mouse-Xenopus genome with tophat (version v2.1.1).
Transcripts were assigned to gene and counted using htseq-count (HTSeq-0.5.4p3).
The M. musculus (mm10) was replaced with H. sapiens (hg38) in experiments with human cells transplanted into Xenopus oocytes.
Assembly: mm10
Assembly: hg38
Supplementary files format and content: exl files include TPM for each sample

source_name: myoblasts

extract_protocol:
RNA was extracted by Qiagen Rneasy Mini Kit and BrUTP incorporated RNA was isolated via immunoprecipitation.
RNA-seq libraries were prepared by Ovation Single Cell RNA-seq System (NuGEN) and 10 ng of BrUTP incorporated RNA was used for each library.

value: myoblasts


title: MYO-NT, Day 2, Biol Rep 1


title: ESC-NT, Day 2, Biol Rep 3

source_name: embryonic stem cells

value: embryonic stem cells


title: HP1cTKO ESCs clone 20 KAP1 ChIP

tag: tissue

value: anti-KAP1, mouse-mono(20C1), GTX80695


title: RNA-Seq of Homo sapiens: U251-Ctrl-LINC02454-KD-Rep1

value: Glioblastoma cells

value: brain


title: RNA-Seq of Homo sapiens: U251-LINC02454-SE-KO-Rep2

value: untreated


title: RNA-Seq of Homo sapiens: U251-LINC02454-SE-KO-Rep1


title: ESC-NT, Day 2, Biol Rep 2


title: HP1cTKO ESCs clone 10 H4K20me3 ChIP


title: CT26_cnt1

value: Large intestine; colon, epithelial


title: HP1cTKO ESCs clone 10 KAP1 ChIP


title: LTBI_9411_2mo-Plasma IgA

city: Bronx

last: Achkar

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

description: IgA

value: Asymptomatic controlled Mtb infection


title: ESC-NT, Day 2, Biol Rep 1


title: RNA-Seq of Homo sapiens: U251-Ctrl-LINC02454-SE-KO-Rep2


title: wt ESCs clone 20 H4K20me3 ChIP

value: WT


title: MEF-NT, Day 2, Biol Rep 3

source_name: embryonic fibroblasts

value: embryonic fibroblasts


title: MYO-NT, Day 2, Biol Rep 3


title: wt ESCs clone 20 KAP1 ChIP


title: RNA-Seq of Homo sapiens: U251-Ctrl-LINC02454-SE-KO-Rep1


title: MEF-NT, Day 2, Biol Rep 2


title: MEF-NT, Day 2, Biol Rep 1


title: wt ESCs clone 10 H4K20me3 ChIP


title: RNA-Seq of Homo sapiens: U87-TMZ-Rep2

value: TMZ 72 h


title: MEF-NT, Day 1, Biol Rep 2


title: wt ESCs clone 10 KAP1 ChIP


title: RNA-Seq of Homo sapiens: U87-TMZ-Rep1


title: Igf1rKO-LE_3

city: Xiamen

first: Wenbo

last: Deng

state: Fujian

address: Xiang'an Road

department: School of Medicine

institute: Xiamen University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR with default parameters
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using EdgeR package of R.
Differential expression genes were normalized to fragments per kilobase of exon model per million mapped reads (RPKM) using EdgeR package in R with the criteria of fold change significantly greater than 2 and P<0.05. Gene ontology (GO) enrichment analysis of the DEGs was analyzed by using DAVID (the Database for Annotation, Visualization and Integrated Discovery, https://david.ncifcrf.gov). GO terms with corrected p <0.05 were considered significantly enriched. Gene Set Enrichment Analysis (GSEA) was performed to determine whether a defined set of genes shows statistically significant, consistent differences between different groups.
Assembly: mm10

source_name: Mouse uteri on pregnant day 4

growth_protocol: Mice were housed in the animal care facility of Xiamen University according to the guidelines for the care and use of laboratory animals. All experimental procedures were approved by the Animal Welfare Committee of Research Organization (X200811), Xiamen University.

extract_protocol:
Uterine horns were excised, trimmed of fat, and cut into 50-mm-long sections and placed into 25 g/L Trypsin (Sigma, T8003) for 6-8 min at 37℃. Then slowly pushed from one side of the uterus to the other, squeezed out luminal epithelial cells. The cells were washed twice in phosphate-buffered saline (PBS) and repelleted. The pellets were lysed with Trizol for RNA extraction. Total RNAs from uteri were extracted by TRIzol and purified by ploy-A before subjected to RNA-Seq.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: C57 mouse decidua

value: epithelium

value: normal pregnancy

tag: developmental stage

value: pregnancy day 4

value: Igf1r KO


title: RNA-Seq of Homo sapiens: U87-DMSO-Rep2

value: DMSO 72 h


title: MEF-NT, Day 1, Biol Rep 1


title: RNA-Seq of Homo sapiens: U87-DMSO-Rep1


title: Igf1rKO-LE_2


title: LTBI_9208_2mo-Plasma IgA

description: IgA


title: LTBI_9311_6mo-BALF IgA

description: IgA


title: Igf1rKO-LE_1


title: LTBI_9208_6mo-Plasma IgA

description: IgA


title: LTBI_9311_6mo-Plasma IgA

description: IgA


title: LTBI_9311_2mo-BALF IgA

description: IgA


title: LTBI_9311_Pre-Plasma IgA

description: IgA


title: LTBI_9311_2mo-Plasma IgA

description: IgA


title: LTBI_9208_Pre-BALF IgA

description: IgA


title: LTBI_9311_Pre-BALF IgA

description: IgA


title: RNA-Seq of Homo sapiens: U251-TMZ-Rep2


title: LTBI_9208_6mo-BALF IgA

description: IgA


title: LTBI_9208_Pre-Plasma IgA

description: IgA


title: LTBI_9208_2mo-BALF IgA

description: IgA


title: TB_10208_6mo-Plasma IgA

description: IgA

value: Symptomatic uncontrolled Mtb infection/TB disease


title: LTBI_6909_Pre-Plasma IgA

description: IgA


title: Control, E10.75, mandible, litter 3

city: Cincinnati

first: Rulang

last: Jiang

address: 3333 Burnet Ave

department: Division of Developmental Biology

institute: Cincinnati Children's Hospital Medical Center

data_processing:
The sequencing reads were mapped to the mouse cDNA (mm10) using Salmon v1.5.2. --seqBias and --validateMappings flags were used during the read mapping.
R package tximport was used to summarize the quantification data at gene level. R package DESeq2 was used for differential gene expression analysis.
Assembly: mm10
Supplementary files format and content: Tab-delimited text format including the TPM values

source_name: distal mandible

extract_protocol:
RNeasy micro kit from Qiagen was used to extract total RNA.
The library construction was performed at the DNA sequencing core at CCHMC using standard illumina sequencing protocols.

value: distal mandible

tag: age


title: Mutant, E10.75, mandible, litter 3


title: RNA-Seq of Homo sapiens: U251-TMZ-Rep1


title: Control, E10.75, mandible, litter 2


title: Mutant, E10.75, mandible, litter 2


title: RNA-Seq of Homo sapiens: U251-DMSO-Rep2


title: LTBI_6909_Pre-BALF IgA

description: IgA


title: WT-LE_2


title: LTBI_6909_6mo-Plasma IgA

description: IgA


title: RNA-Seq of Homo sapiens: U251-DMSO-Rep1


title: WT-LE_1


title: pspD4_17_2

extract_protocol:
To isolate the luminal epithelium, frozen sections of pregnant uteri (20 µm) were mounted on polyethylene naphthalate slides (Leica Microsystems). The target regions in the sections were dissected using the Leica LMD7 (Leica Microsystems, Wetzlar, Germany). Total RNA was extracted from collected cells using RNAeasy Micro Kit Qiagen 74004 and eluted with 14 μl of RNase-free water. Total RNAs from uteri were extracted by TRIzol and purified by ploy-A before subjected to RNA-Seq.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: pseudopregnancy


title: LTBI_6909_6mo-BALF IgA

description: IgA


title: Mutant, E10.75, mandible, litter 1


title: pspD4_17_1


title: Ire1af/f Emx1Cre cortex Polysome 1

description: total RNA (polysome fraction)

data_processing:
Raw reads were aligned to GRCm38.p5 using STAR 2.5.3a with parameters --outFilterMultimapNmax 100 --winAnchormultimapNmax 100 --outSamstrandField intronMotif and the gencode vM16 basic annotation transcriptome
Count table was generated from the resulting bam files using TETranscripts
Fit to a quasi-likelihood negative binomial generalized log-linear model and tested for differential expression using EdgeR
Genome_build: GRCm38.p5

source_name: E18 Cerebral Cortex

extract_protocol:
Ribosome fractionation and polysome purification from E18.5 cortex was performed as published protocol (Kraushar et al., 2021).  RNA was isolated using the Relia-prep RNA mini kit (Promega)
Stranded Total RNAseq libraries were prepared using TruSeq with Ribo-Zero Gold rRNA Removal

value: cerebral cortex


title: pspD4_10_1


title: pspD4_10_2


title: M2 macrophages treated with Folfirinox  replicate_2

city: Marseille

first: Ghislain

last: BIDAUT

address: 27 Bd Leï Roure

department: Bioinformatics

country: France

institute: Centre de Recherche en Cancérologie de Marseille

description:
M2_FOLFI_rep2
M2 macrophages differentiated using M-CSF (5 days) and polarized by IL-4 and IL-13 and treated with 15uM Folfirinox for 48h

data_processing:
Trimming - Removal of adaptater sequences, removal of bases with Phread < 30.
Alignment on reference genome with Subread using subread-align (v1.5.0) (1) with default parameters.
Summarization at the gene level using featurecount.
RPKM were calculated by count normalisaiton by gene length and library size.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes count values for each Sample at the gene level.

source_name: Human healthy blood donor monocytes-derived macrophages

growth_protocol: Human healthy blood donor buffy coats were used to isolate CD14+ monocytes with magnetic bead isolation. Monocytes were plated and treated with 40ng/mL of human recombinant M-CSF for 5 days. Following differentiation with M-CSF, macrophages were treated with human recombinant IL-4 (50ng/mL) and IL-13 (25ng/mL) for 48 hours before cocultures with primary PDAC CAFs and treatment with Folfirinox

extract_protocol:
RNA extraction was performed using the Qiagen Rnaeasy mini kit and RNA quality was tested using the Agilent RNA 6000 Nano kit and the Agilent 2100 Bioanalyzer.
Libraries were prepared with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina protocol according supplier recommendations. Briefly the key stages of this protocol are successively, the purification of PolyA containing mRNA molecules using poly-T oligo attached magnetic beads from 100ng total RNA (with the Magnetic mRNA Isolation Kit from NEB), a fragmentation using divalent cations under elevated temperature to obtain approximately 300bp fragments, double strand cDNA synthesis and finally Illumina adapters ligation and cDNA library amplification by PCR for sequencing.
Sequencing was carried out on Paired End 100b reads on Illumina NovaSeq6000. Image analysis and base calling was performed using Illumina Real Time Analysis with default parameters

treatment_protocol: Macrophages were placed at a 1:1 ratio with primary PDAC CAFs in indirect coculture (transwell inserts, 0.4 microns). Monocultures and cocultures were treated with 15uM of each component of Folfirinox chemotherapy regimen (5'-fluorouracil, irinotecan, and oxaliplatin) for a duration of 48 hours before RNA extraction was performed.

value: M2 macrophages treated with Folfirinox


title: Control, E10.75, mandible, litter 1


title: WT-LE_3


title: M2 macrophages treated with Folfirinox replicate_3

description:
M2_FOLFI_rep3
M2 macrophages differentiated using M-CSF (5 days) and polarized by IL-4 and IL-13 and treated with 15uM Folfirinox for 48h

value: Human healthy blood donor monocytes-derived macrophages


title: M2 macrophages treated with Folfirinox  replicate_1

description:
M2_FOLFI_rep1
M2 macrophages differentiated using M-CSF (5 days) and polarized by IL-4 and IL-13 and treated with 15uM Folfirinox for 48h


title: LTBI_6909_2mo-Plasma IgA

description: IgA


title: M2 macrophages in coculture with CAFs and treated with Folfirinox replicate_3

description:
M2-CAF_FOLFI_rep3
M2 macrophages differentiated using M-CSF (5 days) and polarized by IL-4 and IL-13 in indirect coculture with primary PDAC CAFs for 48h and treated with 15uM Folfirinox


title: LTBI_6909_2mo-BALF IgA

description: IgA


title: LTBI_6709_Pre-Plasma IgA

description: IgA


title: Ire1af/f cortex Polysome 2

description: total RNA (polysome fraction)

value: wild type


title: Ire1af/f Emx1Cre cortex Polysome 2

description: total RNA (polysome fraction)


title: D4_17_2


title: LTBI_6709_Pre-BALF IgA

description: IgA

value: Asymptomatic controlled Mtb infection


title: Ire1af/f cortex Polysome 1

description: total RNA (polysome fraction)


title: M2 macrophages in coculture with CAFs and treated with Folfirinox replicate_1

description:
M2-CAF_FOLFI_rep1
M2 macrophages differentiated using M-CSF (5 days) and polarized by IL-4 and IL-13 in indirect coculture with primary PDAC CAFs for 48h and treated with 15uM Folfirinox

value: WT


title: LTBI_6709_6mo-Plasma IgA

description: IgA


title: M2 macrophages in coculture with CAFs  replicate_3

description:
M2-CAF_CTRL_rep3
M2 macrophages differentiated using M-CSF (5 days) and polarized by IL-4 and IL-13 in indirect coculture with primary PDAC CAFs for 48h

value: M2 macrophages in coculture with CAFs


title: LTBI_6709_6mo-BALF IgA

description: IgA


title: M2 macrophages in coculture with CAFs replicate_2

description:
M2-CAF_CTRL_rep2
M2 macrophages differentiated using M-CSF (5 days) and polarized by IL-4 and IL-13 in indirect coculture with primary PDAC CAFs for 48h


title: Ire1af/f cortex 3

description: total RNA


title: D4_10_1


title: Ire1af/f Emx1Cre cortex 1

description: total RNA


title: M2 macrophages in coculture with CAFs replicate_1

description:
M2-CAF_CTRL_rep1
M2 macrophages differentiated using M-CSF (5 days) and polarized by IL-4 and IL-13 in indirect coculture with primary PDAC CAFs for 48h


title: Ire1af/f cortex 2

description: total RNA


title: M2 macrophages in coculture with CAFs and treated with Folfirinox replicate_2

description:
M2-CAF_FOLFI_rep2
M2 macrophages differentiated using M-CSF (5 days) and polarized by IL-4 and IL-13 in indirect coculture with primary PDAC CAFs for 48h and treated with 15uM Folfirinox


title: M2 macrophages replicate_3

description:
M2_CTRL_rep3
M2 macrophages differentiated using M-CSF (5 days) and polarized by IL-4 and IL-13

value: M2 macrophages control


title: Ire1af/f cortex 1

description: total RNA


title: M2 macrophages replicate_2

description:
M2_CTRL_rep2
M2 macrophages differentiated using M-CSF (5 days) and polarized by IL-4 and IL-13


title: Reactive+JSH23.ATACseq.C

data_processing:
Reads were quality and adaptor trimmed using cutadapt v2.9.
Trimmed reads were then aligned to the mm10 mouse genome using BWA v0.7.15-r1140, sorted and indexed using samtools v1.15.1.
Peaks were called while ignoring duplicates using GENRICH v0.5 in ATACseq mode.
Assembly: mm10
Supplementary files format and content: bed files and bigwig files

source_name: primary reactive astrocytes

extract_protocol:
Nuclei were extracted from cells and treated with transposition mixture containing Nextera Tn5 Transposase for 30 minutes at 37oC with 1000 RPM mixing. Transposed fragments were then purified using Qiagen MinElute columns, PCR amplified, and libraries were purified with Agencourt AMPure XP magnetic beads with a sample to bead ratio of 1:1.2.
Samples were sequenced on an Illumina NovaSeq with paired-end 50bp reads with 100 million reads per sample.

value: primary reactive astrocytes

value: reactive (treated with TNFa, IL1a, C1q) + 5uM JSH-23


title: M2 macrophages replicate_1

description:
M2_CTRL_rep1
M2 macrophages differentiated using M-CSF (5 days) and polarized by IL-4 and IL-13


title: Reactive+JSH23.ATACseq.B


title: D4_17_1

value: C57 mouse decidua

value: epithelium

value: normal pregnancy


title: LTBI_6609_6mo-Plasma IgA

description: IgA


title: KO_pos_33

city: Farmington

first: Marina

last: Yurieva

state: Connecticut

address: 10 Discovery dr

department: Computational Sciences

institute: Jackson Laboratory

description:
sample ID:
Run20.99

data_processing:
Library strategy: 16S rRNA-seq
Demultiplexing for the uploaded fastq files was performed in fastq-multx
Analyses of 16S sequencing data was performed using QIIME (version 1.9.1) on the original NOT demultiplexed fastq files.
Libraries were split using split_libraries_fastq.py script (result is in processed data file seqs.fna)
Samples were rarefied to 20000 reads using multiple_rarefactions.py  script
Assembly: Silva 123 SSURef Nr99
Supplementary files format and content: counts

organism: mouse gut metagenome

source_name: fecal material [ENVO_00002003]

growth_protocol: Frozen bacterial samples were resuspended in 400 µL staining buffer before adding 250 µL 0.1 mm zirconia/silica beads (Biospec), 300 µL Lysis buffer (200 mM NaCl, 200 mM Tris, 20 mM EDTA, pH 8), 200 µL 20% SDS and 500 µL phenol:chloroform:isoamyl alcohol (25:24:1,pH 7.9; Sigma). After incubation on ice for 4 minutes, bacterial cells were homogenized by 2 rounds of bead beating with 2 minutes of incubation on ice in between before centrifugation at 6000 g at 4oC. Aqueous phase was transferred to a Phase Lock Gel tube (Light; 5 PRIME) before an equal volume of phenol:chloroform:isoamyl alcohol was added.

extract_protocol:
Samples were mixed before centrifugation at 16,100 g for 3 minutes at room temperature. DNA precipitation was performed using 1/10 volume of 3 M NaOAc (pH5.5) and 1 volume Isopropanol to the aqueous phase before overnight incubation at 20o C. DNA precipitate was pelleted at 16,100g for 20 minutes at 4oC before washing in 500 µL of absolute EtOH, centrifugation was performed 16,100 g for 3 minutes at 4oC before DNA pellet was for 15 minutes with no heat (miVac GeneVac on Auto Run setting). Lastly, DNA pellet was resuspended in 100 µL of TE buffer (pH 7) and incubated at 50oC for 30 min. 35 U/ml RNase A was added to the DNA pellet before purification and elution in 40 µL Elution Buffer (QIAquick PCRpurification; QIAGEN).
16S rRNA sequencing of the V4 region and bacterial genome sequencing were performed on an Illumina miSeq using barcoded primers.

value: feces

tag: geographic location

value: USA:Farmington, Connecticut

tag: host

value: Mus musculus

tag: host genotype

value: DOCK8 homozygous

tag: iga status

value: positive

tag: molecule subtype


title: Ire1af/f Emx1Cre cortex 3

description: total RNA

tag: genotype

value: cerebral cortex


title: D4_10_2

tag: cell type

value: pregnancy day 4


title: LTBI_6609_Pre-BALF IgA

description: IgA

tag: infection states


title: LTBI_6709_2mo-BALF IgA

description: IgA


title: Reactive+RGFP966.ATACseq.B

value: reactive (treated with TNFa, IL1a, C1q) + 5uM RGFP966


title: LTBI_6609_6mo-BALF IgA

description: IgA

value: Asymptomatic controlled Mtb infection


title: LTBI_6609_Pre-Plasma IgA

description: IgA


title: Ire1af/f Emx1Cre cortex 2

description: total RNA

tag: strain


title: MDA-MB-231-miRNA-shUSP7shDICER-rep2

city: Shanghai

first: Jianxiu

last: Yu

address: Room 202, Building 7, 280 South Chongqing Road

department: Department of Biochemistry and Molecular Cell Biology

institute: Shanghai Jiao Tong University school of medicine

data_processing:
For DU145 mRNA data, paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3).  The high quality reads were aligned to the human reference genome (UCSC hg19) with hisat2 software (v2.0.4). Then, guided by the Ensembl gtf gene annotation file, cuffdiff software (v2.2.1, part of cufflinks) was used to get the FPKM as the expression profiles of LncRNA and mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed LncRNA and mRNA were identified. LncRNA target genes were predicted by the locations to nearby genes. And GO and Pathway analysis were performed on these target genes. GO and Pathway enrichment analysis were also performed based on the differentially expressed mRNAs.
For MDA-MB-231 mRNA data, paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the reference genome (UCSC HG19) with hisat2 software (v2.0.4). Then, guided by the Ensembl gtf gene annotation file, cuffdiff software (part of cufflinks) was used to get the gene level FPKM as the expression profiles of mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed mRNA were identified. GO and Pathway enrichment analysis were performed based on the differentially expressed mRNAs.
For DU145 miRNA data, raw data were generated after sequencing, image analysis, base calling and quality filtering on Illumina sequencer. Firstly, Q30 was used to perform quality control. The adaptor sequences were trimmed and the adaptor-trimmed-reads (>= 15nt) were left by cutadapt software (v1.9.2). Then, trimmed reads from all samples were pooled, and miRDeep2 software (v2.0.0.5) was used to predict novel miRNAs. The trimmed reads were aligned to the merged human pre-miRNA databases (known pre-miRNA from miRBase plus the newly predicted pre-miRNAs) using Novoalign software (v3.02.12) with at most one mismatch. The numbers of mature miRNA mapped tags were defined as the raw expression levels of that miRNA. The read counts were normalized by TPM (tag counts per million aligned miRNAs) approach.
For MDA-MB-231 miRNA data, raw data were generated after sequencing, image analysis, base calling and quality filtering on Illumina sequencer. Firstly, Q30 was used to perform quality control. The adaptor sequences were trimmed and the adaptor-trimmed-reads (>= 15nt) were left by cutadapt software (v1.9.3). Then, trimmed reads from all samples were pooled, and miRDeep2 software (v2.0.0.5) was used to predict novel miRNAs. The trimmed reads were aligned to the merged human pre-miRNA databases (known pre-miRNA from miRBase plus the newly predicted pre-miRNAs) using Novoalign software (v3.02.12) with at most one mismatch. The numbers of mature miRNA mapped tags were defined as the raw expression levels of that miRNA. The read counts were normalized by TPM (tag counts per million aligned miRNAs) approach.
Assembly: hg19 for RNA-Seq, miRBase for miRNA-Seq

extract_protocol:
RNA was extracted from total cell lysates.
RNA and miRNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line


title: KO_neg_33

description:
sample ID:
Run20.98

value: negative


title: Reactive+RGFP966.ATACseq.A


title: KO_pre_33

description:
sample ID:
Run20.97

value: pre-sorted


title: Reactive.ATACseq.C

value: reactive (treated with TNFa, IL1a, C1q)


title: MDA-MB-231-miRNA-shUSP7shDICER-rep1


title: LTBI_6609_2mo-Plasma IgA

description: IgA


title: LTBI_6709_2mo-Plasma IgA

description: IgA


title: Reactive+RGFP966.ATACseq.C

value: primary reactive astrocytes


title: LTBI_6609_2mo-BALF IgA

description: IgA


title: Reactive+JSH23.ATACseq.A

value: reactive (treated with TNFa, IL1a, C1q) + 5uM JSH-23


title: KO_pos_32

description:
sample ID:
Run20.96


title: KO_neg_32

description:
sample ID:
Run20.95


title: MDA-MB-231-miRNA-shUSP7-rep2


title: MDA-MB-231-miRNA-pLKO.1-rep2


title: Reactive.ATACseq.B


title: LTBI_6509_Pre-BALF IgA

description: IgA


title: LTBI_6509_Pre-Plasma IgA

description: IgA


title: Reactive.ATACseq.A


title: MDA-MB-231-miRNA-pLKO.1-rep1


title: Resting.ATAC.C

source_name: primary resting astrocytes

value: primary resting astrocytes

value: resting (untreated)


title: Resting.ATAC.A


title: KO_neg_31

description:
sample ID:
Run20.92


title: KO_pos_31

description:
sample ID:
Run20.93


title: MDA-MB-231-mRNA-shUSP7shDICER-rep2


title: Resting.ATAC.B


title: LTBI_6509_6mo-Plasma IgA

description: IgA


title: MDA-MB-231-mRNA-shUSP7shDICER-rep1


title: KO_pre_31

description:
sample ID:
Run20.91


title: LTBI_6509_6mo-BALF IgA

description: IgA


title: LTBI_6509_2mo-Plasma IgA

description: IgA


title: MDA-MB-231-mRNA-shUSP7-rep2


title: non-lesional ear skin from MRL/+ control mice [HC_MRL_3_S21]

city: New York

first: HSS Genomics

last: Research Center

state: New York

address: 535 E 70th St

department: Research

institute: Hospital for Special Surgery

data_processing:
fastp -q 15 -n 10 -l 20 –detect_adapter_for_pe  -i target_R1.fastq -I target_R2.fastq (fastp v0.19.10)
STAR --readFilesIn target_R1.fastq target_R2.fastq --outSAMtype BAM Unsorted --outFilterMultimapNmax 4 --outFilterType BySJout --outSAMmultNmax 1 --outFilterMismatchNoverReadLmax 0.1 --outSAMstrandField intronMotif --sjdbGTFfile gencode_v33.gtf --outReadsUnmapped Fastx (STAR v2.7.3a)
samtools sort -n target_STAR.Aligned.out.bam | samtools fixmate -rm - - | samtools sort - | samtools markdup -l 800 -rs – target_STAR.Aligned.sortedByCoord.out.bam (samtools v1.9)
featureCounts -p -a gencode_v33.gtf -s 2 -o reverse_stranded.txt target_STAR.Aligned.sortedByCoord.out.bam (featureCounts v2.0.1)
Assembly: mm10
Supplementary files format and content: Tab Separated File containing gene level counts per sample

source_name: ear skin biopsy

growth_protocol: Mice were either bred in-house or purchased from Jackson Laboratory: MRL/+(#000486) and MRL/lpr mice (#000485), B6.Sle1yaa mice (021569) and their B6 controls were either bred in-house or  purchased from Jackson Laboratory.

extract_protocol:
Female MRL/+ and MRL/lpr 12-14 weeks old and 6 month old B6 and B6.Sle1yaa male mice were used for RNA sequencing. RNA was extracted from ear skin using an RNEasy Kit (Qiagen, Germantown, MD) and quality confirmed on a BioAnalyzer 2100 (Agilent Technologies, Santa Clara, CA)
Libraries were prepared with non-stranded and poly-A selection TruSeq RNA Sample Preparation kits. Sequencing libraries were sequenced by the Genomics Core Facility at Weill Cornell Medicine using a HiSeq 2500 (MRL/lpr, MRL/+ samples) and NovaSeq (B6, B6.Sle1yaa) at a depth of 15-30 million mappable paired-end reads per sample.

treatment_protocol: No treatment was applied

value: ear skin biopsy

value: MRL/+

value: 12 weeks

tag: Sex

value: Female


title: LTBI_6509_2mo-BALF IgA

description: IgA


title: MDA-MB-231-miRNA-shUSP7-rep1


title: MDA-MB-231-mRNA-shUSP7-rep1


title: KO_pre_32

description:
sample ID:
Run20.94

value: feces

value: USA:Farmington, Connecticut

value: Mus musculus

value: DOCK8 homozygous


title: MDA-MB-231-mRNA-pLKO.1-rep2


title: Het_neg_30

description:
sample ID:
Run20.89

value: DOCK8 heterozygous


title: Het_pos_29

description:
sample ID:
Run20.87

value: positive


title: Het_pre_30

description:
sample ID:
Run20.88


title: non-lesional ear skin from MRL/+ control mice [HC_MRL_1_S19]


title: non-lesional ear skin from MRL/+ control mice [14_MRL_5_S36]

value: 14 weeks


title: non-lesional ear skin from MRL/+ control mice [HC_MRL_2_S20]


title: LTBI_6309_Pre-Plasma IgA

description: IgA

source_name: Pre-Plasma

value: Asymptomatic controlled Mtb infection


title: MDA-MB-231-mRNA-pLKO.1-rep1


title: Het_neg_29

description:
sample ID:
Run20.86

value: negative


title: LTBI_6309_Pre-BALF IgA

description: IgA

source_name: Pre-BALF


title: Het_pos_30

description:
sample ID:
Run20.90


title: LTBI_6309_6mo-BALF IgA

description: IgA


title: non-lesional ear skin from MRL/+ control mice [14_MRL_3_S34]


title: non-lesional ear skin from MRL/+ control mice [14_MRL_2_S33]


title: non-lesional ear skin from MRL/+ control mice [14_MRL_4_S35]


title: non-lesional ear skin from MRL/+ control mice [HC_MRL_4_S22]


title: FG; PRDM1KD ; Lib515

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

data_processing:
Sequencing reads were aligned to hg38 and dm6 combined genome using STAR aligner. Only uniquely and concordantly aligned read pairs were used for downstream analysis. Read count mapped to each gene was measured using featureCounts with options ‘-O --fracOverlap 0.8’. For spike-in controlled analysis, reads mapped to drosophila genes were also counted using the same method.
Assembly: hg38 & dm6
Supplementary files format and content: Excel file containing read counts per genes. Columns names matche with sample titles. Drosophila genes are prefixed by "dm-"

source_name: Human induced pluripotent stem cells (72.3, male, RRID: CVCL_A1BW)

extract_protocol:
1 million cultured cells were dissociated to single cells with Accutase and were mixed with 100,000 of Drosophila Schneider 2 (S2) cells for a spike-in control. Cells were pelleted and lysed with Aurum Total RNA Lysis Solution (BioRad # 7326802). Total RNA was extracted by Aurum™ Total RNA Mini Kit (BioRad #7326820) and sent to Novogene for library preparation and paired-end-150bp sequencing on an Illumina NovaSeq 6000.
Novogene performed the library construction

value: Human induced pluripotent stem cells (72.3, male, RRID:CVCL_A1BW)

value: Foregut

tag: treatment


title: Het_pre_29

description:
sample ID:
Run20.85

value: pre-sorted


title: FG; Ctrl ; Lib514

value: Ctrl


title: Het_pos_28

description:
sample ID:
Run20.84


title: non-lesional ear skin from MRL/+ control mice [14_MRL_1_S32]

value: ear skin biopsy


title: Het_neg_28

description:
sample ID:
Run20.83


title: FG; PRDM1KD ; Lib513


title: Het_pos_27

description:
sample ID:
Run20.81


title: PM; OCT4KD ; Lib348

value: Paraxial mesoderm


title: Het_pre_28

description:
sample ID:
Run20.82


title: non-lesional ear skin from MRL/lpr SLE mouse model [HC_Ipr_2_S24]

value: MRL/MpJ-Faslpr/J

value: 12 weeks


title: non-lesional ear skin from MRL/lpr SLE mouse model [HC_Ipr_4_S26]

value: Female


title: PM; OCT4KD ; Lib345


title: non-lesional ear skin from MRL/lpr SLE mouse model [HC_Ipr_3_S25]


title: Het_neg_27

description:
sample ID:
Run20.80

value: feces

value: USA:Farmington, Connecticut


title: Ex-Vivo human T-cells, 80BB scRNAseq

first: Michel

last: Sadelain

address: 1275 York Avenue, Box 182

institute: Memorial Sloan Kettering Cancer Cener

description: 10X Genomics

data_processing:
Raw fastq data was processed by Cell Ranger (v6.1.1) multi command with reference assembly GRCh38, to demultiplex cells to original hashtags and to obtain gene counts.
The two replicated were aggregated with Cell Ranger aggr command.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: mouse bone marrow

extract_protocol:
For single-cell RNA sequencing analysis, 5 Mice per group were injected with NALM6 tumour and treated with 1?×?1e5 or 5?×?1e4 19-HIT+ T cells per mouse on day 4 post tumour injection. On day 9 post T cell injection, bone marrow cells were isolated.Cells from mice within one condition were pooled and labelled with PE mouse anti-human CD45 (2D1, Biolegend) and TotalSeq™-B0251 anti-human Hashtag 1 Antibody (Biolegend) in 19-HIT treated mice or TotalSeq™-B0254 anti-human Hashtag 4 Antibody (Biolegend) in 19-HIT80BB treated mice.  Cells were FACS sorted for CD45+ GFP- cells (human T cells, excluding NALM6).  Cells from different conditions were pooled together at a balanced ratio and submitted for 10X 3’ RNA sequencing.
Cells were stained with Trypan blue and Countess II Automated Cell Counter (ThermoFisher) was used to assess both cell number and viability. Following QC, the single cell suspension was loaded onto Chromium Next GEM Chip G (10X Genomics PN 1000120) and GEM generation, cDNA synthesis, cDNA amplification, and library preparation of 15-21,000 cells proceeded using the Next GEM Single Cell 3’ Kit v3.1 (10X Genomics PN 1000268) according to the manufacturer’s protocol. cDNA amplification included 11 cycles and 10 µL of the material was used to prepare sequencing libraries with 8-10 cycles of PCR.

value: mouse bone marrow

value: human HIT T-cell

value: HIT or HIT 80BB


title: PM; Ctrl ; Lib352


title: Het_pre_27

description:
sample ID:
Run20.79

value: Mus musculus

value: DOCK8 heterozygous


title: PM; Ctrl ; Lib351


title: FG; Ctrl ; Lib512


title: non-lesional ear skin from MRL/lpr SLE mouse model [14_lpr_4_S40]

value: 14 weeks


title: non-lesional ear skin from MRL/lpr SLE mouse model [HC_Ipr_1_S23]


title: NE 3D; OCT4KD ; Lib350

value: Human induced pluripotent stem cells (72.3, male, RRID:CVCL_A1BW)

value: Neuroectoderm


title: Het_neg_26

description:
sample ID:
Run20.77

value: negative


title: Het_pre_26

description:
sample ID:
Run20.76

value: pre-sorted


title: non-lesional ear skin from MRL/lpr SLE mouse model [14_lpr_3_S39]

value: ear skin biopsy


title: NE 3D; OCT4KD ; Lib349


title: non-lesional ear skin from MRL/lpr SLE mouse model [14_lpr_2_S38]


title: LTBI_4808_2mo-BALF IgA

description: IgA

data_processing: Spots were considered reactive if the ratio of the median fluorescent intensity (MFI) of the gene was greater than 1.4 x the median of negative control genes

extract_protocol: Plasma was obtained from peripheral blood samples and the BAL procedure was performed as previously described via direct visualization of the airway and lavage of ~ 40 ml normal saline (0.9%). Animal protocols and procedures were approved by the University of Pittsburgh’s Institutional Animal Care and Use Committee before the collection of samples.

value: Asymptomatic controlled Mtb infection


title: LTBI_6309_2mo-Plasma IgA

description: IgA


title: LTBI_23010_Pre-Plasma IgA

description: IgA


title: LTBI_6309_2mo-BALF IgA

description: IgA


title: NE 3D; FOXAKD ; Lib340

value: FOXAKD


title: LTBI_4808_Pre-BALF IgA

description: IgA


title: LTBI_23010_2mo-Plasma IgA

description: IgA


title: LTBI_4808_2mo-Plasma IgA

description: IgA


title: LTBI_22810_Pre-BALF IgA

description: IgA


title: LTBI_23010_Pre-BALF IgA

description: IgA


title: LTBI_23010_2mo-BALF IgA

description: IgA


title: non-lesional ear skin from MRL/lpr SLE mouse model [14_lpr_1_S37]

value: MRL/MpJ-Faslpr/J


title: LTBI_22810_2mo-Plasma IgA

description: IgA


title: Het_pos_26

description:
sample ID:
Run20.78

value: positive


title: LTBI_22810_2mo-BALF IgA

description: IgA


title: NE 3D; FOXAKD ; Lib336


title: NE 3D; Ctrl ; Lib339

value: Ctrl


title: WT_neg_25

description:
sample ID:
Run20.74

value: feces

value: USA:Farmington, Connecticut

value: Wild type


title: LTBI_22810_Pre-Plasma IgA

description: IgA


title: LTBI_22710_3mo-Plasma IgA

description: IgA


title: LTBI_22710_3mo-BALF IgA

description: IgA


title: WT_pre_25

description:
sample ID:
Run20.73


title: LTBI_21910_Pre-Plasma IgA

description: IgA


title: WT_neg_24

description:
sample ID:
Run20.71


title: ME (APS); OCT4KD ; Lib343

value: Mesendoderm


title: WT_pre_24

description:
sample ID:
Run20.70

value: Mus musculus


title: DE; OCT4KD ; Lib347

value: Definitive endoderm


title: WT_pos_25

description:
sample ID:
Run20.75


title: Reactive Astrocytes

description: Primary mouse astrocytes exposed to TNFa, Il1a, and C1q for 24hrs.

data_processing:
Final libraries were sequenced on an Illumina HiSeq 2500 with a read depth of at least 50,000 reads per cell.
Cell Ranger 2.1 was used to align reads to mm10.
Clustering and differential expression analysis was performed using the publicly available Seurat package in R.
Genome_build: mm10
Supplementary_files_format_and_content: 10x Genomics output

source_name: Cortex

extract_protocol:
Cells were prepared for single cell RNAseq according to 10x Genomics sample preparation instructions.
Single cell libraries were prepared according to 10x Genomics instructions for Chormium Single-Cell 3' v2 Chemistry Kit.

value: TNFa, IL1a, C1q

value: Cortex

value: astrocyte


title: NE 3D; Ctrl ; Lib335

value: Human induced pluripotent stem cells (72.3, male, RRID:CVCL_A1BW)

value: Neuroectoderm


title: WT_pos_24

description:
sample ID:
Run20.72


title: WT_pos_23

description:
sample ID:
Run20.69


title: ME (APS); OCT4KD ; Lib346


title: Resting Astrocytes

description: Primary mouse astrocytes.


title: LTBI_21910_Pre-BALF IgA

description: IgA


title: WT_neg_23

description:
sample ID:
Run20.68

value: negative


title: WT_pre_23

description:
sample ID:
Run20.67

value: pre-sorted


title: LTBI_21810_Pre-Plasma IgA

description: IgA

value: Asymptomatic controlled Mtb infection


title: hPSC; OCT4KD 3D ; Lib171

value: Pluripotent stem cells

value: OCT4KD 3Day


title: hPSC; OCT4KD 3D ; Lib168


title: LTBI_21910_2mo-BALF IgA

description: IgA


title: LTBI_21910_2mo-Plasma IgA

description: IgA


title: VT1 cells, 3h BOLD-100 treatment n3

city: Belfast

first: Daryl

last: Griffin

address: 97 Lisburn Road

institute: Queens University, Belfast

data_processing:
Paired 91 end sequencing was conducted with a sequencing depth of 50 million reads, resulting in 75-base pair reads.
Assembly: reads were trimmed based on Phred score from the 3-prime end and then aligned to the human genome (hg38) using TopHat21  (version 2.1.0) with default settings.
Supplementary files format and content: Merged_raw_counts.txt

source_name: Colon adenocarcinoma

growth_protocol: Standard culture conditions

extract_protocol:
total RNA was extracted using RNeasy Mini Kit (Qiagen), according to the manufacturer’s protocol
library preparation was performed with 100ng RNA (Illumina NextSeq 500 kit, Illumina, UK)  according to the manufacturer's instructions. using the KAPA RNA HyperPrep Kit with RiboErase (HMR) (Roche, USA).

treatment_protocol: Control - No treatment, 3H - Treatment with 24µM BOLD-100 for 3 hours, 24H - Treatment with 24µM BOLD-100 for 24 hours.

value: Colon adenocarcinoma

value: BRAFWT/-

value: 24µM BOLD-100 3hours


title: VT1 cells, 3h BOLD-100 treatment n2


title: VT1 cells, 24h BOLD-100 treatment n2

value: 24µM BOLD-100 24hours


title: VT1 cells, 24h BOLD-100 treatment n3


title: VT1 cells, 3h BOLD-100 treatment n1


title: VT1 cells, 24h BOLD-100 treatment n1


title: WT_pos_22

description:
sample ID:
Run20.66

value: feces

value: USA:Farmington, Connecticut

value: Wild type

value: positive


title: VT1 cells, Control n3

value: Control


title: ME (APS); FOXAKD ; Lib9

value: Mesendoderm

value: FOXAKD


title: hPSC; OCT4KD 3D ; Lib165

value: Human induced pluripotent stem cells (72.3, male, RRID:CVCL_A1BW)


title: DE; OCT4KD ; Lib344

value: Definitive endoderm


title: VT1 cells, Control n2


title: VT1 cells, Control n1


title: ME (APS); FOXAKD ; Lib7


title: VACO432 cells, 24h BOLD-100 treatment n3


title: VACO432 cells, 24h BOLD-100 treatment n2


title: ME (APS); FOXAKD ; Lib5


title: WT_neg_22

description:
sample ID:
Run20.65

value: Mus musculus

value: negative


title: WT_neg_21

description:
sample ID:
Run20.62


title: WT_pre_22

description:
sample ID:
Run20.64

value: pre-sorted


title: WT_pos_21

description:
sample ID:
Run20.63