title: 11.3 Wk human fetal, snATAC-seq, rep F1

description: 10X Chromium Single Cell ATAC v1.1

data_processing:
Sequencing reads were aligned to the mouse genome (atac-GRCh38-1.2.0) with the Cell Ranger atac software (version 1.2.0) using STAR aligner on the University of Southern California High Performance Cluster. The samples were aggregated using cellranger-atac aggr.  Non-nucleotide, processed feature-barcode information is provided. Controlled access to raw fastq files is available through dbGaP. The files used in the analysis are provided (fragments.tsv.gz, fragments.tsv.gz.tbi, singlecell.csv, filtered_peak_bc_matrix.h5) compressed into tar.gz files.
Assembly: atac-GRCh38-1.2.0
Supplementary files format and content: fragments.tsv.gz
Supplementary files format and content: fragments.tsv.gz.tbi
Supplementary files format and content: singlecell.csv
Supplementary files format and content: filtered_peak_bc_matrix.h5

extract_protocol:
From the harvested P0 mouse kidneys, nuclei were isolated as previously described in(Wilson et al., 2019). Briefly, flash frozen kidney pieces were thawed on ice and dissected into smaller pieces (<1mm) with a razor blade and then dounced in cold Nuclei EZ Lysis Buffer (Sigma, N3408) supplemented with protease inhibitor (Roche; 05892791001) and RNAse inhibitors (Promega, N2615; Thermo Fisher Scientific, AM2696). The tissue was dounce grinded 30 times with a loose pestle (Sigma, P0485), and then filtered through a 200um strainer (pluriSelect, 43-50200). The tissue was dounce grinded 10 times with a tight pestle, and then incubated for 5 mins on ice. Cells were filtered through 40uM filter (pluriSelect ,43-50040) and pelleted at 500g for 5min at 4°C in a swinging bucket centrifuge. Supernatant was removed and nuclei pellet resuspended in Nuclei EZ lysis buffer with RNAse inhibitors, incubated an additional 5 mins on ice and pelleted again. The final pellet was resuspended in 4°C Nuclei Buffer (10X Genomics, #2000207).
Chromium_NextGEM_SingleCell_ATAC_ReagentKits_v1.1_UserGuide (CG000209)


title: S13-FFPE5_P3

status: Public on Jun 20 2024

type: SRA

city: Scottsdale

first: Xianfeng

last: Chen

state: AZ

address: 13400 E Shea Blvd

country: USA

institute: Mayo Clinic

library_source: genomic

data_processing:
processed with our customoized pipeline which are modified from missionbio tapestri V2 pipeline
Assembly: hg19
Supplementary files format and content: ucsf_chapman.bed
Supplementary files format and content: amplicon design file

molecule: genomic DNA

organism: Homo sapiens

source_name: Surgical resection high grade serous ovarian carcinoma grade 3 stage 3C

extract_protocol:
flow sorting
tapestri single cell sequencing platform
scDNA-seq

tag: tissue


title: S10-FF6_P3

source_name: Surgical resection ovarian endometrriod carcinoma grade 2 stage 3B


title: 11.1 Wk human fetal, snRNA-seq, rep M2

city: Los Angeles

first: Andrew

middle: P

last: McMahon

state: California

address: 1425 San Pablo St, BCC 312

department: Stem Cell Biol & Regen Med

institute: University of Southern California

description: 10X Chromium Single Cell 3' v3

library_source: transcriptomic single cell

data_processing:
Sequencing reads were aligned to the human genome (GRCh38-2020-A) with the Cell Ranger software (version 5.0.1) using STAR aligner on the University of Southern California High Performance Cluster. The samples were aggregated using cellranger aggr. The processed files (filtered_feature_bc_matrix.h5) are provided. Controlled access to raw fastq files is available through dbGaP.
Assembly: GRCh38-2020-A
Supplementary files format and content: filtered_feature_bc_matrix.h5

molecule: polyA RNA

source_name: Kidney tissue

extract_protocol:
Cryopreserved human fetal kidneys were processed with optimized single-nuclei dissociation protocol to minimize potential tissue damage artifacts from frozen samples and loss of intact RNA molecules during the dissociation process. Briefly, the tissues were transported in DMEM (5% FBS, 25mM HEPES), removed from capsules, dissected into <2mm pieces and flash frozen in liquid nitrogen for later isolation. Nuclei isolation from flash frozen tissue was performed by the same protocol used with mouse tissue described above. For sex identification, a small amount of the donor tissue was lysed, and DNA was isolated by incubating in DirectPCR Lysis Reagent (Qiagen, #102-T) with 1% Proteinase K (Roche, 3115879001). Donor tissue was then sexed using primers for Y-specific human SRY (SRY-FOR: CCC ATG AAC GCA TTC ATT GTG TGG/ SRY-REV: ATT TTA GCC TTC CGA CGA GGT CGA TA), and ZFX/ZFY (ZFX/ZFY FOR: GCA CTT CTT TGG TAT CTG AGA AAG T/ ZFX/ZFY REV: ATA ATC ACA TGG AGA GCC ACA AGC T) to confirm DNA isolation quality.
Chromium_SingleCell_3'_ReagentKits_v3_UserGuide (CG000183)

value: Kidney tissue

tag: cell type

value: Kidney cells

tag: age

value: 11.1 Wk human fetal

tag: treatment


title: 11.6 Wk human fetal, snATAC-seq, rep M3

description: 10X Chromium Single Cell ATAC v1.1

value: 11.6 Wk human fetal


title: wt dox_3

city: Würzburg

first: Robert

last: Blum

address: Josef-Schneider-Str. 11

department: Department of Neurology

country: Germany

institute: University Hospital Würzburg

description: stable expression (after lentiviral infection) of doxycycline inducible TrkB-wt

library_source: transcriptomic

data_processing:
Base calling with Illumina NextSeq RTA v3.7.17
FASTQ conversion with bcl2fastq v2.20.0.422
FASTQ quality and adapter trimming using Cutadapt (Martin, 2011) version 2.5 (cutadapt parameters: --nextseq-trim=20 -m 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC)
Alignment of trimmed reads to human genome (GRCh38.p13 primary assembly and mitochondrion) using STAR (Dobin et al., 2013)  v2.7.2b with default parameters based on RefSeq annotation version 109.20210226
Calculation of read counts on exon level summarized for each gene (RefSeq annotation version 109.20210226 for GRCh38.p13) using featureCounts v1.6.4 from the Subread package (Liao et al., 2014). Multi-mapping and multi-overlapping reads were counted strand-specific and reversely stranded with a fractional count for each alignment and overlapping feature (command line parameters: -s 2 -t exon -M -O –fraction).
Genome_build: GRCh38.p13 (primary assembly and mitochondrion)
Supplementary_files_format_and_content: Character (TAB) separated value file containing mRNA abundance measurements

molecule: total RNA

source_name: U87MG (ATCC #HTB-14) cell line

growth_protocol: U87MG stably expressing the lentiviral TrkB constructs (either wt-TrkB, YFF or SQSTM1-NTRK2) were seeded at a density of 200.000 cells in 35 mm cell culture dishes (Falcon). All cells were grown in media containing 1µg/ml Puromycin. The cells were further treated with 1 µg/ml doxycycline to induce expression of the corresponding TrkB-related constructs (Dox on). For control, the solvent DMSO was added. 24 h after Dox-induction, some of the cell culture dishes were treated with 1 µg/ml LOXO-101 (Larotrectinib). After another 24h, cells were lysed and RNA was extracted (Qiagen RNeasy mini kit #74104). As a control, RNA was also extracted from untransformed and uninfected U87MG cells.

extract_protocol:
Total RNA was extracted from cell cultures using the Qiagen RNeasy Mini Kit.
RNA quality was checked using a 2100 Bioanalyzer with the RNA 6000 Nano kit (Agilent Technologies). The RIN for all samples was ≥9.0. DNA libraries suitable for sequencing were prepared from 500 ng of total RNA with oligo-dT capture beads for poly-A-mRNA enrichment using the TruSeq Stranded mRNA Library Preparation Kit (Illumina) according to manufacturer’s instructions (½ volume). After 14 cycles of PCR amplification, the size distribution of the barcoded DNA libraries was estimated ~300 bp by electrophoresis on Agilent DNA 1000 Bioanalyzer microfluidic chips.

treatment_protocol: The cells were treated with 1 µg/ml doxycycline for 48 hours to induce expression of the corresponding TrkB-related constructs (Dox on). To acutely block kinase activity, cells were treted with the Trk kinase inhibitor 1 µg/ml LOXO-101 (Larotrectinib).

value: doxycycline, 48h

tag: genetic background


title: YFF dox_3

description: stable expression (after lentiviral infection) of doxycycline inducible TrkB-YFF mutant


title: YFF ctr_2

value: untreated


title: 10.6 Wk human fetal, snATAC-seq, rep M1

description: 10X Chromium Single Cell ATAC v1.1

value: 10.6 Wk human fetal


title: 11.1 Wk human fetal, snATAC-seq, rep M2

description: 10X Chromium Single Cell ATAC v1.1


title: YFF ctr_1


title: SAMPLE 44

city: HeFei

first: zhang

middle: xiao

last: jing

state: AnHui

address: 81 Meishan Road

department: dermatology

country: China

institute: Anhui Medical University

description: +:Means a positive test. -:Means a negative test. NA:This examination was not performed

data_processing:
In this project, we sequence 45 samples used DNBSEQ platform, averagely generating about  6.67G Gb bases per sample. The average mapping ratio with reference genome is 94.50%, the  average mapping ratio with gene is 66.29%; 17826 genes were identified.
The raw data contains reads of low quality, reads with adaptor sequences and reads with high  levels of N base. Those reads need to be filtered before the data analysis for reliability analysis  results.
Assembly: GCF_000001405.39_GRCh38.p13

source_name: PBMC

extract_protocol: Peripheral venous blood was collected from 45 SLE patients (5ml per patient), PBMC was extracted, Trizol was added and sent to DNBSEQ platform for sequencing.

value: PBMC

tag: disease state

value: SLE

tag: Sex

value: female

tag: esr

tag: crp

tag: aha

tag: snrnp

tag: anti-smith

tag: sledai

tag: group

value: sSLE


title: SAMPLE 45


title: RNA-Seq of HEK293T:C2_Cas13_NT

city: Nanjing

first: Shu

last: Xu

state: Jiangsu Province

address: China Pharmaceutical University

institute: China Pharmaceutical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Assembly: After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Supplementary files format and content: FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.

source_name: cell line

growth_protocol: Cells were maintained in Dulbecco’s modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum (HyClone), 100 U/mL penicillin, and 100 µg/mL streptomycin at 37 °C with 5% CO2 incubation. Cells were seeded into 6-well plates (Corning) 24 h prior to transfection at a density of 200,000 cells per well.

extract_protocol:
Total RNA was prepared from transfection experiments after 72 h using a RNA Isolation Reagent (R701-01, Vazyme). A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations
Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample

treatment_protocol: Cells were transfected by using TransIntro EL Transfection Reagent following the manufacturer’s recommended protocol. For each well of a 6-well plate, 4 μg plasmids were transfected and 500 pmoL of DNA probes were transfected 24 h later.

value: cell line

tag: cell line

value: HEK297T cell

value: Human Embryonic Kidney 293 Cells

tag: genotype

value: TransIntro EL Transfection Reagent


title: SAMPLE 43


title: line ctr_3

description: cell line as control

value: unaltered


title: line ctr_4

description: cell line as control


title: RNA-Seq of HEK293T:D1_Cas13_T

value: HEK298T cell


title: SAMPLE 42


title: RNA-Seq of HEK293T:B2_Taqtth_NT

value: HEK295T cell

value: TaqTth-KRASknockdown-control


title: SAMPLE 40


title: SAMPLE 41


title: SAMPLE 39


title: RNA-Seq of HEK293T:C3_Taqtth_T

value: HEK296T cell

value: TaqTth-KRASknockdown-test


title: SAMPLE 38


title: SAMPLE 37


title: RNA-Seq of HEK293T:A2_siRNA_T

value: HEK293T cell

value: siRNA-KRASknockdown-test


title: SAMPLE 36


title: DMF_not_Formed, scRNAseq

city: New Orleans

first: Alejandra

last: Martinez Lege

state: United States

address: 1430 Tulane Ave

department: Neurosurgery

institute: Tulane University

description: 10X Genomics

data_processing:
10x Cell Ranger V.4.0 was used to generate Fastq files, perform alignment,filtering,barcode counting,UMI counting and aggregation.
Seurat V.4.02 for scRNA-seq
Assembly: mm10
Supplementary files format and content: H5 file filtered-gene-barcode-matrix can be deconvoluted to tsv and mtx files

organism: Mus musculus

source_name: Circle of Willis

extract_protocol:
total RNA
Libraries were prepared from individual cells using the droplet-based method as was outlined by 10x Genomics. Indexed libraries were sequenced on a NextSeq 2000 (Illumina) sequencer using P3 flow cell
v3.chemistry 10X Genomics

value: Circle of Willis

value: DMF


title: line ctr_1

description: cell line as control

value: untreated


title: CE-12

city: Philadelphia

first: Ramkrishna

last: Mitra

state: Pennsylvania

address: 233 S 10th street

institute: Thomas Jefferson University

data_processing:
Adapter sequence trimming was performed by TrimGalore
The tools Hisat2 and StringTie were used to perform sequence mapping and transcript assembling, respectively.
For differential expression analysis, read counts were imported into the tool edgeR.
Assembly: GRCh38
Supplementary files format and content: Ensembl gene IDs and read counts are provided in tab-delimited text files as the processed data files.

growth_protocol: DLBCL parental cell lines were purchased from and cultured as described by ATCC

extract_protocol:
TRIzol Reagent from Invitrogen Cat # 15596026
NEBNext Ultra II RNA Library Preparation Kit for SUDHL6 and Illumina Stranded Total RNA Prep, ligation with RiboZero Plus for SUDHL16.
RNA-sequencing for SUDHL6 and SUDHL16 parental and ABT-199/venetoclax-resistant cell lines were done using Illumina HiSeq 4000 and NovaSeq 6000 platforms, respectively.

treatment_protocol: Parental DLBCL ABT-199/venetoclax-resistant DLBCL cell lines were generated by chronic exposure to gradually increasing concentrations of ABT-199/venetoclax and could grow at a concentration of 10x the original IC50.

value: DLBCL


title: SAMPLE 35

value: PBMC

value: SLE

value: female

value: sSLE


title: SAMPLE 33


title: mouse DRG cell culture, 14 days post infection with Neurog2-Neurog1-DsRed, rep1

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.1
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: dorsal root ganglia

extract_protocol:
Primary DRG cells infected with CAG-Neurog2-Neurog1-DsRed were harvested at 14 dpi in an FCS-coated Falcon. Cells were filtered through a 100 µm cell filter (pluriSelect, Cat#43-10100-40) and sorted using a BD FACS Aria III Cell Sorter (BD Biosciences) based on DsRed fluorescence. Cells were collected through a 100 µm nozzle into 0.04% BSA in 1xPBS. Cells were centrifuged and diluted to a concentration of 1,000 cells/µl in 0.04% BSA in 1xPBS prior to single cell RNA sequencing.
Single-cell isolation and library preparation was performed via 10x Genomics Chromium Next GEM 3’ kit v3.1 following the manufacturer’s instruction. In brief, FACS-sorted cells were subsequently loaded on a 10x Genomics Chip G and encapsulated into Gel Bead-in-Emulsion (GEM) droplets, each containing a single cell along with a unique barcoded bead. Within these GEMs, the mRNA from each cell was reverse transcribed into complementary DNA (cDNA) using reverse transcriptase, with the process occurring on the uniquely barcoded beads. The resulting cDNA was then recovered from the GEM droplets and amplified to prepare sequencing libraries using PCR. During library preparation, additional sequences necessary for sequencing, such as adapter sequences, were incorporated into the cDNA fragments.

value: dorsal root ganglia

tag: developmental stage

value: adult (4-6 weeks)

tag: time

value: 14 days post infection

value: wild type

value: infection with Neurog2-Neurog1-DsRed


title: SAMPLE 32

tag: tissue


city: Vienna

first: Moritz

middle: M

last: Gaidt

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

description: rRNA depleted, total RNA-seq bone marrow immature B cells Ikzf1(AID/AID) Ikzf3(AID/AID) R26(Tir2/Tir2) Ctr (8h)_2

data_processing:
RNA-Seq: Only reads that passed the Illumina quality filtering were processed.  Reads were filtered against rDNA with the Bowtie 2 program, and the remaining reads were aligned with the STAR program version 2.4.2a to the mm10 genome version of December 2011July 2007 (GRCm38NCBI37).  Alignments were quantified at the gene level, using a custom curated and extended version of the RefSeq annotation for mm10 (Woehner et al. 2016), based on a RefSeq data download from December 6, 2018. Annotation entries for introns were created by extrapolating from the annotated exons of each transcript. Quantification was done over the whole gene body, and for exons and introns separately, using subread featureCounts version 2.0.2. To include fragments covering exon-intron boundaries (which are most likely nascent fragments), but exclude pure exon counts, we subtracted exon-only covering paired end aligned fragments from counting, leaving us with intron and intron-exon-boundary covering read counts only. This procedure resulted in three different expression values for each gene – exon, intron, and no_exon.To visualize expression values in bar graph figures, we converted raw counts to normalized values, similar as done in TPMs (Transcripts Per Millions), by using concatenated exon and intron lengths, for exon and intron/no_exon counts, respectively.
Assembly: mm10
Supplementary files format and content: txt = normalized count values, such as TPMs, in ASCII text format tab delimited.

source_name: bone marrow

extract_protocol:
King Fisher RNA isolation, rRNA depletion
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: bone marrow

tag: cell type

value: immature B cells

tag: cell preparation

value: Ex-vivo FACS sorted from bone marrow

value: Ctr (8h)

tag: replicate number


title: SAMPLE 31

tag: disease state

tag: Sex

tag: age


title: SAMPLE 30

tag: esr

tag: crp

tag: aha


title: line ctr_2

description: cell line as control

tag: treatment

tag: genetic background

value: unaltered


title: RNA-Seq of HEK293T:B2_siRNA_NT

value: cell line

tag: cell line

value: HEK294T cell

value: Human Embryonic Kidney 293 Cells

value: siRNA-KRASknockdown-control

value: TransIntro EL Transfection Reagent


title: CE-10

value: DLBCL


title: SAMPLE 29

value: PBMC

value: SLE

value: female

tag: snrnp

tag: anti-smith

tag: sledai

tag: group

value: sSLE


description: rRNA depleted, total RNA-seq bone marrow Pre-B cells Ikzf1(AID/AID) Ikzf3(AID/AID) R26(Tir2/Tir2) 8h 5-Ph-IAA_2

tag: strain

tag: tissue

value: Pre-B cells

tag: genotype

value: 8h 5-Ph-IAA


title: SAMPLE 26


title: SAMPLE 34


description: rRNA depleted, total RNA-seq bone marrow immature B cells Ikzf1(AID/AID) Ikzf3(AID/AID) R26(Tir2/Tir2) Ctr (8h)_1

value: bone marrow

tag: cell type

tag: cell preparation

tag: replicate number


title: SAMPLE 21

tag: disease state

tag: Sex

tag: age

value: mSLE


description: rRNA depleted, total RNA-seq bone marrow immature B cells Ikzf1(AID/AID) Ikzf3(AID/AID) R26(Tir2/Tir2) 8h 5-Ph-IAA_2

value: immature B cells

value: Ex-vivo FACS sorted from bone marrow


title: SAMPLE 28

tag: esr

tag: crp

tag: aha


title: CE-9

tag: cell line


title: SAMPLE 27

tag: snrnp


title: SAMPLE 22

tag: anti-smith


title: SAMPLE 25

tag: sledai


description: rRNA depleted, total RNA-seq bone marrow Pre-B cells Ikzf3(AID/AID) R26(Tir2/Tir2) Ctr_2

value: Ikzf3(AID/AID) R26(Tir2/Tir2)

tag: treatment

value: Ctr


description: rRNA depleted, total RNA-seq bone marrow Pre-B cells Ikzf3(AID/AID) R26(Tir2/Tir2) 8h 5-Ph-IAA_2

tag: strain


title: CE-8


title: SAMPLE 24

tag: tissue

tag: group


title: NHEK, 3H, Sham 0, R2

city: Rennes

first: Frédéric

last: Chalmel

state: France

address: 9 avenue du Pr. Léon Bernard

department: Physiology and physiopathology of the urogenital tract

country: France

institute: Inserm U1085-Irset

description: NHEK treatement during 3 hours Sham 0 Replicate 2, E1

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Samples demultiplexing transforms the raw paired-end fastq files into a single-end fastq file for each sample.
All sixteen bases of the first read (from the read pairs) must have quality scores of at least 10 and the first six bases must correspond exactly to a designed well-specific barcode.
The second reads were aligned to the human reference transcriptome
Assembly: hg38
Supplementary files format and content: bam alignment files obtained from bwa
Supplementary files format and content: Expression file in dat format. Contains for each sample, the number of unique umis (unique molecular identifier) associated with the 28278 genes detected.

source_name: human primary culture keratinocyte (NHEK3N)

growth_protocol: Two different primary culture of human keratinocyte cells that are pools issue from 3 donors and are named HEK_3N and NHEK_3N and were cultured in were cultured onto collagen IV-coated plates in supplemented keratinocyte serum-free medium (SFM). Cell were used between passages 4 and 9. In parallel, the keratinocyte cell line HaCaT was used between passages 5 and 10. They were maintained and exposed in DMEM  All experiments were replicated between 3 to 6 times.

extract_protocol:
RNA was harvested using RNeasy Micro Kit (Qiagen, Germany) including on-column DNase I treatment according to manufacturer’s instructions.
Libraries were prepared from 10 ng of total RNA. Poly(A) tailed mRNAs were tagged with universal adapters, well-specific barcodes and unique molecular identifiers (UMIs) during reverse transcription. Barcoded cDNAs from multiple samples were then pooled, amplified, and tagmented using a transposon-fragmentation approach that enriches for 3′ ends of cDNA. The resulting library of 350-800 bp was sequenced on an Illumina Hiseq 4000.
3'Bulk RNA Barcoding and sequencing (BRB-seq)

treatment_protocol: HEK_3N, NHEK_3N and HaCaT Cells were Sham-exposed or exposed to IPD of 20 mW/cm² or heat exposed to a temperature equivalent to those reached during the MMW exposure.HaCaT cells were expoed either on MMW gradient  5 to 20 mW/cm² during 3 hours or 10 MW/cm² during 14 hours. Heat control were performed at the temperature of clee reached during the exposure.

value: NHEK

tag: cell type

value: human primary culture keratinocyte

tag: exposure


title: SAMPLE 23


description: rRNA depleted, total RNA-seq bone marrow immature B cells Ikzf1(AID/AID) Ikzf3(AID/AID) R26(Tir2/Tir2) 8h 5-Ph-IAA_1

tag: genotype

tag: cell preparation

tag: replicate number


title: SAMPLE 20

tag: disease state

tag: Sex

tag: age


title: NHEK, 3H, Sham 0, R3

description: NHEK treatement during 3 hours Sham 0 Replicate 3, H1


title: SAMPLE 19

tag: esr

tag: crp

tag: aha


title: CE-11

tag: cell line


title: NHEK, 3H, Sham 0, R1

description: NHEK treatement during 3 hours Sham 0 Replicate 1, B1


title: SAMPLE 17

tag: snrnp

tag: anti-smith

tag: sledai


title: NHEK, 3H, HSC 20, R2

description: NHEK treatement during 3 hours Heat Shock Control equivalent to "Expo 20 mW/cm²" Replicate 2, G1


title: SAMPLE 16

tag: tissue


title: SAMPLE 18

tag: group


title: CE-7

tag: cell type


title: SAMPLE 15


description: rRNA depleted, total RNA-seq bone marrow immature B cells Ikzf3(AID/AID) R26(Tir2/Tir2) Ctr_1

tag: strain

tag: treatment


title: NHEK, 3H, HSC 20, R1

description: NHEK treatement during 3 hours Heat Shock Control equivalent to "Expo 20 mW/cm²" Replicate 1, D1

tag: exposure


title: SAMPLE 14


description: rRNA depleted, total RNA-seq bone marrow immature B cells Ikzf3(AID/AID) R26(Tir2/Tir2) 8h 5-Ph-IAA_2

tag: genotype

tag: cell preparation

tag: replicate number


description: rRNA depleted, total RNA-seq bone marrow immature B cells Ikzf3(AID/AID) R26(Tir2/Tir2) 8h 5-Ph-IAA_1


title: SAMPLE 10

tag: disease state

tag: Sex

tag: age


title: SAMPLE 8

tag: esr

tag: crp

tag: aha


title: NHEK, 3H, Expo 20, R2

description: NHEK treatement during 3 hours Exposition at 20 mW/cm² Replicate 2, C1

tag: cell line


description: rRNA depleted, total RNA-seq bone marrow Pre-B cells Ikzf1(AID/AID) Ikzf3(AID/AID) R26(Tir2/Tir2) Ctr_2


title: NHEK, 3H, HSC 20, R3

description: NHEK treatement during 3 hours Heat Shock Control equivalent to "Expo 20 mW/cm²" Replicate 3, A2


title: SAMPLE 9

description: +:Means a positive test. -:Means a negative test. NA:This examination was not performed

tag: snrnp

tag: anti-smith

tag: sledai


title: SAMPLE 13

tag: tissue

tag: group


title: NHEK, 3H, Expo 20, R3

description: NHEK treatement during 3 hours Exposition at 20 mW/cm² Replicate 3, F1

tag: cell type


title: NHEK, 3H, Expo 20, R1

description: NHEK treatement during 3 hours Exposition at 20 mW/cm² Replicate 1, A1

tag: exposure


description: rRNA depleted, total RNA-seq bone marrow Pre-B cells Ikzf1(AID/AID) Ikzf3(AID/AID) R26(Tir2/Tir2) 8h 5-Ph-IAA_1

tag: strain

tag: genotype

tag: treatment


title: SAMPLE 6

tag: disease state


title: SAMPLE 7

tag: Sex


title: HEK3N, 3H, Sham 0, R3

description: HEK3N treatement during 3 hours Sham 0 Replicate 3, H2

source_name: human primary culture keratinocyte (HEK3N)


title: SAMPLE 5

tag: age


description: rRNA depleted, total RNA-seq bone marrow immature B cells Ikzf3(AID/AID) R26(Tir2/Tir2) Ctr_2

tag: cell preparation

tag: replicate number


description: rRNA depleted, total RNA-seq bone marrow Pre-B cells Ikzf3(AID/AID) R26(Tir2/Tir2) 8h 5-Ph-IAA_1


description: rRNA depleted, total RNA-seq bone marrow immature B cells Pax5(AID/AID) R26(Tir2/Tir2) 6h 5-Ph-IAA_2

value: Pax5(AID/AID) R26(Tir2/Tir2)

value: 6h 5-Ph-IAA


title: SAMPLE 2

tag: esr

tag: crp

tag: aha


title: SAMPLE 1

tag: snrnp

tag: anti-smith


title: SAMPLE 3

tag: tissue

tag: sledai


title: HEK3N, 3H, Sham 0, R4

description: HEK3N treatement during 3 hours Sham 0 Replicate 4, C3

tag: cell line

tag: cell type


title: SAMPLE 12

tag: group


title: SAMPLE 11


description: rRNA depleted, total RNA-seq bone marrow immature B cells Pax5(AID/AID) R26(Tir2/Tir2) 6h 5-Ph-IAA_1

tag: strain

tag: genotype


title: HEK3N, 3H, Sham 0, R1

description: HEK3N treatement during 3 hours Sham 0 Replicate 1, B2

tag: exposure


title: HEK293T_KAS-ATAC-seq, rep2

city: Chicago

first: Ruitu

last: Lyu

state: IL

address: 929 E 57th Street

department: Chemistry

institute: The University of Chicago

data_processing:
All data from KAS-ATAC-seq and ATAC-seq were produced in paired-end mode. The preprocessing, read alignment, and read alignments format conversion procedures for KAS-ATAC-seq and ATAC-seq data mirrored those for Opti-KAS-seq and KAS-seq.
Peak calling for KAS-ATAC-seq and ATAC-seq was accomplished via MACS2, targeting sharp peaks with a false discovery rate (FDR) threshold of 0.05.
Deduplicated KAS-seq reads were then transformed into bedGraph and bigWig formats using the deeptools bamCoverage and UCSC tools. Fragment size comparisons within KAS-ATAC-seq and ATAC-seq libraries were facilitated by the ATACseqQC Bioconductor package.
Assembly: hg19
Supplementary files format and content: bed, peaks list.
Supplementary files format and content: bigWig, read density.
Library strategy: KAS-ATAC-seq

growth_protocol: HEK293T cells were purchased from ATCC (CRL11268) and were cultured in DMEM (Gibco 11995) supplemented with 10% (v/v) fetal bovine serum (Gibco), 1% penicillin and streptomycin (Gibco) and grown at 37 °C with 5% CO2.

extract_protocol:
Subsequently, dilute this lysed solution with 1 ml of cold ATAC-RSB that has 0.1% Tween-20 (but devoid of NP40 or digitonin). Mix by inverting the tube five times. Centrifuge this mixture again at 500 RCF for 5 minutes at 4ºC and discard the supernatant. Resuspend the pellet with 100 µl of 10 mM N3-Kethoxial in PBS and then incubate at 37ºC with 500 rpm shaking for 10 minutes. After incubation, wash the nuclei by adding 1 ml of DPBS. Centrifuge the suspension at 500 RCF for 5 minutes at 4ºC, and subsequently remove the supernatant. Resuspend the nuclei pellet in 50 µl of the previously prepared Transposition Mix. Achieve a uniform mixture by pipetting up and down six times. Incubate the mixture in a thermomixer set to 37°C and 1,000 rpm for 30 minutes. Remove the tubes from the thermomixer, and immediately terminate the transposition reaction by adding 250 µL (five volumes) of DNA Binding Buffer from the DNA Clean and Concentrator-5 Kit and mix well by pipetting or inversion. Mix thoroughly and followed by brief centrifugation to collect the contents at the bottom of the tubes. Proceed with purifying the transposed DNA using the kit, according to the manufacturer's instructions.
Elute the purified DNA in 21 µl of elution buffer and store at -20°C for future use. Finally, utilize this eluted gDNA for the Click reaction and perform library preparation and sequencing according to the established ATAC-seq protocol (https://protocolexchange.researchsquare.com/article/nprot-6107/v1).

treatment_protocol: Initiate the procedure by collecting 50,000 viable cells, wash the collected cells with DPBS and centrifuge at 500 RCF for 5 minutes at 4ºC. Resuspend the cell pellet in 50 µl of ATAC-RSB containing 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin. Mix thoroughly by pipetting up and down three times and then incubate on ice for 3 minutes.

value: Human embryonic kidney

value: WT

tag: treatment

value: No treatment


title: HEK293T_ATAC-seq, rep2

data_processing:
All data from KAS-ATAC-seq and ATAC-seq were produced in paired-end mode. The preprocessing, read alignment, and read alignments format conversion procedures for KAS-ATAC-seq and ATAC-seq data mirrored those for Opti-KAS-seq and KAS-seq.
Peak calling for KAS-ATAC-seq and ATAC-seq was accomplished via MACS2, targeting sharp peaks with a false discovery rate (FDR) threshold of 0.05.
Deduplicated KAS-seq reads were then transformed into bedGraph and bigWig formats using the deeptools bamCoverage and UCSC tools. Fragment size comparisons within KAS-ATAC-seq and ATAC-seq libraries were facilitated by the ATACseqQC Bioconductor package.
Assembly: hg19
Supplementary files format and content: bed, peaks list.
Supplementary files format and content: bigWig, read density.


title: HEK293T_KAS-ATAC-seq, rep1


title: HEK3N, 3H, HSC 20, R2

description: HEK3N treatement during 3 hours Heat Shock Control equivalent to "Expo 20 mW/cm²" Replicate 2, F2


title: HEK3N, 3H, HSC 20, R4

description: HEK3N treatement during 3 hours Heat Shock Control equivalent to "Expo 20 mW/cm²" Replicate 4, D3


title: HEK293T_ATAC-seq, rep1


description: rRNA depleted, total RNA-seq bone marrow Pre-B cells Ikzf3(AID/AID) R26(Tir2/Tir2) Ctr_1


description: rRNA depleted, total RNA-seq bone marrow Pre-B cells Pax5(AID/AID) R26(Tir2/Tir2) 6h 5-Ph-IAA_2


title: SAMPLE 4

value: PBMC

tag: disease state

value: SLE

tag: Sex

value: female

tag: age


title: HEK3N, 3H, Sham 0, R2

description: HEK3N treatement during 3 hours Sham 0 Replicate 2, E2


title: HEK3N, 3H, HSC 20, R1

description: HEK3N treatement during 3 hours Heat Shock Control equivalent to "Expo 20 mW/cm²" Replicate 1, C2


description: rRNA depleted, total RNA-seq bone marrow Pre-B cells Pax5(AID/AID) R26(Tir2/Tir2) 6h 5-Ph-IAA_1

value: Pre-B cells

tag: cell preparation

tag: replicate number


title: HEK3N, 3H, HSC 20, R3

description: HEK3N treatement during 3 hours Heat Shock Control equivalent to "Expo 20 mW/cm²" Replicate 3, A3


description: rRNA depleted, total RNA-seq bone marrow Pre-B cells Pax5(AID/AID) Ctr_2

value: bone marrow


title: HEK3N, 3H, Expo 20, R2

description: HEK3N treatement during 3 hours Exposition at 20 mW/cm² Replicate 2, G2


description: rRNA depleted, total RNA-seq bone marrow immature B cells Pax5(AID/AID) Ctr_2


description: rRNA depleted, total RNA-seq bone marrow Pro-B cells Pax5(AID/AID) R26(Tir2/Tir2) 6h 5-Ph-IAA_2

value: Pro-B cells


description: rRNA depleted, total RNA-seq bone marrow immature B cells Pax5(AID/AID) Ctr_1

value: immature B cells


title: HEK3N, 3H, Expo 20, R4

description: HEK3N treatement during 3 hours Exposition at 20 mW/cm² Replicate 4, E3


title: HEK3N, 3H, Expo 20, R1

description: HEK3N treatement during 3 hours Exposition at 20 mW/cm² Replicate 1, D2


description: rRNA depleted, total RNA-seq bone marrow Pro-B cells Pax5(AID/AID) R26(Tir2/Tir2) 6h 5-Ph-IAA_1

value: Ex-vivo FACS sorted from bone marrow


description: rRNA depleted, total RNA-seq bone marrow Pro-B cells Pax5(AID/AID) Ctr_1


title: GCN2 SA100 2h only one repetition

type: RNA

city: Poznan

first: Marcin

last: Rucinski

address: Swiecicki 6

department: Histology and Embriology

country: Poland

institute: Poznan University of Medical Science

description: Gene expression data

hyb_protocol: Biotin-labeled fragments of cDNA (5.5 μg) were hybridized to Affymterix GeneChip Human Genome U219 ArrayStrip (16 h, 45°C).

scan_protocol: The array strips were scanned using an Imaging Station of GeneAtlas System (Thermo Fisher Scientific, MA, USA). The preliminary analysis of the scanned chips was carried out by means of Affymetrix GeneAtlas Operating Software (Affymetrix, Santa Clara, CA, USA).

data_processing: Obtained CEL files were subjected for background correction and normalization using RobustMultiarrayAveraging (RMA) algorithm implemented in affy package of BioConductor.

label: biotin

source_name: HAP1 cell line

label_protocol: The protocol involving transcription in vitro, biotin labelling and cDNA fragmentation for further hybridization was carried out using the Affymetrix GeneChip IVT Express Kit (Affymetrix, Santa Clara, CA, USA)

growth_protocol: HAP cell lines were cultured in Iscove’s modified Dulbecco’s medium (IMDM, Gibco #12440-053) supplemented with 10% FBS (Thermo Fisher Scientific #10270106) and 1% penicillin-streptomycin. All cell lines were maintained at 37°C with 5% CO2.

extract_protocol: Total RNA isolation was performed using the modified Chomczynski method with the use of TRI Reagent (Sigma, St Louis, MO, USA) and the RNeasy Mini Elute Cleanup Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions

treatment_protocol: Control (PAR) and S51A, ΔHRI, ΔGCN2, ΔPKR, ΔPERK HAP1 cells were exposed to lomustine (200 μM, 2 h) or NaAsO2 (100 μM, 2 h).

value: near-haploid human cell line derived from the KBM-7 chronic myelogenous leukemia (CML) cell line

tag: agent

value: lomustine


title: S51A SA100 2h only one repetition

description: Gene expression data


title: GCN2, lomustine, only one repetition

description: Gene expression data


title: PERK lomustine, only one repetition

description: Gene expression data

value: PERK


title: PKR SA100 2h 1 only one repetition

description: Gene expression data

value: PKR


title: PKR, lomustine, only one repetition

description: Gene expression data


title: HRI SA100 2h only one repetition

description: Gene expression data

value: HRI


title: PERK SA100 2h only one repetition

description: Gene expression data


title: S51A lomustine repetition B

description: Gene expression data


title: HRI lomustine repetition A

description: Gene expression data


title: HaCaT, ON, Sham 0, R2

description: HaCaT treatement overnight Sham 0 Replicate 2, E7

source_name: human keratinocyte cell line (HaCat)

value: HaCaT

value: human keratinocyte cell line


title: HRI lomustine repetition B

description: Gene expression data


title: PAR SA100 2h only one repetition

description: Gene expression data

value: PAR


title: HEK3N, 3H, Expo 20, R3

description: HEK3N treatement during 3 hours Exposition at 20 mW/cm² Replicate 3, B3

value: human primary culture keratinocyte


description: rRNA depleted, total RNA-seq bone marrow immature B cells Ebf1(AID/AID) R26(Tir2/Tir2) 6h 5-Ph-IAA_2

value: Ebf1(AID/AID) R26(Tir2/Tir2)

value: 6h 5-Ph-IAA


description: rRNA depleted, total RNA-seq bone marrow Pro-B cells Pax5(AID/AID) Ctr_2

value: Ctr


title: HaCaT, ON, Sham 0, R3

description: HaCaT treatement overnight Sham 0 Replicate 3, H7


description: rRNA depleted, total RNA-seq bone marrow immature B cells Ebf1(AID/AID) R26(Tir2/+) Ctr_2

value: Ebf1(AID/AID) R26(Tir2/+)


title: HaCaT, ON, Sham 0, R1

description: HaCaT treatement overnight Sham 0 Replicate 1, B7


description: rRNA depleted, total RNA-seq bone marrow immature B cells Ebf1(AID/AID) R26(Tir2/Tir2) 6h 5-Ph-IAA_1

value: bone marrow


title: HaCaT, ON, Sham 0, R4

description: HaCaT treatement overnight Sham 0 Replicate 4, C8


description: rRNA depleted, total RNA-seq bone marrow immature B cells Ebf1(AID/AID) R26(Tir2/+) Ctr_1


title: S51A lomustine Repetition A

description: Gene expression data


title: HaCaT, ON, HSC 10, R2

description: HaCaT treatement overnight Heat Shock Control equivalent to "Expo 10 mW/cm²" Replicate 2, F7


title: PAR lomustine repetition B

description: Gene expression data


title: ESTpro::MUTE, treatment, MNase

city: Stanford

first: Dominique

middle: C.

last: Bergmann

address: 371 Jane Stanford Way

department: Biology

institute: Stanford University

description: estrodial.bw

data_processing:
cutadapt to trim the raw reads
picard to remove PCR duplicates
bowtie2 to align the reads to TAIR10 gemone assembly
MACS2 (ChIP-seq) or DANPOS (MNase-seq) to define bound regions
Assembly: TAIR10
Supplementary files format and content: bw files to visualize the enrichment of corresponding reads

organism: Arabidopsis thaliana

source_name: seedling

extract_protocol:
DNA were extracted based on ChIP protocol or MNase-seq protocol (see methods part in the publication)
per manufacturer's instructions

value: seedling

value: estrodial


title: GCN2, no drugs, only one repetition

description: Gene expression data


title: S51A, no drugs, repetition B

description: Gene expression data


title: HaCaT, ON, HSC 10, R4

description: HaCaT treatement overnight Heat Shock Control equivalent to "Expo 10 mW/cm²" Replicate 4, D8


description: rRNA depleted, total RNA-seq bone marrow Pre-B cells Ebf1(AID/AID) R26(Tir2/Tir2) 6h 5-Ph-IAA_2

value: Pre-B cells

value: Ex-vivo FACS sorted from bone marrow


title: HRI no drugs repetition A

description: Gene expression data

value: near-haploid human cell line derived from the KBM-7 chronic myelogenous leukemia (CML) cell line


title: PKR, no drug, only one repetition

description: Gene expression data


title: cardiac allograft, tolerization protocol (DST CoB), rep1

first: Samantha

middle: L

last: Schroth

address: 320 E Superior St

institute: Northwestern University Feinberg School of Medicine

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: cardiac allograft

extract_protocol:
Cardiac allografts were perfused with PBS and subjected to digestion with Collagenase II and DNAse and subjected to independent CD45+ and pan DC magnetic enrichment and re-pooled at a 1:1 ratio per condition
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Briefly, single cells from splenic cell suspenion were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: cardiac allograft

value: BALB/c splenic cell infusion + antiCD40L (D0), anti-CD40L (D7), anti-CD40L (D14)


description: rRNA depleted, total RNA-seq bone marrow Pre-B cells Ebf1(AID/AID) R26(Tir2/Tir2) 6h 5-Ph-IAA_1


title: HRI, no drugs, repetition B

description: Gene expression data

value: HRI


title: cardiac allograft, acute rejection, rep1

description: 10x Genomics


title: PAR lomustine Repetition A

description: Gene expression data

value: lomustine


title: PAR, no drugs, repetition B

description: Gene expression data


title: PERK, no drug, only one repetition

description: Gene expression data

value: PERK


title: S51A no drug repetition A

description: Gene expression data


title: HaCaT, ON, HSC 10, R1

description: HaCaT treatement overnight Heat Shock Control equivalent to "Expo 10 mW/cm²" Replicate 1, C7

value: HaCaT

value: human keratinocyte cell line


description: rRNA depleted, total RNA-seq bone marrow Pre-B cells Ebf1(AID/AID) R26(Tir2/+) Ctr_2


title: PAR no drug repetition A

description: Gene expression data

value: PAR


title: HaCaT, ON, HSC 10, R3

description: HaCaT treatement overnight Heat Shock Control equivalent to "Expo 10 mW/cm²" Replicate 3, A8


title: 36wk_HF_SCN_6

city: Grand Forks

first: Junguk

last: Hur

state: ND

address: 1301 N. Columbia Rd. Stop 9037

department: Biomedical Sciences

institute: University of North Dakota

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then processed using the Tuxedo suite of sequence analysis programs. Reads were mapped to the NCBI reference mouse genome (mm10) to identify transcripts.
Trimmomatic software v0.36 (Bolger et al., 2014; PMID: 24695404) was used to remove the low-quality (Q<30) and sequencing adapters from raw reads. Clean reads were then mapped to the mouse reference genome (mm10) using HISAT2 (Kim et al., 2015; PMID: 25751142). The unique mapped reads to mouse genes were summarized with featureCounts (Liao et al., 2014; PMID: 24227677).
Assembly: NCBI38/mm10
Supplementary files format and content: tab-delimited text files include raw mapped counts for each Sample

source_name: sciatic nerve

extract_protocol:
Total RNA was isolated from DRG and SCN at 12 and 36 weeks of age from SD and HFD mice using a RNeasy Mini Kit (Qiagen, Germantown, MD). TapeStation (Agilent, Santa Clara, CA) was used to evaluate RNA quality and samples with an RNA integrity number of ≥8 were processed with the Illumina TruSeq mRNA Sample Prep v2 kit (Catalog #s RS122-2001, RS-122-2002; Illumina, San Diego, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: sciatic nerve

tag: diet

value: high-fat-diet


title: 36wk_WT_DRG_5

value: dorsal root ganglia

value: standard-diet


title: 36wk_HF_DRG_6


title: HaCaT, ON, Expo 10, R2

description: HaCaT treatement overnight Exposition at 10 mW/cm² Replicate 2, G7


title: 36wk_HF_SCN_5


title: 36wk_HF_DRG_5


description: rRNA depleted, total RNA-seq bone marrow Pre-B cells Ebf1(AID/AID) R26(Tir2/+) Ctr_1

value: bone marrow

value: Ebf1(AID/AID) R26(Tir2/+)

value: Ctr


description: rRNA depleted, total RNA-seq bone marrow Pro-B cells Ebf1(AID/AID) R26(Tir2/Tir2) 6h 5-Ph-IAA_2

value: Pro-B cells

value: Ebf1(AID/AID) R26(Tir2/Tir2)

value: Ex-vivo FACS sorted from bone marrow

value: 6h 5-Ph-IAA


title: ESTpro::MUTE, control, MNase

description: control.bw

value: seedling

value: mock


title: 12wk_HF_DRG_6


title: 36wk_WT_SCN_5


title: HaCaT, ON, Expo 10, R1

description: HaCaT treatement overnight Exposition at 10 mW/cm² Replicate 1, D7


description: rRNA depleted, total RNA-seq bone marrow Pro-B cells Ebf1(AID/AID) R26(Tir2/Tir2) 6h 5-Ph-IAA_1


title: 12wk_HF_DRG_5


title: 12wk_WT_DRG_6


description: rRNA depleted, total RNA-seq bone marrow Pro-B cells Ebf1(AID/AID) R26(Tir2/+) Ctr_2


title: 12wk_WT_DRG_5


title: HaCaT, ON, Expo 10, R4

description: HaCaT treatement overnight Exposition at 10 mW/cm² Replicate 4, E8


title: HaCaT, ON, Expo 10, R3

description: HaCaT treatement overnight Exposition at 10 mW/cm² Replicate 3, B8


title: 12wk_HF_SCN_6


title: HaCaT, 3H, Sham 0, R1

description: HaCaT treatement during 3 hours Sham 0 Replicate 1, F3


description: rRNA depleted, total RNA-seq bone marrow Pro-B cells Ebf1(AID/AID) R26(Tir2/+) Ctr_1


title: 12wk_WT_SCN_6


title: 12wk_HF_SCN_5


title: 36wk_HF_DRG_4


description: rRNA depleted, total RNA-seq bone marrow immature B cells Ikzf1(AID/AID) Ikzf3(AID/AID) R26(Tir2/Tir2) Ctr_2

value: immature B cells


title: 12wk_WT_SCN_5


description: rRNA depleted, total RNA-seq bone marrow immature B cells Ikzf1(AID/AID) Ikzf3(AID/AID) R26(Tir2/Tir2) Ctr_1


title: 36wk_WT_DRG_4


title: 36wk_HF_DRG_3


title: 36wk_WT_DRG_3


title: HaCaT, 3H, Sham 0, R2

description: HaCaT treatement during 3 hours Sham 0 Replicate 2, E4

value: HaCaT


description: rRNA depleted, total RNA-seq bone marrow immature B cells Ikzf1(AID/AID) Ikzf3(AID/AID) R26(Tir2/Tir2) 12h 5-Ph-IAA_2

value: 12h 5-Ph-IAA


title: HaCaT, 3H, Sham 0, R4

description: HaCaT treatement during 3 hours Sham 0 Replicate 4, C6

value: human keratinocyte cell line


title: 36wk_HF_SCN_4

value: sciatic nerve


description: rRNA depleted, total RNA-seq bone marrow immature B cells Ikzf1(AID/AID) Ikzf3(AID/AID) R26(Tir2/Tir2) 12h 5-Ph-IAA_1


title: HaCaT, 3H, Sham 0, R3

description: HaCaT treatement during 3 hours Sham 0 Replicate 3, D5


title: HaCaT, 3H, HSC 5, R1

description: HaCaT treatement during 3 hours Heat Shock Control equivalent to "Expo 5 mW/cm²" Replicate 1, H3


title: 36wk_HF_SCN_3

value: high-fat-diet


title: HaCaT, 3H, HSC 5, R2

description: HaCaT treatement during 3 hours Heat Shock Control equivalent to "Expo 5 mW/cm²" Replicate 2, G4


description: rRNA depleted, total RNA-seq bone marrow Pre-B cells Ikzf1(AID/AID) Ikzf3(AID/AID) R26(Tir2/Tir2) Ctr_1

value: Pre-B cells


title: 36wk_WT_SCN_4

value: standard-diet


description: rRNA depleted, total RNA-seq bone marrow Pre-B cells Ikzf1(AID/AID) Ikzf3(AID/AID) R26(Tir2/Tir2) 12h 5-Ph-IAA_2

value: bone marrow


title: 12wk_HF_DRG_4

value: dorsal root ganglia


title: 36wk_WT_SCN_3


title: HaCaT, 3H, HSC 5, R3

description: HaCaT treatement during 3 hours Heat Shock Control equivalent to "Expo 5 mW/cm²" Replicate 3, F5


description: rRNA depleted, total RNA-seq bone marrow Pre-B cells Ikzf1(AID/AID) Ikzf3(AID/AID) R26(Tir2/Tir2) 12h 5-Ph-IAA_1


title: 12wk_HF_DRG_3


title: 12wk_WT_DRG_4


title: 12wk_WT_DRG_3


title: 12wk_HF_SCN_3


title: 12wk_HF_SCN_4


title: HaCaT, 3H, HSC 5, R4

description: HaCaT treatement during 3 hours Heat Shock Control equivalent to "Expo 5 mW/cm²" Replicate 4, E6


title: 12wk_WT_SCN_4


title: HaCaT, 3H, HSC 20, R1

description: HaCaT treatement during 3 hours Heat Shock Control equivalent to "Expo 20 mW/cm²" Replicate 1, D4


description: rRNA depleted, total RNA-seq bone marrow immature B cells E2A(AID/AID) R26 (Tir2/Tir2) 6h 5-Ph-IAA_1

value: E2A(AID/AID) R26 (Tir2/Tir2)


title: 12wk_WT_SCN_3


title: 36wk_HF_DRG_2


title: HaCaT, 3H, HSC 20, R3

description: HaCaT treatement during 3 hours Heat Shock Control equivalent to "Expo 20 mW/cm²" Replicate 3, B6


title: 36wk_WT_DRG_2


description: rRNA depleted, total RNA-seq bone marrow immature B cells E2A(AID/AID) R26 (Tir2/Tir2) Ctr_2

value: Ctr


title: HaCaT, 3H, HSC 20, R2

description: HaCaT treatement during 3 hours Heat Shock Control equivalent to "Expo 20 mW/cm²" Replicate 2, C5


title: 36wk_HF_DRG_1


title: HaCaT, 3H, HSC 20, R4

description: HaCaT treatement during 3 hours Heat Shock Control equivalent to "Expo 20 mW/cm²" Replicate 4, A7


title: 36wk_WT_DRG_1


description: rRNA depleted, total RNA-seq bone marrow immature B cells E2A(AID/AID) R26 (Tir2/Tir2) Ctr_1


title: 36wk_HF_SCN_2


description: rRNA depleted, total RNA-seq bone marrow Pre-B cells E2A(AID/AID) R26 (Tir2/Tir2) 6h 5-Ph-IAA_2


title: HaCaT, 3H, HSC 10, R3

description: HaCaT treatement during 3 hours Heat Shock Control equivalent to "Expo 10 mW/cm²" Replicate 3, H5


title: 36wk_HF_SCN_1


title: 36wk_WT_SCN_2


description: rRNA depleted, total RNA-seq bone marrow Pre-B cells E2A(AID/AID) R26 (Tir2/Tir2) 6h 5-Ph-IAA_1


title: 36wk_WT_SCN_1


title: HaCaT, 3H, HSC 10, R1

description: HaCaT treatement during 3 hours Heat Shock Control equivalent to "Expo 10 mW/cm²" Replicate 1, B4


title: 12wk_HF_DRG_1


title: 12wk_WT_DRG_2


description: rRNA depleted, total RNA-seq bone marrow Pre-B cells E2A(AID/AID) R26 (Tir2/Tir2) Ctr_1


title: 12wk_WT_DRG_1


title: 12wk_HF_SCN_1


title: HaCaT, 3H, HSC 10, R2

description: HaCaT treatement during 3 hours Heat Shock Control equivalent to "Expo 10 mW/cm²" Replicate 2, A5


description: rRNA depleted, total RNA-seq bone marrow Pro-B cells E2A(AID/AID) R26 (Tir2/Tir2) 6h 5-Ph-IAA_2

value: Pro-B cells


title: HaCaT, 3H, Expo 5, R1

description: HaCaT treatement during 3 hours Exposition at 5 mW/cm² Replicate 1, G3


title: 12wk_HF_SCN_2


description: rRNA depleted, total RNA-seq bone marrow Pro-B cells E2A(AID/AID) R26 (Tir2/Tir2) 6h 5-Ph-IAA_1

value: Ex-vivo FACS sorted from bone marrow


title: HaCaT, 3H, Expo 5, R2

description: HaCaT treatement during 3 hours Exposition at 5 mW/cm² Replicate 2, F4


description: rRNA depleted, total RNA-seq bone marrow Pro-B cells E2A(AID/AID) R26 (Tir2/Tir2) Ctr_2


title: HaCaT, 3H, Expo 5, R3

description: HaCaT treatement during 3 hours Exposition at 5 mW/cm² Replicate 3, E5


title: ExpB_rep3

first: Mingtian

last: Deng

address: 1st weigang

institute: Nanjing Agricultural University

data_processing:
Reads were trimmed to remove adaptors and low-quality bases using fastp (v0.23.4). Reads that passed quality control were mapped to reference genome ARS-UI_Ramb_v2.0 using hisat2 (v2.1.0). All the mapped reads were then sorted and indexed using samtools (v1.9). Transcript quantification was performed through featureCounts (v2.0.1), and the expression of genes was normalized with fragments per kilobase of exon model per million mapped fragments (FPKM)
Assembly: ARS-UI_Ramb_v2.0
Supplementary files format and content: FPKM

organism: Ovis aries

source_name: embryo

extract_protocol:
Direct lysis
SMATR-seq2

value: embryo

tag: developmental stage

value: Expand Blastocyst


title: ExpB_rep2

tag: tissue


description: rRNA depleted, total RNA-seq bone marrow Pro-B cells E2A(AID/AID) R26 (Tir2/Tir2) Ctr_1


title: HaCaT, 3H, HSC 10, R4

description: HaCaT treatement during 3 hours Heat Shock Control equivalent to "Expo 10 mW/cm²" Replicate 4, G6


title: 12wk_HF_DRG_2


title: HaCaT, 3H, Expo 5, R4

description: HaCaT treatement during 3 hours Exposition at 5 mW/cm² Replicate 4, D6


description: rRNA depleted, total RNA-seq bone marrow immature B cells E2A(AID/AID) R26 (Tir2/Tir2) 6h 5-Ph-IAA_2

value: 6h 5-Ph-IAA


description: rRNA depleted, total RNA-seq bone marrow Pre-B cells E2A(AID/AID) R26 (Tir2/Tir2) Ctr_2


description: rRNA depleted, total RNA-seq bone marrow immature B cells Pax5(AID/AID) R26(Tir2/Tir2) 5h 5-Ph-IAA_2

value: immature B cells

value: Pax5(AID/AID) R26(Tir2/Tir2)

value: 5h 5-Ph-IAA


title: EarlyB_rep2

value: Early Blastocyst


title: EarlyB_rep1


description: rRNA depleted, total RNA-seq bone marrow immature B cells Pax5(AID/AID) R26(Tir2/Tir2) 5h 5-Ph-IAA_1


title: Morula_rep3

value: Morula


title: Morula_rep2


title: HaCaT, 3H, Expo 20, R1

description: HaCaT treatement during 3 hours Exposition at 20 mW/cm² Replicate 1, C4

value: HaCaT

value: human keratinocyte cell line


title: 16C_rep2


title: Morula_rep1


title: 12wk_WT_SCN_2

value: sciatic nerve

value: standard-diet


description: rRNA depleted, total RNA-seq bone marrow immature B cells Pax5(AID/AID) R26(Tir2/+) Ctr_1

value: bone marrow

value: Pax5(AID/AID) R26(Tir2/+)


description: rRNA depleted, total RNA-seq bone marrow immature B cells Pax5(AID/AID) R26(Tir2/+) Ctr_2

value: Ctr


title: ExpB_rep4


title: 16C_rep3


title: 16C_rep1


title: HaCaT, 3H, Expo 20, R2

description: HaCaT treatement during 3 hours Exposition at 20 mW/cm² Replicate 2, B5


description: rRNA depleted, total RNA-seq bone marrow Pre-B cells Pax5(AID/AID) R26(Tir2/Tir2) 5h 5-Ph-IAA_2

value: Pre-B cells


title: 12wk_WT_SCN_1


title: HaCaT, 3H, Expo 20, R3

description: HaCaT treatement during 3 hours Exposition at 20 mW/cm² Replicate 3, A6


title: EarlyB_rep3


title: 8C_rep4


title: 8C_rep3


title: HaCaT, 3H, Expo 20, R4

description: HaCaT treatement during 3 hours Exposition at 20 mW/cm² Replicate 4, H6


title: 8C_rep2


title: ExpB_rep1


title: HaCaT, 3H, Expo 10, R3

description: HaCaT treatement during 3 hours Exposition at 10 mW/cm² Replicate 3, G5


description: rRNA depleted, total RNA-seq bone marrow Pre-B cells Pax5(AID/AID) R26(Tir2/Tir2) 5h 5-Ph-IAA_1

value: Ex-vivo FACS sorted from bone marrow


title: HaCaT, 3H, Expo 10, R4

description: HaCaT treatement during 3 hours Exposition at 10 mW/cm² Replicate 4, F6


title: HaCaT, 3H, Expo 10, R2

description: HaCaT treatement during 3 hours Exposition at 10 mW/cm² Replicate 2, H4


title: 4C_rep3

value: embryo


title: 8C_rep1


description: rRNA depleted, total RNA-seq bone marrow Pre-B cells Pax5(AID/AID) R26(Tir2/+) Ctr_1


title: 4C_rep1


title: 4C_rep2


title: HaCaT, 3H, Expo 10, R1

description: HaCaT treatement during 3 hours Exposition at 10 mW/cm² Replicate 1, A4


description: rRNA depleted, total RNA-seq bone marrow Pro-B cells Pax5(AID/AID) R26(Tir2/Tir2) 5h 5-Ph-IAA_2

value: Pro-B cells


title: 2C_rep4


title: 15.6 Wk human fetal, snRNA-seq, rep F2

description: 10X Chromium Single Cell 3' v3

value: Kidney tissue

value: Kidney cells

value: 15.6 Wk human fetal


title: 2C_rep1


description: rRNA depleted, total RNA-seq bone marrow Pro-B cells Pax5(AID/AID) R26(Tir2/+) Ctr_2


title: 15.6 Wk human fetal, snRNA-seq, rep F3

description: 10X Chromium Single Cell 3' v3


description: rRNA depleted, total RNA-seq bone marrow Pro-B cells Pax5(AID/AID) R26(Tir2/Tir2) 5h 5-Ph-IAA_1

value: Pax5(AID/AID) R26(Tir2/Tir2)

value: 5h 5-Ph-IAA


title: 2C_rep3


title: 2C_rep2


title: MII_rep2

source_name: oocyte

value: oocyte

value: MII


description: rRNA depleted, total RNA-seq bone marrow immature B cells Ikzf1(AID/AID) R26(Tir2/Tir2) 8h 5-Ph-IAA_2

value: immature B cells

value: Ikzf1(AID/AID) R26(Tir2/Tir2)

value: 8h 5-Ph-IAA


description: rRNA depleted, total RNA-seq bone marrow Pro-B cells Pax5(AID/AID) R26(Tir2/+) Ctr_1

value: bone marrow


description: rRNA depleted, total RNA-seq bone marrow immature B cells Ikzf1(AID/AID) R26(Tir2/Tir2) 8h 5-Ph-IAA_1


title: HEK293T_DNMT1_KO_BG4_rep

city: Guangzhou

first: Lijun

last: Xiang

state: Guangdong

address: No.55, West of Zhongshan Avenue

department: Guangzhou Key Laboratory of Insect Development Regulation and Application Research

institute: South China Normal University

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
CUT&Tag reads were trimmed from 3' end until the final base had a quality score > 20, using TrimGalore-0.6.7, discarding reads left with < 20 bp
CUT&Tag reads were aligned to the UCSC hg38 genome using Bowtie2 version 2.4.5.
The aligned reads were removed with Picard MarkDuplicates, and the deduplicated BAM files were normalized to the total aligned reads (reads per million, BPM) with the bamCoverage command from deepTools 3.3.0
Peaks were called uing MACS v2.2.7.1 with the significance cut-off q-value <=1E-5
Assembly: hg38
Supplementary files format and content: narrowPeak
Library strategy: CUT&Tag

growth_protocol: DMEM, 15% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
CUT&Tag was performed essentially as described by Kaiwei Liang et al. 2021, with minor modifications according the Hyperactive Universal CUT&Tag Assay Kit protocol (Vazyme, Nanjing, China).One hundred thousand cells were used for the CUT&Tag experiment, and cell counting was performed by using a Cellometer Mini (Nexcelom Bioscience, Boston, MA, USA). pA-Tn5 transposase was used to cut the genome and add a special adaptor sequence to build a library.
Libraries were prepared according to Hyperactive Universal CUT&Tag Assay Kit protocol (Vazyme, Nanjing, China)

value: Human embryonic kidney


description: rRNA depleted, total RNA-seq bone marrow immature B cells Ikzf1(AID/AID) R26(Tir2/+) Ctr_1

value: Ikzf1(AID/AID) R26(Tir2/+)

value: Ctr


description: rRNA depleted, total RNA-seq bone marrow immature B cells Ikzf1(AID/AID) R26(Tir2/+) Ctr_2

value: Ex-vivo FACS sorted from bone marrow


title: MUC7391

city: Munich

first: Stefanie

last: Eyerich

address: Biedersteinderstrasse 29

institute: Center of Allergy and Environment

data_processing:
STAR aligner with human genome reference hg38
Bioconductor package DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: .txt

source_name: lesional skin

growth_protocol: RNA analysis of skin biopsies, skin biopsies were stored at -80°C in RNAlater solution until RNA preparation

extract_protocol:
RNA from skin biopsies was isolated using the QIAzol Lysis Reagent (Qiagen) and miRNeasy Mini Kit (Qiagen) according to manufacturer’s protocol
RNASeq libraries were generated using the TruSeq Stranded Total RNA Kit (Illumina) with Ribo-Zero Depletion (rRNA Removal Mix) according to manufacturer’s high sample protocol. 200 ng of RNA was used as input. DNA was PCR amplified with Illumina primers for 13 cycles. Libraries were sequenced on the Illumina HiSeq 4000 as paired-end with a read length of 2x 150 bp and an average output of 40 Mio reads per sample and end following the manufacturer's protocols.

treatment_protocol: no treatment

tag: diagnosis

value: psoriasis

tag: patient id

tag: gender

value: female

tag: batch id


title: MUC7392

source_name: non-lesional skin


title: MUC7390

value: Atopic eczema


title: MUC7393

value: male


description: rRNA depleted, total RNA-seq bone marrow Pre-B cells Ikzf1(AID/AID) R26(Tir2/Tir2) 8h 5-Ph-IAA_2

tag: strain

tag: cell type

value: Pre-B cells


title: MUC7388

value: Nummular Eczema


title: CD4 T cells Co-culture donor 3 replicate 1

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

data_processing:
The raw reads were first cleaned by removing adapter sequences and poly-x sequences (> 9 nt used for detection) using fastp (Version 0.23.4). Reads with length <18nt after trimming were additionally filtered out.
Sequence pseudo alignment of the resulting high-quality reads to the Human reference genome and quantification of gene level expression (gene model definition from GENCODE release 42) was carried out using Kallisto (Version 0.46.1)
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited transcript abundances

source_name: PMBCs

growth_protocol: MDMS were generated from freshly isolated CD14+ cells by cultiring in high attachment plates RPMI supplemented with human Ab serum for 5 days. Medium was changed for RPMI supplemented with IFNg and LPS for 48h before co-cuclture establishment. Freshly isolated PBMCs were culture for 24h in RPMI supplemented with FBS, GlutaMax and IL-2 before HIV infection with 0.1 MOI.

extract_protocol:
Extraction kit: QIAGEN RNeasy mini kit. Protocol according to manufacturer instructions.
Illumina Stranded mRNA Prep, Ligation (https://www.illumina.com/content/dam/illumina/gcs/assembled-assets/marketing-literature/illumina-stranded-mrna-prep-data-sheet-m-gl-02143/illumina-stranded-mrna-prep-data-sheet-m-gl-02143.pdf)

value: PMBCs

value: CD4+ T cells


title: CD4 T cells monoculture donor 3 replicate 3 HIV infected


title: CD4 T cells Co-culture donor 3 replicate 3


title: CD4 T cells Co-culture donor 3 replicate 2 HIV infected


title: CD4 T cells Co-culture donor 3 replicate 3 HIV infected


title: CD4 T cells Co-culture donor 3 replicate 1 HIV infected


title: CD4 T cells monoculture donor 3 replicate 3


title: MII_rep1

value: oocyte

value: MII


title: CD4 T cells monoculture donor 3 replicate 2 HIV infected


title: CD4 T cells monoculture donor 3 replicate 2


description: rRNA depleted, total RNA-seq bone marrow Pre-B cells Ikzf1(AID/AID) R26(Tir2/Tir2) 8h 5-Ph-IAA_1

tag: genotype

value: Ikzf1(AID/AID) R26(Tir2/Tir2)


title: MUC7387


title: CD4 T cells monoculture donor 3 replicate 1 HIV infected


description: rRNA depleted, total RNA-seq bone marrow Pre-B cells Ikzf1(AID/AID) R26(Tir2/+) Ctr_2

tag: treatment


title: CD4 T cells monoculture donor 3 replicate 1


title: MDMs co-cuclutre donor 3 replicate 3 HIV infected

value: MDMs


title: CD4 T cells Co-culture donor 3 replicate 2


title: MUC7386


title: MDMs co-cuclutre donor 3 replicate 3


title: MDMs co-cuclutre donor 3 replicate 2 HIV infected


title: MUC7389


description: rRNA depleted, total RNA-seq bone marrow Pro-B cells Ikzf1(AID/AID) R26(Tir2/Tir2) 8h 5-Ph-IAA_1

value: bone marrow

value: Pro-B cells

value: 8h 5-Ph-IAA


title: MDMs co-cuclutre donor 3 replicate 2


description: rRNA depleted, total RNA-seq bone marrow Pro-B cells Ikzf1(AID/AID) R26(Tir2/Tir2) 8h 5-Ph-IAA_2


title: MUC7384


title: MDMs co-cuclutre donor 3 replicate 1 HIV infected


title: MDMs co-cuclutre donor 3 replicate 1


title: MUC7383


title: MDMs monoculture donor 3 replicate 3


description: rRNA depleted, total RNA-seq bone marrow Pro-B cells Ikzf1(AID/AID) R26(Tir2/+) Ctr_1

value: Ikzf1(AID/AID) R26(Tir2/+)

value: Ctr


description: rRNA depleted, total RNA-seq bone marrow Pro-B cells Ikzf1(AID/AID) R26(Tir2/+) Ctr_2

value: Ex-vivo FACS sorted from bone marrow


title: CD4 T cells Co-culture donor 2 replicate 3 HIV infected


title: MDMs monoculture donor 3 replicate 1


title: MUC7381


title: MUC7382

value: psoriasis


title: MDMs monoculture donor 3 replicate 2


title: CD4 T cells Co-culture donor 2 replicate 3


description: rRNA depleted, total RNA-seq bone marrow immature B cells E2A(AID/AID) 10h 5-Ph-IAA_1

value: immature B cells

value: 10h 5-Ph-IAA


title: CD4 T cells Co-culture donor 2 replicate 2 HIV infected


title: CD4 T cells Co-culture donor 2 replicate 2


title: CD4 T cells Co-culture donor 2 replicate 1 HIV infected


title: MUC7380

value: male


title: MUC7379


title: MUC7385


description: rRNA depleted, total RNA-seq bone marrow Pre-B cells E2A(AID/AID) 10h 5-Ph-IAA_1

value: Pre-B cells


title: CD4 T cells Co-culture donor 2 replicate 1

value: PMBCs


description: rRNA depleted, total RNA-seq bone marrow immature B cells E2A(AID/AID) 10h 5-Ph-IAA_2


title: CD4 T cells monoculture donor 2 replicate 3 HIV infected

value: CD4+ T cells


description: rRNA depleted, total RNA-seq bone marrow Pre-B cells Ikzf1(AID/AID) R26(Tir2/+) Ctr_1


title: CD4 T cells monoculture donor 2 replicate 3


title: MUC7377

value: Atopic eczema

value: female


title: MUC7378


title: CD4 T cells monoculture donor 2 replicate 2 HIV infected


title: CD4 T cells monoculture donor 2 replicate 2


description: rRNA depleted, total RNA-seq bone marrow Pro-B cells E2A(AID/AID) 10h 5-Ph-IAA_1


description: rRNA depleted, total RNA-seq bone marrow Pre-B cells E2A(AID/AID) 10h 5-Ph-IAA_2


title: CD4 T cells monoculture donor 2 replicate 1


title: CD4 T cells monoculture donor 2 replicate 1 HIV infected


title: MUC7376


title: MDMs co-cuclutre donor 2 replicate 3 HIV infected


title: MUC7375


description: rRNA depleted, total RNA-seq bone marrow Pro-B cells E2A(AID/AID) 10h 5-Ph-IAA_2


title: MDMs co-cuclutre donor 2 replicate 2 HIV infected


title: Cut&Run bone marrow Pre-B cells Wildtype_2

data_processing:
Cut-and-Run-Seq: Only reads that passed the Illumina quality filtering were processed. Reads were aligned with the bowtie program version 2.4.4 (ref. 11) to the mm10 genome version of December 2011 (GRCm38).
Assembly: mm10
Supplementary files format and content: bw (bigwig) = read coverage (reads per million) in bigWIG format
Library strategy: Cut&Run

extract_protocol:
King Fisher RNA isolation, rRNA depletion
Cut&Run libraries were prepared for sequencing using standard Illumina protocols

value: Wildtype


title: MDMs co-cuclutre donor 2 replicate 3

value: MDMs


title: Cut&Run bone marrow Pre-B cells Ebf1(AID/AID)_2

value: bone marrow


title: MUC7372


title: MUC7371


title: Cut&Run bone marrow Pre-B cells Ebf1(AID/AID)_1


title: MDMs monoculture donor 2 replicate 3


title: MDMs co-cuclutre donor 2 replicate 1


title: MDMs co-cuclutre donor 2 replicate 1 HIV infected


title: MUC7370

value: Nummular Eczema


title: Cut&Run bone marrow Pre-B cells E2A(AID/AID) R26 (Tir2/Tir2)_2

value: E2A(AID/AID) R26 (Tir2/Tir2)


title: CD4 T cells Co-culture donor 1 replicate 3 HIV infected


title: MDMs monoculture donor 2 replicate 1


title: MDMs monoculture donor 2 replicate 2


title: MUC7369


title: Cut&Run bone marrow Pre-B cells E2A(AID/AID) R26 (Tir2/Tir2)_1


title: MUC7368


title: CD4 T cells Co-culture donor 1 replicate 2 HIV infected


title: CD4 T cells Co-culture donor 1 replicate 3


title: CD4 T cells Co-culture donor 1 replicate 2


title: MUC7367


title: CD4 T cells Co-culture donor 1 replicate 1 HIV infected


title: MDMs co-cuclutre donor 2 replicate 2


title: Cut&Run bone marrow Pre-B cells Pax5(AID/AID) R26(Tir2/Tir2)_1

value: Pax5(AID/AID) R26(Tir2/Tir2)


title: CD4 T cells monoculture donor 1 replicate 3 HIV infected


title: MUC7366


title: MUC7365


title: CD4 T cells monoculture donor 1 replicate 3


title: Cut&Run bone marrow Pre-B cells Ikzf3(AID/AID)_2


title: CD4 T cells monoculture donor 1 replicate 2 HIV infected


title: CD4 T cells monoculture donor 1 replicate 2


title: CD4 T cells monoculture donor 1 replicate 1 HIV infected


title: Cut&Run bone marrow Pre-B cells Ikzf1(AID/AID)_1


title: MUC7363


title: CD4 T cells monoculture donor 1 replicate 1


title: Cut&Run bone marrow Pre-B cells Ikzf1(AID/AID)_2


title: MDMs co-cuclutre donor 1 replicate 3 HIV infected


title: MDMs co-cuclutre donor 1 replicate 3


title: MUC7362


title: Cut&Run bone marrow Pro-B cells Wildtype_1

value: Pro-B cells


title: Cut&Run bone marrow Pre-B cells Pax5(AID/AID) R26(Tir2/Tir2)_2

value: Ex-vivo FACS sorted from bone marrow


title: MDMs co-cuclutre donor 1 replicate 2


title: Cut&Run bone marrow Pro-B cells Ebf1 (AID/AID)_2

value: Ebf1 (AID/AID)


title: MDMs co-cuclutre donor 1 replicate 1 HIV infected


title: MUC7360

value: psoriasis


title: MDMs co-cuclutre donor 1 replicate 1


title: CD4 T cells Co-culture donor 1 replicate 1


title: MDMs monoculture donor 1 replicate 3


title: Cut&Run bone marrow Pro-B cells Ebf1(AID/AID)_1


title: Cut&Run bone marrow Pre-B cells Ikzf3(AID/AID)_1


title: MUC7356


title: MUC7364


title: Cut&Run bone marrow Pro-B cells E2A(AID/AID) R26 (Tir2/Tir2)_2


title: 77_STI-102

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

data_processing:
Illumina bcl2fastq v2.17.1.14 was used for demultiplexing.
Alignment was performed using STAR version 2.5.2b
Transcript abundance estimates were calculated internal to the STAR aligner using the algorithm of htseq-count
Assembly: GRCh38, Emsembl annotation v86
Supplementary files format and content: comma delimited text file containing ensembl ID, gene symbol, gene description and raw read counts for each sample (in columns) for each annotated transcript (in rows).

source_name: rectal biopsy

extract_protocol:
RNA was isolated from two rectal biopsy pinches for each patient using the RNeasy Micro kit (Qiagen) with on-column DNase digestion. RNA quality was assessed using an Agilent Bioanalyzer
Ten nanograms of total RNA was used as input for cDNA synthesis using the Clontech SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio) according to the manufacturer’s instructions. Amplified cDNA was fragmented and appended with dual-indexed bar codes using the NexteraXT DNA Library Preparation kit (Illumina).

value: rectal biopsy

tag: race group

value: NonBlack

tag: age group

value: Adult

tag: msm

value: MSM

tag: p24 logauc

tag: hiv status

value: HIVNeg

tag: sti status

value: STIPos

tag: batch


title: Cut&Run bone marrow Pro-B cells E2A(AID/AID) R26 (Tir2/Tir2)_1

tag: cell preparation

tag: replicate number


title: 76_STI-100

tag: tissue

value: Black

tag: age

value: Youth

value: HIVPos

value: STINeg


title: 75_STI-099


title: 74_STI-098


title: MDMs co-cuclutre donor 1 replicate 2 HIV infected

value: PMBCs

value: MDMs


title: MUC7355

tag: diagnosis

tag: patient id

tag: gender

value: male


title: MUC7354

value: female

tag: batch id


title: 73_STI-097


title: Cut&Run bone marrow Pro-B cells Pax5(AID/AID) R26(Tir2/Tir2)_1

tag: strain

value: bone marrow

tag: cell type

value: Pro-B cells

tag: genotype

value: Pax5(AID/AID) R26(Tir2/Tir2)

value: Ex-vivo FACS sorted from bone marrow


title: 72_STI-092

value: rectal biopsy

tag: race group

tag: age group


title: MUC7353

value: psoriasis


title: MUC7361


title: 71_STI-087

tag: msm

value: MSM

tag: p24 logauc


title: 70_STI-086

tag: hiv status

value: HIVNeg

tag: sti status


title: Cut&Run bone marrow Pro-B cells Ikzf3(AID/AID)_2

tag: cell preparation


title: MUC7350


title: Cut&Run bone marrow Pro-B cells Ikzf3(AID/AID)_1

tag: replicate number


title: MDMs monoculture donor 1 replicate 2

tag: tissue


title: 68_STI-084

tag: age

value: STIPos

tag: batch


title: MUC7359

tag: diagnosis

tag: patient id


title: 78_STI-103

value: Black

value: Adult


title: 67_STI-082

value: Youth


title: MUC7349

tag: gender

tag: batch id


title: 66_STI-081


title: Cut&Run bone marrow Pro-B cells Ikzf1(AID/AID)_1

tag: strain

tag: cell type


title: MDMs monoculture donor 1 replicate 1


title: MUC7348


title: 65_STI-080

tag: race group

value: HIVPos


title: 64_STI-079

tag: age group


title: 63_STI-078

tag: msm


title: MUC7347


title: MUC7346


title: 61_STI-074

tag: p24 logauc

value: STINeg


title: ATAC-Seq bone marrow immature B cells Ikzf3(AID/AID) R26(Tir2/Tir2) 8h 5-Ph-IAA_2

data_processing:
ATAC-Seq:  Only reads that passed the Illumina quality filtering were processed. Reads were aligned with the bowtie program version 2.3.5.1 to the mm10 genome version of December 2011 (GRCm38), including NZ_CP083274.1 Escherichia coli strain Rosetta2-DE3 chromosome (4.5Mb).
Assembly: mm10
Supplementary files format and content: bw (bigwig) = read coverage (reads per million) in bigWIG format

extract_protocol:
King Fisher RNA isolation, rRNA depletion
ATAC-Seq libraries were prepared for sequencing using standard Illumina protocols

value: immature B cells

tag: genotype

value: Ikzf3(AID/AID) R26(Tir2/Tir2)

tag: treatment

value: 8h 5-Ph-IAA


title: Cut&Run bone marrow Pro-B cells Pax5(AID/AID) R26(Tir2/Tir2)_2

value: bone marrow

tag: cell preparation


title: 62_STI-077

tag: hiv status

tag: sti status


title: 59_STI-071

tag: tissue

tag: age


title: 60_STI-072

tag: batch


title: 58_STI-070


title: 69_STI-085


title: 57_STI-063


title: ATAC-Seq bone marrow immature B cells E2A(AID/AID) R26 (Tir2/Tir2) 6h 5-Ph-IAA_4

value: E2A(AID/AID) R26 (Tir2/Tir2)

value: 6h 5-Ph-IAA

tag: replicate number


title: ATAC-Seq bone marrow immature B cells E2A(AID/AID) R26 (Tir2/Tir2) 6h 5-Ph-IAA_3

value: Ex-vivo FACS sorted from bone marrow


title: MUC7345

tag: diagnosis

tag: patient id

tag: gender

value: male


title: 56_STI-061

value: rectal biopsy


title: MUC7343

value: psoriasis

value: female

tag: batch id


title: MUC7344


title: 55_STI-059

tag: race group

value: MSM


title: 54_STI-057

value: Black

tag: age group

value: Control


title: Cut&Run bone marrow Pro-B cells Ikzf1(AID/AID)_2

tag: strain

tag: cell type

value: Pro-B cells


title: MUC7342

value: Atopic eczema


title: ATAC-Seq bone marrow immature B cells Ebf1(AID/AID) R26(Tir2/Tir2) 6h 5-Ph-IAA_2

tag: genotype

value: Ebf1(AID/AID) R26(Tir2/Tir2)


title: MUC7341


title: ATAC-Seq bone marrow immature B cells E2A(AID/AID) R26 (Tir2/Tir2) Ctr_3

value: immature B cells

tag: treatment

value: Ctr


title: 52_STI-055

value: Youth

tag: msm

tag: p24 logauc

value: HIVPos

value: STIPos


title: 53_STI-056

tag: hiv status

tag: sti status

value: STINeg


title: ATAC-Seq bone marrow immature B cells Ebf1(AID/AID) R26(Tir2/Tir2) 6h 5-Ph-IAA_1

tag: tissue

value: bone marrow

tag: cell preparation

value: Ex-vivo FACS sorted from bone marrow

value: 6h 5-Ph-IAA


title: ATAC-Seq bone marrow immature B cells Ikzf3(AID/AID) R26(Tir2/Tir2) 8h 5-Ph-IAA_1

value: Ikzf3(AID/AID) R26(Tir2/Tir2)

value: 8h 5-Ph-IAA

tag: replicate number


title: MUC7340

tag: diagnosis

value: psoriasis

tag: age

value: female


title: 50_STI-053

value: rectal biopsy

value: Black

value: MSM

tag: batch


title: 49_STI-051

value: HIVNeg


title: MUC7339

tag: patient id

tag: gender

tag: batch id


title: 48_STI-047

tag: race group

tag: age group


title: ATAC-Seq bone marrow immature B cells Ebf1(AID/AID) R26(Tir2/Tir2) Ctr_2

tag: strain

tag: cell type

value: immature B cells

tag: genotype

value: Ebf1(AID/AID) R26(Tir2/Tir2)


title: 47_STI-045

value: Youth

tag: msm

tag: p24 logauc


title: ATAC-Seq bone marrow Pre-B cells Ikzf3(AID/AID) R26(Tir2/Tir2) 8h 5-Ph-IAA_2

value: Pre-B cells

tag: treatment


title: 46_STI-044

tag: tissue

tag: hiv status

value: HIVPos

tag: sti status


title: ATAC-Seq bone marrow Pre-B cells Ikzf3(AID/AID) R26(Tir2/Tir2) 8h 5-Ph-IAA_1

tag: cell preparation

tag: replicate number


title: ATAC-Seq bone marrow immature B cells Ebf1(AID/AID) R26(Tir2/Tir2) Ctr_1

value: Ctr


title: MUC7338

tag: diagnosis

tag: age

value: male


title: MUC7337

tag: patient id

tag: gender


title: 44_STI-042

tag: race group

value: STIPos

tag: batch


title: 45_STI-043

tag: age group

value: Control


title: MUC7336

tag: batch id


title: 42_STI-040


title: 41_STI-039

value: NonBlack

value: STINeg


title: ATAC-Seq bone marrow Pre-B cells E2A(AID/AID) R26 (Tir2/Tir2) 6h 5-Ph-IAA_1

tag: strain

value: bone marrow

tag: cell type

tag: genotype

value: E2A(AID/AID) R26 (Tir2/Tir2)

value: Ex-vivo FACS sorted from bone marrow

value: 6h 5-Ph-IAA


title: 43_STI-041

value: rectal biopsy

value: Black

tag: msm

value: MSM

tag: p24 logauc


title: ATAC-Seq bone marrow Pre-B cells E2A(AID/AID) R26 (Tir2/Tir2) 6h 5-Ph-IAA_2

tag: tissue

tag: treatment


title: MUC7335

value: psoriasis

value: female


title: 40_STI-038

value: Youth

tag: hiv status

value: HIVNeg

tag: sti status


title: 36_STI-033

value: HIVPos


title: MUC7333

tag: diagnosis

value: Atopic eczema


title: 51_STI-054

tag: age


title: 35_STI-032


title: 39_STI-037


title: MUC7334

tag: patient id


title: 37_STI-034


title: 34_STI-031


title: 38_STI-036


title: ATAC-Seq bone marrow Pre-B cells Ebf1(AID/AID) R26(Tir2/Tir2) 6h 5-Ph-IAA_1

value: Pre-B cells

value: Ebf1(AID/AID) R26(Tir2/Tir2)

tag: cell preparation

tag: replicate number


title: MUC7330

tag: gender

value: male


title: ATAC-Seq bone marrow Pre-B cells E2A(AID/AID) R26 (Tir2/Tir2) Ctr_3

value: Ctr


title: MUC7329


title: ATAC-Seq bone marrow Pre-B cells Ebf1(AID/AID) R26(Tir2/Tir2) 6h 5-Ph-IAA_2

value: bone marrow


title: 33_STI-029

tag: race group

tag: age group

value: STINeg

tag: batch


title: 31_STI-026

value: STIPos


title: 28_STI-023

value: Control


title: MUC7310

value: Nummular Eczema

tag: batch id


title: 30_STI-025

value: rectal biopsy

value: Black


title: ATAC-Seq bone marrow Pre-B cells Ebf1(AID/AID) R26(Tir2/Tir2) Ctr_2

tag: strain

tag: cell type

tag: genotype

value: Ex-vivo FACS sorted from bone marrow


title: MUC7309


title: 29_STI-024

tag: tissue

tag: msm

value: MSM

tag: p24 logauc


title: MUC7320

value: female


title: 32_STI-027

value: Youth

tag: hiv status

value: HIVNeg

tag: sti status


title: ATAC-Seq bone marrow Pre-B cells Ebf1(AID/AID) R26(Tir2/Tir2) Ctr_1

tag: treatment


title: ATAC-Seq bone marrow Pro-B cells E2A(AID/AID) R26 (Tir2/Tir2) 6h 5-Ph-IAA_2

value: Pro-B cells

value: E2A(AID/AID) R26 (Tir2/Tir2)

value: 6h 5-Ph-IAA


title: MUC7308

tag: diagnosis

tag: patient id

tag: age


title: 26_STI-020


title: 20_ARM-094


title: 22_STI-001

value: NonBlack


title: MUC7307

tag: gender


title: 27_STI-022

tag: race group


title: ATAC-Seq bone marrow Pro-B cells Ikzf3(AID/AID) R26(Tir2/Tir2) 8h 5-Ph-IAA_2

value: Ikzf3(AID/AID) R26(Tir2/Tir2)

tag: cell preparation

value: 8h 5-Ph-IAA

tag: replicate number


title: 19_ARM-093-V2

tag: age group

value: STINeg

tag: batch


title: ATAC-Seq bone marrow Pro-B cells Ikzf3(AID/AID) R26(Tir2/Tir2) 8h 5-Ph-IAA_1

tag: strain

value: bone marrow

tag: cell type


title: 21_ARM-095

tag: tissue


title: 23_STI-004

tag: msm

value: HIVPos

value: STIPos


title: 18_ARM-090

value: rectal biopsy

value: Adult

tag: p24 logauc


title: 24_STI-016

value: Black

tag: hiv status


title: MUC7306

value: psoriasis

tag: batch id


title: 25_STI-019

value: MSM

tag: sti status


title: ATAC-Seq bone marrow Pro-B cells E2A(AID/AID) R26 (Tir2/Tir2) 6h 5-Ph-IAA_1

tag: genotype

value: Ex-vivo FACS sorted from bone marrow

tag: treatment


title: ATAC-Seq bone marrow Pro-B cells Ebf1(AID/AID) R26(Tir2/Tir2) 6h 5-Ph-IAA_2

value: Ebf1(AID/AID) R26(Tir2/Tir2)


title: ATAC-Seq bone marrow Pro-B cells E2A(AID/AID) R26 (Tir2/Tir2) Ctr_3

value: Pro-B cells

value: Ctr


title: 14_ARM-081

tag: age


title: MUC7305

tag: diagnosis

tag: patient id

tag: gender

value: female


title: 15_ARM-083

tag: race group

value: NonBlack


title: 17_ARM-089-V2

tag: age group


title: 16_ARM-088-V2

tag: batch


title: 13_ARM-077

value: Control


title: 12_ARM-076


title: MUC7303

value: Nummular Eczema

value: male


title: ATAC-Seq bone marrow Pro-B cells Ebf1(AID/AID) R26(Tir2/Tir2) 6h 5-Ph-IAA_1

tag: strain

value: bone marrow

tag: cell preparation

value: 6h 5-Ph-IAA

tag: replicate number


title: ATAC-Seq bone marrow Pro-B cells Ebf1(AID/AID) R26(Tir2/Tir2) Ctr_1

tag: tissue

tag: cell type


title: 10_ARM-074

tag: msm

tag: p24 logauc

tag: hiv status


title: 9_ARM-059

tag: sti status


title: 8_ARM-058


title: MUC7296

tag: batch id


title: ATAC-Seq bone marrow immature B cells Pax5(AID/AID) R26(Tir2/Tir2) 6h 5-Ph-IAA_2

value: immature B cells

tag: genotype

value: Pax5(AID/AID) R26(Tir2/Tir2)

tag: treatment


title: 5_ARM-035-V2

value: rectal biopsy

tag: age

value: Adult


title: 4_ARM-015-V2

value: Black

value: Youth

value: HIVNeg

value: STINeg


title: 6_ARM-036-V2

value: MSM


title: ATAC-Seq bone marrow immature B cells Pax5(AID/AID) R26(Tir2/Tir2) 6h 5-Ph-IAA_1

value: Ex-vivo FACS sorted from bone marrow


title: ATAC-Seq bone marrow immature B cells Pax5(AID/AID) R26(Tir2/Tir2) Ctr_2

value: Ctr


title: MUC7304

tag: diagnosis

tag: patient id

tag: gender


title: MUC7292


title: ATAC-Seq bone marrow Pro-B cells Ebf1(AID/AID) R26(Tir2/Tir2) Ctr_2

value: Pro-B cells

value: Ebf1(AID/AID) R26(Tir2/Tir2)


title: 3_ARM-005-V2

tag: race group

tag: age group

tag: batch


title: 2_ARM-004

value: STIPos


title: MUC7291

value: Nummular Eczema

value: male


title: ATAC-Seq bone marrow immature B cells E2A(AID/AID) R26 (Tir2/Tir2) 6h 5-Ph-IAA_2

tag: strain

value: bone marrow

value: E2A(AID/AID) R26 (Tir2/Tir2)

tag: cell preparation

value: 6h 5-Ph-IAA

tag: replicate number


title: 1_ARM-001

tag: tissue

value: rectal biopsy

tag: msm


title: 11_ARM-075

value: Adult

value: Control

tag: p24 logauc

tag: hiv status


title: MUC7302

value: psoriasis

tag: batch id


title: MUC7301


title: 27_ARM-032

value: Black

tag: sti status


title: 13_ARM-040

value: Youth

value: HIVNeg

value: STINeg


title: MUC7290


title: ATAC-Seq bone marrow immature B cells E2A(AID/AID) R26 (Tir2/Tir2) Ctr_2

tag: cell type

value: immature B cells

tag: genotype

value: Ex-vivo FACS sorted from bone marrow

tag: treatment

value: Ctr


title: MUC7289

tag: diagnosis

tag: patient id

tag: age


title: 12_ARM-036

tag: race group

tag: age group

value: MSM


title: MUC7295

value: Nummular Eczema

tag: gender

value: female


title: 11_ARM-055

value: STIPos

tag: batch


title: ATAC-Seq bone marrow immature B cells E2A(AID/AID) R26 (Tir2/Tir2) Ctr_1

tag: strain

value: bone marrow

value: E2A(AID/AID) R26 (Tir2/Tir2)

tag: cell preparation

tag: replicate number


title: MUC7286

value: male


title: 293T_DNMT1_KO_ATAC

data_processing:
ATAC-seq reads were aligned to human genome hg38. The aligned reads were removed with Picard MarkDuplicates, Blacklisted regions were removed from the BAM file with bedtools intersect, and the deduplicated BAM files were normalized (Bins Per Million mapped reads, BPM) to generate bigwig file with the bamCoverage command from deepTools 3.3.0.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak

extract_protocol:
ATAC-seq was performed as previously described (Li et al. 2021). Briefly, 5×104 cells were collected and washed with cold PBS and centrifuged at 500 g for 5 minutes. Then, the cells were lysed by 50 μl cold lysis buffer (Novoprotein, 10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl, 0.1% NP-40, 0.1% Tween-20, 1% Digitonin) and incubated on ice for 5 minutes. The cells were furthered added with 950 μl cold wash buffer (Novoprotein, 10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl, 0.1% Tween-20) and centrifuged at 500 g for 5 minutes
The pellet was resuspended with 40 μl tagmentation buffer (Novoprotein, N248, 0.3×pbs, 0.1% Tween-20, 0.01% Digitonin, 1×TD buffer, 1×pA-Tn5 transposome Mix) incubated at 37 ℃ for 30 min. The reaction was stopped by adding 10 μl stop buffer (Novoprotein, N248) at 55 ℃ for 5 min. The DNA was further purified with 100 μl Tagment DNA Extract Beads (Novoprotein, N245) and eluted with 37 μl Elution buffer. The purifyied DNA was amplified with 5×AmpliMix (Novoprotein, N248) using N501 and N701 index primer((Novoprotein, N239). The purified DNA libraries were size selected with NovoNGS® DNA Clean Beads (Novoprotein, N240)

tag: cell line

value: Human embryonic kidney


title: ATAC-Seq bone marrow immature B cells Pax5(AID/AID) R26(Tir2/Tir2) Ctr_1

tag: tissue

value: Pax5(AID/AID) R26(Tir2/Tir2)


title: MUC7285

tag: batch id


title: ATAC-Seq bone marrow immature B cells Ikzf1(AID/AID) Ikzf3(AID/AID) R26(Tir2/Tir2) 12h 5-Ph-IAA_2

value: 12h 5-Ph-IAA


title: 35_ARM-054

value: rectal biopsy

value: Black

value: Adult

tag: msm

tag: p24 logauc

tag: hiv status

tag: sti status


title: 293T_WT_ATAC

tag: cell type

tag: genotype

value: WT


title: HEK293T_DNMT1_KO_WGBS

data_processing:
The WGBS libraries were sequenced using NovaSeq 6000 analyzer with paired end reads of 150 bp read length (PE150) according to the manufacturer’s instructions. Low quality bases and adapter sequences were trimmed by using trim_galore. The cleaned reads were mapped back to hg38 genome using BSMAP software version 2.90. The parameter settings used was “-n 0 -v 0.08 -g 1 -p 48”. Methylation ratios were extracted from BSMAP output (SAM) using a Python script (methratio.py) which is distributed with the BSMAP package. In brief, The methylation level was calculated based on the methylated cytosine (mC) percentage in the whole genome as site methylation level = 100× (number of sequences with methylated cytosines (mC)/total number of valid sequences).
Assembly: hg38
Supplementary files format and content: The methylation level  based on the methylated cytosine (mC)

extract_protocol:
DNA was isolated using the Cell Culture DNA Midi Kit from QIAGEN (Qiagen, 13343). Prior to library construction, 1µg sample genome DNA mixed with unmethylated lambda DNA was fragmented using a Bioruptor system to a mean size of approximately 250bp
After fragmentation, the purified randomly fragmented DNA was subsequently treated with a mix of T4 DNA polymerase, Klenow Fragment and T4 polynucleotide kinase to repair, blunt and phosphorylate the ends. The blunt DNA fragments were subsequently 3’ adenylated using Klenow Fragment (3’-5’ exo-) (Enzymatics, P7010-LC-L) and following with ligation to adaptors synthesized with 5’-methylcytosine instead of cytosine using T4 DNA Ligase. Then, the DNA was purified using QIAquick PCR purification kit (Qiagen, 28104). After that, ZYMO EZ DNA Methylation-Gold Kit™ (ZYMO, D5005) was employed to convert unmethylated cytosine into uracil according to the instructions. Finally, the WGBS libraries were generated by PCR amplification using JumpStartTM Taq DNA Polymerase (Sigma, D4184-50UN) and purification using QIAquick PCR purification kit (Qiagen, 28104).

tag: treatment


title: HEK293T_WT_WGBS


title: ATAC-Seq bone marrow immature B cells Ikzf1(AID/AID) Ikzf3(AID/AID) R26(Tir2/Tir2) 12h 5-Ph-IAA_1

value: immature B cells


title: MUC7283

tag: diagnosis

tag: patient id

tag: age


title: MUC7284

tag: gender


title: 32_ARM-051

tag: race group

tag: age group

tag: batch


title: ATAC-Seq bone marrow immature B cells Ikzf1(AID/AID) Ikzf3(AID/AID) R26(Tir2/Tir2) Ctr_2

tag: strain

tag: cell preparation

value: Ex-vivo FACS sorted from bone marrow

tag: replicate number


title: EV-A71 HFMD patient, scRNA-Seq

city: Xian

first: Yaping

last: Li

state: Shaanxi

address: Xincheng District

institute: Xi'an Jiaotong University

description: 10 x Genomics

data_processing:
Cell Ranger software was used for initial quality control, including cell integrity assessment, alignment to the reference genome, and quantification of gene expression from the raw sequencing data.Seurat was utilized for further expression quality control, discarding genes expressed in fewer than three cells. Cells expressing more than 6,000 or fewer 2000 genes were excluded, as were those with mitochondrial gene-derived unique molecular identifiers (UMIs) constituting more than 20% of the total UMIs.
Assembly: CellMarker website (http://xteam.xbio.top/CellMarker/)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Blood

extract_protocol:
For single-cell sequencing, peripheral venous blood (2 ml) from the severe HFMD patient and the control was collected into heparin anticoagulant tubes. PBMCs were then isolated via Ficoll density gradient centrifugation (Lymphocyte Separation Medium, Applygen, Beijing). Cell count and viability were assessed using an automated cell counter to ensure that the single-cell suspension was well dispersed, had high cell viability, and had an accurate count. We immediately subjected freshly extracted PBMC to 10× single-cell sequencing
The entire process includes single-cell counting, single-cell GEM production, reverse transcription, cDNA amplification, library construction, library quality testing, and superior sequencing. The cDNA amplification products were sequentially fragmented, end completed, A-tailed, fragment size sorted, and ligated Head, and the complete library sequencing adaptor was added by PCR to obtain the sequencing library.Concentration required for library quality testing >10ng/ul, and the fragment length is concentrated between 350-500bp.

tag: tissue

value: Blood

tag: disease

value: EV-A71 HFMD

value: PBMC


title: H1299,IgG

city: Harbin

first: Fang

last: Liu

address: Harbin health care road

institute: Harbin Medical University

description: negative control

data_processing:
libarary strategy: CUT＆RUN
After removing adapters using Cutadapt(2.5), CUT＆RUNTools pipeline was employed for data processing and footprint analysis. Viewable bigwig files were generated using deepTools(3.4.1). Enhancers were stitched and super-enhancers were identified using ROSE (https://bitbucket.org/young_computation/rose).
Assembly: hg38
The submits.bed files contain region-based peaks information. The .bw files are CUT＆RUN sequencing signal files. The peaks_Gateway_Enhancers.bed files were generated by using ROSE.

source_name: cell line

extract_protocol:
Cells were treated using Wash Buffer of Epi™CUT＆RUN Assay Kit (Epibiotek, cat. no R1816).
Epi™ CUT＆RUN Assay Kit (Epibiotek, cat. no R1816) was used to peform library construction according to the manufacturer's instructions.

value: cell line

tag: cell line

value: human lung adenocarcinoma cells.


title: H1299,SP1,CUT&RUN


title: H1299,H3k27ac,CUT&RUN


title: MUC7281

value: Nummular Eczema

value: female

tag: batch id


title: ATAC-Seq bone marrow immature B cells Ikzf1(AID/AID) Ikzf3(AID/AID) R26(Tir2/Tir2) Ctr_1

value: bone marrow

tag: cell type

value: Ctr


title: MUC7282


title: HMV-II cells shEZH2 rep3

city: Beijing

first: Haizhen

last: Du

state: Beijing

address: No.52 Fucheng Road, Haidian District

institute: Peking University Cancer Hospital and Institute

data_processing:
Differential expression analysis of two groups was performed using the DESeq2 R package (1.20.0). P <= 0.05 and |log2(foldchange)| >= 0.585 were set as the threshold for significantly differential expression.
Assembly: hg19
Supplementary files format and content: Excel file includes raw counts for each sample

source_name: vaginal

growth_protocol: HMV-II cells were cultured in F10 containing 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted from the cells using TRIzol reagent according to the manufacturer’s instructions.
The mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. The library fragments were purified with the AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained. After the construction of the library, the insert size of the library was detected by the Agilent 2100 bioanalyzer. The library was sequenced by the Illumina NovaSeq 6000. FeatureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. Then FPKM of each gene was calculated based on the gene length and reads count mapped to this gene.

value: vaginal

value: HMV-II

value: melanoma

tag: genotype

value: EZH2 knockdown


title: HMV-II cells shEZH2 rep1

tag: treatment


title: HMV-II cells shEZH2 rep2


title: Healthy control, scRNA-Seq

description: 10 x Genomics

value: normal


title: ATAC-Seq bone marrow immature B cells Ikzf1(AID/AID) R26(Tir2/Tir2) 8h 5-Ph-IAA_2

source_name: bone marrow

value: Ikzf1(AID/AID) R26(Tir2/Tir2)

value: 8h 5-Ph-IAA


title: MUC7278

tag: diagnosis

value: Atopic eczema


title: ATAC-Seq bone marrow immature B cells Ikzf1(AID/AID) R26(Tir2/Tir2) 8h 5-Ph-IAA_1

value: immature B cells

value: Ex-vivo FACS sorted from bone marrow


title: ATAC-Seq bone marrow immature B cells Ikzf1(AID/AID) R26(Tir2/Tir2) Ctr_2


title: HMV-II cells shEZH2 EZH2-ChIP

data_processing:
Raw reads were mapped to the human genome (hg19) using BWA mem (v 0.7.12), and fragment size estimated with MACS2 [68]. Peaks were annotated with ChIPseeker and motifs identified with Homer. A q-value threshold of 0.05 was applied. Validation was performed with ChIP-qPCR.
Assembly: hg19
Supplementary files format and content: bigwig for each sample

extract_protocol:
ChIP assays were performed using the SimpleChIP Enzymatic Chromatin IP Kit (9003, Cell Signaling Technology) following the manufacturer's instructions.
The library was constructed by Novogene Corporation (Beijing, China). Subsequently, pair-end sequencing of sample was performed on Illumina platform (Illumina, CA, USA). Library quality was assessed on the Agilent Bioanalyzer 2100 system.

tag: chip antibody


title: MUC7277

tag: patient id

tag: age


title: HMV-II cells Vector rep1

value: WT


title: ATAC-Seq bone marrow Pro-B cells Pax5(AID/AID) R26(Tir2/Tir2) 6h 5-Ph-IAA_2

value: Pro-B cells

value: Pax5(AID/AID) R26(Tir2/Tir2)

value: 6h 5-Ph-IAA


title: HMV-II cells Vector rep2


title: ATAC-Seq bone marrow immature B cells Ikzf1(AID/AID) R26(Tir2/Tir2) Ctr_1


title: HMV-II cells shEZH2 Input


title: MUC7270

value: Nummular Eczema

tag: gender

value: female


title: HMV-II cells shNC EZH2-ChIP


title: HMV-II cells shNC Input


title: MUC7268

value: male


title: ATAC-Seq bone marrow Pro-B cells Pax5(AID/AID) R26(Tir2/Tir2) 6h 5-Ph-IAA_1

value: bone marrow


title: ATAC-Seq bone marrow Pro-B cells Pax5(AID/AID) R26(Tir2/Tir2) Ctr_2

value: Ctr


title: MUC7267


title: ATAC-Seq bone marrow Pro-B cells Pax5(AID/AID) R26(Tir2/Tir2) Ctr_1


title: HMV-II cells Vector rep3

value: vaginal

value: HMV-II

value: melanoma


title: ATAC-Seq bone marrow Pro-B cells E2A(AID/AID) R26 (Tir2/Tir2) 8h 5-Ph-IAA_2

value: E2A(AID/AID) R26 (Tir2/Tir2)


title: ATAC-Seq bone marrow Pro-B cells E2A(AID/AID) R26 (Tir2/Tir2) Ctr_2


title: MUC7262


title: MUC7263


title: ATAC-Seq bone marrow Pro-B cells Ikzf1(AID/AID) Ikzf3(AID/AID) R26(Tir2/Tir2) 12 5-Ph-IAA_1

value: 12 5-Ph-IAA


title: MUC7266


title: MUC7265


title: ATAC-Seq bone marrow Pro-B cells E2A(AID/AID) R26 (Tir2/Tir2) Ctr_1


title: MUC7257


title: MUC7256


title: MUC7269


title: ATAC-Seq bone marrow Pro-B cells Ikzf1(AID/AID) Ikzf3(AID/AID) R26(Tir2/Tir2) Ctr_1


title: ATAC-Seq bone marrow Pro-B cells Ikzf1(AID/AID) R26(Tir2/Tir2) 8h 5-Ph-IAA_2

value: Ikzf1(AID/AID) R26(Tir2/Tir2)

value: 8h 5-Ph-IAA


title: ATAC-Seq bone marrow Pro-B cells Ikzf1(AID/AID) Ikzf3(AID/AID) R26(Tir2/Tir2) Ctr_2

value: Ex-vivo FACS sorted from bone marrow


title: MUC7258


title: MUC7255


title: ATAC-Seq bone marrow Pro-B cells Ikzf1(AID/AID) R26(Tir2/Tir2) 8h 5-Ph-IAA_1


title: MUC7264


title: MUC7261


title: MUC7248


title: ATAC-Seq bone marrow Pro-B cells Ikzf1(AID/AID) R26(Tir2/Tir2) Ctr_2


title: MUC7247


title: MUC7250


title: ATAC-Seq bone marrow Pro-B cells Ikzf1(AID/AID) R26(Tir2/Tir2) Ctr_1


title: ATAC-Seq bone marrow in vitro pro-B control Rag2 (-/-) Ctr_2

value: in vitro pro-B control


title: ATAC-Seq bone marrow Pro-B cells Ikzf1(AID/AID) Ikzf3(AID/AID) R26(Tir2/Tir2) 12 5-Ph-IAA_2

value: Pro-B cells


title: ATAC-Seq bone marrow Pre-B cells Pax5(AID/AID) R26(Tir2/Tir2) 6 5-Ph-IAA_2

value: Pre-B cells

value: Pax5(AID/AID) R26(Tir2/Tir2)

value: 6 5-Ph-IAA


title: MUC7242

value: Nummular Eczema

value: female


title: ATAC-Seq bone marrow Pre-B cells Pax5(AID/AID) R26(Tir2/Tir2) Ctr_2

value: bone marrow


title: ATAC-Seq bone marrow Pre-B cells Pax5(AID/AID) R26(Tir2/Tir2) Ctr_1

value: Ctr


title: MUC7241


title: MUC7238

value: Atopic eczema

value: male


title: ATAC-Seq bone marrow Pre-B cells E2A(AID/AID) R26 (Tir2/Tir2) 6 5-Ph-IAA_2


title: MUC7237


title: ATAC-Seq bone marrow Pre-B cells E2A(AID/AID) R26 (Tir2/Tir2) Ctr_2


title: MUC4332


title: ATAC-Seq bone marrow Pre-B cells E2A(AID/AID) R26 (Tir2/Tir2) Ctr_1


title: MUC4331


title: ATAC-Seq bone marrow Pre-B cells Ikzf1(AID/AID) Ikzf3(AID/AID) R26(Tir2/Tir2) 12 5-Ph-IAA_1


title: MUC7249


title: ATAC-Seq bone marrow Pre-B cells Ikzf1(AID/AID) Ikzf3(AID/AID) R26(Tir2/Tir2) 12 5-Ph-IAA_2


title: MUC4328


title: MUC4327


title: ATAC-Seq bone marrow Pre-B cells Ikzf1(AID/AID) Ikzf3(AID/AID) R26(Tir2/Tir2) Ctr_2


title: MUC4326


title: ATAC-Seq bone marrow Pre-B cells Ikzf1(AID/AID) Ikzf3(AID/AID) R26(Tir2/Tir2) Ctr_1


title: MUC4325


title: ATAC-Seq bone marrow Pre-B cells Ikzf1(AID/AID) R26(Tir2/Tir2) 8h 5-Ph-IAA_1


title: ATAC-Seq bone marrow Pre-B cells Pax5(AID/AID) R26(Tir2/Tir2) 6 5-Ph-IAA_1


title: MUC4314


title: MUC4322


title: ATAC-Seq bone marrow Pre-B cells Ikzf1(AID/AID) R26(Tir2/Tir2) 8h 5-Ph-IAA_2


title: ATAC-Seq bone marrow Pre-B cells Ikzf1(AID/AID) R26(Tir2/Tir2) Ctr_1


title: MUC4321


title: MUC4313


title: MUC4307

value: psoriasis


title: ATAC-Seq bone marrow Pre-B cells Ikzf1(AID/AID) R26(Tir2/Tir2) Ctr_2


title: MUC4304


title: MUC4308


title: tumor-infiltrating NK cells, ruxolitinib treated mice

city: San Diego

first: John

middle: R

last: Teijaro

state: CA

address: 10550 North Torrey Pines Rd

department: Immunology and Microbial Science

institute: The Scripps Research Institute

description:
RNA isolated from flow-sorted NK cells
bulk RNA-seq

data_processing:
Raw data generated by Illumina sequencers were converted to FASTQ using cellranger mkfastq (10X Genomics) then subjected to quality control using fastqc and fastqcr.
Cell identification, cDNA counting and antibody-dependent tag counting were performed using cellranger v7.0.0 (10X Genomics) with the --include-intron=true option. The processed data uploaded are given as generated by cellranger count in the directory filtered_bc_feature_matrix.
For raw RNA-seq analysis, demultiplexed FASTQ files were aligned to the mouse genome (mm10) using STAR v2.7.6a with Ensembls v101 transcriptome annotations. The processed data provided are raw read counts generated by STAR.
Assembly: mm10
Supplementary files format and content: CITE-seq: count matrices generated by cellranger count
Supplementary files format and content: bulk RNA-seq: raw counts generated by STAR

source_name: tumor

extract_protocol:
Single-cell suspensions were stained with CD45 antibody and viability dye, then live CD45+ cells sorted by flow cytometry. Individual sorted cell samples were stained using the TotalSeq-B hashtag antibodies (Biolegend) according to the manufacturer's specifications and the combined cells were stained using Biolegend's TotalSeq-B protein-targeted antibodies according to the manufacturer's protocol. Stained cells were subjected to library preparation using the 3' single-cell dual index transcriptome kit (10X Genomics) targeting 30,000 total cells. For bulk RNA-seq experiments, cells sorted by flow cytometry were subjected to RNA isolation using the Arcturus PicoPure kit (Thermo Scientific) followed by library preparation targeting polyA+ RNA.
The Chromium Single Cell 3' Reagent Kit v3.1 (Dual Index) (10X Genomics) was used according to the manufacturer's specifications. Bulk RNA-seq libraries were constructed using the SMARTer v4 kit (Takara Bio).
mRNA-derived libraries were constructed independently; a combined library containing hashtag and antibody dependent tag oligos was also constructed (ADT_library). For bulk RNA-seq experiments, polyA+ RNA was converted to cDNA, subjected to amplification and library preparation using SMARTer v4 (Takara) for Illumina single-end sequencing.
CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

value: tumor

value: tumor-infiltrating NK cells

tag: antibodies/tags


title: tumor-infiltrating NK cells, ICB and ruxolitinib treated mice


title: MUC4303