title: Methyl-seq_Young, Obese-23

data_processing:
Reads were mapped to the GRCm38 version of the mouse genome using the Bismark (version 0.17.0) bisulfite converted sequence read aligner. Bismark utilizes the Bowtie2 (version 2.2.4) alignment algorithm as part of its processing pipeline. The MarkDuplicatesWithMateCigar function from the Picard Toolkit (version 2.4.1) was used to eliminate amplification artifacts.
The MethylKit Bioconductor (version 1.2.0) package was used to process, normalize, and analyze differences between samples. Differential methylation was identified both on the base level for individual CpG sites (differentially methylated cytosines; DMC) as well as over 200 base pair sliding windows (differentially methylated windows; DMW) in tileMethylCounts (R version 3.3.0) with a 100 base pair step size. The input was reduced to only those regions that had reads that overlapped with the target regions in the SureSelect capture kit. CpG sites and sliding windows were annotated to their nearest gene according to the mm10 GRCm38v73 version of the mouse transcriptome. The false discovery rate was calculated to control for multiple hypothesis testing for each comparison. For calculating differential methylation, the following parameters were used: overdispersion=”MN”, test=”Chisq”. For A vs Y comparisons of age, diet (O and L) were included as covariates; for O vs L comparisons of diet, age (A and Y) were included as covariates in the model. Default parameters were used for all other packages.
Assembly: GRCm38v73
Supplementary files format and content: bedGraph
Library strategy: Methyl-Seq target enrichment

extract_protocol:
Qiagen's All Prep kit (Qiagen catalog # 80284) standard methods
SureSelectXT Mouse Methyl-Seq Reagent Kit (Agilent Catalog # 931052)
Illumina protocol


title: Aged, Obese-15

status: Public on Dec 21 2023

type: SRA

city: West Lafayette

first: Dianne

last: Little

state: IN

address: 625 Harrison St

department: Basic Medical Sciences

country: USA

institute: Purdue University

library_source: transcriptomic

data_processing:
Reads were mapped to the GRCm38v73 version of the mouse genome and transcriptome using the STAR RNA-seq alignment tool. Reads were kept for subsequent analysis if they mapped to a single genomic location. Read counts for each gene feature for each animal were compiled using the HTSeq tool (Version 0.7.0). The parameters used for HTSeq-Count were set for unstranded RNA-Seq. Counts from all biological replicates were merged into one file using custom Perl scripts to generate a merged read count matrix for all samples. The merged count matrix was used for downstream differential gene expression analysis, and the quality of the count matrix was verified by determining basic statistics including data range and matrix size prior to downstream evaluation. Genes that had at least 5 or more counts in at least 50% of the animals from each group were retained for subsequent analysis. Normalization, gene-wise dispersion, and differential gene expression (DGE) analysis between different groups was carried out using the DESeq2 (version 1.12.4) Bioconductor package with the R statistical programming environment (version 3.4.0). To identify the genes that affected differently by age across different diet groups, interaction analysis was conducted in DESeq2.
Assembly: GRCm38v73
Supplementary files format and content: tab-delimited text; gene_count_matrix

molecule: total RNA

organism: Mus musculus

source_name: Inguinal Fat

extract_protocol:
Qiagen's All Prep kit (Qiagen catalog # 80284) standard methods
Illumina protocol

tag: tissue

value: Inguinal Fat

tag: cell markers

tag: cell type

value: adipose-derived stem cells

tag: genotype

tag: treatment

value: Aged, Obese


title: Aged, Lean-15

value: Aged, Lean


title: Methyl-seq_Young, Obese-21

library_source: genomic

molecule: genomic DNA

tag: cell line

value: Young, Obese


title: Aged, Lean-12


title: Aged, Lean-19


title: Methyl-seq_Young, Obese-20


title: Methyl-seq_Young, Obese-22


title: Aged, Lean-11


title: Methyl-seq_Young, Obese-19


title: Aged, Lean-13


title: Aged, Obese-14


title: Methyl-seq_Young, Lean-27

value: Young, Lean


title: Methyl-seq_Young, Lean-24


title: Methyl-seq_Young, Obese-1


title: Methyl-seq_Aged, Obese-17


title: Methyl-seq_Young, Lean-25


title: Methyl-seq_Young, Lean-26


title: Methyl-seq_Young, Lean-23


title: Methyl-seq_Aged, Obese-14


title: Methyl-seq_Aged, Obese-12


title: Methyl-seq_Aged, Obese-10


title: Methyl-seq_Young, Obese-18


title: Aged, Lean-16


title: Methyl-seq_Aged, Lean-19


title: Methyl-seq_Aged, Lean-20


title: Methyl-seq_Aged, Obese-16


title: Methyl-seq_Aged, Lean-17


title: hHGFtg-hMETtg-BCAT-PBCre-Intact-replicate-1

city: Duarte

first: Zijie

last: Sun

state: CA

address: 1500 E. Duarte Rd.

department: Cancer Biology

institute: City of Hope

data_processing:
Adapter sequences and other redundant sequences were removed from raw paired-end reads using Trimmomatic (v0.39)
polyA were removed using  FASTP (v0.20.0)
Reads were aligned against the mouse genome (mm10) using STAR(v2.7.9).
Read counts were tabulated using HTSeq-count (v2.0.2)
Assembly: UCSC. The mouse genome (mm10).
Supplementary files format and content: Txt file with raw reads for each sample corresponding to each gene

source_name: Prostate tissue

extract_protocol:
RNA samples were extracted from fresh intact or castrated PCa mouse prostate using RNeasy Mini Kit (#74104, Qiagen, Hilden, Germany)
cDNA libraries were prepared using Kapa RNA HyperPrep Kit with RiboErase (KR1351, Kapa Biosystems, Wilmington, MA, USA)

value: Prostate

tag: castrated/intact pca

value: Intact PCa


title: hHGFtg-hMETtg-BCAT-PBCre-Intact-replicate-2


title: Methyl-seq_Aged, Lean-13


title: Methyl-seq_Aged, Lean-12


title: hHGFtg-hMETtg-BCAT-PBCre-Castrated-replicate-3

value: Castrated PCa


title: hHGFtg-hMETtg-BCAT-PBCre-Castrated-replicate-2


title: 6_Liver

city: New York

first: Sander

middle: M

last: Houten

state: NY

address: 1425 Madison Avenue, Box 1498

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Illumina HiSeq2500 for base calling.
Read alignment. STAR (release 2.4.0 g1).
Gene-level read quantification via featureCounts v1.5.2.
Genome_build: Mouse genome mm10 (GRCm38.75).
Supplementary_files_format_and_content: *.txt: Tab-delimited text files containing read count per gene.

molecule: polyA RNA

source_name: liver

extract_protocol:
RNA was isolated using QIAzol lysis reagent followed by purification using the RNeasy kit (Qiagen).
mRNA-focused cDNA libraries were generated using Illumina reagents (polyA capture), and samples were run on an Illumina HiSeq 2500 sequencer to yield a total read depth of approximately 64 million 100 nucleotide paired-end reads per sample.

tag: strain

value: liver

tag: Sex

value: female

value: wt

tag: diet

value: chow


title: hHGFtg-hMETtg-BCAT-PBCre-Castrated-replicate-1


title: 5_Liver


title: 9_Liver


title: 7_Liver


title: 8_Liver


title: 8_Gastroc

source_name: gastroc

value: gastrocnemius muscle


title: 7_Gastroc


title: 6_Gastroc


title: 12_Liver


title: MyoT-Gtx-N3

city: Creteil

first: Joana

last: Esteves de Lima

address: 8 rue du general sarrail

department: IMRB INSERM U955

country: France

institute: INSERM

data_processing:
FASTQ groomer tool (Galaxy version 1.1.5)  (https://usegalaxy.org)
BOWTIE2 (Galaxy Version 2.5.0+galaxy0) (https://usegalaxy.org)
featureCounts (Galaxy Version 2.0.1+galaxy2) (https://usegalaxy.org)
DESeq2 v2.11.40.6+galaxy1 (https://usegalaxy.org)
Assembly: hg38
Supplementary files format and content: tab-delimited txt file includes raw counts for each sample

organism: Homo sapiens

source_name: hiPSC Pci-AFR1

growth_protocol: PCi-MYO were plated at 25K cells/cm2 on Geltrex-coated dishes in Phenocell Myoblast Amplification Medium to allow proliferation. Phenocell Amplification Medium is composed of DMEMF12/Glutamax, 10% Fetal Bovine Serum and N2 supplement supplemented extemporaneously with 100 ng/ml IGF1, 10 ng/ml FGF2, 10 ng/ml Heregulin-B-1 and 4 µM Forskolin. The medium was changed every other day. PCi-MYO were amplified for 4 to 7 days until they reached 90% confluence. Afterwards, to induce the differentiation into myotubes, PCi-MYO were detached using accutase incubation for 5-10 min at 37C and plated at  100K cells/cm2 on Geltrex or Laminin-521-coated dishes in Maturation Medium (PhenoCULT®-MYO,  Phenocell) for 7 days. Maturation Medium was changed every other day.

extract_protocol:
For RNA-seq, 2x105 cells were collected per sample and triplicates were prepared for each condition (MyoB, MyoT-LAM  and MyoT-Gtx) for RNA extraction (Macherey Nagel, 740955) following the manufacturer protocol.
Libraries were prepared with TruSeq Stranded Total RNA Sample preparation kit according to supplier recommendations. Briefly, the key stages of this protocol are successively, the removal of ribosomal RNA fraction from 1µg of total RNA using the Ribo-Zero Gold Kit; fragmentation using divalent cations under elevated temperature to obtain approximately 300bp pieces; double strand cDNA synthesis using reverse transcriptase and random primers, and finally Illumina adapters ligation and cDNA library amplification by PCR for sequencing. Sequencing was carried out on single-end 75bp of Illumina NextSeq500.

value: hiPSC Pci-AFR1

value: hiPSC

value: WT


title: 9_Gastroc


title: Methyl-seq_Aged, Lean-16

value: Inguinal Fat


title: MyoT-Gtx-N1


title: MyoT-Gtx-N2


title: MyoB-N3


title: MyoT-Lam-N1


title: MyoB-N1


title: QKIpan-NM, dimer, rep2

city: Adelaide

first: Katherine

middle: Anne

last: Pillman

state: SA

address: North Terrace

department: Centre for Cancer Biology

country: Australia

institute: Adelaide University

description:
QKIpan-NM_5_6_14_15_merged_peaks_sorted.bed
QKIpan-NM-QKI5-Be_3_4_12_13_5_6_14_15_merged_peaks_sorted.good_peaks-min_reads-10_pct_25.bed

data_processing:
Raw reads were adapter-trimmed and filtered for short sequences using cutadapt v1.3 (Martin, 2011), in paired-end mode (parameters: minimum read length: 18 nt, maximum error-rate: 0.2, minimum adapter overlap: 5 nt). The resulting FASTQ files were analysed and quality checked using FastQC.
Using a custom python script, the spacer sequence (sequence: GTAC)  and degenerate barcode (8 bp) were clipped from the 3’ end of the read and the spacer sequence was added to the header of each read. Where the spacer sequence could not be identified from read 1, it and the barcode were identified from Read 2 instead using a second custom python script.
Reads were mapped in single-end mode against the human reference genome (build GRChr37/hg19) using the iGenomes UCSC hg19 gene annotations with TopHat2 v2.0.10 (Kim et al., 2013, optional parameters: -p 4 --GTF <gene annotation gtf file> -- library-type=fr-firststrand).
The molecular barcodes of reads which had both a) 5’ ends mapping to the same position and b) identical alignment CIGAR strings, were analysed using Python code and reads with barcodes sequences ≤1 edit distance apart were classified as PCR duplicates and collapsed to a single read.
Low-quality alignments were discarded using samtools (Li et al., 2009) (quality threshold: -bq 10).
Alignments from the same antibody but with other technical variations in library preparation method were pooled (CTRL; QKI5-Be; QKIpan-NM). Also, to create a combined peak set, all the QKI samples were combined.
Peak calling was performed separately for each strand using MACS2 2.1.1.20160309 (Zhang et al., 2008) using the CTRL bam file as the control (callpeak program parameters: -t <experimental bam file> -c <control bam file> -f BAM -g hs --keep-dup all --nomodel --shift -15 --extsize 50 -B --call-summits --llocal 0 --slocal 0 --fe-cutoff 3 -q 0.05). The resulting peak files from each strand were merged.
For the peak calling which combined all QKI samples, an additional step was performed to filter out low complexity peaks which were likely artifacts. This used a custom python script to discard peaks which had more than 10 reads but for which more than 25% of those reads mapped to an identical location.
Assembly: Human genome, build hg19
Supplementary files format and content: Bed format peak files

source_name: mesHMLE

growth_protocol: HMLE cells (Mani, Guo et al., 2008) were cultured in HuMEC ready media (ThermoFisher) and induced to undergo EMT by transferring to DMEM: F12 media (1:1) supplemented with 10 μg/ml insulin, 20 ng/ml EGF, 0.5 μg/ml hydrocortisone, 5% fetal calf serum (FCS) and treating with 2.5 ng/ml of TGF-β1 (R&D) for at least 14 days. MesHMLE cells, which are derived from HMLE from prolonged treatment with TGF-β1 (Mani et al., 2008), were maintained in EMT-inducing media without additional TGF-β1.

extract_protocol:
Cells grown to 90% confluency in 100mm dishes were rinsed with ice-cold PBS and UV irradiated with 600 mJ/cm2, 254 nm, in ice-cold PBS using a Stratalinker 1800. Cells were collected by scraping & centrifugation and stored at -80˚C until use. Cell pellets were lysed resuspended using 200 µl of 1 X QLB (1 X PBS, 0.3% SDS, 0.5% deoxycholate, 0.5% Igepal, EDTA-free Complete protease inhibitor cocktail (PIC; Roche, 11873580001) for 15 min, followed by addition of 400 µl of 1 X QDB (1 X PBS, 0.5% deoxycholate, 0.5% Igepal, PIC).
Rep1 libraries were constructed using NEBNext Multiplex small RNA library prep kit for Illumina with substitution of the 3' adapter with 3'SRdeg_DNA; /5rApp/GTACNNNNNNNNAGATCGGAAGAGCACACGTCT/3ddC/. Rep 2 libraries were constructed using a protocol modified from eCLIP (Van Nostrand et al Nat Methods, 2016) using custom adapters: 3' adapter 3'SRdeg_DNA, RT primer SR-RT; 5'-AGACGTGTGCTCTTCCGATCT-3', 5' adapter 5'SR_DNA; 5’P-GATCGTCGGACTGTAGAACTCTGAAC-3’SpC3/. PCR amplification with a common forward primer (NEBNext SR primer for Illumina) and barcoded reverse primers for each sample (NEBNext Index primers for Illumina).
CLIP-seq

value: mesHMLE

value: Breast

value: HITS-CLIP using anti-panQKI antibody (Neuromab, clone N147/6) on mesHMLE cells.

tag: antibody

value: anti-panQKI

tag: fraction

value: CLIP tag RNA

tag: technical replicate

tag: library preparation

value: dimer, modified eCLIP


title: QKI5-Be, monomer, rep1

description:
QKI5-Be_3_4_12_13_merged_peaks_sorted.bed
QKIpan-NM-QKI5-Be_3_4_12_13_5_6_14_15_merged_peaks_sorted.good_peaks-min_reads-10_pct_25.bed

value: HITS-CLIP using anti-QKI5 antibody (Bethyl Cat#A300-183A) on mesHMLE cells

value: monomer, NEBNext Multiplex small RNA library prep


title: QKI5-Be, monomer, rep2

value: monomer, modified eCLIP


title: MyoT-Lam-N3


title: QKIpan-NM, monomer, rep1


title: QKIpan-NM, monomer, rep2


title: QKI5-Be, dimer, rep1

value: dimer, NEBNext Multiplex small RNA library prep


title: QKI5-Be, dimer, rep2


title: 12_Gastroc

value: female


title: 5_Gastroc

value: chow


title: CTRL, dimer, rep2

value: HITS-CLIP size-matched input control from mesHMLE cells

value: input RNA


title: CTRL, monomer, rep2


title: AMS2.RNA

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

data_processing:
RNA-seq data was aligned using the bowtie2 algorithm against the hg19 human reference genome and RSEM v1.2.12 software was used to estimate read counts and RPKM values using gene information from Ensemble transcriptome version GRCh37.p13
Assembly: hg19
Supplementary files format and content: raw counts for all genes

source_name: spontaneous lymphoblastoid cell lines

extract_protocol:
Total RNA was isolated from 2 × 106 cells using the RNeasy Mini Kit (Qiagen, Germany) and treated with deoxyribonuclease (Qiagen, Hilden, Germany), following the manufacturer’s protocol
Sequencing library preparation for SLCLs was completed using the Quantseeq RNA-seq library preparation kit.

tag: disease state

value: active

tag: disease

value: MS

value: spontaneous lymphoblastoid cell lines


title: AMS4.RNA


title: AMS3.RNA


title: SMS3.RNA

value: stable


title: MyoT-Lam-N2

value: hiPSC Pci-AFR1

value: hiPSC

value: WT


title: SMS1.RNA


title: AMS1.RNA


title: MyoB-N2


title: HC2.RNA

value: healthy


title: QKIpan-NM, dimer, rep1

value: mesHMLE

value: Breast

value: HITS-CLIP using anti-panQKI antibody (Neuromab, clone N147/6) on mesHMLE cells.

value: anti-panQKI

value: CLIP tag RNA


title: NB10_NPC

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

data_processing:
Data were analysed using the Lexogen's proprietary Bluebee sequence analysis platform. Trimming using Bbduk and quality control with FASTQC.
Assembly: HGhg38

source_name: Nasopharyngeal carcinoma

extract_protocol:
Qiagen Rneasy microRNA kit with Dnase treatment
Libraries were prepared according to Lexogen's instructions accompanying the Kit (QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina)

value: Nasopharyngeal carcinoma

tag: gender

value: M

tag: age

tag: ebv

value: positive


title: HC1.RNA

tag: cell type


title: NB07_NPC

tag: tissue


title: NB08_NPC


title: NB09_NPC


title: CTRL, monomer, rep1

tag: genotype

tag: treatment

value: HITS-CLIP size-matched input control from mesHMLE cells

value: input RNA

value: monomer, NEBNext Multiplex small RNA library prep


title: CTRL, dimer, rep1

tag: cell line

value: dimer, NEBNext Multiplex small RNA library prep


title: LP45_NPC


title: LP50_NPC

value: F


title: LP46_NPC


title: LP47_NPC


title: LP48_NPC


title: LP42_NPC


title: LP49_NPC


title: LP40_NPC


title: LP44_NPC


title: LP39_NPC


title: LP41_NPC


title: SMS2.RNA

value: stable

value: MS

value: spontaneous lymphoblastoid cell lines


title: LP34_NPC


title: LP37_NPC


title: LP38_NPC


title: LP31_NPC


title: LP36_NPC


title: LP32_NPC


title: LP33_NPC


title: LP35_NPC


title: LP30_NPC


title: LP13_NPC


title: LP12_NPC


title: LP02_NPC


title: LO99_NPC


title: LP10_NPC


title: LP01_NPC


title: LO98_NPC


title: LP00_NPC


title: LP43_NPC


title: LO97_NPC


title: LO77_NPC


title: LO78_NPC


title: LO79_NPC


title: LO72_NPC


title: LO73_NPC


title: LO75_NPC


title: LO74_NPC


title: LO70_NPC


title: LO66_NPC


title: LO71_NPC


title: LO69_NPC


title: LO67_NPC


title: HCI-005_Input

city: ADELAIDE UNIVERSITY

first: Geraldine

last: Laven-Law

state: South Australia

address: Adelaide Health & Med Sci Bldg, Corner George St & North Terrace

institute: The University of Adelaide

data_processing:
Basecalls performed in BaseSpace.
Trimmed FASTQ files were aligned to the hg19 genome assembly using Bowtie2 (Langmead & Salzberg, 2012).
Mapped reads with a minimum MAPQ <10 and duplicate reads were removed using SAMtools (Li et al., 2009).
Peaks were called using MACS2 (Zhang et al., 2008 & Feng et al., 2012) callpeak v2.1.1.20160309 (default settings), with a pooled input sample as the control.
Peaks found in a minimum of 2 replicates (as determined using Cistrome (Liu et al., 2011)) were kept for the consensus peakset.
Genome_build: hg19
Supplementary_files_format_and_content: Four bed files per condtion are provided; three of which contain peaks called from individual replicates (i.e. _1, _2, _3), and one (without a suffix) containing consensus bed files, corresponding to shared peaks found within any two of three replicate experiments. A merged bigwig file, corresponding to a merge of all three replicate experiments, is also provided.

source_name: Breast cancer PDX HCI-005 tumor

growth_protocol: A single patient-derived tumor tissue was divided and implanted into the 4th inguinal mammary gland of 6-week-old female NOD-SCID-IL2γR-/- (NSG) mice. tumors were allowed to grow until reaching ~200 mm^3 size. Mice grafted with PDX HCI-005 received an estrogen pellet to drive tumor growth. This was not required for PDX GAR15-13.

extract_protocol:
tumors were cut into 30 µm slices on a cryostat and fixed with 2 mM disuccinimidyl glutarate for 25 m followed by 1% formaldehyde for 20 m prior to quenching. Chromatin was prepared and subsequently sheared by the Diagenode BioRuptor Pico for 5 cycles (30 sec on, 30 sec off) on ice. Sheared chromatin was immunoprecipitated with 5 µg GATA3 antibody overnight, after coupling to Protein A Dynabeads (10002D). DNA was purified using phenol:chloroform:isoamyl alcohol extraction.
Libraries were prepared according to manufacturer's instructions accompanying the Qiagen Ultralow Input Library Kit (Part #180495).
ChIP-Seq; Illumina NextSeq 500 (High Output v2) single-end 75 bp reads.

treatment_protocol: Mice were randomly assigned to treatment groups and treated with either a vehicle or AR agonist treatmet (GAR15-13; Enobosarm 10 mg/kg/day, HCI-005; DHT pellet). After 5 days, tumors were excised and snap-frozen.

value: PDX model HCI-005

tag: time point

value: Short-term (5 days treatment)

tag: chip antibody

value: none (Pooled input DNA)


title: LO68_NPC


title: LO96_NPC


title: GAR15-13_Input

source_name: Breast cancer PDX GAR15-13 tumor

value: PDX model GAR15-13


title: LO80_NPC


title: GAR15-13_GATA3_Sarm

value: GATA3 (Abcam ab199428)

value: Enobosarm


title: ZR-75-1 GATA3 ChIP E2+DHT Consensus

data_processing:
Basecalls performed in BaseSpace.
Trimmed FASTQ files were aligned to the hg19 genome assembly using Bowtie2 (Langmead & Salzberg, 2012).
Mapped reads with a minimum MAPQ <10 and duplicate reads were removed using SAMtools (Li et al., 2009).
Peaks were called using MACS2 (Zhang et al., 2008 & Feng et al., 2012) with a pooled input sample as the control.
Consensus peaks were called for peaks present in any two of three replicates using BEDTools (Quinlan & Hall 2010).
Genome_build: hg19
Supplementary_files_format_and_content: Four bed files per condtion are provided; three of which contain peaks called from individual replicates (i.e. _1, _2, _3), and one (without a suffix) containing consensus bed files, corresponding to shared peaks found within any two of three replicate experiments. A merged bigwig file, corresponding to a merge of all three replicate experiments, is also provided.

source_name: ZR-75-1 breast cancer cell line

growth_protocol: Cell lines were grown in hormone-deplete conditions (phenol red-free RPMI-1640 + 5% dextran-coated charcoal-stripped FBS) for 72 h

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 m prior to quenching. Chromatin was prepared and subsequently sheared by the Diagenode BioRuptor Plus for 10 cycles (30 sec on, 30 sec off) on ice. Sheared chromatin was immunoprecipitated with 5 µg of GATA3 antibody overnight, after coupling to Protein A Dynabeads (10002D). DNA was purified using phenol:chloroform:isoamyl alcohol extraction.
Libraries were prepared according to manufacturer's instructions accompanying the Qiagen Ultralow Input Library Kit (Part #180495).
ChIP-Seq; Illumina NextSeq 500 (High Output v2) single-end 75 bp reads.

treatment_protocol: Cells were treated for 4 h with either a vehicle (0.001% ethanol), 10 nM E2, 10 nM DHT, or 10 nM E2 + 10 nM DHT

tag: passages


title: ZR-75-1 GATA3 ChIP DHT Consensus

value: DHT


title: ZR-75-1 Pooled input

value: none (Input DNA)


title: HCI-005_GATA3_DHT


title: GAR15-13_GATA3_Veh

value: Vehicle


title: T-47D GATA3 ChIP E2+DHT Consensus

source_name: T-47D breast cancer cell line


title: ZR-75-1 GATA3 ChIP E2 Consensus


title: ZR-75-1 GATA3 ChIP Veh Consensus

value: Veh


title: LO76_NPC

value: Nasopharyngeal carcinoma

value: M

value: positive


title: T-47D Pooled input


title: T-47D GATA3 ChIP E2 Consensus


title: MFM-223 AR ChIP Veh Consensus

source_name: MFM-223 breast cancer cell line

growth_protocol: Cell lines were grown in hormone-deplete conditions (MDA-MB-453; DMEM High Glucose + 5% dextran-coated charcoal-stripped FBS, MFM-223; EMEM + 1x ITS + 5% dextran-coated charcoal-stripped FBS) for 72 h

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 m prior to quenching. Chromatin was prepared and subsequently sheared by the Diagenode BioRuptor Plus for 10 cycles (30 sec on, 30 sec off) on ice. Sheared chromatin was immunoprecipitated with 5 µg GATA3, 5 µg AR, or 2 µg H3K27ac antibody overnight, after coupling to Protein A Dynabeads (10002D). DNA was purified using phenol:chloroform:isoamyl alcohol extraction.
Libraries were prepared according to manufacturer's instructions accompanying the Qiagen Ultralow Input Library Kit (Part #180495).
ChIP-Seq; Illumina NextSeq 500 (High Output v2) single-end 75 bp reads.

treatment_protocol: Cells were treated for 4 h with either a vehicle (0.001% ethanol) or 10 nM DHT.

value: AR (Abcam ab108341)


title: MFM-223 AR ChIP DHT Consensus


title: T-47D GATA3 ChIP DHT Consensus


title: T-47D GATA3 ChIP Veh Consensus


title: MFM-223 H3K27ac ChIP DHT Consensus

value: H3K27ac (Abcam ab4729)


title: MFM-223 Pooled input


title: HCI-005_GATA3_Veh


title: MFM-223 H3K27ac ChIP Veh Consensus


title: MFM-223 GATA3 ChIP DHT Consensus


title: MDA-MB-453 Pooled input

source_name: MDA-MB-453 breast cancer cell line


title: MDA-MB-453 H3K27ac ChIP DHT Consensus


title: MDA-MB-453 H3K27ac ChIP Veh Consensus


title: MDA-MB-453 AR ChIP DHT Consensus


title: MDA-MB-453 GATA3 ChIP DHT Consensus


title: MDA-MB-453 AR ChIP Veh Consensus


title: MDA-MB-453 GATA3 ChIP Veh Consensus


title: MFM-223_DHT_passage_6

data_processing:
Basecalls performed using Illumina software.
Fastq files were trimmed using AdapterRemoval.
Trimmed files were aligned using STAR.
Reads were counted using featureCounts and normalised using Conditional Quantile Normalisation (CQN).
Differential analysis was performed using a Quasi-likelihood GLM fit.
Genome_build: GRCh38 (Ensembl 101)
Supplementary_files_format_and_content: CQN-normalised counts and differentially-expressed genes

growth_protocol: Cells were grown in standard conditions (MDA-MB-453; DMEM High Glucose + 10% FBS, MFM-223; EMEM + 1x ITS + 10% FBS) for 72 h

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy kit according to the manufacturer's instructions.
Libraries were generated using the TruSeq Total RNA HT Library Prep Kit
Total RNA-Seq; Illumina HiSeq 2500 single-end 40 bp reads

treatment_protocol: Cells were treated for 6 h with either a vehicle (0.001% ethanol) or 10 nM DHT

tag: replicate


title: MFM-223_DHT_passage_5


title: MFM-223_DHT_passage_4


title: MFM-223_DHT_passage_3


title: MFM-223_DHT_passage_1


title: MFM-223_Veh_passage_6


title: MFM-223_Veh_passage_4


title: MDA-MB-453_DHT_passage_6


title: MDA-MB-453_DHT_passage_4


title: MFM-223_Veh_passage_3


title: MFM-223_Veh_passage_5


title: MFM-223_Veh_passage_1


title: MFM-223 GATA3 ChIP Veh Consensus


title: MDA-MB-453_DHT_passage_1


title: MDA-MB-453_DHT_passage_2


title: MDA-MB-453_Veh_passage_4


title: MDA-MB-453_Veh_passage_3


title: MDA-MB-453_Veh_passage_6


title: MDA-MB-453_Veh_passage_5


title: MDA-MB-453_DHT_passage_3


title: MDA-MB-453_Veh_passage_1


title: MDA-MB-453_Veh_passage_2


title: TDP-43 ChIP-seq Repicate2

city: Shanghai

first: Xiang

last: Yu

state: Shanghai

address: 800 DongChuan

country: China

institute: Shanghai Jiao Tong University

description: DNA from TDP-43 ChIP Replicate 2

data_processing:
Reads were aligned to the human reference genome (GRCh38) with Bowtie2 (v2.1.0). Mapped reads were sorted with SAMtools (v0.1.19) and BAM files were converted to BED files with bedtools (v2.19.1). Mapped reads were normalized to reads per 10 million reads mapped (RP10M).
To identify TDP-43 binding sites, BED files of three TDP-43 ChIP-seq replicates were concatenated and peak calling was performed with factor analysis strategy using the HOMER (v4.7) findPeaks script. A minimum of 2-fold enrichment compared to the flanking 10 kb, 1.5-fold enrichment over input and a false discovery rate of 0.01 was required (-norm 1e8 -fdr 0.01 -F 1.5 -P 0.01 –L2 –LP 0.01). Putative peaks in each replicate were then filtered, requiring a minimum 1.5-fold enrichment relative to both input and TDP-43 knockdown. Common peaks represent the intersection of the filtered peaks in the three biologic replicates and were used for subsequent analyses.
genome build: GRCh38/hg38
processed data files format and content: bigwig

source_name: human HEK293 cell

growth_protocol: HEK293 cells were maintained in DMEM medium supplemented with 10% fetal bovine serum, 1% penicillin-streptomycin and 1% L-glutamine.

extract_protocol:
ChIP was performed in HEK293 cells and three independent biologic replicates of TDP-43 ChIP were used for downstream high-throughput sequencing. Additionally, as a negative control, TDP-43 ChIP-seq was performed in the context of shRNA-mediated TDP-43 knockdown. TDP-43 was immunoprecipitated using the monoclonal antibody TDP171 (Center for Neurodegenerative Disease Research, Philadelphia, PA). ChIPs were performed using the Chromatin Immunoprecipitation Assay Kit (ThermoFisher Scientific, #17-295) with modifications to the manufacturer protocol. Briefly, HEK293 cells were cross-linked with 1% formaldehyde, quenched with 0.125M glycine, washed and collected in DPBS. Cells were lysed in 1% SDS lysis buffer, sonicated to generate 100-400 base pair fragments and centrifuged to remove insoluble material. The resulting supernatant was diluted 10x in ChIP Dilution Buffer and used for subsequent immunoprecipitations. 250 μg of total protein was used as starting material for each immunoprecipitation. Chromatin was combined with 10 μg of antibody and 40 μL of protein A+G magnetic beads and rotated at 4°C overnight. The following day, magnetic beads were separated and washed in a series of buffers: 1. Low Salt Wash Buffer, 2. High Salt Wash Buffer, 3. LiCl Wash Buffer, 4. TE Buffer x3. Remaining complexes were eluted in 1% SDS and 0.1M NaHCO3 and subsequent to this step, input was processed alongside immunoprecipitations. Cross-links were reversed by addition of 5M NaCl at 65°C overnight. The following day, samples were treated with RNase A for 1 hr at 37°C, followed by addition of 0.5M EDTA, 1M Tris-HCl pH 6.5 and Proteinase K for 1.5 hrs at 45°C. DNA was isolated using MinElute PCR Purification Kit (Qiagen, #28004) and quality assessed on a BioAnalyzer 2100 prior to sequencing.
Sequenced experimental samples included an input, three independent biologic replicates of TDP-43 ChIP and TDP-43 ChIP in the context of TDP-43 knockdown. Libraries were prepared for next generation sequencing following manufacturer’s instructions (Illumina TruSeq ChIP Sample Prep Kit, #IP-202-1012) and contained DNA fragments 125-325 bp in length. Libraries were sequenced on an Illumina HiSeq2000, producing 100 bp single-end reads.

treatment_protocol: see above

value: no treatment

value: TDP171 (Center for Neurodegenerative Research, Philadelphia, PA)

value: ChIP-seq

value: Illumina HiSeq2000 100 bp single-end

tag: fraction

value: TDP-43-bound genomic DNA


title: TDP-43 ChIP-seq Repicate3

description: DNA from TDP-43 ChIP Replicate 3


title: TDP-43 ChIP input

description: Input DNA

value: Genomic DNA


title: TDP-43 KD ChIP-seq

description: DNA from TDP-43 ChIP from TDP-43 knockdown cells

value: Nucleofected with TDP-43 shRNA (Origene, #TR308946) prior to TDP-43 ChIP.


title: MDA-MB-453_DHT_passage_5


title: TDP-43 ChIP-seq Repicate1

description: DNA from TDP-43 ChIP Replicate 1


title: Pat_2132_visit4_NO_response

type: RNA

city: GRANADA

first: Daniel

last: Toro

state: Spain

address: Avenida de la Ilustracion

country: Spain

institute: GENYO

description: Gene expression of Patient 2132, visit4, response: NO, HC

hyb_protocol: Standard Affymetrix protcol

scan_protocol: HTAPS scan was used

data_processing: Data was normalized using rma R package

label: Biotin

source_name: SLE, Patient 2132, visit4, response: NO, HC

label_protocol: NuGEN Ovation

growth_protocol: Whole Blood samples in collected fom PAXgene tubes

extract_protocol: The RNA was extracted with Trizol reagent (Life Technologies) and cleaned up with RNA easy

treatment_protocol: Standard

value: Whole Blood

tag: diagnosis

value: SLE

tag: Sex

value: Female

tag: race

value: W

value: HC

value: NO

tag: sledai

tag: pga

tag: plaquenil


title: Pat_2132_visit3_NO_response

description: Gene expression of Patient 2132, visit3, response: NO, HC

source_name: SLE, Patient 2132, visit3, response: NO, HC


title: Pat_2128_visit4_NO_response

description: Gene expression of Patient 2128, visit4, response: NO, AZA

source_name: SLE, Patient 2128, visit4, response: NO, AZA

value: AZA


title: Pat_2129_visit2_YES_response

description: Gene expression of Patient 2129, visit2, response: YES, MMF

source_name: SLE, Patient 2129, visit2, response: YES, MMF

value: B

value: MMF

value: YES


title: Pat_2129_visit1_YES_response

description: Gene expression of Patient 2129, visit1, response: YES, MMF

source_name: SLE, Patient 2129, visit1, response: YES, MMF


title: Pat_2128_visit7_NO_response

description: Gene expression of Patient 2128, visit7, response: NO, AZA

source_name: SLE, Patient 2128, visit7, response: NO, AZA


title: Pat_2128_visit6_NO_response

description: Gene expression of Patient 2128, visit6, response: NO, AZA

source_name: SLE, Patient 2128, visit6, response: NO, AZA


title: Pat_2132_visit2_NO_response

description: Gene expression of Patient 2132, visit2, response: NO, HC

source_name: SLE, Patient 2132, visit2, response: NO, HC


title: Pat_2128_visit3_NO_response

description: Gene expression of Patient 2128, visit3, response: NO, AZA

source_name: SLE, Patient 2128, visit3, response: NO, AZA


title: Pat_2122_visit1_YES_response

description: Gene expression of Patient 2122, visit1, response: YES, MMF

source_name: SLE, Patient 2122, visit1, response: YES, MMF


title: Pat_2132_visit1_NO_response

description: Gene expression of Patient 2132, visit1, response: NO, HC

source_name: SLE, Patient 2132, visit1, response: NO, HC


title: Pat_2129_visit5_YES_response

description: Gene expression of Patient 2129, visit5, response: YES, MMF

source_name: SLE, Patient 2129, visit5, response: YES, MMF


title: Pat_2119_visit1_NO_response

description: Gene expression of Patient 2119, visit1, response: NO, MMF

source_name: SLE, Patient 2119, visit1, response: NO, MMF


title: Pat_2128_visit5_NO_response

description: Gene expression of Patient 2128, visit5, response: NO, AZA

source_name: SLE, Patient 2128, visit5, response: NO, AZA


title: Pat_2115_visit2_NO_response

description: Gene expression of Patient 2115, visit2, response: NO, HC

source_name: SLE, Patient 2115, visit2, response: NO, HC

value: Male


title: Pat_2125_visit1_NO_response

description: Gene expression of Patient 2125, visit1, response: NO, AZA

source_name: SLE, Patient 2125, visit1, response: NO, AZA


title: Pat_2119_visit5_NO_response

description: Gene expression of Patient 2119, visit5, response: NO, MMF

source_name: SLE, Patient 2119, visit5, response: NO, MMF


title: Pat_2103_visit7_YES_response

description: Gene expression of Patient 2103, visit7, response: YES, MMF

source_name: SLE, Patient 2103, visit7, response: YES, MMF

value: A


title: Pat_2128_visit2_NO_response

description: Gene expression of Patient 2128, visit2, response: NO, AZA

source_name: SLE, Patient 2128, visit2, response: NO, AZA


title: Pat_2119_visit2_NO_response

description: Gene expression of Patient 2119, visit2, response: NO, MMF

source_name: SLE, Patient 2119, visit2, response: NO, MMF


title: Pat_2122_visit2_YES_response

description: Gene expression of Patient 2122, visit2, response: YES, MMF

source_name: SLE, Patient 2122, visit2, response: YES, MMF


title: Pat_2129_visit3_YES_response

description: Gene expression of Patient 2129, visit3, response: YES, MMF

source_name: SLE, Patient 2129, visit3, response: YES, MMF


title: Pat_2122_visit3_YES_response

description: Gene expression of Patient 2122, visit3, response: YES, MMF

source_name: SLE, Patient 2122, visit3, response: YES, MMF


title: Pat_2129_visit4_YES_response

description: Gene expression of Patient 2129, visit4, response: YES, MMF

source_name: SLE, Patient 2129, visit4, response: YES, MMF


title: Pat_2103_visit6_YES_response

description: Gene expression of Patient 2103, visit6, response: YES, MMF

source_name: SLE, Patient 2103, visit6, response: YES, MMF


title: Pat_2125_visit2_NO_response

description: Gene expression of Patient 2125, visit2, response: NO, AZA

source_name: SLE, Patient 2125, visit2, response: NO, AZA


title: Pat_2128_visit1_NO_response

description: Gene expression of Patient 2128, visit1, response: NO, AZA

source_name: SLE, Patient 2128, visit1, response: NO, AZA


title: Pat_2103_visit2_YES_response

description: Gene expression of Patient 2103, visit2, response: YES, MMF

source_name: SLE, Patient 2103, visit2, response: YES, MMF


title: Pat_2103_visit4_YES_response

description: Gene expression of Patient 2103, visit4, response: YES, MMF

source_name: SLE, Patient 2103, visit4, response: YES, MMF


title: Pat_2103_visit1_YES_response

description: Gene expression of Patient 2103, visit1, response: YES, MMF

source_name: SLE, Patient 2103, visit1, response: YES, MMF


title: Pat_2119_visit4_NO_response

description: Gene expression of Patient 2119, visit4, response: NO, MMF

source_name: SLE, Patient 2119, visit4, response: NO, MMF


title: Pat_2119_visit3_NO_response

description: Gene expression of Patient 2119, visit3, response: NO, MMF

source_name: SLE, Patient 2119, visit3, response: NO, MMF


title: Pat_2102_visit2_YES_response

description: Gene expression of Patient 2102, visit2, response: YES, PHC

source_name: SLE, Patient 2102, visit2, response: YES, PHC

value: PHC


title: Pat_2041_visit2_YES_response

description: Gene expression of Patient 2041, visit2, response: YES, HC

source_name: SLE, Patient 2041, visit2, response: YES, HC


title: Pat_2101_visit2_YES_response

description: Gene expression of Patient 2101, visit2, response: YES, HC

source_name: SLE, Patient 2101, visit2, response: YES, HC


title: Pat_2102_visit1_YES_response

description: Gene expression of Patient 2102, visit1, response: YES, PHC

source_name: SLE, Patient 2102, visit1, response: YES, PHC


title: Pat_2101_visit1_YES_response

description: Gene expression of Patient 2101, visit1, response: YES, HC

source_name: SLE, Patient 2101, visit1, response: YES, HC


title: Pat_2086_visit2_YES_response

description: Gene expression of Patient 2086, visit2, response: YES, AZA

source_name: SLE, Patient 2086, visit2, response: YES, AZA


title: Pat_2103_visit5_YES_response

description: Gene expression of Patient 2103, visit5, response: YES, MMF

source_name: SLE, Patient 2103, visit5, response: YES, MMF


title: Pat_2086_visit1_YES_response

description: Gene expression of Patient 2086, visit1, response: YES, AZA

source_name: SLE, Patient 2086, visit1, response: YES, AZA


title: Pat_2041_visit1_YES_response

description: Gene expression of Patient 2041, visit1, response: YES, HC

source_name: SLE, Patient 2041, visit1, response: YES, HC


title: Pat_2103_visit3_YES_response

description: Gene expression of Patient 2103, visit3, response: YES, MMF

source_name: SLE, Patient 2103, visit3, response: YES, MMF


title: Pat_2068_visit2_NO_response

description: Gene expression of Patient 2068, visit2, response: NO, PHC

source_name: SLE, Patient 2068, visit2, response: NO, PHC


title: Pat_2094_visit2_YES_response

description: Gene expression of Patient 2094, visit2, response: YES, MMF

source_name: SLE, Patient 2094, visit2, response: YES, MMF


title: Pat_2068_visit1_NO_response

description: Gene expression of Patient 2068, visit1, response: NO, PHC

source_name: SLE, Patient 2068, visit1, response: NO, PHC


title: Pat_2025_visit1_YES_response

description: Gene expression of Patient 2025, visit1, response: YES, HC

source_name: SLE, Patient 2025, visit1, response: YES, HC


title: Pat_2006_visit2_YES_response

description: Gene expression of Patient 2006, visit2, response: YES, PHC

source_name: SLE, Patient 2006, visit2, response: YES, PHC


title: Pat_2022_visit1_YES_response

description: Gene expression of Patient 2022, visit1, response: YES, AZA

source_name: SLE, Patient 2022, visit1, response: YES, AZA


title: Pat_2006_visit1_YES_response

description: Gene expression of Patient 2006, visit1, response: YES, PHC

source_name: SLE, Patient 2006, visit1, response: YES, PHC


title: Pat_2018_visit2_YES_response

description: Gene expression of Patient 2018, visit2, response: YES, HC

source_name: SLE, Patient 2018, visit2, response: YES, HC


title: Pat_2094_visit1_YES_response

description: Gene expression of Patient 2094, visit1, response: YES, MMF

source_name: SLE, Patient 2094, visit1, response: YES, MMF


title: Pat_2005_visit2_YES_response

description: Gene expression of Patient 2005, visit2, response: YES, AZA

source_name: SLE, Patient 2005, visit2, response: YES, AZA


title: Pat_2115_visit1_NO_response

description: Gene expression of Patient 2115, visit1, response: NO, HC

source_name: SLE, Patient 2115, visit1, response: NO, HC


title: Pat_2009_visit1_YES_response

description: Gene expression of Patient 2009, visit1, response: YES, MMF

source_name: SLE, Patient 2009, visit1, response: YES, MMF


title: Pat_2002_visit1_YES_response

description: Gene expression of Patient 2002, visit1, response: YES, HC

source_name: SLE, Patient 2002, visit1, response: YES, HC


title: Pat_2022_visit2_YES_response

description: Gene expression of Patient 2022, visit2, response: YES, AZA

source_name: SLE, Patient 2022, visit2, response: YES, AZA


title: Pat_1944_visit3_NO_response

description: Gene expression of Patient 1944, visit3, response: NO, HC

source_name: SLE, Patient 1944, visit3, response: NO, HC


title: Pat_1944_visit2_NO_response

description: Gene expression of Patient 1944, visit2, response: NO, HC

source_name: SLE, Patient 1944, visit2, response: NO, HC


title: Pat_2002_visit2_YES_response

description: Gene expression of Patient 2002, visit2, response: YES, HC

source_name: SLE, Patient 2002, visit2, response: YES, HC


title: Pat_1944_visit4_NO_response

description: Gene expression of Patient 1944, visit4, response: NO, HC

source_name: SLE, Patient 1944, visit4, response: NO, HC


title: Pat_2003_visit2_YES_response

description: Gene expression of Patient 2003, visit2, response: YES, HC

source_name: SLE, Patient 2003, visit2, response: YES, HC


title: Pat_2018_visit1_YES_response

description: Gene expression of Patient 2018, visit1, response: YES, HC

source_name: SLE, Patient 2018, visit1, response: YES, HC


title: Pat_1930_visit2_YES_response

description: Gene expression of Patient 1930, visit2, response: YES, MMF

source_name: SLE, Patient 1930, visit2, response: YES, MMF


title: Pat_2005_visit1_YES_response

description: Gene expression of Patient 2005, visit1, response: YES, AZA

source_name: SLE, Patient 2005, visit1, response: YES, AZA


title: Pat_2025_visit2_YES_response

description: Gene expression of Patient 2025, visit2, response: YES, HC

source_name: SLE, Patient 2025, visit2, response: YES, HC


title: Pat_1944_visit1_NO_response

description: Gene expression of Patient 1944, visit1, response: NO, HC

source_name: SLE, Patient 1944, visit1, response: NO, HC


title: Pat_2003_visit1_YES_response

description: Gene expression of Patient 2003, visit1, response: YES, HC

source_name: SLE, Patient 2003, visit1, response: YES, HC


title: Pat_1943_visit1_YES_response

description: Gene expression of Patient 1943, visit1, response: YES, MMF

source_name: SLE, Patient 1943, visit1, response: YES, MMF


title: Pat_1930_visit1_YES_response

description: Gene expression of Patient 1930, visit1, response: YES, MMF

source_name: SLE, Patient 1930, visit1, response: YES, MMF


title: Afa17 100896670186_J

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were processed and normalised using quantile normalisation with BeadStudio software v3.8

label: biotin

source_name: Afa17 2_after

label_protocol: RNA from each sample was labeled according to the manufacturers recommendations (Illumina Gene Expression Profiling Assay Guide).

extract_protocol: RNA was extracted with QIAGEN FFPE RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

tag: specimen

value: Afatinib


title: Afa20 100896670186_K

source_name: Afa20 1_baseline


title: Pat_1943_visit2_YES_response

description: Gene expression of Patient 1943, visit2, response: YES, MMF

source_name: SLE, Patient 1943, visit2, response: YES, MMF


title: Afa16 100896670186_G

source_name: Afa16 1_baseline


title: Afa20 100896670186_L

source_name: Afa20 2_after


title: Pat_1927_visit3_NO_response

description: Gene expression of Patient 1927, visit3, response: NO, AZA

source_name: SLE, Patient 1927, visit3, response: NO, AZA


title: Pat_1927_visit4_NO_response

description: Gene expression of Patient 1927, visit4, response: NO, AZA

source_name: SLE, Patient 1927, visit4, response: NO, AZA


title: Pat_1927_visit2_NO_response

description: Gene expression of Patient 1927, visit2, response: NO, AZA

source_name: SLE, Patient 1927, visit2, response: NO, AZA


title: Afa1 100896670186_B

source_name: Afa1 2_after


title: Afa3 100896670181_J

source_name: Afa3 1_baseline


title: Pat_1924_visit6_NO_response

description: Gene expression of Patient 1924, visit6, response: NO, HC

source_name: SLE, Patient 1924, visit6, response: NO, HC


title: Pat_1926_visit1_YES_response

description: Gene expression of Patient 1926, visit1, response: YES, HC

source_name: SLE, Patient 1926, visit1, response: YES, HC


title: Pat_1927_visit1_NO_response

description: Gene expression of Patient 1927, visit1, response: NO, AZA

source_name: SLE, Patient 1927, visit1, response: NO, AZA


title: Afa13 100896670181_D

source_name: Afa13 1_baseline


title: Pat_1924_visit3_NO_response

description: Gene expression of Patient 1924, visit3, response: NO, HC

source_name: SLE, Patient 1924, visit3, response: NO, HC


title: Afa1 100896670186_A

source_name: Afa1 1_baseline


title: Afa10 100896670181_A

source_name: Afa10 1_baseline


title: Pat_1926_visit2_YES_response

description: Gene expression of Patient 1926, visit2, response: YES, HC

source_name: SLE, Patient 1926, visit2, response: YES, HC


title: Pat_1924_visit1_NO_response

description: Gene expression of Patient 1924, visit1, response: NO, HC

source_name: SLE, Patient 1924, visit1, response: NO, HC


title: Afa7 100896670177_B

source_name: Afa7 2_after


title: Afa17 100896670186_I

source_name: Afa17 1_baseline


title: Afa9 100896670177_H

source_name: Afa9 2_after


title: Afa8 100896670177_D

source_name: Afa8 1_baseline


title: Afa16 100896670186_H

source_name: Afa16 2_after


title: Pat_1924_visit4_NO_response

description: Gene expression of Patient 1924, visit4, response: NO, HC

source_name: SLE, Patient 1924, visit4, response: NO, HC


title: Pat_1924_visit7_NO_response

description: Gene expression of Patient 1924, visit7, response: NO, HC

source_name: SLE, Patient 1924, visit7, response: NO, HC


title: Pat_1913_visit2_YES_response

description: Gene expression of Patient 1913, visit2, response: YES, PHC

source_name: SLE, Patient 1913, visit2, response: YES, PHC


title: Pat_1924_visit2_NO_response

description: Gene expression of Patient 1924, visit2, response: NO, HC

source_name: SLE, Patient 1924, visit2, response: NO, HC


title: Pat_1924_visit5_NO_response

description: Gene expression of Patient 1924, visit5, response: NO, HC

source_name: SLE, Patient 1924, visit5, response: NO, HC


title: Afa9 100896670177_G

source_name: Afa9 1_baseline


title: Afa12 100896670181_C

source_name: Afa12 2_after


title: Afa7 100896670177_A

source_name: Afa7 1_baseline


title: Afa5 100896670175_I

source_name: Afa5 2_after


title: Afa8 100896670177_E

source_name: Afa8 2_after


title: Pat_1913_visit1_YES_response

description: Gene expression of Patient 1913, visit1, response: YES, PHC

source_name: SLE, Patient 1913, visit1, response: YES, PHC


title: Pat_1891_visit2_YES_response

description: Gene expression of Patient 1891, visit2, response: YES, MMF

source_name: SLE, Patient 1891, visit2, response: YES, MMF


title: Afa5 100896670175_H

source_name: Afa5 1_baseline


title: Pat_1888_visit2_YES_response

description: Gene expression of Patient 1888, visit2, response: YES, MMF

source_name: SLE, Patient 1888, visit2, response: YES, MMF


title: Afa4 100896670175_F

source_name: Afa4 2_after


title: Pat_1880_visit2_YES_response

description: Gene expression of Patient 1880, visit2, response: YES, MMF

source_name: SLE, Patient 1880, visit2, response: YES, MMF


title: Pat_1889_visit1_YES_response

description: Gene expression of Patient 1889, visit1, response: YES, MMF

source_name: SLE, Patient 1889, visit1, response: YES, MMF


title: Pat_1889_visit2_YES_response

description: Gene expression of Patient 1889, visit2, response: YES, MMF

source_name: SLE, Patient 1889, visit2, response: YES, MMF


title: Afa34 100896670166_L

source_name: Afa34 2_after


title: Afa34 100896670166_K

source_name: Afa34 1_baseline


title: Afa36 100896670175_C

source_name: Afa36 2_after


title: Pat_1891_visit1_YES_response

description: Gene expression of Patient 1891, visit1, response: YES, MMF

source_name: SLE, Patient 1891, visit1, response: YES, MMF


title: Afa4 100896670175_E

source_name: Afa4 1_baseline


title: Afa26 100896670106_H

source_name: Afa26 2_after


title: Afa36 100896670175_B

source_name: Afa36 1_baseline


title: Pat_2009_visit2_YES_response

description: Gene expression of Patient 2009, visit2, response: YES, MMF

source_name: SLE, Patient 2009, visit2, response: YES, MMF


title: Pat_1880_visit1_YES_response

description: Gene expression of Patient 1880, visit1, response: YES, MMF

source_name: SLE, Patient 1880, visit1, response: YES, MMF


title: Pat_1876_visit1_YES_response

description: Gene expression of Patient 1876, visit1, response: YES, MMF

source_name: SLE, Patient 1876, visit1, response: YES, MMF


title: Pat_1888_visit1_YES_response

description: Gene expression of Patient 1888, visit1, response: YES, MMF

source_name: SLE, Patient 1888, visit1, response: YES, MMF


title: Afa26 100896670106_I

source_name: Afa26 1_baseline


title: Afa3 100896670166_C

source_name: Afa3 2_after


title: Afa24 100896670106_C

source_name: Afa24 2_after


title: Afa25 100896670106_E

source_name: Afa25 1_baseline


title: Pat_1876_visit2_YES_response

description: Gene expression of Patient 1876, visit2, response: YES, MMF

source_name: SLE, Patient 1876, visit2, response: YES, MMF


title: Pat_1871_visit4_YES_response

description: Gene expression of Patient 1871, visit4, response: YES, MMF

source_name: SLE, Patient 1871, visit4, response: YES, MMF


title: Pat_1874_visit1_YES_response

description: Gene expression of Patient 1874, visit1, response: YES, HC

source_name: SLE, Patient 1874, visit1, response: YES, HC


title: Pat_1871_visit3_YES_response

description: Gene expression of Patient 1871, visit3, response: YES, MMF

source_name: SLE, Patient 1871, visit3, response: YES, MMF


title: Pat_1913_visit3_YES_response

description: Gene expression of Patient 1913, visit3, response: YES, PHC

source_name: SLE, Patient 1913, visit3, response: YES, PHC


title: Afa25 100896670106_F

source_name: Afa25 2_after


title: Pat_1874_visit2_YES_response

description: Gene expression of Patient 1874, visit2, response: YES, HC

source_name: SLE, Patient 1874, visit2, response: YES, HC


title: Afa24 100896670106_B

source_name: Afa24 1_baseline


title: Pat_1871_visit2_YES_response

description: Gene expression of Patient 1871, visit2, response: YES, MMF

source_name: SLE, Patient 1871, visit2, response: YES, MMF


title: PBMC, HBV-ACLF3, a-BTLA

city: Quanzhou

first: Xueping

state: Fujian

address: No. 250 East Street

department: Infection Disease

institute: Fujian Medical University Affiliated First Quanzhou hospital

data_processing:
CLC Genomics Workbench v 11.0.1
mRNA-seq reads were trimmed from 3' end until the final base had a quality score > 20, using seqtk v1.0-r82-dirty, discarding reads left with < 25 bp
Trimmed sequence reads were mapped to GRCh38(hg38) using TopHat（version:2.0.9）
The number of Fragments of each gene after TopHat comparison was counted by HTSeq, and then normalized by the original mean of M Values (TMM) method. Finally, the FPKM value of each gene was calculated by Perl script.
Assembly: GRCh38(hg38)
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: PBMC

extract_protocol:
Total RNA was extracted using miRNeasy Mini Kit (Cat# 217004, Qiagen)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).
According to the instructions of the experiment, the purified Total RNA was remove rRNA, fragmented, first-strand cDNA synthesis, second-strand cDNA synthesis, end repair, adding A to the 3 'end, ligating connector, enrichment and other steps to complete the construction of sequencing sample library.

value: PBMC

tag: cell type

tag: group

value: HBV-ACLF

value: XYP, male

value: a-BTLA


title: PBMC, HBV-ACLF2, a-BTLA

tag: tissue

tag: genotype

value: LGW, male


title: PBMC, HBV-ACLF3, PBS

tag: treatment

value: PBS


title: PBMC, HBV-ACLF2, PBS


title: PBMC,CHB3, a-BTLA

value: CHB

value: WHP, male


title: PBMC, HBV-ACLF1, a-BTLA

value: LGF, male


title: Afa12 100896670094_G

source_name: Afa12 1_baseline


title: Afa13 100896670094_K

source_name: Afa13 2_after


title: Afa11 100896670094_D

source_name: Afa11 1_baseline


title: Afa11 100896670094_E

source_name: Afa11 2_after


title: Pat_1869_visit2_NO_response

description: Gene expression of Patient 1869, visit2, response: NO, HC

source_name: SLE, Patient 1869, visit2, response: NO, HC

value: Whole Blood

value: SLE

value: Female

value: HC

value: NO


title: Pat_1866_visit2_YES_response

description: Gene expression of Patient 1866, visit2, response: YES, HC

source_name: SLE, Patient 1866, visit2, response: YES, HC

value: W

value: YES


title: Afa10 100896670094_B

source_name: Afa10 2_after

value: Afatinib


title: PBMC,CHB3, PBS

value: PBMC


title: Pat_1871_visit1_YES_response

description: Gene expression of Patient 1871, visit1, response: YES, MMF

source_name: SLE, Patient 1871, visit1, response: YES, MMF

value: B

value: MMF


title: Pat_1866_visit1_YES_response

description: Gene expression of Patient 1866, visit1, response: YES, HC

source_name: SLE, Patient 1866, visit1, response: YES, HC


title: Pat_1869_visit1_NO_response

description: Gene expression of Patient 1869, visit1, response: NO, HC

source_name: SLE, Patient 1869, visit1, response: NO, HC


title: Pat_1854_visit1_YES_response

description: Gene expression of Patient 1854, visit1, response: YES, HC

source_name: SLE, Patient 1854, visit1, response: YES, HC


title: Pat_1842_visit3_NO_response

description: Gene expression of Patient 1842, visit3, response: NO, HC

source_name: SLE, Patient 1842, visit3, response: NO, HC


title: Pat_1811_visit2_NO_response

description: Gene expression of Patient 1811, visit2, response: NO, PHC

source_name: SLE, Patient 1811, visit2, response: NO, PHC

value: PHC


title: PBMC, CHB2, a-BTLA

value: HQL, male

value: a-BTLA


title: Pat_1842_visit2_NO_response

description: Gene expression of Patient 1842, visit2, response: NO, HC

source_name: SLE, Patient 1842, visit2, response: NO, HC


title: Pat_1842_visit1_NO_response

description: Gene expression of Patient 1842, visit1, response: NO, HC

source_name: SLE, Patient 1842, visit1, response: NO, HC


title: Pat_1811_visit1_NO_response

description: Gene expression of Patient 1811, visit1, response: NO, PHC

source_name: SLE, Patient 1811, visit1, response: NO, PHC


title: PBMC, CHB2, PBS

source_name: PBMC

value: CHB

value: PBS


title: PBMC, HBV-ACLF1, PBS

value: HBV-ACLF

value: LGF, male


title: Pat_1854_visit2_YES_response

description: Gene expression of Patient 1854, visit2, response: YES, HC

source_name: SLE, Patient 1854, visit2, response: YES, HC

value: Whole Blood

value: SLE


title: PBMC, CHB1, PBS

value: ZDL, male


title: PBMC,CHB1, a-BTLA


title: Pat_1869_visit3_NO_response

description: Gene expression of Patient 1869, visit3, response: NO, HC

source_name: SLE, Patient 1869, visit3, response: NO, HC

value: Female

value: HC

value: NO


title: Pat_1807_visit3_NO_response

description: Gene expression of Patient 1807, visit3, response: NO, PHC

source_name: SLE, Patient 1807, visit3, response: NO, PHC


title: PBMC, NC2, PBS

value: NC

value: YYH, male


title: PBMC, NC3, a-BTLA

value: PBMC

value: LJF, female


title: PBMC, NC1, a-BTLA

value: CP, male


title: PBMC, NC1, PBS


title: PBMC, NC3, PBS


title: PBMC, NC2, a-BTLA


title: Pat_1807_visit1_NO_response

description: Gene expression of Patient 1807, visit1, response: NO, PHC

source_name: SLE, Patient 1807, visit1, response: NO, PHC

value: B

value: PHC


title: PT-00251650_T_EA

city: BUFFALO

first: Eduardo

last: Cortes

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequenced reads were mapped to GRCh38 reference GENCODE annotation (p7) using tophat 2.0.13
TopHat aligned BAMs were merged using MergeSamFiles from Picard v1.97
Reads counts are obtained using HTSeq v0.6.1 using intersect-strict option
Assembly: GRCh38.p7 GENCODE v25
Supplementary files format and content: RawCounts.csv. Comma-separated text file. First column indicates gene symbols. Rest of columns include read counts extracted from HTSeq

source_name: Tumor

extract_protocol:
Illumina TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gol
RNA libraries were prepared for sequencing using standard Illumina protocols

value: prostate

value: EA


title: PT-00237328_T_EA


title: Pat_1806_visit1_YES_response

description: Gene expression of Patient 1806, visit1, response: YES, HC

source_name: SLE, Patient 1806, visit1, response: YES, HC

value: W

value: YES


title: Pat_1792_visit3_YES_response

description: Gene expression of Patient 1792, visit3, response: YES, HC

source_name: SLE, Patient 1792, visit3, response: YES, HC

value: Whole Blood


title: Pat_1806_visit2_YES_response

description: Gene expression of Patient 1806, visit2, response: YES, HC

source_name: SLE, Patient 1806, visit2, response: YES, HC

value: SLE


title: Pat_1806_visit3_YES_response

description: Gene expression of Patient 1806, visit3, response: YES, HC

source_name: SLE, Patient 1806, visit3, response: YES, HC


title: Pat_1785_visit2_YES_response

description: Gene expression of Patient 1785, visit2, response: YES, MMF

source_name: SLE, Patient 1785, visit2, response: YES, MMF

value: O

value: MMF


title: PT-00233979_T_EA


title: Pat_1792_visit4_YES_response

description: Gene expression of Patient 1792, visit4, response: YES, HC

source_name: SLE, Patient 1792, visit4, response: YES, HC

value: Female

value: HC


title: PT-00235895_NT_EA

source_name: Adjacent Tumor


title: PT-00251650_NT_EA


title: Pat_1792_visit2_YES_response

description: Gene expression of Patient 1792, visit2, response: YES, HC

source_name: SLE, Patient 1792, visit2, response: YES, HC


title: PT-00237328_NT_EA


title: Pat_1792_visit1_YES_response

description: Gene expression of Patient 1792, visit1, response: YES, HC

source_name: SLE, Patient 1792, visit1, response: YES, HC


title: PT-00235895_T_EA


title: PT-00233979_NT_EA


title: PT-00231995_T_EA


title: PT-00231995_NT_EA


title: PT-00231846_NT_EA


title: Pat_1718_visit1_YES_response

description: Gene expression of Patient 1718, visit1, response: YES, HC

source_name: SLE, Patient 1718, visit1, response: YES, HC

value: A


title: Pat_1723_visit1_NO_response

description: Gene expression of Patient 1723, visit1, response: NO, MMF

source_name: SLE, Patient 1723, visit1, response: NO, MMF

value: NO


title: Pat_1718_visit2_YES_response

description: Gene expression of Patient 1718, visit2, response: YES, HC

source_name: SLE, Patient 1718, visit2, response: YES, HC


title: Pat_1702_visit1_NO_response

description: Gene expression of Patient 1702, visit1, response: NO, AZA

source_name: SLE, Patient 1702, visit1, response: NO, AZA

value: AZA


title: Pat_1785_visit1_YES_response

description: Gene expression of Patient 1785, visit1, response: YES, MMF

source_name: SLE, Patient 1785, visit1, response: YES, MMF


title: Pat_1702_visit3_NO_response

description: Gene expression of Patient 1702, visit3, response: NO, AZA

source_name: SLE, Patient 1702, visit3, response: NO, AZA


title: PT-00231182_T_EA


title: Pat_1699_visit4_NO_response

description: Gene expression of Patient 1699, visit4, response: NO, AZA

source_name: SLE, Patient 1699, visit4, response: NO, AZA


title: Pat_1702_visit2_NO_response

description: Gene expression of Patient 1702, visit2, response: NO, AZA

source_name: SLE, Patient 1702, visit2, response: NO, AZA


title: PT-00231182_NT_EA


title: PT-00231030_NT_EA


title: PT-00231030_T_EA

source_name: Tumor


title: PT-00231846_T_EA


title: PT-00225395_T_EA


title: PT-00228928_NT_EA


title: PT-00225395_NT_EA


title: Pat_1699_visit1_NO_response

description: Gene expression of Patient 1699, visit1, response: NO, AZA

source_name: SLE, Patient 1699, visit1, response: NO, AZA


title: PT-00228928_T_EA


title: Pat_1699_visit2_NO_response

description: Gene expression of Patient 1699, visit2, response: NO, AZA

source_name: SLE, Patient 1699, visit2, response: NO, AZA


title: Pat_1723_visit2_NO_response

description: Gene expression of Patient 1723, visit2, response: NO, MMF

source_name: SLE, Patient 1723, visit2, response: NO, MMF


title: Pat_1699_visit3_NO_response

description: Gene expression of Patient 1699, visit3, response: NO, AZA

source_name: SLE, Patient 1699, visit3, response: NO, AZA


title: Pat_1679_visit3_NO_response

description: Gene expression of Patient 1679, visit3, response: NO, AZA

source_name: SLE, Patient 1679, visit3, response: NO, AZA


title: Pat_1807_visit2_NO_response

description: Gene expression of Patient 1807, visit2, response: NO, PHC

source_name: SLE, Patient 1807, visit2, response: NO, PHC


title: Pat_1679_visit1_NO_response

description: Gene expression of Patient 1679, visit1, response: NO, AZA

source_name: SLE, Patient 1679, visit1, response: NO, AZA


title: Pat_1679_visit2_NO_response

description: Gene expression of Patient 1679, visit2, response: NO, AZA

source_name: SLE, Patient 1679, visit2, response: NO, AZA


title: Pat_1667_visit2_YES_response

description: Gene expression of Patient 1667, visit2, response: YES, HC

source_name: SLE, Patient 1667, visit2, response: YES, HC


title: PT-00225118_T_EA


title: Pat_1667_visit1_YES_response

description: Gene expression of Patient 1667, visit1, response: YES, HC

source_name: SLE, Patient 1667, visit1, response: YES, HC


title: PT-00225118_NT_EA

source_name: Adjacent Tumor


title: Pat_1657_visit2_YES_response

description: Gene expression of Patient 1657, visit2, response: YES, HC

source_name: SLE, Patient 1657, visit2, response: YES, HC


title: PT-00222678_NT_EA


title: PT-00217159_T_EA


title: PT-00222678_T_EA


title: PT-00219496_NT_EA


title: Pat_1657_visit1_YES_response

description: Gene expression of Patient 1657, visit1, response: YES, HC

source_name: SLE, Patient 1657, visit1, response: YES, HC


title: Pat_1642_visit3_YES_response

description: Gene expression of Patient 1642, visit3, response: YES, HC

source_name: SLE, Patient 1642, visit3, response: YES, HC


title: PT-00216325_T_EA


title: PT-00216325_NT_EA


title: PT-00217159_NT_EA


title: Pat_1642_visit2_YES_response

description: Gene expression of Patient 1642, visit2, response: YES, HC

source_name: SLE, Patient 1642, visit2, response: YES, HC


title: Pat_1642_visit1_YES_response

description: Gene expression of Patient 1642, visit1, response: YES, HC

source_name: SLE, Patient 1642, visit1, response: YES, HC


title: PT-00214592_T_EA

source_name: Tumor


title: PT-00219496_T_EA


title: Pat_1619_visit2_YES_response

description: Gene expression of Patient 1619, visit2, response: YES, PHC

source_name: SLE, Patient 1619, visit2, response: YES, PHC


title: Pat_1619_visit1_YES_response

description: Gene expression of Patient 1619, visit1, response: YES, PHC

source_name: SLE, Patient 1619, visit1, response: YES, PHC


title: PT-00211536_T_EA


title: Pat_1585_visit2_YES_response

description: Gene expression of Patient 1585, visit2, response: YES, MMF

source_name: SLE, Patient 1585, visit2, response: YES, MMF


title: Pat_1583_visit1_YES_response

description: Gene expression of Patient 1583, visit1, response: YES, PHC

source_name: SLE, Patient 1583, visit1, response: YES, PHC


title: PT-00211536_NT_EA


title: PT-00196174_T_EA


title: PT-00197815_NT_EA


title: PT-00197815_T_EA


title: Pat_1579_visit1_YES_response

description: Gene expression of Patient 1579, visit1, response: YES, HC

source_name: SLE, Patient 1579, visit1, response: YES, HC


title: PT-00196174_NT_EA


title: Pat_1582_visit1_NO_response

description: Gene expression of Patient 1582, visit1, response: NO, MMF

source_name: SLE, Patient 1582, visit1, response: NO, MMF


title: Pat_1543_visit3_YES_response

description: Gene expression of Patient 1543, visit3, response: YES, HC

source_name: SLE, Patient 1543, visit3, response: YES, HC


title: PT-00194466_T_EA


title: Pat_1583_visit2_YES_response

description: Gene expression of Patient 1583, visit2, response: YES, PHC

source_name: SLE, Patient 1583, visit2, response: YES, PHC


title: Pat_1539_visit2_YES_response

description: Gene expression of Patient 1539, visit2, response: YES, HC

source_name: SLE, Patient 1539, visit2, response: YES, HC


title: Pat_1579_visit2_YES_response

description: Gene expression of Patient 1579, visit2, response: YES, HC

source_name: SLE, Patient 1579, visit2, response: YES, HC


title: PT-00194466_NT_EA

source_name: Adjacent Tumor


title: Pat_1539_visit1_YES_response

description: Gene expression of Patient 1539, visit1, response: YES, HC

source_name: SLE, Patient 1539, visit1, response: YES, HC


title: PT-00194498_T_EA


title: Pat_1513_visit2_YES_response

description: Gene expression of Patient 1513, visit2, response: YES, AZA

source_name: SLE, Patient 1513, visit2, response: YES, AZA


title: PT-00214592_NT_EA


title: PT-00194403_NT_EA


title: PT-00194498_NT_EA


title: PT-00194403_T_EA


title: PT-00193829_NT_EA


title: PT-00193829_T_EA


title: Pat_1505_visit2_YES_response

description: Gene expression of Patient 1505, visit2, response: YES, PHC

source_name: SLE, Patient 1505, visit2, response: YES, PHC


title: PT-00193649_NT_EA


title: Pat_1543_visit1_YES_response

description: Gene expression of Patient 1543, visit1, response: YES, HC

source_name: SLE, Patient 1543, visit1, response: YES, HC


title: PT-00193349_T_EA


title: Pat_1478_visit4_YES_response

description: Gene expression of Patient 1478, visit4, response: YES, HC

source_name: SLE, Patient 1478, visit4, response: YES, HC


title: Pat_1513_visit1_YES_response

description: Gene expression of Patient 1513, visit1, response: YES, AZA

source_name: SLE, Patient 1513, visit1, response: YES, AZA


title: Pat_1478_visit5_YES_response

description: Gene expression of Patient 1478, visit5, response: YES, HC

source_name: SLE, Patient 1478, visit5, response: YES, HC


title: Pat_1478_visit3_YES_response

description: Gene expression of Patient 1478, visit3, response: YES, HC

source_name: SLE, Patient 1478, visit3, response: YES, HC


title: Pat_1478_visit1_YES_response

description: Gene expression of Patient 1478, visit1, response: YES, HC

source_name: SLE, Patient 1478, visit1, response: YES, HC


title: Pat_1505_visit1_YES_response

description: Gene expression of Patient 1505, visit1, response: YES, PHC

source_name: SLE, Patient 1505, visit1, response: YES, PHC


title: PT-00193649_T_EA

source_name: Tumor


title: PT-00193349_NT_EA


title: PT-00193228_NT_EA


title: PT-00193110_T_EA


title: PT-00193228_T_EA


title: PT-00193110_NT_EA


title: PT-00191831_T_EA


title: PT-00191831_NT_EA


title: Pat_1478_visit2_YES_response

description: Gene expression of Patient 1478, visit2, response: YES, HC

source_name: SLE, Patient 1478, visit2, response: YES, HC


title: Pat_1585_visit1_YES_response

description: Gene expression of Patient 1585, visit1, response: YES, MMF

source_name: SLE, Patient 1585, visit1, response: YES, MMF


title: PT-00179840_T_EA


title: Pat_1428_visit2_YES_response

description: Gene expression of Patient 1428, visit2, response: YES, HC

source_name: SLE, Patient 1428, visit2, response: YES, HC


title: PT-00191716_T_EA


title: Pat_1409_visit2_YES_response

description: Gene expression of Patient 1409, visit2, response: YES, MMF

source_name: SLE, Patient 1409, visit2, response: YES, MMF


title: Pat_1463_visit2_NO_response

description: Gene expression of Patient 1463, visit2, response: NO, MMF

source_name: SLE, Patient 1463, visit2, response: NO, MMF


title: PT-00179840_NT_EA

source_name: Adjacent Tumor


title: Pat_1428_visit1_YES_response

description: Gene expression of Patient 1428, visit1, response: YES, HC

source_name: SLE, Patient 1428, visit1, response: YES, HC


title: Pat_1384_visit2_YES_response

description: Gene expression of Patient 1384, visit2, response: YES, HC

source_name: SLE, Patient 1384, visit2, response: YES, HC


title: Pat_1409_visit1_YES_response

description: Gene expression of Patient 1409, visit1, response: YES, MMF

source_name: SLE, Patient 1409, visit1, response: YES, MMF


title: Pat_1392_visit1_YES_response

description: Gene expression of Patient 1392, visit1, response: YES, HC

source_name: SLE, Patient 1392, visit1, response: YES, HC


title: Pat_1409_visit3_YES_response

description: Gene expression of Patient 1409, visit3, response: YES, MMF

source_name: SLE, Patient 1409, visit3, response: YES, MMF


title: PT-00190763_T_EA


title: Pat_1463_visit3_NO_response

description: Gene expression of Patient 1463, visit3, response: NO, MMF

source_name: SLE, Patient 1463, visit3, response: NO, MMF


title: Pat_1392_visit2_YES_response

description: Gene expression of Patient 1392, visit2, response: YES, HC

source_name: SLE, Patient 1392, visit2, response: YES, HC


title: Pat_1373_visit1_YES_response

description: Gene expression of Patient 1373, visit1, response: YES, HC

source_name: SLE, Patient 1373, visit1, response: YES, HC


title: Pat_1543_visit2_YES_response

description: Gene expression of Patient 1543, visit2, response: YES, HC

source_name: SLE, Patient 1543, visit2, response: YES, HC


title: Pat_1463_visit1_NO_response

description: Gene expression of Patient 1463, visit1, response: NO, MMF

source_name: SLE, Patient 1463, visit1, response: NO, MMF


title: Pat_1384_visit1_YES_response

description: Gene expression of Patient 1384, visit1, response: YES, HC

source_name: SLE, Patient 1384, visit1, response: YES, HC


title: PT-00177543_NT_EA


title: PT-00282384_NT_AA

value: AA


title: PT-00177543_T_EA

source_name: Tumor


title: Pat_1373_visit2_YES_response

description: Gene expression of Patient 1373, visit2, response: YES, HC

source_name: SLE, Patient 1373, visit2, response: YES, HC


title: PT-00191716_NT_EA


title: PT-00267366_T_AA


title: PT-00238051_T_AA


title: PT-00267366_NT_AA


title: PT-00282384_T_AA


title: PT-00238051_NT_AA


title: Pat_1369_visit2_YES_response

description: Gene expression of Patient 1369, visit2, response: YES, MMF

source_name: SLE, Patient 1369, visit2, response: YES, MMF


title: PT-00237623_T_AA


title: PT-00237623_NT_AA


title: Pat_1369_visit1_YES_response

description: Gene expression of Patient 1369, visit1, response: YES, MMF

source_name: SLE, Patient 1369, visit1, response: YES, MMF


title: Pat_1361_visit2_YES_response

description: Gene expression of Patient 1361, visit2, response: YES, HC

source_name: SLE, Patient 1361, visit2, response: YES, HC


title: PT-00236614_T_AA


title: Pat_1361_visit1_YES_response

description: Gene expression of Patient 1361, visit1, response: YES, HC

source_name: SLE, Patient 1361, visit1, response: YES, HC


title: Pat_1358_visit2_YES_response

description: Gene expression of Patient 1358, visit2, response: YES, HC

source_name: SLE, Patient 1358, visit2, response: YES, HC


title: Pat_1351_visit1_YES_response

description: Gene expression of Patient 1351, visit1, response: YES, AZA

source_name: SLE, Patient 1351, visit1, response: YES, AZA


title: PT-00236614_NT_AA

source_name: Adjacent Tumor


title: PT-00235411_T_AA


title: PT-00235411_NT_AA


title: Pat_1351_visit2_YES_response

description: Gene expression of Patient 1351, visit2, response: YES, AZA

source_name: SLE, Patient 1351, visit2, response: YES, AZA


title: Pat_1342_visit2_YES_response

description: Gene expression of Patient 1342, visit2, response: YES, HC

source_name: SLE, Patient 1342, visit2, response: YES, HC


title: PT-00229031_NT_AA


title: Pat_1342_visit1_YES_response

description: Gene expression of Patient 1342, visit1, response: YES, HC

source_name: SLE, Patient 1342, visit1, response: YES, HC


title: Pat_1337_visit2_YES_response

description: Gene expression of Patient 1337, visit2, response: YES, HC

source_name: SLE, Patient 1337, visit2, response: YES, HC


title: PT-00227158_T_AA


title: PT-00227158_NT_AA


title: Pat_1337_visit1_YES_response

description: Gene expression of Patient 1337, visit1, response: YES, HC

source_name: SLE, Patient 1337, visit1, response: YES, HC


title: PT-00220025_T_AA


title: PT-00224181_NT_AA


title: Pat_1358_visit1_YES_response

description: Gene expression of Patient 1358, visit1, response: YES, HC

source_name: SLE, Patient 1358, visit1, response: YES, HC


title: PT-00216463_T_AA


title: Pat_1336_visit2_YES_response

description: Gene expression of Patient 1336, visit2, response: YES, HC

source_name: SLE, Patient 1336, visit2, response: YES, HC


title: PT-00229031_T_AA


title: Pat_1336_visit1_YES_response

description: Gene expression of Patient 1336, visit1, response: YES, HC

source_name: SLE, Patient 1336, visit1, response: YES, HC


title: Pat_1335_visit5_YES_response

description: Gene expression of Patient 1335, visit5, response: YES, MMF

source_name: SLE, Patient 1335, visit5, response: YES, MMF


title: Pat_1335_visit4_YES_response

description: Gene expression of Patient 1335, visit4, response: YES, MMF

source_name: SLE, Patient 1335, visit4, response: YES, MMF


title: Pat_1335_visit3_YES_response

description: Gene expression of Patient 1335, visit3, response: YES, MMF

source_name: SLE, Patient 1335, visit3, response: YES, MMF


title: Pat_1335_visit2_YES_response

description: Gene expression of Patient 1335, visit2, response: YES, MMF

source_name: SLE, Patient 1335, visit2, response: YES, MMF


title: PT-00220025_NT_AA


title: Pat_1319_visit2_YES_response

description: Gene expression of Patient 1319, visit2, response: YES, PHC

source_name: SLE, Patient 1319, visit2, response: YES, PHC


title: Pat_1335_visit6_YES_response

description: Gene expression of Patient 1335, visit6, response: YES, MMF

source_name: SLE, Patient 1335, visit6, response: YES, MMF


title: Pat_1335_visit1_YES_response

description: Gene expression of Patient 1335, visit1, response: YES, MMF

source_name: SLE, Patient 1335, visit1, response: YES, MMF


title: Pat_1319_visit1_YES_response

description: Gene expression of Patient 1319, visit1, response: YES, PHC

source_name: SLE, Patient 1319, visit1, response: YES, PHC


title: Pat_1309_visit2_NO_response

description: Gene expression of Patient 1309, visit2, response: NO, PHC

source_name: SLE, Patient 1309, visit2, response: NO, PHC


title: PT-00224181_T_AA

source_name: Tumor


title: PT-00214541_T_AA


title: PT-00216417_NT_AA

source_name: Adjacent Tumor


title: PT-00214541_NT_AA


title: PT-00208975_T_AA


title: PT-00208975_NT_AA


title: PT-00201372_NT_AA


title: PT-00200672_NT_AA


title: Pat_1285_visit1_YES_response

description: Gene expression of Patient 1285, visit1, response: YES, HC

source_name: SLE, Patient 1285, visit1, response: YES, HC


title: Pat_1281_visit1_YES_response

description: Gene expression of Patient 1281, visit1, response: YES, PHC

source_name: SLE, Patient 1281, visit1, response: YES, PHC


title: Pat_1285_visit2_YES_response

description: Gene expression of Patient 1285, visit2, response: YES, HC

source_name: SLE, Patient 1285, visit2, response: YES, HC


title: Pat_1309_visit1_NO_response

description: Gene expression of Patient 1309, visit1, response: NO, PHC

source_name: SLE, Patient 1309, visit1, response: NO, PHC


title: PT-00216417_T_AA


title: Pat_1281_visit2_YES_response

description: Gene expression of Patient 1281, visit2, response: YES, PHC

source_name: SLE, Patient 1281, visit2, response: YES, PHC


title: Pat_1273_visit2_YES_response

description: Gene expression of Patient 1273, visit2, response: YES, MMF

source_name: SLE, Patient 1273, visit2, response: YES, MMF

value: Male


title: PT-00197746_T_AA


title: Pat_1269_visit3_NO_response

description: Gene expression of Patient 1269, visit3, response: NO, HC

source_name: SLE, Patient 1269, visit3, response: NO, HC


title: PT-00216463_NT_AA


title: PT-00197746_NT_AA


title: PT-00195907_NT_AA


title: PT-00195907_T_AA


title: PT-00195338_T_AA


title: PT-00201372_T_AA


title: PT-00195338_NT_AA


title: PT-00200672_T_AA


title: Pat_1269_visit2_NO_response

description: Gene expression of Patient 1269, visit2, response: NO, HC

source_name: SLE, Patient 1269, visit2, response: NO, HC


title: Pat_1261_visit2_YES_response

description: Gene expression of Patient 1261, visit2, response: YES, HC

source_name: SLE, Patient 1261, visit2, response: YES, HC

value: B


title: Pat_1269_visit1_NO_response

description: Gene expression of Patient 1269, visit1, response: NO, HC

source_name: SLE, Patient 1269, visit1, response: NO, HC


title: PT-00192088_T_AA


title: PT-00192088_NT_AA


title: Pat_1275_visit1_YES_response

description: Gene expression of Patient 1275, visit1, response: YES, HC

source_name: SLE, Patient 1275, visit1, response: YES, HC


title: Pat_1261_visit1_YES_response

description: Gene expression of Patient 1261, visit1, response: YES, HC

source_name: SLE, Patient 1261, visit1, response: YES, HC


title: Pat_1253_visit2_NO_response

description: Gene expression of Patient 1253, visit2, response: NO, AZA

source_name: SLE, Patient 1253, visit2, response: NO, AZA


title: Pat_1253_visit1_NO_response

description: Gene expression of Patient 1253, visit1, response: NO, AZA

source_name: SLE, Patient 1253, visit1, response: NO, AZA


title: Pat_1227_visit3_NO_response

description: Gene expression of Patient 1227, visit3, response: NO, MMF

source_name: SLE, Patient 1227, visit3, response: NO, MMF


title: PT-00190805_T_AA

source_name: Tumor


title: PT-00190362_T_AA


title: PT-00190805_NT_AA

source_name: Adjacent Tumor


title: Pat_1273_visit1_YES_response

description: Gene expression of Patient 1273, visit1, response: YES, MMF

source_name: SLE, Patient 1273, visit1, response: YES, MMF


title: Pat_1227_visit1_NO_response

description: Gene expression of Patient 1227, visit1, response: NO, MMF

source_name: SLE, Patient 1227, visit1, response: NO, MMF


title: Pat_1227_visit2_NO_response

description: Gene expression of Patient 1227, visit2, response: NO, MMF

source_name: SLE, Patient 1227, visit2, response: NO, MMF


title: Pat_1216_visit2_YES_response

description: Gene expression of Patient 1216, visit2, response: YES, HC

source_name: SLE, Patient 1216, visit2, response: YES, HC


title: PT-00195211_T_AA


title: PT-00190334_NT_AA


title: PT-00190362_NT_AA


title: PT-00190334_T_AA


title: PT-00189570_T_AA


title: Pat_1275_visit2_YES_response

description: Gene expression of Patient 1275, visit2, response: YES, HC

source_name: SLE, Patient 1275, visit2, response: YES, HC


title: PT-00189562_T_AA


title: Pat_1216_visit1_YES_response

description: Gene expression of Patient 1216, visit1, response: YES, HC

source_name: SLE, Patient 1216, visit1, response: YES, HC


title: Pat_1206_visit3_YES_response

description: Gene expression of Patient 1206, visit3, response: YES, MMF

source_name: SLE, Patient 1206, visit3, response: YES, MMF


title: Pat_1206_visit4_YES_response

description: Gene expression of Patient 1206, visit4, response: YES, MMF

source_name: SLE, Patient 1206, visit4, response: YES, MMF


title: Pat_1206_visit1_YES_response

description: Gene expression of Patient 1206, visit1, response: YES, MMF

source_name: SLE, Patient 1206, visit1, response: YES, MMF


title: Pat_1206_visit2_YES_response

description: Gene expression of Patient 1206, visit2, response: YES, MMF

source_name: SLE, Patient 1206, visit2, response: YES, MMF


title: Pat_1182_visit3_YES_response

description: Gene expression of Patient 1182, visit3, response: YES, HC

source_name: SLE, Patient 1182, visit3, response: YES, HC


title: Pat_1182_visit1_YES_response

description: Gene expression of Patient 1182, visit1, response: YES, HC

source_name: SLE, Patient 1182, visit1, response: YES, HC


title: PT-00187338_NT_AA


title: PT-00188738_T_AA


title: PT-00187338_T_AA


title: PT-00180319_T_AA


title: Pat_1179_visit3_YES_response

description: Gene expression of Patient 1179, visit3, response: YES, MMF

source_name: SLE, Patient 1179, visit3, response: YES, MMF


title: PT-00153875_T_AA


title: PT-00162955_T_AA


title: PT-00153875_NT_AA


title: PT-00162955_NT_AA


title: NCI-H1299 Cells, si-ZBTB11, rep 2

city: Beijing

first: Donglai

last: Wang

address: #5 Dong Dan San Tiao

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

data_processing:
The index of the reference genome (hg38) was built using HISAT2 v2.0.5, and paired-end clean reads were aligned to the reference genome using HISAT2 v2.0.5
FeatureCounts v1.5.0-p3 was used to count the read numbers mapped to each gene.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include read count values for each Sample

growth_protocol: NCI-H1299 cells were cultured in DMEM supplemented with 10% (vol/vol) FBS.

extract_protocol:
Trasfected NCI-H1299 cells were lysed by TRIzol® reagent, followed by RNA precipitation by isopropanol and ethanol sequentially. After air drying, the RNA pellet was redissolved in an appropriate volume of DNase/RNase-free H2O.
The sequencing libraries were generated using the NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, E7530L) following the manufacturer’s protocol.

treatment_protocol: NCI-H1299 was transfected with si-Ctr, si-ZBTB11 and si-SET oligo using Lipofectamine 3000 according to the manufacurer`s protocol.

tag: cell line

value: Human lung adenocarcinoma

value: ZBTB11 knockdown

value: si-ZBTB11 treatment


title: NCI-H1299 Cells, si-SET, rep 2

value: SET knockdown

value: si-SET treatment


title: PT-00180319_NT_AA

value: prostate


title: NCI-H1299 Cells, si-ZBTB11, rep 1


title: NCI-H1299 Cells, si-SET, rep 1


title: Pat_1176_visit6_YES_response

description: Gene expression of Patient 1176, visit6, response: YES, PHC

source_name: SLE, Patient 1176, visit6, response: YES, PHC

value: Whole Blood

value: SLE

value: PHC

value: YES


title: Pat_1176_visit4_YES_response

description: Gene expression of Patient 1176, visit4, response: YES, PHC

source_name: SLE, Patient 1176, visit4, response: YES, PHC

value: Female


title: Pat_1179_visit1_YES_response

description: Gene expression of Patient 1179, visit1, response: YES, MMF

source_name: SLE, Patient 1179, visit1, response: YES, MMF

value: MMF


title: Pat_1176_visit3_YES_response

description: Gene expression of Patient 1176, visit3, response: YES, PHC

source_name: SLE, Patient 1176, visit3, response: YES, PHC


title: NCI-H1299 Cells, si-Ctr, rep 2

value: WT

value: si-Ctr treatment


title: Pat_1176_visit2_YES_response

description: Gene expression of Patient 1176, visit2, response: YES, PHC

source_name: SLE, Patient 1176, visit2, response: YES, PHC


title: Pat_1179_visit2_YES_response

description: Gene expression of Patient 1179, visit2, response: YES, MMF

source_name: SLE, Patient 1179, visit2, response: YES, MMF


title: Pat_1176_visit5_YES_response

description: Gene expression of Patient 1176, visit5, response: YES, PHC

source_name: SLE, Patient 1176, visit5, response: YES, PHC


title: Pat_1176_visit1_YES_response

description: Gene expression of Patient 1176, visit1, response: YES, PHC

source_name: SLE, Patient 1176, visit1, response: YES, PHC


title: Pat_1174_visit3_YES_response

description: Gene expression of Patient 1174, visit3, response: YES, MMF

source_name: SLE, Patient 1174, visit3, response: YES, MMF


title: Pat_1174_visit2_YES_response

description: Gene expression of Patient 1174, visit2, response: YES, MMF

source_name: SLE, Patient 1174, visit2, response: YES, MMF


title: Pat_1162_visit2_YES_response

description: Gene expression of Patient 1162, visit2, response: YES, HC

source_name: SLE, Patient 1162, visit2, response: YES, HC

value: HC


title: NCI-H1299 Cells, si-Ctr, rep 1


title: ZR-75-1_DHT_passage_2

source_name: ZR-75-1 breast cancer cell line

growth_protocol: Cells were grown in hormone-deplete conditions (phenol red-free RPMI-1640 + 5% dextran-coated charcoal-stripped FBS) for 72h

extract_protocol:
Total RNA was extracted using Zymo Direct-Zol RNA kit, according to the manufacturer's instructions.
Libraries were generated using the TruSeq Stranded Total RNA HT Library Prep Kit
Total RNA-Seq; Illumina HiSeq 2500 single-end 40 bp reads

value: DHT


title: ZR-75-1_DHT_passage_3


title: Pat_1174_visit1_YES_response

description: Gene expression of Patient 1174, visit1, response: YES, MMF

source_name: SLE, Patient 1174, visit1, response: YES, MMF

value: B


title: Pat_1162_visit1_YES_response

description: Gene expression of Patient 1162, visit1, response: YES, HC

source_name: SLE, Patient 1162, visit1, response: YES, HC


title: ZR-75-1_DHT_passage_1


title: ZR-75-1_Veh_passage_4

value: Veh


title: ZR-75-1_DHT_passage_4


title: ZR-75-1_Veh_passage_3


title: ZR-75-1_Veh_passage_2


title: Pat_1182_visit2_YES_response

description: Gene expression of Patient 1182, visit2, response: YES, HC

source_name: SLE, Patient 1182, visit2, response: YES, HC

value: W


title: T-47D_DHT_passage_4

source_name: T-47D breast cancer cell line


title: ZR-75-1_Veh_passage_1


title: Pat_1161_visit2_YES_response

description: Gene expression of Patient 1161, visit2, response: YES, HC

source_name: SLE, Patient 1161, visit2, response: YES, HC

value: O


title: T-47D_DHT_passage_3


title: Pat_1161_visit1_YES_response

description: Gene expression of Patient 1161, visit1, response: YES, HC

source_name: SLE, Patient 1161, visit1, response: YES, HC


title: Pat_1135_visit2_YES_response

description: Gene expression of Patient 1135, visit2, response: YES, AZA

source_name: SLE, Patient 1135, visit2, response: YES, AZA

value: AZA


title: Pat_1107_visit2_YES_response

description: Gene expression of Patient 1107, visit2, response: YES, MMF

source_name: SLE, Patient 1107, visit2, response: YES, MMF


title: Pat_1135_visit1_YES_response

description: Gene expression of Patient 1135, visit1, response: YES, AZA

source_name: SLE, Patient 1135, visit1, response: YES, AZA


title: Pat_1161_visit3_YES_response

description: Gene expression of Patient 1161, visit3, response: YES, HC

source_name: SLE, Patient 1161, visit3, response: YES, HC


title: Pat_1135_visit3_YES_response

description: Gene expression of Patient 1135, visit3, response: YES, AZA

source_name: SLE, Patient 1135, visit3, response: YES, AZA


title: Pat_1105_visit2_YES_response

description: Gene expression of Patient 1105, visit2, response: YES, HC

source_name: SLE, Patient 1105, visit2, response: YES, HC


title: T-47D_DHT_passage_1


title: Pat_1107_visit1_YES_response

description: Gene expression of Patient 1107, visit1, response: YES, MMF

source_name: SLE, Patient 1107, visit1, response: YES, MMF


title: Pat_1101_visit2_NO_response

description: Gene expression of Patient 1101, visit2, response: NO, MMF

source_name: SLE, Patient 1101, visit2, response: NO, MMF

value: NO


title: Pat_1105_visit1_YES_response

description: Gene expression of Patient 1105, visit1, response: YES, HC

source_name: SLE, Patient 1105, visit1, response: YES, HC


title: T-47D_Veh_passage_3


title: T-47D_Veh_passage_4


title: Pat_1093_visit3_YES_response

description: Gene expression of Patient 1093, visit3, response: YES, HC

source_name: SLE, Patient 1093, visit3, response: YES, HC


title: T-47D_Veh_passage_2


title: T-47D_Veh_passage_1


title: T-47D_DHT_passage_2


title: Pat_1093_visit2_YES_response

description: Gene expression of Patient 1093, visit2, response: YES, HC

source_name: SLE, Patient 1093, visit2, response: YES, HC


title: L56_V0_CD4_EM

city: Zurich

first: Hubert

last: Rehrauer

address: Winterthurerstr. 190

department: FGCZ

country: Switzerland

institute: ETH Zurich / University of Zurich

data_processing:
Basecalls performed using illumina's bcl2fastq.
Sequenced reads were trimmed for adaptor sequence, low complexity and low quality sequences. Then reads were aligned to Ensembl GRCh37.p13 genome assembly using RSEM 1.2.22 with following parameters: --calc-ci
Genome_build: GRCh37.p13
Supplementary_files_format_and_content: tab-delimited text files include raw counts values for each sample.

source_name: effector memory T cells

growth_protocol: CD14+ monocytes and effector memory T cells collected from PBMC

extract_protocol: Illumina TruSeq RNA

tag: condition

value: Before Fingolimod therapy


title: L50_V0_CD4_EM


title: L56_V9_CD4_EM

value: After Fingolimod therapy


title: L50_V9_CD4_EM


title: L46_V9_CD4_EM


title: L46_V0_CD4_EM


title: L43_V9_CD4_EM


title: Pat_1093_visit1_YES_response

description: Gene expression of Patient 1093, visit1, response: YES, HC

source_name: SLE, Patient 1093, visit1, response: YES, HC

value: Whole Blood

value: SLE


title: L43_V0_CD4_EM


title: Pat_1077_visit2_NO_response

description: Gene expression of Patient 1077, visit2, response: NO, MMF

source_name: SLE, Patient 1077, visit2, response: NO, MMF

value: Male


title: Pat_1077_visit1_NO_response

description: Gene expression of Patient 1077, visit1, response: NO, MMF

source_name: SLE, Patient 1077, visit1, response: NO, MMF


title: Pat_1053_visit2_NO_response

description: Gene expression of Patient 1053, visit2, response: NO, PHC

source_name: SLE, Patient 1053, visit2, response: NO, PHC

value: Female

value: PHC


title: Pat_1075_visit2_YES_response

description: Gene expression of Patient 1075, visit2, response: YES, AZA

source_name: SLE, Patient 1075, visit2, response: YES, AZA

value: YES


title: L41_V9_CD4_EM


title: Pat_1052_visit4_YES_response

description: Gene expression of Patient 1052, visit4, response: YES, HC

source_name: SLE, Patient 1052, visit4, response: YES, HC


title: Pat_1101_visit1_NO_response

description: Gene expression of Patient 1101, visit1, response: NO, MMF

source_name: SLE, Patient 1101, visit1, response: NO, MMF

value: MMF


title: Pat_1052_visit2_YES_response

description: Gene expression of Patient 1052, visit2, response: YES, HC

source_name: SLE, Patient 1052, visit2, response: YES, HC

value: HC


title: Pat_1052_visit3_YES_response

description: Gene expression of Patient 1052, visit3, response: YES, HC

source_name: SLE, Patient 1052, visit3, response: YES, HC


title: Pat_1075_visit1_YES_response

description: Gene expression of Patient 1075, visit1, response: YES, AZA

source_name: SLE, Patient 1075, visit1, response: YES, AZA


title: L36_V9_CD4_EM


title: Pat_1053_visit1_NO_response

description: Gene expression of Patient 1053, visit1, response: NO, PHC

source_name: SLE, Patient 1053, visit1, response: NO, PHC


title: Pat_1052_visit5_YES_response

description: Gene expression of Patient 1052, visit5, response: YES, HC

source_name: SLE, Patient 1052, visit5, response: YES, HC


title: L56_MONOS_V0

source_name: monocytes


title: L36_V0_CD4_EM


title: L50_MONOS_V9


title: Pat_1052_visit1_YES_response

description: Gene expression of Patient 1052, visit1, response: YES, HC

source_name: SLE, Patient 1052, visit1, response: YES, HC


title: L41_V0_CD4_EM


title: L56_MONOS_V9


title: L46_MONOS_V9


title: L46_MONOS_V0


title: L43_MONOS_V9


title: Pat_1049_visit2_YES_response

description: Gene expression of Patient 1049, visit2, response: YES, HC

source_name: SLE, Patient 1049, visit2, response: YES, HC


title: Pat_1049_visit1_YES_response

description: Gene expression of Patient 1049, visit1, response: YES, HC

source_name: SLE, Patient 1049, visit1, response: YES, HC


title: Pat_1037_visit1_YES_response

description: Gene expression of Patient 1037, visit1, response: YES, HC

source_name: SLE, Patient 1037, visit1, response: YES, HC


title: L43_MONOS_V0


title: Pat_1042_visit1_YES_response

description: Gene expression of Patient 1042, visit1, response: YES, HC

source_name: SLE, Patient 1042, visit1, response: YES, HC


title: Pat_1050_visit2_NO_response

description: Gene expression of Patient 1050, visit2, response: NO, PHC

source_name: SLE, Patient 1050, visit2, response: NO, PHC


title: Pat_1037_visit2_YES_response

description: Gene expression of Patient 1037, visit2, response: YES, HC

source_name: SLE, Patient 1037, visit2, response: YES, HC


title: Pat_1050_visit1_NO_response

description: Gene expression of Patient 1050, visit1, response: NO, PHC

source_name: SLE, Patient 1050, visit1, response: NO, PHC


title: Pat_1042_visit2_YES_response

description: Gene expression of Patient 1042, visit2, response: YES, HC

source_name: SLE, Patient 1042, visit2, response: YES, HC


title: L41_MONOS_V0


title: L50_MONOS_V0


title: L41_MONOS_V9


title: Pat_1034_visit2_NO_response

description: Gene expression of Patient 1034, visit2, response: NO, HC

source_name: SLE, Patient 1034, visit2, response: NO, HC


title: L36_MONOS_V9


title: Pat_1007_visit2_YES_response

description: Gene expression of Patient 1007, visit2, response: YES, HC

source_name: SLE, Patient 1007, visit2, response: YES, HC


title: Pat_1007_visit1_YES_response

description: Gene expression of Patient 1007, visit1, response: YES, HC

source_name: SLE, Patient 1007, visit1, response: YES, HC


title: Pat_1005_visit2_YES_response

description: Gene expression of Patient 1005, visit2, response: YES, PHC

source_name: SLE, Patient 1005, visit2, response: YES, PHC


title: RGI5_Rap3

city: Gwangju

first: Jungmook

last: Kim

address: 77, yongbong-ro

department: Bioenergy science and technology

country: South Korea

institute: Chonnam national university

description: 100 nM of rapamycin

data_processing:
The quantification of transcript expression was performed using Salmon
Differential expression analysis was performed using DESeq2
Genome_build: Araport11
Supplementary_files_format_and_content: abundance measurements

organism: Arabidopsis thaliana

growth_protocol: Seedlings were grown for 7 days after germination.

extract_protocol:
Total RNA from each samples was isolated using an RNeasy Plant Mini Kit (Qiagen, Japan)
The isolated total RNA was processed for preparing mRNA sequencing library using the Illumina TruSeq Stranded mRNA Sample preparation kit (Illumina) accoding to the manufacturer’s protocol.

treatment_protocol: Each plant was transferred on a filter paper containing 1/2 MS solution with mock, 100 nM rapamycin (RiD-RGI5/BAK1) or 1 µM rapamycin (RiD-RGI1/BAK1) and incubated for 4 hours with gentle shaking in light at 23°C. WT plants were treated with 100 nM RGF1 peptide for 4 hours.

tag: ecotype

value: root from 7-day-old-germination

tag: agent

value: 100 nM of rapamycin


title: RGI5_Rap2

description: 100 nM of rapamycin


title: L36_MONOS_V0


title: RGI5_DMSO4

description: mock

value: mock


title: RGI5_DMSO2

description: mock


title: Pat_981_visit3_NO_response

description: Gene expression of Patient 981, visit3, response: NO, PHC

source_name: SLE, Patient 981, visit3, response: NO, PHC

value: W


title: Pat_1005_visit1_YES_response

description: Gene expression of Patient 1005, visit1, response: YES, PHC

source_name: SLE, Patient 1005, visit1, response: YES, PHC


title: col5_Rap4

description: 100 nM of rapamycin

value: WT


title: RGI5_DMSO1

description: mock


title: RGI5_Rap1

description: 100 nM of rapamycin


title: Pat_959_visit2_YES_response

description: Gene expression of Patient 959, visit2, response: YES, PHC

source_name: SLE, Patient 959, visit2, response: YES, PHC

value: B


title: Pat_981_visit1_NO_response

description: Gene expression of Patient 981, visit1, response: NO, PHC

source_name: SLE, Patient 981, visit1, response: NO, PHC

value: NO


title: Pat_981_visit2_NO_response

description: Gene expression of Patient 981, visit2, response: NO, PHC

source_name: SLE, Patient 981, visit2, response: NO, PHC


title: col5_Rap3

description: 100 nM of rapamycin


title: col5_DMSO4

description: mock


title: col5_Rap2

description: 100 nM of rapamycin


title: col5_DMSO3

description: mock


title: Pat_959_visit1_YES_response

description: Gene expression of Patient 959, visit1, response: YES, PHC

source_name: SLE, Patient 959, visit1, response: YES, PHC


title: Pat_958_visit1_YES_response

description: Gene expression of Patient 958, visit1, response: YES, MMF

source_name: SLE, Patient 958, visit1, response: YES, MMF


title: RGI1_Rap3

description: 1 μM of rapamycin

value: 1 microM of rapamycin


title: RGI1_Rap2

description: 1 μM of rapamycin


title: Pat_965_visit2_YES_response

description: Gene expression of Patient 965, visit2, response: YES, HC

source_name: SLE, Patient 965, visit2, response: YES, HC


title: Pat_958_visit2_YES_response

description: Gene expression of Patient 958, visit2, response: YES, MMF

source_name: SLE, Patient 958, visit2, response: YES, MMF


title: Pat_954_visit2_YES_response

description: Gene expression of Patient 954, visit2, response: YES, HC

source_name: SLE, Patient 954, visit2, response: YES, HC


title: RGI1_Rap1

description: 1 μM of rapamycin


title: col5_DMSO2

description: mock


title: Pat_903_visit3_YES_response

description: Gene expression of Patient 903, visit3, response: YES, HC

source_name: SLE, Patient 903, visit3, response: YES, HC


title: Pat_954_visit1_YES_response

description: Gene expression of Patient 954, visit1, response: YES, HC

source_name: SLE, Patient 954, visit1, response: YES, HC


title: Pat_946_visit2_NO_response

description: Gene expression of Patient 946, visit2, response: NO, MMF

source_name: SLE, Patient 946, visit2, response: NO, MMF

value: A