title: HiC_shScr

value: shScramble


title: DSS-T-1

status: Public on Jan 17 2025

type: SRA

city: Shanghai

first: Zhe

last: Cui

address: No.1058, Huan Zhen Bei Road, Baoshan District, Shanghai

country: China

institute: Department of General Surgery, Baoshan Branch, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University

library_source: transcriptomic

data_processing:
The raw data was checked by FastQC v
Clean reads were aligned to the human genome using STAR 2.5
The expression of the transcript was calculated by FPKM using Cuffnorm
Differentially expression transcripts were determined using DESeq v1.22.1
Function and signaling pathway enrichment analysis using GO and KEGG database
Assembly: mm9
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: colon

extract_protocol:
RNA was isolated using the standard TRIzol protocol.
Stand-specific libraries were constructed using the TruSeq RNA sample prepartion kit (Illumina).

tag: condition

value: colitis

tag: tissue

value: colon

tag: genotype

value: WT

tag: treatment

value: DSS+thymopentin


title: DSS-N-3

value: DSS+normal saline


title: PBMCs_85 [sample442]

type: genomic

city: Innsbruck

first: Martin

last: Widschwendter

address: Innrain 52

country: Austria

institute: University of Innsbruck

description: PBMC biology in a mouse on a normal diet

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing:
Minfi v1.46
Average Beta

label: Cy5 and Cy3

molecule: genomic DNA

source_name: PBMCs, Mouse DNA

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was isolated from cells and different organs using AllPrep DNA/RNA Mini Kits (cat #80204, Qiagen Ltd), following the manufacturer’s protocol.

tag: Sex

value: Female

value: PBMC

tag: diet

value: Normal diet

value: MPA/DMBA- MIF-

value: Intervention set

value: No

value: No tumor


title: PBMCs_84 [sample441]

description: PBMC biology in a mouse treated with medroxyprogesterone (MPA, P) and 7,12-dimethylbenzanthracene (DMBA, D), on a ketogenic diet, and treated with Mifepristone (M)

value: Ketogenic diet

value: MPA/DMBA+ MIF+

value: Validaton set

value: Tumor


title: PBMCs_82 [sample439]


title: PBMCs_81 [sample438]


title: PBMCs_79 [sample436]

description: PBMC biology in a mouse treated with medroxyprogesterone (MPA, P) and 7,12-dimethylbenzanthracene (DMBA, D) and on a ketogenic diet

value: MPA/DMBA+ MIF-

value: Yes


title: PBMCs_78 [sample435]


title: PBMCs_80 [sample437]


title: PBMCs_77 [sample434]


title: PBMCs_71 [sample428]

description: PBMC biology in a mouse treated with medroxyprogesterone (MPA, P) and 7,12-dimethylbenzanthracene (DMBA, D), on a normal diet, and treated with Mifepristone (M)


title: PBMCs_76 [sample433]


title: PBMCs_74 [sample431]


title: PBMCs_72 [sample429]


title: PBMCs_70 [sample427]


title: PBMCs_69 [sample426]


title: PBMCs_75 [sample432]


title: PBMCs_73 [sample430]


title: PBMCs_68 [sample425]

description: PBMC biology in a mouse treated with medroxyprogesterone (MPA, P) and 7,12-dimethylbenzanthracene (DMBA, D) and on a normal diet


title: PBMCs_65 [sample422]


title: DA-SPII8h-2

city: Paris

first: Maxime

last: Wery

address: 26 rue d'Ulm

country: France

institute: Institut Curie

data_processing:
After removal of adapter sequences, reads were mapped to the reference genome using version 2.1.0 of Bowtie2 (no mismatch).
Tag densities for genes, dubious ORFs, sn(o)RNAs, tRNAs and several classes of lncRNAs (including CUTs, SUTs, XUTs and MUTs) were obtained using uniquely mapped 18-23 nt reads, after normalization on the total number of 18-23 nt reads that uniquely mapped on ORFs.
Genome_build: S. cerevisiae S288C

organism: Saccharomyces cerevisiae

source_name: Yeast cells

extract_protocol:
Total RNA was extracted using the hot phenol procedure
Small-RNA libraries were constructed using the TruSeq Small RNA kit (Illumina), starting from total RNA.

tag: genotype/variation

value: DCR1 AGO1

tag: Stage

value: after 8 hours of meiosis induction

tag: replicate


title: PBMCs_66 [sample423]


title: PBMCs_67 [sample424]


title: PBMCs_61 [sample418]

description: PBMC biology in a mouse on a ketogenic diet and treated with Mifepristone (M)

value: MPA/DMBA- MIF+


title: PBMCs_60 [sample417]


title: PBMCs_63 [sample420]


title: PBMCs_64 [sample421]


title: DA-YPD-2

value: grown in YPD medium (vegetative growth)


title: DA-SPII8h-1


title: PBMCs_62 [sample419]

value: Female


title: DA-YPD-1


title: PBMCs_86 [sample416]

value: PBMC


title: PBMCs_83 [sample440]


title: PBMCs_59 [sample415]

description: PBMC biology in a mouse on a ketogenic diet


title: PBMCs_58 [sample414]


title: WT-SPII8h-1

value: wild type


title: PBMCs_57 [sample413]

description: PBMC biology in a mouse on a normal diet and treated with Mifepristone (M)

value: Normal diet


title: PBMCs_55 [sample411]

value: Intervention set


title: WT-YPD-1


title: WT-YPD-2


title: BV-2 cells, young, LPS treated, N5

city: Stockholm

last: Skandik

address: Nobels vag 13

country: Sweden

institute: Karolinska Institutet

description: Library name: 20_BV2_young_LPS_N5

data_processing:
Sample quality was assessed using FastQC (v0.11.8).
Reads were aligned to a reference built from Ensembl GRCh38 genome sequences using STAR (v2.6.1d).
Counts for each gene were obtained using featureCounts (v1.5.1) using the GRCm38.101 GTF file from Ensembl.
Bioconductor package DESEq2 was used for count normalization and sample group comparisons, generating log2 fold changes, Wald test p-values and p-value adjustments for multiple testing (Benjamini-Hochberg method).
Assembly: GRCh38/hg19
Supplementary files format and content: Tab-delimited matrix of raw counts for all samples

source_name: brain

growth_protocol: BV_2 microglia were maintained in DMEM (high glucose, Glutamax) with addition of 10% FBS and PENSTREP (100 µg/ml penicillin and 100 µg/ml streptomycin) at 37°C in humified 5 % CO2 atmosphere.

extract_protocol:
Total RNA was isolated using the RNeasy Plus Mini kit (Qiagen) with an additional step of Dnase treatment. The yield and quality of the isolated RNA were analysed using NanoDrop spectrophotometer. Total RNA samples were subjected to quality control with Agilent Tapestation according to the manufacturer’s instructions.
To construct libraries suitable for Illumina sequencing, the Illumina stranded mRNA prep ligation sample preparation protocol was used with starting concentration of 200 ng total RNA. The protocol includes mRNA isolation, cDNA synthesis, ligation of adapters and amplification of indexed libraries. The yield and quality of the amplified libraries were analysed using Qubit by ThermoFisher Scientific and quality was further checked by using Agilent Tapestation. The indexed cDNA libraries were normalized and combined, and the pools were sequenced.

treatment_protocol: BV-2 microglial cells were treated with bacterial LPS (100 ng/ml) for 6 hours.

value: brain

tag: cell line

tag: cell type

value: microglia

value: WT

value: LPS, 6 hours

tag: batch


title: PBMCs_53 [sample409]

value: MPA/DMBA- MIF-

value: No

value: No tumor


title: PBMCs_52 [sample408]


title: BV-2 cells, young, LPS treated, N4

description: Library name: 16_BV2_young_LPS_N4


title: PBMCs_51 [sample407]

value: Ketogenic diet

value: MPA/DMBA+ MIF+

value: Validaton set

value: Yes

value: Tumor


title: PBMCs_50 [sample406]

value: Female


title: PBMCs_56 [sample412]

value: PBMC

value: MPA/DMBA- MIF+


title: PBMCs_48 [sample404]


title: BV-2 cells, aged, untreated, N4

description: Library name: 13_BV2_aged_untr_N4


title: WT-SPII8h-2

value: wild type

value: after 8 hours of meiosis induction


title: BV-2 cells, young, LPS treated, N3

description: Library name: 12_BV2_young_LPS_N3

value: brain


title: BV-2 cells, young, untreated, N3

description: Library name: 11_BV2_young_untr_N3

value: microglia


title: PBMCs_47 [sample403]


title: PBMCs_49 [sample405]


title: BV-2 cells, aged, LPS treated, N3

description: Library name: 10_BV2_aged_LPS_N3

value: WT


title: PBMCs_45 [sample401]

value: MPA/DMBA+ MIF-


title: BV-2 cells, aged, untreated, N3

description: Library name: 9_BV2_aged_untr_N3


title: BV-2 cells, aged, untreated, N5

description: Library name: 17_BV2_aged_untr_N5


title: BV-2 cells, aged, LPS treated, N4

description: Library name: 14_BV2_aged_LPS_N4

value: LPS, 6 hours


title: PBMCs_44 [sample400]


title: PBMCs_54 [sample410]

value: Normal diet

value: MPA/DMBA- MIF-

value: Intervention set

value: No


title: PBMCs_43 [sample399]

value: Ketogenic diet

value: Validaton set


title: PBMCs_46 [sample402]

value: MPA/DMBA+ MIF+

value: No tumor


title: BV-2 cells, young, untreated, N5

description: Library name: 19_BV2_young_untr_N5


title: PBMCs_42 [sample398]

value: Female

value: PBMC

value: Yes

value: Tumor


title: BV-2 cells, young, untreated, N2

description: Library name: 7_BV2_young_untr_N2

value: brain


title: BV-2 cells, aged, LPS treated, N5

description: Library name: 18_BV2_aged_LPS_N5

value: microglia


title: BV-2 cells, aged, LPS treated, N2

description: Library name: 6_BV2_aged_LPS_N2

value: WT


title: PBMCs_41 [sample397]

value: MPA/DMBA+ MIF-


title: BV-2 cells, young, untreated, N4

description: Library name: 15_BV2_young_untr_N4


title: BV-2 cells, aged, untreated, N2

description: Library name: 5_BV2_aged_untr_N2


title: PBMCs_40 [sample396]


title: PBMCs_39 [sample395]


title: BV-2 cells, young, untreated, N1

description: Library name: 3_BV2_young_untr_N1


title: PBMCs_38 [sample394]


title: PBMCs_37 [sample393]


title: BV-2 cells, aged, LPS treated, N1

description: Library name: 2_BV2_aged_LPS_N1

value: LPS, 6 hours


title: PBMCs_36 [sample392]

value: Normal diet


title: BV-2 cells, aged, untreated, N1

description: Library name: 1_BV2_aged_untr_N1


title: PBMCs_35 [sample391]


title: BV-2 cells, young, LPS treated, N2

description: Library name: 8_BV2_young_LPS_N2


title: PBMCs_34 [sample390]


title: PBMCs_33 [sample389]


title: PBMCs_32 [sample388]


title: PBMCs_28 [sample384]

value: MPA/DMBA- MIF+


title: PBMCs_31 [sample387]

value: Intervention set


title: WT-Veh-rep4

type: RNA

city: Irvine

first: Robert

middle: Paul

last: Krattli Jr

state: CA

address: 811 Health Sciences Road, MedSci B-120

department: Anatomy and Neurobiology

country: USA

institute: University of California, Irvine

description: Total RNA isolated from fresh-frozen brain samples, no amplification of genetic material

hyb_protocol: For each 12-lane cartridge, 70 µl of Master Mix were combined with 42 µl of the fluorescent labeled Reporter CodeSet, flicked to mix, and briefly spun down before 8 µl of combined solution were added to each lane. 5 µl of total RNA (20 ng/µl) per sample was then added to individual lanes. Next, 2 µl of the biotin Capture ProbeSet was added to each lane. Then, loaded cartridges were placed in a thermocycler at 65 degrees Celsius for approximately 20 hours. Following hybridization, cartridges are loaded onto nCounter Prep Station (NanoString™) to perform liquid transfers, magnetic bead separations, and immobilization of molecular labels on the sample cartridge surface. Protocol as described per the manufacturer’s instructions: NanoString™ (Seattle, WA).

scan_protocol: Scanning of hybridized cartridges was performed on an nCounter Digital Analyzer (NanoString™) per the manufacturer’s instructions: NanoString™ (Seattle, WA).

data_processing: The raw value data were normalized utilizing a two-step normalization process: an initial Positive Control Normalization, followed by a CodeSet Content Normalization using 13 internalized housekeeping genes that accompanied the Neuroinflammation Panel. Both processes were performed by the nSolver Analysis Software 4.0 (NanoString™).

label: Color-Coded Reporter Probe

source_name: fresh-frozen brain tissue

label_protocol: 5 µl of total RNA (20 ng/µl) per sample were labeled with a fluorescent Reporter ProbeSet per the manufacturer’s instructions: NanoString™ (Seattle, WA).

extract_protocol: Total RNA was isolated from 100 mg of fresh-frozen brain tissue per sample. Brain samples were first homogenized in QIAzol Lysis Reagent (Qiagen) and then underwent RNA isolation with RNeasy Plus Universal Mini Kit (Qiagen) to obtain minimum of 100ng of unreplicated RNA, whose purity was verified with both NanoDrop (ThermoFisher) and Bioanalyzer 2100 (Agilent Technologies).

value: fresh-frozen brain tissue

value: male

tag: strain

tag: ev treatment

value: No

tag: ev cell line


title: WT-Veh-rep3


title: PBMCs_29 [sample385]

value: Ketogenic diet

value: Validaton set


title: AD-iMGL-rep4

value: iMGL


title: AD-iMGL-rep3


title: AD-iMGL-rep5


title: BV-2 cells, young, LPS treated, N1

description: Library name: 4_BV2_young_LPS_N1


title: AD-iMGL-rep2


title: WT-Veh-rep1


title: PBMCs_30 [sample386]

value: Female

value: PBMC


title: PBMCs_26 [sample382]

value: MPA/DMBA- MIF-

value: No tumor


title: AD-hNSC-rep5

value: Yes

value: EnStem-A


title: WT-Veh-rep2


title: PBMCs_27 [sample383]


title: PBMCs_25 [sample381]


title: PBMCs_24 [sample380]


title: PBMCs_23 [sample379]


title: AD-hNSC-rep4


title: AD-hNSC-rep2


title: AD-hNSC-rep3


title: AD-hNSC-rep1


title: AD-Veh-rep4


title: Oviduct_85 [sample374]

description: Oviduct biology in a mouse on a normal diet

source_name: Oviduct, Mouse DNA, Tissue

value: Oviduct


title: AD-iMGL-rep1


title: AD-Veh-rep3


title: AD-Veh-rep1


title: AD-Veh-rep2


title: ATAC-seq, HBV cccDNA, intermediate2 nucleosomes,  In vitro Experiment2

city: New York

first: Andres

last: Mansisidor

state: NY

address: 1230 York Ave Box 176

department: Laboratory of Genome Architecture and Dynamics

institute: Rockefeller University

description:
Library name: Sample 121
ATAC-seq

library_source: genomic

data_processing:
UMI demultiplexing (custom script)
adapter trimming (custom script)
alignment to HBV genome (Bowtie2 v2.3.4.3)
nucleosome coverage mapping (nucleoATAC)
Bedgraphs from both RNA- and MNase-seq were plotted using Sushi package v1.30.0 in R v4.1.0
Assembly: NC_003977.2 (offset by 500 bp)
Supplementary files format and content: bedgraph files that include coverage of fragment centers (50 bp windows)
adapter trimming (TrimGalore v0.4.5, cutadapt v1.15, FastQC v0.11.5)
alignment to hg38 and HBV genome (bowtie2 v2.3.4.1
deduplication (Picard Tools v2.16.0)
For read counts related to the in vitro chromatin assembly of the HBV genome, the percentage of mapped reads was determined based on the total number of unique reads in the de-duplicated bam files
Assembly: hg38 (human alignment), NC_003977.2 (offset by 500 bp, HBV alignment)

organism: Hepatitis B virus

source_name: in vitro

extract_protocol:
In vivo MNase-seq was performed on purified nuclei at different timepoints after transfection with HBV cccDNA or on in vitro reconstituted chromatin.
For MNase-seq on in vitro reconstituted chromatin, titration of MNase was performed to determine enzyme concentrations that yielded partial- , fully-, or over-digested chromatin arrays. Chromatinized DNA (100 ng) was digested using MNase (NEB) in 25 µL reactions with 2.5–25 units of enzymes that was incubated for 5 minutes at 37°C before 1 mM of CaCl2 was added and incubation continued for another 5 minutes at 37°C. The reaction was stopped by adding 20 mM EDTA and 1% SDS. DNA was subsequently purified using Clean and Concentrated-5 DNA columns (Zymo). Sequencing libraries were prepared using NEBNext Ultra II DNA Library Prep Kit – DNA repair, End Prep, USER, and Ligation of Unique Dual Index Barcodes or Unique Dual Index UMI Adaptors (NEB). Barcoding PCR was consistently carried out using only 5 PCR cycles with NEBNext High-Fidelity 2X PCR Mix and subsequent size selection using agarose gel or beads (Ampure XP). For MNase-seq on cell cultured samples, HEK293T cells were transfected with recombinant cccDNA 4 or 24-hours prior to harvest for MNase-seq. The nuclei of HEK293, HepG2.2.15, and HepAD38 cells were purified by incubating cells in Nuclei isolation buffer for 10 minutes (0.1% Igepal, 0.1% Triton X -100, 1 mM DTT in 1 X PBS), mechanically lysing with 10 strokes of loose (A) pestle Dounce homogenizer, and washing nuclei twice in 10 mL of Wash Buffer with Tween (10 mM Tris-HCl pH 7.5, 2.5 mM NaCl, 3 mM MgCl2, and 0.1% Tween-20). Titration of MNase was similarly performed to determine enzyme concentrations that yielded partial- , fully-, or over-digested genomic DNA. MNase (NEB) was added to 2 x 106 nuclei in 50 µL reaction volume with 125–2000 units of enzyme that was incubated for 5 minutes at 37 °C before 1 mM of CaCl2 was added and incubation continued for another 5 minutes at 37 °C. The reaction was stopped by adding 20 mM EDTA and 1 % SDS. DNA was subsequently purified using Clean and Concentrated-5 DNA columns (Zymo). Sequencing libraries were prepared using NEBNext Ultra II DNA Library Prep Kit – DNA repair, End Prep, USER, and Ligation of Unique Dual Index UMI Adaptors (NEB). Barcoding PCR was consistently carried out with NEBNext High-Fidelity 2X PCR Mix and subsequent size selection using agarose gel or beads (Ampure XP). Libraries were then pooled and enriched for HBV-containing reads using custom-designed xGen Lockdown probes (Integrated DNA Technology) of 60 bp each tiling the entire HBV genome and oligo capture protocol was followed per manufacture’s protocol. Enriched libraries were subsequently amplified using 11 PCR cycles with NEBNext High-Fidelity 2X PCR Mix and purified using Ampure XP beads.
Following assembly, HBV minichromosomes were submitted at MSKCC’s Epigenetics Research Innovation Lab for processing. ATAC-seq was carried out as previously described with minor modifications using in house prepared transposase (Tn5) enzyme. Upon Mg precipitation, two replicates were used and analyzed for each condition. Briefly, a total of 130 ng chromatinized material was reconstituted in 50 μL transposition buffer containing 25 μL TD buffer (2 0mM Tris HCl pH 7.5, 10 mM MgCl2, 20 % Dimethyl Formamide), 2.5 μL Tn5 transposase, 0.1 % Tween20, 0.01 % Digitonin, 16.5 µl 1X PBS and 5.4 μL ddH2O. Samples were then incubated at 37 °C for 25 min. DNA was isolated using a ZYMO Kit (D4014).
ATAC-seq libraries were prepared using NEBNext High-Fidelity 2X PCR Master Mix (NEB, #M0541), a uniquely barcoded primer per sample, and a universal primer. Samples were first subjected to 5 cycles of initial amplification in order to identify the number or cycles needed for each partially amplified library. Upon completion of final amplification, samples were subject to a dual size selection (0.55x–1.5x) using SPRIselect beads (Beckman Coulter, B23317). Fragment distribution of libraries was assessed with an Agilent Bioanalyzer and the sequencing libraries were sent to the MSKCC Integrated Genomics Operation core facility for sequencing on a NovaSeq 6000 flow cell in a 50 bp paired-end (50PE) mode.

value: in vitro

value: not applicable

value: reconstituted nucleosomes


title: Oviduct_84 [sample373]

description: Oviduct biology in a mouse treated with medroxyprogesterone (MPA, P) and 7,12-dimethylbenzanthracene (DMBA, D), on a ketogenic diet, and treated with Mifepristone (M)

value: MPA/DMBA+ MIF+

value: Tumor


title: Oviduct_82 [sample371]


title: Oviduct_83 [sample372]


title: ATAC-seq, HBV cccDNA, intermediate nucleosomes,  In vitro Experiment2

description:
Library name: Sample 119
ATAC-seq


title: Oviduct_81 [sample370]


title: ATAC-seq, HBV cccDNA, intermediate nucleosomes,  In vitro Experiment1

description:
Library name: Sample 118
ATAC-seq


title: ATAC-seq, HBV cccDNA, undersaturated nucleosomes,  In vitro Experiment2

description:
Library name: Sample 117
ATAC-seq


title: ATAC-seq, HBV cccDNA, intermediate2 nucleosomes,  In vitro Experiment1

description:
Library name: Sample 120
ATAC-seq


title: Oviduct_80 [sample369]


title: Oviduct_79 [sample368]

description: Oviduct biology in a mouse treated with medroxyprogesterone (MPA, P) and 7,12-dimethylbenzanthracene (DMBA, D) and on a ketogenic diet

value: MPA/DMBA+ MIF-


title: PBMCs_22 [sample378]

value: Normal diet

value: MPA/DMBA- MIF+

value: Intervention set

value: No


title: ATAC-seq, HBV cccDNA, empty, In vitro Experiment2

description:
Library name: Sample 115
ATAC-seq


title: Oviduct_78 [sample367]

value: Female

value: Ketogenic diet

value: Validaton set


title: ATAC-seq, HBV cccDNA, undersaturated nucleosomes,  In vitro Experiment1

description:
Library name: Sample 116
ATAC-seq


title: PBMCs_21 [sample377]

value: PBMC

value: No tumor


title: Oviduct_77 [sample366]

value: Yes


title: ATAC-seq, HBV cccDNA, empty, In vitro Experiment1

description:
Library name: Sample 114
ATAC-seq


title: Oviduct_76 [sample365]

value: Oviduct


title: PBMCs_19 [sample375]

value: MPA/DMBA- MIF-


title: PBMCs_20 [sample376]


title: Oviduct_75 [sample364]


title: Oviduct_74 [sample363]

description: Oviduct biology in a mouse treated with medroxyprogesterone (MPA, P) and 7,12-dimethylbenzanthracene (DMBA, D), on a normal diet, and treated with Mifepristone (M)


title: PSG6

city: Caparica

first: Pedro

middle: M.

last: Costa

address: Campus de Caparica

department: Department of Life Sciences

country: Portugal

institute: NOVA School of Science and Technology, NOVA University of Lisbon

data_processing:
Data quality was assessed with the FastQC quality-control tool v0.11.9 for high throughput sequence data. Reads with low-quality and the Illumina adapter were trimmed by using TrimGalore v0.6.6.
Reads were combined and assembled with Trinity v2.6.6.
Coding regions within the assembled transcriptome were predicted using TransDecoder v5.5.0.
Reads were mapped against the respective assembled transcriptome with Kallisto v0.43.0.
The Tximport v1.18.0 package was used to import the data into R.
Assembly: NA
Supplementary files format and content: xlsx: Data frame with the predicted coding region with homology matching against Swiss-Prot database (UniProt release 2023_03): expression values (mean Counts), e-value, %ID,  annotation and nucleotide. sequence
Supplementary files format and content: fasta: Nucleotide sequence of the predicted coding regions that had homology matching against Swiss-Prot database.

molecule: polyA RNA

organism: Sepia officinalis

source_name: Posterior salivary gland

extract_protocol:
Total RNA of posterior salivary glands was isolated from whole-tissue preserved in RNAlater using the RNeasy Protect Mini Kit combined with on-column DNA digestion with the RNase-Free DNase Set (all from Qiagen, Hilden, Germany).
Library preparation was done using Stranded mRNA Library Preparation Kit and the generated RNA fragments were sequenced in Illumina NovaSeq platform (Illumina, San Diego, CA, USA), with a mean length of 150 bp paired-end reads at the scale of 40 million reads.

value: Posterior salivary gland

value: wild type


title: Oviduct_73 [sample362]

value: MPA/DMBA+ MIF+


title: SDL-TOPO library prepared from 25 pg of genomic DNA extracted from cdc9-7 mutant of budding yeast cells

city: Kashiwa

first: Fumihito

last: Miura

state: Chiba

address: Kashiwanoha 5-1-5

department: Graduate School of Frontier Sciences

country: Japan

institute: The University of Tokyo

description: Library name: Lagging-seq library 08

data_processing:
The libraries were sequence determined with the Illumina iSeq 100 system, and obtained reads were mapped on the sacCer3 reference genome with bowtie2. The exported bam file was converted to a bigwig file using bedtools and bedGraphToBigWig. The bigwig file was visualized with IGV.
Assembly: sacSer3
Supplementary files format and content: bigwig format of read depth

growth_protocol: Budding yeast strain BY20149 (MATa ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 ura3-1 cdc9-7, W303 background) was provided by the National Bio-Resource Project (NBRP) – Yeast, Japan. A single colony was inoculated in 10 mL YPD media (2%(w/v) glucose, 2% (w/v) peptone, and 1% (w/v) yeast extract) and cultivated at 30°C overnight with shaking at 250 RPM. The 1 mL of grown cells were diluted 1:9 with the same media and cultivated again at 30°C for 2 h.

extract_protocol:
Cells were collected with centrifugation, washed once with water, and served for genomic DNA extraction using Genomic-tip 100/G from Qiagen following the yeast-specific protocol provided by the manufacturer.
A 14.5 μL reaction containing the indicated amount of genomic DNA, 2.5 μL 10x SDL buffer, 1 μL rSAP (NEB) was prepared and incubated at 37°C for 15 min and 95°C for 5 min. Then, the reaction was supplemented with 7.5 μL PEG600, 1 μL each 10 mM ATP, 10 μM P-AR-thio5-NH2, and 5 mg/ml SDL. The reaction was incubated at 37°C for 1 h and 95 °C for 5min. Subsequently, the solution was supplemented with 15 µL of water, 5 µL of 10×PCR buffer (Takara Bio Inc.), 4 µL of 2.5 mM dNTPs, 1 µL of 50 µM NH2-AF (Supplementary Table S1), and five units of GeneTaq hot start (Nippon gene, Toyama, Japan) and incubated sequentially at 95°C for 3 min, 55°C for 5 min, and 72°C for 5 min. Then, 50 µL of AxyPrep Mag PCR clean and 50 µL of isopropanol were added and incubated at 5 min. The beads were washed twice with 200 µL of the solution containing 19% (v/v) PEG #400, 1 M NaCl, and 50 mM Tris-HCl, pH 8.0, and rinsed once with 70%(v/v) ethanol. The purified DNA was eluted with 25 µL of 10 mM Tris-Acetate, pH 8.0. To the purified DNA solution, 15 µL of water, 5 µL of 10×ExTaq buffer, 4 µL of 2.5 mM dNTPs, 1 µL of ExTaq HS, 1 µL of 20 µM Primer-3, 1 µL of 20 µM Index primer, and 1 µL of 5 ng/µl VOC for TA were added. After sequential incubation at 25°C for 5 min, 72°C for 5 min, and 95°C for 3 min, appropriate cycles of three-step incubations for 15 s at 95°C, 55°C, and 72°C, and a final extension at 72°C for 1 min were performed.


title: SDL-TOPO library prepared from 250 pg of genomic DNA extracted from cdc9-7 mutant of budding yeast cells

description: Library name: Lagging-seq library 06


title: SDL-TOPO library prepared from 75 pg of genomic DNA extracted from cdc9-7 mutant of budding yeast cells

description: Library name: Lagging-seq library 07


title: Oviduct_70 [sample359]

value: Tumor


title: SDL-TOPO library prepared from 750 pg of genomic DNA extracted from cdc9-7 mutant of budding yeast cells

description: Library name: Lagging-seq library 05


title: Oviduct_71 [sample360]


title: Oviduct_69 [sample358]


title: SDL-TOPO library prepared from 7.5 ng of genomic DNA extracted from cdc9-7 mutant of budding yeast cells

description: Library name: Lagging-seq library 03


title: SDL-TOPO library prepared from 25 ng of genomic DNA extracted from cdc9-7 mutant of budding yeast cells

description: Library name: Lagging-seq library 02


title: Oviduct_68 [sample357]

description: Oviduct biology in a mouse treated with medroxyprogesterone (MPA, P) and 7,12-dimethylbenzanthracene (DMBA, D) and on a normal diet

value: MPA/DMBA+ MIF-


title: Oviduct_67 [sample356]

value: Normal diet


title: SDL-TOPO library prepared from 75 ng of genomic DNA extracted from cdc9-7 mutant of budding yeast cells

description: Library name: Lagging-seq library 01


title: Oviduct_65 [sample354]


title: IMR90-tPBAT

data_processing:
Reads were mapped on mixed reference of human genome hg19 and lammbda phage genome using in-house program BMap.
Alignments exported from BMap were summarized into a binary file in graph format using in-house program MPTC.
The methylation levels and coverage were exported from the file in graph format using in-hose program MethExport
Assembly: Human hg19
Supplementary files format and content: bedGraph

organism: Homo sapiens

source_name: tPBAT library prepared from IMR90 genomic DNA

growth_protocol: The IMR-90 cells were grown in MEM supplemented with 10% FBS.

extract_protocol:
Genomic DNA was extracted with Qiagen's DNeasy Blood & Tissue kit following to manufacture's protocol.
The library preparations were done with tPBAT (Miura F et al., 2019, Nucleic Acids Res, 47, e85) and sPBAT, which is related to this submission.

treatment_protocol: No treatment was performed.


title: IMR90-sPBAT

source_name: sPBAT library prepared from IMR90 genomic DNA


title: PSG8


title: PSG7


title: Oviduct_63 [sample352]


title: HUDEP2_KD_replicate_2

city: Rochester

first: Laurie

last: Steiner

address: 601 Elmwood Ave

department: Pediatrics

institute: University of Rochester

description: Library name: KD_2

data_processing:
aligned to hg38 using STAR
RPKM normalization using bamCoverage
Assembly: hg38
Supplementary files format and content: bigwig

extract_protocol:
Qiagen RNAeasy
Preparation and sequencing of poly-A mRNA sequencing libraries were performed by URMC using TruSeq Stranded mRNA

value: erythroid


title: HUDEP2_KD_replicate_3

description: Library name: KD_3


title: Oviduct_66 [sample355]

value: Intervention set


title: Oviduct_62 [sample351]


title: Oviduct_61 [sample350]

description: Oviduct biology in a mouse on a ketogenic diet and treated with Mifepristone (M)

value: MPA/DMBA- MIF+

value: No


title: HUDEP2_KD_replicate_1

description: Library name: KD_1


title: Oviduct_72 [sample361]

value: Female


title: HUDEP2_YYFF_replicate_3

description: Library name: YYFF_3


title: SDL-TOPO library prepared from 2.5 ng of genomic DNA extracted from cdc9-7 mutant of budding yeast cells

description: Library name: Lagging-seq library 04


title: Oviduct_60 [sample349]

value: Ketogenic diet

value: Validaton set


title: HUDEP2_YYFF_replicate_2

description: Library name: YYFF_2


title: Oviduct_86 [sample348]

value: No tumor


title: HUDEP2_OE_replicate_3

description: Library name: OE_3


title: Oviduct_59 [sample347]

description: Oviduct biology in a mouse on a ketogenic diet


title: HUDEP2_OE_replicate_2

description: Library name: OE_2


title: Oviduct_57 [sample345]

description: Oviduct biology in a mouse on a normal diet and treated with Mifepristone (M)


title: Oviduct_58 [sample346]


title: Oviduct_64 [sample353]

value: Yes


title: HUDEP2_OE_replicate_1

description: Library name: OE_1


title: Oviduct_55 [sample343]

value: Oviduct


title: Oviduct_56 [sample344]


title: HUDEP2_EV_replicate_3

description: Library name: EV_3

value: EV


title: HUDEP2_EV_replicate_1

description: Library name: EV_1


title: Oviduct_54 [sample342]

value: MPA/DMBA- MIF-


title: Oviduct_51 [sample339]


title: Oviduct_52 [sample340]


title: Oviduct_53 [sample341]


title: HUDEP2_EV_replicate_2

description: Library name: EV_2


title: Human PBMC-derived CD4 T cells Th1_PATIENT_AL_RNA

city: Philadlephia

first: Daniel

last: Beiting

state: Pennsylvania

address: 380 S. University Avenue

institute: University of Pennsylvania

description: Library name: Th1_PATIENT_AL_RNA

data_processing:
Raw Fastq files were pseudoaligned using Kallisto software (version > 0.44.0). Abundance output from Kallisto were read into R using tximport and gene-level count information are provided here.
Assembly: hg38
Supplementary files format and content: Raw_Counts_RNA_Fig3.txt contains the kallisto pseudoaligned counts from the first cohort of lupus patients and healthy controls and includes multiple CD4 T cell subsets.
Supplementary files format and content: Raw_Counts_RNA_Fig5.txt contains the kallisto pseudoaligned counts from the first and second cohorts of lupus patients and healthy controls and includes only Naïve CD4 T cells.
Supplementary files format and content: Raw_Counts_RNA_Fig6.txt contains the kallisto pseudoaligned counts from the first , second, and third  cohorts of lupus patients and healthy controls and includes only Naïve CD4 T cells.

source_name: Blood

extract_protocol:
Cryopreserved PBMCs were thawed and enriched using negative selection (Stem Cell technologies human CD4 Isolation kit #100-0696) ) for CD4 T cells. They were then stained with flourescent antibodies and cells were sorted using flourescent activated cell sorter (Aria C). CD45RA+CD27+ naive TH, CXCR5+PD1+ICOS+CD38+ AcTfh, CXCR5+PD1+ICOSCD38- cTfh, and CXCR5-PD1-CXCR3+ Th1 cells were sorted. In most cases, 5000 cells were sorted. Immediately following sorting, cells were processed for RNA-seq following manufacturer protocols (Takara SMART-Seq® v4 Ultra Low Input RNA Kit). Cells were processed directly to cDNA without separate RNA isolation per the protocol.
Libaries were prepared following standard protocols and utilizing Illumina indexes. Fractionation and size selection were performed. Size selection was done using bead-based enrichment.

value: Blood

tag: timpoint

value: A

tag: disease

value: Lupus

tag: treatment arb_active

tag: treatment arb_type

tag: treatment rituximab_ever

tag: treatment rituximab_active

tag: treatment acei_active

tag: disease _severity_sledai

tag: ethnicity

value: Not Hispanic or Latino/a

tag: race

value: White


title: Human PBMC-derived CD4 T cells Th1_PATIENT_AP_RNA

description: Library name: Th1_PATIENT_AP_RNA

tag: tissue

tag: Sex

value: Healthy

value: UKN


title: Oviduct_50 [sample338]

tag: diet

tag: treatment

value: MPA/DMBA+ MIF+


title: Human PBMC-derived CD4 T cells Th1_PATIENT_AF_RNA

description: Library name: Th1_PATIENT_AF_RNA

tag: cell type

tag: batch

value: No

value: Black/AfricanAmerican


title: Oviduct_49 [sample337]

value: Female

value: Ketogenic diet

value: Tumor


title: Human PBMC-derived CD4 T cells Th1_PATIENT_AE_RNA

description: Library name: Th1_PATIENT_AE_RNA

value: Yes

value: Hispanic or Latino/a


title: HUDEP2_YYFF_replicate_1

description: Library name: YYFF_1

tag: cell line

value: erythroid

tag: genotype


title: Human PBMC-derived CD4 T cells Th1_PATIENT_AG_RNA

description: Library name: Th1_PATIENT_AG_RNA

tag: timpoint

tag: disease

value: Losartan

value: yes


title: Oviduct_47 [sample335]

value: Oviduct

value: Validaton set

value: No tumor


title: Human PBMC-derived CD4 T cells Th1_CONTROL_BH_RNA

description: Library name: Th1_CONTROL_BH_RNA

value: Blood

value: A

tag: treatment arb_active

tag: treatment arb_type


title: Human PBMC-derived CD4 T cells Th1_PATIENT_AD_RNA

description: Library name: Th1_PATIENT_AD_RNA

value: Healthy

tag: treatment rituximab_ever

tag: treatment rituximab_active

value: UKN


title: Human PBMC-derived CD4 T cells Th1_CONTROL_BE_RNA

description: Library name: Th1_CONTROL_BE_RNA

tag: treatment acei_active

tag: disease _severity_sledai


title: Oviduct_48 [sample336]

value: MPA/DMBA+ MIF+

value: No


title: Oviduct_45 [sample333]

value: Female

value: MPA/DMBA+ MIF-


title: Oviduct_44 [sample332]

value: Ketogenic diet

value: Tumor


title: Human PBMC-derived CD4 T cells Th1_CONTROL_BC_RNA

description: Library name: Th1_CONTROL_BC_RNA

tag: ethnicity

tag: race


title: Human PBMC-derived CD4 T cells NaiveCD4_PATIENT_Q_RNA

description: Library name: NaiveCD4_PATIENT_Q_RNA

tag: tissue

tag: Sex

value: Lupus

value: Yes

value: Not Hispanic or Latino/a

value: White


title: Oviduct_43 [sample331]

value: Oviduct

tag: diet

tag: treatment


title: Human PBMC-derived CD4 T cells NaiveCD4_PATIENT_N_RNA

description: Library name: NaiveCD4_PATIENT_N_RNA

tag: cell type

tag: batch


title: Oviduct_41 [sample329]

value: Validaton set


title: Oviduct_40 [sample328]

value: Normal diet

value: Intervention set


title: Human PBMC-derived CD4 T cells NaiveCD4_PATIENT_L_RNA

description: Library name: NaiveCD4_PATIENT_L_RNA

value: Blood

value: A

value: Black/AfricanAmerican


title: Human PBMC-derived CD4 T cells NaiveCD4_PATIENT_K_RNA

description: Library name: NaiveCD4_PATIENT_K_RNA

value: Asian


title: Oviduct_39 [sample327]

value: MPA/DMBA+ MIF+

value: No

value: No tumor


title: Oviduct_38 [sample326]

value: Female


title: Human PBMC-derived CD4 T cells NaiveCD4_PATIENT_J_RNA

description: Library name: NaiveCD4_PATIENT_J_RNA


title: Human PBMC-derived CD4 T cells NaiveCD4_PATIENT_H_RNA

description: Library name: NaiveCD4_PATIENT_H_RNA


title: Oviduct_36 [sample324]


title: Oviduct_35 [sample323]

value: MPA/DMBA+ MIF-

value: Tumor


title: Oviduct_46 [sample334]

value: Ketogenic diet


title: Oviduct_37 [sample325]


title: Oviduct_42 [sample330]

value: Yes


title: Human PBMC-derived CD4 T cells NaiveCD4_PATIENT_E_RNA

description: Library name: NaiveCD4_PATIENT_E_RNA

value: Lupus

value: Valasartan

value: Not Hispanic or Latino/a


title: Human PBMC-derived CD4 T cells NaiveCD4_PATIENT_G_RNA

description: Library name: NaiveCD4_PATIENT_G_RNA


title: Oviduct_33 [sample321]

value: Oviduct

value: Normal diet


title: Human PBMC-derived CD4 T cells NaiveCD4_PATIENT_AH_RNA

description: Library name: NaiveCD4_PATIENT_AH_RNA

value: Blood


title: Oviduct_31 [sample319]

value: Intervention set


title: Human PBMC-derived CD4 T cells NaiveCD4_PATIENT_AG_RNA

description: Library name: NaiveCD4_PATIENT_AG_RNA

value: A

value: Losartan

value: yes

value: Black/AfricanAmerican


title: Human PBMC-derived CD4 T cells NaiveCD4_PATIENT_AP_RNA

description: Library name: NaiveCD4_PATIENT_AP_RNA

value: Healthy

value: No

value: UKN


title: Oviduct_29 [sample317]

value: Female

value: MPA/DMBA- MIF+

value: Validaton set

value: No tumor


title: Oviduct_30 [sample318]

value: MPA/DMBA+ MIF-

value: Yes

value: Tumor


title: Human PBMC-derived CD4 T cells NaiveCD4_PATIENT_P_RNA

description: Library name: NaiveCD4_PATIENT_P_RNA

value: Lupus

value: Not Hispanic or Latino/a


title: Human PBMC-derived CD4 T cells NaiveCD4_PATIENT_AE_RNA

description: Library name: NaiveCD4_PATIENT_AE_RNA

value: Blood

value: Hispanic or Latino/a

value: White


title: Oviduct_32 [sample320]

value: Oviduct

value: Normal diet

value: Intervention set


title: Oviduct_28 [sample316]

value: Ketogenic diet

value: No


title: Human PBMC-derived CD4 T cells NaiveCD4_PATIENT_A_RNA

description: Library name: NaiveCD4_PATIENT_A_RNA

value: Female

value: A

value: Black/AfricanAmerican


title: Oviduct_27 [sample315]

value: MPA/DMBA- MIF+

value: Validaton set

value: No tumor


title: Oviduct_26 [sample314]

value: MPA/DMBA- MIF-


title: Oviduct_34 [sample322]

value: MPA/DMBA+ MIF-

value: Yes

value: Tumor


title: Oviduct_23 [sample311]


title: Human PBMC-derived CD4 T cells NaiveCD4_CONTROL_BG_RNA

description: Library name: NaiveCD4_CONTROL_BG_RNA

value: Blood

value: Healthy

value: UKN


title: Human PBMC-derived CD4 T cells NaiveCD4_CONTROL_BF_RNA

description: Library name: NaiveCD4_CONTROL_BF_RNA


title: Oviduct_24 [sample312]

value: Oviduct


title: Oviduct_22 [sample310]

value: Normal diet

value: Intervention set


title: Oviduct_25 [sample313]

value: Ketogenic diet

value: No


title: Human PBMC-derived CD4 T cells NaiveCD4_PATIENT_AL_RNA

description: Library name: NaiveCD4_PATIENT_AL_RNA

value: Female

value: A

value: Lupus

value: Not Hispanic or Latino/a

value: White


title: Human PBMC-derived CD4 T cells NaiveCD4_CONTROL_BC_RNA

description: Library name: NaiveCD4_CONTROL_BC_RNA


title: Human PBMC-derived CD4 T cells NaiveCD4_CONTROL_BE_RNA

description: Library name: NaiveCD4_CONTROL_BE_RNA


title: Human PBMC-derived CD4 T cells NaiveCD4_CONTROL_BD_RNA

description: Library name: NaiveCD4_CONTROL_BD_RNA

value: Male


title: Human PBMC-derived CD4 T cells NaiveCD4_PATIENT_AF_RNA

description: Library name: NaiveCD4_PATIENT_AF_RNA

value: Black/AfricanAmerican


title: Oviduct_21 [sample309]

value: MPA/DMBA- MIF+

value: No tumor


title: Oviduct_20 [sample308]

value: MPA/DMBA- MIF-


title: Oviduct_19 [sample307]


title: Human PBMC-derived CD4 T cells NaiveCD4_CONTROL_BA_RNA

description: Library name: NaiveCD4_CONTROL_BA_RNA

value: Blood

value: Healthy


title: Human PBMC-derived CD4 T cells cTfh_PATIENT_E_RNA

description: Library name: cTfh_PATIENT_E_RNA

value: cTfh

value: Yes

value: Valasartan


title: Cervix_84 [sample305]

description: Cervix biology in a mouse treated with medroxyprogesterone (MPA, P) and 7,12-dimethylbenzanthracene (DMBA, D), on a ketogenic diet, and treated with Mifepristone (M)

source_name: Cervix, Mouse DNA, Tissue

value: Cervix

value: Ketogenic diet

value: MPA/DMBA+ MIF+

value: Validaton set

value: Tumor


title: Human PBMC-derived CD4 T cells cTfh_PATIENT_C_RNA

description: Library name: cTfh_PATIENT_C_RNA

value: A

value: Lupus

value: No

value: Not Hispanic or Latino/a


title: Human PBMC-derived CD4 T cells NaiveCD4_PATIENT_AD_RNA

description: Library name: NaiveCD4_PATIENT_AD_RNA

value: Female

value: UKN


title: Cervix_85 [sample306]

description: Cervix biology in a mouse on a normal diet

value: Normal diet

value: MPA/DMBA- MIF-

value: Intervention set

value: No tumor


title: Cervix_82 [sample303]


title: Human PBMC-derived CD4 T cells cTfh_PATIENT_AP_RNA

description: Library name: cTfh_PATIENT_AP_RNA

value: Blood

value: cTfh

value: Healthy


title: Human PBMC-derived CD4 T cells cTfh_PATIENT_AL_RNA

description: Library name: cTfh_PATIENT_AL_RNA

value: White


title: Human PBMC-derived CD4 T cells NaiveCD4_CONTROL_BH_RNA

description: Library name: NaiveCD4_CONTROL_BH_RNA


title: Human PBMC-derived CD4 T cells cTfh_PATIENT_AG_RNA

description: Library name: cTfh_PATIENT_AG_RNA

value: Yes

value: Losartan

value: yes

value: Black/AfricanAmerican


title: Cervix_81 [sample302]

value: Cervix

value: Ketogenic diet

value: MPA/DMBA+ MIF+

value: Validaton set


title: Cervix_80 [sample301]

value: Female

value: No


title: Cervix_78 [sample299]

description: Cervix biology in a mouse treated with medroxyprogesterone (MPA, P) and 7,12-dimethylbenzanthracene (DMBA, D) and on a ketogenic diet

value: MPA/DMBA+ MIF-


title: Human PBMC-derived CD4 T cells cTfh_PATIENT_AD_RNA

description: Library name: cTfh_PATIENT_AD_RNA

value: A

value: UKN


title: Human PBMC-derived CD4 T cells cTfh_CONTROL_BK_RNA

description: Library name: cTfh_CONTROL_BK_RNA

value: Blood


title: Cervix_79 [sample300]

value: Tumor


title: Human PBMC-derived CD4 T cells cTfh_PATIENT_AE_RNA

description: Library name: cTfh_PATIENT_AE_RNA

value: cTfh

value: Lupus

value: Hispanic or Latino/a


title: Human PBMC-derived CD4 T cells cTfh_PATIENT_A_RNA

description: Library name: cTfh_PATIENT_A_RNA

value: Not Hispanic or Latino/a


title: Human PBMC-derived CD4 T cells NaiveCD4_CONTROL_BB_RNA

description: Library name: NaiveCD4_CONTROL_BB_RNA

value: Healthy


title: Human PBMC-derived CD4 T cells cTfh_CONTROL_BH_RNA

description: Library name: cTfh_CONTROL_BH_RNA


title: Cervix_77 [sample298]

value: Yes


title: Cervix_76 [sample297]

value: Cervix


title: Cervix_74 [sample295]

description: Cervix biology in a mouse treated with medroxyprogesterone (MPA, P) and 7,12-dimethylbenzanthracene (DMBA, D), on a normal diet, and treated with Mifepristone (M)

value: Normal diet

value: Intervention set

value: No tumor


title: Human PBMC-derived CD4 T cells cTfh_CONTROL_BG_RNA

description: Library name: cTfh_CONTROL_BG_RNA

value: Female


title: Human PBMC-derived CD4 T cells cTfh_CONTROL_BF_RNA

description: Library name: cTfh_CONTROL_BF_RNA


title: Human PBMC-derived CD4 T cells cTfh_CONTROL_BE_RNA

description: Library name: cTfh_CONTROL_BE_RNA


title: Cervix_75 [sample296]

value: Ketogenic diet

value: Validaton set


title: Cervix_72 [sample293]

value: MPA/DMBA+ MIF+


title: Human PBMC-derived CD4 T cells cTfh_CONTROL_BD_RNA

description: Library name: cTfh_CONTROL_BD_RNA

value: Male

value: A

value: UKN


title: Cervix_73 [sample294]

value: No


title: Human PBMC-derived CD4 T cells cTfh_CONTROL_BC_RNA

description: Library name: cTfh_CONTROL_BC_RNA

value: Blood

value: cTfh


title: Cervix_71 [sample292]

value: Tumor


title: Cervix_83 [sample304]


title: Human PBMC-derived CD4 T cells cTfh_CONTROL_BB_RNA

description: Library name: cTfh_CONTROL_BB_RNA

value: Healthy


title: Cervix_68 [sample289]

description: Cervix biology in a mouse treated with medroxyprogesterone (MPA, P) and 7,12-dimethylbenzanthracene (DMBA, D) and on a normal diet

value: MPA/DMBA+ MIF-

value: Yes


title: Human PBMC-derived CD4 T cells AcTfh_PATIENT_G_RNA

description: Library name: AcTfh_PATIENT_G_RNA

value: AcTfh

value: Lupus

value: Not Hispanic or Latino/a

value: Asian


title: Human PBMC-derived CD4 T cells cTfh_CONTROL_BA_RNA

description: Library name: cTfh_CONTROL_BA_RNA


title: Cervix_70 [sample291]

value: Female

value: Cervix

value: Normal diet

value: Intervention set


title: Cervix_69 [sample290]

value: MPA/DMBA+ MIF+


title: Cervix_64 [sample285]


title: Cervix_65 [sample286]


title: Human PBMC-derived CD4 T cells AcTfh_PATIENT_B_RNA

description: Library name: AcTfh_PATIENT_B_RNA

value: A

value: Black/AfricanAmerican


title: Human PBMC-derived CD4 T cells AcTfh_PATIENT_AP_RNA

description: Library name: AcTfh_PATIENT_AP_RNA

value: Blood

value: No

value: UKN


title: Cervix_67 [sample288]

value: Tumor


title: Human PBMC-derived CD4 T cells AcTfh_PATIENT_AL_RNA

description: Library name: AcTfh_PATIENT_AL_RNA

value: White


title: Human PBMC-derived CD4 T cells AcTfh_PATIENT_AG_RNA

description: Library name: AcTfh_PATIENT_AG_RNA

value: Yes

value: Losartan

value: yes


title: Cervix_63 [sample284]

value: MPA/DMBA+ MIF-


title: Human PBMC-derived CD4 T cells AcTfh_PATIENT_AF_RNA

description: Library name: AcTfh_PATIENT_AF_RNA

value: AcTfh

value: Lupus

value: Not Hispanic or Latino/a


title: Human PBMC-derived CD4 T cells AcTfh_PATIENT_AD_RNA

description: Library name: AcTfh_PATIENT_AD_RNA

value: Female

value: Healthy


title: Cervix_62 [sample283]

value: Cervix

value: Ketogenic diet

value: Validaton set


title: Cervix_60 [sample281]

description: Cervix biology in a mouse on a ketogenic diet and treated with Mifepristone (M)

value: MPA/DMBA- MIF+

value: No tumor


title: Cervix_61 [sample282]

value: No


title: Human PBMC-derived CD4 T cells AcTfh_PATIENT_A_RNA

description: Library name: AcTfh_PATIENT_A_RNA

value: Blood

value: A

value: Black/AfricanAmerican


title: Cervix_86 [sample280]


title: Human PBMC-derived CD4 T cells AcTfh_CONTROL_BK_RNA

description: Library name: AcTfh_CONTROL_BK_RNA

value: UKN


title: Cervix_59 [sample279]

description: Cervix biology in a mouse on a ketogenic diet

value: MPA/DMBA- MIF-


title: Human PBMC-derived CD4 T cells AcTfh_CONTROL_BJ_RNA

description: Library name: AcTfh_CONTROL_BJ_RNA

value: Male


title: Human PBMC-derived CD4 T cells AcTfh_CONTROL_BD_RNA

description: Library name: AcTfh_CONTROL_BD_RNA

value: AcTfh


title: Cervix_66 [sample287]

value: Normal diet

value: MPA/DMBA+ MIF-

value: Intervention set

value: Yes

value: Tumor


title: Human PBMC-derived CD4 T cells AcTfh_CONTROL_BF_RNA

description: Library name: AcTfh_CONTROL_BF_RNA

value: Female

value: Healthy


title: Cervix_58 [sample278]

value: Cervix

value: Ketogenic diet

value: Validaton set


title: Human PBMC-derived CD4 T cells AcTfh_CONTROL_BC_RNA

description: Library name: AcTfh_CONTROL_BC_RNA

value: Blood


title: Cervix_57 [sample277]

description: Cervix biology in a mouse on a normal diet and treated with Mifepristone (M)

value: MPA/DMBA- MIF+

value: No

value: No tumor


title: Human PBMC-derived CD4 T cells AcTfh_CONTROL_BE_RNA

description: Library name: AcTfh_CONTROL_BE_RNA

value: A

value: UKN


title: Cervix_56 [sample276]


title: Cervix_54 [sample274]

value: MPA/DMBA- MIF-


title: Human PBMC-derived CD4 T cells AcTfh_PATIENT_C_RNA

description: Library name: AcTfh_PATIENT_C_RNA

value: Male

value: AcTfh

value: Lupus

value: Not Hispanic or Latino/a

value: Black/AfricanAmerican


title: Human PBMC-derived CD4 T cells AcTfh_CONTROL_BB_RNA

description: Library name: AcTfh_CONTROL_BB_RNA

value: Female


title: Human PBMC-derived CD4 T cells AcTfh_CONTROL_BA_RNA

description: Library name: AcTfh_CONTROL_BA_RNA

value: Healthy


title: Cervix_53 [sample273]

value: Cervix

value: Normal diet

value: Intervention set


title: Human blood-derived CD4 T cell Th1_PATIENT_AL_ATAC

description: Library name: Th1_PATIENT_AL_ATAC

data_processing:
Raw fastq Files were put through the ENCODE ATAC-seq pipeline in batches (up to seven samples of like cell type). ENCODE output of IDR (reproducible stringently called peaks) were then merged across different samples to create a consensus peak list. Bedtools Coverage function was then used to generate count level data for each peak in the consensus data set for each sample. This information was input into R for further analysis.
Assembly: hg38
Supplementary files format and content: Raw_unfiltered_ATAC_Fig1_Fig2.txt contains data from multiple CD4 T cell populations from the first cohort of lupus patients and healthy controls. The bulk isolated ATAC data is presented in the form of count data for stringently called consensus peaks. Consensus peaks were generated from merging individual peak sets reported.
Supplementary files format and content: Raw_unfiltered_ATAC_Fig5.txt  contains data from Naive CD4 T cells from the first and second cohorts of lupus patients and healthy controls. The bulk isolated ATAC data is presented in the form of count data for stringently called consensus peaks. Consensus peaks were generated from merging individual peak sets reported. Consensus peaks reflect the addition of new data in a second cohort which may change peaks.
Supplementary files format and content: Raw_unfiltered_ATAC_fig6.txt contains data from Naive CD4 T cells from the first, second, and third cohorts of lupus patients and healthy controls. The bulk isolated ATAC data is presented in the form of count data for stringently called consensus peaks. Consensus peaks were generated from merging individual peak sets reported. Consensus peaks reflect the addition of new data in a third cohort which may change peaks.

extract_protocol:
Cryopreserved PBMCs were thawed and enriched using negative selection (Stem Cell technologies human CD4 Isolation kit #100-0696) ) for CD4 T cells. They were then stained with flourescent antibodies and cells were sorted using flourescent activated cell sorter (Aria C). CD45RA+CD27+ naive TH, CXCR5+PD1+ICOS+CD38+ AcTfh, CXCR5+PD1+ICOSCD38- cTfh, and CXCR5-PD1-CXCR3+ Th1 cells were sorted. In most cases, 5000 cells were sorted. Immediately following sorting, cells were processed for ATAC-seq. OMNI ATAC protocol was followed (PMID: 28846090). Cells were transposed for 40 minutes in 37 degree still water bath before DNA was isoalted with Zymogen Clean and Concentrate Kit.
Libaries were prepared following standard protocols and utilizing Illumina indexes. Fractionation and size selection were performed. Size selection was done using bead-based enrichment.

value: Blood

value: CXCR5 negative PD-1 negative Non Nave T cells that are CXCR3 positive

value: White


title: Human blood-derived CD4 T cell Th1_PATIENT_AG_ATAC

description: Library name: Th1_PATIENT_AG_ATAC

value: Yes

value: Losartan

value: yes

value: No


title: Cervix_55 [sample275]

value: MPA/DMBA- MIF+

value: No tumor


title: Cervix_52 [sample272]

value: MPA/DMBA- MIF-


title: Cervix_51 [sample271]

value: Ketogenic diet

value: MPA/DMBA+ MIF+

value: Validaton set

value: Tumor


title: Cervix_49 [sample269]

value: Female

value: Cervix


title: Cervix_47 [sample267]


title: Cervix_50 [sample270]


title: Human blood-derived CD4 T cell Th1_PATIENT_AF_ATAC

description: Library name: Th1_PATIENT_AF_ATAC

value: A

value: Lupus

value: Not Hispanic or Latino/a

value: Black/AfricanAmerican


title: Human PBMC-derived CD4 T cells AcTfh_CONTROL_BH_RNA

description: Library name: AcTfh_CONTROL_BH_RNA

value: Blood

value: AcTfh

value: Healthy

value: UKN


title: Cervix_48 [sample268]

value: No


title: Human blood-derived CD4 T cell Th1_PATIENT_AD_ATAC

description: Library name: Th1_PATIENT_AD_ATAC

value: CXCR5 negative PD-1 negative Non Nave T cells that are CXCR3 positive


title: Cervix_46 [sample266]

value: No tumor


title: Human blood-derived CD4 T cell Th1_CONTROL_BH_ATAC

description: Library name: Th1_CONTROL_BH_ATAC


title: Human blood-derived CD4 T cell Th1_CONTROL_BE_ATAC

description: Library name: Th1_CONTROL_BE_ATAC


title: Cervix_45 [sample265]

value: Ketogenic diet

value: MPA/DMBA+ MIF-

value: Yes


title: Human blood-derived CD4 T cell Th1_CONTROL_BC_ATAC

description: Library name: Th1_CONTROL_BC_ATAC


title: Cervix_44 [sample264]

value: Validaton set

value: Tumor


title: Human blood-derived CD4 T cell NaiveCD4_PATIENT_Q_ATAC

description: Library name: NaiveCD4_PATIENT_Q_ATAC

value: Female

value: CD45RA positive CD27 positive CD4 positive T cells

value: Losartan

value: yes

value: White


title: Cervix_43 [sample263]

value: Cervix


title: Human blood-derived CD4 T cell NaiveCD4_PATIENT_P_ATAC

description: Library name: NaiveCD4_PATIENT_P_ATAC

value: Blood

value: A

value: Lupus

value: Not Hispanic or Latino/a

value: Black/AfricanAmerican


title: Human blood-derived CD4 T cell NaiveCD4_PATIENT_N_ATAC

description: Library name: NaiveCD4_PATIENT_N_ATAC

value: No


title: Cervix_41 [sample261]

value: Ketogenic diet


title: Human blood-derived CD4 T cell Th1_PATIENT_AE_ATAC

description: Library name: Th1_PATIENT_AE_ATAC

value: CXCR5 negative PD-1 negative Non Nave T cells that are CXCR3 positive

value: Hispanic or Latino/a


title: Human blood-derived CD4 T cell NaiveCD4_PATIENT_M_ATAC

description: Library name: NaiveCD4_PATIENT_M_ATAC


title: Human blood-derived CD4 T cell NaiveCD4_PATIENT_L_ATAC

description: Library name: NaiveCD4_PATIENT_L_ATAC


title: Cervix_38 [sample258]

value: Normal diet

value: MPA/DMBA+ MIF+

value: Intervention set

value: No tumor


title: Cervix_40 [sample260]

value: Female

value: Yes

value: Tumor


title: Cervix_37 [sample257]

value: Cervix


title: Cervix_39 [sample259]


title: Human blood-derived CD4 T cell NaiveCD4_PATIENT_K_ATAC

description: Library name: NaiveCD4_PATIENT_K_ATAC

value: Blood

value: CD45RA positive CD27 positive CD4 positive T cells

value: Asian


title: Cervix_36 [sample256]


title: Human blood-derived CD4 T cell NaiveCD4_PATIENT_H_ATAC

description: Library name: NaiveCD4_PATIENT_H_ATAC

value: A

value: Lupus

value: Not Hispanic or Latino/a

value: White


title: Human blood-derived CD4 T cell NaiveCD4_PATIENT_J_ATAC

description: Library name: NaiveCD4_PATIENT_J_ATAC

value: No

value: Black/AfricanAmerican


title: Cervix_34 [sample254]

value: Normal diet

value: MPA/DMBA+ MIF-


title: Cervix_35 [sample255]

value: Intervention set


title: Human blood-derived CD4 T cell NaiveCD4_PATIENT_G_ATAC

description: Library name: NaiveCD4_PATIENT_G_ATAC


title: Human blood-derived CD4 T cell NaiveCD4_PATIENT_E_ATAC

description: Library name: NaiveCD4_PATIENT_E_ATAC

value: Valasartan


title: Human blood-derived CD4 T cell NaiveCD4_PATIENT_F_ATAC

description: Library name: NaiveCD4_PATIENT_F_ATAC

value: Female


title: Cervix_42 [sample262]

value: Ketogenic diet

value: Validaton set

value: Yes


title: Cervix_33 [sample253]

value: Cervix

value: Tumor


title: Cervix_32 [sample252]


title: Human blood-derived CD4 T cell NaiveCD4_PATIENT_C_ATAC

description: Library name: NaiveCD4_PATIENT_C_ATAC

value: Blood

value: Male

value: CD45RA positive CD27 positive CD4 positive T cells


title: Human blood-derived CD4 T cell NaiveCD4_PATIENT_D_ATAC

description: Library name: NaiveCD4_PATIENT_D_ATAC

value: A

value: Lupus

value: Not Hispanic or Latino/a


title: Cervix_30 [sample250]


title: Human blood-derived CD4 T cell NaiveCD4_PATIENT_B_ATAC

description: Library name: NaiveCD4_PATIENT_B_ATAC

value: No

value: Black/AfricanAmerican


title: Cervix_28 [sample248]

value: MPA/DMBA- MIF+

value: No tumor


title: Human blood-derived CD4 T cell NaiveCD4_PATIENT_AL_ATAC

description: Library name: NaiveCD4_PATIENT_AL_ATAC

value: White


title: Cervix_27 [sample247]

value: Female


title: Human blood-derived CD4 T cell NaiveCD4_PATIENT_AJ_ATAC

description: Library name: NaiveCD4_PATIENT_AJ_ATAC


title: Cervix_26 [sample246]

value: Ketogenic diet

value: MPA/DMBA- MIF-


title: Cervix_24 [sample244]

value: Validaton set


title: Human blood-derived CD4 T cell NaiveCD4_PATIENT_AK_ATAC

description: Library name: NaiveCD4_PATIENT_AK_ATAC


title: Human blood-derived CD4 T cell NaiveCD4_PATIENT_AH_ATAC

description: Library name: NaiveCD4_PATIENT_AH_ATAC


title: FSTD8_10

status: Public on Jan 18 2025

city: California

first: Natalia

middle: Faraj

last: Murad

address: 500 Parnassus Ave

department: HemOnc

institute: University of California, San Francisco

description:
Library name: Sample 30
Column name in counts.csv file: FSTD8_10

data_processing:
Paired-end clean reads were aligned to the reference genome Felis_catus_9.0 using Hisat2 v2.0.5.
FeatureCounts v1.5.0-p380 was used to count the reads numbers mapped to each gene.
Assembly: Felis_catus_9.0
Supplementary files format and content: tab delimited file including raw counts for each sample

organism: Felis catus

source_name: oral cavity

extract_protocol:
RNA was extracted using the Direct-zol RNA Miniprep kit (Zymo Research) according to the manufacturer’s modified protocol for “RNA purification from the aqueous phase after Tri Reagent extraction”.
Tumor samples were crushed in liquid nitrogen, mixed with 500µL Trizol, and further lysed using a bead mill. Chloroform (100 µL) was added to the lysate, mixed well, and the mixture subjected to centrifugation. The aqueous phase was removed, mixed with an equal volume of 100% ethanol and added to a Zymo-Spin IICR column. After centrifugation and a quick wash, on-column DNA digestion was performed, followed by additional washes. Total RNA was eluted with 50 µL of RNAse/DNAse-free water and 1 µg was submitted to Novogene Co. for quality testing, library prep, and sequencing.

value: oral cavity

value: mucosal surface

tag: genotype

value: tumor

tag: time

value: Day 8


title: Cervix_25 [sample245]

value: Cervix


title: Human blood-derived CD4 T cell NaiveCD4_PATIENT_AD_ATAC

description: Library name: NaiveCD4_PATIENT_AD_ATAC

value: Blood

value: CD45RA positive CD27 positive CD4 positive T cells

tag: timpoint

value: A

tag: disease

value: Healthy

value: UKN


title: Human blood-derived CD4 T cell NaiveCD4_PATIENT_AE_ATAC

description: Library name: NaiveCD4_PATIENT_AE_ATAC

value: Lupus

tag: treatment arb_active

value: No

tag: treatment arb_type

value: Yes

value: Hispanic or Latino/a


title: Cervix_22 [sample242]

value: Female

value: Normal diet

value: MPA/DMBA- MIF+

value: Intervention set

value: No tumor


title: Cervix_21 [sample241]


title: Human blood-derived CD4 T cell NaiveCD4_PATIENT_A_ATAC

description: Library name: NaiveCD4_PATIENT_A_ATAC

tag: treatment rituximab_ever

tag: treatment rituximab_active

value: Not Hispanic or Latino/a

value: Black/AfricanAmerican


title: Cervix_23 [sample243]

value: Cervix


title: Human blood-derived CD4 T cell NaiveCD4_CONTROL_BQ_ATAC

description: Library name: NaiveCD4_CONTROL_BQ_ATAC

value: Blood

tag: treatment acei_active

tag: disease _severity_sledai


title: Human blood-derived CD4 T cell NaiveCD4_PATIENT_AF_ATAC

description: Library name: NaiveCD4_PATIENT_AF_ATAC

value: CD45RA positive CD27 positive CD4 positive T cells

tag: ethnicity

tag: race


title: Cervix_20 [sample240]

tag: Sex

tag: tissue

value: MPA/DMBA- MIF-


title: Human blood-derived CD4 T cell NaiveCD4_CONTROL_BN_ATAC

description: Library name: NaiveCD4_CONTROL_BN_ATAC

value: A

value: Healthy


title: Cervix_31 [sample251]

tag: diet

tag: treatment

value: MPA/DMBA+ MIF-

value: Tumor


title: Cervix_29 [sample249]

value: Ketogenic diet

value: Validaton set

value: No


title: Breast_tumor_84 [sample238]

description: Breast tumor biology in a mouse treated with medroxyprogesterone (MPA, P) and 7,12-dimethylbenzanthracene (DMBA, D), on a ketogenic diet, and treated with Mifepristone (M)

source_name: Breast tumor, Mouse DNA, Tissue

value: Female

value: Breast tumor

value: MPA/DMBA+ MIF+


title: Cervix_19 [sample239]

value: Normal diet

value: Intervention set

value: No tumor


title: Human blood-derived CD4 T cell NaiveCD4_CONTROL_BM_ATAC

description: Library name: NaiveCD4_CONTROL_BM_ATAC

tag: cell type

tag: batch

value: UKN


title: Human blood-derived CD4 T cell NaiveCD4_CONTROL_BH_ATAC

description: Library name: NaiveCD4_CONTROL_BH_ATAC

value: Blood


title: Human blood-derived CD4 T cell NaiveCD4_CONTROL_BJ_ATAC

description: Library name: NaiveCD4_CONTROL_BJ_ATAC

value: Male

value: CD45RA positive CD27 positive CD4 positive T cells


title: Human blood-derived CD4 T cell NaiveCD4_PATIENT_AG_ATAC

description: Library name: NaiveCD4_PATIENT_AG_ATAC

value: A

value: Lupus

value: Yes

value: Losartan

value: yes

value: Not Hispanic or Latino/a

value: Black/AfricanAmerican


title: Human blood-derived CD4 T cell NaiveCD4_CONTROL_BG_ATAC

description: Library name: NaiveCD4_CONTROL_BG_ATAC

value: Female

value: Healthy


title: Breast_tumor_76 [sample235]

description: Breast tumor biology in a mouse treated with medroxyprogesterone (MPA, P) and 7,12-dimethylbenzanthracene (DMBA, D) and on a ketogenic diet

value: Breast tumor

value: Ketogenic diet

value: MPA/DMBA+ MIF-

value: Validaton set

value: No

value: Tumor


title: Breast_tumor_77 [sample236]


title: Human blood-derived CD4 T cell NaiveCD4_CONTROL_BF_ATAC

description: Library name: NaiveCD4_CONTROL_BF_ATAC

value: Blood

value: UKN


title: Human blood-derived CD4 T cell NaiveCD4_CONTROL_BE_ATAC

description: Library name: NaiveCD4_CONTROL_BE_ATAC

value: CD45RA positive CD27 positive CD4 positive T cells

value: A


title: Breast_tumor_70 [sample232]

description: Breast tumor biology in a mouse treated with medroxyprogesterone (MPA, P) and 7,12-dimethylbenzanthracene (DMBA, D), on a normal diet, and treated with Mifepristone (M)

value: Normal diet

value: MPA/DMBA+ MIF+

value: Intervention set

value: Yes


title: Breast_tumor_68 [sample230]

description: Breast tumor biology in a mouse treated with medroxyprogesterone (MPA, P) and 7,12-dimethylbenzanthracene (DMBA, D) and on a normal diet


title: Breast_tumor_72 [sample233]


title: Breast_tumor_67 [sample229]


title: Breast_tumor_66 [sample228]


title: Human blood-derived CD4 T cell cTfh_PATIENT_E_ATAC

description: Library name: cTfh_PATIENT_E_ATAC

value: ICOS negative CD38 negative CXCR5 positive PD-1 positive Non-nave CD4 T cells

value: Lupus

value: Valasartan

value: Not Hispanic or Latino/a

value: Black/AfricanAmerican


title: Breast_tumor_69 [sample231]

value: Female

value: Breast tumor


title: Human blood-derived CD4 T cell NaiveCD4_CONTROL_BC_ATAC

description: Library name: NaiveCD4_CONTROL_BC_ATAC

value: Healthy


title: Human blood-derived CD4 T cell NaiveCD4_CONTROL_BD_ATAC

description: Library name: NaiveCD4_CONTROL_BD_ATAC

value: Male


title: Human blood-derived CD4 T cell cTfh_PATIENT_G_ATAC

description: Library name: cTfh_PATIENT_G_ATAC

value: Blood

value: No

value: Asian


title: Human blood-derived CD4 T cell NaiveCD4_CONTROL_BA_ATAC

description: Library name: NaiveCD4_CONTROL_BA_ATAC

value: CD45RA positive CD27 positive CD4 positive T cells

value: A

value: UKN


title: Breast_tumor_64 [sample226]

value: Normal diet

value: MPA/DMBA+ MIF-

value: Intervention set

value: Tumor


title: Breast_tumor_65 [sample227]

value: Yes


title: Human blood-derived CD4 T cell cTfh_PATIENT_D_ATAC

description: Library name: cTfh_PATIENT_D_ATAC

value: ICOS negative CD38 negative CXCR5 positive PD-1 positive Non-nave CD4 T cells

value: Lupus

value: Not Hispanic or Latino/a

value: White


title: Human blood-derived CD4 T cell cTfh_PATIENT_C_ATAC

description: Library name: cTfh_PATIENT_C_ATAC

value: Black/AfricanAmerican


title: Breast_tumor_79 [sample237]

value: Female

value: Breast tumor

value: Ketogenic diet

value: Validaton set


title: Human blood-derived CD4 T cell cTfh_PATIENT_AL_ATAC

description: Library name: cTfh_PATIENT_AL_ATAC

value: Blood

value: No


title: Breast_tumor_62 [sample224]


title: Breast_tumor_63 [sample225]


title: Breast_tumor_51 [sample223]

value: MPA/DMBA+ MIF+


title: Breast_tumor_45 [sample222]


title: Human blood-derived CD4 T cell cTfh_PATIENT_AK_ATAC

description: Library name: cTfh_PATIENT_AK_ATAC

value: A


title: Human blood-derived CD4 T cell cTfh_PATIENT_AJ_ATAC

description: Library name: cTfh_PATIENT_AJ_ATAC


title: Breast_tumor_75 [sample234]

value: MPA/DMBA+ MIF-


title: Breast_tumor_44 [sample221]


title: Human blood-derived CD4 T cell cTfh_PATIENT_AG_ATAC

description: Library name: cTfh_PATIENT_AG_ATAC

value: Losartan

value: yes


title: Human blood-derived CD4 T cell cTfh_PATIENT_AF_ATAC

description: Library name: cTfh_PATIENT_AF_ATAC


title: Breast_tumor_43 [sample220]

value: Yes

value: Tumor


title: Human blood-derived CD4 T cell cTfh_PATIENT_AE_ATAC

description: Library name: cTfh_PATIENT_AE_ATAC

value: ICOS negative CD38 negative CXCR5 positive PD-1 positive Non-nave CD4 T cells

value: Lupus

value: Hispanic or Latino/a


title: Breast_tumor_41 [sample219]


title: Human blood-derived CD4 T cell cTfh_PATIENT_AD_ATAC

description: Library name: cTfh_PATIENT_AD_ATAC

value: Healthy

value: UKN


title: Human blood-derived CD4 T cell cTfh_PATIENT_A_ATAC

description: Library name: cTfh_PATIENT_A_ATAC

value: Female

value: Not Hispanic or Latino/a

value: Black/AfricanAmerican


title: Human blood-derived CD4 T cell cTfh_CONTROL_BP_ATAC

description: Library name: cTfh_CONTROL_BP_ATAC

value: Blood


title: Breast_tumor_35 [sample217]

value: Breast tumor

value: Normal diet

value: Intervention set


title: Breast_tumor_33 [sample215]

value: MPA/DMBA+ MIF-


title: Human blood-derived CD4 T cell cTfh_CONTROL_BQ_ATAC

description: Library name: cTfh_CONTROL_BQ_ATAC

value: A


title: Breast_tumor_30 [sample212]


title: Breast_tumor_31 [sample213]


title: Human blood-derived CD4 T cell cTfh_PATIENT_B_ATAC

description: Library name: cTfh_PATIENT_B_ATAC

value: No


title: Breast_tumor_32 [sample214]

value: Yes


title: Human blood-derived CD4 T cell cTfh_CONTROL_BH_ATAC

description: Library name: cTfh_CONTROL_BH_ATAC


title: Human blood-derived CD4 T cell cTfh_CONTROL_BJ_ATAC

description: Library name: cTfh_CONTROL_BJ_ATAC

value: Male


title: Human blood-derived CD4 T cell cTfh_CONTROL_BM_ATAC

description: Library name: cTfh_CONTROL_BM_ATAC

value: ICOS negative CD38 negative CXCR5 positive PD-1 positive Non-nave CD4 T cells


title: Breast_85 [sample211]

description: Breast biology in a mouse on a normal diet

source_name: Breast, Mouse DNA, Tissue

value: Breast

value: MPA/DMBA- MIF-

value: No tumor


title: Human blood-derived CD4 T cell cTfh_CONTROL_BG_ATAC

description: Library name: cTfh_CONTROL_BG_ATAC

value: Healthy

value: UKN


title: Human blood-derived CD4 T cell cTfh_CONTROL_BF_ATAC

description: Library name: cTfh_CONTROL_BF_ATAC

value: Female


title: Breast_82 [sample208]

description: Breast biology in a mouse treated with medroxyprogesterone (MPA, P) and 7,12-dimethylbenzanthracene (DMBA, D), on a ketogenic diet, and treated with Mifepristone (M)

value: Ketogenic diet

value: MPA/DMBA+ MIF+

value: Validaton set


title: Breast_83 [sample209]

value: Tumor


title: Breast_81 [sample207]


title: Breast_84 [sample210]


title: Breast_80 [sample206]


title: Breast_tumor_40 [sample218]

value: Breast tumor

value: Normal diet

value: Intervention set


title: Breast_tumor_34 [sample216]

value: MPA/DMBA+ MIF-


title: Human blood-derived CD4 T cell cTfh_CONTROL_BC_ATAC

description: Library name: cTfh_CONTROL_BC_ATAC

value: Blood

value: A


title: Human blood-derived CD4 T cell AcTfh_PATIENT_G_ATAC

description: Library name: AcTfh_PATIENT_G_ATAC

value: ICOS positive CD38 positive CXCR5 positive PD-1 positive Non-nave CD4 T cells

value: Lupus

value: No

value: Not Hispanic or Latino/a

value: Asian


title: Human blood-derived CD4 T cell cTfh_CONTROL_BD_ATAC

description: Library name: cTfh_CONTROL_BD_ATAC

value: Male

value: ICOS negative CD38 negative CXCR5 positive PD-1 positive Non-nave CD4 T cells

value: Healthy

value: UKN


title: Human blood-derived CD4 T cell AcTfh_PATIENT_F_ATAC

description: Library name: AcTfh_PATIENT_F_ATAC

value: Female

value: White


title: Breast_78 [sample204]

description: Breast biology in a mouse treated with medroxyprogesterone (MPA, P) and 7,12-dimethylbenzanthracene (DMBA, D) and on a ketogenic diet

value: Breast

value: Ketogenic diet

value: Validaton set

value: No tumor


title: Breast_77 [sample203]

value: MPA/DMBA+ MIF-

value: Yes

value: Tumor


title: Human blood-derived CD4 T cell cTfh_CONTROL_BN_ATAC

description: Library name: cTfh_CONTROL_BN_ATAC

value: Blood

value: A


title: Human blood-derived CD4 T cell AcTfh_PATIENT_B_ATAC

description: Library name: AcTfh_PATIENT_B_ATAC

value: ICOS positive CD38 positive CXCR5 positive PD-1 positive Non-nave CD4 T cells

value: Lupus

value: No

value: Not Hispanic or Latino/a

value: Black/AfricanAmerican


title: Human blood-derived CD4 T cell AcTfh_PATIENT_E_ATAC

description: Library name: AcTfh_PATIENT_E_ATAC

value: Valasartan


title: Breast_76 [sample202]

value: Female


title: Breast_74 [sample200]

description: Breast biology in a mouse treated with medroxyprogesterone (MPA, P) and 7,12-dimethylbenzanthracene (DMBA, D), on a normal diet, and treated with Mifepristone (M)

value: Normal diet

value: MPA/DMBA+ MIF+

value: Intervention set


title: Human blood-derived CD4 T cell AcTfh_PATIENT_AL_ATAC

description: Library name: AcTfh_PATIENT_AL_ATAC

value: White


title: Breast_73 [sample199]

value: Breast

value: No tumor


title: Human blood-derived CD4 T cell AcTfh_PATIENT_AK_ATAC

description: Library name: AcTfh_PATIENT_AK_ATAC


title: Human blood-derived CD4 T cell AcTfh_PATIENT_AJ_ATAC

description: Library name: AcTfh_PATIENT_AJ_ATAC

value: Yes


title: Human blood-derived CD4 T cell AcTfh_PATIENT_AG_ATAC

description: Library name: AcTfh_PATIENT_AG_ATAC

value: Losartan

value: yes


title: Breast_71 [sample197]

value: Tumor


title: Breast_70 [sample196]


title: Human blood-derived CD4 T cell cTfh_CONTROL_BE_ATAC

description: Library name: cTfh_CONTROL_BE_ATAC

value: Blood

value: ICOS negative CD38 negative CXCR5 positive PD-1 positive Non-nave CD4 T cells

value: A

value: Healthy

value: UKN


title: Human blood-derived CD4 T cell AcTfh_PATIENT_AE_ATAC

description: Library name: AcTfh_PATIENT_AE_ATAC

value: ICOS positive CD38 positive CXCR5 positive PD-1 positive Non-nave CD4 T cells

value: Lupus

value: No

value: Hispanic or Latino/a


title: Breast_69 [sample195]

value: Female

value: Normal diet

value: MPA/DMBA+ MIF+

value: Intervention set


title: Breast_79 [sample205]

value: Breast

value: Ketogenic diet

value: MPA/DMBA+ MIF-

value: Validaton set

value: Yes


title: Breast_66 [sample192]

description: Breast biology in a mouse treated with medroxyprogesterone (MPA, P) and 7,12-dimethylbenzanthracene (DMBA, D) and on a normal diet

value: Tumor


title: Human blood-derived CD4 T cell AcTfh_PATIENT_C_ATAC

description: Library name: AcTfh_PATIENT_C_ATAC

value: Blood

value: Male

value: A

value: Not Hispanic or Latino/a

value: Black/AfricanAmerican


title: Breast_68 [sample194]


title: Human blood-derived CD4 T cell AcTfh_CONTROL_BP_ATAC

description: Library name: AcTfh_CONTROL_BP_ATAC

value: ICOS positive CD38 positive CXCR5 positive PD-1 positive Non-nave CD4 T cells

value: Healthy

value: UKN


title: Human blood-derived CD4 T cell AcTfh_PATIENT_AF_ATAC

description: Library name: AcTfh_PATIENT_AF_ATAC

value: Female

value: Lupus

value: No


title: Human blood-derived CD4 T cell AcTfh_PATIENT_A_ATAC

description: Library name: AcTfh_PATIENT_A_ATAC


title: Breast_67 [sample193]

value: Breast

value: Normal diet

value: Intervention set


title: Human blood-derived CD4 T cell AcTfh_PATIENT_AD_ATAC

description: Library name: AcTfh_PATIENT_AD_ATAC


title: Breast_65 [sample191]

value: MPA/DMBA+ MIF-


title: Human blood-derived CD4 T cell AcTfh_CONTROL_BM_ATAC

description: Library name: AcTfh_CONTROL_BM_ATAC


title: Breast_64 [sample190]

value: Yes


title: Human blood-derived CD4 T cell AcTfh_CONTROL_BN_ATAC

description: Library name: AcTfh_CONTROL_BN_ATAC


title: Breast_75 [sample201]

value: Ketogenic diet

value: Validaton set

value: Tumor


title: Human blood-derived CD4 T cell AcTfh_CONTROL_BH_ATAC

description: Library name: AcTfh_CONTROL_BH_ATAC

value: Blood

value: A


title: Human blood-derived CD4 T cell AcTfh_CONTROL_BJ_ATAC

description: Library name: AcTfh_CONTROL_BJ_ATAC

value: Male


title: Breast_72 [sample198]

value: MPA/DMBA+ MIF+


title: Human blood-derived CD4 T cell AcTfh_CONTROL_BF_ATAC

description: Library name: AcTfh_CONTROL_BF_ATAC

value: ICOS positive CD38 positive CXCR5 positive PD-1 positive Non-nave CD4 T cells

value: Healthy


title: Breast_63 [sample189]

value: Female


title: Breast_61 [sample187]

description: Breast biology in a mouse on a ketogenic diet and treated with Mifepristone (M)

value: MPA/DMBA- MIF+

value: No tumor


title: Human blood-derived CD4 T cell AcTfh_CONTROL_BG_ATAC

description: Library name: AcTfh_CONTROL_BG_ATAC

value: UKN


title: Breast_60 [sample186]

value: Breast

value: No


title: Human blood-derived CD4 T cell AcTfh_CONTROL_BE_ATAC

description: Library name: AcTfh_CONTROL_BE_ATAC


title: Breast_59 [sample185]

description: Breast biology in a mouse on a ketogenic diet

value: MPA/DMBA- MIF-


title: Human blood-derived CD4 T cell AcTfh_CONTROL_BD_ATAC

description: Library name: AcTfh_CONTROL_BD_ATAC


title: Human blood-derived CD4 T cell AcTfh_CONTROL_BC_ATAC

description: Library name: AcTfh_CONTROL_BC_ATAC


title: Breast_57 [sample183]

description: Breast biology in a mouse on a normal diet and treated with Mifepristone (M)

value: Normal diet

value: Intervention set


title: Human blood-derived CD4 T cell AcTfh_CONTROL_BA_ATAC

description: Library name: AcTfh_CONTROL_BA_ATAC


title: Breast_55 [sample181]


title: Breast_56 [sample182]


title: Breast_62 [sample188]

value: Ketogenic diet

value: MPA/DMBA+ MIF-

value: Validaton set

value: Yes


title: scARC library, group 08, 1 hr

city: Evanston

first: Jubao

last: Duan

state: IL

address: 1001 University Place

department: Center for Psychiatric Genetics

institute: NorthShore University HealthSystem

description:
Library name: scARC_Library_8_6
Library 08, unstimulated, contains cell line CD0000008, CD0000025, CD0000026

library_source: other

data_processing:
10x Genomics Chromium single cell Multiome sequencing libraries were sequenced at UMGC on Novaseq S4 platform targeting pair-end (2 x 150bp) 50k reads per nuclei for ATAC library and 25K reads per nuclei for gene expression library. Briefly, after raw data collection, Illumina’s BCL2FASTQ software was used to de-multiplex and assemble the fastq files corresponding to reads (R1/R2) and indices (i5/i7) for Cell Ranger ARC. The fastq files were subsequently processed by 10x Genomics Cell Ranger ARC (v2.0.2) and aligned twice to both the human GRCh38.p14 genome and a contingent of human GRCh38.p14 and mouse GRCm38 provided by 10x Genomics for efficient identification and removal of rodent astrocytes. For snATAC-seq, the per-library Transcription Start Sites (TSS) enrichment score is usually between 7-9 and the Fraction of high-quality Reads overlapping Peaks (FRiP) is usually between 40%-80%. We excluded cells with >15% of the reads mapped to mitochondrial genes, cells with > 8,000 or < 400 number of features, and cells with > 40,000 or <500 number of UMI counts (filtered by 400 < nCount < 8,000 using Seurat).
For each library that contains cells derived from 3-4 iPSC lines, barcode-level identification was performed separately for snRNA-seq (GEX) and snATAC-seq data with genotyping information of all donors. Briefly, the BAM files generated from GEX and ATAC assays (gex_possorted_bam.bam and atac_possorted_bam.bam) were processed by demuxlet (Kang et al., 2018) with known genotype information provided as .vcf files. Barcodes (cells) identified as singlets with P1 likelihood (p1LLK) < 1x10-8 were collected, and only barcodes positively identified in both GEX and ATAC assays were retained for downstream analysis.
snRNA-seq (GEX) data were processed by extracting gene expression data from the .h5 files generated by Cell Ranger ARC. Only barcodes (cells) confidently assigned to individual iPSC lines were retained. With Seurat 5.1.0(Hao et al., 2024), for cell type assignmentsTo assign cell type identity, Leiden clustering was performed at the library level based on the first 30 PCs (or appropriate as determined by the elbowplot) and subsequently by comparing cell clusters and their marker gene expressions (GAD1, GAD2, SLC17A6, SLC17A7, NEFM) and added as metadata. The library-level gene expression matrices were subsequently collated in Seurat 5.1.0(Hao et al., 2024) as one large object with cell line-specific metadata assigned. Harmony (Korsunsky et al., 2019) was used to integrate the library-level gene matrices and removed sequencing batch-derived effects.
For snATAC-seq data, the aggregation function of Cell Ranger ARC was used to merge and generate new fragment files for MACS2-based peak calling with the CallPeaks() function in Signac(Stuart et al., 2021) with default settings. We made two merged fragment files, one containing all libraries from batch 024 (18 cell lines) and the other from batch 018, 024, 025, and 029 (76 cell lines). From each fragment file, we iterated througugh the combinations of cell types (NEFM+ glut, NEFM- glut, GABA) and stimulation stages (0 hr, 1 hr, 6 hr), which generated nine peak sets (cell type x time). We further generated a union peak set from batch 024 by setting CallPeaks(combine.peaks = TRUE) for peak analysis across different cell types. Finally, peaks that fell within the ENCODE blacklisted regions were removed. We also removed peaks that fall within chromosomes X and Y and the mitochondrial genome regions.
Assembly: hg38/GRCh38
Supplementary files format and content: atac_fragments.tsv.gz, snATAC-seq fragment files
Supplementary files format and content: h5, count matrices snATAC and snRNA-seq
Supplementary files format and content: .cloupe, 10x Genomics Loupe data file

molecule: other

source_name: Neuron

growth_protocol: We differentiated iPSC lines into both excitatory and inhibitory neurons and co-cultured with rate glial cells. For excitatory neuron differentiation, we used the method to derive Ngn2-glutamatergic neuron {Zhang, 2013 #6824}  with minor modifications. On DIV0, 60-80% confluent iPSCs were dissociated into single cells using accutase and replated into Matrigel-coated 6-w plate at 5 x 105 cells per well in mTeSRPlus media with 5M ROCK inhibitor, together with appropriate amount of rtTA virus and Ngn2-puro virus. On DIV1, media was refreshed with mTeSRplus containing 5M ROCK inhibitor and 2g/ml doxycycline. On DIV2 - DIV4, cells were treated with neural culture media (Neuralbasal media with 1x B27Plus and 1x Glutamax) supplemented with 2g/ml puromycin, 2g/ml doxycycline to remove non-transduced cells. On DIV5 - DIV6, puromycin was withdrawn and cells were treated with neural culture media with 2ug/ml doxycycline. On DIV7, cells would be ready for replating. For generating excitatory neurons, we used the method to derive Ascl1/Dlx2-GABAergic neurons {Yang, 2017 #7817} with minopr modifications. On DIV0, 60-80% confluent iPSCs were dissociated into single cells using accutase and replated into Matrigel-coated 6-w plate at 7 x 105 cells per well in mTeSRPlus media with 5M ROCK inhibitor together with rtTA virus, Ascl1-puro virus and Dlx2-hygro virus. On DIV1, media was refreshed with mTeSRplus containing 5M ROCK inhibitor and 2g/ml doxycycline. From DIV2 - DIV4, cells were treated with neural culture media supplemented with 2g/ml puromycin, 150g/ml hygromycin and 2g/ml doxycycline to remove non-transduced cells. On DIV5 - DIV6, cells were treated with neural culture media with 2g/ml doxycycline and 2M AraC. Cells would be ready for replating on DIV7. To co-culture the excitatory and inhibitory neurons,  on DIV7, separately cultured Ngn2-glutamatergic neurons, Ascl1/Dlx2-GABAergic neurons and primary rat cortical astrocytes (Thermofisher; N7745100) were dissociated using accutase at 37C for 15-20min. Ngn2-glutamatergic neurons, Ascl1/Dlx2-GABAergic neurons and astrocytes were replated at 5:5:1 ratio onto Matrigel pre-coated 12-well plate in neural culture media supplemented with 2g/ml doxycycline, 10ng/ml BDNF, 10ng/ml GDNF, 10ng/ml NT-3 and 1% FBS. For each co-culture,  we pooled cells from 3-4 donor lines with equal proportion. On DIV8, we refilled cells with more media. From DIV9 – DIV33, media was refreshed every three days with half volume change. Doxycycline was withdrawn at DIV14 and 1uMµM AraC was added in the media from DIV8-DIV17 to ensure neuron purity. DIV33 neurons were used for KCI stimulation.

extract_protocol:
After stimulation, cells were briefly washed with 1x PBS and dissociated in accutase at 37C for 40min with gentle shaking. After accutase incubation, we pipetted cells multiple times and filtered suspension twice with 40m tip filter (Sigma# BAH136800040-50EA) to obtain single cells. The washed cells were subjected to fresh nuclei isolation following 10x Genomics’ protocols (CG000365 and CG000338). For each library, around 15,000 freshly isolated nuclei were loaded for GEM capture targeting 10,000 nuclei recovery.
The pre-amplified DNAs (for snATAC-seq) and cDNAs (for snRNA-seq) were shipped to University of Minnesota Genomics Center  (UMGC) for sn-multiomics sequencing library construction following 10x Genomics’ standard protocol.

treatment_protocol: To model neuron activation, we followed previously used protocol to treat the cells with KCI {Boulting, 2021 #8234}. Briefly, 24hr before stimulation, old media was aspirated and DIV33 neuron co-culture were silenced in neural culture media supplemented with 1M TTX and 100M DL-AP5. The next day, we added fresh culture media with warmed depolarization solution (10mM HEPES, 170mM KCl, 1mM MgCl2, 2mM CaCl2) to initiate KCI stimulation. We prepared three conditions with different treatment duration (0hr, 1hr and 6hr). After stimulation, cells were dissociated for 10x Genomics’ sn-Multiomics sequencing library preparation.

value: Neuron

tag: cell line

value: cultured glutamatergic and GABAergic neurons derived from iPS cells


title: Breast_54 [sample180]


title: scARC library, group 02, 6 hr

description:
Library name: scARC_Library_2_6
Library 02, 6 hr post stimulation, contains cell line CD0000027 and CD0000054


title: scARC library, group 08, 6 hr

description:
Library name: scARC_Library_8_1
Library 08, 6 hr post stimulation, contains cell line CD0000008, CD0000025, CD0000026


title: scARC library, group 08, 0 hr

description:
Library name: scARC_Library_8_0
Library 08, 1 hr post stimulation, contains cell line CD0000008, CD0000025, CD0000026


title: Breast_52 [sample178]


title: scARC library, group 02, 1 hr

description:
Library name: scARC_Library_2_1
Library 02, 1 hr post stimulation, contains cell line CD0000027 and CD0000054


title: Breast_53 [sample179]


title: Breast_51 [sample177]

value: MPA/DMBA+ MIF+

value: Tumor


title: Breast_48 [sample174]

value: Female


title: normal human astrocytes, miR-423-3p mimics, rep3

city: Jinan

first: Ziyi

last: Tang

state: Shandong

address: 107 Wenhuaxi Rd

institute: Shandong University

description: Library name: A423_3

data_processing:
The genome of human genome version of hg38 was used as reference. The sequencing quality were assessed with FastQC (v0.11.5)[1] and then low quality data were filtered using NGSQC (v2.3.3)[2].The clean reads were then aligned to the reference genome using HISAT2 (v2.1.0) [3]with default parameters. The processed reads from each sample were aligned using HISAT2 against the reference genome. The gene expression analyses were performed with StringTie (v1.3.3b)[4]. DESeq(v1.28.0)[5] was used to analyze the DEGs between samples. Thousands of independent statistical hypothesis testing was conducted on DEGs, separately. Then a p-value was obtained, which was corrected by FDR method. And Corrected P-value (q-value) was calculated by correcting using BH method. p-value or q-value were used to conduct significance analysis. Parameters for classifying significantly DEGs are ≥2-fold differences (|log2FC|≥1, FC: the fold change of expressions) in the transcript abundance and p ≤ 0.05.
Assembly: hg38
Supplementary files format and content: excel file including FPKM values for all samples was uploaded following the raw data

source_name: normal human astrocytes

extract_protocol:
Total RNA was extracted with Trizol (Invitrogen) and assessed with Agilent 2100 BioAnalyzer (Agilent Technologies, Santa Clara, CA, USA) and Qubit Fluorometer (Invitrogen).
RNA-seq libraries were generated and sequenced by CapitalBio Technology (Beijing, China).

value: normal human astrocytes


title: Breast_50 [sample176]

value: No tumor


title: Breast_49 [sample175]


title: normal human astrocytes, miR-423-3p mimics, rep1

description: Library name: A423_1


title: scARC library, group 02, 0 hr

description:
Library name: scARC_Library_2_0
Library 02, unstimulated, contains cell line CD0000027 and CD0000054


title: normal human astrocytes, miR-423-3p mimics, rep2

description: Library name: A423_2


title: Breast_47 [sample173]


title: Breast_46 [sample172]


title: Breast_58 [sample184]


title: normal human astrocytes, miR-control ,rep2

description: Library name: nc2


title: normal human astrocytes, miR-control ,rep1

description: Library name: nc1


title: 105796_022

city: Huddinge

first: Lars

last: Muhl

address: Blickagången 6

department: MedH

description:
Library name: sample 27
150 bp

data_processing:
adapter trimming and quality filtering using fastp v0.23.2
mapping to human GRCh38.p13 using  STAR2 v2.7.10
BAM files indexed with samtools v1.10
feature counting with HTSeq v2.0.2
Library prepararion, sequencing, and sequence analysis was performed by GenomeScan (www.genomescan.nl)
Assembly: human GRCh38
Supplementary files format and content: table as txt-file containing raw counts

source_name: lung cancer

extract_protocol:
a maximum of 5 x 10um thick FFPE tissue sections per sample  using the Rneasy  FFPE kit (#73504, Qiagen, Hilden, Germany)
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760S/L). rRNA depletion using the rRNA-depletion kit (NEB #E6310).

value: lung cancer

value: Male

tag: disease stage

value: CR

tag: tumor type

value: AC

tag: pla

value: high

value: batch 3


title: Breast_44 [sample170]

value: Breast

value: Ketogenic diet


title: 105796_018

description:
Library name: sample 26
150 bp

value: SD


title: Breast_42 [sample168]

value: MPA/DMBA+ MIF-

value: Validaton set

value: Yes


title: Breast_43 [sample169]


title: Breast_41 [sample167]


title: 105796_016

description:
Library name: sample 25
150 bp


title: 105796_012

description:
Library name: sample 24
150 bp

value: SqCC


title: Breast_40 [sample166]

value: Normal diet

value: MPA/DMBA+ MIF+

value: Intervention set

value: Tumor


title: Breast_39 [sample165]

value: Female

value: No

value: No tumor


title: Breast_37 [sample163]


title: 105796_010

description:
Library name: sample 22
150 bp

value: lung cancer

value: Male

value: PD

value: AC


title: normal human astrocytes, miR-control ,rep3

description: Library name: nc3

value: normal human astrocytes


title: 105796_011

description:
Library name: sample 23
150 bp

value: CR

value: high

value: batch 3


title: 105796_009

description:
Library name: sample 21
150 bp

value: low


title: Breast_38 [sample164]

value: Breast


title: Breast_34 [sample160]

value: Normal diet

value: MPA/DMBA+ MIF-

value: Yes


title: Breast_35 [sample161]

value: Intervention set

value: Tumor


title: Breast_36 [sample162]

value: Female

value: MPA/DMBA+ MIF+

value: No


title: 105796_002

description:
Library name: sample 17
150 bp

value: lung cancer

value: SqCC

value: batch 2


title: Breast_45 [sample171]

value: Ketogenic diet

value: Validaton set


title: 105796_006

description:
Library name: sample 19
150 bp

value: SD

value: AC

value: high


title: Breast_33 [sample159]

value: Breast


title: 105691_068

description:
Library name: sample 16
150 bp

value: Male

value: PD

value: low


title: Breast_31 [sample157]

value: Normal diet

value: MPA/DMBA+ MIF-

value: Intervention set

value: Yes


title: Breast_32 [sample158]

value: Female

value: Tumor


title: 105691_065

description:
Library name: sample 15
150 bp

value: lung cancer

value: CR

value: other


title: 105691_063

description:
Library name: sample 13
150 bp

value: batch 2


title: Breast_30 [sample156]


title: Breast_28 [sample154]

value: Ketogenic diet

value: MPA/DMBA- MIF+

value: Validaton set

value: No

value: No tumor


title: 105691_057

description:
Library name: sample 11
150 bp

value: Male

value: PD

value: AC


title: 105691_061

description:
Library name: sample 12
150 bp

value: SqCC

value: low


title: 105691_056

description:
Library name: sample 10
150 bp

value: SD


title: Breast_27 [sample153]

value: Female

value: Breast


title: 105796_007

description:
Library name: sample 20
150 bp

value: lung cancer

value: high

value: batch 3


title: 105796_003

description:
Library name: sample 18
150 bp

value: CR


title: Breast_25 [sample151]

value: Ketogenic diet

value: MPA/DMBA- MIF-


title: Breast_24 [sample150]

value: Validaton set


title: 105691_054

description:
Library name: sample 9
150 bp

value: batch 2


title: Breast_23 [sample149]

value: Normal diet

value: MPA/DMBA- MIF+

value: Intervention set

value: No

value: No tumor


title: 105691_044

description:
Library name: sample 6
150 bp

value: Male

value: SqCC


title: Breast_22 [sample148]

value: Female


title: 105691_053

description:
Library name: sample 8
150 bp

value: PD

value: AC

value: low


title: 105691_047

description:
Library name: sample 7
150 bp

value: lung cancer

value: other

value: high


title: 105691_041

description:
Library name: sample 5
150 bp


title: 105691_038

description:
Library name: sample 4
150 bp

value: SD


title: Breast_21 [sample147]

value: Breast


title: Breast_20 [sample146]

value: MPA/DMBA- MIF-


title: 105691_036

description:
Library name: sample 3
150 bp

value: batch 2


title: Breast_19 [sample145]

value: Normal diet


title: 105691_026

description:
Library name: sample 1
150 bp


title: 105691_064

description:
Library name: sample 14
150 bp


title: 105691_033

description:
Library name: sample 2
150 bp


title: Breast_29 [sample155]

value: Ketogenic diet

value: MPA/DMBA- MIF+

value: Validaton set


title: Spleen_13 [sample143]

description: Spleen biology in a mouse treated with medroxyprogesterone (MPA, P) and 7,12-dimethylbenzanthracene (DMBA, D) and on a normal diet

source_name: Spleen, Mouse DNA, Tissue

value: Spleen

value: MPA/DMBA+ MIF-

value: Discovery set

value: No

value: No tumor


title: Spleen_12 [sample142]

value: Female


title: Spleen_11 [sample141]


title: Breast_26 [sample152]


title: PBMCs_16 [sample140]

description: PBMC biology in a mouse treated with medroxyprogesterone (MPA, P) and 7,12-dimethylbenzanthracene (DMBA, D) and on a normal diet

source_name: PBMCs, Mouse DNA

value: PBMC


title: PBMCs_10 [sample135]


title: PBMCs_15 [sample139]


title: PBMCs_14 [sample138]


title: PBMCs_12 [sample137]


title: Oviduct_16 [sample134]

description: Oviduct biology in a mouse treated with medroxyprogesterone (MPA, P) and 7,12-dimethylbenzanthracene (DMBA, D) and on a normal diet

value: Oviduct


title: PBMCs_11 [sample136]


title: Oviduct_14 [sample133]


title: Oviduct_12 [sample131]


title: Lung_12 [sample126]

description: Lung biology in a mouse treated with medroxyprogesterone (MPA, P) and 7,12-dimethylbenzanthracene (DMBA, D) and on a normal diet

source_name: Lung, Mouse DNA, Tissue

value: Lung


title: Lung_17 [sample124]


title: Lung_10 [sample125]


title: Oviduct_13 [sample132]


title: Oviduct_11 [sample130]


title: Lung_16 [sample128]


title: Oviduct_10 [sample129]


title: Lung_18 [sample123]


title: Spleen_14 [sample144]


title: Liver_14 [sample121]

description: Liver biology in a mouse treated with medroxyprogesterone (MPA, P) and 7,12-dimethylbenzanthracene (DMBA, D) and on a normal diet

source_name: Liver, Mouse DNA, Tissue

value: Liver


title: XD1B wildtype young panicle

city: Chongqing

first: Zhongcheng

last: Li

address: Chongqing

institute: Southwest University

description: Library name: XD1B young panicle

data_processing:
CLC Genomics Workbench v 11.0.1 was used for data processing.
Sequence reads were trimmed for adaptor sequence and low-quality sequence using CLC Genomics Workbench (parameter - Quality limit: 0.05).
Trimmed sequence reads were mapped to the NIP genome using CLC Genomics Workbench (parameters - Mismatch cost: 2, Insertion cost: 3, Deletion cost: 3, Length fraction: 0.8, Similarity fraction: 0.8).
Read count extraction and normalization were performed using CLC Genomics Workbench.
Assembly: NIP genome (RGAP 7.0)
Supplementary files format and content: Tab-delimited text files include RPKM values for each sample.

organism: Oryza sativa

source_name: young inflorescences

extract_protocol:
Total RNA was extracted with Promega plant total RNA extraction kit (Tiangen, Beijing, China) following the manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: young inflorescences

tag: sample type

value: <2cm young panicle

tag: genotype

value: XD1B WT


title: lf2 mutant young panicle

description: Library name: lf2 mutant young panicle

value: LF2 mutant


title: ECs+ implantation-3

city: Guangzhou

first: Zhenxing

last: Wang

state: Guangdong

address: Guangzhou, P. R. China.

department: School of Materials Science and Engineering

institute: South China University of Technology

description:
Library name: ECs+ implantation-3
normal-3

data_processing:
fastp
hisat2
htseq
DESeq2
clusterProfiler
Assembly: GCF_000003025.6_Sscrofa11.1
Supplementary files format and content: the raw count file and normalization TPM expression file with tsv format

organism: Sus scrofa

source_name: penile corpus cavernosum

extract_protocol:
not collection
TruSeq RNA Library Prep Kit v2

value: penile corpus cavernosum


title: Liver_16 [sample122]

data_processing:
Minfi v1.46
Average Beta

extract_protocol: DNA was isolated from cells and different organs using AllPrep DNA/RNA Mini Kits (cat #80204, Qiagen Ltd), following the manufacturer’s protocol.

value: Normal diet


title: ECs+ implantation-2

description:
Library name: ECs+ implantation-2
normal-3


title: Liver_13 [sample120]


title: ECs+ implantation-1

description:
Library name: ECs+ implantation-1
normal-3


title: normal-3

description:
Library name: normal-3
normal-3


title: normal-2

description:
Library name: normal-2
normal-2


title: Liver_12 [sample119]


title: defect-3

description:
Library name: defect-3
defect-3


title: defect-2

description:
Library name: defect-2
defect-2


title: implantation B-3

description:
Library name: implantation B-3
implantation B-3


title: Liver_10 [sample117]


title: defect-1

description:
Library name: defect-1
defect-1


title: implantation B-2

description:
Library name: implantation B-2
implantation B-2


title: normal-1

description:
Library name: normal-1
normal-1


title: Liver_11 [sample118]


title: Kidney_14 [sample115]

description: Kidney biology in a mouse treated with medroxyprogesterone (MPA, P) and 7,12-dimethylbenzanthracene (DMBA, D) and on a normal diet

source_name: Kidney, Mouse DNA, Tissue

value: Kidney


title: Kidney_13 [sample114]


title: implantation A-2

description:
Library name: implantation A-2
implantation A-2


title: implantation A-3

description:
Library name: implantation A-3
implantation A-3


title: implantation B-1

description:
Library name: implantation B-1
implantation B-1


title: macrophage, infected with Mtb-ZLM for 24h, Rep2

city: Honolulu

first: Sladjana

last: Prisic

state: HI

address: 1800 East-West Rd

institute: University of Hawaii

data_processing:
The RNA-seq paired-end reads in FASTQ format were explored using FastQC and cleaned using Trimmomatic. The cleaning procedure included trimming low quality reads from both 3’ and 5’ ends until a base pair of Phred quality score of 30 (99.9% accurate) or greater was found, and filtering out reads having mean quality score less than 30 and length below 20 nucleotides. The house mouse (Mus musculus) reference genome (GRCm38) was indexed and aligned against by HiSAT. The resulting SAM (Sequence Alignment and Mapped) files were sorted and converted to BAM files using SAMtools, and then used to generate count reads using HTSeq.
Assembly: GRCm38
Supplementary files format and content: non-normalized count data are provided. Ensembl gene accession numbers are provided.

growth_protocol: M. tuberculosis mc2 6206 bacteria (Mtb) were cultured in Sauton's medium supplemented with 6μM zinc sulfate (zinc-replete medium - ZRM) or Sauton's medium without zinc sumplementation (zinc-limited medium - ZLM).  The auxotroph also needs 50 μg/mL L-Leucine and 48 μg/mL D-pantothenate supplemetation. Bacteria were grown for 8 days, harvested and enriched for single cells before the infection. RAW 264.7 cell line was cultured in DMEM with 10% fetal bovine serum.

extract_protocol:
TRIzol reagent was added to the macrophages at 4 hpi and 24 hpi, the TRIzol extractions were collected, and centrifuged to remove debris and pellet Mtb. RNA was isolated and purified using the PureLink RNA mini kit (ThermoFisher).
Ribosomal RNA was depleted from the samples using Ribo-Zero plus rRNA depletion kit (Illumina®, Cat. #:20037135) before being sequenced on an Illumina® HiSeq platform for generation of 150 base pair paired end reads. RNA sequencing (RNAseq) was performed by GENEWIZ® (South Plainfield, NJ 07080).

treatment_protocol: After 8 days of growth in ZRM and ZLM Sautons media, Mtb aggregates were removed by centrifuging the cultures at 800 xg for 10 minutes followed by passing them through 10 μm strainers once. Mtb grown in ZRM (Mtb-ZLM) and Mtb grown in ZLM (Mtb-ZLM) were resuspended in ZRM and ZLM, respectively. Macrophages were infected with Mtb-ZRM and Mtb-ZLM, and ZRM and ZLM were added to macrophages as controls. Macrophage RNA was harvested from all conditions at 4 hours post-infection (hpi) and 24 hpi.

value: macrophage-like

value: macrophages infected with Mtb-ZLM at 24hpi


title: Kidney_12 [sample113]

value: MPA/DMBA+ MIF-

value: Discovery set


title: macrophage, infected with Mtb-ZLM for 24h, Rep3


title: macrophage, infected with Mtb-ZRM for 24h, Rep3

value: macrophages infected with Mtb-ZRM at 24hpi


title: macrophage, infected with Mtb-ZRM for 24h, Rep1


title: macrophage, infected with Mtb-ZLM for 24h, Rep1


title: Kidney_11 [sample112]

value: Female

value: No

value: No tumor


title: macrophage, infected with Mtb-ZRM for 24h, Rep2