title: T cells from donor 3 cultured in hypoxia-rep2

first: Gokce

last: OGUZ

address: 60 Biopolis St, GENOME, #02-01

department: Bioinformatics Consulting and Training Platform

institute: Genome Institute of Singapore

data_processing:
raw fastq files were examined for quality using FastQC (v0.11.9) and MultiQC (v1.10)
paired fastq files were aligned to human genome hg38 using HISAT2(v2.2.1).
count were quantified from BAM files using featureCounts(v2.0.2)
Genome_build: hg38
Supplementary_files_format_and_content: TPM normalized gene count in csv format

source_name: human PBMC

extract_protocol: Human pan-T cells were collected from co-culture and lysed directly with Trizol (Invitrogen) as described above. Total RNA was isolated and purified with the RNeasy Mini Kit (Qiagen, USA). The RNA samples were sent to Novogene AIT (Singapore) for sequencing and mRNA library generation.

value: Hypoxia

value: Human T cells


title: KS_Rep2

status: Public on Jun 21 2022

type: SRA

city: La Jolla

first: Yunjiang

last: Qiu

state: CA

address: 9500 Gilman Drive

country: USA

institute: University of California, San Diego

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software was used for basecalling.
Reads were aligned to the hg19 reference genome using STAR 2.4.2a with default parameters.
Only uniquely mapped reads were kept for further analysis.
FPKM values for each gene were computed using cufflinks v2.2.1 with default parameters according to Gencode human annotation release 24.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values

molecule: total RNA

organism: Homo sapiens

source_name: U87-MG cells

growth_protocol: Cells were cultured in DMEM supplemented with 10% FBS.

extract_protocol:
Total RNAs were extracted by TRIzol (Thermo Fisher Scientific) from U87-MG cells with or without SEMA3s treatment.
The resulting RNA was then used to prepare libraries using Illumina TruSeq Stranded mRNA Library Prep Kit Set A (Illumina, RS- 122-2101) or Set B (Illumina, RS-122-2102).

treatment_protocol: Cells were treated with 500 ng/ml recombinant SEMA3A proteins for 6 hours.

tag: genotype

value: KO

tag: treatment


title: KS_Rep3


title: T cells from donor 3 cultured in normoxia-rep2

city: Singapore

country: Singapore

value: Normoxia

tag: cell type


title: ADULT_DAY_3_rep1

type: RNA

city: Providence

first: Gerard

middle: J

last: Nau

state: RI

address: 593 Eddy St.

department: Medicine

institute: Alpert School of Medicine at Brown University

hyb_protocol: Labeled cRNA (1.65 µg) was hybridized to Whole Mouse Genome 4x44K microarrays (Agilent) following the manufacturer’s recommendations.  Array chambers were placed in a rotating hybridization oven (10 rpm, 65°C) for 17 hours. After hybridization, arrays were washed using pre-warmed (37°C) gene expression wash buffer 2 (Agilent) and scanned immediately in an Agilent G2565 microarray scanner

scan_protocol: Arrays were washed using pre-warmed (37°C) gene expression wash buffer 2 (Agilent) and scanned immediately in an Agilent G2565 microarray scanner.

data_processing: Summary expression files of each microarray scan were generated using limma: (a)  (backgroundCorrect(dat, method="normexp", offset=1)), then (b) normalized using  (normalizeBetweenArrays(dat$E, method="quantile")), then (c) the probe with the highest intensity (for a given gene) was selected as the representative of that gene.

organism: Mus musculus

source_name: Lung, ADULT, DAY, 3, rep1

label_protocol: Five hundred ng of total lung RNA was reverse transcribed to cDNA and processed to cyanine-3 labeled cRNA using the one-color Quick Amp Labeling Kit (Agilent) according to the product handbook.  Labeled cRNA samples were purified using the RNeasy mini kit (QIAGEN).  Cy-3 integration and cRNA amplification were assessed using spectrophotometry, and samples with approximately 10 pmole Cy3/ug cRNA integration and greater than 5 µg total cRNA yield were hybridized to arrays.

extract_protocol: Whole mouse lungs were homogenized in 2 ml MagNA lyser Green Bead tubes (Roche Applied Science) with 1 mL TRI-reagent (Molecular Research Center, Inc.) at 6000 rpm for 1 min.  Homogenates were transferred to 1.5 mL RNase-free safe-lock tubes (Eppendorf) containing 1 mL of TRI-Reagent (Molecular Research Center).  For RNA isolation with TRI-Reagent, the manufacturer’s protocol for phase separation and RNA precipitation were followed except that samples were placed at -80°C overnight after adding isopropanol. To complete the isolation, tubes were thawed on ice, RNA was pelleted by centrifugation (12,000 rpm, 45 min, 4°C), and pellets were washed twice with cold 75% RNase-free ethanol (1 mL, 12,000 rpm, 10 min, 4°C).  After removing the ethanol wash, RNA pellets were dried for 3-5 minutes on the bench top, and then resuspended in 50 µL RNase-free water.  RNA was stored at -80°C until microarray labeling.  RNA integrity was evaluated using the Agilent RNA 6000 Nano Kit and 2100 BioAnalyzer according to the product handbooks.  RNA quantity was measured using a DU 800 UV/Vis Spectrophotometer (Beckman Coulter).

treatment_protocol: Mice were anesthetized (ketamine and xylazine mix) and intranasally instilled with 50 μl of PBS containing 50-100 pfu of PR8.

tag: strain

value: BALB/c

tag: tissue

value: left lung

tag: Sex

value: Female

tag: age group

value: ADULT

tag: timepoint

value: DAY 3


title: T cells from donor 3 cultured in normoxia-rep1


title: AGED_DAY_3_rep1

source_name: Lung, AGED, DAY, 3, rep1

value: AGED


title: Pancreas_14dpa

city: Dresden

first: Prateek

last: Chawla

state: Saxony

address: Fetscherstrasse 105

department: CRTD

country: Germany

institute: TU Dresden

description:
10x Single Cell RNA Seq
mRNA

data_processing:
bcl2fastq_1: Pancreas_Control, Pancreas_2dpa and Pancreas_7dpa were run with bcl2fastq2 2.19.1.
bcl2fastq_2: Pancreas_0dap and Pancreas_14dpa were run with bcl2fastq2 2.20.0.
Reference build: Cellranger needs a reference. Here GRCz11 was used and 3 transgenic genes were added to avoid false alignments to the main references. The genes are YFP, mCherry and NTR.
Alignment: Processing of sequencing data was done with the cellranger pipeline (cellranger-4.0.0).
Genome_build: GRCz11
Supplementary_files_format_and_content: Tar archives contain the cellranger filtered feature barcode folder; the 3 files per folder are explained here: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/matrices

organism: Danio rerio

source_name: Zebrafish pancreas

extract_protocol:
Trypsin based dissociation followed by FACS sorting of alive cells.
Library prep was performed according to the 10x protocol.

tag: strain/background

value: AB

tag: genotype/variation

value: Wildtype, expressing NTR gene under the insulin promoter

value: Pancreatic cells

value: Pooled male and female

tag: age

value: Adult

value: MTZ treatment for 24 hours

tag: time point

value: Dissection at 14 days after MTZ


title: cDC2 flox rep2 (RNA-seq)

city: Lund

first: Jonas

last: Ungerback

address: Klinikgatan 26

department: Division of Molecular Hematology

country: Sweden

institute: Lund University

description:
analyzeRepeats_immuno_samples.raw_exon_counts.txt
cDC2_flox.rep2

data_processing:
RNA-seq: RNA-sequence pre-processing  RNA-sequenced reads were trimmed Trimmomatiic (v0.38) for removal of adapter –and low quality sequences. Resulting reads were then mapped onto the mouse genome build mm10 with STAR (v2.6.0) (Dobin et al, 2013)  and post-processed with RSEM (v. 1.2.30) (http://deweylab.github.io/RSEM/) (Li et al, 2011) according to the settings in the ENCODE long-rna-seq-pipeline (https://github.com/ENCODE-DCC/long-rna-seq-pipeline/blob/master/DAC/STAR_RSEM.sh) with the minor modifications that settings “--output-genome-bam --sampling-for-bam” was added to rsem-calculate-expression. STAR and RSEM reference libraries were created from genome build mm10 together with the Ensembl gene model file Mus_musculus.NCBIM37.66.gtf. The resulting bam-files were used to create HOMER tag directories (makeTagDirectory with –keepAll setting). For analysis of statistical significance among differentially expressed genes the raw gene counts were derived from each tag directory with analyzeRepeats.pl with the –noadj -condenseGenes options and tested for differential gene expression using the DESeq2 package ( https://www.bioconductor.org/packages/devel/bioc/html/DESeq2.html) (Love et al, 2014 #38) via HOMER getDifferentialExpression.pl.  t.
ATAC-seq: Reads were trimmed using Trimmomatic and mapped to mm10 (Gencode build GRCm38.p5) with Bowtie2 (v. 2.3.4) (Langmead et al, 2012). PCR duplicates were removed with Picard MarkDuplicates (v. 2.15.0) and files were further filtered for mapq score of 10 using Samtools (v. 1.7). Peak calling from the mapq10 filtered bam files (duplicates) was performed using the Kundaje lab ATAC-seq pipeline (https://www.encodeproject.org/pipelines/ENCPL792NWO/) with MACS2 and IDR (irreproducible discovery rate) threshhold set to 0.05 and 0.1, respectively. Samtools was used to remove mitochondrial reads prior to peak calling. From each processed duplicate, the Optimal peak set was used for downstream analysis.
Genome_build: mm10 (GRCm38.p5)
Supplementary_files_format_and_content: RNA-seq: Raw count matrix derived with HOMER tools analyzeRepeats.pl rna mm10 -condenseGenes -count exons -raw -d {path-to-tagdirs}    ATAC-seq: IDR-processed MACS2 peak file. Filtered bam-files were processed with Kundaje lab ATAC-seq pipeline (https://www.encodeproject.org/pipelines/ENCPL792NWO/) with MACS2 and IDR (irreproducible discovery rate) threshhold set to 0.05 and 0.1, respectively.

source_name: conventional dendritic cell

extract_protocol:
RNA-seq: Cells were FACS sorted based on the following surface parameters. Common pre-gate to all samples: Live, Singlets, CD11c+ Lin- (CD19, TCRb, B220, NK1.1). cDC1_migratory_XCR1Cre+_IRF4_flox (MHC-II high GFP+ XCR1+ CD11b-); cDC1_migratory_XCR1Cre-_IRF4_flox (MHC-II high XCR1+ CD11b-); cDC1_resident_XCR1Cre+_IRF4_flox (MHC-II low GFP+ XCR1+ CD11b-); cDC1_resident_XCR1Cre-_IRF4_flox (MHC-II low XCR1+ CD11b-); cDC1_wt (MHC-II hi YFP+); cDC2_wt (MHC-II hi YFP- CD11b+); ex_cDC1 (MHC-II hi YFP+); cDC2_flox (MHC-II hi YFP- CD11b+); DKO ( MHC-II hi YFP+); RNeasy Micro Kit  according to manufacturers protocol (Qiagen) and analyzed on an Agilent 2100 Bioanalyzer with the RNA 6000 nano kit (Agilent).   ATAC-seq: Briefly, sorted cells (same populations as in RNA-seq: cDC1, cDC2_wt, ex_cDC1 and cDC2_flox) were rinsed with resuspension buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl and 3 mM MgCl2 in sterile water), lysed and immediately after added tagmentation reaction mix from the Nextera DNA library preparation kit (Illumina). After 30  min incubation at 37C, samples were cleaned up using MinElute PCR purification kit (Qiagen). The libraries were constructed and barcoded using a Nextera library preparation kit (Illumina). The final amplified libraries were purified and size-selected (x1.2 bead-to-DNA ratio for ~100-150bp cutoff DNA size) using SPRI select (Beckman-Coulter). Each biological sample was run in triplicates. Libraries were sequenced paired-end on HiSeq2500 (Illumina) using 50 cycles paired-end mode (Illumina).
RNA-seq: RNA was extracted with RNeasy Micro kit (Qiagen). Revere transcription and amplification was performed using Ovation RNA-Seq System V2 kit (NuGEN). Amplified cDNA was purified using the MinElute Reaction Cleanup kit (Qiagen). Final librariers were constructed and indexed with the Ovation Ultralow system V2 kit (NuGEN) and quantified by Agilent 2100 Bioanalyzer (High sensitivity DNA kit).    ATAC-seq:  ATAC-seq library preparation was done as described in (Corces et al. 2017) using Transposomes from Nextera DNA library preparation kit (Illumina) and custom primers. Libraries were run paired-end on the Illumina HiSeq2500.

value: XCR1-cre.Irf8fl/fl. R26R.EYFP

value: mesenteric lymph nodes

value: 8-16 weeks


title: ADULT_DAY_3_rep2

source_name: Lung, ADULT, DAY, 3, rep2


title: AGED_DAY_1_rep3

source_name: Lung, AGED, DAY, 1, rep3

value: DAY 1


title: ex_cDC1_IRF4_IRF8.DKO.rep1 (RNA-seq)

description:
analyzeRepeats_immuno_samples.raw_exon_counts.txt
ex_cDC1_IRF4_IRF8.DKO.rep1


title: T cells from donor 1 cultured in hypoxia-rep2

value: Hypoxia

value: Human T cells


title: KC_Rep1

value: KO


title: cDC2 flox rep1 (RNA-seq)

description:
analyzeRepeats_immuno_samples.raw_exon_counts.txt
cDC2_flox.rep1


title: Pancreas_2dpa

description:
10x Single Cell RNA Seq
mRNA

value: Dissection at 2 days after MTZ


title: DC1 wt rep2 (ATAC-seq)

description: DC1_wt_out_ppr.IDR0.1.filt.no_chrY.narrowPeak

library_source: genomic

molecule: genomic DNA

value: XCR1-cre. R26R.EYFP

value: 12 weeks


title: ex cDC1 rep3+B42:B43 (RNA-seq)

description:
analyzeRepeats_immuno_samples.raw_exon_counts.txt
ex_cDC1.rep3


title: T cells from donor 1 cultured in hypoxia-rep1


title: Pancreas_0dpa

description:
10x Single Cell RNA Seq
mRNA

value: AB

value: Dissection at 0 days after MTZ


title: T cells from donor 1 cultured in normoxia-rep2

value: Normoxia


title: Pancreas_Control

description:
10x Single Cell RNA Seq
mRNA

value: Wildtype, expressing NTR gene under the insulin promoter

value: Pancreatic cells

value: Pooled male and female

value: Untreated


title: cDC2 flox rep3 (RNA-seq)

description:
analyzeRepeats_immuno_samples.raw_exon_counts.txt
cDC2_flox.rep3

value: XCR1-cre.Irf8fl/fl. R26R.EYFP


title: ex cDC1 rep2 (RNA-seq)

description:
analyzeRepeats_immuno_samples.raw_exon_counts.txt
ex_cDC1.rep2

value: mesenteric lymph nodes


title: AGED_DAY_1_rep1

source_name: Lung, AGED, DAY, 1, rep1

value: BALB/c

value: left lung

value: Female

value: AGED


title: T cells from donor 3 cultured in hypoxia-rep1

value: Hypoxia

value: Human T cells


title: T cells from donor 1 cultured in normoxia-rep1


title: Pancreas_7dpa

description:
10x Single Cell RNA Seq
mRNA

value: Adult

value: MTZ treatment for 24 hours

value: Dissection at 7 days after MTZ


title: ADULT_DAY_1_rep3

source_name: Lung, ADULT, DAY, 1, rep3

value: ADULT

value: DAY 1


title: AGED_DAY_1_rep2

source_name: Lung, AGED, DAY, 1, rep2


title: T cells from donor 2 cultured in hypoxia-rep2


title: T cells from donor 2 cultured in hypoxia-rep1


title: cDC2 wt rep3 (RNA-seq)

description:
analyzeRepeats_immuno_samples.raw_exon_counts.txt
cDC2_wt.rep3

value: XCR1-cre. R26R.EYFP

value: 8-16 weeks


title: EVnega_rep3

city: Nagoya

first: Hiroshi

middle: I.

last: Suzuki

address: 65 Tsurumai-cho, Showa-ku

department: DIvision of Molecular Oncology, Graduate School of Medicine

country: Japan

institute: Nagoya University

data_processing:
RNAseq samples were analyzed by NovaSeq 6000 instrument (Illumina).
The sequencing reads were aligned to the reference genome (rn6) using STAR (v2.5.3). Reads on each refSeq gene were counted with HTSeq (v0.6.0) using intersection-strict mode, and edgeR package in R was used to identify the differentially expressed genes with FDR threshold of 0.1. After filtering out genes with a maximum count per million (CPM) across all samples less than 1, trimmed mean of M-values normalization (TMM) method and generalized linear models were used to compare gene expression data.
Genome_build: rn6
Supplementary_files_format_and_content: Summary txt file includes normalized CPM values.

organism: Rattus norvegicus

source_name: M2 macrophage

growth_protocol: Rat anti-inflammatory macrophages were collected by flowcytometry for four groups including control (physiological condition), GN (glomerulonephritis condition without ASCs treatment), EVs+ (EVs transferred condition under glomerulonephritis), and EVs− (EVs untransferred condition under glomerulonephritis)

extract_protocol:
RNA was extracted using RNeasy Plus Micro Kit (Qiagen).
Libraries for RNA-seq were prepared using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech) and Nextera XT DNA Library Prep Kit (Illumina) and were subjected to paired-end sequencing using NovaSeq 6000 instrument (Illumina).

treatment_protocol: Cells were directly subjected to RNA-seq analysis.

value: WKY /Ncrj

value: M2 macrophage

tag: disease condition

value: GN (nephritis), EV-negative


title: ex cDC1 rep1 (RNA-seq)

description:
analyzeRepeats_immuno_samples.raw_exon_counts.txt
ex_cDC1.rep1

value: XCR1-cre.Irf8fl/fl. R26R.EYFP

value: mesenteric lymph nodes


title: EVnega_rep2


title: cDC2 wt rep1 (RNA-seq)

description:
analyzeRepeats_immuno_samples.raw_exon_counts.txt
cDC2_wt.rep1


title: a rabbit IUA sample with hUCB-MSCs transplantation

city: Zhengzhou

first: Yong

last: Zhang

state: State...

address: Tongbaibei NO.16 Zhongyuan district, Zhengzhou

country: China

institute: Zhengzhou University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The Cell Ranger software pipeline (version 5.0.0) provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells.
We processed the unique molecular identifier (UMI) count matrix using the R package Seurat(version 3.1.1).
Assembly: ribbit reference genome, oryCun2

organism: Oryctolagus cuniculus

source_name: The uterine mucosa

extract_protocol: The dually edited Mel-RM (Mel-RM.DE) cells were serum starved for 96 h and the endometrial quiescent cells were sorted, washed twice and re-suspended in cold PBS (calcium and magnesium free) with 0.04% FBS. Cell number and viability were determined using hemocytometer and Trypan Blue staining and 1´105 cells were subjected to10´ Genomics sequencing according to the manufacturer’s protocol by Shanghai OE Biotech co., LTD (Shanghai, China). Briefly, viable endometrial cells isolated from dually edited Mel-RM cells after serum starvation were analyzed using the 10´ Genomics Chromium Droplet platform with unique transcript counting through barcoding with unique molecular identifiers (UMIs). Cell Ranger 3.1.0 and Seurat 3.1.1 were used to analyze the sequencing results.

value: All cells

value: The uterine mucosa

value: New Zealand

value: 14 weeks old


title: T cells from donor 2 cultured in normoxia-rep2

value: Normoxia

value: Human T cells


title: EVnega_rep1


title: ADULT_DAY_1_rep2

source_name: Lung, ADULT, DAY, 1, rep2

value: BALB/c

value: left lung

value: Female


title: AGED_DAY_0_rep2

source_name: Lung, AGED, DAY, 0, rep2

value: AGED

value: DAY 0


title: ADULT_DAY_1_rep1

source_name: Lung, ADULT, DAY, 1, rep1

value: ADULT

value: DAY 1


title: EVposi_rep3

value: WKY /Ncrj

value: M2 macrophage

value: GN (nephritis), EV-positive


title: AGED_DAY_0_rep3

source_name: Lung, AGED, DAY, 0, rep3


title: EVposi_rep2


title: cDC1 wt rep2 (RNA-seq)

description:
analyzeRepeats_immuno_samples.raw_exon_counts.txt
cDC1_wt.rep2

value: XCR1-cre. R26R.EYFP

value: mesenteric lymph nodes

value: 8-16 weeks


title: EVposi_rep1


title: ADULT_DAY_0_rep3

source_name: Lung, ADULT, DAY, 0, rep3


title: B.1.351-ID24_2nd

city: Bethesda

first: Hye Kyung

last: Lee

state: MD

address: 8 CENTER DR RM 107

department: National Institute of Diabetes and Digestive and Kidney (NIDDK)

institute: National Institutes of Health (NIH)

data_processing:
RNA-seq data were trimmed using trimmomatic (Bolger et al., Bioinformatics, 2014) and subsequently aligned to the reference genome hg19 applying STAR RNA-seq aligner (Dobin et al., Bioinformatics, 2013). HTSeq(Anders et al., Bioinformatics, 2015) was applied for obtain HTSeq counts.
HTSeq(Anders et al., Bioinformatics, 2015) was applied for obtain HTSeq counts.
Genome_build: hg19
Supplementary_files_format_and_content: HTSeq counts from RNA-seq samples

molecule: polyA RNA

source_name: PBMCs

growth_protocol: Blood samples were collected from the COVID-19 patients infected by variant B.1.351.

extract_protocol:
The buffy coat was extracted by centrifuge after blood sample collection and RBC was removed using RBC lysis buffer in the buffy coat. Total RNA was isolated using a Maxwell RSC simply RNA Blood purification kit.
Libraries for sequencing were prepared with TruSeq Stranded mRNA Kit following standard Illumina protocols.

tag: gender

tag: disease state

value: COVID-19_B.1.351 varient

tag: severity

value: moderate

tag: geographical location

value: Ischgl, Austria

value: PBMC


title: ADULT_DAY_0_rep2

source_name: Lung, ADULT, DAY, 0, rep2

value: BALB/c


title: T cells from donor 2 cultured in normoxia-rep1

source_name: human PBMC

value: Normoxia

value: Human T cells


title: cDC1 wt rep3 (RNA-seq)

description:
analyzeRepeats_immuno_samples.raw_exon_counts.txt
cDC1_wt.rep3


title: B.1.351-ID24_3rd

value: Female


title: AGED_DAY_0_rep1

source_name: Lung, AGED, DAY, 0, rep1

value: left lung

value: AGED

value: DAY 0


title: GN_rep2

value: WKY /Ncrj

value: GN (nephritis)


title: cDC1 wt rep1 (RNA-seq)

description:
analyzeRepeats_immuno_samples.raw_exon_counts.txt
cDC1_wt.rep1

source_name: conventional dendritic cell


title: cDC1 resident XCR1Cre- IRF4 flox rep1 (RNA-seq)

description:
analyzeRepeats_immuno_samples.raw_exon_counts.txt
cDC1_resident_XCR1Cre-_IRF4_flox.rep1


title: B.1.351-ID24_1st


title: Control_rep2

value: M2 macrophage

value: control


title: B.1.351-ID14_1st


title: BM cells, Mx1-Cre Sf3b1-K700E: Inv(3)_rep3

city: Suita

first: Masaki

last: Nomura

state: Osaka

address: 2-2, Yamadaoka

department: Department of Cancer Pathology

institute: Graduate School of Medicine, The University of Osaka

data_processing:
bcl2fastq
nf-core/rnaseq 3.0
Genome_build: mm10
Supplementary_files_format_and_content: gene expression (counts, TPMs, FPKMs)

source_name: Lineage- cKit+ bone marrow cells in femora and tibiae

extract_protocol:
RNA was extracted using RNeasy columns (Qiagen) per manufacturer’s instructions.
RNA was poly(A)-selected, and unstranded Illumina libraries were prepared with the standard TruSeq protocol

treatment_protocol: Four weeks after BMT, the recipient mice received 20 mg/kg pIpC injection every other day for a total of 3 doses.

tag: donor genotype

tag: recipient genotype

tag: timing of preparation

value: 6 months after pIpC injection

value: bone marrow


title: cDC1 resident XCR1Cre- IRF4 flox rep3 (RNA-seq)

description:
analyzeRepeats_immuno_samples.raw_exon_counts.txt
cDC1_resident_XCR1Cre-_IRF4_flox.rep3

tag: strain

value: mesenteric lymph nodes

value: 8-16 weeks


title: B.1.351-ID14_2nd

value: COVID-19_B.1.351 varient

value: moderate

value: Ischgl, Austria

tag: cell type


title: cDC1 resident XCR1Cre+ IRF4 flox rep2 (RNA-seq)

description:
analyzeRepeats_immuno_samples.raw_exon_counts.txt
cDC1_resident_XCR1Cre+_IRF4_flox.rep2

tag: tissue


title: BM cells, Mx1-Cre Sf3b1-K700E: Inv(3)_rep2


title: cDC1 resident XCR1Cre+ IRF4 flox rep1 (RNA-seq)

description:
analyzeRepeats_immuno_samples.raw_exon_counts.txt
cDC1_resident_XCR1Cre+_IRF4_flox.rep1


title: ADULT_DAY_0_rep1

source_name: Lung, ADULT, DAY, 0, rep1

value: BALB/c

tag: Sex

tag: age group

value: ADULT


title: B.1.351-ID7_2nd

value: Male

value: severe

value: PBMC


title: cDC1 migratory XCR1Cre- IRF4 flox rep3 (RNA-seq)

description:
analyzeRepeats_immuno_samples.raw_exon_counts.txt
cDC1_migratory_XCR1Cre-_IRF4_flox.rep3


title: cDC2 wt rep2 (RNA-seq)

description:
analyzeRepeats_immuno_samples.raw_exon_counts.txt
cDC2_wt.rep2

value: XCR1-cre. R26R.EYFP


title: GN_rep1

value: WKY /Ncrj


title: BM cells, Mx1-Cre Sf3b1-K700E_rep3


title: B.1.351-ID6_3rd

value: Female


title: BM cells, Mx1-Cre Sf3b1-K700E: Inv(3)_rep1


title: B.1.351-ID7_1st


title: cDC1 resident XCR1Cre+ IRF4 flox rep3 (RNA-seq)

description:
analyzeRepeats_immuno_samples.raw_exon_counts.txt
cDC1_resident_XCR1Cre+_IRF4_flox.rep3


title: B.1.351-ID6_2nd


title: cDC1 migratory XCR1Cre- IRF4 flox rep2 (RNA-seq)

description:
analyzeRepeats_immuno_samples.raw_exon_counts.txt
cDC1_migratory_XCR1Cre-_IRF4_flox.rep2


title: B.1.351-ID6_1st


title: cDC1 resident XCR1Cre- IRF4 flox rep2 (RNA-seq)

description:
analyzeRepeats_immuno_samples.raw_exon_counts.txt
cDC1_resident_XCR1Cre-_IRF4_flox.rep2


title: Control_rep1

value: M2 macrophage


title: B.1.351-ID7_3rd


title: BM cells, Mx1-Cre Sf3b1-K700E_rep2


title: cDC1 migratory XCR1Cre- IRF4 flox rep1 (RNA-seq)

description:
analyzeRepeats_immuno_samples.raw_exon_counts.txt
cDC1_migratory_XCR1Cre-_IRF4_flox.rep1


title: B.1.351-ID5_4th


title: BM cells, Mx1-Cre Sf3b1-K700E_rep1


title: cDC1 migratory XCR1Cre+ IRF4 flox rep3 (RNA-seq)

description:
analyzeRepeats_immuno_samples.raw_exon_counts.txt
cDC1_migratory_XCR1Cre+_IRF4_flox.rep3


title: B.1.351-ID5_3rd


title: cDC1 migratory XCR1Cre+ IRF4 flox rep2 (RNA-seq)

description:
analyzeRepeats_immuno_samples.raw_exon_counts.txt
cDC1_migratory_XCR1Cre+_IRF4_flox.rep2


title: BM cells, Mx1-Cre Inv(3)_rep3


title: B.1.351-ID5_2nd


title: B.1.351-ID5_1st


title: cDC1 migratory XCR1Cre+ IRF4 flox rep1 (RNA-seq)

description:
analyzeRepeats_immuno_samples.raw_exon_counts.txt
cDC1_migratory_XCR1Cre+_IRF4_flox.rep1


title: BM cells, Mx1-Cre Inv(3)_rep1


title: WT-Veh-2WV

city: New York

first: Igor

last: Dolgalev

state: New York

address: 550 1st Ave

institute: NYU Grossman School of Medicine

description:
counts.raw.csv.gz
counts.normalized.csv.gz
counts.tpm.csv.gz

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
The sequencing reads were adapter- and quality-trimmed with Trimmomatic.
The sequencing reads were aligned to the mouse genome (build mm10/GRCm38) using the splice-aware STAR aligner.
The featureCounts program was utilized to generate counts for each gene.
The raw counts were normalized using the DESeq2 R package.
Genome_build: mm10
Supplementary_files_format_and_content: CSV files contain raw and normalized counts for all genes and samples.

source_name: Embryo

extract_protocol:
RNA was extracted from treated cells with MASM7 or MFI8 using Rneasy kit from Qiagen (#74104).  Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Embryonic Fibroblasts

value: Embryo

tag: treatment

value: Vehicle


title: BM cells, Mx1-Cre Inv(3)_rep2

value: 6 months after pIpC injection

value: bone marrow


title: BM cells, Mx1-Cre_rep3


title: EVI1_18_colony

data_processing:
RNA-seq rawdata was cleaned by FastP(PE mode) and aligned to GRCm38 by Hisat2(2.2.1)
Data were  filtered using Samtools and converted to BAM files
Read counted by FeatureCount from Subreads Packages(R)
Counts data was normalized by edgeR with significant differience genes were screened out
Assembly: GRCm38
Supplementary files format and content: raw counts, Differentially expressed gene Excel

source_name: Lineage- bone marrow cells in femora, tibiae and pelvis

growth_protocol: Lineage negative bone marrow cells isolated with MACS (Miltenyi) were precultured overnight and infected with pMYs-IG-EVI1-WT or +18 the next day. Three days after infection, 10,000 of GFP-sorted cells were cultured in Methocult M3434 (STEM CELL Technologies, #03434) for about 3 weeks.

extract_protocol:
RNA was extracted using RNeasy mini kit (Qiagen) following the manufacturer’s protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: transduced vector

tag: expression type

value: stably expressed

tag: expression level

value: retroviral overexpression


title: WT-MFI8-2WM


title: B.1.351-ID4_1st

tag: age

value: COVID-19_B.1.351 varient

value: Ischgl, Austria


title: B.1.351-ID3_3rd

tag: gender

value: mild


title: B.1.351-ID3_2nd

value: Male

tag: disease state


title: WT-MFI8-1WM


title: WT-Veh-1WV


title: EVI1_WT_colony


title: BM cells, Mx1-Cre_rep2


title: WT-MASM7-2WB


title: BM cells, Mx1-Cre_rep1


title: B.1.351-ID3_1st

tag: severity


title: CK2αfl/fldLck-Cre Rep 3

first: Wei

last: Yang

state: NY

address: Belfer Research Building,Room 760B,413 E. 69th Street

department: Department of Medicine

institute: Weill Cornell Medicine

data_processing:
Genewiz took the sequenced reads and trimmed to remove possible adapter sequences and nucleotides with poor quality bases (error rate < 0.05) at the ends. After trimming, sequence reads shorter than 30 nucleotides were discarded.
Genewiz took the remaining sequence reads and aligned to the Mus musculsus genome with CLC Genomics Server program. Gene hit counts were measured and RPKM values were calculated.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized counts of each genes for each samples

source_name: CD8+ T

growth_protocol: CD45.2 OT-I CK2αfl/fl and CD45.2 OT-I CK2α-/- CD8+ T-cells were transfer into CD45.1 B6 seperately, then host mice were infection with listeria monocytogenes-OVA for 7 days

extract_protocol:
CD45.2 CD8+ T were collected, centrifuged and washed for 3 times. Then RNA was isolated using the miRNeasy Mini Kit
RNA was sent to Genewiz for their standard library construction

value: Spleen

value: CD8+ T cell

tag: infection

value: Listeria monocytogenes infection

tag: genotype/variation

value: KO


title: CK2αfl/fldLck-Cre Rep 2


title: WT-MASM7-1WB


title: B.1.351-ID2_4th

value: Female

value: severe

tag: geographical location

value: PBMC


title: B.1.351-ID2_3rd


title: B.1.351-ID2_2nd


title: Adap-KO rep3

city: Suzhou

first: Hebin

last: Liu

address: 199 Renai Road

department: Institutes of Biology and Medical Sciences

institute: Soochow University

data_processing:
Illumina Casava1.8 software was used for basecalling.
Sequenced reads were aligned to mouse genome (mm10) using Hisat2 (v 2.0.5), and counted by featureCounts (v 1.5.0-p3).
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts and annotations for every gene in every sample

source_name: Splenic macrophage

extract_protocol:
RNA was extracted from splenic macrophages using Trizol reagent.
Sequencing library was prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina. The mRNA was enriched using the oligo (dT) magnetic beads, fragmented, and reversed-transcribed to cDNA using random hexamer primers and M-MuLV Reverse Transcriptase. Double strand cDNA was synthesized, added adenine at the 3’ end, and ligated with sequencing adaptors. The fragments were purified with AMPure XP system (Beckman Coulter), amplified by PCR and subjected to library quality control using the Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System.

tag: genotype

value: Adap-KO

value: Splenic macrophage


title: post_m01: Mouse 1 posterior jejunum

city: Mainz

first: Frank

last: Rühle

address: Ackermannweg 4

department: Bioinformatics Core Facility

institute: Institute of Molecular Biology (IMB)

data_processing:
Library strategy: MARS-Seq
Cell pool libraries were sequenced on an Illumina NextSeq500 machine in paired end mode with 69 bp read length for R1 and 16 bp for R2 (contains UMI and cell barcode).
Cell pool demultiplexing of MARS-Seq raw data was performed using Illumina’s bcl2fastq conversion software v.2.19.
UMI-tools v.1.0.0 was used to extract Unique Molecular Identifiers (UMI) and cell barcodes from R2 using the barcode pattern "CCCCCCCNNNNNNNN" and to add them to the respective R1 read name. Cell barcodes were filtered with a corresponding cell barcode whitelist.
Cutadapt v.1.18 was used to trim Illumina adapter sequences of raw reads and to remove a 5’ stretch of 5 random nucleotides.
Reads were to the mouse reference genome GRCm38 with STAR v.2.6.1b.
Cell-wise UMI deduplication and read summarization at gene level was performed using UMI-tools v.1.0.0.
Further downstream processing in R v3.5.1 included QC filtering of cells by removing cells with library sizes < 1,000 or > 50,000 (potential doublets) reads, detected features < 250 or portion of reads mapping to mitochondrial genes > 25%. Genes with no expression in 95% of the cells were filtered out.
Read counts were normalized using cell-specific size factors and log2-transformed as implemented in the scater R-package.
Data was adjusted for effects between sequenced batches and for cell cycle phase by using continuous G1/G2M scores estimated from expression data.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: QC-filtered matrix table with log normalized gene counts for every gene and every cell

source_name: small intestine

extract_protocol:
The mouse small intestines were dissected in 12 equal pieces. The 3rd (anterior jejunum) and 7th (posterior jejunum) parts were used for single cell RNA-sequencing. The small intestines were cut in pieces of 1 cm2, placed into 50 ml conical tubes and washed 3 times for 20 min with 25 ml of PBS/ 5 mM EDTA on a rocking plate at room temperature. Villi were mechanically removed by gentle shaking 3 times and trituration using a 25 ml pipette. Crypts were separated from the intestine by vigorous shaking 2 times. Both villi and crypts were collected by centrifugation at 200g for 5 min, washed twice with PBS. Cells from the villi and crypts were mixed at 1:1 ratio. To isolate epithelial cells, single cell suspensions were stained with APC–conjugated anti-EpCAM 1:1000 (eBioscience) antibody for 30 min at room temperature. Fluorescence-activated cell sorting was performed using BD FACS Aria III SORP cell sorter (100 μm nozzle). Living cells were gated by DAPI dye exclusion. Single EpCAM+ cells were sorted in 386 well plates.
Single cell libraries (pooled) were constructed using the MARS-Seq protocol as described by Jaitin DA, et al. Science 343, 776–9 (2014).

value: posterior jejunum

tag: background

value: mixed CD-1:C57BL/6

value: 120 days

value: small intestinal epithelial cells


title: post_m03: Mouse 3 posterior jejunum

tag: cell type


title: Adap-KO rep1

tag: strain

tag: tissue


title: post_m02: Mouse 2 posterior jejunum


title: CK2αfl/fldLck-Cre Rep 1


title: Adap-KO rep2


title: WT rep3

value: wild type


title: CK2αfl/fl Control Rep 3

value: WT


title: CK2αfl/fl Control Rep 2


title: ant_m03: Mouse 3 anterior jejunum

value: anterior jejunum


title: B.1.351-ID2_1st

value: COVID-19_B.1.351 varient

value: Ischgl, Austria


title: B.1.351-ID1_3rd

value: moderate


title: ant_m02: Mouse 2 anterior jejunum


title: CK2αfl/fl Control Rep 1

value: Spleen

value: CD8+ T cell

value: Listeria monocytogenes infection


title: ant_m01: Mouse 1 anterior jejunum


title: B.1.351-ID1_2nd

value: Female


title: WT rep2


title: WT rep1


title: osrdr2-3-pa-R2 mRNA-seq

city: Nanjing

first: Lili

last: Wang

address: Weigang No.1

institute: Nanjing Agricultural University

data_processing:
Low-quality reads had been eliminated.
All reads were mapped onto the O.sativa genome (MSU version 7.0) by Tophat.
Expression level were normalized through fragments per kilobase of exon model per million mapped reads (FPKM).
Supplementary_files_format_and_content: tdf, gene_exp.txt

organism: Oryza sativa

source_name: young panicle

growth_protocol: RIce plants grown in soil in Hannan province

extract_protocol:
RNA was extrated using TRIzol method.
1.Total RNA used DNaseI to digest DNA, and enriched mRNA using magnetic beads with Oligo(dT).
2.Adding reagent in Thermomixer to interrupt mRNA into short fragments.
3.The fragmented mRNA was used as template to synthesize the first strand of cDNA, and then synthesized the second strand.
4.Purified by using the kit, and repaired the adhesive termination, added the base "A" and adapter in the CDNA 3'end, then selected 200-300bp fragments and performed PCR amplification.
5.The libraries were checked with Agilent 2100 Bioanalyzer and ABI Real-Time PCR System, the qualified libraries were sequenced using sequencing platform.

tag: cultivar

value: japonica

value: panicle

value: DES1 mutant


title: C4_CypDko_flu

city: Chicago

first: Luis

middle: B

last: Barreiro

address: 900 E 57th Street

institute: University of Chicago

description:
bulk RNA library
JD-MD_C4_NEY922A14-24_S17

data_processing:
Fastqs were trimmed using Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) in paired-end mode (-q 20 --phred33)
Reads were pseudoaligned to mm10 using kallisto's quant function (Bray et al.) in paired-end mode
Quantification estimates were obtained from abundance.h5 files using the R package tximport (Soneson et al.)
Genome_build: mm10.81
Supplementary_files_format_and_content: Mus_musculus.mm10.81.kallisto.gene_level.raw_counts.txt includes raw count values for each sample; Mus_musculus.mm10.81.kallisto.gene_level.lengthScaledTPM_counts.txt includes counts from abundance estimates scaled using the average transcript length across samples and the library size

source_name: CypD knockout_flu-infected_NK cells

growth_protocol: Six to ten-week old C57BL/6J mice were bred at the RI-MUHC, Montreal, QC, Canada. Experiment were performed age- and sex-matched mice and all animal studies were conducted in accordance with the guidelines of and approved by the Animal Research Ethics Board of McGill University (project ID: 5860).

extract_protocol:
Splenocytes were harvested and pure pan-NK cells were isolated using the EasySep Mouse NK Cell Isolation Kit (StemCell). Cell purity was then ascertained by flow cytometry and cells were lysed and prepped for RNA-Seq.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were intranasally infected with 50 PFU of PR8 H1N1 influenza A virus (IAV). At 5 days post-infection, animals were sacrificed and their spleens extracted.

tag: strain background

value: CypD knockout

tag: treatment

value: flu-infected

value: purified splenic NK cells


title: T60d_2

city: Xiangtan

first: chen

middle: chen

state: Hunan province

address: Heping Street

department: School of Life and Health Sciences

institute: Hunan University of Science and Technology

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by removing reads containing sequencing adapter; removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; removing reads whose unknown base(‘N’ base) ratio is more than 5%.
The clean reads were mapped to GRCz11/dnaRer11 using HISAT2(v2.0.4) pipeline.
Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set (GCF_000002035.6_GRCz11), then expression level of gene was calculated by RSEM(v1.2.12).
Differential expression analysis was performed using the DESeq2(v1.4.5) with Q value ≤ 0.05.
GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper (https://en.wikipedia.org/wiki/ Hypergeometric_distribution) based on Hypergeometric test.
The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value≤ 0.05) by Bonferroni.
Assembly: dnaRer11
Supplementary files format and content: tab-delimited text files include genes expression and read count for each Sample

source_name: Whole fish

growth_protocol: The AB strain were maintained in a glass aquarium with a circulating water system at 28±0.5℃, with photoperiods of 14L-10D, and the number of fish in each 5-liter tank was 50-55.

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12,000xg at 4℃, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000xg for 10 minutes at 4C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4℃. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4℃ to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25μL~100μL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
RNA libraries for RNA-seq were prepared using standard BGISEQ-500 protocols. Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. Afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

treatment_protocol: The control group was kept at 28℃, whereas the thermal treatment group was exposed to 35℃for 10 days during 25-35 dpf. And each group had three biological replicates. After the treatment, fish were returned at 28℃ until the fish reached to sexual maturity (90 dpf).

value: Whole fish

value: AB

value: Wide type

tag: development stage

value: heat-shock


title: T60d_3


title: T60d_1


title: T45d_3


title: C3_CypDko_flu

description:
bulk RNA library
JD-MD_C3_NEY922A14-23_S16


title: Nip-pa-R1 mRNA-seq

value: control


title: RNA2-mock_rep2

city: Wuhan

first: Ying

address: Shizishan

institute: Huazhong Agricultural University

data_processing:
RNA-seq: analysis was performed using  Hisat2 (v 2.1.0) and FeatureCounts in the Subread package (v1.6.5)
ATAC-seq:analysis was performed using  BWA-MEM (v.0.7.15) , MACS2 (v2.1.2)
Genome_build: Arabidopsis genome (TAIR10) was obtained from Ensembl (http://plants.ensembl.org/).
Supplementary_files_format_and_content: *BIGWIG , the genome coverage of each sample

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: Plants were grown in soil (KEKKILA) in a growth room at 21°C, 45% humidity, and 75 μE m-2 s-1 light with a 12-hr-light/12-hr-dark photoperiod. Ten-day-old seedlings were cultured on half-strength Murashige and Skoog (1/2MS) plates containing 1% sucrose and 0.8% agar, and grown under the same condition as above.

extract_protocol:
Protoplasts were isolated from 4-week-old wild type Arabidopsis plants, and then resuspend the protoplasts in WI solution at a density of 1 x 10^6 /ml. For ATAC-seq, lysed protoplasts and collected the nuclei, the pellet was incubated with Tn5 for later to construct sequencing libraries.
Ribosomal RNA (rRNA) depletion bulk RNA-seq to determine whether enhancer drives RNA synthesis at enhancers. Ribosomal RNA was depleted using Ribo-Zero kit. Equal amounts of RNA from biological replicates were pooled for RNA-seq library construction.

tag: Stage

value: Arabidopsis seedling

tag: ecotype

value: seedling

value: CHX treated for 1 hr.


title: B.1.351-ID1_1st

tag: age

tag: gender

value: COVID-19_B.1.351 varient

value: moderate

value: Ischgl, Austria

value: PBMC


title: Nip-pa-R2 mRNA-seq

value: japonica

value: panicle


title: T45d_1


title: RNA2-mock_rep3


title: C2_CypDko_flu

description:
bulk RNA library
JD-MD_C2_NEY922A14-22_S15

value: CypD knockout


title: T45d_2


title: RNA2-INA_rep3

value: CHX pre-treated for 1 hr and INA treated for 1 hr.


title: C1_CypDko_flu

description:
bulk RNA library
JD-MD_C1_NEY922A14-21_S14

value: flu-infected

value: purified splenic NK cells


title: osrdr2-3-pa-R1 mRNA-seq

value: DES1 mutant


title: W4_WT_flu

description:
bulk RNA library
JD-MD_W4_NEY922A14-19_S11

source_name: wild type_flu-infected_NK cells

value: wild type


title: T35d_2

value: Whole fish

value: AB

value: Wide type

value: heat-shock


title: RNA2-mock_rep1

value: Arabidopsis seedling

value: seedling

value: CHX treated for 1 hr.


title: W3_WT_flu

description:
bulk RNA library
JD-MD_W3_NEY922A14-18_S10


title: W2_WT_flu

description:
bulk RNA library
JD-MD_W2_NEY922A14-17_S9


title: T35d_3


title: RNA2-INA_rep2


title: C0_CypDko_NI

description:
bulk RNA library
JD-MD_C0_NEY922A14-20_S13

source_name: CypD knockout_control_NK cells

value: control


title: RNA2-pep2_rep3

value: CHX pre-treated for 1 hr and pep2 treated for 1 hr.


title: RNA2-INA_rep1


title: T35d_1


title: W1_WT_flu

description:
bulk RNA library
JD-MD_W1_NEY922A14-16_S8


title: C45d_3


title: C60d_3


title: EC-enriched murine lung cells

city: Helsinki

first: Andrey

last: Anisimov

address: Haartmaninkatu 8

department: Faculty of medicine

country: Finland

institute: University of Helsinki

data_processing:
The Cell Ranger v 2.1.1 mkfastq and count pipelines (10x Genomics, Pleasanton, CA) were used to demultiplex and convert Chromium single-cell 3’ RNA-sequencing barcodes and read data to FASTQ files and to generate aligned reads and gene-cell matrices.
Reads were aligned to mouse reference genome mm10
Cells were filtered based on the number of genes and the percentage of mitochondrial genes.
Genome_build: mm10
Supplementary_files_format_and_content: tsv, mtx output files

source_name: Lung

growth_protocol: Mice were maintained in standard housing conditions

extract_protocol:
Mice were euthanized by overdose of anaesthetics (Ketaminol/Rompun) and briefly perfused with PBS. Lungs were harvested and left lobes of the lungs were dissociated with 0.5 mg/mL Collagenase H (Roche), 0.5 U/mL of Dispase II (Sigma), 1 U/mL DNase I (Thermo Scientific) and 1% (w/v) BSA (Biowest). Dissociated cells were washed once with PBS and stained with Alexa-antibody-conjugates, specific for CD31. CD31+DAPI- were sorted using BD Influx flow. The sorted fraction had approximately 60-70% endothelial cells (CD31+), and that was used for scRNAseq.
Subsequent cDNA purification, amplification (12 cycles) and library construction (sample index PCR 14 cycles) was performed as instructed
Sample libraries were sequenced on the Illumina NovaSeq 6000 system using S1 flow cell (Illumina)

treatment_protocol: Mice have received 5 shots of tamoxifen (2 mg/dose/day) during 5 cosecutive days, when they were 6 weeks old. They served as a control in multiorgan profiling project.

value: 11 weeks

value: Lung


title: W0_WT_NI

description:
bulk RNA library
JD-MD_W0_NEY922A14-15_S7

source_name: wild type_control_NK cells


title: st16.5 Posterior Globe_Temporal_Rep3

city: Athens

first: Douglas

last: Menke

state: GA

address: 500 DW Brooks Drive

institute: University of Georgia

data_processing:
Sequenced reads were mapped to AnoSag2.1 genome using hisat2 v2.2.1 with the default parameters
Reads mapped to the exons of transcript were counted using the R function featureCounts in the Rsubread package v2.4.2
Genome_build: AnoSag2.1
Supplementary_files_format_and_content: tab-delimited text files contain raw counts for each sample ...

organism: Anolis sagrei

source_name: Embryonic eye

growth_protocol: Tissues from three different subregions of posterior globe of the eye were collected from Anolis sagrei embryos at stage 16.5

extract_protocol:
Total RNA was isolated using the mirVana RNA Isolation Kit (ThermoFisher Scientific).
Libraries were constructed with TruSeq Stranded mRNA Sample Prep Kit for Illumina. Libraries were sequenced on the Illumina NextSeq 500 platform

tag: developmental stage

value: Sanger stage 16.5

tag: specific sample collection location

value: posterior globe - temporal quadrant


title: st16.5 Posterior Globe_Temporal_Rep2


title: RNA2-NLP20_rep2

value: CHX pre-treated for 1 hr and NLP20 treated for 1 hr.


title: C60d_1


title: RNA2-pep2_rep1


title: C60d_2


title: st16.5 Posterior Globe_Temporal_Rep1


title: st16.5 Posterior Globe_Temporal_Rep5


title: RNA2-pep2_rep2


title: RNA2-NLP20_rep3


title: C45d_2


title: C45d_1


title: C35d_1


title: RNA2-NLP20_rep1


title: st16.5 Posterior Globe_Temporal_Rep4


title: st16.5 Posterior Globe_Nasal_Rep5

value: posterior globe - nasal quadrant


title: C35d_3


title: RNA2-chitin_rep1

value: CHX pre-treated for 1 hr and chitin treated for 1 hr.


title: RNA2-chitin_rep2


title: st16.5 Posterior Globe_Nasal_Rep3


title: C35d_2


title: C25d_2


title: RNA2-chitin_rep3


title: st16.5 Posterior Globe_Nasal_Rep4


title: RNA1-mock_rep2


title: RNA1-mock_rep1


title: ATAC_rep2

source_name: plant leaf

value: Arabidopsis protoplasts

value: plant leaf


title: st16.5 Posterior Globe_Nasal_Rep2


title: S2 cells -- ssDrip+RNaseH_R1

city: Nashville

first: Jared

last: Nordman

state: TN

address: 465 21st Ave S

department: Biological Sciences

institute: Vanderbilt University

data_processing:
Library strategy: ssDRIP-Seq
Adapters trimmed using Trimmomatic.
Aligned to dm6 genome with bowtie using local settings.
Duplicates marked with picardTools
Strand-specific bam files were made with samtools.
Peaks called with stranded bam files with MACS2 against RNase H treated control.
Genome_build: dm6
Supplementary_files_format_and_content: peak text files

organism: Drosophila melanogaster

source_name: Cell culture line

growth_protocol: Oregon R flies were expanded into population cages containing grape juice plates supplemented with wet yeast. Population cages were kept at 25°C in a humidified room and plates were changed daily. Before embryo collections, flies were precleared for at least one hour to minimize the number of late-stage embryos. Embryos were collected and aged at 25°C as necessary to obtain embryos that were 2-3 or 14-16 hours old.

extract_protocol:
Lysates were prepared with proteinase K and SDS. DNA was phenol:chloroform purified and precipitated with ethanol. Sonication was done to fragment DNA.
Libraries were prepared according to Swift Bioscience's instructions accompanying the Accel-NGS 1S DNA Library kit (Part# 10024). Briefly, DNA was denatured and adaptase was added to each DNA strand. Extension was performed. Ligation of indexing primer was performed, and then indexing PCR. Sample was cleaned using SpriSelect beads, and quality was assessed on BioAnalyzer. Samples were sequenced on Illumina Novaseq by core according to manufacturer’s instructions.

value: S2 cultured cells

tag: biomaterial

value: untreated


title: S2 cells -- ssDrip_R2


title: ATAC_rep1


title: S2 cells - Input_R2


title: C25d_1

value: Whole fish

value: AB

value: Wide type


title: S2 cells - Input_R1


title: RNA1-flg22_rep2

value: Arabidopsis seedling

value: seedling

value: CHX pre-treated for 1 hr and flg22 treated for 1 hr.


title: st16.5 Posterior Globe_Nasal_Rep1


title: RNA1-flg22_rep1


title: 14-16hr Embryos - ssDrip_R2

value: Whole embryos

value: OregonR


title: 14-16hr Embryos - ssDrip+RNaseH_R1


title: st16.5 Posterior Globe_Central_Rep5

value: Sanger stage 16.5

value: posterior globe - central quadrant


title: 4T1_NC3

city: Hangzhou

first: Mingqian

last: Li

address: Gucui Road 234

institute: Tongde hospital of Zhejiang Province

description: Normal 3

data_processing:
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: GrCM38/mm10
Supplementary files format and content: tab-delimited text files include COUNT values for each Sample

organism: Mus

growth_protocol: Cells were cultured with  RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS, ExCell Bio, China) at 37°C under a humidified 5% CO2 incubator

extract_protocol:
the cells were extracted by the Trizol method.
RNA library were prepared for sequencing using standard Illumina protocol

treatment_protocol: The 4T1 cells were seeded in a six-well plate at the number of 5×105 cells/well. After overnight, 10 μg/mL IPA was added for 24 h

tag: cell line


title: st16.5 Posterior Globe_Central_Rep2


title: C25d_3

tag: genotype

value: control


title: st16.5 Posterior Globe_Central_Rep4


title: st16.5 Posterior Globe_Central_Rep3


title: 4T1_IPA3

value: 10ug/ml IPA


title: rabbit IUA sample2 treated with hUCB-MSCs

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded.
The reads contaminated with adaptor sequences were trimmed.clean data were mapped to the reference genome of oryCun2 using STRA software (version 2.5.3a) with default parameters.
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKMs were calculated.
Assembly: ribbit reference genome, oryCun2
Supplementary files format and content: tab-delimited text files include read count values for each sample

source_name: All cells

extract_protocol:
Total RNAs were extracted by Trizol method, RNA purity was detected by spectrophotometer, RNA integrity was analyzed by agarose gel electrophoresis and Agilent 2100 BioAnalyzer
The Library was constructed using Illumina’s NEBNext® UltraTM RNA Library Prep Kit. Illumina platform was used for library sequencing and 150 bp paired terminal reading was generated to obtain the sequence information of the fragment to be measured.

value: 14 weeks old

value: All cells

value: IUA

value: hUCB-MSCs

tag: time

value: Day 28


title: st16.5 Posterior Globe_Central_Rep1


title: 4T1_IPA2


title: 4T1_IPA1


title: rabbit IUA sample3  treated with hUCB-MSCs

tag: cell type


title: 14-16hr Embryos - Input_R2

source_name: Embryo

tag: strain

value: untreated


title: 4T1_NC1

description: Normal 1


title: rabbit IUA sample3 without treated with hUCB-MSCs


title: T48Lm-3-G1

city: Xining

first: Delin

last: Qi

address: No. 251, Ningda Road

institute: Qinghai university

description: rainbow trout

data_processing:
Reads obtained from the sequencing machines included raw reads containing adapters or low quality bases which would affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered according to the following rules: 1) Removing reads containing adapters; 2) Removing reads consisting of all A bases; 3) Removing reads containing more than 10% of unknown nucleotides (N); 4) Removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
Short reads alignment tool Bowtie2 (2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads were then removed. The remaining reads were further used in assembly and analysis of transcriptome.
The rRNA removed reads of each sample were then mapped to reference genome by TopHat2 (version 2.1.1), respectively. The alignment parameters were as follows: 1) Maximum read mismatch is 2; 2) Disables the coverage based search for junctions; 3) The distance between mate-pair reads is 50bp; 4) The standard deviation for the distribution on inner distance between mate-pair reads is 80bp.
After aligned with reference genome, unmapped reads (or mapped very poorly) were then re-aligned with Bowtie2, the enriched unmapped reads were split into smaller segments which were then used to find potential splice sites. The section and the section position of these short segments were predicted as well. A set of splice sites was built with initial unmapped reads by TopHat2 without relying on the known genes annotation. Not only be used for identifying expressed genes and their quantitative expression, the sequence alignment will also be helpful to find alternative splicing and new transcripts.
Assembly: Oncorhynchus mykiss Omyk_1.1
Supplementary files format and content: genes_fpkm_expression.txt: Tab-delimited text file includes count and FPKM values for each Sample.

organism: Oncorhynchus mykiss

source_name: liver tissues

extract_protocol:
The samples were collected immediately, then flash-frozen in liquid nitrogen, and total RNA was extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: tissue

value: liver tissues

value: IHNV infection

value: wild-type


title: 14-16hr Embryos - Input_R1


title: 14-16hr Embryos - ssDrip_R1


title: 4T1_NC2

description: Normal 2


title: S2 cells -- ssDrip_R1

value: S2 cultured cells


title: 2-3hr Embryos  - ssDrip_R1


title: bamRNAi_hs-bam_polysome_1

city: Albany

first: Prashanth

last: Rangan

address: 1400 Washington

institute: RNA Institute

data_processing:
Sequenced reads were aligned and raw counts generated using STAR (version 2.6.1c) against the D. melanogaster genome/assembly (UCSC dm6).
Genome_build: UCSC dm6

source_name: Ovaries

growth_protocol: Flies ready for heat shock were placed at 37°C for 2 hours, moved to room temperature for 4 hours and placed back into 37°C for 2 additional hours. Flies were then left overnight at room temperature and the same heat shocking procedure was repeated for a total of 2 days. Flies were then dissected in 1x PBS.

extract_protocol:
RNA was isolated using TRIzol (Invitrogen, 15596026) (for input samples) or phenol-chloroform treatment (for polysome samples) , treated with DNase (TURBO DNA-free Kit, Life Technologies, AM1907). To generate mRNA-enriched libraries total RNA was treated with poly(A)tail selection beads.
Following the manufacturer's instructions of the NEXTflex Rapid Directional RNAseq Kit (Bioo Scientific Corp, NOVA-5138-08), except RNA was fragmented for 13 minutes

treatment_protocol: Samples were lysed in polysome lysis buffer and either loaded on to polysome gradients (samples labeled polysome) or kept as input (samples labeled input)

value: dissected 3-5 days post-eclosion

tag: experiment

value: polysome-seq

tag: polysome fraction (input/polysome)

value: polysome

value: UAS-Dicer2;NosGAL4 > bam RNAi; hs-bam


title: rabbit IUA sample1 treated with hUCB-MSCs

first: Yong

address: Tongbaibei NO.16 Zhongyuan district, Zhengzhou

institute: Zhengzhou University

tag: treatment


title: 2-3hr Embryos  - Input_R2

value: Whole embryos

value: OregonR


title: rabbit IUA sample1 without treated with hUCB-MSCs


title: C48Lm-2-G1

description: rainbow trout

value: control


title: 2-3hr Embryos  - Input_R1

value: Oregon R


title: C48Lm-1-G1

description: rainbow trout


title: bamRNAi_hs-bam_input_1

value: input


title: 2-3hr Embryos  - ssDrip_R2


title: 2-3hr Embryos  - ssDrip+RNaseH_R1


title: SNB19 ZBTB18 FL-mut Rep2

status: Public on Jun 20 2022

city: Freiburg

first: Maria Stella

last: Carro

address: Breisacherstraße 64

institute: Freiburg University Medical Center

data_processing:
Basecalling was performed by Albacore implemented in the nanopore software.
Postprocessing was performed using the NanoPoreSeq pipeline, available at github (https://github.com/heilandd/NanoPoreSeq)
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: SNB19 cells

growth_protocol: SNB19 cells were grown in DMEM +10% FBS

extract_protocol:
RNA was extracted with Trizol reagent. We then performed mRNA purification from total RNA samples using the Dynabeads mRNA Purification Kit (Thermo Fisher Scientific, Carlsbad, USA).
Library was prepared using the Low Input by PCR Barcoding Kit and the cDNA-PCR Sequencing Kit (Oxford Nanopore Technologies, Oxford, United Kingdom) as recommended by the manufacturer.

treatment_protocol: SNB19 cells were transduced with lentiviral particles expressing specific proteins  (EV, ZBTB18, ZBTB18-mut, ZBTB18 SF, ZBTB18 SF-mut)

value: Glioblastoma cell

tag: transduced

value: ZBTB18 full length-mut (FL-mut)


title: SNB19 ZBTB18 FL-mut Rep1


title: SNB19 ZBTB18 FL-mut Rep3


title: SNB19 ZBTB18 SF-Nte Rep1

value: ZBTB18 short form Nte (SF-Nte)


title: T48Lm-2-G1

description: rainbow trout


title: SNB19 ZBTB18 SF-mut Rep3

value: ZBTB18 short form Nte mut (SF-mut)


title: T48Lm-1-G1

description: rainbow trout

value: liver tissues


title: SNB19 ZBTB18 SF-mut Rep2


title: bamRNAi_hs-bam_polysome_3


title: C48Lm-3-G1

description: rainbow trout


title: bamRNAi_hs-bam_input_3


title: SNB19 EV Rep2

value: Empty vector (EV)


title: rabbit IUA sample2 without treated with hUCB-MSCs

city: Zhengzhou

value: 14 weeks old

value: All cells

value: IUA

value: Day 28


title: SNB19 ZBTB18 SF-mut Rep1


title: Temp = 25degC, replicate5

city: Berkeley

first: Jonathon

last: Stillman

state: ca

address: 3040 Valley Life Sciences Building #3140

department: Integrative Biology

institute: University of California Berkeley

data_processing:
To prepare libraries for analysis, sequences were trimmed to remove Illumina adaptors (stringency = 1) and bases with a Phred quality score under 20 using Trim_Galore! (V 0.3.0).  Trimmed reads were 32.0 Â± 1.2 % of the total, 11.0 Â± 1.8 % of which were quality trimmed, and 0.51 Â± 0.02 % of the bases were trimmed.  FLASH (V 1.2.8) was used to join overlapping paired end reads in order to make longer reads for de novo assembly and to eliminate artificial double counting of mapped read overlap regions.  The number of reads processed by FLASH was 10.4 Â± 2.0 X 106 , with 37.8 Â± 5.5% of the reads combined, and 11.6 Â±1.0% of sequence pairs removed.
De novo transcriptome assembly was performed using Trinity (V r2013-11-10) (http://trinityrnaseq.sourceforge.net/) (Grabherr 2011). Trinity was used to conduct the assembly using a minimum kmer coverage = 2.   The assembled transcriptome contained n=135858 contigs.  The transcriptome was annotated against the SwissProt database using Trinotate (V 1.1) , with BLASTx of nucleotide sequences (resulting in n=37464 annotated contigs), and BLASTp (n=31743 annotated) and PFAM (n=30225 annotated) analyses of TransDecoder (V 2.0) produced protein sequences.  Gene ontology annotation was found for n=35024 contigs.
Libraries were mapped to the de novo transcriptome for that species using Bowtie2 (V 2.0.6) and counted using eXpress (V 1.5.1) (http://bio.math.berkeley.edu/eXpress/), a read mapper that probabilistically assigns reads that ambiguously map to multiple loci, thus minimizing issues arising from redundant putative transcripts in de novo assembled transcriptomes (Roberts & Pachter, 2013) . Library size (# of mapped reads) was compared visually using boxplots to ensure that there was no library size variation.  On average 93.8 Â± 1.0 % of reads in each library mapped to the transcriptome.
Statistical analysis of differential gene expression was performed in R using the Bioconductor package EdgeR (V 1.2.4) (http://www.bioconductor.org/packages/release/bioc/html/edgeR.html) (Robinson 2010) to identify genes with expression that varied across temperature. We used likelihood ratio tests (LRT) with false-discovery rate correction to identify genes that had differential expression between any two acclimation treatments within a given species. Transcripts with expression of less than 2 reads/million mapped in less than 4 samples were removed from the analysis, which resulted in the retention of n=30092 transcripts in the analysis.  Transcripts with a false-discovery rate corrected P-value of less than 0.05 and a fold-change â‰¥ 4 (for up-regulation) or â‰¤ 0.25 (for down-regulation) were identified as statistically differentially expressed genes (DEGs) in each LRT, which yielded a set of n=2586 DEGs.   Differentially expressed transcripts were log2base transformed and median-centered based on the global within-species median.
Supplementary files format and content: Processed data represent median-centered log2 transformed FPKM values.
Supplementary files format and content: Processed data from all samples are provided in a single file.

organism: Dicosmoecus gilvipes

source_name: thorax

extract_protocol:
Animals were flash-frozen in liquid nitrogen and the thorax was dissected on dry ice and placed frozen into Tri Reagent (MRC). The thorax was used to maximize muscle tissue and minimize digestive tract symbiont contamination. Thorax tissue was homogenized under liquid N2 using a TissueLyser II (Qiagen 85300) for 5-10 sec and RNA was extracted using the manufacturerâ€™s polysaccharide/proteoglycan removal modified protocol, using BCP and High Salt Precipitation Solution (MRC). Purified RNA was assessed for quantity and quality using a Bioanalyzer (Agilent) and only samples with little to no degradation and adequate concentration were used in subsequent steps.
For each exposure temperature, equal amounts of total RNA from each individual were used to make n=5 independent pooled RNA samples.  Those n=5 pooled RNA samples were used to make RNAseq libraries following the Illumina Tru-Seq RNA v2 kit.

value: thorax

value: Temp = 25degC


title: SNB19 ZBTB18 FL Rep3

value: ZBTB18 full length (FL)


title: SNB19 ZBTB18 SF-Nte Rep2


title: SNB19 ZBTB18 FL Rep2


title: Temp = 20degC, replicate4

value: Temp = 20degC


title: Temp = 20degC, replicate1


title: Temp = 15.5degC, replicate5

value: Temp = 15.5degC


title: Temp = 15.5degC, replicate4


title: Temp = 20degC, replicate2


title: SNB19 EV Rep3


title: SNB19 ZBTB18 FL Rep1


title: SNB19 ZBTB18 SF-Nte Rep3


title: SNB19 EV Rep1


title: Temp = 15.5degC, replicate3


title: Temp = 28.6degC, replicate4

value: Temp = 28.6degC


title: Temp = 28.6degC, replicate5


title: Temp = 28.6degC, replicate2


title: variant V2

city: Guangzhou

first: Pengxia

state: Guangdong

address: 164 Xingang West Rd

department: South China Sea Institute of Oceanology

institute: Chinese Academy of Sciences

data_processing:
Sequencing was carried out using a 2x150 paired-end (PE) configuration.
image analysis and base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument.
image analysis and base calling were conducted by the NovaSeq Control Software (NCS) + OLB + GAPipeline-1.6 (Illumina) on the NovaSeq instrument.
image analysis and base calling were conducted by the Zebeacall on the MGI2000 instrument.
Assembly: Reference genome sequence of Vibrio alginolyticus SCSIO 43097 download from NCBI (accession number is CP071840-CP071841) was used for read alignment.
Supplementary files format and content: WT_1_2_3 and variant_V1_V2_V3.xls (the raw count and FPKM of the wild type strain and its variants V1,V2 and V3 of Vibrio alginolyticus SCSIO 43097)
Supplementary files format and content: variant V1_V2 vs WT 1_2_3.xls (Gene expression of the variants V1 and V2 compared with the wild type strain SCSIO 43097 .by RNA-seq)

organism: Vibrio alginolyticus

source_name: SCSIO 43097

growth_protocol: The cells of WT and variants were cultured in 2216E liquid at 30°C until the OD600 reached 0.8-1.

extract_protocol:
Total RNA was isolated using Tiangen RNAprep Pure Cell (Tiangen Biotech, China) following the manufacturer’s instructions.
1μg total RNA was used for following library preparation. Next generation sequencing library preparations were constructed according to the manufacturer’s protocol.

value: SCSIO 43097

value: variant


title: variant V1


title: WT colony 2

value: wild type strain


title: WT colony 3


title: Temp = 25degC, replicate3


title: Temp = 25degC, replicate2


title: Temp = 20degC, replicate5


title: Temp = 20degC, replicate3


title: C1-M-H

city: Taipei

first: Chen-Si

last: Lin

address: No. 1, Sec. 4, Roosevelt Road

department: Department of Veterinary Medicine

country: Taiwan

institute: Nationwide Taiwan University

description:
peak group:
MCGF

data_processing:
The sequencing quality processing tool (FASTX-Toolkit http://hannonlab.cshl.edu/fastx_toolkit/) was used to filter out low quality sequencing reads. The command was “fastq_quality_filter –Q33 –q 20 –p 70”. “-q 20” indicated that the minimum phred score was 20 (20 means the sequencing error rate is 0.1% to a base) and “-p 70” indicated that the minimum percent of bases must have “-q” quality ≥70%
BWA (http://bio-bwa.sourceforge.net/) was used to align sequencing reads with Dog genome sequences (CanFam3.1) which were got from NCBI.
MACS2 (https://github.com/taoliu/MACS) was employed to identify hypermethylated peaks according to the results of sequencing alignment.
Genome_build: CanFam3.1
Supplementary_files_format_and_content: hypermethylated peaks (excel format)

organism: Canis lupus familiaris

source_name: lymph node

extract_protocol:
Tumor cells from cHGBL cases were collected via fine needle aspiration of the enlarged lymph nodes and preserved in RPMI medium until genomic DNA extraction. Whole blood was collected from each healthy dog and peripheral blood mononuclear cells were separated by Ficoll-Paque PLUS gradient centrifugation for genomic DNA extraction. Total genomic DNA was extracted from no more than 5 x 106 cells using Genomic DNA isolation Kit.
A total amount of 800 pg captured DNA (meDNA captured sample) was taken for library preparation using QIAseq Ultralow Input Library Kit according to the manufacturer’s protocol. Briefly, the double-stranded DNA was end-repaired and 3’end adenylated followed by adapter ligation and PCR amplification. The length of library fragments ranging from 200 bp and 1 kb were further selected using AMPure XP beads. The fragment size of the resulting library was validated using Agilent 2200 TapeStation-D1000 Screentape system. The library was quantitatively measured by Kapa Library Quantification Kit for Illumina platform and Qubit dsDNA HS Assay kit. The library was sequenced using a 150 bp paired-end protocol on an Illumina Novaseq.

tag: breed

value: schnauzer

value: lymph node

value: 10 years

tag: disease state

value: high-grade B-cell lymphoma

tag: tumor stage

value: IV

tag: fraction

value: MethylCap DNA


title: H4-L

description:
peak group:
LHG

source_name: peripheral blood mononuclear cells

value: poodle (standard)

value: blood

tag: age

value: 5 years

value: healthy control


title: Temp = 25degC, replicate4

value: thorax

value: Temp = 25degC


title: Temp = 28.6degC, replicate1


title: Temp = 15.5degC, replicate2

value: Temp = 15.5degC


title: C2-M-H

description:
peak group:
MCGF

value: mixed

value: IV-V


title: C8-M-H

description:
peak group:
MCGF

value: dachshund

value: III


title: Temp = 15.5degC, replicate1


title: H3-L

description:
peak group:
LHG

value: golden retriever

value: 2 years


title: Temp = 28.6degC, replicate3

value: Temp = 28.6degC


title: Temp = 25degC, replicate1


title: WT colony 1

value: SCSIO 43097

value: wild type strain


title: C2-L

description:
peak group:
LCGF

value: lymph node

value: 10 years

value: high-grade B-cell lymphoma

value: MethylCap DNA


title: H3-M-H

description:
peak group:
MHG

value: blood

value: healthy control


title: CL10-L

description:
peak group:
LCGF

value: 13 years

value: V


title: CL10-M-H

description:
peak group:
MCGF


title: H2-M-H

description:
peak group:
MHG

value: mixed

value: 7 years


title: variant V3

value: variant


title: C5-M-H

description:
peak group:
MCGF

value: 5 years

value: IV


title: ATAC_E95_PT_rep1

city: Geneva

first: Aurelie

last: Hintermann

address: 30 quai Ernest-Ansermet

department: Genetics and Evolution

country: Switzerland

institute: University of Geneva

description:
ATAC E9.5 posterior trunk
ATAC

data_processing:
All scripts are available on https://gitlab.unige.ch/Aurelie.Hintermann/hintermannetal2022
Sequenced DNA fragments were processed as previously reported in (Amândio et al., 2020) with a minor modification on a local Galaxy server: the BAM file was converted to BED prior to peak calling with bedtools version 2.30.0
Peak calling was done using MACS2 (v2.1.1.20160309) callpeak (--no-model --shift -100 --extsize 200 --call-summits --keep-dup all).
Peak regions for each condition were obtained from the union of the peak region of both replicates with bedtools merge (v2.30.0) and extended by 660 bp each side with bedtools slop.
Each replicate was normalized per million reads mapped in their own peaks, subsetted in the HoxD region (mm10,chr2:73000000-77000000 ; galGal6, chr7:13000000-17000000) and the neq2 coverage is the mean of normalized replicates
Assembly: mm10
Assembly: galGal6
Supplementary files format and content: bigwig: coverage from MACS2
Supplementary files format and content: narrowPeak: narrowPeak from MACS2
Supplementary files format and content: bedgraph: replicates were  normalized to the number of million reads falling in their own peaks, subsetted in the HoxD region (mm10,chr2:73000000-77000000 ; galGal6, chr7:13000000-17000000) and averaged.
Supplementary files format and content: bed: narrowPeaks of both replicates were pooled, extended by 660 bp each side and then merged to obtain non-overlapping intervals.

extract_protocol:
ATAC-seq experiments were performed as described in (Bolt et al., 2022)
ATAC-seq librairies were prepared as described in (Bolt et al., 2022)

tag: developmental stage

value: WT

tag: dissection

value: A portion of tissue corresponding to the tailbud, presomitic mesoderm, and 2-3 somite pairs, was micro-dissected from one E9.5 embryo.


title: C5-L

description:
peak group:
LCGF


title: H4-M-H

description:
peak group:
MHG

value: poodle (standard)


title: B171_del

city: Parkville

first: Peter

last: Hickey

address: 1G Royal Parade

country: Australia

institute: WEHI

data_processing:
Base calling using Real-Time Analysis v2.4.6, demultiplexing and fastq.gz file generation using bcl2fastq conversion software v2.15.0.4
Quality control and adapter trimming were performed with FastQC and Trim_galore!
Reads were aligned to the mm10 reference genome using TopHat
Expression values in reads per million (RPM) were determine using the Seqmonk package (www.bioinformatics.babraham.ac.uk/projects/seqmonk/), using the RNA-seq Quantitation Pipeline
The gene counts matrix was analysed for differential expression using the quasi-likelihood framework from the edgeR (v3.32.1) R/Bioconductor package
All code used to perform differential expression analysis of the RNA-seq data is available from https://github.com/WEHISCORE/C086_Kinkel
Genome_build: GRCm38
Supplementary_files_format_and_content: Female samples: table with raw gene counts for every gene and every sample as well as average read count for each experimental group
Supplementary_files_format_and_content: Male samples: table with raw gene counts for every gene and every sample as well as average read count for each experimental group
Supplementary_files_format_and_content: Female samples: table of results from differential expression analysis
Supplementary_files_format_and_content: Male samples: table of results from differential expression analysis

source_name: Bone marrow derived 12-16 month old B cells

extract_protocol:
Bone marrow cells were flushed from femurs, stained with antibodies against CD45.2, B220 and Mac1, subjected to fluorescence activated cell sorting to purify CD45.2+ B220+ Mac1- cells. RNA was extracted using a Zymo RNA/DNA purification kit.
RNAseq libraries were preprared using an Illumina Truseq RNA prepartion kit

value: B cells

value: Smchd1[del/del] Vav.Cre[T/+]

tag: Sex

value: male


title: B217_del

tag: genotype


title: C1-L

description:
peak group:
LCGF

value: schnauzer

value: lymph node

value: 10 years

value: high-grade B-cell lymphoma


title: B200_del

value: female


title: C8-L

description:
peak group:
LCGF

value: dachshund

value: III

value: MethylCap DNA


title: B173_het

value: Smchd1[del/+] Vav.Cre[T/+]


title: B194_het


title: H2-L

description:
peak group:
LHG

value: mixed

value: blood

value: 7 years

value: healthy control


title: ATAC_E125_WP_rep1

description:
ATAC E12.5 whisker pad
ATAC

value: WT

value: One pair of whisker pad was micro-dissected from one E12.5 embryo.


title: ATAC_E125_WP_rep2

description:
ATAC E12.5 whisker pad
ATAC


title: ATAC_E125_FB_rep1

description:
ATAC E12.5 forebrain
ATAC

value: One telencephalon was micro-dissected from one E12.5 embryo.


title: ATAC_E125_FB_rep2

description:
ATAC E12.5 forebrain
ATAC


title: B190_del

value: B cells

value: Smchd1[del/del] Vav.Cre[T/+]


title: ATAC_E95_PT_rep2

description:
ATAC E9.5 posterior trunk
ATAC

value: A portion of tissue corresponding to the tailbud, presomitic mesoderm, and 2-3 somite pairs, was micro-dissected from one E9.5 embryo.


title: B203_het


title: B212_del

value: male


title: B196_del


title: Forebrain culture, Control replicate3

city: Isehara

first: Takatoshi

last: Iijima

state: Kanagawa

address: 143 Shimokasuya

department: School of Medicine

institute: Tokai University

description:
gene expression, alternative splicing in the differentiated neurons
726_1C

hyb_protocol: Fluorescent dye-labeled cRNA was hybridized to SurePrint G3 Mouse Exon 2x400K arrays (Agilent Technologies, CA, USA); hybridization and washing were performed on Agilent’s microarray platform, according to manufacture's protocols.

scan_protocol: Scaned using microarray scanner G2690D

data_processing: All scanned images were analyzed using Agilent feature extraction software (v11.5.1.1). Raw data were imported with GeneSpring GX software (v13.0, Agilent Technologies, CA, USA) with adapted by 75 percentile shift normalization

source_name: forebrain culture #3

label_protocol: Total RNA was amplified using the Low Input Quick Amp WT Labeling Kit, One-Color*3 (Agilent), according to the manufacturer’s instructions (Agilent Technologies, Santa Clara, USA). 100 ng of total RNA was reverse-transcribed into double-stranded cDNA, which was translated into cRNA in the presence of Cy3-dCTP and amplified by T7 RNA polymerase.

extract_protocol: Total RNA was prepared using NucleoSpin RNA XS (Takara, Japan) and quantified using a NanoDrop-1000 spectrophotometer. The quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: Embryonic brain (forebrain)

value: wild-type (MNRI)

value: control


title: B213_het


title: B189_het

value: female


title: B214_het


title: Forebrain culture, Control replicate2

description:
gene expression, alternative splicing in the differentiated neurons
718_1C

source_name: forebrain culture #2


title: Forebrain culture, Control replicate1

description:
gene expression, alternative splicing in the differentiated neurons
703_4C

source_name: forebrain culture #1


title: Forebrain culture, VPA replicate3

description:
gene expression, alternative splicing in the differentiated neurons
726_2V

value: VPA


title: B243_del


title: Forebrain culture, VPA replicate2

description:
gene expression, alternative splicing in the differentiated neurons
718_2V


title: Forebrain culture, VPA replicate1

description:
gene expression, alternative splicing in the differentiated neurons
703_5V


title: YTcKO+H151_1

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

description: Gene expression of YAP/TAZ KO fibroblasts after STING inhibition

data_processing:
Raw reads were trimmed for adapters, polyA read through, and low-quality tails (quality < Q20) using BBDuk (version 37.02; sourceforge.net/projects/bbmap/). Reads shorter than 35 bp were also removed resulting on average 19.4M trimmed reads per sample.
Reads were subsequently aligned to the mouse reference genome (mm10) using STAR (version 2.5.3a) and setting the STAR parameters as indicated in the Lexogen data analysis guidelines (see https://www.lexogen.com/quantseq-data-analysis/ for details).
Raw gene counts were obtained using the featureCounts function of the Rsubread R package (version 1.30.3) and the Gencode gene annotation for mm10 genome.
Gene counts were normalized to counts per million mapped reads (CPM) using the edgeR package; only genes with a CPM greater than 1 in at least 2 samples were further retained for differential analysis.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file with CPM values for each sample

source_name: Primary dermal fibroblast culture

growth_protocol: DMEM-F12 medium, supplemented with 20% Fetal Bovine Serum (FBS), L-Glutamine and antibiotics.

extract_protocol:
RNA extraction was performed with NucleoSpin 8 RNA Core Kit (Macherey-Nagel) according to the manufacturer’s instructions, using an automated system (Freedom EVO, Tecan).
RNA-seq libraries were prepared with QuantSeq 3’mRNA-Seq Library Prep kit (LEXOGEN), according to manufacturer’s instructions.

treatment_protocol: 1 μM 4OH-Tamoxifen, alone or in combination with 1 µM H-15, was added to the full gowth medium for 72 hr.

value: Primary dermal fibroblasts

tag: strain/genotype

value: R26-CAG-CreER; Yap1 fl/fl; Wwtr1 fl/fl

tag: experimental conditions

value: 72hr treatment with 1 μM 4OH-Tamoxifen and 1 µM H-151 (STING inhibitor)


title: Control_2

description: Gene expression of control fibroblasts

tag: cell type

value: Yap1 fl/fl; Wwtr1 fl/fl

value: 72hr treatment with 1 μM 4OH-Tamoxifen


title: CD14+_Mono

city: Cambridge

first: Vinay

last: Kartha

state: MA

address: 7 Divinity Ave

institute: Harvard University

description: PBMCs isolated for CD14+ cells

data_processing:
Cell barcodes and UMIs were parsed from read 1 and written into the read name of the corresponding read in the read 2 fastq. All read 2 files with valid cell barcodes were aligned using STAR (v2.5.2b) to hg19 (UCSC; PAR masked) reference genome. Reads that aligned to abundant features (chrM, rRNA, and sncRNA) were filtered from the analysis.
Transcript counts per barcode were then generated by counting the number of unique genic UMIs for each read with a minimum mapping quality of 12 that aligned unambiguously to an annotated exon in the RefSeq annotation of hg19. The distribution of unique genic UMI per barcode was then filtered to separate barcodes present in droplets with cells from barcodes present in cell-free droplets.
Gene-mapped counts were then loaded into R as a Seurat object (Stuart et al., 2019) and used for downstream analysis. Genes with at least 1 UMI across cells were retained, and cells with number of unique feature counts > 200 and < 5000 were initially retained.  Normalization and scaling of RNA gene expression levels was performed using the SCTransform function. scRNA cell barcode doublets were inferred using DoubletFinder (McGinnis et al., 2019; Stuart et al., 2019) and removed.
Genome_build: hg19
Supplementary_files_format_and_content: Decomposed counts matrix. Counts data is indexed by gene (row), cell (column), and count where the geneNames file and cellMeta file provide annotations for rows and columns.

source_name: Human PBMCs

growth_protocol: Cryopreserved human isolated peripheral blood CD4+, CD8+, CD14+, CD19+ and CD56+ cells were purchased from Allcells. Cells were quickly thawed in a 37°C water bath, rinsed with culture medium (IMDM medium supplemented with 10% FBS and 1% Pen/Strep) and then treated with 0.2 U/μL DNase I (Thermo Fisher Scientific) in 10 mL of culture medium at 37°C for 30 min. After DNase I treatment, cells were washed with medium once and then twice with ice cold 1x PBS + 0.1% BSA. Cells were then filtered with a 35 μm cell strainer (Corning) and cell viability and concentration were measured with trypan blue on the TC20 Automated Cell Counter (Bio-Rad). Cell viability was greater than 80% for all samples.

extract_protocol: scRNA-seq libraries were generated using the SureCell WTA 3′ Library Prep Kit for the ddSEQ System (20014280, Illumina) with the following modifications. A higher concentration of beads was used to obtain 1,000-2,000 single-cells per emulsion, whilst minimizing the number of droplets with multiple beads to < 10%. Furthermore, Bst 2.0 WarmStart (M0538S, NEB) was added to the droplet mix to perform temperature activated second strand synthesis in droplets.

tag: isolation marker


title: differentiated ureteric bud lineages, day 7 (nephric duct) and day 18 (collecting duct)

city: Boston

first: Kyle

last: McCracken

state: Massachusetts

address: 4 Blackfan Circle

institute: Brigham and Women's Hospital

description: BD Rhapsody

data_processing:
Raw data were uploaded and processed on the BD Rhapsody WTA Analysis Pipeline on the Seven Bridges Genomics cloud platform. Sequences were quality filtered and aligned to the human mRNA reference genome. Samples were de-multiplexed based on Sample Tags, and cell-gene count matrices were generated for each sample. Further analyses were performed using the R package Seurat (v4.0.4).
Raw data files here are multiplexed and therefore the same for both day 7 (SampleTag_02) and day 18 (SampleTag_06) samples. They can be de-multiplexed in the Seven Bridges analysis pipeline. The 'S2' files contain sequencing data for the sample barcode library.
Assembly: hg38
Supplementary files format and content: Processed data files are individual count matrices downloaded from the WTA Analysis on Seven Bridges Genomics. They are already de-multiplexed.

source_name: nephric duct spheroid and collecting duct organoid

extract_protocol:
Organoids were isolated from matrigel culture by incubation in Cell Recovery Solution (Corning) on ice for 15-20 minutes, with gentle trituration using a wide-bore P1000 pipet every 3-4 minutes. Once separated from Matrigel, thte structures were washed in PBS once, then pelleted by gravity. The organoids were dissociated into single cells in TrypLE Express for 10-12 minutes at 37 degrees. The suspensions were washed once PBS and filtered through a 70 um reversible cell strainer. The cells were then pelleted by centrifugation at 400 xg for 4 minutes, resuspended and labelled using BD Human Single Cell Multiplexing Kit.
Labelled samples, day 7 (SampleTag_02) and day 18 (SampleTag_06), were pooled into a single cell suspension. Cells were loaded into BD Rhapsody cartridge and libraries were prepared using the BD Whole Transcriptome Amplification (WTA) kit at the Single Cell Sequencing core at Harvard Medical School. The sample library was combined with the Sample Tag library (3%), and sequencing using an Illumina NextSeq 550 High Output kit at the Biopolymers Facility at Harvard Medical School.

treatment_protocol: Directed differentiation of hESCs (WA09) into three-dimensional ureteric bud (UB) organoids was performed. Spheroids were isolated at day 7 of differentiation, corresponding to the nephric duct stage. Additional samples were collected at day 18, corresponding to the differentiated collecting duct stage.

tag: tissue

tag: cell line

value: WT


title: B242_het

value: Smchd1[del/+] Vav.Cre[T/+]

tag: strain


title: Plate number LCE504

description: mixed sample (non-demultiplexed)

data_processing:
gene and ERCC count matrix generated using scPipe 1.12.0
reads were aligned using Rsubread 2.4.2
All code used to perform data processing and analysis of the RNA-seq data are available from https://github.com/WEHISCORE/C086_Kinkel
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: CSV, gene count matrix, rows represent genes and each column is a well, values corresponding to read counts
Supplementary_files_format_and_content: CSV, ERCC count matrix, rows represent ERCC spike-in sequences and each column is a well, values corresponding to read counts
Supplementary_files_format_and_content: CSV, sample sheet, rows represent a well and columns contain metadata on the sample in the well

source_name: Bone marrow derived LT-HSCs

extract_protocol:
Bone marrow cells were flushed from femurs and tibiae, depleted for lineage+ cells using magnetic bead depletion, stained with antibodies and subjected to fluorescence activated cell sorting to purify  Ter119- Gr1- Mac1- CD3- Ly6G- B220- c-kit+ Sca1+ Flt3- CD48- CD150+ LT-HSCs.
Minibulk transcriptome libraries were generated using the CelSeq2 protocol (Hashimshony et al., 2016 Genome Biol.) with the following adaptations: Second strand synthesis was performed using NEBNext Second Strand Synthesis module (NEB, #E6111S) in a final reaction volume of 8 µl and NucleoMag NGS Clean-up and Size select magnetic beads (Macherey-Nagel, 7449970.5) were used for all DNA purification and size selection steps.

value: Smchd1[del/+] Vav.Cre[T/+] Smchd1[del/del] Vav.Cre[T/+]


title: B210_del

value: B cells


title: B202_het


title: B167_het


title: B166_del

value: Smchd1[del/del] Vav.Cre[T/+]


title: CD56+_NK

description: PBMCs isolated for CD56+ cells


title: YTcKO+H151_2


title: YTcKO_2

description: Gene expression of YAP/TAZ KO fibroblasts


title: scRNA-seq_PMA_6h_Donor1

growth_protocol: Cryopreserved human peripheral blood mononuclear cells (PBMCs) were purchased from Allcells. Cells were quickly thawed in a 37°C water bath, rinsed with culture medium (RPMI 1640 medium supplemented with 15% FBS and 1% Pen/Strep) and then treated with 0.2 U/μL DNase I in 10mL of culture medium at 37°C for 30 min. After DNase I treatment, cells were washed with medium once, filtered with a 35 μm cell strainer and cell viability and concentration were measured with trypan blue on the TC20 Automated Cell Counter. Cell viability was greater than 90% for all samples.

extract_protocol:
After stimulation, cells were harvested and washed twice with ice cold 1x PBS + 0.1% BSA and cell viability and concentration were measured with trypan blue on the TC20 Automated Cell Counter.
scRNA-seq libraries were generated using the SureCell WTA 3′ Library Prep Kit for the ddSEQ System (20014280, Illumina) with the following modifications. A higher concentration of beads was used to obtain 1,000-2,000 single-cells per emulsion, whilst minimizing the number of droplets with multiple beads to < 10%. Furthermore, Bst 2.0 WarmStart (M0538S, NEB) was added to the droplet mix to perform temperature activated second strand synthesis in droplets.

treatment_protocol: Cells were plated at a concentration of 1 x 10^6 cell/mL, rested at 37°C and 5% CO2 for 1 h and then treated with the specified concentrations of the following stimulants (or DMSO as a control) for either 1 h or 6 h: 1) 20 ng/mL Lipopolysaccharide (LPS), 2) 50 ng/mL Phorbol 12-myristate 13-acetate (PMA) + 250 ng/mL Ionomycin calcium salt, 3) 20 ng/mL Interferon gamma (IFN-Ɣ). For the Golgi inhibitor experiments, cells were incubated for 6 h with GolgiPlug at a 1:1000 dilution plus stimulants at the concentrations indicated above (or GolgiPlug only as a control).

value: PBMC

tag: stimulation

value: PMA/ionomycin

tag: donor

value: Donor 1

tag: time

value: 6 h


title: scRNA-seq_PMAGolgiPlug_6h_Donor1

value: PMA/ionomycin + Golgi inhibitor


title: scRNA-seq_PMA_6h_Donor3

value: Donor 3


title: scRNA-seq_PMA_1h_Donor4

value: Donor 4

value: 1 h


title: scRNA-seq_PMA_1h_Donor2

value: Donor 2


title: scRNA-seq_LPSGolgiPlug_6h_Donor2

value: LPS + Golgi inhibitor


title: YTcKO_1

value: Primary dermal fibroblasts

value: R26-CAG-CreER; Yap1 fl/fl; Wwtr1 fl/fl


title: Control_1

description: Gene expression of control fibroblasts

value: Yap1 fl/fl; Wwtr1 fl/fl

value: 72hr treatment with 1 μM 4OH-Tamoxifen


title: scRNA-seq_LPS_1h_Donor4

value: LPS


title: scRNA-seq_LPS_6h_Donor1


title: CD19+

description: PBMCs isolated for CD19+ cells


title: scRNA-seq_PMA_1h_Donor1


title: CD8+_T

description: PBMCs isolated for CD8+ cells


title: scRNA-seq_PMAGolgiPlug_6h_Donor3


title: scRNA-seq_IFN_6h_Donor2

value: Interferon gamma


title: scRNA-seq_IFN_6h_Donor3


title: scRNA-seq_ControlGolgiPlug_6h_Donor3

value: Control + Golgi inhibitor


title: scRNA-seq_PMA_1h_Donor3

value: PBMC


title: scRNA-seq_PMA_6h_Donor2

value: PMA/ionomycin


title: scRNA-seq_LPSGolgiPlug_6h_Donor1

value: Donor 1


title: scRNA-seq_LPS_6h_Donor4

value: 6 h


title: scRNA-seq_LPS_6h_Donor2


title: scRNA-seq_LPS_6h_Donor3


title: CD4+_T

description: PBMCs isolated for CD4+ cells


title: scRNA-seq_IFNGolgiPlug_6h_Donor1

value: Interferon gamma + Golgi inhibitor


title: scRNA-seq_LPS_1h_Donor3

value: Donor 3


title: scRNA-seq_Control_6h_Donor2

value: Control


title: scRNA-seq_LPS_1h_Donor2

value: 1 h


title: scRNA-seq_LPS_1h_Donor1


title: scRNA-seq_PMAGolgiPlug_6h_Donor2

value: PMA/ionomycin + Golgi inhibitor

value: Donor 2


title: scRNA-seq_IFNGolgiPlug_6h_Donor3


title: scRNA-seq_LPSGolgiPlug_6h_Donor3

value: LPS + Golgi inhibitor


title: scRNA-seq_Control_1h_Donor2


title: scRNA-seq_Control_1h_Donor1


title: scRNA-seq_IFNGolgiPlug_6h_Donor2


title: scRNA-seq_PMA_6h_Donor4

value: Donor 4


title: scRNA-seq_IFN_1h_Donor3


title: scRNA-seq_IFN_6h_Donor1


title: scRNA-seq_IFN_1h_Donor1


title: ATAC-seq_PMAGolgiPlug_6h_Donor1

data_processing:
Per-read bead barcodes were parsed and trimmed using UMI-TOOLs (https://github.com/CGATOxford/UMI-tools). Constitutive elements of the bead barcodes were assigned to the closest known sequence allowing for up to 1 mismatch per 6-mer or 7-mer (mean >99% parsing efficiency across experiments).
Paired-end reads were aligned to hg19 using BWA (http://bio-bwa.sourceforge.net/) on the Illumina BaseSpace online application.
We used bead-based ATAC-seq processing (BAP) (https://github.com/caleblareau/bap), to identify systematic biases (i.e. reads aligning to an inordinately large number of barcodes), barcode-aware deduplicate reads, and perform merging of multiple bead barcode instances associated with the same cell. Barcode merging is necessary due to the nature of the BioRad SureCell scATAC-seq procedure used in this study, which enables multiple beads per droplet. BAP uses as input an alignment (.bam) file for a given experiment with a bead barcode identifier indicated by a SAM tag.
Genome-wide chromatin accessibility peaks were called using MACS v2 (MACS2) (Zhang et al., 2008) on the merged aligned scATAC-seq reads per treatment condition, generating a list of peak summit calls per condition. As previously described, summits were then ranked per condition based on their FDR score (from MACS2), and the summit scores rank-normalized such that the normalized summit scores rendered are comparable across conditions (Satpathy et al., 2019). Peak summits were then padded by 400 bases on either end (generating 801 bp windows), and overlapping peak windows filtered iteratively such that windows with higher scores were retained at each step. This resulted in a filtered list of disjoint peaks (n=219,136), which were finally resized to 301 bp (i.e. + 150 bp from each peak summit) and used for all downstream analyses.
A matrix of reads in peaks counts for single cells was obtained by counting the number of uniquely aligned fragments (with coordinates offset +4/-5 bp for the +/- strand to adjust for Tn5 integration) overlapping the determined peak window genomic ranges, grouped by cell barcode ID, done using custom R code
Genome_build: hg19
Supplementary_files_format_and_content: Peak file (BED) contains chromsome, start and end coordinates for determined chromatin accessibility peak window ranges. cellMeta file contains single cell barcode information for the final set of filtered scATAC stimulation cells used in the analysis. Fragments.tsv.gz files contain all Tn5-corrected coordinates for aligned fragments generated using BAP, which can be used to overlap with peaks to get counts of Tn5 insertions falling within peaks for each cell barcode.

extract_protocol:
After stimulation, cells were harvested and washed twice with ice cold 1x PBS + 0.1% BSA and cell viability and concentration were measured with trypan blue on the TC20 Automated Cell Counter. For a detailed description of tagmentation protocols and buffer formulations refer to the SureCell ATAC-Seq Library Prep Kit User Guide (17004620, Bio-Rad). Harvested cells and tagmentation related buffers were chilled on ice. Lysis was performed simultaneously with tagmentation. Washed and pelleted cells were resuspended in Whole Cell Tagmentation Mix containing 0.1% Tween-20, 0.01% Digitonin, 1x PBS supplemented with 0.1% BSA, ATAC Tagmentation Buffer and ATAC Tagmentation Enzyme (ATAC Tagmentation Buffer and Enzyme are both included in the SureCell ATAC-Seq Library Prep Kit (17004620, Bio-Rad)). Cells were mixed and agitated on a ThermoMixer for 30 min at 37°C. Tagmented cells were kept on ice prior to encapsulation.
Tagmented cells were loaded onto a ddSEQ Single-Cell Isolator. Single-cell ATAC-seq libraries were prepared using the SureCell ATAC-Seq Library Prep Kit (17004620, Bio-Rad) and SureCell ddSEQ Index Kit (12009360, Bio-Rad). Bead barcoding and sample indexing were performed in a C1000 Touch™ Thermal cycler with a 96-Deep Well Reaction Module: 37°C for 30 min, 85°C for 10 min, 72°C for 5 min, 98°C for 30 sec, 8 cycles of 98°C for 10 sec, 55°C for 30 sec, and 72°C for 60 sec, and a single 72°C extension for 5 min to finish. Emulsions were broken and products cleaned up using Ampure XP beads. Barcoded amplicons were further amplified using a C1000 Touch™ Thermal cycler with a 96-Deep Well Reaction Module: 98°C for 30 sec, 6-9 cycles (cycle number depending on the cell input, Section 4 Table 3 of the User Guide) of 98°C for 10 sec, 55°C for 30 sec, and 72°C for 60 sec, and a single 72°C extension for 5 min to finish. PCR products were purified using Ampure XP beads and quantified on an Agilent Bioanalyzer using the High-Sensitivity DNA kit. Libraries were loaded at 1.5 pM on a NextSeq 550 using the NextSeq High Output Kit and sequencing was performed using the following read protocol: Read 1 118 cycles, i7 index read 8 cycles, and Read 2 40 cycles. A custom sequencing primer is required for Read 1 (16005986, Bio-Rad; included in the kit).


title: ATAC-seq_PMAGolgiPlug_6h_Donor2


title: scRNA-seq_ControlGolgiPlug_6h_Donor2


title: scRNA-seq_ControlGolgiPlug_6h_Donor1


title: scRNA-seq_Control_6h_Donor4


title: ATAC-seq_PMA_6h_Donor1


title: ATAC-seq_PMA_6h_Donor2


title: ATAC-seq_PMA_6h_Donor4


title: scRNA-seq_Control_6h_Donor1


title: ATAC-seq_PMA_1h_Donor3


title: ATAC-seq_PMA_1h_Donor4


title: scRNA-seq_Control_6h_Donor3


title: scRNA-seq_Control_1h_Donor3


title: scRNA-seq_IFN_1h_Donor2


title: ATAC-seq_LPSGolgiPlug_6h_Donor3


title: scRNA-seq_Control_1h_Donor4


title: ATAC-seq_PMAGolgiPlug_6h_Donor3


title: ATAC-seq_PMA_1h_Donor1


title: ATAC-seq_LPS_6h_Donor4


title: ATAC-seq_PMA_6h_Donor3


title: ATAC-seq_PMA_1h_Donor2


title: ATAC-seq_LPS_6h_Donor2


title: ATAC-seq_LPS_6h_Donor1