title: SJSA-1 cells, ZNF217 KD #2

city: Minneapolis

first: Lauren

last: Mills

state: MN

address: 420 Delaware St SE

department: Department of Pediatrics

institute: University of Minnesota

description:
SJSAKD2
rawCounts_SJSA1.txt
DESeq2_results_TPMs_SJSA1_Ctl-KD.xlsx

data_processing:
Illumina specific adapters and low quality sequences were removed with Trimmomatic
Reads that passed QC were aligned to GRCh38 with HISAT2
Gene level count data was generated using Subread featrurecount and Ensembl annotations
Differential expression tests were performed using DESeq2 using Control - KD as the design
Genome_build: GRCh38
Supplementary_files_format_and_content: Excel file with DESeq2 results and TPM values for each gene
tab delimited text with raw counts for each gene

source_name: cell line

extract_protocol:
Total RNA was extracted using the PureLink RNA extraction kit from Thermo
Library was constructed in the University of Minnesota Genomics Core (UMGC) using standard methodology

value: ZNF217 knockdown


title: SJSA-1 cells, CON #2

status: Public on Mar 24 2020

type: SRA

country: USA

description:
SJSA1CON2
rawCounts_SJSA1.txt
DESeq2_results_TPMs_SJSA1_Ctl-KD.xlsx

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: genotype

value: control


title: LN229 Ctr_H3K27ac ChIP

city: New York

first: Markus

last: Siegelin

institute: Columbia University Medical Center

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using bwa mem
peaks were called using macs version 2.1.2 with the default setting
Genome_build: hg19
Supplementary_files_format_and_content: wig files were generated using deepTools; Scores represent depth

molecule: genomic DNA

growth_protocol: Glioblastoma cells were grown in 10% FBS/DMEM in 5% CO2 incubator.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: U87 and LN229 were treated with 0.05 uM for 3 weeksand harvested for ChIP.

tag: cell type

value: glioblastoma cells

tag: passages

tag: chip antibody


title: SJSA-1 cells, CON #1

description:
SJSA1CON1
rawCounts_SJSA1.txt
DESeq2_results_TPMs_SJSA1_Ctl-KD.xlsx


title: LN229 PbR_Input2


title: U87 Ctr_Input


title: U87 PbR_Input


title: U87 PbR_Input2


title: U87 PbR_H3K27ac ChIP


title: U87 Ctr_H3K27ac ChIP


title: KinaseScreen_OVCA420

city: Ottawa

first: David

last: Cook

state: ON

address: 501 Smyth Rd

department: Cancer Therapeutics Program

country: Canada

institute: Ottawa Hospital Research Institute

description:
MULTI-seq pool of OVCA420 cells treated with TGFB1, EGF, or TNF along with 22 independent kinase inhibitors
A549_KinaseScreen_UMI_matrix.csv.gz
A549_KinaseScreen_metadata.csv.gz
DU145_KinaseScreen_UMI_matrix.csv.gz
DU145_KinaseScreen_metadata.csv.gz
MCF7_KinaseScreen_UMI_matrix.csv.gz
MCF7_KinaseScreen_metadata.csv.gz
OVCA420_KinaseScreen_UMI_matrix.csv.gz
OVCA420_KinaseScreen_metadata.csv.gz
KinaseScreen_unfiltered_UMI_matrix.csv.gz
KinaseScreen_unfiltered_metadata.csv.gz
KinaseScreen_OVCA420_barcode_counts.csv.gz
KinaseScreen_OVCA420_barcode_annotations.csv.gz

data_processing:
Raw sequencing reads were processed using CellRanger v2.2.0 (Time course data) or v3.0.2 (kinase inhibitor screens). The GRCh38 build of the human genome was used for both. Except for explicitly setting --expect-cells=25000, default parameters were used for all samples. MULTI-seq barcode libraries were simply trimmed to 26bp (v2 libraries) or 28bp (v3 libraries) using Trimmomatic v0.36 prior to demultiplexing.
Sample demultiplexing was performed using the deMULTIplex R package v1.0.2.
Genome_build: GRCh38
Supplementary_files_format_and_content: UMI count matrix: Gene-by-cell matrix containing unprocessed transcript counts for each cell. Cell metadata for UMI count matrix: Cell-by-variable table containing various metadata (eg. Cell line, treatment, time point, etc) for each cell in the UMI count matrix. MULTI-seq barcode UMI count matrix: Cell-by-barcode matrix of MULTI-seq barcode counts for each cell that was used to demultiplex samples. MULTI-seq barcode sample annotation: Table describing which samples were labelled with which MULTI-seq barcode for each replicate of the experiments.

source_name: Cell Lines

growth_protocol: All cell lines were cultured in DMEM (high-glucose) + 10% fetal calf serum

extract_protocol:
Cells were lysed in droplets in the 10x Genomics Chromium system.
cDNA synthesis and library construction was performed using the 10x Genomics Single Cell 3' Reagent Kit (v2 for Time Course data, v3 for Kinase Inhibitor Screens)
3' scRNA-seq


title: KinaseScreen_MCF7

description:
MULTI-seq pool of MCF7 cells treated with TGFB1, EGF, or TNF along with 22 independent kinase inhibitors
A549_KinaseScreen_UMI_matrix.csv.gz
A549_KinaseScreen_metadata.csv.gz
DU145_KinaseScreen_UMI_matrix.csv.gz
DU145_KinaseScreen_metadata.csv.gz
MCF7_KinaseScreen_UMI_matrix.csv.gz
MCF7_KinaseScreen_metadata.csv.gz
OVCA420_KinaseScreen_UMI_matrix.csv.gz
OVCA420_KinaseScreen_metadata.csv.gz
KinaseScreen_unfiltered_UMI_matrix.csv.gz
KinaseScreen_unfiltered_metadata.csv.gz
KinaseScreen_MCF7_barcode_counts.csv.gz
KinaseScreen_MCF7_barcode_annotations.csv.gz


title: TimeCrouse_Pool6

description:
MULTI-seq pool of A549, DU145, MCF7, and OVCA420 cells treated with TGFB1, EGF, or TNF for various periods of time
A549_TGFB1_TimeCourse_UMI_matrix.csv.gz
A549_TGFB1_TimeCourse_metadata.csv.gz
A549_EGF_TimeCourse_UMI_matrix.csv.gz
A549_EGF_TimeCourse_metadata.csv.gz
A549_TNF_TimeCourse_UMI_matrix.csv.gz
A549_TNF_TimeCourse_metadata.csv.gz
DU145_TGFB1_TimeCourse_UMI_matrix.csv.gz
DU145_TGFB1_TimeCourse_metadata.csv.gz
DU145_EGF_TimeCourse_UMI_matrix.csv.gz
DU145_EGF_TimeCourse_metadata.csv.gz
DU145_TNF_TimeCourse_UMI_matrix.csv.gz
DU145_TNF_TimeCourse_metadata.csv.gz
MCF7_TGFB1_TimeCourse_UMI_matrix.csv.gz
MCF7_TGFB1_TimeCourse_metadata.csv.gz
MCF7_EGF_TimeCourse_UMI_matrix.csv.gz
MCF7_EGF_TimeCourse_metadata.csv.gz
MCF7_TNF_TimeCourse_UMI_matrix.csv.gz
MCF7_TNF_TimeCourse_metadata.csv.gz
OVCA420_TGFB1_TimeCourse_UMI_matrix.csv.gz
OVCA420_TGFB1_TimeCourse_metadata.csv.gz
OVCA420_EGF_TimeCourse_UMI_matrix.csv.gz
OVCA420_EGF_TimeCourse_metadata.csv.gz
OVCA420_TNF_TimeCourse_UMI_matrix.csv.gz
OVCA420_TNF_TimeCourse_metadata.csv.gz
TimeCourse_Mix4b_barcode_counts.csv.gz
TimeCourse_Mix4b_barcode_annotations.csv.gz

value: A549, DU145, MCF7, and OVCA420


title: KinaseScreen_A549

description:
MULTI-seq pool of A549 cells treated with TGFB1, EGF, or TNF along with 22 independent kinase inhibitors
A549_KinaseScreen_UMI_matrix.csv.gz
A549_KinaseScreen_metadata.csv.gz
DU145_KinaseScreen_UMI_matrix.csv.gz
DU145_KinaseScreen_metadata.csv.gz
MCF7_KinaseScreen_UMI_matrix.csv.gz
MCF7_KinaseScreen_metadata.csv.gz
OVCA420_KinaseScreen_UMI_matrix.csv.gz
OVCA420_KinaseScreen_metadata.csv.gz
KinaseScreen_unfiltered_UMI_matrix.csv.gz
KinaseScreen_unfiltered_metadata.csv.gz
KinaseScreen_A549_barcode_counts.csv.gz
KinaseScreen_A549_barcode_annotations.csv.gz


title: TimeCourse_Pool5

description:
MULTI-seq pool of A549, DU145, MCF7, and OVCA420 cells treated with TGFB1, EGF, or TNF for various periods of time
A549_TGFB1_TimeCourse_UMI_matrix.csv.gz
A549_TGFB1_TimeCourse_metadata.csv.gz
A549_EGF_TimeCourse_UMI_matrix.csv.gz
A549_EGF_TimeCourse_metadata.csv.gz
A549_TNF_TimeCourse_UMI_matrix.csv.gz
A549_TNF_TimeCourse_metadata.csv.gz
DU145_TGFB1_TimeCourse_UMI_matrix.csv.gz
DU145_TGFB1_TimeCourse_metadata.csv.gz
DU145_EGF_TimeCourse_UMI_matrix.csv.gz
DU145_EGF_TimeCourse_metadata.csv.gz
DU145_TNF_TimeCourse_UMI_matrix.csv.gz
DU145_TNF_TimeCourse_metadata.csv.gz
MCF7_TGFB1_TimeCourse_UMI_matrix.csv.gz
MCF7_TGFB1_TimeCourse_metadata.csv.gz
MCF7_EGF_TimeCourse_UMI_matrix.csv.gz
MCF7_EGF_TimeCourse_metadata.csv.gz
MCF7_TNF_TimeCourse_UMI_matrix.csv.gz
MCF7_TNF_TimeCourse_metadata.csv.gz
OVCA420_TGFB1_TimeCourse_UMI_matrix.csv.gz
OVCA420_TGFB1_TimeCourse_metadata.csv.gz
OVCA420_EGF_TimeCourse_UMI_matrix.csv.gz
OVCA420_EGF_TimeCourse_metadata.csv.gz
OVCA420_TNF_TimeCourse_UMI_matrix.csv.gz
OVCA420_TNF_TimeCourse_metadata.csv.gz
TimeCourse_Mix4a_barcode_counts.csv.gz
TimeCourse_Mix4a_barcode_annotations.csv.gz


title: LN229 PbR_H3K27ac ChIP


title: Vehicle replicate 4, GFP+ cells from 3 mice [CP3_041015]

type: RNA

city: Lexington

first: Timothy

middle: S

last: McClintock

state: Kentucky

address: 508 Medical Science Buildi

department: Physiology

institute: University of kentucky

description: mRNA abundance data

hyb_protocol: after fragmentation cRNA was hybridized for 16 hr at 45C on Mouse GeneChip 1.0 ST arrays. These were washed and stained in an Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using an Affymetrix GCS3000 7G Scanner

data_processing: The data were analyzed with Affymetrix Gene Expression Console software using default analysis settings and global scaling as normalization method.

label: biotin

organism: Mus musculus

source_name: Olfactory mucosa; Vehicle-stimulated

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 50 - 100 ng of total RNA.

growth_protocol: 18 mice of both sexes, ages 7 - 12 weeks, were placed individuallly in clean air chambers for 40 hrs under air flow of 3.1L/min

extract_protocol: Mice were euthanized, olfactory mucosa were dissected, dissociated, and subjected to FACS.

treatment_protocol: After 26 hrs, half the mice were intermittently stimulated with vehicle (filtered air) or odorant for 10 sec every 20 min.

tag: treatment

value: vehicle (filtered air)

value: FACS sample, GFP+


title: SJSA-1 cells, ZNF217 KD #1

description:
SJSAKD1
rawCounts_SJSA1.txt
DESeq2_results_TPMs_SJSA1_Ctl-KD.xlsx


title: TimeCourse_Pool4

description:
MULTI-seq pool of A549, DU145, MCF7, and OVCA420 cells treated with TGFB1, EGF, or TNF for various periods of time
A549_TGFB1_TimeCourse_UMI_matrix.csv.gz
A549_TGFB1_TimeCourse_metadata.csv.gz
A549_EGF_TimeCourse_UMI_matrix.csv.gz
A549_EGF_TimeCourse_metadata.csv.gz
A549_TNF_TimeCourse_UMI_matrix.csv.gz
A549_TNF_TimeCourse_metadata.csv.gz
DU145_TGFB1_TimeCourse_UMI_matrix.csv.gz
DU145_TGFB1_TimeCourse_metadata.csv.gz
DU145_EGF_TimeCourse_UMI_matrix.csv.gz
DU145_EGF_TimeCourse_metadata.csv.gz
DU145_TNF_TimeCourse_UMI_matrix.csv.gz
DU145_TNF_TimeCourse_metadata.csv.gz
MCF7_TGFB1_TimeCourse_UMI_matrix.csv.gz
MCF7_TGFB1_TimeCourse_metadata.csv.gz
MCF7_EGF_TimeCourse_UMI_matrix.csv.gz
MCF7_EGF_TimeCourse_metadata.csv.gz
MCF7_TNF_TimeCourse_UMI_matrix.csv.gz
MCF7_TNF_TimeCourse_metadata.csv.gz
OVCA420_TGFB1_TimeCourse_UMI_matrix.csv.gz
OVCA420_TGFB1_TimeCourse_metadata.csv.gz
OVCA420_EGF_TimeCourse_UMI_matrix.csv.gz
OVCA420_EGF_TimeCourse_metadata.csv.gz
OVCA420_TNF_TimeCourse_UMI_matrix.csv.gz
OVCA420_TNF_TimeCourse_metadata.csv.gz
TimeCourse_Mix3b_barcode_counts.csv.gz
TimeCourse_Mix3b_barcode_annotations.csv.gz


title: TimeCourse_Pool3

description:
MULTI-seq pool of A549, DU145, MCF7, and OVCA420 cells treated with TGFB1, EGF, or TNF for various periods of time
A549_TGFB1_TimeCourse_UMI_matrix.csv.gz
A549_TGFB1_TimeCourse_metadata.csv.gz
A549_EGF_TimeCourse_UMI_matrix.csv.gz
A549_EGF_TimeCourse_metadata.csv.gz
A549_TNF_TimeCourse_UMI_matrix.csv.gz
A549_TNF_TimeCourse_metadata.csv.gz
DU145_TGFB1_TimeCourse_UMI_matrix.csv.gz
DU145_TGFB1_TimeCourse_metadata.csv.gz
DU145_EGF_TimeCourse_UMI_matrix.csv.gz
DU145_EGF_TimeCourse_metadata.csv.gz
DU145_TNF_TimeCourse_UMI_matrix.csv.gz
DU145_TNF_TimeCourse_metadata.csv.gz
MCF7_TGFB1_TimeCourse_UMI_matrix.csv.gz
MCF7_TGFB1_TimeCourse_metadata.csv.gz
MCF7_EGF_TimeCourse_UMI_matrix.csv.gz
MCF7_EGF_TimeCourse_metadata.csv.gz
MCF7_TNF_TimeCourse_UMI_matrix.csv.gz
MCF7_TNF_TimeCourse_metadata.csv.gz
OVCA420_TGFB1_TimeCourse_UMI_matrix.csv.gz
OVCA420_TGFB1_TimeCourse_metadata.csv.gz
OVCA420_EGF_TimeCourse_UMI_matrix.csv.gz
OVCA420_EGF_TimeCourse_metadata.csv.gz
OVCA420_TNF_TimeCourse_UMI_matrix.csv.gz
OVCA420_TNF_TimeCourse_metadata.csv.gz
TimeCourse_Mix3a_barcode_counts.csv.gz
TimeCourse_Mix3a_barcode_annotations.csv.gz


title: TimeCourse_Pool2

description:
MULTI-seq pool of A549, DU145, MCF7, and OVCA420 cells treated with TGFB1, EGF, or TNF for various periods of time
A549_TGFB1_TimeCourse_UMI_matrix.csv.gz
A549_TGFB1_TimeCourse_metadata.csv.gz
A549_EGF_TimeCourse_UMI_matrix.csv.gz
A549_EGF_TimeCourse_metadata.csv.gz
A549_TNF_TimeCourse_UMI_matrix.csv.gz
A549_TNF_TimeCourse_metadata.csv.gz
DU145_TGFB1_TimeCourse_UMI_matrix.csv.gz
DU145_TGFB1_TimeCourse_metadata.csv.gz
DU145_EGF_TimeCourse_UMI_matrix.csv.gz
DU145_EGF_TimeCourse_metadata.csv.gz
DU145_TNF_TimeCourse_UMI_matrix.csv.gz
DU145_TNF_TimeCourse_metadata.csv.gz
MCF7_TGFB1_TimeCourse_UMI_matrix.csv.gz
MCF7_TGFB1_TimeCourse_metadata.csv.gz
MCF7_EGF_TimeCourse_UMI_matrix.csv.gz
MCF7_EGF_TimeCourse_metadata.csv.gz
MCF7_TNF_TimeCourse_UMI_matrix.csv.gz
MCF7_TNF_TimeCourse_metadata.csv.gz
OVCA420_TGFB1_TimeCourse_UMI_matrix.csv.gz
OVCA420_TGFB1_TimeCourse_metadata.csv.gz
OVCA420_EGF_TimeCourse_UMI_matrix.csv.gz
OVCA420_EGF_TimeCourse_metadata.csv.gz
OVCA420_TNF_TimeCourse_UMI_matrix.csv.gz
OVCA420_TNF_TimeCourse_metadata.csv.gz
TimeCourse_Mix2_barcode_counts.csv.gz
TimeCourse_Mix2_barcode_annotations.csv.gz


title: TimeCourse_Pool1

description:
MULTI-seq pool of A549, DU145, MCF7, and OVCA420 cells treated with TGFB1, EGF, or TNF for various periods of time
A549_TGFB1_TimeCourse_UMI_matrix.csv.gz
A549_TGFB1_TimeCourse_metadata.csv.gz
A549_EGF_TimeCourse_UMI_matrix.csv.gz
A549_EGF_TimeCourse_metadata.csv.gz
A549_TNF_TimeCourse_UMI_matrix.csv.gz
A549_TNF_TimeCourse_metadata.csv.gz
DU145_TGFB1_TimeCourse_UMI_matrix.csv.gz
DU145_TGFB1_TimeCourse_metadata.csv.gz
DU145_EGF_TimeCourse_UMI_matrix.csv.gz
DU145_EGF_TimeCourse_metadata.csv.gz
DU145_TNF_TimeCourse_UMI_matrix.csv.gz
DU145_TNF_TimeCourse_metadata.csv.gz
MCF7_TGFB1_TimeCourse_UMI_matrix.csv.gz
MCF7_TGFB1_TimeCourse_metadata.csv.gz
MCF7_EGF_TimeCourse_UMI_matrix.csv.gz
MCF7_EGF_TimeCourse_metadata.csv.gz
MCF7_TNF_TimeCourse_UMI_matrix.csv.gz
MCF7_TNF_TimeCourse_metadata.csv.gz
OVCA420_TGFB1_TimeCourse_UMI_matrix.csv.gz
OVCA420_TGFB1_TimeCourse_metadata.csv.gz
OVCA420_EGF_TimeCourse_UMI_matrix.csv.gz
OVCA420_EGF_TimeCourse_metadata.csv.gz
OVCA420_TNF_TimeCourse_UMI_matrix.csv.gz
OVCA420_TNF_TimeCourse_metadata.csv.gz
TimeCourse_Mix1_barcode_counts.csv.gz
TimeCourse_Mix1_barcode_annotations.csv.gz


title: LN229 Ctr_Input


title: Vehicle replicate 2, GFP- cells from 3 mice [CN2_041015]

description: mRNA abundance data

value: FACS sample, GFP-


title: Vehicle replicate 4, GFP- cells from 3 mice [CN3_041015]

description: mRNA abundance data


title: vWAT, 20 weeks, control, rep 5

city: Lausanne

first: Richard

last: Coward

address: Dorothy Hodgkin Building, Whitson Street, Bristol

department: Bristol Medical School

country: United Kingdom

institute: Bristol Royal hospital for Sick Children & University of Bristol

data_processing:
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.8)
Reads were filtered for low complexity with reaper (v. 15-065)
Reads were aligned against Mus musculus.GRCm38.86 genome using STAR (v. 2.5.2b)
The number of read counts per gene locus was summarized with htseq-count (v. 0.6.1) using Mus musculus.GRCm38.86 gene annotation.
Genome_build: Mus musculus.GRCm38.86
Supplementary_files_format_and_content: Tab-separated .txt files with gene-level read counts

source_name: visceral (epididymal) adipose tissue

growth_protocol: C57/BL6 male, 4-wk-old (at time of sacrifice), mice were housed in  a 12 h light/12 h dark (LD) regimen  with water and food available ad libitum. All mice were fed  with a 10% in fat chow diet (D12450J, Research Diet) for two weeks. At 6 weeks of age they were either shifted to a high fat diet containing 60% in fat (D12492, Research Diet) or kept in control diet for 1, 8 and 20 weeks.  At each time time point, 20 mice were sacrified using CO2. Subcutaneous and viceral adipose tissue were immediately collected, snap-frozen in liquid nitrogen and kept at −80°C for RNA extraction and chromatin preparation. For chromatin preparation, aliquats of 4 grams of adipose tissue were homogenized on dry ice and immediately crosslinked in 45ml of PBS containing 0.5% formaldehyde. All animal care and handling was performed according to the Swiss law for animal protection

extract_protocol:
Trizol extraction of total RNA, followed by purification with Lipid RNeasy Mini Kit (Qiagen). After quality check,  total RNA from 4-10 individual mice of the same experimental group were pooled for RNA-seq.
RNA-seq libraries were prepared using the Illumina Truseq Stranded mRNA protocol

treatment_protocol: All mice were fed  with a 10% in fat chow diet (D12450J, Research Diet) for two weeks. At 6 weeks of age a total of 170 and 180 mice were put on HFD (D12492, Research Diet) and chow diet (D12450J, Research Diet, respectively. Mice were sacrified after 1, 8 or 20 week of diet.

tag: strain

tag: age

value: 26 weeks

tag: Sex

value: male

tag: diet

value: Control chow diet (D12450J)

tag: time

value: 20 weeks

tag: tissue

value: visceral (epididymal) adipose tissue


title: Vehicle replicate 2, GFP+cells from 3 mice [CP2_041015]

description: mRNA abundance data


title: KinaseScreen_DU145

description:
MULTI-seq pool of DU145 cells treated with TGFB1, EGF, or TNF along with 22 independent kinase inhibitors
A549_KinaseScreen_UMI_matrix.csv.gz
A549_KinaseScreen_metadata.csv.gz
DU145_KinaseScreen_UMI_matrix.csv.gz
DU145_KinaseScreen_metadata.csv.gz
MCF7_KinaseScreen_UMI_matrix.csv.gz
MCF7_KinaseScreen_metadata.csv.gz
OVCA420_KinaseScreen_UMI_matrix.csv.gz
OVCA420_KinaseScreen_metadata.csv.gz
KinaseScreen_unfiltered_UMI_matrix.csv.gz
KinaseScreen_unfiltered_metadata.csv.gz
KinaseScreen_DU145_barcode_counts.csv.gz
KinaseScreen_DU145_barcode_annotations.csv.gz


title: pho1-7_SE_rep1

city: Illkirch-Graffenstaden

first: Jules

last: Deforges

address: Boulevard Gonthier d'Andernach

country: France

institute: Transgene SA

data_processing:
reads mapped in Hisat2
Readcount with Htseq-count
Genome_build: TAIR10
Supplementary_files_format_and_content: Tables with readcounts within annotated exons
Supplementary_files_format_and_content: Tables with readcounts within newly identified 3’UTR extensions.

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana seedlings

growth_protocol: Plants were grown in Oil Dri US special granulates (http://www.oildri.com/) that were fertilized weekly with a commercial fertilizer (Wuxal; Maag; http://www.maag-garden.ch). Plants were grown in a phytotron with long-day conditions with 16 h of light at 21°C and 8 h of dark at 20°C.

extract_protocol:
Rneasy Plant mini kit (Qiagen)
TrueSeq stranded kit (Illumina)

tag: ecotype

value: 3 weeks old roots

tag: growth condition

value: Pots

tag: genetic background

tag: library type

value: single end


title: pho1-7_SE_rep2


title: Vehicle replicate 1, GFP+ cells from 3 mice [CP1_041015]

description: mRNA abundance data


title: pho1-7hpr1-5_SE_rep1


title: pho1-7hpr1-5_SE_rep2


title: Vehicle replicate 1, GFP- cells from 3 mice [CN1_041015]

description: mRNA abundance data


title: Odor replicate 4, GFP- cells from 3 mice [CAN3_041015]

description: mRNA abundance data

source_name: Olfactory mucosa; citrus accord-stimulated

value: odorant for 10 sec every 20 min


title: Odor replicate 4, GFP+ cells from 3 mice [CAP3_041015]

description: mRNA abundance data


title: pho1-7tex1-4_SE_rep2


title: pho1-7tex1-4_SE_rep1


title: col0_SE_rep2

value: wild type col0


title: Odor replicate 3, GFP- cells from 3 mice [CAN2_041015]

description: mRNA abundance data


title: col0_SE_rep1


title: Odor replicate 3, GFP+ cells from 3 mice [CAP2_041015]

description: mRNA abundance data


title: tex1-4_PE_rep3

growth_protocol: Plants were grown in half strength Murashige and Skoog (MS) salts (Duchefa M0255) containing 1% sucrose (Applichem, A4734) and .07% agar (Applichem, A2111)

value: 10 day old roots

value: Petri dishes

value: paired end


title: tex1-4_PE_rep2


title: col0_PE_rep3


title: tex1-4_PE_rep1


title: Odor replicate 2, GFP- cells from 3 mice [CAN1_041015]

description: mRNA abundance data


title: Odor replicate 2, GFP+ cells from 3 mice [CAP1_041015]

description: mRNA abundance data


title: Male rat primary hepatocyte _triadimefon-3.7

city: Research Triangle Park

first: Christopher

last: Corton

state: NC

address: 109 TW Alexander Dr.

institute: US-EPA

data_processing:
TempO-Seq data are analyzed using the Tempo-SeqR software package using the statistical computing language R. The input for TempO-Seq data analysis is a folder of zipped FASTQ files. Each FASTQ file contains the reads and quality scores for one sample. Each FASTQ file is aligned using the Bowtie algorithm to a pseudo-transcriptome input by the user. The output for TempO-Seq data analysis is a table of counts with each column representing a sample and each row representing a gene.
Data normalization was not done
Supplementary_files_format_and_content: Corton_29_Chem_data_matrix.txt (counts)

organism: Rattus norvegicus

source_name: Hepatocytes

growth_protocol: Male rat primary hepatocytes were isolated from liver samples and plated on collagen-coated plates.

extract_protocol: Purified RNA was examined for gene expression changes using the rat TempO-Seq targeted RNA-Seq platform (BioSpyder, Inc; Carlsbad CA). In addition to the 29 test chemicals, a number of reference chemicals were examined at one concentration (17beta-estradiol, Dexamethasone, GW4046, Oltipraz, Pregnenolone 16-alpha-carbonitrile, Sulforaphane, TCPOBOP, Testosterone, WY-14,643).

treatment_protocol: Primary hepatocytes were treated with DMSO (0.1%) or 6 concentrations of chemical (100 or 33.3 uM as the top concentration with a log2 step-down of dose level). Cells were treated for 24 hrs.

value: Male

tag: chemical

value: triadimefon

tag: dose

value: primary hepatocytes


title: Male rat primary hepatocyte _triadimefon-11.1


title: Male rat primary hepatocyte _triadimefon-0.4


title: col0_PE_rep2


title: Male rat primary hepatocyte _triadimefon-33.3


title: Male rat primary hepatocyte _DMSO rep8

value: DMSO

value: uM


title: Male rat primary hepatocyte _DMSO rep9


title: Male rat primary hepatocyte _triadimefon-100


title: Male rat primary hepatocyte _DMSO rep7


title: Male rat primary hepatocyte _dexamethasone-10

value: dexamethasone

value: 10 uM


title: 18-Dual_S6

city: Columbus

first: Justin

middle: Ray

last: Kaspar

state: OH

address: 305 W 12th Ave

department: Biosciences

institute: The Ohio State University

description: repeat 2 of 3

data_processing:
Step 1: FASTQ Groomer
Step 2: FASTQ Quality Trimmer
Step 3: Cutadapt removing GATCGGAAGAGCACACGTCTGAACTCCAGTCAC
Step 4: Map with Bowtie for Illumina
Step 5: sort
Step 6: htseq-count (see our publication for details)
Genome_build: NC_004350.2
Supplementary_files_format_and_content: Read counts obtained from step 6: htseq-count, listed along side each open reading frame

organism: Streptococcus mutans

source_name: Whole cell lysate

growth_protocol: Bacterial cells used for extraction of RNA were grown in CDM medium, in the presence of 5% CO2 at 37°C without agitation, until they reached mid-exponential phase (OD600 ≈ 0.5)

extract_protocol:
Total RNA was extracted from bacterial cells using the RNeasy Mini kit (Qiagen), with chromosomal DNA removed using a DNase I kit (Qiagen). To remove 16S and 23S rRNAs, 10 µg of total RNA was treated using the MICROBExpressTM Bacterial mRNA Enrichment Kit
cDNA libraries were created from 100 ng enriched mRNA samples using the NEBNext Ultra Directional RNA Library Prep kit for Illumina and NEBNext multiplex Oligos for Illumina (New England Biolabs, Ipswich, MA) following instructions from the supplier.
RNA-Seq: single-ended short reads were obtained from a set of bar-coded cDNA libraries

treatment_protocol: Cells were harvested by centrifugation at 4°C for 5 min, treated with bacterial RNAprotect Bacteria Reagent (Qiagen), and immediately stored at -80°C.

value: directly cocultured with S. sp. A12 OD600 nm = 0.5

tag: genotype

value: UA159 wild-type


title: 16-Dual_S8

description: repeat 1 of 3


title: col0_PE_rep1


title: 19-Dual_S12

description: repeat 3 of 3


title: Male rat primary hepatocyte _DMSO rep5

tag: cell type


title: Male rat primary hepatocyte _DMSO rep6


title: Male rat primary hepatocyte _testosterone-10

value: testosterone


title: 25-A12sup_S4

description: repeat 2 of 3

value: grown in S. sp. A12 supernatant to OD600 nm = 0.5


title: 23-A12sup_S10

description: repeat 1 of 3


title: Male rat primary hepatocyte _17beta-estradiol-10


title: Male rat primary hepatocyte _DMSO rep4


title: 27-A12sup_S4

description: repeat 3 of 3


title: Male rat primary hepatocyte _sulforaphane-10

value: sulforaphane


title: 21-UA159sup_S14

description: repeat 2 of 3

value: grown in own supernatant to OD600 nm = 0.5


title: Male rat primary hepatocyte _Pregnenolone-16alpha-carbonitrile-15

value: Pregnenolone 16alpha carbinonitrile

value: 15 uM


title: Male rat primary hepatocyte _triadimefon-1.2


title: Male rat primary hepatocyte _Wyeth-14,643-15


title: Male rat primary hepatocyte _DEHP-0.4

value: DEHP


title: Male rat primary hepatocyte _oltipraz-30

value: oltipraz

value: 30 uM


title: Discovery_ASD_F_14

city: Davis

first: Charles

middle: E

last: Mordaunt

state: CA

address: 3318 Tupper Hall, One Shields Ave

department: Medical Microbiology and Immunology

institute: University of California, Davis

data_processing:
Filtered raw fastq files using Illumina quality flag
Followed CpG_Me workflow v1.0 which included the steps below.
Trimmed to remove adapters and 5' and 3' methylation bias with Trim Galore! v0.4.5
Aligned to hg38 reference genome with Bismark v0.19.1
Removed PCR duplicates with Bismark v0.19.1
Extracted CpG methylation counts at all covered sites to generate genome-wide cytosine methylation reports with Bismark v0.19.1
Genome_build: hg38
Supplementary_files_format_and_content: Bismark genome-wide cytosine methylation report for each sample with columns for chromosome, CpG position, strand, methylated count, unmethylated count, dinucleotide context, and trinucleotide context

source_name: umbilical cord blood

extract_protocol:
DNA was extracted from whole umbilical cord blood using the Gentra Puregene Blood Kit (Qiagen).
DNA was bisulfite converted with the EZ DNA Methylation Lightning kit (Zymo). WGBS libraries were prepared from 100ng of bisulfite-converted DNA using the TruSeq DNA Methylation kit (Illumina) with indexed PCR primers and a 14-cycle PCR program.

tag: sample set

value: Discovery

value: umbilical cord blood

tag: diagnosis

value: ASD

value: F

tag: study

value: MARBLES


title: Discovery_ASD_F_12


title: Discovery_ASD_F_11


title: Discovery_ASD_F_13


title: Male rat primary hepatocyte _DEHP-11.1

value: Male

value: primary hepatocytes


title: Male rat primary hepatocyte _DEHP-1.2


title: Discovery_ASD_F_10


title: Male rat primary hepatocyte _DEHP-33.3


title: Male rat primary hepatocyte _DEHP-3.7


title: Discovery_ASD_F_09


title: Discovery_ASD_F_07


title: Male rat primary hepatocyte _cyproconazole-0.4

value: cyproconazole


title: 22-UA159sup_S11

description: repeat 3 of 3

tag: strain

tag: treatment

value: UA159 wild-type


title: Male rat primary hepatocyte _DEHP-100

tag: Sex


title: Male rat primary hepatocyte _cyproconazole-3.7


title: Discovery_ASD_F_05

value: EARLI


title: Male rat primary hepatocyte _TCPOBOP-1.5

value: TCPOBOP


title: Male rat primary hepatocyte _cyproconazole-1.2


title: Discovery_ASD_F_03


title: Male rat primary hepatocyte _cyproconazole-11.1


title: Male rat primary hepatocyte _cyproconazole-33.3


title: Discovery_ASD_F_01


title: Discovery_ASD_F_08


title: Male rat primary hepatocyte _GW 4046-1.5


title: 20-UA159sup_S7

description: repeat 1 of 3

value: grown in own supernatant to OD600 nm = 0.5


title: Male rat primary hepatocyte _oxadiazon-0.4

value: oxadiazon


title: Male rat primary hepatocyte _cyproconazole-100


title: Discovery_ASD_F_15


title: Male rat primary hepatocyte _oxadiazon-3.7


title: Discovery_ASD_M_31

value: M


title: Discovery_ASD_F_06


title: Discovery_ASD_M_33


title: Discovery_ASD_M_32


title: Male rat primary hepatocyte _oxadiazon-11.1


title: Discovery_ASD_F_04


title: Discovery_ASD_M_30


title: Male rat primary hepatocyte _oxadiazon-100


title: Male rat primary hepatocyte _cyclanilide-0.4

value: cyclanilide


title: Discovery_ASD_M_27


title: Male rat primary hepatocyte _oxadiazon-1.2


title: Discovery_ASD_M_29


title: Male rat primary hepatocyte _oxadiazon-33.3


title: Discovery_ASD_F_02


title: Male rat primary hepatocyte _cyclanilide-1.2


title: Discovery_ASD_M_26


title: Male rat primary hepatocyte _cyclanilide-3.7


title: Discovery_ASD_M_25


title: Male rat primary hepatocyte _cyclanilide-11.1


title: Discovery_ASD_M_24


title: Discovery_ASD_M_23


title: Male rat primary hepatocyte _cyclanilide-33.3


title: Discovery_ASD_M_22


title: Discovery_ASD_M_28


title: Male rat primary hepatocyte _PFOA-0.4

value: PFOA


title: Male rat primary hepatocyte _cyclanilide-100


title: Male rat primary hepatocyte _PFOA-1.2


title: Male rat primary hepatocyte _PFOA-3.7


title: Discovery_ASD_M_20


title: Discovery_ASD_M_18


title: Discovery_ASD_M_21


title: Male rat primary hepatocyte _PFOA-100


title: Discovery_ASD_M_17


title: Male rat primary hepatocyte _PFOA-33.3


title: Discovery_ASD_M_16


title: Discovery_ASD_M_15


title: Discovery_ASD_M_14


title: Discovery_ASD_M_13


title: Male rat primary hepatocyte _S-bioallethrin-1.2

value: S-Bioallethrin


title: Male rat primary hepatocyte _S-bioallethrin-0.4


title: Male rat primary hepatocyte _S-bioallethrin-3.7


title: Discovery_ASD_M_12

value: Discovery


title: Male rat primary hepatocyte _S-bioallethrin-11.1


title: Discovery_ASD_M_11

value: umbilical cord blood


title: Male rat primary hepatocyte _S-bioallethrin-33.3


title: Male rat primary hepatocyte _S-bioallethrin-100


title: Discovery_ASD_M_10

value: ASD


title: Discovery_ASD_M_09


title: Male rat primary hepatocyte _carbaryl-0.4

value: carbaryl


title: Discovery_ASD_M_08


title: Male rat primary hepatocyte _PFOA-11.1


title: Male rat primary hepatocyte _carbaryl-1.2


title: Discovery_ASD_M_19


title: Male rat primary hepatocyte _carbaryl-3.7


title: Discovery_ASD_M_07


title: Discovery_ASD_M_05


title: Discovery_ASD_M_06


title: Male rat primary hepatocyte _carbaryl-100


title: Male rat primary hepatocyte _carbaryl-33.3


title: Discovery_ASD_M_04


title: Male rat primary hepatocyte _dimethenamid-3.7

value: dimethenamid


title: Male rat primary hepatocyte _dimethenamid-1.2

value: Male


title: Male rat primary hepatocyte _dimethenamid-0.4

value: primary hepatocytes


title: Discovery_ASD_M_01


title: Male rat primary hepatocyte _dimethenamid-33.3


title: Discovery_ASD_M_03


title: Male rat primary hepatocyte _dimethenamid-11.1


title: Discovery_TD_F_13

value: TD

value: F

value: MARBLES


title: Discovery_TD_F_12


title: Discovery_TD_F_15


title: Discovery_TD_F_14


title: Male rat primary hepatocyte _PFOS-0.4

value: PFOS


title: Male rat primary hepatocyte _PFOS-1.2


title: Discovery_TD_F_10


title: Male rat primary hepatocyte _PFOS-3.7


title: Male rat primary hepatocyte _PFOS-11.1


title: Male rat primary hepatocyte _carbaryl-11.1


title: Male rat primary hepatocyte _PFOS-33.3


title: Discovery_TD_F_09


title: Discovery_TD_F_08


title: Male rat primary hepatocyte _PFOS-100


title: Discovery_TD_F_06

value: EARLI


title: Discovery_TD_F_05


title: Male rat primary hepatocyte _dimethenamid-100


title: Discovery_TD_F_04


title: Male rat primary hepatocyte _dichlobenil-3.7

value: dichlobenil


title: Discovery_TD_F_03


title: Male rat primary hepatocyte _dichlobenil-11.1


title: Discovery_TD_F_01


title: Male rat primary hepatocyte _dichlobenil-100


title: Discovery_TD_M_35

value: M


title: Discovery_TD_F_02


title: Male rat primary hepatocyte _triticonazole-0.4

value: triticonazole


title: Discovery_TD_M_34


title: Discovery_TD_F_11


title: Male rat primary hepatocyte _triticonazole-1.2


title: Male rat primary hepatocyte _dichlobenil-0.4


title: Male rat primary hepatocyte _triticonazole-33.3


title: Discovery_TD_M_30


title: Male rat primary hepatocyte _triticonazole-3.7


title: Discovery_TD_M_33


title: Discovery_TD_M_32


title: Male rat primary hepatocyte _dichlobenil-1.2


title: Discovery_TD_F_07


title: Discovery_TD_M_31


title: Male rat primary hepatocyte _dichlobenil-33.3


title: Discovery_TD_M_29


title: Male rat primary hepatocyte _cyprodinil-0.4

value: cyprodinil


title: S15_NL

first: Emma

last: Guttman

state: New York

address: 1425 Madison Ave

institute: Icahn School of Medicine at Mt. SInai

data_processing:
The R1 bases 1-16 and 17-26 were tagged with cell barcode "SC" and unique molecular indifier (UMI) "XM," respectively.
Reads with low quality bases were removed, and the 3' end was trimmed to remove poly(A) sequences of length≥6.
Reads were aligned to the human genome reference using STAR aligner, allowing up to three mismatches.
Genes expressed in fewer than three cells, and cells with fewer than 100 or greater than 5,000 genes were filtered out to eliminate partial cells and doublets.
Ubiquitously expressed ribosomal protein-coding (RPS and RPL) and MALAT noncoding RNA, miRNA, and snoRNA genes were excluded.
Genome_build: hg38
Supplementary_files_format_and_content: Txt files with count matrices of normalized feature expression measurements that are scaled by 10,000 and log-transformed

source_name: Skin cells

extract_protocol:
Cryopreserved skin biopsies were thawed, dissociated in a Liberase solution twice, and then dissociated again in a Trypsin solution. The tissues were subsequently re-suspended in PBS-bovine serum albumin.
The Chromium Single Cell 3' Reagent Kit V2 (10x Genomics) was used to generate single-cell libraries, according to manufacturer instructions. The library was sequenced on the Illumina HiSeq 2500 platform.

tag: disease

value: Atopic dermatitis

tag: tissue type

value: Non-lesional

tag: frozen vs. fresh

value: Frozen


title: S16_NL


title: S17_H

value: Healthy


title: Male rat primary hepatocyte _cyprodinil-1.2


title: Male rat primary hepatocyte _cyprodinil-100


title: S14_NL


title: Discovery_TD_M_28

value: Discovery

tag: tissue

value: umbilical cord blood


title: Discovery_TD_M_26


title: Male rat primary hepatocyte _cyprodinil-33.3

value: Male


title: Male rat primary hepatocyte _cyprodinil-11.1

value: primary hepatocytes


title: Discovery_TD_M_27

value: TD


title: Male rat primary hepatocyte _fludioxonil-1.2

value: fludioxonil


title: S13_H


title: Male rat primary hepatocyte _fludioxonil-0.4


title: Male rat primary hepatocyte _triticonazole-11.1


title: Male rat primary hepatocyte _triticonazole-100


title: Male rat primary hepatocyte _fludioxonil-3.7


title: Discovery_TD_M_25


title: Male rat primary hepatocyte _cyprodinil-3.7


title: Discovery_TD_M_24


title: Male rat primary hepatocyte _fludioxonil-100


title: S12_H


title: Male rat primary hepatocyte _fludioxonil-33.3


title: S11_NL


title: Male rat primary hepatocyte _simazine-0.4

value: simazine


title: Male rat primary hepatocyte _fludioxonil-11.1


title: Discovery_TD_M_23


title: Male rat primary hepatocyte _simazine-1.2


title: S10_H


title: Discovery_TD_M_22


title: S9_H


title: Male rat primary hepatocyte _simazine-3.7


title: Male rat primary hepatocyte _DMSO rep3

value: DMSO

value: uM


title: Discovery_TD_M_21

value: EARLI


title: Male rat primary hepatocyte _DMSO rep2


title: Male rat primary hepatocyte _DMSO rep1


title: S8_H

value: Fresh


title: Male rat primary hepatocyte _simazine-11.1


title: Discovery_TD_M_19

value: M


title: Male rat primary hepatocyte _simazine-33.3


title: Discovery_TD_M_20


title: S7_LS

value: Lesional


title: Male rat primary hepatocyte _isoxaflutole-1.2

value: isoxaflutole


title: Male rat primary hepatocyte _isoxaflutole-0.4


title: S6_H


title: Male rat primary hepatocyte _isoxaflutole-11.1


title: Male rat primary hepatocyte _isoxaflutole-33.3


title: Discovery_TD_M_17


title: S4_H


title: Male rat primary hepatocyte _isoxaflutole-100


title: Discovery_TD_M_18


title: Male rat primary hepatocyte _isoxaflutole-3.7


title: S3_NL

value: Atopic dermatitis

value: Non-lesional


title: Male rat primary hepatocyte _dithiopyr-0.14

value: dithiopyr


title: Discovery_TD_M_16

value: Discovery


title: S2_LS

value: Frozen


title: Male rat primary hepatocyte _dithiopyr-3.7

value: Male


title: Male rat primary hepatocyte _dithiopyr-1.2

value: primary hepatocytes


title: Male rat primary hepatocyte _dithiopyr-0.4


title: Discovery_TD_M_15

value: umbilical cord blood

value: TD


title: Discovery_TD_M_14


title: Male rat primary hepatocyte _dithiopyr-11.1


title: S1_LS


title: Male rat primary hepatocyte _simazine-100

value: simazine


title: Male rat primary hepatocyte _ametryn-0.14

value: ametryn


title: Male rat primary hepatocyte _dithiopyr-33.3


title: R30dm

city: Amsterdam

first: Rocco

last: Sciarrillo

state: North Holland

address: De Boelelaan 1117

department: Hematology

country: Netherlands

institute: Amsterdam UMC

data_processing:
Annotation-aware gapped alignment of sequencing reads to the reference genome (hg19, GRCh37) was performed using STAR version 2.3.0
A gene annotation (.gtf file) was compiled from then NCBI refGene table using UCSC table browser
Alignment files were sorted and indexed with picard tools version 1.115
Post-mapping quality control was performed by RSeQC version 2.3.6 and samtools version 0.1.19
Count matrix was generated by using HTSeq-0.61p1
Genome_build: hg19
Supplementary_files_format_and_content: The file "count_matrix_samples_sciarrillo" is a matrix of read counts provided per each sample and ordered per gene name.

source_name: cell line CCFR-CEM (ATCC CCL-119)

growth_protocol: Mononuclear bone marrow or peripheral blood cells from pediatric leukemia patients were isolated by Ficoll Isopaque centrifugation and washed two times in PBS containing 0.1% bovine serum albumin. CEMWT and R30dm cell lines were maintained in RPMI-1640 medium supplemented with 10% fetal calf serum and 100 units/mL penicillin G, and 100μg/mL streptomycin sulphate.

extract_protocol:
Total RNA was extracted from patient samples and cell lines (exposed or unexposed to Pladienolide-B) using the RNeasy mini kit (Qiagen).
Sequencing libraries were prepared with the Illumina TruSeq Stranded mRNA Library Prep LT Kit (RS-122-2201) and Agencount AMPure XP beads according to manufacturer protocols. RNA quality was checked with RNA 6000 Nano Kit on a 2100 Bioanalyzer (Agilent). Sequencing reaction was performed on Illumina HiSeq 2500 by using HT-v4-SR100 chip or RAPID-SR100 chip (samples ALL2, ALL21, ALL30, ALL33, ALL8 and ALL9).

treatment_protocol: CEM and R30dm cell lines were treated with 4 nM Pladienolide-B for 6 hours prior to RNA extraction.

value: Peripheral blood


title: S5_LS


title: Male rat primary hepatocyte _ametryn-0.4


title: Discovery_TD_M_12

value: EARLI


title: R30dm_4PladB


title: Discovery_TD_M_11


title: CEMWT


title: Male rat primary hepatocyte _ametryn-33.3


title: Male rat primary hepatocyte _ametryn-1.2


title: Male rat primary hepatocyte _ametryn-3.7


title: Male rat primary hepatocyte _ametryn-11.1


title: Male rat primary hepatocyte _imazalil-0.14

value: imazalil


title: CEMWT_4PladB


title: Male rat primary hepatocyte _imazalil-0.4


title: Discovery_TD_M_10

value: M


title: ALL9

source_name: Mononuclear cells


title: Male rat primary hepatocyte _imazalil-1.2


title: Discovery_TD_M_09


title: Male rat primary hepatocyte _imazalil-3.7


title: Male rat primary hepatocyte _imazalil-11.1


title: Discovery_TD_M_08


title: ALL8

value: Bone marrow


title: Discovery_ASD_M_02

value: ASD


title: Discovery_TD_M_13


title: Male rat primary hepatocyte _acetochlor-0.14

value: acetochlor


title: Discovery_TD_M_07


title: ALL7


title: ALL6


title: Male rat primary hepatocyte _acetochlor-3.7


title: Male rat primary hepatocyte _acetochlor-11.1


title: ALL5


title: Male rat primary hepatocyte _acetochlor-33.3


title: Discovery_TD_M_04


title: Male rat primary hepatocyte _alachlor-0.14

value: alachlor


title: Male rat primary hepatocyte _acetochlor-1.2


title: Discovery_TD_M_05


title: ALL4


title: Discovery_TD_M_03


title: Male rat primary hepatocyte _alachlor-1.2


title: Male rat primary hepatocyte _alachlor-3.7


title: Male rat primary hepatocyte _imazalil-33.3


title: Male rat primary hepatocyte _alachlor-11.1


title: Male rat primary hepatocyte _alachlor-33.3


title: ALL37


title: Discovery_TD_M_01


title: Male rat primary hepatocyte _acetochlor-0.4


title: Discovery_TD_M_06


title: ALL35


title: ALL36


title: Male rat primary hepatocyte _triflumizole-1.2

value: triflumizole


title: Male rat primary hepatocyte _triflumizole-0.4


title: Male rat primary hepatocyte _triflumizole-3.7


title: Male rat primary hepatocyte _triflumizole-11.1


title: ALL34


title: Male rat primary hepatocyte _triflumizole-33.3


title: Male rat primary hepatocyte _alachlor-0.4


title: Male rat primary hepatocyte _hexaconazole-0.14

value: hexaconazole


title: ALL33


title: Discovery_TD_M_02

value: Discovery


title: ALL38


title: Male rat primary hepatocyte _hexaconazole-1.2

value: Male


title: ALL32


title: Male rat primary hepatocyte _hexaconazole-3.7

value: primary hepatocytes


title: ALL31


title: Male rat primary hepatocyte _hexaconazole-11.1


title: Male rat primary hepatocyte _hexaconazole-33.3


title: LPM, LPS, patient 4

city: Jena

first: Sven

last: Stengel

address: Am Klinikum 1

department: Clinic for Internal Medicine IV

country: Germany

institute: Jena University Hospital

description: Gene expression data from large peritoneal macrophages of patient with liver cirrhosis isolated from ascitic fluid after treatment with 10 ng/ml LPS

hyb_protocol: According to manufacture protocol (GeneChip® WT PLUS Reagent Kit, ThermoFisher Scientific). Complentary DNA was hybridized for 16 hr at 45C and 60 rpm on a Clariom S HT 24 array plate.

scan_protocol: Clariom S HT 24 array plate was scanned using an Affymetrix GeneTitan Scanner.

data_processing: CHP files were created using Transcriptome analysis concole (TAC, ThermoFisher Scientific). GC Correction, SST (Signal Space Transformation), RMA background and quantile normalization were applied. Differential gene expression between SPMs and LPMs was analyzed in steady state or following LPS stimulation. Before extracting differentially expressed genes, patient dependent differences were eliminated using repeated measure option (pairwise analysis or batch effect removal) of TAC software package.

source_name: Large Peritoneal Macrophages treated with LPS 40 ng/ml for 3h, BioSample 4

label_protocol: Biotinylated cDNAs were prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip WT PLUS Reagent Kit).

growth_protocol: Sorted PM subsets were seeded in cell culture plates at a density of about 100k cell per cm2 (0.75 – 1.0 mio cells per well) in RPMI supplemented with 10% FCS and 1% L-glutamine-penicillin-streptomycinand for 3h.

extract_protocol: Total RNA was extracted using NucleoSpin RNA Kit (Macherey-Nagel) according to manufactures protocol. The RNA concentration and purity were determined spectrophotometrically. RNA integrity was determinded using the Agilent RNA Screen Tape System on a TapeStation 2200 instrument (Agilent Technologies).

treatment_protocol: Cells were treated with 10 ng/mL lipopolysaccharide (LPS) from E. coli K12 (InvivoGen) or left untreated (control)

tag: patient

value: peritoneal macrophages

tag: pm subset

value: LPM

value: LPS


title: Male rat primary hepatocyte _tetraconazole-0.14

value: tetraconazole


title: Male rat primary hepatocyte _triflumizole-0.14


title: Male rat primary hepatocyte _tetraconazole-1.2


title: ALL30

value: Peripheral blood


title: ALL3


title: Male rat primary hepatocyte _tetraconazole-0.4


title: Male rat primary hepatocyte _tetraconazole-3.7


title: Male rat primary hepatocyte _tetraconazole-11.1


title: Male rat primary hepatocyte _hexaconazole-0.4


title: Male rat primary hepatocyte _tetraconazole-33.3


title: ALL29


title: Male rat primary hepatocyte _Bensulide-0.14

value: Bensulide


title: ALL28


title: Male rat primary hepatocyte _Bensulide-0.4


title: Male rat primary hepatocyte _Bensulide-1.2


title: LPM, untreated, patient 4

description: Gene expression data from large peritoneal macrophages of patient with liver cirrhosis isolated from ascitic fluid in steady state

source_name: Large Peritoneal Macrophages medium without LPS for 3h, BioSample 4

value: untreated


title: SPM, LPS, patient 4

description: Gene expression data from small peritoneal macrophages of patient with liver cirrhosis isolated from ascitic fluid after treatment with 10 ng/ml LPS

source_name: Small Peritoneal Macrophages treated with LPS 40 ng/ml for 3h, BioSample 4

value: SPM


title: SPM, untreated, patient 4

description: Gene expression data from small peritoneal macrophages of patient with liver cirrhosis isolated from ascitic fluid in steady state

source_name: Small Peritoneal Macrophages medium without LPS for 3h, BioSample 4


title: LPM, LPS, patient 3

source_name: Large Peritoneal Macrophages treated with LPS 30 ng/ml for 3h, BioSample 3


title: LPM, untreated, patient 3

source_name: Large Peritoneal Macrophages medium without LPS for 3h, BioSample 3


title: SPM, LPS, patient 3

source_name: Small Peritoneal Macrophages treated with LPS 30 ng/ml for 3h, BioSample 3


title: Male rat primary hepatocyte _Bensulide-3.7


title: SPM, untreated, patient 3

source_name: Small Peritoneal Macrophages medium without LPS for 3h, BioSample 3


title: ALL27

value: Bone marrow


title: LPM, LPS, patient 2

source_name: Large Peritoneal Macrophages treated with LPS 20 ng/ml for 3h, BioSample 2


title: Male rat primary hepatocyte _Bensulide-11.1


title: ALL26


title: Male rat primary hepatocyte _Bensulide-33.3


title: LPM, untreated, patient 2

source_name: Large Peritoneal Macrophages medium without LPS for 3h, BioSample 2


title: Male rat primary hepatocyte _flusilazole-0.14

value: flusilazole


title: Male rat primary hepatocyte _flusilazole-0.4


title: Male rat primary hepatocyte _flusilazole-1.2


title: ALL25


title: ALL24


title: Male rat primary hepatocyte _flusilazole-3.7


title: Male rat primary hepatocyte _flusilazole-11.1


title: ALL23


title: Male rat primary hepatocyte _flusilazole-33.3


title: SPM, LPS, patient 2

source_name: Small Peritoneal Macrophages treated with LPS 20 ng/ml for 3h, BioSample 2


title: Male rat primary hepatocyte _Bisphenol A-0.14

source_name: Hepatocytes

value: Bisphenol A


title: SPM, untreated, patient 2

source_name: Small Peritoneal Macrophages medium without LPS for 3h, BioSample 2


title: ALL22


title: Male rat primary hepatocyte _Bisphenol A-0.4


title: LPM, untreated, patient 1

source_name: Large Peritoneal Macrophages medium without LPS for 3h, BioSample 1


title: ALL21


title: Male rat primary hepatocyte _Bisphenol A-1.2


title: ALL20


title: Male rat primary hepatocyte _Bisphenol A-3.7


title: Male rat primary hepatocyte _Bisphenol A-11.1


title: Male rat primary hepatocyte _Bisphenol A-33.3


title: Male rat primary hepatocyte _etoxazole-0.14

value: etoxazole


title: SPM, LPS, patient 1

source_name: Small Peritoneal Macrophages treated with LPS 10 ng/ml for 3h, BioSample 1


title: Male rat primary hepatocyte _etoxazole-0.4


title: ALL19


title: Male rat primary hepatocyte _etoxazole-1.2


title: SPM, untreated, patient 1

source_name: Small Peritoneal Macrophages medium without LPS for 3h, BioSample 1


title: Male rat primary hepatocyte _etoxazole-3.7


title: Male rat primary hepatocyte _etoxazole-11.1


title: 201RS9

city: Cambridge

first: Philip

last: Wigge

address: 47 Bateman street

department: Sainsbury Laboratory

institute: Cambridge University

data_processing:
genome build:  Bd21-v3.1
Adapters were trimmed off from raw reads with Trimmomatic with argument "ILLUMINACLIP:$FA_ADAPTER:6:30:10 LEADING:3 TRAILING:3 MINLEN:36 SLIDINGWINDOW:4:15".
Raw reads were aligned with Hisat2 with arguments "--no-mixed --rna-strandness RF --dta --fr" to produce a SAM file.
Duplicate reads were removed with Picard using default setting
Alignments in SAM file were assembled into transcripts abundances with stringtie with argument "--rf".
Supplementary_files_format_and_content: .stringtie.count.txt: TSV table containing abundance of transcripts with bed-formatted coordinates.
Supplementary_files_format_and_content: RPKM.bw:  RPKM normalised bigwig files

organism: Brachypodium distachyon

source_name: fully expanded leaves

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in LD (20 h light/4 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 4 weeks at ZT0 by snap-freezing in liquid nitrogen.

extract_protocol:
Qiagen RNeasy Mini Kit (74104) was used to extract RNA. RNA quality and integrity were assessed on the Agilent 2200 TapeStation system.
Library preparation was performed with 1µg total RNA using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (E7420L). The libraries were sequenced on a NextSeq500 (Illumina) running a final pooled library. Each pool contained 24 to 30 samples and was sequenced using NextSeq® 500/550 High Output Kit v2 (150 cycles) TG-160-2002 on a NextSeq500 (Illumina).

value: phyC

tag: cultivar

value: fully expanded leaves

tag: photoperiod

value: LD (20 h light/4 h dark)

tag: temperature

tag: replicate

value: single

tag: time

value: collected after 4 weeks at ZT0


title: 201RS7

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in LD (20 h light/4 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 4 weeks at ZT20 by snap-freezing in liquid nitrogen.

tag: genotype

value: collected after 4 weeks at ZT20


title: 201RS6

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in LD (20 h light/4 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 4 weeks at ZT16 by snap-freezing in liquid nitrogen.

value: collected after 4 weeks at ZT16


title: 201RS8

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in LD (20 h light/4 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 4 weeks at ZT22 by snap-freezing in liquid nitrogen.

value: collected after 4 weeks at ZT22


title: 201RS5

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in LD (20 h light/4 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 4 weeks at ZT12 by snap-freezing in liquid nitrogen.

value: collected after 4 weeks at ZT12


title: LPM, LPS, patient 1

source_name: Large Peritoneal Macrophages treated with LPS 10 ng/ml for 3h, BioSample 1

tag: cell type

value: peritoneal macrophages

value: LPM

value: LPS


title: ALL17

source_name: Mononuclear cells


title: Male rat primary hepatocyte _triclosan-0.14

value: Male

tag: chemical

value: triclosan

tag: dose

value: primary hepatocytes


title: Male rat primary hepatocyte _etoxazole-33.3


title: Male rat primary hepatocyte _triclosan-0.4


title: 201RS4

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in LD (20 h light/4 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 4 weeks at ZT8 by snap-freezing in liquid nitrogen.

value: collected after 4 weeks at ZT8


title: ALL16

value: Bone marrow


title: Male rat primary hepatocyte _triclosan-3.7


title: 201RS3

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in LD (20 h light/4 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 4 weeks at ZT4 by snap-freezing in liquid nitrogen.

value: collected after 4 weeks at ZT4


title: ALL2


title: Male rat primary hepatocyte _triclosan-11.1


title: ALL15


title: Male rat primary hepatocyte_triclosan-33.3


title: ALL14

value: Peripheral blood


title: 201RS22

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in LD (20 h light/4 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 3 weeks at ZT20 by snap-freezing in liquid nitrogen.

value: fully expanded leaves

value: LD (20 h light/4 h dark)

value: collected after 3 weeks at ZT20


title: ALL13


title: WT_cDC2_2

city: Tokyo

first: Takeshi

last: Nitta

address: 7-3-1 Hongo, Bunkyo-ku

department: Department of Immunology,

country: Japan

institute: Graduate School of Medicine and Faculty of Medicine, The University of Tokyo

data_processing:
Data were acquired on an Ion Proton sequencer (Thermo Fisher) and analyzed using CLC genomics Workbench v12 (CLC) and GeneSpring (Agilent).
Supplementary_files_format_and_content: Excel files include RPKM values for each sample

source_name: FACS-sorted primary cell

extract_protocol:
Cells were collected by FACS sorting. Total RNA was extracted using RNeasy micro kit (QIAGEN).
cDNA was synthesized and amplified using SMART-seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech Laboratories)

value: conventional type 2 dendritic cell (cDC2)

tag: strain

value: wild type

tag: age

value: thymus


title: WT_cDC1_2

value: conventional type 1 dendritic cell (cDC1)


title: WT_pDC_1

value: plasmacytoid dendritic cell (pDC)


title: 201RS21

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in LD (20 h light/4 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 3 weeks at ZT16 by snap-freezing in liquid nitrogen.

value: single

value: collected after 3 weeks at ZT16


title: WT_cDC1_1


title: WT_pDC_2


title: ALL18


title: 201RS20

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in LD (20 h light/4 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 3 weeks at ZT12 by snap-freezing in liquid nitrogen.

value: collected after 3 weeks at ZT12


title: deltaTEC_mTEClo_2

value: mTEC lo

value: Ltbr (flox/flox) FoxN1-Cre


title: ALL11


title: deltaTEC_mTEClo_1


title: deltaFb_mTEClo_2

value: Ltbr (flox/flox) Twist2-Cre


title: ALL10

value: Bone marrow


title: deltaFb_mTEClo_1


title: LTbRflox_mTEClo_2

value: Ltbr (flox/flox)


title: ALL1


title: 201RS23

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in LD (20 h light/4 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 3 weeks at ZT22 by snap-freezing in liquid nitrogen.

value: collected after 3 weeks at ZT22


title: deltaTEC_mTEChi_2

value: mTEC hi


title: 201RS18

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in LD (20 h light/4 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 3 weeks at ZT4 by snap-freezing in liquid nitrogen.

value: fully expanded leaves

value: LD (20 h light/4 h dark)

value: collected after 3 weeks at ZT4


title: LTbRflox_mTEClo_1


title: 201RS2

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in LD (20 h light/4 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 4 weeks at ZT1 by snap-freezing in liquid nitrogen.

value: collected after 4 weeks at ZT1


title: deltaTEC_mTEChi_1

value: thymus


title: Eos KO4

first: Ken

last: Oestreich

state: Ohio

address: 460 W 12th Avenue, 740 Biomedical Research Tower

data_processing:
Reads were mapped to the GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2
Bioconductor package DESeq2 was used to generate p-values and log2 fold changes
Genome_build: GRCm38
Supplementary_files_format_and_content: processed files are provided as .xls summary tables, representing gene counts and associated P values

source_name: CD4+ T cells

growth_protocol: Naïve CD4+ T cells (wild type or Ikzf4-/- (Eos KO)) were stimulated on plate-bound anti-CD3 and anti-CD28 in the presence of Th1-polarizing conditions for 72h.

extract_protocol:
Total RNA was isolated from cell pellets using the Macherey-Nagel Nucleospin RNA isolation kit according to the manufacturer's instructions.
Libraries were generated and sequenced according to standard protocols from GENEWIZ, Inc., to which the samples were sent for library preparation and analysis.

value: CD4+ T cells

tag: culturing conditions

value: Th1-polarizing conditions on anti-CD3/anti-CD28 stimulation for 72h


title: WT_cDC2_1

value: conventional type 2 dendritic cell (cDC2)

value: wild type


title: 201RS17

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in LD (20 h light/4 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 3 weeks at ZT0 by snap-freezing in liquid nitrogen.

value: single

value: collected after 3 weeks at ZT0


title: deltaFb_mTEChi_2


title: Eos KO3


title: Male rat primary hepatocyte _triclosan-1.2

growth_protocol: Male rat primary hepatocytes were isolated from liver samples and plated on collagen-coated plates.

tag: Sex

value: Male

value: triclosan

value: primary hepatocytes


title: deltaFb_mTEChi_1

value: Ltbr (flox/flox) Twist2-Cre


title: 201RS16

value: phyC

value: collected after 4 weeks at ZT22


title: LTbRflox_mTEChi_2

value: mTEC hi

value: Ltbr (flox/flox)


title: ALL12

growth_protocol: Mononuclear bone marrow or peripheral blood cells from pediatric leukemia patients were isolated by Ficoll Isopaque centrifugation and washed two times in PBS containing 0.1% bovine serum albumin. CEMWT and R30dm cell lines were maintained in RPMI-1640 medium supplemented with 10% fetal calf serum and 100 units/mL penicillin G, and 100μg/mL streptomycin sulphate.

value: Bone marrow


title: LTbRflox_mTEChi_1


title: deltaFb_mFb_4

value: thymic medullary fibroblast (mFb)


title: Eos KO2


title: 201RS15

value: fully expanded leaves

value: LD (20 h light/4 h dark)

value: collected after 4 weeks at ZT20


title: deltaFb_mFb_2

value: thymus


title: WT4

value: CD4+ T cells

value: Th1-polarizing conditions on anti-CD3/anti-CD28 stimulation for 72h

value: wild type


title: deltaFb_mFb_1


title: 201RS19

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in LD (20 h light/4 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 3 weeks at ZT8 by snap-freezing in liquid nitrogen.

value: single

value: collected after 3 weeks at ZT8


title: Eos KO1


title: deltaFb_mFb_3


title: 201RS13

value: collected after 4 weeks at ZT12


title: deltaFb_capFb_3

value: thymic capsular fibroblast (capFb)

value: Ltbr (flox/flox) Twist2-Cre


title: 201RS14

value: phyC

value: collected after 4 weeks at ZT16


title: deltaFb_capFb_2


title: deltaFb_capFb_4


title: WT3


title: 201RS11

value: collected after 4 weeks at ZT4


title: WT_mLN-FRC_2

value: mesenteric lymph node FRC

value: mesenteric lymph nodes


title: 201RS12

value: fully expanded leaves

value: collected after 4 weeks at ZT8


title: WT_sLN-FRC_2

value: skin-draining lymph node FRC

value: axillary and inguinal lymph nodes


title: WT1

value: CD4+ T cells


title: WT_mLN-FRC_1


title: 201RS10

value: LD (20 h light/4 h dark)

value: collected after 4 weeks at ZT1


title: WT_sLN-FRC_1

value: wild type


title: WT_mTEC_2

value: medullary thymic epithelial cell (mTEC)

value: thymus


title: WT_cTEC_2

value: cortical thymic epithelial cell (cTEC)


title: Idoxuridine_single_cell_rnaseq

city: San Francisco

first: Ravi

last: Desai

address: 1650 Owens Street

department: Biochemistry and Biophysics

institute: University of California, San Francisco

data_processing:
Data were aligned to mm10 genome using 10x Cell Ranger v2. The gene-barcode matrices were then filtered and normalized with Seurat using the “LogNormalize” gene scaling method.
Genome_build: mm10

source_name: Embryonic stem cells (E14)

growth_protocol: Mouse E14 embryonic stem cells (mESCs, male) were cultured in feeder-free conditions on gelatin-coated plates with ESGRO-2i medium (Millipore, cat#SF016-200).

extract_protocol:
After treatment, cells were trypsinized with trypLE and spun down for 5 min at 90 x g. Single-cell suspensions were prepared in dpbs at a concentration of 83,000 cells/1ml.
~3000 cells from each sample were loaded into a chip and processed with the Chromium Single Cell Controller (10x Genomics).  To generate single-cell gel beads in emulsion (GEMs), DMSO- and Idoxuridine- treated samples were assigned unique indexes using Single Cell 3′ Library and Gel Bead Kit V2 (10x Genomics, 120237). Sequencing was performed on an Illumina HiSeq 4000 with paired end setup specific for 10x libraries. On average, sequencing generated 100k  reads per cell.

treatment_protocol: For noise enhancer testing, mESCs were treated with either 10 mM Idoxuridine (Sigma, cat#I7125) or DMSO for 24 hours in 2i/LIF

tag: treatment

value: 10uM Idoxuridine


title: DMSO_single_cell_rnaseq

value: dmso


title: 201RS1

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in LD (20 h light/4 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 4 weeks at ZT0 by snap-freezing in liquid nitrogen.

tag: tissue

value: single

value: collected after 4 weeks at ZT0


title: WT_mTEC_1


title: WT_cTEC_1


title: 199RS9

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in SD (12 h light/12 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 6 weeks at ZT0 by snap-freezing in liquid nitrogen.

value: SD (12 h light/12 h dark)

value: collected after 6 weeks at ZT0


title: deltaFb_capFb_1

value: thymic capsular fibroblast (capFb)

value: Ltbr (flox/flox) Twist2-Cre


title: LTbRflox_PC_2

value: thymic pericyte (PC)

value: Ltbr (flox/flox)


title: 199RS7

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in SD (12 h light/12 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 6 weeks at ZT20 by snap-freezing in liquid nitrogen.

value: fully expanded leaves

value: collected after 6 weeks at ZT20


title: LTbRflox_PC_1


title: WT_PC_2


title: WT2

value: CD4+ T cells

value: Th1-polarizing conditions on anti-CD3/anti-CD28 stimulation for 72h


title: WT_PC_1

value: wild type


title: E8.0_Body_EC76

city: Beijing

first: Zongcheng

last: Li

address: No. 8 East Street, Fengtai District

country: China

institute: Fifth Medical Center of Chinese PLA General Hospital

data_processing:
Read 1 is biological.
Read 2 is technical.  The barcode is the first eight bases from the beginning and UMI is the next 8 bases (i.e., barcode is 1-8 bp and UMI is 9-16 bp in read 2 of length 150 bp.).
Illumina CASAVA version 1.8 were used to the basecalling.
For modified STRT-seq data, raw reads were first split for each cell by specific barcode sequence attached in Read 2. The TSO sequence and polyA tail sequence were trimmed for the corresponding Read 1 after UMI information was aligned to it. Reads with adapter contaminants or low-quality bases (N > 10%) were discarded. Subsequently, we aligned the stripped Read 1 sequences to mm10 mouse transcriptome (UCSC) using tophat2 (version 2.0.12). Uniquely mapped reads were counted by HTSeq package and grouped by the cell-specific barcodes. Duplicated transcripts were removed based on the UMI information for each gene. Finally, for each individual cell, the copy number of transcripts of a given gene was the number of the distinct UMIs of that gene.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include UMI values for each cell

molecule: polyA RNA

source_name: mouse embryonic cells

extract_protocol:
modified STRT-seq
A modified STRT-seq protocol was applied for single-cell RNA-seq. Briefly, sorted single cells in good condition were picked into lysis by mouth pipetting, and the scRNA-seq libraries were constructed based on STRT-seq with some modifications. cDNAs were synthesized using sample-specific 25-nt oligo-dT primer containing 8-nt barcode (TCAGACGTGTGCTCTTCCGATCT-XXXXXXXX-DDDDDDDD-T25, X representing sample-specific barcode while D standing for unique molecular identifiers (UMI).  After reverse transcription and second-strand cDNA synthesis, the cDNAs were amplified by 16 cycles of PCR using ISPCR primer and 3’ Anchor primer. Samples were pooled and purified using Agencourt AMPure XP beads . 4 cycles of PCR were performed to introduce index sequence  and subsequently, 400 ng cDNAs were fragmented to around 300 bp by Covaris S2. After being incubated with Dynabeads MyOneTM Streptavidin C1 beads (Thermo Fisher, 65002) for 1 hour at room temperature, cDNA Libraries were generated using KAPA Hyper Prep Kit (Kapa Biosystems, kk8505). After adaptor ligation, the libraries were amplified by 8 cycles of PCR using QP2 primer and short universal primer. The libraries were sequenced on Illumina Hiseq 4000 platform in 150 bp pair-ended manner

value: Body

value: embryonic cells

tag: development stage


title: E11.0_AGM_T1_EC81

value: AGM


title: E11.0_AGM_T1_EC82


title: LTbRflox_mFb_4

value: thymic medullary fibroblast (mFb)

value: thymus


title: 199RS6

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in SD (12 h light/12 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 6 weeks at ZT16 by snap-freezing in liquid nitrogen.

value: single

value: collected after 6 weeks at ZT16


title: 199RS5

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in SD (12 h light/12 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 6 weeks at ZT12 by snap-freezing in liquid nitrogen.

value: SD (12 h light/12 h dark)

value: collected after 6 weeks at ZT12


title: E8.0_Body_EC75


title: LTbRflox_mFb_3


title: 199RS4

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in SD (12 h light/12 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 6 weeks at ZT8 by snap-freezing in liquid nitrogen.

value: collected after 6 weeks at ZT8


title: LTbRflox_mFb_2


title: E10.0_AGM_PK44_EC74


title: WT_mFb_2


title: WT_mFb_1


title: E10.0_AGM_Neurl3_NE


title: E10.0_AGM_PK44_EC73


title: WT_EC_1

value: thymic endothelial cell (EC)


title: LTbRflox_capFb_3

value: thymic capsular fibroblast (capFb)

value: Ltbr (flox/flox)


title: 199RS8

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in SD (12 h light/12 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 6 weeks at ZT22 by snap-freezing in liquid nitrogen.

value: fully expanded leaves

value: collected after 6 weeks at ZT22


title: WT_EC_2


title: 199RS2

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in SD (12 h light/12 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 6 weeks at ZT1 by snap-freezing in liquid nitrogen.

value: collected after 6 weeks at ZT1


title: 199RS3

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in SD (12 h light/12 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 6 weeks at ZT4 by snap-freezing in liquid nitrogen.

value: collected after 6 weeks at ZT4


title: E11.0_DA_EC64

value: DA


title: LTbRflox_capFb_2


title: LTbRflox_capFb_1


title: WT_capFb_1

value: wild type


title: 199RS15

value: collected after 6 weeks at ZT20


title: 199RS16


title: Fraction1_gp38+

value: thymic fibroblast (fraction 1)


title: 199RS14


title: 199RS13


title: E10.0_DA_EC47

value: embryonic cells


title: LTbRflox_mFb_1

value: thymic medullary fibroblast (mFb)

value: thymus


title: E8.5_Body_EC40

value: Body


title: E10.0_DA_EC46


title: 199RS12

value: SD (12 h light/12 h dark)

value: single


title: E8.5_Body_EC39


title: 199RS11


title: E8.5_Body_EC38


title: E8.5_Body_EC37


title: 199RS10


title: E10.5_DA_EC63


title: E9.0_Body_EC36


title: 199RS1

value: collected after 6 weeks at ZT0


title: 196RS9

value: LD (20 h light/4 h dark)

value: collected after 3 weeks at ZT0


title: Fraction5-6_gp38+

value: thymic fibroblast (fraction 5-6)


title: E9.0_Body_EC35


title: 196RS8

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in LD (20 h light/4 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 3 weeks at ZT22 by snap-freezing in liquid nitrogen.

value: fully expanded leaves

value: collected after 3 weeks at ZT22


title: E9.0_Body_EC34


title: 196RS7

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in LD (20 h light/4 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 3 weeks at ZT20 by snap-freezing in liquid nitrogen.

value: collected after 3 weeks at ZT20


title: 196RS5

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in LD (20 h light/4 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 3 weeks at ZT12 by snap-freezing in liquid nitrogen.

value: collected after 3 weeks at ZT12


title: 196RS6

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in LD (20 h light/4 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 3 weeks at ZT16 by snap-freezing in liquid nitrogen.

value: collected after 3 weeks at ZT16


title: E9.0_Body_EC33


title: E10.0_Body_EC32


title: E10.0_Body_EC31


title: 196RS4

value: collected after 3 weeks at ZT8


title: 196RS3

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in LD (20 h light/4 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 3 weeks at ZT4 by snap-freezing in liquid nitrogen.

value: collected after 3 weeks at ZT4


title: E10.0_Body_EC30

value: embryonic cells


title: E10.0_Body_EC29


title: 196RS16


title: 196RS2

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in LD (20 h light/4 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 3 weeks at ZT1 by snap-freezing in liquid nitrogen.

value: collected after 3 weeks at ZT1


title: E8.5_Body_EC28


title: E8.5_Body_EC27


title: 196RS15


title: E8.5_Body_EC22


title: E8.5_Body_EC21


title: 196RS13


title: E8.5_Body_EC20


title: 196RS12

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in LD (20 h light/4 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 3 weeks at ZT8 by snap-freezing in liquid nitrogen.


title: 196RS14


title: 196RS11


title: E9.5_Body_EC19


title: E9.5_Body_EC18


title: 196RS10


title: E9.5_Body_EC17


title: blast cells, bone marrow, z342_401

type: genomic

city: Lublin

first: Monika

last: Szelest

address: ul. Antoniego Gębali 6

department: Laboratory of Genetic Diagnostics

country: Poland

institute: Medical University of Lublin

hyb_protocol: The 250 ng of genomic DNA from the leukemic cells was subjected to microarray examination according to the manufacturer's protocols as follows: i) Digestion with the restriction enzyme NspI; ii) adapter ligation, polymerase chain reaction (PCR) amplification and magnetic bead purification; iii) fragmentation and end-labeling with biotin; iv) washing and staining using a GeneChip ® Fluidics Station 450; and v) scanning using an Affymetrix GeneChip Scanner 3000 7G (Affymetrix). Scanned data files were generated using Affymetrix GeneChip Command Console Software,  and analyzed with Affymetrix Chromosome Analysis Suite v 3.3 (Affymetrix).

data_processing:
To calculate the copy number of altered regions, the data were normalized to baseline reference intensities using NA 32.3 FFPE v.2 reference model (Affymetrix). The hidden Markov model available within the software package was used to determine the copy number states (CN) and their breakpoints. Thresholds of log 2 ratio ≥0.58 and ≤1 were used to categorize altered regions as CN variation (CNV) gains (amplifications) and copy number losses (deletions), respectively. To prevent the detection of false-positive CNVs arising due to microarray unspecific signals, only regions that involved at least 50 consecutive probes were considered in the analysis of gains or losses in this study. Amplificationsand deletions were analyzed separately. To exclude aberrations representing common normal CNVs, all the identified CNVs were compared with those reported in the Database of Genomic Variants ( http://projects.tcag.ca/variation/ ). To identify the genes involved in the CNVs further, the UCSC database ( http://genome.ucsc.edu) and Ensemble (http://www.ensembl.org) were used.
Gene annotation and gene overlap were determined using the human genome build 19 and NetAffx (http://www.affymetrix.com).The obtained data were analyzed based on two different criteria: genome-wide CNVs and leukemia-associated region/gene-specific CNAs (leukemia genes_all_20150505; Fullerton Overlap Map_hg19).

source_name: blast cells, bone marrow

growth_protocol: Karyotypes are prepared from mitotic cells that have been arrested in the metaphase or prometaphase portion of the cell cycle, when chromosomes assume their most condensed conformations. For cancer diagnoses, typical specimens include bone marrow samples. The process of generating a karyotype begins with the short-term culture of cells derived from a specimen. After a period of cell growth and multiplication, dividing cells are arrested in metaphase by addition of colchicine, which poisons the mitotic spindle. The cells are next treated with a hypotonic solution that causes their nuclei to swell and the cells to burst. The nuclei are then treated with a chemical fixative, dropped on a glass slide, and treated with various stains that reveal structural features of the chromosomes.

extract_protocol: The researched material was the genomic DNA extracted from bone marrow samples using the QIAamp DNA Blood Mini Kit (Qiagen, Hilden, Germany).

tag: disease state

value: acute lymphoblastic leukemia

value: bone marrow

value: blast cells

tag: gender

value: F


title: 196RS1

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in LD (20 h light/4 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 3 weeks at ZT0 by snap-freezing in liquid nitrogen.

tag: cultivar

tag: photoperiod

value: single


title: blast cells, bone marrow, 1733

scan_protocol: The 250 ng of genomic DNA from the leukemic cells was subjected to microarray examination according to the manufacturer's protocols as follows: i) Digestion with the restriction enzyme NspI; ii) adapter ligation, polymerase chain reaction (PCR) amplification and magnetic bead purification; iii) fragmentation and end-labeling with biotin; iv) washing and staining using a GeneChip ® Fluidics Station 450; and v) scanning using an Affymetrix GeneChip Scanner 3000 7G (Affymetrix). Scanned data files were generated using Affymetrix GeneChip Command Console Software,  and analyzed with Affymetrix Chromosome Analysis Suite v 3.3 (Affymetrix).

treatment_protocol: After a period of cell growth and multiplication, dividing cells are arrested in metaphase by addition of colchicine, which poisons the mitotic spindle. The cells are next treated with a hypotonic solution that causes their nuclei to swell and the cells to burst. The nuclei are then treated with a chemical fixative, dropped on a glass slide, and treated with various stains that reveal structural features of the chromosomes.

value: M


title: blast cells, bone marrow, Y00349

label_protocol: The 250 ng of genomic DNA from the leukemic cells was subjected to microarray examination according to the manufacturer's protocols as follows: i) Digestion with the restriction enzyme NspI; ii) adapter ligation, polymerase chain reaction (PCR) amplification and magnetic bead purification; iii) fragmentation and end-labeling with biotin; iv) washing and staining using a GeneChip ® Fluidics Station 450; and v) scanning using an Affymetrix GeneChip Scanner 3000 7G (Affymetrix). Scanned data files were generated using Affymetrix GeneChip Command Console Software,  and analyzed with Affymetrix Chromosome Analysis Suite v 3.3 (Affymetrix).


title: blast cells, bone marrow, Y01588


title: blast cells, bone marrow, 163


title: blast cells, bone marrow, z793_401


title: 193RS9

value: LD (20 h light/4 h dark)

tag: temperature

tag: replicate


title: blast cells, bone marrow, Y02265


title: blast cells, bone marrow, 920


title: 193RS8

tag: genotype

tag: time

value: collected after 3 weeks at ZT0


title: blast cells, bone marrow, 1309

tag: cell type


title: blast cells, bone marrow, Y01966


title: E9.0_Body_EC15

value: Body


title: blast cells, bone marrow, 1606


title: blast cells, bone marrow, 5741


title: blast cells, bone marrow, 6482


title: blast cells, bone marrow, 856


title: blast cells, bone marrow, 1301


title: blast cells, bone marrow, 1200


title: blast cells, bone marrow, 7657


title: 193RS7

value: fully expanded leaves

value: collected after 3 weeks at ZT22


title: 193RS6

value: collected after 3 weeks at ZT20


title: blast cells, bone marrow, YAR


title: E9.0_Body_EC13


title: E9.0_Body_EC12


title: E9.5_Body_EC16


title: blast cells, bone marrow, Y01980


title: blast cells, bone marrow, 975


title: E9.5_Body_EC11


title: blast cells, bone marrow, E01468


title: 193RS5

value: collected after 3 weeks at ZT16


title: E9.5_Body_EC10


title: blast cells, bone marrow, 1067


title: w303_400_rep1

city: Delft

first: Diederik

last: Laman Trip

address: Van der Maasweg 9

department: Bionanoscience

institute: Delft University of Technology

description:
No-growth culture at 40.5C. Initial density approx. 48.000 cells/mL, final density approx. 400.000 cells/mL after ~3 days, biological replicate 1.
processed data file: genes.fpkm_tracking.txt

data_processing:
Illumina RTA 1.18.54 was used for base-calling.
Sequenced reads were trimmed for the adapter sequences and filtered from short or low-quality sequences using Bbduk (Bbmap_38.36).
Sequenced reads were subsequently aligned to the Saccharomyces cerevisiae reference genome (Ensembl, R64-1-1) using TopHat2 (tophat2 -p 8 -G).
Next, expressed genes were assembled (cufflinks -p 8 -o), merged (cuffmerge -p 8) and Fragments Per Kilobase Million (FPKM) values were calculated (cuffdiff -o -p 8 -L) as described in Trapnell et al., Nat Protoc. (2012).
Finally, genes with at least 2-fold difference expression when compared to the reference were categorized by Gene Ontologies with AmiGO2.
Genome_build: Saccharomyces cerevisiae, Ensembl R64-1-1
Supplementary_files_format_and_content: genes.fpkm_tracking.txt: Tab-delimited text file includes FPKM values per condition per gene.

organism: Saccharomyces cerevisiae

growth_protocol: Cells were cultured in defined minimal media (SD) consisting of Yeast Nitrogen Base, Complete Supplement Mixture and 2% glucose. Cultures were covered with breathable film, incubated in a compressor-cooled high-precision thermostatic incubator at the desired temperature, and constantly shaken at 400rpm.

extract_protocol:
RNA was extracted from each cell-pellet with the RiboPure Yeast Kit 830 (Ambion, Life Technologies) as described by its protocol.
The cDNA library was prepared with the 3' mRNA-Seq library preparation kit (Quant-Seq, Lexogen) as described by its protocol.

treatment_protocol: Cells were collected in 50-mL tubes and spun down in a pre-cooled centrifuge.

tag: incubation temperature


title: w303_400_rep2

description:
No-growth culture at 40.5C. Initial density approx. 48.000 cells/mL, final density approx. 400.000 cells/mL after ~3 days, biological replicate 2.
processed data file: genes.fpkm_tracking.txt

tag: strain


title: 193RS2


title: w303_390_rep3

description:
Log-phase growth at 39.1C. Initial density approx. 10.000 cells/mL, final density approx. 1.700.000 cells/mL after ~4 days, biological replicate 3.
processed data file: genes.fpkm_tracking.txt


title: 193RS4

value: collected after 3 weeks at ZT12


title: E9.5_Body_EC9


title: E9.5_Body_EC8


title: w303_390_rep2

description:
Log-phase growth at 39.1C. Initial density approx. 10.000 cells/mL, final density approx. 1.700.000 cells/mL after ~4 days, biological replicate 2.
processed data file: genes.fpkm_tracking.txt


title: 193RS14


title: blast cells, bone marrow, Y01604

tag: age


title: w303_390_rep1

description:
Log-phase growth at 39.1C. Initial density approx. 10.000 cells/mL, final density approx. 1.200.000 cells/mL after ~3 days, biological replicate 1.
processed data file: genes.fpkm_tracking.txt


title: blast cells, bone marrow, Y02140

value: unkonown


title: 193RS13


title: 193RS3

value: collected after 3 weeks at ZT8


title: blast cells, bone marrow, Y01358


title: E10.0_Body_EC6

value: embryonic cells


title: E10.0_Body_EC7


title: blast cells, bone marrow, Y87

value: acute lymphoblastic leukemia


title: w303_300_rep3

description:
Log-phase growth at 30.0C, approx. 1.2M cells/mL, biological replicate 3.
processed data file: genes.fpkm_tracking.txt


title: 193RS12


title: blast cells, bone marrow, 986_982

value: bone marrow


title: E9.0_Body_EC14


title: w303_300_rep2

description:
Log-phase growth at 30.0C, approx. 1.2M cells/mL, biological replicate 2.
processed data file: genes.fpkm_tracking.txt


title: w303_300_rep1

description:
Log-phase growth at 30.0C, approx. 1.2M cells/mL, biological replicate 1.
processed data file: genes.fpkm_tracking.txt


title: 193RS10


title: E10.0_Body_EC4


title: blast cells, bone marrow, z219_401

value: blast cells


title: 16_IN_control

city: Los Angeles

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

description:
16_S31_L00*
2017-9106

data_processing:
Aligned to mm10 using STAR spliced read aligner
Count read using HT-seq and using mm10 RefSeq as reference
Normalization (TMM), quantitation (logCPM) and differential expression analysis using edgeR and limma voom.
Genome_build: mm10
Supplementary_files_format_and_content: logCPM values

extract_protocol:
Input and IP samples underwent DNA depletion and RNA purification with the RNeasy Micro Plus kit (Qiagen). Integrity of the eluted RNA was analyzed by a 2100 Bioanalyzer (Agilent).
Sequencing libraries were prepared using Illumina TruSeq RNA sample prep kit following manufacturer's protocol.  After library preparation, amplified double-stranded cDNA was fragmented into 125 bp (Covaris-S2, Woburn, MA) DNA fragments, which were (200 ng) end-repaired to generate blunt ends with 5’- phosphates and 3’- hydroxyls and adapters ligated.

treatment_protocol: Tamoxifen was injected i.p. at 2 months to induce the expression of Ribotag in astrocytes. After 1 month, mice were stressed by putting them in un bucket with water for 20 minutes. Mice rested for 90 minutes in their homecage before RNA extraction. Control mice stayed in their home cage all the time.

tag: strain background

tag: genotype/variation

value: 3 m

value: Control

value: somatosensory cortex

tag: molecule subtype

value: cleared lysate as the input and control


title: 193RS11

tag: tissue

value: LD (20 h light/4 h dark)

value: single


title: 169RS34

data_processing:
genome build:  Bd21-v3.1
Adapters were trimmed off using Trimmomatic with "ILLUMINACLIP:$FA_ADAPTER:2:10:5:1"
The trimmed reads were aligned using Tophat with "--max-multihits --library-type fr-firststrand --no-mixed"
Duplicate reads were removed with Picard using default setting
Alignments in SAM file were assembled into transcripts abundances using htseq-count with "-r name -s no -f bam -t exon -i gene_id" against the GTF annotation"
Supplementary_files_format_and_content: _htseq_count.ct.txt: TSV table containing htseq-counted transcript abundances.

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in LD (20 h light/4 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 10 day at ZT4 by snap-freezing in liquid nitrogen.

value: fully expanded leaves

value: collected after 10 day at ZT4


title: 15_IP_stress

description:
15_S30_L00*
2017-9106

tag: treatment

value: Stress

tag: ip antibody

value: Anti-HA.11 Epitope Tag Antibody (Biolegend #901514)

value: astrocyte-specific ribosome-associated RNA precipitated via a hemagglutinin (HA) tag


title: 14_IN_control

description:
14_S29_L00*
2017-9106


title: 169RS33

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in LD (20 h light/4 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 8day at ZT4 by snap-freezing in liquid nitrogen.

value: collected after 8day at ZT4


title: 169RS32

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in LD (20 h light/4 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 6day at ZT4 by snap-freezing in liquid nitrogen.

value: collected after 6day at ZT4


title: 13_IP_control

description:
13_S28_L00*
2017-9106


title: 169RS31

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in LD (20 h light/4 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 4day at ZT4 by snap-freezing in liquid nitrogen.

value: collected after 4day at ZT4


title: blast cells, bone marrow, 682

tag: disease state

value: acute lymphoblastic leukemia

tag: gender

value: F


title: 193RS1

tag: cultivar

tag: photoperiod

value: collected after 3 weeks at ZT0


title: Cg_GABA_(NH4)2SO4_vs_GABA_K2SO4_4

city: Juelich

first: Tino

last: Polen

state: NRW

address: Wilhelm-Johnen-Str 1

department: IBG-1: Biotechnology

institute: Forschungszentrum Jülich GmbH

hyb_protocol: Purified cDNA samples to be compared were pooled and the prepared two-color samples were hybridized at 65°C while rotating for 16 hours using Agilent’s Gene Expression Hybridization Kit, hybridization oven and hybridization chamber. After hybridization the arrays were washed using Agilent’s Wash Buffer Kit according to the manufacturer’s instructions.

scan_protocol: Fluorescence of hybridized DNA microarrays was determined at 532 nm (Cy3) and 635 nm (Cy5) at 5 μm resolution with a GenePix 4000B laser scanner and GenePix Pro 6.0 software (Molecular Devices, Sunnyvale, CA, USA). Fluorescence images were saved to raw data files in TIFF format (GenePix Pro 6.0). Quantitative TIFF image analysis was carried out using GenePix image analysis software and results were saved as GPR-file (GenePix Pro 6.0).

data_processing: For ratio calculation and ratio normalization, GPR-files were processed using the BioConductor R-packages limma and marray (http://www.bioconductor.org).

organism: Corynebacterium glutamicum

label_protocol: Synthesis of fluorescently labelled cDNA were carried out as described in Lange, C., D. Rittmann, V. F. Wendisch, M. Bott, and H. Sahm. 2003. Global expression profiling and physiological characterization of Corynebacterium glutamicum grown in the presence of L-valine. Appl. Environm. Microbiol. 69:2521-2532 and in Möker, N., M. Brocker, S. Schaffer, R. Krämer, S. Morbach & M. Bott. 2004. Deletion of the genes encoding the MtrA-MtrB two-component system of Corynebacterium glutamicum has a strong influence on cell morphology, antibiotics susceptibility and expression of genes involved in osmoprotection. Mol. Microbiol. 54: 420-438.

growth_protocol: For precultivation of C. glutamicum, brain heart infusion (BHI) medium (Becton Dickinson and Company, New Jersey, USA) with 90 g L-1 sorbitol were used. The cells of these precultures were harvested by centrifugation (5,000×g, 4°C, 10 min), and washed twice by PBS buffer (pH 7.0). The main cultures were inoculated to an OD of 1 in CGXII minimal medium with GABA and K2SO4 or (NH4)2SO4. At an OD of 5 the cells were harvested by centrifugation (4120 x g, 10 min and 4 °C). The cell pellet was subsequently frozen in liquid nitrogen and stored at -70°C.

extract_protocol: The preparation of total RNA was performed as described previously with the RNeasy Kit from Qiagen (Möker, N., M. Brocker, S. Schaffer, R. Krämer, S. Morbach & M. Bott, (2004) Deletion of the genes encoding the MtrA-MtrB two-component system of Corynebacterium glutamicum has a strong influence on cell morphology, antibiotics susceptibility and expression of genes involved in osmoprotection. Mol Microbiol 54: 420-438.)

treatment_protocol: see growth protocol

tag: agent