title: 2Sa_2Sa_deletion_1D_rep3 [RNA-seq_rRNA removal]

description:
TB-2Sa_deletion_gene_exp_rRNA_depletion_bioreps.txt
TB-2Sa_gene_exp_rRNA_depletion_bioreps.txt
2Sa_2Sa_deletion_1D_H44
TB2Sa_disomy_comparison_rRNA_depletion
TB-2Sa_deletion_disomy_comparison_rRNA_depletion
TB-2Sa_deletion_gene_exp_rRNA_depletion.txt
TB-2Sa_gene_exp_rRNA_depletion.txt


title: 2Sa_2Sa_deletion_1D_rep4 [RNA-seq_rRNA removal]

status: Public on Feb 22 2021

type: SRA

city: Columbia

first: James

last: Birchler

state: MO

address: 310 Tucker Hall

country: USA

institute: University of Missouri-Columbia

description:
TB-2Sa_deletion_gene_exp_rRNA_depletion_bioreps.txt
TB-2Sa_gene_exp_rRNA_depletion_bioreps.txt
2Sa_2Sa_deletion_1D_H45
TB2Sa_disomy_comparison_rRNA_depletion
TB-2Sa_deletion_disomy_comparison_rRNA_depletion
TB-2Sa_deletion_gene_exp_rRNA_depletion.txt
TB-2Sa_gene_exp_rRNA_depletion.txt

library_source: transcriptomic

data_processing:
RNA-seq (rRNA removal): Adaptors at the 3' end of the reads were trimmed using cutadapt. Low quality reads were removed using the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/, fastq_quality_filter -Q 33 -q 20 -p 80). The remaining reads were aligned to ERCC sequences using TopHat2 with default parameters. Non-ERCC reads were aligned to the maize chloroplast and mitochondrial genome using TopHat2 with default parameters. Non-ERCC and non-organelle reads were aligned to the maize reference genome W22v2 along with the maize chloroplast and mitochondrial genome using TopHat2 with default parameters. Normalized read counts were generated by Cuffdiff (--raw-mapped-norm) for each comparison.
RNA-seq (mRNA selection): Adaptors at the 3' end of the reads were trimmed using cutadapt. Low quality reads were removed using the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/, fastq_quality_filter -Q 33 -q 20 -p 80). The remaining reads were aligned to ERCC sequences using TopHat2 with default parameters. Non-ERCC reads were aligned to the maize reference genome W22v2 along with the maize chloroplast and mitochondrial genome using TopHat2 with default parameters. Normalized read counts were generated by Cuffdiff (--raw-mapped-norm) for each comparison.
DNA-seq: Adaptor trimming and low-quality read removal were performed the same as in mRNA-seq data process. Then the remaining DNA reads were aligned to the maize reference genome W22v2 along with the maize chloroplast and mitochondrial genome using Bowtie 2 with default parameters. A custom perl script was used for extraction of uniquely mapped read counts from the gene regions or 1Mb genome region. The counts from the gene region were then subjected to RPKM normalization.
Genome_build: W22v2 along with the maize chloroplast and mitochondrial genome (Springer et al., 2018; Bosacchi et al., 2015; Clifton et al., 2004).
Supplementary_files_format_and_content: Tab-delimited text files including tables showing cuffdiff normalized counts and differential gene expression analyses and tables reporting RPKM normalized counts in DNA-seq.

molecule: total RNA

organism: Zea mays

source_name: Leaf tissue

growth_protocol: 45-day grown in the greenhouse

extract_protocol:
RNA extracted by mirVana™ miRNA Isolation Kit; DNA extracted by DNeasy Plant Mini Kit (QIAGEN)
TruSeq library construction

tag: age

tag: rna/dna-seq approaches

value: ribosomal RNAs depletion


title: bladder tumour 2103

type: RNA

city: Leeds

first: Margaret

middle: A

last: Knowles

state: West Yorkshire

address: Becket Street

department: LICAP

country: United Kingdom

institute: University of Leeds

description: bladder tumour

hyb_protocol: Microarrays were washed and stained using the Affymetrix GeneChip Hybridization, Wash, and Stain Kit according to manufacturer's instructions using the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Microarrays were scanned using an Affymetrix GeneChip 7G microarray scanner.

data_processing:
Data QC was analysed using Affymetrix Expression Console Software and samples were normalised using RMA.
HTA-2_0.r3.pgf
HTA-2_0.r3.Psrs.mps

label: biotin

organism: Homo sapiens

source_name: fresh frozen bladder tumour tissue

label_protocol: Total RNA was amplified using the Affymetrix GeneChip WT PLUS Reagent Kit according to manufacturer's instructions. The resulting cDNA was quantified using OD (NanoDrop). The cDNA was normalised and hybridised onto Affymetrix Human Transcriptome 2.0 microarrays for 16 hours at 45 degrees C.

growth_protocol: not applicable

extract_protocol: Total RNA was extracted from fresh frozen tissue samples comprising at least 70% tumour using an RNeasy  Plus Micro Kit (Qiagen). The protocol for fibrous tissue was followed with the inclusion of an on-column DNase digestion step

treatment_protocol: not applicable

tag: tumour stage

value: tumour stageT1


title: bladder tumour 2100

description: bladder tumour

value: tumour stageTa


title: 2Sa_2Sa_deletion_1D_rep2 [RNA-seq_rRNA removal]

description:
TB-2Sa_deletion_gene_exp_rRNA_depletion_bioreps.txt
TB-2Sa_gene_exp_rRNA_depletion_bioreps.txt
2Sa_2Sa_deletion_1D_H43
TB2Sa_disomy_comparison_rRNA_depletion
TB-2Sa_deletion_disomy_comparison_rRNA_depletion
TB-2Sa_deletion_gene_exp_rRNA_depletion.txt
TB-2Sa_gene_exp_rRNA_depletion.txt


title: 2Sa_2Sa_deletion_1D_rep1 [RNA-seq_rRNA removal]

description:
TB-2Sa_deletion_gene_exp_rRNA_depletion_bioreps.txt
TB-2Sa_gene_exp_rRNA_depletion_bioreps.txt
2Sa_2Sa_deletion_1D_H39
TB2Sa_disomy_comparison_rRNA_depletion
TB-2Sa_deletion_disomy_comparison_rRNA_depletion
TB-2Sa_deletion_gene_exp_rRNA_depletion.txt
TB-2Sa_gene_exp_rRNA_depletion.txt


title: 1La_5Lb_8Lc_1D_rep3 [RNA-seq_rRNA removal]

description:
TB-1La_gene_exp_rRNA_depletion_bioreps.txt
TB-5Lb_gene_exp_rRNA_depletion_bioreps.txt
TB-8Lc_gene_exp_rRNA_depletion_bioreps.txt
1La_5Lb_8Lc_1D_H26
TB-1La_disomy_comparison_rRNA_depletion
TB-5Lb_disomy_comparison_rRNA_depletion
TB-8Lc_disomy_comparison_rRNA_depletion
TB-1La_gene_exp_rRNA_depletion.txt
TB-5Lb_gene_exp_rRNA_depletion.txt
TB-8Lc_gene_exp_rRNA_depletion.txt


title: bladder tumour 2086

description: bladder tumour


title: bladder tumour 2074

description: bladder tumour


title: bladder tumour 2064

description: bladder tumour


title: 1La_5Lb_8Lc_1D_rep1 [RNA-seq_rRNA removal]

description:
TB-1La_gene_exp_rRNA_depletion_bioreps.txt
TB-5Lb_gene_exp_rRNA_depletion_bioreps.txt
TB-8Lc_gene_exp_rRNA_depletion_bioreps.txt
1La_5Lb_8Lc_1D_H23
TB-1La_disomy_comparison_rRNA_depletion
TB-5Lb_disomy_comparison_rRNA_depletion
TB-8Lc_disomy_comparison_rRNA_depletion
TB-1La_gene_exp_rRNA_depletion.txt
TB-5Lb_gene_exp_rRNA_depletion.txt
TB-8Lc_gene_exp_rRNA_depletion.txt


title: 1La_5Lb_8Lc_1D_rep2 [RNA-seq_rRNA removal]

description:
TB-1La_gene_exp_rRNA_depletion_bioreps.txt
TB-5Lb_gene_exp_rRNA_depletion_bioreps.txt
TB-8Lc_gene_exp_rRNA_depletion_bioreps.txt
1La_5Lb_8Lc_1D_H24
TB-1La_disomy_comparison_rRNA_depletion
TB-5Lb_disomy_comparison_rRNA_depletion
TB-8Lc_disomy_comparison_rRNA_depletion
TB-1La_gene_exp_rRNA_depletion.txt
TB-5Lb_gene_exp_rRNA_depletion.txt
TB-8Lc_gene_exp_rRNA_depletion.txt


title: bladder tumour 2063

description: bladder tumour


title: 4Sa_9Sd_1D_rep4 [RNA-seq_rRNA removal]

description:
TB-4Sa_gene_exp_rRNA_depletion_bioreps.txt
TB-9Sd_gene_exp_rRNA_depletion_bioreps.txt
4Sa_9Sd_1D_H20
TB-4Sa_disomy_comparison_rRNA_depletion
TB-9Sd_disomy_comparison_rRNA_depletion
TB-4Sa_gene_exp_rRNA_depletion.txt
TB-9Sd_gene_exp_rRNA_depletion.txt


title: bladder tumour 2055

description: bladder tumour


title: 1La_5Lb_8Lc_1D_rep4 [RNA-seq_rRNA removal]

description:
TB-1La_gene_exp_rRNA_depletion_bioreps.txt
TB-5Lb_gene_exp_rRNA_depletion_bioreps.txt
TB-8Lc_gene_exp_rRNA_depletion_bioreps.txt
1La_5Lb_8Lc_1D_H27
TB-1La_disomy_comparison_rRNA_depletion
TB-5Lb_disomy_comparison_rRNA_depletion
TB-8Lc_disomy_comparison_rRNA_depletion
TB-1La_gene_exp_rRNA_depletion.txt
TB-5Lb_gene_exp_rRNA_depletion.txt
TB-8Lc_gene_exp_rRNA_depletion.txt


title: bladder tumour 2082

description: bladder tumour


title: bladder tumour 2058

description: bladder tumour


title: 4Sa_9Sd_1D_rep3 [RNA-seq_rRNA removal]

description:
TB-4Sa_gene_exp_rRNA_depletion_bioreps.txt
TB-9Sd_gene_exp_rRNA_depletion_bioreps.txt
4Sa_9Sd_1D_H19
TB-4Sa_disomy_comparison_rRNA_depletion
TB-9Sd_disomy_comparison_rRNA_depletion
TB-4Sa_gene_exp_rRNA_depletion.txt
TB-9Sd_gene_exp_rRNA_depletion.txt


title: bladder tumour 2056

description: bladder tumour


title: bladder tumour 2037

description: bladder tumour


title: bladder tumour 2065

description: bladder tumour


title: bladder tumour 2046

description: bladder tumour


title: bladder tumour 2032

description: bladder tumour


title: bladder tumour 2033

description: bladder tumour


title: bladder tumour 2047

description: bladder tumour


title: 4Sa_9Sd_1D_rep1 [RNA-seq_rRNA removal]

description:
TB-4Sa_gene_exp_rRNA_depletion_bioreps.txt
TB-9Sd_gene_exp_rRNA_depletion_bioreps.txt
4Sa_9Sd_1D_H17
TB-4Sa_disomy_comparison_rRNA_depletion
TB-9Sd_disomy_comparison_rRNA_depletion
TB-4Sa_gene_exp_rRNA_depletion.txt
TB-9Sd_gene_exp_rRNA_depletion.txt


title: bladder tumour 2020

description: bladder tumour


title: bladder tumour 2013

description: bladder tumour


title: bladder tumour 2000

description: bladder tumour


title: 9Sd_2D_rep2 [RNA-seq_rRNA removal]

description:
TB-9Sd_gene_exp_rRNA_depletion_bioreps.txt
9Sd_2D_9S12
TB-9Sd_disomy_comparison_rRNA_depletion
TB-9Sd_gene_exp_rRNA_depletion.txt


title: 9Lc_2D_rep5 [RNA-seq_rRNA removal]

description:
TB-9Lc_gene_exp_rRNA_depletion_bioreps.txt
9Lc_2D_9Lc44
TB-9Lc_disomy_comparison_rRNA_depletion
TB-9Lc_gene_exp_rRNA_depletion.txt


title: 9Sd_2D_rep1 [RNA-seq_rRNA removal]

description:
TB-9Sd_gene_exp_rRNA_depletion_bioreps.txt
9Sd_2D_9S11
TB-9Sd_disomy_comparison_rRNA_depletion
TB-9Sd_gene_exp_rRNA_depletion.txt


title: 9Lc_2D_rep4 [RNA-seq_rRNA removal]

description:
TB-9Lc_gene_exp_rRNA_depletion_bioreps.txt
9Lc_2D_9Lc43
TB-9Lc_disomy_comparison_rRNA_depletion
TB-9Lc_gene_exp_rRNA_depletion.txt


title: bladder tumour 2012

description: bladder tumour


title: bladder tumour 2022

description: bladder tumour


title: 9Sd_2D_rep4 [RNA-seq_rRNA removal]

description:
TB-9Sd_gene_exp_rRNA_depletion_bioreps.txt
9Sd_2D_9S9
TB-9Sd_disomy_comparison_rRNA_depletion
TB-9Sd_gene_exp_rRNA_depletion.txt


title: 8Lc_2D_rep4 [RNA-seq_rRNA removal]

description:
TB-8Lc_gene_exp_rRNA_depletion_bioreps.txt
8Lc_2D_8L20
TB-8Lc_disomy_comparison_rRNA_depletion
TB-8Lc_gene_exp_rRNA_depletion.txt


title: bladder tumour 1992

description: bladder tumour


title: bladder tumour 1991

description: bladder tumour


title: bladder tumour 1978

description: bladder tumour


title: 8Lc_2D_rep3 [RNA-seq_rRNA removal]

description:
TB-8Lc_gene_exp_rRNA_depletion_bioreps.txt
8Lc_2D_8L16
TB-8Lc_disomy_comparison_rRNA_depletion
TB-8Lc_gene_exp_rRNA_depletion.txt


title: 9Lc_2D_rep3 [RNA-seq_rRNA removal]

description:
TB-9Lc_gene_exp_rRNA_depletion_bioreps.txt
9Lc_2D_9Lc38
TB-9Lc_disomy_comparison_rRNA_depletion
TB-9Lc_gene_exp_rRNA_depletion.txt


title: bladder tumour 1974

description: bladder tumour


title: 9Lc_2D_rep2 [RNA-seq_rRNA removal]

description:
TB-9Lc_gene_exp_rRNA_depletion_bioreps.txt
9Lc_2D_9Lc35
TB-9Lc_disomy_comparison_rRNA_depletion
TB-9Lc_gene_exp_rRNA_depletion.txt


title: 9Lc_2D_rep1 [RNA-seq_rRNA removal]

description:
TB-9Lc_gene_exp_rRNA_depletion_bioreps.txt
9Lc_2D_9Lc34
TB-9Lc_disomy_comparison_rRNA_depletion
TB-9Lc_gene_exp_rRNA_depletion.txt


title: bladder tumour 1971

description: bladder tumour


title: 7Sc_2D_rep4 [RNA-seq_rRNA removal]

description:
TB-7Sc_gene_exp_rRNA_depletion_bioreps.txt
7Sc_2D_7S5
TB-7Sc_disomy_comparison_rRNA_depletion
TB-7Sc_gene_exp_rRNA_depletion.txt


title: bladder tumour 1972

description: bladder tumour


title: 9Sd_2D_rep3 [RNA-seq_rRNA removal]

description:
TB-9Sd_gene_exp_rRNA_depletion_bioreps.txt
9Sd_2D_9S13
TB-9Sd_disomy_comparison_rRNA_depletion
TB-9Sd_gene_exp_rRNA_depletion.txt


title: bladder tumour 1968

description: bladder tumour


title: 8Lc_2D_rep2 [RNA-seq_rRNA removal]

description:
TB-8Lc_gene_exp_rRNA_depletion_bioreps.txt
8Lc_2D_8L13
TB-8Lc_disomy_comparison_rRNA_depletion
TB-8Lc_gene_exp_rRNA_depletion.txt


title: 8Lc_2D_rep1 [RNA-seq_rRNA removal]

description:
TB-8Lc_gene_exp_rRNA_depletion_bioreps.txt
8Lc_2D_8L12
TB-8Lc_disomy_comparison_rRNA_depletion
TB-8Lc_gene_exp_rRNA_depletion.txt


title: 7Sc_2D_rep2 [RNA-seq_rRNA removal]

description:
TB-7Sc_gene_exp_rRNA_depletion_bioreps.txt
7Sc_2D_7S11
TB-7Sc_disomy_comparison_rRNA_depletion
TB-7Sc_gene_exp_rRNA_depletion.txt


title: 7Sc_2D_rep3 [RNA-seq_rRNA removal]

description:
TB-7Sc_gene_exp_rRNA_depletion_bioreps.txt
7Sc_2D_7S35
TB-7Sc_disomy_comparison_rRNA_depletion
TB-7Sc_gene_exp_rRNA_depletion.txt


title: 7Lb_2D_rep4 [RNA-seq_rRNA removal]

description:
TB-7Lb_gene_exp_rRNA_depletion_bioreps.txt
7Lb_2D_7Lb47
TB-7Lb_disomy_comparison_rRNA_depletion
TB-7Lb_gene_exp_rRNA_depletion.txt


title: bladder tumour 1947

description: bladder tumour


title: 7Lb_2D_rep3 [RNA-seq_rRNA removal]

description:
TB-7Lb_gene_exp_rRNA_depletion_bioreps.txt
7Lb_2D_7Lb42
TB-7Lb_disomy_comparison_rRNA_depletion
TB-7Lb_gene_exp_rRNA_depletion.txt


title: bladder tumour 1931

description: bladder tumour


title: bladder tumour 1934

description: bladder tumour


title: bladder tumour 1932

description: bladder tumour


title: bladder tumour 1860

description: bladder tumour


title: 7Lb_2D_rep2 [RNA-seq_rRNA removal]

description:
TB-7Lb_gene_exp_rRNA_depletion_bioreps.txt
7Lb_2D_7Lb41
TB-7Lb_disomy_comparison_rRNA_depletion
TB-7Lb_gene_exp_rRNA_depletion.txt


title: bladder tumour 1853

description: bladder tumour


title: 7Lb_2D_rep1 [RNA-seq_rRNA removal]

description:
TB-7Lb_gene_exp_rRNA_depletion_bioreps.txt
7Lb_2D_7Lb23
TB-7Lb_disomy_comparison_rRNA_depletion
TB-7Lb_gene_exp_rRNA_depletion.txt


title: bladder tumour 1933

description: bladder tumour


title: bladder tumour 1831

description: bladder tumour


title: bladder tumour 1930

description: bladder tumour


title: bladder tumour 1810

description: bladder tumour


title: 6Lc_2D_rep2 [RNA-seq_rRNA removal]

description:
TB-6Lc_gene_exp_rRNA_depletion_bioreps.txt
6Lc_2D_6Lc29
TB-6Lc_disomy_comparison_rRNA_depletion
TB-6Lc_gene_exp_rRNA_depletion.txt


title: 5Sc_2D_rep3 [RNA-seq_rRNA removal]

description:
TB-5Sc_gene_exp_rRNA_depletion_bioreps.txt
5Sc_2D_5SCh5
TB-5Sc_disomy_comparison_rRNA_depletion
TB-5Sc_gene_exp_rRNA_depletion.txt


title: 5Sc_2D_rep2 [RNA-seq_rRNA removal]

description:
TB-5Sc_gene_exp_rRNA_depletion_bioreps.txt
5Sc_2D_5SCh14
TB-5Sc_disomy_comparison_rRNA_depletion
TB-5Sc_gene_exp_rRNA_depletion.txt


title: bladder tumour 1798

description: bladder tumour


title: bladder tumour 1858

description: bladder tumour


title: 5Sc_2D_rep1 [RNA-seq_rRNA removal]

description:
TB-5Sc_gene_exp_rRNA_depletion_bioreps.txt
5Sc_2D_5SCh10
TB-5Sc_disomy_comparison_rRNA_depletion
TB-5Sc_gene_exp_rRNA_depletion.txt


title: bladder tumour 1817

description: bladder tumour


title: 5Sc_1D_rep4 [RNA-seq_rRNA removal]

description:
TB-5Sc_gene_exp_rRNA_depletion_bioreps.txt
5Sc_1D_5SCh6
TB-5Sc_disomy_comparison_rRNA_depletion
TB-5Sc_gene_exp_rRNA_depletion.txt


title: 5Sc_2D_rep4 [RNA-seq_rRNA removal]

description:
TB-5Sc_gene_exp_rRNA_depletion_bioreps.txt
5Sc_2D_5SCh7
TB-5Sc_disomy_comparison_rRNA_depletion
TB-5Sc_gene_exp_rRNA_depletion.txt


title: 7Sc_2D_rep1 [RNA-seq_rRNA removal]

description:
TB-7Sc_gene_exp_rRNA_depletion_bioreps.txt
7Sc_2D_7S1
TB-7Sc_disomy_comparison_rRNA_depletion
TB-7Sc_gene_exp_rRNA_depletion.txt


title: bladder tumour 1747

description: bladder tumour


title: 5Sc_1D_rep1 [RNA-seq_rRNA removal]

description:
TB-5Sc_gene_exp_rRNA_depletion_bioreps.txt
5Sc_1D_5SCh11
TB-5Sc_disomy_comparison_rRNA_depletion
TB-5Sc_gene_exp_rRNA_depletion.txt


title: 5Sc_1D_rep3 [RNA-seq_rRNA removal]

description:
TB-5Sc_gene_exp_rRNA_depletion_bioreps.txt
5Sc_1D_5SCh4
TB-5Sc_disomy_comparison_rRNA_depletion
TB-5Sc_gene_exp_rRNA_depletion.txt


title: bladder tumour 1766

description: bladder tumour


title: bladder tumour 1745

description: bladder tumour


title: bladder tumour 1735

description: bladder tumour


title: 6Lc_2D_rep3 [RNA-seq_rRNA removal]

description:
TB-6Lc_gene_exp_rRNA_depletion_bioreps.txt
6Lc_2D_6Lc9
TB-6Lc_disomy_comparison_rRNA_depletion
TB-6Lc_gene_exp_rRNA_depletion.txt


title: bladder tumour 1709

description: bladder tumour


title: bladder tumour 1719

description: bladder tumour


title: bladder tumour 1732

description: bladder tumour


title: bladder tumour 1629

description: bladder tumour


title: 5Sc_1D_rep2 [RNA-seq_rRNA removal]

description:
TB-5Sc_gene_exp_rRNA_depletion_bioreps.txt
5Sc_1D_5SCh18
TB-5Sc_disomy_comparison_rRNA_depletion
TB-5Sc_gene_exp_rRNA_depletion.txt


title: bladder tumour 1679

description: bladder tumour


title: bladder tumour 1729

description: bladder tumour


title: bladder tumour 1633

description: bladder tumour


title: 4Sa_2D_rep2 [RNA-seq_rRNA removal]

description:
TB-4Sa_gene_exp_rRNA_depletion_bioreps.txt
4Sa_2D_4S5
TB-4Sa_disomy_comparison_rRNA_depletion
TB-4Sa_gene_exp_rRNA_depletion.txt


title: 5Lb_2D_rep4 [RNA-seq_rRNA removal]

description:
TB-5Lb_gene_exp_rRNA_depletion_bioreps.txt
5Lb_2D_5L9
TB-5Lb_disomy_comparison_rRNA_depletion
TB-5Lb_gene_exp_rRNA_depletion.txt


title: 5Lb_2D_rep3 [RNA-seq_rRNA removal]

description:
TB-5Lb_gene_exp_rRNA_depletion_bioreps.txt
5Lb_2D_5L8
TB-5Lb_disomy_comparison_rRNA_depletion
TB-5Lb_gene_exp_rRNA_depletion.txt


title: 5Lb_2D_rep2 [RNA-seq_rRNA removal]

description:
TB-5Lb_gene_exp_rRNA_depletion_bioreps.txt
5Lb_2D_5L6
TB-5Lb_disomy_comparison_rRNA_depletion
TB-5Lb_gene_exp_rRNA_depletion.txt


title: 4Sa_2D_rep3 [RNA-seq_rRNA removal]

description:
TB-4Sa_gene_exp_rRNA_depletion_bioreps.txt
4Sa_2D_4S8
TB-4Sa_disomy_comparison_rRNA_depletion
TB-4Sa_gene_exp_rRNA_depletion.txt


title: 4Sa_2D_rep1 [RNA-seq_rRNA removal]

description:
TB-4Sa_gene_exp_rRNA_depletion_bioreps.txt
4Sa_2D_4S3
TB-4Sa_disomy_comparison_rRNA_depletion
TB-4Sa_gene_exp_rRNA_depletion.txt


title: 4Sa_9Sd_1D_rep2 [RNA-seq_rRNA removal]

description:
TB-4Sa_gene_exp_rRNA_depletion_bioreps.txt
TB-9Sd_gene_exp_rRNA_depletion_bioreps.txt
4Sa_9Sd_1D_H18
TB-4Sa_disomy_comparison_rRNA_depletion
TB-9Sd_disomy_comparison_rRNA_depletion
TB-4Sa_gene_exp_rRNA_depletion.txt
TB-9Sd_gene_exp_rRNA_depletion.txt


title: 5Lb_2D_rep1 [RNA-seq_rRNA removal]

description:
TB-5Lb_gene_exp_rRNA_depletion_bioreps.txt
5Lb_2D_5L17
TB-5Lb_disomy_comparison_rRNA_depletion
TB-5Lb_gene_exp_rRNA_depletion.txt


title: bladder tumour 1567

description: bladder tumour


title: bladder tumour 1559

description: bladder tumour


title: 4Lb_2D_rep4 [RNA-seq_rRNA removal]

description:
TB-4Lb_gene_exp_rRNA_depletion_bioreps.txt
4Lb_2D_4Lb50
TB-4Lb_disomy_comparison_rRNA_depletion
TB-4Lb_gene_exp_rRNA_depletion.txt


title: bladder tumour 1685

description: bladder tumour


title: 4Lb_2D_rep3 [RNA-seq_rRNA removal]

description:
TB-4Lb_gene_exp_rRNA_depletion_bioreps.txt
4Lb_2D_4Lb49
TB-4Lb_disomy_comparison_rRNA_depletion
TB-4Lb_gene_exp_rRNA_depletion.txt


title: bladder tumour 1530

description: bladder tumour


title: 4Lb_2D_rep5 [RNA-seq_rRNA removal]

description:
TB-4Lb_gene_exp_rRNA_depletion_bioreps.txt
4Lb_2D_4Lb52
TB-4Lb_disomy_comparison_rRNA_depletion
TB-4Lb_gene_exp_rRNA_depletion.txt


title: 4Lb_2D_rep2 [RNA-seq_rRNA removal]

description:
TB-4Lb_gene_exp_rRNA_depletion_bioreps.txt
4Lb_2D_4Lb48
TB-4Lb_disomy_comparison_rRNA_depletion
TB-4Lb_gene_exp_rRNA_depletion.txt


title: bladder tumour 1566

description: bladder tumour


title: 3Sb_2D_rep5 [RNA-seq_rRNA removal]

description:
TB-3Sb_gene_exp_rRNA_depletion_bioreps.txt
3Sb_2D_3Sb28
TB-3Sb_disomy_comparison_rRNA_depletion
TB-3Sb_gene_exp_rRNA_depletion.txt


title: 4Lb_2D_rep1 [RNA-seq_rRNA removal]

description:
TB-4Lb_gene_exp_rRNA_depletion_bioreps.txt
4Lb_2D_4Lb34
TB-4Lb_disomy_comparison_rRNA_depletion
TB-4Lb_gene_exp_rRNA_depletion.txt


title: bladder tumour 1520

description: bladder tumour


title: bladder tumour 1527

description: bladder tumour


title: 3Sb_2D_rep4 [RNA-seq_rRNA removal]

description:
TB-3Sb_gene_exp_rRNA_depletion_bioreps.txt
3Sb_2D_3Sb26
TB-3Sb_disomy_comparison_rRNA_depletion
TB-3Sb_gene_exp_rRNA_depletion.txt


title: bladder tumour 1481

description: bladder tumour


title: bladder tumour 1514

description: bladder tumour


title: 3Sb_2D_rep2 [RNA-seq_rRNA removal]

description:
TB-3Sb_gene_exp_rRNA_depletion_bioreps.txt
3Sb_2D_3Sb24
TB-3Sb_disomy_comparison_rRNA_depletion
TB-3Sb_gene_exp_rRNA_depletion.txt


title: bladder tumour 1521

description: bladder tumour


title: bladder tumour 1473

description: bladder tumour


title: 3La_2D_rep3 [RNA-seq_rRNA removal]

description:
TB-3La_gene_exp_rRNA_depletion_bioreps.txt
3La_2D_3L36
TB-3La_disomy_comparison_rRNA_depletion
TB-3La_gene_exp_rRNA_depletion.txt


title: bladder tumour 1498

description: bladder tumour


title: 3La_2D_rep4 [RNA-seq_rRNA removal]

description:
TB-3La_gene_exp_rRNA_depletion_bioreps.txt
3La_2D_3L9
TB-3La_disomy_comparison_rRNA_depletion
TB-3La_gene_exp_rRNA_depletion.txt


title: bladder tumour 1467

description: bladder tumour


title: bladder tumour 1517

description: bladder tumour


title: bladder tumour 1503

description: bladder tumour


title: 6Lc_2D_rep1 [RNA-seq_rRNA removal]

description:
TB-6Lc_gene_exp_rRNA_depletion_bioreps.txt
6Lc_2D_6Lc18
TB-6Lc_disomy_comparison_rRNA_depletion
TB-6Lc_gene_exp_rRNA_depletion.txt


title: 3Sb_2D_rep3 [RNA-seq_rRNA removal]

description:
TB-3Sb_gene_exp_rRNA_depletion_bioreps.txt
3Sb_2D_3Sb25
TB-3Sb_disomy_comparison_rRNA_depletion
TB-3Sb_gene_exp_rRNA_depletion.txt


title: bladder tumour 1474

description: bladder tumour


title: bladder tumour 1453

description: bladder tumour


title: 3Sb_2D_rep1 [RNA-seq_rRNA removal]

description:
TB-3Sb_gene_exp_rRNA_depletion_bioreps.txt
3Sb_2D_3Sb20
TB-3Sb_disomy_comparison_rRNA_depletion
TB-3Sb_gene_exp_rRNA_depletion.txt


title: bladder tumour 1500

description: bladder tumour


title: 3La_2D_rep1 [RNA-seq_rRNA removal]

description:
TB-3La_gene_exp_rRNA_depletion_bioreps.txt
3La_2D_3L10
TB-3La_disomy_comparison_rRNA_depletion
TB-3La_gene_exp_rRNA_depletion.txt


title: 3La_2D_rep2 [RNA-seq_rRNA removal]

description:
TB-3La_gene_exp_rRNA_depletion_bioreps.txt
3La_2D_3L33
TB-3La_disomy_comparison_rRNA_depletion
TB-3La_gene_exp_rRNA_depletion.txt


title: bladder tumour 1440

description: bladder tumour


title: 2Sa_2D_rep4 [RNA-seq_rRNA removal]

description:
TB-2Sa_gene_exp_rRNA_depletion_bioreps.txt
2Sa_2D_2S9
TB-2Sa_disomy_comparison_rRNA_depletion
TB-2Sa_gene_exp_rRNA_depletion.txt


title: bladder tumour 1457

description: bladder tumour


title: 2Sa_2D_rep2 [RNA-seq_rRNA removal]

description:
TB-2Sa_gene_exp_rRNA_depletion_bioreps.txt
2Sa_2D_2S16
TB-2Sa_disomy_comparison_rRNA_depletion
TB-2Sa_gene_exp_rRNA_depletion.txt


title: 2Sa_2D_rep3 [RNA-seq_rRNA removal]

description:
TB-2Sa_gene_exp_rRNA_depletion_bioreps.txt
2Sa_2D_2S17
TB-2Sa_disomy_comparison_rRNA_depletion
TB-2Sa_gene_exp_rRNA_depletion.txt


title: 2Sa_2D_rep1 [RNA-seq_rRNA removal]

description:
TB-2Sa_gene_exp_rRNA_depletion_bioreps.txt
2Sa_2D_2S10
TB-2Sa_disomy_comparison_rRNA_depletion
TB-2Sa_gene_exp_rRNA_depletion.txt


title: 2Sa_deletion_2D_rep3 [RNA-seq_rRNA removal]

description:
TB-2Sa_deletion_gene_exp_rRNA_depletion_bioreps.txt
2Sa_deletion_2D_2S8
TB-2Sa_deletion_disomy_comparison_rRNA_depletion
TB-2Sa_deletion_gene_exp_rRNA_depletion.txt


title: 2Sa_deletion_2D_rep2 [RNA-seq_rRNA removal]

description:
TB-2Sa_deletion_gene_exp_rRNA_depletion_bioreps.txt
2Sa_deletion_2D_2S7
TB-2Sa_deletion_disomy_comparison_rRNA_depletion
TB-2Sa_deletion_gene_exp_rRNA_depletion.txt


title: 1Sb_2D_rep6 [RNA-seq_rRNA removal]

description:
TB-1Sb_gene_exp_rRNA_depletion_bioreps.txt
1Sb_2D_1S9
TB-1Sb_disomy_comparison_rRNA_depletion
TB-1Sb_gene_exp_rRNA_depletion.txt


title: bladder tumour 1436

description: bladder tumour


title: 2Sa_deletion_2D_rep1 [RNA-seq_rRNA removal]

description:
TB-2Sa_deletion_gene_exp_rRNA_depletion_bioreps.txt
2Sa_deletion_2D_2S5
TB-2Sa_deletion_disomy_comparison_rRNA_depletion
TB-2Sa_deletion_gene_exp_rRNA_depletion.txt


title: 1Sb_2D_rep3 [RNA-seq_rRNA removal]

description:
TB-1Sb_gene_exp_rRNA_depletion_bioreps.txt
1Sb_2D_1S168
TB-1Sb_disomy_comparison_rRNA_depletion
TB-1Sb_gene_exp_rRNA_depletion.txt


title: bladder tumour 1443

description: bladder tumour


title: 1Sb_2D_rep4 [RNA-seq_rRNA removal]

description:
TB-1Sb_gene_exp_rRNA_depletion_bioreps.txt
1Sb_2D_1S169
TB-1Sb_disomy_comparison_rRNA_depletion
TB-1Sb_gene_exp_rRNA_depletion.txt


title: 1Sb_2D_rep2 [RNA-seq_rRNA removal]

description:
TB-1Sb_gene_exp_rRNA_depletion_bioreps.txt
1Sb_2D_1S158
TB-1Sb_disomy_comparison_rRNA_depletion
TB-1Sb_gene_exp_rRNA_depletion.txt


title: bladder tumour 1419

description: bladder tumour


title: bladder tumour 1485

description: bladder tumour


title: bladder tumour 1407

description: bladder tumour


title: 1Sb_2D_rep1 [RNA-seq_rRNA removal]

description:
TB-1Sb_gene_exp_rRNA_depletion_bioreps.txt
1Sb_2D_1S154
TB-1Sb_disomy_comparison_rRNA_depletion
TB-1Sb_gene_exp_rRNA_depletion.txt


title: bladder tumour 1428

description: bladder tumour


title: bladder tumour 1408

description: bladder tumour


title: 1La_2D_rep4 [RNA-seq_rRNA removal]

description:
TB-1La_gene_exp_rRNA_depletion_bioreps.txt
1La_2D_1L5
TB-1La_disomy_comparison_rRNA_depletion
TB-1La_gene_exp_rRNA_depletion.txt


title: 1Sb_2D_rep5 [RNA-seq_rRNA removal]

description:
TB-1Sb_gene_exp_rRNA_depletion_bioreps.txt
1Sb_2D_1S170
TB-1Sb_disomy_comparison_rRNA_depletion
TB-1Sb_gene_exp_rRNA_depletion.txt


title: 1La_2D_rep3 [RNA-seq_rRNA removal]

description:
TB-1La_gene_exp_rRNA_depletion_bioreps.txt
1La_2D_1L19
TB-1La_disomy_comparison_rRNA_depletion
TB-1La_gene_exp_rRNA_depletion.txt


title: bladder tumour 1390

description: bladder tumour


title: bladder tumour 1392

description: bladder tumour


title: bladder tumour 1387

description: bladder tumour


title: bladder tumour 1385

description: bladder tumour


title: bladder tumour 1361

description: bladder tumour


title: bladder tumour 1395

description: bladder tumour


title: bladder tumour 1358

description: bladder tumour


title: 1La_2D_rep2 [RNA-seq_rRNA removal]

description:
TB-1La_gene_exp_rRNA_depletion_bioreps.txt
1La_2D_1L11
TB-1La_disomy_comparison_rRNA_depletion
TB-1La_gene_exp_rRNA_depletion.txt


title: bladder tumour 1337

description: bladder tumour


title: bladder tumour 1383

description: bladder tumour


title: 1La_2D_rep1 [RNA-seq_rRNA removal]

description:
TB-1La_gene_exp_rRNA_depletion_bioreps.txt
1La_2D_1L10
TB-1La_disomy_comparison_rRNA_depletion
TB-1La_gene_exp_rRNA_depletion.txt


title: 10L19_2D_rep5 [RNA-seq_rRNA removal]

description:
TB-10L19_gene_exp_rRNA_depletion_bioreps.txt
10L19_2D_10L1962
TB-10L19_disomy_comparison_rRNA_depletion
TB-10L19_gene_exp_rRNA_depletion.txt


title: 10L19_2D_rep4 [RNA-seq_rRNA removal]

description:
TB-10L19_gene_exp_rRNA_depletion_bioreps.txt
10L19_2D_10L1961
TB-10L19_disomy_comparison_rRNA_depletion
TB-10L19_gene_exp_rRNA_depletion.txt


title: 10L19_2D_rep3 [RNA-seq_rRNA removal]

description:
TB-10L19_gene_exp_rRNA_depletion_bioreps.txt
10L19_2D_10L1960
TB-10L19_disomy_comparison_rRNA_depletion
TB-10L19_gene_exp_rRNA_depletion.txt


title: bladder tumour 1335

description: bladder tumour


title: 10L19_2D_rep2 [RNA-seq_rRNA removal]

description:
TB-10L19_gene_exp_rRNA_depletion_bioreps.txt
10L19_2D_10L1935
TB-10L19_disomy_comparison_rRNA_depletion
TB-10L19_gene_exp_rRNA_depletion.txt


title: bladder tumour 1326

description: bladder tumour


title: bladder tumour 1325

description: bladder tumour


title: 10L19_2D_rep1 [RNA-seq_rRNA removal]

description:
TB-10L19_gene_exp_rRNA_depletion_bioreps.txt
10L19_2D_10L1934
TB-10L19_disomy_comparison_rRNA_depletion
TB-10L19_gene_exp_rRNA_depletion.txt


title: bladder tumour 1318

description: bladder tumour


title: 5637 cells no antibody rep_1

city: Philadelphia

first: M

middle: Celeste

last: Simon

state: Pennsylvania

address: 421 Curie Boulevard, Rm 456 BRB II/III

department: Abramson Family Cancer Research Institute

institute: University of Pennsylvania

description:
DJS7_Input
Input control

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.4.
ChIP-seq reads were aligned to the mm10 genome assembly using EasyAlign version 3.2.
Peaks were called using PeaksFind version 2.2 with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3).
Bam files were processed into tag directories with homer.
Tag directories were summarized into bedgraph files with homer.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: bedgraph files indicating genomic coverage for each sample.

molecule: genomic DNA

source_name: 5637 urothelial carcinoma cells

growth_protocol: 5637 Human UC cells were cultured in RPMI supplemented with 10% FBS.

extract_protocol:
Whole cell extracts of cells crosslinked with 1% formaldehyde for 15 minutes at room temperature, followed by quenching with 125 mM glycine for 5 minutes.
Sonication via a Diagenode Bioruptor followed by centrifugation to remove cellular debris from sheared chromatin.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).

treatment_protocol: 5637 UC cells evaluated by chromatin-precipitation followed by deep sequencing for PPARg, RXR, and IgG controls to investigate PPARg occupancy genome-wide in UC.

tag: cell line

tag: cell type

value: urothelial carcinoma cells

tag: chip antibody


title: 5637 cells no antibody rep_2

description:
DJS8_Input
Input control


title: 5637 cells IgG antibody rep_2

description:
DJS4_IgG
IgG control

value: Normal Rabbit IgG (Cell Signaling Technologies, cat. 2729)


title: 5637 cells RXR antibody rep_1

description:
DJS5_RXR
RXR Ab
RXRalpha/beta/gamma (Santa Cruz, cat. sc-774)


title: 5637 cells RXR antibody rep_2

description:
DJS6_RXR
RXR Ab
RXRalpha/beta/gamma (Santa Cruz, cat. sc-774)


title: 5637 cells PPARg antibody rep_2

description:
DJS2_PPARg
PPARg Ab

value: PPARg (Santa Cruz, cat. sc-7196)


title: bladder tumour 1315

description: bladder tumour


title: 5637 cells PPARg antibody rep_1

description:
DJS1_PPARg
PPARg Ab


title: Parental cells, PPARG inhibitor treated rep_4

description:
CTT4
16samp_counts_salmonTxi.csv

data_processing:
Standard Illumina Casava pipeline for basecalling, demultiplexing and adapter trimming to yield fastq files.
Raw data were counted against transcripts described in Gencode v28 using salmon.
Counts per gene were summarized from transcript counts using tximport.
Genome_build: GRCh38.p12 - Gencode v28
Supplementary_files_format_and_content: 16samp_counts_salmonTxi.csv: Ensembl gene IDs with raw counts per sample - comma-separated values.

growth_protocol: Human 5637 UC cells were grown in RPMI supplemented with 10% FBS.

extract_protocol:
Total RNA was isolated from four technical replicates of each experimental treatment using TRIzol (ThermoFisher Scientific cat. # 15596026) and RNeasy.
NEBNext Ultra II RNA Library Prep Kit for Illumina was used to prepare ~250-300 bp insert cDNA, non-directional libraries according to manufacturer's instructions at Novogene Corporation.

treatment_protocol: 5637 cells were either untreated controls, or treated with 100 nM T0070907 to inhibit PPARg  or two different sgRNAs (PPARG sgRNA 6 and PPARG sgRNA 9).

tag: treatment

value: PPARg inhibitor (100 nM T0070907), 96 hrs


title: Parental cells, PPARG inhibitor treated rep_3

description:
CTT3
16samp_counts_salmonTxi.csv


title: bladder tumour 1305

description: bladder tumour


title: bladder tumour 1313

description: bladder tumour


title: bladder tumour 1289

description: bladder tumour


title: bladder tumour 1285

description: bladder tumour


title: bladder tumour 1307

description: bladder tumour


title: bladder tumour 1300

description: bladder tumour


title: 5637 cells IgG antibody rep_1

description:
DJS3_IgG
IgG control


title: bladder tumour 1279

description: bladder tumour


title: bladder tumour 1252

description: bladder tumour


title: Parental cells, PPARG inhibitor treated rep_1

description:
CTT1
16samp_counts_salmonTxi.csv


title: bladder tumour 1283

description: bladder tumour


title: Parental cells, DMSO treated rep_4

description:
CTD4
16samp_counts_salmonTxi.csv

value: DMSO control, 96 hrs


title: bladder tumour 1234

description: bladder tumour


title: bladder tumour 1249

description: bladder tumour


title: bladder tumour 1273

description: bladder tumour


title: Parental cells, DMSO treated rep_1

description:
CTD1
16samp_counts_salmonTxi.csv


title: PPARG sgRNA #9 rep_4

description:
CR94
16samp_counts_salmonTxi.csv

value: PPARG sgRNA #9


title: bladder tumour 1222

description: bladder tumour


title: bladder tumour 1213

description: bladder tumour


title: PPARG sgRNA #9 rep_3

description:
CR93
16samp_counts_salmonTxi.csv


title: bladder tumour 1214

description: bladder tumour


title: Parental cells, DMSO treated rep_3

description:
CTD3
16samp_counts_salmonTxi.csv


title: PPARG sgRNA #9 rep_2

description:
CR92
16samp_counts_salmonTxi.csv


title: bladder tumour 1211

description: bladder tumour


title: bladder tumour 1210

description: bladder tumour


title: PPARG sgRNA #9 rep_1

description:
CR91
16samp_counts_salmonTxi.csv


title: Parental cells, DMSO treated rep_2

description:
CTD2
16samp_counts_salmonTxi.csv


title: PPARG sgRNA #6 rep_3

description:
CR63
16samp_counts_salmonTxi.csv

value: PPARG sgRNA #6


title: bladder tumour 1181

description: bladder tumour


title: PPARG sgRNA #6 rep_2

description:
CR62
16samp_counts_salmonTxi.csv


title: PPARG sgRNA #6 rep_1

description:
CR61
16samp_counts_salmonTxi.csv


title: bladder tumour 1145

description: bladder tumour


title: bladder tumour 1144

description: bladder tumour


title: bladder tumour 1124

description: bladder tumour


title: PPARG sgRNA #6 rep_4

description:
CR64
16samp_counts_salmonTxi.csv


title: bladder tumour 1142

description: bladder tumour


title: bladder tumour 1177

description: bladder tumour


title: Asynchronous_IPSc_mut_rep1

city: Goettingen

first: Argyris

last: Papantonis

address: Robert-Koch-Str 40

department: Department of Pathology

country: Germany

institute: University Medical Center Goettingen

data_processing:
mapped with Bowtie2 to hg38 and dm6
filtered to remove non-primary, unmapped, duplicate and mitochondrial reads
spike-in scaling factors calculated from dm6 mapped reads with ChIPseqSpike
scaled with spike-in scaling factors and RPKM normalized with Deeptools to produce bigwig files
Genome_build: hg38

source_name: induced pluripotent stem cells

extract_protocol:
Transposase-accessible chromatin was obtained from frozen human IPSc and D. Melanogaster S2 cells according to ATAC-seq protocol (Buenrostro et al. 2013; 2015), with modifications. Briefly, 100 000 IPSc cells per replicate were spiked-in with 200 S2 cells, washed in PBS and lysed in cell lysis buffer (10 mM Tris-Hcl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.1% Tween-20 and 0.01% digitonin) for 3 minutes (Corces et al. 2017). Lysates were washed with washing buffer (10 mM Tris-Hcl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20) and pelleted. Isolated nuclei were resuspended in transposase reaction mix (25 ul 2X TD buffer, 16.5 ul 1X PBS, 0.5 ul 10% Tween-20, 0.5 ul 1% digitonin, 2.5 ul of Tn5 Transposase and 5 ul of nuclease-free H2O) and incubated at 37°C for 30 minutes on thermomixer at 1000 rpm. Transposase reaction was terminated by addition of stop buffer (50 mM Tris-Hcl pH 8, 10 mM EDTA, 1% SDS) (Stewart-Morgan, Reverón-Gómez, and Groth 2019). Reaction components were removed with DNA Clean&Concentrator kit (Zymo) and extracted chromatin was used for library construction and subsequent sequencing.
Standard DNA library prep (Buenrostro et al 2015)

tag: passage

value: Passage 45

tag: genotype

value: CHD6 Mutant


title: Asynchronous_IPSc_mut_rep2


title: Asynchronous_IPSc_wt_rep1

value: Passage 19

value: Wild-type


title: bladder tumour 1137

description: bladder tumour


title: bladder tumour 1138

description: bladder tumour


title: Asynchronous_IPSc_wt_rep2


title: Parental cells, PPARG inhibitor treated rep_2

description:
CTT2
16samp_counts_salmonTxi.csv


title: bladder tumour 1167

description: bladder tumour


title: bladder tumour 1103

description: bladder tumour


title: A549 cells treated with DEX for 12hr 12h after DEX removal - rep2

city: Durham

first: Charles

last: Gersbach

state: North Carolina

address: 101 science drive rm 2323

institute: Duke University

description:
A549.rna_seq.dedex.12h.rep2
processed data file: A549.rna_seq.dedex.12h.rep2.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

data_processing:
Sequences for TruSeq Illumina adapters were removed from the raw reads using Trimmomatic v0.32 (Bolger et al., 2014).
Reads were aligned against the latest mouse reference genome (GRCh38) using the aligner STAR v2.4.1a following the proposed 2-pass strategy, removing alignments containing non-canonical splice junctions (--outFilterIntronMotifs RemoveNoncanonical)
Aligned reads were assigned to genes in the GENCODE v22 comprehensive gene annotation using the featureCounts command in the subread package with default settings (v1.4.6-p4)
Differential expression analysis was performed using DESeq2 (v1.22.0) running on R (v3.5.1). Briefly, raw counts were imported and filtered to remove genes with low or no expression, that is, keeping genes having two or more counts per million (CPMs) in two or more samples.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited files with TPM gene counts

source_name: A549 treated with DEX for 12h, 12h after DEX removal

growth_protocol: Seeded out 10 M seed stock of A549 cells. Changed media after 48 hours. Performed a 1:10 split into 10 plates after 72 hours. Performed a6:12 split into 12 plates 72 hours later. Performed a final 12:48 split into 12 plates and into 12 6-well plates

extract_protocol:
Harvested plates at timepoints (0,0.5, 1, 2 3, 4, 5, 6, 7, 8, 10, 12) by removing media, washing with 3 mL PBS twice, and lysing with RLT+ beta-mercaptoethanol
Cleaned total RNA with Qiagen RNA midiprep kits, and used Illumina mRNA prep kits

treatment_protocol: Treated with 3 uL of 100 uM Dexamethasone dissolved in Ethanol for 12 hours. After 12 hours, removed the media containing dexamethasone and replaced with media that did not contain dex

tag: cell line background

tag: tissue/cell type

value: adenocarcinomic human alveolar basal epithelial

value: DEX for 12h, 12h after DEX removal


title: A549 cells treated with DEX for 12hr 12h after DEX removal - rep3

description:
A549.rna_seq.dedex.12h.rep3
processed data file: A549.rna_seq.dedex.12h.rep3.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: bladder tumour 1115

description: bladder tumour


title: bladder tumour 1094

description: bladder tumour


title: A549 cells treated with DEX for 12hr 12h after DEX removal - rep1

description:
A549.rna_seq.dedex.12h.rep1
processed data file: A549.rna_seq.dedex.12h.rep1.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: A549 cells treated with DEX for 12hr 10h after DEX removal - rep3

description:
A549.rna_seq.dedex.10h.rep3
processed data file: A549.rna_seq.dedex.10h.rep3.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: A549 treated with DEX for 12h, 10h after DEX removal

value: DEX for 12h, 10h after DEX removal


title: bladder tumour 1106

description: bladder tumour


title: bladder tumour 1087

description: bladder tumour


title: bladder tumour 1117

description: bladder tumour


title: A549 cells treated with DEX for 12hr 08h after DEX removal - rep2

description:
A549.rna_seq.dedex.08h.rep2
processed data file: A549.rna_seq.dedex.08h.rep2.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: A549 treated with DEX for 12h, 08h after DEX removal

value: DEX for 12h, 08h after DEX removal


title: A549 cells treated with DEX for 12hr 08h after DEX removal - rep3

description:
A549.rna_seq.dedex.08h.rep3
processed data file: A549.rna_seq.dedex.08h.rep3.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: bladder tumour 1083

description: bladder tumour


title: bladder tumour 1081

description: bladder tumour

value: tumour stageT1


title: A549 cells treated with DEX for 12hr 07h after DEX removal - rep3

description:
A549.rna_seq.dedex.07h.rep3
processed data file: A549.rna_seq.dedex.07h.rep3.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: A549 treated with DEX for 12h, 07h after DEX removal

value: DEX for 12h, 07h after DEX removal


title: bladder tumour 1067

description: bladder tumour

value: tumour stageTa


title: A549 cells treated with DEX for 12hr 10h after DEX removal - rep2

description:
A549.rna_seq.dedex.10h.rep2
processed data file: A549.rna_seq.dedex.10h.rep2.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: bladder tumour 1058

description: bladder tumour


title: A549 cells treated with DEX for 12hr 10h after DEX removal - rep1

description:
A549.rna_seq.dedex.10h.rep1
processed data file: A549.rna_seq.dedex.10h.rep1.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: bladder tumour 1062

description: bladder tumour


title: A549 cells treated with DEX for 12hr 07h after DEX removal - rep1

description:
A549.rna_seq.dedex.07h.rep1
processed data file: A549.rna_seq.dedex.07h.rep1.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: bladder tumour 1063

description: bladder tumour


title: bladder tumour 1053

description: bladder tumour


title: A549 cells treated with DEX for 12hr 06h after DEX removal - rep3

description:
A549.rna_seq.dedex.06h.rep3
processed data file: A549.rna_seq.dedex.06h.rep3.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: A549 treated with DEX for 12h, 06h after DEX removal

value: DEX for 12h, 06h after DEX removal


title: bladder tumour 1047

description: bladder tumour


title: A549 cells treated with DEX for 12hr 08h after DEX removal - rep1

description:
A549.rna_seq.dedex.08h.rep1
processed data file: A549.rna_seq.dedex.08h.rep1.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: bladder tumour 1016

description: bladder tumour


title: A549 cells treated with DEX for 12hr 07h after DEX removal - rep2

description:
A549.rna_seq.dedex.07h.rep2
processed data file: A549.rna_seq.dedex.07h.rep2.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: A549 cells treated with DEX for 12hr 06h after DEX removal - rep2

description:
A549.rna_seq.dedex.06h.rep2
processed data file: A549.rna_seq.dedex.06h.rep2.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: A549 cells treated with DEX for 12hr 06h after DEX removal - rep1

description:
A549.rna_seq.dedex.06h.rep1
processed data file: A549.rna_seq.dedex.06h.rep1.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: A549 cells treated with DEX for 12hr 05h after DEX removal - rep3

description:
A549.rna_seq.dedex.05h.rep3
processed data file: A549.rna_seq.dedex.05h.rep3.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: A549 treated with DEX for 12h, 05h after DEX removal

value: DEX for 12h, 05h after DEX removal


title: bladder tumour 1023

description: bladder tumour


title: bladder tumour 1038

description: bladder tumour


title: A549 cells treated with DEX for 12hr 05h after DEX removal - rep1

description:
A549.rna_seq.dedex.05h.rep1
processed data file: A549.rna_seq.dedex.05h.rep1.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: bladder tumour 990

description: bladder tumour


title: A549 cells treated with DEX for 12hr 04h after DEX removal - rep2

description:
A549.rna_seq.dedex.04h.rep2
processed data file: A549.rna_seq.dedex.04h.rep2.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: A549 treated with DEX for 12h, 04h after DEX removal

value: DEX for 12h, 04h after DEX removal


title: bladder tumour 1017

description: bladder tumour


title: A549 cells treated with DEX for 12hr 04h after DEX removal - rep3

description:
A549.rna_seq.dedex.04h.rep3
processed data file: A549.rna_seq.dedex.04h.rep3.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: A549 cells treated with DEX for 12hr 05h after DEX removal - rep2

description:
A549.rna_seq.dedex.05h.rep2
processed data file: A549.rna_seq.dedex.05h.rep2.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: A549 cells treated with DEX for 12hr 03h after DEX removal - rep2

description:
A549.rna_seq.dedex.03h.rep2
processed data file: A549.rna_seq.dedex.03h.rep2.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: A549 treated with DEX for 12h, 03h after DEX removal

value: DEX for 12h, 03h after DEX removal


title: bladder tumour 981

description: bladder tumour


title: A549 cells treated with DEX for 12hr 02h after DEX removal - rep3

description:
A549.rna_seq.dedex.02h.rep3
processed data file: A549.rna_seq.dedex.02h.rep3.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: A549 treated with DEX for 12h, 02h after DEX removal

value: DEX for 12h, 02h after DEX removal


title: bladder tumour 940

description: bladder tumour


title: A549 cells treated with DEX for 12hr 03h after DEX removal - rep1

description:
A549.rna_seq.dedex.03h.rep1
processed data file: A549.rna_seq.dedex.03h.rep1.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: bladder tumour 936

description: bladder tumour


title: A549 cells treated with DEX for 12hr 02h after DEX removal - rep1

description:
A549.rna_seq.dedex.02h.rep1
processed data file: A549.rna_seq.dedex.02h.rep1.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: bladder tumour 930

description: bladder tumour


title: bladder tumour 933

description: bladder tumour


title: A549 cells treated with DEX for 12hr 02h after DEX removal - rep2

description:
A549.rna_seq.dedex.02h.rep2
processed data file: A549.rna_seq.dedex.02h.rep2.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: A549 cells treated with DEX for 12hr 01h after DEX removal - rep3

description:
A549.rna_seq.dedex.01h.rep3
processed data file: A549.rna_seq.dedex.01h.rep3.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: A549 treated with DEX for 12h, 01h after DEX removal

value: DEX for 12h, 01h after DEX removal


title: A549 cells treated with DEX for 12hr 04h after DEX removal - rep1

description:
A549.rna_seq.dedex.04h.rep1
processed data file: A549.rna_seq.dedex.04h.rep1.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: bladder tumour 811

description: bladder tumour


title: bladder tumour 865

description: bladder tumour


title: bladder tumour 894

description: bladder tumour


title: bladder tumour 866

description: bladder tumour


title: bladder tumour 787

description: bladder tumour


title: bladder tumour 589

description: bladder tumour


title: A549 cells treated with DEX for 12hr 01h after DEX removal - rep2

description:
A549.rna_seq.dedex.01h.rep2
processed data file: A549.rna_seq.dedex.01h.rep2.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: bladder tumour 934

description: bladder tumour


title: A549 cells treated with DEX for 12hr - rep3

description:
A549.rna_seq.dedex.00h.rep3
processed data file: A549.rna_seq.dedex.00h.rep3.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: A549 treated with DEX for 12h

value: DEX for 12h


title: A549 cells treated with DEX for 12hr 01h after DEX removal - rep1

description:
A549.rna_seq.dedex.01h.rep1
processed data file: A549.rna_seq.dedex.01h.rep1.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: bladder tumour 578

description: bladder tumour


title: bladder tumour 705

description: bladder tumour


title: bladder tumour 571

description: bladder tumour


title: A549 cells treated with DEX for 12hr - rep2

description:
A549.rna_seq.dedex.00h.rep2
processed data file: A549.rna_seq.dedex.00h.rep2.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: A549 cells treated with DEX for 12hr - rep1

description:
A549.rna_seq.dedex.00h.rep1
processed data file: A549.rna_seq.dedex.00h.rep1.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: bladder tumour 672

description: bladder tumour


title: bladder tumour 675

description: bladder tumour


title: A549 cells treated with DEX for 12hr 00h30m after DEX removal - rep3

description:
A549.rna_seq.dedex.00h30m.rep3
processed data file: A549.rna_seq.dedex.00h30m.rep3.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: A549 treated with DEX for 12h, 00h30m after DEX removal

value: DEX for 12h, 00h30m after DEX removal


title: A549 cells treated with DEX for 12hr 00h30m after DEX removal - rep2

description:
A549.rna_seq.dedex.00h30m.rep2
processed data file: A549.rna_seq.dedex.00h30m.rep2.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Modified A549 cells with TFCP2L1 Overexpressed and treated with DEX for 12h - rep2

description:
A549_OE_TFCP2L1.rnaseq.dex.12h.rep2
processed data file: A549_OE_TFCP2L1.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: Modified A549_TFCP2L1 Overexpressed and treated with DEX for 12h

treatment_protocol:
Seeded out 10 M seed stock of A549 cells. Changed media after 48 hours. Performed a 1:10 split into 10 plates after 72 hours. Performed a6:12 split into 12 plates 72 hours later. Performed a final 12:48 split into 12 plates and into 12 6-well plates
Treated with 3 uL of 100 uM Dexamethasone dissolved in Ethanol for 12 hours. After 12 hours, removed the media containing dexamethasone and replaced with media that did not contain dex

tag: genotype/variation

value: TFCP2L1 Overexpressed

value: dexamethasone (DEX)

tag: time point


title: A549 cells treated with DEX for 12hr 03h after DEX removal - rep3

description:
A549.rna_seq.dedex.03h.rep3
processed data file: A549.rna_seq.dedex.03h.rep3.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

value: adenocarcinomic human alveolar basal epithelial


title: Modified A549 cells with TFCP2L1 Overexpressed and treated with DEX for 12h - rep1

description:
A549_OE_TFCP2L1.rnaseq.dex.12h.rep1
processed data file: A549_OE_TFCP2L1.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: A549 cells treated with DEX for 12hr 00h30m after DEX removal - rep1

description:
A549.rna_seq.dedex.00h30m.rep1
processed data file: A549.rna_seq.dedex.00h30m.rep1.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Modified A549 cells with TFCP2L1 Overexpressed and treated with DEX for 08h - rep3

description:
A549_OE_TFCP2L1.rnaseq.dex.08h.rep3
processed data file: A549_OE_TFCP2L1.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: Modified A549_TFCP2L1 Overexpressed and treated with DEX for 08h


title: bladder tumour 567

description: bladder tumour

source_name: fresh frozen bladder tumour tissue


title: bladder tumour 555

description: bladder tumour


title: Modified A549 cells with TFCP2L1 Overexpressed and treated with DEX for 08h - rep1

description:
A549_OE_TFCP2L1.rnaseq.dex.08h.rep1
processed data file: A549_OE_TFCP2L1.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Modified A549 cells with TFCP2L1 Overexpressed and treated with DEX for 04h - rep2

description:
A549_OE_TFCP2L1.rnaseq.dex.04h.rep2
processed data file: A549_OE_TFCP2L1.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: Modified A549_TFCP2L1 Overexpressed and treated with DEX for 04h


title: bladder tumour 557

description: bladder tumour


title: bladder tumour 535

description: bladder tumour


title: bladder tumour 544

description: bladder tumour


title: Modified A549 cells with TFCP2L1 Overexpressed and treated with DEX for 04h - rep3

description:
A549_OE_TFCP2L1.rnaseq.dex.04h.rep3
processed data file: A549_OE_TFCP2L1.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Modified A549 cells with TFCP2L1 Overexpressed and treated with DEX for 08h - rep2

description:
A549_OE_TFCP2L1.rnaseq.dex.08h.rep2
processed data file: A549_OE_TFCP2L1.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Modified A549 cells with TFCP2L1 Overexpressed and treated with DEX for 12h - rep3

description:
processed data file: A549_OE_TFCP2L1.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt
A549_OE_TFCP2L1.rnaseq.dex.12h.rep3

growth_protocol: Seeded 2 and a half 6-well plates at 0.55 M cells (.092 M cells per well) in a total volume of 3 mL per well for a total of 15 wells per line. Let cells grow to 80-90% confluency.

extract_protocol:
Harvested plates at timepoints (0,1, 4, 8, and 12) by removing media, washing with 3 mL PBS twice, and lysing with RLT+ beta-mercaptoethanol
Cleaned total RNA with Qiagen RNA midiprep kits, and used Illumina mRNA prep kits

treatment_protocol: Treated with 3 uL of 100 uM Dexamethasone dissolved in Ethanol at 1 hr, 4 hr, 8 hr and 12 hr


title: Modified A549 cells with TFCP2L1 Overexpressed and treated with DEX for 04h - rep1

description:
A549_OE_TFCP2L1.rnaseq.dex.04h.rep1
processed data file: A549_OE_TFCP2L1.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: bladder tumour 494

description: bladder tumour


title: Modified A549 cells with TFCP2L1 Overexpressed and treated with DEX for 01h - rep2

description:
A549_OE_TFCP2L1.rnaseq.dex.01h.rep2
processed data file: A549_OE_TFCP2L1.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: Modified A549_TFCP2L1 Overexpressed and treated with DEX for 01h


title: bladder tumour 534

description: bladder tumour


title: bladder tumour 419

description: bladder tumour


title: Modified A549 cells with TFCP2L1 Overexpressed and treated with DEX for 01h - rep3

description:
A549_OE_TFCP2L1.rnaseq.dex.01h.rep3
processed data file: A549_OE_TFCP2L1.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: bladder tumour 411

description: bladder tumour


title: bladder tumour 435

description: bladder tumour


title: Modified A549 cells with TFCP2L1 Overexpressed and treated with DEX for 00h - rep3

description:
A549_OE_TFCP2L1.rnaseq.dex.00h.rep3
processed data file: A549_OE_TFCP2L1.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: Modified A549_TFCP2L1 Overexpressed and treated with DEX for 00h


title: Modified A549 cells with TFCP2L1 Overexpressed and treated with DEX for 00h - rep1

description:
A549_OE_TFCP2L1.rnaseq.dex.00h.rep1
processed data file: A549_OE_TFCP2L1.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: bladder tumour 418

description: bladder tumour


title: Modified A549 cells with TFCP2L1 Overexpressed and treated with DEX for 00h - rep2

description:
A549_OE_TFCP2L1.rnaseq.dex.00h.rep2
processed data file: A549_OE_TFCP2L1.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Modified A549 cells with OCT4 Overexpressed and treated with DEX for 12h - rep3

description:
A549_OE_OCT4.rnaseq.dex.12h.rep3
processed data file: A549_OE_OCT4.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: Modified A549_OCT4 Overexpressed and treated with DEX for 12h

value: OCT4 Overexpressed


title: liver, CLPDCA-4

city: Winston Salem

first: Matthew

middle: Allan

last: Quinn

state: NC

address: 575 N Patterson Ave

department: Pathology

institute: Wake Forest School of Medicine

data_processing:
Raw reads were filtered to exclude pairs with average base quality <20.
Filtered reads pairs were mapped against  mm10 by STAR v2.5 with parameters "--outSAMattrIHstart 0 --outFilterType BySJout --alignSJoverhangMin 8 --limitBAMsortRAM 55000000000 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical".
Counts per gene per sample were collected by featureCounts (Subread v1.5.0-p1) with parameters "-s0 -Sfr -p".
Coverage tracks were generated by STAR v2.5 with parameters “--runMode inputAlignmentsFromBAM --outWigType bedGraph --outWigStrand Unstranded --outWigNorm None”, normalized with size factors as determined by DESeq2, then converted to bigWig format with UCSC utility bedGraphToBigWig.
Genome_build: mm10
Supplementary_files_format_and_content: coverage tracks in bigWig format; RNAseq counts-per-gene in tab-delimited text format

organism: Mus musculus

source_name: liver

extract_protocol:
Livers were homogenized in trizol followed by phenol:chloroform extraction. RNA was further purified with the BioRad Total RNA isolation kit
TruSeq RNA library kit V2

treatment_protocol: Surgieres were performed and 24 hours later mice were injected with respective drugs and liver harvested 6 hours post-injection (30 hours post-surgery)

tag: tissue

value: whole liver

tag: strain

tag: disease state

value: septic

value: cecal ligation puncture with dichloroacetate


title: liver, Sham-1

value: control

value: sham surgical procedure


title: liver, Sham-4


title: liver, Sham-2


title: liver, Sham-3


title: Modified A549 cells with OCT4 Overexpressed and treated with DEX for 12h - rep2

description:
A549_OE_OCT4.rnaseq.dex.12h.rep2
processed data file: A549_OE_OCT4.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Modified A549 cells with OCT4 Overexpressed and treated with DEX for 12h - rep1

description:
A549_OE_OCT4.rnaseq.dex.12h.rep1
processed data file: A549_OE_OCT4.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: liver, CLPDCA-3


title: Modified A549 cells with OCT4 Overexpressed and treated with DEX for 08h - rep3

description:
A549_OE_OCT4.rnaseq.dex.08h.rep3
processed data file: A549_OE_OCT4.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: Modified A549_OCT4 Overexpressed and treated with DEX for 08h


title: liver, CLPDCA-2


title: Modified A549 cells with TFCP2L1 Overexpressed and treated with DEX for 01h - rep1

description:
A549_OE_TFCP2L1.rnaseq.dex.01h.rep1
processed data file: A549_OE_TFCP2L1.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: bladder tumour 66

description: bladder tumour

value: tumour stageTa


title: bladder tumour 437

description: bladder tumour


title: bladder tumour 390

description: bladder tumour


title: Modified A549 cells with OCT4 Overexpressed and treated with DEX for 08h - rep2

description:
A549_OE_OCT4.rnaseq.dex.08h.rep2
processed data file: A549_OE_OCT4.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: bladder tumour 315

description: bladder tumour

value: tumour stageT1


title: bladder tumour 377

description: bladder tumour


title: bladder tumour 132

description: bladder tumour


title: bladder tumour 393

description: bladder tumour


title: bladder tumour 103

description: bladder tumour


title: bladder tumour 239

description: bladder tumour


title: bladder tumour 94

description: bladder tumour


title: Modified A549 cells with OCT4 Overexpressed and treated with DEX for 08h - rep1

description:
A549_OE_OCT4.rnaseq.dex.08h.rep1
processed data file: A549_OE_OCT4.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: liver, CLP-4

value: cecal ligation puncture


title: Modified A549 cells with OCT4 Overexpressed and treated with DEX for 04h - rep2

description:
A549_OE_OCT4.rnaseq.dex.04h.rep2
processed data file: A549_OE_OCT4.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: Modified A549_OCT4 Overexpressed and treated with DEX for 04h


title: liver, CLP-2


title: liver, CLP-3


title: liver, CLP-1


title: Modified A549 cells with OCT4 Overexpressed and treated with DEX for 04h - rep1

description:
A549_OE_OCT4.rnaseq.dex.04h.rep1
processed data file: A549_OE_OCT4.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: liver, CLPDCA-1


title: Modified A549 cells with OCT4 Overexpressed and treated with DEX for 01h - rep2

description:
A549_OE_OCT4.rnaseq.dex.01h.rep2
processed data file: A549_OE_OCT4.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: Modified A549_OCT4 Overexpressed and treated with DEX for 01h


title: Modified A549 cells with OCT4 Overexpressed and treated with DEX for 01h - rep3

description:
A549_OE_OCT4.rnaseq.dex.01h.rep3
processed data file: A549_OE_OCT4.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Modified A549 cells with OCT4 Overexpressed and treated with DEX for 00h - rep2

description:
A549_OE_OCT4.rnaseq.dex.00h.rep2
processed data file: A549_OE_OCT4.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: Modified A549_OCT4 Overexpressed and treated with DEX for 00h


title: Modified A549 cells with OCT4 Overexpressed and treated with DEX for 01h - rep1

description:
A549_OE_OCT4.rnaseq.dex.01h.rep1
processed data file: A549_OE_OCT4.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Modified A549 cells with OCT4 Overexpressed and treated with DEX for 00h - rep3

description:
A549_OE_OCT4.rnaseq.dex.00h.rep3
processed data file: A549_OE_OCT4.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: TIL_sc-seq - ADT/HTO

city: Melbourne

first: Conor

last: Kearney

address: Grattan Street

country: Australia

institute: Peter MacCallum cancer Centre

description: CK-06-20-glycan-B16-MC38-TIL-5-Surface_S3

data_processing:
Cell Ranger: Reads were aligned to the mm10 reference genome, cellular barcodes were de-multiplexed and unique molecular identifiers (UMI) and antibody capture (Antibody Derived Tags (ADT) and Hashtag oligos (HTO)) were quantified using 10x Genomics' Cell Ranger software (version 3.1.0). Cell barcodes containing RNA or antibody counts from cells from more than one sample (inter-sample doublets) were identified using Seurat's HTODemux function. Barcodes containing counts from more than one cell within the same sample (intra-sample doublets) were identified using the Scrublet python package (version 0.2.1) (21). A cutoff of more than one median absolute deviation (MAD) value above the median Scrublet score was chosen. Cells identified as either type of doublet were removed from the analysis. Relative transcription factor activity in each cell was estimated using the Single-Cell Regulatory Network Inference And Clustering (SCENIC) method (22). Area-under-curve (AUC) scores for transcription factors were calculated based on inferred gene regulatory networks using the pyscenic python package (version 0.9.19). Gene expression and antibody count matrices were processed in R (version 3.6.1) using the Seurat R package (version 3.1.0) (23). RNA transcript counts for barcodes identified as cells by Cell Ranger were normalized using sctransform via Seurat's SCTransform function. The counts were first transformed with no covariates in the sctransform model then cell cycle phase scores were estimated using Seurat's CellCycleScoring function with mouse homologues of the cell cycle gene sets provided by Seurat. The sctransform normalization was then rerun with the cell cycle phase scores and the percent of raw RNA counts belonging to mitochondrial genes for each cell as variables to be regressed out in the model. ADT counts were log1p transformed and scaled (Z score) or normalized using centered log ratio (CLR) transformation, with either method producing a similar result.  Principal component analysis (PCA) was then performed on the sctransform scaled RNA expression values for genes with residual variance in the sctransform model greater than 1.3. A shared-nearest-neighbours (SNN) network was calculated using the top 10 principal components using the FindNeighbors function with k-nearest neighbors set to 50 and cosine distance metric. The SNN network was then used to identify cell populations using the FindClusters function using the Louvain algorithm with resolution parameter 0.6. Uniform Manifold Approximation and Projection (UMAP) values were also calculated using the RunUMAP function with the top 10 principal components as input and parameters n.neighbors=50 and metric="cosine". Monocle3 was utilized for pseudotime analysis using default setting.
Genome_build: NOT PROVIDED
Supplementary_files_format_and_content: Cell Ranger output

source_name: Tumor-infiltrating T cells

growth_protocol: MC38-OVA cells were grown subcutaneously in C57BL/6 mice

extract_protocol:
Tumors were harvested, processed and FAC sorted for TCRB+CD3+CD90.2+CD11b- cells followed by ADT and HTO tagging and droplet encapsulation for single cell sequencing using 10xGenomics platform
All samples were prepared using the 10x Genomics Single Cell 5′  protocol according to the manufacturer’s instructions up until the cDNA amplification step (10x Genomics, USA). Two picomoles of HTO and ADT additive oligonucleotides were spiked into the cDNA amplification PCR, and cDNA was amplified according to the 10x Single Cell 3′ v3 protocol (10x Genomics, USA). Following cDNA amplification, 0.6X SPRI was used to separate the large cDNA fraction derived from cellular mRNAs (retained on beads) from the ADT- and Cell Hashtag (HTO)-containing fraction (in supernatant). The cDNA fraction was processed according to the 10x Genomics Single Cell 3′ v3 protocol to generate the transcriptome library; indexing was done using Chromium i7 Multiplex Kit. An additional 1.4X reaction volume of SPRI beads was added to the ADT/HTO fraction to bring the ratio up to 2.0X. The beads were washed with 80% ethanol, eluted in water, and an additional round of 2.0X SPRI performed to remove excess single-stranded oligonucleotides from cDNA amplification. After final elution, separate PCRs were set up to generate the CITE-seq ADT library (SI-PCR and RPI-x primers) and the HTO library (SI-PCR and D7xx_s).
Standard 10X genomics library prep

treatment_protocol: Tumors were harvested on day 14 for SUGAR-seq

tag: mouse strain

tag: tumor type

value: MC38-OVA or B16-Ova subcutaneous

tag: target/sample (oligo barcode)

value: PD1 (GAAAGTCAAAGCACT); Tim3 (ATTGGCACTCAGATG); Biotin (CGGTATATCAACAGA); hash#1 (ACCCACCAGTAAGAC); hash#2 (GGTCGAGAGCATTCA)

tag: molecule type

value: Oligonucleotide


title: TIL_sc-seq - TCR

description: CK_06_20_glycan_B16_MC38_TIL_5_VDJ_SI-GA-A1_1_HF7YTDSXY_GGTTTACT

value: total RNA


title: TIL_sc-seq - GEX

description: CK_06_20_glycan_B16_MC38_TIL_5_SI-GA-A2_1_HF7YTDSXY_TTTCATGA


title: sc-seq - ADT/HTO [Glycan-seq-mouseT-cells_S8]


title: Modified A549 cells with OCT4 Overexpressed and treated with DEX for 00h - rep1

description:
A549_OE_OCT4.rnaseq.dex.00h.rep1
processed data file: A549_OE_OCT4.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: sc-seq - GEX [CS_C_GEX_S4]


title: L-Pha low_ATAC-seq [CK-2L_S26]

data_processing:
Bcl2fastq v2.17.1.14 was used for de-multiplexing. The Fastq files generated by sequencing were aligned to the mouse reference genome (GRCm38/mm10) using bowtie (v2.2.3). Samtools (v1.8) was used for manipulation of SAM and BAM files, after which MACS (v2.0.10) was used for peak calling. Browser viewable TDF files were generated using IGVTools (v2.3.72) and ChIP-Seq tracks were visualized using IGV (v2.3.55). Differentially accessible regions were quantitative analyzed using Rsubread featureCounts on merged reference bed file containing all peaks identified across treatment conditions after which the limma-voom package was used for statistical analysis of differentially accessible regions. Subsequently, = HOMER (v4.8.3) was used for motif analysis on MACS2 peak summits using FindMotifGenome.pl for differentially accessible regions using all summits as a background set with the -bg option. ATAC-seq peaks were annotated to genes using the AnnotatePeaks.pl function after which R was used for visualization.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: bigwig

growth_protocol: B16-OVA cells were grown subcutaneously in C57BL/6 mice

extract_protocol:
Tumors were harvested, processed and FACS sorted for TCRB+CD3+ and L-Pha low or high TILs, followed by ATAC-seq
Cells were washed once in ice-cold PBS and lysed in ATAC lysis buffer (0.1% Tween-20, 0.1% NP-40, 3mM MgCl2, 10mM NaCl, 10mM Tris HCl pH 7.4). Tagmentation was performed with Tn5 transposase and 2x TD Buffer (Nextera DNA Library Prep Kit, Ilumina) for 30 minutes at 37°C. Tagmented DNA was purified using a MinElute colum (Qiagen, 28004) and amplified for 12 cycles using 2x KAPA HiFi HotStart ReadyMix (Kapa Biosystems, KK2602). The amplified libraries were purified using MinElute columns (Qiagen) and sequenced on an Ilumina NextSeq 500 with 75 bp single-end reads. Library QC and quantification was performed using D1000 high-sensitivity screen tape with 4200 TapeStation Instrument (Agilent Technologies) and size selected for between 200 bp and 700 bp using a Pippin Prep system (Sage Science).
Nextera DNA Library Prep Kit, Ilumina

value: B16-Ova subcutaneous

value: Tumor-infiltrating T cells

tag: cell subtype

value: L-Pha low


title: L-Pha high_ATAC-seq [CK-2H_S27]

tag: cell type

value: L-Pha high


title: Modified A549 cells with KLF9 Overexpressed and treated with DEX for 12h - rep2

description:
A549_OE_KLF9.rnaseq.dex.12h.rep2
processed data file: A549_OE_KLF9.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: Modified A549_KLF9 Overexpressed and treated with DEX for 12h

value: adenocarcinomic human alveolar basal epithelial

value: KLF9 Overexpressed

value: dexamethasone (DEX)


title: L-Pha low_ATAC-seq [CK-1L_S24]


title: L-Pha high_ATAC-seq [CK-1H_S25]


title: Modified A549 cells with KLF9 Overexpressed and treated with DEX for 12h - rep1

description:
A549_OE_KLF9.rnaseq.dex.12h.rep1
processed data file: A549_OE_KLF9.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Modified A549 cells with OCT4 Overexpressed and treated with DEX for 04h - rep3

description:
A549_OE_OCT4.rnaseq.dex.04h.rep3
processed data file: A549_OE_OCT4.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

value: OCT4 Overexpressed


title: 3H_S62_3'RNA seq 6

data_processing:
Libraries were sequenced on the Illumina NextSeq 500 to obtain 75 b.p. single-end reads. Sequencing files were de-multiplexed using Bcl2fastq (v2.17.1.14) to generate FASTQ files on which QC was performed using FASTQC (v0.11.5). Sequencing reads were trimmed using cutadapt (v1.7) and aligned to the human reference genome (Hg19) using HISAT2 (v2.1.0). Read counting across genomic features was performed using FeatureCounts (from the Subread package, v1.5.0) prior to differential gene expression analysis using Voom/Limma. Gene set enrichment analyses were performed using GSEA software (Broad Institute) and barcode plots were plotted using ReplotGSEA.R (part of the Rtoolbox R package).
Genome_build: human reference genome (Hg19)
Supplementary_files_format_and_content: logcounts, counts

extract_protocol:
Tumors were harvested, processed and FAC sorted for TCRB+CD3 cells followed by lysis in trizol and 3'RNA seq
Libraries were prepared using the QuantSeq 3'mRNA Seq library prep kit for Illumina (Leogen, Vienna, Austria)

treatment_protocol: Tumors were harvested on day 14 for bulk 3' RNA seq


title: Modified A549 cells with KLF9 Overexpressed and treated with DEX for 08h - rep3

description:
A549_OE_KLF9.rnaseq.dex.08h.rep3
processed data file: A549_OE_KLF9.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: Modified A549_KLF9 Overexpressed and treated with DEX for 08h


title: 3L_S61_3'RNA seq 5


title: 2H_S60_3'RNA seq 4


title: Modified A549 cells with KLF9 Overexpressed and treated with DEX for 08h - rep2

description:
A549_OE_KLF9.rnaseq.dex.08h.rep2
processed data file: A549_OE_KLF9.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: 1H_S58_3'RNA seq 2


title: Modified A549 cells with KLF9 Overexpressed and treated with DEX for 08h - rep1

description:
A549_OE_KLF9.rnaseq.dex.08h.rep1
processed data file: A549_OE_KLF9.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: 2L_S59_3'RNA seq 3


title: Modified A549 cells with KLF9 Overexpressed and treated with DEX for 04h - rep3

description:
A549_OE_KLF9.rnaseq.dex.04h.rep3
processed data file: A549_OE_KLF9.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: Modified A549_KLF9 Overexpressed and treated with DEX for 04h


title: 1L_S57_3'RNA seq 1


title: Modified A549 cells with KLF9 Overexpressed and treated with DEX for 04h - rep1

description:
A549_OE_KLF9.rnaseq.dex.04h.rep1
processed data file: A549_OE_KLF9.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Modified A549 cells with KLF9 Overexpressed and treated with DEX for 04h - rep2

description:
A549_OE_KLF9.rnaseq.dex.04h.rep2
processed data file: A549_OE_KLF9.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Wounded_TZ

city: Bron

first: Hector

last: Hernandez-Vargas

state: Rhone

address: 36 bis Rue de la Batterie

country: France

institute: Genomics Consulting

description: 10xGenomics 3’scRNAseq protocol

data_processing:
Illumina bcl files were basecalled, demultiplexed and aligned to the mouse mm10 genome using the cellranger software (version 3.1.0, 10xGenomics)
Raw counts were imported into R and single cell data was analyzed with the 'Seurat' package v.3.2.2
After filtering for library size (between 200 and 5000 features per cell) and mitochondrial gene expression (less than 25%), pre-processing was performed using Seurat functions for counts normalization (NormalizeData using the  LogNormalize method), scaling (ScaleData using the 2000 most variable features), dimension reduction with principal component analysis (PCA) (RunPCA with default parameters), construction of a Shared Nearest Neighbor (SNN) graph (FindNeighbors using 10 dimensions of reduction as input) and clustering (FindClustering with a resolution of 0.2).
Data was adjusted for cell cycle using the CellCycleScoring function and regressing for S and G2/M phases scores.
After visualization with Uniform Manifold Approximation and Projection (UMAP) dimensional reduction technique, contaminating cell types were filtered out (i.e. anal glands, hair follicle and fibroblasts) followed by rescaling of each dataset.
Genome_build: mm10
Supplementary_files_format_and_content: csv files containing normalized expression matrices. Suggested cell identities have been added to the first row (rowname = “Identity”)
Supplementary_files_format_and_content: filtered feature matrices (output of cellranger count)

source_name: anorectal junction

extract_protocol:
After tissue dissection and dissociation, FACS purified suspended cells were partitioned into nanoliter-scale Gel Bead-In-Emulsions (GEMs) with the Chromium Single Cell Controller (10XGenomics)
Cell encapsulation, barcoding, and library preparation followed the standard scRNAseq protocol comprising reverse transcription, amplification, and indexing (10xGenomics).
Sequencing was performed using a NextSeq Illumina device (Illumina).

treatment_protocol: Wounded condition: cells were prepared 1 week post wound with EDTA

value: anorectal epithelial cells


title: Modified A549 cells with KLF9 Overexpressed and treated with DEX for 01h - rep3

description:
A549_OE_KLF9.rnaseq.dex.01h.rep3
processed data file: A549_OE_KLF9.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: Modified A549_KLF9 Overexpressed and treated with DEX for 01h


title: Normal_TZ

description: 10xGenomics 3’scRNAseq protocol


title: Modified A549 cells with KLF9 Overexpressed and treated with DEX for 12h - rep3

description:
A549_OE_KLF9.rnaseq.dex.12h.rep3
processed data file: A549_OE_KLF9.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Modified A549 cells with KLF9 Overexpressed and treated with DEX for 01h - rep1

description:
A549_OE_KLF9.rnaseq.dex.01h.rep1
processed data file: A549_OE_KLF9.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Rest_micro_+Vehicle_rep5

city: Framingham

first: Joseph

last: Gans

state: Ma

address: 49 New York Ave

department: Genomics

institute: Sanofi Genzyme

data_processing:
Illumina bcl2fastq conversion software V2.20 used to demultiplex and strip Illumina adaptors
Omicsoft Array Studio V10.0 used to filter rRNA, tRNA, ERCC, and poor quality reads using a q-score cutoff of 20
Omicsoft Array Studio V10.0 used for alignment to Mouse B38 reference genome using the Ensembl.R90 Gene Model
Omicsoft Array Studio V10.0 used for quantification and FPKM conversion using "Report Gene/Transcript Counts" function.
Omicsoft Array Studio V10.0 used to subset protein coding genes only and filtering low FPKM using 0.1 as a cutoff.
Omicsoft Array Studio V10.0 used for data normalization to the 75th quantile
Omicsoft Array Studio V10.0 used for data transformation where a constant of 1 was added prior to a log2 transformation.
Genome_build: GRCm38
Supplementary_files_format_and_content: All processed data is provided as normalized Log2 transformed FPKM with rows containing gene identifiers and columns describing the samples.  Raw counts are also provided.

source_name: Sorted Cells from Brain

extract_protocol:
Cells were flow sorted directly into lysis buffer from the PicoPure RNA Isolation Kit (KIT0202).  Cell numbers ranged from 100-380,000.  Samples were then incubated at 42C for 30min prior to storage at -80C.  RNA extraction was carried out using the standard protocol for cell pellets (PicoPure) with the addition of a DNase treatment step.
RNA was quantified and quality checked using Nanodrop 8000 and Agilent's RNA 6000 Pico Kit (CAT# 5067-1513).  RNA was normalized to 1ng as starting input for Clontech's SMART-Seq V4 Ultra Low Input RNA Kit (CAT# 634891).  Several samples with very low input were maxed at the highest allowable volume.  Using this kit for low input samples, we captured mRNA, converted to cDNA, and amplified cDNA using either 11 or 17 cycles, depending on the sample input (higher cycles for the few samples with very low input).  Next, we used Illumina's Nextera XT Kit (CAT# FC-131-1096) to Tagment Illumina adaptors, PCR amplify to add dual sample indices i7/i5, and necessary bead clean-up steps to ensure a high quality library ready for sequencing on the Illumina NextSeq500.

value: brain

value: microglia

tag: activation status

value: resting

tag: disease induction

value: Cortical MS

tag: phenotype

value: Vehicle


title: Modified A549 cells with KLF9 Overexpressed and treated with DEX for 01h - rep2

description:
A549_OE_KLF9.rnaseq.dex.01h.rep2
processed data file: A549_OE_KLF9.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

tag: treatment


title: Rest_micro_+Vehicle_rep3


title: Rest_micro_+Vehicle_rep2


title: Rest_micro_+Vehicle_rep4


title: Modified A549 cells with KLF9 Overexpressed and treated with DEX for 00h - rep2

description:
A549_OE_KLF9.rnaseq.dex.00h.rep2
processed data file: A549_OE_KLF9.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: Modified A549_KLF9 Overexpressed and treated with DEX for 00h

tag: cell line background


title: Modified A549 cells with KLF6 Overexpressed and treated with DEX for 12h - rep2

description:
A549_OE_KLF6.rnaseq.dex.12h.rep2
processed data file: A549_OE_KLF6.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: Modified A549_KLF6 Overexpressed and treated with DEX for 12h

tag: tissue/cell type

value: KLF6 Overexpressed


title: Modified A549 cells with KLF6 Overexpressed and treated with DEX for 12h - rep3

description:
A549_OE_KLF6.rnaseq.dex.12h.rep3
processed data file: A549_OE_KLF6.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

tag: genotype/variation


title: Modified A549 cells with KLF9 Overexpressed and treated with DEX for 00h - rep3

description:
A549_OE_KLF9.rnaseq.dex.00h.rep3
processed data file: A549_OE_KLF9.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

tag: time point


title: Rest_micro_+CSF1R_rep6

tag: tissue

value: CSF1R inh


title: Rest_micro_+CSF1R_rep5


title: Rest_micro_+CSF1R_rep4


title: Rest_micro_+Vehicle_rep1


title: Modified A549 cells with KLF6 Overexpressed and treated with DEX for 12h - rep1

description:
A549_OE_KLF6.rnaseq.dex.12h.rep1
processed data file: A549_OE_KLF6.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Modified A549 cells with KLF6 Overexpressed and treated with DEX for 08h - rep3

description:
A549_OE_KLF6.rnaseq.dex.08h.rep3
processed data file: A549_OE_KLF6.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: Modified A549_KLF6 Overexpressed and treated with DEX for 08h


title: Rest_micro_+CSF1R_rep3


title: Modified A549 cells with KLF6 Overexpressed and treated with DEX for 08h - rep2

description:
A549_OE_KLF6.rnaseq.dex.08h.rep2
processed data file: A549_OE_KLF6.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Rest_micro_+CSF1R_rep2


title: Rest_micro_+CSF1R_rep1


title: Act_bloodphago_+Vehicle_rep5

value: blood-derived phagocytes

value: activated


title: Act_bloodphago_+Vehicle_rep4


title: Modified A549 cells with KLF6 Overexpressed and treated with DEX for 04h - rep2

description:
A549_OE_KLF6.rnaseq.dex.04h.rep2
processed data file: A549_OE_KLF6.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: Modified A549_KLF6 Overexpressed and treated with DEX for 04h


title: Modified A549 cells with KLF6 Overexpressed and treated with DEX for 04h - rep3

description:
A549_OE_KLF6.rnaseq.dex.04h.rep3
processed data file: A549_OE_KLF6.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Modified A549 cells with KLF6 Overexpressed and treated with DEX for 08h - rep1

description:
A549_OE_KLF6.rnaseq.dex.08h.rep1
processed data file: A549_OE_KLF6.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Act_bloodphago_+Vehicle_rep3


title: Modified A549 cells with KLF6 Overexpressed and treated with DEX for 04h - rep1

description:
A549_OE_KLF6.rnaseq.dex.04h.rep1
processed data file: A549_OE_KLF6.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Modified A549 cells with KLF6 Overexpressed and treated with DEX for 01h - rep3

description:
A549_OE_KLF6.rnaseq.dex.01h.rep3
processed data file: A549_OE_KLF6.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: Modified A549_KLF6 Overexpressed and treated with DEX for 01h


title: Act_bloodphago_+Vehicle_rep2


title: Modified A549 cells with KLF6 Overexpressed and treated with DEX for 01h - rep2

description:
A549_OE_KLF6.rnaseq.dex.01h.rep2
processed data file: A549_OE_KLF6.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Act_bloodphago_+Vehicle_rep1


title: Modified A549 cells with KLF9 Overexpressed and treated with DEX for 00h - rep1

description:
A549_OE_KLF9.rnaseq.dex.00h.rep1
processed data file: A549_OE_KLF9.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Act_bloodphago_+CSF1R_rep6


title: Act_bloodphago_+CSF1R_rep5


title: Act_bloodphago_+CSF1R_rep3


title: Act_bloodphago_+CSF1R_rep4


title: Modified A549 cells with KLF6 Overexpressed and treated with DEX for 00h - rep1

description:
A549_OE_KLF6.rnaseq.dex.00h.rep1
processed data file: A549_OE_KLF6.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: Modified A549_KLF6 Overexpressed and treated with DEX for 00h


title: Modified A549 cells with KLF15 Overexpressed and treated with DEX for 12h - rep3

description:
A549_OE_KLF15.rnaseq.dex.12h.rep3
processed data file: A549_OE_KLF15.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: Modified A549_KLF15 Overexpressed and treated with DEX for 12h

value: KLF15 Overexpressed


title: Modified A549 cells with KLF15 Overexpressed and treated with DEX for 12h - rep2

description:
A549_OE_KLF15.rnaseq.dex.12h.rep2
processed data file: A549_OE_KLF15.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Act_bloodphago_+CSF1R_rep2


title: Modified A549 cells with KLF15 Overexpressed and treated with DEX for 12h - rep1

description:
A549_OE_KLF15.rnaseq.dex.12h.rep1
processed data file: A549_OE_KLF15.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Act_micro_+Vehicle_rep5


title: Modified A549 cells with KLF15 Overexpressed and treated with DEX for 08h - rep3

description:
A549_OE_KLF15.rnaseq.dex.08h.rep3
processed data file: A549_OE_KLF15.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: Modified A549_KLF15 Overexpressed and treated with DEX for 08h


title: Modified A549 cells with KLF6 Overexpressed and treated with DEX for 00h - rep2

description:
A549_OE_KLF6.rnaseq.dex.00h.rep2
processed data file: A549_OE_KLF6.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Act_micro_+Vehicle_rep4


title: Modified A549 cells with KLF15 Overexpressed and treated with DEX for 08h - rep2

description:
A549_OE_KLF15.rnaseq.dex.08h.rep2
processed data file: A549_OE_KLF15.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Act_micro_+Vehicle_rep3


title: Act_micro_+Vehicle_rep2


title: Act_micro_+Vehicle_rep1


title: Modified A549 cells with KLF15 Overexpressed and treated with DEX for 08h - rep1

description:
A549_OE_KLF15.rnaseq.dex.08h.rep1
processed data file: A549_OE_KLF15.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Modified A549 cells with KLF15 Overexpressed and treated with DEX for 04h - rep2

description:
A549_OE_KLF15.rnaseq.dex.04h.rep2
processed data file: A549_OE_KLF15.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: Modified A549_KLF15 Overexpressed and treated with DEX for 04h


title: Modified A549 cells with KLF15 Overexpressed and treated with DEX for 01h - rep3

description:
A549_OE_KLF15.rnaseq.dex.01h.rep3
processed data file: A549_OE_KLF15.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: Modified A549_KLF15 Overexpressed and treated with DEX for 01h


title: Modified A549 cells with KLF6 Overexpressed and treated with DEX for 01h - rep1

description:
A549_OE_KLF6.rnaseq.dex.01h.rep1
processed data file: A549_OE_KLF6.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Modified A549 cells with KLF15 Overexpressed and treated with DEX for 04h - rep3

description:
A549_OE_KLF15.rnaseq.dex.04h.rep3
processed data file: A549_OE_KLF15.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Modified A549 cells with KLF6 Overexpressed and treated with DEX for 00h - rep3

description:
A549_OE_KLF6.rnaseq.dex.00h.rep3
processed data file: A549_OE_KLF6.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Modified A549 cells with KLF15 Overexpressed and treated with DEX for 01h - rep2

description:
A549_OE_KLF15.rnaseq.dex.01h.rep2
processed data file: A549_OE_KLF15.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Modified A549 cells with KLF15 Overexpressed and treated with DEX for 04h - rep1

description:
A549_OE_KLF15.rnaseq.dex.04h.rep1
processed data file: A549_OE_KLF15.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Act_micro_+CSF1R_rep3


title: Act_micro_+CSF1R_rep4


title: Act_micro_+CSF1R_rep6


title: Act_micro_+CSF1R_rep5


title: Modified A549 cells with KLF15 Overexpressed and treated with DEX for 01h - rep1

description:
A549_OE_KLF15.rnaseq.dex.01h.rep1
processed data file: A549_OE_KLF15.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Act_bloodphago_+CSF1R_rep1


title: Act_micro_+CSF1R_rep1


title: Modified A549 cells with KLF15 Overexpressed and treated with DEX for 00h - rep3

description:
A549_OE_KLF15.rnaseq.dex.00h.rep3
processed data file: A549_OE_KLF15.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: Modified A549_KLF15 Overexpressed and treated with DEX for 00h


title: Act_micro_+CSF1R_rep2


title: Modified A549 cells with KLF15 Overexpressed and treated with DEX for 00h - rep2

description:
A549_OE_KLF15.rnaseq.dex.00h.rep2
processed data file: A549_OE_KLF15.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Modified A549 cells with FOXO3 Overexpressed and treated with DEX for 12h - rep3

description:
A549_OE_FOXO3.rnaseq.dex.12h.rep3
processed data file: A549_OE_FOXO3.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: Modified A549_FOXO3 Overexpressed and treated with DEX for 12h

value: FOXO3 Overexpressed


title: 1-a

city: Göttingen

first: Andre

last: Fischer

state: NDS

address: Von-Siebold-Str. 3a

department: Epigenetics and Systems Medicine in Neurodegenerative Diseases

institute: DZNE Göttingen

description: synaptic RNAs, total and small

data_processing:
Illumina’s bcl2fastq (v2.20.2) was used for adapter trimming and converting the base calls
Trimming of 3’ adapters for smallRNASeq data was done using cutadapt (v1.11.0)
totalRNASeq reads were aligned using the STAR aligner (v2.5.2b)
smallRNASeq reads were aligned using the mapper.pl script from mirdeep2 (v2.0.1.2) which uses bowtie (v1.1.2)
TotalRNASeq read counts were generated using featureCounts (v1.5.1)
smallRNA read counts were generated with the quantifier.pl script from mirdeep2 (v2.0.1.2)
All read counts were normalized according to library size to transcript per million (TPM)
Genome_build: mm10
Supplementary_files_format_and_content: excel file containing raw and normalized read counts

source_name: Hippocampus primary culture from E17 mouse

growth_protocol: cells were seeded on PDMS (coated with 0.5mg/ml PDL in borate buffer) and cultured in Neurobasal Plus with GlutaMax, Penicilin/Strep and B27 Plus supplement

extract_protocol:
Synaptosome RNA was extracted via Trizol, synaptic RNA from microfluidic chambers was isolated with the GenElute™ Single Cell RNA Purification Kit after cutting the synaptic compartment out of the chamber
Synaptosome small RNA libraries were done via NEBNext Small RNA Library Prep Kit, synaptosome toal RNA libraries via Illumina Truseq total RNA kit. Microfluidic total RNA libraries were prepared with Takara´s SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian, microfluidic chamber small RNA with Takara´s  SMARTer smRNA-Seq Kit for Illumina

treatment_protocol: as indicated, samples were treated with 50mM of KCl for 2h

tag: strain

tag: age

value: DIV14 from E17

tag: stimulation


title: 11-a

description: synaptic RNAs, total and small


title: Modified A549 cells with KLF15 Overexpressed and treated with DEX for 00h - rep1

description:
A549_OE_KLF15.rnaseq.dex.00h.rep1
processed data file: A549_OE_KLF15.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

value: adenocarcinomic human alveolar basal epithelial


title: Modified A549 cells with FOXO3 Overexpressed and treated with DEX for 12h - rep2

description:
A549_OE_FOXO3.rnaseq.dex.12h.rep2
processed data file: A549_OE_FOXO3.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: 3

description: synaptic RNAs, total and small


title: 9

description: synaptic RNAs, total and small


title: Modified A549 cells with FOXO3 Overexpressed and treated with DEX for 08h - rep3

description:
A549_OE_FOXO3.rnaseq.dex.08h.rep3
processed data file: A549_OE_FOXO3.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: Modified A549_FOXO3 Overexpressed and treated with DEX for 08h


title: Modified A549 cells with FOXO3 Overexpressed and treated with DEX for 08h - rep2

description:
A549_OE_FOXO3.rnaseq.dex.08h.rep2
processed data file: A549_OE_FOXO3.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Ctrl3

description: synaptic RNAs, total and small


title: KCL1a

description: synaptic RNAs, total and small

value: KCL for 2h


title: KCL1

description: synaptic RNAs, total and small


title: Modified A549 cells with FOXO3 Overexpressed and treated with DEX for 08h - rep1

description:
A549_OE_FOXO3.rnaseq.dex.08h.rep1
processed data file: A549_OE_FOXO3.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

value: dexamethasone (DEX)


title: Modified A549 cells with FOXO3 Overexpressed and treated with DEX for 04h - rep2

description:
A549_OE_FOXO3.rnaseq.dex.04h.rep2
processed data file: A549_OE_FOXO3.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: Modified A549_FOXO3 Overexpressed and treated with DEX for 04h


title: Ctrl4

description: synaptic RNAs, total and small


title: KCL4

description: synaptic RNAs, total and small


title: Modified A549 cells with FOXO3 Overexpressed and treated with DEX for 04h - rep1

description:
A549_OE_FOXO3.rnaseq.dex.04h.rep1
processed data file: A549_OE_FOXO3.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt