title: whole blood gene expression profile_ALS06779

description: unique sample


title: whole blood gene expression profile_ALS04457

status: Public on Apr 05 2018

type: RNA

city: Utrecht

first: Jan

middle: Herman

last: Veldink

state: Utrecht

address: Heidelberglaan 100, F.02.230

department: Neurology, Brain Center Rudolf Magnus

country: Netherlands

institute: University Medical Center Utrecht

description: unique sample

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
The data were normalised using quantile normalisation with IlluminaGUI in R
Before RNA hybridization, samples were randomized to avoid batch effects correlated to the diagnosis. Samples were hybridized to Illumina’s HumanHT-12 version 4 BeadChips according to manufacturer’s protocol (Illumina, Inc., San Diego, CA, U.S.A.).
Final Reports from Illumina’s GenomeStudio were imported in R (http://.cran.r-project.org). After quantile normalization, gender was checked by expression of gender-specific Y chromosomal probes (JARID1D and RPS4Y1). Samples with gender mismatches were excluded. Subsequently expression values were log2 transformed and quantile normalized. Arrays were projected along the first and second principal component and outliers were dismissed. This resulted in the exclusion of 34 patients and 33 control subjects from the training set and exclusion of 13 patients and 7 control subjects from the test-validation set.
High quality probes were selected, including true autosomal probes only. Using the BLAT function in UCSC’s Genome Browser, all probes were aligned to the NCBI reference genome build 36. Probes with multiple BLAT hits with a sequence homology of > 95% were defined as aspecific and excluded from further analysis. We looked for retired probes using the RefSeq and UniGene (build #228) databases. Retired probes were excluded from further analysis. Finally, probes with identical probe IDs that overlapped between the Illumina HumanHT12 v3 and v4 platform were selected.
Surrogate variable analysis: To eliminate expression heterogeneity caused by known and unknown technical and biological background, data from both training and test sets were combined and normalized, applying surrogate variable analysis (SVA). This produces surrogate variables for which expression levels can be corrected by calculating residuals in a linear regression model. In previous studies, this correction has been proven to reduce batch-specific background noise, thereby increasing the ability to detect biologically meaningful signals.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: whole blood_ALS

label_protocol: The Illumina TotalPrep‐96 RNA Amplification Kit was used to generate Biotin labeled (biotin‐16‐UTP), amplified cRNA starting from 200ng total RNA.

extract_protocol: Venous blood was collected in PAXgene tubes stabilizing messengerRNA (mRNA). PAXgene extraction kits (Qiagen) for RNA extraction were used according to the manufacturer’s protocol. Globin reduction treatments were not performed. Quality of isolated RNA was assessed using the Agilent 2100 Bioanalyzer system.

tag: Sex

value: m

tag: diagnosis

value: ALS

value: s

tag: censored


title: whole blood gene expression profile_ALS06778

description: unique sample

source_name: whole blood_CON

value: v

value: CON


title: whole blood gene expression profile_ALS06177

description: unique sample


title: S810

type: SRA

city: Ann Arbor

first: Antonio

middle: Marcondes

last: Lerario

state: MI

address: 109 Zina Pitcher Place, 1528 BSRB

department: MEND

country: USA

institute: University of Michigan

description: Illumina TruSeq RNA Sample Prep Kit

library_source: transcriptomic

data_processing:
Illumina Casava1.9 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to hg38 whole genome using STAR v2.5.2_b with parameters --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignEndsType EndToEnd --sjdbScore 1
counts were generated by featureCounts v1.5.1 with parameters -p -t exon -g gene_id -B -T8 -M -O --fraction
normalized log2-transformed count table was generated by the voom function from the R/Bioconductor limma package
mouse data was processed according to lexogen proprietary software
Genome_build: hg38/mm10
Supplementary_files_format_and_content: tab-delimited matrices including raw counts and log2-normalized counts for all samples.

source_name: brain biopsy

extract_protocol:
Total RNA was extracted from flow cytometry-sorted microglia cells using an RNeasy and AllPrep Micro Kit (Qiagen) and from whole brain tissue using RNeasy Lipid Tissue Mini kit (Qiagen), according to the manufacturer's protocol. Illumina TruSeq RNA Sample Prep Kit was used with 60 ng of total RNA for the construction of sequencing libraries of 23 samples. Clontech SMARTer Stranded Total RNA-Seq Kit - Pico Input (Takara Bio, Japan) cDNA libraries were prepared for 16 samples starting with 500 pg of total RNA.
Human RNA libraries were prepared for sequencing using standard Illumina and Clontech protocols. Mouse  RNA samples were prepared with a Quantseq 3’mRNA-Seq kit. (Lexogen, USA)

tag: tissue

value: brain

tag: age

tag: gender

value: M


title: whole blood gene expression profile_ALS04856

description: unique sample


title: whole blood gene expression profile_ALS05332

description: unique sample

source_name: whole blood_MIM

value: MIM


title: whole blood gene expression profile_ALS06777

description: unique sample


title: S969

description: Illumina TruSeq RNA Sample Prep Kit

value: F


title: S861

description: Illumina TruSeq RNA Sample Prep Kit


title: whole blood gene expression profile_ALS04667

description: unique sample

value: b


title: whole blood gene expression profile_ALS06147

description: unique sample


title: whole blood gene expression profile_ALS06780

description: unique sample


title: whole blood gene expression profile_ALS04476

description: unique sample


title: whole blood gene expression profile_ALS06172

description: unique sample


title: S947

description: Illumina TruSeq RNA Sample Prep Kit


title: FL HSC 1

city: Cambridge

first: Michael

last: Guo

state: MA

address: 415 Main St

institute: Broad Institute

description: miRNA

hyb_protocol: Nanostring miRNA profiling was performed according to manufacturer's specifications.

data_processing: RCC files were processed through the nSOLVER software to normalize for negative and positive controls and filter for probes with counts >10. These values were then normalized by the average geometric means across all lanes. Filtering was done as suggested by nSOLVER recommendations.

label: NanoString labels

source_name: CB PROG

growth_protocol: Refer to the STAR methods of the related manuscript.

extract_protocol: RNA was extracted using miRNeasy (Qiagen)

treatment_protocol: HSC, PROG and HPC cells isolated according to specific panels of cell surface markers. Full details on the STAR methods of the related manuscript.

tag: cell type

value: Cord Blood Hematopoietic Progenitor Cells


title: whole blood gene expression profile_ALS04806

description: unique sample


title: S805

description: Illumina TruSeq RNA Sample Prep Kit


title: whole blood gene expression profile_ALS04314

description: unique sample


title: CB PROG 3

description: miRNA

scan_protocol: Nanostring miRNA profiling was performed according to manufacturer's specifications.

source_name: BM PROG

value: Bone Marrow Hematopoietic Progenitor Cells


title: whole blood gene expression profile_ALS06137

description: unique sample


title: whole blood gene expression profile_ALS06808

description: unique sample


title: CB PROG 1

description: miRNA

label_protocol: Nanostring miRNA profiling was performed according to manufacturer's specifications.


title: whole blood gene expression profile_ALS04562

description: unique sample


title: whole blood gene expression profile_ALS04468

description: unique sample


title: whole blood gene expression profile_ALS06116

description: unique sample


title: CB HSC 3

description: miRNA

source_name: FL HSC

value: Fetal Liver Hematopoietic Stem Cells


title: whole blood gene expression profile_ALS06937

description: unique sample


title: whole blood gene expression profile_ALS06944

description: unique sample


title: CB PROG 2

description: miRNA


title: CB HSC 1

description: miRNA


title: whole blood gene expression profile_ALS06014

description: unique sample


title: whole blood gene expression profile_ALS04155

description: unique sample


title: whole blood gene expression profile_ALS06051

description: unique sample


title: whole blood gene expression profile_ALS05632

description: unique sample


title: whole blood gene expression profile_ALS03855

description: unique sample


title: whole blood gene expression profile_ALS04187

description: unique sample


title: whole blood gene expression profile_ALS04523

description: unique sample


title: whole blood gene expression profile_ALS06052

description: unique sample


title: whole blood gene expression profile_ALS04363

description: unique sample


title: CB HSC 2

description: miRNA


title: whole blood gene expression profile_ALS06938

description: unique sample


title: whole blood gene expression profile_ALS05987

description: unique sample


title: whole blood gene expression profile_ALS06066

description: unique sample


title: whole blood gene expression profile_ALS06803

description: unique sample


title: whole blood gene expression profile_ALS05884

description: unique sample


title: BM PROG 3

description: miRNA

source_name: CB HSC

value: Cord Blood Hematopoietic Stem Cells


title: BM PROG 2

description: miRNA


title: BM PROG 1

description: miRNA


title: BM HSC 3

description: miRNA

source_name: BM HSC

value: Bone Marrow Hematopoietic Stem Cells


title: whole blood gene expression profile_ALS05883

description: unique sample


title: whole blood gene expression profile_ALS04184

description: unique sample


title: whole blood gene expression profile_ALS06104

description: unique sample


title: BM HSC 2

description: miRNA


title: whole blood gene expression profile_ALS05854

description: unique sample


title: Glass Bio replicate 2

city: Pune

first: Kundan

last: Sengupta

state: Maharashtra

address: Dr. Homi Bhabha Road, Near NCL Innovation Park, Pashan

department: Biology

country: India

institute: Indian Institute of Science Education and Research (IISER), Pune

data_processing:
Raw processing and QC: Illumina HiSeq raw reads were quality checked using FastQC. Illumina raw reads were processed by in-house script for adapters and low quality base trimming towards 3' end.
Alignment of reads to reference genome: Tophat-2.0.7,  fast splice junction mapper, was used to align RNA-Seq reads to human genome using the ultra high-throughput short read aligner Bowtie, and then mapping results were analyzed to identify splice junctions between exons. Cufflinks-2.0.1 was used to assemble the transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.
Differential gene expression analysis: Cuffdiff program in Cufflinks-2.0.1 was used to find significant changes in transcript expression.  Merged GTF file produced by Cuffmerge was used as input in Cuffdiff. The group wise merged gtf files used as input in Cuffdiff, coverted to FASTA format have been provided as processed data (Merged transcripts).
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Excel files with FPKM, fold change, p value, q value etc for all up, down and neutrally regulated transcripts for given sample (compared to reference sample)

molecule: polyA RNA

source_name: mammalian cell line (human)

growth_protocol: DLD-1 colorectal adenocarcinoma cells were obtained from Thomas Ried (NCI, NIH, Bethesda USA). DLD-1 cells were maintained in RPMI media (Invitrogen, RPMI 1640, 11875-093) supplemented with 10% Fetal Bovine Serum (FBS, Invitrogen, 6140-079 Carlsbad, USA) and antibiotics - Penicillin (100 U/mL) and Streptomycin (100 μg/ml, Invitrogen, 15070-063) at 37°C with 5% CO2.

extract_protocol:
After 90 mins, cells were harvested in Trizol reagent and outsourced for sequencing to Genotypic Technology, Bangalore, India
RNA library preparation was performed using standard Illumina protocols

treatment_protocol: DLD-1 cells growing on regular tissue culture plastic substrates were detached using 0.05% Trypsin-EDTA and equal number of cells were re-seeded on softer matrices (2 kPa and 55 kPa) and collagen (100 µg/ml) coated glass coverslips for 90 minutes.

tag: matrix condition

value: on Glass matrix for 90 minutes

tag: cell line

value: DLD-1 colorectal adenocarcinoma cell line


title: whole blood gene expression profile_ALS05552

description: unique sample


title: 55 kPa Bio replicate 2

value: on 55 kPa matrix for 90 minutes


title: whole blood gene expression profile_ALS05421

description: unique sample


title: Glass Bio replicate 1

value: on Glass for 90 minutes


title: BM HSC 1

description: miRNA


title: whole blood gene expression profile_ALS06578

description: unique sample


title: whole blood gene expression profile_ALS07913

description: unique sample

value: m

value: ALS

value: s


title: 55 kPa Bio replicate 1


title: whole blood gene expression profile_ALS05730

description: unique sample

value: v


title: whole blood gene expression profile_ALS06752

description: unique sample

value: CON


title: whole blood gene expression profile_ALS06547

description: unique sample


title: whole blood gene expression profile_ALS06556

description: unique sample


title: 2 kPa Bio replicate 2

value: on 2 kPa matrix for 90 minutes


title: whole blood gene expression profile_ALS03348

description: unique sample

value: MIM


title: whole blood gene expression profile_ALS06554

description: unique sample


title: whole blood gene expression profile_ALS03458

description: unique sample


title: 2 kPa Bio replicate 1


title: whole blood gene expression profile_ALS07018

description: unique sample


title: whole blood gene expression profile_ALS07048

description: unique sample


title: whole blood gene expression profile_ALS06539

description: unique sample


title: whole blood gene expression profile_ALS04884

description: unique sample


title: 13773 - Oac 4

city: Saint Louis

first: Jonathan

last: Lin

state: MO

address: 660 S. Euclid Ave, Campus Box 8096

institute: Washington University School of Medicine

hyb_protocol: We followed manufacturer's instructions.

scan_protocol: not provided

data_processing: We processed the array results with Affymetrix Expression Console (v1.3.1.187) at standard settings (RMA background correction, median polish summarization, and quantile normalization).

organism: Mus musculus

source_name: peritoneal macrophages

label_protocol: We labeled each sample with FlashTagTM Biotin HSR RNA labeling kits (Affymetrix).

extract_protocol: We extracted RNA with the mirVana miRNA isolation kit (Thermo Fisher).

value: female

value: peritoneal macrophages

value: 18 months

tag: treatment

value: 25 μg/ml acLDL for 24 hours


title: 13772 - Oox 4

value: 25 μg/ml oxLDL for 24 hours


title: whole blood gene expression profile_ALS06989

description: unique sample


title: 13771 - Out 4

value: untreated


title: whole blood gene expression profile_ALS06169

description: unique sample


title: whole blood gene expression profile_ALS06785

description: unique sample


title: whole blood gene expression profile_ALS05575

description: unique sample


title: 13769 - Oox 3


title: whole blood gene expression profile_ALS04766

description: unique sample


title: whole blood gene expression profile_ALS06117

description: unique sample


title: 13770 - Oac 3


title: whole blood gene expression profile_ALS05991

description: unique sample


title: whole blood gene expression profile_ALS06487

description: unique sample

value: b


title: 13767 - Oac 2


title: whole blood gene expression profile_ALS06859

description: unique sample


title: 13768 - Out 3


title: 13766 - Oox 2


title: whole blood gene expression profile_ALS05990

description: unique sample


title: whole blood gene expression profile_ALS06159

description: unique sample


title: whole blood gene expression profile_ALS05786

description: unique sample


title: whole blood gene expression profile_ALS05077

description: unique sample


title: whole blood gene expression profile_ALS06966

description: unique sample


title: whole blood gene expression profile_ALS05695

description: unique sample


title: whole blood gene expression profile_ALS05870

description: unique sample


title: whole blood gene expression profile_ALS06968

description: unique sample


title: whole blood gene expression profile_ALS06466

description: unique sample


title: 13764 - Oac 1


title: whole blood gene expression profile_ALS06753

description: unique sample


title: 13765 - Out 2


title: 13763 - Oox 1


title: 13761 - Yac 4

description: outlier sample -- no processed data available

value: 3 months


title: whole blood gene expression profile_ALS06289

description: unique sample


title: whole blood gene expression profile_ALS06940

description: unique sample


title: whole blood gene expression profile_ALS03219

description: unique sample


title: whole blood gene expression profile_ALS05690

description: unique sample


title: whole blood gene expression profile_ALS05261

description: unique sample


title: whole blood gene expression profile_ALS06703

description: unique sample


title: whole blood gene expression profile_ALS06194

description: unique sample


title: 13760 - Yox 4


title: 13762 - Out 1


title: whole blood gene expression profile_ALS04668

description: unique sample


title: whole blood gene expression profile_ALS06180

description: unique sample


title: 13756 - Yut 3


title: 13758 - Yac 3


title: 13759 - Yut 4


title: whole blood gene expression profile_ALS06061

description: unique sample


title: whole blood gene expression profile_ALS06936

description: unique sample


title: whole blood gene expression profile_ALS04861

description: unique sample


title: 13754 - Yox 2


title: 13755 - Yac 2


title: whole blood gene expression profile_ALS05938

description: unique sample


title: whole blood gene expression profile_ALS06708

description: unique sample


title: whole blood gene expression profile_ALS06053

description: unique sample


title: whole blood gene expression profile_ALS05079

description: unique sample


title: whole blood gene expression profile_ALS06093

description: unique sample


title: whole blood gene expression profile_ALS04518

description: unique sample


title: whole blood gene expression profile_ALS03867

description: unique sample


title: whole blood gene expression profile_ALS04520

description: unique sample


title: 13757 - Yox 3


title: whole blood gene expression profile_ALS06571

description: unique sample


title: whole blood gene expression profile_ALS06680

description: unique sample


title: whole blood gene expression profile_ALS04365

description: unique sample


title: whole blood gene expression profile_ALS05988

description: unique sample


title: whole blood gene expression profile_ALS04151

description: unique sample


title: whole blood gene expression profile_ALS03412

description: unique sample


title: whole blood gene expression profile_ALS04354

description: unique sample


title: whole blood gene expression profile_ALS06537

description: unique sample


title: whole blood gene expression profile_ALS07136

description: unique sample


title: 13750 - Yut 1


title: 13753 - Yut 2


title: 13751 - Yox 1


title: 13752 - Yac 1


title: whole blood gene expression profile_ALS05875

description: unique sample


title: whole blood gene expression profile_ALS05763

description: unique sample


title: whole blood gene expression profile_ALS07133

description: unique sample


title: whole blood gene expression profile_ALS06134

description: unique sample


title: whole blood gene expression profile_ALS01305

description: unique sample


title: whole blood gene expression profile_ALS05847

description: unique sample


title: RelAZFDRRM + isoleucine starved rep2

city: Copenhagen

first: Kenn

last: Gerdes

address: Ole Maaloesvej 5

country: Denmark

institute: University of Copenhagen

description:
CRAC
NG-A4_NNNTCTCTAGC_ZFDRRM+val2
MG1655relAΔZFDΔRRM::HTF

data_processing:
fastq_quality_filter -q 30 -Q 33 -i<(cat NG-8549_CAT_lib91426_4106_1_1.fastq.bz2 | bunzip2 -c) -o NG-A1.fastq #quality filtering
pyBarcodeFilter.py -f NG-A1.fastq -b barcodes.txt #demultiplex in respect to 5' barcode
cutadapt NG-A1_NNNCACTAGC_cont.fastq -a TGGAATT -m 12 -o cont.trimmed.fastq #trimming of 3' end linker
pyFastqDuplicateRemover.py -f cont.trimmed.fastq -o cont.trimmed.collapsed.fasta #removal of PCR duplicates
bowtie2-build ecoli_masked.fa ecoli bowtie2 -x ecoli -f cont.trimmed.collapsed.fasta > cont.sam #alignment using masked genome file
Genome_build: NC_000913.3
Supplementary_files_format_and_content: *_count_output_reads.gtf: Mapped read coordinates in GTF format.

organism: Escherichia coli

source_name: RelAZFDRRM + isoleucine starved bacterial cells

growth_protocol: Bacterial cells were grown in MOPS (morpholinepropanesulfonic acid) minimal medium at 30C supplemented with 0.2% glucose and with all nucleobases (10 µg ml-1 of each).

extract_protocol:
The cells were subsequently UV-C crosslinked and harvested by centrifugation, washed in ice-cold phosphate-buffered saline (PBS) and snap frozen in liquid nitrogen. The pellets were stored at -80C. The HTF tagged proteins were then purified, linkers ligated to crosslinked RNA, cDNA synthesized and DNA libraries generated as described in Winther et al. 2018.
Libraries were constructed as per Winther et al. 2018.

treatment_protocol: Non-starved cultures were collected at OD600=0.2 and isoleucine starved cultures were collected after incubation with 500μg/mL L-Valine for 30 min (samples indicated by +val).

tag: strain/background

tag: growth condition

value: isoleucine starved

tag: antibody


title: whole blood gene expression profile_ALS05762

description: unique sample


title: whole blood gene expression profile_ALS06749

description: unique sample


title: RelAZFDRRM + isoleucine starved rep1

description:
CRAC
NG-A3_NNNGTGAGC_ZFDRRM+val1
MG1655relAΔZFDΔRRM::HTF


title: whole blood gene expression profile_ALS03353

description: unique sample


title: whole blood gene expression profile_ALS06120

description: unique sample


title: whole blood gene expression profile_ALS06559

description: unique sample


title: whole blood gene expression profile_ALS05691

description: unique sample


title: whole blood gene expression profile_ALS06567

description: unique sample


title: HuR KO 1

city: Cleveland

first: Tomasz

middle: M

last: Herjan

state: Ohio

address: 9500 Euclid Avenue

department: Immunology

institute: Cleveland Clinic Foundation

description: Gene expression data from total brain tissue of Thy1Cre-ERT2-EYFPHuRf/f (designed as KO) mouse

hyb_protocol: The labeled RNA were hybridized for 16 hr at 45°C on GeneChip 2.0 Arrays. GeneChips were washed and stained in the AffymetrixFluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: MAS5.0, using Affymetrix default analysis settings and global scaling as normalization method

source_name: mouse brain: Thy1Cre-ERT2-EYFPHuRf/f (designed as KO)

label_protocol: Biotinylated RNA was prepared according to Affymetrix WT Plus Labeling Kit from 150 ng total RNA

growth_protocol: 91 days old, tamoxifen-injected mice were used for brain isolation

extract_protocol: Brain was isolated, homogenized and total RNA was extracted in TRIzol reagentusingmanufacturer's protocol

treatment_protocol: Cre expression was induced through Tamoxifen administration to conditional neuron-specific HuR-deficient mice (Thy1Cre-ERT2-EYFPHuRf/f) and control mice (Thy1Cre-ERT2-EYFPHuRf/+) of either sex at 10 and 11 weeks of age

value: total brain tissue

tag: genotype

value: Thy1Cre-ERT2-EYFPHuRf/f (designed as K

value: 91 days old


title: HuR WT 1

description: Gene expression data from total brain tissue of Thy1Cre-ERT2-EYFPHuRf/+ (designed as WT) mouse

source_name: mouse brain: Thy1Cre-ERT2-EYFPHuRf/+ (designed as WT)


title: HuR KO 2


title: HuR WT 3

value: Thy1Cre-ERT2-EYFPHuRf/+ (designed as WT)


title: HuR WT 2


title: whole blood gene expression profile_ALS00508

description: unique sample

value: m


title: whole blood gene expression profile_ALS04414

description: unique sample

value: v

value: ALS

value: s


title: whole blood gene expression profile_ALS08029

description: unique sample


title: whole blood gene expression profile_ALS07120

description: unique sample


title: whole blood gene expression profile_ALS05521

description: unique sample


title: whole blood gene expression profile_ALS05704

description: unique sample


title: whole blood gene expression profile_ALS06294

description: unique sample

value: MIM


title: HuR KO 3


title: RelAZFDRRM rep2

description:
CRAC
NG-A4_NNNCACTAGC_ZFDRRM2
MG1655relAΔZFDΔRRM::HTF

source_name: RelAZFDRRM bacterial cells

value: non-starved


title: whole blood gene expression profile_ALS05098

description: unique sample


title: RelARRM + isoleucine starved

description:
CRAC
NG-A2_NNNGTGAGC_RRM+val1
MG1655relAΔRRM::HTF

source_name: RelARRM + isoleucine starved bacterial cells


title: RelAZFDRRM rep1

description:
CRAC
NG-A3_NNNCGCTTAGC_ZFDRRM1
MG1655relAΔZFDΔRRM::HTF


title: RelARRM

description:
CRAC
NG-A2_NNNCGCTTAGC_RRM1
MG1655relAΔRRM::HTF

source_name: RelARRM bacterial cells


title: HPC-5F_CTRL_1

data_processing:
Alignment was performed using TopHat v2.0.14 using default parameters
Alignment performed to hg19 and with Gencode v19 as the transcriptome index
Transcript quantification performed using the cuffquant tool within Cufflinks v2.2.1 using default parameters
Calculation of transcript FPKM performed using the cuffnorm tool within Cufflinks v2.2.1 using default parameters
Calculation of differential expression performed using the cuffdiff tool within Cufflinks v2.2.1 using default parameters
Genome_build: hg19
Supplementary_files_format_and_content: Text files with gene/isoform names/IDs and expression in FPKM

extract_protocol:
RNA was extracted using miRNeasy (Qiagen)
RNA-seq libraries were prepared from 100ng of total RNA using the Truseq RNA Sample Preparation kit v2 (Illumina)

treatment_protocol: HPC-5F cells were transduced with a control (CTRL), HMGA2-L (LONG), HMGA2-S (SHORT) or CLK3 ORF lentiviral over-expression vectors. Full details on the STAR methods of the related manuscript.

value: IPSC-derived Hematopoietic Progenitor Cells (transduced with lentivirus)


title: HPC-5F_CLK3_2


title: HPC-5F_CTRL_2


title: RelAH432E rep2

description:
CRAC
NG-A5_NNNTAAGC_H432E2

source_name: RelAH432E bacterial cells


title: RelAH432E + isoleucine starved rep1

description:
CRAC
NG-A3_NNNATTAGC_H432E+val1

source_name: RelAH432E + isoleucine starved bacterial cells


title: RelAH432E + isoleucine starved rep2

description:
CRAC
NG-A5_NNNATTAGC_H432E+val2


title: HPC-5F_HMGA2_LONG_2


title: HPC-5F_CLK3_1


title: whole blood gene expression profile_ALS06202

description: unique sample


title: whole blood gene expression profile_ALS05995

description: unique sample

source_name: whole blood_CON

value: CON


title: whole blood gene expression profile_ALS05548

description: unique sample

source_name: whole blood_ALS


title: HPC-5F_HMGA2_LONG_1


title: whole blood gene expression profile_ALS06704

description: unique sample


title: whole blood gene expression profile_ALS07020

description: unique sample


title: whole blood gene expression profile_ALS06816

description: unique sample


title: whole blood gene expression profile_ALS07017

description: unique sample


title: whole blood gene expression profile_ALS05268

description: unique sample


title: whole blood gene expression profile_ALS06083

description: unique sample

source_name: whole blood_MIM


title: whole blood gene expression profile_ALS06390

description: unique sample


title: whole blood gene expression profile_ALS06056

description: unique sample


title: whole blood gene expression profile_ALS05271

description: unique sample


title: whole blood gene expression profile_ALS06510

description: unique sample


title: whole blood gene expression profile_ALS06939

description: unique sample


title: whole blood gene expression profile_ALS06928

description: unique sample


title: whole blood gene expression profile_ALS05094

description: unique sample


title: RelAH432E rep1

description:
CRAC
NG-A3_NNNTAAGC_H432E1


title: RelA + isoleucine starved rep2

description:
CRAC
NG-A2_NNNTCTCTAGC_rela+val2

source_name: RelA + isoleucine starved bacterial cells


title: whole blood gene expression profile_ALS05264

description: unique sample


title: HPC-5F_HMGA2_SHORT_1


title: HPC-5F_HMGA2_SHORT_2


title: whole blood gene expression profile_ALS05943

description: unique sample


title: RelA + isoleucine starved rep1

description:
CRAC
NG-A1_NNNATTAGC_rela+val1


title: RelA rep1

description:
CRAC
NG-A1_NNNTAAGC_rela1

source_name: RelA bacterial cells


title: whole blood gene expression profile_ALS06561

description: unique sample


title: K562_AID-BRD4_clone-2_Pol2_DMSO

city: Vienna

first: Matthias

last: Muhar

address: Campus-Vienna-Biocenter 1

country: Austria

institute: Research Institute for Molecular Pathology

description: ChIP-seq of Pol2 using ca 10% untreated mouse cells as spike-in for global normalization.

library_source: genomic

data_processing:
A hybrid reference genome was prepared by merging human and mouse genomic sequences (GRCh38 and mm10) and reads were aligned against this hybrid genome using bowtie2 v2.2.9 (--sensitive) and subsequently separated into human and mouse bins.
The read coverage of each track was calculated using deeptools v2.5.0.1 and re-scaled using the relative fraction of mouse reads stemming from spiked-in chromatin as normalization factor prior to subtraction of the respective input signal.
Genome_build: GRCh38 and mm10
Supplementary_files_format_and_content: bigWig

molecule: genomic DNA

extract_protocol:
Cells were cross-linked with 1% formaldehyde (10’, RT). Nuclei were isolated, lysed, and chromatin was sheared by sonication. Mouse chromatin (ratio 10:1, human:mouse) was added for internal normalization. Antibodies against total Pol2, Pol2-S2p or Pol2-S5p (active motif) were added overnight at 4° and captured with magnetic sepharose beads for 2h at 4°C. Beads were washed, immune complexes eluted, and cross-links reversed for 6h at 65°C. Genomic DNA was recovered by phenol-chloroform extraction and ethanol precipitation.
Deep sequencing libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina.

tag: genetic modification

value: AID-BRD4 / SFFV-OsTir1-T2A-BlastR

tag: 4su labeling time before harvest (min)


title: LH8_fox1_F3

city: New York

first: Long

last: He

department: cancer center

institute: WCMC

data_processing:
The raw RNA-seq reads were aligned to mouse reference genome (mm9) using Bowtie with default parameters.
Only uniquely mapped reads were retained and processed using SPP package for peak calling (FDR < 0.01).
CEAS was employed subsequently for characterization of genome-wide protein-DNA interaction patterns.
MEME-ChIP was used for de novo motif identification based on DNA sequences for the top 200 significant peaks.
Genome_build: mm9
Supplementary_files_format_and_content: narrowpeak files attached are the processed ChIP-seq results

source_name: MEFs

growth_protocol: DMEM

extract_protocol:
Lysates were clarified from sonicated nuclei and Foxk1-DNA complexes were isolated with Foxk1 antibody.
DNA library was made with NEBNext® DNA Library Prep Master Mix kit (E6040S)


title: Control

description:
CRAC
NG-A1_NNNCACTAGC_cont

source_name: Control bacterial cells


title: K562_AID-BRD4_clone-2_Pol2-S5P_IAA

description: ChIP-seq of S5-phosphorylated Pol2 using ca 10% untreated mouse cells as spike-in for global normalization.

value: 100µM indole-3-acetic acid, 60 min

value: S5-phosphorylated Pol2


title: Control + isoleucine starved

description:
CRAC
NG-A1_NNNTCTCTAGC_cont+val

source_name: Control + isoleucine starved bacterial cells


title: whole blood gene expression profile_ALS06188

description: unique sample


title: whole blood gene expression profile_ALS04848

description: unique sample

value: b


title: K562_AID-BRD4_clone-2_input_IAA

description: ChIP-seq input using ca 10% untreated mouse cells as spike-in for global normalization.


title: whole blood gene expression profile_ALS05052

description: unique sample


title: RelA rep2

description:
CRAC
NG-A2_NNNCACTAGC_rela2


title: LH6_fox1_F1


title: K562_AID-BRD4_clone-2_input_DMSO


title: LH7_fox1_F2


title: whole blood gene expression profile_ALS06226

description: unique sample


title: whole blood gene expression profile_ALS05606

description: unique sample


title: K562_AID-BRD4_clone-2_Pol2-S5P_DMSO


title: whole blood gene expression profile_ALS05083

description: unique sample


title: whole blood gene expression profile_ALS06681

description: unique sample


title: whole blood gene expression profile_ALS06224

description: unique sample


title: whole blood gene expression profile_ALS04814

description: unique sample


title: whole blood gene expression profile_ALS04833

description: unique sample


title: K562_AID-BRD4_Pol2-S2P_DMSO

description: ChIP-seq of S2-phosphorylated Pol2 using ca 10% untreated mouse cells as spike-in for global normalization.

value: S2-phosphorylated Pol2


title: LH4_IgG1_I2

value: IgG


title: whole blood gene expression profile_ALS06183

description: unique sample


title: whole blood gene expression profile_ALS05767

description: unique sample


title: whole blood gene expression profile_ALS04390

description: unique sample


title: whole blood gene expression profile_ALS05522

description: unique sample


title: K562_AID-BRD4_clone-2_Pol2_IAA


title: K562_AID-BRD4_Pol2-S5P_DMSO


title: whole blood gene expression profile_ALS05089

description: unique sample


title: K562_AID-BRD4_Pol2-S2P_IAA


title: LH5_IgG1_I3


title: K562_AID-BRD4_Pol2_DMSO


title: LH3_IgG1_I1


title: K562_AID-BRD4_Pol2-S5P_IAA


title: whole blood gene expression profile_ALS06184

description: unique sample


title: whole blood gene expression profile_ALS04409

description: unique sample


title: whole blood gene expression profile_ALS05080

description: unique sample


title: LH2_Input_2


title: LH1_Input_1


title: K562_AID-BRD4_Pol2_IAA


title: whole blood gene expression profile_ALS03879

description: unique sample


title: whole blood gene expression profile_ALS06000

description: unique sample


title: whole blood gene expression profile_ALS04438

description: unique sample


title: whole blood gene expression profile_ALS04032

description: unique sample


title: whole blood gene expression profile_ALS05797

description: unique sample


title: K562_AID-BRD4_input_DMSO


title: shFoxk1+Foxk1-2

hyb_protocol: standard Affymetrix

scan_protocol: standard Affymetrix

data_processing: RMA normalization (Bioconductor R affy package)

label_protocol: Biotinylated RNA were prepared according to the standard Affymetrix protocol.

extract_protocol: RNAeasy kit from Qiagen

value: MEFs

tag: genotype/variation


title: K562_MYC-AID_clone-3

data_processing:
Raw reads were adapter trimmed using cutadapt through the trim_galore (v0.3.7) wrapper tool with adapter overlaps set to 3bp for trimming (--stringency 3).
Trimmed reads were processed using SlamDunk v0.2.4 running the 'map' procedure in QuantSeq mode (slamdunk map -5 12 -n 100 -q) and 'filter' procedure using SlamDunk's multimapper recovery strategy (slamdunk filter -b bed) aligning against the human genome (UCSC version GRCh38).
Reads were quantified using featureCounts in stranded mode (-s 1) and counting multimappers (-M).
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-separated table output from featureCounts displaying genomic feature coordinates and length as well as read counts for the respective samples.

extract_protocol:
Total RNA was extracted using a commercial column purification kit.
3'UTR sequencing libraries were generated from 500ng total RNA using a commercial kit (QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina, Lexogen).

value: MYC-AID


title: whole blood gene expression profile_ALS05961

description: unique sample

tag: Sex


title: K562_MYC-AID_clone-2


title: K562_MYC-AID_clone-1


title: whole blood gene expression profile_ALS06029

description: unique sample

tag: diagnosis


title: whole blood gene expression profile_ALS04807

description: unique sample

tag: censored


title: whole blood gene expression profile_ALS06050

description: unique sample


title: whole blood gene expression profile_ALS04172

description: unique sample


title: whole blood gene expression profile_ALS04521

description: unique sample


title: whole blood gene expression profile_ALS06045

description: unique sample


title: K562_AID-BRD4_clone-2


title: whole blood gene expression profile_ALS04334

description: unique sample


title: whole blood gene expression profile_ALS04333

description: unique sample


title: K562_AID-BRD4_clone-3


title: shFoxk1+Foxk1-3


title: shFoxk1-3


title: K562_AID-BRD4_input_IAA


title: shFoxk1+Foxk1-1


title: shFoxk1-2


title: K562_AID-BRD4_clone-1


title: whole blood gene expression profile_ALS06260

description: unique sample


title: K562_wt_clone-12


title: whole blood gene expression profile_ALS05942

description: unique sample


title: whole blood gene expression profile_ALS04332

description: unique sample


title: whole blood gene expression profile_ALS04139

description: unique sample


title: whole blood gene expression profile_ALS05882

description: unique sample


title: HPC_2

data_processing:
Align was performed using TopHat v2.0.14 using default parameters.
Alignment performed to hg19 and with Gencode v17 as the transcriptome index.
Transcript quantification performed using the cuffquant tool within Cufflinks v2.2.1 using default parameters and a custom transciptome index.
Calculation of transcript FPKM performed using the cuffnorm tool within Cufflinks v2.2.1 using default parameters.
Calculation of differential expression performed using the cuffdiff tool within Cufflinks v2.2.1 using default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: Text files with gene/isoform names/IDs and expression in FPKM

source_name: HPC

extract_protocol:
RNA was extracted using miRNeasy (Qiagen)
RNA-seq libraries were prepared from 100ng of total RNA using the Truseq RNA Sample Preparation kit v2 (Illumina)
Paired-end 101 bp reads

value: IPSC-derived Hematopoietic Progenitor Cells


title: shGFP-3


title: HPC_3


title: whole blood gene expression profile_ALS03718

description: unique sample

value: m


title: whole blood gene expression profile_ALS03729

description: unique sample


title: whole blood gene expression profile_ALS07130

description: unique sample

value: v


title: shFoxk1-1


title: whole blood gene expression profile_ALS03901

description: unique sample

value: ALS


title: whole blood gene expression profile_ALS05873

description: unique sample

value: s


title: whole blood gene expression profile_ALS04157

description: unique sample

value: MIM


title: shGFP-2


title: shGFP-1


title: K562_wt_clone-11


title: HPC_1


title: K562_wt_clone-9


title: ChIP_5F_CTRL_2_k4me2

data_processing:
Alignment: bowtie2 (v2.2.1)
1kb tile coverage was calculated using the 'bedtools coverage' command.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.1kbCounts.txt: Tab-delimited text files; The processed data files have the following columns: [1] Chromosome, [2] Start, [3] End, [4] Tile ID, [5] The number of features in reads that overlapped (by at least one base pair) the tile, [6] The number of bases in the tile that had non-zero coverage from reads, [7] The length of the tile, [8] The fraction of bases in the tile that had non-zero coverage from reads.

extract_protocol:
antibody epitope: H3K4me2. Vendor: Diagenode. Catalog number: 035-050
antibody epitope: V5. Vendor: MBL intl. Catalog number: M167-3. Lot: #5
ChIP-seq libraries were prepared from 1-10 ng of DNA, using an end-repair/tailing/ligation-based protocol, as previously described (Cacchiarelli et al., 2015)
Single-end 50 bp reads

treatment_protocol: HPC-5F cells were transduced with a control (CTRL), V5-tagged HMGA2-L (LONG) or HMGA2-S (SHORT) ORF lentiviral over-expression vectors. Full details on the STAR methods of the related manuscript.

tag: overexpression

value: Control

tag: chip antibody


title: K562_wt_clone-10


title: K562_wt_clone-8


title: ChIP_5F_CTRL_2_WCE

description: Whole cell extract

value: IPSC-derived Hematopoietic Progenitor Cells (transduced with lentivirus)


title: K562_wt_clone-7


title: ChIP_5F_CTRL_2_V5


title: ChIP_5F_CTRL_1_k4me2


title: K562_wt_clone-5


title: MPM.FFPE.008_PD

city: HOUSTON

first: Hyun-Sung

last: Lee

state: TX

address: One Baylor Plaza

department: Surgery

institute: BAYLOR COLLEGE OF MEDICINE

description: To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.

hyb_protocol: Labeled, amplified material (750 ng per array) was hybridized to the Illumina HumanHT-12 V4.0 expression beadchip according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA).

scan_protocol: Arrays were scanned with an Illumina Bead array Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the Manufacturer's instructions

data_processing: Array data processing were performed on Illumina BeadStudio software. We normalized gene expression data using Quantile normalization and log2 transformatoin. To export to a data matrix, Sample Gene Profile option of this software was used.

label: Biotin

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to Illumina's recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina. TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations using spectrophotometer (Nanodrop, ND-1000)

extract_protocol: Total RNA was isolated from tissues with mirVana RNA Isolation labeling kit (Ambion Inc) according to the manufacturer protocol. RNA quality and integrity were confirmed by ExperionTM Automated Electrophoresis System (BIO-RAD)

value: nivolumab


title: K562_wt_clone-4


title: MPM.FFPE.006_PD


title: K562_wt_clone-6


title: MPM.FFPE.010_CR

value: pembrolizumab


title: MPM.FFPE.007_PR


title: ChIP_5F_CTRL_1_V5


title: MPM.FFPE.005_PD


title: MPM.FFPE.004_SD


title: MPM.FFPE.009_PD


title: K562_wt_clone-3


title: ChIP_5F_CTRL_1_WCE

description: Whole cell extract


title: MPM.FFPE.002_CR


title: human.MPM.012

tag: disease state

value: malignant pleural mesothelioma

value: Treatment-naive


title: human.MPM.011


title: human.MPM.010


title: K562_wt_clone-2


title: ChIP_5F_SHORT_2_k4me2

value: V5-tagged HMGA2-S


title: MPM.FFPE.003_SD


title: human.MPM.008


title: K562_wt_bulk


title: human.MPM.005


title: K562_wt_clone-1


title: ChIP_5F_SHORT_2_WCE

description: Whole cell extract


title: KOD7_14

city: Indianapolis

first: Joseph

last: Bidwell

state: Indiana

address: 635 Barnhill Dive

department: Anatomy and Cell Biology

institute: Indiana University School of Medicine

description: WT=wild type; KO=knockout; D3=day 3; D7=Day 7; _#=replicate code for individual cell wells

data_processing:
Raw reads were filtered into clean reads by employing the following rules: (i) remove reads in which the percentage of bases with quality <10 was >50%
(ii) remove reads in which unknown bases were more than 10%;
(iii) remove reads with adapters;
(iv) map the clean reads to Mus musculus reference mm10 using STAR (version 2.4.2a);
(v) gene-based expression levels were quantified with featureCounts;
(vi) differential expression of genes across different treatments was determined with edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: An Excel file which contains average, relative expression values (cpm) for genes above cutoff. These represent average of 4 replicates.

source_name: mesenchymal stem/progenitor cells (MSPCs)

growth_protocol: Cells were seeded into 12-well plates at either 10,000 cells/well (25 cells/mm2) or 25,000 cells/well (62 cells/mm2). The cells seeded at the lower density were maintained in Mesencult MediaTM + Mesencult Stimulatory SupplementTM (non-differentiating medium) for 3 days post-seeding and then harvested for total RNA. Cells plated at the higher density were maintained in α-MEM complete medium throughout the experiment. At 48 hours post-seeding the medium was refreshed with the ascorbic acid, dexamethasone, and BGP supplement. These cells were harvested at 7 days post-seeding as early osteogenic cells.

extract_protocol:
Total RNA was harvested using RNeasy (Qiagen, Valencia, CA) and measured for quality using the Agilent 2100 Bioanalyzer, and Qubit 2.0 Fluorometer. All RNA integrity numbers (RIN) ranged between 8.2-9.7.
The total RNA samples were submitted to the Beijing Genomics Institute (BGI) for transcriptome sequencing. In brief, magnetic beads with Oligo (dT) were used to isolate mRNA. The mRNA was fragmented and then constructed into HiSeq 2000 strand-specific libraries. The 2 × 100-nt paired-end reads were generated by Illumina HiSeqTM 2000. Clean reads filtered from raw sequence reads were returned from BGI.

treatment_protocol: Cells harvested at Day 3 were maintained in Mesencult MediaTM + Mesencult Stimulatory SupplementTM (non-differentiating medium) and not treated. Cells harvested at Day 7 were seeded in α-MEM supplemented with 100 IU/mL penicillin, 100 µg/mL streptomycin, 25 µg/mL amphotericin, 2 mM L-glutamine (Gibco BRL, Life technologies; Grand Island, NY, USA) and 10% fetal bovine serum (Sigma-Aldrich, St. Louis, MO). At 48 hours post-seeding the medium was refreshed and further supplemented with ascorbic acid (5 µg/mL; Sigma-Aldrich), dexamethasone (10 nM; Sigma-Aldrich), and 10 mM glycerol 2-phosphate disodium salt hydrate (BGP) (Sigma-Aldrich).

tag: cell type

value: bone marrow-derived MSPCs

tag: passages

value: passage 5-10

value: KO

tag: time

value: 7 days days post-seeding

tag: strain

tag: rin value


title: ChIP_5F_SHORT_1_k4me2

tag: cell line


title: KOD7_15


title: KOD7_16


title: human.MPM.007

tag: treatment


title: ChIP_5F_SHORT_2_V5


title: ChIP_5F_SHORT_1_V5

growth_protocol: Refer to the Supplemental Experimental Procedures of the related manuscript.

extract_protocol:
Antibody epitope: H3K4me2. Vendor: Active Motif. Catalog number: 39141. Lot: #01008001.
Antibody epitope: V5. Vendor: MBL intl. Catalog number: M167-3. Lot: #5.
ChIP-seq Illumina libraries were prepared and analyzed as previously described (Mikkelsen et al., 2010).


title: ChIP_5F_SHORT_1_WCE

description: Whole cell extract

treatment_protocol: Refer to the Supplemental Experimental Procedures of the related manuscript.


title: human.MPM.009


title: ChIP_5F_LONG_2_WCE

description: Whole cell extract

value: V5-tagged HMGA2-L


title: WTD7_9

tag: genotype

value: WT


title: KOD3_8

value: 3 days days post-seeding


title: KOD3_7


title: KOD3_6


title: KOD7_13


title: WTD7_11


title: K562_5uM_JQ1_rep-1_exp-4

data_processing:
Library strategy: SLAM-seq
Raw reads were adapter trimmed using cutadapt through the trim_galore (v0.3.7) wrapper tool with adapter overlaps set to 3bp for trimming (--stringency 3).
Trimmed reads were processed using SlamDunk v0.2.4 running the full analysis procedure (slamdunk all) and aligning against the human genome (UCSC version GRCh38),  trimming 12 bp from the 5’ end (-5 12), reporting up to 100 alignments for multimappers (-n 100) and activating multimapper retainment strategy (-m), filtering for variants with a variant fraction of 0.2 (-mv 0.2), filtering with a base-quality cutoff of 27 (-mbq 27) and stringency filter set to 2 (requiring ≥ 2 T>C conversions per read).
Genome_build: GRCh38
Supplementary_files_format_and_content: SlamDunk v0.2.4 output containing UTR coordinates named by EntrezID, raw and normalized read counts, as well as T>C conversion statistics. For details see http://t-neumann.github.io/slamdunk/docs.html

extract_protocol:
Total RNA was extracted using a commercial column purification kit and treated with iodoacetamide for alkylation of 4-thiouridine.
3'UTR sequencing libraries were generated from 500ng of alkylated total RNA using a commercial kit (QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina, Lexogen).

value: 5µM JQ1, 90 min


title: K562_5uM_JQ1_rep-2_exp-4


title: K562_1uM_JQ1_rep-2_exp-4

value: 1µM JQ1, 90 min


title: K562_1uM_JQ1_rep-3_exp-4


title: WTD7_10


title: K562_5uM_JQ1_rep-3_exp-4


title: WTD7_10b


title: ChIP_5F_LONG_2_V5


title: KOD3_5


title: WTD3_1b


title: K562_1uM_JQ1_rep-1_exp-4


title: MPM.FFPE.001_CR


title: human.MPM.006


title: human.MPM.003


title: WTD3_4


title: WTD3_3


title: human.MPM.004


title: human.MPM.002


title: ChIP_5F_LONG_1_k4me2

growth_protocol: HPC-5F cells were transduced with a control (CTRL), V5-tagged HMGA2-L (LONG) or HMGA2-S (SHORT) ORF lentiviral over-expression vectors. Full details on the STAR methods of the related manuscript.

treatment_protocol: Refer to the STAR methods of the related manuscript.


title: human.MPM.001


title: WTD3_1


title: Input

data_processing:
ChIP-seq (Illumina) ChIP and Input DNAs were prepared for amplification by converting overhangs into phosphorylated blunt ends and adding an adenine to the 3’-ends.
Illumina genomic adapters were ligated and the sample was size-fractionated (200–300 bp) on an agarose gel. After a final PCR amplification step (18 cycles), the resulting DNA libraries were quantified and sequenced on HiSeq 2000
Sequences (50nt reads, single end) were aligned to the mouse genome (mm10) using the Burrows-Wheeler algorithm
Alignments were extended in silico at their 3’-ends to a length of 150 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 BAR and bigWig files. ZFP384 peak locations were determined using the MACS algorithm (v1.4.2) with a cutoff of P = 1e-7.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig file that contains peak information for Znf384 (Nmp4) binding sites in MC3T3 cells treated with vehicle (negative controls)
Supplementary_files_format_and_content: BigWig file that contains peak information for Znf384 (Nmp4) binding sites in MC3T3 cells treated with 25nM hPTH (1-34) for 1 hour.
Supplementary_files_format_and_content: BigWig file that contains peak information for DNA Polymerase II binding sites in MC3T3 cells treated with vehicle (negative controls)
Supplementary_files_format_and_content: BigWig file that contains peak information for DNA polymerase II binding sites in MC3T3 cells treated with 25nM hPTH (1-34) for 1 hour
Supplementary_files_format_and_content: BigWig file contains Input control data sequenced to 10-11 million reads

growth_protocol: Cells from ATCC (MC3T3-E1 subclone 4) were maintained in a-MEM supplemented with 100-IU/mL penicillin, 100-µg/mL streptomycin, 25-µg/mL amphotericin, 2mM L-glutamine (Gibco BRL), ascorbic acid (50 µg/mL; Sigma-Aldrich), and 10% fetal bovine serum (Sigma-Aldrich). Cells were seeded into twenty-one 150-mm plates at an initial density of 50,000 cells/plate (320 cells/cm2) and maintained in a-MEM complete medium plus ascorbic acid. On day 14 post-seeding, cells were treated with 25nM hPTH (1–34) or vehicle control for 1 hour before harvest.

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 minutes and quenched with 0.125M glycine. Cell pellets were frozen in an ethanol dry ice bath and shipped to Active Motif for FactorPath analysis. The chromatin was isolated from the pellets by adding lysis buffer followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300–500 bp. Genomic DNA (Input) was prepared by treating aliquots of chromatin with ribonuclease, proteinase K and heat for decross-linking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a NanoDrop spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30 µg) was precleared with protein A agarose beads (Invitrogen, Thermo Fisher Scientific). Genomic DNA regions of interest were isolated using 4-µg antibody against ZNF384 (lot A57874; Sigma HPA004051). Complexes were washed, eluted from the beads with SDS buffer, and subjected to ribonuclease and proteinase K treatment. Cross-links were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.
ChIP-seq (Illumina) ChIP and Input DNAs were prepared for amplification by converting overhangs into phosphorylated blunt ends and adding an adenine to the 3’-ends. Illumina genomic adapters were ligated and the sample was size-fractionated (200–300 bp) on an agarose gel. After a final PCR amplification step (18 cycles), the resulting DNA libraries were quantified and sequenced on HiSeq 2000.
Sequences (50nt reads, single end) were aligned to the mouse genome (mm10) using the Burrows-Wheeler algorithm. Alignments were extended in silico at their 3’-ends to a length of 150 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 BAR and bigWig files. ZFP384 peak locations were determined using the MACS algorithm (v1.4.2) with a cutoff of P = 1e-7.

value: MC3T3-E1 subclone 4

value: Preosteoblast

tag: medium

value: 14 days in osteogenic medium

tag: differentiation agent

value: differentiated 14 days with ascorbic acid


title: ChIP_5F_LONG_1_V5

value: IPSC-derived Hematopoietic Progenitor Cells (transduced with lentivirus)


title: ChIP_5F_LONG_2_k4me2


title: ChIP_5F_LONG_1_WCE

description: Whole cell extract


title: Pol II ChIP-seq PTH

treatment_protocol: On day 14 post-seeding, cells were treated with 25nM hPTH (1–34) or vehicle control for 1 hour before harvest.

value: PTH

value: RNA Pol II (Abcam,catalog# ab5095, lot# GR84118-2)


title: K562_DMSO_rep-1_exp-4

description:
K562_1uM-JQ1_deseq_out.tsv
K562_5uM-JQ1_deseq_out.tsv

tag: 4su labeling time before harvest (min)


title: Pol II ChIP-seq vehicle

value: vehicle


title: MV4-11_5uM_JQ1_rep-3_exp-2


title: CB_PROG_3

data_processing:
Align was performed using TopHat v2.0.14 using default parameters.
Alignment performed to hg19 and with Gencode v17 as the transcriptome index.
Transcript quantification performed using the cuffquant tool within Cufflinks v2.2.1 using default parameters and a custom transcriptome index.
Calculation of transcript FPKM performed using the cuffnorm tool within Cufflinks v2.2.1 using default parameters.
Calculation of differential expression performed using the cuffdiff tool within Cufflinks v2.2.1 using default parameters.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Text files with gene/isoform names/IDs and expression in FPKM

source_name: CB PROG

growth_protocol: Refer to the STAR methods of the related manuscript

extract_protocol:
RNA was extracted using miRNeasy (Qiagen)
RNA-seq libraries were prepared from 100ng of total RNA using the Truseq RNA Sample Preparation kit v2 (Illumina)
Paired-end 101 bp reads.

value: Cord blood hematopoietic progenitor cells


title: K562_DMSO_rep-3_exp-4


title: Nmp4 ChIP-seq vehicle

value: ZNF384 (Sigma, catalog# HPA004051, lot# A57874)


title: FL_PROG_3

source_name: FL PROG

value: Fetal liver hematopoietic progenitor cells


title: K562_DMSO_rep-2_exp-4


title: MV4-11_5uM_JQ1_rep-1_exp-2


title: FL_PROG_2


title: Nmp4 ChIP-seq PTH


title: MV4-11_1uM_JQ1_rep-2_exp-2


title: MV4-11_5uM_JQ1_rep-2_exp-2


title: FL_PROG_1


title: MV4-11_DMSO_rep-1_exp-2

description:
MV4-11_1uM-JQ1_deseq_out.tsv
MV4-11_5uM-JQ1_deseq_out.tsv


title: MV4-11_1uM_JQ1_rep-3_exp-2


title: MV4-11_DMSO_rep-3_exp-2


title: CB_PROG_1


title: MV4-11_1uM_JQ1_rep-1_exp-2


title: CB_PROG_2


title: BM_PROG_3

source_name: BM PROG

value: Bone marrow hematopoietic progenitor cells


title: BM_PROG_2


title: BM_PROG_1


title: CB_HSC_3

source_name: CB HSC

value: Cord blood hematopoietic stem cells


title: K562_AID-BRD4_DMSO_rep-2

tag: genetic modification

value: AID-BRD4 / SFFV-OsTir1-T2A-BlastR


title: FL_HSC_3

source_name: FL HSC

value: Fetal liver hematopoietic stem cells


title: K562_AID-BRD4_IAA_rep-3

value: 100µM indole-3-acetic acid, 90 min


title: K562_AID-BRD4_DMSO_rep-1


title: MV4-11_DMSO_rep-2_exp-2


title: FL_HSC_1


title: FL_HSC_2


title: CB_HSC_2


title: K562_AID-BRD4_DMSO_rep-3


title: K562_SOP-ctrl_IAA-rep-3


title: BM_HSC_2

source_name: BM HSC

value: Bone marrow hematopoietic stem cells


title: BM_HSC_1


title: K562_SOP-ctrl_IAA-rep-1


title: K562_AID-BRD4_IAA_rep-2


title: CB_HSC_1


title: K562_SOP-ctrl_DMSO-rep-3


title: BM_HSC_3


title: K562_AID-BRD4_IAA_rep-1


title: BM_HSC_CTRL_2

data_processing:
Alignment was performed using TopHat v2.0.14 using default parameters.
Alignment performed to hg19 and with Gencode v19 as the transcriptome index.
Transcript quantification performed using the cuffquant tool within Cufflinks v2.2.1 using default parameters.
Calculation of transcript FPKM performed using the cuffnorm tool within Cufflinks v2.2.1 using default parameters.
Calculation of differential expression performed using the cuffdiff tool within Cufflinks v2.2.1 using default parameters.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.exp.txt: Tab-delimited text files with gene/isoform names/IDs and expression in FPKM.

extract_protocol:
RNA extracted using miRNeasy (Qiagen).
Generated from 1-5 ng of total RNA for each biological replicate using Clontech Smart-seq v4 kit.
Paired-end 101 bp reads.

treatment_protocol: Cells were infected with lentiviruses for overexpression of CLK3, HMGA2-S, HMGA2-L or control empty vector (refer to the Supplemental Experimental Procedures of the related manuscript).

value: PSMAL empty vector


title: K562_SOP-ctrl_IAA-rep-2


title: BM_HSC_CLK3_2

extract_protocol:
RNA was extracted using miRNeasy (Qiagen)
RNA-seq libraries were prepared from 1-5ng of total RNA using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech) in combination with the Nextera XT DNA Library Preparation Kit from 150pg of cDNA (Illumina).
Pair-end 101 bp reads

treatment_protocol: BM-HSC cells were transduced with a control (CTRL), HMGA2-S+3'UTRwt (SHORT) or CLK3 lentiviral over-expression vectors. Full details on the STAR methods of the related manuscript.

value: Bone Marrow Hematopoietic Stem Cells (transduced with lentivirus)


title: BM_HSC_HMGA2_SHORT_2

treatment_protocol:
RNA was extracted using miRNeasy (Qiagen)
RNA-seq libraries were prepared from 1-5ng of total RNA using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech) in combination with the Nextera XT DNA Library Preparation Kit from 150pg of cDNA (Illumina).
Pair-end 101 bp reads

tag: characteristics


title: BM_HSC_CTRL_1

value: CTRL empty vector


title: K562_SOP-ctrl_DMSO-rep-2


title: K562_SOP-ctrl_DMSO-rep-1


title: BM_HSC_CLK3_1


title: BM_HSC_HMGA2_SHORT_1


title: st10_rep2

city: Takatsuki

first: Hiroki

last: Oda

state: Osaka

address: 1-1 Murasaki-cho

country: Japan

institute: JT Biohistory Research Hall

data_processing:
Base call and quality scoring were performed by the Real Time Analysis software application during Illumina's sequencing runs.
Sequence reads were trimmed for adaptor and primer sequences and low-quality sequences using the CLC Genomics Workbench 7.0.3 (Qiagen) with the following parameter settings: trim using quality scores, limit=0.05; trim ambiguous nucleotides, maximum number of ambiguities=2; filter on length, discard reads below length=30. Trimmed reads were then aligned to Ptep_1.0 genome assembly using the BLAT algorithm version 34 in the DDBJ Read Annotation Pipeline with default settings.
The output alignments were filtered based on quality, coverage, and uniqueness using a perl script filterPSL.pl available from the AUGUSTUS 3.0.1 scripts folder. The parameter settings were as follows: minimum coverage, 60%; minimum percent identity, 90%; unique threshold, 0.96. The filtered alignments were converted into sam files with a custom perl script.
Using the sam files, abundance of mRNAs against AUGUSTUS gene models (Schwager et al., 2017, BMC Biol. 15, 62) was calculated with htseq-count v. 0.6.1p1 in -s reverse, -m union settings and was normalized in Reads Per Kilobase of exon per Million reads (RPKM).
The alignments were converted into wig files using a script aln2wig available from the AUGUSTUS 3.0.1 scripts folder.
Genome_build: Ptep_1.0
Supplementary_files_format_and_content: tab-delimited text file includes RPKM values for gene models and the features of the gene models.
Supplementary_files_format_and_content: wig files ; Scores represent normalized read coverage (per 10 million reads).

organism: Parasteatoda tepidariorum

source_name: spider embryos

growth_protocol: Embryos were incubated at 25˚C until they reached the appropriate stages.

extract_protocol:
Poly(A) mRNA was extracted using the Dynabeads mRNA DIRECT Kit (Ambion) from 10-100 embryos of each successive developmental stage.
mRNA was fragmented using the NEBNext Rnase III RNA Fragmentation Module (New England BioLabs). Sequencing libraries were constructed from fragmented RNA using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs) and NEBNext Multiplex Oligos for Illumina (Index Primers Set 1, New England BioLabs).

tag: isolate

value: Osaka

tag: tissue

value: whole embryo

tag: developmental stage

value: stage 10 (~78 h AEL)


title: st6_rep2

value: stage 6 (42-43 h AEL)


title: RAT 5 morphine tolerance

city: Changsha

first: Jiali

last: Shao

state: Hunan

address: 281 Tongzipo Road, Changsha, Hunan, China

department: Department of Anesthesiology

country: China

institute: The affiliated Cancer Hospital of Xiangya School of Medicine, Central South University

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C)

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 5 out of 10 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering and combined analysis were performed using homemade scripts.

organism: Rattus norvegicus

source_name: morphine tolerance group_spinal cord

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA were extracted using Trizol. The RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: morphine tolerance group were intrathecally injected with 10 μg(10μl) morphine twice daily for 7 consecutive days, while normal saline group were intrathecally injected with 10μl normal saline twice daily for 7 consecutive days

value: Sprague Dawley

tag: gender

value: male

tag: weight

tag: injected with

value: 10μl(10μg) morphine, twice daily for 7 consecutive days

value: spinal cord

value: morphine


title: RAT 4 morphine tolerance


title: RAT 9 normal saline

source_name: normal saline group_spinal cord

value: 10μl normal saline, twice daily for 7 consecutive days

value: normal saline


title: RAT 7 normal saline


title: Dglycerol/BYGlicerol

city: Recife

first: Marcos

middle: Antonio

last: Morais

state: Pernambuco

address: Av. Moraes Rego, 1235

department: Department of Genetics

country: Brazil

institute: Federal University of Pernambuco

hyb_protocol: Two arrays, corresponding to biological duplicate, were used for each sample combination: parental glycerol (Cy5, Target ) x parental glucose (Cy3, reference); Damp glycerol (Cy5, Target) x Damp glucose (Cy3 reference); Damp glucose (Cy5, Target) x parental glucose (Cy3, reference); Damp glycerol (Cy5, Target) x parental glycerol (Cy3, reference). Target and reference cRNA samples were mixed and the hybridizations were performed on yeast gene expression 8x15K spots slides (cat. nr. G4813A-016322, Agilent, USA) at 65 ºC for 17 hours at 10 r.pm. in the Microarray Hybridization Oven (cat. nr. G2545A, Agilent, USA).

scan_protocol: The slides were placed into the High-Resolution Microarray Scanner (cat. nr. G2505-60502, Agilent, USA). The fluorescence data were extracted (.txt files) for each spot  by using Scan Control 8.5.1 software (Agilent, USA)

data_processing: Data were then analyzed using the R statistical language with the specific LIMMA and MArray  packages. Background correction was done with normexp method. Robust spline and quantile methods were used for normalization within and between arrays, respectively. A list of differentially expressed genes was generated by applying adjusted p-values for multiple tests. Groups of genes with statistical significance (Adj.p<0.05) were utilized

organism: Saccharomyces cerevisiae

source_name: Damp Glycerol

label_protocol: Synthesis of cDNA and labelling was performed by Two-Color Low Input Quick Amp Labeling Kit (cat. nr. 5190-2306, Agilent, USA), with Two-Color RNA spike-in kit for internal control (cat. nr. 5188-5279, Agilent, USA). For yeast samples, 100 ng of purified RNA was used for labelling.

growth_protocol: Cell from BY4741 strain and DampERG12 mutants, which express 10% of parental MVK activity, were grown in complete synthetic YNB medium containing glucose (20 g/L) in flasks at 30ºC and 150 rpm in a rotatory shaker to mid-exponential growth phase (OD600nm = 1), collected, washed in water, suspended in in the same medium containing either glucose (20 g/L) or glycerol (20 g/L) at an initial cell density of OD600 0.1 and cultivated in the same conditions until the cultures reach to OD600 0.5 (maximal OD reached by mutant cells in glycerol). Cells were recovered from 20 mL of cultures, centrifuged and stored at -80ºC until use.

extract_protocol: total RNA in the lysates was purified by using RNAspin Mini RNA Isolation Kit (cat. nr. 25-0500-71, GE HealthCare, USA) following manufacturer´s instructions and suspended in 25 μl nuclease-free water.

treatment_protocol: The cultures were centrifuged and each one was re-suspended with YPD medium pH 2.5 adjusted with sulfuric acid. After incubation for 1 h at 30°C with orbital agitation (150 rpm), the cells were recovered by centrifugation and immediately used to RNA extraction

tag: strain/genotype

value: DampERG12 mutants

tag: carbon source

value: glycerol

source_name: Parental glycerol

value: BY4741 strain


title: Dglucose/ByGlucose

source_name: Damp Glucose

value: glucose

source_name: Parental glucose


title: st8_rep2

value: stage 8 (~60 h AEL)


title: st5l_rep2

value: stage 5 late (36-37 h AEL)


title: RAT 6 normal saline

tag: strain


title: Dglycerol/Dglucose

source_name: Damp glucose


title: RAT 8 normal saline


title: RAT 10 normal saline


title: RAT 2 morphine tolerance


title: RAT 3 morphine tolerance


title: MG CD4+T cell 5

type: genomic

city: Chang Sha

first: jingjiao

last: chen

state: Hu Nan

address: Renmin

institute: xiangya hospital

description:
MG CD4+T cell
Sample name: 26

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

source_name: CD4 +T cells of patients with MG

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions

value: peripheral venous blood

tag: cell type

value: CD4 +T cells

tag: diagnosis

value: myasthenia gravis

tag: age


title: st5e_rep2

value: Osaka

value: whole embryo

value: stage 5 early (31-32 h AEL)


title: Control CD4+T cell 6

description:
Control CD4+T cell
Sample name: C8

source_name: CD4 +T cells of control

value: healthy control

value: male


title: RAT 1 morphine tolerance

value: Sprague Dawley

value: 10μl(10μg) morphine, twice daily for 7 consecutive days

value: spinal cord

tag: treatment

value: morphine


title: st4_rep2

value: stage 4 (25-26 h AEL)


title: ByGlycerol/ByGlucose

value: BY4741 strain

value: glycerol


title: MG CD4+T cell 2

description:
MG CD4+T cell
Sample name: 17


title: Control CD4+T cell 5

description:
Control CD4+T cell
Sample name: C6

value: female


title: st1_rep2

value: stage 1 (16-cell stage, ~9 h AEL)


title: MG CD4+T cell 1

description:
MG CD4+T cell
Sample name: 15

value: peripheral venous blood


title: MG CD4+T cell 4

description:
MG CD4+T cell
Sample name: 24

value: CD4 +T cells


title: st3_rep2

value: stage 3 (20-21 h AEL)


title: st2_rep2

value: Osaka

value: stage 2 (256-cell stage, ~15 h AEL)


title: Control CD4+T cell 2

description:
Control CD4+T cell
Sample name: C3


title: st8_rep1

value: whole embryo

value: stage 8 (~60 h AEL)


title: st10_rep1

value: stage 10 (~78 h AEL)


title: st7_rep1

value: stage 7 (~50 h AEL)


title: st6_rep1

value: stage 6 (42-43 h AEL)


title: H111 ∆hamD chem 3

city: Zürich

first: Gabriella

last: Pessi

address: Winterthurerstrasse 190

country: Switzerland

institute: University of Zürich

description: 20171004.A-Anu_6_R1 (GE)

data_processing:
The sequences of the reads were quality trimmed using the program fastq_quality_trimmer.
Sequencing reads were mapped to the Bc H111 genome (Carlier et al. 2014) using CLC Genomics Workbench v7.0 (CLCbio) allowing up to 2 mismatches per read.
RNA-Seq count data were subsequently analyzed with the DESeq software (Anders & Huber 2010).
Genome_build: H111 genome sequence (accession no. HG938370, HG938371, and HG938372)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include RPKM and mean values for each sample.

organism: Burkholderia cenocepacia H111

source_name: Bc H111 planktonic cells

extract_protocol:
Cells were flash frozen on dry ice, and RNA was harvested using hot phenol protocol (Pessi et al. 2007). Ds cDNA was produced and nugen libraries obtained.
RNA libraries were prepared using Ovation® Complete Prokaryotic RNA-Seq Library System.

tag: genotype/variation

value: chemical complementation of hamD mutant

tag: growth phase

value: planktonic cells, OD600 equal 1

tag: medium

value: AB minimal medium with glycerol as C-source, supplemented with Valdiazen (100 uM)


title: H111 ∆hamD chem 2

description: 20171004.A-Anu_5_R1 (GE)


title: H111 ∆hamD 3

description: 20171004.A-Anu_4_R1 (GE)

value: hamD mutant

value: AB minimal medium with glycerol as C-source


title: Control CD4+T cell 1

description:
Control CD4+T cell
Sample name: C1

value: healthy control

value: male


title: st5e_rep1

value: stage 5 early (31-32 h AEL)


title: st4_rep1

value: stage 4 (25-26 h AEL)


title: H111 wild type 2

description: 20171004.A-Anu_1_R1 (GE)

value: wild type


title: Control CD4+T cell 3

description:
Control CD4+T cell
Sample name: C4

value: peripheral venous blood

value: CD4 +T cells


title: Control CD4+T cell 4

description:
Control CD4+T cell
Sample name: C5


title: H111 ∆hamD chem 1


title: H111 wild type 3

description: 20171004.A-Anu_2_R1 (GE)


title: H111 ∆hamD 2

description: 20171004.A-Anu_3_R1 (GE)


title: primary porcine buccal pouch mucosal cells at 30 days of culture rep2

city: Poznań

first: Marcin

last: Ruciński

state: Wielkopolska

address: Święcickiego 6

department: Histology and Embryology

country: Poland

institute: Poznań University of Medical Sciences

description:
Gene Expression data from primary porcine buccal pouch mucosal cells at 30 days of culture
30D.2

hyb_protocol: Biotin-labeled fragments of cDNA (5.5 μg) were hybridized to the Affymetrix® Canine Gene 1.1 ST Array Strip (48°C/20 h), washed and stained using the Affymetrix GeneAtlas Fluidics Station according to the manufacturer technical protocol

scan_protocol: The array strips were scanned employing Imaging Station of the GeneAtlas System.

data_processing: Obtained cell files were submitted to bioconductor and R programing lenguage. Each CEL file was merged with a description file.  In order to correct background, normalize, and summarize results, we used the Robust Multiarray Averaging (RMA) algorithm.

organism: Sus scrofa

source_name: 9 months old crossbred landrace glits

label_protocol: Biotin labeling and fragmentation were performed by Affymetrix GeneChip® WT Terminal Labeling and Hybridization (Affymetrix).

growth_protocol: In this study we used landrace crossbred gilts (n=30). They had mean age of 155 days and the mean weight was 100kg.

extract_protocol: Total RNA was extracted from samples using TRI Reagent (Sigma, St Louis, MO, USA) and RNeasy MinElute cleanup Kit (Qiagen, Hilden, Germany). Subsequently total RNA (100 ng) from each pooled sample was subjected to two round, sense cDNA amplification (Ambion® WT Expression Kit).

treatment_protocol: Mucosa cells were surgically removed using sterile surgical blades and then were incubated with collagenase I for 25 min. Next, the cells were washed three times by centrifugation. The final cell pellet was resuspended in DMEM supplemented with 10% fetal calf serum (FCS; Sigma Aldrich, Madison, USA) and 10,000 U×mL−1 penicillin G, 10 mg×mL−1 streptomycin, and 25 μg×mL−1 amphotericin B. The cells were cultured at 37oC in humidified atmosphere of 5 % CO2.

value: poricne bucal pouch mucosa

value: in vitro culture

tag: time

value: 30 days of culture


title: primary porcine buccal pouch mucosal cells at 15 days of culture rep1

description:
Gene Expression data from primary porcine buccal pouch mucosal cells at 15 days of culture
15D.1

value: 15 days of culture


title: primary porcine buccal pouch mucosal cells at 7 days of culture rep2

description:
Gene Expression data from primary porcine buccal pouch mucosal cells at 7 days of culture
7D.2

value: 7 days of culture


title: primary porcine buccal pouch mucosal cells at 15 days of culture rep2

description:
Gene Expression data from primary porcine buccal pouch mucosal cells at 15 days of culture
15D.2


title: primary porcine buccal pouch mucosal cells at 30 days of culture rep1

description:
Gene Expression data from primary porcine buccal pouch mucosal cells at 30 days of culture
30D.1


title: st1_rep1

tag: isolate

value: Osaka

value: whole embryo

value: stage 1 (16-cell stage, ~9 h AEL)


title: MG CD4+T cell 3

description:
MG CD4+T cell
Sample name: 18

tag: tissue

value: myasthenia gravis

value: female


title: st2_rep1

tag: developmental stage

value: stage 2 (256-cell stage, ~15 h AEL)


title: MG CD4+T cell 6

description:
MG CD4+T cell
Sample name: 28

tag: gender

value: male


title: H111 ∆hamD 1

value: hamD mutant

value: planktonic cells, OD600 equal 1

value: AB minimal medium with glycerol as C-source


title: A20_24-3

status: Public on Apr 04 2018

city: Los Angeles

first: Ling

state: CA

address: 2011 Zonal Avenue, 600

department: Department of Medicine

institute: University of Southern California

data_processing:
Reads were trimmed based on quality score and adaptor sequences removed using Trimmomatic
Alignment to the human genome (ver. GRCh38.p7) performed using ultra-fast aligner STAR
Differential gene expression analysis performed with R/Bioconductor package DESeq2
Statistical analysis performed in Rstudio ver 1.0.136 and R ver. 3.3.3
Genome_build: GRCh38.p7
Supplementary_files_format_and_content: readCounts

growth_protocol: RKO cells routinely maintained in DMEM +10% fetal calf serum

extract_protocol:
Total RNA extracted using Qiagen Rneasy Plus Minikit (#74134)
RNAseq libraries prepared using 500ng of total RNA and Kapa mRNA HyperPrep Kit

treatment_protocol: Cells were treated with 50ng/mL of recombinant human wnt3a for 24 hours

tag: cell line

value: RKO

value: Colon Cancer Cell Line

tag: sirna

tag: stimulation

value: recombinant human wnt3a

value: 24 hours


title: A20_24-4


title: st3_rep1

value: stage 3 (20-21 h AEL)


title: H111 wild type 1

value: wild type


title: A20_24-1


title: A20_24-2


title: CNTL_24-2

value: Control


title: Control_CHX

city: Hangzhou

first: Yuanhui

last: Mao

state: Zhejiang

address: 1369 West Wenyi Road

institute: Zhejiang University

data_processing:
Library strategy: Ribo-seq
For replicate 1, the 3' adaptor AAAAAAAAAA and low quality bases were trimmed by Cutadapt. The trimmed reads were mapped to Human transcriptom (GRCh38.81) by Bowtie, using parameters: -a --best -m1 --strata. Two mismatches were permitted.
For replicate 2, the 3' adaptor CTGTAGGCACCATCAAT were trimmed by Cutadapt. The first 6 nucleotide and the last 4 nucleotides were also clipped after adaptor removal. The trimmed reads were mapped to Human transcriptom (GRCh38.81) by Bowtie, using parameters: -a --best -m1 --strata. Two mismatches were permitted. The PCR duplicates were removed from the mapped reads using the methods in Lecanda et al., 2016 (PMID: 27450428)
Genome_build: GRCh38.81
Supplementary_files_format_and_content: RPKM values in text files

growth_protocol: Wild-type human embryonic kidney (HEK) 293T cells immortalized with SV40 Large T antigen were plated at a concentration of 4.0 x 104 cells/cm2 and allowed to grow overnight before growth medium was replaced with experimental control or amino acid-deficient medium.

extract_protocol:
Equal aliquots of the ribosome fractions separated by sucrose gradient were pooled and treated with E. coli RNase I (Ambion) to digest regions of mRNAs not protected by ribosomes. RNAs were extracted using TRIzol LS.
cDNA libraries were constructed from the ribosome-protected mRNA fragments by poly(A)tailing and reverse transcription using barcode containing oligonucleotides (one for each treatment condition). For deep sequencing, the cDNA library was amplified by PCR using the Phusion High-Fidelity polymerase and primers containing Illumina cluster generation sequences. Equal amounts of barcoded samples for the three conditions were mixed together, and approximately 3–5 pM of the pooled DNA sample was used for cluster generation followed by deep sequencing.

treatment_protocol: Experimental control medium was the same as normal growth medium with the following changes: medium was prepared using DMEM that lacked sulfur amino acids, histidine, leucine and arginine (custom prepared by Gibco/Invitrogen) and was supplemented with 10% dialyzed FBS and L-cysteine, L-methionine, L-histidine, L-leucine and L-arginine to levels found in normal DMEM. Methionine-deficient (Met-), leucine-deficient (Leu-) and arginine deficient (Arg-) media were prepared similarly except the respective amino acids were not added back to the deficient DMEM.

value: HEK293T cells immortalized with SV40 Large T antigen

tag: molecule

value: ribosomes protected RNA

tag: condition

value: Control, AA sufficient, CHX pre-treated


title: Arg-_no_CHX

value: Arg starvation over night, no CHX pre-treated


title: Met-_CHX

value: Met starvation over night, CHX pre-treated


title: Leu-_CHX

value: Leu starvation over night, CHX pre-treated


title: Met-_no_CHX

value: Met starvation over night, no CHX pre-treated


title: Control_no_CHX

value: Control, AA sufficient, no CHX pre-treated


title: CNTL_24-4

tag: cell type


title: CNTL_24-3


title: primary porcine buccal pouch mucosal cells at 7 days of culture rep1

description:
Gene Expression data from primary porcine buccal pouch mucosal cells at 7 days of culture
7D.1

value: poricne bucal pouch mucosa

value: in vitro culture

value: 7 days of culture


title: CNTL_24-1

value: RKO

value: Colon Cancer Cell Line


title: Leu-_no_CHX

value: Leu starvation over night, no CHX pre-treated


title: Arg-_CHX

value: Arg starvation over night, CHX pre-treated


title: st7_rep2

value: Osaka

value: whole embryo

value: stage 7 (~50 h AEL)


title: Sequencing data from the shoot tips of one pillar peach branch - pillar tree #10

city: East Lansing

first: Courtney

last: Hollender

address: 1066 Bogue St

department: Dept. of Horticulture

institute: Michigan State University

description:
Sequencing data from the shoot tips of one pillar peach branch. This is a biolical replicate. It is from a pillar tree that we call #10
These peach trees were from a segregating F2 population from a cross between  parents used only for breeding purposes. The  trees sequenced here are not cultivar varieties. Lengthy detail on their origin can be found in the supplementary section of the  paper Hollender et al (2018) Hort Research. The standard trees used here are the same trees (and the same raw data) used for the RNAseq experiment described in  Hollender et al (2018) PNAS and the pillar trees used for this study are from the same population as well.

data_processing:
Barcodes were removed from Raw Reads and then the sequences were trimmed based on qualtiy and ambiguity using CLC Genomics workbench 10.1
The remaining reads were aligned against the Peach Genome Version 2 using CLC Genomics workbench 10.1
Differential expression analysis was performed using CLC Genomics workbench 10.1 Basic Variant Detection tool with the following modifications to the default parameters: Ploidy = 6, minimum coverage = 20, minimum count = 4, minimum frequency = 8.0.
Supplementary_files_format_and_content: TPM

organism: Prunus persica

source_name: Lateral shoot (branch) tips of trees

growth_protocol: Trees were grown in a field at the USDA ARS Appalachian Fruit Research Station

extract_protocol:
RNA was extracted using the Omega SQ total RNA kit with the addition of 2% PVP to the lysis buffer
50 bp Illumina Truseq uppaired libraries were constructed at the gemoics resources core facility at Weill Cornell College of Medicine
50 bp RNAseq unpaired reads

treatment_protocol: No Treatments

value: Mature tree

value: branch tip

tag: growth habit

value: pillar growth habit


title: Sequencing data from the shoot tips of one pillar peach branch - pillar tree #7

description:
Sequencing data from the shoot tips of one pillar peach branch. This is a biolical replicate. It is from a pillar tree that we call #7
These peach trees were from a segregating F2 population from a cross between  parents used only for breeding purposes. The  trees sequenced here are not cultivar varieties. Lengthy detail on their origin can be found in the supplementary section of the  paper Hollender et al (2018) Hort Research. The standard trees used here are the same trees (and the same raw data) used for the RNAseq experiment described in  Hollender et al (2018) PNAS and the pillar trees used for this study are from the same population as well.


title: Sequencing data from the shoot tips of one standard peach branch - standard tree #9

description:
Sequencing data from the shoot tips of one standard peach branch. This is a biolical replicate. It is from a standard tree that we call #9
These peach trees were from a segregating F2 population from a cross between  parents used only for breeding purposes. The  trees sequenced here are not cultivar varieties. Lengthy detail on their origin can be found in the supplementary section of the  paper Hollender et al (2018) Hort Research. The standard trees used here are the same trees (and the same raw data) used for the RNAseq experiment described in  Hollender et al (2018) PNAS and the pillar trees used for this study are from the same population as well.

value: standard growth habit


title: Sequencing data from the shoot tips of one standard peach branch - standard tree #10

description:
Sequencing data from the shoot tips of one standard peach branch. This is a biolical replicate. It is from a standard tree that we call #10
These peach trees were from a segregating F2 population from a cross between  parents used only for breeding purposes. The  trees sequenced here are not cultivar varieties. Lengthy detail on their origin can be found in the supplementary section of the  paper Hollender et al (2018) Hort Research. The standard trees used here are the same trees (and the same raw data) used for the RNAseq experiment described in  Hollender et al (2018) PNAS and the pillar trees used for this study are from the same population as well.


title: Sequencing data from the shoot tips of one pillar peach branch - pillar tree #4

description:
Sequencing data from the shoot tips of one pillar peach branch. This is a biolical replicate. It is from a pillar tree that we call #4
These peach trees were from a segregating F2 population from a cross between  parents used only for breeding purposes. The  trees sequenced here are not cultivar varieties. Lengthy detail on their origin can be found in the supplementary section of the  paper Hollender et al (2018) Hort Research. The standard trees used here are the same trees (and the same raw data) used for the RNAseq experiment described in  Hollender et al (2018) PNAS and the pillar trees used for this study are from the same population as well.


title: Sequencing data from the shoot tips of one standard peach branch - standard tree #7

description:
Sequencing data from the shoot tips of one standard peach branch. This is a biological replicate. It is from a standard tree that we called #7
These peach trees were from a segregating F2 population from a cross between  parents used only for breeding purposes. The  trees sequenced here are not cultivar varieties. Lengthy detail on their origin can be found in the supplementary section of the  paper Hollender et al (2018) Hort Research. The standard trees used here are the same trees (and the same raw data) used for the RNAseq experiment described in  Hollender et al (2018) PNAS and the pillar trees used for this study are from the same population as well.


title: SNU-216-CD133-1

city: Seoul

first: Tae-Min

last: Kim

address: Seocho-Gu, Banpo-Dong

department: Dept of Medical Informatics

country: South Korea

institute: The Catholic University of Korea, College of Medicine

description:
Gastric cancer celllines (SNU-216), CD133- subpopulation by FACS sorting, replicate 1
SAMPLE 7

hyb_protocol: A Whole-Genome Expression Direct Hybridization Kit (Illumina) was used to hybridize 750 ng of cRNA from each sample to Human HT-12 v3 expression BeadChips (Illumina) at 58°C overnight.

scan_protocol: BeadChip was scanned with a BeadArray reader (Illumina).

data_processing: Data processing was performed with BeadStudio (Illumina).

source_name: SNU-216 celllines, CD133-, replicate 1

label_protocol: Labelling was performed according to manufacturer (Illumina) specifications.

growth_protocol: Cells were maintained in RPMI1640 medium (Hyclone, USA) supplemented with 10% (v/v) calf serum (Hyclone) at 37°C in a 5% (v/v) CO2 humidified atmosphere.

extract_protocol: Total RNA was isolated from sorted cells using the Iso-RNA Lysis Reagent (5PRIME, USA) according to the manufacturer’s protocol.

treatment_protocol: MoFlo XDP flow cytometry (Beckman Coulter, USA) was employed to sort cell lines into CD133+ and CD133- populations.

value: Gastric cancer cell line

tag: cell markers


title: SNU-601-CD133-1

description:
Gastric cancer celllines (SNU-601), CD133- subpopulation by FACS sorting, replicate 1
SAMPLE 11

source_name: SNU-601 celllines, CD133-, replicate 1


title: SNU-601-CD133+2

description:
Gastric cancer celllines (SNU-601), CD133+ subpopulation by FACS sorting, replicate 2
SAMPLE 10

source_name: SNU-601 celllines, CD133+, replicate 2


title: SNU-601-CD133+1

description:
Gastric cancer celllines (SNU-601), CD133+ subpopulation by FACS sorting, replicate 1
SAMPLE 9

source_name: SNU-601 celllines, CD133+, replicate 1


title: SNU-601-CD133-2

description:
Gastric cancer celllines (SNU-601), CD133- subpopulation by FACS sorting, replicate 2
SAMPLE 12

source_name: SNU-601 celllines, CD133-, replicate 2


title: SNU-216-CD133+2

description:
Gastric cancer celllines (SNU-216), CD133+ subpopulation by FACS sorting, replicate 2
SAMPLE 6

source_name: SNU-216 celllines, CD133+, replicate 2


title: C3H_tumor_3

city: Tsukuba

first: Keiko

last: Nohara

address: 16-2 Onogawa

department: Center for Health and Environmental Risk Research

institute: National Institute for Environmental Studies

description: Gene expression of liver tumor_3

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x GE hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE Ver 2.0Microarrays (G4858A) for 17 hours at 65℃ in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37℃ GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G4900DA) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent) using default parameters (protocol GE1_1200_Jun14 and Grid: 074809_D_F_20150624) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Low RNA Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

growth_protocol: pregnant F0 C3H/HeN mice were purchased from CLEA Japan (Tokyo, Japan) and F1 and F2 pups in the control group were given free access to a standard diet (CA-1; CLEA Japan) and tap water.  C3H mice of 74~75 weeks were used in this analysis.

extract_protocol: RNA was prepared using the RNeasy Mini Kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations.  The protocol includes an on-column DNase digestion.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: liver

value: male


title: KATO-III-CD133-2

description:
Gastric cancer celllines (KATO-III), CD133- subpopulation by FACS sorting, replicate 2
SAMPLE 4

source_name: KATO-III celllines, CD133-, replicate 2

value: KATO-III


title: Sequencing data from the shoot tips of one pillar peach branch - pillar tree #8

description:
Sequencing data from the shoot tips of one pillar peach branch. This is a biolical replicate. It is from a pillar tree that we call #8
These peach trees were from a segregating F2 population from a cross between  parents used only for breeding purposes. The  trees sequenced here are not cultivar varieties. Lengthy detail on their origin can be found in the supplementary section of the  paper Hollender et al (2018) Hort Research. The standard trees used here are the same trees (and the same raw data) used for the RNAseq experiment described in  Hollender et al (2018) PNAS and the pillar trees used for this study are from the same population as well.


title: SNU-216-CD133-2

description:
Gastric cancer celllines (SNU-216), CD133- subpopulation by FACS sorting, replicate 2
SAMPLE 8

source_name: SNU-216 celllines, CD133-, replicate 2


title: C3H_normal_2

description: Gene expression of normal liver_2


title: C3H_tumor_2

description: Gene expression of liver tumor_2


title: KATO-III-CD133+1

description:
Gastric cancer celllines (KATO-III), CD133+ subpopulation by FACS sorting, replicate 1
SAMPLE 1

source_name: KATO-III celllines, CD133+, replicate 1


title: C3H_normal_3

description: Gene expression of normal liver_3


title: Sequencing data from the shoot tips of one standard peach branch - standard tree #8

description:
Sequencing data from the shoot tips of one standard peach branch. This is a biological replicate. It is from a standard tree that we call #8
These peach trees were from a segregating F2 population from a cross between  parents used only for breeding purposes. The  trees sequenced here are not cultivar varieties. Lengthy detail on their origin can be found in the supplementary section of the  paper Hollender et al (2018) Hort Research. The standard trees used here are the same trees (and the same raw data) used for the RNAseq experiment described in  Hollender et al (2018) PNAS and the pillar trees used for this study are from the same population as well.


title: KATO-III-CD133-1

description:
Gastric cancer celllines (KATO-III), CD133- subpopulation by FACS sorting, replicate 1
SAMPLE 3

source_name: KATO-III celllines, CD133-, replicate 1


title: SNU-216-CD133+1

description:
Gastric cancer celllines (SNU-216), CD133+ subpopulation by FACS sorting, replicate 1
SAMPLE 5

source_name: SNU-216 celllines, CD133+, replicate 1


title: KATO-III-CD133+2

description:
Gastric cancer celllines (KATO-III), CD133+ subpopulation by FACS sorting, replicate 2
SAMPLE 2

source_name: KATO-III celllines, CD133+, replicate 2


title: CCTt15

data_processing:
Bisulfite-treated sequencing reads were aligned by a paired-end alignment method for a unique  best hit to the mouse reference genome (NCBI/mm10) using the Bismark program
adapter trimming and quality control was performed using Trim Galore  (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). The aligned data were used  for analyzing DNA methylation profiles using a methylKit package on R
The aligned data were used for analyzing DNA methylation profiles using a methylKit package on R
DMCs were extracted using methylKit for the cytosines in CpG sites with ≥10 reads in  coverage and ≥25% methylation differences between normal and tumor tissues using the logistic  regression method. DMRs were detected for regions containing ≥3 CpG sites and at least 1  DMC and with ≥30% absolute mean CpG methylation difference by using an eDMR package on  R
Promoter DMRs, which were defined as regions within ±2000 bp from TSSs for Refseq  transcripts, were extracted using bedtools 2.25.0 (bedtools.readthedocs.io).
Genome_build: mm10
Supplementary_files_format_and_content: Excel file containing the results of DMRs between 3 normal liver tissues and 3 liver tumor tissues, and the distance of DMRs from closest gene calculated by bedtools.

source_name: Liver

extract_protocol:
Tissues were lysed in lysis buffer, treated with RNase, and purified with a phenol-chloroform mixture
RRBS libraries were prepared from genomic DNA of 3 normal liver tissues and 3 tumor tissues  having a Ha-ras mutation according to the protocol reported by Boyle et al (Genome Biol. 2012, 13:R92. doi: 10.1186/gb-2012-13-10-r92). with some modifications. Briefly, 100 ng of genomic DNA was digested with MspI, subjected to gapfilling  and A-tailing, and ligated with TruSeq adaptors included in the TruSeq DNA Sample Prep  Kit (FC-121-1001, Illumina). After DNA size selection and ligation efficiency were checked,  adaptor-ligated DNA was subjected to bisulfite conversion and amplified by PCR. The PCR  products were cleaned-up using Agencourt AMPure XP beads

tag: strain

tag: age

value: 74 weeks

tag: normal or tumor

value: tumor


title: CCTt10


title: C3H_normal_1

description: Gene expression of normal liver_1


title: C3H_tumor_1

description: Gene expression of liver tumor_1


title: CCTt8


title: CCN6

value: normal


title: st5l_rep1

source_name: spider embryos

value: stage 5 late (36-37 h AEL)


title: CCN5