title: Bcl-xAS-transfected 786-O cells_replicate 4_Cy3 vs. Control empty vector-transfected 786-O cells_replicate 4_Cy5

description:
Bcl-xAS_rep4_Cy3/Ctl_rep4_Cy5
Bcl-xAS-transfected 786-O cells, biological replicate 4 of 4, Cy3 labelled vs. empty vector-transfected 786-O cells, biological replicate 4 of 4, Cy5 labelled.


title: X6_G9

status: Public on Mar 02 2021

type: SRA

city: Dresden

first: Gerd

last: Kempermann

state: Saxony

address: Tatzberg 41

country: Germany

institute: German Center for Neurodegenerative Diseases (DZNE)

library_source: transcriptomic

data_processing:
Quality control with FASTQC
Data were demultiplexed using bcl2fastq2 v2.20 and aligned to the mouse reference transcriptome mm10 using kallisto v0.44.0 with default parameters.
Transcript levels were quantified as transcripts per million reads (TPM) and then summarized to the gene level.
Cells with fewer than 10 reads for at least  500 genes were removed from further analysis.
The pagoda2 package was used for variance normalisation (gam.k = 10), identification of cell clusters (PCA: nPcs = 100,  n.odgenes = 3e3; k-nearest neighbor: k = 50, perplexity = 30, min.group.size = 10) and t-distributed stochastic neighbor embedding (t-SNE). Log-transformed normalised gene expression values were then exported from pagoda2 for further analyses.
Genome_build: mm10
Supplementary_files_format_and_content: tsv: tab-delimited transcript abundances; csv: matrix of normalised and log-transformed expression values summarised by gene.

molecule: total RNA

organism: Mus musculus

source_name: WT_dentate gyrus; adult-born neural precursor cell_T1

growth_protocol: Mice were housed in standard polycarbonate cages (Type II, Tecniplast) and maintained on a 12 h light/dark cycle. Food and water were provided ad libitum.

extract_protocol:
Single cells from dissociated hippocampus tissue were sorted by fluorescence cell cytometry and collected into a 384-well plates pre-loaded with 2.3 µl lysis buffer (50 mM guanidine hydrochloride, 17.4 mM dNTPs, 2.2 µM SMART dT30VN primer).
Smart-Seq2 libraries were generated using Tecan Freedom EVO and Nanodrop II (Bionex) systems.

tag: genotype

value: WT

tag: animal id

tag: tissue/cell type

tag: cell type


title: cast_x_B6_1xE3_5_bla_3

city: Vienna

first: Martin

last: Leeb

address: Dr.-Bohr-Gasse 9/3

department: Max Perutz Labs

country: Austria

institute: University of Vienna

data_processing:
Reads were aligned using STAR (version 2.5.2b)
Mapped reads of different lanes were merged and sorted using samtools (version 1.9-92)
The Allelome.Pro pipeline was used to retrieve strain specific counts from intermediate results
Mapped reads were converted to bedgraphs using the genomecov function from bedtools (version: v2.28.0-33-g0f45761)
Bedgraphs were converted to bigwig files using the bedGraphToBigWig function from UCSC
Genome_build: mm10
Supplementary_files_format_and_content: CSV (strain specific reads for each sample from forward and reverse cross)

molecule: polyA RNA

source_name: E3.5 blastocyst reverse cross (cast x B6)

extract_protocol:
Single E3.5 blastocysts were derived from Mus musculus musculus C57BL/6 (B6) x Mus musculus castaneus (cast) reciprocal natural matings and directly lysed for RNA extraction without in vitro culture.
SMART-Seq2


title: Bcl-xAS-transfected 786-O cells_replicate 3_Cy3 vs. Control empty vector-transfected 786-O cells_replicate 3_Cy5

type: RNA

city: New York

first: Angela

middle: A.

last: Fachel

state: New York

address: 1300 York Ave

country: USA

institute: Weill Cornell Medicine

description:
Bcl-xAS_rep3_Cy3/Ctl_rep3_Cy5
Bcl-xAS-transfected 786-O cells, biological replicate 3 of 4, Cy3 labelled vs. empty vector-transfected 786-O cells, biological replicate 3 of 4, Cy5 labelled.

hyb_protocol: 300 ng of cRNA was hybridized following the Agilent Two-color Low Input Quick Amp Labeling Protocol Version 6.5.

scan_protocol: Scanned on an Agilent G2565CA Microarray Scanner System.

data_processing: Linear and lowess-normalized data (Processed Signal Column by Feature Extractor Agilent Software v.10.7.1.1) was transformed to log2 ratios for test/reference samples.

organism: Homo sapiens

label_protocol: 200 ng of total RNA was labelled following the Agilent Two-color Low Input Quick Amp Labeling Protocol Version 6.5.

growth_protocol: 786-O cells were cultivated in 147.8 cm2 cell culture plates with Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% FBS. To perform four biological replicates, we cultivated four plates in parallel.

extract_protocol: Total RNA was extracted with Trizol reagent following the manufacturer's instructions. Total RNA was DNase-I-treated and purified using the Illustra RNAspin Mini kit (GE Healthcare) following the manufacturer's instructions.

treatment_protocol: Cells were transfected with 6 μg of Bcl-xAS expression construct or with 6 μg of empty vector (pCEP) as control using 3:1 FuGENE HD reagent (Promega). At 24 h after transfection, total RNA was extracted.

tag: cell line

tag: original tissue

value: clear cell renal cell cancer (CCRCC)

tag: transfection

value: control

source_name: Bcl-xAS-transfected 786-O cells

value: Bcl-xAS


title: Bcl-xAS-transfected 786-O cells_replicate 1_Cy3 vs. Control empty vector-transfected 786-O cells_replicate 1_Cy5

description:
Bcl-xAS_rep1_Cy3/Ctl_rep1_Cy5
Bcl-xAS-transfected 786-O cells, biological replicate 1 of 4, Cy3 labelled vs. empty vector-transfected 786-O cells, biological replicate 1 of 4, Cy5 labelled.


title: PHH_D6_HCV6h

city: Hannover

first: Birthe

middle: Maren

last: Tegtmeyer

address: Feodor-Lynen-Str. 7

institute: TWINCORE - Centre for Experimental and Clinical Infection Research

description:
BT20_3
6hpi NI vs. Jc1 Expression Browser

data_processing:
Transcriptomic analyses were performed using CLC Genomics Workbench (Qiagen, Aarhaus)
Generated Fastq files were mapped against the hg38 human reference genome with annotated gene and mRNA tracks.
Gene expression was calculated for individual transcripts as reads per kilobase per million bases mapped (RPKM).
Genome_build: hg38
Supplementary_files_format_and_content: xlsx documents include total counts & RPKM values for each gene and each condition and additionally, fold change and statistical values

source_name: hepatocytes

extract_protocol:
Cells were either lysed in 350 μl RA1 buffer supplemented with β-mercaptoethanol (Macherey-Nagel) or in 1 ml Trizol reagent (Invitrogen) (PHH D1-3 samples) and lysates stored at -80°C until processing. We extracted the total RNA and DNA according to the manufacturer's instructions.
RNA sequencing library generated with ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre, Illumina)

tag: hcv

value: infected

tag: phh donor

tag: time

value: 6 hours


title: X6_B9

value: dentate gyrus; adult-born neural precursor cell


title: cast_x_B6_1xE3_5_bla_2

value: E3.5 blastocyst reverse cross (cast x B6)


title: PHH_D6_UV6h

description:
BT20_2
6hpi NI vs. UV Expression Browser

value: UV-inactivated HCV control


title: PHH_D6_mock6h

description:
BT20_1
6hpi NI vs. Jc1 Expression Browser
6hpi NI vs. UV Expression Browser

value: mock control, conditioned medium


title: cast_x_B6_1xE3_5_bla_1


title: X6_M8

source_name: WT_dentate gyrus; adult-born neural precursor cell_T4


title: PHH_D5_HCV72h

description:
BT48
72hpi NI vs. Jc1 Expression Browser
Canonical pathways PHH 72hpi
Upstream regulators_PHH 72hpi NI vs Jc1_List

value: 72 hours


title: X6_L8


title: SPERM2

city: Shanghai

first: Zhen

last: Liu

state: Shanghai

address: 320 Yue-Yang Rd

department: Center for Excellence in Brain Science and Intelligence Technology (CEBSIT)

country: China

institute: Institute of Neuroscience (ION), Chinese Academy of Sciences

library_source: genomic

data_processing:
Illumina Hiseq 2000 used for basecalling.
Quality control. Read sequences produced by the Illumina pipeline in FastQ format were first pre-processed through in-house perl scripts. Firstly, as a subset of reads contained all of part of the 3 adapter oligonucleotide sequence, every read was scanned for the adapter sequence, and if detected the read was filtered out. Secondly, since some reads had unknown base in their sequences, the percentage of Ns in each read was calculated, and if the percentage of Ns was larger than 10% the read was removed. Thirdly, reads with low quality (PHRED score <= 5, and percentage of the low quality bases >= 50%) were trimmed. At the same time, Q20, Q30 and GC  content of the data were calculated. The remaining reads that passed the filters were called as clean reads and all of the subsequent analyses were based on them.
Reads mapping to the reference genome. Bismark software (version 0.12.5; Krueger F, 2011) was used to perform alignments of bisulfite-treated reads to a reference genome with the default parameters. The reference genome was firstly transformed into bisulfite-converted version (C-to-T and G-to- A converted) and then indexed using bowtie2 (Langmead B, 2012).
Genome_build: Macaca_fascicularis_5.0
Supplementary_files_format_and_content: bigWig files were generated for earch sample  by deepTools 3.5.0 (bamCoverage)

molecule: genomic DNA

organism: Macaca fascicularis

source_name: sperm

extract_protocol:
A total amount of 5.2 microgram genomic DNA spiked with 26 ng lambda DNA were fragmented by sonication to 200-300bp with Covaris S220, followed by end repair and adenylation. Cytosine-methylated barcodes were ligated to sonicated DNA as per manufacturer s instructions. Then these DNA fragments were treated twice with bisulfite using EZ DNA Methylation-GoldTMKit (Zymo Research). And the resulting single-strand DNA fragments were PCR amplificated using KAPA HiFi HotStart Uracil + ReadyMix (2X). Library concentration was quantified by Qubit 2.0 Flurometer (Life Technologies, CA, USA) and quantitative PCR, and the insert size was checked on Agilent Bioanalyzer 2100 system.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq 2000/2500 platform.

tag: tissue

value: sperm

value: naturally-matured monkey (#2)


title: SPERM49

value: sexual precocious monkey (#49)


title: X6_J8


title: B6_x_cast_1xE3_5_bla_3

source_name: E3.5 blastocyst forward cross (B6 x cast)


title: PHH_D5_UV72h

description:
BT47
72hpi NI vs. UV Expression Browser


title: X6_I8


title: B6_x_cast_1xE3_5_bla_2

value: E3.5 blastocyst forward cross (B6 x cast)


title: PHH_D5_mock72h

description:
BT46
72hpi NI vs. Jc1 Expression Browser
72hpi NI vs. UV Expression Browser
Canonical pathways PHH 72hpi
Upstream regulators_PHH 72hpi NI vs Jc1_List


title: X6_F8

source_name: WT_dentate gyrus; adult-born neural precursor cell_T1b


title: X6_A8


title: PHH_D5_HCV6h

description:
BT45
6hpi NI vs. Jc1 Expression Browser


title: B6_x_cast_1xE3_5_bla_1


title: X6_O7


title: PHH_D5_UV6h

description:
BT44
6hpi NI vs. UV Expression Browser


title: PHH_D4_HCV72h

description:
BT42
72hpi NI vs. Jc1 Expression Browser
Canonical pathways PHH 72hpi
Upstream regulators_PHH 72hpi NI vs Jc1_List


title: X6_M7


title: genomic DNA from brochoscopic biopsy sample [P11130085_Lu]

type: genomic

city: Ulm

first: Ole

last: Ammerpohl

address: Albert-Einstein-Allee 11

institute: UK Ulm

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using iScan Reader using standard recommended Illumina scanner setting

data_processing:
GenomeStudio software V2011.1
The MatrixProcessed_PB3.txt contains Average Beta; GenomeStudio was used for data normalization ("normalization based on internal controls").
The MatrixSignal_PB3.txt contains Unmethylated and methylated signal intensities

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from bronchoscopic biopsie samples using Qiagen DNeasy Kit according to standard instructions

tag: donor id

tag: histology (diagnosis by pathologists based on one single specimen)

value: control, no malignant cells, diagnosis definite

tag: diagnosis (final clinical diagnosis for the patient)

value: squamous cell carcinoma

value: brochoscopic biopsy sample


title: genomic DNA from brochoscopic biopsy sample [P12130087_L]

value: probably benign, diagnosis not definite

value: adenocarcinoma


title: PHH_D4_mock72h

description:
BT40
72hpi NI vs. Jc1 Expression Browser
72hpi NI vs. UV Expression Browser
Canonical pathways PHH 72hpi
Upstream regulators_PHH 72hpi NI vs Jc1_List


title: genomic DNA from brochoscopic biopsy sample [P12130087_T]

value: probably tumor sample,  diagnosis not definite


title: PHH_D4_UV72h

description:
BT41
72hpi NI vs. UV Expression Browser


title: X6_L7

value: WT


title: X6_K7


title: PKR2 overexpressing heart [12wk_TG2_392.4]

city: Nantes

first: Marja

last: Steenman

address: 8 quai Moncousu

country: France

institute: L'institut du thorax

hyb_protocol: 1650 ng of Cy3-labeled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 55 µl of 2x Agilent Hi-RPM hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Microarrays (G4122F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent). Next, microarrays were washed 30 seconds in acetonitrile and 30 seconds in Stabilization and Drying Solution.

scan_protocol: Slides were scanned immediately after washing on the Agilent G2565CA Microarray Scanner using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1-v5_95_Feb07 and Grid: 014868_D_20070820) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Data were normalized using R statistical software. Raw values of all probes on all arrays were normalized against a virtual median chip (median raw intensity per row) using a locally weighted scattered plot smoother analysis (LOWESS). Values for replicate probes were averaged. The data were filtered to 20,000 probes to remove probes with low intensity values.

source_name: heart from 12wk old mice overexpressing PKR2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the Low Input QuickAmp Labeling Kit One-Color (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted using Tri-Reagent. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was assessed using an Agilent 2100 Bioanalyzer.

tag: genotype/variation

value: PKR2 overexpression

value: heart

tag: gender

value: male

tag: age

value: 12 weeks


title: PHH_D4_HCV6h

description:
BT39
6hpi NI vs. Jc1 Expression Browser

value: infected

value: 6 hours


title: PKR2 overexpressing heart [12wk_TG2_332.4]


title: PKR2 overexpressing heart [12wk_TG2_331.4]


title: WT heart [12wk_WT_392.2]

source_name: heart from 12wk old WT mice


title: WT heart [12wk_WT_333.3]


title: PKR2 overexpressing heart [12wk_TG2_333.4]


title: WT heart [12wk_WT_330.3]


title: genomic DNA from brochoscopic biopsy sample [P11130085_Tu]

value: tumor sample, diagnosis definite


title: Bcl-xAS-transfected 786-O cells_replicate 1_Cy5 vs. Control empty vector-transfected 786-O cells_replicate 1_Cy3

description:
Bcl-xAS_rep1_Cy5/Ctl_rep1_Cy3
Bcl-xAS-transfected 786-O cells, biological replicate 1 of 4, Cy5 labelled vs. empty vector-transfected 786-O cells, biological replicate 1 of 4, Cy3 labelled.

value: clear cell renal cell cancer (CCRCC)

value: Bcl-xAS

value: control


title: X6_J7

tag: genotype

value: dentate gyrus; adult-born neural precursor cell


title: PHH_D4_UV6h

description:
BT38
6hpi NI vs. UV Expression Browser

value: UV-inactivated HCV control


title: WT heart [12wk_WT_329.4]


title: X6_H7

tag: animal id


title: genomic DNA from brochoscopic biopsy sample [P11130083_T]

value: squamous cell carcinoma

value: brochoscopic biopsy sample


title: X6_E7

tag: tissue/cell type


title: PHH_D4_mock6h

description:
BT37
6hpi NI vs. Jc1 Expression Browser
6hpi NI vs. UV Expression Browser

value: mock control, conditioned medium


title: genomic DNA from brochoscopic biopsy sample [P11130083_L]

value: control, no malignant cells, diagnosis definite


title: X6_N7

value: WT

tag: cell type


title: PHH_D5_mock6h

description:
BT43
6hpi NI vs. Jc1 Expression Browser
6hpi NI vs. UV Expression Browser


title: PHH_D3_HCV72h [re-analyzed GSM3874414]

description:
GSM3874414
HCVJc1MOI1_E269-RNA7_R1
72hpi NI vs. Jc1 Expression Browser
Canonical pathways PHH 72hpi
Upstream regulators_PHH 72hpi NI vs Jc1_List

value: 72 hours


title: X6_C7


title: genomic DNA from brochoscopic biopsy sample [P11130082_L]

value: small cell carcinoma


title: PHH_D3_mock72h [re-analyzed GSM3874413]

description:
GSM3874413
Mockinfection_E269-RNA8_R1
72hpi NI vs. Jc1 Expression Browser
Canonical pathways PHH 72hpi
Upstream regulators_PHH 72hpi NI vs Jc1_List


title: genomic DNA from brochoscopic biopsy sample [P11130082_T]


title: PHH_D3_HCV6h [re-analyzed GSM3874412]

description:
GSM3874412
HCVJc1MOI1_E269-RNA4_R1
6hpi NI vs. Jc1 Expression Browser


title: X6_B7


title: B-CPAP cells, shLDHA_2

city: Tianjin

first: Xiukun

last: Hou

address: Huanhu Road

institute: Tianjin Cancer Institute and Hospital

data_processing:
Illumina RTA software used for image identification and basecalling.
Adaptor sequence and low-quality sequence were trimmed by Trim Galore, then sequence reads were mapped to hg38 genome using Hisat2 with default parameters.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg38
Supplementary_files_format_and_content: Raw_count.xlsx

source_name: B-CPAP cells

extract_protocol:
Total RNA was extracted with Trizon Reagen (CWBIO) and was subjected to DNase Ｉ(Thermo Scientific) for 30min
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol (VAHTS mRNA-seq V2 Library Prep Kit for Illumina). The mRNA fragmentation and priming was performed using VAHTSFirst Strand Synthesis Reaction Buffer and VAHTS Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double-stranded cDNA（byAxyPrep Mag PCR Clean-up (Axygen)was then treated with End Prep Enzyme Mix to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using AxyPrep Mag PCR Clean-up (Axygen), and fragments of ~360 bp (with the approximate insert size of 300 bp) were recovered. Each sample was then amplified by PCR for 11 cycles using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six-base index allowing for multiplexing. The PCR products were cleaned up using AxyPrep Mag PCR Clean-up (Axygen), validated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified by Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA, USA).

tag: cell line

value: papillary thyroid carcinoma cell line B-CPAP

tag: treatment

value: LDHA knockdown


title: X6_P6


title: PHH_D3_mock6h [re-analyzed GSM3874411]

description:
GSM3874411
Mockinfection_E269-RNA_R1
6hpi NI vs. Jc1 Expression Browser


title: genomic DNA from brochoscopic biopsy sample [P10140153_L]


title: genomic DNA from brochoscopic biopsy sample [P10140153_T]


title: genomic DNA from brochoscopic biopsy sample [P10130078_L]

value: probably tumor sample,  diagnosis not definite


title: B-CPAP cells, shGFP_2


title: B-CPAP cells, shGFP_1


title: PHH_D2_HCV72h [re-analyzed GSM3874422]

description:
GSM3874422
E321_RNA7HCVinfection72h_GACGAC_L008
72hpi NI vs. Jc1 Expression Browser
Canonical pathways PHH 72hpi
Upstream regulators_PHH 72hpi NI vs Jc1_List

value: infected


title: genomic DNA from brochoscopic biopsy sample [P10130078_T]


title: PHH_D2_mock72h [re-analyzed GSM3874421]

description:
GSM3874421
E321_RNA8Mockinfection72h_TAATCG_L008
72hpi NI vs. Jc1 Expression Browser
Canonical pathways PHH 72hpi
Upstream regulators_PHH 72hpi NI vs Jc1_List


title: PHH_D2_HCV6h [re-analyzed GSM3874420]

description:
GSM3874420
E321_RNA5HCVinfection6h_CTATAC_L005
6hpi NI vs. Jc1 Expression Browser

value: 6 hours


title: X6_D6


title: X6_F6


title: X6_K6


title: shTRIM28-1% O2-#2 [SUM159-shTRIM28-1pct-2]

city: Baltimore

first: Gregg

middle: Leonard

last: Semenza

state: Maryland

address: 733 North Broadway

institute: Johns Hopkins University

data_processing:
The Fastq files were subjected to quality check and analyzed by Genialis (https://www.genialis.com/)
First, reads are preprocessed by BBDuk which removes adapters, trims reads for quality from the 3'-end, and discards reads that are too short after trimming. Next, preprocessed reads are aligned by STAR aligner. Aligned reads are summarized to gene-level counts by the featureCounts tool.
astQC reports, alignment statistics and rRNA/globin depletion rate QC information is automatically summarized by the MultiQC tool.
The dataset is normalised within DESEq2, and fold change and log2(FC) are reported/computed from that.
The Fastq files were subjected to quality check and analyzed by Genialis (https://www.genialis.com/)
Genome_build: Homo sapiens_GRCh38_ens92
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample, Matrix table with raw gene counts for every gene and every sample

source_name: SUM159_TRIM28 knockdown_1% O2

growth_protocol: SUM159 cells were maintained DMEM/F12 (50:50) medium. The culture media were supplemented with 10% (vol/vol) fetal bovine serum (FBS) and 1% (vol/vol) penicillin-streptomycin. Cells were cultured at 37°C in a 5% CO2, 95% air incubator.

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) and treated with DNase (Qiagen).
Library preparation and sequencing using the Illumina NovaSeq 6000 were performed by Johns Hopkins Genetics Resources Core Facility High-Throughput Sequencing Center.

treatment_protocol: SUM159 subclones were seeded into 6-well plates in three biological replicates and exposed to 20% or 1% O2 for 24 hours.

value: breast cancer cell line

value: TRIM28 knockdown


title: PHH_D2_mock6h [re-analyzed GSM3874419]

description:
GSM3874419
E321_RNA6Mockinfection6h_CTCAGA_L005
6hpi NI vs. Jc1 Expression Browser


title: shTRIM28-1% O2-#3 [SUM159-shTRIM28-1pct-3]


title: shTRIM28-20% O2-#3 [SUM159-shTRIM28-20pct-3]

source_name: SUM159_TRIM28 knockdown_20% O2


title: X6_P5


title: shTRIM28-1% O2-#1 [SUM159-shTRIM28-1pct-1]


title: B-CPAP cells, shLDHA_1


title: genomic DNA from brochoscopic biopsy sample [P10130076_T]

value: tumor sample, diagnosis definite

value: adenocarcinoma


title: genomic DNA from brochoscopic biopsy sample [P10130077_L]


title: PHH_D1_mock72h [re-analyzed GSM3874417]

description:
GSM3874417
E313_8_Mock72h
72hpi NI vs. Jc1 Expression Browser
Canonical pathways PHH 72hpi
Upstream regulators_PHH 72hpi NI vs Jc1_List


title: X6_L6

value: dentate gyrus; adult-born neural precursor cell


title: PHH_D1_HCV72h [re-analyzed GSM3874418]

description:
GSM3874418
E313_7_HCV72h
72hpi NI vs. Jc1 Expression Browser
Canonical pathways PHH 72hpi
Upstream regulators_PHH 72hpi NI vs Jc1_List


title: shTRIM28-20% O2-#2 [SUM159-shTRIM28-20pct-2]


title: genomic DNA from brochoscopic biopsy sample [P10130076_L]


title: X6_N5


title: PHH_D1_HCV6h [re-analyzed GSM3874416]

description:
GSM3874416
E313_5_HCV6h
6hpi NI vs. Jc1 Expression Browser


title: X6_M5


title: genomic DNA from brochoscopic biopsy sample [P10130074_T]

value: probably benign, diagnosis not definite

value: no malignancy


title: PHH_D1_mock6h [re-analyzed GSM3874415]

description:
GSM3874415
E313_6_Mock6h
6hpi NI vs. Jc1 Expression Browser

value: mock control, conditioned medium


title: genomic DNA from brochoscopic biopsy sample [P10130074_L]

value: brochoscopic biopsy sample


title: X6_L5

value: WT


title: genomic DNA from brochoscopic biopsy sample [P10130077_T]

value: squamous cell carcinoma


title: shTRIM28-20% O2-#1 [SUM159-shTRIM28-20pct-1]


title: Huh-7.5_HCV6 72hpi

description:
BT52
Expression Browser_Huh7.5 72hpi NI vs Jc1
Canonical pathways Huh-7.5 72hpi
Upstream regulators_Huh7.5 72hpi NI vs Jc1_List

source_name: hepatocellular carcinoma

value: 72 hours


title: shDNA-PKcs-1% O2-#3 [SUM159-shDNA-PKcs-1pct-3]

source_name: SUM159_DNA-PKcs knockdown_1% O2

value: DNA-PKcs knockdown


title: genomic DNA from brochoscopic biopsy sample [P10130073_Tu]


title: Huh-7.5_HCV5 72hpi

description:
BT36
Expression Browser_Huh7.5 72hpi NI vs Jc1
Canonical pathways Huh-7.5 72hpi
Upstream regulators_Huh7.5 72hpi NI vs Jc1_List


title: genomic DNA from brochoscopic biopsy sample [P10130073_Lu]

value: control, no malignant cells, diagnosis definite


title: shDNA-PKcs-1% O2-#2 [SUM159-shDNA-PKcs-1pct-2]


title: shDNA-PKcs-1% O2-#1 [SUM159-shDNA-PKcs-1pct-1]


title: X6_G5


title: X6_O5


title: Huh-7.5_HCV4 72hpi

description:
BT30
Expression Browser_Huh7.5 72hpi NI vs Jc1
Canonical pathways Huh-7.5 72hpi
Upstream regulators_Huh7.5 72hpi NI vs Jc1_List


title: shDNA-PKcs-20% O2-#3 [SUM159-shDNA-PKcs-20pct-3]

source_name: SUM159_DNA-PKcs knockdown_20% O2


title: genomic DNA from brochoscopic biopsy sample [P10130072_L]

value: probably tumor sample,  diagnosis not definite

value: small cell carcinoma


title: X6_A5


title: Huh-7.5_mock6 72hpi

description:
BT51
Expression Browser_Huh7.5 72hpi NI vs Jc1
Canonical pathways Huh-7.5 72hpi
Upstream regulators_Huh7.5 72hpi NI vs Jc1_List

value: mock control


title: shDNA-PKcs-20% O2-#2 [SUM159-shDNA-PKcs-20pct-2]

value: breast cancer cell line


title: genomic DNA from brochoscopic biopsy sample [P10130072_T]


title: shDNA-PKcs-20% O2-#1 [SUM159-shDNA-PKcs-20pct-1]


title: Huh-7.5_mock5 72hpi

description:
BT34
Expression Browser_Huh7.5 72hpi NI vs Jc1
Canonical pathways Huh-7.5 72hpi
Upstream regulators_Huh7.5 72hpi NI vs Jc1_List


title: genomic DNA from brochoscopic biopsy sample [P09130069_L]


title: X6_N4

source_name: WT_dentate gyrus; adult-born neural precursor cell_T3


title: Huh-7.5_mock4 72hpi

description:
BT28
Expression Browser_Huh7.5 72hpi NI vs Jc1
Canonical pathways Huh-7.5 72hpi
Upstream regulators_Huh7.5 72hpi NI vs Jc1_List


title: Huh-7.5_HCV6 6hpi

description:
BT50
Expression Browser_Huh7.5 6hpi NI vs Jc1

value: infected

value: 6 hours


title: X6_L4

source_name: WT_dentate gyrus; adult-born neural precursor cell_T1


title: X6_P4


title: genomic DNA from brochoscopic biopsy sample [P09130064_Tu]

value: tumor sample, diagnosis definite


title: shDKD-1% O2-#3 [SUM159-shDKD-1pct-3]

source_name: SUM159_HIF-1α and HIF-2α double knockdown_1% O2

value: HIF-1alpha and HIF-2alpha double knockdown


title: Huh-7.5_HCV5 6hpi

description:
BT33
Expression Browser_Huh7.5 6hpi NI vs Jc1


title: shDKD-1% O2-#1 [SUM159-shDKD-1pct-1]


title: X6_K5

value: dentate gyrus; adult-born neural precursor cell


title: X6_J4


title: X6_K4


title: shDKD-1% O2-#2 [SUM159-shDKD-1pct-2]


title: shDKD-20% O2-#3 [SUM159-shDKD-20pct-3]

source_name: SUM159_HIF-1α and HIF-2α double knockdown_20% O2


title: genomic DNA from brochoscopic biopsy sample [P09130064_Lu]


title: genomic DNA from brochoscopic biopsy sample [P09130063_T]

value: adenocarcinoma


title: Huh-7.5_HCV4 6hpi

description:
BT27
Expression Browser_Huh7.5 6hpi NI vs Jc1


title: Huh-7.5_mock6 6hpi

description:
BT49
Expression Browser_Huh7.5 6hpi NI vs Jc1


title: genomic DNA from brochoscopic biopsy sample [P09130063_L]


title: shDKD-20% O2-#2 [SUM159-shDKD-20pct-2]


title: X6_H4


title: Huh-7.5_mock5 6hpi

description:
BT31
Expression Browser_Huh7.5 6hpi NI vs Jc1


title: shDKD-20% O2-#1 [SUM159-shDKD-20pct-1]


title: genomic DNA from brochoscopic biopsy sample [P09130069_T]


title: X6_G4

source_name: WT_dentate gyrus; adult-born neural precursor cell_T2


title: genomic DNA from brochoscopic biopsy sample [P09130061_T]


title: Huh-7.5_mock4 6hpi

description:
BT25
Expression Browser_Huh7.5 6hpi NI vs Jc1


title: shNTC-1% O2-#3 [SUM159-shNTC-1pct-3]

source_name: SUM159_non-targeting control_1% O2

value: non-targeting control


title: genomic DNA from brochoscopic biopsy sample [P09130057_T]

value: brochoscopic biopsy sample


title: X6_K3

value: WT


title: Huh-7.5_hIRF1_3 [re-analyzed GSM3874410]

description:
GSM3874410
hIRF1_S9_L002
Expression Browser_ IRF1vsempty
Canonical pathways Huh-7.5 IRF1
Upstream regulators_IRF1 vs empty_List

tag: ectopic expression


title: shNTC-1% O2-#1 [SUM159-shNTC-1pct-1]


title: shNTC-1% O2-#2 [SUM159-shNTC-1pct-2]


title: X6_J3


title: Huh-7.5_hIRF1_2 [re-analyzed GSM3874409]

description:
GSM3874409
hIRF1_P11_S31_L003
Expression Browser_ IRF1vsempty
Canonical pathways Huh-7.5 IRF1
Upstream regulators_IRF1 vs empty_List


title: Huh-7.5_hIRF1_1 [re-analyzed GSM3874408]

description:
GSM3874408
hIRF1_P9_S30_L003
Expression Browser_ IRF1vsempty
Canonical pathways Huh-7.5 IRF1
Upstream regulators_IRF1 vs empty_List


title: X6_I3


title: genomic DNA from brochoscopic biopsy sample [P09130057_L]

value: probably benign, diagnosis not definite


title: X6_I4


title: genomic DNA from brochoscopic biopsy sample [P08130055_L]


title: shNTC-20% O2-#2 [SUM159-shNTC-20pct-2]

source_name: SUM159_non-targeting control_20% O2


title: shNTC-20% O2-#3 [SUM159-shNTC-20pct-3]


title: shNTC-20% O2-#1 [SUM159-shNTC-20pct-1]


title: Huh-7.5_HCV2 [re-analyzed GSM3874406]

description:
GSM3874406
19_72hr_empty_HCV_S9_L002
Expression Browser_Huh7.5 72hpi NI vs Jc1
Canonical pathways Huh-7.5 72hpi
Upstream regulators_Huh7.5 72hpi NI vs Jc1_List

tag: hcv

value: 72 hours


title: X6_B2


title: genomic DNA from brochoscopic biopsy sample [P08130054_T]

value: squamous cell carcinoma


title: Huh-7.5_HCV1 [re-analyzed GSM3874405]

description:
GSM3874405
2b_Empty_HCV_S18_L004
Expression Browser_Huh7.5 72hpi NI vs Jc1
Canonical pathways Huh-7.5 72hpi
Upstream regulators_Huh7.5 72hpi NI vs Jc1_List


title: genomic DNA from brochoscopic biopsy sample [P08130054_L]

value: control, no malignant cells, diagnosis definite


title: X6_L1


title: genomic DNA from brochoscopic biopsy sample [P09130061_L]

value: probably tumor sample,  diagnosis not definite


title: siCTRL-rep3

city: reykjavik

first: Ramile

last: Dilshat

address: Sturlugata 8

department: Biochemistry and Molecular biology

country: Iceland

institute: University of Iceland

data_processing:
RNA-seq reads were aligned using Kallisto with --bootstrap 100
Differential expressed genes were called using Sleuth
Reads from ChIP-seq were aligned using Bowtie2 and Peaks were called using MACS
Genome_build: GRCh38 for RNA-seq and hg19 for ChIP-seq
Supplementary_files_format_and_content: bed
Supplementary_files_format_and_content: bigWig
Supplementary_files_format_and_content: count matrix

source_name: skin melanoma cell line

extract_protocol: RNA was extracted using RNA isolatoin kit and treated with DNase I.

tag: sirna

value: siCTRL


title: X6_B4

source_name: WT_dentate gyrus; adult-born neural precursor cell_T1b


title: Huh-7.5_mock3 [re-analyzed GSM3874404]

description:
GSM3874404
Empty_S8_L002
Expression Browser_Huh7.5 72hpi NI vs Jc1
Canonical pathways Huh-7.5 72hpi
Upstream regulators_Huh7.5 72hpi NI vs Jc1_List
Expression Browser_ IRF1vsempty
Canonical pathways Huh-7.5 IRF1
Upstream regulators_IRF1 vs empty_List

value: mock control

tag: time


title: siCTRL-rep2


title: genomic DNA from brochoscopic biopsy sample [P08130053_T]

tag: tissue


title: X6_H1


title: genomic DNA from brochoscopic biopsy sample [P08130053_L]

tag: donor id


title: genomic DNA from brochoscopic biopsy sample [P08130055_T]

tag: histology (diagnosis by pathologists based on one single specimen)


title: Huh-7.5_mock1 [re-analyzed GSM3874402]

description:
GSM3874402
1a_Empty_Un_S12_L003
Expression Browser_Huh7.5 72hpi NI vs Jc1
Canonical pathways Huh-7.5 72hpi
Upstream regulators_Huh7.5 72hpi NI vs Jc1_List
Expression Browser_ IRF1vsempty
Canonical pathways Huh-7.5 IRF1
Upstream regulators_IRF1 vs empty_List


title: siCTRL-rep1


title: Mixed WT and KO T cells (hashtags)

city: Melbourne

first: Ian

last: Parish

state: VIC

address: 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

data_processing:
Demultiplexing, alignment, filtering and UMI counting was performed with Cell Ranger 3.1.0 using the cellranger count command.
The filtered_feature_bc_matrix.h5 file (output by Cell Ranger) for both gene expression and hashtag samples were loaded in R merged based on cell barcodes common samples.
WT and cKO cells were labeled with the Biolegend TotalSeq -C0301
anti-mouse Hashtag 1 or TotalSeq -C0302 anti-mouse Hashtag 2
antibodies respectively according to manufacturer s instructions. The
sequenced hashtags are in the IP-HTO-V2_S1_* fastq files. (The other
set of fastq files are the mRNA sequences for the same cells). The
matrix HTO_filtered_feature_bc_matrix.h5 has two rows, "WT" and "KO",
and each column corresponds to a cell barcode. The values in the
matrix are the UMI counts for each hashtag in each cell.
Genome_build: mm10
Supplementary_files_format_and_content: The .h5 files contain a gene or hashtag by cell barcode matrix.

source_name: T cells

extract_protocol:
At day 20 p.i., CD8+CD44int-hi H-2DbGP33-41-tetramer stained cells were isolated by fluorescence activated cell sorting, labelled with hashtags, mixed and then analysed by scRNAseq.
Cell capture and library preparations were performed using the 10x Genomics Chromium system, the Chromium Single Cell 5' Library & Gel Bead Kit (v1.0 chemistry) and the Chromium Single Cell 5' Feature Barcode Library Kit. Single-cell and feature (hashtag) libraries were generated using the Chromium Controller and Single Cell 5’ Library & Gel Bead Kit and Chip A Kit (10x Genomics) according to the manufacturer’s protocol.

treatment_protocol: CD4 depleted WT or cKO mice were infected with 2x10^6 pfu LCMV-Cl13 i.v.

tag: strain

value: LCMV H-2Kb GP33-41-specific CD8+ T cells

value: Mixture of CD4-cre+ Egr2 flox/flox and CD4-cre+ Egr2+/+ littermate cells


title: WT-4: EGR2 WT replicate 2

data_processing:
Reads were trimmed in paired-end mode using Trim_Galore version 0.4.5_dev
Trimmed reads were aligned to GRCm38.p6 using BWA MEM v0.7.17
The resulting bam files were deduplicated with MarkDuplicates (Picard) v2.19.0
Bam converted to bedGraph using genomeCoverageBed from bedtools
bedGraph coverted to Bigwig using bedGraphToBigWig from KentUtils
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Bigwig (bw)

source_name: Sorted LCMV-specific CD8+ T cells

extract_protocol:
At day 20 p.i., CD8+CD44int-hi H-2DbGP33-41-tetramer stained cells were isolated by fluorescence activated cell sorting and subjected to ATACseq analysis
ATACseq library preparation was conducted based on a published protocol (Buenrostro et al, Nat Methods, 2013).

value: LCMV H-2Kb GP33-41-specific CD8+ T cell

value: CD4-cre+ Egr2+/+

tag: disease state

value: chronic LCMV infection


title: Huh-7.5_mock2 [re-analyzed GSM3874403]

description:
GSM3874403
1b_Empty_Un_S17_L003
Expression Browser_Huh7.5 72hpi NI vs Jc1
Canonical pathways Huh-7.5 72hpi
Upstream regulators_Huh7.5 72hpi NI vs Jc1_List
Expression Browser_ IRF1vsempty
Canonical pathways Huh-7.5 IRF1
Upstream regulators_IRF1 vs empty_List


title: genomic DNA from brochoscopic biopsy sample [P07140141_T]

value: tumor sample, diagnosis definite

tag: diagnosis (final clinical diagnosis for the patient)


title: X6_E2

value: dentate gyrus; adult-born neural precursor cell


title: TN Patient 9

city: London

first: Samah

last: Alimam

address: Great Maze Pond

department: Cancer Genetics

country: United Kingdom

institute: KCL

data_processing:
Reads were trimmed using Trimmomatic RPKM.
Aligned to the hg19 genome using STAR 2 Pass Aligner
Raw gene expression counts were extracted using Rsubread feature counts
Raw counts were normalised using limma voom for differential analysis
Raw counts were also normalised by counts per million (cpm) for further analysis
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes normalized read counts (CPM) values for each Sample
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each Sample

source_name: PBMC (Peripheral blood mononuclear cells)

extract_protocol:
RNA was extracted from PBMCs using Trizol reagent (Life Technologies).
Libraries were prepared using the Illumina TruSeq Stranded RNA kit following the manufacturer’s instructions and sequenced using an Illumina HiSeq 2500 instrument.

tag: individual

value: TN Patient

tag: mutation status

value: TN (Triple negative)


title: siIRF4-rep3


title: genomic DNA from brochoscopic biopsy sample [P07140141_L]

value: adenocarcinoma

value: brochoscopic biopsy sample


title: TN Patient 8

value: PBMC (Peripheral blood mononuclear cells)


title: WT-2: EGR2 WT replicate 1

tag: genotype


title: Huh-7.5_HCV3 [re-analyzed GSM3874407]

description:
GSM3874407
L470_EMPTYplusHCV_A_S37
Expression Browser_Huh7.5 72hpi NI vs Jc1
Canonical pathways Huh-7.5 72hpi
Upstream regulators_Huh7.5 72hpi NI vs Jc1_List

value: infected

value: 72 hours


title: siIRF4-rep2


title: siIRF4-rep1


title: KO-3: EGR2 KO replicate 2

value: CD4-cre+ Egr2 flox/flox


title: TN Patient 7


title: genomic DNA from brochoscopic biopsy sample [P07140137_L]

value: control, no malignant cells, diagnosis definite

value: small cell carcinoma


title: KO-1: EGR2 KO replicate 1


title: TN Patient 6


title: genomic DNA from brochoscopic biopsy sample [P07140136_T]


title: UTSW_BC82

city: Dallas

first: Jane

last: Zhu

state: Texas

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

description:
raw_transcript_counts.csv
filtered_normalized_stablized_expression.csv

data_processing:
Raw sequencing reads were converted to FASTQ with bcl2fastq (version 2.20)
Data trimmed using Bbmap (version 38.5)
Pseudoaligned to the human GENCODE v32 transcriptome and quantified using Salmon (version 1.3.0)
Genome_build: Human GENCODE v32
Supplementary_files_format_and_content: Adjusted for size factors and dispersion, normalized, and variance stablized using DESeq2 (version 1.28.1)

source_name: blood

extract_protocol:
Total RNA isolated and purified using Rneasy Plus 96 Kit (Qiagen). Quality was assessed using Bioanalyzer RNA 6000 pico assays
100 ng of each RNA sample was used as input for conversion to sequencing libraries using a KAPA RNA HyperPrep Kit with RiboErase (Roche)

value: DLE

tag: Sex

value: Female

tag: ethnicity

value: C

value: blood


title: UTSW_BC83

value: Male


title: TN Patient 5

tag: cell type


title: GFP positive replicate 2

data_processing:
Reads were aligned to the mouse genome reference (GRCm38/mm10) sequence using HiSat2 (Kim et al., 2015) with default parameters.
Read counts were then generated for each gene in each sample using FeatureCounts from the Subread package (v1.5.0-p3).
Supplementary_files_format_and_content: counts

source_name: Sorted CD8+ T cells

extract_protocol:
At day 20 p.i., GFP+ and GFP- CD8+CD44int-hiPD-1+Slamf6+Tim3- splenocytes were isolated by fluorescence activated cell sorting. Total RNA was isolated using Trizol LS (Thermo Fisher Scientific) according to manufacturer’s instructions.
RNA-seq libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.
Directional RNA-seq

treatment_protocol: Egr2-GFP reporter mice were infected with 2x10^6 pfu LCMV-Cl13 i.v.

value: CD8+CD44int-hiPD-1+Slamf6+Tim3- cells

tag: background


title: UTSW_BC81

value: AA


title: TN Patient 4

value: TN Patient


title: UTSW_BC79

value: O


title: UTSW_BC78


title: TN Patient 3

value: TN (Triple negative)


title: GFP positive replicate 1


title: GFP negative replicate 1


title: UTSW_BC77


title: TN Patient 2


title: genomic DNA from brochoscopic biopsy sample [P07140133_L]

value: brochoscopic biopsy sample


title: genomic DNA from brochoscopic biopsy sample [P07140133_T]

value: tumor sample, diagnosis definite


title: Macrophages infected with Mtb BJN starve condition rep2

city: Bangkok

first: Marisa

last: Ponpuak

address: 272 Rama 6 Road

country: Thailand

institute: Department of Microbiology, Faculty of Science, Mahidol University

data_processing:
RTA software v2 used for basecalling
Sequenced reads were trimmed for adaptor sequence, and filtered low-quality sequence, then mapped to GRCm38 whole genome using TopHat v2.0 with specific --library type fr-firststrand
StringTie and prepDE.py were used to assemble and extract transcript reads. Transcripts_count_matrix was then created and subjected to edgeR for differential transcript exprssion analysis.
Gene ontology and pathway enrichment analyses were performed using differentially expressed transcripts on web-based bioinformatics tool DAVID 6.8 (https://david.ncifcrf.gov/).
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Raw264.7 macrophages

extract_protocol:
Total RNAs were collected and isolated using TRI Reagent and Ambion® RiboPure™ (Thermo Fisher Scientific). Illumina TruSeq Stranded mRNA Library Prep Kit (Cat#RS-122-2101) was used with 500 ng of total.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: Raw264.7 macrophages

value: macrophage

tag: mtb infection

value: infected with autophagy-resistant Beijing strain

tag: autophagy induction

value: induced by starvation


title: genomic DNA from brochoscopic biopsy sample [P07140137_T]

value: small cell carcinoma


title: UTSW_BC76

value: DLE


title: TN Patient 12

value: PBMC (Peripheral blood mononuclear cells)


title: genomic DNA from brochoscopic biopsy sample [P07140131_L]

value: control, no malignant cells, diagnosis definite


title: Macrophages infected with Mtb BJN starve condition rep1


title: Macrophages infected with Mtb BJN full condition rep2

value: uninduced


title: UTSW_BC75

value: Female

value: blood


title: TN Patient 10


title: UTSW_BC74

value: Male

value: AA


title: GFP negative replicate 2

value: CD8+CD44int-hiPD-1+Slamf6+Tim3- cells


title: genomic DNA from brochoscopic biopsy sample [P07140130_L]

value: squamous cell carcinoma


title: genomic DNA from brochoscopic biopsy sample [P07140136_L]

value: adenocarcinoma

value: brochoscopic biopsy sample


title: TN Patient 1

value: TN Patient

value: TN (Triple negative)


title: UTSW_BC73


title: Macrophages infected with Mtb H37RV starve condition rep2

value: Raw264.7 macrophages

value: macrophage

value: infected with autophagy-sensitive reference strain H37Rv


title: genomic DNA from brochoscopic biopsy sample [P07130046_T]

value: tumor sample, diagnosis definite


title: genomic DNA from brochoscopic biopsy sample [P07140131_T]

value: small cell carcinoma


title: JAK2 Patient 3

value: JAK2 Patient

value: JAK2 (JAK2 mutation)

value: PBMC (Peripheral blood mononuclear cells)


title: Macrophages infected with Mtb H37RV starve condition rep1

value: induced by starvation


title: genomic DNA from brochoscopic biopsy sample [P07130044_T]

value: probably benign, diagnosis not definite


title: JAK2 Patient 2


title: genomic DNA from brochoscopic biopsy sample [P07130044_L]


title: UTSW_BC71

value: DLE

value: Male

value: AA

value: blood


title: JAK2 Patient 1


title: UTSW_BC69

value: Female


title: Macrophages infected with Mtb H37RV full condition rep1

value: uninduced


title: TN Patient 11

value: TN Patient

value: TN (Triple negative)


title: genomic DNA from brochoscopic biopsy sample [P07140130_T]

value: squamous cell carcinoma

value: brochoscopic biopsy sample


title: genomic DNA from brochoscopic biopsy sample [P07130042_T]


title: Macrophages starve condition rep2

value: Raw264.7 macrophages

value: macrophage

value: uninfected


title: Macrophages infected with Mtb BJN full condition rep1

value: infected with autophagy-resistant Beijing strain


title: genomic DNA from brochoscopic biopsy sample [P07130042_L]


title: Healthy Control 3

value: Healthy Control 3

value: CTRL (Healthy Control)

value: PBMC (Peripheral blood mononuclear cells)


title: UTSW_BC67

value: DLE

value: O


title: Macrophages starve condition rep1

value: induced by starvation


title: Healthy Control 2

value: Healthy Control 2


title: genomic DNA from brochoscopic biopsy sample [P06140126_T]

value: tumor sample, diagnosis definite

value: small cell carcinoma


title: UTSW_BC65

value: Male

value: AA

value: blood


title: UTSW_BC72

value: Female

value: C


title: Macrophages full condition rep2

value: Raw264.7 macrophages

value: macrophage

value: uninduced


title: genomic DNA from brochoscopic biopsy sample [P07130046_L]

value: control, no malignant cells, diagnosis definite

value: adenocarcinoma

value: brochoscopic biopsy sample


title: genomic DNA from brochoscopic biopsy sample [P06140126_L]


title: Macrophages full condition rep1

value: uninfected


title: Macrophages infected with Mtb H37RV full condition rep2

value: infected with autophagy-sensitive reference strain H37Rv


title: UTSW_BC64

value: DLE


title: UTSW_BC70


title: CALR Patient 3

value: CALR Patient

value: CALR (Calreticulin mutation)

value: PBMC (Peripheral blood mononuclear cells)


title: Healthy Control 4

value: Healthy Control 4

value: CTRL (Healthy Control)


title: CALR Patient 2


title: genomic DNA from brochoscopic biopsy sample [P06130031_T]

value: probably benign, diagnosis not definite


title: UTSW_BC63

value: Female

value: AA

value: blood


title: CALR Patient 1


title: genomic DNA from brochoscopic biopsy sample [P06130031_L]


title: UTSW_BC61


title: KO2  48 h

city: Carmel

first: Kai

last: Yang

state: Indiana

address: 12598 pembrooke circle

department: Pediatrics

institute: School of Medicine, IUPUI

data_processing:
The sequencing data was assessed using FastQC (Babraham Bioinfomatics, Cambridge, UK).
Uniquely mapped sequencing reads were assigned to mm10 refGene genes using featureCounts (from subread) (Liao et al., 2014). Genes with read count per million (CPM) >0.5 in more than 3 of the samples were kept.
The data were further normalized using RPKM (Reads Per Kilobase Million). Differential gene expression analysis was conducted by using DESeq2 method with an FDR less than 0.05 as the significant cutoff (Love et al., 2014).
Pathway enrichment analyses were conducted by hypergeometric tests against mouse Gene Ontology and MsigDB v6 canonical pathways, with P less than 0.01 as the significant cutoff (Subramanian et al., 2005)
For selected pathways, GSEA enrichment score and ssGSEA sample-wise enrichment score were used for visualization (Subramanian et al., 2005).
Genome_build: The sequencing data was mapped to the mouse genome (UCSC mm10) using STAR RNA-seq aligner (Dobin et al., 2013) with the parameter: “—outSAMmapqUNIQUE 60”.
Supplementary_files_format_and_content: The processed data are in an excel file containing raw counts of seqeuncing reads

source_name: Stimulated with aCD3-CD28/IL-2 for 48 h

growth_protocol: For α-CD3-CD28/IL-2 stimulation, sorted WT and BATF-deficient Treg cells were cultured in Click’s medium (plus β-mercaptoethanol) supplemented with 10% (vol/vol) FBS and 1% (vol/vol) penicillin–streptomycin.

extract_protocol:
RNA of WT and BATF-deficient Treg cells was extracted using the RNeasy Micro Kit (Qiagen)
RNA (600 ng/ sample) was used to prepare single indexed strand specific cDNA library using TruSeq stranded mRNA library prep kit (Illumina). The library prep was assessed for quantity and size distribution using Qubit and Agilent 2100 Bioanalyzer.

treatment_protocol: WT and BATF-deficient Treg cells were stimulated with plate-bound α-CD3-CD28 (5 μg/ml) in the presence of IL-2 (200 U/ml) for 48 h

tag: age

value: 7 weeks

value: Treg


title: KO3  48 h


title: genomic DNA from brochoscopic biopsy sample [P05140125_T]

value: others (?), unknown

tag: tissue


title: KO1  48 h


title: genomic DNA from brochoscopic biopsy sample [P05140125_L]

tag: donor id


title: UTSW_BC59

value: TLE

value: C


title: Healthy Control 1

value: Healthy Control 1


title: WT3  48 h

value: WT


title: genomic DNA from brochoscopic biopsy sample [P05140123_T]

tag: histology (diagnosis by pathologists based on one single specimen)

value: tumor sample, diagnosis definite

value: adenocarcinoma

value: brochoscopic biopsy sample


title: UTSW_BC58

value: Male


title: WT2  48 h

tag: strain


title: G66

city: Tel Aviv

first: Tamar

last: Geiger

address: Levanon st

country: Israel

institute: Tel Aviv University

data_processing:
Resulting reads were trimmed and quality filtered using Trimmomatic (Bolger et al., 2014)
Salmon quasi-mapping tool (Patro et al., 2017) was used for expression quantification against the transcriptome compiled from the Ensembl human hg38 genome assembly
R package DESeq2 (Love et al., 2014) was used to convert transcripts per million (TPM) quantifications to gene level, as well as to perform log2 transformation and variance stabilizing transformations (VST) normalization of the counts for downstream analysis
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file includes DESeq2-VST transformed values for each sample

source_name: GBM tumor tissue

extract_protocol:
RNA was extracted from fresh frozen GBM tissues of human patients using EZ RNAII isolation kit (Biological Industries, Bet Haemek, Israel) according to manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease state

value: GBM (IV)

tag: gender

value: M

tag: survival (days)

value: GBM tumor tissue


title: G68

value: F


title: G67


title: genomic DNA from brochoscopic biopsy sample [P05140123_L]

value: control, no malignant cells, diagnosis definite

tag: diagnosis (final clinical diagnosis for the patient)


title: UTSW_BC56

value: O

value: blood


title: genomic DNA from brochoscopic biopsy sample [P05130030_T]

value: probably benign, diagnosis not definite

value: small cell carcinoma


title: WT1  48 h

value: 7 weeks

tag: genotype

value: Treg


title: UTSW_BC55

value: TLE

tag: Sex

value: C


title: G65


title: KO3 Unstimulated

source_name: Unstimulated


title: UTSW_BC62

value: DLE

tag: ethnicity

value: AA


title: genomic DNA from brochoscopic biopsy sample [P05130030_L]

value: brochoscopic biopsy sample


title: UTSW_BC53

value: Female


title: G64

value: GBM (IV)


title: genomic DNA from brochoscopic biopsy sample [P05130027_T]

value: tumor sample, diagnosis definite

value: others (?), unknown


title: KO1 Unstimulated

tag: cell type


title: G62

value: M

value: WT

value: GBM tumor tissue


title: genomic DNA from brochoscopic biopsy sample [P05130027_L]

value: control, no malignant cells, diagnosis definite


title: UTSW_BC54

value: blood


title: G63

value: F


title: UTSW_BC51


title: genomic DNA from brochoscopic biopsy sample [P05130026_T]

value: squamous cell carcinoma


title: WT2 Unstimulated

value: 7 weeks

value: Treg


title: UTSW_BC52

value: TLE

value: Male

value: C


title: G60


title: UTSW_BC50

value: LP

value: AA


title: WT3 Unstimulated


title: G61

value: GBM (IV)


title: WT1 Unstimulated


title: genomic DNA from brochoscopic biopsy sample [P05130026_L]

value: brochoscopic biopsy sample


title: UTSW_BC47

value: DLE

value: Female


title: T cell Input control

data_processing:
The Fastq ﬁles were aligned to the mouse reference genome (GRCm38/mm10) using bowtie2 (v2.3.3).
Samtools (v1.4.1) was used to convert the sam file to bam, remove duplicates and sort.
MACS (v2.1.1) was used for peak-calling to identify significantly enriched peaks (FDR<0.05)
Genome_build: mm10
Supplementary_files_format_and_content: peak bed file

extract_protocol:
~60x106 CD8+ T cells from 8 mice were resuspended in PBS and crossed-linked with fresh formaldehyde solution for 30 min at room temperature. Excess formaldehyde was quenched with 125mM Glycine. Cells were incubated with nuclear extraction buffer with protease inhibitors on ice for 5 min. Nuclear extracts were resuspended in sonication buffer and sonicated using the Covaris S220 Focused Ultrasonicator.  Protein A and Protein G Dynabeads were washed and resuspended in ChIP IP buffer then  added to diluted lysates with 20µg of a previously validated polyclonal anti-EGR2 ChIP antibody (ab43020, Abcam). IP samples were incubated overnight at 4oC. Protein A/G beads were washed then incubated with Reverse Crosslinking Buffer containing 45mg Proteinase K at 55oC for 1h and the supernatant was then isolated and incubated at 65oC overnight. DNA was isolated using the ChIP DNA Clean & Concentrator Kit (Zymo Research).
Indexed libraries were prepared using KAPA Hyper Prep Kit for Illumina platforms  and the SeqCap Adapter Kit (Roche) following vendor’s instructions. Library QC and quantiﬁcation was performed using D1000 high-sensitivity screen tape with a 4200 TapeStation Instrument (Agilent Technologies) and size selected for between 200 bp and 500 bp using a Pippin Prep system.

treatment_protocol: C57BL/6J mice were infected with 2x10^6 pfu LCMV-Cl13 Cl13, and at day 20 p.i. spleen and lymph nodes were isolated from the mice and pooled. CD8+ T cells were then isolated by MACS enrichment (Miltenyi) according to manufacturer’s instructions.

tag: antibody

value: CD8+ T cell

tag: background


title: UTSW_BC46


title: G59

value: M

value: GBM tumor tissue


title: G58


title: G57


title: KO2 Unstimulated


title: genomic DNA from brochoscopic biopsy sample [P05130025_L]

value: probably benign, diagnosis not definite


title: EGR2 KO replicate 2

data_processing:
Reads were aligned to the mouse genome reference (GRCm38/mm10) sequence using HiSat2 (Kim et al., 2015) with default parameters.
Read counts were then generated for each gene in each sample using FeatureCounts from the Subread package (v1.5.0-p3).

extract_protocol:
At day 20 p.i., CD8+CD44int-hi H-2DbGP33-41-tetramer stained cells were isolated by fluorescence activated cell sorting. Total RNA was isolated using Trizol LS (Thermo Fisher Scientific) according to manufacturer’s instructions
RNA-seq libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.

value: LCMV H-2Kb GP33-41-specific CD8+ T cell

value: CD4-cre+ Egr2 flox/flox


title: T cell EGR2 ChIP

value: ab43020, Abcam


title: genomic DNA from brochoscopic biopsy sample [P05130022_Tu]

value: tumor sample, diagnosis definite

value: non small cell carcinoma


title: UTSW_BC44

value: Male

value: AS

value: blood


title: UTSW_BC45

value: C


title: G56

value: GBM (IV)

value: F

value: MUT


title: EGR2 KO replicate 1


title: genomic DNA from brochoscopic biopsy sample [P05130022_Lu]

value: control, no malignant cells, diagnosis definite

value: brochoscopic biopsy sample


title: UTSW_BC43

value: DLE

value: Female

value: AA


title: G55

value: M

value: GBM tumor tissue


title: EGR2 WT replicate 2

value: LCMV H-2Kb GP33-41-specific CD8+ T cell

value: CD4-cre+ Egr2+/+


title: genomic DNA from brochoscopic biopsy sample [P04140119_T]

value: probably benign, diagnosis not definite

value: non small cell carcinoma


title: G54


title: UTSW_BC42

value: Male

value: H


title: EGR2 WT replicate 1


title: genomic DNA from brochoscopic biopsy sample [P04140119_L]


title: genomic DNA from brochoscopic biopsy sample [P05130025_T]

value: squamous cell carcinoma


title: G53

value: GBM (IV)


title: UTSW_BC41

value: blood


title: G52

value: WT


title: genomic DNA from brochoscopic biopsy sample [P04140117_T]

value: tumor sample, diagnosis definite

value: small cell carcinoma


title: UTSW_BC40

value: DLE


title: WT_Sp1

city: Kiel

first: Seyed Mohammd Mahdi

last: Rasa

state: Schleswig-Holstein

address: Michaelisstrasse 5

department: Institut for Immunology

institute: Universitätsklinikum Schleswig-Holstein

description: ChIP (DNA sequencing)

data_processing:
Fastq files quality check was performed with FastQC (v0.11.5).
Fastq files mapping to mm9 genome was performed by using Bowtie (v1.1.2) with --best --strata -m 1 parameters.
Duplicate reads were removed using a custom script.
Wig files were made using macs14 (v1.4.2) with --nolambda parameter.
The Wig files were converted to tdf file using igvtools (v2.3.97)
Genome_build: mm9
Supplementary_files_format_and_content: tdf

source_name: aNSCs

growth_protocol: Young (around 2-4 months old)  male and female wild-type C57BL6/J mice were group housed and maintained in a specific pathogen-free animal facility in Fritz Lipmann Institute with 12 h of light/dark cycle and fed with a standard mouse chow.

extract_protocol:
aNSCs were isolated from adult mice (between 2 and 4 months old) as previously described (Walker and Kempermann;2014) and expanded In-vitro. 2x106 Cells were cross-linked by adding formaldehyde 1% for 10 min at room temperature, quenched with 0.125 M Glycine for 5 min at room temperature, and then washed three times in phosphate-buffered saline (PBS) before freezing. Pellets were suspended in 0.25 ml SDS lysis buffer (50 mM HEPES-KOH, 140 mM NaCl, 1mM EDTA , 0.1% Triton X-100, 0.1% Sodium Deoxycholate, 1% SDS, 10 µM NaB and protease inhibitors), incubated on a rotator for 30 min at 4oC, sonicated for 20 min at 4°C, and then centrifuged at 14,000 rpm for 10 min at 4°C. Supernatants were diluted 10-fold with ChIP dilution buffer (1% Triton X-100, 2mM EDTA, 20mM Tris-HCL, 150 mM NaCl, 10 µM NaB and protease inhibitors) (25 µl were kept as input) and incubated overnight in gentle rotation at 4°C with 4 µg of antibody. The following antibodies were used: rabbit anti-SP1 (Millipore), rabbit anti-acetyl-Histone 3 (Millipore), mouse anti-TRRAP (Euromedex) and rabbit anti-acetyl-Histone 4 (Millipore). After that, 40 µl of preblocked protein-G-conjugated magnetic beads (DYNAL, Thermo Fischer) were added and incubated for 2h in a rotator at 4°C. The immunoprecipitated complexes were washed three times in low-salt wash buffer (0.1% SDS,1% Triton X-100, 2mM EDTA, 20mM Tris-HCL, 150 mM NaCl), one time in high-salt wash buffer (0.1% SDS,1% Triton X-100, 2mM EDTA, 20mM Tris-HCL, 500 mM NaCl) and one time in TE buffer. The complexes were eluted by adding 0.2 ml of Elution buffer (TE 1x, 1 % SDS, 150 mM NaCl, 5mM DTT) for 30 min in rotation at room temperature. The de-crosslinking was performed at 65 °C overnight. De-crosslinked DNA was purified using QiaQuick PCR Purification Kit (Quiagen) according to the manufacture’s instruction.
Approximately 10 ng of purified ChIP DNA were end-repaired, dA-tailed, and adaptor-ligated using the TruSeq ChIP Sample Preparation Kit (illumina) following the manufacturer’s instructions. The size of the library was checked using Fragment Analyzer (Agilent) and the library was sequenced on the NextSeq500 platform (illumina).

treatment_protocol: Cells were treated with 4-OHT (1mM) for 5 days before the DNA isolation

tag: genotype/variation

value: Trrap fl/+;CreER

tag: antibodies

value: anti-SP1 (Millipore)

tag: treatment

value: 4-OHT treatment


title: G51

tag: age

value: M

tag: tissue

value: GBM tumor tissue


title: genomic DNA from brochoscopic biopsy sample [P04130019_T]

tag: donor id

tag: histology (diagnosis by pathologists based on one single specimen)

value: adenocarcinoma

value: brochoscopic biopsy sample


title: genomic DNA from brochoscopic biopsy sample [P04140117_L]

value: control, no malignant cells, diagnosis definite


title: UTSW_BC39

tag: disease state

value: Female

value: AA


title: G50

tag: gender


title: WT_H4ac

description: ChIP (DNA sequencing)

tag: strain

value: anti-acetyl-Histone 4 (Millipore)


title: genomic DNA from brochoscopic biopsy sample [P04130019_L]

tag: diagnosis (final clinical diagnosis for the patient)


title: UTSW_BC36

value: SCLE

value: H


title: G49

value: GBM (IV)

value: F

tag: survival (days)


title: G48


title: KO_Sp1

description: ChIP (DNA sequencing)

value: Trrap fl/fl;CreER


title: genomic DNA from brochoscopic biopsy sample [P03140113_T]

value: probably benign, diagnosis not definite

value: small cell carcinoma


title: WT_H3ac

description: ChIP (DNA sequencing)

value: Trrap fl/+;CreER

value: acetyl-Histone 3 (Millipore)


title: UTSW_BC30

value: DLE

tag: Sex

value: C

value: blood


title: UTSW_BC32

tag: ethnicity


title: genomic DNA from brochoscopic biopsy sample [P03140113_L]

value: brochoscopic biopsy sample


title: G47

value: GBM tumor tissue


title: KO_input

description: ChIP (DNA sequencing)

value: 4-OHT treatment


title: genomic DNA from brochoscopic biopsy sample [P03140111_T]

value: tumor sample, diagnosis definite


title: genomic DNA from brochoscopic biopsy sample [P03140111_L]

value: control, no malignant cells, diagnosis definite


title: UTSW_BC23

value: Female

value: AA


title: G46

value: GBM (IV)


title: KO_H4ac

description: ChIP (DNA sequencing)

value: anti-acetyl-Histone 4 (Millipore)


title: WT_input

description: ChIP (DNA sequencing)


title: G45

value: M


title: UTSW_BC22


title: BM_MSC05_act

city: Madrid

first: Luis

last: Rodriguez-Rodriguez

address: Calle Prof Martin Lagos

department: Rheumatology

country: Spain

institute: Instituto de Investigación Sanitaria San Carlos

data_processing:
The raw sequence reads (FASTQ format) were aligned to the cDNA sequences of the human GRCh37 reference assembly available in UCSC Genome Browser (http://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.2bit), using the Rsubread Bioconductor package v1.20.3, using the default settings, and reporting only uniquely mapped reads.
Read summarization was performed with featureCounts, using the in-built gene annotations from the NCBI RefSeq for Hg19, included in the Rsubread package. Mapped reads for each sample were summarized into the meta-feature “gene,” thus obtaining gene-level expression counts that were used as input for gene expression analysis.
We removed those genes with low expression according to the number of counts for million mapped reads (CPMs). We set a threshold of at least 1 count per million (CPM), in at least 4 of the 5 active and/or 4 of the 5 resting samples.
To adjust for variable sequencing depths between samples, the raw gene counts were normalized using a weighted trimmed mean of the log expression ratios (Trimmed Mean of M values [TMM] algorithm) as implemented in the edgeR Bioconductor package
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Bone marrow mesenchymal stem cells

growth_protocol: BM-MSCs (2 × 105 cells) were cultured alone for 24 h in non-treated Falcon® 6-wells flat bottom plates (Corning) in complete low-glucose DMEM (Lonza Group Ltd., Basel, Switzerland) at 37 °C and 5% CO2. After this time, the medium was replaced by supplemented RPMI.

extract_protocol:
Total RNA from BM-MSCs was extracted using the RNeasy Mini Kit (Qiagen Iberia, Madrid, Spain), according to the manufacturer’s protocol. RNA concentration was quantified spectrophotometrically (Nanodrop ND-1000, Wilmington, DE), and its quality and integrity assessed by capillary electrophoresis on an Agilent 2100 Bioanalyzer (Agilent Technologies. Spain).
Barcoded cDNA libraries were prepared from poly(A) enriched mRNA using NebNext Ultra Directional RNA Library Prep Kit (New England Biolabs, Spain). Pooled libraries were sequenced on an Illumina NextSeq 500 instrument to generate on average 32.9 million single-end reads of 76 bp length. To avoid a batch effect bias, all samples were run simultaneously twice, and results merged.

treatment_protocol: PBMCs (2 × 106 cells) were added to the wells in ratio 1:10 (BM-MSC:PBMCs) mostly based on cellular and cellular membrane size. In some wells, anti-CD3-/anti-CD28-coated beads (Dynabeads® Human T-Activator; Life Technologies) were also added at a ratio of 1 bead per 4 PBMCs. Three days after co-culturing, supernatant was collected removing the anti-CD3-/anti-CD28-coated beads as well as PBMCs not attached to the BM-MSCs. Furthermore, those weakly attached to the surface of the BM-MSCs were collected by gently pipetting the bottom of each plate with clean RPMI.

tag: cell type

value: mesenchymal stem cell

value: resting PBMCs


title: genomic DNA from brochoscopic biopsy sample [P03140107_T]

data_processing:
GenomeStudio software V2011.1
The MatrixProcessed_PB3.txt contains Average Beta; GenomeStudio was used for data normalization ("normalization based on internal controls").
The MatrixSignal_PB3.txt contains Unmethylated and methylated signal intensities

extract_protocol: genomic DNA was extracted and purified from bronchoscopic biopsie samples using Qiagen DNeasy Kit according to standard instructions

value: squamous cell carcinoma


title: genomic DNA from brochoscopic biopsy sample [P03140107_L]


title: BM_MSC05

value: activated PBMCs


title: UTSW_BC21

value: DLE

value: Male


title: UTSW_BC18

value: blood


title: G43


title: G44


title: genomic DNA from brochoscopic biopsy sample [P02140103_T]

value: brochoscopic biopsy sample


title: genomic DNA from brochoscopic biopsy sample [P02140103_L]


title: BM_MSC04_act


title: BM_MSC04


title: genomic DNA from brochoscopic biopsy sample [P02140101_T]

value: small cell carcinoma


title: G42

value: GBM tumor tissue


title: BM_MSC03_act


title: UTSW_BC16


title: UTSW_BC28

value: SCLE

value: C


title: UTSW_BC15

value: Female


title: G40


title: KO_H3ac

description: ChIP (DNA sequencing)

value: Trrap fl/fl;CreER

value: acetyl-Histone 3 (Millipore)

value: 4-OHT treatment


title: BM_MSC03


title: G39

value: GBM (IV)

value: M


title: UTSW_BC14


title: genomic DNA from brochoscopic biopsy sample [P02140101_L]

value: control, no malignant cells, diagnosis definite


title: genomic DNA from brochoscopic biopsy sample [P02140100_T]

value: tumor sample, diagnosis definite

value: adenocarcinoma


title: G38


title: UTSW_BC13

value: DLE


title: BM_MSC02_act

value: mesenchymal stem cell

value: resting PBMCs


title: genomic DNA from brochoscopic biopsy sample [P02140100_L]

value: brochoscopic biopsy sample


title: UTSW_BC12

value: AA

value: blood


title: G37

value: F

value: GBM tumor tissue


title: genomic DNA from brochoscopic biopsy sample [P02140095_T]

value: squamous cell carcinoma


title: BM_MSC01_act


title: UTSW_BC17

value: Male


title: G36


title: UTSW_BC11

value: LP

value: Female


title: BM_MSC01

value: activated PBMCs


title: genomic DNA from brochoscopic biopsy sample [P02140095_L]


title: genomic DNA from brochoscopic biopsy sample [P02140094_T]

value: large cell carcinoma


title: UTSW_BC10

value: TLE

value: C


title: G35

value: GBM (IV)

value: M


title: UTSW_BC09


title: G34

value: WT


title: genomic DNA from brochoscopic biopsy sample [P02140094_L]

value: control, no malignant cells, diagnosis definite


title: OM-10.1 -SP - Stim 2

city: Jupiter

first: Adam

last: Getzler

state: FL

address: 130 Scripps Way

institute: TSRI-FL

data_processing:
Raw FASTQC files were filtered for read quality using trim-galore version 0.6.1 with the following options: –clip_R1 5 –clip_R2 5 –trim-n –paired
Trimmed reads were aligned to the human transcriptome (GRCh38v100) with the HIV-1 genome added as an additional chromosome (REFSEQ release 202) using salmon version 0.14.1 with the validateMappings option
Aligned transcriptomes were mapped to genes, and differential gene expression was called using tximport version 1.16.1 and DESeq2 version 1.28.1, respectively
TPMs were determined using the countsFromAbundance = “lengthScaledTPM” option in tximport
Genome_build: H. Sapiens: GRCh38v100; HIV-1: REFSEQ 202

growth_protocol: Cells were maintained in RPMI 1640 (Gibco) supplemented with 2.0 mM l-glutamine/100 U/ml penicillin/100 μg/ml streptomycin (Gibco) and 10% heat-inactivated fetal bovine serum (FBS) (Atlas Biologicals; catalog no. FS-0500-AD) (complete RPMI) and cultured at 37°C and 5% CO2. Cells were passaged every 3 days.

extract_protocol:
Total RNA was extracted using the RNeasy kit (Qiagen; no. 74106)
 RNA was DNase treated using the TURBO DNA-free kit (Invitrogen; no. AM1907).mRNA was selectively isolated from total RNA (500 ng) using poly-T oligonucleotides attached to magnetic beads according to the manufacturer’s guidelines in the NEBNext poly(A) mRNA magnetic isolation module (catalog no. E7490; NEB, Ipswich, MA). The library preparation from the enriched mRNA was conducted according to NEBNext Ultra II directional RNA kit (catalog no. E7760; NEB, Ipswich, MA).

treatment_protocol: 45 days of treatment with ART and 10 μM SP or DMSO followed by stimulation with 1 μM prostratin (LC Laboratories; no. P-4462-1MG)

tag: drug treatment

value: Spironolactone

tag: stimulation

value: prostratin

tag: cell line

value: Cloned from HL-60 cells that survived an acute in vitro HIV-1 infection


title: G33

value: F


title: OM-10.1 - DMSO - Stim 2

value: DMSO


title: UTSW_BC08

value: blood


title: genomic DNA from brochoscopic biopsy sample [P01150170_T]

value: tumor sample, diagnosis definite

value: non small cell carcinoma

value: brochoscopic biopsy sample


title: G32

value: GBM tumor tissue


title: UTSW_BC07

value: DLE

value: Female

value: H


title: BM_MSC02

value: mesenchymal stem cell

value: activated PBMCs


title: OM-10.1 - DMSO - NoStim 2


title: genomic DNA from brochoscopic biopsy sample [P01150170_L]


title: G31

value: GBM (IV)

value: M


title: UTSW_BC06

value: SCLE

value: C


title: genomic DNA from brochoscopic biopsy sample [P01140093_T]

value: squamous cell carcinoma


title: G30

value: WT


title: UTSW_BC04


title: OM-10.1 - DMSO - Stim

value: DMSO

value: Cloned from HL-60 cells that survived an acute in vitro HIV-1 infection


title: G29


title: OM-10.1 -SP - NoStim

value: Spironolactone

value: prostratin


title: OM-10.1 -SP - Stim


title: genomic DNA from brochoscopic biopsy sample [77473_Tu]

value: tumor sample, diagnosis definite

value: non small cell carcinoma

value: brochoscopic biopsy sample


title: G28

value: GBM tumor tissue


title: genomic DNA from brochoscopic biopsy sample [77473_Lu]

value: control, no malignant cells, diagnosis definite


title: OM-10.1 - DMSO - NoStim


title: genomic DNA from brochoscopic biopsy sample [P01140093_L]


title: UTSW_BC05

value: Female

value: blood


title: G27

value: GBM (IV)


title: genomic DNA from brochoscopic biopsy sample [77213_T]


title: G26

value: M


title: OM-10.1 -SP - NoStim 2


title: P7.2017

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

data_processing:
CellRanger software (v3.0.2) (10X Genomics) (default parameters)
Hashtag count matrices were obtained from CITE-Seq-Count package (https://zenodo.org/record/2590196) (default parameters).
Genome_build: hg38
Supplementary_files_format_and_content: comma-separated text file with cell x genes count matrix
Supplementary_files_format_and_content: count matrix for all cells from all samples in matrix.mtx. Cell ID in barcodes.tsv. Genes in genes.tsv. Metadata (including in particular the hastag counts for each cell ID) in metadata.tsv

source_name: CD4 T cell

extract_protocol:
PBMC were thawed, washed and cells were stained with fluorophore-conjugated +- DNA-conjugated antibodies (for cohort 2) for cell sorting by flow cytometry and sample pooling for single cell RNAseq library construction (10x Genomics, Single Cell 3′ Reagent Kit (V2 or V3 chemistry, cohort 1 and cohort2, respectively)
RNA libraries were prepared for sequencing using standard 10X Genomics Single Cell 3′ Reagent Kit (V2 or V3 chemistry)

value: peripheral blood

tag: donor

tag: genotype

value: IPEX

tag: center

value: Paris

tag: cohort

value: no

value: yes

value: FKHD

value: exon 12

value: keratitis, blepharitis, rhinitis

value: eczema

tag: triad

tag: enteropathy

tag: eczema

value: severe

value: asthma

value: cow milk

value: dust mite, pollen

value: keratitis, blepharitis, chronic sinusitis

tag: hyperige

value: anti-AIE75, anti-transglutaminase

value: rapamycin, inhaled corticosteroids

tag: outcome

value: alive

tag: hash

value: TGATGGCCTATTGGG

tag: platform


title: genomic DNA from brochoscopic biopsy sample [77213_L]

tag: donor id

tag: histology (diagnosis by pathologists based on one single specimen)

value: control, no malignant cells, diagnosis definite

tag: diagnosis (final clinical diagnosis for the patient)

value: squamous cell carcinoma

tag: tissue

value: brochoscopic biopsy sample


title: Homo_ips_3

city: Shenzhen

first: Minglin

last: Ou

address: No.1017, Dongmen North Road, Luohu District

department: Clinical Medical Research Center of The Second Clinical Medical College

institute: Jinan University

description: Pooled sample of Human iPS cell line 1(ips_M3)-derived cells and Human iPS cell line 2(ips_F3)-derived cells.

data_processing:
Clean reads were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
The basic statistics of the reads were performed by FastQC software.
We used a set of analysis pipeline in the Cell Ranger Single-Cell Software Suite for the data merging, barcode processing, gene counting and alignments.
Genome_build: GRCh38
Supplementary_files_format_and_content: They included barcodes.tsv, genes.tsv and matrix.mtx files. The matrix.mtx file contains the UMI counts, while the other two files contain the cell barcodes and the gene annotation.

extract_protocol:
For each group of samples, about 10000 living cells, including 5000 cells from cell line 1 and 5000 from cell line 2 were loaded for the generation of gel bead-in-emulsion.
The cell samples collected at different time points in the cardiac differentiation process were used for single-cell RNA sequencing library preparation by Chromium Single Cell 3' Reagent kit  and Chromium Controller (10X Genomics) according to the manufacturer's instruction.

tag: time point

tag: Sex

value: not applicable

tag: cell type

value: Human iPS-derived cell


title: G25

tag: disease state

value: GBM (IV)

tag: age

tag: gender

value: F

value: WT

tag: survival (days)

value: GBM tumor tissue


title: B2

value: peripheral blood

tag: donor

tag: genotype

value: IPEX

tag: center

value: Boston

tag: cohort

value: yes

value: no

value: M

value: ZF

value: exon 6

value: diarrhea

value: eczema

tag: triad

tag: enteropathy

value: Yes

value: severe

value: No

value: corticosteroids

value: TTCCGCCTCTCTTTG


title: Homo_ips_2

description: Pooled sample of Human iPS cell line 1(ips_M2)-derived cells and Human iPS cell line 2(ips_F2)-derived cells.

value: not applicable

value: Human iPS-derived cell


title: genomic DNA from brochoscopic biopsy sample [77146_Tu]

tag: donor id

value: probably tumor sample,  diagnosis not definite

value: squamous cell carcinoma

value: brochoscopic biopsy sample


title: HD15

value: peripheral blood

value: HD

value: Boston

value: yes

value: well child visit

tag: hash

value: GGTTGCCAGATGTCA

tag: platform


title: G24

value: GBM (IV)

value: M

tag: tissue

value: GBM tumor tissue


title: Homo_ips_1

description: Pooled sample of Human iPS cell line 1(ips_M1)-derived cells and Human iPS cell line 2(ips_F1)-derived cells.

tag: time point


title: genomic DNA from brochoscopic biopsy sample [77146_Lu]

tag: histology (diagnosis by pathologists based on one single specimen)

tag: diagnosis (final clinical diagnosis for the patient)


title: G23

tag: disease state

value: F

value: WT


title: P7.2016b

value: IPEX

value: Paris

value: no

tag: Sex

value: FKHD

value: exon 12

value: keratitis, blepharitis, rhinitis

value: eczema

tag: eczema

value: severe

value: asthma

value: cow milk

value: dust mite, pollen

value: keratitis, blepharitis, chronic sinusitis

tag: hyperige

value: anti-AIE75, anti-transglutaminase

tag: outcome

value: alive

value: GTCAACTCTTTAGCG


title: G41

value: GBM (IV)

tag: age

tag: gender

value: M

tag: survival (days)

value: GBM tumor tissue


title: genomic DNA from brochoscopic biopsy sample [76964_T]

value: probably tumor sample,  diagnosis not definite

value: non small cell carcinoma

value: brochoscopic biopsy sample


title: HD16

value: peripheral blood

tag: donor

tag: genotype

value: HD

tag: center

value: Paris

tag: cohort

value: no

value: yes

value: elbow fracture

value: TGTCTTTCCTGCCAG


title: UTSW_BC03

value: SCLE

value: Female

tag: ethnicity

value: AA

value: blood


title: Homo_ips_0

description: Pooled sample of Human iPS cell line 1(ips_M0) and Human iPS cell line 2(ips_F0).

value: not applicable

tag: cell type

value: Human iPS cell


title: genomic DNA from brochoscopic biopsy sample [76964_L]

tag: donor id

value: probably benign, diagnosis not definite

tag: tissue


title: UTSW_BC01

value: C


title: Homo_ips_M3

description: Human iPS-derived cells collected at the fourth time point (after 240 hours culture) in the cardiac differentiation; it also is defined as M-iPS-3 in our study.

data_processing:
Clean reads were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Clean reads then mapped to the reference genome using Hisat2 v2.0.5.
Differential expression analysis was performed using the edgeR R package (3.18.1).
Genome_build: GRCh38
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample

extract_protocol:
Total RNA of the cells was extracted by TRIzol (Invitrogen), and 3 μg RNA was taken for each transcriptome library preparation.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

value: male

value: Human iPS-derived cell


title: Homo_ips_F3

description: Human iPS-derived cells collected at the fourth time point (after 240 hours culture) in the cardiac differentiation; it also is defined as F-iPS-3 in our study.

value: female


title: genomic DNA from brochoscopic biopsy sample [76701_T]

tag: histology (diagnosis by pathologists based on one single specimen)

tag: diagnosis (final clinical diagnosis for the patient)

value: small cell carcinoma

value: brochoscopic biopsy sample


title: B6

value: peripheral blood

value: IPEX

value: Boston

tag: Sex

value: M

value: FKHD

value: exon 12

value: diabetes

value: eczema

tag: triad

tag: enteropathy

value: mild

value: no

value: cow milk

value: post-transplant autoimmune hemolytic anemia

value: tacrolimus, IVIG

value: alive

tag: hash

value: AGTAAGTTCAGCGTA

tag: platform


title: G22

tag: disease state

value: GBM (IV)

tag: age

tag: gender

value: WT

value: GBM tumor tissue


title: G21

tag: survival (days)


title: M2

value: peripheral blood

tag: donor

tag: genotype

value: Het

tag: center

value: yes

value: F


title: Homo_ips_F2

description: Human iPS-derived cells collected at the third time point (after 96 hours culture) in the cardiac differentiation; it also is defined as F-iPS-2 in our study.

value: female

value: Human iPS-derived cell


title: genomic DNA from brochoscopic biopsy sample [76701_L]

value: probably tumor sample,  diagnosis not definite

value: small cell carcinoma

value: brochoscopic biopsy sample


title: G19


title: G20


title: HD12

value: HD

value: Boston

tag: cohort

value: M

value: annual physical exam, h/o urethral stricture s/p surgery

value: AAGTATCGTTTCGCA


title: Homo_ips_M2

description: Human iPS-derived cells collected at the third time point (after 96 hours culture) in the cardiac differentiation; it also is defined as M-iPS-2 in our study.

value: male


title: G18

value: GBM (IV)

value: WT


title: dct_8

city: Berlin

first: Oliver

last: Nagel

address: Hindenburgdamm 30

department: Department of Gastroenterology, Rheumatology and Infectious Diseases

institute: Charité - Universitätsmedizin Berlin

description:
101035
dct_wt_vs_ko_diff_expr.csv
raw_counts.csv

data_processing:
Basecalling: Casava 1.8
Readmaping: STAR 2.5, default parameters
count reads: GenomicRanges 1.36.1
remove unwanted variation RUVSeq 1.18.0
differential expression analysis: DESeq2 v 1.24.0
Genome_build: GRCm38
Supplementary_files_format_and_content: csv: raw counts, diff. exp. results

source_name: kidney, distal convoluted tubule

growth_protocol: Mice were housed under standardized conditions (12 hr light/dark cycle; 22–24°C temperature; 55% ± 15% humidity ad libitum access to standard diet and water).

extract_protocol:
Rneasy Plus Micro kit
Illumina Nextera XT DNA sample preparation protocol

treatment_protocol: Mice were sacrificed by terminal blood collection and decapitation under deep anesthesia (5% isoflurane). Kidneys were removed immediately. After decapsulation thin transversal slices were cut for either enzymatic tubule preparation or kept in incubation solution on ice for electrophysiological measurements. For RNA preparation 10 PCTs and approx. 20 DCTs per kidney were pooled, snap frozen and stored at -80°C until further processing for RNA-Seq.

value: Cldn10a KO

value: kidney, distal convoluted tubule


title: Homo_ips_F1

description: Human iPS-derived cells collected at the second time point (after 48 hours culture) in the cardiac differentiation; it also is defined as F-iPS-1 in our study.


title: B1.2017b

value: peripheral blood

value: IPEX

value: yes

value: Nterm

value: exon 5

value: failure to thrive

value: diarrhea

value: no

tag: eczema

value: autoimmune gastritis

tag: hyperige

tag: outcome

value: alive

value: GTCAACTCTTTAGCG


title: G17

value: M

tag: tissue

value: GBM tumor tissue


title: Homo_ips_M1

description: Human iPS-derived cells collected at the second time point (after 48 hours culture) in the cardiac differentiation; it also is defined as M-iPS-1 in our study.

tag: Sex

value: male

value: Human iPS-derived cell


title: G16

value: GBM (IV)


title: dct_6

description:
101031
dct_wt_vs_ko_diff_expr.csv
raw_counts.csv

value: Cldn10a KO

value: kidney, distal convoluted tubule


title: HD13

value: peripheral blood

value: HD

value: Boston

value: back pain

value: GGTTGCCAGATGTCA


title: G15

value: WT


title: dct_5

description:
101029
dct_wt_vs_ko_diff_expr.csv
raw_counts.csv


title: Homo_ips_M0

description: Human iPS cell generated from male urine cells; it also is defined as M-iPS-0 in our study.

value: Human iPS cell


title: B4.2017b

value: IPEX

value: yes

value: RBR

value: exon 9

tag: triad

value: no

value: TGATGGCCTATTGGG


title: HD14

value: M

value: urology f/u bilateral retractile testes

value: TGTCTTTCCTGCCAG


title: dct_4

description:
101021
dct_wt_vs_ko_diff_expr.csv
raw_counts.csv

value: kidney, distal convoluted tubule


title: G14

value: GBM (IV)

value: GBM tumor tissue


title: G13


title: P5.2017

value: peripheral blood

value: Paris

value: splicing (donor site)

value: intron 8

value: proteinuria

value: diabetes

tag: enteropathy

value: mild

value: cow milk

value: azathioprine, tacrolimus

value: alive, stable

value: TTCCGCCTCTCTTTG


title: B5.b

value: IPEX

value: Boston

value: yes

value: M

value: FKHD

value: exon 12

tag: hash


title: G12

value: GBM (IV)

value: F

value: WT

value: GBM tumor tissue


title: P4.2015

value: peripheral blood

value: Paris

value: splicing (acceptor site)

value: intron 7

value: no

value: severe

value: yes (dyspraxy, ADHD)

value: asthma

value: egg, gluten

value: anaphylatic shock, asthma

value: bronchial dilation

value: ANA, anti-insulin, anti-GAD

value: rapamycin, inhaled corticosteroids

value: alive

value: GTCAACTCTTTAGCG

tag: platform


title: G11

tag: disease state

value: GBM (IV)

value: F

value: WT


title: dct_7

description:
101033
dct_wt_vs_ko_diff_expr.csv
raw_counts.csv

value: Cldn10a KO

value: kidney, distal convoluted tubule


title: dct_1

description:
101015
dct_wt_vs_ko_diff_expr.csv
raw_counts.csv


title: HD09

value: peripheral blood

value: HD

value: Paris

value: yes

value: M

value: congenital torticollis

value: AAGTATCGTTTCGCA


title: G10

tag: age

value: MUT

value: GBM tumor tissue


title: pct_7

description:
97797
pct_wt_vs_ko_diff_expr.csv
raw_counts.csv

source_name: kidney, proximal tubule

value: kidney, proximal tubule


title: Homo_ips_F0

description: Human iPS cell generated from male urine cells; it also is defined as F-iPS-0 in our study.

value: female

value: Human iPS cell


title: pct_6

description:
97795
pct_wt_vs_ko_diff_expr.csv
raw_counts.csv


title: M5

value: Het

value: no

value: AGTAAGTTCAGCGTA


title: G9

value: GBM (IV)

tag: gender

value: F

value: WT


title: HD11

value: peripheral blood

value: HD

value: phalangeal fracture

value: TGTCTTTCCTGCCAG


title: P4.2017

value: IPEX

value: Paris

value: yes

value: M

value: splicing (acceptor site)

value: intron 7

value: diabetes

value: severe

value: yes (dyspraxy, ADHD)

value: asthma

value: egg, gluten

value: anaphylatic shock, asthma

value: bronchial dilation

value: ANA, anti-insulin, anti-GAD

value: rapamycin, inhaled corticosteroids

value: alive

value: TGATGGCCTATTGGG


title: dct_3

description:
101019
dct_wt_vs_ko_diff_expr.csv
raw_counts.csv

value: WT

value: kidney, distal convoluted tubule


title: pct_5

description:
101025
pct_wt_vs_ko_diff_expr.csv
raw_counts.csv

value: Cldn10a KO

value: kidney, proximal tubule


title: dct_2

description:
101017
dct_wt_vs_ko_diff_expr.csv
raw_counts.csv


title: G7

value: GBM (IV)

value: M

tag: survival (days)

value: GBM tumor tissue


title: HD06

value: peripheral blood

tag: donor

value: HD

value: Paris

value: yes

value: Surgical referral :trauma orthopaedic - no past medical history


title: B5.a

tag: genotype

value: IPEX

value: Boston

value: no

value: FKHD

value: exon 12


title: G8

value: WT


title: G6

value: F


title: pct_2

description:
101011
pct_wt_vs_ko_diff_expr.csv
raw_counts.csv


title: liver graft_7 d_NMP_rep1

first: Hongli

last: Song

state: Tianjin

address: No. 24 Fukang Road, Nankai District

department: Department of Organ Transplantation

institute: Tianjin First Central Hospital

description: Gene expression after 7 d in transplanted liver of rat

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60° C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human Gene Expression（8*60K）for 17 hours at 65° C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37° C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

organism: Rattus norvegicus

source_name: liver graft, 7 d, NMP, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions.

treatment_protocol: BMMSCs were isolated from rat bone marrow and modified with the adenovirus for heme oxygenase 1 (HO-1) gene.Saline solution, BMMSCs or HO-1/BMMSCs were perfused into the donor liver in vitro using a normothermic machine perfusion (NMP) system, followed by liver transplantation. The rats were divided into the following five groups according to the different liver treatments: sham operated (Sham) group; static cold storage (SCS) group; NMP group; NMP combined with BMMSCs (BMP) group; and NMP combined with HO-1/BMMSCs (HMP) group.

tag: treatment

value: NMP

value: male

value: liver graft


title: G5

value: GBM (IV)


title: liver graft_7 d_NMP+HO-1/BMMSCs_rep1

source_name: liver graft, 7 d, NMP+HO-1/BMMSCs, replicate 1


title: B4.2017a

tag: center

tag: cohort

value: M

value: RBR

value: exon 9

value: alive


title: B7

value: peripheral blood

value: yes

value: follow-up visit

value: diarrhea

value: neonatal respiratory distress syndrome

tag: hyperige

value: deceased


title: liver graft_7 d_NMP+BMMSCs_rep1

source_name: liver graft, 7 d, NMP+BMMSCs, replicate 1

value: NMP+BMMSCs


title: pct_1

description:
101009
pct_wt_vs_ko_diff_expr.csv
raw_counts.csv

value: WT

value: kidney, proximal tubule


title: HD03

value: HD

value: Paris

value: Surgical referral :trauma orthopaedic - no past medical history


title: G3

value: GBM (IV)

value: GBM tumor tissue


title: liver graft_7 d_SCS_rep1

source_name: liver graft, 7 d, SCS, replicate 1

value: SCS

value: male

value: liver graft


title: pct_4

description:
101023
pct_wt_vs_ko_diff_expr.csv
raw_counts.csv

value: Cldn10a KO


title: Naked mole rat TRF1 in normoxia condition_Sample B

city: Brussels

first: Frederick

last: Libert

address: 808 route de Lennik

department: IRIBHM

country: Belgium

institute: ULB

description:
14-NormoMouseB-11
Naked mole rat TRF1 wild type.
normo-hypo_NMR-TRF1_mutant-wt.csv

data_processing:
Sequenced reads were trimmed for adaptor sequence.
Paired-end reads were mapped against the mouse reference genome (GRCm38.p4/mm10) using the STAR software to generate read alignments.
The annotation file Mus_musculus.GRCm38.90.gtf was obtained from the ftp.Ensembl.org server.
Following transcript assembly, gene level counts were obtained using HTSeq.
Genome_build: GRCm38.p4/mm10
Supplementary_files_format_and_content: normo-hypo_NMR-TRF1_mutant-wt.csv: Normalized abundance measurements in CPM.

source_name: tMEF cells

growth_protocol: Cells were grown in DEM with 10% fetal calf serum and antibiotic-antimycotic.

extract_protocol:
Total RNA was extracted with the MicroElute total RNA kit (Omega Bio-Tek) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard TruSeq RNA Illumina protocols.

treatment_protocol: Cells were grown in 1% O2 (hypoxia) or atmospheric oxygen (normoxia).

tag: genotype/variation

value: naked mole rat TRF1 wild type

tag: cell type

value: tMEF cells

value: Normoxia


title: HD02

tag: tissue

value: peripheral blood

value: yes

tag: Sex

value: M


title: liver graft_7 d_sham operated_rep1

source_name: liver graft, 7 d, sham operated, replicate 1

value: sham operated


title: Naked mole rat TRF1 in normoxia condition_Sample A

description:
13-NormoMouseA-8
Naked mole rat TRF1 wild type.
normo-hypo_NMR-TRF1_mutant-wt.csv


title: pct_3

description:
101013
pct_wt_vs_ko_diff_expr.csv
raw_counts.csv

value: WT

value: kidney, proximal tubule


title: Double mutant GLAD/TIN of naked mole rat TRF1 in hypoxia condition_Sample B

description:
12-Hypo-Dbmut-B
Double mutant GLAD/TIN of naked mole rat TRF1.
normo-hypo_NMR-TRF1_mutant-wt.csv

value: double mutant GLAD/TIN of naked mole rat TRF1

value: Hypoxia


title: HD01

value: HD

value: Paris

value: Surgical referral :trauma orthopaedic - no past medical history


title: G1

value: GBM (IV)

value: GBM tumor tissue


title: G4


title: P3

value: IPEX

value: no

value: Nterm

value: exon 3

value: diarrhea

value: eczema

tag: triad

tag: enteropathy

tag: eczema

value: severe

value: yes (kidney transplant 2014)

value: yes (sensitive neuropathy, hypersignal in the white matter)

value: cow milk

value: anti-GAD65, anti-langherans island, antiI-AE

value: rapamycin, tacrolimus

value: yes (Kidney april 2014 and Bone marrow oct 2015)

tag: outcome

value: deceased secondary to BMT and kidney transplant complications


title: Mutant TIN of naked mole rat TRF1 in hypoxia condition_Sample B

description:
10-Hypo-TIN-B
Mutant TIN of naked mole rat TRF1.
normo-hypo_NMR-TRF1_mutant-wt.csv

value: mutant TIN of naked mole rat TRF1

value: tMEF cells

value: Hypoxia


title: Mutant TIN of naked mole rat TRF1 in hypoxia condition_Sample A

description:
9-Hypo-TIN-A
Mutant TIN of naked mole rat TRF1.
normo-hypo_NMR-TRF1_mutant-wt.csv


title: G2

tag: disease state

value: GBM (IV)

tag: age

value: M

value: GBM tumor tissue


title: P4.2016

value: peripheral blood

value: IPEX

value: Paris

value: yes

value: splicing (acceptor site)

value: intron 7

value: follow-up visit

value: diabetes

value: no

value: yes (dyspraxy, ADHD)

value: asthma

value: egg, gluten

value: anaphylatic shock, asthma

value: bronchial dilation

value: ANA, anti-insulin, anti-GAD

value: rapamycin, inhaled corticosteroids

value: alive

tag: hash

tag: platform


title: Mutant GLAD of naked mole rat TRF1 in hypoxia condition_Sample B

description:
8-Hypo-GLAD-B
Mutant GLAD of naked mole rat TRF1.
normo-hypo_NMR-TRF1_mutant-wt.csv

value: mutant GLAD of naked mole rat TRF1

value: tMEF cells

value: Hypoxia


title: P1

value: peripheral blood

tag: donor

tag: genotype

value: IPEX

value: Paris

value: yes

value: M

value: promoter and exon 1

value: diarrhea

value: eczema

value: mild

value: chronic bronchitis, bacterial  pneumonia

value: cow milk, eggs, gluten, fruits

value: rapamycin


title: Double mutant GLAD/TIN of naked mole rat TRF1 in hypoxia condition_Sample A

description:
11-Hypo-Dbmut-A
Double mutant GLAD/TIN of naked mole rat TRF1.
normo-hypo_NMR-TRF1_mutant-wt.csv

value: double mutant GLAD/TIN of naked mole rat TRF1

tag: treatment


title: Mutant GLAD of naked mole rat TRF1 in hypoxia condition_Sample A

description:
7-Hypo-GLAD-A
Mutant GLAD of naked mole rat TRF1.
normo-hypo_NMR-TRF1_mutant-wt.csv


title: WM983B-HA15RES

city: Debrecen

first: Viktoria

last: Koroknai

address: 26/B Kassai str.

department: Department of Public Health and Epidemiology

country: Hungary

institute: University of Debrecen

description: HA15 resistant WM983B cell line

data_processing:
Raw sequencing data (fastq) were aligned to human reference genome version GRCh38 using HISAT2 algorithm and BAM files were generated. Downstream analysis was performed using StrandNGS software (www.strand-ngs.com).
BAM files were imported into the software DESeq1 algorithm was used for normalization.
To identify differentially expressed genes between conditions Moderated T-Test with Benjamini-Hochberg FDR for multiple testing correction was used.
Genome_build: hg38
Supplementary_files_format_and_content: raw and normalized abundance measurements

source_name: melanoma cell line

growth_protocol: The cells were cultured in RPMI-1640 medium (Lonza Group Ltd., Basel, Switzerland) and supplemented with 10 % foetal bovine serum (Gibco, CA, USA), 2 mmol/L glutamine, and antibiotics at 37°C.

extract_protocol:
RNeasy Mini Kit (Qiagen GmbH, Hilden, Germany) was used to isolate total RNA from the melanoma cell lines.
cDNA libraries for RNA-Seq analyses were prepared from 1 μg total RNA using Ultra II RNA Sample Prep kit (New England BioLabs Inc., USA) according to the manufacturer’s protocol.

treatment_protocol: WM983B melanoma cell line was seeded at a low density in T/25 flasks until the cells reached 80% confluence. Then, the cells were switched to a medium containing 10 µM HA15 and increasing the concentration. until 30 µM HA15 and cultured. The surviving cells were fed with a medium containing 30 µM HA15 every 3 days until cells reached the 80% confluence (~10 weeks). The resistant cell lines were designated as WM983B-HA15RES. On the other hand, WM983B  cells  were starved for 14 hours, designated as WM983B-14HR-STARV

tag: tumor stage

value: metastatic

tag: cell line


title: original WM983B cell line

description: original WM983B cell line


title: WM983B-14HR-STARV

description: WM983B cell line after 14 hours of starvation


title: Cel.seq.exp.13

city: New York

first: Jinyang

last: Li

address: 1230 York Ave

institute: The Rockefeller University

data_processing:
trim R1 reads to 12 bp and R2 reads to 36 bp using cutadapt
process of trimmed fastq files with UMI-Tools using extract function
mapping reads using STAR
sort bam files using samtools
index bam files using samtools
counting molecules using UMI-Tools using count function
merge all UMI results together using bash join function
Genome_build: mm10
Supplementary_files_format_and_content: UMI count for each cell and sample information for each cell

source_name: liver metastasis and primary tumor

growth_protocol: 6419c5 pancreatic tumor cells were inoculated to the pancreas of C57/Bl6 mice

extract_protocol:
Tumor cells were isolated via photoconversion-based isolation protocol from liver metastasis and primary tumor in a mouse pancreatic cancer model
Libraries were constructed by following the cel-seq2 procedure by the developer’s protocol
Cel-seq2 single cell RNAseq library

tag: cell line for implantation

tag: genetic background


title: Cel.seq.exp.12