title: E24 MEF wt P25 4H_0002 AICAR 2mM

source_name: MEF, WT, AICAR


title: E24 MEF wt P25 4H_0004 AICAR 2mM

status: Public on Mar 04 2019

type: RNA

city: Lausanne

first: Frederic

last: Raymond

address: Campus EPFL - Quartier de l'Innovation

department: Functional Genomics

country: Switzerland

institute: Nestle Institute of Health Sciences

hyb_protocol: Affymetrix hybridization procedure.

scan_protocol: Affymetrix GeneChip scanner 3000 7G.

data_processing: Data were background subtracted, log2 transformed, and quantile normalized using RMA in Partek GS software.

label: Biotin

molecule: total RNA

organism: Mus musculus

label_protocol: Labeled-cRNA was performed following TotalPrep RNA Amplification Kit. cRNA fragmentation was done following Affymetrix procedure, prior to hybridization.

growth_protocol:
C57BL/6 mice were obtained from Jackson Laboratories.
Mouse embryonic fibroblasts (MEFs) control or AMPK α1-/-/α2-/- were cultured in DMEM-Glutamax supplemented with 10% fetal calf serum (FCS) and 1% penicillin streptomycin. Cells were treated with vehicle (DMSO), AICAR 2 mM or 991 10 μM for 4 h and subsequently harvested.
Primary hepatocytes were isolated by collagenase perfusion and prepared as previously described (Fullerton et al., 2009). More in details, cells were plated on collagen-coated plates in M199-Glutamax containing 10% FCS, 1% penicillin streptomycin, 1 M HEPES, 10 nM insulin, 200 nM T3, 100 nM dexamethasone, and allowed to adhere for 4 h. Then cells were washed with PBS and provided with media comprising M199-Glutamax, 1% penicillin streptomycin and 100 nM dexamethasone. Hepatocytes were incubated overnight at 37 °C, and the experiments were performed the following morning. Briefly, hepatocytes were exposed to vehicle (DMSO), AICAR 300 μM or 991 3 μM for 4 h and then harvested.

extract_protocol: Total RNA was extracted using the RNAdvance Tissue Kit (A32645; Agencourt) and quantified by RiboGreen (R11490; ThermoFisher). RNA integrity was determined by Fragment Analyzer.

tag: strain/background

tag: cell type

value: MEF

tag: genotype/variation

value: WT

tag: treatment

value: AICAR

tag: technical replicate

tag: biological replicate

value: Not Applicable


title: Hko4_No_2_b1

source_name: Hepatocytes, dKO, Vehicle

value: Hepatocytes

value: AMPK alpha1-/- alpha2-/-

value: Vehicle


title: E24 MEF wt P25 4H_0003 991 10uM

source_name: MEF, WT, 991


title: E24 MEF wt P25 4H_0004 991 10uM


title: Performance_Post_11

type: SRA

city: Helsinki

first: Irma

last: Järvelä

address: Department of Medical Genetics, University of Helsinki, P.O. Box 720

department: Department of Medical Genetics

country: Finland

institute: University of Helsinki

library_source: transcriptomic

data_processing:
Bustard 1.9.3 was used for basecalling.
Sequenced reads were trimmed for 3' adaptors  and filtered for shorter (<15 bp) and low-quality reads (quality<20) with Trim Galore! V0.3.7.
Reads are then mapped to human genome reference (GRCh38, Ensembl release 76) using bowtie v1.1.2 requiring perfect match for a seed length of 18 and selecting only unique alignment
miRNA expressions were quantified from the alignments using HTSeq version 0.6.1p1 according to miRBase release 20 annotations.
Genome_build: GRCh38, Ensembl release 76
Supplementary_files_format_and_content: tab-delimited text file with miRNA count for all samples

organism: Homo sapiens

source_name: human peripheral whole blood, after music-performance

extract_protocol:
2.5ml of peripheral blood was drawn into PAXgene Blood RNA tubes (PreAnalytiX GmbH, Hombrechtikon, Switzerland) before and after music-performance and RNA was isolated using either the PAXgene Blood miRNA Kit as per the kit manual.
small RNA libraries were prepared using NEBNext® Small RNA Library Prep Set using standard Illumina protocols

tag: tissue

value: peripheral blood

tag: ethnicity

value: Finnish

value: music-performance


title: E24 MEF wt P25 4H_0001 No Treat

source_name: MEF, WT, Vehicle


title: E24 MEF wt P25 4H_0003 AICAR 2mM


title: E24 MEF dko P25 4H_0004 AICAR 2mM

source_name: MEF, dKO, AICAR


title: E24 MEF dko P25 4H_0004 No Treat

source_name: MEF, dKO, Vehicle


title: Hko4_AICAR_300uM_4_b1

source_name: Hepatocytes, dKO, AICAR


title: E24 MEF dko P25 4H_0003 991 10uM

source_name: MEF, dKO, 991


title: E24 MEF wt P25 4H_0001 AICAR 2mM


title: Performance_Pre_11

source_name: human peripheral whole blood, before music-performance

value: baseline


title: E24 MEF dko P25 4H_0002 991 10uM


title: E24 MEF dko P25 4H_0001 991 10uM


title: E24 MEF wt P25 4H_0002 991 10uM


title: Performance_Pre_10


title: E24 MEF wt P25 4H_0003 No Treat


title: E24 MEF dko P25 4H_0003 AICAR 2mM


title: E24 MEF dko P25 4H_0001 AICAR 2mM


title: E24 MEF dko P25 4H_0002 AICAR 2mM


title: E24 MEF dko P25 4H_0004 991 10uM


title: E24 MEF wt P25 4H_0002 No Treat


title: E24 MEF dko P25 4H_0001 No Treat


title: E24 MEF dko P25 4H_0003 No Treat


title: Performance_Post_9


title: Performance_Pre_9


title: Performance_Pre_8


title: Performance_Post_8


title: Performance_Post_7


title: Performance_Post_10


title: Performance_Pre_7


title: Performance_Pre_5


title: Performance_Pre_6


title: Performance_Pre_3


title: Performance_Post_3


title: Performance_Post_2


title: Performance_Pre_2


title: Performance_Post_1


title: Performance_Pre_1


title: pombe_h90-1_input_PE

city: Edinburgh

first: Robin

last: Allshire

state: Midlothian

address: Max Born Cresent

country: United Kingdom

institute: The University of Edinburgh

library_source: genomic

data_processing:
ChIP-seq reads were aligned to reference genome using Bowtie2
Genome_build: Pombe: ASM294v2.20
Genome_build: S. japonicus: GCA_000149845
Genome_build: S. croyphylus: assembly genome
Genome_build: S. octosporus: assembly genome
Supplementary_files_format_and_content: bigwig files were generated deeptools normalized by RPKM

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: cell

growth_protocol: cell were gwon in rich medium (YES).

extract_protocol:
Lysates were prepared using standard bead beating procedure, sonicated to achieve fragmements of 200-400bp and clarified by centrifugation at 17000g.
Libraries were prepared using standard Illumina pipeline.

value: whole cells

tag: strain

tag: chip antibody

value: input


title: pombe_input_PE

value: wild-type


title: pombe_H3K9_RA_PE


title: pombe_cenpa_PE

value: cenpa


title: pombe_input_RA_PE


title: pombe_h90-2_H3K9_PE


title: pombe_h90-1_H3K9_PE


title: Performance_Post_6


title: Performance_Post_5


title: RET_BL21

city: Chicago

first: Alexander

last: Mankin

state: Illinois (IL)

address: 900 S. Ashland Avenue Room 3056

department: Pharmacognosy

country: USA

institute: University of Illinois at Chicago

data_processing:
library strategy: Ribo-seq
Reads were trimmed with Cutadapt 1.1.a
Reads were first aligned to a ncRNA fasta file and the unmapped reads were subsequently mapped to the respective genomes with Bowtie 1.1.2
P-sites of the ribosomes were mapped as 15 nts away from the 3prime end of the read and used to calculate nucleotide rpm
Genome_build: U00096, CP001509_3
Supplementary_files_format_and_content: wig, rpm values of the calculated ribosmal P-site

organism: Escherichia coli

source_name: Bacterial culture

extract_protocol:
Ribosome protected fragments were isolated as described in Oh et al. 2011
Libraries were generated as described in Oh et al. 2011

value: Retapamulin


title: No_Drug_BL21

value: none (untreated)


title: E24 MEF dko P25 4H_0002 No Treat

value: MEF


title: pombe_h90-2_INPUT_PE

value: INPUT


title: 254706910029_b3 - nda9_NI_3days_1 vs Ctrl_NI_3days_1

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: arabidopsis thaliana (columbia)  mutant (col0) -  dev.stage (boyes et al. plant cell 2001): boyes: 1.05

hyb_protocol: Ctrl_NI_3days_1 Cy5 / nda9_NI_3days_1 Cy3 : 20pmol.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 50%, Cy5:635nm,pmt voltage 700V,laser power 45%

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, total RNA  .

growth_protocol: whole plant - Media=Agar plates with MS-255 medium, 1% w/v sucrose Temperature=24°C Light=long day

treatment_protocol: Name:Estradiol-Inducible_3days - compound based treatment - compound addition,estradiol,earthworms:quantity 185uM time 0day . Seedlings are grown on plates with 35 mL solid agar medium. Treatment is through addition of 2 mL liquid medium with 185 µM estradiol to each agar plate.

tag: ecotype

value: Control

tag: developmental stage

value: Boyes 1.05 (Boyes et al. Plant Cell 2001)

tag: time point

value: day 3


title: 254706910029_b1 - nda9_NI_4days_1 vs Ctrl_NI_4days_1

hyb_protocol: Ctrl_NI_4days_1 Cy5 / nda9_NI_4days_1 Cy3 : 20pmol.

treatment_protocol: Name:Estradiol-Inducible_4days - compound based treatment - compound addition,estradiol,earthworms:quantity 185uM time 0day . Seedlings are grown on plates with 35 mL solid agar medium. Treatment is through addition of 2 mL liquid medium with 185 µM estradiol to each agar plate.

value: day 4


title: 254706910029_b4 - Ctrl_NI_3days_1 vs nda9_NI_3days_1

hyb_protocol: nda9_NI_3days_1 Cy5 / Ctrl_NI_3days_1 Cy3 : 20pmol.


title: 254706910029_b2 - Ctrl_NI_4days_1 vs nda9_NI_4days_1

hyb_protocol: nda9_NI_4days_1 Cy5 / Ctrl_NI_4days_1 Cy3 : 20pmol.


title: 254706910028_b2 - Ctrl_NI_2days_1 vs nda9_NI_2days_1

hyb_protocol: nda9_NI_2days_1 Cy5 / Ctrl_NI_2days_1 Cy3 : 20pmol.

treatment_protocol: Name:Estradiol-Inducible_2days - compound based treatment - compound addition,estradiol,earthworms:quantity 185uM time 0day . Seedlings are grown on plates with 35 mL solid agar medium. Treatment is through addition of 2 mL liquid medium with 185 µM estradiol to each agar plate.

value: day 2


title: 254706910020_b4 - Ctrl_LI_4days_1 vs nda9_LI_4days_1

hyb_protocol: nda9_LI_4days_1 Cy5 / Ctrl_LI_4days_1 Cy3 : 20pmol.


title: 254706910019_b3 - nda9_LI_2days_1 vs Ctrl_LI_2days_1

hyb_protocol: Ctrl_LI_2days_1 Cy5 / nda9_LI_2days_1 Cy3 : 20pmol.


title: 254706910019_b2 - Ctrl_LI_3days_1 vs nda9_LI_3days_1

hyb_protocol: nda9_LI_3days_1 Cy5 / Ctrl_LI_3days_1 Cy3 : 20pmol.


title: 254706910028_b4 - Ctrl_NI_1day_1 vs nda9_NI_1day_1

hyb_protocol: nda9_NI_1day_1 Cy5 / Ctrl_NI_1day_1 Cy3 : 20pmol.

treatment_protocol: Name:Estradiol-Inducible_1day - compound based treatment - compound addition,estradiol,earthworms:quantity 185uM time 0day . Seedlings are grown on plates with 35 mL solid agar medium. Treatment is through addition of 2 mL liquid medium with 185 µM estradiol to each agar plate.

value: day 1


title: NHDF cells, single-cell RNA-seq, non-synchronous 37C infection, 5hpi, Replicate 5

city: Berlin

first: Emanuel

last: Wyler

address: Robert Roessle Str 10

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max Delbrück Center for Molecular Medicine

description:
scRNA-seq
HSV1scRNA_rawcounts_allcells.txt.gz
scRNAseq_Rep45_morethan2000genes_normcounts.txt

data_processing:
Bulk RNA-seq reads were mapped to the hg38 reference using Tophat2 (Kim et al. 2013, PMID: 23618408).
Reads were counted using quasR (Gaidatzis et al. 2015, PMID: 25417205) with the Gencode gene annotation version 28 and stored in the file bulk_RNA-seq_readcounts.txt.gz
Single-cell RNA-seq data was processed using the PiGx pipeline (Wurmus et al. 2018, PMID: 30277498) to yield the raw counts in HSV1scRNA_rawcounts_allcells.txt.gz
After filtering cells with less than 2000 detected genes, normalized counts, cell cycle phase and tSNE coordinates were calculated using the Seurat package (Butler et al., 2018, PMID: 29608179) and stored in the files xx. Cell cyle marker genes were taken from Kowalczyk et al. 2015, PMID: 26430063.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-separated text

molecule: polyA RNA

source_name: NHDF primary human fibroblasts

growth_protocol: Primary human juveline foreskin fibroblasts (Promocell C-12300) were cultured in DMEM supplemented with 10% Fetal Bovine Serum (FBS), 100 units/ml penicillin, 100 µg/ml streptomycin, and non-essential amino acids.

extract_protocol:
Drop-seq
For bulk RNA-sequencing, Cells were resuspended in Trizol and, following Chloroform-mediate phase separation, RNA extracted from the aqueous phase using the CC-25 kit (Zymo). For scRNA-seq, cells were fixed in 80% methanol and analysed using the Drop-Seq protocol (Macosko et al. 2015, PMID: 26000488)
See column "library construction protocol" in the SAMPLES section.

treatment_protocol: Cells were infected with Herpes simplex virus 1 as indicated.

tag: hsv-1 infection

value: Infected 5h before harvesting

tag: infection protocol

value: MOI 10, 30min 37 degree, conditioned medium

tag: rna isolation

value: single-cell RNA


title: 254706910028_b1 - nda9_NI_2days_1 vs Ctrl_NI_2days_1

hyb_protocol: Ctrl_NI_2days_1 Cy5 / nda9_NI_2days_1 Cy3 : 20pmol.


title: 254706910010_b4 - Ctrl_HI_2days_1 vs nda9_HI_2days_1

hyb_protocol: nda9_HI_2days_1 Cy5 / Ctrl_HI_2days_1 Cy3 : 20pmol.


title: 254706910020_b2 - Ctrl_NI_0day_1 vs nda9_NI_0day_1

hyb_protocol: nda9_NI_0day_1 Cy5 / Ctrl_NI_0day_1 Cy3 : 20pmol.

treatment_protocol: Name:Estradiol-Inducible_0day - compound based treatment - compound addition,estradiol,earthworms:quantity 185uM time 0day . Seedlings are grown on plates with 35 mL solid agar medium. Treatment is through addition of 2 mL liquid medium with 185 µM estradiol to each agar plate.

value: day 0


title: 254706910020_b3 - nda9_LI_4days_1 vs Ctrl_LI_4days_1

hyb_protocol: Ctrl_LI_4days_1 Cy5 / nda9_LI_4days_1 Cy3 : 20pmol.


title: 254706910019_b1 - nda9_LI_3days_1 vs Ctrl_LI_3days_1

hyb_protocol: Ctrl_LI_3days_1 Cy5 / nda9_LI_3days_1 Cy3 : 20pmol.


title: NHDF cells, single-cell RNA-seq, non-synchronous 37C infection, 5hpi, Replicate 4


title: 254706910018_b1 - nda9_LI_1day_1 vs Ctrl_LI_1day_1

hyb_protocol: Ctrl_LI_1day_1 Cy5 / nda9_LI_1day_1 Cy3 : 20pmol.


title: 254706910018_b4 - Ctrl_LI_0day_1 vs nda9_LI_0day_1

hyb_protocol: nda9_LI_0day_1 Cy5 / Ctrl_LI_0day_1 Cy3 : 20pmol.


title: 254706910020_b1 - nda9_NI_0day_1 vs Ctrl_NI_0day_1

hyb_protocol: Ctrl_NI_0day_1 Cy5 / nda9_NI_0day_1 Cy3 : 20pmol.


title: 254706910008_b2 - Ctrl_HI_0day_1 vs nda9_HI_0day_1

hyb_protocol: nda9_HI_0day_1 Cy5 / Ctrl_HI_0day_1 Cy3 : 20pmol.


title: 254706910017_b3 - nda9_HI_3days_1 vs Ctrl_HI_3days_1

hyb_protocol: Ctrl_HI_3days_1 Cy5 / nda9_HI_3days_1 Cy3 : 20pmol.


title: NHDF cells, single-cell RNA-seq, non-synchronous 37C infection, 3hpi, Replicate 4

value: Infected 3h before harvesting


title: 254706910018_b3 - nda9_LI_0day_1 vs Ctrl_LI_0day_1

hyb_protocol: Ctrl_LI_0day_1 Cy5 / nda9_LI_0day_1 Cy3 : 20pmol.


title: 254706910017_b2 - Ctrl_HI_4days_1 vs nda9_HI_4days_1

hyb_protocol: nda9_HI_4days_1 Cy5 / Ctrl_HI_4days_1 Cy3 : 20pmol.


title: 254706910019_b4 - Ctrl_LI_2days_1 vs nda9_LI_2days_1

hyb_protocol: nda9_LI_2days_1 Cy5 / Ctrl_LI_2days_1 Cy3 : 20pmol.


title: 254706910017_b1 - nda9_HI_4days_1 vs Ctrl_HI_4days_1

hyb_protocol: Ctrl_HI_4days_1 Cy5 / nda9_HI_4days_1 Cy3 : 20pmol.


title: 254706910028_b3 - nda9_NI_1day_1 vs Ctrl_NI_1day_1

hyb_protocol: Ctrl_NI_1day_1 Cy5 / nda9_NI_1day_1 Cy3 : 20pmol.


title: 254706910008_b3 - nda9_HI_1day_1 vs Ctrl_HI_1day_1

hyb_protocol: Ctrl_HI_1day_1 Cy5 / nda9_HI_1day_1 Cy3 : 20pmol.


title: 254706910008_b4 - Ctrl_HI_1day_1 vs nda9_HI_1day_1

hyb_protocol: nda9_HI_1day_1 Cy5 / Ctrl_HI_1day_1 Cy3 : 20pmol.


title: NHDF cells, single-cell RNA-seq, non-synchronous 37C infection, 3hpi, Replicate 5


title: 254706910018_b2 - Ctrl_LI_1day_1 vs nda9_LI_1day_1

hyb_protocol: nda9_LI_1day_1 Cy5 / Ctrl_LI_1day_1 Cy3 : 20pmol.


title: NHDF cells, stranded polyA RNA-seq, non-synchronous 37C mock infection, 1hpi

description:
Stranded RNA-seq
bulk_RNA-seq_readcounts.txt

extract_protocol:
TruSeq Stranded mRNA Library Prep Kit
For bulk RNA-sequencing, Cells were resuspended in Trizol and, following Chloroform-mediate phase separation, RNA extracted from the aqueous phase using the CC-25 kit (Zymo). For scRNA-seq, cells were fixed in 80% methanol and analysed using the Drop-Seq protocol (Macosko et al. 2015, PMID: 26000488)
See column "library construction protocol" in the SAMPLES section.

value: Mock-infected 1h before harvesting

value: mock, 30min 37 degree, conditioned medium

value: total RNA

tag: adapter sequence

value: GATCGGAAGAGCACACGT


title: 254706910010_b3 - nda9_HI_2days_1 vs Ctrl_HI_2days_1

hyb_protocol: Ctrl_HI_2days_1 Cy5 / nda9_HI_2days_1 Cy3 : 20pmol.


title: 254706910017_b4 - Ctrl_HI_3days_1 vs nda9_HI_3days_1

hyb_protocol: nda9_HI_3days_1 Cy5 / Ctrl_HI_3days_1 Cy3 : 20pmol.


title: 254706910008_b1 - nda9_HI_0day_1 vs Ctrl_HI_0day_1

hyb_protocol: Ctrl_HI_0day_1 Cy5 / nda9_HI_0day_1 Cy3 : 20pmol.


title: NHDF cells, single-cell RNA-seq, non-synchronous 37C infection, 1hpi, Replicate 5

value: Infected 1h before harvesting


title: NHDF cells, single-cell RNA-seq, non-synchronous 37C infection, uninfected, Replicate 5

value: Uninfected


title: NHDF cells, stranded polyA RNA-seq, non-synchronous 37C mock infection, uninfected


title: NHDF cells, stranded polyA RNA-seq, non-synchronous 37C mock infection, 5hpi

value: Mock-infected 5h before harvesting


title: NHDF cells, single-cell RNA-seq, non-synchronous 37C infection, uninfected, Replicate 4


title: NHDF cells, stranded polyA RNA-seq, non-synchronous 37C infection, 5hpi, Replicate 4


title: NHDF cells, single-cell RNA-seq, synchronous 4C infection, 5hpi, Replicate 2

description:
scRNA-seq
HSV1scRNA_rawcounts_allcells.txt.gz
scRNAseq_Rep23_morethan2000genes_normcounts.txt.gz

value: MOI 10, 1h 4 degree, new medium


title: NHDF cells, stranded polyA RNA-seq, non-synchronous 37C infection, 3hpi, Replicate 4


title: NHDF cells, single-cell RNA-seq, synchronous 4C infection, 5hpi, Replicate 3


title: NHDF cells, single-cell RNA-seq, synchronous 4C infection, 3hpi, Replicate 2


title: NHDF cells, single-cell RNA-seq, synchronous 4C infection, 1hpi, Replicate 3


title: NHDF cells, stranded polyA RNA-seq, non-synchronous 37C infection, 3hpi, Replicate 5


title: NHDF cells, single-cell RNA-seq, synchronous 4C infection, 3hpi, Replicate 3


title: NHDF cells, single-cell RNA-seq, synchronous 4C infection, 1hpi, Replicate 2


title: NHDF cells, stranded polyA RNA-seq, non-synchronous 37C infection, 1hpi, Replicate 5


title: NHDF cells, stranded polyA RNA-seq, non-synchronous 37C infection, 1hpi, Replicate 4


title: NHDF cells, stranded polyA RNA-seq, non-synchronous 37C infection, uninfected, Replicate 5


title: NHDF cells, single-cell RNA-seq, synchronous 4C infection, uninfected, Replicate 2


title: NHDF cells, single-cell RNA-seq, synchronous 4C infection, uninfected, Replicate 3


title: NHDF cells, stranded polyA RNA-seq, synchronous 4C infection, 5hpi, Replicate 2


title: NHDF cells, single-cell RNA-seq, synchronous 4C infection, 5hpi, pilot replicate 1

description:
scRNA-seq
HSV1scRNA_rawcounts_allcells.txt.gz
scRNAseq_Rep1_morethan2000genes_normcounts.txt.gz


title: NHDF cells, stranded polyA RNA-seq, synchronous 4C infection, 5hpi, Replicate 3


title: NHDF cells, single-cell RNA-seq, synchronous 4C infection, 3hpi, pilot replicate 1


title: NHDF cells, stranded polyA RNA-seq, synchronous 4C infection, 3hpi, Replicate 3


title: NHDF cells, stranded polyA RNA-seq, non-synchronous 37C mock infection, 3hpi

value: Mock-infected 3h before harvesting


title: NHDF cells, stranded polyA RNA-seq, synchronous 4C infection, 3hpi, Replicate 2


title: NHDF cells, single-cell RNA-seq, synchronous 4C infection, uninfected, pilot replicate 1


title: NHDF cells, stranded polyA RNA-seq, synchronous 4C infection, 1hpi, Replicate 3


title: NHDF cells, stranded polyA RNA-seq, synchronous 4C infection, 1hpi, Replicate 2


title: NHDF cells, stranded polyA RNA-seq, synchronous 4C infection, uninfected, Replicate 3


title: Patient H4

city: boston

first: Liam

last: Cornell

state: MASSACHUSETTS

address: 450 brookline avenue

institute: Dana-Farber Cancer Institute

description: RNA derived from CDK4/6 inhibitor treated patient biopsy

data_processing: Raw counts were normalised to Counts per million. CPM was used for direct comparisons between patient phenotypes. Genome_build: hg19

source_name: CDK4/6 inhibitor treated patient biopsy

extract_protocol:
Qiagen's AllPrep DNA/RNA/miRNA Universal
NEBNext® Small RNA Library Prep Set for Illumina, as per manufacturers instructions

treatment_protocol: All patients were treated with a CDK4/6

tag: sample type

value: Tissue

tag: cdk4/6 inhibitor phenotype

value: Intrinsic Resistance


title: Patient H5

value: Aquired Resistance


title: NHDF cells, stranded polyA RNA-seq, synchronous 4C infection, uninfected, Replicate 2


title: Patient H3

value: Sensitive


title: NHDF cells, stranded polyA RNA-seq, non-synchronous 37C infection, uninfected, Replicate 4

value: MOI 10, 30min 37 degree, conditioned medium


title: EPAS1-/- 786-O cells, single cell clone #3

city: Hangzhou

first: Yilong

last: Zou

state: Zhejiang

address: Shilongshan Road #18, Cloud Town, Xihu District

department: School of Life Sciences

country: China

institute: Westlake University

data_processing:
Raw paired-end 150bp/150bp sequencing reads were mapped to human genome build hg19 using Bowtie2 (v2.3.1) with standard settings. In average 66% of read pairs were uniquely mapped to the hg19 genome.
Mapped reads were counted to gene features by the htseq-count function from HTSeq (version 0.9.1) with standard settings.
Read count matrix was normalized to library size with DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: Normalized read counts in txt format

source_name: 786-O cell culture

growth_protocol: 786-O cells were cultured at 37 °C with 5% CO2 in RPMI medium containing 10% FBS.

extract_protocol:
Total RNA was extracted from adherent 786-O cells using the RNeasy Mini Kit (Qiagen Inc.) according to manufacturer's instructions.
RNA sequencing library was prepared using NEBNext Ultra RNA Library Prep Kit following manufacturer’s recommendations. Briefly, mRNAs were first enriched with Oligod(T) beads and fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized, end repaired and adenylated at 3’ends. Universal adapter was ligated to cDNA fragments, followed by index addition and library enrichment with limited cycle PCR. Sequencing libraries were validated using the Agilent Tapestation 4200, and quantified using Qubit 2.0 Fluorometer as well as by quantitative PCR.
The sequencing libraries were multiplexed and clustered on one lane of a flowcell. After clustering, the flowcell was loaded on the Illumina HiSeq instrument according to manufacturer’s instructions.  The samples were sequenced using a 2x150 Paired End (PE) configuration.  Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mis-match was allowed for index sequence identification.

treatment_protocol: WT 786-O cells were treated with DMSO or 10uM HIF-2a antagonist compound C2 (Scheuermann et al., Nature Chemical Biology 2013) for 3 days prior to RNA extraction.

tag: genotype/variation


title: Patient H1


title: wildtype EPAS1+/+ 786-O cells, treated with HIF2a antagonist compound C2

value: wildtype EPAS1+/+ 786-O


title: Patient H2


title: NHDF cells, single-cell RNA-seq, non-synchronous 37C infection, 1hpi, Replicate 4

value: single-cell RNA


title: wildtype EPAS1+/+ 786-O cells, replicate 2


title: Patient G3


title: Patient G4


title: EPAS1-/- 786-O cells, single cell clone #2


title: wildtype EPAS1+/+ 786-O cells, treated with DMSO


title: EPAS1-/- 786-O cells, single cell clone #1


title: Patient G5


title: wildtype EPAS1+/+ 786-O cells, replicate 1


title: Patient G2


title: Patient G1


title: Patient F5


title: CRC121Li_I_REST

city: New York

first: Richard

last: Koche

state: NY

address: 430 East 67th Street

institute: Sloan Kettering Institute

data_processing:
ChIP-seq reads were trimmed and filtered for quaity with trim_galore v0.4.5, backed by version 1.15 of cutadapt. 15 was used as the quality setting.
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie2 version 2.3.4 with the default settings.
Duplicate reads were removed with MarkDuplicates in Picard, version 2.16.0.
Peaks in ChIP-seq read density were called with version 2.1.1.20160309 of MACS2. 0.001 was the setting for the p-value option, with "BAM" as the format setting and the "--nomdel" option activated.
For read density visualization, bigWig files were created with the bamToBed, slopBed, and genomeCoverageBed programs in version 2.27.1 of bedtools, and wigToBigWig in v359 of the UCSC utilities.
Genome_build: mm9
Supplementary_files_format_and_content: Each bigWig file was generated from the corresponding aligned BAM by using bamToBed, slopBed, and genomeCoverageBed in version 2.27.1 of bedtools, and wigToBigWig in v359 of the UCSC utilities.

source_name: ChIP-seq of REST in intact organoid

extract_protocol:
Extraction of material for sequencing was performed as in http://dx.doi.org/10.1038/nature13736
Libraries were prepared according to Roche's instructions accompanying the kapa htp library prep kit, and DNA was amplified with 12 PCR cycles.

value: CRC121 organoid

value: REST (Millipore Sigma, 07-579, lot 2843200)


title: Patient F4


title: Patient F6


title: CRC121Li_D_REST

source_name: ChIP-seq of REST in dissociated organoid


title: CRC121Li_I_input

source_name: Input DNA for REST ChIP-seq in context of organoid integrity


title: Patient F3


title: Patient F2


title: CRC121Li_D_input

source_name: Input DNA for REST ChIP-seq in context of organoid dissociation


title: CRC107LishCTRL_I_REST

value: CRC107 organoid


title: Patient E3


title: Patient E5


title: NHDF cells, stranded polyA RNA-seq, non-synchronous 37C infection, 5hpi, Replicate 5

value: Infected 5h before harvesting

value: total RNA


title: CRC107LishCTRL_D_Input


title: CRC107LishCTRL_D_REST


title: Patient E1


title: Patient E4


title: jap_INPUT

organism: Schizosaccharomyces japonicus

value: whole cells

value: h+

value: INPUT


title: Patient D6


title: jap_H3K9_SE


title: Patient D5


title: CRC107LishCDH1_REST

source_name: ChIP-seq of REST in context of shRNA knockdown of CDH1


title: Patient E6


title: Patient D3


title: jap_cenpa_SE

value: cenpa


title: Patient D2


title: Patient D1


title: 4-day ML210 treatment

data_processing:
Library strategy: CRISPR screen
raw data includes sequencing reads for the sgRNAs in the library
Sequence mapping and counting: For CRISPR screen data analysis, the sgRNA sequences were mapped to a reference file containing all SpCas9 sgRNAs in the library and the sgRNA-associated barcodes were counted and mapped to the barcode reference file. The reference file containing all the sgRNAs in the Brunello library is included in this submission, and can be found publicly at https://media.addgene.org/cms/filer_public/8b/4c/8b4c89d9-eac1-44b2-bb2f-8fea95672705/broadgpp-brunello-library-contents.txt .
Read count normalization: The read count matrix was normalized to reads per million reads (RPM) within each condition.
Supplementary_files_format_and_content: The read count matrix is presented as a txt file.

source_name: 4-day ML210 treatment

growth_protocol: 786-O cells were cultured in RPMI-1640 (Gibco) media supplemented with 10% fetal bovine serum (Gibco) and 1% penicillin/streptomycin in a humidified incubator at 37°C with 5% CO2.

extract_protocol:
Genomic DNA from cell pellets was purified using the QIAamp DNA Blood Maxi/Midi/Mini kits (Qiagen) according to the manufacturer’s protocols and quantified using a Nanodrop 2000 (Thermo Fisher Scientific).
sgRNA cassettes were PCR-amplified and barcoded with sequencing adaptors utilizing ExTaq DNA Polymerase (Clontech). PCR products were purified with Agencourt AMPure XP SPRI beads (Beckman Coulter A63880) according to the manufacturer’s instructions, quantified using a Nanodrop 2000, pooled into a master sequencing pool, and sequenced on a MiSeq sequencer (Illumina) with 300nt single-end reads, loaded at 60% with a 5% spike-in of PhiX DNA.

treatment_protocol: Prior to screening, the viral titer and volume was pre-determined with pilot experiments to ensure about 30% infection rate in the screening experiment and caution was taken to minimize multiple constructs transduced into the same cell. Optimized surface area for cell growth was pre-determined in pilot experiments to avoid over confluence during screening. Puromycin concentrations were pre-determined with pilot experiments before the screen. For the screening experiment, 150 million 786-O-Cas9 cells were infected with a lentiviral library containing 77,441 sgRNA targeting 18,000 genes in the human genome to ensure each sgRNA is represented by at least 500 cells on average47. For the infection, cells added with the calculated lentivirus volume were supplemented with 4mg/mL of polybrene and centrifuged at 950xg for 2 hours. Fresh media was added at a 1:1 ratio post-centrifugation. Infected cells were selected with 2mg/mL of puromycin for 96 hours, expanded for another 4 days to reach the desired cell number and split for DMSO or 5mM ML210 treatment. At least 40 million cells were used for each treatment condition to keep the minimum presentation number for each sgRNA above 500. Cells were exposed to ML210 treatment for 4, 6, or 8 days before being cultured in drug-free media for recovery and expansion for 24h.

tag: cell line

tag: cell type

value: clear-cell carcinoma


title: CRC107LishCTRL_I_Input


title: DMSO treatment

source_name: DMSO treatment


title: Patient D4

value: Tissue


title: Patient C6


title: Patient F1

value: Intrinsic Resistance


title: 6-day ML210 treatment

source_name: 6-day ML210 treatment


title: Patient C5


title: PBDE.337

city: Duarte

first: Noriko

last: Kanaya

address: 1500 East Duarte

department: Cancer Biology

institute: Beckman Research Institute at City of Hope

description:
Kapa Stranded mRNA library
RNA-Seq data, PBDE treatment in Mouse Xenograft, replicate 2

data_processing:
Illumina RTA was used to create .bcl files, and bcl2fastq 1.8 software was used for base calling (for samples split between flowcells and later merged per run)
Reads aligned using TopHat2 (v2.0.14), with --no-coverage-search (with --library-type fr-firststrand for stranded library samples)
Unique reads quantified using htseq-count (version 0.6.0), with database generated from TxDb.Hsapiens.UCSC.hg19.knownGene (Bioconductor annotations, downloaded 6/8/2016), with strand was set to "reverse"
Genome_build: hg19
Supplementary_files_format_and_content: FPKM normalized expression (using quantified reads and TxDb annotations in R) and read counts (calculated using htseq-count).  Log2(FPKM+0.1) values are anti-logged to provide linear values (with low FPKM values appearing as 0)

source_name: PBDE treatment in NSG Mouse Xenograft, replicate 2

growth_protocol: Tumor pieces of ER+ PDX (COH-SC31) were surgically inoculated in female NSG mice

extract_protocol:
RNease kit (QIAGEN)
KAPA stranded mRNA kit
stranded mRNA RNA-Seq

treatment_protocol: Mice were exposed to mixture of PBDEs through diet (PBDE-47; 1mg/kg/day, PBDE-100; 0.056mg/kg/day and PBDE-153; 0.126mg/kg/day)

tag: treatment

value: PBDE


title: Patient C3

value: Sensitive


title: PBDE.333

description:
Kapa Stranded mRNA library
RNA-Seq data, PBDE treatment in Mouse Xenograft, replicate 1

source_name: PBDE treatment in NSG Mouse Xenograft, replicate 1


title: Patient E2


title: DMSO.339

description:
Kapa Stranded mRNA library
RNA-Seq data, Control treatment in Mouse Xenograft, replicate 3

source_name: Control treatment in NSG Mouse Xenograft, replicate 3

value: Control


title: Patient C4

value: Aquired Resistance


title: DMSO.332

description:
Kapa Stranded mRNA library
RNA-Seq data, Control treatment in Mouse Xenograft, replicate 2

source_name: Control treatment in NSG Mouse Xenograft, replicate 2


title: CDA

city: Tokyo

first: Hiroshi

last: Kohara

address: 4-6-1 Shirokanedai, Minato-ku

department: Division of ALA Advanced Medical Research

country: Japan

institute: Institute of Medical Science, the University of Tokyo

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v3; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of two samples were log2-transformed and normalized by the quantile algorithm with the Bioconductor.

source_name: CD235a(+) cells derived from CDA patient-derived iPSC

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

growth_protocol: In vitro differentiation of iPSCs into CD34(+) hematopoietic progenitor cells was induced via embryoid body formation in DMEM supplemented with 10% FBS; Differentiation of CD34(+) cells into erythroblastic cells was induced in RPMI1640 supplemented with IL-3, stem cell factor (SCF), and erythropoietin (EOP).

extract_protocol: Total RNA was isolated from tissues using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega)

tag: cells


title: Patient C1


title: DMSO.331

description:
Kapa Stranded mRNA library
RNA-Seq data, Control treatment in Mouse Xenograft, replicate 1

source_name: Control treatment in NSG Mouse Xenograft, replicate 1


title: Patient B6


title: Patient B5


title: 8-day ML210 treatment

source_name: 8-day ML210 treatment


title: Control

source_name: CD235a(+) cells derived from healthy donor control iPSC


title: Patient B4

source_name: CDK4/6 inhibitor treated patient biopsy


title: ILC3_D6_S20

city: Zurich

first: Ge

last: Tan

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich

institute: University of Zurich

data_processing:
Basecalls performed with bcl2fastq-1.8.4
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
RNA-Seq reads were aligned to Ensembl GRCh38.p10 genome assembly using STAR 2.5.4b
Counts were generated by featureCounts of Rsubread 1.28.1
Genome_build: GRCh38.p10

source_name: Group 3 innate lymphoid cells (ILC3)

growth_protocol: N/A (the cells were isolated ex vivo, without culture)

extract_protocol:
The three ILC subsets were isolated using flow cytometry. In brief, CD3, CD14 and CD19 cells were MACS (Miltenyi Biotec, Bergisch Gladbach, Germany) depleted and then sorted using a FACS Aria flow cytometer (BD Bioscience, Allschwil, Switzerland). Staining procedure for sorting should be also included here. In brief, lymphocytes were initially gated based on FSC and SSC, and then dead cells were excluded using a Fixable Viability Dye (eBioscience, Frankfurt, Germany). We then gated on the linage-CD127+ viable lymphocytes population, of which the CD161mid/+ cells were the main ILC containing population. The three ILC subsets were finally distinguished based on their differential expression of c-kit, CRTH2 and NKp44. The sorted ILC populations (from N = 6 individuals) were immediately re-sorted (2-round sorting) into 96-w plate, 1000 cells per well or as close as possible.
RNA libraries were prepared for sequencing using Clontech SMARTer - Low Input Mammalian kit.

treatment_protocol: N/A (the cells were isolated ex vivo, without treatment

tag: condition

tag: donor


title: Patient B3


title: ILC3_D7_S21


title: ILC3_D4_S18


title: Patient B2


title: CRC107LishCDH1_Input

source_name: Input DNA for REST ChIP-seq in context of shRNA knockdown of CDH1

tag: tissue

tag: chip antibody


title: ILC3_D3_S17


title: Patient A6


title: Patient A5


title: Patient A3


title: ILC2_D7_S14

source_name: Group 2 innate lymphoid cells (ILC2)


title: ILC3_D1_S15


title: Patient A4


title: ILC2_D6_S13


title: T47D mir-432-5p captured RNA 3

description: RNA captured using a biotin labelled miR-432-5p, performed in parental T47D cells.

data_processing:
FKPM was calculated, data presented in the manuscript is dirived from FKPM
FKPM averages for sample repeats which were >0 but <1 was rounded to 1.
DESeq2 analysis was also performed and attached
Genome_build: hg19
Supplementary_files_format_and_content: Excel spreadsheets of both FKPM and DESeq2 are attached

source_name: T47D cells

growth_protocol: Cells were exponentially gowing on standard, ATCC recommented medium

extract_protocol:
RNA was extraced using TRIZOL + column purification
Illumina TruSeq stranded mRNAseq, as per manufacturers guidelines

treatment_protocol: Biotin labelled miRNA was transfected using lipofectamine 3000

value: Immortalized cell line


title: ILC2_D3_S10


title: ILC2_D4_S11


title: ILC2_D2_S9


title: T47D control RNA 3

description: Control RNA from untreated parental T47D cells


title: Patient C2


title: PA4595-2

city: Hong Kong

first: Xin

last: DENG

address: 1/F, Block 1, To Yuen Building, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong

department: Department of Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

description:
processed data file: 4595_double_gene_exp.txt
sample_2 (hl49951)

data_processing:
Bacterial RNA-seq reads were mapped to the P. auruginosa genome by using TopHat (version 2.0.0), with two mismatches allowed
Only the uniquely mapped reads were kept for the subsequent analyses.
The gene differential expression analysis was performed using Cuffdiff software (version 2.0.0)
Genome_build: Pseudomonas aeruginosa PAO1 (ASM676v1, NC 002516.2)
Supplementary_files_format_and_content: File containing comparisons between PA4595 mutant and wild-type.  value_1 and value_2 are the FPKMs of sample_1(hlpack1) and sample_2(hl49951), respectively.

organism: Pseudomonas aeruginosa PAO1

source_name: liquid culture in LB (Luria-Bertani)  medium

growth_protocol: LB

extract_protocol:
To examine the effect of PA4595 on the transcriptome, 2 ml of mid-log-phase (OD600= 0.6) bacterial cultures (PAO1 and ∆PA4595 strains) were collected by centrifugation (12,000 rpm, 4℃). An RNeasy minikit (Qiagen) was used for subsequent RNA purification with DNaseI (NEB) treatment. After removing rRNA by using the MICROBExpress kit (Ambion), mRNA was used to generate the cDNA library according to the TruSeq RNA sample prep kit protocol (Illumina), which was then sequenced using the HiSeq 2000 system (Illumina). Bacterial RNA-seq reads were mapped to the P. auruginosa genome (ASM676v1, NC 002516.2) by using TopHat (version 2.0.0), with two mismatches allowed. Only the uniquely mapped reads were kept for the subsequent analyses. The gene differential expression analysis was performed using Cuffdiff software (version 2.0.0). GO enrich-ment analyses were conducted on all differentially transcribed genes using DAVID before data sets were imported into Cytoscape with an Enrichment Map plugin. The each sample in RNA-seq assay was repeated twice.
TruSeq RNA sample prep kit protocol (Illumina)

treatment_protocol: grow until mid-log phase in LB

tag: genotype

value: PA4595 mutant


title: T47D mir-432-5p captured RNA 2


title: PA4595-1


title: Patient A1


title: PBDE.340

description:
Kapa Stranded mRNA library
RNA-Seq data, PBDE treatment in Mouse Xenograft, replicate 3

source_name: PBDE treatment in NSG Mouse Xenograft, replicate 3


title: T47D mir-432-5p captured RNA 1


title: T47D control RNA 1


title: CK-1

description:
processed data file: 4595_double_gene_exp.txt
sample_1 (hlpack1)

value: WT


title: T47D control RNA 2


title: RNA from parental cells gown in resistant cell media repeat 3

description:
All experiments were conducted at Exiqon Services, Denmark. The quality of the total RNA was verified by an Agilent 2100 Bioanalyzer profile. 750 ng total RNA from both sample and reference was labeled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY LNA™ microRNA Hi-Power Labeling Kit, Hy3™/Hy5™ (Exiqon, Denmark) following the procedure described by the manufacturer. The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY LNA™ microRNA Array 7th Gen (Exiqon, Denmark), which contains capture probes targeting all microRNAs for human, mouse or rat registered in the miRBASE 18.0. The hybridization was performed according to the miRCURY LNA™ microRNA Array Instruction manual using a Tecan HS4800™ hybridization station (Tecan, Austria). After hybridization the microarray slides were scanned and stored in an ozone free environment (ozone level below 2.0 ppb) in order to prevent potential bleaching of the fluorescent dyes. The miRCURY LNA™ microRNA Array slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene® 9 (miRCURY LNA™ microRNA Array Analysis Software, Exiqon, Denmark). The quantified signals were background corrected (Normexp with offset value 10, see Ritchie et al. 2007) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.
0_Exiiqon files are the reference files

hyb_protocol: The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY LNA™ microRNA Array 7th Gen (Exiqon, Denmark), which contains capture probes targeting all microRNAs for human, mouse or rat registered in the miRBASE 18.0. The hybridization was performed according to the miRCURY LNA™ microRNA Array Instruction manual using a Tecan HS4800™ hybridization station (Tecan, Austria). Spike-in controls were added in various concentrations in both the Hy3™ and the Hy5™ labeling reactions giving the opportunity to evaluate the labeling reaction, hybridization, and the performance of the array experiment in general. The high correlation (R2>0.95) of the signal intensities across all slides shown in the tables below for both the Hy3™ and Hy5™  channels indicates that both labeling and hybridization were successful. 52 different spike-in controls were added in concentrations covering the full signal range. Each spike-in control has 4 replicates of capture probes on the array.

data_processing: The quantified signals were background corrected (Normexp with offset value 10, see Ritchie et al. 2007) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm. Data normalization was performed to minimize differences between the colors in an intensity dependent manner. Normalization was performed using Lowess (Locally Weighted Scatterplot Smoothing) normalization. Lowess uses a locally established regression to smooth the M/A (log ratio/log mean-intensity) scatterplot toward a linear distribution. The Lowess algorithm works under the assumption that the majority of the signals between samples do not differ and it enforces equal overall means on all signal intensities. Therefore, Lowess allows the correction of systematic deviations in the MA plot resulting in an intensity dependent adjustment of MA-data to a straight line. We have found this normalization to produce the best within-slide normalization and thereby minimize the intensity-dependent differences between the dyes. Array slide quality was also assessed using 52 different spole-in controls.

growth_protocol: Parental T47D cells are were grown as directed by ATCC, resistant cells were cultured in the same way with the addition of 100 nM palbociclib to the medium.

extract_protocol: RNA was extracted using invitrogens "recoverall" kit according to the manufacturer guidelines

treatment_protocol: "M" samples were parental T47D cells, which had been cultured in conditioned medium for 48 hours.

source_name: reference

value: reference


title: ILC3_D2_S16


title: ILC1_D4_S4

source_name: Group 1 innate lymphoid cells (ILC1)


title: ILC1_D3_S3


title: ILC1_D6_S6


title: ILC1_D7_S7


title: Patient A2


title: RNA from parental cells gown in resistant cell media repeat 2

scan_protocol: After hybridization the microarray slides were scanned and stored in an ozone free environment (ozone level below 2.0 ppb) in order to prevent potential bleaching of the fluorescent dyes. The miRCURY LNA™ microRNA Array slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene® 9 (miRCURY LNA™ microRNA Array Analysis Software, Exiqon, Denmark).

label_protocol: 750 ng total RNA from both sample and reference was labeled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY LNA™ microRNA Hi-Power Labeling Kit, Hy3™/Hy5™ (Exiqon, Denmark) following the procedure described by the manufacturer.


title: RNA-Seq stat R3

city: Leipzig

first: Olga

last: Bondareva

state: Saxony

address: Philipp-Rosenthal-Straße 27

department: HI-MAG

institute: Helmholtz Zentrum München

data_processing:
Sequenced reads were trimmed for adaptor sequence and corrected for duplicates, then mapped to Homo sapiens whole genome hg19 using (i) Bowtie2 for ChIP-Seq data and (ii) TopHat for RNA-Seq data. Replicates were merged.
The peak calling procedure for H3K27ac ChIP-Seq data was performed using MACS2 software and differential peaks between oscillatory shear stress vs. static conditions were determined using bdgdiff function with following parameters: -q 0.01 , -g 100, -l 200.
The differential gene expression analysis was performed using Cuffdiff; adjusted P-value > 0.05
Genome_build: hg19
Supplementary_files_format_and_content: Differential H3K27ac peaks in oscillatory vs. static condition and common peaks are in BED format: cond1 = oscillatory-specific; cond2 = static-specific
Supplementary_files_format_and_content: Normalized abundance measurements from Cuffdiff are in tab-delimited TXT format

source_name: Human umbilical vein endothelial cells

growth_protocol: Human umbilical vein endothelial cells (HUVECs) were isolated and cultivated from human umbilical cord veins as described elsewhere (PMID: 8338136).

extract_protocol:
Total mRNA and genomic DNA were directly isolated from HUVEC after shear stress experiments, further DNA-histone complexes were precipitated and purified using H3K27ac antibody.
ChIP and RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Experiments and respective controls were performed in parallel. Cells were exposed to shear stress of ± 3 dyn/cm2 (for oscillatory treatment) or kept under static conditions for 6 h at 37°C and with constant CO2 perfusion.

value: Human umbilical vein endothelial cells

value: Static


title: RNA from parental cells gown in resistant cell media repeat 1


title: pabociclib resistant cell RNA repeat 3


title: RNA-Seq osc R3

value: Oscillatory shear stress


title: ILC2_D1_S8


title: Parental cell RNA repeat 3


title: pabociclib resistant cell RNA repeat 1


title: CK-2


title: RNA-Seq stat R2


title: ILC1_D1_S1


title: Control group #5

city: Boston

first: Johannes

last: Schlondorff

state: MA

address: 99 Brookline Ave, RN304B

department: Nephrology

institute: Beth Israel Deaconess Medical Center

data_processing:
Bioinformatic analysis of RNA-seq data from freshly isolated mouse glomeruli, including sequence quality evaluation, read trimming and mapping, hit counting, and differential gene expression analysis were performed through GeneWiz.
Trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b, unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2, and DESeq2 was used to compare gene expression between experimental groups.
The Wald test was used to generate p-values and log2 fold changes. Genes with adjusted p-values <0.05 and absolute log2 fold changes >1 were considered differentially expressed genes for each comparison.
Genome_build: Mus musculus GRCm38.
Supplementary_files_format_and_content: Excel file including gene hit count for each sample, average gene hit, log 2 fold difference between Cosmc KO group and control and associated p-value

source_name: Glomeruli

extract_protocol:
Glomeruli were isolated by Dynabead perfusion technique from 1 month old control(n=5) and Podo-Cre; CosmcY/flox(n=4) male animals.  RNA was isolation using Rneasy Plus Mini kit (Qiagen).
Libraries were generated by GeneWiz using standard protocols with polyA enriched RNA.  Samples were run on Illumina HiSeq, PE 2x150

tag: strain

value: Podo-Cre; Cosmc Y/+

tag: age (days)


title: PPT.PBDE153.2

description:
Stranded polyA library
RNA-Seq data, PPT+PBDE153 treatment in MCF7 cells, replicate 2

data_processing:
Illumina RTA was used to create .bcl files, and bcl2fastq 1.8 software was used for base calling (for samples split between flowcells and later merged per run)
Reads aligned using TopHat2 (v2.0.14), with --no-coverage-search (with --library-type fr-firststrand for stranded library samples)
Unique reads quantified using htseq-count (version 0.6.0), with database generated from TxDb.Hsapiens.UCSC.hg19.knownGene (Bioconductor annotations, downloaded 6/8/2016), with strand was set to "reverse"
Genome_build: hg19
Supplementary_files_format_and_content: RPKM normalized expression (using quantified reads and TxDb annotations in R) and read counts (calculated using htseq-count)

growth_protocol: Prior to the assay, cells were incubated for 2 days with phenol red-free MEM containing 10% charcoal-treated-FBS and then seeded in 6 cm dish at 8 × 105 cells per dish.

extract_protocol:
Trizole
KAPA stranded polyA kit

treatment_protocol: MCF7 cells were treated with DMSO (0.2%), PPT (10 nM), PPT (10 nM) + MMP (1 μM), PBDE47 (20 μM), PPT (10 nM) + PBDE100 (20 μM), and PPT (10 nM) + PBDE153 (20 μM) for 24 hours.

tag: batch


title: Parental cell RNA repeat 2


title: PPT.PBDE153.3

description:
Stranded polyA library
RNA-Seq data, PPT+PBDE153 treatment in MCF7 cells, replicate 3


title: Parental cell RNA repeat 1


title: RNA-Seq stat R1


title: Cosmc KO group #4

value: Podo-Cre; Cosmc Y/flox


title: RNA-Seq osc R1


title: RNA-Seq osc R2


title: Control group #3

value: Cosmc Y/+


title: PPT.PBDE100.2

description:
Stranded polyA library
RNA-Seq data, PPT+PBDE100 treatment in MCF7 cells, replicate 2


title: Cosmc KO group #3


title: Control group #2

value: Cosmc Y/flox


title: PPT.PBDE100.3

description:
Stranded polyA library
RNA-Seq data, PPT+PBDE100 treatment in MCF7 cells, replicate 3


title: Control group #4


title: Input osc R2


title: Cosmc KO group #1


title: ILC1_D2_S2


title: pabociclib resistant cell RNA repeat 2


title: Control group #1


title: PBDE47.3

description:
Stranded polyA library
RNA-Seq data, PBDE47 treatment in MCF7 cells, replicate 3


title: PPT.PBDE153.1

description:
Stranded polyA library
RNA-Seq data, PPT+PBDE153 treatment in MCF7 cells, replicate 1


title: Input stat R1


title: Input osc R1


title: Cosmc KO group #2


title: Input stat R2


title: H3K27ac stat R2

description:
H3K27ac_osc_vs_stat_cond2.bed
H3K27ac_osc_vs_stat_common.bed

value: H3K27ac (Abcam, ab4729)


title: H3K27ac osc R2

description:
H3K27ac_osc_vs_stat_cond1.bed
H3K27ac_osc_vs_stat_common.bed


title: PBDE47.1

description:
Stranded polyA library
RNA-Seq data, PBDE47 treatment in MCF7 cells, replicate 1


title: PPT.MPP.3

description:
Stranded polyA library
RNA-Seq data, PPT+MPP treatment in MCF7 cells, replicate 3

value: PPT+MPP


title: PBDE47.2

description:
Stranded polyA library
RNA-Seq data, PBDE47 treatment in MCF7 cells, replicate 2


title: Ex-Resistant Cell RNA dataset 2 repeat 3

description: Gene Expression data

hyb_protocol: HG_U133_2_plus array was carried out as per manufacturers instructions

data_processing: Data was normalised using RMA.

label: biotin

extract_protocol: RNA was extracted using invitrogens recoverall kit according to the manufacturer guidelines

treatment_protocol: Palbociclib resistant cells were grown with 100 nM palbociclib containing medium. Ex-resistant cells were T47D cells, cutured to resistance then grown in drug free medium for 7 weeks +.


title: Ex-Resistant Cell RNA dataset 2 repeat 1

description: Gene Expression data

scan_protocol: HG_U133_2_plus array was carried out as per manufacturers instructions


title: H3K27ac stat R1


title: PPT.PBDE100.1

description:
Stranded polyA library
RNA-Seq data, PPT+PBDE100 treatment in MCF7 cells, replicate 1


title: PPT.MPP.1

description:
Stranded polyA library
RNA-Seq data, PPT+MPP treatment in MCF7 cells, replicate 1


title: Ex-Resistant Cell RNA dataset 2 repeat 2

description: Gene Expression data

label_protocol: HG_U133_2_plus array was carried out as per manufacturers instructions


title: H3K27ac osc R1


title: PPT.3

description:
Stranded polyA library
RNA-Seq data, PPT treatment in MCF7 cells, replicate 3

value: PPT


title: pabociclib resistant cell RNA dataset 2 repeat 1

description: Gene Expression data


title: Parental cell RNA dataset 2 repeat 2

description: Gene Expression data


title: Parental cell RNA dataset 2 repeat 1

description: Gene Expression data


title: Parental cell RNA dataset 2 repeat 3

description: Gene Expression data


title: pabociclib resistant cell RNA dataset 1 repeat 1

description: Gene Expression data


title: Parental cell RNA dataset 1 repeat 3

description: Gene Expression data


title: pabociclib resistant cell RNA dataset 1 repeat 2

description: Gene Expression data


title: pabociclib resistant cell RNA dataset 1 repeat 3

description: Gene Expression data


title: PPT.MPP.2

description:
Stranded polyA library
RNA-Seq data, PPT+MPP treatment in MCF7 cells, replicate 2


title: pabociclib resistant cell RNA dataset 2 repeat 2

description: Gene Expression data


title: Control.3

description:
Stranded polyA library
RNA-Seq data, Control treatment in MCF7 cells, replicate 3


title: PPT.2

description:
Stranded polyA library
RNA-Seq data, PPT treatment in MCF7 cells, replicate 2


title: Control.1

description:
Stranded polyA library
RNA-Seq data, Control treatment in MCF7 cells, replicate 1


title: Control.2

description:
Stranded polyA library
RNA-Seq data, Control treatment in MCF7 cells, replicate 2


title: pabociclib resistant cell RNA dataset 2 repeat 3

description: Gene Expression data


title: Parental cell RNA dataset 1 repeat 1

description: Gene Expression data


title: Parental cell RNA dataset 1 repeat 2

description: Gene Expression data


title: Sample11_NHD13 transgenic, Lyl1 knockout DN thymocytes rep 2

city: Clayton

first: Wei

last: Shi

state: Victoria

address: Wellington Rd

country: Australia

institute: Monash University

description:
replicate 2
Sample11

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw intensity values were background corrected and normalized by the neqc method. Probes were filtered as ‘not expressed’ if they failed to achieve a BeadStudio detection P value of 0.05 on at least one array. Manufacturer probe annotation was used. Linear models were fitted to genes using Bioconductor R package limma. Differences in expression were assessed with empirical Bayes moderated t-statistics. Genes were considered to have different expression if they achieved a false-discovery rate of less than 0.05 and also a fold change greater than 2.

label_protocol: Standard Illumina labelling protocol

extract_protocol: RNA was prepared using the RNeasy Mini Kit (Qiagen).Approximately 300 ng of total RNA was labelled and hybridised to Illumina MouseWG-6 v2.0 Expression BeadChips (Illumina) according to Illumina standard protocols.

tag: strain background

value: NHD13 transgenic, Lyl1 knockout

tag: age

value: 2-3 months

value: Thymus

value: sorted CD4-CD8 double-negative (DN) thymocytes


title: Sample8_NHD13 transgenic DN thymocytes rep 2

description:
replicate 2
Sample8

source_name: NHD13 transgenic DN thymocytes

value: NHD13 transgenic


title: Sample10_NHD13 transgenic, Lyl1 knockout DN thymocytes rep 1

description:
replicate 1
Sample10


title: Sample4_Wild-type DN thymocytes rep 4

description:
replicate 4
Sample4

source_name: Wild-type DN thymocytes

value: wild type


title: Sample6_Wild-type DN thymocytes rep 6

description:
replicate 6
Sample6


title: Sample12_NHD13 transgenic, Lyl1 knockout DN thymocytes rep 3

description:
replicate 3
Sample12


title: PPT.1

description:
Stranded polyA library
RNA-Seq data, PPT treatment in MCF7 cells, replicate 1


title: Sample9_NHD13 transgenic DN thymocytes rep 3

description:
replicate 3
Sample9


title: oct_input_RA_PE

data_processing:
ChIP-seq reads were aligned to reference genome using Bowtie2
Genome_build: Pombe: ASM294v2.20
Genome_build: S. japonicus: GCA_000149845
Genome_build: S. croyphylus: assembly genome
Genome_build: S. octosporus: assembly genome
Supplementary_files_format_and_content: bigwig files were generated deeptools normalized by RPKM

organism: Schizosaccharomyces octosporus

source_name: cell

extract_protocol:
Lysates were prepared using standard bead beating procedure, sonicated to achieve fragmements of 200-400bp and clarified by centrifugation at 17000g.
Libraries were prepared using standard Illumina pipeline.

value: whole cells

value: wild-type

value: input


title: Sample2_Wild-type DN thymocytes rep 2

description:
replicate 2
Sample2


title: oct_H3K9_PE


title: Sample3_Wild-type DN thymocytes rep 3

description:
replicate 3
Sample3


title: oct_H3K9_RA_PE


title: oct_CENPA_PE

value: CENPA


title: oct_INPUT_SE

value: INPUT


title: oct_input_PE


title: oct_H3K9_SE


title: Sample7_NHD13 transgenic DN thymocytes rep 1

description:
replicate 1
Sample7


title: Sample1_Wild-type DN thymocytes rep 1

description:
replicate 1
Sample1


title: Sample5_Wild-type DN thymocytes rep 5

description:
replicate 5
Sample5


title: E16R002d01: D1 HUVEC-1 80rpm Rcab

city: Tübingen

first: Jakob

last: Admard

address: Calwerstr. 7

department: Institut für Medizinische Genetik und Angewandte Genomik

institute: Universitätsklinikum Tübingen

description: isolated from the vein of the umbilical cord

hyb_protocol: Following fragmentation, 15 ug cRNA were hybridized for 16 h at 45°C on GeneChip HG-U219 or GeneChip HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed using Affymetrix Expression Console with RMA as normalization method

source_name: Human umbilical vein endothelial cells, RCαβ treated, fluid shear condition

label_protocol: Biotinylated cRNA were prepared according to the standard GeneChip WT Kit protocol from 100ng total RNA.

growth_protocol: Human umbilical vein endothelial cells (HUVECs) were cultured according to the manufacturer’s instructions (Promocell, passages < 5), in complete endothelial cell growth medium containing 2% heat-inactivated fetal bovine serum (FBS) and 1% penicillin-streptomycin (P/S)

extract_protocol: Cells were collected and total RNA was extracted from the cells.

treatment_protocol: Endothelial cells stimulated  with 200 nM RCαβ or 200 ng/ml HGF

value: Human umbilical vein endothelial cells

tag: passage

value: passage 1


title: oct_CENPA_SE


title: E16R002d03: D3 HUVEC-3 80rpm Rcab


title: E16R002b02: B2 HUVEC-2 Static Rcab

source_name: Human umbilical vein endothelial cells, RCαβ treated, static condition


title: Patient 36

city: Grand Rapids

first: Eric

last: Kort

state: MI

address: 333 Bostwick NE

institute: Van Andel Research Institute

data_processing:
The sequencing data was aligned to the human genome  (assembly GRCh38) and unique feature counts obtained using the software pipeline developed by the inDrop manufacturer (version 0.3, https://github.com/indrops/indrops).
Matrix was filtered to remove any row with less than 500 total transcript counts (these were assumed to represent empty droplets containing only background RNA from lysed cells)
Genome_build: GRCh38
Supplementary_files_format_and_content: An RDS (R data file) file containing raw counts for 61,861 cells and 42,024 genes as a dgCMatrix object. Requires R with the Matrix package installed to load, but smaller and faster than the text file (below).
Supplementary_files_format_and_content: An RDS (R data file) file containing sample level metadata required to reproduce analysis in our forthcoming paper
Supplementary_files_format_and_content: A TAB (tab delmited text file) file containing the same data as the RDS file, but readable by a wide range of software.
Supplementary_files_format_and_content: A TAB (tab delimited text file) file containing the same metadata as the above file but readable in a wide range of software

source_name: Primary cells

extract_protocol:
PBMCs were isolated by Ficoll gradient, and cryopreserved in CryoStor (Sigma-Aldrich) at approximately 4x106 cells per vial.
Cells were encapsulated and librariers prepared following the manufacturers protocols (1CellBio, Watertown, MA).  Briefly, Thawed, sorted and diluted cells were encapsulated along with barcoded beads and reverse transcription reagents using the inDrop platform (1CellBio, Watertown, MA).  Flow rates were adjusted periodically throughout the experiment, with the help of high speed video microscopy, to ensure that the number of droplets containing one bead was maximized while minimizing droplets with two or more beads.  Run times were calculated to capture 1500 cells per sample.  Each sample was run on a separate, freshly silanized microfluidics device.  Reverse transcription was performed following the manufacturer’s protocol.  Briefly, barcoding oligo were cleaved by exposing each droplet emulsion aliquot to UV light for 10 minutes. The emulsions were then incubated at 50°C for one hour, and then 70°C for 15 minutes.  The emulsion was then broken, and the aqueous phase containing the cDNA removed. The cDNA was cleaned up MinElute columns (Qiagen, Hilden, Germany) and excess barcodes enzymatically removed.  Second strand synthesis was performed using the NEBNext Ultra II second strand synthesis kit (NEB, Ipswich, MA) according to the manufacturer’s protocol. The samples were then again cleaned up on MinElute columns, and sample integrity confirmed by Bioanalyzer (Agilent, Santa Clara, CA).  In vitro transcription was then performed using the NEB HiScribe High Yield RNA synthesis kit according to the manufacturer’s instructions.  Sample integrity was again verified by Bioanalyzer. The IVT products were then reverse transcribed using random hexamers. Amplifciation cycles were optimized by diagnostic qPCR, and then the samples were amplified using unique PE1/PE2 indexing primers such that samples could be pooled prior to sequencing. Amplified cDNA was then cleaned up using AMPure beads (Beckman Coulter, Indianapolis, IN).  Library integrity and fragment size was confirmed by BioAnalyzer prior to sequencing.

value: PBMCs

tag: disease state

value: VA-ECLS patient

value: Survived

value: Died


title: E16R002b03: B3 HUVEC-3 Static Rcab


title: Patient 37


title: Patient 35


title: E16R002d02: D2 HUVEC-2 80rpm Rcab


title: Patient 34


title: E16R002a01: A1 HUVEC-1 Static ctrl

source_name: Human umbilical vein endothelial cells, untreated, static condition


title: HBsAg carrier sample94_control

type: genomic

city: Taipei

first: Ming-Whei

last: Yu

address: Room 522 No.17, Xuzhou Road Zhongzheng District, Taipei City 10055, Taiwan

department: Graduate Institute of Epidemiology and Preventive Medicine, College of Public Health

country: Taiwan

institute: National Taiwan University

description: genomic DNA from SAMPLE 94

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium HumanMethylation450 Beadchip using standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing:
GenomeStudio v1.1.0
Raw_signal_intensities.txt (linked as a supplementary file on the Series record) reports unmethylated and methylated signal intensities

label: Cy3, Cy5

source_name: HBsAg-positive peripheral leukocytes

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from peripheral leukocyte samples

tag: individual

value: HBsAg carrier

tag: disease status

value: control

tag: gender

value: male

tag: tissue fraction

value: Buffy coat

value: peripheral leukocyte


title: E16R002b01: B1 HUVEC-1 Static Rcab


title: E16R002a02: A2 HUVEC-2 Static ctrl


title: E16R002a03: A3 HUVEC-3 Static ctrl


title: HBsAg carrier sample93_case

description: genomic DNA from SAMPLE 93

value: case

tag: cell type


title: Patient 33


title: Patient 30


title: HBsAg carrier sample96_control

description: genomic DNA from SAMPLE 96


title: Patient 29


title: Patient 31


title: Patient 28


title: HBsAg carrier sample91_case

description: genomic DNA from SAMPLE 91


title: Patient 27


title: Patient 26


title: Patient 32


title: Patient 25


title: Patient 23


title: HBsAg carrier sample86_control

description: genomic DNA from SAMPLE 86


title: Patient 21


title: HBsAg carrier sample85_case

description: genomic DNA from SAMPLE 85


title: HBsAg carrier sample83_case

description: genomic DNA from SAMPLE 83


title: HBsAg carrier sample87_case

description: genomic DNA from SAMPLE 87


title: HBsAg carrier sample90_control

description: genomic DNA from SAMPLE 90


title: HBsAg carrier sample84_control

description: genomic DNA from SAMPLE 84


title: Patient 22


title: HBsAg carrier sample89_case

description: genomic DNA from SAMPLE 89


title: HBsAg carrier sample81_case

description: genomic DNA from SAMPLE 81


title: Patient 20


title: HBsAg carrier sample92_control

description: genomic DNA from SAMPLE 92


title: HBsAg carrier sample78_control

description: genomic DNA from SAMPLE 78


title: Patient 38


title: Patient 24


title: Patient 17


title: HBsAg carrier sample75_case

description: genomic DNA from SAMPLE 75


title: HBsAg carrier sample88_control

description: genomic DNA from SAMPLE 88


title: Patient 18


title: HBsAg carrier sample95_case

description: genomic DNA from SAMPLE 95


title: HBsAg carrier sample80_control

description: genomic DNA from SAMPLE 80


title: HBsAg carrier sample74_control

description: genomic DNA from SAMPLE 74


title: HBsAg carrier sample77_case

description: genomic DNA from SAMPLE 77


title: Patient 19


title: Patient 14


title: Patient 15


title: HBsAg carrier sample70_control

description: genomic DNA from SAMPLE 70


title: Patient 16


title: Patient 12


title: Patient 13


title: Patient 9


title: HBsAg carrier sample68_control

description: genomic DNA from SAMPLE 68


title: HBsAg carrier sample79_case

description: genomic DNA from SAMPLE 79


title: HBsAg carrier sample82_control

description: genomic DNA from SAMPLE 82


title: HBsAg carrier sample71_case

description: genomic DNA from SAMPLE 71


title: HBsAg carrier sample73_case

description: genomic DNA from SAMPLE 73


title: Patient 7


title: Patient 6


title: HBsAg carrier sample67_case

description: genomic DNA from SAMPLE 67


title: Patient 5


title: Patient 4


title: HBsAg carrier sample76_control

description: genomic DNA from SAMPLE 76


title: Patient 3


title: Patient 2


title: HBsAg carrier sample64_control

description: genomic DNA from SAMPLE 64


title: Patient 1


title: HBsAg carrier sample63_case

description: genomic DNA from SAMPLE 63


title: HBsAg carrier sample66_control

description: genomic DNA from SAMPLE 66


title: 03_uninfected_mtb_24h_C

city: Seattle

first: Eliza

last: Peterson

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

description: uninfected

data_processing:
Raw FASTQ read data were processed using the R package DuffyNGS
Genome_build: Mycobacterium tuberculosis H37Rv ASM19595v2 and Mus musculus GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text files includes RPKM and read counts for each sample.

organism: Mycobacterium tuberculosis

source_name: bacterial culture

extract_protocol:
Cell pellets in TRIzol were transferred to a tube containing Lysing Matrix B (QBiogene, Inc.), and vigorously shaken at max speed for 30 s in a FastPrep 120 homogenizer (QBiogene) three times. This mixture was centrifuged at max speed for 1 min and the supernatant was transferred to a fresh tube. RNA was isolated using chloroform/isopropanol extraction method with DNase treatment. Total RNA was depleted of rRNA using Illumina RiboZero Gold Epidemiology kit.
RNA libraries for Path-seq were prepared using the SureSelectXT strand-specific RNA target enrichment for Illumina multiplexed sequencing using custom MTB probes (assembly M_tub_h37rv_ASM19595v2_32_1). RNA libraries for RNA-seq were prepared using the SureSelectXT strand-specific RNA kit, but were not hybridized to probes.

value: M. tuberculosis H37Rv

value: bacterial culture

value: wildtype


title: HBsAg carrier sample65_case

description: genomic DNA from SAMPLE 65


title: 02_uninfected_mtb_24h_B

description: uninfected


title: 01_uninfected_mtb_24h_A

description: uninfected


title: HBsAg carrier sample72_control

description: genomic DNA from SAMPLE 72


title: Patient 11


title: HBsAg carrier sample62_control

description: genomic DNA from SAMPLE 62


title: 21-mtb-no-inf-24h_C

description: uninfected, processed by Path-seq

data_processing:
Raw FASTQ read data were processed using the R package DuffyNGS
Genome_build: Mycobacterium tuberculosis H37Rv ASM19595v2 and Mus Musculus GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text files includes RPKM and read countss for each sample, meta-data (time and dissolved oxygen for each sample)

extract_protocol:
Cell pellets in TRIzol were transferred to a tube containing Lysing Matrix B (QBiogene, Inc.), and vigorously shaken at max speed for 30 s in a FastPrep 120 homogenizer (QBiogene) three times. This mixture was centrifuged at max speed for 1 min and the supernatant was transferred to a fresh tube. RNA was isolated using the Direct-zol RNA MicroPrep kit (Zymol Research) according to manufacturer’s instruction with on-column DNase treatment. Total RNA was depleted of rRNA using Illumina RiboZero Gold Epidemiology kit.
RNA libraries for Path-seq were prepared using the SureSelectXT strand-specific RNA target enrichment for Illumina multiplexed sequencing using custom MTB probes (assembly M_tub_h37rv_ASM19595v2_32_1). RNA libraries for RNA-seq were prepared using the SureSelectXT strand-specific RNA kit, but were not hybridized to probes.


title: 20-mtb-no-inf-24h_B

description: uninfected, processed by Path-seq


title: HBsAg carrier sample57_case

description: genomic DNA from SAMPLE 57


title: HBsAg carrier sample59_case

description: genomic DNA from SAMPLE 59


title: 19-mtb-no-inf-24h_A

description: uninfected, processed by Path-seq


title: HBsAg carrier sample58_control

description: genomic DNA from SAMPLE 58


title: HBsAg carrier sample51_case

description: genomic DNA from SAMPLE 51


title: Patient 10


title: HBsAg carrier sample69_case

description: genomic DNA from SAMPLE 69


title: 11-mtb-no-inf-8h_B

description: uninfected, processed by Path-seq

value: 8 h


title: 10-mtb-no-inf-8h_A

description: uninfected, processed by Path-seq


title: HBsAg carrier sample55_case

description: genomic DNA from SAMPLE 55


title: HBsAg carrier sample49_case

description: genomic DNA from SAMPLE 49


title: HBsAg carrier sample53_case

description: genomic DNA from SAMPLE 53


title: 01-mtb-no-inf-2h_A

description: uninfected, processed by Path-seq

value: 2 h


title: 03-mtb-no-inf-2h_C

description: uninfected, processed by Path-seq


title: HBsAg carrier sample52_control

description: genomic DNA from SAMPLE 52


title: 02-mtb-no-inf-2h_B

description: uninfected, processed by Path-seq


title: T26_120h_46.92oxygen_C

data_processing:
Illumina RiboZero bacteria kit was used for rRNA depletion. Samples were sequenced on the NextSeq sequencing instrumetn in mid output 150 v2 flow cell. Paired-end 75 bp reads were checked for technical artifacts using FastQC following Illumina default quality filtering steps. Raw FASTQ read data were aligned using Bowtie2 and processed using the R package DuffyNGS.
Genome_build: Mycobacterium tuberculosis H37Rv ASM19595v2
Supplementary_files_format_and_content: tab-delimited text file includes RPKM for each sample, meta-data (time and dissolved oxygen for each sample)

extract_protocol:
Biological triplicate cultures (A-C) of M. tuberculosis H37Rv wildtype in 7H9 media, were grown as 750 mL cultures in 2L spinner flasks, at 37ºC, 5%CO2. Mass flow controllers were used to adjust the amount of nitrogen and air flowing into the headspace. Sample were collected via syringe through sampling port. After harvesting, cells were spun down, flash frozen as cell pellets and kept frozen at -80 until RNA isolation. Cell pellets were resuspended in lysing buffer and transferred to a tube containing Lysing Matrix B, and vigorously shaken at max speed for 30 s in a FastPrep 120 homogenizer three times. This mixture was centrifuged at max speed for 1 min and the supernatant was transferred to a fresh tube. RNA was isolated using chloroform/isopropanol extraction with DNase treatment.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: dissolved oxygen


title: HBsAg carrier sample56_control

description: genomic DNA from SAMPLE 56


title: T26_120h_46.92oxygen_B


title: Patient 8


title: HBsAg carrier sample50_control

description: genomic DNA from SAMPLE 50


title: T26_120h_46.92oxygen_A


title: HBsAg carrier sample48_control

description: genomic DNA from SAMPLE 48


title: HBsAg carrier sample60_control

description: genomic DNA from SAMPLE 60


title: HBsAg carrier sample46_control

description: genomic DNA from SAMPLE 46


title: T25_116h_10.89oxygen_C


title: HBsAg carrier sample54_control

description: genomic DNA from SAMPLE 54


title: T25_116h_10.89oxygen_B


title: T25_116h_10.89oxygen_A


title: HBsAg carrier sample44_control

description: genomic DNA from SAMPLE 44


title: HBsAg carrier sample41_case

description: genomic DNA from SAMPLE 41


title: HBsAg carrier sample43_case

description: genomic DNA from SAMPLE 43


title: T24_115h_6oxygen_C

value: 6 % DO


title: HBsAg carrier sample47_case

description: genomic DNA from SAMPLE 47


title: HBsAg carrier sample45_case

description: genomic DNA from SAMPLE 45


title: T24_115h_6oxygen_A


title: HBsAg carrier sample61_case

description: genomic DNA from SAMPLE 61


title: HBsAg carrier sample42_control

description: genomic DNA from SAMPLE 42


title: T23_114.5h_3.84oxygen_B


title: T24_115h_6oxygen_B


title: T23_114.5h_3.84oxygen_C


title: T22_114h_0.45oxygen_C


title: T23_114.5h_3.84oxygen_A


title: HBsAg carrier sample38_control

description: genomic DNA from SAMPLE 38


title: 27-BMDM-no-inf-24h_C

description: uninfected, standard RNA-seq

source_name: BMDMs

value: BMDMs


title: 26-BMDM-no-inf-24h_B

description: uninfected, standard RNA-seq


title: T22_114h_0.45oxygen_A


title: T21_112h_0oxygen_C

value: 0 % DO


title: HBsAg carrier sample37_case

description: genomic DNA from SAMPLE 37


title: T22_114h_0.45oxygen_B


title: 25-BMDM-no-inf-24h_A

description: uninfected, standard RNA-seq


title: HBsAg carrier sample34_control

description: genomic DNA from SAMPLE 34


title: HBsAg carrier sample33_case

description: genomic DNA from SAMPLE 33


title: T21_112h_0oxygen_B


title: HBsAg carrier sample39_case

description: genomic DNA from SAMPLE 39


title: HBsAg carrier sample36_control

description: genomic DNA from SAMPLE 36


title: T21_112h_0oxygen_A


title: 17-BMDM-no-inf-8h_B

description: uninfected, standard RNA-seq


title: 18-BMDM-no-inf-8h_C

description: uninfected, standard RNA-seq


title: 12-mtb-no-inf-8h_C

description: uninfected, processed by Path-seq


title: T20_94h_0oxygen_B


title: T20_94h_0oxygen_C


title: HBsAg carrier sample27_case

description: genomic DNA from SAMPLE 27


title: 09-BMDM-no-inf-2h_C

description: uninfected, standard RNA-seq


title: HBsAg carrier sample29_case

description: genomic DNA from SAMPLE 29


title: T20_94h_0oxygen_A


title: 08-BMDM-no-inf-2h_B

description: uninfected, standard RNA-seq


title: T19_88h_0oxygen_C


title: HBsAg carrier sample32_control

description: genomic DNA from SAMPLE 32


title: HBsAg carrier sample22_control

description: genomic DNA from SAMPLE 22


title: 07-BMDM-no-inf-2h_A

description: uninfected, standard RNA-seq


title: HBsAg carrier sample35_case

description: genomic DNA from SAMPLE 35


title: HBsAg carrier sample30_control

description: genomic DNA from SAMPLE 30


title: T19_88h_0oxygen_B


title: T19_88h_0oxygen_A


title: T18_70h_0oxygen_C


title: CU3D1

city: Gent

first: Jana

last: Asselman

address: Coupure Links 653 (Building F, 2nd floor)

country: Belgium

institute: Ghent University

description: NormalizedCountsTranscriptome.txt

data_processing:
Reads were trimmed using trimmomatric version 0.32 to remove any adaptor sequences
The trimmed reads were mapped against the Daphnia magna transcriptome using tophat version 2.1.1
The HTSeq was used to generate the count tables
Raw counts were filtered, whereby only genes with a cpm above 1 in at least 3 samples were retained
Filtered counts were normalized using edgeR standard normalization method
Genome_build: http://arthropods.eugenes.org/EvidentialGene/daphnia/daphnia_magna/Genes/earlyaccess/dmagset7finloc9b.puban.mrna.gz
Supplementary_files_format_and_content: They contain normalized counts in a tab delimited format

organism: Daphnia magna

source_name: whole body

growth_protocol: Animals were cultured in M4 medium under a 16:8 light:dark cycle and fed daily

extract_protocol: RNA was extracted using the Qiagen RNEasy kit following manufacturers instruction including DNAse digestion

treatment_protocol: Animals were exposed to copper, arsenic, a mixture of both for 1, 2 or 4 days

tag: exposure time

value: 1 day

value: whole body

tag: treatment

value: copper


title: HBsAg carrier sample23_case

description: genomic DNA from SAMPLE 23

value: HBsAg carrier


title: HBsAg carrier sample40_control

description: genomic DNA from SAMPLE 40

value: control


title: CU4D1

description: NormalizedCountsTranscriptome.txt

tag: tissue


title: HBsAg carrier sample25_case

description: genomic DNA from SAMPLE 25

value: male


title: T18_70h_0oxygen_B

tag: genotype


title: HBsAg carrier sample28_control

description: genomic DNA from SAMPLE 28

value: Buffy coat


title: HBsAg carrier sample20_control

description: genomic DNA from SAMPLE 20

value: peripheral leukocyte


title: CU1D1

description: NormalizedCountsTranscriptome.txt


title: HBsAg carrier sample31_case

description: genomic DNA from SAMPLE 31

value: case


title: CT4D1

description: NormalizedCountsTranscriptome.txt


title: T17_64h_0oxygen_C

tag: strain


title: T18_70h_0oxygen_A


title: HBsAg carrier sample19_case

description: genomic DNA from SAMPLE 19


title: CT3D1

description: NormalizedCountsTranscriptome.txt


title: T17_64h_0oxygen_B


title: CT2D1

description: NormalizedCountsTranscriptome.txt


title: HBsAg carrier sample18_control

description: genomic DNA from SAMPLE 18


title: T17_64h_0oxygen_A


title: CT1D1

description: NormalizedCountsTranscriptome.txt


title: T16_54h_0oxygen_F


title: AC4D4

description: NormalizedCountsTranscriptome.txt

value: 4 days

value: copper+arsenic


title: HBsAg carrier sample26_control

description: genomic DNA from SAMPLE 26


title: T16_54h_0oxygen_D

value: wildtype


title: AC3D4

description: NormalizedCountsTranscriptome.txt


title: HBsAg carrier sample24_control

description: genomic DNA from SAMPLE 24


title: HBsAg carrier sample17_case

description: genomic DNA from SAMPLE 17


title: T16_54h_0oxygen_E


title: HBsAg carrier sample15_case

description: genomic DNA from SAMPLE 15


title: 16-BMDM-no-inf-8h_A

description: uninfected, standard RNA-seq

value: 8 h


title: AC2D4

description: NormalizedCountsTranscriptome.txt


title: HBsAg carrier sample21_case

description: genomic DNA from SAMPLE 21


title: HBsAg carrier sample14_control

description: genomic DNA from SAMPLE 14


title: AC1D4

description: NormalizedCountsTranscriptome.txt


title: AS4D4

description: NormalizedCountsTranscriptome.txt

value: arsenic


title: HBsAg carrier sample12_control

description: genomic DNA from SAMPLE 12


title: HBsAg carrier sample11_case

description: genomic DNA from SAMPLE 11


title: T16_54h_0oxygen_A


title: T16_54h_0oxygen_B


title: T16_54h_0oxygen_C


title: AS3D4

description: NormalizedCountsTranscriptome.txt


title: T14_52h_0oxygen_C


title: T14_52h_0oxygen_B


title: AS2D4

description: NormalizedCountsTranscriptome.txt


title: si3

city: Xi‘an’

first: Jiaxing

last: Sun

state: Shaanxi

address: Changlexi 169#

institute: Fourth Military Medical University

data_processing:
The clean reads were aligned to the reference genome using TopHat (Broad Institute). During read alignment, a maximum of two mismatches and a gap length of 2 bps were allowed. The functional annotations of genetic variants were generated using ANNOVAR. Read alignments were processed by Cufflinks software package to determine the differential expression of genes.
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text files include counts and RPKM values for each Sample

source_name: human umbilical vein endothelial cells

growth_protocol: Cells at passages 2–6 were used and cultured in EC medium (ECM) (ScienCell) supplemented with 5% FBS, EC growth supplements (ECGS), 100 U/mL penicillin and 100 μg/mL streptomycin in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
HUVECs were transfected with siSNAI1 or NC and cultured in complete ECM for 24h. Cells were then starved in ECM with 0.5 % FBS and without ECGS for 24h following VEGF-165 stimulus at 50 ng/mL for 6h. RNA was extracted, sequenced and analyzed by RiboBio. In brief, total RNA was isolated from cells using TRIzol reagent (Invitrogen) according to the manufacturer's protocol. RNA purity was assessed using the ND-1000 Nanodrop. Each RNA sample had an A260:A280 ratio above 1.8 and A260:A230 ratio above 2.0. RNA integrity was evaluated using the Agilent 2200 TapeStation (Agilent Technologies, USA) and each sample had the RINe above 7.0.
RNA libraries were prepared for sequencing using standard Illumina protocols. mRNAs were isolated from total RNA and fragmented to approximately 200bp, and subsequently subjected to first strand and second strand cDNA synthesis following by adaptor ligation and enrichment with a low-cycle according to instructions of TruSeq® RNA LT/HT Sample Prep Kit (Illumina, USA). The purified library products were evaluated using the Agilent 2200 TapeStation and Qubit®2.0(Life Technologies,USA) and then diluted to 10 pmol/L for cluster generation in situ on the HiSeq3000 pair-end flow cell followed by sequencing (2×150 bp) on HiSeq 3000.

value: endothelial

value: umbilical vein

tag: sirna


title: HBsAg carrier sample8_control

description: genomic DNA from SAMPLE 8


title: AS1D4

description: NormalizedCountsTranscriptome.txt


title: HBsAg carrier sample13_case

description: genomic DNA from SAMPLE 13


title: si2


title: CU4D4

description: NormalizedCountsTranscriptome.txt


title: HBsAg carrier sample16_control

description: genomic DNA from SAMPLE 16


title: T13_50h_0oxygen_C

value: 0 % DO


title: NC3

value: NC


title: CU3D4

description: NormalizedCountsTranscriptome.txt

value: whole body


title: CU2D4

description: NormalizedCountsTranscriptome.txt

value: copper


title: NC2


title: HBsAg carrier sample6_control

description: genomic DNA from SAMPLE 6

value: HBsAg carrier


title: HBsAg carrier sample7_case

description: genomic DNA from SAMPLE 7


title: NC1


title: CU1D4

description: NormalizedCountsTranscriptome.txt


title: T12_49h_0oxygen_C


title: CT4D4

description: NormalizedCountsTranscriptome.txt

value: control


title: HBsAg carrier sample9_case

description: genomic DNA from SAMPLE 9

value: male


title: T13_50h_0oxygen_A


title: CT3D4

description: NormalizedCountsTranscriptome.txt


title: HBsAg carrier sample3_case

description: genomic DNA from SAMPLE 3

value: Buffy coat


title: T12_49h_0oxygen_A


title: T12_49h_0oxygen_B


title: CT2D4

description: NormalizedCountsTranscriptome.txt


title: T11_48h_0oxygen_C


title: HBsAg carrier sample4_control

description: genomic DNA from SAMPLE 4

value: peripheral leukocyte


title: CT1D4

description: NormalizedCountsTranscriptome.txt


title: HBsAg carrier sample10_control

description: genomic DNA from SAMPLE 10


title: HBsAg carrier sample1_case

description: genomic DNA from SAMPLE 1

value: case


title: T11_48h_0oxygen_B


title: HBsAg carrier sample5_case

description: genomic DNA from SAMPLE 5


title: HBsAg carrier sample2_control

description: genomic DNA from SAMPLE 2


title: CU2D1

description: NormalizedCountsTranscriptome.txt

value: 1 day


title: T11_48h_0oxygen_A


title: AC4D2

description: NormalizedCountsTranscriptome.txt

value: 2 days

value: copper+arsenic


title: AC3D2

description: NormalizedCountsTranscriptome.txt


title: T10_47h_0oxygen_C

value: wildtype


title: AC2D2

description: NormalizedCountsTranscriptome.txt


title: T10_47h_0oxygen_B


title: AC1D2

description: NormalizedCountsTranscriptome.txt


title: E13R040d03: D3 (200ng/ml_HGF)

description: isolated from the vein of the umbilical cord (promocell)

source_name: Human umbilical vein endothelial cells, HGF treated

value: Human umbilical vein endothelial cells

value: passage 4


title: E13R040d02: D2 (200ng/ml_HGF)


title: T10_47h_0oxygen_A


title: AS4D2

description: NormalizedCountsTranscriptome.txt

value: arsenic


title: E13R040d01: D1 (200ng/ml_HGF)


title: AS3D2

description: NormalizedCountsTranscriptome.txt


title: E13R040b02: B2 (Bolus200nM_RCab)

source_name: Human umbilical vein endothelial cells, RCαβ treated


title: AS2D2

description: NormalizedCountsTranscriptome.txt


title: T9_46h_0.41oxygen_A


title: E13R040a03: A3 (no treatment)

source_name: Human umbilical vein endothelial cells, untreated


title: MSMEG_0916_induced

data_processing:
Samples were sequenced on the NextSeq sequencing instrument in mid output 150 v2 flow cell. Unpaired 75 bp reads were checked for technical artifacts using FastQC following Illumina default quality filtering steps. Raw FASTQ read data were processed using the R package DuffyNGS.
Genome_build: Mycobacterium smegmatis mc2155 ASM1500v1
Supplementary_files_format_and_content: csv  file containing identified ChIP-peak with scores and significance as described in Minch et al (2015) Nature Communications.

organism: Mycolicibacterium smegmatis

extract_protocol:
Biological triplicate cultures of M. smegmatis containing pDTCF-MSMEG_0916 in 7H9 media, were grown as 50 mL cultures , at 37ºC, 5%CO2, for 4 hours in the presence or absence of 100 ng/ml anhydrotetracycline.
DNA libraries were prepared for sequencing using ThruPLEX DNA-seq Kit (Rubicon) standard protocols

treatment_protocol: induced sample treated with 100 ng/ml Atc for overexpression of MSMEG_0916

tag: genotype/variation

value: MSM pDTCF-MSMEG_0916 indcued

tag: treated with

value: 100 ng/ml ATc

tag: treatment time

value: 4 hour


title: E13R040b03: B3 (Bolus200nM_RCab)

tag: passage


title: CU3D2

description: NormalizedCountsTranscriptome.txt

value: whole body

value: copper


title: T8_45h_2.93oxygen_B

tag: age


title: CU4D2

description: NormalizedCountsTranscriptome.txt


title: 11_Msm_916_induced

data_processing:
Illumina RiboZero bacteria kit was used for rRNA depletion. Samples were sequenced on the NextSeq sequencing instrumetn in mid output 150 v2 flow cell. Paired-end 75 bp reads were checked for technical artifacts using FastQC following Illumina default quality filtering steps. Raw FASTQ read data were processed using the R package DuffyNGS.
Genome_build: Mycobacterium smegmatis mc2155 ASM1500v1
Supplementary_files_format_and_content: tab-delimited text file includes RPKM for each sample

extract_protocol:
Biological triplicate cultures of M. smegmatis containing pDTCF-MSMEG_0916 in 7H9 media, were grown as 10 mL cultures in 50mL flasks, at 37ºC, 5%CO2, for 4 hours in the presence or absence of 100 ng/ml anhydrotetracycline. After harvesting, cells were spun down, resuspended in Trizol, and frozen at -80 until RNA isolation. Cell pellets in TRIzol were transferred to a tube containing Lysing Matrix B, and vigorously shaken at max speed for 30 s in a FastPrep 120 homogenizer three times. This mixture was centrifuged at max speed for 1 min and the supernatant was transferred to a fresh tube. RNA was isolated using the Direct-zol RNA MicroPrep kit (Zymol Research) according to manufacturer’s instruction with on-column DNase treatment.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: induced samples treated with 100 ng/ml Atc for overexpression of MSMEG_0916

value: MSM pDTCF-MSMEG_0916 induced

tag: time point

tag: agent


title: E13R040b01: B1 (Bolus200nM_RCab)


title: E13R040a04: A4 (no treatment)


title: T14_52h_0oxygen_A

value: 0 % DO


title: E13R040a02: A2 (no treatment)


title: T9_46h_0.41oxygen_B


title: AS1D2

description: NormalizedCountsTranscriptome.txt


title: T8_45h_2.93oxygen_A


title: 12_Msm_916_induced


title: E13R040a01: A1 (no treatment)


title: CU2D2

description: NormalizedCountsTranscriptome.txt


title: 10_Msm_916_induced


title: T9_46h_0.41oxygen_C


title: 09_Msm_916_uninduced

value: MSM pDTCF-MSMEG_0916 uninduced

value: 0 ng/ml ATc


title: T7_44h_4.31oxygen_C


title: CU1D2

description: NormalizedCountsTranscriptome.txt


title: MSMEG_0916_uninduced

value: MSM pDTCF-MSMEG_0916 unindcued


title: T8_45h_2.93oxygen_C


title: T7_44h_4.31oxygen_B


title: 08_Msm_916_uninduced


title: CT3D2

description: NormalizedCountsTranscriptome.txt

value: control


title: 07_Msm_916_uninduced


title: T7_44h_4.31oxygen_A


title: T6_43h_6.13oxygen_C


title: 03_mmu_inf_mtb_24h_C

description: infected

organism:
Mycobacterium tuberculosis
Mus musculus

source_name: mouse infection

value: M. tuberculosis H37Rv and M. musculus C57BL/6 mice

value: MTB infected mouse alveolar macrophages


title: CT1D2

description: NormalizedCountsTranscriptome.txt

value: 2 days


title: 02_mmu_inf_mtb_24h_B

description: infected

value: wildtype


title: AC4D1

description: NormalizedCountsTranscriptome.txt

value: 1 day

value: copper+arsenic


title: T6_43h_6.13oxygen_A


title: CT2D2

description: NormalizedCountsTranscriptome.txt


title: T5_42h_7.49oxygen_C


title: 01_mmu_inf_mtb_24h_A

description: infected


title: T5_42h_7.49oxygen_B


title: 24-mtb-BMDM-inf-24h-RNA-seq_C

description: infected, standard RNA-seq

source_name: M. tuberculosis infected BMDMs

value: M. tuberculosis infected BMDMs


title: 23-mtb-BMDM-inf-24h-RNA-seq_B

description: infected, standard RNA-seq


title: CT4D2

description: NormalizedCountsTranscriptome.txt


title: 22-mtb-BMDM-inf-24h-RNA-seq_A

description: infected, standard RNA-seq


title: AC2D1

description: NormalizedCountsTranscriptome.txt


title: AC1D1

description: NormalizedCountsTranscriptome.txt


title: T4_41h_8.82oxygen_C


title: AS4D1

description: NormalizedCountsTranscriptome.txt

value: arsenic


title: T4_41h_8.82oxygen_B


title: 15-mtb-BMDM-inf-8h-RNA-seq_C

description: infected, standard RNA-seq

value: 8 h


title: T6_43h_6.13oxygen_B


title: T4_41h_8.82oxygen_A


title: T3_40h_11.51oxygen_C


title: T5_42h_7.49oxygen_A


title: 06-mtb-BMDM-inf-2h-RNA-seq_C

description: infected, standard RNA-seq

value: 2 h


title: AS2D1

description: NormalizedCountsTranscriptome.txt

value: whole body


title: T3_40h_11.51oxygen_B


title: 14-mtb-BMDM-inf-8h-RNA-seq_B

description: infected, standard RNA-seq


title: T3_40h_11.51oxygen_A


title: AC3D1

description: NormalizedCountsTranscriptome.txt


title: T2_23h_42.77oxygen_C


title: 04-mtb-BMDM-inf-2h-RNA-seq_A

description: infected, standard RNA-seq


title: 05-mtb-BMDM-inf-2h-RNA-seq_B

description: infected, standard RNA-seq


title: KO4

city: Rockville

first: Tongwu

last: Zhang

state: MD

address: 9609 Medical Center Drive

department: Division of Cancer Epidemiology & Genetics

institute: National Cancer Institute

description: RNA was purified using Rneasy Fibrous Tissue Kit

hyb_protocol: The reaction mixes were loaded onto the Nanostring nCounter Prep Station for binding and wahing.

scan_protocol: The resulting cartridge was transferred to the Nanostring nCounter digital analyzer for scanning

data_processing:
The data collection was done by Nanostring nCounter digital analyzer. Quantified expression data were analyzed using Nanostring nSolver Analysis software v2.0.
Data were log2-transformed and used for further analysis. Student's t-test was applied to compare normalized expression values between groups.

label: Biotin & color-coded tag

source_name: Yumm1.5 melanoma

label_protocol: For each Nanostring assay, an aliquot of 100ng RNA was mixed with a Nanostring code set mix and incubated at 65 C for overnight.

growth_protocol: Yumm1.5 cells wer cultured in DMEM media.

extract_protocol: RNA from tumors was purified using Rneasy Fibrous Tissue Kit.Purity and concentration of extracted RNA were checked and quantified by reading at 260 and 280 nm in a NanoDrop spectrophotometer (Thermo Fisher)

treatment_protocol: Yumm1.5 tumor cells were injected into WT or Rnf5-/- mice.The tumor were collected at day 10 after injection.

value: melanoma

tag: cell line

tag: mouse genotype

value: Rnf5 KO


title: 24-mtb-BMDM-inf-24h-Path-seq_C

description: infected, processed by Path-seq


title: si1

tag: cell type

value: endothelial

value: umbilical vein


title: KO3


title: 23-mtb-BMDM-inf-24h-Path-seq_B

description: infected, processed by Path-seq


title: T2_23h_42.77oxygen_B

tag: dissolved oxygen


title: cry_input_RA_PE

city: Edinburgh

first: Robin

last: Allshire

address: Max Born Cresent

institute: The University of Edinburgh

organism: Schizosaccharomyces cryophilus

growth_protocol: cell were gwon in rich medium (YES).

value: whole cells

value: wild-type

tag: chip antibody

value: input


title: AS3D1

description: NormalizedCountsTranscriptome.txt

tag: exposure time

tag: treatment


title: T2_23h_42.77oxygen_A

tag: genotype


title: 22-mtb-BMDM-inf-24h-Path-seq_A

description: infected, processed by Path-seq

tag: strain

value: M. tuberculosis H37Rv and M. musculus C57BL/6 mice

tag: tissue


title: T13_50h_0oxygen_B

value: 0 % DO


title: T1_17h_57.63oxygen_C

value: wildtype


title: cry_input_PE


title: 15-mtb-BMDM-inf-8h-Path-seq_C

description: infected, processed by Path-seq


title: T1_17h_57.63oxygen_B


title: 13-mtb-BMDM-inf-8h-RNA-seq_A

description: infected, standard RNA-seq


title: KO2


title: 14-mtb-BMDM-inf-8h-Path-seq_B

description: infected, processed by Path-seq


title: KO5


title: 13-mtb-BMDM-inf-8h-Path-seq_A

description: infected, processed by Path-seq


title: cry_H3K9_PE


title: T1_17h_57.63oxygen_A


title: KO1


title: cry_H3K9_RA_PE


title: cry_CENPA_PE

value: CENPA


title: 06-mtb-BMDM-inf-2h-Path-seq_C

description: infected, processed by Path-seq


title: cry_INPUT

value: INPUT


title: AS1D1

description: NormalizedCountsTranscriptome.txt

value: 1 day


title: WT4

value: WT


title: 05-mtb-BMDM-inf-2h-Path-seq_B

description: infected, processed by Path-seq

value: M. tuberculosis infected BMDMs


title: T0_0h_81.62oxygen_B

value: 0 h


title: T0_0h_81.62oxygen_A


title: cry_CENPA_SE


title: WT1


title: 04-mtb-BMDM-inf-2h-Path-seq_A

description: infected, processed by Path-seq

value: 2 h


title: L046T

status: Public on Mar 03 2019

city: Beijing

first: Ying

last: Jiang

address: Life Science Park Road

institute: National Center for Protein Sciences (Beijing)

description:
HCC.RNA-seq.35.samples.fpkm.txt
418T

data_processing:
RNA-seq reads per sample were mapped to the reference using Tophat11 v2.0.12. The reference consists of the human reference genome and the Ensembl annotated human transcriptome (GRCh37/hg19 assembly). The mapped reads were processed using cufflinks12 v2.2.1 with the ‘classic-fpkm’ library normalization method and ‘fr-unstranded’ library type to quantitate gene expression against Ensembl transcript annotation.
Genome_build: hg19
Supplementary_files_format_and_content: The processed data file L*.fpkm.txt has two columns. The first represets the Ensembl gene ID, and the second represents the FPKM of the corresponding gene.

extract_protocol:
The TRIzol method was used for RNA extraction of liver tissues. RNA degradation and contamination were monitored on 1% agarose gels. RNA purity was checked using the Nano Photometer® spectrophotometer (IMPLEN, CA, USA). RNA concentration was measured using the Qubit® RNA Assay Kit in Qubit® 2.0 Fluorometer (Life Technologies, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using the NEBNext® Ultra™ RNA Library PrepKit for Illumina® (NEB, USA) following the manufacturer’s recommendations, and index codes were added to attribute sequences to each sample.

value: HCC

tag: tumor stage

value: early stage


title: L047T

description:
HCC.RNA-seq.35.samples.fpkm.txt
419T


title: WT5

value: melanoma


title: L056T

description:
HCC.RNA-seq.35.samples.fpkm.txt
429T


title: L076T

description:
HCC.RNA-seq.35.samples.fpkm.txt
4T


title: L044T

description:
HCC.RNA-seq.35.samples.fpkm.txt
416T