title: Single_cell_RNASeq [D93]

city: Heidelberg

first: Ana

last: Martin-Villalba

state: Deutschland

address: Im Neuenheimer Feld 280

department: Molekulare Neurobiologie (A290)

institute: German Cancer Research Center (DKFZ)

description:
mRNA_with_poly_a_tail
D93

data_processing:
Basecalls performed using llumina bcl2fastq 2.17.1.14
Before alignment, adapter sequences in raw reads were trimmed by Btrim64 (http://graphics.med.yale.edu/trim)
Trimmed reads were mapped to mouse genome (ENSEMBL Release 84) using STAR-2.5.2a
Expression level of each gene was quantified in unites by transcript per million (TPM) and fragments per kilobase of transcript per million fragments mapped (FPKM) using RSEM v1.2.30 with default parameters.To compare expression levels of different genes across samples, we performed an additional TMM (trimmed mean of M-values) normalization on TPM using Trinity (http://trinityRNA-seq.github.io/) based on edgeR (abbreviated TMM-TPM). The purpose of this normalization is to account for differences in total cellular RNA production across all cells.
We developed custom R scripts based on FactoMineR library (http://factominer.free.fr/) performing PCA analysis on gene expression matrices.PCA analysis was performed on cells passed quality control. Subsequently, genes with the highest correlation coefficient with one of the first six principal components were identified using dimdesc function in FactoMineR. Hierarchical clustering was performed on cells and on the genes identified by PCA using Euclidean distance or correlation metric.
Genome_build: mm10
Supplementary_files_format_and_content: Gene expression matrices (TPM value) of each gene in each cells in CSV format

extract_protocol:
Mice were sacrificed at the indicated timepoints, when the cortex and the meninges were microdissected, digested into a single-cell suspension and DiI-positive cells were sorted by flow cytometry. Sorted cells were processed for single-cell RNA-se
Single cell RNA seq library preparation protocol was done as previously described in Llorens-Bobadilla et al., 2015

treatment_protocol: Meninges from P0 neonatal mice were microdissected and digested into a single-cell suspension. Pdgfrb-expressing cells were enriched via one round of MACS isolation (Pdgfr_plus). Individual cells were picked and processed for single-cell RNA-seq as described (our paper). In a parallel set of experiments, DiI was injected into the subarachnoid region of P0 mice.

tag: age

value: Meninges


title: siControl rep2

status: Public on Nov 23 2016

type: SRA

city: Munich

first: Stefan

last: Krebs

address: Feodor-Lynen-Str. 25

department: Gene Center

country: Germany

institute: Ludwig-Maximilian University

library_source: transcriptomic

data_processing:
Basecalling was done by RTA1.18.64
Truseq adapter and polyA were removed
reads were aligned to the human genome by STAR RNAseq read mapper
reads overlapping with annotated genes were counted with HTseq count
variance stabilisation and differential gene expression were done by DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: raw count table from HTseq count and vst tranformed expression values from DEseq2

molecule: total RNA

organism: Homo sapiens

source_name: siControl rep2

extract_protocol:
Total RNA was purified using the Trizol standard protocol and treated with heat-labile dsDNAse (Thermo scientific)
libraries were produced from 150ng total RNA with Nugen complete RNAseq library system according to the manufacturers protocol.

tag: tissue

value: colon cancer

tag: cell line


title: Single_cell_RNASeq [D91]

description:
mRNA_with_poly_a_tail
D91

organism: Mus musculus

tag: gender


title: Single_cell_RNASeq [D95]

description:
mRNA_with_poly_a_tail
D95


title: Single_cell_RNASeq [D94]

description:
mRNA_with_poly_a_tail
D94


title: Single_cell_RNASeq [D92]

description:
mRNA_with_poly_a_tail
D92


title: Single_cell_RNASeq [D9]

description:
mRNA_with_poly_a_tail
D9


title: siADNP rep2

source_name: siADNP rep2


title: Single_cell_RNASeq [D89]

description:
mRNA_with_poly_a_tail
D89


title: Single_cell_RNASeq [D87]

description:
mRNA_with_poly_a_tail
D87


title: Single_cell_RNASeq [D84]

description:
mRNA_with_poly_a_tail
D84


title: 06-02-Normal

city: Farmington

first: Allen

last: Mo

state: CT

address: 263 Farmington Avenue

department: Center for Molecular Medicine

country: USA

institute: UConn Health

description: Each biopsy specimen requires four separate library preps: epithelia, stroma and two RNA Ampliseq Panels

data_processing:
IonTorrent Suite (v4.4) for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, mapped to targetted regions using coverageAnalysis plugin and aligned to hg19_RNA_CanTran_v1
Total reads were normalized to one million per panel, and all samples were combined into one large processed datamatrix (possible pseudogenes were removed)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file with RPKM values for each sample panel

source_name: Colon tissue biopsy during colonoscopy

extract_protocol:
OCT-embedded colon biopisies were sectioned at 9-um thickness onto PEN membrance slides and subjected to LCM of stromal and epithelial cells onto separate caps. RNA was extracted from caps using Picopure RNA isolation kit following manufacturer's protocols. Half of extracted RNA was used for each library preparation panel
RNA libraries were prepared for sequencing using standard IonTorrent RNA Ampliseq protocols for two separate panels (Apoptosis and custom Senesence). Libraries were barcoded with IonXpress Adapters.
Targetted RNA-seq, Barcoded (provided in the barcode.txt) to run 4 samples per 318 chip
each raw data file is named as 'Patient#-Biopsy#-Epithelia/Stroma-Apoptosis/Senescence Panel-ACF/Normal' and the original file names  (associated with each sample)/their checksums are included in the barcode.txt.

tag: patient #

tag: biopsy #

value: biopsied normal colon

tag: mutation

tag: cell type

value: laser capture microdissected epithelial cells


title: HDAC3_WT_Veh_2

status: Public on Nov 26 2016

city: Boston

first: Manashree

last: Damle

state: MA

address: 185 Cambridge Street

department: Molecular Biology

institute: Massachusetts General Hospital

library_source: genomic

data_processing:
ChIP-seq peaks were called using HOMER. Peaks above  4-fold over KO and above 1rpm were kept.
RNAseq normalized counts were generated using Htseq and differential gene expression was found using DESeq2.
Genome_build: mm9
Supplementary_files_format_and_content: bed file with called peaks; Excel file with DESeq output.

molecule: genomic DNA

source_name: Isolated islets

extract_protocol:
Islets were isolated and processed immdiately for RNA extraction with Trizol, or fixed with 1% formaldehyde for ChIP.
Libraries were prepared using standard Illumina protocols

treatment_protocol: C57BL6/J mice on normal chow were gavaged tamoxifen (2mg/day) or corn oil vehicle daily for 5 days 2 weeks prior to islet isolation.

tag: strain

value: islets

value: 10 weeks

tag: genotype


title: Single_cell_RNASeq [D73]

description:
mRNA_with_poly_a_tail
D73


title: Single_cell_RNASeq [D82]

description:
mRNA_with_poly_a_tail
D82


title: Single_cell_RNASeq [D67]

description:
mRNA_with_poly_a_tail
D67


title: Single_cell_RNASeq [D7]

description:
mRNA_with_poly_a_tail
D7


title: Single_cell_RNASeq [D66]

description:
mRNA_with_poly_a_tail
D66


title: Single_cell_RNASeq [D63]

description:
mRNA_with_poly_a_tail
D63


title: Single_cell_RNASeq [D62]

description:
mRNA_with_poly_a_tail
D62


title: Single_cell_RNASeq [D60]

description:
mRNA_with_poly_a_tail
D60


title: Single_cell_RNASeq [D6]

description:
mRNA_with_poly_a_tail
D6


title: Single_cell_RNASeq [D58]

description:
mRNA_with_poly_a_tail
D58


title: Single_cell_RNASeq [D55]

description:
mRNA_with_poly_a_tail
D55


title: Single_cell_RNASeq [D49]

description:
mRNA_with_poly_a_tail
D49


title: Single_cell_RNASeq [D43]

description:
mRNA_with_poly_a_tail
D43


title: Single_cell_RNASeq [D36]

description:
mRNA_with_poly_a_tail
D36


title: Single_cell_RNASeq [D4]

description:
mRNA_with_poly_a_tail
D4


title: Single_cell_RNASeq [D38]

description:
mRNA_with_poly_a_tail
D38


title: Single_cell_RNASeq [D37]

description:
mRNA_with_poly_a_tail
D37


title: Single_cell_RNASeq [D31]

description:
mRNA_with_poly_a_tail
D31


title: Single_cell_RNASeq [D30]

description:
mRNA_with_poly_a_tail
D30


title: Single_cell_RNASeq [D29]

description:
mRNA_with_poly_a_tail
D29


title: Single_cell_RNASeq [D83]

description:
mRNA_with_poly_a_tail
D83


title: Single_cell_RNASeq [D26]

description:
mRNA_with_poly_a_tail
D26


title: Single_cell_RNASeq [D24]

description:
mRNA_with_poly_a_tail
D24


title: Single_cell_RNASeq [D21]

description:
mRNA_with_poly_a_tail
D21


title: Single_cell_RNASeq [D20]

description:
mRNA_with_poly_a_tail
D20


title: Single_cell_RNASeq [D74]

description:
mRNA_with_poly_a_tail
D74


title: Single_cell_RNASeq [D27]

description:
mRNA_with_poly_a_tail
D27


title: Single_cell_RNASeq [D19]

description:
mRNA_with_poly_a_tail
D19


title: Single_cell_RNASeq [D15]

description:
mRNA_with_poly_a_tail
D15


title: Single_cell_RNASeq [D14]

description:
mRNA_with_poly_a_tail
D14


title: Single_cell_RNASeq [C76]

description:
mRNA_with_poly_a_tail
C76


title: Single_cell_RNASeq [D1]

description:
mRNA_with_poly_a_tail
D1


title: Single_cell_RNASeq [D50]

description:
mRNA_with_poly_a_tail
D50


title: Single_cell_RNASeq [C75]

description:
mRNA_with_poly_a_tail
C75


title: Single_cell_RNASeq [C63]

description:
mRNA_with_poly_a_tail
C63


title: Single_cell_RNASeq [C45]

description:
mRNA_with_poly_a_tail
C45


title: Single_cell_RNASeq [C44]

description:
mRNA_with_poly_a_tail
C44


title: Single_cell_RNASeq [D32]

description:
mRNA_with_poly_a_tail
D32


title: Single_cell_RNASeq [C33]

description:
mRNA_with_poly_a_tail
C33


title: Single_cell_RNASeq [C42]

description:
mRNA_with_poly_a_tail
C42


title: Single_cell_RNASeq [C32]

description:
mRNA_with_poly_a_tail
C32


title: Single_cell_RNASeq [C34]

description:
mRNA_with_poly_a_tail
C34


title: Single_cell_RNASeq [C26]

description:
mRNA_with_poly_a_tail
C26


title: Single_cell_RNASeq [C28]

description:
mRNA_with_poly_a_tail
C28


title: Single_cell_RNASeq [D2]

description:
mRNA_with_poly_a_tail
D2


title: Single_cell_RNASeq [C12]

description:
mRNA_with_poly_a_tail
C12


title: AF9 myeloid-1

city: Cincinnati

first: Shan

last: Lin

state: OH

address: 3333 Burnet Avenue, CCHMC

department: EHCB

institute: Cincinnati Children's Hospital Medical Center

description: processed data file: Myeloid Af4 vs AF9 all gene result.txt

data_processing:
bcl files were demultiplexed and converted to fastq files using bcl2fastq in Casava 1.8
fastq seqences were aligned to hg19 using Tophat
number of reads was calculated for each Entrez gene
differential expression analysis was performed using Deseq
Genome_build: hg19
Supplementary_files_format_and_content: DESeq output with appended columns containing RPKM values for samples.

source_name: CD34+ HSPCs

growth_protocol: Lymphoid cells were extracted from mouse bone marrow, red blood cells were lysed. Myeloid culture cells were maintaind in IMDM with 10% FBS and 10ng/mL of SCF, TPO, Flt3 ligand, IL-3 and IL-6

extract_protocol:
Cells were sorted. Total RNA was isolated from sorted cells using RNeasy Mini Kit (Qiagen).
PrepX mRNA Library kit (WaferGen)  was used with 1 ug of total RNA for the construction of sequencing libraries, the libraries were clustered by using IIIumina TruSeq PE Cluster kit

tag: lineage

value: myeloid

tag: cell etiology

value: PBPC


title: AF9 myeloid-2


title: Single_cell_RNASeq [C14]

description:
mRNA_with_poly_a_tail
C14


title: Single_cell_RNASeq [D16]

description:
mRNA_with_poly_a_tail
D16


title: Single_cell_RNASeq [C89]

description:
mRNA_with_poly_a_tail
C89


title: AF9 myeloid-3

value: UCB


title: Af4 myeloid-4


title: Single_cell_RNASeq [C93]

description:
mRNA_with_poly_a_tail
C93


title: Af4 myeloid-2


title: Single_cell_RNASeq [C11]

description:
mRNA_with_poly_a_tail
C11


title: Af4 myeloid-3


title: Af4 myeloid-1


title: Single_cell_RNASeq [C10]

description:
mRNA_with_poly_a_tail
C10


title: Single_cell_RNASeq [C60]

description:
mRNA_with_poly_a_tail
C60


title: AF9 ALL-2

description: processed data file: ALL Af4_vs_AF9 all gene result.txt

value: lymphoid


title: Single_cell_RNASeq [B95]

description:
mRNA_with_poly_a_tail
B95


title: Single_cell_RNASeq [C37]

description:
mRNA_with_poly_a_tail
C37


title: Af4 ALL-5


title: AF9 myeloid-4


title: Single_cell_RNASeq [B94]

description:
mRNA_with_poly_a_tail
B94


title: Af4 ALL-3

description: processed data file: AF4_vs_proB all gene result.txt


title: Af4 ALL-2


title: Af4 ALL-4


title: Single_cell_RNASeq [B9]

description:
mRNA_with_poly_a_tail
B9


title: proB-3

value: Ctrl


title: proB-2


title: proB-1


title: AF9 ALL-3


title: Single_cell_RNASeq [B86]

description:
mRNA_with_poly_a_tail
B86


title: Single_cell_RNASeq [B83]

description:
mRNA_with_poly_a_tail
B83


title: Single_cell_RNASeq [B8]

description:
mRNA_with_poly_a_tail
B8


title: Single_cell_RNASeq [B87]

description:
mRNA_with_poly_a_tail
B87


title: Single_cell_RNASeq [B82]

description:
mRNA_with_poly_a_tail
B82


title: Single_cell_RNASeq [B88]

description:
mRNA_with_poly_a_tail
B88


title: Single_cell_RNASeq [B79]

description:
mRNA_with_poly_a_tail
B79


title: Single_cell_RNASeq [B75]

description:
mRNA_with_poly_a_tail
B75


title: Single_cell_RNASeq [B77]

description:
mRNA_with_poly_a_tail
B77


title: Single_cell_RNASeq [B85]

description:
mRNA_with_poly_a_tail
B85


title: Single_cell_RNASeq [B84]

description:
mRNA_with_poly_a_tail
B84


title: AF9 ALL-1


title: Single_cell_RNASeq [B73]

description:
mRNA_with_poly_a_tail
B73


title: Single_cell_RNASeq [B74]

description:
mRNA_with_poly_a_tail
B74


title: Single_cell_RNASeq [B69]

description:
mRNA_with_poly_a_tail
B69


title: Single_cell_RNASeq [B68]

description:
mRNA_with_poly_a_tail
B68


title: Single_cell_RNASeq [B71]

description:
mRNA_with_poly_a_tail
B71


title: Single_cell_RNASeq [B90]

description:
mRNA_with_poly_a_tail
B90


title: Af4 ALL-6


title: Af4 ALL-1


title: Single_cell_RNASeq [B67]

description:
mRNA_with_poly_a_tail
B67


title: Single_cell_RNASeq [B66]

description:
mRNA_with_poly_a_tail
B66


title: Single_cell_RNASeq [B89]

description:
mRNA_with_poly_a_tail
B89


title: Single_cell_RNASeq [B64]

description:
mRNA_with_poly_a_tail
B64


title: Wild-type Vogels Minimal Medium with chitosan 16h

city: San Vicente

first: Federico

last: Lopez-Moya

state: Alicante

address: San Vicente Road S/N

department: Marine Science and Applied Biology

country: Spain

institute: University of Alicante

data_processing:
Illumina Casava1.7 software used for basecalling
Sequenced libraries were mapped against predicted transcripts from the Neurospora crassa OR74A genome (v10) with TopHat (v2.0.4) and the short sequence aligner Bowtie (v2.0.0.6).
Transcript abundance measured as FPKMs (Fragments Per Kilobase transcript model per Million fragments mapped) was calculated using Cufflinks (v 2.0.2) using counts that exclusively mapped to predicted transcripts to estimate the FPKM denominator
Genome_build: N. crassa OR74A; NC12
Supplementary_files_format_and_content: Transcript abundance measurement; FPKMs

organism: Neurospora crassa OR74A

growth_protocol: VMM salts diluted 100 times with 2% sucrose was used as a culture media, we adopted this media because chitosan precipitated with some salts included in standard VMM. Time-course experiments of germination were assessed every 2h for 24h under continuous light, shaking at 200 rpm and 25ºC. N. crassa conidia sensitivity to chitosan was evaluated using selected media, with sub-lethal concentrations of chitosan (0.1-1 µg ml-1). Finally we performed the experiment to determine the transcriptomic response of N. crassa to chitosan in a final concentration of 0.5 µg ml-1 of this compound. We selected a chitosan dose that resulted in a 50% inhibition of germination respect to the control (IC50). The percentage of N. crassa conidial germination with chitosan for 2, 4, 6, 8, 10, 12 and 16h after inoculation was measured. Finally we studied the transcriptomic response at 4, 8 and 16h.

extract_protocol:
N. crassa samples were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain info

tag: genotype/variation

value: wild type

tag: cultured in

value: Culture media + chitosan (0.5 µg ml-1)

tag: time point


title: Wild-type Vogels Minimal Medium with chitosan 8h


title: Wild-type Vogels Minimal Medium with chitosan 4h


title: Wild-type Vogels Minimal Medium 4h

source_name: Wild-type Vogels Minimal Medium

value: control culture media


title: V-01

city: Pretoria

first: Stanford

last: Kwenda

state: Gauteng

address: Lunnon Road, Hilcrest

department: Microbiology and Plant Pathology Forestry and Agricultural Biotechnology Institute (FABI)

country: South Africa

institute: University of Pretoria

data_processing:
Base-calling and adapter sequence removal were done at BGI-Shenzhen
Strand-specific sequencing reads for each cultivar were quality checked using FASTQC (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc) and mapped to the potato reference genome (Genome assembly: PGSC_DM_v4.03; http://solanaceae.plantbiology.msu.edu/pgsc_download.shtml) using TopHat2 (version 2.0.13)
Transcript assembly was performed using Cufflinks (version 2.2.1)
Coding Potential Calculator (CPC) was used to differentiate candidate lncRNA transcripts from mRNAs
InterproScan used as an additional filter to remove all candidate lncRNA transcripts with similarities to protein domains and signatures in the InterPro database
Genome_build: PGSC_DM_v4.03
Supplementary_files_format_and_content: txt files containing read counts for lncRNAs

organism: Solanum tuberosum

source_name: stem tissues

growth_protocol: Potato tubers were grown in the greenhouse under standard conditions (22 to 26 °C, 16 h light/ 8 h dark photoperiod and 70% relative humidity)

extract_protocol:
Total RNA was extracted from potato stems using the QIAGEN RNeasy plant mini kit (Qiagen) including DNAse treatment (Qiagen). For the preparation of strand-specific libraries, total RNA was was pooled from five time-points(0, 6,12,24,72 hours post inoculation; hpi) for cultivars BP1 and Valor.
The construction of whole transcriptome libraries and sequencing were carried out at the Beijing Genomics Institute (BGI-Shenzhen, China).  cDNA libraries were sequenced using standard Illumina protocols for strand-specific RNA-seq.

treatment_protocol: Stem inoculations were done as previously described in (Kubheka et al 2013), except that we used wild-type P. carotovorum subsp. brasiliense strain 1692 for the inoculations and inoculated plants were assessed and sampled at 0, 6, 12, 24, and 72 hours post inoculation (hpi) in triplicates (three plants were pooled together for each biological replicate)

value: stem

tag: cultivar

value: Valor

tag: phenotype

value: susceptible


title: Wild-type Vogels Minimal Medium 16h


title: ChIP-seq_STJ0537_input

first: Peter

middle: J

last: Park

address: 10 Shattuck St

department: Center for Biomedical Informatics

institute: Harvard Medical School

data_processing:
The sequenced reads were aligned to the hg19 genome assembly using Bowtie 0.12.6, allowing up to 10 matches (‘-m 10 --best’ options).
Reads on the 24 assembled chromosomes excluding the encode blacklisted regions were kept for downstream analysis.
For batches with low library complexity (<70% in any sample), only one read was preserved mapping to each position (denoted "1read")
Peaks of cross-correlation profiles were identified to estimate the typical fragment size for each sample.  Each read was considered to represent a signal at half typical fragment size from the 5' end.
Genomic profiles for visualization were generated using a sigma=100bp Gaussian smoothing after library size normalization
Genome_build: hg19
Supplementary_files_format_and_content: wig files depict genomic profiles after a sigma=100bp Gaussian smoothing.

growth_protocol: primary tissue

extract_protocol:
lysis (SDS) of sonicated (Branson) nuclei, ChIP with antibodies and Dynabeads
single read Illumina

tag: tissue id

tag: tissue source/type

value: primary kidney rhabdoid tumor tissue


title: Single_cell_RNASeq [B58]

description:
mRNA_with_poly_a_tail
B58

tag: age

tag: tissue

tag: gender


title: B-01

value: tolerant


title: ChIP-seq_STJ0090_input


title: Single_cell_RNASeq [B61]

description:
mRNA_with_poly_a_tail
B61


title: Single_cell_RNASeq [B59]

description:
mRNA_with_poly_a_tail
B59


title: Single_cell_RNASeq [B57]

description:
mRNA_with_poly_a_tail
B57


title: Wild-type Vogels Minimal Medium 8h


title: Single_cell_RNASeq [B55]

description:
mRNA_with_poly_a_tail
B55


title: ChIP-seq_BCH2698_input

value: primary brain rhabdoid tumor tissue


title: Single_cell_RNASeq [B6]

description:
mRNA_with_poly_a_tail
B6


title: ChIP-seq_STJ0347_input


title: ChIP-seq_STJ0537_H3K27ac

tag: chip antibody

value: H3K27ac (Active Motif 39133)


title: ChIP-seq_STJ0347_H3K27ac


title: Single_cell_RNASeq [B51]

description:
mRNA_with_poly_a_tail
B51


title: Single_cell_RNASeq [B5]

description:
mRNA_with_poly_a_tail
B5


title: ChIP-seq_STJ0090_H3K27ac


title: ChIP-seq_BCH2698_H3K27ac


title: Single_cell_RNASeq [B48]

description:
mRNA_with_poly_a_tail
B48


title: Single_cell_RNASeq [B46]

description:
mRNA_with_poly_a_tail
B46


title: Single_cell_RNASeq [B45]

description:
mRNA_with_poly_a_tail
B45


title: PF1_H3K27me3-ve_input

city: Ann Arbor

first: Sriram

last: Venneti

state: MI

address: 3520E MSRB 1, 1150 W. Medical Center Dr.

institute: University of Michigan

data_processing:
Sequencing reads that passed the quality filter were aligned to human genome- hg19 using bowtie version 1.0.0 with default parameters. Each sample was normalized by Reads Per Kilobase per Million mapped (RPKM). H3K27me3 peaks were called using mosaics one-sample analysis (Binning size for genome= 200 bp, threshold= 8, minsize= 200 bp, maxgap= 2000 bp).  Occupancy analysis was performed using bedtools to determine differential H3K27me3-enriched regions between different samples.
Genome_build: GRCh37
Supplementary_files_format_and_content: H3K27me3 peaks. Columns: chrID, peakStart, peakStop, peakSize, logAveP, logMinP, aveChipCount, maxChipCount, map, GC.

source_name: Posterior Fossa Ependymoma

extract_protocol:
Ependymoma samples were homogenized and fixed in 1% formaldehyde for 10 min at room temperature. Crosslinking was quenched with the addition of 125 mM glycine for 5 min. Samples were then lysed in SDS lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl) and sonicated with Bioruptor (Diagenode) to 200-500 bp fragments. After centrifugation, the lysates were diluted with dilution buffer (167 mM NaCl, 0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl) and incubated with 10 µg of anti-H3K27me3 antibody (9733, Cell Signaling Technology) bound to Dynal magnetic beads (Invitrogen) overnight at 4¡C. Magnetic beads were washed with low salt buffer (150 mM NaCl; 0.1% SDS; 1% Triton X-100; 1 mM EDTA; 50 mM Tris-HCl), high salt buffer (500 mM NaCl; 0.1% SDS; 1% Triton X-100; 1 mM EDTA; 50 mM Tris-HCl), LiCl buffer (150 mM LiCl; 0.5% Na deoxycholate; 0.1% SDS; 1% Nonidet P-40; 1 mM EDTA; 50 mM Tris-HCl) and TE buffer (1 mM EDTA; 10 mM Tris-HCl). ChIP DNA was eluted and recovered using Qiagen PCR purification kit.
ChIP sequencing libraries were prepared according to the Illumina TruSeq protocol and were sequenced on the HiSeq 2000.

treatment_protocol: Noine

value: Posterior Fossa Ependymoma

tag: subgroup

value: Low global H3K27me3


title: ST5_H3K27me3+ve_input

source_name: Supratentorial Ependymoma

value: Supratentorial Ependymoma

value: High global H3K27me3


title: ST4_H3K27me3+ve_input


title: PF6_H3K27me3-ve_input


title: ST6_H3K27me3+ve_H3K27me3

value: anti-H3K27me3 antibody (9733, Cell Signaling Technology)


title: Single_cell_RNASeq [B42]

description:
mRNA_with_poly_a_tail
B42


title: Single_cell_RNASeq [B43]

description:
mRNA_with_poly_a_tail
B43


title: PF5_H3K27me3-ve_input


title: Single_cell_RNASeq [B39]

description:
mRNA_with_poly_a_tail
B39


title: Single_cell_RNASeq [B53]

description:
mRNA_with_poly_a_tail
B53


title: Single_cell_RNASeq [B44]

description:
mRNA_with_poly_a_tail
B44


title: Single_cell_RNASeq [B38]

description:
mRNA_with_poly_a_tail
B38


title: PF1_H3K27me3-ve_H3K27me3


title: Single_cell_RNASeq [B37]

description:
mRNA_with_poly_a_tail
B37


title: Single_cell_RNASeq [B41]

description:
mRNA_with_poly_a_tail
B41


title: ST5_H3K27me3+ve_H3K27me3


title: PF6_H3K27me3-ve_H3K27me3


title: ST4_H3K27me3+ve_H3K27me3


title: Single_cell_RNASeq [B36]

description:
mRNA_with_poly_a_tail
B36


title: Single_cell_RNASeq [B30]

description:
mRNA_with_poly_a_tail
B30


title: ST6_H3K27me3+ve_input


title: ST3_H3K27me3+ve

description: High global H3K27me3

data_processing:
All sequenced libraries were mapped to the human genome (hg19) using TopHat(v.2.0.3) [5] with the following parameters: '-r 70 --mate-std-dec 90'. A custom GTF file that includes both RefSeq information (from the UCSC genome browser) and the ERCC transcript information was used (--GTF $SEQCLB/hg19_150_ERCC.gtf) along with the transcriptome index option (--transcriptome-index $SEQCLIB/hg19_150_ERCC). Genes shorter than 150 bp were excluded from this GTF file. HTSeq (v.0.5.3p3) [15] was used to generate the count matrix with the following parameters: 'htseq-count -m intersection-strict -s no' with the same GTF file used for the alignment step ($SEQCLIB/hg19_150_ERCC.gtf).
Genome_build: GRCh37
Supplementary_files_format_and_content: counts

extract_protocol:
RNA was isolated using Trizol (15596-026, Invitrogen) and treated with DNase (9003-98-9, Sigma).
RNA sequencing, libraries were prepared according to the Illumina TruSeq protocol and were sequenced on the HiSeq 2000


title: Single_cell_RNASeq [B28]

description:
mRNA_with_poly_a_tail
B28


title: Single_cell_RNASeq [B27]

description:
mRNA_with_poly_a_tail
B27


title: ST2_H3K27me3+ve

description: High global H3K27me3


title: Single_cell_RNASeq [B25]

description:
mRNA_with_poly_a_tail
B25


title: ST1_H3K27me3+ve

description: High global H3K27me3


title: PF4_H3K27me3-ve

description: Low global H3K27me3


title: Single_cell_RNASeq [B23]

description:
mRNA_with_poly_a_tail
B23


title: Single_cell_RNASeq [B19]

description:
mRNA_with_poly_a_tail
B19


title: PF3_H3K27me3-ve

description: Low global H3K27me3


title: Single_cell_RNASeq [B18]

description:
mRNA_with_poly_a_tail
B18


title: PF13_H3K27me3-ve

description: Low global H3K27me3


title: Single_cell_RNASeq [B16]

description:
mRNA_with_poly_a_tail
B16


title: Single_cell_RNASeq [B15]

description:
mRNA_with_poly_a_tail
B15


title: Single_cell_RNASeq [B34]

description:
mRNA_with_poly_a_tail
B34


title: PF1_H3K27me3-ve

description: Low global H3K27me3


title: Single_cell_RNASeq [B10]

description:
mRNA_with_poly_a_tail
B10


title: PF5_H3K27me3-ve_H3K27me3


title: Single_cell_RNASeq [A96]

description:
mRNA_with_poly_a_tail
A96


title: HIO+ENS_Phox2b_Homo3

first: Michael

middle: A

last: Helmrath

address: 3333 Burnet Avenue

department: CuSTOM

description: Single-end 75bp, 30 million reads

data_processing:
Following removal of primers and barcodes, RNA-seq analysis was performed entirely in Strand NGS software (Agilent Technologies, Santa Clara, CA).
The samples were aligned against the GRCh37 genome model. Multiply mapping reads were removed and aligned reads were filtered on base quality, with a quality threshold >=30 and zero ‘Ns’ allowed in each read. The aligned gene read counts were quantified and used to compute reads per kilobase per million reads (RPKMs) for each transcript in each sample.
Raw counts were normalized using the DESeq algorithm, thresholded to 1, and baselined to the median of all samples.
Genome_build: GRCh37
Supplementary_files_format_and_content: Normalized expression matrix

molecule: polyA RNA

extract_protocol:
Samples were placed into DNase- and RNase-free 1.5 ml microfuge tubes containing RA1 lysis buffer. Total RNA from organoids was isolated using NucleoSpin RNA isolation Kit (Macherey-Nagel). Isolation was carried out according to the manufacturers’ protocol.
Whole-transcriptome (RNA) sequencing was performed at the CCHMC DNA Sequencing and Genotyping Core. Following RNA isolation, the RNA was quantified (Qubit RNA Assay Kit, Life Technologies, Inc.) and quality controlled. 1000 ng was used as input for the Illumina TruSeq RNA prep kit (Illumina, Inc.) RNA-seq libraries were prepared using the Illumina TruSeq RNA preparation kit and sequenced on the Illumina Hi-Seq 2000 with single-end 75-bp, 30 million reads (Illumina, San Diego, CA).

value: ES derived human intestinal organoid

tag: cell line

value: H1 (WA-01) + WTC10 Phox2B null (Y14X/Y14X)

value: 28 days

tag: type

value: in vitro


title: HIO+ENS_Phox2b_Homo2

description: Single-end 75bp, 30 million reads


title: Single_cell_RNASeq [A95]

description:
mRNA_with_poly_a_tail
A95


title: Single_cell_RNASeq [B1]

description:
mRNA_with_poly_a_tail
B1


title: HIO+ENS_Phox2b_Het2

description: Single-end 75bp, 30 million reads

value: H1 (WA-01) + WTC10 Phox2B het (+/Y14X)


title: Single_cell_RNASeq [A93]

description:
mRNA_with_poly_a_tail
A93


title: HIO+ENS_Phox2b_Het3

description: Single-end 75bp, 30 million reads


title: HIO+ENS_Phox2b_Het1

description: Single-end 75bp, 30 million reads


title: HIO+ENS_Phox2b_Homo1

description: Single-end 75bp, 30 million reads


title: HIO+ENS_3

description: Single-end 75bp, 30 million reads

source_name: HIO+ENS


title: Single_cell_RNASeq [A91]

description:
mRNA_with_poly_a_tail
A91


title: HIO+ENS_2

description: Single-end 75bp, 30 million reads


title: Single_cell_RNASeq [A90]

description:
mRNA_with_poly_a_tail
A90


title: Single_cell_RNASeq [A92]

description:
mRNA_with_poly_a_tail
A92


title: HIO+ENS_1

description: Single-end 75bp, 30 million reads


title: Single_cell_RNASeq [A89]

description:
mRNA_with_poly_a_tail
A89


title: PF14_H3K27me3-ve

description: Low global H3K27me3


title: PF18_H3K27me3+ve

data_processing:
All the paired-end reads were aligned to the human reference GRCh37 augmented by splice junctions from Ensembl (Flicek et al. 2012) 75 using STAR 2.3 (Dobin et al. 2013) with default settings in two-pass alignment filtering mode “--outFilterType BySJout.” Only primary alignments were kept, duplicate fragments were marked using SAMtools (Li et al. 2009), and BAM files were sorted using novosort (http://www.novocraft.com/products/novosort/). The number of reads spanning each splice junction was obtained from the “SJ.out.tab” file provided by STAR.
Reads overlapping Ensemble genes were counted using featureCounts
Genome_build: GRCh37
Supplementary_files_format_and_content: counts

extract_protocol:
RNA was isolated using Trizol (15596-026, Invitrogen) and treated with DNase (9003-98-9, Sigma).
RNA sequencing, libraries were prepared according to the Illumina TruSeq protocol and were sequenced on the HiSeq 2500


title: PF17_H3K27me3+ve


title: Single_cell_RNASeq [A88]

description:
mRNA_with_poly_a_tail
A88


title: HIO_2

description: Single-end 75bp, 30 million reads

source_name: HIO


title: Single_cell_RNASeq [A87]

description:
mRNA_with_poly_a_tail
A87


title: Single_cell_RNASeq [A84]

description:
mRNA_with_poly_a_tail
A84


title: PF15_H3K27me3+ve


title: Single_cell_RNASeq [A86]

description:
mRNA_with_poly_a_tail
A86


title: HIO_1

description: Single-end 75bp, 30 million reads


title: PF10_ H3K27me3-ve


title: PF11_ H3K27me3-ve


title: Single_cell_RNASeq [A83]

description:
mRNA_with_poly_a_tail
A83


title: PF9_ H3K27me3-ve


title: Single_cell_RNASeq [A80]

description:
mRNA_with_poly_a_tail
A80


title: Single_cell_RNASeq [A77]

description:
mRNA_with_poly_a_tail
A77


title: Single_cell_RNASeq [A81]

description:
mRNA_with_poly_a_tail
A81


title: PF7_ H3K27me3-ve


title: PF4_ H3K27me3-ve


title: uMSC-Exo [miRNA-seq]

city: Shanghai

first: Chen

last: Xu

address: No, 800, Rd. Xiangyin

country: China

institute: The Second Military Medical University

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a) 30% base quality <13 b) read length < 17bp c) adaptor sequence.
Utilizing the BWA software, we mapped the clean data to miRBase 21.0 Homo Sapiens miRNA database and GRCH37.p13 genome.
count counting
Genome_build:  hg19_GRCh37 / miRBase 21.0
Supplementary_files_format_and_content: txt file contain counts for each sample

growth_protocol: HEK293T and uMSCs are cultured in T75 flasks for exosome preparation. The medium used for exosome collection were modified by using an exosome-free culture medium. In brief, we first centrifuged fetal bovine serum at 120,000g 4C overnight to exclude any serum exosomes from the product. The supernatant were syringed through a 0.22μm filter before use. DMEM with 10% exosome-free FBS were used for both uMSC and HEK293T culture.

extract_protocol:
Total RNA was extracted from exosomes. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for miRNA purification. miRNA was purified by miRNeasy Mini Kit (Qiagen) and the purification result was validated by Gel electrophoresis.
The complementary DNA (cDNA) libraries for single-end sequencing were prepared using Ion Total RNA-Seq Kit v2.0 (Life Technologies) according to the manufacturer’s instructions. The cDNA libraries were then processed for the Proton Sequencing process according to the commercially available protocols. Samples were diluted and mixed, the mixture was processed on a OneTouch 2 instrument (Life Technologies) and enriched on a OneTouch 2 ES station (Life Technologies) for preparing the template-positive Ion PI™ Ion Sphere™ Particles (Life Technologies) according to Ion PI™ Template OT2 200 Kit v2.0 (Life Technologies). After enrichment, the mixed template-positive Ion PI™ Ion Sphere™ Particles of samples was loaded on to 1 P1v2 Proton Chip (Life Technologies) and sequenced on Proton Sequencers according to Ion PI Sequencing 200 Kit v2.0 (Life Technologies) by NovelBio Corp. Laboratory, Shanghai.

treatment_protocol: Culture medium collection started when cells reach 90% confluence. The medium were collected every other day.

value: uMSC

tag: cell type

value: umbilical cord mesenchymal stem cells

tag: passage

tag: sample type

value: Exosomes


title: HEK293T-Exo [miRNA-seq]

value: Human Embryonic Kidney cells


title: Single_cell_RNASeq [A75]

description:
mRNA_with_poly_a_tail
A75


title: Single_cell_RNASeq [A76]

description:
mRNA_with_poly_a_tail
A76


title: PF5_ H3K27me3-ve


title: Single_cell_RNASeq [A74]

description:
mRNA_with_poly_a_tail
A74


title: Single_cell_RNASeq [A73]

description:
mRNA_with_poly_a_tail
A73


title: HIO_3

description: Single-end 75bp, 30 million reads


title: PF16_H3K27me3+ve


title: PF2_ H3K27me3-ve


title: Single_cell_RNASeq [A72]

description:
mRNA_with_poly_a_tail
A72


title: Single_cell_RNASeq [A69]

description:
mRNA_with_poly_a_tail
A69


title: PF1_ H3K27me3-ve


title: Single_cell_RNASeq [A67]

description:
mRNA_with_poly_a_tail
A67


title: HEK293_Flag-ZMYND8_ChIP-seq (replicate_2)

city: St. Petersburg

first: Alexander

last: Kanapin

address: 7/9 University Emb.

department: Institute for Translational Biomedicine

country: Russia

institute: St Petersburg Universoty

data_processing:
Basecalling was with bclToFastq (Illumina basecaller) version 1.8.4
The FASTQ files for ZMYND8, H3K14ac, H3K27ac were mapped to the human reference genome (hg19) by BWA-MEM using default parameters allowing up to two mismatches.
The genome ChIP-seq profiles for ZMYND8, H3K14ac, H3K27ac were generated using HOMER
The ChIP-seq profiles were normalized to GC content, 109 total tag numbers and peaks were called at FDR<=10-3.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig, peaks bed

growth_protocol: Flp-In T-REx HEK293 cells, stably carrying inducible full length 3xFLAG-ZMYND8, were maintained in DMEM, GlutaMAX supplement (Cat.#10566-016; Gibco), supplemented with 10 % heat-inactivated foetal bovine serum (FBS - Sigma), 100 U/mL penicillin (Gibco), 100 µg/mL streptomycin (Gibco), and 200µg/ml Hygromycin (Invitrogen). Cells were grown at 37 °C in a humidified cabinet at 5 % CO2.

extract_protocol:
The ChIP DNA was collected using the SimpleChIP™ Enzymatic Chromatin IP Kit (Cell Signaling Technology #9005), according to the manufacturer’s protocol. Briefly, HEK293 cells were collected from 15 cm plates and treated with 1 % formaldehyde (cross-linking) for 10 min and 125 mM Glycine for another 5 min (quenching) at room temperature. After washing three times with 1X PBS, cells were lysed in buffer A for 10 min on ice, then washed once in buffer B. Cells were re-suspended in buffer B, then treated with MNase (2000 gel units per 100 ml reaction) at 37 ˚C for 30 min, before the digestion was stopped by adding EDTA (10 μl 0.5 mM EDTA per 100 μl reaction). Chromatin extracts were harvested following complete lysis of nuclei by sonication.
Libraries were constructed using Wafergen’s PrepX Complete ILMN 32i DNA Library Kit (cat number 400076) with an input of 5ng where available using the Apollo 324

treatment_protocol: For Flag-ZMYND8 ChIP-seq pull-down by anti-Flag antibody, Flp-In T-Rex HEK293 cells carrying inducible full length 3xFLAG-ZMYND8 were treated with 10 nM Doxycycline to induce the overexpression of Flag-ZMYND8.

value: Flag (Sigma, F1804)


title: HEK293_Flag-ZMYND8_ChIP-seq (replicate_1)


title: Single_cell_RNASeq [A66]

description:
mRNA_with_poly_a_tail
A66


title: Single_cell_RNASeq [A65]

description:
mRNA_with_poly_a_tail
A65


title: ConvR1_HFHS

city: Madison

first: John

middle: M.

last: Denu

state: Wisconsin

address: 330 N. Orchard Street

department: Biomolecular Chemistry

institute: University of Wisconsin-Madison

data_processing:
The first 10bp were trimmed to eliminate GC bias at the beginning of each read (FastX trimmer).
The 6bp Illumina adapter sequences were then clipped (FastX Clipper)
A quality filter was applied to eliminate any reads with a quality score < 30 (FastX Quality Filter).
Reads were then aligned to the mm9 reference genome constructed to include only annotated genes (NM_RegSeqs) by Bowtie 2 alignment (seed length = 28, 2 mismatches per seed allowed).
Expression level determined using RSEM v 1.2.23
Genome_build: mm9
Supplementary_files_format_and_content: txt file containing gene expression  values in expected counts, TPM, and FPKM (.resultts)

source_name: liver

growth_protocol: Animal care and study protocols were approved by the University of Wisconsin - Madison Animal Care and Use Committee. Mice were housed in the Microbial Sciences Building vivarium. Conventionally-raised (ConvR) and germ-free (GF) C57BL/6J mice were bred at the University of Wisconsin-Madison to generate mice used in this study. ConvR and GF mice were housed in separate plastic flexible vinyl gnotobiotic isolators. Conventionalized (ConvD) mice were generated by colonizing GF C57BL/6J with fresh cecal contents were collected from 15-week old conventionally-raised C57BL/6J mice maintained on a chow diet diet (n = 2 mice per donor cecal microbiota samples per experiment). Immediately after sacrifice, fresh cecal contents from donor mice were re-suspended in Mega Medium (1:100 w/v) in an anaerobic chamber. Suspensions were transferred into anaerobic sealed tubes and used to colonize mice in a sterile biological safety cabinet. Germ-free 15-week-old C57Bl/6J male mice were inoculated via a single oral gavage with ~0.2 ml of cecal incolula (Turnbaugh et al., 2009) and kept in sealed filter-top gnotobiotic cages for 4 weeks. Mice were group housed by colonization status and diet (3-5 mice/cage) under standard conditions (12 h light:dark, temperature- and humidity-controlled conditions), and received ad libitum access to water and food. After 3 weeks of age, mice were maintained on either a control breeder chow (5021, Lab Diet, 23.7%-kcal fat, 53.2% carbohydrate, 23.1% protein) or a high-fat high-sucrose (HF/HS) diet (TD.08811, Envigo Teklad, 44.6%-kcal fat, 40.6% carbohydrate, 14.8% protein). Diets were sterilized by irradiation and autoclaving. Sterility of germ-free animals was assessed by incubating freshly collected fecal samples under aerobic and anaerobic conditions using standard microbiology methods. Final dissection and data collection were performed at 19-weeks of age.

extract_protocol:
RNA was extracted using a Qiagen RNA-easy minikit
Library was constructed using the Illumina TruSeq Stranded mRNA Library Preparation Kit

treatment_protocol: C57BL/6J mice were (1) maintained germ-free throughout the experiment, (2) allowed to acquire a microbitoa from birth to adulthood (conventionally raised, ConvR), or (3) colonized with a complete (uncultured) microbiota harvested from ConvR donors (conventionalized, ConvD)

tag: colonization status

value: conventionally raised (ConvR)

tag: strain

tag: diet

value: HF/HS


title: ConvR3_HFHS


title: Single_cell_RNASeq [A63]

description:
mRNA_with_poly_a_tail
A63

value: Meninges


title: Single_cell_RNASeq [A60]

description:
mRNA_with_poly_a_tail
A60


title: PF3_ H3K27me3-ve

value: Posterior Fossa Ependymoma

value: Low global H3K27me3


title: Single_cell_RNASeq [A61]

description:
mRNA_with_poly_a_tail
A61


title: PF8_ H3K27me3-ve


title: GF2_HFHS

value: germ-free


title: Single_cell_RNASeq [A6]

description:
mRNA_with_poly_a_tail
A6


title: GF1_HFHS

value: high fat, high sucrose (HF/HS)


title: ConvR2_HFHS


title: ConvD2_chow

value: conventionalized (ConvD)

value: chow


title: ConvD3_chow


title: ConvD1_chow


title: Single_cell_RNASeq [A59]

description:
mRNA_with_poly_a_tail
A59


title: GF3_HFHS


title: Single_cell_RNASeq [A56]

description:
mRNA_with_poly_a_tail
A56


title: ConvR3_chow


title: Single_cell_RNASeq [A55]

description:
mRNA_with_poly_a_tail
A55


title: HEK293_Flag-input DNA

source_name: HEK293_Flag-input DNA


title: RCH_P300_ChIPseq

city: Oxford

first: Thomas

last: Milne

address: John Radcliffe Hospital

department: Molecular Haematology Unit

country: United Kingdom

institute: Weatherall Institute of Molecular Medicine

data_processing:
Nascent RNA-seq reads were aligned to the hg18 genome using STAR
Read counts were determined using featureCounts (Subread package)
ChIP-seq reads were aligned to the hg18 genome using bowtie version 1.1.2 with following parameters: p1 m2 best strata sam. Duplicates were removed prior to subsequent analysis
CaptureC reads were mapped and analysed using the CaptureC 'CCanalyser3' pipeline (https://github.com/telenius/captureC/releases) using bowtie2 for paired-end reads with genome build hg18
Genome_build: hg18
Supplementary_files_format_and_content: Rpkm table was generated using edgeR
Supplementary_files_format_and_content: CaptureC_combinedReads.txt is a text file containing the reads from the WIG file of the Capture-C track, around the region that is investigated.

source_name: Leukemia cell line (RCH-ACV)

growth_protocol: Cells were continuously grown in IMDM (SEM) or RPMI1640 (RCH-ACV) with 10-20% FBS, split when they reached a density of 1-2X10e6 down to 5X10e5

extract_protocol:
108 fixed cells were lysed in 1% SDS lysis buffer. Samples were sonicated and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's protocol accompanying the NEBNext DNA (Part# E6040) or Ultra RNA (Part# E7530) Library Prep Master Mix Set.

value: Paediatric pre B-cell line derived from cALL with t(1;19)(q23;p13) translocation


title: Single_cell_RNASeq [A54]

description:
mRNA_with_poly_a_tail
A54


title: ConvR2_chow


title: 180h-4

city: La Jolla

first: Nathan

last: Lewis

state: CA

address: 9500 Gilman Dr. MC 0760

institute: UCSD

description: Sample taken at t=180, replicate #4

data_processing:
FastQC (Andrews, 2010) was used to assess read quality.
Trimmomatic v0.32 (Bolger et al., 2014) was used to trim reads with adapters or low quality scores.
STAR2.4.0a (Dobin et al., 2013) was used to align trimmed reads to the CHO-K1 genome (Xu et al., 2011).
Mapping results were stored using SAMtools 1.0(Li et al., 2009).
Cufflinks 2.2.1 (Trapnell et al., 2010) was used to assemble mapped reads and quantify expression levels.
Genome_build: CHOK1 reference genome from ncbi ftp site: ftp://ftp.ncbi.nlm.nih.gov/genomes/Cricetulus_griseus/CHR_Un/cgr_ref_CriGri_1.0_chrUn.fa.gz
Supplementary_files_format_and_content: Tab delimited file containing FPKM measurements for genes.

organism: Cricetulus griseus

source_name: CHO-S

growth_protocol: CHO-S (Life Technologies # A11557-01) cells were cultured in CD CHO medium (Life Technologies # 10743-029) supplemented with 8 mM L-glutamine (Life Technologies # 25030-024), Anti-clumping agent 1:500 (Life Technologies # 0010057 AE), and Pen-Strep 1:100 (Life Technologies # 15140-122) in 2 L Corning shake flasks (Sigma # 431255) with 400 mL medium. All cultures were maintained in an incubator kept at 37°C, 5% CO2, 70% humidity and 25 mm throw, shaking at 120 rpm.

extract_protocol:
5 x 10^6 cells were harvested for transcriptomic analysis via RNA-Seq. Cells were centrifuged and the pellet resuspended in 2%/98% DTT/RLT buffer and stored at -80°C. RNA was extracted with Qiagen's RNeasy mini kit (Qiagen #74104) according to manufacturer's protocol with on-column DNase digestion.
RNA libraries for sequencing were prepared using TruSeq Stranded mRNA Sample prep kit with 96 dual indexes (Illumina, CA, USA) according to the manufacturer’s instructions with the following changes. The protocols were automated using an Agilent NGS workstation (Agilent, CA, USA) using purification steps as previously described (Borgström et al., 2011; Lundin et al., 2010). Libraries were clustered using cBot and sequenced on HiSeq2500 (HiSeq Control Software 2.2.38/RTA 1.18.61) with a 2x126 setup in RapidHighOutput mode.

value: CHO-S

tag: time after seeding (h)


title: MLL-AF4_ChIPSeq

city: Birmingham

first: Salam

middle: Adli

last: Assi

address: IBR

department: Institute for Cancer and Genomic Sciences

institute: University of Birmingham

data_processing:
Quality of reads was verified using FASTQC analysis
Sequences reads in fastq format were mapped onto the reference human genome version hg38, Genome Reference Consortium GRCh38. The Illumina reads were aligned to the human genome using Bowtie2
Reads that were uniquely aligned to chromosomal positions were retained and duplicate reads were removed from the aligned data using Picard tools.
The filtered aligned reads were used to generate density profiles using “genomeCoverageBed” function from bedtools
Genome_build: hg38
Supplementary_files_format_and_content: bedGraph

source_name: FLAG_MLL-AF4_ ChIPseq

growth_protocol: Human CD34+ hematopoietic stem and progenitor cells expressing MLL-Af4 were transplanted into NSG mice, the CD19+ leukemic cells were extracted from mouse bone marrow for ChIP-seq

extract_protocol:
ChIP-Seq assay were performed essentially as previously described (Ptasinska et al., 2014). Antibody against Flag (Sigma, M2)  was used for IP. Cells were first washed with PBS and then cross-linked with 0.83 mg/ml Di(N-succinimidyl) glutarate (DSG) (Sigma) for 45 minutes at room temperature with rotation. Cells were washed four times with PBS and further crosslinked in PBS with 1% formaldehyde (~0.34 M) for 10 minutes at room temperature. All crosslinking reactions were quenched by adding 4 volumes of PBS and 0.125 M glycine, cells were washed twice in PBS and incubated with Buffer A (10 mM HEPES pH 8.0, 10 mM EDTA, 0.5 mM EGTA, 0.25% Triton X-100, proteinase inhibitor cocktail (Roche UK, Burgess Hill, UK) and 0.1 mM PMSF), incubated for 10 min at 4°C with rotation, and centrifuged 5 min at 500 x g at 4 °C. The pellet was resuspended in 10 ml of ice–cold Buffer B (10 mM HEPES pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.01% Triton X-100, protease inhibitor cocktail and 0.1 mM PMSF), incubated for 10 min at 4 °C with rotation and centrifuged for 5 min at 500 x g at 4 °C. Cells were resuspended in 600 μl of ice-cold ChIP lysis buffer (25 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.25% SDS, protease inhibitor cocktail and 0.1 mM PMSF), incubated 10 min on ice and sonicated at 5 °C using a Bioruptor™ (Diagenode) to generate fragments an average length of 500 bp (10 min with 30 s “ON” and “OFF” cycles, power setting high). The lysates were centrifuged for 5 min at 16,000 x g at 4 °C and the supernatants were diluted with two volumes of ice-cold ChIP dilution buffer (25 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 7.5% glycerol, protease inhibitor cocktail and 0.1 mM PMSF). For each IP, 15 μl of Dynabeads® protein G (Dynal) were pre–incubated with 50 μg BSA and 1-2 μg antibody for 2 h at 4 °C with rotation. The blocked antibody-bound protein G mix was added to 20–25 μg chromatin in a total volume of 500 μl diluted ChIP lysis buffer and incubated for 2 h at 4°C with rotation. After magnetic separation the beads were washed once with 1 ml wash buffer 1 (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), twice with 1 ml wash buffer 2 (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), once with 1 ml LiCl buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% Na-deoxycholate) and twice with 1 ml TE/NaCl buffer (10 mM Tris-HCl pH 8.0, 50 mM NaCl, 1 mM EDTA). For each wash the beads were mixed with ice-cold washing buffers for 10 min at 4 °C. The immunoprecipitated DNA was eluted two times with 50 μl ChIP elution buffer (100 mM NaHCO3, 1% SDS) for 15 min at RT with shaking. At this step the input control (1% of the starting material) was included in the experimental procedure after first adjusting the final volume to 100 μl with ChIP elution buffer. The eluted DNA was incubated overnight at 65 °C in the presence of 50 μg proteinase K. The DNA was finally purified using Agencourt AMPure (Beckman Coulter) magnetic beads according to the manufacturer’s instructions, eluted with 50 μl x TE and analysed by qPCR using SYBR Green reagents.
KAPA Hyper Prep Kit, Kapa biosystems

treatment_protocol: untreated cells

tag: host strain

value: NSG mouse

tag: transplanted with

value: mouse bone marrow

value: CD19+ leukemic cells

value: anti-Flag antibody (Sigma, M2)


title: ConvR1_chow


title: Single_cell_RNASeq [A53]

description:
mRNA_with_poly_a_tail
A53

data_processing:
Basecalls performed using llumina bcl2fastq 2.17.1.14
Before alignment, adapter sequences in raw reads were trimmed by Btrim64 (http://graphics.med.yale.edu/trim)
Trimmed reads were mapped to mouse genome (ENSEMBL Release 84) using STAR-2.5.2a
Expression level of each gene was quantified in unites by transcript per million (TPM) and fragments per kilobase of transcript per million fragments mapped (FPKM) using RSEM v1.2.30 with default parameters.To compare expression levels of different genes across samples, we performed an additional TMM (trimmed mean of M-values) normalization on TPM using Trinity (http://trinityRNA-seq.github.io/) based on edgeR (abbreviated TMM-TPM). The purpose of this normalization is to account for differences in total cellular RNA production across all cells.
We developed custom R scripts based on FactoMineR library (http://factominer.free.fr/) performing PCA analysis on gene expression matrices.PCA analysis was performed on cells passed quality control. Subsequently, genes with the highest correlation coefficient with one of the first six principal components were identified using dimdesc function in FactoMineR. Hierarchical clustering was performed on cells and on the genes identified by PCA using Euclidean distance or correlation metric.
Genome_build: mm10
Supplementary_files_format_and_content: Gene expression matrices (TPM value) of each gene in each cells in CSV format

extract_protocol:
Mice were sacrificed at the indicated timepoints, when the cortex and the meninges were microdissected, digested into a single-cell suspension and DiI-positive cells were sorted by flow cytometry. Sorted cells were processed for single-cell RNA-se
Single cell RNA seq library preparation protocol was done as previously described in Llorens-Bobadilla et al., 2015


title: 180h-2

description: Sample taken at t=180, replicate #2


title: GF3_chow


title: Single_cell_RNASeq [A52]

description:
mRNA_with_poly_a_tail
A52


title: PF6_ H3K27me3-ve


title: 168h-4

description: Sample taken at t=168, replicate #4


title: 180h-1

description: Sample taken at t=180, replicate #1


title: GF1_chow


title: GST:Repo-Man_1

first: Silvia

last: Salatino

address: Roosevelt Drive

institute: Wellcome Centre for Human Genetics

data_processing:
Approximately 60-80 million read pairs were produced per sample and mapped to the human reference genome (hs37d5 version of build 37) using Stampy.
Aligned bam files from two individual sequencing lanes were merged using Picard.
Mapped reads were analysed for standard ChIP-Seq quality metrics; in particular, for each sample, the Normalized Strand Cross-correlation and the Relative Strand Cross-correlation was calculated.
Peaks were called using the software MACS2 with default parameters for narrow regions.
Genome_build: hs37d5 (GRCh37 + decoy)

source_name: HeLa cells

growth_protocol: HeLa cells were grown in DMEM supplemented with 10% FBS and 1% Penicillin-Streptomycin (Invitrogen Gibco) at 37°C with 5% CO2

extract_protocol:
HeLa lysates were prepared and nucleosomes extracted via Mnase digestion. Nucleosomes were incubated with GST:Repo-Man and GST alone. DNA was extracted and sent to sequencing.
Libraries were prepared using Wafergen’s PrepX ILM DNA Library Kits. Standard Illumina adapters were used.

value: HeLa

tag: phenotype

value: adherent


title: GST_alone_1


title: GST_alone_2


title: GST:Repo-Man_2


title: 168h-3

description: Sample taken at t=168, replicate #3


title: Single_cell_RNASeq [A48]

first: Ana

last: Martin-Villalba

address: Im Neuenheimer Feld 280

description:
mRNA_with_poly_a_tail
A48

tag: age


title: 168h-2

description: Sample taken at t=168, replicate #2


title: Single_cell_RNASeq [A51]

description:
mRNA_with_poly_a_tail
A51

tag: tissue


title: Single_cell_RNASeq [A49]

description:
mRNA_with_poly_a_tail
A49

tag: gender


title: HEK293_input DNA

data_processing:
Basecalling was with bclToFastq (Illumina basecaller) version 1.8.4
Alignment was with stampy, version 1.0.23 after pre-mapping with BWA version 0.7, the reference genome being 'hs37d5', which is GRCh37 with decoy, as used by 1000 Genomes.
The FASTQ files for ZMYND8, H3K14ac, H3K27ac were mapped to the human reference genome (hg19) by BWA-MEM using default parameters allowing up to two mismatches.
The genome ChIP-seq profiles for ZMYND8, H3K14ac, H3K27ac were generated using HOMER
The ChIP-seq profiles were normalized to GC content, 109 total tag numbers and peaks were called at FDR<=10-3.
Genome_build: hg19
Supplementary_files_format_and_content: Bed and bigWig files with CHiPSeq peaks and density of tags

source_name: Kidney

growth_protocol: Flp-In T-REx HEK293 cells, stably expressing full length 3xFLAG-ZMYND8 or 3xFLAG-ZMYND8 N228F mutant, were maintained in DMEM, GlutaMAXTM supplement (Cat.#10566-016; Gibco), supplemented with 10 % heat-inactivated foetal bovine serum (FBS - Sigma), 100 U/mL penicillin (Gibco), 100 µg/mL streptomycin (Gibco), and 200µg/ml Hygromycin (Invitrogen). Cells were grown at 37 °C in a humidified cabinet at 5 % CO2.

tag: chip antibody


title: Single_cell_RNASeq [A47]

description:
mRNA_with_poly_a_tail
A47


title: 168h-1

description: Sample taken at t=168, replicate #1


title: HEK293_H3K27ac_ChIP-seq (replicate_2)

value: H3K27ac (Millipore, 07-595)


title: ConvD3

treatment_protocol: C57BL/6J mice were (1) maintained germ-free throughout the experiment, (2) maintained germ-free throughout the experiment and supplemented with a mixture of short chain fatty acids via drinking water supplied ad lib, or (3) colonized with a complete (uncultured) microbiota harvested from ConvR donors (conventionalized, ConvD)

tag: supplement


title: ConvD1


title: ConvD2


title: 180h-3

description: Sample taken at t=180, replicate #3

tag: cell line


title: 156h-4

description: Sample taken at t=156, replicate #4


title: Single_cell_RNASeq [A45]

description:
mRNA_with_poly_a_tail
A45


title: GF+SCFA3

value: acetate(67.5mM), propionate (25.9 mM), butyrate (40mM) via filter-sterilized drinking water supplied ad lib


title: HEK293_H3K14ac_ChIP-seq (replicate_2)

value: H3K14ac (Millipore, 07-353)


title: GF2_chow


title: 156h-3

description: Sample taken at t=156, replicate #3


title: GF+SCFA2


title: Single_cell_RNASeq [A42]

description:
mRNA_with_poly_a_tail
A42

value: Meninges


title: HEK293_H3K14ac_ChIP-seq (replicate_1)


title: 156h-2

description: Sample taken at t=156, replicate #2


title: HEK293_ZMYND8_ChIP-seq (replicate_2)

value: ZMYND8(Bethyl Laboratory, A302-089A)


title: GF+SCFA1

value: germ-free


title: Single_cell_RNASeq [A41]

description:
mRNA_with_poly_a_tail
A41


title: 156h-1

description: Sample taken at t=156, replicate #1


title: GF3


title: Single_cell_RNASeq [A46]

description:
mRNA_with_poly_a_tail
A46


title: HEK293_H3K27ac_ChIP-seq (replicate_1)


title: 144h-4

description: Sample taken at t=144, replicate #4


title: Single_cell_RNASeq [A4]

description:
mRNA_with_poly_a_tail
A4


title: Single_cell_RNASeq [A37]

description:
mRNA_with_poly_a_tail
A37


title: GF1


title: Single_cell_RNASeq [A36]

description:
mRNA_with_poly_a_tail
A36


title: GF2


title: 144h-2

description: Sample taken at t=144, replicate #2


title: HEK293_ZMYND8_ChIP-seq (replicate_1)


title: 144h-3

description: Sample taken at t=144, replicate #3


title: 144h-1

description: Sample taken at t=144, replicate #1


title: Math1::Cre; Rosa tdTomato; Hoxa2+/fl; Hoxb2fl/fl rep 3

city: Basel

first: Tim

last: Roloff

address: Maulbeerstrasse 66

department: Functional Genomics

country: Switzerland

institute: FMI

data_processing:
HCS 2.2.58 was used with default parameters for base calling.
bcl2fastq 1.8.4 (Illumina) was used to generate fastq files
Raw reads were preprocessed using the R/Bioconductor package QuasR: Reads with more than 2Ns were removed with the function preprocessReads(). The remaining reads were aligned to mm10 using the qAlign() with splicedAlignments=TRUE and the following parameters: Rbowtie v1.4.0 (parameters: -max_intron 400000 -min_intron 20000 -max_multi_hit 10 -selectSingleHit TRUE -seed_mismatch 1 -read_mismatch 2 -try_hard yes)
The QuasR function qCount() was used to extract a table with raw read counts per gene for all Ensembl genes for each sample.
Genome_build: mm10
Supplementary_files_format_and_content: table containig raw read counts per gene. First column: Ensembl gene ID, second column: number of unique, non-masked bases for all exons of the gene.

source_name: Cochlear Nucleaus

extract_protocol:
Pregnant females were sacrificed at gestational day e18.5 to retrieve mutant and wild type embryos. Embryos were than hand dissected to extract cochlear nuclei. The collected tissue was than incubated with Trypsin 0.5% in DMEM at 37°C while shacking. Trypsin was blocked with DMEM complemented with FBS 10% and cells were mechanically dissociated on ice using a pasteur glass pipet. Cells were washed 3 times in DMEM. 30000 cells per sample were than FACS sorted and collected in Lysis buffer. RNA was extracted using the Picopure extraction kit. For each replicate sample 3 littermate embrios were pulled together. Embryos for each sample come from a different pregnant mother.
Libraries were constructed from 2ng total RNA with the TotalScript RNA-seq kit (Epicentre) using a mix of poly-A and random primers and 14 cycles of PCR for the amplification. Each library were barcoded and all 8 libraries pooled equimolarly. The pool was sequenced on 3 different lanes on an Illumina HiSeq2500 sequencer.

tag: developmental stage

value: FACS sorted cells

tag: genotype

value: mutant


title: Math1::Cre; Rosa tdTomato; Hoxa2+/fl; Hoxb2fl/fl rep 4


title: Single_cell_RNASeq [A34]

institute: German Cancer Research Center (DKFZ)

description:
mRNA_with_poly_a_tail
A34


title: Math1::Cre; Rosa tdTomato; Hoxa2+/fl; Hoxb2fl/fl rep 2


title: 132h-4

description: Sample taken at t=132, replicate #4


title: Single_cell_RNASeq [A33]

description:
mRNA_with_poly_a_tail
A33


title: 132h-3

description: Sample taken at t=132, replicate #3


title: Math1::Cre; Rosa tdTomato; Hoxa2+/fl; Hoxb2fl/fl rep 1


title: Single_cell_RNASeq [A31]

description:
mRNA_with_poly_a_tail
A31


title: 132h-2

description: Sample taken at t=132, replicate #2


title: Single_cell_RNASeq [A30]

description:
mRNA_with_poly_a_tail
A30


title: 132h-1

description: Sample taken at t=132, replicate #1


title: Math1::Cre; Rosa tdTomato rep 3

value: wt


title: Math1::Cre; Rosa tdTomato rep 2


title: Single_cell_RNASeq [A28]

description:
mRNA_with_poly_a_tail
A28


title: 120h-4

description: Sample taken at t=120, replicate #4


title: Math1::Cre; Rosa tdTomato rep 4


title: SEM_2umEPZ5676_Rep3

description: nascent RNA

data_processing:
Nascent RNA-seq reads were aligned to the hg18 genome using STAR
Read counts were determined using featureCounts (Subread package)
Genome_build: hg18
Supplementary_files_format_and_content: Rpkm tables (.txt) were generated using edgeR

source_name: Leukemia cell line (SEM)

growth_protocol: SEM cells were continuously grown in IMDM with 10-20% FBS, split when they reached a density of 1-2X10e6 down to 5X10e5

extract_protocol:
Nascent RNA-seq: 108 4sU-treated cells were lysed in 10ml Trizol. RNA was extracted using chloroform and precipitated with EtOH. 4sU RNA was biotinylated with 1mg/ml Biotin-HPDP and nascent RNA was enriched for using streptavidin-coated beads.
Libraries were prepared according to Illumina's protocol accompanying the Ultra RNA Library Prep Master Mix Set (Part# E7530).

treatment_protocol: cells were treated with 2µM EPZ-5676 for 7 days

tag: cell type

value: Paediatric pro B-cell line derived from ALL with t(4;11)(q21;q23) translocation


title: Single_cell_RNASeq [A26]

description:
mRNA_with_poly_a_tail
A26


title: Single_cell_RNASeq [A23]

description:
mRNA_with_poly_a_tail
A23


title: Math1::Cre; Rosa tdTomato rep 1


title: S- 3

city: Poznań

first: Zofia

last: Szweykowska-Kulińska

address: Umultowska 89

department: Department of Gene Expression

country: Poland

institute: Adam Mickiewicz University

data_processing:
Mapping to all mature A.thaliana miRNA from miRBase (release 21)  enriched with 4 sequences not deposited in the database (miR319a.2, miR319b.2, miR319c.2 and miR163.2) performed using script countreads_mirna.pl from the analysis package described here (Eminaga et al., 2013).
Mapping to A.thaliana genome done with the usage of Bowtie version 1.0.0.
cmp_mirna.pl - script from the analysis package was run to obtain normalized count reads. Each 3 results from every replicate for every condition were averaged. A custom python script was used to calculate fold change and p-value between every condition and its control. Fold change was obtained using averaged data. P-value was calculated with the usage f_oneway function from Python scipy.statts (version 0.15.1) module that performs a 1-way ANOVA test. using data for every replicate from the given condition and every replicate from the control (to include standard deviation).
Genome_build: A.thaliana TAIR10 genome release

organism: Arabidopsis thaliana

source_name: Col-0, wt, 15 days old seedlings

growth_protocol: Arabidopsis thaliana (L.) Heynh, Col-0 wild type plants and homozygous line ΔmiR319b (SALK_037093) (Sobkowiak et al., 2012) were used in the experiments. The wild type plants were grown after stratification at 16h/8h day/night cycles at 22°C on 0.8% agar ½ MS plates for the following abiotic stress conditions: 250mM NaCl excess, 10µM Cu excess, 10µM Cd excess, Cu deficiency, S deficiency.

extract_protocol:
Total RNA enriched with small RNA was isolated from 100mg of 15-day old seedlings and 1.13 growth stage (Boyes et al., 2001) plant leaves using a protocol as previously described (Kruszka et al., 2013). NGS dedicated RNA was verified with regard to its concentration and integrity using Agilent RNA 6000 Nano Kit (Agilent Technologies, Inc., Waldbronn, Germany).
Libraries were prepared by BGI Tech Solutions, Hongkong, CO., limited.

treatment_protocol: The stresses were applied for 14-day old seedlings in ½ MS liquid medium for 24 hours. For heat stress, different sets of plates containing 14-day old seedlings were transferred into 37°C condition for 0.5 and 6 hours. For salinity, Cu excess and Cd excess stress inductions up to 250mM NaCl, 10µM CuSO4 and 10µM CdSO4 were added to ½ MS liquid media, respectively (Fig.S1 (A) upper panel). For Cu and S deficiency stresses, 0.1µM CuSO4*5H2O was eliminated and all sulphates were replaced by equivalent chloride salts, respectively. For progressive drought experiment, after stratification Arabidopsis thaliana (L.) Heynh, Col-0 wild type plants were grown at 16h, 22°C /8h, 15°C day/night cycles in 70% SWC (soil water content) soil in a Conviron controlled environment at 50-60% relative humidity and 200µmol·m2·s light intensity. The stress was applied at 1.10 growth stage (Boyes et al., 2001) by water withholding, and continued until the soil moisture level reached 30% SWC (3 days before wilting) and 20%SWC (wilting), both for three different plant batches. The experiment was monitored by leaf relative water content (RWC) measurements (Weatherly, 1951). All stress experiments were done in three biological replicates.

tag: stress conditions

value: 24h sulfur deficiency

tag: biological replicate

tag: organ

value: seedling

tag: growth stage

value: 15 days old seedlings


title: 120h-1

description: Sample taken at t=120, replicate #1

value: CHO-S

tag: time after seeding (h)


title: 120h-3

description: Sample taken at t=120, replicate #3


title: SEM_2umEPZ5676_Rep2

description: nascent RNA


title: S- 2


title: 120h-2

description: Sample taken at t=120, replicate #2


title: S- 1


title: Single_cell_RNASeq [A22]

description:
mRNA_with_poly_a_tail
A22


title: Cd+ 3

value: 24h cadmium [10μM] excess


title: Single_cell_RNASeq [A21]

description:
mRNA_with_poly_a_tail
A21


title: Single_cell_RNASeq [A20]

description:
mRNA_with_poly_a_tail
A20


title: SEM_0umEPZ5676_Rep3

description: nascent RNA

treatment_protocol: cells were treated with DMSO for 7 days


title: 108h-3

description: Sample taken at t=108, replicate #3


title: Cd+ 2


title: Single_cell_RNASeq [A29]

description:
mRNA_with_poly_a_tail
A29


title: 108h-2

description: Sample taken at t=108, replicate #2


title: Cd+ 1


title: Cu+ 3

value: 24h copper [10μM] excess


title: 108h-1

description: Sample taken at t=108, replicate #1


title: Single_cell_RNASeq [A14]

description:
mRNA_with_poly_a_tail
A14


title: SEM_0umEPZ5676_Rep1

description: nascent RNA


title: 96h-4

description: Sample taken at t=96, replicate #4


title: Cu+ 2


title: Cu+ 1


title: Single_cell_RNASeq [A13]

description:
mRNA_with_poly_a_tail
A13


title: 96h-3

description: Sample taken at t=96, replicate #3


title: SEM_2umEPZ5676_Rep1

description: nascent RNA


title: Cu- 3

value: 24h copper deficiency


title: 96h-2

description: Sample taken at t=96, replicate #2


title: SEM_siMLLAF4_Rep1

description: nascent RNA

extract_protocol:
108 4sU-treated cells were lysed in 10ml Trizol. RNA was extracted using chloroform and precipitated with EtOH. 4sU RNA was biotinylated with 1mg/ml Biotin-HPDP and nascent RNA was enriched for using streptavidin-coated beads.
Libraries were prepared according to Illumina's protocol accompanying the NEBNext DNA (Part# E6040) or Ultra RNA (Part# E7530) Library Prep Master Mix Set.

treatment_protocol: cells were treated with 300pmol siMA6 (MLL-AF4)


title: 108h-4

description: Sample taken at t=108, replicate #4


title: RNA-seq_H4_2i paired-end

city: Evanston

first: Liqun

last: Xi

state: IL

address: 2006 Sheridan Road

department: Statistics

institute: Northwestern University

data_processing:
Reads were mapped to the mouse (mm9) genome using Bowtie (http://bowtie-bio.sourceforge.net/index.shtml). We mapped the paired-end reads by allowing 0 to 3 mismatches progressively. The reads were first aligned under the most stringent criterion (i.e., 0 mismatch). Then in the following steps, unaligned reads from previous runs were re-aligned using less stringent mismatch criteria. This strategy helps balance the success rate of sequence alignment (considering sequencing errors) and the chance of mis-alignment due to homologies. If one read (paired) was aligned to n multiple locations, each location was assigned with a read frequency 1/n. The alignment yielded ~ 4,390 million cleavages on each strand. For the MNase maps, we applied the same alignment strategy, but only the uniquely mapped reads were used in the chemical analysis.
Genome_build: mm9
Supplementary_files_format_and_content:
unique.map_95pc.txt.gz: Total two columns, 1st is chromosome number (from 1 to 22 as described), 2nd is selected nucleosome center
*score.txt.gz;
1st-column: chromosome number (from 1, 2, …, to 22, where 1 represents chr1, …, 19 represents chr19;  20 for chrX,  21 for chrY,  22 for chrM)
2nd-column: position on the chromosome
3rd-column: the score (if a position is not listed, the score at this position is Zero)
*gtf.gz: output from tophat & cufflinks, FPKM are included

growth_protocol: H4S47C-expressing ES cells were cultured in M15 media with Lif and 2i without feeders prior to the mapping experiments.

extract_protocol:
Total RNA was isolated from cultured mouse ES cells with TRIzol Reagent (Life Technologies) according to the manufacturer’s instructions.
For RNA-seq analysis, total RNA samples from WT and H4S47C ES cells were used to construct RNA-seq libraries with a TruSeq Stranded Total RNA Library Prep Kit (Illumina). The library sequencing was performed using a HiSeq 2000 platform at the Genomics Facility of University of Chicago.

value: mouse embryonic stem cells

tag: genotype/variation

value: expressing H4S47C

tag: treated with

value: 2i culture condition

tag: molecule subtype

value: total RNA


title: Cu- 2


title: 84h-3

description: Sample taken at t=84, replicate #3


title: NaCl+ 3

value: 24h NaCl [250mM] excess


title: RNA-seq_H4_Lif paired-end

value: Lif culture condition


title: SEM_0umEPZ5676_Rep2

description: nascent RNA


title: 96h-1

description: Sample taken at t=96, replicate #1


title: RNA-seq_WT_2i paired-end

value: wild type; parent


title: 84h-4

description: Sample taken at t=84, replicate #4


title: Single_cell_RNASeq [A17]

city: Heidelberg

description:
mRNA_with_poly_a_tail
A17

tag: age

value: Meninges


title: 84h-2

description: Sample taken at t=84, replicate #2


title: NaCl+ 2


title: MNAse-Partial_15U  paired-end

extract_protocol:
For partial MNase digestion, ES cells were harvested and permeabilized as described for chemical mapping. Cells were resuspended in MNase buffer (150 mM sucrose, 50 mM Tris-HCl pH 7.4, 50 mM NaCl, 0.5 mM MgCl2, 0.01% NP-40, 0.15 mM spermine, 0.5 mM spermidine) and incubated with 5 U/mL or 15 U/mL MNase at 37°C. The reactions were terminated with Stop Buffer (10 mM Tris-HCl pH 7.4, 100 mM NaCl, 10 mM EDTA, 1% SDS) after a 5 min digestion, when roughly 15% of genomic DNA was cleaved into mononucleosome sized fragments.  The nucleosomal DNA fragment was resolved on a 1.5% agarose gel and gel-purified for sequencing.
Library prepared according to Illumina HiSeq protocol.

value: nucleosomal DNA


title: C 3

value: Control for sulfur deficiency, copper deficiency, copper excess, cadmium excess, NaCl excess stresses


title: 84h-1

description: Sample taken at t=84, replicate #1


title: NaCl+ 1


title: RNA-seq_WT_Lif paired-end


title: 72h-4

description: Sample taken at t=72, replicate #4


title: MNase-H4  paired-end

extract_protocol:
Complete MNase digestion of nucleosomal DNA in mouse ES cells was performed as recently described (Sebeson et al., 2015). The resulting mononucleosomal DNA   was gel purified for library construction.
Library prepared according to Illumina HiSeq protocol.


title: C 1


title: Cu- 1


title: 72h-3

description: Sample taken at t=72, replicate #3


title: C 2


title: 72h-2

description: Sample taken at t=72, replicate #2


title: Chemical  paired-end

extract_protocol:
For the chemical map: The cells were harvested for mapping reactions as previously described with specific modifications for mouse ES cells (Brogaard et al., 2012). First, trypsinized ES cells were pelleted and washed in permeabilization buffer (150 mM sucrose, 80 mM KCl, 35 mM Hepes pH 7.4, 5 mM K2HPO4, 5 mM MgCl2). Second, cells were permeabilized with L-α-lysophosphatidylcholine at a final concentration of 100 μg/mL for 5 min. Permeabilized cells were then washed in wash buffer (150 mM sucrose, 5 mM MgCl2, 0.01% NP-40). Third, the cell pellets were resuspended in labeling buffer (150 mM Sucrose, 10mM Tris-HCl pH 7.4, 15 mM NaCl, 60 mM KCl, 5 mM MgCl2, 0.01% NP-40, 0.5 mM spermidine, 0.15 mM spermine), and incubated with 1.4 mM N-(1,10-Phenanthrolin-5-yl)iodoacetamide (Biotium) for 2 hrs at RT. Fourth, following washes with mapping buffer (150 mM Sucrose, 50 mM Tris-HCl pH 7.5, 2.5 mM NaCl, 60 mM KCl, 5 mM MgCl2, 0.01% NP-40, 0.5 mM spermidine, 0.15 mM spermine), the labeled cells were incubated with 0.15 mM CuCl2 for 2 min. The pellets were washed again and resuspended in mapping buffer and subjected to 20 min of hydroxyl radical cleavage using 6 mM of 3-mercaptopropanoic acid (Sigma) and 6 mM of H2O2. The mapping reaction was quenched with 2.8 mM Neocuproine (Alfa Aesar). Lastly, to extract chemically cleaved DNA, the cell pellets were lysed in a buffer containing 10 mM Tris-HCl pH8.0, 25 mM EDTA, 100 mM NaCl, 0.5% SDS, and 0.2 mg/mL proteinase K at 55°C for 4 hrs. Following phenol/chloroform extraction, ethanol precipitation, and RNase A treatment, the purified DNA was resolved on a 2.25% NuSieve 3:1 (Lonza) agarose gel. DNA fragments between two adjacent nucleosomes (~100 to 300 bp) were gel-purified.
DNA ends were blunted using first NEB’s Klenow Polymerase large fragment, then processed further using Lucigen’s DNATerminator End Repair Kit. DNAs were adapter ligated and PCR amplified according to Illumina HiSeq protocol.


title: H 6 III

value: 6h heat (37˚C)


title: 72h-1

description: Sample taken at t=72, replicate #1


title: H 0.5 II

value: 0.5h heat (37˚C)

value: seedling


title: H 0.5 III

value: 15 days old seedlings


title: H 0.5 I


title: H 0 III

value: Control for heat stresses


title: Day60

city: Taian

first: Yuding

last: Wang

address: No. 61, Daizong Street

institute: Shandong Agricultural University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Cufflinks are used for assemble transcripts and remap and quanlity gene-expression level, which is estimate by FPKM value.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Sus scrofa

source_name: longissimus dorsi muscle

extract_protocol:
RNA was extracted from longissimus dorsi muscle samples (stored at −80°C) according to the EZNA Tissue RNA Kit instruction manual. RNA sequencing libraries were generated using the NEB Next Ultra RNA Library Prep Kit for Illumina (Cat# E7420L).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A total of 12 pure castrated male Laiwu pigs reared under similar environmental and feeding conditions were selected at four developments periods: 60, 120, 240 and 400 days of age

tag: tissue

value: muscle

value: 60 days old

value: wild type


title: H 6 I


title: D20 III

source_name: Col-0, wt,  30 days old adult plants

value: 20%FC drought

value: rossette leaves

value: 30 days old adult plants


title: D20 II


title: Day120

value: 120 days old


title: H 0 II


title: H 6 II


title: Day240

value: 240 days old


title: ZMEL1 METASTATIC REP 4

city: New York

first: Richard

middle: Mark

last: White

state: NY

address: 1275 York Avenue MB 424

department: Cancer Biology & Genetics

institute: Memorial Sloan Kettering Cancer Center

data_processing:
GSNAP alignment to Av9 zebrafish reference genome
Read counts extracted with HTSeq
Differential expression with DeSeq2
Zebrafish genes converted to human orthologs using DIOPT
Genome_build: Zv9
Supplementary_files_format_and_content: XLSX sheet with normalized read counts output from HTSeq

organism: Danio rerio

source_name: ZMEL1 cells in vivo

growth_protocol: in vitro: DMEM/10% FCS/1X glutamax/28.5C     in vivo: growth in the zebrafish from 2-21dpf

extract_protocol:
Cells were FACS sorted and total RNA isolated with Zymo kits
Illumina TruSeq

tag: tissue type

value: melanoma


title: MNase-WT  paired-end

value: mouse embryonic stem cells

value: expressing H4S47C


title: ZMEL1 METASTATIC REP 3


title: C20 III

value: Control for 20%SWC drought


title: Mnase-Partial_5U  paired-end

value: nucleosomal DNA


title: C20 II


title: D30 IV

source_name: Col-0, wt,  27 days old adult plants

value: 30%FC drought

value: 27 days old adult plants


title: ZMEL1 METASTATIC REP 2


title: Day400

value: 400 days old


title: GSC-222_rep1

city: Nagoya

first: Keisuke

last: Katsushima

address: 1 Kawasumi, Mizuho-cho, Mizuho-ku

department: Department of Epigenomics

country: Japan

institute: Nagoya City University Graduate School of Medical Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Obtained data were removed PCR duplication and aligned with TopHat 2.0.13 to hg19 with default parameters.
Expression differences (Reads Per Kilobase of exon per Megabase of library size ;RPKM) between two GSC lines were calculated with Cuffdiff 2.2.1.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Giloma stem cell, 222, replicate 1

growth_protocol: GSCs were cultured in Neurobasal Medium (Life Technologies, Carlsbad, CA) containing N2 and B27 supplements (Life Technologies), along with human recombinant basic fibroblast growth factor and epidermal growth factor (20 ng/ml each; R&D Systems, Minneapolis, MN).  at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol:
Total RNA was extracted from GSCs using TRIzol (Life Technologies).
The RNA-seq libraries were prepared using a paired-end RNA Sequencing Sample Prep Kit (Illumina). 2 μg of total RNA was used as the starting material, and the polyadenylated RNAs were selected using Sera-Mag Magnetic Oligo(dT) Beads (Illumina). First-strand cDNA synthesis was performed using SuperScript II (Life Technologies), and second-strand cDNA synthesis was performed using DNA Pol I in the supplied GEX second-strand reaction buffer (Illumina). Paired-end adaptors were ligated to the cDNA fragments. PCR (eight cycles) was performed with Phusion High-Fidelity DNA Polymerase (Finnzymes Oy, Espoo). The PCR products were cleaned up with Agencourt AMPure XP magnetic beads (Beckman Coulter).

value: Human glioblastoma

tag: gender

value: male


title: D30 III


title: GSC-1228_rep1

source_name: Giloma stem cell, 1228, replicate 1


title: H 0 I

value: Control for heat stresses

value: seedling

value: 15 days old seedlings


title: D20 IV

value: 20%FC drought

value: rossette leaves


title: ZMEL1 METASTATIC REP 1


title: D30 II


title: C30 IV

value: Control for 30%SWC drought


title: ZMEL1 IN VITRO REP 1

source_name: ZMEL1 cells in vitro


title: ZMEL1 IN VITRO REP 2


title: C20 IV

value: 30 days old adult plants


title: WT

city: Nanjing

first: Ying

last: Huang

address: 1 wenyuan rd

department: Microbiology

institute: Nanjing Normal University

description: yHL

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked forploy-N and low-quality sequence, then Index of the reference genome was built using Bowtie v2.2.3 and. Reads were blasted to the reference genome using TopHat v2.0.12
Numbers of reads per kilobase of exon region in a gene per million mapped reads (RPKM). RPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Trapnell, Cole, et al., 2010).
Genome_build: ASM294v2
Supplementary_files_format_and_content: tab-delimited .txt file includes RPKM values for each Sample

organism: Schizosaccharomyces pombe

source_name: Schizosaccharomyces pombe cells, WT

extract_protocol:
Cells were digested, RNA was harvested using Trizol reagent. Illumina NEBNext®Ultra™ RNA Library Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: growth phase

value: logarithmic phase

value: wild type


title: C30 III


title: C30 II


title: Single_cell_RNASeq [A40]

department: Molekulare Neurobiologie (A290)

description:
mRNA_with_poly_a_tail
A40

value: Meninges


title: Mock_shoot_rep1

status: Public on Nov 22 2016

city: Riverside

first: Yasemin

last: Bektas

address: 2150 Batchelor Hall

department: Botany and Plant Sciences

institute: University of California, Riverside

data_processing:
Sequence reads were analyzed using TopHat for alignment of reads to the TAIR10 Arabidopsis genome annotation.
Differentially expressed genes (DEGs) were identified by comparing read counts from DPMP-treated samples versus their respective mock controls by EdgeR using a Bonferroni-corrected false discovery rate (FDR)-cut off of 0.05.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

growth_protocol: Arabidopsis plants were grown for 14 days on ½ MS agar plates containing either 3 µM DPMP  or mock (solvent only).

extract_protocol:
After 14 days, plant tissue was separated into shoot and root parts using blade. To prevent any tissue contamination, seedlings were cut into three parts, and root-shoot intersection areas were discarded. Total RNA was isolated from Shoot and root separately by using TRIZOL.
Libraries were prepared with the NEBNext Ultra RNA library prep kit by following manufacturer’s instruction.

tag: accession

tag: agent

value: control

value: shoot

value: 14 days old


title: Mock_root_rep2

tag: genotype

value: root


title: 3 µM DPMP_shoot_rep1

source_name: 3 µM DPMP_shoot

value: DPMP


title: 3 µM DPMP_root_rep1

source_name: 3 µM DPMP_root


title: 3 µM DPMP_root_rep2


title: 3 µM DPMP_shoot_rep2


title: ChIP repeat two

city: Rehovot

first: Gilgi

last: Friedlander

address: Hertzel st

country: Israel

institute: Weizmann Institute of Science

data_processing:
Reads were demultiplexed
Adapters were trimmed using the cutadapt tool
The reads were aligned uniquely to the mouse genome (mm9)
Bound regions were detected using MACS2 (version 2.0.10.20131216)
(Duplicates were combined)
Genome_build: mm9
Supplementary_files_format_and_content: bed files of MACS2 peaks

source_name: hippocampus_CTCF ChIP

extract_protocol:
Magna Chip tissue immunoprecipitation kit
In-house ChIP-Seq protocol

tag: strain

value: hippocampus

tag: chip antibody

value: CTCF millipore antibody (07-729)


title: cko knockout repeat one

data_processing:
Reads were demultiplexed
Adapters were trimmed from sequences using cutadapt tool
Reads that mapped to rRNA were removed
The rest of the reads were aligned to the mm10 genome built using Tophat (v2.0.10)
Read counting to Refseq genes was done with HTseq-count (version 0.6.1p1)
Differential expression analysis was performed with DESeq2 (1.6.3)
Genome_build: mm10
Supplementary_files_format_and_content: Excel file includes the raw counts, normalized counts, fold change, p-value and FDR

source_name: cko knockout_hippocampus

extract_protocol:
mRNAeasy qiagen RNA extraction kit
Truseq illumina library kit

value: CTCF cko


title: input repeat one

source_name: hippocampus_CTCF input


title: input repeat two


title: wt repeat one


title: wt repeat three


title: wt repeat two


title: ChIP repeat one


title: cko knockout repeat two


title: Mock_root_rep1


title: 5p4_35cfoxc1

city: Denver

first: Lianghua

last: Bin

state: Colorado

address: 1400 Jackson street

department: Department of Pediatrics

institute: National Jewish Health

data_processing:
RTA v1.12 software used for base-calling
Sequence aliggnment used CASAVA v1.8 software
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: differentiated keratinocytes with FOXC1 siRNA

growth_protocol: Foreskin keratinocytes were purchased from from Invitrogen (Portland, OR) and maintained in EpiLife Medium containing 0.06 mM CaCl2 and S7 supplemental reagent (Invitrogen) under standard tissue culture conditions.

extract_protocol:
Total RNA was extracted using QIAzol®Lysis reagent (QIAGEN, MD).
RNA purity and concentration was measured on an Agilent Bioanalyzer (Agilent Technol., Palo Alto, CA). A total of 5 µg total RNA was treated with Ribo-ZeroTM  Magnetic Kit (Epicentre) to deplete ribosome RNA (rRNA). After rRNA depletion, the RNA was used to prepare the Illumina HiSeq libraries according to manufacturer’s instructions of the TruSeq RNA kit.

treatment_protocol: The cells were seeded in 24 well-dishes at 1x105/well to form a 80% of confluent monolayer.  The following day, the cells were transfected with siRNA duplexes using Invitrogen lipofectamine 2000.   After 24 hours of incubation with siRNA duplexes, the cells were kept in undifferentiated condition or undergone Ca2+-induced differentiation for 5 days.  The cells were then harvested for RNA extraction.

tag: cell type

value: Keratinocytes

tag: differentiation stage

value: differentiated for 5 days


title: 5p4_33cfoxc1

source_name: undifferentiated keratinocytes with FOXC1 siRNA

value: Undifferentiated


title: 5p4_34cfoxc1


title: Mock_shoot_rep2


title: ppr10 deletion

source_name: Schizosaccharomyces pombe cells, ppr10 deletion

value: ppr10 deletion


title: 5p4_31cfoxc1


title: 5p4_30c

source_name: differentiated keratinocytes with scrambled siRNA


title: 5p4_27c

source_name: undifferentiated keratinocytes with scrambled siRNA

value: keratinocytes


title: 5p4_28c


title: cko knockout repeat three


title: 5p4_25c


title: 5p4_29c


title: D1

data_processing:
RTA v1.12 software used for base-calling
Sequence aliggnment used CASAVA v1.8 software
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Keratinocytes differentiated in 1.3mM Ca2+ for 24 hours

growth_protocol: Foreskin keratinocytes were purchased from from Invitrogen (Portland, OR) and maintained in EpiLife Medium containing 0.06 mM CaCl2 and S7 supplemental reagent (Invitrogen) under standard tissue culture conditions.  The cells were seeded in 6 well-dishes at 1x106/well to form a confluent monolayer.  The following day, the cells were subjected to differentiation by increasing CaCl2 to 1.3mM in the culture media. The cells were harvested for RNA extraction before differentiation, differentiation for 24 hours, 48 huors, 72 hours, 96 hours and 120 hours.

value: keratinocyte

tag: treatment

value: differentiated in 1.3mM Ca2+

tag: time

value: 24 hours


title: D2

source_name: Keratinocytes differentiated in 1.3mM Ca2+ for 48 hours

value: 48 hours


title: D5

source_name: Keratinocytes differentiated in 1.3mM Ca2+ for 120 hours

value: 120 hours


title: D3

source_name: Keratinocytes differentiated in 1.3mM Ca2+ for 72 hours

value: 72 hours


title: UD

source_name: Undifferentiated normal human keratinocytes

value: undifferentiated

value: control


title: D4

source_name: Keratinocytes differentiated in 1.3mM Ca2+ for 96 hours

value: 96 hours


title: H3K4me3_MV4-11R_ChIPSeq

first: Christian

last: Rohde

address: Im Neuenheimer Feld 410

institute: Heidelberg University

data_processing:
Sequencing of ChIP-seq samples produced single-end 42bp reads after removal of multiplex index sequence tags. Reads were trimmed for low quality nucleotides and mapped to the hg19 human genome sequence using Bowtie v0.12.7 (Langmead et al., 2009) using the parameters "-S -m 1".
Aligned datasets were filtered for multiple reads at the same position occurring after PCR amplication. Where more than one read mapped to the same position and at the same strand duplicates were removed.
The reads were extended to 200 bp length, and the number of reads at a given position was counted and saved as a fixedStep wig file with 100 bp resolution. Values are denominated in fragments pr. Mreads pr. kbp.
Genome_build: hg19
Supplementary_files_format_and_content: Wig: fixedStep Wiggle file containing densities with 100 bp resolution of aligned and filtered reads.

growth_protocol: MV4-11 and MV4-11R cells cultured in IMDM (Life Technologies, Darmstadt, Germany) supplemented with 10% fetal bovine serum (VWR International, Darmstadt, Germany) at a density of 2 to 10 x105 cells/mL in a humid incubator with 5% CO2 at 37°C.

extract_protocol:
ChIP protocol: Cells were fixed for 10 min in culture media containing 1% formaldehyde and were processed for ChIP as previously described (Dietrich et al, PLOS Genetics 2012). Briefly, formaldehyde fixed chromatin was sonicated in IP buffer (IP buffer =2 volume SDS Buffer : 1 volume Triton Dilution Buffer; SDS Buffer-  100mM NaCl  50mM Tris-Cl, pH8.1, 5mM EDTA, pH 8.0, 0.2% NaN3, 2% SDS; Triton Dilution Buffer- 100mM Tris-Cl, pH 8.6, 100mM NaCl, 5mM EDTA, pH 8.0, 0.2% NaN3, 5.0% Triton X-100) using Branson Sonifier (4 cycles of 30 sec each at 20% amplitude). 15ug DNA (sonicated chromatin) was used for each ChIP in IP buffer. Antibodies used: Rabbit IgG (DAKO), rabbit anti-REST (Millipore, 07-579), anti-SUZ12 (Rabbit monoclonal, Cell signaling). Samples were incubated with antibodies overnight at 40C and immunocomplexes were precipitated with protein A-sepharose beads with 3 hr rotation at 40C. After subsequent washes the samples were decrosslinked overnight at 650C (shaking) in 1%SDS, 0.1M NaHCO3. Finally, ChIP DNA was purified using Qiagen PCR purification kit. The ChIPs were validated at REST and Polycomb target genes by qPCR. ChIP DNA from three parallel ChIPs were pooled and 10 ng was used for making ChIP-seq libraries. The libraries were prepared using “ChIP seq DNA sample preparation kit” from Illumina following manufacturer’s instructions. Individual samples were run in a single lane on HiSeq2000 (Illumina). Basecalls were performed using on-instrument real time analysis (RTA). Mapping was performed with bowtie allowing for <=2 mismatches and only including reads that were mapped to a single position to hg18. The number of reads in 100 bp sections of the genome were counted genome-wide. A normal distribution was fitted to the counts, and the distribution with the least root-mean-square deviation was used as model for the background in the datasets. Thresholds were set so that windows that scored positive had p-values < 0.001 compared to the background distribution. A ChIP-sequenced IgG-control was used as a negative control and handled in the same way. Only windows scoring positive for REST or Suz12, but not IgG, were included for downstream analysis. Also windows where the positive signal (normalized to dataset size) did not exceed the negative signal (normalized to dataset size) at least threefold were omitted from downstream analysis. Datasets were analyzed this way four times in 25 bp shifts, thereby reducing the number of regions that scored negative due to a division of the reads into neighboring sections. Overlapping positive windows and positive windows within 100bp for REST and 500bp for Suz12 of each other were merged. The position of the border was refined by shifting the window in one bp steps until the window scored positive (without scoring positive in the negative control sample) starting at a distance of one window-size from the regions border. Genomic positions were transferred to hg19 using the UCSC liftover tool (http://genome.ucsc.edu/cgi-bin/hgLiftOver).
The libraries were prepared using “ChIP seq DNA sample preparation kit” from NEB following manufacturer’s instructions.

treatment_protocol: The MV4-11R cell line was regularly cultured in the presence of 140 nM PKC412 but grown in normal medium without PKC412 for at least 96 hours before start of individual experiments.

tag: cell line

value: Acute Myeloid Leukemia (AML) cell line

tag: drug resistance

value: resistant

tag: ezh2 expression

value: low

tag: chip antibody vendor

value: Cell signaling

tag: chip antibody cat. #


title: IgG_MV4-11_ChIPSeq

value: sensitive

value: high

value: IgG

value: DAKO


title: H3K27me3_MV4-11R_ChIPSeq

value: Cell Signalling


title: H3K27ac_MV4-11_ChIPSeq

value: Abcam


title: ssm_15121002_NC14_18_rep3

first: Shelby

last: Blythe

address: Northwestern University, Hogan Hall, 2205 Tech Drive

department: Molecular Biosciences

data_processing:
Sequenced reads were barcode-split and adapters were removed using TrimGalore.
Trimmed reads were mapped to the Drosophila melanogaster genome (dm6) using BWA with default parameters.
Alignments were converted to .bam format, duplicates were marked with Picard MarkDuplicates, and reads were filtered for quality score (>= 30), duplication, and were required to be mapped, properly paired, and non secondary alignments.
Only reads corresponding to chr2L, chr2R, chr3L, chr3R, chr4, and chrX were considered for further analysis.
Paired end read fragments <= 98 bp were considered to have originated from 'open' chromatin. Replicates were pooled, and average coverage over open regions was calculated over 10 bp discrete windows. These data are provided as .wig formatted files in the processed data file deposit.
Peaks were called with Zinba on pooled biological replicates spanning either the entire timecourse (per genotype) or spanning entire cell cycles (NC11, NC12, NC13, per genotype). The peaks are provided as a tab-delimited table with annotations.
Nucleosomes within 2500bp regions flanking the maximum open position as called by Zinba were called using NucleoATAC. Both smoothed nucleosome profiles and dyad position/occupancy scores are provided in the processed data file deposit.
Genome_build: dm6
Supplementary_files_format_and_content: Peaks are provided as a tab-delimited text file with additional logical indexers that indicate categories of peak as determined by analysis. Coverage of reads originating from open chromatin are provided as .wig files for each timepoint and genotype. Predicted nucleosome positions are provided in two formats: smoothed nucleosome profiles from NucleoATAC are provided in bedgraph format, and dyad positions and estimated occupancy are provided in a .bed format.

organism: Drosophila melanogaster

growth_protocol: Adults were allowed to lay eggs on yeasted apple juice agar plates. Adults were between 4 and 12 days old for embryo collection.

extract_protocol:
Embryos were observed under a fluorescent microscope until they reached the desired timepoint. Embryos were dechorionated in 4% bleach for 1 minute, washed extensively with water, and macerated in a small volume of extraction buffer. Nuclear pellets were collected and briefly frozen on dry ice.
Frozen nuclear pellets were thawed and fragmented using the Nextera Tn5 transposase solution (Illumina), 2.5 ul per 10 ul reaction. Fragmentation was for 30 minutes at 37 degrees with shaking. Samples were cleaned up with a Qiagen minelute kit and subjected to limited PCR amplification with barcoded primers.

value: w ssm[185b]; His2Av-GFP

value: haploid (sesame)

tag: timepoint

tag: sex type

value: haploid

value: Pool 4

value: TGCTGGGT


title: H3K27me3_MV4-11_ChIPSeq


title: ssm_15121005_NC14_09_rep4

value: Pool 2

value: GTGTGGTG


title: ssm_15120903_NC14_12_rep2

value: CGAGGCTG


title: IgG_MV4-11R_ChIPSeq

value: Acute Myeloid Leukemia (AML) cell line

value: resistant


title: 5p4_32cfoxc1

value: Keratinocytes

value: Undifferentiated


title: H3K4me3_MV4-11_ChIPSeq

value: sensitive

value: high

value: Cell signaling


title: ssm_15121006_NC14_15_rep3

value: TGGGTTTC


title: ssm_15120803_NC14_09_rep1

value: AGGCAGAA


title: ssm_15120904_NC14_18_rep2

value: w ssm[185b]; His2Av-GFP

value: AAGAGGCA


title: ssm_15120806_NC14_18_rep1

value: haploid (sesame)

value: haploid

value: Pool 1

value: TAGGCATG


title: ssm_15120905_NC14_06_rep2

value: Pool 3

value: GTAGAGGA


title: ssm_15120906_NC14_15_rep2

value: GTCGTGAT


title: ssm_15120805_NC14_15_rep1

value: Pool 4

value: GGACTCCT


title: ssm_15120908_NC14_09_rep3

value: Pool 2

value: TGGATCTG


title: ssm_15121004_NC14_06_rep3

value: AGGTTGGG


title: ssm_15121001_NC14_12_rep3

value: CCGTTTGT


title: ssm_15120902_NC14_09_rep2

value: CAGAGAGG


title: ssm_15120907_NC14_03_rep3

value: ACCACTGT


title: H3K27ac_MV4-11R_ChIPSeq

value: Acute Myeloid Leukemia (AML) cell line

value: resistant

value: low

value: Abcam


title: ssm_15121003_NC14_03_rep4

value: w ssm[185b]; His2Av-GFP

value: haploid (sesame)

value: haploid

value: GAGGGGTT