title: KRT5-traced transformed bladder cells [CTB056]

description:
CTB056
RIN: 10
processed data files:
raw_counts_unfiltered.txt.gz
raw_counts.filtered_4_counts.txt.gz
regularized_log_transform.filtered_4_counts.txt.gz
DKO_Dataset1_DEG.xlsx

value: KRT5-CreERT2, p53flox/flox, Ptenflox/flox, Rosa26YFP/+

value: 5 months


title: KD1B_8

status: Public on Jan 01 2019

type: SRA

city: Amsterdam

first: Kat

last: Moore

address: Plesmanlaan 125

country: Netherlands

institute: Sanquin Research

description:
B6
The cell line is derived from an erythroblast culture started from fetal liver of F1 mice (FVB/n x C57BL/6) both heterozygous for the Trp53 deletion described in [Clarke AR, Purdie CA, Harrison DJ, et al. Thymocyte apoptosis induced by p53-dependent and independent pathways. Nature. 1993; 362(6423):849-852].
Tis7 knockdown 1 rep B, time point 8.
shRNA sequence (5'-3'): CCGGGCAGTACCACTTGCAGACAAACTCGAGTTTGTCTGCAAGTGGTACTGCTTTTTG
processed data file: Tis_rawcounts.txt

library_source: transcriptomic

data_processing:
Raw fastq aligned to genome using Splice Transcripts Alignment to a Reference (STAR) v2.4, with parameters --quantMode GeneCounts --outFilterMultimapNmax 20 and -sjDBGTFfile with an Ensembl gtf file accessed on 17-Sept-2017.
Resulting raw (unnormalized) read counts were analyzed with DESeq2 using Wald test for pairwise comparisons and a likelihood ratio test to model the time course experiment.
Genome_build: mm10/GRCm38.p5
Supplementary_files_format_and_content: Tis_rawcounts.txt: Tab-delimited text file includes raw read counts.

molecule: total RNA

organism: Mus musculus

source_name: Erythroblasts, KD1

growth_protocol: Murine erythroblasts, isolated from p53-/- mouse fetal livers, were cultured in Stempro supplemented with L-glutamine and Pen/Strep (Thermo Fisher), 0.5 U/ml erythropoietin (Epo, Jansen-Cilag), 1% stem cell factor (supernatant) and 1 nM dexamethasone (Sigma).

extract_protocol:
RNeasy Plus Kit (Qiagen).
Performed by Novogene, Co., LTD. Oligo(dt) bead isolation followed by cDNA synthesis with random hexamers and second strand synthesis using Illumina brand buffer, dNTPs, RNase H and DNA pol I. The final cDNA library was completed after a series of terminal repair, A-tailing, adapter ligation, size selection and PCR enrichment.

treatment_protocol: For stress induction, erythroblasts were treated with 2.5 µg/ml Tunicamycin (Sigma) for 0, 4 and 8 hours.

tag: genotype/variation

tag: cell type

value: Erythroblasts

tag: tissue origin

value: fetal liver

tag: shRNA type

value: anti-Tis7 1

tag: tunicamycin exposure (hours)

tag: replicate

value: B


title: KD2B_4

description:
B8
The cell line is derived from an erythroblast culture started from fetal liver of F1 mice (FVB/n x C57BL/6) both heterozygous for the Trp53 deletion described in [Clarke AR, Purdie CA, Harrison DJ, et al. Thymocyte apoptosis induced by p53-dependent and independent pathways. Nature. 1993; 362(6423):849-852].
Tis7 knockdown 2 rep B, time point 4.
shRNA sequence (5'-3'): CCGGCAGTACCACTTGCAGACAAATCTCGAGATTTGTCTGCAAGTGGTACTGTTTTTG
processed data file: Tis_rawcounts.txt

source_name: Erythroblasts, KD2

value: anti-Tis7 2


title: ScB_8

description:
B3
The cell line is derived from an erythroblast culture started from fetal liver of F1 mice (FVB/n x C57BL/6) both heterozygous for the Trp53 deletion described in [Clarke AR, Purdie CA, Harrison DJ, et al. Thymocyte apoptosis induced by p53-dependent and independent pathways. Nature. 1993; 362(6423):849-852].
Control shRNA rep B, time point 8.
shRNA sequence (5'-3'): CCGGCAACAAGATGAAGAGCACCAACTCGAGTTGGTGCTCTTCATCTTGTTGTTTTT
processed data file: Tis_rawcounts.txt

source_name: Erythroblasts, control

value: Sc


title: ScB_0

description:
B1
The cell line is derived from an erythroblast culture started from fetal liver of F1 mice (FVB/n x C57BL/6) both heterozygous for the Trp53 deletion described in [Clarke AR, Purdie CA, Harrison DJ, et al. Thymocyte apoptosis induced by p53-dependent and independent pathways. Nature. 1993; 362(6423):849-852].
Control shRNA rep B, time point 0.
shRNA sequence (5'-3'): CCGGCAACAAGATGAAGAGCACCAACTCGAGTTGGTGCTCTTCATCTTGTTGTTTTT
processed data file: Tis_rawcounts.txt


title: KD1B_0

description:
B4
The cell line is derived from an erythroblast culture started from fetal liver of F1 mice (FVB/n x C57BL/6) both heterozygous for the Trp53 deletion described in [Clarke AR, Purdie CA, Harrison DJ, et al. Thymocyte apoptosis induced by p53-dependent and independent pathways. Nature. 1993; 362(6423):849-852].
Tis7 knockdown 1 rep B, time point 0.
shRNA sequence (5'-3'): CCGGGCAGTACCACTTGCAGACAAACTCGAGTTTGTCTGCAAGTGGTACTGCTTTTTG
processed data file: Tis_rawcounts.txt


title: ChIPseq_H4ac_TX1072_Hdac3KO_24h_Dox_Rep2

city: Paris

first: Aurélie

last: Bousard

address: 26, rue d'Ulm

country: France

institute: Institut Curie

library_source: genomic

data_processing:
Adapters and low quality bases (<Q20) have been removed with TrimGalore (v0.4.0) (Krueger) and Cutadapt (1.8.2) (Martin et al, 2011).
An ‘N-masked” genome has been generated with SNPSplit (0.3.2) {Krueger, 2016 #2319} which is a version of the mouse reference genome mm10 where all the polymorphic sites for the hybrid strain Mus musculus CAST/EiJ and Mus musculus C57BL/6 are masked by ambiguity nucleobase ‘N’. For all samples, reads were then mapped to the ‘N-masked” genome with Bowtie2 (2.2.5) (Langmead B and Salzberg S, 2012) with options [KOend-to-end -N1 -q].
Duplicates were discarded with Picard MarkDuplicates (1.65) with options [REMOVE_DUPLICATES=true] (DePristo et al., 2011) and reads mapped on blacklisted regions from Encode Consortium (Dunham et al., 2012) were discarded.
SNPSplit (0.3.2) {Krueger, 2016 #2319} was then used to generate allele-specific BAM files by separating the alignment into two distinct alleles (CAST and B6) based on SNPs information downloaded on Sanger {Keane, 2011 #1133}.
Bigwig files were created with bedtools genomeCoverageBed (2.25.0) (Quinlan and Hall, 2010), using a scale factor calculated on the total library (10.000.000/total reads) for both allele specific bigwigs, and loaded on UCSC genome browser (Kent et al., 2002).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

molecule: genomic DNA

growth_protocol: TX1072 (mouse, female, [Mus musculus castaneus X C57BL/6] embryonic stem cells) cells have been previously derived in the lab {Schulz, 2014 #1419}. Hdac3-/-clones have been derived from the TX1072 line by CRISPR/Cas9 targeting. Cells were cultured on gelatin-coated plates in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 15% foetal bovine serum, 2-mercaptoethanol (0.1mM), LIF(1000u/mL) and 2i (PD0325901 [0.4 mM], CHIR99021 [3 mM]) {Ying, 2008 #767}.

extract_protocol:
Cells were collected using Accutase (Thermo Fisher Scientific), washed twice in ice-cold PBS and counted. Typically, 3.5mln cells were used per immunoprecipitation (IP). A fraction of cells was always used for RNA/FISH verification of Xist induction. Cell pellet was resuspended in 90ul (per 10mln cells) of Lysis Buffer (50mM Tris-HCl, pH7.5; 150mM NaCl;
0.1% sodium deoxycholate;
1% Triton X-100;
5mM CaCl2; Protease Inhibitor Cocktail; 5mM sodium butyrate). After lysing cells on ice for 10min we added 62ul (per 10mln cells) of Lysis Buffer with MNase (500ul buffer + 0.5ul MNase). Chromatin was digested for exactly 10min at 37°C and reaction was stopped by the addition of 20mM EGTA. To remove uindigested debris the lysates were centrifuged at 13000rpm for 5min at 4°C. Supernatant was transferred to a fresh tube, an equal volume of STOP Buffer (50mM Tris-HCl, pH7.5; 150mM NaCl;
0.1% sodium deoxycholate;
1% Triton X-100;
30mM EGTA;
30mM EDTA; Protease Inhibitor Cocktail; 5mM sodium butyrate) was added, samples were stored on ice.  5ul of lysate was digested in 45ul of ProtK Digestion Buffer (20mM HEPES; 1mM EDTA; 0.5% SDS) for 30min at 56°C. 50ul of AMPure XP beads were added to the digested lysate together with 60ul of 20% PEG8000 1.25M NaCl. After mixing the samples were incubated for 15min at RT. Beads were separated on a magnet and washed twice with 80% Ethanol for 30sec. DNA was eluted in 12ul of Low-EDTA TE and DNA concentration was measured using Qubit DNA High-Sensitivity kit. These measurements were used to normalise lysate concentration between samples. DNA isolated in this step was used as the input sample. The volume of each undigested lysate was adjusted for equal concentration and to obtain 1mL per IP using a 1:1 mix of Lysis Buffer and STOP Buffer.  We have washed twice anti-mouse Dynabeads (50ul/IP) and Protein-A Dynabeads (10ul/IP) in Blocking Buffer (0.5% BSA; 0.5% Tween in PBS). Beads were then resuspended in Blocking buffer and coated with antibodies for 4hrs at 4°C (anti-mouse Dynabeads: H3K9ac[1ug/IP], H3K4me3[2.5ug/IP], H3K27ac[1ug/IP]; Protein-A dynabeads: H3K4me1[0.4ug/IP], H3K27me3[1ug/IP], H2AK119Ub[0.4ug/IP], H4ac[2ug/IP]). Once coated beads were magnet-separated and resuspended in 1mL of concentration-adjusted lysate. Samples were left rotating overnight at 4°C.  Following day beads were magnet-separated and washed quickly with ice-cold washing buffers. anti-H3K4me3 IP was washed 8 times with Low Salt Buffer (0.1% SDS;
1% TritonX-100;
2 mM EDTA;
20 mM Tris-HCl, pH 8.1; 150 mM NaCl;
0.1% sodium deoxycholate). All remaining IPs were washed 4-times with Low Salt Buffer, 2-times with High Salt Buffer (0.1% SDS;
1% TritonX-100;
2 mM EDTA;
20 mM Tris-HCl, pH 8.1; 360 mM NaCl;
0.1% sodium deoxycholate) and 2-times with LiCl buffer (0.25 M LiCl;
1% NP40;1.1% sodium deoxycholate; 1 mM EDTA; 10 mM Tris-HCl pH 8.1). Prior to elution all samples were rinsed once in TE. ChIP-DNA was eluted in ProtK-Digestion buffer for 15min at 56 °C. Beads were separated and the supernatant was further digested for another 2hrs at 56 °C. DNA was isolated using AMPure XP beads as described for the input sample.  For each nChIPseq, 0.5ul of each sample was used for qPCR validation of enrichment at control regions. 0.5ul of input samples were also used to verify the digestion efficiency using D1000 tapestation.
Library preparation was done using Ovation® Ultralow Library System V2 following suppliers protocol. Amplified libraries were size-selected for dinucleotide fraction (350-600bp fragments) using agarose gel-separation and MinElute Gel Extraction Kit (Qiagen). Sample quality was inspected using D1000 tapestation. Samples were sequenced with Illumina HiSeq 2500 using PE100 mode.

treatment_protocol: TX1072 based ESC lines were plated at a density of 1.8mln/T75 flask. After 24hrs of culture in DMEM/15%FCS+LIF+2i cell the medium was supplemented with doxycycline (1ug/ml). Cells were then collected at regular intervals.

tag: strain background

value: CAST / C57BL/6

tag: cell line

tag: condition

value: 24h Dox

tag: assay

value: ChIPseq

tag: target

tag: antibody


title: ScA_8

description:
A3
The cell line is derived from an erythroblast culture started from fetal liver of F1 mice (FVB/n x C57BL/6) both heterozygous for the Trp53 deletion described in [Clarke AR, Purdie CA, Harrison DJ, et al. Thymocyte apoptosis induced by p53-dependent and independent pathways. Nature. 1993; 362(6423):849-852].
Control shRNA rep A, time point 8.
shRNA sequence (5'-3'): CCGGCAACAAGATGAAGAGCACCAACTCGAGTTGGTGCTCTTCATCTTGTTGTTTTT
processed data file: Tis_rawcounts.txt

value: A


title: ScA_4

description:
A2
The cell line is derived from an erythroblast culture started from fetal liver of F1 mice (FVB/n x C57BL/6) both heterozygous for the Trp53 deletion described in [Clarke AR, Purdie CA, Harrison DJ, et al. Thymocyte apoptosis induced by p53-dependent and independent pathways. Nature. 1993; 362(6423):849-852].
Control shRNA rep A, time point 4.
shRNA sequence (5'-3'): CCGGCAACAAGATGAAGAGCACCAACTCGAGTTGGTGCTCTTCATCTTGTTGTTTTT
processed data file: Tis_rawcounts.txt


title: totalES_02

city: Wako

first: Itoshi

last: NIKAIDO

state: Saitama

address: 2-1 Hirosawa

department: Center for Biosystems Dynamics Research

country: Japan

institute: RIKEN

data_processing:
FASTQ files were generated using bcl2fastq (v2.16.0.10).
Count and TPM files were generated using Sailfish 0.9.2 with GENCODE M9
Genome_build: mm10

source_name: ES_diluted total RNA

growth_protocol: 5G6GR mouse ES cells were cultured in a feeder-free gelatin-coated dish in 10% fetal calf serum containing Glasgow minimal essential medium (GMEM; Sigma-Aldrich), 1000 U/mL leukemia inhibitory factor (ESGRO; Invitrogen), 100 µmol/l 2-mercaptoethanol (Nacalai Tesque), 1× non-essential amino acids (Life Technologies), 1 mmol/L sodium pyruvate (Life Technologies), 2 mmol/L L-glutamine (Nacalai Tesque), 0.5× penicillin/streptomycin (Life Technologies), 0.5 ug/ml puromycin (Sigma) and 10 µg/mL blasticidin (Life Technologies).

extract_protocol:
Total RNA was extracted using a Direct-zol RNA MiniPrep Kit (Zymo Research).
We prepared RT-RamDA sequencing library from single-stranded amplified cDNA by using a DNA SMART ChIP-Seq Kit (Clontech). Before performing DNA SMART ChIP-Seq Kit, for digesting remaining RNA, 1 µl of RNase mix [2.5 x NEB buffer 3 (New England Biolabs), 0.1 U RNase H (Thermo Fisher) and RNase If (New England Biolabs) in RNase-free water] was added to 3 µl of RT-RamDA product from diluted 10 pg of total mESC RNA. RNase treatment was carried out at 37°C for 30 min. After RNase treatment, immediately cDNAs were purified by using 12 µl of AMPure XP SPRI beads (Beckman Coulter). Washed AMPure XP beads attached to single-stranded cDNAs were directly eluted using 8 μl of 1 × DNA Dilution Buffer (Clontech) and mixed well using a vortex mixer and pipetting. Sequencing library preparation was performed according to the manual instructions, except that the reaction volume was modified to 1/2.5. Seventeen cycles of PCR were applied for the library DNA. When we performed ribosomal RNA depleted total RNA-seq using diluted 200 ng of total mESC RNA, we utilized a KAPA RNA HyperPrep Kit with RiboErase (Kapa Biosystems) for the preparation of sequencing library DNA according to the manual instructions. Seven cycles of PCR were applied for the library DNA. Quality control of sequencing library DNA was carried out using a Bioanalyzer Agilent High-Sensitivity DNA Kit (Agilent) and a KAPA library quantification kit (Kapa Biosystems).

value: Embryonic stem (ES) cell

tag: sample type

value: purified total RNA

tag: starting amount

tag: method subtype

value: KAPA RNA HyperPrep Kit with RiboErase

tag: rt primer


title: totalES_03


title: KD2A_0

description:
A7
The cell line is derived from an erythroblast culture started from fetal liver of F1 mice (FVB/n x C57BL/6) both heterozygous for the Trp53 deletion described in [Clarke AR, Purdie CA, Harrison DJ, et al. Thymocyte apoptosis induced by p53-dependent and independent pathways. Nature. 1993; 362(6423):849-852].
Tis7 knockdown 2 rep A, time point 0.
shRNA sequence (5'-3'): CCGGCAGTACCACTTGCAGACAAATCTCGAGATTTGTCTGCAAGTGGTACTGTTTTTG
processed data file: Tis_rawcounts.txt


title: KD2A_4

description:
A8
The cell line is derived from an erythroblast culture started from fetal liver of F1 mice (FVB/n x C57BL/6) both heterozygous for the Trp53 deletion described in [Clarke AR, Purdie CA, Harrison DJ, et al. Thymocyte apoptosis induced by p53-dependent and independent pathways. Nature. 1993; 362(6423):849-852].
Tis7 knockdown 2 rep A, time point 4.
shRNA sequence (5'-3'): CCGGCAGTACCACTTGCAGACAAATCTCGAGATTTGTCTGCAAGTGGTACTGTTTTTG
processed data file: Tis_rawcounts.txt


title: KD1A_0

description:
A4
The cell line is derived from an erythroblast culture started from fetal liver of F1 mice (FVB/n x C57BL/6) both heterozygous for the Trp53 deletion described in [Clarke AR, Purdie CA, Harrison DJ, et al. Thymocyte apoptosis induced by p53-dependent and independent pathways. Nature. 1993; 362(6423):849-852].
Tis7 knockdown 1 rep A, time point 0.
shRNA sequence (5'-3'): CCGGGCAGTACCACTTGCAGACAAACTCGAGTTTGTCTGCAAGTGGTACTGCTTTTTG
processed data file: Tis_rawcounts.txt


title: KD2A_8

description:
A9
The cell line is derived from an erythroblast culture started from fetal liver of F1 mice (FVB/n x C57BL/6) both heterozygous for the Trp53 deletion described in [Clarke AR, Purdie CA, Harrison DJ, et al. Thymocyte apoptosis induced by p53-dependent and independent pathways. Nature. 1993; 362(6423):849-852].
Tis7 knockdown 2 rep A, time point 8.
shRNA sequence (5'-3'): CCGGCAGTACCACTTGCAGACAAATCTCGAGATTTGTCTGCAAGTGGTACTGTTTTTG
processed data file: Tis_rawcounts.txt


title: totalES_01


title: KD1A_8

description:
A6
The cell line is derived from an erythroblast culture started from fetal liver of F1 mice (FVB/n x C57BL/6) both heterozygous for the Trp53 deletion described in [Clarke AR, Purdie CA, Harrison DJ, et al. Thymocyte apoptosis induced by p53-dependent and independent pathways. Nature. 1993; 362(6423):849-852].
Tis7 knockdown 1 rep A, time point 8.
shRNA sequence (5'-3'): CCGGGCAGTACCACTTGCAGACAAACTCGAGTTTGTCTGCAAGTGGTACTGCTTTTTG
processed data file: Tis_rawcounts.txt


title: KD2B_0

description:
B7
The cell line is derived from an erythroblast culture started from fetal liver of F1 mice (FVB/n x C57BL/6) both heterozygous for the Trp53 deletion described in [Clarke AR, Purdie CA, Harrison DJ, et al. Thymocyte apoptosis induced by p53-dependent and independent pathways. Nature. 1993; 362(6423):849-852].
Tis7 knockdown 2 rep B, time point 0.
shRNA sequence (5'-3'): CCGGCAGTACCACTTGCAGACAAATCTCGAGATTTGTCTGCAAGTGGTACTGTTTTTG
processed data file: Tis_rawcounts.txt


title: KD1A_4

description:
A5
The cell line is derived from an erythroblast culture started from fetal liver of F1 mice (FVB/n x C57BL/6) both heterozygous for the Trp53 deletion described in [Clarke AR, Purdie CA, Harrison DJ, et al. Thymocyte apoptosis induced by p53-dependent and independent pathways. Nature. 1993; 362(6423):849-852].
Tis7 knockdown 1 rep A, time point 4.
shRNA sequence (5'-3'): CCGGGCAGTACCACTTGCAGACAAACTCGAGTTTGTCTGCAAGTGGTACTGCTTTTTG
processed data file: Tis_rawcounts.txt


title: KD1B_4

description:
B5
The cell line is derived from an erythroblast culture started from fetal liver of F1 mice (FVB/n x C57BL/6) both heterozygous for the Trp53 deletion described in [Clarke AR, Purdie CA, Harrison DJ, et al. Thymocyte apoptosis induced by p53-dependent and independent pathways. Nature. 1993; 362(6423):849-852].
Tis7 knockdown 1 rep B, time point 4.
shRNA sequence (5'-3'): CCGGGCAGTACCACTTGCAGACAAACTCGAGTTTGTCTGCAAGTGGTACTGCTTTTTG
processed data file: Tis_rawcounts.txt


title: ChIPseq_H4ac_TX1072_Hdac3KO_0h_Dox_Rep2

value: 0h Dox


title: ScB_4

description:
B2
The cell line is derived from an erythroblast culture started from fetal liver of F1 mice (FVB/n x C57BL/6) both heterozygous for the Trp53 deletion described in [Clarke AR, Purdie CA, Harrison DJ, et al. Thymocyte apoptosis induced by p53-dependent and independent pathways. Nature. 1993; 362(6423):849-852].
Control shRNA rep B, time point 4.
shRNA sequence (5'-3'): CCGGCAACAAGATGAAGAGCACCAACTCGAGTTGGTGCTCTTCATCTTGTTGTTTTT
processed data file: Tis_rawcounts.txt


title: ScA_0

description:
A1
The cell line is derived from an erythroblast culture started from fetal liver of F1 mice (FVB/n x C57BL/6) both heterozygous for the Trp53 deletion described in [Clarke AR, Purdie CA, Harrison DJ, et al. Thymocyte apoptosis induced by p53-dependent and independent pathways. Nature. 1993; 362(6423):849-852].
Control shRNA rep A, time point 0.
shRNA sequence (5'-3'): CCGGCAACAAGATGAAGAGCACCAACTCGAGTTGGTGCTCTTCATCTTGTTGTTTTT
processed data file: Tis_rawcounts.txt


title: Donor 3 MSCs, normoxia treated, with TGFb

type: RNA

city: Philadelphia

first: Lachlan

middle: James

last: Smith

state: Pennsylvania

address: 371 Stemmler Hall, 3450 Hamilton Walk

department: Department of Orthopaedic Surgery

country: USA

institute: University of Pennsylvania

description:
D5N1
Gene expression data from bovine bone marrow-derived MSCs preconditioned in normoxia with TGFb

hyb_protocol: Five and a half micrograms of labeled cDNA were added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to Bovine Gene 1.0 ST GeneChips (Affymetrix Inc., Santa Clara CA) using the GeneChip Hybridization oven 645. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: A GeneChip 3000 7G scanner was used to collect fluorescence signal.

data_processing: Probe intensities were normalized using RMA as implemented in Partek Genomics Suite (v6.6, Partek, Inc., St. Louis, MO), yielding normalized log2-transformed gene expression intensities.

label: biotin

organism: Bos taurus

source_name: bovine bone marrow-derived MSCs preconditioned in normoxia (21% O2) with TGFb

label_protocol: 250ng of total RNA was converted to first-strand cDNA using reverse transcriptase primed by poly(T) and random oligomers that incorporated the T7 promoter sequence. Second-strand cDNA synthesis was followed by in vitro transcription with T7 RNA polymerase for linear amplification of each transcript, and the resulting cRNA was converted to cDNA, fragmented, assessed by Bioanalyzer, and biotinylated by terminal transferase end labeling.

growth_protocol: Bone marrow-derived MSCs were isolated from juvenile (age < 6 months) bovine femurs and tibiae. Following the initial isolation, MSCs were expanded to confluence through a single initial passage in standard tissue culture conditions with normal oxygen tension (atmospheric, 21% O2), 5% CO2, in basal medium comprised of high glucose (4.5 g/L) Dulbecco’s Modified Eagle medium (DMEM; ThermoFisher Scientific; Waltham, MA), 10% fetal bovine serum (FBS; ThermoFisher Scientific; Waltham, MA), and 1% penicillin, streptomycin, and fungizone (PSF; ThermoFisher Scientific; Waltham, MA).

extract_protocol: RNA was isolated from each sample using serial TRIzol (Ambion; Austin, TX)-chloroform extractions, and were in-column treated with RNase-free DNase (Qiagen; Valencia, CA) on miRNeasy columns (Qiagen; Valencia, CA) and eluted following the manufacturer’s protocols.

treatment_protocol: Cells were then passaged and expanded (preconditioned) in basal medium in one of four different conditions for one week: 1) N0: normoxia (21% O2); 2) N1: normoxia + TGF-β3 (10 ng/mL, R&D Systems; Minneapolis, MN); 3) H0: hypoxia (2% O2); 4) H1:  hypoxia + TGF-β3. Hypoxic culture was carried out continuously in an environmental workstation (Hypoxystation 35; Hypoxygen, MD, USA) that enabled media changes without exposure to atmospheric conditions.

value: bone-marrow derived mesenchymal stem cells

tag: age

value: juvenile (less than 6 months of age)

tag: tissue

value: femurs and tibiae


title: Donor 3 MSCs, hypoxia treated, no TGFb

description:
D5H0
Gene expression data from bovine bone marrow-derived MSCs preconditioned in hypoxia without TGFb

source_name: bovine bone marrow-derived MSCs preconditioned in hypoxia (2% O2) without TGFb

tag: cell type


title: Donor 2 MSCs, hypoxia treated, with TGFb

description:
D2H1
Gene expression data from bovine bone marrow-derived MSCs preconditioned in hypoxia with TGFb

source_name: bovine bone marrow-derived MSCs preconditioned in hypoxia (2% O2) with TGFb


title: Donor 2 MSCs, normoxia treated, no TGFb

description:
D2N0
Gene expression data from bovine bone marrow-derived MSCs preconditioned in normoxia without TGFb

source_name: bovine bone marrow-derived MSCs preconditioned in normoxia (21% O2) without TGFb


title: Donor 3 MSCs, hypoxia treated, with TGFb

description:
D5H1
Gene expression data from bovine bone marrow-derived MSCs preconditioned in hypoxia with TGFb


title: Donor 2 MSCs, hypoxia treated, no TGFb

description:
D2H0
Gene expression data from bovine bone marrow-derived MSCs preconditioned in hypoxia without TGFb


title: Donor 2 MSCs, normoxia treated, with TGFb

description:
D2N1
Gene expression data from bovine bone marrow-derived MSCs preconditioned in normoxia with TGFb


title: Donor 1 MSCs, normoxia treated, no TGFb

description:
D1N0
Gene expression data from bovine bone marrow-derived MSCs preconditioned in normoxia without TGFb


title: Donor 1 MSCs, hypoxia treated, with TGFb

description:
D1H1
Gene expression data from bovine bone marrow-derived MSCs preconditioned in hypoxia with TGFb


title: Donor 1 MSCs, normoxia treated, with TGFb

description:
D1N1
Gene expression data from bovine bone marrow-derived MSCs preconditioned in normoxia with TGFb


title: Donor 3 MSCs, normoxia treated, no TGFb

description:
D5N0
Gene expression data from bovine bone marrow-derived MSCs preconditioned in normoxia without TGFb


title: Donor 1 MSCs, hypoxia treated, no TGFb

description:
D1H0
Gene expression data from bovine bone marrow-derived MSCs preconditioned in hypoxia without TGFb


title: Low_anti-CD4_2

city: Charleston

first: Zhenwu

last: Luo

state: SC

address: 173 Ashley Ave

department: Immunology & Microbiology

institute: Medical University of South Carolina

description: Gene expression data from low anti-CD4

hyb_protocol: Affymetrix Human GeneChip U133 Plus 2.0 Array was used for RNA hybridization and labeling assay

scan_protocol: not provided

data_processing: Biological profiles of distinct genes were analyzed and clustered using iPathway

organism: Homo sapiens

source_name: Purified human B cells

label_protocol: total RNA were sent to do the gene expression microarray

growth_protocol: B cells were purified from fresh isolated PBMC

extract_protocol: RNeasy Micro kit

treatment_protocol: No treatment

tag: diagnosis

value: HIV+

value: blood

value: Purified human B cells

tag: flu vaccine

tag: gender

value: M


title: High_anti-CD4_1

description: Gene expression data from high anti-CD4


title: OPM2_control

city: Singapore

first: Zhigang

last: Xie

address: 14 Medical Drive, CeLS Building #02-07

department: CSI Singapore

country: Singapore

institute: National University of Singapore

description: Gene expression data from OPM2-control cells

hyb_protocol: Following labeling, biotin labeled ss-cDNA were hybridized for 16 hr at 45C on GeneChip™ Human Gene 2.0 ST Array (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing:
The data were analyzed with GeneSpring 13.1 using default analysis settings as normalization method.
The normalization strategy: The data were filtered on expression (20.0 - 100.0)th percentile in the raw data and at least one of the samples in each condition pairs (KMS11_control vs KMS11_ShMI, KMS18_control vs KMS18_ShMI, KMS34_control vs KMS34_ShMI and OPM2_control vs OPM2_ShMI) have value within range.
Entities that meet the fold change cut-off of 1.0 fold were analyzed.

source_name: OPM2 cells, control

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix protocol from 5.5 ug single-stranded cDNA (WT Plus Reagent Kit Assay Manual, 2013, Affymetrix).

growth_protocol: Human t(4;14) MM cell lines were maintained in RPMI 1640, supplemented with 10% fetal calf serum (FCS), 100 U/mL penicillin and 100 μg/mL streptomycin. Cells were grown at 37C in a humidified atmosphere with 5% CO2.

extract_protocol: Total RNA was extracted by using the Qiagen RNeasy Mini kit (Germany).

treatment_protocol: Cells were infected with lentiviruses in the presence of 8 µg/mL polybrene (Sigma-Aldrich). Twenty four hours after infection, infection mixtures were replaced with normal growth medium. Cells were incubated at 37C in a humidified, 5% CO2 atmosphere for 48 h and subsequently collected for RNA extraction.

value: Multiple Myeloma Cell Line OPM2

tag: genotype/variation

value: control


title: High_anti-CD4_2

description: Gene expression data from high anti-CD4


title: KMS34_ShMI

description: Gene expression data from KMS34-shMMSETI cells

source_name: KMS34 cells, ShMMSETI

value: Multiple Myeloma Cell Line KMS34

value: MMSETI knockdown


title: High_anti-CD4_4

description: Gene expression data from high anti-CD4

value: F


title: Low_anti-CD4_3

description: Gene expression data from low anti-CD4


title: OPM2_ShMI

description: Gene expression data from OPM2-shMMSETI cells

source_name: OPM2 cells, ShMMSETI


title: Low_anti-CD4_4

description: Gene expression data from low anti-CD4


title: Low_anti-CD4_6

description: Gene expression data from low anti-CD4


title: High_anti-CD4_3

description: Gene expression data from high anti-CD4


title: Low_anti-CD4_5

description: Gene expression data from low anti-CD4


title: Low_anti-CD4_1

description: Gene expression data from low anti-CD4


title: KMS34_control

description: Gene expression data from KMS34-control cells

source_name: KMS34 cells, control


title: KMS18_ShMI

description: Gene expression data from KMS18-shMMSETI cells

source_name: KMS18 cells, ShMMSETI

value: Multiple Myeloma Cell Line KMS18


title: KMS11_ShMI

description: Gene expression data from KMS11-shMMSETI cells

source_name: KMS11 cells, ShMMSETI

value: Multiple Myeloma Cell Line KMS11


title: KMS18_control

description: Gene expression data from KMS18-control cells

source_name: KMS18 cells, control


title: 4672 Non-Peripheral Neuropathy

city: Edmonton

first: William

middle: George

last: Branton

state: Alberta

address: 611 HMRC University of Alberta

department: Medicine

country: Canada

institute: University of Alberta

description: miRNA expression data from blood serum

hyb_protocol: labeled samples were hybridized to Affymetrix miRNA 3.0 GeneChip array at 48 °C for 16 h

scan_protocol: Arrays were stained and washed on Affymetrix GeneChip Fluidics 450 following manufacturer's protocol and scanned with Affymetrix GeneChip Scanner 3000 7G System

data_processing: GeneSpring (version 12.6, Agilent Technologies) were used to normalize the data  based on the Robust Multiarray Average algorithm, in which data are background-corrected, log 2 transformed and quartile normalized

label: Biotin

source_name: serum

label_protocol: 8 µg total RNA labelled with Affymetrix FlashTag Biotin HSR kit as per manufacturer's instructions

growth_protocol: Archived post mortem human neocortex

extract_protocol: Qiagen miRNeasy serum/plasma kit extraction as per manufacturer's instructions

tag: Sex

value: male

value: Non-Peripheral Neuropathy


title: Scramble-3

city: Winnipeg

first: Tamra

last: Werbowetski-Ogilvie

state: Manitoba

address: 611-745 Bannatyne Avenue

department: Biochemistry & Medical Genetics

institute: University of Manitoba

hyb_protocol: Affymetrix Standard Whole Genome Sense Target Labeling and Hybridization Protocol P/N 703174 Rev.2.

scan_protocol: An Affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays. Gene expression intensities were calculated using Affymetrix Gene Chip Command Console.

data_processing: Affymetrix Expression Console was used to generate RMA expression values from the CEL files

growth_protocol: D283 tumorspheres were grown in ultra low-attachment plates in Neural Proliferation Media consisting of Dulbecco’s modified Eagle’s medium (DMEM)/F12 supplemented with 1% N2 (Gibco), 1% B27 (Gibco), 20 ng/ml epidermal growth factor (EGF; R&D Systems), and 20 ng/ml basic fibroblast growth factor (bFGF; R&D Systems).

treatment_protocol: OTX2 was knocked down in D283 tumorspheres using Silencer select siRNAs (Life Technologies), while a non-silencing (scramble) siRNA was used as a negative control. For microarrays, OTX2 was knocked down using the siRNAs s9931.

tag: cell line

value: scramble control


title: OTx2KD-9931-3

label_protocol: Affymetrix Standard Whole Genome Sense Target Labeling and Hybridization Protocol P/N 703174 Rev.2.


title: OTx2KD-9931-2

extract_protocol: Affymetrix Standard Whole Genome Sense Target Labeling and Hybridization Protocol P/N 703174 Rev.2.


title: Scramble-2


title: 3629 Peripheral Neuropathy

description: miRNA expression data from blood serum

tag: condition

value: Peripheral Neuropathy


title: 4608 Non-Peripheral Neuropathy

description: miRNA expression data from blood serum


title: 4429 Peripheral Neuropathy

description: miRNA expression data from blood serum

value: female


title: 3904 Non-Peripheral Neuropathy

description: miRNA expression data from blood serum


title: 3465 Non-Peripheral Neuropathy

description: miRNA expression data from blood serum


title: KMS11_control

description: Gene expression data from KMS11-control cells

source_name: KMS11 cells, control


title: 2924 Non-Peripheral Neuropathy

description: miRNA expression data from blood serum


title: 2899 Non-Peripheral Neuropathy

description: miRNA expression data from blood serum


title: 3050 Peripheral Neuropathy

description: miRNA expression data from blood serum


title: 3343 Non-Peripheral Neuropathy

description: miRNA expression data from blood serum


title: 3536 Non-Peripheral Neuropathy

description: miRNA expression data from blood serum


title: 3249 Peripheral Neuropathy

description: miRNA expression data from blood serum


title: 2631 Non-Peripheral Neuropathy

description: miRNA expression data from blood serum


title: 2638 Non-Peripheral Neuropathy

description: miRNA expression data from blood serum


title: 3025 Non-Peripheral Neuropathy

description: miRNA expression data from blood serum


title: 2170 Non-Peripheral Neuropathy

description: miRNA expression data from blood serum


title: 2858 Non-Peripheral Neuropathy

description: miRNA expression data from blood serum


title: 2179 Non-Peripheral Neuropathy

description: miRNA expression data from blood serum


title: 2653 Non-Peripheral Neuropathy

description: miRNA expression data from blood serum


title: 2517 Non-Peripheral Neuropathy

description: miRNA expression data from blood serum


title: 3266 Non-Peripheral Neuropathy

description: miRNA expression data from blood serum


title: 2238 Non-Peripheral Neuropathy

description: miRNA expression data from blood serum


title: 1989 Non-Peripheral Neuropathy

description: miRNA expression data from blood serum


title: 2263 Non-Peripheral Neuropathy

description: miRNA expression data from blood serum


title: 1805 Peripheral Neuropathy

description: miRNA expression data from blood serum


title: 1794 Non-Peripheral Neuropathy

description: miRNA expression data from blood serum


title: 2495 Non-Peripheral Neuropathy

description: miRNA expression data from blood serum


title: 1594 Peripheral Neuropathy

description: miRNA expression data from blood serum


title: 3239 Non-Peripheral Neuropathy

description: miRNA expression data from blood serum


title: 1660 Peripheral Neuropathy

description: miRNA expression data from blood serum


title: 1538 Non-Peripheral Neuropathy

description: miRNA expression data from blood serum


title: OTx2KD-9931-1


title: 1361 Non-Peripheral Neuropathy

description: miRNA expression data from blood serum


title: 1119 Peripheral Neuropathy

description: miRNA expression data from blood serum


title: 1219 Peripheral Neuropathy

description: miRNA expression data from blood serum


title: 1293 Peripheral Neuropathy

description: miRNA expression data from blood serum


title: 1359 Non-Peripheral Neuropathy

description: miRNA expression data from blood serum


title: 1348 Non-Peripheral Neuropathy

description: miRNA expression data from blood serum


title: 1328 Peripheral Neuropathy

description: miRNA expression data from blood serum


title: 1523 Non-Peripheral Neuropathy

description: miRNA expression data from blood serum


title: 1483 Peripheral Neuropathy

description: miRNA expression data from blood serum


title: 916 Peripheral Neuropathy

description: miRNA expression data from blood serum


title: 774 Peripheral Neuropathy

description: miRNA expression data from blood serum


title: 797 Non-Peripheral Neuropathy

description: miRNA expression data from blood serum


title: 684 Non-Peripheral Neuropathy

description: miRNA expression data from blood serum


title: 733 Peripheral Neuropathy

description: miRNA expression data from blood serum


title: 954 Peripheral Neuropathy

description: miRNA expression data from blood serum


title: 1423 Peripheral Neuropathy

description: miRNA expression data from blood serum


title: 402 Non-Peripheral Neuropathy

description: miRNA expression data from blood serum


title: 1453 Non-Peripheral Neuropathy

description: miRNA expression data from blood serum


title: 973 Non-Peripheral Neuropathy

description: miRNA expression data from blood serum


title: 3955 Non-Peripheral Neuropathy

description: miRNA expression data from blood serum


title: DTA1_3

city: Los Angeles

first: Lauriane

last: Galle

state: California

address: 1450 Biggy Street NRT 5509

institute: University of Southern California

data_processing:
Illumina Casava1.7 software used for basecalling, algorithm: bcl2fastq-v2.17.1.14
RNAseq data were analyzed using Partek® Flow® software, version 7.0 Copyright ©; 2018
Raw reads were first trimmed based on Quality Score (min quality level 20, trim from both ends, min read length 25)
Trimmed reads were aligned to mm10 with Gencode M16 as guidance using STAR 2.5.3a
Aligned reads were quantified to Gencode M16 genes using Partek E/M
Raw read counts were filtered (exclude a feature where its maximum reads <= 10 in all samples) and normalized (offset by 1 and then upper-quartile normalization)
Normalized reads counts were tested for differential expression using Partek's GSA algorithm.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file with raw read counts

source_name: DTA1_sorted ILC2s

extract_protocol:
Total RNA was isolated using MicroRNAeasy (Qiagen, Valencia, California). 10ng of input RNA was used to produce cDNA for downstream library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Freshly isolated ILC2s after 3 i.p. injections of 1µg rm-IL33 were stimulated with rm-IL-2 (10ng/mL) and rm-IL-7 (10ng/mL) at 37°C with GITR agonist DTA-1 (5µg/mL) or the isotype control for 48 hours.

tag: strain

value: 8 weeks

tag: treatment

value: visceral adipose tissue

value: sorted Type-2 innate lymphoid cells (ILC2s)


title: 106 Peripheral Neuropathy

description: miRNA expression data from blood serum


title: 994 Non-Peripheral Neuropathy

description: miRNA expression data from blood serum


title: 193 Peripheral Neuropathy

description: miRNA expression data from blood serum


title: Isotype_3

source_name: Isotype_sorted ILC2s

value: isotype control


title: DTA1_1


title: 29 Non-Peripheral Neuropathy

description: miRNA expression data from blood serum


title: Isotype_2


title: DTA1_2


title: 1049 Peripheral Neuropathy

description: miRNA expression data from blood serum


title: 251 Non-Peripheral Neuropathy

description: miRNA expression data from blood serum


title: Isotype_1


title: 488 Peripheral Neuropathy

description: miRNA expression data from blood serum


title: 1497 Peripheral Neuropathy

description: miRNA expression data from blood serum


title: 226 Non-Peripheral Neuropathy

description: miRNA expression data from blood serum


title: 466 Peripheral Neuropathy

description: miRNA expression data from blood serum


title: 48 Peripheral Neuropathy

description: miRNA expression data from blood serum


title: 37 Peripheral Neuropathy

description: miRNA expression data from blood serum


title: 1239 Non-Peripheral Neuropathy

description: miRNA expression data from blood serum


title: 1054 Non-Peripheral Neuropathy

description: miRNA expression data from blood serum


title: 542 Peripheral Neuropathy

description: miRNA expression data from blood serum


title: 1118 Peripheral Neuropathy

description: miRNA expression data from blood serum


title: 15_p53KO_G2_Rep1

city: La Jolla

first: Francesca

last: Boscolo

state: CA

address: 9500 Gilman Drive

department: Reproductive Medicine

institute: UCSD

data_processing:
Read data was processed in BasebeadSpace
Reads were alligned using STAR aligner with default settings
Differential expression analysis was performed using the Cufflinks Cuffdiff package
Pathway analysis was performed employing IPA, GSEA, and CE
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include fpkm values for each Sample

source_name: Hind limb muscles

extract_protocol:
Muscles were removed, digested in collagenase and dispase, and isolated through flow cytometry using CD34 and alpha-7 integrin as positive markers and CD31, CD11b, CD45, and Sca-1 as negative markers; RNA isolation was performed using Qiagen RNaesy Micro kit (Cat. number: 74004); Libraries were preared using NEBNext Ultra II Directional RNA Library Prep kit for Illumina
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Muscle

value: from 2 to 3 months old

tag: genotype


title: 13_p53WT_G2_Rep1

value: p53 WT


title: 16_p53KO_G2_Rep2


title: 12_p53KO_3dai_Rep3

source_name: Tibialis Anterior


title: 1280 Peripheral Neuropathy

description: miRNA expression data from blood serum


title: 09_p53WT_3dai_Rep3


title: 08_p53WT_3dai_Rep2


title: 2553 Peripheral Neuropathy

description: miRNA expression data from blood serum


title: Scramble-1


title: 07_p53WT_3dai_Rep1


title: 05_p53KO_Rep2


title: 06_p53KO_Rep3


title: 04_p53KO_Rep1


title: 10_p53KO_3dai_Rep1


title: 03_p53WT_Rep3


title: 01_p53WT_Rep1


title: 14_p53WT_G2_Rep2


title: 02_p53WT_Rep2


title: WT  PA infected 2

city: Chicago

first: Zarema

middle: H

last: Arbieva

state: IL

address: 835 S. Wolcott A301

department: RRC

institute: UIC

data_processing:
Illumina Bcl2fastq 2.17 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using BWA mem v0.7.15
Raw counts were calculated using featureCounts v 1.5.1, given the gene annotation of mm10

source_name: Lung

extract_protocol:
Lungs were removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. Lexogen 3' mRNA-seq Library Prep Kit  was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Age- and weight-matched male WT, Sphk1-/-, and Sphk2-/- mice were administrated a single intratracheal infusion of sterile PBS or PA103 in P (1x106 CFU/mouse). After 24 h of treatment,  lung tissue was collected.

value: Lung

value: WT

tag: infection

value: PA103 in P (1x106 CFU/mouse)


title: WT  PA infected 3


title: Sphk2 KO Control 3

value: Sphk2 KO

value: control


title: WT  Control 2

value: male


title: WT  Control 3


title: Sphk2 KO PA infected 1


title: WT  PA infected 1


title: 11_p53KO_3dai_Rep2


title: Sphk2 KO PA infected 3


title: Sphk2 KO PA infected 2


title: H3K27ac-ChIP-Seq

city: Ann Arbor

first: Vesa

middle: Matti

last: Kaartinen

state: MI

address: 1011 N. University

department: BMS

institute: University of Michigan

data_processing:
Sequences: Standard Illumina software base-calling and quality-control filtering was applied
Sequences (75 nt reads, single end) were aligned to the mouse genome (hg19/mm10) using the BWA algorithm (v0.7.12, default parameters).
Aligns were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWIG files.
Peak locations were determined using the MACS algorithm (v2.1.0) with a cutoff of pvalue = 1E-7. --- or e.g.: Peak calling was done with the SICER script (SICER v1.1; FDR 1E-10, gap=600).
Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations
Genome_build: mm10
Supplementary_files_format_and_content: BW = signal map in bigWIG format (UCSC)
Supplementary_files_format_and_content: BED = standard BED file containing MACS peaks (narrowPeak format for MACS2)

source_name: Embryoid bodies

growth_protocol: Mouse ES cells were derived from Trim33FF: UbcCreERT2 blastocysts. ESCs were passaged in serum-containing medium (Life Technologies, Cat. No. 16141-061), dissociating with TrypLE Express (Life Technologies, Cat. No. 12605-010) and maintained in serum replacement medium (Knock Out Serum Replacement Cat No. 10828-010, Life Technologies) in a base medium of 1:1 Knock Out Dulbecco’s Modified Eagle’s Medium and Ham’s F12. Trim33FF::UbcCreERT2 ESCs were maintained under feeder-free culture conditions on gelatin-coated dishes in the presence of 2i (1.0μM PD0325901  and 3μM CHIR99021; Stemgent) and LIF (Millipore; ESG 1106). EB formation and differentiation were carried out per the ATCC protocol in 20% serum containing medium (http://diyhpl.us/~bryan/irc/protocol-online/protocol-cache/Embryoid_Body_Formation.pdf). Both the media for non-differentiatiing and differentiating conditions were supplemented by Glutamine (GlutaMAX-l, Life Technologies, Cat. No. 35050-061), β-mercaptoethanol (Life Technologies, Cat. No. 21985-023) and Penicillin/Streptomycin (Life Technologies, Cat. No.15140-122).

extract_protocol:
Embryoid bodies from 20 10-cm dishes were harvested at day 6 and fixed immediately with 1% p-formaldehyde for 15 minutes at room temperature followed by quenching with 0.125M (final conc) Glycine. Lysates were sonicated with a microtip sonicator to shear the DNA. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. For each ChIP reaction, 30 ug of chromatin was precleared with protein A agarose beads (Invitrogen). ChIP reaction was set up using precleared chromatin and antibody and incubated overnight at 4 C. Protein A agarose beads were added and incubation at 4 C was continued for another 3 hr. Immune complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on HiSeq 2500/NextSeq 500.

value: Day 6 embryoid bodies from mouse embryonic stem cells

tag: passage numbers of mes cells used

value: From 8 to 12

value: Outbred - B6:129Sv

tag: chip antibody

value: anti-H3K27ac (Active Motif 39133)


title: Sphk2 KO Control 1

value: 8 weeks


title: CTCF-ChIP-Seq

value: anti-CTCF (Active Motif 61311)


title: Fsep_Replicate2

city: New York

first: Peter

last: Sims

state: NY

address: 3960 Broadway, 2nd Floor, Room 203AC

institute: Columbia University

data_processing:
Read 1 and read 2 fastq files were generated on basespace.
12-nt cell barcodes (CBs) and 8-nt unique molecular identifiers (UMIs) were extracted from read 1. Degenerate CBs containing either 'N's or more than four consecutive 'G's were discarded. Synthesis errors, which can result in truncated 11-nt cell barcodes, were corrected.
Read 2 were trimmed to remove poly(A) tails (> dA(7)) from the 3'-ends of each read. Any resulting fragment shorter than 24 nucleotides were discarded.
Trimmed reads were aligned to the Mus musculus genome and transcriptome annotation (GRCm38, Gencode annotation vM10) using STAR v.2.5.0 with parameters --sjdbOverhang 65 --twopassMode Basic --outSAMtype BAM Unsorted. Only reads with unique, strand-specific alignments to exons were kept for further analysis.
All reads with the same CB, UMI, and gene mapping were collapsed to represent a single molecule. To correct for sequencing errors in UMIs, we further collapsed UMIs that were within Hamming distance 1 of another UMI with the same barcode and gene. To correct for sequencing errors in cell barcodes, we then collapsed CBs that were within Hamming distance one of another cell barcode, had at least 20 unique UMI-gene pairs, and had at least 75% overlap of their UMI-gene pairs. Finally, we repeated UMI error correction and collapse using the error-corrected CBs. A digital gene expression matrix was then generated from these corrected barcode-UMI-gene triplets. We note that for any experiments conducted using the 'V' base modified Drop-seq beads, we adjusted our analytical pipeline to recognize truncated CBs by the presence of excessive 'T' bases one nucleotide downstream of the position used in the pipeline described above.
Genome_build: GRCm38
Supplementary_files_format_and_content: 29319_cells.matrix.txt (Replicates 1) and 13055_cells.matrix.txt (Replicates 2) contain the gene expression level of each individual cell. 29319_cells_id.txt (Replicates 1) and 13055_cells_id.txt (Replicates 2) contain ordered cell IDs for each cell in the gene expression matrix.

molecule: polyA RNA

source_name: Ventricular-Subventricular Zone

extract_protocol:
mRNA molecules were captured using bead-bound oligo dT(30).
Captured mRNA molecules were reverse transcribed to obtain cDNA which is then amplified by PCR reactions (14 cycles). Aliquots of amplified cDNA from each sample were pooled and purified with AMPure XP beads. The purified cDNA PCR product was used as the input for Nextera XT reactions to generate sequencing library.

value: Ventricular-Subventricular Zone (V-SVZ) cells

value: Female

tag: location

value: Septal

value: hGFAP::CreERT2; R26RCAG-tdTomato

tag: number of cells sequenced

tag: number of cells retained after initial filtering

tag: number of animals


title: Flat_Replicate2

tag: tissue

value: Lateral


title: Input DNA

tag: cell type


title: NT_3_R1

city: Boston

first: Alexander

last: Gimelbrant

state: Massachusetts

address: 450 Brookline Avenue

institute: Dana-Farber Cancer Institute and Harvard Medical School

data_processing:
alignment using TopHat (v 2.1.1)aligner against mm10 assembly
cufflinks (v2.1.1)
cuffmerge (v 2.1.1)
cuffdiff (v2.1.1)
Supplementary_files_format_and_content: IFN_gene_exp.diff.txt
Supplementary_files_format_and_content: IFN_RNA-Seq_all.csv

source_name: macrophages

growth_protocol: Mouse femurs and tibias were homogenized in DMEM (Corning cellgro) containing 2% FBS. Bone marrow cells were filtered through a 70-μm strainer (Falcon, REF352350) and further purified on a gradient of NycoPrep A-1.077 (Axis-Shield PoC AS, Oslo, Norway). Purified bone marrow cells were cultured in DMEM/F12 containing 10% FBS, 1 ng/mL recombinant mouse interleukin-3 (rmIL-3, R&D Systems, Minneapolis, MN, USA), and 10% L-929 cell conditioned medium as a source of colony stimulation factor-1 (CSF-1) for 3 days. Non-adherent cells were collected and expanded in DMEM/F12 containing 10% FBS and 20% L-929 cell conditioned medium in the ultra-low cluster plates (Corning, Acton, MA, USA) for additional 3 days. Cells were plated in tissue culture plastic ware in DMEM/F12 containing 10% FBS and 10% L-929 conditioned medium to form a monolayer of macrophages for 4 days with a media change on day 2.

extract_protocol:
Agilent Ampure Beads
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The media was substituted with the fresh medis, supplemented with the indicated amounts of IFNg and incubated for 8h.

tag: time of the differentiation


title: NT_2_R1


title: Trim33-ChIP-Seq

value: anti-Trim33 (Bethyl A301-060A)


title: NT_1_R1


title: IFN_2_1_R1

value: IFN, 2 U/ml


title: IFN_20_3_R1

value: IFN, 20 U


title: IFN_20_1_R1


title: IFN_2_3_R1


title: Msep_Replicate2

tag: gender

value: Male


title: Mlat_Replicate2


title: IFN_20_2_R1


title: WT  Control 1

value: Lung

tag: genotype/variation

value: WT

value: control

tag: age


title: IFN_02_2_R1

value: IFN, 0.2 U/ml


title: 1h_50ng_2

data_processing:
alignment using TopHat (v 2.1.1)aligner against mm10 assembly
cufflinks (v2.1.1)
cuffmerge (v 2.1.1)
cuffdiff (v2.1.1)
Supplementary_files_format_and_content: RNA-Seq_fpkm1.xlsx: FPKM for all samples after the cuffdif normalization and merging of the replicates
Supplementary_files_format_and_content: TB_gene_exp.diff.txt: raw cuffdiff output

growth_protocol: Mouse femurs and tibias were homogenized in DMEM (Corning cellgro) containing 2% FBS. Bone marrow cells were filtered through a 70-?m strainer (Falcon, REF352350) and further purified on a gradient of NycoPrep A-1.077 (Axis-Shield PoC AS, Oslo, Norway). Purified bone marrow cells were cultured in DMEM/F12 containing 10% FBS, 1 ng/mL recombinant mouse interleukin-3 (rmIL-3, R&D Systems, Minneapolis, MN, USA), and 10% L-929 cell conditioned medium as a source of colony stimulation factor-1 (CSF-1) for 3 days. Non-adherent cells were collected and expanded in DMEM/F12 containing 10% FBS and 20% L-929 cell conditioned medium in the ultra-low cluster plates (Corning, Acton, MA, USA) for additional 3 days. Cells were plated in tissue culture plastic ware in DMEM/F12 containing 10% FBS and 10% L-929 conditioned medium to form a monolayer of macrophages for 4 days with a media change on day 2.

treatment_protocol: The media was substituted with the fresh medis, supplemented with the indicated amounts of TNFa and incubated fr 8h.

value: TNFa 50 ng


title: IFN_02_1_R1


title: 1h_2ng_2

value: TNFa 2 ng


title: 1h_NT1_2

value: TNFa n/a


title: 1h_2ng_1


title: IFN_02_3_R1


title: B6_50ng_2


title: 1h_NT1_1


title: IFN_2_2_R1


title: B6_50ng_1


title: B6_10ng_1

value: TNFa 10 ng


title: B6_2ng_2


title: B6_2ng_1


title: B6_NT1_2


title: B6_10ng_2


title: B6_NT_1


title: KO-Refed2

city: Memphis

first: John

last: Crispino

state: Tennessee

address: 262 DANNY THOMAS PL

institute: St. Jude Children's Research

data_processing:
Illumina adapters were trimmed using cutadapt with default parameters
Trimmed Reads were aligned to mm10 using STAR and default parameters
Gene expression was quantified using htseq-count and default parameters
Differential expression was carried out with DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized reads counts (by DESeq2) for each sample.

source_name: KO-Refed, liver

extract_protocol:
Mice was fasted overnignt and refed for 4 hours
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

value: 12 weeks

value: Refed


title: KO-Refed1


title: WT-Refed1

source_name: WT-Refed, liver


title: KO-Fasted1

source_name: KO-Fasted, liver

value: Fasted


title: WT-Fasted2

source_name: WT-Fasted, liver


title: KO-Fasted2


title: WT-Fasted1


title: WT-Refed2


title: Sphk2 KO Control 2

value: Sphk2 KO

value: 8 weeks

value: male


title: 1h_50ng_1


title: Fsep_Replicate1

value: Ventricular-Subventricular Zone (V-SVZ) cells

value: Female

value: Septal

value: hGFAP::CreERT2; R26RCAG-tdTomato

tag: throughput

value: High


title: 1h_10ng_2

tag: strain


title: 1h_10ng_1

tag: treatment


title: Msep_Replicate1

value: Male


title: E5-23 M6K T2

city: Dallas

first: Hao

last: Zhu

state: Texas

address: 6000 Harry Hines Blvd

institute: UT Southwestern Medical Center

data_processing:
library strategy: Target-DNA-sequencing
BCL files from Illumina Nextseq 500 sequencing were converted to FASTQ files by bcl2fastq (Illumina). After trimming by trim_galore package, BWA-MEM (version 0.7.15) was used to align FASTQ files to reference genome GRCm38 with subsequent processing by Samtools (version 1.3) and Nudup.py (Nugen) to ensure proper file formatting and remove duplicates. Alignments were then recalibrated and realigned by GATK (version 3.5).
To detect somatic variants in tumor samples, we use the somatic variant detection program Mutect (version 1.1.7). 50 tumor samples were called against a panel of 3 normal liver samples from two WT C3H/HeJ mice to the reference genome GRCm38. Variants passed the Mutect high-confidence somatic mutation filters were selected and further filtered against from known SNVs in C3H/HeJ mice provided by  http://ftp-mouse.sanger.ac.uk (mgp.v3).
Genome_build: GRCm38
Supplementary_files_format_and_content: vcf file

source_name: C3H/HeJ_E2f8 KO_frozen liver tumor tissue

extract_protocol:
The genomic DNA was extracted using QIAGEN AllPrep DNA/RNA Kit (Cat. 80204). Integrity of genomic DNA was assessed by electrophoresis on 1% agarose gels, and concentration was determined by nanodrop. gDNA was sonicated into 500bp fragments and purified using Genomic DNA Clean & Concentrator Kit (ZYMO RESEARCH).
The DNA library was prepared using Ovation Target Enrichment System (NuGEN) following the manufacturer’s instructions. Target genes were selected from human HCC and mouse sequencing studies (Bard-Chapeau et al., 2014; Keng et al., 2009; Shen et al., 2016) and some well-known cancer related genes. The target probes were synthesized by NuGEN. More than 99.5% of the probes had >90% coverage. The sequencing was performed using a 150 bp single-end protocol on Illumina NextSeq 500 platform.

treatment_protocol: The mice were injected with one dose DEN (75ug/g) at P27.Tumors were harvested after 5 months.

tag: genotype or sirna treatment

value: E2f8 KO

value: about 177 days old

value: liver tumor


title: E5-23 M6K T1


title: E5-23 M4K T1


title: E5-23 M4K T2


title: E5-30 M10H T1

source_name: C3H/HeJ_E2f8 Het_frozen liver tumor tissue

value: E2f8 Het


title: E5-23 M1H T2


title: E5-23 M7H T1


title: E5-23 M1H T1


title: E5-30 M7W T2

source_name: C3H/HeJ_E2f8 WT_frozen liver tumor tissue

value: E2f8 WT


title: E5-30 M7W T1


title: Mlat_Replicate1

value: Lateral


title: E5-23 M8W T1


title: E5-30 M2W T1


title: C3H M N4

source_name: C3H/HeJ_WT_normal liver tissue

treatment_protocol: Wild type C3H/HeJ mice, no treatment.

value: WT

value: about 90 days old

value: normal liver


title: E5-30 M2W T2


title: Flat_Replicate1


title: C3H M N1


title: 7-82 M5E T1

source_name: C3H/HeJ_siE2f8_frozen liver tumor tissue

treatment_protocol: The mice were treated with in vivo siRNA against E2f8 from P8-10 to P20-22, twice/week, four doses in total. Then at P24-26, one dose of DEN (75ug/g) was injected to mice.Tumors were harvested after 6 months.

value: about 205 days old


title: 7-7 M4E T1


title: 7-7 M4E T2


title: 7-82 M5E T2


title: C3H M N2


title: E5-30 M10H T2


title: 7-4 M4E T1


title: 7-3 M2ET2


title: 7-3 M2E T1


title: 6-30 M2E T1


title: 7-22 M3E T2


title: 6-30 M2E T2


title: 7-22 M3E T1


title: 7-82 M8S T1

source_name: C3H/HeJ_siCtrl_frozen liver tumor tissue

treatment_protocol: The mice were treated with negative control siRNA from P8-10 to P20-22, twice/week, four doses in total. Then at P24-26, one dose of DEN (75ug/g) was injected to mice.Tumors were harvested after 6 months.

value: siCtrl


title: 7-3 M4S T1


title: 7-3 M4S T2


title: 7-4 M6S T1


title: 7-3 M3S T2


title: 7-81 M3S T1


title: 7-22 M6S T1


title: 7-3 M3S T1


title: 7-4 M6S T2


title: 6-30 M4S T1


title: 6-30 M3S T2


title: 7-4 M4E T2


title: 7-82 M3A T1

source_name: C3H/HeJ_siAnln_frozen liver tumor tissue

treatment_protocol: The mice were treated with in vivo siRNA against Anln from P8-10 to P20-22, twice/week, four doses in total. Then at P24-26, one dose of DEN (75ug/g) was injected to mice. Tumors were harvested after 6 months.

value: siAnln


title: 6-30 M3S T1


title: 7-82 M3A T2


title: 7-4 M3A T1


title: 7-3 M3A T2


title: 7-7 M1A T1


title: 7-7 M1A T2


title: 7-22 M2A T1


title: 7-3 M1A T2


title: 6-30 M1A T1


title: 7-3 M1A T1


title: Sma17_RamDA_10pg_dT_C04

source_name: ES_diluted total RNA

value: Embryonic stem (ES) cell

tag: sample type

value: purified total RNA

tag: starting amount

value: 10 pg

tag: method subtype

value: RT-RamDA

tag: rt primer

value: dT


title: Sma17_RamDA_10pg_dT_B04


title: Sma17_RamDA_10pg_NSRdT_B06

value: NSR and dT


title: Sma17_RamDA_10pg_NSRdT_C06


title: Sma17_RamDA_10pg_dT_A04


title: Sma17_RamDA_10pg_N6_A02


title: Sma17_RamDA_10pg_NSR_C03

value: NSR


title: Sma17_RamDA_10pg_NSRdT_A06


title: Sma17_RamDA_10pg_NSR_B03


title: Sma17_RamDA_10pg_N6dT_C05

value: N6 and dT


title: Sma17_RamDA_10pg_N6_C02


title: Sma17_RamDA_10pg_N6dT_B05


title: Sma17_RamDA_10pg_N6dT_A05


title: 7-22 M2A T2

value: liver tumor


title: 6-30 M1A T2


title: Sma17_RamDA_10pg_NSR_A03


title: Sma17_RamDA_10pg_N6_B02


city: Minneapolis

first: Dong Seong

last: Cho

state: MN

address: 421 Washington Ave S.E.

department: Chemical Engineering and Materials Science

institute: University of Minnesota

description: Gene expression data from rESC grown on feeder-dependent condition

hyb_protocol: Standard Affymetrix hybridization protocol for GeneChip Rat Gene 1.0 ST array (Affymetrix) was performed by the University of Chicago Genomics Facility.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner in the University of Chicago Genomics Facility.

data_processing: The data were processed by RMA summarization and normalized by linear normalization.

organism: Rattus norvegicus

source_name: rESC (feeder)

label_protocol: Standard Affymetrix biotin labelling protocol was performed by the University of Chicago Genomics Facility.

growth_protocol: rESCs were cultured with N2B27 medium supplemented with 3 µM CHIR99021 and 0.5 µM PD0325901 on mouse embryonic fibroblast feeder layers. For feeder-free culture, rESCs were cultured with N2B27 medium supplemented with 3 µM CHIR99021, 2 µM PD0325901, and 5 ng/mL human BMP4 on laminin coated plates.

extract_protocol: Total RNA was extracted using Rneasy micro kit (Qiagen) with the manufacturer's protocol.

treatment_protocol: rESCs were differentiated into cHypoSCs by culturing under rat multipotent adult progenitor cell maintenance medium (Subramanian et al., 2010) that contains LIF, EGF, PDGF, and 2% fetal bovine serum.

tag: used resc cell line


description: Gene expression data from cHypoSCs derived from rESC grown on feeder-dependent condition, D7

source_name: D7 (feeder)


description: Gene expression data from cHypoSCs derived from rESC grown on feeder-free condition, D17, biological rep1

source_name: D17 (feeder-free)


description: Gene expression data from cHypoSCs derived from rESC grown on feeder-free condition, D7, biological rep2

source_name: D7 (feeder-free)


description: Gene expression data from cHypoSCs derived from rESC grown on feeder-free condition, D7, biological rep1


description: Gene expression data from cHypoSCs derived from rESC grown on feeder-free condition, D32, biological rep2

source_name: D32 (feeder-free)


description: Gene expression data from cHypoSCs derived from rESC grown on feeder-free condition, D17, biological rep2


description: Gene expression data from cHypoSCs derived from rESC grown on feeder-dependent condition, D17

source_name: D17 (feeder)


title: Rag2/pfp_KO_TH_3

city: Seoul

first: Yun-Jung

last: Choi

address: 120 Neungdon-ro,Gwangjib-gu

department: Animal biotechnology

country: South Korea

institute: KONKUK University

description:
KO TH
replicate 3

hyb_protocol: 750 ng of labeled cRNA samples were hybridized to each Mouse Ref-8 v2.0 Expression Beadchip for 17h at 58°C, according to the manufacturer's instructions (Illumina, Inc., San Diego, USA)

scan_protocol: Arrays were scanned with an Illumina bead array Reader confocal scanner according to the manufacturer's instructions.

data_processing: Raw data were extracted using the software provided by the manufacturer (Illumina GenomeStudio v2011.1 (Gene Expression Module v1.9.0)). Array probes transformed by logarithm and normalized by quantile method

label_protocol: Total RNA was amplified and purified using TargetAmp-Nano Labeling Kit for Illumina Expression BeadChip (EPICENTRE, Madison, USA) to yield biotinylated cRNA according to the manufacturer’s instructions. Briefly, 500 ng of total RNA was reverse-transcribed to cDNA using a T7 oligo(dT) primer. Second-strand cDNA was synthesized, in vitro transcribed, and labeled with biotin-NTP. After purification, the cRNA was quantified using the ND-1000 Spectrophotometer (NanoDrop, Wilmington, USA).

extract_protocol: Total RNA was extracted and purified from the thymus of Rag2/pfp mouse using RNeasy columns (Qiagen; Valencia, CA, USA) according to the manufacturer's  protocol. The RNA quality was verified using an Agilent Bioanalyzer 2100 (Agilent Technologies; Palo Alto, CA, USA). Generation of double-stranded cDNA, preparation and labeling of cRNA, hybridization to Illumina Mouse Ref-8 v2 expression BeadChip (Illumina), washing, and scanning with Illumina Bead Array Reader Conforcal Scanner (Illumina, Inc.).

value: Thymus

tag: genotype

value: Rag2/pfp KO


title: Wild_mouse_spleen_2

description:
WT SP2
replicate2

extract_protocol: Total RNA was extracted and purified from the spleen of Rag2/pfp mouse using RNeasy columns (Qiagen; Valencia, CA, USA) according to the manufacturer's  protocol. The RNA quality was verified using an Agilent Bioanalyzer 2100 (Agilent Technologies; Palo Alto, CA, USA). Generation of double-stranded cDNA, preparation and labeling of cRNA, hybridization to Illumina Mouse Ref-8 v2 expression BeadChip (Illumina), washing, and scanning with Illumina Bead Array Reader Conforcal Scanner (Illumina, Inc.).

value: spleen

value: Wild type


description: Gene expression data from cHypoSCs derived from rESC grown on feeder-dependent condition, D32

source_name: D32 (feeder)


title: RD26-IOE+EST 5h biological replicate 1

city: Postdam

first: Salma

last: Balazadeh

address: Am Muehlenberg 1

department: Stitt

country: Germany

institute: MPIMP

description: RD26-IOE lines treated with 10µM EST for 5h

hyb_protocol: Labelling, hybridisation, washing, staining, and scanning procedures were performed by an Affymetrix authorized service provider (ATLAS Biolabs, Berlin, Germany) as described in the Affymetrix technical manual.

data_processing: Raw data (CEL files) obtained from RNA hybridisation experiments were normalized with the affyPLM package from the Bioconductor software project (Gentleman et al., 2004) using the GCRMA that uses GC content of probes in normalization with RMA (Robust Multiple array Average) and  gives one value for each probe set instead of keeping probe level information (Wu et al., 2004). The transcriptional changes were determined by subtracting the normalized signal intensity of the control samples from that of induced samples.

organism: Arabidopsis thaliana

source_name: Arabidopsis WT-Col-0 Seedlings treated with EST

growth_protocol: Seeds were surface-sterilized for 1 min in 70% ethanol and then in sterilisation solution (20% sodium hypochlorite) for 30 min. After sterilization, the seeds were sown on half-strength MS medium (Murashige and Skoog, 1962), supplemented with 1% (w/v) sucrose and solidified with 0.7% (w/v) phytoagar and appropriate antibiotics. After imbibition, the seeds were stratified at 4°C for 3 days. The seeds were germinated at 22°C under a 16-h day (140 µmol m-2 s-1) / 8-h night regime. The 2-week-old Arabidopsis seedlings were carefully removed from plates  and subjected to EST or mock treatments.

extract_protocol: RNeasy Plant Mini Kit (Qiagen)

treatment_protocol: After two weeks, seedlings were transferred to liquid MS medium while shaking. β-Estradiol (Sigma-Aldrich) was added to the medium to a final concentration of 10 μM. Subsequently, seedlings were harvested at 2h or 5h after addition of estradiol. Ethanol (0.1% [v/v]) was added to control seedlings (mock treatment).

value: Seedlings

tag: cultivar

value: two-week-old


description: Gene expression data from cHypoSCs derived from rESC grown on feeder-free condition, D32, biological rep1


title: rESC grown on feeder-free condition

description: Gene expression data from rESC grown on feeder-free condition, biological rep1

source_name: rESC (feeder-free)


title: RD26-IOE+Mock 5h biological replicate 2

description: RD26-IOE lines treated with 0.01/ EtOH for 5h

scan_protocol: Labelling, hybridisation, washing, staining, and scanning procedures were performed by an Affymetrix authorized service provider (ATLAS Biolabs, Berlin, Germany) as described in the Affymetrix technical manual.

source_name: Arabidopsis WT-Col-0 Seedlings treated with EtOH

tag: tissue


title: RD26-IOE+Mock 5h biological replicate 1

label_protocol: Labelling, hybridisation, washing, staining, and scanning procedures were performed by an Affymetrix authorized service provider (ATLAS Biolabs, Berlin, Germany) as described in the Affymetrix technical manual.


title: RD26-IOE+Mock 2h

description: RD26-IOE lines treated with 0.01/ EtOH for 2h


title: Wild_mouse_TH_1

description:
WT TH4
replicate 1


title: Rag2/pfp_KO_TH_1

description:
KO TH4
replicate 1


title: Wild_mouse_TH_3

description:
WT TH
replicate 3


title: Wild_mouse_TH_2

description:
WT TH5
replicate 2


title: Wild_mouse_spleen_1

description:
WT SP4
replicate1


title: RD26-IOE+EST 2h

description: RD26-IOE lines treated with 10µM EST for 2h


title: Rag2/pfp_KO_TH_2

description:
KO TH5
replicate 2


title: Rag2/pfp_KO_spleen_3

description:
KO SP1
replicate3


title: Wild_mouse_spleen_3

description:
WT SP3
replicate3


title: RD26-IOE+EST 5h biological replicate 2


title: Rag2/pfp_KO_spleen_2

description:
KO SP7
replicate2


title: Wild_mouse_LN_3

description:
WT_LN3
replicate 3

extract_protocol: Total RNA was extracted and purified from the LN (lymph node) of Rag2/pfp mouse using RNeasy columns (Qiagen; Valencia, CA, USA) according to the manufacturer's  protocol. The RNA quality was verified using an Agilent Bioanalyzer 2100 (Agilent Technologies; Palo Alto, CA, USA). Generation of double-stranded cDNA, preparation and labeling of cRNA, hybridization to Illumina Mouse Ref-8 v2 expression BeadChip (Illumina), washing, and scanning with Illumina Bead Array Reader Conforcal Scanner (Illumina, Inc.).

value: Lymph node


title: Wild_mouse_LN_2

description:
WT_LN2
replicate 2


title: Rag2/pfp_KO_LN_2

description:
Rag_pfp_LN2
replicate 2


title: Wild_mouse_LN_1

description:
WT_LN1
replicate 1


title: Rag2/pfp_KO_spleen_1

description:
KO SP4
replicate1


title: Rag2/pfp_KO_LN_3

description:
Rag_pfp_LN3
replicate 3


title: Rag2/pfp_KO_LN_1

description:
Rag_pfp_LN1
replicate 1


title: ACC-09

type: genomic

first: Arnoud

last: Boot

state: Singapore

address: 8 college road

institute: Duke-NUS Medical School

hyb_protocol: DNA was bisulfite converted using the EZ DNA methylation gold kit. Hybridization was performed according to the illumina protocol.

scan_protocol: Standard Illumina Protocol

data_processing: Data was normalized using the BMIQ function from the wateRmelon package in R with nfit=5000. probes with detection pval. ## 1370 sites were removed as beadcount <3 in 5 % of samples ## 5118 sites having 1 % of samples with a detection p-value greater than 0.05 were removed ## final filtering: sites with total intensity (methylated + unmethylated) <2000 were removed.

label: Cy3 and Cy5

source_name: Oncocytic adrenocrotical carcinoma

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was isolated using the DNA isolation was performed using the Wizard Genomic DNA Purification Kit (Promega

value: Oncocytic adrenocrotical carcinoma

value: Yes


title: ACC-10


title: 14A_C

city: London

first: Vitor

last: Teixeira

address: 5 University Street

country: United Kingdom

institute: University College London

hyb_protocol: Hybridization on the 450K BeadArray according to Illumina’s Infinium HD protocol

scan_protocol: Illumina’s iScan fluorescent system was used to scan and image the arrays.

data_processing: Raw data loaded into Bioconductor environment using ChAMP import method.

source_name: Human preinvasive lung squamous cell carcinoma lesions

label_protocol: 200 ng of DNA were bisulfite converted using the EZ DNA methylation kit according to the manufacturer’s modified protocol for Illumina’s Infinium 450K assay

extract_protocol: DNA from the micro-dissected tissue and bronchial brushing samples was extracted using QIAGEN’s QIAmp DNA Mini and Micro kits, respectively .

treatment_protocol: CIS lesions were isolated using laser capture microdissection.

value: Preinvasive lung squamous cell carcinoma lesions

tag: lesion outcome

value: Control


title: 45A_P

value: Progressive


title: 13A_C


title: 53_P


title: 16A_C


title: 29_R

value: Regressive


title: 2_R


title: 54_P


title: 52_P


title: 23_R


title: 17A_C


title: 4B_C


title: 28_R


title: 31_R


title: 8B_C


title: 28_P


title: 1A_C


title: 7B_C


title: 5_R


title: 17_P


title: 51_P


title: 55_P


title: 15B_C


title: 15_R


title: 17B_C


title: 16B_C


title: 44A_P


title: 22_P


title: 17_R


title: 1B_C


title: 19_R


title: 2A_C


title: 12B_C


title: 8A_C


title: 104_C


title: 6A_C


title: 9A_C


title: 3A_C


title: 5B_C


title: 12A_C


title: 6B_C


title: 5A_C


title: 2B_C


title: 102_C


title: 13B_C


title: 26_R


title: 24_R


title: 41_P


title: 11A_C


title: 42_P


title: 11B_C


title: 30_P


title: 12_C


title: 60_C


title: 7A_C


title: 4A_C


title: 10B_C


title: 7_R


title: H07HT3

city: Utrecht

first: Basten

last: Snoek

address: Padualaan

department: Mol. Plant. Physiology

institute: Utrecht University

data_processing:
Quality Control (QC) was performed in house on the raw sequencing reads prior to analysis using FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc).
Subsequently the raw reads were aligned to the Arabidopsis genome (TAIR10) using TopHat v2.0.131 with the parameter settings: ‘bowtie’, ‘no-novel-juncs’, ‘p 6’, ‘G’, ‘min-intron-length 40’, ‘max-intron-length 2000’.
Aligned reads were summarized over annotated gene models using HTSeq-count v0.6.12 with settings: ‘-stranded no’, ‘-i gene_id’. From the TAIR10 GTF file all ORFs of which the annotation starts with ‘CPuORF’ were manually removed prior summarization to avoid not counting all double annotated genes.
Sample counts were depth-adjusted and differential expression was determined using the DESeq package with default settings
Genome_build: TAIR 10
Supplementary_files_format_and_content: Tab-delimited text with normalized counts

source_name: hda9-1 mutant_7 day-old seedling_27°C

growth_protocol: Seeds were stratified on 1% MS-Agar plates at 4oC in the dark. Thereafter, plates were moved to a growth cabinet at the indicated temperature at 22°C or 27°C, in short day photoperiod (8h light/16h dark) at app. 100 umol m-2 s-1 PAR light intensity

extract_protocol:
Seeds were harvested at the moment of dawn (lights on), and snap frozen in liquid Nitrogen. RNA was isolated using the Sigma Spectrum Plant Total RNA isolation kit and gDNA was removed by on-column DNAse treatment (Sigma-Aldrich). RNA integrity and concentration was checked using RNA 6000 Nano Chips on a Bioanalyzer (Agilent-2100). For RNA-seq library preparation in total 3 samples were prepared for each genotype, treatment and time-point, by combining isolated RNA of 3 individually harvested batches per sample.
Illumina TruSeq RNA Library preparation and Illumina HiSeq2500 (high-throughput) single-end 50 bp sequencing was outsourced to Macrogen, Korea.

treatment_protocol: control or high temperature conditions (22°C vs 27°C)

tag: ecotype background

value: hda9-1 mutant

value: 7 day-old

tag: growth condition

value: control temperature 27°C

value: 7 day-old whole mount seedling


title: H07HT2

tag: genotype/variation


title: H07HT1

tag: age


title: P07HT3

source_name: pif4-2 mutant_7 day-old seedling_27°C

value: pif4-2 mutant


title: 21_R


title: 9B_P


title: 12_R


title: P07HT2


title: 32_P


title: P07HT1


title: 1_P


title: 27_P


title: 29_P


title: 20_R


title: 38_P


title: C07HT3

source_name: wild type_7 day-old seedling_27°C

value: wild type


title: 5_P


title: 9_R


title: 11_P


title: 14_P


title: 19_P


title: 15_P


title: C07HT2


title: 12_P


title: 24_P


title: 37_P


title: 10_P


title: C07HT1


title: 36_P


title: 3_P


title: 7_P


title: H07C3

source_name: hda9-1 mutant_7 day-old seedling_22°C

value: control temperature 22°C


title: H07C2


title: H07C1


title: 26_P


title: 31_P


title: P07C2

source_name: pif4-2 mutant_7 day-old seedling_22°C


title: 10_R


title: P07C1


title: 6_P


title: 8_P


title: C07C3

source_name: wild type_7 day-old seedling_22°C


title: P07C3


title: C07C2


title: 8_R


title: MXL_LST

city: Shanghai

first: Liangliang

state: Shanghai

address: NO. 168, Changhai Road, Yangpu

country: China

institute: Changhai Hospital of Shanghai

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

scan_protocol: Illumina Infinium HumanMethylation450 (HM450) Bead- Chips (Illumina, San Diego, CA) were used for these studies in Shanghai Biotechnology Corporation.

data_processing:
DNA methylation profiling data were processed by the Methylation Module of GenomeStudio v1.9 software using default parameters (Illumina).
Methylation values for individual CpG sites were obtained as β-values, calculated as the ratio of the methylated signal intensity to the sum of both methylated and unmethylated signals after background subtraction.
The β-values were reported as a DNA methylation score ranging from 0 (non-methylated) to 1 (completely methylated).

label: Cy5 and Cy3

source_name: Rectal LST

label_protocol: Standard Illumina protocol for Human Methylation450 DNA Analysis bead chip

extract_protocol: DNA was isolated using a micro DNA isolation kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions.

treatment_protocol: Genomic DNA was extracted and bisulfite modifies DNA extraction from snap-frozen tissues used for the studies as described previously.

tag: gender

value: Female

value: Rectum

tag: tissue type

value: Villous adenoma

tag: size (cm)

tag: operation way

value: ESD


title: CBX_LST

value: Villioustublar adenoma

tag: tumor stage

value: LIN

value: EMR


title: 13_P

value: Preinvasive lung squamous cell carcinoma lesions


title: CBX_LSTP

source_name: Normal rectal mucosa

value: Normal mucosa


title: LAW_LSTP

value: Male


title: C07C1


title: XJX_LST

source_name: Sigmoid colon LST

value: Sigmoid colon


title: MXL_LSTP


title: H48HT3

source_name: hda9-1 mutant_2 day-old seedling_27°C

value: hda9-1 mutant

value: 2 day-old

value: 2 day-old whole mount seedling


title: WMD_LSTP


title: XJX_LSTP

source_name: Normal sigmoid colon mucosa


title: HWB_LST


title: HWB_LSTP


title: YHF_LSTP

source_name: Normal desending colon mucosa

value: Desending colon


title: H48HT1

value: control temperature 27°C


title: WMD_LST


title: H48HT2


title: TGH_LSTP


title: P48HT3

source_name: pif4-2 mutant_2 day-old seedling_27°C

value: pif4-2 mutant


title: YGW_LSTP

value: Female


title: YHF_LST

source_name: Desending colon LST

value: Low-grade intraepithelial neoplasia (LIN)


title: QZS_LST

value: Rectum

value: High-grade intraepithelial neoplasia (HIN)


title: QZS_LSTP


title: P48HT2


title: TGH_LST

value: Villioustublar adenoma

value: ESD


title: P48HT1


title: SAMPLE 146 SQ

city: Seattle

first: Sean

last: Maden

state: WA

address: 1100 Fairview Ave N

department: Clinical Research

institute: Fred Hutch

description: Squamous tissue

hyb_protocol: Illumina Infinium HD Methylation protocol

scan_protocol: Imaged with iScan+ using Methylation NXT scan setting

data_processing: GenomeStudio v2011.1 with Methylation Module v1.9.0

source_name: Tissue core or slide

extract_protocol: DNA from formalin fixed paraffin-embedded (FFPE) cores or tissue sections

value: male


title: C48HT2

source_name: wild type_2 day-old seedling_27°C

value: wild type


title: YGW_LST

value: Villous adenoma

value: LIN; HIN partly


title: C48HT1


title: SAMPLE 142 SQ

description: Squamous tissue

label_protocol: Illumina Infinium HD Methylation protocol

value: female


title: SAMPLE 148 SQ

description: Squamous tissue


title: H48C3

source_name: hda9-1 mutant_2 day-old seedling_22°C

value: hda9-1 mutant

value: control temperature 22°C


title: SAMPLE 145 SQ

description: Squamous tissue


title: H48C2

value: 2 day-old

value: 2 day-old whole mount seedling


title: SAMPLE 135 SQ

description: Squamous tissue


title: SAMPLE 136 SQ

description: Squamous tissue


title: SAMPLE 147 SQ

description: Squamous tissue


title: SAMPLE 141 SQ

description: Squamous tissue


title: LAW_LST

value: Male

value: EMR


title: H48C1


title: SAMPLE 143 SQ

description: Squamous tissue


title: P48C3

source_name: pif4-2 mutant_2 day-old seedling_22°C

value: pif4-2 mutant


title: SAMPLE 140 SQ

description: Squamous tissue


title: SAMPLE 144 SQ

description: Squamous tissue


title: SAMPLE 139 SQ

description: Squamous tissue


title: SAMPLE 137 SQ

description: Squamous tissue


title: SAMPLE 132 SQ

description: Squamous tissue


title: SAMPLE 138 SQ

description: Squamous tissue


title: P48C2


title: C48C3

source_name: wild type_2 day-old seedling_22°C


title: P48C1


title: SAMPLE 130 SQ

description: Squamous tissue


title: C48HT3

value: control temperature 27°C


title: SAMPLE 127 SQ

description: Squamous tissue


title: SAMPLE 128 SQ

description: Squamous tissue


title: C48C2


title: SAMPLE 121 SQ

description: Squamous tissue


title: SAMPLE 133 SQ

description: Squamous tissue


title: SAMPLE 131 SQ

description: Squamous tissue


title: SAMPLE 117 SQ

description: Squamous tissue


title: SAMPLE 120 SQ

description: Squamous tissue


title: SAMPLE 118 SQ

description: Squamous tissue


title: SAMPLE 119 SQ

description: Squamous tissue


title: C48C1


title: SAMPLE 113 SQ

description: Squamous tissue


title: SAMPLE 116 SQ

description: Squamous tissue


title: SAMPLE 123 SQ

description: Squamous tissue


title: SAMPLE 124 SQ

description: Squamous tissue


title: SAMPLE 115 SQ

description: Squamous tissue


title: SAMPLE 126 SQ

description: Squamous tissue


title: SAMPLE 112 SQ

description: Squamous tissue


title: SAMPLE 125 SQ

description: Squamous tissue


title: SAMPLE 122 SQ

description: Squamous tissue


title: M2: OV2008-miR328-sample 2

city: Columbus

first: Qi-En

last: Wang

state: OH

address: 420 W.12th Avenue

department: Radiation Oncology

institute: The Ohio State University

description: Gene expression data from OV2008 cells transfected with NC miRNA

hyb_protocol: Following fragment and label, 5.2 μg of single-strand DNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Human transcriptome array 2.0. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.   Following fragment and label, 5.2 ug of single-strand DNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Human transcriptome array 2.0. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.  Following fragment and label, 5.2 ug of single-strand DNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Human transcriptome array 2.0. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: OV2008 cells transfected with miR328-M-sample 2

label_protocol: Amplified and biotinylated sense-strand DNA were prepared according to the standard Affymetrix protocol from 100ng total RNA  Amplified and biotinylated sense-strand DNA were prepared according to the standard Affymetrix protocol from 100ng total RNA  Amplified and biotinylated sense-strand DNA were prepared according to the standard Affymetrix protocol from 100ng total RNA

growth_protocol: Cells were grown in RPMI 1640 medium supplemented with 10% (v/v) fetal bovine serum (FBS), and maintained in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: cell type

value: ovarian cancer

tag: cell line


title: M1: OV2008-miR328-sample 1

source_name: OV2008 cells transfected with miR328-M-sample 1


title: A2L0694_THC-SIV

city: San Antonio

first: Mahesh

last: Mohan

address: 8715 West Military Road

department: Host Pathogen Interaction Program

institute: Southwest National Primate Research Center

description:
A2L0694
Test

data_processing:
QuantStudio run files representing all treatment groups and timepoints were analyzed using ExpressionSuite Software (Life Tech). The results from the ExpressionSuite software analysis containing five columns (well, sample, detector, task and CT values) were saved as a tab-delimited text file which was later imported and analyzed using the Omics Office StatMiner qPCR analysis software, TIBCO Spotfire (Perkin Elmer, Waltham, MA). Omics Office StatMiner Software utilizes the comparative Cτ (ΔΔCτ) method to rapidly and accurately quantify relative gene expression across many genes and samples.
miRNA expression data was normalized using the global normalization method.
In all experiments, the CT upper limit was set to 28 meaning that all miRNA detectors with a CT value greater than or equal to 28 were excluded.
Due to the small sample size and exploratory nature of the study, multiple comparisons correction was not applied.
Omics Statminer software automatically calculates all deltadeltaCT based fold-change calculations and provides p values from the uploaded QuantStudio data files.
Non-normalized matrix worksheet reports non-normalized signal.
Normalized matrix worksheet reports normalized signal (normalization using global normalization).
Fold-Change worksheet reports test/control (i.e., VEH-SIV, THC-SIV vs Uninfected control) ratios.

label: not provided

organism: Macaca mulatta

source_name: Colon

label_protocol: microRNA profiling was performed using the TaqMan® OpenArray® Human microRNA panels (Life Tech) following the manufacturer’s instructions. Reverse transcription was first performed from 350 ng of total RNA using the microRNA reverse transcription kit. 2.5 µL of cDNA was preamplified using the TaqMan® PreAmp Master Mix kit. Preamplified products were first diluted and then loaded onto to TLDA plates. TLDA plates were run on the ABI 7900 HT Fast PCR system following the manufacturer’s recommended thermal cycling conditions.

extract_protocol: Total RNA (small and large) was extracted using the miRNeasy Mini kit (Qiagen). On-column DNase digestion was also performed to eliminate contaminating genomic DNA.

treatment_protocol: 17 animals were infected intravenously with 100 TCID50 SIVmac251 and 6 remained uninfected.

value: Colon

tag: infection

value: Simian immunodeficiency virus (SIV)

tag: treatment

value: Delta-9-tetrahydrocannabinol (THC)


title: C3: OV2008-NC-sample 3

source_name: OV2008 cells transfected with NC miRNA-sample 3


title: SAMPLE 109 SQ

description: Squamous tissue

value: male


title: SAMPLE 105 SQ

description: Squamous tissue


title: C2: OV2008-NC-sample 2

source_name: OV2008 cells transfected with NC miRNA-sample 2


title: SAMPLE 104 SQ

description: Squamous tissue


title: C1: OV2008-NC-sample 1

source_name: OV2008 cells transfected with NC miRNA-sample 1


title: IA04_THC-SIV

description:
IA04
Test


title: SAMPLE 134 SQ

description: Squamous tissue


title: JB82_THC-SIV

description:
JB82
Test


title: SAMPLE 106 SQ

description: Squamous tissue


title: SAMPLE 129 SQ

description: Squamous tissue


title: SAMPLE 107 SQ

description: Squamous tissue


title: HI09_THC-SIV

description:
HI09
Test


title: SAMPLE 108 SQ

description: Squamous tissue


title: SAMPLE 103 SQ

description: Squamous tissue


title: SAMPLE 114 SQ

description: Squamous tissue


title: SAMPLE 102 SQ

description: Squamous tissue


title: M3: OV2008-miR328-sample 3

source_name: OV2008 cells transfected with miR328-M-sample 3


title: SAMPLE 101 SQ

description: Squamous tissue


title: SAMPLE 111 SQ

description: Squamous tissue


title: HT48_THC-SIV

description:
HT48
Test


title: SAMPLE 99 SQ

description: Squamous tissue


title: IA83_THC-SIV

description:
IA83
Test


title: SAMPLE 98 SQ

description: Squamous tissue


title: SAMPLE 97 SQ

description: Squamous tissue


title: SAMPLE 100 SQ

description: Squamous tissue


title: SAMPLE 96 SQ

description: Squamous tissue


title: HD08.90D_VEH-SIV

description:
HD08.90D
Test

value: Vehicle


title: SAMPLE 89 EAC

description: Esophageal adenocarcinoma


title: SAMPLE 91 EAC

description: Esophageal adenocarcinoma


title: SAMPLE 95 SQ

description: Squamous tissue


title: SAMPLE 110 SQ

description: Squamous tissue


title: SAMPLE 93 SQ

description: Squamous tissue


title: SAMPLE 87 EAC

description: Esophageal adenocarcinoma


title: SAMPLE 92 EAC

description: Esophageal adenocarcinoma


title: SAMPLE 90 EAC

description: Esophageal adenocarcinoma


title: SAMPLE 88 EAC

description: Esophageal adenocarcinoma


title: GH25_VEH-SIV

description:
GH25
Test


title: GA19_VEH-SIV

description:
GA19
Test


title: SAMPLE 83 EAC

description: Esophageal adenocarcinoma


title: GV60_THC-SIV

description:
GV60
Test


title: SAMPLE 86 EAC

description: Esophageal adenocarcinoma


title: JC81_VEH-SIV

description:
JC81
Test


title: SAMPLE 85 EAC

description: Esophageal adenocarcinoma


title: SAMPLE 81 EAC

description: Esophageal adenocarcinoma


title: SAMPLE 82 EAC

description: Esophageal adenocarcinoma


title: SAMPLE 80 EAC

description: Esophageal adenocarcinoma


title: HB31_VEH-SIV

description:
HB31
Test


title: IH69_THC-SIV

description:
IH69
Test


title: HV48_VEH-SIV

description:
HV48
Test


title: SAMPLE 79 EAC

description: Esophageal adenocarcinoma


title: SAMPLE 94 SQ

description: Squamous tissue


title: IH96_VEH-SIV

description:
IH96
Test


title: HT22_Uninfected

description:
HT22
Control

value: Uninfected

value: Untreated


title: SAMPLE 77 EAC

description: Esophageal adenocarcinoma


title: HR42_Uninfected

description:
HR42
Control


title: SAMPLE 78 EAC

description: Esophageal adenocarcinoma


title: SAMPLE 74 EAC

description: Esophageal adenocarcinoma


title: SAMPLE 84 EAC

description: Esophageal adenocarcinoma


title: SAMPLE 76 EAC

description: Esophageal adenocarcinoma


title: SAMPLE 69 BE.EAC

description: nondysplastic Barrett's sample from Esophageal Adenocarcinoma patient

value: non-dysplastic


title: SAMPLE 75 EAC

description: Esophageal adenocarcinoma


title: SAMPLE 72 EAC

description: Esophageal adenocarcinoma


title: HF54_Uninfected

description:
HF54
Control


title: EH80_Uninfected

description:
EH80
Control


title: SAMPLE 71 EAC

description: Esophageal adenocarcinoma


title: SAMPLE 67 BE.EAC


title: IN24_VEH-SIV

description:
IN24
Test


title: SAMPLE 73 EAC

description: Esophageal adenocarcinoma


title: SAMPLE 66 BE.EAC


title: FT11_VEH-SIV

description:
FT11
Test


title: EL66_Uninfected

description:
EL66
Control


title: SAMPLE 64 BE.EAC


title: SAMPLE 65 BE.EAC


title: SAMPLE 61 BE.BE

description: nondysplastic Barrett's sample from Barrett's patient


title: SAMPLE 62 BE.BE


title: EH70_Uninfected

description:
EH70
Control


title: SAMPLE 55 BE.BE

value: female


title: SAMPLE 59 BE.BE


title: SAMPLE 58 BE.BE


title: SAMPLE 63 BE.EAC


title: Tri-DS3, +Cont shRNA,+Shh+Pur,D14

city: Houston

first: Ying

last: Liu

address: 1825 Pressler

institute: UTHealth

description: replicate 1

data_processing:
Fastq files were generated using the Bc12Fastq software, version 1.8.4. The genome sequence was then indexed using the rsem-prepare-reference command. Each fastq file was trimmed using the fqtrim program, and then aligned to the human genome using the rsem-calculate-expression (version 1.2.31) command to calculate FPKM (fragments per kilobase of transcript per million mapped reads) values.
All the results have been generated by our standard pipelines utilizing STAR as the aligner and RSEM as the tool for annotation and quantification at both gene and isoform levels.
The Excel files give normalized expression abundance in TPM and FPKM values for all the available genes.
The FPKM value (Fragments Per Kilobase of transcript per Million mapped reads) is the FPKM-normalized expression value for each gene/isoform. However, TPM (Transcripts Per Kilobase Million) has now becoming quite popular. TPM is very similar to FPKM. The only difference is the order of operations. Here’s how you calculate TPM: Divide the read counts by the length of each gene in kilobases. This gives you reads per kilobase (RPK). Count up all the RPK values in a sample and divide this number by 1,000,000. This is your “per million” scaling factor. Divide the RPK values by the “per million” scaling factor. This gives you the TPM value.
when calculating TPM, the only difference is that you normalize for gene length first, and then normalize for sequencing depth. However, the effects of this difference are quite profound. When you use TPM, the sum of all TPMs in each sample are the same. This makes it easier to compare the proportion of reads that mapped to a gene in each sample. In contrast, with RPKM and FPKM, the sum of the normalized reads in each sample may be different, and this makes it harder to compare samples directly.
In order to analyze the transcripts, FPKM > 1 was set as cutoff to filter transcripts. |Fold change | > 1.5 was set as criteria to filter differential expressed genes (DEGs). Upregulated and downregulated DEGs were mapped to each chromosome and the number of DEGs in each chromosome was counted. Functional enrichment analysis was performed using DAVID online tool (Huang da et al., 2009a; Huang da et al., 2009b) and visualized using GraphPad. Heatmaps were generated using pheatmap package of R. Correlations with Brainspan data were performed in R using only genes common to both experiments.  The average of the Spearman correlation coefficient is presented for all the combinations of organoid sample replicates or Brainspan samples matching the labeled condition.
Genome_build: hg19
Supplementary_files_format_and_content: Excel files containing FPKM data

source_name: Cultured human iPSC-neural differentiated cells

growth_protocol: Organoids (5-week old) generated from hiPSC lines derived from two DS patients (patient DS1 and DS3 and corresponding cell lines include DS1, control1, isogenic Tri-DS3 and Di-DS3, Tri-DS3+ContshRNA, and Tri-DS3+OLIG2shRNA hiPSCs) were used for RNA-sequencing. For each cell line, total 40-60 organoids collected from three batches of organoid cultures were pool together for RNA extraction and sample preparation. By pooling organoids, we increased the chances of identifying genes that were commonly up- or down-regulated in the three batches of cultures, whereas on the other hand, we decreased the chances of identifying genes that had varied expression levels in the three batches of cultures.

extract_protocol: Total RNA was prepared with RNAeasy kit (Qiagen) (Chen et al., 2014) and libraries were constructed using 600 ng of total RNA from each sample and the TruSeqV2 kit from Illumina (Illumina, San Diego, CA) following manufacturers suggested protocol. The libraries were subjected to 75 bp paired read sequencing using a NextSeq500 Illumina sequencer to generate approximately 30 to 36 million paired-reads per sample.

tag: individual

value: DS patient DS3

value: iPSC derived cells

value: +Cont shRNA,+Shh+Pur,D14


title: SAMPLE 68 BE.EAC


title: SAMPLE 70 EAC

description: Esophageal adenocarcinoma


title: SAMPLE 60 BE.BE


title: DS1, +Shh+Pur, D14

description: replicate 1

value: DS patient DS1

value: +Shh+Pur, D14


title: SAMPLE 57 BE.BE


title: SAMPLE 51 BE.BE


title: Tri-DS3, +Shh+Pur,D14

description: replicate 1


title: SAMPLE 52 BE.BE


title: SAMPLE 45 BE.BE


title: Di-DS3, +Shh+Pur,D14

description: replicate 1


title: SAMPLE 50 BE.BE


title: SAMPLE 46 BE.BE


title: SAMPLE 47 BE.BE


title: SAMPLE 48 BE.BE


title: SK-N-BE-2C [58_total_run329_H12_JQ1]

city: Ghent

first: Celine

last: Everaert

address: De Pintelaan 185

country: Belgium

institute: University Ghent

data_processing:
Alligment with STAR v2.5.3 :STAR --runThreadN 10 --outFileNamePrefix outdir --readFilesIn sample.fastq --genomeDir star_index --sjdbGTFfile gtf_index --outSAMtype BAM SortedByCoordinate --outReadsUnmapped Fastx --twopassMode Basic --outSAMmultNmax 1 --outSAMprimaryFlag AllBestScore --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 0
Quantification with Kallisto v0.43.1. For polyA: kallisto quant -t 10 -i kallisto_index --single -l 200 -s 20 -o outdir sample.fastq; For total: kallisto quant -t 10 -i kallisto_index –rf-stranded --single -l 200 -s 20 -o outdir sample.fastq
Genome_build: hg38
Supplementary_files_format_and_content: abundance.tsv output for kallisto

source_name: cell line

extract_protocol:
Cells were lysed and cDNA was synthesized according to the SMARTer single cell total RNA sequencing protocol on script hub (Fluidigm).
polyA+ RNA-seq libraries were generated using the SMART-seq ultra low input RNA kit for the Fluidigm C1 system. Total RNA-seq libraries were generated using a single cell adapted SMARTer stranded total RNA-seq v2 kit pico input mammalian protocol.

tag: mrna seq

value: total


title: SAMPLE 42 BE.BE


title: SAMPLE 54 BE.BE


title: SAMPLE 41 BE.BE


title: SAMPLE 43 BE.BE


title: SK-N-BE-2C [53_total_run329_H4]

value: vehicle


title: SAMPLE 44 BE.BE


title: Cont1, +Shh+Pur, D14

description: replicate 1

value: control


title: SK-N-BE-2C [52_total_run329_H2]


title: SAMPLE 40 BE.BE


title: SK-N-BE-2C [51_total_run329_H1_JQ1]


title: SK-N-BE-2C [50_total_run329_G12_JQ1]


title: SAMPLE 38 BE.BE


title: SK-N-BE-2C [56_total_run329_H10_JQ1]


title: SAMPLE 37 BE.BE


title: SAMPLE 36 BE.BE


title: SK-N-BE-2C [54_total_run329_H5]


title: SAMPLE 53 BE.BE


title: SK-N-BE-2C [49_total_run329_G11]


title: SAMPLE 56 BE.BE


title: SAMPLE 49 BE.BE


title: SAMPLE 32 BE.BE


title: SK-N-BE-2C [48_total_run329_G10_JQ1]


title: SAMPLE 30 BE.BE


title: SK-N-BE-2C [47_total_run329_G7_JQ1]


title: SAMPLE 33 BE.BE


title: SAMPLE 39 BE.BE


title: SAMPLE 34 BE.BE


title: SK-N-BE-2C [46_total_run329_G6]


title: SK-N-BE-2C [57_total_run329_H11_JQ1]


title: SAMPLE 35 BE.BE


title: SAMPLE 27 BE.BE


title: SAMPLE 26 BE.BE


title: SAMPLE 25 BE.BE


title: SK-N-BE-2C [45_total_run329_G5_JQ1]


title: Tri-DS3, +OLIG2 shRNA,+Shh+Pur,D14

description: replicate 1

value: +OLIG2 shRNA,+Shh+Pur,D14


title: SK-N-BE-2C [44_total_run329_G4_JQ1]


title: SAMPLE 31 BE.BE


title: SAMPLE 23 BE.BE


title: SAMPLE 28 BE.BE