title: RNA-seq_Bcat_ChoroidPlexus_Bound_R1

data_processing:
Library strategy: RiboTag immunoprecipitation
RNA-seq data was generated from papain dissociated adult Tie2-GFP cerebellum, anterior pituitary, and posterior pituitary, with and without beta-catenin stabilization: (1) GFP-negative FACS-sorted cells and (2) GFP-positive FACS-sorted cells.  RNA-seq was also performed on mice expressing RiboTag in ECs. Salmon version 0.10.2 (Patro et al., 2017) was used to quantify expression of transcripts from RNA-seq experiments using mm10/GRCm38_92 Ensembl transcriptome (salmon quant -l A -g Mus_musculus.GRCm38.92.chr.gtf.gz --validateMappings --rangeFactorizationBins 4 --incompatPrior 0.0 -- useVBOpt --seqBias --gcBias --posBias --biasSpeedSamp 10). To visualize RNA-seq data on an IGV browser (Robinson et al., 2011; Thorvaldsdóttir et al., 2013), kallisto version 0.44.0 (Bray et al., 2016) was used to generate alignment bam files (kallisto quant --bias --single -l 250 -s 25 --genomebam -g Mus_musculus.GRCm38.92.chr.gtf.gz -c mouse.mm10.genome) and then deepTools was used to generate bigwig files (bamCoverage -bs 1 --normalizeUsing RPKM). To convert transcript-level abundances to the gene-level for further downstream analyses, we used tximport (Soneson et al., 2015). Differentially expressed genes were identified using EBSeq version 1.20.0 (Leng and Kendziorski, 2015).
Genome_build: mm10
Supplementary_files_format_and_content: text with TPM

source_name: Bound from beta-catenin stabilized choroid plexus

extract_protocol:
Immunoprecipitation performed with Anti-HA.11 Epitope Tag Antibody from Covance, Catalog# MMS-101R. To prepare total RNA, 350 μl of Qiagen RLT buffer was added to the RiboTag immunoprecipitated samples or to the input samples. Total RNA was prepared according to manufacturer’s instructions using the RNeasy Plus Micro kit (Qiagen), and the quantity and quality of the RNA were assessed using a Bioanalyzer (Agilent).
For RNA-seq, total RNA was converted to cDNA and amplified (Ovation Ultralow System V2-32, 0342HV, NuGEN Technologies, San Carlos, CA). Amplified cDNA was fragmented, end-repaired, linker-adapted, and single-end sequenced for 75 cycles on a NextSeq500 (Illumina Inc.).

value: RiboTag; Pdgfb-CreER; BcatEx3fl

value: Choroid Plexus


title: C13_Treg_H3K27ac

status: Public on Mar 26 2019

type: SRA

city: Hershey

first: Yasin

last: Uzun

state: PA

address: 700 HMC Crescent Rd

department: Department of Pediatrics

country: USA

institute: Pennsylvania State University College of Medicine

library_source: genomic

data_processing:
Basecalls performed using Illumina Casava version 1.8
ChIP-Seq reads were mapped to human genome (hg9) using Bowtie2. Only uniquely mapped reads with fewer than 2 mismatches were used for downstream analyses.
[.wig] Aligned reads were quantified in 200bp windows along the genome
[.bed] Every subject has one input control for each cell (Th1 and Treg).
All the peaks were called using input control as the background.
Peaks were called using MACS 1.4 in default settings with FDR cutoff 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: variableStep Wiggle format text file

molecule: genomic DNA

organism: Homo sapiens

source_name: Effector memory TREG cells

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared using ThruPLEX® DNA-seq Kit (Rubicon Genomics) according to the protocol from the vendor. Qubit, bioanalyzer and KAPA qPCR were done before pooling for sequencing on HiSeq 2500 platform.

tag: disease state

value: control

tag: individual

tag: tissue

value: Peripheral Blood

tag: cell type

value: Effector memory TREG cells

tag: chip antibody

value: H3K27ac (Abcam, ab4729)


title: RNA-seq_WT_ChoroidPlexus_Bound_R2

city: Baltimore

first: Mark

middle: F

last: Sabbagh

state: MD

address: 725 North Wolfe Street

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

source_name: Bound from wild-type choroid plexus

growth_protocol: Adult mice were housed in our animal facility with 12 h light/dark cycles and food ab libitum. Animals were used for analysis in accordance with protocols approved by the Institutional Animal Care and Use Committee

tag: genotype

value: RiboTag; Pdgfb-CreER

tag: age

value: Adult

tag: Sex

value: Male

value: Vascular endothelial cells


title: RNA-seq_Bcat_ChoroidPlexus_Bound_R2


title: C13_Th1_H3K27ac

source_name: Effector memory TH1 cells

value: Effector memory TH1 cells


title: C12_Treg_Input


title: C12_Treg_H3K4me1

value: H3K4me1 (Abcam, ab8895)


title: C12_Th1_Input


title: RNA-seq_WT_ChoroidPlexus_Input_R2

source_name: Input from wild-type choroid plexus

value: Whole Tissue


title: C12_Th1_H3K4me1


title: C12_Th1_H3K27ac


title: RNA-seq_Bcat_Cortex_Bound_R2

source_name: Bound from beta-catenin stabilized cortex

value: Cortex


title: RNA-seq_WT_ChoroidPlexus_Input_R1


title: RNA-seq_Bcat_ChoroidPlexus_Input_R2

source_name: Input from beta-catenin stabilized choroid plexus


title: RNA-seq_Bcat_Cortex_Bound_R1


title: RNA-seq_Bcat_Cortex_Input_R1

source_name: Input from beta-catenin stabilized cortex


title: Otel-SV40-R2-EV

type: RNA

city: Paris

first: Nicolas

last: Manel

address: 12 rue Lhomond

department: INSERM U932

country: France

institute: Institut Curie

description: Gene expression data from non-depleted cells

hyb_protocol: Hybridization was performed using 5 micrograms of biotinylated target, which was incubated with the GeneChip Human gene 2.0 array (Affymetrix) at 45 °C for 16–20 h. After hybridization, nonspecifically bound material was removed by washing and specifically bound target was detected using the GeneChip Hybridization, Wash and Stain kit, and the GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: The arrays were scanned using the GeneChip Scanner 3000 7G (Affymetrix) and raw data was extracted from the scanned images and analyzed with the Affymetrix Power Tools software package (Affymetrix).

data_processing: Raw data were treated, normalized and summarized using oligo R package.

label: biotin

source_name: SV40-transformed human skin fibroblasts

label_protocol: Using 100ng of total RNA, double-stranded cDNA was synthesized with random hexamers tagged with a T7 promoter sequence. The double-stranded cDNA was subsequently used as a template and amplified by T7 RNA polymerase producing many copies of antisense cRNA. In the second cycle of cDNA synthesis, random hexamers are used to prime reverse transcription of the cRNA from the first cycle to produce single-stranded DNA in the sense orientation. cDNA was synthesized using the GeneChip WT (Whole Transcript) Sense Target Labeling and Control Reagents kit as described by the manufacturer (Affymetrix). The sense cDNA was then fragmented by uracil DNA glycosylase and apurinic/apyrimidic endonuclease-1 and biotin-labeled with terminal deoxynucleotidyl transferase using the GeneChip WT Terminal labeling kit (Affymetrix).

growth_protocol: Skin human SV40-fibroblasts were transduced by lentivirus to depleted BLM or not by CRISPR-Cas9. Cells were selected with puromycine.

extract_protocol: 48h after seeding, total RNA was extracted with Nucleospin kit and eluted in 40µl (Nanodrop quantification).

treatment_protocol: BLM-depleted or non-depleted cells were seed and allow to grow for 48h.

value: WT


title: C11_Treg_Input


title: C11_Th1_H3K27ac


title: RNA-seq_WT_Cortex_Input_R1

source_name: Input from wild-type cortex


title: C11_Th1_H3K4me1


title: RNA-seq_WT_Cortex_Bound_R2

source_name: Bound from wild-type cortex


title: C11_Th1_Input


title: RNA-seq_Bcat_PosteriorPituitary_GFPpos_R2

data_processing:
RNA-seq data was generated from papain dissociated adult Tie2-GFP cerebellum, anterior pituitary, and posterior pituitary, with and without beta-catenin stabilization: (1) GFP-negative FACS-sorted cells and (2) GFP-positive FACS-sorted cells.  RNA-seq was also performed on mice expressing RiboTag in ECs. Salmon version 0.10.2 (Patro et al., 2017) was used to quantify expression of transcripts from RNA-seq experiments using mm10/GRCm38_92 Ensembl transcriptome (salmon quant -l A -g Mus_musculus.GRCm38.92.chr.gtf.gz --validateMappings --rangeFactorizationBins 4 --incompatPrior 0.0 -- useVBOpt --seqBias --gcBias --posBias --biasSpeedSamp 10). To visualize RNA-seq data on an IGV browser (Robinson et al., 2011; Thorvaldsdóttir et al., 2013), kallisto version 0.44.0 (Bray et al., 2016) was used to generate alignment bam files (kallisto quant --bias --single -l 250 -s 25 --genomebam -g Mus_musculus.GRCm38.92.chr.gtf.gz -c mouse.mm10.genome) and then deepTools was used to generate bigwig files (bamCoverage -bs 1 --normalizeUsing RPKM). To convert transcript-level abundances to the gene-level for further downstream analyses, we used tximport (Soneson et al., 2015). Differentially expressed genes were identified using EBSeq version 1.20.0 (Leng and Kendziorski, 2015).
Genome_build: mm10
Supplementary_files_format_and_content: text with TPM and .bw

source_name: beta-catenin stabilized GFP-positive sorted cells from posterior pituitary

extract_protocol:
RNA was extracted from  from GFP-positive and GFP-negative FACS sorted cells using the RNeasy Micro Plus kit (74034, QIAGEN, Venlo, Netherlands).
For RNA-seq, total RNA was converted to cDNA and amplified (Ovation Ultralow System V2-32, 0342HV, NuGEN Technologies, San Carlos, CA). Amplified cDNA was fragmented, end-repaired, linker-adapted, and single-end sequenced for 75 cycles on a NextSeq500 (Illumina Inc.).

value: Tie2-GFP; Pdgfb-CreER; BcatEx3fl

value: Posterior Pituitary


title: C11_Treg_H3K27ac


title: RNA-seq_WT_Cortex_Input_R2


title: CT_VT_RT_96h_3

city: Tuebingen

first: Stefan

last: Czemmel

address: Auf der Morgenstelle 10

department: University of Tuebingen

country: Germany

institute: Quantitative Biology Center (QBiC)

data_processing:
Data was filtered using fastqc 0.11.4
Reads were aligned to hg19 using Tophat 2 with parameters --no-coverage-search -p 2 -G
Read features were counted using htseq 0.6.1p2
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table containing all counts in csv format

growth_protocol: LNZ308 glioma cells were cultured in Dulbecco's Modified Eagle Medium (Thermo Fisher Scientific, Waltham, USA) supplemented with 10% fetal bovine serum and 50 μg/ml gentamycin (Thermo Fisher Scientific).

extract_protocol:
RNA was isolated using RNeasy Mini kit (Qiagen, Hilden, Germany) according to manufacturer’s instructions.
TruSeq Stranded RNA Sample Prep Kit (Illumina)

treatment_protocol: LNZ308 glioma cells were treated in Dulbecco's Modified Eagle Medium (Thermo Fisher Scientific, Waltham, USA) containing 50 μg/ml gentamycin (Thermo Fisher Scientific) with respective treatment regimen as described. The treatment medium was strictly serum-free throughout the course of the experiment.

value: glioblastoma cell line

tag: time

tag: treatment

value: triple treatment chemotherapy - viral therapy - radiotherapy

tag: cell line


title: CT_VT_RT_96h_2


title: RNA-seq_Bcat_PosteriorPituitary_GFPpos_R1


title: RNA-seq_Bcat_ChoroidPlexus_Input_R1

value: RiboTag; Pdgfb-CreER; BcatEx3fl

value: Choroid Plexus


title: RNA-seq_WT_ChoroidPlexus_Bound_R1


title: RNA-seq_Bcat_PosteriorPituitary_GFPneg_R2

data_processing:
RNA-seq data was generated from papain dissociated adult Tie2-GFP cerebellum, anterior pituitary, and posterior pituitary, with and without beta-catenin stabilization: (1) GFP-negative FACS-sorted cells and (2) GFP-positive FACS-sorted cells.  RNA-seq was also performed on mice expressing RiboTag in ECs. Salmon version 0.10.2 (Patro et al., 2017) was used to quantify expression of transcripts from RNA-seq experiments using mm10/GRCm38_92 Ensembl transcriptome (salmon quant -l A -g Mus_musculus.GRCm38.92.chr.gtf.gz --validateMappings --rangeFactorizationBins 4 --incompatPrior 0.0 -- useVBOpt --seqBias --gcBias --posBias --biasSpeedSamp 10). To visualize RNA-seq data on an IGV browser (Robinson et al., 2011; Thorvaldsdóttir et al., 2013), kallisto version 0.44.0 (Bray et al., 2016) was used to generate alignment bam files (kallisto quant --bias --single -l 250 -s 25 --genomebam -g Mus_musculus.GRCm38.92.chr.gtf.gz -c mouse.mm10.genome) and then deepTools was used to generate bigwig files (bamCoverage -bs 1 --normalizeUsing RPKM). To convert transcript-level abundances to the gene-level for further downstream analyses, we used tximport (Soneson et al., 2015). Differentially expressed genes were identified using EBSeq version 1.20.0 (Leng and Kendziorski, 2015).
Genome_build: mm10
Supplementary_files_format_and_content: text with TPM

source_name: beta-catenin stabilized GFP-negative sorted cells from posterior pituitary

value: Non-endothelial


title: CT_VT_RT_96h_1


title: RNA-seq_Bcat_PosteriorPituitary_GFPneg_R1


title: CT_VT_RT_36h_3


title: CT_VT_RT_36h_2


title: C12_Treg_H3K27ac

value: control

value: Peripheral Blood

value: Effector memory TREG cells

value: H3K27ac (Abcam, ab4729)


title: RNA-seq_WT_PosteriorPituitary_GFPpos_R2

source_name: Wild-Type GFP-positive sorted cells from posterior pituitary

value: Adult

value: Male

value: Vascular endothelial cells


title: CT_VT_96h_2

value: double treatment chemotherapy - viral therapy


title: CT_VT_RT_36h_1


title: CT_VT_96h_3


title: RNA-seq_Bcat_AnteriorPituitary_GFPpos_R2

source_name: beta-catenin stabilized GFP-positive sorted cells from anterior pituitary


title: RNA-seq_WT_PosteriorPituitary_GFPneg_R2

source_name: Wild-Type GFP-negative sorted cells from posterior pituitary


title: RNA-seq_WT_Cortex_Bound_R1

value: RiboTag; Pdgfb-CreER

value: Cortex


title: CT_VT_96h_1


title: CT_VT_36h_3


title: RNA-seq_WT_PosteriorPituitary_GFPneg_R1


title: RNA-seq_Bcat_AnteriorPituitary_GFPpos_R1

value: Tie2-GFP; Pdgfb-CreER; BcatEx3fl

value: Anterior Pituitary


title: RNA-seq_Bcat_Cortex_Input_R2

value: Whole Tissue


title: RNA-seq_WT_AnteriorPituitary_GFPpos_R1

source_name: Wild-Type GFP-positive sorted cells from anterior pituitary


title: CT_VT_36h_2

value: glioblastoma cell line


title: RNA-seq_Bcat_AnteriorPituitary_GFPneg_R1

source_name: beta-catenin stabilized GFP-negative sorted cells from anterior pituitary


title: CTL_CT_96h_1

value: Control Chemotherapy


title: RNA-seq_Bcat_AnteriorPituitary_GFPneg_R2


title: CT_VT_36h_1


title: CTL_CT_96h_2


title: RNA-seq_WT_AnteriorPituitary_GFPpos_R2


title: CTL_CT_96h_3


title: RNA-seq_WT_AnteriorPituitary_GFPneg_R2

source_name: Wild-Type GFP-negative sorted cells from anterior pituitary


title: RNA-seq_Bcat_Cerebellum_GFPpos_R2

source_name: beta-catenin stabilized GFP-positive sorted cells from cerebellum

value: Cerebellum


title: RNA-seq_WT_AnteriorPituitary_GFPneg_R1

value: Non-endothelial


title: RNA-seq_Bcat_Cerebellum_GFPpos_R1


title: RNA-seq_WT_PosteriorPituitary_GFPpos_R1

value: Posterior Pituitary


title: CTL_CT_36h_3


title: CTL_CT_36h_2


title: CT_96h_2

value: Chemotherapy


title: RNA-seq_WT_Cerebellum_GFPneg_R2

source_name: Wild-Type GFP-negative sorted cells from cerebellum


title: CTL_CT_36h_1


title: RNA-seq_WT_Cerebellum_GFPpos_R1

source_name: Wild-Type GFP-positive sorted cells from cerebellum


title: RNA-seq_WT_Cerebellum_GFPpos_R2


title: RNA-seq_Bcat_Cerebellum_GFPneg_R1

source_name: beta-catenin stabilized GFP-negative sorted cells from cerebellum


title: CT_96h_3


title: CT_36h_3


title: RNA-seq_Bcat_Cerebellum_GFPneg_R2


title: CT_96h_1


title: CT_36h_1


title: CT_36h_2


title: CTL_R_V_96h_2

value: Control double treatment radiotherapy and viral therapy


title: RNA-seq_WT_Cerebellum_GFPneg_R1


title: E3 CFP CD24-

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
FASTQ files were output using standard Illumina protocols and software.
Reads were aligned to the mouse genome by Rsubread 1.29.6.
Read counts were summarized by Entrez Gene ID using featureCounts and Rsubread's built-in NCBI annotation. Read counts were separately obtained for each exon. Supplementary files provide both gene-level and exon-level counts.
Genome_build: mm10 (NCBI build 38.1)
Supplementary_files_format_and_content: tab-delimited text files; columns represent Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene.

source_name: Live lineage-negative tumor cells

extract_protocol:
RNA was isolated from freshly sorted cells with the miRNeasy Micro Kit (50) (Qiagen Catalog #217084).
mRNA reverse transcription cDNA libraries were prepared using either the TruSeq RNA Sample preparation kit (Illumina) or the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech) following the manufacturer’s instructions.

tag: strain

tag: tumor

tag: fluorescent marker

value: CFP

value: lineage-negative tumor cells

tag: cell population

tag: sequencing date

tag: sample id

tag: library preparation protocol

value: TruSeq


title: CTL_R_V_96h_1


title: K4 GFP CD24-

value: GFP


title: E3 RFP CD24+

value: RFP


title: CTL_R_V_96h_3


title: E3 CFP CD24+


title: RT_96h_3

value: radiotherapy


title: E3 RFP CD24-


title: CTL_R_V_36h_2


title: CTL_R_V_36h_1


title: E3 YFP CD24+

value: YFP


title: E2 YFP CD24-


title: RT_36h_3


title: E2 YFP CD24+


title: RT_96h_2


title: E1 CFP CD24+


title: RT_96h_1


title: K2 CFP CD24-


title: RT_36h_1


title: VT_96h_3

value: viral therapy


title: E1 CFP CD24-


title: VT_36h_3


title: RT_36h_2


title: K2 RFP CD24-


title: VT_96h_2


title: E3 YFP CD24-


title: K2 GFP CD24+


title: CTL_R_V_36h_3


title: K2 RFP CD24+


title: K5 CFP CD24-

value: Clontech


title: VT_36h_2


title: K2 GFP CD24-


title: P6-2

city: Wuxi

first: Lanmei

last: Wang

address: East Shanshui Road 9

country: China

institute: Freshwater Fisheries Research Centre of Chinese Academy of Fishery Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Quality control of sequencing reads was analyzed using FastQC software. Also, sequences with poor quality, 3’ adaptor absense, 5’ adaptor contaminants and short trimmed length was defined as disordered reads and removed prior to further analysis.
The remaining sequences were first mapped to the whole genome sequence of common carp using the SOAP2 program (v2.20)16 with no more than 2 mismatches. Then, rRNAs, tRNAs, snRNAs and snoRNAs were filter out from the mapped sequences by blasting against Rfam (http://rfam.sanger.ac.uk/) and NCBI GenBank (http://www.ncbi.nlm.nih.gov/genbank/) databases. The rest sequences were then aligned to the miRNA precursor of common carp in the miRBase version 21 database (http://www.mirbase.org/) to identify conserved miRNAs. The final unannotated sRNAs reads were submitted to predict candidate novel miRNAs using MIREAP software.
MiRNA abundance of each library was quantified using TPM normalizion method.
EdgeR R package was used to identify differentially expressed miRNAs (DEMs) based on the miRNAs expression values. The cut-off criteria for DEMs was |log2(Fold Change)|≥1 and FDR≤0.05 between two groups.
Genome_build: GCF_000951615.1
Supplementary_files_format_and_content: tab-delimited text files include rawcount number for each Sample

organism: Cyprinus carpio

source_name: 1 dph larva_embryo

growth_protocol: The common carp used in the experiment is a new fish variety derived from the original parents of Jian carp (C. carpio var. jian), Huanghe carp (C. carpio haematopterus) and Heilongjiang common carp (C. carpio haermatopterus) after five generations combined selection by Freshwater Fisheries Research Center (FFRC), Chinese Academy of Fishery Sciences (CAFS), which is designated as FFRC No.2 strain common carp. Embryos were obtained by natural spawning.

extract_protocol:
Total RNA was isolated using the standard TRIzol (Invitrogen) protocol
Genomic DNA was removed prior to RNA purity and integrity evaluation. An equal amount of total RNA of each stage was pooled separately. Ligated with 3’ and 5’ adapters (Illumina, San Diego, CA, USA) using T4 ligase (New England Biolabs), purified RNA was reverse-transcribed into the first strand cDNA and then amplified by PCR. The final sRNA sequencing library was prepared by purified the nucleotide fractions at 140–150 bp length.
Illumina HiSeq 2500 for 50 bp single-end sequencing

treatment_protocol: The stages of embryonic development were observed and photographed under an microscope. The test samples consisted of six embryonic stages: cleavage stage(2 hours post-fertilization (hpf) embryos) (P1), blastocyst stage (6 hpf) (P2), gastrulation stage (12 hpf) (P3), organ formation stage (20 hpf) (P4), hatching stage (64 hpf) (P5) and 1 dph larva (P6) (Supplementary fig). All samples were immediately frozen in liquid nitrogen and then stored at −80 °C for further use.

value: FFRC No.2 strain

value: WT

tag: developmental stage

value: 1 dph larva

value: embryo


title: P6-3

tag: tissue


title: K2 CFP CD24+

tag: cell type


title: BLANK_0h_2

value: glioblastoma cell line

value: no  treatment


title: VT_36h_1


title: K5 CFP CD24+


title: BLANK_0h_3


title: BLANK_0h_1


title: K5 RFP CD24-


title: VT_96h_1


title: P5-3

source_name: hatching stage (64 hpf)_embryo

value: hatching stage (64 hpf)


title: P5-2


title: K5 RFP CD24+


title: P4-3

source_name: organ formation (20 hpf)_embryo

value: organ formation (20 hpf)


title: P5-1


title: P4-2


title: 53482

city: Leipzig

first: Torsten

last: Thalheim

address: Härtelstr. 16 – 18

department: Interdisciplinary Centre for Bioinformatics

institute: Leipzig University

description:
940_53482
Mouse9
processed data file: genelist_mm9_modifications.csv

data_processing:
The sequenced reads underwent a quality trimming using cutadapt to ensure a minimum read length of 40 bases and a Phred quality score above 20.
The high-quality reads were mapped to the mouse reference genome NCBI37/mm9 using the software tool segemehl 0.2.0 with parameter settings “-s -t 8”.
Histone modification peaks were identified by applying MACS 1.4.2 with the H3pan data as control and the following, modification independent parameter settings: “--nomodel -w --space = 30 --bw 300 --pvalue 1e-5”. Modification dependent is the parameter “--shiftsize”, which has been set to 200 (H3K4me3) and 600 (H3K27me3, H3K36me3).
The histone modification peak lists were summarized for each genotype and treatment. A peak is accepted, if it is detected in both replicates or in one replicate with a high reliability (MACS fold enrichment > 5.0). Finally, a peak is assigned to be within the promoter region of genes ((TSS) ± 1000 bases) and the gene bodies. If the overlap with a promoter or body region is at least 5%, the respective gene-associated histone is considered as modified.
X- and Y-chromosome is excluded from the analysis.
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: genelist_mm9_modifications.csv: Processed data is stored in comma-separated value format and provides modification profiles of mouse genes. The list includes those genes that show a modification in at least one of the lysines K4, K27 or K36 of histone 3 only. If the lysine is modified, the respective value is '1', otherwise '0' (unmodified). In the respective columns ([Plus|Plus_irr|Minus|Minus_irr]_H3K[4|27|36]me3), Plus/Minus refers to the non-irradiated samples and Plus_irr/Minus_irr refers to the irradiated samples. Furthermore, Plus/Minus identifies the genotype, though Plus is associated with VC-/-Msh2LoxP/LoxP (Msh2+/+) and Minus is associated with VC+/?Msh2LoxP/LoxP (Msh2-/-). In addition, beside the gene's name, the following data is provided: ensID: ensemble transcription ID, chr: chromosome, strand, txStart, txEnd: start and end position.

source_name: jejunum

growth_protocol: The mouse strains B6.SJL-Tg(Villin-Cre)997Gum/J and B6.Cg-Msh2tm2.1Rak/J were obtained from The Jackson Laboratory (Bar Harbor, USA). By crossing both, the conditional Msh2 allele has been placed under the control of the Villin-Cre transgene. Mice were genotyped as described {Kucherlapati, 2010}. VC+/?Msh2LoxP/LoxP (Msh2-/-) and VC-/-Msh2flox/flox (Msh2+/+) mice were bred under specific pathogen-free conditions. A mouse duplet consisted of one Msh2-/- and one Msh2+/+ mouse from one litter.

extract_protocol:
Samples were dissected, shock frozen without delay, and stored in liquid nitrogen until further use. Chromatin was prepared from up to 50 mg tissue using SDS Shearing Buffer and the truChlP Tissue Chromatin Shearing Kit (Covaris, Brighton, UK). ChIPs were run on the IP-Star compact system using the Auto iDeal ChIP-seq kit for histones (Diagenode, Seraing, Belgium).
Library preparations were performed according to the TruSeq LT PCR free or TruSeq Nano DNA Kit instructions (Illumina, San Diego, USA). Sequencing was performed on the Illumina HiSeq 4000 with 76 bp paired-end sequencings.

treatment_protocol: 3-month-old mice were placed in the radiation unit (X-ray generator, Gulmay D3225, round tube 170 mm, radiation level at 2.5 cm: 1.068 Gy/min). One pair of mice of each genotype was irradiated with a total dose of 0.5 Gy, while the other pair was left non-radiated. All mice were killed after 28 days.

tag: strain/background

tag: genotype/variation

value: 4 months

value: jejunum

value: radiation

tag: chip antibody


title: 53486

description:
940_53486
Mouse9, control
processed data file: genelist_mm9_modifications.csv

tag: age

value: H3pan (Diagenode, cat. no. C15200011, lot 001)


title: K5 GFP CD24-

value: GFP

value: lineage-negative tumor cells


title: K5 GFP CD24+


title: P4-1

tag: genotype


title: 53472

description:
812_53472
Mouse8
processed data file: genelist_mm9_modifications.csv

tag: treatment


title: K5 YFP CD24-

value: YFP


title: K5 YFP CD24+


title: K4 CFP CD24+

value: CFP

value: TruSeq


title: P3-2

source_name: gastrulation (12 hpf)_embryo

value: FFRC No.2 strain

value: gastrulation (12 hpf)


title: P3-3

value: WT


title: P6-1

value: 1 dph larva

value: embryo


title: K4 CFP CD24-


title: K4 YFP CD24-


title: Tuberculoid Leprosy skin biopsy 6

city: Sacramento

first: Dennis

middle: Jay

last: Montoya

state: CA

address: 2700 Stockton Blvd #2354

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

data_processing:
Reads with poor quality were trimmed by Trim Galore! (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore) and high quality reads were mapped to the hg19 human genome via STAR (Dobin et al., 2013).  Unmapped reads after human genome alignment were mapped to the Br4923 M. leprae genome (Assembly ASM2668v1).  The sum of exonic reads per gene were counted using HTSeq (Anders) using the GENCODE GRCh37-mapped version Release 24 (Harrow et al., 2012).  Although, M. leprae 23S was calculated by a 96bp region (1343455-1343551).
Genome_build: human hg19 and Br4923 M. leprae genome (Assembly ASM2668v1)
Supplementary_files_format_and_content: Filtered exonic read counts (containing genes with ≥ 5 reads in at least one patient group) from bacterial and human transcriptomes were normalized via DESeq2 (Love et al., 2014) using default parameters, except for basing scaling factors on only human genes.  DESeq2 normalized counts per M. leprae gene or Human gene were output for processed expression files

organism:
Mycobacterium leprae
Homo sapiens

source_name: skin

extract_protocol:
Six millimeter punch biopsies were taken near the border of the lesion and specimens were embedded in OCT medium (Ames, Elkhar, IN) then flash frozen in liquid nitrogen. Frozen tissue sections of nine L-lep, nine RR, and six T-lep frozen skin lesions were cut into multiple ten micron sections and lysed in Qiagen RLT buffer with 0.1% b-mercaptoethanol (Invitrogen).  To ensure efficient lysis of mycobacterial cell wall, lysates were homogenized with 0.1mm silica beads (MP Biomedicals, Santa Ana, CA) in the FastPrep3000 twice at a setting of 6.5 for 45s. RNA was extracted via Qiagen AllPrep Kit (Qiagen, Hilden, Germany).
Ribosomal RNA was depleted with the Illumina Ribo-Zero Gold rRNA Removal Kit (Epidemiology) before sequencing library preparation with the Illumina Truseq Stranded Total RNA Sample Preparation Kit. Libraries were sequenced on the HiSeq2000 Sequencer (Illumina) at single-end 50 bp reads.

tag: diagnosis

value: Tuberculoid Leprosy (TL)

tag: host gender

value: Male

value: skin


title: K4 YFP CD24+

tag: strain

tag: tumor


title: 53468

description:
812_53468
Mouse8
processed data file: genelist_mm9_modifications.csv

value: 4 months

value: H3K4me3 (Diagenode)


title: Tuberculoid Leprosy skin biopsy 5


title: 53474

description:
812_53474
Mouse8
processed data file: genelist_mm9_modifications.csv

value: jejunum

value: H3K27me3 (Diagenode, cat. no. C15410069, lot A1821D13)


title: K4 RFP CD24-

tag: fluorescent marker

value: RFP

tag: cell population


title: 53478

description:
940_53478
Mouse9
processed data file: genelist_mm9_modifications.csv

value: radiation


title: 53484

description:
940_53484
Mouse9
processed data file: genelist_mm9_modifications.csv


title: P3-1


title: P2-3

source_name: blastocyst (6 hpf)_embryo

value: blastocyst (6 hpf)


title: P2-2


title: 53494

description:
399_53494
Mouse7
processed data file: genelist_mm9_modifications.csv


title: 53492

description:
399_53492
Mouse7
processed data file: genelist_mm9_modifications.csv


title: K4 GFP CD24+

value: GFP

value: lineage-negative tumor cells

tag: sequencing date

tag: sample id


title: K4 RFP CD24+

tag: library preparation protocol

value: TruSeq


title: Tuberculoid Leprosy skin biopsy 4

value: Female

tag: tissue


title: Tuberculoid Leprosy skin biopsy 3


title: 53488

description:
399_53488
Mouse7
processed data file: genelist_mm9_modifications.csv


title: P2-1

value: FFRC No.2 strain

value: WT

tag: developmental stage


title: Tuberculoid Leprosy skin biopsy 2


title: P1-2

source_name: cleavage (2 hours post-fertilization hpf)_embryo

value: embryo


title: 53476

description:
812_53476
Mouse8, control
processed data file: genelist_mm9_modifications.csv

tag: strain/background

value: H3pan (Diagenode, cat. no. C15200011, lot 001)


title: 44767

description:
347_44767
Mouse5
processed data file: genelist_mm9_modifications.csv

tag: genotype/variation


title: NCH421k

city: Luxembourg

first: Arnaud

last: Muller

address: 84 Val Fleuri

department: DONC

country: Luxembourg

institute: LIH

description: FACS-sorted viable cells

data_processing:
The FASTQ files were assembled from the raw BCL files using Illumina’s bcl2fastq converter and ran through the FASTQC codes [Babraham bioinformatics; https://www.bioinformatics.babraham.ac.uk/projects/fastqc/] to check for consistency in library qualities. . The monitored quality assessment parameters were a) quality per base sequence (especially for the read 2 of the gene), b) per base N content, c) per base sequence content and d) overrepresented sequences. Libraries that showed significant deviation were re-sequenced.
The FASTQ files were then merged and converted to binaries using PICARD’s fastqtosam algorithm.
The sequencing reads were converted to a digital gene expression matrix (DGE) using the Drop-seq bioinformatics pipeline from PMID: 26000488
Genome_build: hg19
Supplementary_files_format_and_content: The data is provided in the format of digital expression matrix (DGE), containing unfiltered events representing cell barcodes detected upon scRNA-seq. tab-delimited text files include raw counts

molecule: polyA RNA

source_name: GBM cell cultures in vitro

growth_protocol: Patient-derived orthotopic xenografts (PDOXs) were derived from 3D tumor spheroids implanted intracranially to nude mice. NCH644 and NCH421k cells were cultured in serum-free stem cell media To obtain a pure population of single viable cells all GBM cultures were FACS-sorted (NCH644, NCH421k bulk cultures and NCH644 subpopulations P2 and P6). For GBM PDOXs we have pre-selected hCD90 positive tumor cells. FACS-sorted populations were collected in HBSS, 0.5% BSA at 4°C.

extract_protocol:
Experiments followed the original Drop-seq protocol (PMID: 26000488) with minor changes described in PMID: 30206190.
The 3’ end enriched cDNA libraries were prepared by tagmentation reaction of 600 pg cDNA library using the standard Nextera XT tagmentation kit (Illumina). Reactions were performed according to the manufacturer’s instructions, except for the 400 nM primer sets.

treatment_protocol: No treatment was performed

value: cells derived from in vitro culture

value: No treatment


title: P1-3

value: cleavage (2 hours post-fertilization hpf)


title: 53498

description:
344_53498
Mouse6, in replacement for Mouse5, H3K27me3 (measurement failed)
processed data file: genelist_mm9_modifications.csv

value: 4 months

tag: chip antibody


title: Reversal reaction leprosy skin biopsy 9

value: Reversal Reaction Leprosy (RR)

tag: age

value: Male

value: skin


title: NCH644 subpopulation 2

description: FACS-sorted CD133+CD44-A2B5+CD15+ cells


title: Reversal reaction leprosy skin biopsy 8A


title: P1-1

tag: genotype


title: NCH644 subpopulation 6

description: FACS-sorted CD133+CD44+A2B5+CD15+ cells

tag: treatment


title: Tuberculoid Leprosy skin biopsy 1

tag: diagnosis

value: Tuberculoid Leprosy (TL)


title: NCH644

description: FACS-sorted viable cells


title: 44766

description:
347_44766
Mouse5
processed data file: genelist_mm9_modifications.csv

value: jejunum

value: H3K4me3 (Diagenode)


title: PDOX P13

description: FACS-sorted hCD90 PDOX tumor cells

source_name: tumor cells derived from GBM PDOX

value: cells derived from tissue


title: 53500

description:
344_53500
Mouse6, control, in replacement for Mouse5, H3K27me3 (measurement failed)
processed data file: genelist_mm9_modifications.csv


title: Reversal reaction leprosy skin biopsy 8B


title: 44765

description:
347_44765
Mouse5, control
processed data file: genelist_mm9_modifications.csv


title: Reversal reaction leprosy skin biopsy 7

tag: host gender


title: C11_Treg_H3K4me1

source_name: Effector memory TREG cells

tag: disease state

value: control

tag: individual

value: Peripheral Blood

tag: cell type

value: Effector memory TREG cells

value: H3K4me1 (Abcam, ab8895)


title: PDOX P3

description: FACS-sorted hCD90 PDOX tumor cells


title: Reversal reaction leprosy skin biopsy 6

value: Female


title: 53496

description:
399_53496
Mouse7, control
processed data file: genelist_mm9_modifications.csv

value: radiation

value: H3pan (Diagenode, cat. no. C15200011, lot 001)


title: 43580

description:
813_43580
Mouse4
processed data file: genelist_mm9_modifications.csv

value: H3K27me3 (Diagenode, cat. no. C15410069, lot A1821D13)


title: 43578

description:
813_43578
Mouse4
processed data file: genelist_mm9_modifications.csv


title: Reversal reaction leprosy skin biopsy 4


title: IMR32_400THZ_1

city: Boston

first: Ruben

last: Dries

address: 360 Longwood Ave

department: Computational Biology

institute: DFCI

hyb_protocol: Following fragmentation, 12.5 ug of aRNA were hybridized at 45C for 16 hr at 60RPM on GeneChip Arrays (PrimeView). GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manurfacturer's instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 and images were extracted with Affymetrix GeneChip Expression Console.

data_processing: Microarray data were analyzed using a custom CDF file (GPL16043) that contained the mapping information of the ERCC probes used in the spike-in RNAs. The data were analyzed with Bioconductor using the MAS5 normalization method. Briefly, all chip data were imported in R (version 3.1.3) using the affy package, converted into expression values using the expresso command, normalized to take into account the different numbers of cells and spike-ins used in the different experiments and renormalized using loess regression fitted to the spike-in probes.

source_name: IMR32 cells

label_protocol: Biotinylated aRNA was prepared according to the standard Affymetrix protocol from 100 ng of total RNA (GeneChip 3' IVT Express Kit User Manual, Affymetrix).

growth_protocol: IMR-32 and Kelly cells were grown in RPMI-1640 media supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin

extract_protocol: Biological duplicates (equivalent to 5 x 10e6 cells per replicate) were collected and homogenized in 1ml of TRIzol Reagent (Ambion), purified using the mirVANA miRNA isolation kit (Ambion) following the manufacturer’s instructions and re-suspended in 50 ml nuclease-free water  (Ambion). Total RNA was spiked-in with ERCC RNA Spike-In Mix (Ambion), treated with DNA-freeTM DNase I (Ambion) and analyzed on an Agilent 2100 Bioanalyzer (Agilent Technologies) for integrity.

treatment_protocol: Cells were incubated for 6 h in the presence of DMSO or THZ531 (100nM, 400nM) before performing RNA extraction.

tag: cell line


title: IMR32_400THZ_2


title: IMR_GFP_rep1

description:
processed data file:
all_IMR_CDK_KD_sub_peaks.narrowPeak
IMR_polyA_GFP_forwardRawCov.bw
IMR_polyA_GFP_reverseRawCov.bw

data_processing:
Single-end 100bp reads were filtered with bbduk.sh and parameters “k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=20 minlength=75 ref=truseq_rna.fa.gz”
STAR (v2.5.1b) was used to align reads to the human genome (GRCh38) with the following parameters “--outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD --outSAMtype BAM SortedByCoordinate”.
Strand specific coverage profiles were created with the bamCoverage command (DeepTools v2.5.4) with parameters “--normalizeUsingRPKM –filterRNAstrand –bs 50".
Biological replicates were merged using "samtools merge" and processed as described for the individual replicates.
PolyA-seq peaks were called using MACS2 (v 2.1.1) and parameters “--nomodel --extsize 100 --shift 0”.
Genome_build: GRCh38
Supplementary_files_format_and_content: Peaks and bigWig coverage files for merged replicates.

growth_protocol: IMR-32 cells were grown in RPMI-1640 media supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin

extract_protocol:
Biological duplicated were collected and RNA extraction was performed with TRIzol (Ambion) following the manufacturers’ instructions. Total RNA was treated with DNase I (Invitrogen).
Sequencing libraries were prepared with the RNA-seq library kit (QuantSeq 3’ mRNA Sequencing REV, Lexogen) following the manufacturers’ instructions.

treatment_protocol: pLKO.1 plasmids containing shRNA sequences targeting CDK12 and CDK13 were obtained from the RNAi Consortium of the Broad Institute (Broad Institute, Cambridge, MA); Briefly, the constructs were transfected into HEK293T cells with helper plasmids: pCMV-dR8.91 and pMD2.G-VSV-for virus production. Cells were then transduced with virus, followed by puromycin selection for two days.

value: neuroblastoma cells

value: shGFP


title: IMR32_100_1


title: IMR_GFP_rep2


title: IMR_CDK13_sh704_rep2

description:
processed data file:
all_IMR_CDK_KD_sub_peaks.narrowPeak
IMR_polyA_CDK13_sh_forwardRawCov.bw
IMR_polyA_CDK13_sh_reverseRawCov.bw

value: CDK13 sh704


title: IMR32_100_2


title: 43577

description:
813_43577
Mouse4
processed data file: genelist_mm9_modifications.csv

value: 4 months


title: IMR32_DMSO_2

value: DMSO


title: Reversal reaction leprosy skin biopsy 2

value: Reversal Reaction Leprosy (RR)

value: skin


title: PDOX P8

description: FACS-sorted hCD90 PDOX tumor cells

value: No treatment


title: IMR32_DMSO_1


title: IMR_CDK13_sh704_rep1


title: 44749

description:
811_44749
Mouse3
processed data file: genelist_mm9_modifications.csv

value: jejunum


title: Reversal reaction leprosy skin biopsy 5


title: Reversal reaction leprosy skin biopsy 3


title: Lepromatous leprosy skin biopsy 9

value: Lepromatous leprosy (LL)


title: IMR_CDK13_sh701_rep2

value: CDK13 sh701


title: IMR_CDK13_sh701_rep1


title: Kelly_100THZ_2

source_name: Kelly cells

value: Kelly


title: Kelly_400THZ_1


title: Lepromatous leprosy skin biopsy 8


title: 43567

description:
813_43567
Mouse4, control
processed data file: genelist_mm9_modifications.csv


title: 44746

description:
811_44746
Mouse3
processed data file: genelist_mm9_modifications.csv

value: H3K4me3 (Diagenode)


title: IMR_CDK12_sh98_rep2

description:
processed data file:
all_IMR_CDK_KD_sub_peaks.narrowPeak
IMR_polyA_CDK12_sh_forwardRawCov.bw
IMR_polyA_CDK12_sh_reverseRawCov.bw

value: CDK12 sh98


title: Kelly_400THZ_2


title: 44747

description:
811_44747
Mouse3
processed data file: genelist_mm9_modifications.csv


title: Reversal reaction leprosy skin biopsy 1

value: Female


title: Kelly_100THZ_1


title: Lepromatous leprosy skin biopsy 7A


title: 43583

description:
345_43583
Mouse2
processed data file: genelist_mm9_modifications.csv

value: radiation


title: IMR_CDK12_sh98_rep1


title: Lepromatous leprosy skin biopsy 7B


title: Kelly_DMSO_2


title: Lepromatous leprosy skin biopsy 5

value: Male


title: Lepromatous leprosy skin biopsy 6


title: IMR_CDK12_sh22_rep2

value: neuroblastoma cells

value: CDK12 sh22


title: IMR_CDK12_sh22_rep1


title: 53504

description:
345_53504
Mouse2, control, for 53502
processed data file: genelist_mm9_modifications.csv

value: H3pan (Diagenode, cat. no. C15200011, lot 001)


title: Lepromatous leprosy skin biopsy 4


title: 43585

description:
345_43585
Mouse2
processed data file: genelist_mm9_modifications.csv

value: 4 months

value: H3K27me3 (Diagenode, cat. no. C15410069, lot A1821D13)


title: Kelly_E9R_THZ531_6h_1 [RNA-seq]

description:
processed data file:
all_Kelly_KellyE9R_polyAseq_peaks.narrowPeak

growth_protocol: Kelly and Kelly E9R  cells were grown in RPMI-1640 media supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin

treatment_protocol: Cells were incubated for 6 hours in the presence of DMSO or THZ531  (400nM) before performing RNA extraction.

value: Kelly E9R

value: THZ531 6h


title: 44745

description:
811_44745
Mouse3, control
processed data file: genelist_mm9_modifications.csv


title: 53502

description:
345_53502
Mouse2
processed data file: genelist_mm9_modifications.csv


title: Kelly_E9R_DMSO_2 [RNA-seq]

value: DMSO


title: Lepromatous leprosy skin biopsy 3

value: skin


title: 43561

description:
343_43561
Mouse1
processed data file: genelist_mm9_modifications.csv

value: jejunum


title: Lepromatous leprosy skin biopsy 2

value: Lepromatous leprosy (LL)


title: 43555

description:
343_43555
Mouse1
processed data file: genelist_mm9_modifications.csv


title: 43581

description:
345_43581
Mouse2, control, for 43583, 43585
processed data file: genelist_mm9_modifications.csv


title: 43559

description:
343_43559
Mouse1
processed data file: genelist_mm9_modifications.csv


title: Lepromatous leprosy skin biopsy 1


title: 43556

description:
343_43556
Mouse1, control
processed data file: genelist_mm9_modifications.csv


title: Kelly_THZ531_6h_2 [RNA-seq]

value: Kelly


title: Kelly_THZ531_6h_1 [RNA-seq]


title: Kelly_E9R_THZ531_6h_2 [RNA-seq]


title: Kelly_DMSO_1 [RNA-seq]


title: Kelly_DMSO_1


title: siZNF598 replicate 2 IL-1

city: Copenhagen

first: Christopher

last: Tiedje

address: Blegdamsvej 3B

department: Department of Molecular and Cellular Medicine (ICMM)

country: Denmark

institute: University of Copenhagen

description: NEBNext index 12 primer

data_processing:
All steps except demultiplexing were performed in the Galaxy suite.
After demultiplexing fastq files were groomed (FASTQ Groomer Galaxy Version 1.0.4) and adapter- and quality-trimmed using "Trim Galore!" (Galaxy Version 0.4.2). The reads were then mapped against hg19 (b37) using RNA STAR (Galaxy Version 2.5.2b-0)
For differential gene expression analysis, count tables from the mapped sequencing data were generated and used in DeSeq2 to identify regulated transcripts.
Genome_build: hg19 (b37)
Supplementary_files_format_and_content: The different DeSeq2 comparisons are provided as tab-delimited .txt files

source_name: bone

growth_protocol: U2OS cells were maintained and propagated in DMEM medium supplemented with 10% fetal calf serum and Pen/Strep

extract_protocol:
After stimulation cells were directly lyzed in TRIZol and total RNAs were extracted according to the manufacturer's protocol
Total RNA libraries were generated using the NEBNext Ultra II Directional RNA Library Kit (New England Biolabs #E7765) after rRNA-depletion using the NEBNext rRNA depletion kit (New England Biolabs #6310). To facilitate multiplexing oif libraries indexed primers (New England Biolabs #E7335) were used. 500 ng of total RNA per sample were used as input material.

treatment_protocol: Cells were transcfected with either a mis-match (siMM) or ZNF598-specific (siZNF598) siRNAs using RNAiMAX (Life Technologies) and were left non-stimulated (ns) or stimulated with IL-1 beta (2ng/ml final concentration, Peprotech) for 1h

value: U2OS osteosarcoma, epithelial

value: 1h IL-1 beta (2ng/ml final)

value: siZNF598, specific


title: siZNF598 replicate 2 ns

description: NEBNext index 9 primer

value: non-stimulated


title: Kelly_DMSO_2 [RNA-seq]


title: Kelly_E9R_DMSO_1 [RNA-seq]


title: siCTRL replicate 1 IL-1

description: NEBNext index 3 primer

treatment_protocol: Cells were transcfected with either a mis-match Control (siCTRL) or ZNF598-specific (siZNF598) siRNAs using RNAiMAX (Life Technologies) and were left non-stimulated (ns) or stimulated with IL-1 beta (2ng/ml final concentration, Peprotech) for 1h

value: siMM, control


title: siZNF598 replicate 1 IL-1

description: NEBNext index 7 primer


title: Sub-acute C2 rep4

city: Toronto

first: Stephenie

last: Prokopec

state: Ontario

address: 661 University Avenue, Suite 510

country: Canada

institute: Ontario Institute for Cancer Research

hyb_protocol: Manufacturer's recommended protocols as followed by the TCAG Facility at the Hospital for Sick Kid's in Toronto, Canada

data_processing: Raw array data (CEL files) were loaded into the R statistical environment using the affy package (v1.48.0) of the BioConductor library. Data was investigated for distributional homogeneity, then pre-processed using the RMA algorithm. The custom Probe to Entrez Gene ID map, ragene20strnentrezgcdf (v21.0.0) was used for annotation.

organism: Rattus norvegicus

source_name: C2 treated_sub-acute

growth_protocol: Animals were housed individually (acute exposure) or groups of 2-3 (sub-acute exposure) in ventilated plastic cages lined with aspen wood bedding. The housing environment was maintained at 22 ± 1°C with relative humidity at 38-75% (average 50%). Artificial illumination was maintained on a 12/12 hour light/dark cycle. Commercial pelleted rat chow and filtered, UV-irradiated tap water were available ad libitum.

extract_protocol: Total RNA was isolated using the Sigma-Aldrich GenElute™ Mammalian total RNA isolation kit at the University of Helsinki (Finland).

treatment_protocol: Animals in the acute exposure group were treated by oral gavage with a single bolus of either one dosage of C2 (100 mg/kg) dissolved in PEG-400 vehicle or vehicle alone (5mL/kg) on day 0 and samples collected on day 1. For the sub-acute exposure, animals were administered repeated doses of C2 (100 mg/kg/day) or vehicle control (PEG-400, 5ml/kg/day) daily for 5 consecutive days (days 0-4) and euthanized on day 9.

tag: strain

value: Sprague-Dawley

tag: Sex

value: male

value: 10 weeks

value: repeat dose C2

tag: exposure

value: 10 days

value: liver


title: Sub-acute C2 rep3

scan_protocol: Manufacturer's recommended protocols as followed by the TCAG Facility at the Hospital for Sick Kid's in Toronto, Canada

tag: tissue


title: siCTRL replicate 2 IL-1

description: NEBNext index 5 primer


title: siCTRL replicate 1 ns

description: NEBNext index 2 primer


title: siZNF598 replicate 1 ns

description: NEBNext index 6 primer


title: IMR_THZ_30min_2

description:
nascent RNA
processed data files:
IMR_THZ_30min_forwardCov.bw
IMR_THZ_30min_reverseCov.bw
IMR_THZ_30min_2_forwardCov.bw
IMR_THZ_30min_2_reverseCov.bw

data_processing:
Paired-end 75bp reads were mapped to the human genome (GRCh38) concatenated with ERCC spike-in sequences using STAR (v2.5.1b) and default parameters.
Properly mapped reads were extracted using samtools (v1.3.1) and parameters “-q 7 and –f 83,99,147,163”.
Library size normalization was based on individual spike-in reads counted with samtools idxstats and used as input for estimateSizeFactorsForMatrix (DESeq2).
Strand specific coverage files were created with bamCoverage (DeepTools v2.5.4) with previously calculated sizefactors and parameters “--scaleFactor --normalizeUsingRPKM –filterRNAstrand –bs 100".
Biological replicates were merged using "samtools merge" and processed as described for the individual replicates.
Genome_build: GRCh38
Supplementary_files_format_and_content: bigWig coverage files for both individual replicates and merged replicates.

growth_protocol: IMR-32  cells were grown in RPMI-1640 media supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin

extract_protocol:
RNA extraction was performed with TRIzol (Ambion) following the manufacturers’ instructions. Total RNA was treated with DNase I (Invitrogen). Subsequently, the purified RNA was fragmented on a BioRuptor Next Gen (Diagenode) at high power for one cycle of 30’’/30’’ ON/OFF.
Sequencing libraries were prepared with the RNA-seq library kit (TruSeq Stranded Total RNA RiboZero Gold, Illumina)

treatment_protocol: Cells were incubated for 30min and 2 hours in the presence of DMSO or THZ531  (400nM) and labeled in media for 10 min with 500 μM 4-thiouridine before performing RNA extraction.

value: THZ531 30min

tag: cancer

value: Neuroblastoma


title: siCTRL replicate 2 ns

description: NEBNext index 4 primer


title: Sub-acute C2 rep1

label_protocol: Manufacturer's recommended protocols as followed by the TCAG Facility at the Hospital for Sick Kid's in Toronto, Canada


title: IMR_THZ_2h_1

description:
nascent RNA
processed data files:
IMR_THZ_2h_forwardCov.bw
IMR_THZ_2h_reverseCov.bw
IMR_THZ_2h_1_forwardCov.bw
IMR_THZ_2h_1_reverseCov.bw

value: THZ531 2h


title: Sub-acute PEG-400 rep6

source_name: PEG-400 treated_sub-acute

value: repeat dose PEG-400 vehicle


title: IMR_THZ_30min_3

description:
nascent RNA
processed data files:
IMR_THZ_30min_forwardCov.bw
IMR_THZ_30min_reverseCov.bw
IMR_THZ_30min_3_forwardCov.bw
IMR_THZ_30min_3_reverseCov.bw


title: IMR_DMSO_2

description:
nascent RNA
processed data files:
IMR_DMSO_forwardCov.bw (merged)
IMR_DMSO_reverseCov.bw (merged)
IMR_DMSO_2_forwardCov.bw
IMR_DMSO_2_reverseCov.bw

value: DMSO


title: Sub-acute PEG-400 rep3


title: IMR_THZ_30min_1

description:
nascent RNA
processed data files:
IMR_THZ_30min_forwardCov.bw
IMR_THZ_30min_reverseCov.bw
IMR_THZ_30min_1_forwardCov.bw
IMR_THZ_30min_1_reverseCov.bw


title: IMR_DMSO_1

description:
nascent RNA
processed data files:
IMR_DMSO_forwardCov.bw (merged)
IMR_DMSO_reverseCov.bw (merged)
IMR_DMSO_1_forwardCov.bw
IMR_DMSO_1_reverseCov.bw


title: Sub-acute C2 rep2


title: Acute C2 rep3

source_name: C2 treated_acute

value: single dose C2

value: 1 day


title: Sub-acute PEG-400 rep1


title: IMR_THZ_2h_3

description:
nascent RNA
processed data files:
IMR_THZ_2h_forwardCov.bw
IMR_THZ_2h_reverseCov.bw
IMR_THZ_2h_3_forwardCov.bw
IMR_THZ_2h_3_reverseCov.bw


title: Sub-acute PEG-400 rep5


title: Sub-acute PEG-400 rep2


title: RNA-seq_THZ_6h_2

description:
processed data files:
all_quantseq_peaks.narrowPeak
IMR_quantseq_THZ_6h.selected_forwardCov.bw
IMR_quantseq_THZ_6h.selected_reverseCov.bw

data_processing:
Single-end 100bp reads were filtered with bbduk.sh and parameters “k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=20 minlength=75 ref=truseq_rna.fa.gz”
STAR (v2.5.1b) was used to align reads to the human genome (GRCh38) with the following parameters “--outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD --outSAMtype BAM SortedByCoordinate”.
Strand specific coverage profiles were created with the bamCoverage command (DeepTools v2.5.4) with parameters “--normalizeUsingRPKM –filterRNAstrand –bs 50".
Biological replicates were merged using "samtools merge" and processed as described for the individual replicates.
PolyA-seq peaks were called using MACS2 (v 2.1.1) and parameters “--nomodel --extsize 100 --shift 0”.
Genome_build: GRCh38
Supplementary_files_format_and_content: Peaks and bigWig coverage files for both individual replicates and merged replicates.

treatment_protocol: Cells were incubated for 2 and 6 hours in the presence of DMSO or THZ531  (400nM) before performing RNA extraction.

value: THZ531 6h


title: Acute PEG-400 rep6

source_name: PEG-400 treated_acute

value: single dose PEG-400 vehicle


title: Acute C2 rep1


title: IMR_THZ_2h_2

description:
nascent RNA
processed data files:
IMR_THZ_2h_forwardCov.bw
IMR_THZ_2h_reverseCov.bw
IMR_THZ_2h_2_forwardCov.bw
IMR_THZ_2h_2_reverseCov.bw


title: Acute C2 rep6


title: 21KO10_1_3

city: Nagoya

first: Chieko

last: Sugita

state: Aichi

address: Chikusa-ku Furo-cho

department: Center for Gene Research

country: Japan

institute: Nagoya University

description: Gene expression of 21KO-10 protonema cells

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >16.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent custom Oligo Microarrays (G2509F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent Sure Scan using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5um high sensitivity, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5 (Agilent) using default parameters (protocol GE1-1105_Oct12 and Grid: 084494_D_F_20161121) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Physcomitrium patens

source_name: 4 day old 21KO-10 protonemata

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 150 ng RNA using the One-Color Low Input Quick-Amp WT Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop 2000 Spectrophotometer.

growth_protocol: protonemal tissue was grown on cellophane-overlaid BCD media supplemented with 50mM ammonium tartarate  and 0.5% glucose under continuous light (30 micromole photons m-2 sec-1)at 25ºC

extract_protocol: Total cellular RNA was extracted with Isogen II (Nippon gene), purified with phenol/chloroform/isoamyl alcohol, and treated with DNase I (TaKaRa).

value: PpPPR_21 Knock OUT mutant #10

value: protonemata


title: IMR_DMSO_3

description:
nascent RNA
processed data files:
IMR_DMSO_forwardCov.bw (merged)
IMR_DMSO_reverseCov.bw (merged)
IMR_DMSO_3_forwardCov.bw
IMR_DMSO_3_reverseCov.bw


title: RNA-seq_THZ_6h_1


title: Sub-acute PEG-400 rep4

value: Sprague-Dawley


title: Acute C2 rep5

value: male


title: Acute PEG-400 rep3

value: 10 weeks


title: Acute PEG-400 rep5


title: 21KO184_2_3

description: Gene expression of 21KO-184 protonema cells

source_name: 4 day old 21KO-184 protonemata

value: PpPPR_21 Knock OUT mutant #184


title: Acute C2 rep4


title: RNA-seq_THZ_2h_2

description:
processed data files:
all_quantseq_peaks.narrowPeak
IMR_quantseq_THZ_2h.selected_forwardCov.bw
IMR_quantseq_THZ_2h.selected_reverseCov.bw


title: Acute PEG-400 rep4


title: Acute C2 rep2


title: RNA-seq_DMSO_2

description:
processed data files:
all_quantseq_peaks.narrowPeak
IMR_quantseq_DMSO.selected_forwardCov.bw
IMR_quantseq_DMSO.selected_reverseCov.bw


title: WT + CP Rep 3

city: Nashville

first: Eric

last: Skaar

state: TN

department: Pathology, Microbiology, and Immunology

institute: Vanderbilt University Medical Center

data_processing:
Illumina CASAVA-1.8.2 for FASTQ conversion and demultiplexing
Sequences were processed using Bayesian adapter trimmer Scythe v0.992 to trim 3 = adapter contaminants from reads.
EDGE-pro v1.3 was used to align reads with Bowtie2 v2.1.0
FASTA of the reference genome sequence, protein translation table with coordinates of protein coding genes, and a table with coordinates of tRNA and rRNA genes were downloaded from NCBI.
EDGE-pro was run with default parameters, except for defining read length as 50 bp and using 16 threads on a 64-core Linux server.
Genome_build: NCBI Acinetobacter baumannii ATCC 17978 uid17477
Supplementary_files_format_and_content: Excel file with base mean expression in each condition, fold change, p value, and adjusted p value

organism: Acinetobacter baumannii

source_name: WT A. baumannii strain ATCC 17978

growth_protocol: Bacterial cultures were grown in 60% LB, 40% CP buffer (20 mM Tris-HCL pH 7.5, 100 mM NaCl, 5 mM 2-mercaptoethanol, 3 mM CaCl2) with 250 ug/ml CP added for 7 hours at 37 C.

extract_protocol:
Bacterial cultures were frozen in 1:1 ice cold acetone:ethanol. They were later thawed and RNA was extracted with TRIzol reagent and Qiagen Rneasy kit. Illumina TruSeq RNA Sample Prep Kit was used with 1.5 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: wild type

value: 250 ug/ml calprotectin (CP) added for 7 hrs


title: RNA-seq_DMSO_1


title: RNA-seq_THZ_2h_1


title: WT + CP Rep 1


title: WT + CP Rep 2


title: Acute PEG-400 rep1

value: liver


title: WT Rep 3


title: WT Rep 2


title: Acute PEG-400 rep2


title: Type3 D2; Type3 condition stimulated blood ILC2

city: Utrecht

first: Balthasar

middle: Adrianus

last: Heesters

state: Utrecht

address: Universiteitsweg 99

department: Pharmaceutical Sciences

country: Netherlands

institute: Utrecht University

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: R/Bioconductor, limma rma

source_name: ILC2 from peripheral blood after 7 day culture with IL2, IL-1β, IL-23, and TGF-β.

label_protocol: Briefly, PB was enriched for ILCs by immunomagnetic cell sorting, using a negative selection of CD3, CD14, CD16 and CD19 with Mojosort magnetic cell separation system (BioLegend, San Diego, CA, USA) Tonsillar mononuclear cells were depleted of CD3 and CD19 cells by MACS depletion. The cells suspensions were stained with antibodies against Lineage (CD1a, CD3, CD4, CD5, CD14, CD19, CD16, CD34, CD94, CD123, BDCA2, TCRαβ, TCRγδ, FcER1α), CD45, CD161, CD127, CD117, CRTH2, KLRG1, NKp44, NKp46, CD56 and IL-1R1. Cells were sorted on a FACSAria, purity of the sorted cells in all experiments was >99%.

growth_protocol: ILC2s were cultured for 7 days in Yssels with 1% human serum with either IL-2 (20 U/ml), IL-33 (and all other cytokines 50 ng/ml), and TSLP or IL-2, IL-1β, IL-23, and TGF-β.

extract_protocol: Buffy coats were provided by the blood bank (Sanquin, Amsterdam). The collection and use of all human samples was approved by the Medical Ethical Committee of the AMC and with informed consent. Peripheral blood were isolated by Ficoll-Hypaque density gradient (Lymphoprep; Axis-Shield). Cell suspensions were filtered through a 70- µm cell strainer. Subsequently, ILCs were isolated as described previously .

value: Peripheral Blood

tag: donor


title: Mouse1 with rCPS1 rep2

city: Ann Arbor

first: M. Bishr

last: Omary

state: Michigan

address: Rm 7720 Medical Science II, 1137 E. Catherine St.

department: Molecular and Integrative Physiology

institute: University of Michigan

description:
8 weeks old FVB/N male mice
Gene expression data from hepatic macrophages of mouse injected with recombinant CPS1 and acetaminophen

hyb_protocol: Following labeling procedure, 2.53 ug of cDNA were hybridized at 48C on [Array], and were washed and stained using the Affymetrix GeneTitan system (software version 4.3.0.1592)

scan_protocol: Arrays were scanned using the Affymetrix GeneTitan system (software version 4.3.0.1592)

data_processing: Data was analyzed using the oligo and limma Bioconductor package implemented in the R-statistical language version 3.4.0. RMA was used to fit log2 transformed expression values.

source_name: 8 weeks old FVB/N male mice

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix Plus WT kit protocol (GeneChip® WT Plus Reagent Kit Manual P/N 703174 Rev. 2) from 400 ng total RNA

extract_protocol: Qiagen Rneasy protocols

treatment_protocol: Recombinant CPS1 (50ug) or transferrin (25ug) by tail vein injection and acetaminophen (350 mg/kg) by intraperitoneal injection were administered into FVB/N male mice.

value: 8 wk

value: FVB/N


title: Type3 D1; Type3 condition stimulated blood ILC2

value: from peripheral blood after 7 day culture with IL2, IL-1β, IL-23, and TGF-β.


title: Type3 D3; Type3 condition stimulated blood ILC2


title: WT Rep 1

tag: genotype/variation


title: Type2 D3; Type2 condition stimulated blood ILC2

source_name: ILC2 from peripheral blood after 7 day culture with IL2, IL33 and TSLP


title: Type2 D2; Type2 condition stimulated blood ILC2

value: from peripheral blood after 7 day culture with IL2, IL33 and TSLP


title: P. salmonis_cell intracellular vs. free cultures bacterium_exponential phase_rep3

city: Santiago

first: Rodrigo

last: Pulgar

state: Metropolitana

address: El Líbano 5524, Macul

department: INTA

country: Chile

institute: University of Chile

description: Bacterium grown in cell free media until exponential phase

hyb_protocol: Microarray hybridization  Cy3 and Cy5 labeled RNA samples were hybridized in the 8 x 15 K slides using Agilent Gene Expression Hybridization Kit. Briefly, 300 ng of each amplified and labeled samples were mixed with blocking agent and fragmentation buffer, incubated 30 minutes at 60°C, followed by 1 min on ice, and then 2x hybridization buffer was added. The mix was added onto the slide and incubated in a hybridization oven at 65°C for 17 hours. Then, slides were sequentially rinsed with GE Wash Buffer 1 at room temperature for 1 min and then with GE Wash Buffer 2 for 1 min at 37°C. Finally, slides were dried at room temperature.

scan_protocol: Microarrays slides were scanned using the Microarray Scanner (G2565CA) from Agilent Technologies at 5 μm resolution and at high and low photo multiplier voltages to optimize the dynamic range of the image. Data were extracted from images using the Agilent Feature Extraction 10.7.3.1 software (Agilent Technologies) with default protocols and settings. Quality of microarray images was examined by inspection of foreground (FG) and background (BG) values of red (R) and green (G) channels in each slide

data_processing:
Data were background corrected using a normexp procedure and normalized between channels using an intensity dependent normalization procedure (loess). Linear models were fitted to log2 expression data for each gene across the microarrays. In each case, the coefficient of the model represented the estimated fold-change between samples. Values were used to compute a moderated t-statistics using a simple Bayesian model and raw p-values were corrected for multiple testing using a false discovery rate (FDR) of 0.05.
Genes with FDR < 0.05 and a fold-change threshold > 2 fold were acknowledged as differentially expressed (DEGs). All calculations were performed on R statistical software environment running on Linux or Windows machine, using limma package. Values represent loess normalized log2 (intracellular/cell free cultured bacterium)

organism: Piscirickettsia salmonis

source_name: cell free cultures bacterium grown until exponential phase

label_protocol: Labeling of RNA samples  One hundred ng of RNA isolated from exponentially growing P. salmonis or from P. salmonis-infected SHK-1 cells were labeled using Low Input Quick Amp kit (Agilent) following manufacturer´s instructions. The resulting cRNA with incorporated CNTP-Cy3 or CNTP-Cy5 was purified using RNeasy Kit (QIAGen). The quantity and quality of cRNA and label incorporation were determined by NanoQuant Spectrophotometer (Tecan Technologies).

extract_protocol: RNA extraction from P. salmonis   To isolate total RNA from exponential-phase P. salmonis cultures, cells were collected from the broth by centrifugation and the pellet was resuspended in 0.5 mL of RNAWIZ (Ambion), mixed with 200 µL of zirconia beads and bacterial cells were disrupted using the Fast-prep 24 (MP) in three cycles of 40 s at 5.0 M/s with intervals of 5 min on ice. The bacterial lysate was recovered by centrifugation and zirconia beads were discarded. The bacterial lysate was mixed with 0.2 volumes of chloroform and then centrifuged. The aqueous phase was mixed with 0.5 volumes of 100% ethanol and bacterial RNA was purified by passing through a filter cartridge (Quiagen), successive washes were carried out according to manufacturer´s instructions. RNA was eluted with 0.1 mL of TE buffer in DEPC-treated water and incubated for 30 min at 37°C with RNase-Free DNase I (Ambion) to remove residual genomic DNA. The quantity and quality of RNA were determined by measuring the absorbance at 260/280 nm using a NanoQuant Spectrophotometer (Tecan Technologies) and integrity was confirmed using 2200 TapeStation Bioanalyzer (Agilent Technologies).    RNA extraction from P. salmonis-infected SHK-1 cells  To isolate RNA from intracellular growing P. salmonis, monolayers of infected SHK-1 cells were rinsed with PBS, re-suspended in 1.0 mL of RNAWIZ (Ambion) and total RNA was purified by using the RiboPure-Bacteria kit (Ambion) following manufacturer`s instructions. The fraction of intracellular P. salmonis RNA was enriched by subtracting eukaryotic ribosomal and messenger RNA using the MICROBEnrich™ Kit (Life Technologies). Briefly, 25 µg of total RNA were mixed with 10 µL of oligocapture in 300 µL of binding buffer. The mixes were incubated at 70 °C by 10 min, and at 37 °C by 1 h. Then, magnetic oligo-MagBeads were added and incubated at 37° C by 15 min, the beads were captured by using a magnetic stand and the supernatant containing bacterial enriched RNA was recovered. The recovered RNA was precipitated with sodium acetate, ethanol 100% and glycogen and incubated at -20°C overnight. The pellets were centrifuged at 4°C, washed twice with cold 70% ethanol and resuspended in 40 µL of TE buffer. The quantity and quality of RNA were determined by NanoQuant Spectrophotometer (Tecan Technologies) and 2200 TapeStation Bioanalyzer (Agilent Technologies).

tag: source

value: ATCC

source_name: exponential phase

tag: isolated

value: Chile, 1989

tag: type

value: bacterium grown inside of SHK-1 cell line during 12 days


title: Sub-acute C2 rep5

tag: age

tag: treatment

value: repeat dose C2

value: 10 days


title: Mouse1 with rTF rep3

description:
8 weeks old FVB/N male mice
Gene expression data from hepatic macrophages of mouse injected with recombinant transferrin and acetaminophen


title: Mouse1 with rCPS1 rep1


title: Baseline D2; Fresh blood ILC2

source_name: Freshly isolated ILC2 from peripheral blood

value: Freshly isolated


title: P. salmonis_cell intracellular vs. free cultures bacterium_exponential phase_rep2


title: Mouse1 with rTF rep2

value: male


title: Mouse1 with rCPS1 rep3


title: Baseline D1; Fresh blood ILC2


title: Baseline D3; Fresh blood ILC2


title: Mouse1 with rCPS1 rep4


title: Type2 D1; Type2 condition stimulated blood ILC2


title: 6RE4: RE KO timepoint6 rep4

status: Public on Mar 25 2019

city: Barcelona

first: Aikaterini

last: Symeonidi

state: Barcelona

address: Baldiri i Reixac, 10

department: Oncology

country: Spain

institute: Institut for Research in Biomedicine (IRB-Barcelona)

description: RE KO timepoint6 rep4

data_processing:
Sequenced reads were trimmed for adaptor sequence and quality correction with Trimmomatic
Then mapped to the mm10 reference genome with Tophat version 2.1.1 with parameters --no-novel-juncs --read-realign-edit-dist 0 -N 2 -p 4 -g 1 -r 200 --no-discordant --no-mixed –b2-sensitive
Read count over the Ensembl transcripts GRCm38.81 was performed with htseq-counts
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files of count data

source_name: interfollicular epidermis

growth_protocol: For the transcriptomic studies of circadian oscillations 4 females (8 weeks old) were used per genotype at each of the six time points. Mice were maintained in a standard 12h light:12h darkness photoperiod at 22ºC degrees and had ad libitum access to standard chow diet.

extract_protocol:
Immediately after sacrifice 1cm2 backskin samples were collected for histology. Skin samples were scraped with a scalpel to remove the hypodermis and then floated on dispase 1mg/ml (Sigma-Aldrich) dissolved in PBS for approximately 40 min at 37ºC, allowing the interfollicular epidermis to be separated from the dermis. Dispase was inactivated with 15% chelated fetal bovine serum (GIBCO) diluted in EMEM medium without calcium (Lonza). The interfollicular epidermis was mechanically disaggregated and dissociated and sequentially filtered through a 100-mm and a 40-mm filter. Cells were counted and cell pellets of 1 million cells were frozen for later RNA extraction. RNA was extracted using TRIzol (Sigma-Aldrich).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: interfollicular epidermis

value: 8 weeks

tag: genotype

value: Bmal1-stopFL/K14-Cre (RE)


title: 6RE2: RE KO timepoint6 rep2

description: RE KO timepoint6 rep2


title: Mouse1 with rTF rep1


title: 6RE3: RE KO timepoint6 rep3

description: RE KO timepoint6 rep3


title: 5RE4: RE KO timepoint5 rep4

description: RE KO timepoint5 rep4


title: 5RE3: RE KO timepoint5 rep3

description: RE KO timepoint5 rep3


title: 5RE2: RE KO timepoint5 rep2

description: RE KO timepoint5 rep2


title: 5RE1: RE KO timepoint5 rep1

description: RE KO timepoint5 rep1


title: P. salmonis_cell intracellular vs. free cultures bacterium_exponential phase_rep1


title: Mouse1 with rTF rep4


title: 4RE4: RE KO timepoint4 rep4

description: RE KO timepoint4 rep4


title: 4RE3: RE KO timepoint4 rep3

description: RE KO timepoint4 rep3


title: 4RE2: RE KO timepoint4 rep2

description: RE KO timepoint4 rep2


title: 3RE4: RE KO timepoint3 rep4

description: RE KO timepoint3 rep4


title: 4RE1: RE KO timepoint4 rep1

description: RE KO timepoint4 rep1


title: 6RE1: RE KO timepoint6 rep1

description: RE KO timepoint6 rep1


title: XY FOXL2_Rep2

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression from E14.5 XY FOXL2+ gonads

hyb_protocol: 5.5 μg micrograms of amplified biotin-cDNAs were fragmented and hybridized to each array for 16 hours at 45°C in a rotating hybridization oven. Array slides were stained with streptavidin/phycoerythrin then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual protocol FS450-0001.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000.

data_processing: Data was obtained using the GeneChip® Command Console software.

source_name: E14.5 XY FOXL2+ gonads

label_protocol: One hundred nanograms (100 ng) of total RNA were amplified and labeled as directed using the Affymetrix WT Plus Reagent Kit (WT Plus Kit).

extract_protocol: A single pair of gonads (14.5 dpc) was separated from the mesonephros and was used as one biological replicate (4 biological replicates were included for each genotype). Total RNA was isolated using Picopure extraction kit (Arcturus). RNA quality and concentration were determined using N Agilent 2100 BioAnalyzer (Agilent Technologies, Santa Clara, California)

treatment_protocol: All embryos used in this study resulted from the crossing between Rosa26-CAG-LSL-Foxl2+/f and Sf1-cre+/Tg mice. The genotype of the gonads used in this study is as follows: XX and XY control:  Rosa26+/+; Sf1-Cre+/Tg  and XY FOXL2+:  XY Rosa26-CAG-LSL-Foxl2+/f; Sf1-cre+/Tg

value: mixed 129Sv and C57Bl/6J

value: Fetal gonads

value: XY Rosa26-CAG-LSL-Foxl2+/f; Sf1-cre+/Tg


title: RNA121210CK_26374_prep2_CCGTCC_L007

city: Beaverton

first: Noah

last: Berlow

address: 12655 SW Beaverdam Rd

institute: CC-TDI

description:
genetically engineered mouse model
U23674

data_processing:
raw reads aligned to hg19 human reference genome (PCB490) or mouse reference genome mm10 (U23674, CTX-mouse) using bowtie 2.0 short read aligner
aligned transcripts were quantified using Cufflinks quantifier
Genome_build: hg19 human genome
Genome_build: mm10 mouse genome
Supplementary_files_format_and_content: result files are In tabular format. These files have quantified FPKM data with additional information

source_name: tumor

extract_protocol:
RNA isolation from snap frozen tissue  was performed at Oregon Health and Science University (OHSU)
library construction was performed at OHSU

tag: tumor type

value: alveolar rhabdomyosarcoma


title: RNA121210CK_muscle-CTX_injured_CGATGT_L007

description:
immunocompitent mouse
CTX-mouse

source_name: normal

treatment_protocol: mouse limb was injected with cardiotoxin to induce damage and initiate wound response

value: cardiotoxin


title: XY Control_Rep3

description: Gene expression from E14.5 XY gonads

source_name: E14.5 XY gonads

value: XY Rosa26+/+; Sf1-Cre+/Tg


title: XY Control_Rep1

description: Gene expression from E14.5 XY gonads


title: 3RE3: RE KO timepoint3 rep3

description: RE KO timepoint3 rep3


title: 3RE2: RE KO timepoint3 rep2

description: RE KO timepoint3 rep2


title: XX Control_Rep3

description: Gene expression from E14.5 XX gonads

source_name: E14.5 XX gonads

value: XX Rosa26+/+; Sf1-Cre+/Tg


title: XX Control_Rep1

description: Gene expression from E14.5 XX gonads


title: XY Control_Rep2

description: Gene expression from E14.5 XY gonads


title: 2RE3: RE KO timepoint2 rep3

description: RE KO timepoint2 rep3


title: 2RE4: RE KO timepoint2 rep4

description: RE KO timepoint2 rep4


title: 3RE1: RE KO timepoint3 rep1

description: RE KO timepoint3 rep1


title: XX Control_Rep4

description: Gene expression from E14.5 XX gonads


title: XX Control_Rep2

description: Gene expression from E14.5 XX gonads


title: XY FOXL2_Rep4


title: XY FOXL2_Rep3


title: XY FOXL2_Rep1


title: XY Control_Rep4

description: Gene expression from E14.5 XY gonads


title: 6KO3: LD KO timepoint6 rep3

description: LD KO timepoint6 rep3

value: Bmal1-stopFL (KO)


title: 5KO3: LD KO timepoint5 rep3

description: LD KO timepoint5 rep3


title: 5KO1: LD KO timepoint5 rep1

description: LD KO timepoint5 rep1


title: 5KO4: LD KO timepoint5 rep4

description: LD KO timepoint5 rep4


title: 3KO2: LD KO timepoint3 rep2

description: LD KO timepoint3 rep2


title: 4KO1: LD KO timepoint4 rep1

description: LD KO timepoint4 rep1


title: 2KO4: LD KO timepoint2 rep4

description: LD KO timepoint2 rep4


title: 3KO4: LD KO timepoint3 rep4

description: LD KO timepoint3 rep4


title: 2KO2: LD KO timepoint2 rep2

description: LD KO timepoint2 rep2


title: 3KO1: LD KO timepoint3 rep1

description: LD KO timepoint3 rep1


title: 4KO4: LD KO timepoint4 rep4

description: LD KO timepoint4 rep4


title: 4KO2: LD KO timepoint4 rep2

description: LD KO timepoint4 rep2


title: 1KO4: LD KO timepoint1 rep4

description: LD KO timepoint1 rep4


title: 3KO3: LD KO timepoint3 rep3

description: LD KO timepoint3 rep3


title: 1KO3: LD KO timepoint1 rep3

description: LD KO timepoint1 rep3


title: 1RE2: RE KO timepoint1 rep2

description: RE KO timepoint1 rep2


title: 2KO1: LD KO timepoint2 rep1

description: LD KO timepoint2 rep1


title: 4KO3: LD KO timepoint4 rep3

description: LD KO timepoint4 rep3


title: 1KO2: LD KO timepoint1 rep2

description: LD KO timepoint1 rep2


title: 1RE4: RE KO timepoint1 rep4

description: RE KO timepoint1 rep4


title: 2RE1: RE KO timepoint2 rep1

description: RE KO timepoint2 rep1


title: 2KO3: LD KO timepoint2 rep3

description: LD KO timepoint2 rep3


title: 6WT3: LD WT timepoint6 rep3

description: LD WT timepoint6 rep3

value: K14-Cre (WT)


title: 5KO2: LD KO timepoint5 rep2

description: LD KO timepoint5 rep2


title: 6WT1: LD WT timepoint6 rep1

description: LD WT timepoint6 rep1


title: 1KO1: LD KO timepoint1 rep1

description: LD KO timepoint1 rep1


title: 6WT4: LD WT timepoint6 rep4

description: LD WT timepoint6 rep4


title: 6KO1: LD KO timepoint6 rep1

description: LD KO timepoint6 rep1


title: 5WT1: LD WT timepoint5 rep1

description: LD WT timepoint5 rep1


title: 6KO2: LD KO timepoint6 rep2

description: LD KO timepoint6 rep2


title: 4WT1: LD WT timepoint4 rep1

description: LD WT timepoint4 rep1


title: 3WT3: LD WT timepoint3 rep3

description: LD WT timepoint3 rep3


title: 4WT2: LD WT timepoint4 rep2

description: LD WT timepoint4 rep2


title: 5WT2: LD WT timepoint5 rep2

description: LD WT timepoint5 rep2


title: 5WT4: LD WT timepoint5 rep4

description: LD WT timepoint5 rep4


title: 4WT4: LD WT timepoint4 rep4

description: LD WT timepoint4 rep4


title: 2WT1: LD WT timepoint2 rep1

description: LD WT timepoint2 rep1


title: 2WT2: LD WT timepoint2 rep2

description: LD WT timepoint2 rep2


title: 4WT3: LD WT timepoint4 rep3

description: LD WT timepoint4 rep3


title: 3WT4: LD WT timepoint3 rep4

description: LD WT timepoint3 rep4


title: 3WT1: LD WT timepoint3 rep1

description: LD WT timepoint3 rep1


title: 1WT3: LD WT timepoint1 rep3

description: LD WT timepoint1 rep3


title: 2RE2: RE KO timepoint2 rep2

description: RE KO timepoint2 rep2


title: 2WT3: LD WT timepoint2 rep3

description: LD WT timepoint2 rep3


title: 2WT4: LD WT timepoint2 rep4

description: LD WT timepoint2 rep4


title: 1WT4: LD WT timepoint1 rep4

description: LD WT timepoint1 rep4


title: 3WT2: LD WT timepoint3 rep2

description: LD WT timepoint3 rep2


title: 1WT2: LD WT timepoint1 rep2

description: LD WT timepoint1 rep2


title: 1RE3: RE KO timepoint1 rep3

description: RE KO timepoint1 rep3


title: F508delCFBE41o- miRseq [Urban_2_V6_S30]

city: Pittsburgh

first: Donald

middle: B.

last: DeFranco

address: 7041 Biomedical Sciences Tower 3

department: Department of Pharmacology and Chemical Biology

institute: University of Pittsburgh

description:
Urban_2_V6_S30
Cystic fibrosis bronchial epithelial cells stably expressing F508del-CFTR.
processed data file: raw_counts.xlsx

data_processing:
The raw QIAseq miRNA sequencing files were uploaded to GeneGlobe Data Analysis Center (Qiagen) for quality control, alignment to the human reference genome (GRCh38) and expression quantification.
Briefly, 3’ adapter and low quality bases are trimmed off from reads first using cutadapt. Reads with less than 16bp insert sequences or with less than 10bp UMI sequences are discarded. The remaining reads were collapsed to UMI counts and aligned to miRBase (release v21) mature and hairpin databases sequentially using Bowtie v1.2.
All reads assigned to a particular miRNA or piRNA ID are counted, and the associated UMIs are clustered to count unique molecules. The primary analysis output file is downloaded from GeneGlobe.
EdgeR package is used for the differential analysis based on UMI counts for miRNA. miRNAs were filtered from the analysis if their count per million (as computed by edgeR's cpm function) was not greater than 2 in at least half of the samples.
The trimmed mean of M-values normalization method implemented in edgeR is used for normalization.
Genome_build: GRCh38
Supplementary_files_format_and_content: raw_counts.xlsx: Excel file includes reads and UMI counts.

source_name: F508delCFBE41o- Cells

growth_protocol: Immortalized human bronchial epithelial cell models: CFBE41o- (bronchial epithelial cells): stably expressing F508del-CFTR were cultured in Minimum Essential Media (MEM) containing 10% Fetal bovine serum (FBS), 50µg/mL streptomycin, 50U/mL Penicillin, 2mM L-Glutamine, 0.55 µg/mL Puromycin (2.2 µg/mL Puromycin for F508del-CFBE41o- cells). Cells were split at 90% confluency were seeded (~1 million/24mm insert) on 24mm inserts (Corning) coated with 10% collagen (PureCol, Type I Bovine Collagen Solution, Advanced BioMatrix) in Opti-MEM (1X Opti-MEM Reduced Serum Medium, gibco, Life Technologies) and cultured in air liquid interface (ALI) for 7-8 days.

extract_protocol:
Total RNA was isolated from cell lysate using the Quick-RNA Miniprep Kit (Zymo Research, R1054) according to the manufacturer’s instructions, with additional on-column DNase treatment with the RNase-free DNase Set (Zymo) to remove contaminating genomic DNA.
100ng of total RNA was used with the QIAseqTM miRNA Library Kit (Qiagen, Maryland, USA) following manufacturer’s instruction.
3’ and 5’ adapters were ligated to total input RNA. Reverse transcription, followed by PCR, was used to create cDNA constructs. PCR was performed with primers that anneal to the ends of the adapters. Quality was examined using Agilent Bioanalyzer Tapestation 2200 and Qubit 2.0 Fluorometer with miRNA library pre sequencing QC protocol mentioned in the QIAseqTM miRNA Library Kit. The cDNA libraries were pooled at a final concentration of 2.5pM. Cluster generation and 75 bp single read single-indexed sequencing was performed on Illumina NextSeq 500’s.

treatment_protocol: Human TGF-b1 (Sigma, St. Louis, MO) or vehicle control (4 mM HCl+1 mg/mL BSA) was used at concentration (15 ng/mL) for the treatment of cells on 24mm inserts (basolaterally) for 24 hour.

value: F508del transfected immortalized (CFBE) cells

tag: passages

value: HCL+BSA


title: F508delCFBE41o- miRseq [Urban_2_V4_S28]

description:
Urban_2_V4_S28
Cystic fibrosis bronchial epithelial cells stably expressing F508del-CFTR.
processed data file: raw_counts.xlsx

tag: cell type


title: F508delCFBE41o- miRseq [Urban_2_V5_S29]

description:
Urban_2_V5_S29
Cystic fibrosis bronchial epithelial cells stably expressing F508del-CFTR.
processed data file: raw_counts.xlsx

tag: cell line


title: F508delCFBE41o- miRseq [Urban_2_V3_S27]

description:
Urban_2_V3_S27
Cystic fibrosis bronchial epithelial cells stably expressing F508del-CFTR.
processed data file: raw_counts.xlsx


title: DD RE timepoint6 rep3

data_processing:
Sequenced reads were trimmed for adaptor sequence and quality correction with Trimmomatic
Then mapped to the mm10 reference genome with Tophat version 2.1.1 with parameters --no-novel-juncs --read-realign-edit-dist 0 -N 2 -p 4 -g 1 -r 200 --no-discordant --no-mixed –b2-sensitive
Read count over the Ensembl transcripts GRCm38.81 was performed with featureCounts
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files of count data

source_name: DD RE timepoint6_interfollicular epidermis

growth_protocol: For the transcriptomic studies of circadian oscillations 4 females (8 weeks old) were used per genotype at each of the six time points. Mice were maintained in a standard 12h light:12h darkness photoperiod at 22ºC degrees and had ad libitum access to standard chow diet. For the darkness experiment (DD) mice were transferred to 24h darkness per day at 7 weeks of age and kept in darkness in total for 156h to 176h.

tag: strain


title: 1WT1: LD WT timepoint1 rep1

description: LD WT timepoint1 rep1


title: F508delCFBE41o- miRseq [Urban_2_V2_S26]

description:
Urban_2_V2_S26
Cystic fibrosis bronchial epithelial cells stably expressing F508del-CFTR.
processed data file: raw_counts.xlsx


title: F508delCFBE41o- miRseq [Urban_2_V1_S25]

description:
Urban_2_V1_S25
Cystic fibrosis bronchial epithelial cells stably expressing F508del-CFTR.
processed data file: raw_counts.xlsx


title: DD RE timepoint6 rep4


title: F508delCFBE41o- miRseq [Urban_2_T3_S21]

description:
Urban_2_T3_S21
Cystic fibrosis bronchial epithelial cells stably expressing F508del-CFTR.
TGFβ1
processed data file: raw_counts.xlsx


title: F508delCFBE41o- miRseq [Urban_2_T4_S22]

description:
Urban_2_T4_S22
Cystic fibrosis bronchial epithelial cells stably expressing F508del-CFTR.
TGFβ1
processed data file: raw_counts.xlsx


title: Alcoholic_F_T_AA2698

city: Indianapolis

first: Jeanette

middle: Nance

last: McClintick

state: IN

address: 635 Barnhill Dr.

department: Biochemistry & Molecular Biology

institute: Indiana University School of Medicine

description:
McClintick_LCL_data_2019.xlsx
24T

data_processing:
Sequencing reads (75 bases, single reads) were mapped to the human hg19 reference genome using an in-house mapping pipeline (Breese & Liu, 2013) that utilizes bfast-0.7.0a (Homer, Merriman, & Nelson, 2009)
reads were truncated where the average quality fell below 10 within a window size of 5, and then reads of <35 bases were discarded.
Reads mapped to rRNA/tRNAs were discarded. The remaining reads were mapped to reference genome hg19 and to a splice-junction library created in house. The genomic and splice-junction library maps were then merged. Reads mapped to multiple positions in the genome were excluded from further analysis.
The gene-based expression levels were calculated using bamutils from NGSUtils, based on the RefSeq gene annotation of hg19.
counts per million (CPM) from EdgeR
filter out low expressing genes, remove genes for which the cpm>=2 in fewer than 20 samples
Genome_build: hg19
Supplementary_files_format_and_content: CPM (count per million reads) for each gene

source_name: Lymphoblastoid cell line

extract_protocol:
cells were harvested and lysed with buffer RLT plus, and RNA extractions were conducted using the QIAsymphony RNA extraction protocol
Samples were processed by polyA capture using Dynabeads mRNA DIRECT Micro Kit (Life Technologies, Carlsbad, CA) starting with 1.5 mg of total RNA. PolyA RNA was processed using Life Technologies SOLiDTM Total RNAseq kit (Life Technologies, Carlsbad, CA). Sequencing beads were produced separately for each batch using the SOLiDTM EZBeadTM System (Life Technologies, Carlsbad, CA). Each batch was sequenced separately on a SOLiD 5500xl DNA sequencer (ThermoFisher/ Life Technolgies, Carlsbad, CA).

treatment_protocol: For the RNA sequencing experiment, 2 x 106 LCLs from each of 21 AD and 21 control individuals were seeded in 10 ml of RPMI1640 medium supplemented with 15% FBS, 2 mM glutamine. Cells were cultured in the absence or presence of 75 mM ethanol for 48 h, at which time cells were harvested

tag: phenotype

value: Alcoholic

tag: gender

value: F

value: ethanol 48h

tag: library/sequencing batch

tag: ID


title: Alcoholic_F_U_AA2698

description:
McClintick_LCL_data_2019.xlsx
24U

value: untreated


title: F508delCFBE41o- miRseq [Urban_2_T5_S23]

description:
Urban_2_T5_S23
Cystic fibrosis bronchial epithelial cells stably expressing F508del-CFTR.
TGFβ1
processed data file: raw_counts.xlsx


title: DD RE timepoint6 rep2

value: 8 weeks

tag: tissue

value: interfollicular epidermis


title: DD RE timepoint5 rep3

source_name: DD RE timepoint5_interfollicular epidermis

tag: genotype/variation

value: Bmal1-stopFL/K14-Cre (RE)


title: Alcoholic_M_U_AA2140

description:
McClintick_LCL_data_2019.xlsx
20U

value: M


title: Alcoholic_M_U_AA2178

description:
McClintick_LCL_data_2019.xlsx
14U


title: TM_siATF4-3_Rep3

city: Oslo

first: Adnan

last: Hashim

state: Oslo

address: NCMM - Forskningsparken, House 1, 3rd Floor - Gaustadalléen 21

department: NCMM (Centre for Molecular Medicine Norway)

country: Norway

institute: UiO (University of Oslo)

data_processing:
Raw reads were aligned to the human genome (hg19), and splice junctions were mapped using TopHat v2.1.0 with default parameters
Gene based read counts were obtained using featureCount v1.5.0-p1
To perform normalization and statistical evaluation with negative binomial model between conditions on the count data, we used DESeq2 v1.10.1 Biconductor package
Genes were considered differentially expressed when showing an absolute log2 fold change (treatment/control) ≥ 1 with adjusted p-value (padj) ≤0.05.
Genome_build: hg19
Supplementary_files_format_and_content: txt files contain gene counts that can be used as input of DESE2

source_name: LNCaP cells

growth_protocol: Cells were grown in RPMI 1640 supplemented with 10% FBS. The experiments were carried out in 12 well plate format.

extract_protocol:
RNeasy (Qiagen) kit with on-column DNase digestion. Qiashredder (Qiagen) was used to enhance lysis.
Strand-specific TrueSeq RNA-seq library prep

treatment_protocol: LNCaP cells were reverse transfected with non-targeting siRNA (siCtrl), two oligos siEIF2AK3, or two oligos ATF4. siCtrl cells were treated with DMSO, 2.5 ug/mL tunicamycin, or 2.5 ug/mL L tunicamcin in combination with 100 nM of the PERK inhibitor GSK2606414. Cells transfected with siEIF2AK3 and siATF4 were treated with 2.5 ug/mL tunicamycin. Cells were harvested two days after transfection and subsequent 18 h treatments.

value: LNCaP cells

value: Metastatic prostate cancer cell line

value: siATF4 oligo 2, 2.5 ug/mL TM


title: TM_siATF4-3_Rep4


title: Alcoholic_M_T_AA2140

description:
McClintick_LCL_data_2019.xlsx
20T


title: F508delCFBE41o- miRseq [Urban_2_T2_S20]

description:
Urban_2_T2_S20
Cystic fibrosis bronchial epithelial cells stably expressing F508del-CFTR.
TGFβ1
processed data file: raw_counts.xlsx


title: DD RE timepoint5 rep4


title: DD RE timepoint6 rep1


title: 6KO4: LD KO timepoint6 rep4

description: LD KO timepoint6 rep4


title: F508delCFBE41o- miRseq [Urban_2_T6_S24]

description:
Urban_2_T6_S24
Cystic fibrosis bronchial epithelial cells stably expressing F508del-CFTR.
TGFβ1
processed data file: raw_counts.xlsx


title: F508delCFBE41o- miRseq [Urban_2_T1_S19]

description:
Urban_2_T1_S19
Cystic fibrosis bronchial epithelial cells stably expressing F508del-CFTR.
TGFβ1
processed data file: raw_counts.xlsx


title: Alcoholic_M_T_AA2178

description:
McClintick_LCL_data_2019.xlsx
14T


title: TM_siATF4-3_Rep1


title: TM_siATF4-2_Rep3

value: siATF4 oligo 1, 2.5 ug/mL TM


title: DD RE timepoint4 rep4

source_name: DD RE timepoint4_interfollicular epidermis


title: 1RE1: RE KO timepoint1 rep1

description: RE KO timepoint1 rep1


title: TM_siATF4-3_Rep2


title: DD RE timepoint5 rep1


title: DD RE timepoint4 rep2


title: Alcoholic_F_T_AA2031

description:
McClintick_LCL_data_2019.xlsx
12T


title: Control_M_U_AA2218

description:
McClintick_LCL_data_2019.xlsx
13U

value: Control


title: TM_siPERK-3_Rep1

value: siPERK oligo 2, 2.5 ug/mL TM


title: DD RE timepoint3 rep4

source_name: DD RE timepoint3_interfollicular epidermis


title: Control_M_T_AA2218

description:
McClintick_LCL_data_2019.xlsx
13T


title: TM_siPERK-3_Rep4


title: Control_M_U_AA1118

description:
McClintick_LCL_data_2019.xlsx
9U


title: TM_siPERK-3_Rep3


title: TM_siATF4-2_Rep2


title: DD RE timepoint4 rep1


title: DD RE timepoint4 rep3


title: TM_siATF4-2_Rep1


title: Alcoholic_F_U_AA2031

description:
McClintick_LCL_data_2019.xlsx
12U


title: TM_siPERK-1_Rep2

value: siPERK oligo 1, 2.5 ug/mL TM


title: DD RE timepoint5 rep2


title: Control_M_T_AA1118

description:
McClintick_LCL_data_2019.xlsx
9T


title: TM_PERKi_siCtrl_Rep_3

value: siCtrl, 2.5 ug/mL TM, 100 nM PERKi


title: DD RE timepoint3 rep2


title: TM_siPERK-3_Rep2


title: Control_F_T_AA0802

description:
McClintick_LCL_data_2019.xlsx
8T


title: TM_siPERK-1_Rep1


title: TM_PERKi_siCtrl_Rep_4


title: DD RE timepoint3 rep1


title: TM_PERKi_siCtrl_Rep_1


title: Control_F_U_AA0802

description:
McClintick_LCL_data_2019.xlsx
8U


title: TM_siCtrl_Rep_2

value: siCtrl, 2.5 ug/mL TM


title: TM_siPERK-1_Rep4


title: TM_PERKi_siCtrl_Rep_2


title: TM_siPERK-1_Rep3


title: TM_siCtrl_Rep_3


title: 6WT2: LD WT timepoint6 rep2

description: LD WT timepoint6 rep2

value: K14-Cre (WT)


title: TM_siCtrl_Rep_1


title: DMSO_siCtrl_Rep_3

value: siCtrl, DMSO


title: Alcoholic_F_U_AA2628

description:
McClintick_LCL_data_2019.xlsx
29U

value: Alcoholic

value: F


title: TM_siCtrl_Rep_4


title: Control_F_T_AA0708

description:
McClintick_LCL_data_2019.xlsx
7T

value: ethanol 48h


title: Control_F_U_AA0708

description:
McClintick_LCL_data_2019.xlsx
7U

value: untreated


title: DD RE timepoint2 rep4

source_name: DD RE timepoint2_interfollicular epidermis

value: 8 weeks

value: Bmal1-stopFL/K14-Cre (RE)

value: interfollicular epidermis


title: DD RE timepoint3 rep3


title: TM_siATF4-2_Rep4

value: LNCaP cells

value: Metastatic prostate cancer cell line


title: Alcoholic_F_U_AA0190

description:
McClintick_LCL_data_2019.xlsx
26U


title: DMSO_siCtrl_Rep_4


title: DD RE timepoint2 rep2


title: Alcoholic_F_T_AA2628

description:
McClintick_LCL_data_2019.xlsx
29T


title: DD RE timepoint1 rep3

source_name: DD RE timepoint1_interfollicular epidermis


title: MDA_MFP_Rep2

city: New York City

first: Lin

last: Tian

state: New York

address: Mortimer B. Zuckerman Research Center, 417 East 68th Street

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

description:
MDA_MFP = MDA231 cells injected in mammary fat pad in mouse, and 4 weeks after the injection, tumor was isolated and was processed to get single cell suspension, and MDA231 cells were selected by culturing them in DMEM High glucose media with 10% Fetal Bovine Serum containing 200 ug/mL Hygromycin and 8 ug/mL Blasticidin, and RNA from the surviving cells were sequenced after 2 passages.
Counts_expressed_normalized_inVitro.csv

data_processing:
Samples were barcoded
run on a Hiseq 2000 platform in a 125bp/125bp paired-end run, using the TruSeq SBS Kit v3 (Illumina).
An average of 25 million paired reads were generated per sample.
The data were analyzed using the STAR-HTSeq-DESeq2 pipeline as previously described.
Flura-seq in vivo experiments were aligned to hybrid genome containing combined human and mouse genome. Mouse gene is indicated by "m" in front of the gene name whereas human gene is indicated by "h" in front of the gene name. For the other remaining experiments, the reads were aligned to human genome.
Genome_build: hg19, mm10, Hybrid genome containing hg19 and mm10
Supplementary_files_format_and_content: Two separate count files in csv format are provided for two different profiling methods (Counts_expressed_normalized_Fluraseq.csv, Counts_expressed_normalized_inVitro.csv)

source_name: MDA231 MFP Xenograft

growth_protocol: MDA231 cells  were cultured in DMEM with 10% fetal bovine serum (FBS), 2 mM L-Glutamine, 200 ug/mL Hygromycin and 8 ug/mL Blasticidin.

extract_protocol:
mRNAs were isolated by Oligo dT magnetic beads. Either the mRNAs were sequenced directly or immunoprecipitated with anti-BrdU antibody, and bound mRNAs were eluted using BrdU solution, and the eluted mRNAs were sequenced.
TruSeq RNA Sample Prep Kit v2 (Illumina) following the manufacturer’s instructions. For the immunopurified RNAs, the RNAs were amplified by SMARTer amplification and library was prepared by Nextera Kit followinf manufacturer's protocol.

tag: metastatic derivative

value: Fat pad

tag: reporter gene

value: Firefly Luciferase

tag: protocol

value: Isolated from Fat pad


title: DMSO_siCtrl_Rep_1


title: DMSO_siCtrl_Rep_2


title: Alcoholic_F_T_AA0190

description:
McClintick_LCL_data_2019.xlsx
26T


title: DD RE timepoint1 rep2

tag: age


title: MDA_MFP_Rep3


title: DD RE timepoint1 rep4


title: RNA140925CK_1_pcb00490-5_tu_rna_ATCACG_L001

description:
primary human tissue
PCB490

value: epithelioid sarcoma

tag: treatment


title: DD RE timepoint1 rep1


title: DD RE timepoint2 rep1


title: DD KO timepoint6 rep4

source_name: DD KO timepoint6_interfollicular epidermis

value: Bmal1-stopFL (KO)


title: DD KO timepoint6 rep3


title: MDA_Brain_Rep2

description:
MDA_Brain = MDA231 cells injected intracardiacally in mouse, and 4 weeks after the injection, mouse brain was processed to get single cell suspension, and MDA231 cells were selected by culturing them in DMEM High glucose media with 10% Fetal Bovine Serum containing 200 ug/mL Hygromycin and 8 ug/mL Blasticidin, and RNA from the surviving cells were sequenced after 2 passages.
Counts_expressed_normalized_inVitro.csv

source_name: MDA231 Brain Xenograft

value: Brain

value: Isolated from brain


title: MDA_MFP_Rep1


title: DD RE timepoint2 rep3


title: MDA_Lung_Rep3

description:
MDA_Lung = MDA231 cells injected intracardiacally in mouse, and 4 weeks after the injection, mouse lung was processed to get single cell suspension, and MDA231 cells were selected by culturing them in DMEM High glucose media with 10% Fetal Bovine Serum containing 200 ug/mL Hygromycin and 8 ug/mL Blasticidin, and RNA from the surviving cells were sequenced after 2 passages.
Counts_expressed_normalized_inVitro.csv

source_name: MDA231 Lung Xenograft

value: Lung

value: Isolated from Lung


title: MDA_Brain_Rep3


title: Alcoholic_M_U_AA2314

description:
McClintick_LCL_data_2019.xlsx
22U

value: Alcoholic

value: M


title: Alcoholic_M_T_AA0342

description:
McClintick_LCL_data_2019.xlsx
25T

value: ethanol 48h


title: DD KO timepoint6 rep2

value: 8 weeks