title: DP_Mouse302_SeqID_73449

source_name: DP thymocytes

value: DP thymocytes


title: SP4_Mouse4220_SeqID_73444

status: Public on Apr 04 2018

type: SRA

city: Ann Arbor

first: Tomonori

last: Hosoya

state: MI

address: 109 Zina Pitcher Place

department: CDB

country: USA

institute: University of Michigan

library_source: genomic

data_processing:
In order to account for sequencing depth differences between each library, we down-sampled reads (keeping read pairs intact) to the median depth of all libraries after the pruning steps. This ensures that sequencing depth does not confound this analysis.
After this step, we combined all replicates from each stage into a single BAM file to increase sequencing depth (ranging from 120 to 134 million reads per stage) and called peaks using macs2 with options --nomodel --shift -50 --extsize 100  -B --keep-dup all.
macs2 analyses. Files with .fdr0.05.noBlackList.bed extension are the coordinates of the peak calls for each sample. Additionally, we removed peaks with FDR < 0.05 and in non-mappable regions (blacklisted) to generate a more stringent peak set.
We used CENTIPEDE to generate the posterior probability of each motif instance being bound. We subsequently selected motifs that had a posterior >= 0.99 and fully intersected an ATAC-seq peak in their sample of origin to be considered as bound motifs (footprints).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig, bed

molecule: genomic DNA

organism: Mus musculus

source_name: CD4 SP thymocytes

extract_protocol: Libraries were prepared following  Buenrostro et al, 2013 Nat Methods 10:1213-1218.

treatment_protocol: Single-cell suspension isolated from thymus were stained for cell surface marker, and then each stage of thymoctytes were isolated by flow cytometer

tag: cell type

value: CD4 SP thymocytes

tag: strain

tag: age

value: 9 weeks old

tag: genotype

value: wild type


title: SP8_Mouse4220_SeqID_73445

source_name: CD8 SP thymocytes

value: CD8 SP thymocytes


title: SP4_Mouse300_SeqID_73438


title: DN_Mouse300_SeqID_73436

source_name: DN thymocytes

value: DN thymocytes


title: DP_Mouse4220_SeqID_73443


title: na_2

city: Vancouver

first: Mark

middle: Steven

last: Cembrowski

state: BC

address: 2350 Health Sciences Mall

department: Cellular and Physiological Sciences

country: Canada

institute: University of British Columbia

description:
processed data file:
gene_exp.diff
genes.read_group_tracking
genes.fpkm_tracking

library_source: transcriptomic

data_processing:
As described in methods of manuscript
Genome_build: mm9
Supplementary_files_format_and_content: Tab delimited files containing FPKM values and pairwise DE calls for population-level RNA-seq, as well as tab delimited files for single-cell quanitification

molecule: total RNA

source_name: subPCs projecting to NA

extract_protocol:
Manual sorting to purify for fluorescent neurons from microdissected slices was performed according to previous methods (Hempel et al., 2007).
As described in methods of manuscript.

tag: location

value: Subiculum

value: Subiculum pyramidal cell

tag: sample type

value: bulk


title: SP8_Mouse300_SeqID_73439


title: SP8_Mouse4144_SeqID_73433


title: DP_Mouse300_SeqID_73437


title: SP4_Mouse4144_SeqID_73432


title: DP_Mouse4144_SeqID_73431


title: SP4_Mouse302_SeqID_73450


title: DN_Mouse302_SeqID_73448


title: CLL-03_1088_Control

status: Public on Apr 03 2018

city: New Orleans

first: Nakhle

last: Saba

state: LA

address: 1415 Tulane Ave, Room 118

department: Internal Medicine/Hematology

institute: Tulane University

description:
processed data file:
CLL-1088_TreatedvsControl.results.txt

data_processing:
Base calling using Illumina HiSeq Control Software v.3.3.67
Paired-end reads aligned to reference transcriptome and expression values calculated using RSEM v.1.2.25 using default bowtie1 aligner with parameters rsem-calculate-expression -p 24 --paried-end --no-bam-output --append-names.  Genes.results files include read counts and normalized expression values for each transcript.
Differential expression testing performed using EBSeq v.1.2.0
Genome_build: Homo sapiens GRCh38
Supplementary_files_format_and_content: Tab-delimited text files ending in ".genes.results.txt" were generated using RSEM and include read counts and expression values for each transcript.  Tab-delimted text files ending in ".results.txt" were generated using EBSeq and include posterior probabilities that a transcript is equally or differentially expressed as well as posterior and real fold changes.

organism: Homo sapiens

growth_protocol: Primary CLL cells were incubated with or without the MALT1 inhibitor MI-2 for 8h in RPMI + 10% FBS

extract_protocol:
Total RNA was extracted from CD-19 purified CLL PBMC’s using standard protocols of the RNeasy kit from Qiagen
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 2 μM of MI-2 for 8h or an equivalent ammount of DMSO (control)

value: Chronic Lymphocytic Leukemia (CLL) Primary Cells

tag: purification

value: CD19-selected on-column

tag: treated with

value: none (untreated control)

tag: fresh at purification (not from viably frozen)

value: yes


title: CLL-11_1064_Treatment

description:
processed data file:
CLL-1064_TreatedvsControl.results.txt

value: 2 µM MI-2 for 8hrs


title: DN_Mouse4144_SeqID_73430


title: CLL-07_1074_Control

description:
processed data file:
CLL-1074_TreatedvsControl.results.txt


title: CLL-03_1088_Treatment


title: CLL-11_1064_Control


title: Ly6clow/CX3CR1high_day30_R2

city: Madrid

first: Fatima

last: Sanchez-Cabo

address: Melchor Fernandez Almagro

country: Spain

institute: CNIC

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequencing adaptor contaminations were removed from reads using cutadapt software (version 1.3) and the resulting reads were mapped and quantified on the transcriptome (GRCm38) using RSEM (version 1.2.20)
Estimated counts from RSEM were normalized applying the trimmed mean of M-values (TMM) method from edgeR (version 3.14.0)
Resulting log2 counts per million (CPM) were used as proxy of gene expression
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include log2CPMs for each sample

source_name: Cardiac macrophages

extract_protocol:
Total RNA was isolated from three independent biological replicates using miRNeasy Micro Kit with RNeasy MinElute Spin Columns (Qiagen) with DNaseI treatment.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cryoinjury was used as myocardial infarction model. Animals were sacrificed by CO2 inhalation 3, 7 and 30 days post-MI. Samples from healthy animals were not subjected to any surgery and were included as control.

tag: tissue

value: Heart

value: 2-3 month

tag: condition

value: 30 days post cryoinjury


title: Ly6clow/CX3CR1high_day30_R1


title: Ly6clow/CX3CR1high_day7_R2

value: 7 days post cryoinjury


title: Ly6chigh/CX3CR1low_day3_R3

value: 3 days post cryoinjury


title: Ly6clow/CX3CR1high_day7_R1


title: MVP Human Brain Total RNA (Agilent, cat 540005) - Positive Control 45

city: Durham

first: David

last: Severson

state: North Carolina

address: 2301 Erwin Road

department: Department of Surgery

institute: Duke University Health System

description:
Smartseq2 on wells containing dilute whole brain and ERCC spike-in molecules
raw_counts.tsv
brainandblanks_adjustedcpm_counts.tsv
brainonly_adjustedcpm_counts.tsv

data_processing:
Libraries were mapped to hg19 using STAR v2.5.2a with the GENCODE (release 25) annotation.
Aligned reads were filtered to remove exact position duplicates.
Transcriptome features were counted using HTseq with the intersection-strict parameter.
Genes were removed with zero observations across all samples to produce the raw_counts.tsv file.
An adjusted cpm normalization was applied as described by Hicks et al. using edgeR v3.12.1. The normalization was applied across all 93 samples to yield the file brainandblanks_adjustedcpm_counts.tsv and across only brain total RNA samples to yield the processed file brainonly_adjustedcpm_counts.tsv.
Genome_build: hg19
Supplementary_files_format_and_content: The raw_counts.tsv contains the feature counts without normalization for all 93 samples. The brainandblanks_adjustedcpm_counts.tsv file contains the adjusted cpm normalized counts for all 93 samples, and the brain_only_adjustedcpm_counts.tsv contains the adjusted cpm normalized counts restricted to the samples obtained from dilute total brain RNA. In all three tab-delimited count matrix files, the columns are samples and the rows are ENSEMBL gene id tags.

source_name: brain

extract_protocol:
ERCC spike-in standards and either water or dilute whole brain total RNA (Agilent Technologies, catalog #540005) were converted to cDNA using Smartseq2 protocol.
Libraries were prepared using Fludigm’s recommendations for Illumina NexteraXT at ¼ volume with minor modifcations.
Single cell RNA-sequencing

value: brain

value: Total RNA (diluted to 10pg/μL)

tag: treatment

value: positive control


title: MVP Human Brain Total RNA (Agilent, cat 540005) - Positive Control 46


title: MVP Human Brain Total RNA (Agilent, cat 540005) - Positive Control 48


title: MVP Human Brain Total RNA (Agilent, cat 540005) - Positive Control 43


title: Ly6chigh/CX3CR1low_day3_R2


title: MVP Human Brain Total RNA (Agilent, cat 540005) - Positive Control 42


title: MVP Human Brain Total RNA (Agilent, cat 540005) - Positive Control 41


title: Ly6chigh/CX3CR1low_day3_R1


title: MVP Human Brain Total RNA (Agilent, cat 540005) - Positive Control 40


title: Ly6clow/CX3CR1high_day0_R2

value: uninfarcted heart


title: MVP Human Brain Total RNA (Agilent, cat 540005) - Positive Control 39


title: MVP Human Brain Total RNA (Agilent, cat 540005) - Positive Control 47


title: Ly6clow/CX3CR1high_day0_R3


title: CLL-07_1074_Treatment


title: Ly6clow/CX3CR1high_day30_R3


title: Ly6clow/CX3CR1high_day0_R1


title: Ly6clow/CX3CR1high_day7_R3


title: MVP Human Brain Total RNA (Agilent, cat 540005) - Positive Control 38


title: MVP Human Brain Total RNA (Agilent, cat 540005) - Positive Control 36


title: MVP Human Brain Total RNA (Agilent, cat 540005) - Positive Control 37


title: MVP Human Brain Total RNA (Agilent, cat 540005) - Positive Control 35


title: MVP Human Brain Total RNA (Agilent, cat 540005) - Positive Control 34


title: MVP Human Brain Total RNA (Agilent, cat 540005) - Positive Control 44


title: MVP Human Brain Total RNA (Agilent, cat 540005) - Positive Control 32


title: MVP Human Brain Total RNA (Agilent, cat 540005) - Positive Control 30


title: MVP Human Brain Total RNA (Agilent, cat 540005) - Positive Control 29


title: MVP Human Brain Total RNA (Agilent, cat 540005) - Positive Control 28


title: MVP Human Brain Total RNA (Agilent, cat 540005) - Positive Control 27


title: MVP Human Brain Total RNA (Agilent, cat 540005) - Positive Control 25


title: MVP Human Brain Total RNA (Agilent, cat 540005) - Positive Control 21


title: MVP Human Brain Total RNA (Agilent, cat 540005) - Positive Control 24


title: MVP Human Brain Total RNA (Agilent, cat 540005) - Positive Control 22


title: MVP Human Brain Total RNA (Agilent, cat 540005) - Positive Control 18


title: MVP Human Brain Total RNA (Agilent, cat 540005) - Positive Control 26


title: MVP Human Brain Total RNA (Agilent, cat 540005) - Positive Control 17


title: MVP Human Brain Total RNA (Agilent, cat 540005) - Positive Control 23


title: MVP Human Brain Total RNA (Agilent, cat 540005) - Positive Control 19


title: rpoB-hypoxia_rep1

city: Baltimore

first: Petros

middle: Constantine

last: Karakousis

state: MD

address: 733 North Broadway

department: Department of Infectious Diseases

institute: Johns Hopkins University School of Medicine

data_processing:
Base calls performed using Casava v1.8.2.
EDGE-pro v1.3.1 with default settings was used to align reads to the CDC1551 genome and output *.rpkm files. bash was used to concatenate the multiple files (one per contig) into a single *.rpkm file per sample. The edgeToDeseq.perl script provided with EDGE-pro was used to combine these *.rpkm files into a single deseqFile (for input into DESeq2).
R with DESeq2 v1.16.1 was used to compute log2FC and p-values for all comparisons.
Genome_build: Mycobacterium tuberculosis CDC1551 (GenBank assembly accession: GCA_000669715.1)
Supplementary_files_format_and_content: *.rpkm files are plain text and contain counts of reads mapping to each gene (and RPKM) as generated by EDGE-pro (concatenated with bash). *.csv files are plain text (comma-separated-values format) generated by custom R scripts with DESeq2. The *.csv files report high-level comparisons between the stress conditions (PBS, hypoxia, phosphate-depletion) and rich medium condition (7H9) along with other useful information.

organism: Mycobacterium tuberculosis

source_name: rpoB-hypoxia

growth_protocol: Bacteria were grown to log phase in rich medium (7H9) and reimmersed in PBS/0.05% Tween-80 (PBS), Dubos-Tween-Albumin (hypoxia), or 7H9 medium without phosphate (Phosphate-depleted). See Methods section of papers for additional details.

extract_protocol:
Bacteria were spun down at 4C and immersed in Trizol. Mixture was then beat-beated for 4 minutes. Chloroform:Isoamyl (24:1) was used to extract the RNA. Turbo DNAse was used to remove remaining gDNA.
RNA was converted to cDNA and an NGS library was constructed using the Encore Complete Prokaryotic RNA-Seq DR Mulitplex Systems 1-8 and 9-16 kit from NuGen (Part No. 0326 and 0327).

tag: stress condition

value: rpoB-hypoxia


title: rpoB-Phosphate-depleted_rep3

source_name: rpoB-Phosphate-depleted

value: Phosphate-depleted


title: rpoB-hypoxia_rep2


title: MVP Human Brain Total RNA (Agilent, cat 540005) - Positive Control 20


title: MVP Human Brain Total RNA (Agilent, cat 540005) - Positive Control 16


title: rpoB-Phosphate-depleted_rep2


title: rpoB-Phosphate-depleted_rep1


title: MVP Human Brain Total RNA (Agilent, cat 540005) - Positive Control 15


title: MVP Human Brain Total RNA (Agilent, cat 540005) - Positive Control 14


title: rpoB-PBS_rep2

source_name: rpoB-PBS

value: rpoB-PBS


title: MVP Human Brain Total RNA (Agilent, cat 540005) - Positive Control 12


title: MVP Human Brain Total RNA (Agilent, cat 540005) - Positive Control 13


title: MVP Human Brain Total RNA (Agilent, cat 540005) - Positive Control 33


title: MVP Human Brain Total RNA (Agilent, cat 540005) - Positive Control 11


title: rpoB-7H9_rep4


title: rpoB-PBS_rep1


title: MVP Human Brain Total RNA (Agilent, cat 540005) - Positive Control 31


title: MVP Human Brain Total RNA (Agilent, cat 540005) - Positive Control 10


title: rpoB-7H9_rep3


title: rpoB-7H9_rep2


title: MVP Human Brain Total RNA (Agilent, cat 540005) - Positive Control 9


title: Blank - Negative Control 45

description:
Smartseq2 on wells containing only water and ERCC spike-in molecules
raw_counts.tsv
brainandblanks_adjustedcpm_counts.tsv

organism: other sequences

source_name: water

value: blank

value: water

value: negative control


title: hypoxia_rep2

source_name: hypoxia

value: hypoxia


title: MVP Human Brain Total RNA (Agilent, cat 540005) - Positive Control 7


title: Blank - Negative Control 44


title: hypoxia_rep1


title: rpoB-7H9_rep1


title: MVP Human Brain Total RNA (Agilent, cat 540005) - Positive Control 5


title: MVP Human Brain Total RNA (Agilent, cat 540005) - Positive Control 8


title: MVP Human Brain Total RNA (Agilent, cat 540005) - Positive Control 6


title: Blank - Negative Control 43


title: P1WT3treated_HNGJVAFXX_AGTCAA

city: Bentley

first: Irina

last: Kuznetsova

state: WA

address: Building 304, Kent Street

department: The Centre for Crop and Disease Management

country: Australia

institute: Curtin University

data_processing:
Alignmnet with HISAT2 2.0.5
Alignments were filtered to retain only properly paired, primary alignments with SAMtools 1.5
Read pairs that aligned to the mitochondria were realigned to the mitochondrial genome sequence with with HISAT2 2.0.5 (--no-spliced-alignment)
Gene-level counts were produced with featureCounts 1.5.1 (--largestOverlap -s 2)
Differential expression analysis was performed with DESeq2 1.16.1 (padj<0.05 considered significant)
GO for control samples were achived with goseq 1.28.0, R package
Statistics against mitochondrial genome positions were calculated with pysamstats 1.0.1 Python utility (pysamstats –fasta –type variation_strand)
Quantification of pseudouridylation was performed as described by Antonicka et al.2017
Genome_build: mm10

source_name: WT3 CMC treated

growth_protocol: Total RNA isolated from hearts

extract_protocol: standart TruSeq library preparation

treatment_protocol: Total heart RNA was isolated and cytoplasmic rRNA depletion was performed using a Ribo-Zero rRNA removal kit (Illumina). CMC (N-cyclohexyl-N’-(2-morpholinoethyl)carbodiimide methop-toluenesulfonate; Santa- Cruz Biotechnology) modification was performed as described by Antonicka et.al. (Antonicka et al., 2017).

value: heart

value: Wild type


title: Blank - Negative Control 42


title: Phosphate-depleted_rep2

source_name: Phosphate-depleted


title: Phosphate-depleted_rep1


title: MVP Human Brain Total RNA (Agilent, cat 540005) - Positive Control 4


title: Blank - Negative Control 40


title: Blank - Negative Control 41


title: Phosphate-depleted_rep3


title: Blank - Negative Control 39


title: MVP Human Brain Total RNA (Agilent, cat 540005) - Positive Control 3


title: PBS_rep3

source_name: PBS

value: PBS


title: MVP Human Brain Total RNA (Agilent, cat 540005) - Positive Control 1


title: PBS_rep2


title: P1WT1treated_HNGJVAFXX_GGCTAC

source_name: WT1 CMC treated


title: P1WT2treated_HNGJVAFXX_CTTGTA

source_name: WT2 CMC treated


title: P1KO3treated_HNGJVAFXX_CCGTCC

source_name: KO3 CMC treated

value: PTCD1 knockout


title: MVP Human Brain Total RNA (Agilent, cat 540005) - Positive Control 2


title: P1KO2treated_HNGJVAFXX_ATGTCA

source_name: KO2 CMC terated


title: Blank - Negative Control 38


title: Blank - Negative Control 37


title: P1KO1treated_HNGJVAFXX_AGTTCC

source_name: KO1 CMC treated


title: Blank - Negative Control 36


title: P1WT3control_HNGJVAFXX_GATCTG

source_name: WT3 control


title: 7H9_rep2


title: P1WT2control_HNGJVAFXX_GCCAAT

source_name: WT2 control


title: Blank - Negative Control 35


title: 7H9_rep1


title: P1WT1control_HNGJVAFXX_ACAGTG

source_name: WT1 control


title: Blank - Negative Control 33


title: P1KO2control_HNGJVAFXX_CTGATC

source_name: KO2 control


title: Blank - Negative Control 32


title: Blank - Negative Control 31


title: P1KO1control_HNGJVAFXX_ACTTGA

source_name: KO1 control


title: Blank - Negative Control 30


title: Blank - Negative Control 29


title: Blank - Negative Control 27


title: Blank - Negative Control 24


title: Blank - Negative Control 28


title: 7H9_rep3


title: WT

city: Hong Kong

first: Gang

last: LI

address: Shatin

department: Department of Orthopaedics & Traumatology

country: Hong Kong

institute: The Chinese University of Hong Kong

data_processing:
Base-calling: Illumina GA Pipeline v1.5 software used for base-calling.
Filtering of raw data: Sequenced reads were trimmed for adaptor sequence, high content of unknown bases and low-quality reads. After filtering, the remaining reads are called "clean reads". Quality control were performed on clean data through drawing base composition chart and quality distribution chart.
Alignment assess: After data quality statistics, clean reads were mapped to mm9 whole genome using Bowtie (Langmead B, et al 2009)
Gene expression: Fragments Per Kilobase of Exon Per Million Fragments Mapped (FPKM) were calculated using a software package of RSEM (RNASeq by Expectation Maximization, by Li B and Dewey C N.,  2011). Briefly, the formula of FPKM is FPKM=10^6C/(NL/10^3). Given to be the expression of gene A , C to be number of fragments that are uniquely aligned to gene A , N to be total number of fragments that  are uniquely aligned to all genes, and L to be number of bases on gene A. The FPKM method is able to eliminate the influence of different  gene length and sequencing discrepancy on the calculation of gene expression
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: WT, tendon derived stem cell

growth_protocol: isolated TDSCs were cultured in low glucose Dulbecco’s modified Eagle’s medium (LG-DMEM), 10% fetal bovine serum, 100U/mL penicillin, 100 mg/mL streptomycin, and 2mM L-glutamine (all from Invitrogen, USA). Cells were passaged when the cells become confluent. Cells at passage 4 were collected for RNA-seq analysis

extract_protocol:
When the cells become confluent in 10cm dish at Passage 4, cells were collected after washing with PBS. RNA was harvested using Trizol reagent.
The total RNA samples are first treated with DNase I to degrade any possible  DNA contamination. Then the mRNA is enriched by using the oligo(dT) magnetic beads. Mixed with the fragmentation buffer, the mRNA is  fragmented into short fragments. Then the first strand of cDNA is synthesized by using random hexamer-primer. Buffer, dNTPs, RNase H and  DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End reparation and 3’-  end single nucleotide A (adenine) addition is then performed. Finally, sequencing adaptors are ligated to the fragments. The fragments are  enriched by PCR amplification. During the QC step, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used to  qualify and quantify of the sample library. The library products are ready for sequencing via Illumina HiSeqTM 2000.

treatment_protocol: no treatment for the cells

value: tail tendon derived stem cell

tag: passage

tag: genotype/variation

value: wild type


title: Blank - Negative Control 25


title: DF508-2

source_name: CFTRΔF508, tendon derived stem cell


title: Blank - Negative Control 23

source_name: water


title: Blank - Negative Control 22


title: Blank - Negative Control 26


title: DF508-1


title: Blank - Negative Control 34


title: P1KO3control_HNGJVAFXX_TAGCTT

source_name: KO3 control


title: Blank - Negative Control 21


title: Heat_treated_SK36 strain_T30_Rep3

city: Richmond

first: Fadi

middle: Elias

last: El-Rami

state: VA

address: 521 N 11th Str, wood bldg, room 424

department: Microbiology & Immunology

institute: Virginia Commonwealth University

description:
Replicate 3
Processed data file: SK36-treated-vs-Untreated-SK36.txt

data_processing:
Standard Illumina pipeline. Real Time Analysis (RTA v. 1.18.66.3) software used for image processing, intensity extraction and basecalling based on intensities. CHASTITY software used for quality filter of basecalling.
Reads obtained from RNA-sequencing were aligned against the Streptococcus sanguinis SK36 genome using Rockhopper v. 2.03.
Analyses were run on default parameter settings to obtain expression data of the treated samples compared to untreated SK36. Significance was represented by a q-value ≤ 0.01 adjusted for a false discovery rate of 1%.
Genome_build: Streptococcus sanguinis reference genome
Supplementary_files_format_and_content: SK36-treated-vs-Untreated-SK36.txt: Tab-delimited text file includes transcription and translation start/stop site, strand direction, gene name and ID, gene product, raw and normalized counts for each replicate, Reads Per Kilobase of exon per Megabase of library size (RPKM), expression, p-value and Rockhopper's adjusted q-value for the mutant expression vs. the wild-type SK36 expression.

organism: Streptococcus sanguinis SK36

source_name: Heaticillin-treated SK36 after 30 min

growth_protocol: Untreated cells were incubated at 37°C under anaerobic conditions in brain-heart infusion media and harvested at late-log phase. Other cells were heat-treated at late-log phase for either 10, 20, or 30 minutes.

extract_protocol:
Cells were lysed and RNA was extracted by FastPrep lysing matrix beads. Clean-up and DNase I treatment was conducted by QIAGEN RNeasy mini kit, according to the manufacturer's protocol. Illumina RiboZero Magnetic Kit for bacteria was used to deplete ribosomal RNA from 2 µg of total RNA.
NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs) was used for the RNA-seq library preparation according to the manufacturer’s protocol. Briefly, ribosomal-depleted RNA was fragmented followed by first-strand cDNA synthesis from random primers using ProtoScript II Reverse Transcriptase (New England BioLabs). Second strand cDNA was synthesized and purified. End repair was performed on the double-stranded cDNA and primed with the addition of 5’-phosphorylated dA-tailed ends using T4 DNA polymerase, Klenow DNA polymerase and T4 polynucleotide kinase (New England BioLabs). This was immediately followed by adaptor ligation (New England BioLabs) and purified. Samples were PCR-amplified for 12 cycles with Phusion HiFi polymerase (New England Biolabs) with paired-end primers and a randomly chosen unique barcode (NEB Next Multiplex Oligos for Illumina - Index Primers 1,2,3,5,6,8,9,10,12,22,23,25). Agencourt AMPure XP Beads (Beckman Coulter) were used for all purification steps.

tag: strain/background

tag: growth phase

value: late-log

value: Heat

tag: treatment duration

value: 30 min


title: Heat_treated_SK36 strain_T30_Rep2

description:
Replicate 2
Processed data file: SK36-treated-vs-Untreated-SK36.txt


title: Heat_treated_SK36 strain_T30_Rep1

description:
Replicate 1
Processed data file: SK36-treated-vs-Untreated-SK36.txt


title: Heat_treated_SK36 strain_T20_Rep1

source_name: Heaticillin-treated SK36 after 20 min

value: 20 min


title: Heat_treated_SK36 strain_T20_Rep3


title: Heat_treated_SK36 strain_T20_Rep2


title: Blank - Negative Control 20


title: Blank - Negative Control 19


title: Heat_treated_SK36 strain_T10_Rep3

source_name: Heaticillin-treated SK36 after 10 min

value: 10 min


title: Blank - Negative Control 18


title: Heat_treated_SK36 strain_T10_Rep2


title: PBS_rep1

source_name: PBS


title: Blank - Negative Control 17


title: Blank - Negative Control 16


title: Heat_treated_SK36 strain_T10_Rep1


title: GL

city: Chengdu

first: Yu

middle: NMN

last: Jiang

state: Sichuan

address: Shizishan road 4#

country: China

institute: Institute of Horticulture, Sichuan Academy of Agricultural Sciences

description: FPKM.txt

data_processing:
Basecalls performed using CASAVA version 1.7
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
Raw reads after quality control testing were then assembled using trinity software
count counting
Genome_build: Assemble Genome
Supplementary_files_format_and_content: TXT file contain counts for each sample

organism: Cymbidium longibracteatum

source_name: Cymbidium 'Longchangsu'with green leaf

growth_protocol: The YL and GL plants were grown for one year under controlled temperature of 25/20°C (day/night) in mericlone nursery

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: On the base of Cymbidium longibracteatu 'Longchangsu' (abbreviated as GL in this study), we induced a yellowing rhizomes group by tissue culture, thereby establishing a clonal variation of the rhizome; then, by inducing the rhizome differentiation and years of subculture, we cultivated variation plantlets with a stabile leaf art. The stabile leaf art showed verge line pattern leaves，and the new species is named as Cymbidium longibracteatu 'Longchangsu' with verge line pattern leaves(abbreviated as YL in this study ).

value: leaf

tag: phenotype

value: green

value: parent


title: YL

description: FPKM.txt

source_name: Cymbidium 'Longchangsu'with yellow leaf

value: yellow

value: mutant


title: Blank - Negative Control 15

value: blank

value: water

value: negative control


title: Untreated_SK36 strain_Rep2

source_name: Untreated SK36


title: Untreated_SK36 strain_Rep3


title: Blank - Negative Control 14


title: Blank - Negative Control 12


title: Blank - Negative Control 10


title: Blank - Negative Control 8


title: Blank - Negative Control 7


title: Blank - Negative Control 6


title: Blank - Negative Control 5


title: Blank - Negative Control 4


title: RNAseq_Setdb1 cKO iMEFs_4OHT_siDnmt1_2

status: Public on Apr 02 2018

city: Wako

first: Masaki

last: Kato

state: Saitama

address: 2-1 Hirosawa

country: Japan

institute: RIKEN

data_processing:
We aligned reads to the reference genome (UCSC mm9) using TopHat (version 2.0.12 and 2.1.1) with the exception of “-g 1”.
Mm9 Refseq gtf file was downloaded from UCSC (http://genome.ucsc.edu) in Oct 22, 2014 and applied as gene annotation file.
After obtaining the aligned bam files, the Cufflinks algorithm was used to calculate FPKM with the Refseq gtf file.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: iMEF

growth_protocol: Cells were cultured in DMEM (Nacalai: 08458-45) with MEM non-essential amino acids (Gibco: 11140-035), 2-mercaptoethanol (used at 0.1 mM, Nacalai), 10% FBS. Cells were split every three days.

extract_protocol:
Total RNA was extracted with RNeasy mini kit (QIAGEN: 74134).
RNA libraries were prepared for sequencing using Illumina TruSeq RNA Sample Prep Kit protocols

treatment_protocol: For knockdown, siRNAs targeting Dnmt1 or control siRNA was transfected into Setdb1 cKO iMEFs using RNAiMAX. Transfected cells were passaged 24 h after transfection. A second transfection was conducted with the same reagents on the following day. Cells were harvested at day 6 and RNA was isolated. For simultaneous KO of Setdb1, 4OHT was added at day 0.

tag: cell type

value: iMEF (Setdb1 cKO iMEF)

tag: treatments

value: day 6 after 4OHT treatment with Dnmt1 siRNA


title: RNAseq_Setdb1 cKO iMEFs_4OHT_siDnmt1_1


title: Blank - Negative Control 3


title: Blank - Negative Control 1


title: RNAseq_Setdb1 cKO iMEFs_4OHT_2

value: day 6 after 4OHT treatment with ctrl siRNA


title: RNAseq_Setdb1 cKO iMEFs_4OHT_1


title: RNAseq_Setdb1 cKO iMEFs_siDnmt1_2

value: Transfected with Dnmt1 siRNA


title: input_ChIPseq_Setdb1 cKO iMEFs_KO

data_processing:
Sequence reads were mapped to the Mouse genome (mm9, July 2007) using BOWTIE2 (version 2.2.3). The default BOWTIE2 mapping of multi-hits reads to one of the possible genomic locations was used.
Peak-calling: Peak detection was performed with MACS2 (version 2.1.0.20140616) (PubMed ID: 18798982) and peaks were reported in BED format (q value< 0.005).
The DeepTools package (http://deeptools.github.io) was used to compute the differences between ChIP and Input samples. bigWig files were generated using bamCompare with option arguments “–normalizeUsingRPKM –ratio subtract –binSize 10”.
Genome_build: mm9
Supplementary_files_format_and_content: bed files were generated using MACS2. bigwig files were generated using DeepTools package

extract_protocol:
The chromatin was digested with MNase. After IP, stringent washes, RNase and proteinase K treatment, DNA was extracted using PCR purification kit (QIAGEN). ChIP-seq library was prepared with KAPA hyperprep kit (KAPA biosystems) for the single read Illumina HiSeq 1500 platform.
ChIP-seq library were prepared with KAPA hyperprep kit (KAPA biosystems) for the single read Illumina HiSeq 1500 platform.

treatment_protocol: For KO 4OHT was treated for first 4days then cells were harvested at day 7

tag: time point

value: day 7 after 4OHT treatment

tag: chip antibody


title: RNAseq_Setdb1 cKO iMEFs_siCtrl_1

value: Transfected with control siRNA


title: RNAseq_Setdb1 cKO iMEFs_siDnmt1_1


title: H3K9me3_ChIPseq_Setdb1 cKO iMEFs_WT

value: no treatment


title: RNAseq_Setdb1 cKO iMEFs_siCtrl_2


title: H3K9me3_ChIPseq_Setdb1 cKO iMEFs_KO


title: Blank - Negative Control 11

tag: sample type


title: input_ChIPseq_Setdb1 cKO iMEFs_WT


title: Blank - Negative Control 9


title: Blank - Negative Control 2


title: RNAseq_Setdb1 cKO iMEFs_4OHT5_1

data_processing:
We aligned reads to the reference genome (UCSC mm9) using TopHat (version 2.0.12 and 2.1.1) with  "-g 1" parameter.
Mm9 Refseq gtf file was downloaded from UCSC (http://genome.ucsc.edu) in Oct 22, 2014 and applied as gene annotation file.
the Cufflinks algorithm was used to calculate FPKM with the Refseq gtf file, and two comparisons were done (WT vs cKO, WT vs cKO long culture)
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted with RNeasy mini kit (QIAGEN: 74134).
rRNA was removed using epicentre's Ribo-Zero rRNA Removal kit. Illumina TruSeq RNA Sample Prep Kit was used for the construction of sequencing libraries.

treatment_protocol: For KO 4OHT was treated for first 4days then cells were harvested at day 5

value: day 5 after 4OHT treatment


title: RNAseq_Setdb1 cKO iMEFs_WT_3


title: RNAseq_Setdb1 cKO iMEFs_4OHT5_2


title: RNAseq_Setdb1 KO iMEFs_long_3

value: more than 2weeks after 4OHT treatment


title: RNAseq_Setdb1 KO iMEFs_long_2


title: H3K9me3_ChIPseq_forebrain E14.5_WT2

data_processing:
Sequence reads were mapped to the Mouse genome (mm9, July 2007) using BOWTIE2 (version 2.2.3). The default BOWTIE2 mapping of multi-hits reads to one of the possible genomic locations was used.
Peak-calling: Peak detection was performed with MACS2 (PubMed ID: 18798982) and extended fragment pileup was saved into wig format.
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using MACS2

source_name: fetal forebrain E14.5

extract_protocol:
After dissection, cells were cross-linked by 5 min of 1% formaldehyde treatment at 37˚C. The chromatin was sonicated using Bioruptor UCD-250. After IP, stringent washes, reverse cross-linked and proteinase K treatment, DNA was extracted using PCR purification kit (QIAGEN).
ChIP-seq library were prepared with ChIP-seq sample prep kit (illumina) for the paired end read Illumina HiSeq 2000 platform.

treatment_protocol: Mice did not recieve any treatment

tag: strain


title: input_ChIPseq_forebrain E14.5_WT


title: RNAseq_Setdb1 cKO iMEFs_4OHT5_3


title: RNAseq_Setdb1 KO iMEFs_long_1


title: RNAseq_Setdb1 cKO iMEFs_WT_1


title: braintissue from strain ISS/IbgTejJ replicate ISS_3

city: Aurora, CO

first: Katerina

last: Kechris

state: CO

address: Mail Stop B119, 13001 E. 17th Place

department: Colorado School of Public Health

description:
size-selected RNA
RSEM_counts_NVE.csv

data_processing:
samples were aligned using Bowtie (version 1.1.1)
Fastx toolkit  was used to clip adapters and filter reads for quality (>95% Q20 bases)
quantification for statistical analyses was performed with RSEM (version 1.2.19) to estimate counts for a miRNA transcriptome consisting of the mouse miRBase database (as downloaded on 11/19/2014)
As the SAL and NVE datasets were analyzed separately, miRNA features were filtered to only include the miRNAs that had at least 3 samples with a Counts Per Million (CPM) value greater than 1 based on the RSEM quantitation in both data sets independently
Genome_build: transcript database consisting of all NM and NR mouse transcripts in RefSeq (Release 67)
Supplementary_files_format_and_content: counts

source_name: brain, right hemisphere

extract_protocol:
RNA was collected from whole brain (right hemisphere) using the RNeasy Plus Universal Midi, Mini, and minElute kits for RNA sequencing (Qiagen, Valencia, CA, USA).
Libraries were constructed using the Illumina TruSeq Small RNA Sample Prep kit (Illumina, San Diego, CA, USA).  Fragments between 20-35 bp were size selected

treatment_protocol: Storage in RNA later

value: ISS/IbgTejJ

value: Brain, right hemisphere

tag: age

value: 10 weeks

tag: Sex

value: male

tag: sequencing batch

tag: experimental treatment

value: Boris Tabakoff, Professor, University of Colorado Anschutz Medical Campus Pharmacy and Pharmaceutical Sciences Building (SOP) 12850 East Montview Boulevard, Aurora, Colorado 80045

value: tissue

value: healthy

value: RNAlater, Rneasy Plus Universal Midi,Mini, and minElute kits (Qiagen), Illumina TruSeq Small RNA sample Prep Kit

tag: description

value: Tissue sample from  Brain, right hemisphere from strain ISS/IbgTejJ to be used for miRNA extraction and sequencing


title: braintissue from strain ILS/IbgTejJ replicate ILS_2

institute: University of Colorado Anschutz Medical Campus

description:
size-selected RNA
RSEM_counts_NVE.csv

value: ILS/IbgTejJ

tag: tissue

tag: treatment

value: Tissue sample from  Brain, right hemisphere from strain ILS/IbgTejJ to be used for miRNA extraction and sequencing


title: Blank - Negative Control 13

value: blank

value: water

value: negative control


title: braintissue from strain ISS/IbgTejJ replicate S13

description:
size-selected RNA
RSEM_counts_SAL.csv

source_name: whole brain, minus cerebellum

value: Whole brain (minus cerebellum)

value: 0.01 ml/g normal saline treatment

value: Richard Radcliffe, University of Colorado, Skaggs School of Pharmacy and Pharmaceutical Sciences, Mail Stop C238, 12850 E. Montview Blvd. V20-3124, Aurora, CO 80048

value: healthy, saline treated

value: Tissue sample from  whole brain (minus cerebellum) from strain ISS/IbgTejJ to be used for miRNA extraction and sequencing


title: braintissue from strain ISS/IbgTejJ replicate S15

description:
size-selected RNA
RSEM_counts_SAL.csv

value: ISS/IbgTejJ

value: 10 weeks

value: Richard Radcliffe, University of Colorado, Skaggs School of Pharmacy and Pharmaceutical Sciences, Mail Stop C238, 12850 E. Montview Blvd. V20-3124, Aurora, CO 80050


title: braintissue from strain ILS/IbgTejJ replicate ILS_1

description:
size-selected RNA
RSEM_counts_NVE.csv

value: Brain, right hemisphere

value: male

value: Boris Tabakoff, Professor, University of Colorado Anschutz Medical Campus Pharmacy and Pharmaceutical Sciences Building (SOP) 12850 East Montview Boulevard, Aurora, Colorado 80045

value: tissue


title: braintissue from strain ISS/IbgTejJ replicate ISS_4

description:
size-selected RNA
RSEM_counts_NVE.csv

value: healthy

value: RNAlater, Rneasy Plus Universal Midi,Mini, and minElute kits (Qiagen), Illumina TruSeq Small RNA sample Prep Kit

value: Tissue sample from  Brain, right hemisphere from strain ISS/IbgTejJ to be used for miRNA extraction and sequencing


title: braintissue from strain ILS/IbgTejJ replicate S15

description:
size-selected RNA
RSEM_counts_SAL.csv

value: ILS/IbgTejJ

value: Richard Radcliffe, University of Colorado, Skaggs School of Pharmacy and Pharmaceutical Sciences, Mail Stop C238, 12850 E. Montview Blvd. V20-3124, Aurora, CO 80047

value: Tissue sample from  whole brain (minus cerebellum) from strain ILS/IbgTejJ to be used for miRNA extraction and sequencing


title: braintissue from strain ISS/IbgTejJ replicate S14

description:
size-selected RNA
RSEM_counts_SAL.csv

value: Whole brain (minus cerebellum)

value: 0.01 ml/g normal saline treatment

value: Richard Radcliffe, University of Colorado, Skaggs School of Pharmacy and Pharmaceutical Sciences, Mail Stop C238, 12850 E. Montview Blvd. V20-3124, Aurora, CO 80049


title: braintissue from strain ILS/IbgTejJ replicate ILS_3

description:
size-selected RNA
RSEM_counts_NVE.csv

value: Tissue sample from  Brain, right hemisphere from strain ILS/IbgTejJ to be used for miRNA extraction and sequencing


title: H3K9me3_ChIPseq_forebrain E14.5_WT1

value: no treatment


title: Paneth Enriched Organoid

city: Cambridge

first: Jose

last: Ordovas-Montanes

state: MA

address: 77 Massachusetts Ave

department: IMES

institute: Massachusetts Institute of Technology

data_processing:
Illumina bcl2fastq2.17.1.14 was used to generate fastqs from bcl files
STAR was used to align data to app
Aligned reads were collapsed to cell barcodes and UMIs using DropSeq Tools
Digitial Gene Expression matrices (See Processed Data) were generated using DropSeq Tools
Genome_build: mm10
Used R Script (GEO_Merge_Script.R) to merge three samples together before input into Seurat.

extract_protocol:
Seq-Well Protocol: Samples were processed as described in Gierahn et al. Nature Methods 2017.
Detailed Protocol: Nature Protocols Exchange DOI: 10.1038

value: Intestinal organoids

tag: exposure

value: ENR+CD


title: Untreated_SK36 strain_Rep1

tag: strain/background

tag: growth phase

value: late-log


title: ISC Enriched Organoid

source_name: OrgISC

value: ENR+CV


title: braintissue from strain ILS/IbgTejJ replicate S13

description:
size-selected RNA
RSEM_counts_SAL.csv

value: 10 weeks

value: male

value: Richard Radcliffe, University of Colorado, Skaggs School of Pharmacy and Pharmaceutical Sciences, Mail Stop C238, 12850 E. Montview Blvd. V20-3124, Aurora, CO 80045

value: healthy, saline treated


title: Control Organoid

value: ENR


title: braintissue from strain ILS/IbgTejJ replicate S14

description:
size-selected RNA
RSEM_counts_SAL.csv

value: ILS/IbgTejJ

value: Richard Radcliffe, University of Colorado, Skaggs School of Pharmacy and Pharmaceutical Sciences, Mail Stop C238, 12850 E. Montview Blvd. V20-3124, Aurora, CO 80046

value: tissue

value: RNAlater, Rneasy Plus Universal Midi,Mini, and minElute kits (Qiagen), Illumina TruSeq Small RNA sample Prep Kit


title: RNAseq_Setdb1 cKO iMEFs_WT_2

value: iMEF (Setdb1 cKO iMEF)


title: braintissue from strain ISS/IbgTejJ replicate ISS_2

description:
size-selected RNA
RSEM_counts_NVE.csv

value: ISS/IbgTejJ

value: Brain, right hemisphere

value: Boris Tabakoff, Professor, University of Colorado Anschutz Medical Campus Pharmacy and Pharmaceutical Sciences Building (SOP) 12850 East Montview Boulevard, Aurora, Colorado 80045

value: healthy

value: Tissue sample from  Brain, right hemisphere from strain ISS/IbgTejJ to be used for miRNA extraction and sequencing


title: Whole 28 hpf embryos, replicate 3

status: Public on Apr 01 2018

city: Pittsburgh

first: Charles

middle: A

last: Ettensohn

state: PA

address: 4400 Fifth Avenue

institute: Carnegie Mellon University

description:
DNase-seq
U0126_Control_RPS.bed

data_processing:
Adapter sequences were trimmed using Cutadapt (v1.9)
Reads were mapped to the S. purpuratus genome v 3.1 using Bowtie2 (v2.1.0) with default parameters
Bowtie2 SAM output format was converted to BAM format and PCR duplications were removed and read counts were equalized using Samtools v1.3
Bedtools (v2.19.1) was used to convert the BAM output into BED format.
Fseq (v1.85) was used to call peaks using parameters -f 0 and -t 2
The fraction of reads within peaks (the FRiP score) was calculated using Bedtools (v2.19.1) by extracting and counting all reads within peaks and dividing by the total number of reads mapped.
Separate reference peak sets (RPSs) were generated for the DNase-seq and ATAC- seq data by first identifying all replicate peaks that overlapped by at least 75% non-reciprocally and then merging all such peaks across samples separately for the DNase-seq or ATAC-seq data using Bedops (v2.4.2)
Read counts corresponding to peaks in the RPS were generated using HTSeq (v0.6.0)
Differential peaks were identified using DESeq2
Genome_build: Strongylocentrotus purpuratus genome version 3.1 (Spur_3.1)
Supplementary_files_format_and_content: BED files contain peaks called by Fseq (v1.85), and the reference peak set (RPS) generated by merging the peaks using Bedops(v2.4.2). .txt files contain read counts corresponding to the peaks in the RPS, generated by HTseq (v0.6.0).

organism: Strongylocentrotus purpuratus

source_name: 28 hours post fertilization embryo

growth_protocol: S. purpuratus eggs fertilized and cultured in artificial sea water at 15 degrees Celcius

extract_protocol:
Nuclei were extracted using lysis buffer washes and DNase-seq was performed: 10 million nuclei per replicate were digested with 0-400 units DNase 1 for 3 mins at 37 degrees. Digested fragements < 500 bp were purified.
Truseq library kit used to generate Illumina HiSeq sequencing library by USC Epigenome Center

tag: developmental stage

value: 28 hours post fertilization


title: U0126-treated PMC(-) 28 hpf embryos, replicate 2

description:
DNase-seq
U0126_Control_RPS.bed

treatment_protocol: 10 uM of U0126 in DMSO was added at the 2-cell stage and PMC(-) embryos were collected at 28 hpf


title: U0126-treated PMC(-) 28 hpf embryos, replicate 1

description:
DNase-seq
U0126_Control_RPS.bed


title: U0126-treated PMC(-) 28 hpf embryos, replicate 3

description:
DNase-seq
U0126_Control_RPS.bed


title: WT #2

city: Daejeon

first: Gou Young

last: Koh

address: 291  Daehak-ro

department: Center for Vascular Research

country: South Korea

institute: Institute for Basic Science

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: Endothelial cells in mouse infarct heart.

growth_protocol: To explore roles of Angiopoietin-2 in endothelial cells of myocardial infarct border, we generated Angpt2i∆/∆ mouse by crossing Angpt2fl/fl mouse with UBC-Cre-ERT2 mouse.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: All mice subject to myocardial infarct (MI) or Sham procedure were 8-week to 10-week old male C57BL/6 mice. For Angpt2i∆/∆ mice, 4-week-old male mice were injected with tamoxifen (2 mg, for consecutive injections, i.p.) to induce cre recombination.

value: FACS sorted Heart endothelial cells

value: 8-week to 10-week old

tag: genotype

value: wild-type

tag: cell type

value: Infarct border zone endothelial cells were isolated from C57BL/6 mice (n=3-4), then were digested, enriched for CD45- cells and sorted for hematopoietic lineage marker-/CD31+ endothelial cells.


title: WT #4


title: A2Δ #2

value: UBC-Cre-ERT2 Angpt2fl/fl


title: A2Δ #1


title: A2Δ #3


title: 41116: shT52-2_#1

city: Vienna

first: Stefan

last: Benke

state: Vienna

address: Dr. Bohr-Gasse 9

country: Austria

institute: Max F. Perutz Laboratories, University of Vienna

data_processing:
The reads obtained from the instrument were base called using the instrument manufacturer’s base calling software
Demultiplexing was performed using Illumina2bam
The reads were aligned against the Homo sapiens reference genome (UCSC hg19 release) with STAR version 2.5.1b using the 2-pass alignment mode and reads mapping to ribosomal RNAs were removed
The number of reads aligned within each gene was counted using the HTSeq tool (version 0.5.4p3)
Counts were normalized using the TMM normalization method of the edgeR R/Bioconductor package (R version 3.3.1, Bioconductor version 3.3)
Differential expression analysis was performed using Deseq2 (v. 1.10.1) on data normalized to effective library size using an adjusted p-value cutoff of 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: processed_file.csv: comma separated values file format. Contains read counts as put out by Htseq normalized to effective library size. 41109_geneCounts.txt - 41120_geneCounts.txt: text file. Contain read counts as put out by Htseq.

source_name: U87MG glioblastoma cells

growth_protocol: U87MG cells were cultured using DMEM supplemented with 10% fetal calf serum and 1% penicillin/streptomycin. Stably transduced cells were cultured in the presence of 3µg/ml puromycin.

extract_protocol:
Total RNA was isolated using Trizol reagent according to the manufacturer's recommendations.
1µg of RNA was used for polyA enrichment and Next Generation Sequencing library preparation using a SENSE mRNA-Seq library prep kit V2 (Lexogen, 001.24) according to the manufacturer’s recommendations

treatment_protocol: For inducion of shRNA expression, cells were treated with doxycycline (2µg/ml) for five days.

value: U87MG glioblastoma cells

tag: shRNA type

value: TRIM52 targeting

tag: replicate

tag: shRNA number


title: MLL4_Female_KDM6A-WT_ChIP-Seq_R1

city: Washington

first: Alexandros

last: Tzatsos

state: DC

address: 800 22nd St NW SEH 8850

department: GW Cancer Center

institute: George Washington University

data_processing:
1. All the raw sequencing data were mapped to Mus musculus genome assembly NCBI build 37 using bowtie 1.1.2. Only the uniquely aligned reads were kept.
2. Aligned reads were used to call peaks using SICER v1 with window size 200 bp and FDR 1e-8 for histone modifications and FDR 1e-4 for Kdm6a and Kmt2d. 200bp, 400bp, 600bp were used as the gap size for H3K4me3, H3K27ac, and H3K27me3 respectively. 600 bp was used for the fragment size.Reads with the same coordinate information were considered as duplicates and were discarded.
Genome_build: NCBI build 37, mm9
Supplementary_files_format_and_content: Processed data are the peaks in BED4 format (chrom+start+end+intensity).

source_name: pancreas

growth_protocol: F12/DMEM supplemented with EGF

extract_protocol: Libraries were prepared according to Illumina's protocol and libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: antibody

value: Cell line established from K6A null murine pancreatic cancer


title: 41120: shT52-2_#2


title: WT #1

tag: strain

tag: age


title: 41118: shNT-2_#2

value: non-targeting control


title: 41119: shT52-1_#2


title: 41109: shNT-1_#1


title: 41115: shT52-1_#1


title: MLL4_Female_KDM6A-KO_ChIP-Seq_R1


title: Whole 28 hpf embryos, replicate 1

description:
DNase-seq
U0126_Control_RPS.bed


title: Whole 28 hpf embryos, replicate 2

description:
DNase-seq
U0126_Control_RPS.bed


title: H3K27me3_Female_KDM6A-WT_ChIP-Seq_R1


title: WT #3


title: E10.5 RET NULL GUT REP3

first: Sumantra

last: Chatterjee

address: 733 N Broadway, Room 572

department: Institute of Genetic Medicine

description: E10.5 RET_WT_NULL.txt

data_processing:
Broad Institute’s Picard Pipeline was used for de-multiplexing and data aggregation
The resultant BAM files were sorted and conveted to fastq files for each paierd end using bam2fastq-1.1.0
The files were thenmapped to the mouse genome mm10 index file uisng Tophat2 with the following attributes --library-type fr-unstranded -G (unstranded and pair end)
Successfully mapped reads were used to assemble transcripts and estimate their abundances ((FPKM) using Cufflinks
assembled transcripts  for replicates for each genotype were merged using cuffmerge and differential expression test was done using cuffdiff
Genome_build: mm10
Supplementary_files_format_and_content: Cuffdiff output file in txt format showing FPKM values for each gene at both genotypes plus test statistics, fold change and significance

source_name: Gut

extract_protocol:
Guts were dissected out in cold leibovitz medium and RNA was extracted and cleaned using a Trizol Rneasy column hybrid method
cDNA  was prepared  by oligo dT beads to select mRNA from the total RNA sample followed by heat fragmentation and cDNA synthesis from the RNA template as part of the Illumina Tru Seq™ RNA Sample Preparation protocol. The resultant cDNA then was used for library preparation (end repair, base ‘A’ addition, adapter ligation, and enrichment) using standard Illumina protocols.

tag: development stage

tag: genotype/variation

value: Ret null


title: E10.5 RET NULL GUT REP1

description: E10.5 RET_WT_NULL.txt


title: E10.5 RET NULL GUT REP2

description: E10.5 RET_WT_NULL.txt


title: H3K4me3_Female_KDM6A-WT_ChIP-Seq_R1


title: E10.5 WT GUT REP3

description: E10.5 RET_WT_NULL.txt

value: Wildtype


title: H3K27ac_Female_KDM6A-WT_ChIP-Seq_R1


title: H3K4me1_Male_KDM6A-KO_ChIP-Seq_R1


title: E10.5 WT GUT REP2

description: E10.5 RET_WT_NULL.txt


title: E10.5 WT GUT REP1

description: E10.5 RET_WT_NULL.txt


title: H3K4me1_Female_KDM6A-WT_ChIP-Seq_R1


title: 41117: shNT-1_#2


title: 41114: shNT-2_#1


title: cstKDM6A_Female_KDM6A-WT_ChIP-Seq_R1


title: cstKDM6A_Female_KDM6A-KO_ChIP-Seq_R1


title: H3K4me1_Female_KDM6A-KO_ChIP-Seq_R1


title: Input_Female_KDM6A-WT_ChIP-Seq_R1

value: IgG


title: PDX 2_mm9

city: Toronto

first: Daniel

last: De Carvalho

state: ON

address: 101 College St

institute: Princess Margaret Cancer Centre

description:
raw data aligned to mm9
plasma cfDNA from mice with Colorectal Cancer PDX

data_processing:
library strategy: MeDIP-seq and cfMeDIP-seq
FastQ files for these samples  were sequenced on Illumina HiSeq 2000 and Illumina HiSeq 2500.
FastQ files were aligned to hg19 and mm9 using Bowtie1 with default parameters to yield raw SAM files.
SAM files were converted to raw BAM files using Samtools; unaligned reads were retained.
Genome_build: hg19; mm9
Supplementary_files_format_and_content: processed data files not provided for PDX samples. Conclusions for these samples were based solely on alignments. The raw data for these samples are represented by BAM files. One bam file was aligned to hg19. The other bam file was aligned to mm9.

growth_protocol: HCT116 cells were grown with McCoy Media supplemented with 10% FBS and 1% Penicillin/Streptomycin in 75cm2 flasks at 37˚C and 5% CO2. MM1.S cells were grown with IMDM medium supplemented with 5% FBS in 75cm2 flasks at 37˚C and 5% CO2.

extract_protocol:
The genomic DNA of the collected cells were extracted using Thermofisher PureLink® Genomic DNA Kit and eluted in EB buffer, prior to being sheared using a Covaris M220 shearing instrument to mimic cell free DNA size distribution. antibody: MeDIP kit manufacturer Diagenode; Kit Catalog #: C02010021; the lot number of antibodies include: Lot GF-003, LotD006
The libraries were prepared using the Kapa Hyper Prep Kit.

value: plasma

value: cell free DNA


title: PDX 1_hg19

description:
raw data aligned to hg19
plasma cfDNA from mice with Colorectal Cancer PDX


title: Input Control 2_mm9

description:
raw data aligned to mm9
plasma cfDNA from input control mice

source_name: plasma cfDNA from input control mice


title: PDX 2_hg19

source_name: plasma cfDNA from mice with Colorectal Cancer PDX


title: H3K27ac_male_KDM6A-WT_ChIP-Seq

data_processing:
1. All the raw sequencing data were mapped to Mus musculus genome assembly NCBI build 37 using bowtie 1.1.2. Only the uniquely aligned reads were kept.
2. Aligned reads were used to call peaks using SICER v1 using window size 200 bp and FDR 1e-8. 200Bp, 400bp, 600bp were used as the gap size for H3K4me3, H3K27ac, and H3K27me3 respectively. Reads with the same coordinate information were considered as duplicates and were discarded. Please contact us if you need the aligned BED or BAM file for the input library.
Genome_build: NCBI build 37, mm9
Supplementary_files_format_and_content: Processed data are the peaks in BED4 format (chrom+start+end+intensity).

value: mixed C57BL/6-SV129


title: Input Control 1_mm9


title: Input Control 1_hg19

description:
raw data aligned to hg19
plasma cfDNA from input control mice


title: H3K27ac_male_KDM6A-KO_ChIP-Seq


title: H3K27ac_Female_KDM6A-KO_ChIP-Seq


title: H3K4me1_Male_KDM6A-WT_ChIP-Seq_R1


title: H3K27me3_male_KDM6A-WT_ChIP-Seq


title: H3K27me3_male_KDM6A-KO_ChIP-Seq


title: H3K4me3_male_KDM6A-KO_ChIP-Seq


title: H3K27me3_Female_KDM6A-KO_ChIP-Seq


title: PLU1_ChIPSeq

city: Chicago

first: Elizaveta

middle: V

last: Benevolenskaya

state: IL

address: 900 S. Ashland Ave.

department: Biochemistry and Molecular Genetics

institute: University of Illinois at Chicago

description: Chromatin IP against PLU1

data_processing:
Alignment: Sequence reads were obtained using the Illumina Genome Analyzer Pipeline and reads were mapped to the human (March, 2006) genomes (NCBI36/hg18) using BOWTIE aligner program (version 0.11.3) (http://bowtie-bio.sourceforge.net/index.shtml) (Ref: Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25.) All reads mapping uniquely with two or fewer mismatches were retained.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)

source_name: Chromatin IP against PLU1

growth_protocol: MCF7 breast adenocarcinoma cells were grown in DMEM (Invitrogen) containing 10% fetal bovine serum (FBS) and antibiotics.

extract_protocol: ChIP and genomic library preparation was performed as described (Beshiri, M.L, A. Islam A, D.C. DeWaal, W.F. Richter, Love J, N. Lopez-Bigas, and E.V. Benevolenskaya. 2010. Genome-wide Analysis using ChIP to Identify Isoform-specific Gene Targets. JoVE. 41. http://www.jove.com/index/details.stp?id=2101, doi: 10.3791/2101).  After adapter ligation DNA was PCR amplified with Illumina primers for 18 cycles and library fragments of ~400 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: cell line

value: breast adenocarcinoma cells

tag: cell differnetiation protocol

value: MCF7 [vehicle]

tag: cell treatment

value: Cells were hormone-deprived for at least 3 days and then treated with vehicle for 45 minutes.

tag: chip antibody

value: 4439 (Anti-JARID1B antibody, ABE239, EMD Millipore)


title: RBP2_E2_ChIPSeq_1

description: Chromatin IP against RBP2

source_name: Chromatin IP against RBP2

value: MCF7 [ER-treated]

value: Cells were hormone-deprived for at least 3 days and then treated with 100 nM 17Î²-estradiol (Sigma) for 45 minutes.

value: 2469 (non-commercial, unpublished)


title: RBP2_E2_ChIPSeq_2

description: Chromatin IP against RBP2


title: MCF7_input_gDNA

description: input DNA

source_name: input DNA


title: PDX 1_mm9

tag: tissue


title: Ulcerative colitis Colon Biopsy 8881B1 Non-Inflamed

first: William

last: Gordon

address: 1 Portland Street

institute: Pfizer Inc

data_processing:
STAR used for mapping and alignment 2.4.0k
Featurecounts used for gene quantification 1.4.6
EdgerR used for differential analysis
Genome_build: Hg38
Supplementary_files_format_and_content: .xlsx contains raw reads for all samples

extract_protocol:
Qiazol extraction of total RNA was performed according to the manufacturer's instructions.
Libraries were constructed using Illumina's Neoprep system according to the manufacturers instructions
stranded polyA based prep

treatment_protocol: Colon biopsies were placed in RNAlater and stored at -80 until processed

tag: status

value: Non-Inflamed

tag: site

value: Brigham and Women's Hospital

tag: location

value: Ascending

tag: subject


title: H3K4me3_Female_KDM6A-KO_ChIP-Seq


title: Ulcerative colitis Colon Biopsy 8881A1 Non-Inflamed


title: Ulcerative colitis Colon Biopsy 8881F2 Inflamed

value: Inflamed

value: Sigmoid


title: Ulcerative colitis Colon Biopsy 8879B1 Non-Inflamed

value: Tranverse


title: RBP2_ChIPSeq_1

description: Chromatin IP against RBP2

tag: cell type


title: RBP2_ChIPSeq_2

description: Chromatin IP against RBP2


title: Input Control 2_hg19


title: H3K4me3_male_KDM6A-WT_ChIP-Seq


title: Ulcerative colitis Colon Biopsy 8879A1 Non-Inflamed


title: Ulcerative colitis Colon Biopsy 8881 E2 Inflamed

source_name: Colon_8881 E2


title: Ulcerative colitis Colon Biopsy 8874B1 Non-Inflamed


title: Ulcerative colitis Colon Biopsy 8878B1 Non-Inflamed


title: Ulcerative colitis Colon Biopsy 8878 E4 Inflamed

source_name: Colon_8878 E4


title: Ulcerative colitis Colon Biopsy 8874D1 Inflamed

value: Large


title: Ulcerative colitis Colon Biopsy 8878D2 Inflamed


title: Ulcerative colitis Colon Biopsy 8855D1 Non-Inflamed

value: Descending


title: Ulcerative colitis Colon Biopsy 8855D2 Non-Inflamed


title: Ulcerative colitis Colon Biopsy 8855A3 Inflamed


title: Ulcerative colitis Colon Biopsy 8874A1 Non-Inflamed


title: Ulcerative colitis Colon Biopsy 8879D1 Inflamed


title: Ulcerative colitis Colon Biopsy 8874F2 Inflamed


title: Ulcerative colitis Colon Biopsy 8879 E2 Inflamed

source_name: Colon_8879 E2


title: Ulcerative colitis Colon Biopsy 8855A2 Inflamed


title: Ulcerative colitis Colon Biopsy 8854A3 Non-Inflamed


title: Ulcerative colitis Colon Biopsy 8854D2 Inflamed


title: Ulcerative colitis Colon Biopsy 8854D1 Inflamed


title: Ulcerative colitis Colon Biopsy 1214+6 Inflamed

value: Boston Children's Hospital


title: Ulcerative colitis Colon Biopsy 1214-4 Non-Inflamed


title: Ulcerative colitis Colon Biopsy 1214-3 Non-Inflamed


title: Ulcerative colitis Colon Biopsy 1192+5 Inflamed

value: Rectum


title: Ulcerative colitis Colon Biopsy 1192-3 Non-Inflamed


title: Ulcerative colitis Colon Biopsy 1192-1 Non-Inflamed


title: Ulcerative colitis Colon Biopsy 8878C1 Non-Inflamed


title: Ulcerative colitis Colon Biopsy 1192+6 Inflamed


title: Ulcerative colitis Colon Biopsy 1077+4 Inflamed


title: Ulcerative colitis Colon Biopsy 1077+1 Inflamed


title: Ulcerative colitis Colon Biopsy 1057+6 Inflamed


title: Ulcerative colitis Colon Biopsy 1077-2 Non-Inflamed


title: Ulcerative colitis Colon Biopsy 1057-1 Non-Inflamed


title: Ulcerative colitis Colon Biopsy 1057+4 Inflamed


title: Ulcerative colitis Colon Biopsy 877-4 Non-Inflamed


title: Ulcerative colitis Colon Biopsy 1077-1 Non-Inflamed


title: Ulcerative colitis Colon Biopsy 877+6 Inflamed


title: Ulcerative colitis Colon Biopsy 877-2 Non-Inflamed


title: Ulcerative colitis Colon Biopsy 157+6 Inflamed


title: Ulcerative colitis Colon Biopsy 157+3 Inflamed


title: Ulcerative colitis Colon Biopsy 1214+4 Inflamed


title: Ulcerative colitis Colon Biopsy 8854A1 Non-Inflamed


title: Ulcerative colitis Colon Biopsy 157-4 Non-Inflamed


title: Ulcerative colitis Colon Biopsy 157-3 Non-Inflamed


title: RD 100 nM Tram, 6 hrs

city: Bethesda

first: Javed

last: Khan

address: 37 Convent Dr.

department: Genetics Branch

institute: NCI, NIH

data_processing:
RNA-seq reads were aligned to the hg19 reference genome using TopHat.
Gene expression values were calculated as Fragments Per Kilobase of transcript per Million mapped reads (FPKM) using Cufflinks and the UCSC reference at the gene level.
Differential gene expression was determined using Cuffdiff (http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/).
Genome_build: Hg19
Supplementary_files_format_and_content: FPKM files are provided in txt format at the gene-level

source_name: RMS cell line, mutant NRAS

growth_protocol: Cell lines were grown in DMEM supplemented with 10%FBS and Pen/Strep.

extract_protocol:
RNA was extracted from FN-RMS cell lines using the RNeasy mini kit (Qiagen).
Standard Illumina barcodes were introduced during library preparation
RNA-seq Paired-End

treatment_protocol: Drug was dissolved in DMSO to a stock conentration of 10 mM, and additionally diluted in DMEM to a final concentration of 10 or 100 nM (or DMSO of equivilent final volume), exposing cells for 6, 24 or 48 hours before extracting RNA.

tag: treatment time

value: 6 hours

tag: treatment

value: 100 nM Trametinib


title: RD 100 nM Tram, 48 hrs

value: 48 hours


title: RD 100 nM Tram, 24 hrs

value: 24 hours


title: RD 10 nM Tram, 48 hrs

value: 10 nM Trametinib


title: RD 10 nM Tram, 6 hrs


title: RD 10 nM Tram, 24 hrs


title: RD untreated

value: untreated


title: RD DMSO

value: DMSO


title: RD si control

value: si RNA control scramble


title: RD si MEK1

value: si RNA MEK1


title: Ulcerative colitis Colon Biopsy 877+3 Inflamed


title: CTR DMSO

source_name: RMS cell line, mutant HRAS


title: CTR T48 PolII

description:
DNA (ChIP-enriched)
ChIP samples harvested after 1% formaldehyde fixation for 12 minutes, sonicated, processed and ChIP-enriched via standard protocols (Active Motif ChIP-IT HS kit) with indicated antibodies.  DNase samples were treated with DNaseI (fresh growing cells, without fixation). DNaseI (Roche 04-716-728-001) was added to the cells (0.25 to 0.5 units) and incubated for 5 minutes at 37 ˚C.  The digestion was halted with 50 µL of stop buffer (9.5 mL H2O + 100 µL 1M TrisHCl pH 7.4 + 20µL 5M NaCl + 200µL 0.5 M EDTA, with 150 µL 10% SDS and 125 µL proteinase K added just before use).  Proteinase K activation at 55 ˚C for 1 hour was followed by DNA purification by column (MiniElute PCR purification kit, Qiagen).

data_processing:
ChIP enriched DNA reads were mapped to reference genome using BWA version 0.7.10
The ChIP-seq and DNase-seq peaks were called by MACS2 version 2.1.0.  DNase was run in paired-end mode
The enhancers were identified using ROSE2 pipeline in bamliquidator 1.3
Enrichment of known and de novo motifs were found using HOMER version 4.8.2
Chromatin states were learned using ChromeHMM version 1.10
Genome_build: Hg19
Supplementary_files_format_and_content: peak files are tab delimited text files for each sample.

extract_protocol:
DNA was extracted from ChIP-seq samples prepared following the Active Motif ChIP-IT High Sensitivity kit protocol.  DNase DNA purification was performed by column (MiniElute PCR purification kit, Qiagen).
Standard Illumina barcodes were introduced during library preparation
ChIP-seq and DNase-seq

treatment_protocol: Cells were treated with either DMSO or Trametinib (100 nM) for 48 hours in complete media.

tag: antibody

value: Pol II, Santa Cruz (cat sc-899, lot # K1115 pAb)

tag: enrichment target

value: PolII

tag: target function

value: Transcription

tag: time

value: 48 hr

value: Trametinib 100nM


title: CTR D48 PolII


title: CTR 100 nM Tram, 48 hrs


title: CTR 100 nM Tram, 24 hrs


title: CTR 100 nM Tram, 6 hrs


title: Ulcerative colitis Colon Biopsy 1057-2 Non-Inflamed

value: Non-Inflamed

value: Ascending


title: CTR T48 MYOD1

value: MyoD, Santa Cruz (cat sc-32758, lot I1113)

value: Myogenic Transcription Factor


title: CTR D48 MYOD1 rep 1


title: CTR D48 input rep 2

description:
DNA (genomic input control)
ChIP samples harvested after 1% formaldehyde fixation for 12 minutes, sonicated, processed and ChIP-enriched via standard protocols (Active Motif ChIP-IT HS kit) with indicated antibodies.  DNase samples were treated with DNaseI (fresh growing cells, without fixation). DNaseI (Roche 04-716-728-001) was added to the cells (0.25 to 0.5 units) and incubated for 5 minutes at 37 ˚C.  The digestion was halted with 50 µL of stop buffer (9.5 mL H2O + 100 µL 1M TrisHCl pH 7.4 + 20µL 5M NaCl + 200µL 0.5 M EDTA, with 150 µL 10% SDS and 125 µL proteinase K added just before use).  Proteinase K activation at 55 ˚C for 1 hour was followed by DNA purification by column (MiniElute PCR purification kit, Qiagen).

value: input

value: input control


title: CTR 10 nM Tram, 48 hrs

value: 48 hours


title: CTR T48 input


title: CTR untreated


title: CTR D48 H3K4me1

value: H3K4me1, Active Motif (cat39141, lot01008001 pAb)

value: Poised enhancers and promoters


title: CTR D48 H3K36me3

value: H3K36me3, Active Motif (cat61021, lot01515006 mAb)

value: Transcriptional Elongation

value: DMSO


title: CTR D48 input rep 1

value: Input

value: control


title: CTR T48 H3K27me3 rep 1

value: H3K27me3, Active Motif (cat39155, lot pAb)

value: Polycomb Repressed and Heterochromatin


title: CTR D48 H3K27me3 rep 1

value: 48 hr


title: CTR T48 H3K27ac rep 1

value: H3K27ac, Active Motif (cat39133, lot 31814008 pAb)

value: Active enhancers

value: Trametinib 100nM


title: CTR 10 nM Tram, 24 hrs

value: 24 hours

value: 10 nM Trametinib


title: CTR D48 H3K4me2

value: H3K4me2, Active Motif (cat39141, lot01008001 pAb)


title: CTR T48 H3K27me3 rep 2

value: anti-trimethyl-histone H3 Lys27, Millipore (Cat 07-449, lot 2686928 pAb)


title: CTR T48 MYOG

value: Myogenin, Thermo (cat MA5-11486 mAb)

value: MYOG

value: Transcription Factor


title: CTR D48 H3K4me3

value: H3K4me3, Active Motif (cat39159, lot pAb)

value: Active genes/promoters


title: CTR T48 EZH2

value: EZH2, Active motif (cat39901 lot 27210001 pAb)

value: Polycomb Complex


title: CTR D48 ERK

value: anti-MAP Kinase 2, Millipore (cat 05-0157, lot 2654214 mAb)

value: ERKmp

value: Nuclear Kinase

value: DMSO


title: siRNA scrambled control replicate 3

city: Martinsried

first: Andreas

last: Pichlmair

state: Bayern

address: Am Klopferspitz 18

department: Mann

country: Germany

institute: Max-Planck Institut für Biochemie

data_processing:
Primary data analysis was done using Illumina’s real-time analysis software (RTA)
Sequenced reads containing adaptor sequences were discarded, remaining reads were trimmed, then mapped to the GRCh37 genome assembly and ensembl gene-annotation version 70 using tophat v2.0.9 ( parameters: -G --max-bundle-frags 25M, otherwise default settings)
Transcript/gene levels were quantified against ensembl gene annotation version 70 using cufflinks 2.2.1
Stabilized fold change ratios were calculated as the ratio of sample FPKMs each shifted by +2, discarding genes with read counts below 10.
Genome_build: GRCh37
Supplementary_files_format_and_content: Table (as tab separated values) with FPKM values, stabilized fold changes and p-values for all quantifiable genes as output by cuffdiff

source_name: HeLa S3_siRNA scrambled control

growth_protocol: HeLa S3 cells were routinely maintained in DMEM (GE Healthcare Life Sciences) containing 10% foetal calf serum (GE Healthcare Life Sciences) and antibiotics (100 U/ml penicillin, 100 μg/ml streptomycin)

extract_protocol:
Cells were washed in cold PBS and lysed in RNA extraction lysis buffer (Macherey-Nagel). Total RNA was prepared according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols. Library preparation and RNA sequencing was performed by Max Planck-Genome-Centre Cologne, Germany (http://mpgc.mpipz.mpg.de/home/).

treatment_protocol: TNF-a (20 ng/ml, PeproTech) was applied to the cells for 2 hours

value: HeLa S3

tag: passage

tag: genotype/variation

value: siRNA scrambled control


title: CTR D48 H3K27me3 rep 2

value: Polycomb Repressed and Heterochromatin

value: 48 hr


title: siRNA scrambled control replicate 1

tag: cell line


title: siRNA GTF2b knockdown plus TNF stimulation replicate 1

source_name: HeLa S3_siRNA GTF2b knockdown plus TNF stimulation

value: siRNA GTF2b knockdown

tag: stimulated with

value: 20ng/ml TNF-a for 2hrs


title: CTR D48 MYOG

value: Myogenin, Thermo (cat MA5-11486 mAb)


title: siRNA scrambled control plus TNF stimulation replicate 3

source_name: HeLa S3_siRNA scrambled control plus TNF stimulation


title: CTR T48 H3K27ac rep 2

value: H3K27ac, Active Motif (cat39133, lot 31814008 pAb)

value: Active enhancers

value: Trametinib 100nM


title: siRNA scrambled control plus TNF stimulation replicate 2


title: CTR D48 H3K27ac


title: CTR 10 nM Tram, 6 hrs

value: 6 hours

value: 10 nM Trametinib


title: CTR T48 ERK


title: siRNA GTF2b knockdown replicate 2

source_name: HeLa S3_siRNA GTF2b knockdown


title: CTR DNase 48h rep 3

description:
DNA (DNase-sensitive regions)
ChIP samples harvested after 1% formaldehyde fixation for 12 minutes, sonicated, processed and ChIP-enriched via standard protocols (Active Motif ChIP-IT HS kit) with indicated antibodies.  DNase samples were treated with DNaseI (fresh growing cells, without fixation). DNaseI (Roche 04-716-728-001) was added to the cells (0.25 to 0.5 units) and incubated for 5 minutes at 37 ˚C.  The digestion was halted with 50 µL of stop buffer (9.5 mL H2O + 100 µL 1M TrisHCl pH 7.4 + 20µL 5M NaCl + 200µL 0.5 M EDTA, with 150 µL 10% SDS and 125 µL proteinase K added just before use).  Proteinase K activation at 55 ˚C for 1 hour was followed by DNA purification by column (MiniElute PCR purification kit, Qiagen).

value: DNase

value: Open Chromatin


title: CTR D48 EZH2

value: EZH2, Active motif (cat39901 lot 27210001 pAb)

value: Polycomb Complex


title: siRNA scrambled control replicate 2


title: CTR D48 MYOD1 rep 2

value: MyoD, Santa Cruz (cat sc-32758, lot I1113)

value: Myogenic Transcription Factor

value: DMSO


title: rTHOV delta ML infection replicate2

source_name: HeLa S3_rTHOV delta ML infection

treatment_protocol: Cells were infected with rTHOV at MOI 1 for 1 hour at 4°C. The medium was exchanged and cells were incubated for 16 hours.

value: HeLa S3

tag: infected with

value: rTHOV delta ML


title: CTR DNase 48h rep 1

value: 48 hr


title: rTHOV delta ML infection replicate1


title: CTR DNase Tram 48h rep 3


title: siRNA GTF2b knockdown plus TNF stimulation replicate 3

value: siRNA GTF2b knockdown

value: 20ng/ml TNF-a for 2hrs


title: siRNA GTF2b knockdown plus TNF stimulation replicate 2


title: rTHOV ML SW-mutant infection replicate3

source_name: HeLa S3_rTHOV ML SW-mutant infection

value: rTHOV ML SW-mutant


title: rTHOV ML SW-mutant infection replicate2


title: CTR DNase Tram 48h rep 1


title: siRNA scrambled control plus TNF stimulation replicate 1

value: siRNA scrambled control


title: rTHOV ML SW-mutant infection replicate1


title: siRNA GTF2b knockdown replicate 3


title: Mock-infected control replicate2

source_name: HeLa S3_Mock-infected control

value: mock (control)


title: siRNA GTF2b knockdown replicate 1


title: CTR DNase 48h rep 2


title: rTHOV delta ML infection replicate3


title: Mock-infected control replicate1


title: Mock-infected control replicate3


title: CTR DNase DMSO 48h rep 3


title: 100% MM1.S

description:
genomic DNA sheared to mimic cell-free DNA
Sample 5713

data_processing:
library strategy: MeDIP-seq and cfMeDIP-seq
FastQ files were aligned to hg19 using Bowtie version 0.12.9 with default parameters to yield raw SAM files.
SAM files were converted to raw BAM files using Samtools; unaligned reads were retained.
The MEDIPS software package was used to generate Rdata objects containing RPKM values from each sample's BAM files; the function createSet() was used with genome hg19, all 24 main chromosomes, window size 300 bp, extend size 160 bp, shift size 0 bp & uniq=TRUE.
Using the Rdata objects, the exportWIG() function in the MEDIPS package was used to output the RPKMs for each Sample into .wig.gz files.
Genome_build: hg19
Supplementary_files_format_and_content: wig files containing RPKM values

source_name: Multiple Myeloma

extract_protocol:
The genomic DNA of the collected cells were extracted using Thermofisher PureLink® Genomic DNA Kit and eluted in EB buffer, prior to being sheared using a Covaris M220 shearing instrument to mimic cell free DNA size distribution. antibody: MeDIP kit manufacturer Diagenode; Kit Catalog #: C02010021; the lot number of antibodies include: Lot GF-003, LotD006
The libraries were prepared using the Kapa Hyper Prep Kit

tag: cell line(s)

value: Multiple Myeloma

tag: dilution


title: CTR DNase Tram 48h rep 2

value: Trametinib 100nM


title: 0.001% HCT116

description:
genomic DNA sheared to mimic cell-free DNA
Sample 5711

source_name: Colon colorectal carcinoma & Multiple Myeloma

value: HCT116 & MM.1S


title: CTR DNase DMSO 48h rep 2

value: DNase

value: Open Chromatin


title: CTR DNase DMSO 48h rep 1


title: 1ng rep2

description:
genomic DNA sheared to mimic cell-free DNA
Sample 5676

data_processing:
library strategy: MeDIP-seq and cfMeDIP-seq
FastQ files were aligned to hg19 using Bowtie version 0.12.9 with default parameters to yield raw SAM files.
SAM files were converted to raw BAM files using Samtools; unaligned reads were retained.
The MEDIPS software package was used to generate Rdata objects containing RPKM values from each sample's BAM files; the function createSet() was used with genome hg19, all 24 main chromosomes, window size 300 bp, extend size 165 bp, shift size 0 bp & uniq=TRUE.
Using the Rdata objects, the exportWIG() function in the MEDIPS package was used to output the RPKMs for each Sample into .wig.gz files.
Genome_build: hg19
Supplementary_files_format_and_content: wig files containing RPKM values

source_name: Colon colorectal carcinoma

growth_protocol: HCT116 cells were grown with McCoy Media supplemented with 10% FBS and 1% Penicillin/Streptomycin in 75cm2 flasks at 37˚C and 5% CO2

extract_protocol:
The genomic DNA of the collected cells were extracted using Thermofisher PureLink® Genomic DNA Kit and eluted in EB buffer, prior to being sheared using a Covaris M220 shearing instrument to a target size of 150 bp.The sheared product was size selected and purified with the MinElute Gel Extraction kit (Qiagen) to 100-250 bp and 250-400 bp. The concentration of the purified fragments was measured through Qubit prior to pooling with a ratio of 10:1 of 100-250 bp:250-400 bp DNA product to make test samples with the following DNA amounts: 100 ng, 10 ng, 5 ng and 1 ng. antibody: MeDIP kit manufacturer Diagenode; Kit Catalog #: C02010021; the lot number of antibodies include: Lot GF-003, LotD006
The libraries were prepared using the Kapa Hyper Prep Kit

value: Colon colorectal carcinoma

tag: dna amount


title: rTHOV wild type infection replicate2

source_name: HeLa S3_rTHOV wild type infection

value: rTHOV wild type


title: rTHOV wild type infection replicate1


title: 5ng rep2

description:
genomic DNA sheared to mimic cell-free DNA
Sample 5674


title: 100ng rep1

description:
genomic DNA sheared to mimic cell-free DNA
Sample 5669


title: 100ng rep2

description:
genomic DNA sheared to mimic cell-free DNA
Sample 5670


title: 0.01% HCT116

description:
genomic DNA sheared to mimic cell-free DNA
Sample 5710

value: Colon colorectal carcinoma & Multiple Myeloma


title: r4gal4_svpi_0_7m_2

city: Binghamton

first: Laura

middle: Palanker

last: Musselman

state: New York

address: 4400 Vestal Parkway East

department: Biological Sciences

institute: Binghamton University

data_processing:
To produce bed alignments, sequenced reads were aligned to the D. melanogaster UCSC dm3 assembly using Tophat (v1.3.2) and Bowtie (v0.12.7). Default Tophat settings were used.
Gene expression was quantified by processing the Tophat produced bam alignments with Cufflinks (v1.1.0) and the modENCODE MB8 annotation.
Genome_build: D. melanogaster UCSC dm3 assembly
Supplementary_files_format_and_content: Excel worksheet "GEO upload processed data" containing normalized abundance for each raw dataset using EdgeR, indexed by FlyBase Gene Name

organism: Drosophila melanogaster

source_name: 0.7M_Svpi_fat body

growth_protocol: Wild-type males (VDRC's 60100 control stock or 100762 UAS-Svpi stock) were crossed to r4-GAL4 driver line virgin females to produce offspring whose fat bodies were to be isolated and profiled. Larval offspring were collected at the end of larval development (also known as the wandering third instar stage)

extract_protocol:
Fat bodies were homogenized in Trizol and total RNA isolated after DNAse digestion.
RiboZero subtraction was used to remove rRNA and then reverse transcription, size exclusion, amplification, and bar coding produced the final library.
Reads using bar-coded cDNA were generated by Illumina Hi-Seq analyzer.

treatment_protocol: Larvae were reared on control (0.15M) or high-sugar (0.7M) diets using a modified Bloomington semi-defined food as previously described (J Biol Chem 288(12):8028-42). Fat bodies were isolated by fine dissection, shearing and separation by centrifugation.

tag: strain/genotype

value: VDRC's 100762 stock crossed with a UAS-Dcr2 (X); r4-GAL4 stock

tag: developmental stage

value: wandering third instar larva

tag: Sex

value: female

tag: reared on

value: 0.7M sucrose (high sugar) diet

tag: tissue

value: fat body


title: r4gal4_svpi_0_7m_3


title: 0.1% HCT116

description:
genomic DNA sheared to mimic cell-free DNA
Sample 5709

tag: cell type


title: r4gal4_svpi_0_7m_1


title: 1% HCT116

description:
genomic DNA sheared to mimic cell-free DNA
Sample 5708


title: 10% HCT116

description:
genomic DNA sheared to mimic cell-free DNA
Sample 5707

growth_protocol: HCT116 cells were grown with McCoy Media supplemented with 10% FBS and 1% Penicillin/Streptomycin in 75cm2 flasks at 37˚C and 5% CO2. MM1.2 cells were grown with IMDM medium supplemented with 5% FBS in 75cm2 flasks at 37˚C and 5% CO2.


title: input control

description:
genomic DNA sheared to mimic cell-free DNA
Sample 5677


title: 100% HCT116

description:
genomic DNA sheared to mimic cell-free DNA
Sample 5706


title: r4gal4_svpi_0_15m_1

source_name: 0.15M_Svpi_fat body

value: 0.15M sucrose (control) diet


title: r4gal4_v60100_0_15m_3

source_name: 0.15M_ctrl_fat body

value: VDRC's 60100 stock crossed with a UAS-Dcr2 (X); r4-GAL4 stock


title: 1ng rep1

description:
genomic DNA sheared to mimic cell-free DNA
Sample 5675


title: 10ng rep1

description:
genomic DNA sheared to mimic cell-free DNA
Sample 5671


title: 5ng rep1

description:
genomic DNA sheared to mimic cell-free DNA
Sample 5673


title: 10ng rep2

description:
genomic DNA sheared to mimic cell-free DNA
Sample 5672


title: r4gal4_v60100_0_7m_2

source_name: 0.7M_ctrl_fat body


title: EsgTS + Dm0 + UPD 3

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

description: ISCs/EBs with expression of Lamin Dm0 and UPD.

data_processing:
Sequence images were transformed to BCL files with the Illumina BaseCaller software and samples were demultiplexed to FASTQ files with CASAVA (version 1.8.2).
Sequences were aligned to the genome reference sequence of Drosophila melanogaster (assembly version BDGP 5) using STAR (Dobin et al., 2012, version 2.3) with 2 mismatches in 50 bp.
Subsequently, filtering of unique hits and counting of reads overlapping with exons was conducted with featureCounts (Liao et al., 2014, subread version 1.5.0-p1, Ensembl annotation version 74).
Genome_build: BDGP5 (Release 5)
Supplementary_files_format_and_content: *_geneCounts.txt: Tab-delimited text files include raw counts.

source_name: intestinal stem cells/progenitor cells, Lamin Dm0 + UPD

extract_protocol:
About 100 guts were dissected per sample and the intestinal cells dissociated (pipetting in dissociation buffer). GFP-positive ISCs/EBs were sorted by FACS and RNA isolated by kit (Arcturus Pico pure RNA isolation kit).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Expression of Dm0 and UPD was induced for 5 days by temperature shift to 29°C.

tag: strain/stock

value: EsgTS

value: Esg-Gal4, tub-GAL80TS, UAS-nlsGFP

value: intestinal stem cells/progenitor cells

tag: treatment

value: Lamin Dm0 and UPD


title: r4gal4_svpi_0_15m_3


title: EsgTS + UPD 2

description: ISCs/EBs with expression of Jak/Stat ligand UPD.

source_name: intestinal stem cells/progenitor cells, UPD

value: Jak/Stat ligand UPD


title: RBP2_ChIPSeq

description: Chromatin IP against RBP2

data_processing:
Alignment: Sequence reads were obtained using the Illumina Genome Analyzer Pipeline and reads were  mapped to the mouse (July, 2007) genomes (NCBI37/mm9) using BOWTIE aligner program (http://bowtie-bio.sourceforge.net/index.shtml) (Ref: Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25.) All reads mapping uniquely with two or fewer mismatches were retained.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)

source_name: Chromatin IP against RBP2

growth_protocol: Cells were grown in Claycomb Medium (Sigma) supplemented with 10% Fetal bovine serum (Sigma, Lot #116K8400), 2 mM  L-Glutamine, 0.1 mM Norepinephrine and antibiotics in gelatin/fibronectin coated flasks upto 95% confluency.

extract_protocol: ChIP and genomic library preparation was performed as described (Beshiri, M.L, A. Islam A, D.C. DeWaal, W.F. Richter, Love J, N. Lopez-Bigas, and E.V. Benevolenskaya. 2010. Genome-wide Analysis using ChIP to Identify Isoform-specific Gene Targets. JoVE. 41. http://www.jove.com/index/details.stp?id=2101, doi: 10.3791/2101).  After adapter ligation DNA was PCR amplified with Illumina primers for 18 cycles and library fragments of ~320 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: strain

value: HL-1 cells

value: cardiac muscle cell line

tag: chip antibody

value: 1416(Benevolenskaya et al., Mol Cell 18, 623-635)


title: EsgTS + UPD 1

tag: genotype/variation


title: EsgTS + Dm0 2

description: ISCs/EBs with expression of Lamin Dm0.

source_name: intestinal stem cells/progenitor cells, Lamin Dm0

value: Lamin Dm0


title: EsgTS + Dm0 3

description: ISCs/EBs with expression of Lamin Dm0.


title: EsgTS + Dm0 + UPD 1


title: r4gal4_svpi_0_15m_2


title: rTHOV wild type infection replicate3

tag: cell line

value: HeLa S3

tag: passage

value: rTHOV wild type


title: r4gal4_v60100_0_15m_1

value: wandering third instar larva


title: r4gal4_v60100_0_15m_2

value: female


title: HL1_input_gDNA

description: input DNA

source_name: input DNA


title: JARID2_ChIPSeq

description: Chromatin IP against JARID2

source_name: Chromatin IP against JARID2

value: BL3844(kindly provided by Eric W. McIntush, Bethyl Laboratories, Inc.)


title: r4gal4_v60100_0_7m_3

value: 0.7M sucrose (high sugar) diet

value: fat body


title: OX-AtSRT1 rep2

city: Wuhan

first: Xiaoyun

last: Liu

state: Hubei

address: Economic and Technological Development Zone, Sanjiaohu Road, No. 8

institute: Jianghan university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR10 whole genome using TopHat v2.1.1 with default parameters
Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) were calculated using cufflinks v2.2.1. differentially expressed genes were calculated useing cuffdiff which is one of tools in cuffliniks with default parameters and TAIR10 gtf file. Each sample has 3 replications.
Genome_build: TAIR10
Supplementary_files_format_and_content: excel files include FPKM values of R and OX compared to col.

organism: Arabidopsis thaliana

source_name: leaf, stem, root

growth_protocol: 14 days-Seedlings seedlings were grown in 1/2 MS in the Snijders Climate Chamber (Micro Clima) from wild-type (Col) and RNAi line of SRT1(line RNAi-1) (R) and overexpression line (line OX-SRT1-1)(OX)

extract_protocol:
Arabidopsis seedlings were flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Seedling stage

tag: age

value: 14-days under normal growth conditions

tag: genotype

value: overexpreession line

value: leaf, stem, root


title: EsgTS 3

description: ISCs/EBs (control).

source_name: intestinal stem cells/progenitor cells, control

value: EsgTS

value: Esg-Gal4, tub-GAL80TS, UAS-nlsGFP

value: intestinal stem cells/progenitor cells

value: control


title: EsgTS + Dm0 + UPD 2

value: Lamin Dm0 and UPD


title: col rep3

value: wild type


title: R-AtSRT1 rep1

value: RNAi line


title: EsgTS + UPD 3

value: Jak/Stat ligand UPD


title: col rep1


title: OX-AtSRT1 rep3


title: PMCs isolated from 24 hpf embryos, replicate 1

description:
ATAC-seq
PMC_Other_RPS.bed

data_processing:
Adapter sequences were trimmed using Cutadapt (v1.9)
Reads were mapped to the S. purpuratus genome v 3.1 using Bowtie2 (v2.1.0) with default parameters
Bowtie2 SAM output format was converted to BAM format and PCR duplications were removed and read counts were equalized using Samtools v1.3
Bedtools (v2.19.1) was used to convert the BAM output into BED format.
Fseq (v1.85) was used to call peaks using parameters -f 0 and -t 2
The fraction of reads within peaks (the FRiP score) was calculated using Bedtools (v2.19.1) by extracting and counting all reads within peaks and dividing by the total number of reads mapped.
Separate reference peak sets (RPSs) were generated for the DNase-seq and ATAC- seq data by first identifying all replicate peaks that overlapped by at least 75% non-reciprocally and then merging all such peaks across samples separately for the DNase-seq or ATAC-seq data using Bedops (v2.4.2)
Read counts corresponding to peaks in the RPS were generated using HTSeq (v0.6.0)
Differential peaks were identified using DESeq2
Genome_build: Strongylocentrotus purpuratus genome version 3.1 (Spur_3.1)
Supplementary_files_format_and_content: BED files contain peaks called by Fseq (v1.85), and the reference peak set (RPS) generated by merging the peaks using Bedops(v2.4.2). .txt files contain read counts corresponding to the peaks in the RPS, generated by HTseq (v0.6.0).

source_name: 24 hours post fertilization isolated PMC cells

extract_protocol:
Nuclei were extracted using lysis buffer washes and ATAC-seq was performed: 150,000 nuclei were digested with 2.5 ul Tn5 transposase and a Nextera library was created.
Nextera library kit used to generate Illumina sequencing library for NextSeq

value: 24 hours post fertilization


title: EsgTS + Dm0 1

description: ISCs/EBs with expression of Lamin Dm0.

value: Lamin Dm0


title: EsgTS 2

description: ISCs/EBs (control).


title: EsgTS 1

description: ISCs/EBs (control).


title: PMCs isolated from 24 hpf embryos, replicate 2

description:
ATAC-seq
PMC_Other_RPS.bed


title: R-AtSRT1 rep3


title: col rep2


title: R-AtSRT1 rep2


title: Other, non-PMC cells isolated from 24 hpf embryos, replicate 2

description:
ATAC-seq
PMC_Other_RPS.bed

source_name: 24 hours post fertilization isolated non-PMC cells


title: ire1a1b_TM_rep3

status: Public on Mar 31 2018

city: Ames

first: Stephen

last: Howell

state: Iowa

address: 1035A Roy J. Carver Co-Laboratory 1111 WOI Road

department: Department of Genetics, Development and Cell Biology

institute: Plant Sciences Institute

description: Arabidopsis thaliana 7-days Seedlings

data_processing:
All paired end data with read length 250 bp were aligned to Arabidopsis TAIR10 genome, using STAR (version 2.4.0 with parameters “--outFilterMultimapNmax 10 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.10”)
Subsequently, reads count of each annotated gene was calculated by htseq-count (version 0.6.0 with parameters “-t mRNA -m intersection-nonempty --stranded no”).
Next, significantly differently expressed genes (DEGs) between each two samples were extracted with cutoff FDR (false discovery rate) < 0.01 using DESeq2
Genome_build: TAIR10
Supplementary_files_format_and_content: txt files, count

molecule: polyA RNA

source_name: Arabidopsis thaliana 7-days Seedlings

growth_protocol: Seeds from WT, ire1b and ire1a ire1b were germinated and vertically grown on 100 mm × 100 mm square plates (Fisher Scientific) with 1/2 MS-0 media for 7 days.

extract_protocol:
Samples were harvested by sucking out the liquid with paper towel, and immediately ground into powder in liquid nitrogen. Total RNA extraction was extracted by using RNeasy Plant Mini Kit (QIAGEN, Cat. No. 74904).
RNA-seq libraries were prepared with paired-end and 250 nt

treatment_protocol: Seedlings with similar size were picked up and treated with DMSO (as the control) or with 5μg/mL TM in 6-well cell culture plates with liquid 1/2 MS-0 media (2.2g/L, 5% sucrose) for 6h.

value: seedlings

value: ire1a/ire1b double mutant

tag: replicate


title: ire1a1b_DMSO_rep2

description: Arabidopsis thaliana 7-days Seedlings


title: ire1b_TM_rep3

description: Arabidopsis thaliana 7-days Seedlings

value: ire1b mutant


title: ire1a1b_TM_rep2

description: Arabidopsis thaliana 7-days Seedlings


title: ire1a1b_TM_rep1

description: Arabidopsis thaliana 7-days Seedlings


title: ire1b_DMSO_rep3

description: Arabidopsis thaliana 7-days Seedlings


title: ire1b_DMSO_rep2

description: Arabidopsis thaliana 7-days Seedlings


title: WT_TM_rep3

description: Arabidopsis thaliana 7-days Seedlings


title: Other, non-PMC cells isolated from 24 hpf embryos, replicate 1

description:
ATAC-seq
PMC_Other_RPS.bed


title: ire1a1b_DMSO_rep3

description: Arabidopsis thaliana 7-days Seedlings


title: OX-AtSRT1 rep1

value: Seedling stage


title: ire1a1b_DMSO_rep1

description: Arabidopsis thaliana 7-days Seedlings


title: ire1b_TM_rep1

description: Arabidopsis thaliana 7-days Seedlings


title: WT_DMSO_rep1

description: Arabidopsis thaliana 7-days Seedlings


title: tg_rabbit IgG_ChIP-Seq

city: Essen

first: Cyrus

last: Khandanpour

state: NRW

address: Hufelandstr. 55

department: Department of Hematology

institute: University Hospital Of Essen

data_processing:
Basecalls were performed using CASAVA version 1.8.2
ChIP-seq reads were aligned to the mm10 genome assembly using the Unipro-UGENE software using the BWA-MEM algorithm. Workflow:  Filtration of the Input sequencing reads by the CASAVA header, cutting of adaptersequences, trimming of the sequencing reads by quality, mapping of the reads to reference sequence mouse MM10 (GRCm38), filtratoin of aligned reads by SAM-tools to remove reads with low mapping quality, unaligned / unpaired reads etc, removal of PCR duplicates, conversion to BAM format. The workflow also performs quality control of the data with FastQC: first on the input FASTQ files, second after the preprocessing step.
BAM-file indexes were generated using samtools
BAM files were analyzed using SeqMonk V 0.32.1 and peak-probes were defined using the MACS algorithm using Chip-Seq samples CK31.bam,CK34.bam and IgG control samples CK32.bam,CK35.bam. Fragment size was 300. Significance threshold was 1.0E-5.. Quantitated with Read Count Quantitation using All Reads correcting for total count only in probes per million reads log transformed. Quantitation output was generated by SeqMonk as "feature report" quantitating probes overlapping annotated genes.
Subsequently, H3K9ac probe-levels were analyzed by ALtAnalyze V2.0 (default parameters but: data type: Other ID; platform: Ensembl; process expression file; species: Mm, filter_method: z-score, z_threshold: 1.96, p_val_threshold: 0.05, change_threshold: 2, sort_only_by_zscore: yes, analysis_method: non-UI, enrichment_type: ORA, ORA Parameters: mod: Ensembl, permutations: FisherExactTest, resources_to_analyze: all
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Matrix table of normalized abundance measurements as tab delimited txt-file with gene level probe quantitations and additional information: Chr, Start, End, Feature ID, Description, No. Sublocations, No. Probes, Mean CK31.bam, StDev CK31.bam, Mean CK34.bam, StDev CK34.bam

source_name: leukemic bone marrow cells

extract_protocol:
Bone marrow (BM) cells were isolated from Gfi1bfl/fl MxCretg NUP98/HOXD13tg and Gfi1bfl/fl MxCrewt Nup98/HOXD13 mice. BM cells were homogenised and ery lysis was performed. 1x10^7 cells were fixed with 1% formaldehyde and sonicated for 20 min. Histone-DNA antibody were isolated with antibody
Libraries were prepared using the NEBNext® UltraTM DNA Library Prep Kit for Illumina®. Samples were pooled after quality check.

value: Gfi1b(fl/fl) x Nup98(tg) x MxCre(tg)

value: bone marrow

value: leukemic bone marrow cells

tag: chip-antibody

value: rabbit-IgG, Sigma, I5006


title: ire1b_DMSO_rep1

description: Arabidopsis thaliana 7-days Seedlings


title: WT_rabbit IgG_ChIP-Seq

value: Gfi1b(fl/fl) x Nup98(tg) x MxCre(wt)


title: r4gal4_v60100_0_7m_1

tag: strain/genotype

value: VDRC's 60100 stock crossed with a UAS-Dcr2 (X); r4-GAL4 stock

value: wandering third instar larva

value: female

value: 0.7M sucrose (high sugar) diet

value: fat body


title: WT_H3K9ac_ChIP-Seq


title: WAF-MS417-1 (A518_1)

city: New York

first: Martin

middle: J.

last: Walsh

state: NY

address: One Gustave L. Levy Pl.

department: Structural and Chemical Biology

institute: Mount Sinai School of Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
After filtering contaminant (aligned) reads, sequenced reads were then mapped to mm9 genome, RefSeq exons, splicing junctions using BWA v0.7.3 alignment algorithm
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Huber et al., Journal of immunology, 2012. In short, uniquely aligned reads to the exon and splicing-junction sites for each transcript  were counted and normalized by the size of the transcript and by the size of the library.
RNA for RNA-seq was extracted from white abdominal fat collected from 2 control and 3 treated animals. Expression was compared between control and treated mice matched by weight at the beginning of the treatment ( A518_2/A518_1, A518_2/A518_3 and A518_5/A518_4). Expression change expressed as log2ratio for the 3 comparisons was then averaged.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: white abdominal fat (WAF)

growth_protocol: Male ob/ob B6 mice were obtained from Taconic. They were single caged and pair fed a regular chow diet where the amount of food given to each control mouse corresponded to the mean amount ate by treated mice, fed ad libitum, the previous day.

extract_protocol:
White abdominal fat (WAF) was removed, flash frozen, and RNA was harvested using Trizol reagent.
RNA-seq libraries were prepared from Tryzol extracted RNA samples from which rRNA was removed using Ribo-ZeroTM and following the TruSeq Stranded Total RNA Sample Prep kit protocol (Illumina).

treatment_protocol: At 10 weeks of age mice were being injected, by IP injection, with vehicle only (DMSO diluted in PBS) or MS417.  For the first 15 days mice were injected with a lower dose of 2.5mg/kg. For the remaining 2 weeks the higher 5mg/kg dose of MS417 was used.

value: white abdominal fat

value: 14 weeks


title: WAF-control-1 (A518_2)

value: DMSO


title: WT_TM_rep2

description: Arabidopsis thaliana 7-days Seedlings

value: seedlings

value: wild type


title: WAF-control-2 (A518_4)


title: tg_H3K9ac_ChIP-Seq


title: WT_TM_rep1

description: Arabidopsis thaliana 7-days Seedlings


title: WAF-MS417-3 (A518_5)


title: WT_DMSO_rep3

description: Arabidopsis thaliana 7-days Seedlings


title: WT_DMSO_rep2

description: Arabidopsis thaliana 7-days Seedlings


title: WAF-MS417-2 (A518_3)