title: BJELM_RNA_PolII_ChIP-seq

city: Illkirch; Strasbourg

first: Valeriya

last: Malysheva

address: 1 rue Laurent Fries

country: France

institute: IGBMC

description:
Transformed BJELM fibroblast cells (cancer cells)
ChIP against RNA PolII

data_processing:
Prepared sequencing libraries were sequenced on the Illumina instrument HiSeq2000. Regular Illumina pipelines were used for image processing and base calling.
bed files obtained from the aligned profiles using peak calling tools MeDiChi-seq (for RNA PolII and H3K9ac, H3K4me3, H3K27ac marks) ann SICER tool (for H3K27me3) with the input datasets as a negative control
Genome_build: hg19
Supplementary_files_format_and_content: wig and bed (peak annotation information)

growth_protocol: BJELM cells were cultured in monolayer conditions Dulbecco’s modified Eagle’s medium (DMEM)/M199 (4:1) (with 4.5 g/l glucose) supplemented with 10% of heat inactivated fetal calf serum (FCS),G-418 (400 µg/µl), Hygromycin (400 µg/µl) and puromycin (1 µg/ml) and continuously grown with 10-6 M 4-hydroxytamoxyfen (4-OHT).

extract_protocol:
cells were fixed with 1% para-formaldehyde (Electron Microscopy Sciences) for 30 minutes at room temperature. ChIP assays were performed following previously described conditions: chromatin sonication and immunoprecipitation in lysis buffer (50mM Tris–HCl pH=8, 140mM NaCl, 1mM EDTA, 1% Triton, 0.1% Na-deoxycholate) complemented with protease inhibitor cocktail (Roche 11873580001); 2x washes with lysis buffer; 2x washes with lysis buffer containing 500mM NaCl; 2x washes with washing buffer (10mM Tris–HCl pH=8, 250mM LiCl, 0.5% NP-40, 1mM EDTA, 0.5% Na-deoxycholate); 2x washes with 1x TE buffer; elution at 65°1C; 15 min at 65°C in elution buffer (50mM Tris–HCl pH=8, 10mM EDTA, 1% SDS); overnight decrosslinking at 65C followed by PCI purification. qPCR-qualified ChIP assays were quantified (Qubit dsDNA HS assay kit; Invitrogen); 10 ng of the ChIPed material was used for preparing Illumina sequencing libraries.
Libraries were prepared following a multiplexing approach (NEXTflexTM ChIP-seq Bioo Scientific kit;  ref: 5143-02).

value: BJELM

value: foreskin fibroblast cells

value: polyclonal anti-RNA-PolII (H-224)

tag: chip antibody supplier

value: Santa Cruz Biotechnology

tag: chip antibody catalog#

tag: chip antibody lot #


title: BJELM_input

status: Public on May 13 2016

type: SRA

description:
Transformed BJELM fibroblast cells (cancer cells)
Whole cell extract (input)

library_source: genomic

data_processing:
Prepared sequencing libraries were sequenced on the Illumina instrument HiSeq2000. Regular Illumina pipelines were used for image processing and base calling.
Genome_build: hg19
Supplementary_files_format_and_content: wig

molecule: genomic DNA

organism: Homo sapiens

tag: cell line

tag: cell type

tag: chip antibody

value: no antibody


title: BJELM_H3K27ac_ChIP-seq

description:
Transformed BJELM fibroblast cells (cancer cells)
ChIP against H3K27ac

value: abcam


title: BJELM_H3K27me3_ChIP-seq

description:
Transformed BJELM fibroblast cells (cancer cells)
ChIP against H3K27me3

value: millipore


title: RNA_H3.3 K36M 1

city: Madison

first: Peter

middle: W

last: Lewis

state: Wisconsin

address: 330 N Orchard Street

department: Department of Biomolecular Chemistry

country: USA

institute: University of Wisconsin-Madison

description:
RNA_MedianNorm_H33_WT_K36M
RNA_MedianNorm_H31_H33_xenografts
RNA_medianNorm_wt_K36M-siRNA-control

library_source: transcriptomic

data_processing:
Reads were aligned using bowtie 1.0.0 with default parameters
Expression for annotated refseq genes was determined using RSEM 1.2.12 with default parameters
the data-matrix was normalized by median-normalization
Genome_build: mm9
Supplementary_files_format_and_content: tab separated files containing median normalized 'expected-counts'

molecule: total RNA

organism: Mus musculus

source_name: C3H10T1/2 cells

growth_protocol: C3H10T1/2 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Invitrogen) with 10% fetal bovine serum (FBS, CellGro).

extract_protocol:
RNA was isolated using Trizol (Invitrogen).
libraries were prepared according to the Illumina TruSeq protocol

treatment_protocol: 2x10^6 H3.3K36M cells were mixed with Matrigel and injected subcutaneously into both flanks of 6-8 weeks old athymic female SCID mice. Tumors were harvested 5-6 weeks post-injection.

value: C3H embryo-derived mesenchymal multipotent cells

tag: genotype

value: Stably expressing FLAG-HA-tagged K36M mutant H3.3

tag: passages

value: Passage 10-15


title: BJELM_H3K4me3_ChIP-seq

description:
Transformed BJELM fibroblast cells (cancer cells)
ChIP against H3K4me3


title: BJEL_H3K27me3_ChIP-seq

description:
Immortalized BJEL fibroblast cells (pretransformed)
ChIP against H3K27me3

growth_protocol: BJEL cells were cultured in monolayer conditions Dulbecco’s modified Eagle’s medium (DMEM)/M199 (4:1) (with 4.5 g/l glucose) supplemented with 10% of heat inactivated fetal calf serum (FCS), G-418 (400 µg/µl) and Hygromycin (400 µg/µl).

value: BJEL


title: BJELM_H3K9ac_ChIP-seq

description:
Transformed BJELM fibroblast cells (cancer cells)
ChIP against H3K9ac


title: BJEL_RNA_PolII_ChIP-seq

description:
Immortalized BJEL fibroblast cells (pretransformed)
ChIP against RNA PolII


title: BJEL_input

description:
Immortalized BJEL fibroblast cells (pretransformed)
Whole cell extract (input)


title: RNA_H3.1 K36R

description: exon.vst.tsv

data_processing:
Raw reads are trimmed for quality (phred33 >= 30) and length (n >= 30) using Trimmomatic (v. 0.32). Illumina adaptor sequences are clipped off using the palindromic mode.
Perform a sliding window trimming, cutting once the average quality within the window falls below 30. Cut 3 bases off the start of each read, if below quality 30. Cut 3 bases off the end of each read, if above quality 30. Cut the first 4 bases at the start of each read. Drop short reads (n <= 30).
Reads are aligned to the UCSC mm10 genome with STAR v2.3.0e using default settings, which removes multimapping reads. Feature annotation is provided by UCSC knownGene.
Read counting is done with featureCounts v1.4.4. Unless stated otherwise, default settings are used. Read summarization is done at the gene symbol level. The minimum mapping quality score for a read to be counted is 3. Only primary alignments are counted. Reads rather than fragments are counted. Only reads mapping to exons are considered.
Expression data is variance-stabilized using the VST algorithm provided by the DESeq2 R package.
Genome_build: mm10
Supplementary_files_format_and_content: tab separated file containing read counts normalized with the variance-stabilized transformation

value: Stably expressing FLAG-HA-tagged K36R mutant H3.1


title: BJEL_H3K9ac_ChIP-seq

description:
Immortalized BJEL fibroblast cells (pretransformed)
ChIP against H3K9ac


title: BJ_input

description:
Primary human BJ foreskin fibroblasts (normal cells)
Whole cell extract (input)

growth_protocol: BJ cells were cultured in monolayer conditions Dulbecco’s modified Eagle’s medium (DMEM)/M199 (4:1) (with 4.5 g/l glucose) supplemented with 10% of heat inactivated fetal calf serum (FCS).

value: BJ


title: 1ug_hESCs_RNA_#2

city: beijing

first: yujiao

last: dang

address: Yihe road

country: China

institute: BIOPIC

description: singel cell  RNA seq

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Reads were trimmed to remove the adapter sequences and low quality bases.
RNA-seq reads were aligned to the human refference genome (hg19) using Tophat software
Raw read counts and RPKM calculated by HTSeq
Genome_build: hg19
Supplementary_files_format_and_content: txt files reflect RPKM of each gene in Refseq.

source_name: human stem cells

growth_protocol: The oocytes and embryos for this study were donated from volunteer women with the informed consent signed.

extract_protocol:
The RNAs in individual oocyte or embryo were reverse transcribed and amplified using the single RNA-seq method we recently developed.
Libraries were constructed with TruSeq DNA library preparation kit (Illumina)

treatment_protocol: Oocytes, zygotes and 2-cell-stage embryos were collected at appropriate time based on the embryonic development.

tag: tissue

value: stem cells

tag: passage


title: 1ug_hESCs_RNA_#3

description: singel cell  RNA seq


title: OsGRF6_ChIPSeq

city: Wuhan

first: Wang

last: Kun

state: Hubei

address: Ba-yi Road

institute: wuhan university

data_processing:
Sequence reads for ChIP-Seq is 100bp paired-end and quality control was performed by Fastqc, and then low quality reads and adaptor contamination were deleted. For downstream analysis, data were mapped to Release 7 of the Michigan State University Rice Genome using Bowtie and MACS for peaks calling.
For RNA-Seq, the clean reads were mapped to the rice genome using the Cufflink software. Gene expression was calculated according to the fragments per kilobase of exon per Million fragments mapped (FPKM) method.
Genome_build: MSU rice genome 7.0
Supplementary_files_format_and_content: Tab-delimited text file include FPKM values for each RNA-Seq data. Tab-delimited text file include peaks location for ChIP-Seq data.

organism: Oryza sativa

source_name: Callus

extract_protocol:
For ChIP, Lysates were clarified from sonicated nuclei and OsGRF6-DNA complexes were isolated with antibody. For RNA-seq, total RNAs were extracted with Trizol according to manufacturer’s manual.
For ChIP-Seq library construction, cross-linked chromatin was fragmented into 150-300bp, and then fragmented DNA was used for library construction and sequencing by Illumina Hiseq2000. RNA-Seq library construction was performed by using Illumina TruSeq kit

tag: antibody

value: anti-GFP (Abcam AB290)

tag: genotype/variation

value: p35S:GRF6-GFP transgenic lines


title: BJ_RNA_PolII_ChIP-seq

description:
Primary human BJ foreskin fibroblasts (normal cells)
ChIP against RNA PolII


title: CFBE ctrl rep 3

city: Hanover

first: Katja

last: Koeppen

state: NH

address: 504 Remsen

institute: Geisel School of Medicine at Dartmouth

description: Sample 11

data_processing:
Data analysis was performed with CLC Genomics Workbench.
Adaptors were trimmed and sequences were aligned to the PA14 reference genome.
Pileup tables of uniquely mapped reads were compiled for each sample.
Genome_build: Pseudomonas aeruginosa UCBPP-PA14, complete genome; NC_008463.1
Supplementary_files_format_and_content: Each speadsheet in the 'Unique reads.xls' contains the reads that uniquely mapped to PA14 reference for each sample. Each spreadsheet nubmer (e.g. 1,2,…11,12) correspond to the sample number indicated in the description field.

source_name: CFBE ctrl

growth_protocol: PA14 was grown in LB medium for 16 h at 37°C and 225 rpm

extract_protocol:
RNA was extracted with the miRNeasy kit (Qiagen)
TruSeq Small RNA Library Preparation Kit (Illumina)
50 bp single end RNA-Seq with Illumina HiSeq

treatment_protocol: OMVs were isolated by ultracentrifugation of filtered supernatant and purified on an Optiprep gradient. Host cells were incubated with OMVs for 30 min at 37°C. Unexposed host cells served as negative controls.

value: bronchial epithelial cells


title: CFBE ctrl rep 2

description: Sample 9


title: 1ug_hESCs_RNA_#1

description: singel cell  RNA seq


title: BJ_H3K27me3_ChIP-seq

description:
Primary human BJ foreskin fibroblasts (normal cells)
ChIP against H3K27me3


title: BJ_H3K27ac_ChIP-seq

description:
Primary human BJ foreskin fibroblasts (normal cells)
ChIP against H3K27ac


title: BJ_H3K9ac_ChIP-seq

description:
Primary human BJ foreskin fibroblasts (normal cells)
ChIP against H3K9ac


title: primary HBE ctrl donor 2

description: Sample 3

source_name: primary HBE ctrl

value: primary human bronchial epithelial (HBE) cells


title: primary HBE ctrl donor 1

description: Sample 1


title: BJ_H3K4me3_ChIP-seq

description:
Primary human BJ foreskin fibroblasts (normal cells)
ChIP against H3K4me3

value: foreskin fibroblast cells


title: CFBE ctrl rep 1

description: Sample 7


title: BJEL_H3K27ac_ChIP-seq

description:
Immortalized BJEL fibroblast cells (pretransformed)
ChIP against H3K27ac


title: BJEL_H3K4me3_ChIP-seq

description:
Immortalized BJEL fibroblast cells (pretransformed)
ChIP against H3K4me3


title: ERKO_FOXA2_E2

city: Rennes

first: Raphaël

last: Métivier

address: Campus de Beaulieu

institute: CNRS UMR 6290

description: ChIP

data_processing:
Basecalls were performed using CASAVA (v1.8. or v1.8.2) to produce fastq files. When multiple files were generated,they were concatenated into a single one.
Reads were aligned to the mm9 reference genome assembly using bowtie (Langmead et al., Genome Biol., 2009) with parameters allowing at most one mismatch and selected for unique mapping onto the genome.
Extracted reads were  converted to .wig signal files using samtools (Li et al., Bioinformatics, 2009) and MACS (Zhang et al., Genome Biol, 2008) with default parameters, incluing a normalization step towards the input sequences.
To minimize the bias of diverging sequencing depths between different ChIP samples prepared with the same antibody, the signal intensities of a given .wig were linearly normalized so as to be comparable to the .wig file with the highest sequencing depth.
Genome_build: mm9
Supplementary_files_format_and_content: .wig files containing MACS (v1.4) signals normalized to input reads

source_name: liver

growth_protocol: Wild-type breeders (ERWT) were obtained from the same parents as were the ERKO mice. Genotyping was systematically performed on DNA prepared from breedings’ tails. Mice were housed in cages in groups of 5 and kept in a temperature-controlled facility on an artificial 12h light-dark cycle.

extract_protocol:
Livers were sliced into small pieces and disrupted in 2 ml PBS through a 21G syringe needle. Cells from one liver were fixed in 10 ml PBS containing 1% formaldehyde for 10 min at room temperature. The cross-linking was next stopped by incubation with glycine at 0.125M final concentration at room temperature under gentle agitation. Cells were recovered by centrifugation at 2,500 x g at 4°C, washed twice with PBS and then lysed in 1 ml of specific buffer [10mM Tris-HCl (pH 8.0), 10mM NaCl, 3 mM MgCl2, 0.5% Igepal]. Extraction of nuclei was performed by applying 40 strokes of potter on the suspension in an ice-cold mortar and further incubation for 5 min at 4°C. Nuclei suspensions originating from each liver were divided into 2 and the membrane debris were eliminated by 2 washes in 2 ml of PBS and centrifugation at 1,000 x g at 4°C. Nuclei were then lysed in 4 ml of nuclei lysis buffer [10 mM EDTA, 50 mM Tris-HCl (pH 8.0), 1% SDS] by incubation on ice during 10 min and three rounds of 20 sec sonication using a Branson 250 apparatus at 50% power. Samples were allowed to cool down 1 min on ice between each sonication pulse. SDS was then neutralized by adding 400 µl of 10% Triton X-100 and chromatin further sonicated into fragments of 150-400 bp mean size by 2 additional 14 min sonications of the lysed nuclei (divided into 12 aliquots of 300 µl) in a BioRuptor apparatus (Diagenode) operating at high intensity with 30 sec on/off duty cycles. Chromatin was then cleared through a 10 min centrifugation at 10,000 x g and the supernatants pooled for further use. ChIP experiments were performed using 300 µl of these chromatin preparations. A tenth of this fraction (30 µl) served to prepare the input DNA, while the rest was diluted 5-fold in IP buffer [2 mM EDTA, 100 mM NaCl, 20 mM Tris-HCl (pH 8.1), and 0.5%Triton X-100] containing 10 μg of yeast tRNA. Immunoprecipitations were performed overnight at 4°C under rocking using 2 μg of antibodies. Complexes were recovered after a 4 hr incubation at 4°C with 5 μg yeast tRNA and 60 μl of 50% protein A or G-Sepharose (Amersham Pharmacia Biosciences) slurry. Precipitates were then serially washed, using 300 μl of Washing Buffers (WB) I [2 mM EDTA, 20 mM Tris-HCl (pH 8.1), 0.1% SDS, 1% Triton X-100, 150 mMNaCl], WB II [2 mM EDTA, 20 mM Tris-HCl (pH 8.1), 0.1% SDS, 1% Triton X-100, 500 mM NaCl], WB III [1 mM EDTA, 10 mM Tris-HCl (pH 8.1), 1% NP-40, 1% Deoxycholate, 0.25 M LiCl] and then twice with 1 mM EDTA, 10 mM Tris-HCl (pH 8.1). Precipitated complexes were removed from the beads through two sequential incubations of the beads with 75 μl of 1% SDS+ 0.1 M NaHCO3 during 15 min with strong agitation. Cross-linking of input and immunoprecipitated samples was reversed by heat at 65°C overnight. DNA was purified on NucleoSpin™ columns (Macherey-Nagel) using NTB buffer.
Multiplexed libraries (x3) were prepared according to Illumina's instructions by IGBMC sequencing facility (Strasbourg, France)

treatment_protocol: Mice were ovariectomized at 4 weeks of age and were treated by oral gavage with placebo (P, castor oil 5% EtOH) or estradiol (E2, 1mg/kg) at 9 weeks of age. Folllowing anesthesia by injection of ketamine (100 mg/kg) and xylazine (10 mg/kg) by intraperitoneal route, mice were sacrificed 1 hour after gavage. Blood was collected by retroorbital prelevement and liver sample was snap-frozen in liquid nitrogen and stored at -80°C.

tag: strain

tag: hormone treatment

value: Antibody Mix:clone 3C10 (Millipore) + ab23630 (Abcam)


title: ERKO_H3K27ac_E2

description: ChIP

value: ab4729 (Abcam)


title: ERKO_H3K4me2_E2

description: ChIP

value: 07-030 (Millipore)


title: Th17_ATAC_rep1

city: Saint Louis

first: Eugene

middle: M

last: Oltz

state: Missouri

address: 660 Euclid Ave, Campus Box 8118

department: Pathology & Immumonolgy

institute: Washington University in St Louis

description: ATAC DNA

data_processing:
Library strategy: ATAC-Seq
Basecalls performed using CASAVA.
Sequencing tags from FAIRE- and ChIP-Seq were aligned to the reference genome (build GRCh37/hg19) with Novoalign.
ChIP: MACS was used to identify ChIP peaks by comparison of matched treatment to input samples using the following changes to the default settings: --nomodel --shiftsize=150 (H3K27ac), --nomodel --shiftsize=100 (H3K4me3). ATAC: Samples were processed with MACS using the following changes to default settings, --nomodel --shiftsize=50.
Genome_build: hg19
Supplementary_files_format_and_content: Wig files were generated using MACS.

source_name: Tonsils

extract_protocol:
ChIP Samples: Preparation of samples for ChIP was carried out as described (Brind'Amour et al, 2015). Pre-cleared chromatin was subjected to immunoprecipitation overnight at 4°C with acetylated H3K27 antibody or trimethylated H3K4 antibody, conjugated to Dynabeads coated with Protein-A. Samples were washed as described (Brind'Amour et al, 2015) and DNA was purified with phenol:chloroform:isoamylalcohol (25:24:1, pH 8) using Maxtract tubes (Qiagen), then precipitated overnight. ATAC Samples. Preparation of samples for ATAC was carried out as described (Buenrostro et al, 2015). Aliquots of 25,000 cells were lysed (10mM Tris-Cl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% NP40), pellets were resuspended in 50µl of transposition mix (Tagment DNA buffer, Tagment DNA enzyme, Illumina), and incubated at 37oC (30 min). Samples were purified using MinElute spin columns (Qiagen).
ChIP Samples: ChIP or input DNA was used for indexed library preparation, pooled (4-6 samples), and subjected to 50 bp single-end sequencing per manufacturer’s protocol (Illumina HiSeq2500). ATAC Samples. Nextera index adapters (i7 and i5) were used to amplify transposed DNA fragments (Illumina). Libraries were purified using AMPure XP beans (Beckman-Coulter), pooled (2-3 samples) and subjected to PE50 sequencing on an Illumina HiSeq2500.

tag: markers


title: NK_ATAC_rep1

description: ATAC DNA

source_name: peripheral blood

value: NK


title: ILC3_ATAC_rep1

description: ATAC DNA


title: ILC1_ATAC_rep1

description: ATAC DNA


title: ILC3_ATAC_rep2

description: ATAC DNA


title: ILC1_ATAC_rep2

description: ATAC DNA


title: ERWT_H3K27ac_E2

description: ChIP

value: Esr1 wt


title: ERWT_ER_E2

description: two replicates

value: Antibody Mix:MC20 (SantaCruz) + ab10 (TE111-SD1) (Abcam)


title: ERWT_ER_P

description: two replicates

value: Placebo


title: ERKO_ER_E2

description: ChIP


title: ERWT_FOXA2_E2

description: two replicates


title: ERKO_Input

description: Input


title: ERWT_H3K4me2_E2

description: ChIP


title: Th17_ATAC_rep2

description: ATAC DNA


title: NK_ATAC_rep2

description: ATAC DNA


title: NK_input

description: Input DNA

data_processing:
Basecalls performed using CASAVA.
Sequencing tags from FAIRE- and ChIP-Seq were aligned to the reference genome (build GRCh37/hg19) with Novoalign.
ChIP: MACS was used to identify ChIP peaks by comparison of matched treatment to input samples using the following changes to the default settings: --nomodel --shiftsize=150 (H3K27ac), --nomodel --shiftsize=100 (H3K4me3). ATAC: Samples were processed with MACS using the following changes to default settings, --nomodel --shiftsize=50.
Genome_build: hg19
Supplementary_files_format_and_content: Wig files were generated using MACS.


title: ERWT_Input 1

description: Input


title: NK_K27ac_rep1

description: antibody: H3K27ac (Abcam #ab4729, lot GR184333-2)


title: Th17_input

description: Input DNA


title: NK_K27ac_rep2


title: H3K27me3_ChIPseq_H3.1K36M

description:
ChIP-DNA using H3K27me3 antibody (Cell Signaling, 9733, lot 10)
mouse C3H10T1/2 cells and Drosophila S2 cells were mixed in 1:1 ratio prior to library preparation

data_processing:
a custom genome, termed mm9-dm6, was created by combining both Mus musculus genome built, mm9 and Drosophila melanogaster genome built, dm6
Reads that passed the quality score were aligned to mm9_dm6 custom genome using bowtie 1.0.0 with default parameters
Sample normalization factors (Rx) for reads aligned to mouse genome were determined as 1 over the number of reads mapping to Drosophila genome per million base-pair
Genome_build: mm9-dm6 custom genome
Supplementary_files_format_and_content: tab-separated abundance measurement containing the reference (reads aligned to dm6 genome) normalized intensities in each sample

organism:
Drosophila melanogaster
Mus musculus

source_name: C3H10T1/2 cells & S2 cells

growth_protocol: C3H10T1/2 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Invitrogen) with 10% fetal bovine serum (FBS, CellGro). Drosophila S2 cells were cultured in Schneiderís Drosophila Medium (Invitrogen) containing 10% heat-inactivated FBS (CellGro).

extract_protocol:
~2x10^7 C3H10T1/2 cells were lysed using digesting buffer (50 mM Tris-HCl pH 7.6, 1 mM CaCl2 and 0.2% Triton X-100) and digested with micrococcal nuclease to obtain mono-nucleosomes. The chromatin were then dialyzed into RIPA buffer (10 mM Tris pH 7.6, 1 mM EDTA, 0.1% SDS, 0.1% Na-Deoxycholate, 1% Triton X-100) for 2 h at 4°C. After centrifugation, soluble chromatin was spiked-in with soluble chromatin from Drosophila S2 cells that was similarly prepared and equivalent to 5% of the mouse cell chromatin. The mixed soluble chromatin was incubated with αH3K36me3 (Active Motif, 61101), αH3K36me2 (Millipore, 07-369) or αH3K27me3 (Cell Signaling Tech, 9733) antibody bound to 75 μl protein A or protein G Dynal magnetic beads (Invitrogen) and incubated overnight at 4°C, with 5% kept as input DNA. Magnetic beads were washed with RIPA buffer and LiCl buffer (0.25 M LiCl, 0.5% NP40, 0.5% Na-Deoxycholate) and chromatin was eluted. ChIP DNA was treated with Proteinase K (Roche) and recovered using Qiagen PCR purification kit.
libraries were prepared according to the Illumina TruSeq protocol

value: C3H10T1/2:C3H embryo-derived mesenchymal progenitor cells; S2:derived from a primary culture of late stage (20-24 hours old) Drosophila melanogaster embryos

value: C3H10T1/2:Stably expressing FLAG-HA-tagged K36M mutant H3.1; S2:None

value: C3H10T1/2:Passage 10-15; S2:unknown


title: NK_K4me3_rep2

description: antibody: H3K4me3 (Abcam #ab8580, lot GR224429-1)


title: H3K36me2_ChIPseq_H3.1K36M

description:
ChIP-DNA using H3K36me2 antibody (Millipore, 07-369-I, lot number 2475921)
mouse C3H10T1/2 cells and Drosophila S2 cells were mixed in 1:1 ratio prior to library preparation


title: Th17_K27ac_rep2


title: ERWT_Input 2

description: Input


title: Input_DNA_H3.3K36M

description:
5% input DNA
mouse C3H10T1/2 cells and Drosophila S2 cells were mixed in 1:1 ratio prior to library preparation


title: NK_K4me3_rep1


title: H3K36me2 ChIPseq_H3.1WT

value: C3H10T1/2:Stably expressing FLAG-HA-tagged wildtype H3.1; S2:None


title: Th17_K4me3_rep2


title: Th17_K4me3_rep1


title: Input_DNA_H3.3WT


title: Regenerating zebrafish hearts H3K27Ac ChIP-Seq, 1

city: Durham

first: Ravi

last: Karra

state: NC

address: 464 Nanaline Duke, 307 Research Drive

department: Cell Biology

institute: Duke

description: differential_ac_genome_corrected_treat_afterfiting_all.wig.gz

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the Zv9 genome assembly using Bowtie2
Differential peaks were identified using MACS with parameters effective genome size = 1.70e+09; band width = 300; model fold = 10,30; pvalue cutoff = 1.00e-05; Range for calculating regional lambda is: 1000 bps and 10000 bps
Genome_build: zv9

organism: Danio rerio

source_name: Regenerating zebrafish hearts

extract_protocol:
Ablation protocol: bact2:loxP-mCherry-stop-loxP-DTA;cmcl2:CreER zebrafish were treated with tamoxifen or vehicle
Hearts were extracted 7 days post incubation.  Ventricles were dissected and rinsed in heparin.
ChIP was performed after sonication using the MagnifyChIP kit using.  ChIP was done using an antibody directed against H3K27Ac (ActiveMotif).
Bowman, S. K. et al. Multiplexed Illumina sequencing libraries from picogram quantities of DNA. BMC Genomics 14, 466 (2013)

tag: injury conditions

value: Whole hearts following genetic ablation of cardiomyocytes by recombination of ZCAT fish with tamoxifen

tag: days post injury

value: 7 days post incubation with tamoxifen

value: H3K27Ac (Active Motif)


title: Uninjured zebrafish hearts H3K27Ac ChIP-Seq, 1

description: differential_ac_genome_corrected_control_afterfiting_all.wig.gz

source_name: Uninjured zebrafish hearts

value: Whole hearts following treatment of  ZCAT fish with vehicle

value: 7 days post incubation with vehicle


title: H3K27me3_ChIPseq_H3.1WT


title: Regenerating zebrafish hearts H3K27Ac ChIP-Seq, 2


title: UHRR umiseq

city: Martinsried

first: Swati

last: Parekh

address: Grosshaderner Str. 2

department: Biology II

country: Germany

institute: Ludwig Maximillians University Munich

description:
Processed data file: uhrr_umiseq_read_counts.txt
Processed data file: uhrr_umiseq_umi_counts.txt
Processed data file: uhrr_umiseq_barcodes.txt

data_processing:
Base-calls were performed with Illumina bcl2fastq.
All cDNA reads were aligned with NextGenMap 0.4.12. Smart-seq2 reads were mapped to genome, whereas UMI-seq reads were mapped to Ensembl GRCh37.74 cDNA.
Smart-seq2 reads were mapped to hg19+ERCC reference and assigned to genes using FeatureCount method in Rsubread package.
UMI-seq reads were tagged with its mate-pair UMI after masking bases below 10 quality score; mapped to Ensembl GRCh37.74 cDNA; total read count and unique read count tables were generated.
Genome_build: Ensembl GRCh37.74
Supplementary_files_format_and_content: uhrr_smartseq_read_counts.txt: Tab-delimited text file with raw read counts for the Smart-seq2 method.
Supplementary_files_format_and_content: uhrr_umiseq_read_counts.txt: Tab-delimited text file with raw read counts for the UMI-seq method.
Supplementary_files_format_and_content: uhrr_umiseq_umi_counts.txt: Tab-delimited text file with unique gene-wise counts for the UMI-seq dataset.

source_name: Universal Human Reference RNA, UMI-seq

extract_protocol:
Stratagene Universal Human Reference RNA (UHRR; catalog #740000).
Library preparations for UMI-seq were performed using a modified version of Soumillon et al. 2014 for use with bulk RNA.

tag: sample type

value: reference RNA

tag: library preparation

value: UMI-seq


title: UHRR smartseq H

description: Processed data file: uhrr_smartseq_read_counts.txt

data_processing:
Base-calls were performed with Illumina bcl2fastq.
All cDNA reads were aligned with NextGenMap 0.4.12. Smart-seq2 reads were mapped to genome, whereas UMI-seq reads were mapped to Ensembl GRCh37.74 cDNA.
Smart-seq2 reads were mapped to hg19+ERCC reference and assigned to genes using FeatureCount method in Rsubread package.
UMI-seq reads were tagged with its mate-pair UMI after masking bases below 10 quality score; mapped to Ensembl GRCh37.74 cDNA; total read count and unique read count tables were generated.
Genome_build: GRCh37 (hg19) and ERCC synthetic spike-in reference
Supplementary_files_format_and_content: uhrr_smartseq_read_counts.txt: Tab-delimited text file with raw read counts for the Smart-seq2 method.
Supplementary_files_format_and_content: uhrr_umiseq_read_counts.txt: Tab-delimited text file with raw read counts for the UMI-seq method.
Supplementary_files_format_and_content: uhrr_umiseq_umi_counts.txt: Tab-delimited text file with unique gene-wise counts for the UMI-seq dataset.

source_name: Universal Human Reference RNA, Smart-seq2

extract_protocol:
Stratagene Universal Human Reference RNA (UHRR; catalog #740000).
Library preparations were performed with the Smart-seq2 protocol from UHRR as described in Picelli et al. 2013.


title: UHRR smartseq J


title: Th1_K4me3_rep1


title: Th1_K27ac_rep1


title: Th1_input

description: Input DNA


title: Uninjured zebrafish hearts H3K27Ac ChIP-Seq, 2


title: UHRR smartseq D


title: UHRR smartseq E


title: UHRR smartseq G


title: Th1_K27ac_rep2


title: UHRR smartseq F


title: UHRR smartseq C


title: ILC3_input

description: Input DNA


title: Th17_K27ac_rep1


title: UHRR smartseq B


title: UHRR smartseq A


title: Th1_K4me3_rep2


title: UHRR smartseq I


title: Cbx2_ChIPseq_H3.3WT

description: ChIP-DNA using Cbx2 antibody Bethyl Laboratories, catalog number A302-524A)

data_processing:
Reads that passed the quality score were aligned using bowtie 1.0.0 with default parameters
Peaks were called using mosaics (threshold = 20, FDR= 0.05, maxgap = 10000bp, minsize = 5000bp, binSize= 200bp, two component model, Input-Only analysis)
RPKM-normalized read intensities in the peaks were determined for the H3.3WT and H3.3K36M samples
Genome_build: mm9
Supplementary_files_format_and_content: tab-separated file containing genomic coordinates for Cbx2 peaks and rpkm-normalized read-counts for H3.3WT and H3.3K36M samples for each peak

extract_protocol:
~2x10^7 cells were fixed with 1% formaldehyde for 10 min at room temperature and then quenched with 125 mM glycine for 5 min. Cells were then lysed in SDS lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl) and sonicated for 1 h with Bioruptor (Diagenode) to obtain mononucleosomes. After centrifugation, the lysates were diluted with dilution buffer (167 mM NaCl, 0.01% SDS, 1.1% TritonX-100, 1.2 mM EDTA, 16.7 mM Tris-HCl) and incubated with αCbx2 (Active Motif, 39663) antibody bound to 75 μl protein A Dynal magnetic beads (Invitrogen) and incubated overnight at 4°C, with 5% kept as input DNA. 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, treated with Proteinase K (Roche) and recovered using Qiagen PCR purification kit.
libraries were prepared according to the Illumina TruSeq protocol

value: C3H embryo-derived mesenchymal progenitor cells

value: Stably expressing FLAG-HA-tagged wildtype H3.3

value: Passage 10-15


title: ILC3_K27ac_rep3


title: ILC3_K27ac_rep1


title: ILC3_K4me3_rep3


title: ILC3_K4me3_rep1


title: ILC3_K4me3_rep2


title: VSV infected 2

city: shanghai

first: ql

last: zheng

address: xiangyin

institute: immunity

data_processing:
After linker sequence removal and quality trimming, sequence mapping was performed using Bowtie with default parameters (build mm9).
Bioinformatic and motif enrichment analysis was performed as described previously(Moore, M.J. et al. Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis. Nat Protoc 9, 263-293 (2014).)
Genome_build: mm9
Supplementary_files_format_and_content: xlsx files containing the peak number,the chromosomal location, depth and fold enrichment of the peaks obtained from the iCLIP experiments

growth_protocol: Cells were grown in DMEM-based media supplemented with 10% FBS

extract_protocol:
Cells were UV cross-linked and prepared as described previously (Huppertz, I. et al. iCLIP: protein-RNA interactions at nucleotide resolution. Methods 65, 274-287 (2014)) and immunprecipitation of DDX46 using an anti-DDX46 antibody obtained from Abcam (ab72083).
RNA library constructed as described previously (Huppertz, I. et al. iCLIP: protein-RNA interactions at nucleotide resolution. Methods 65, 274-287 (2014))

treatment_protocol: RAW264.7 cells were infected with or without VSV for 6 h

tag: iclip antibody


title: Sample 96

city: Boston

first: Andrew

last: Lutas

state: MA

address: 200 Longwood Ave

department: Neurobiology

institute: Harvard Medical School

description: Column name in processed data:  q31_0

data_processing:
Reads were generated using an Illumina Nextseq500
Data were separated by barcode and aligned using Tophat version 2.0.10 (Kim et al. 2013) with default settings. Transcripts were quantified using the Cufflinks suite version 2.2.1 (Trapnell et al. 2012).
Data are processed through CuffNorm if 50% of the reads align and there are at least 100,000 aligned pairs per sample. Normalization used the default settings, including “geometric” normalization, which normalizes samples based on the median expression level in each sample.
For samples that pass the filtering critia for CuffNorm, gene expression levels are reported as fragments per kilobase pair per million mapped reads (FPKM)
Genome_build: mm10
Supplementary_files_format_and_content: Text file contains FPKM values for 80 samples that passed initial quality control

molecule: polyA RNA

source_name: postnatal day 16_GFP positive

extract_protocol:
Individual neurons were lysed in 5µL of TCL buffer (qiagen) and total RNA was purified using RNA-SPRI beads.
The Smart-seq2 protocol (Picelli et al., 2014) was used to prepare libraries. cDNA was subject to transposon-based fragmentation that used dual-indexing to barcode each fragment of each converted transcript with a combination of barcodes specific to each sample.

tag: age

value: postnatal day 16

value: brain

tag: tissue subtype

value: Substantia nigra pars reticulata (SNr)

tag: gfp

value: GFP positive

value: GFP-positive GABAergic SNr neurons

value: GTAGAGGA

value: TTACTTAA


title: Sample 95

description: Column name in processed data:  q12_0

tag: cell type

value: AAGAGGCA


title: VSV infected 1


title: ILC1_K27ac_rep1


title: uninfected 1


title: Sample 94

description: Column name in processed data:  q1_0

value: CGAGGCTG


title: uninfected 2


title: Sample 93

description: Column name in processed data:  q10_0

value: GCTACGCT


title: ILC1_K4me3_rep2


title: ILC1_K4me3_rep1


title: Sample 91

description: Column name in processed data:  q29_0

value: CTCTCTAC


title: Sample 90

description: Column name in processed data:  q38_0

value: TAGGCATG


title: Sample 89

description: Column name in processed data:  q4_0

value: GGACTCCT


title: H3.1WT-HA_ChIPseq_H3.1WT

description: ChIP-DNA using HA antibody (Biolegend, catalog number 901501, lot number B201938)

data_processing:
Reads that passed the quality score were aligned using bowtie 1.0.0 with default parameters
Peaks were called using mosaics (threshold = 20, FDR= 0.05, maxgap = 10000bp, minsize = 5000bp, binSize= 200bp, two component model, Input-Only analysis)
RPKM-normalized read intensities in the peaks were determined for the H3.3WT and H3.3K36M samples
Genome_build: mm9
Supplementary_files_format_and_content: tab-separated file containing genomic coordinates for HA-tagged H3.3/H3.1 K36M peaks
Supplementary_files_format_and_content: tab-separated file containing RPKM enrichment of H3.1WT, H3.1K36M, H3.3WT and H3.3K36M in genomic bins (10000 bp each)

tag: genotype

value: Stably expressing FLAG-HA-tagged wildtype H3.1

tag: passages


title: ILC3_K27ac_rep2


title: Sample 88

description: Column name in processed data:  q13_0

tag: tissue

value: TCCTGAGC


title: Sample 86

description: Column name in processed data:  q74_0

source_name: postnatal day 16_GFP negative

value: GFP negative

value: GFP-negative SNr cells

value: CGTACTAG


title: Sample 85

description: Column name in processed data:  q45_0

value: postnatal day 16

value: brain

value: TAAGGCGA


title: ILC1_K27ac_rep2


title: S11-1065-Chondroblastoma-K36M

data_processing:
Raw reads are trimmed for quality (phred33 >= 30) and length (n >= 30) using Trimmomatic (v. 0.32). Illumina adaptor sequences are clipped off using the palindromic mode.
Perform a sliding window trimming, cutting once the average quality within the window falls below 30. Cut 3 bases off the start of each read, if below quality 30. Cut 3 bases off the end of each read, if above quality 30. Cut the first 4 bases at the start of each read. Drop short reads (n <= 30).
Reads are aligned to the UCSC hg19 genome with STAR v2.3.0e using default settings, which removes multimapping reads. Feature annotation is provided by UCSC knownGene.
Read counting is done with featureCounts v1.4.4. Unless stated otherwise, default settings are used. Read summarization is done at the gene symbol level. The minimum mapping quality score for a read to be counted is 3. Only primary alignments are counted. Reads rather than fragments are counted. Only reads mapping to exons are considered.
Expression data is variance-stabilized using the VST algorithm provided by the DESeq2 R package.
Genome_build: hg19
Supplementary_files_format_and_content: tab separated file containing read counts normalized with the variance-stabilized transformation

source_name: patient tumor sample

extract_protocol:
Flash-frozen tumor specimens were homogenized and RNA was harvested using Trizol reagent. Illumina TruSeq Stranded Total RNA with Ribo-Zero Human/Mouse/Rat was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tumor type

value: chondroblastoma

value: histone H3.3 K36M mutant


title: ten_hESCs_#3

description: singel cell  RNA seq

extract_protocol:
The RNAs in individual oocyte or embryo were reverse transcribed and amplified using the single RNA-seq method we recently developed.
Libraries were constructed with TruSeq DNA library preparation kit (Illumina)
RNA-seq (single-cell)

value: stem cells

tag: passage


title: Sample 83

description: Column name in processed data:  q48_0

tag: strain

value: Substantia nigra pars reticulata (SNr)

value: GFP positive

value: GFP-positive GABAergic SNr neurons

value: AAGAGGCA

value: ACGCCGGA


title: ten_hESCs_#4

description: singel cell  RNA seq


title: Sample 84

description: Column name in processed data:  q72_0

value: GTAGAGGA


title: ILC1_K4me3_rep3


title: ten_hESCs_#1

description: singel cell  RNA seq


title: S03-5700-Chondroblastoma-K36M


title: IHRT264-Chondroblastoma-K36M


title: IHRT1586-Chondroblastoma-K36M


title: Sample 82

description: Column name in processed data:  q56_0

value: CGAGGCTG


title: Sample 79

description: Column name in processed data:  q39_0

value: CTCTCTAC


title: Sample 78

description: Column name in processed data:  q32_0

value: TAGGCATG


title: IHRT1352-Chondroblastoma-WT

value: histone H3 wildtype


title: Sample 77

description: Column name in processed data:  q21_0

value: GFP negative

value: GFP-negative SNr cells

value: GGACTCCT


title: IHRT1221-Chondroblastoma-WT


title: IHRT907-Chondroblastoma-WT


title: Sample 76

description: Column name in processed data:  q9_0

value: postnatal day 16

value: brain

value: TCCTGAGC


title: TE_#3

description: single cell  RNA seq

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Reads were trimmed to remove the adapter sequences and low quality bases.
RNA-seq reads were aligned to the human refference genome (hg19) using Tophat software
Raw read counts and RPKM calculated by HTSeq
Genome_build: hg19
Supplementary_files_format_and_content: txt files reflect RPKM of each gene with Refseq ID.

source_name: human TE

value: TE


title: ten_hESCs_#2

description: singel cell  RNA seq

value: stem cells


title: Sample 75

description: Column name in processed data:  q70_0

value: Substantia nigra pars reticulata (SNr)

value: AGGCAGAA


title: TE_#2

description: single cell  RNA seq


title: Sample 74

description: Column name in processed data:  q61_0

source_name: postnatal day 15_GFP positive

value: postnatal day 15

value: GFP positive

value: GFP-positive GABAergic SNr neurons

value: CGTACTAG


title: Sample 81

description: Column name in processed data:  q14_0

value: GCTACGCT

value: ACGCCGGA


title: Sample 73

description: Column name in processed data:  q54_0

value: TAAGGCGA


title: Sample 70

description: Column name in processed data:  q63_0

source_name: postnatal day 15_GFP negative

value: GFP negative

value: CGAGGCTG

value: CGTTCATA


title: Sample 69

description: Column name in processed data:  q78_0


title: TE_#1

description: single cell  RNA seq


title: ICM_#1

description: single cell  RNA seq

source_name: human ICM

value: ICM


title: IHRT498-Chondroblastoma-K36M

value: chondroblastoma

value: histone H3.3 K36M mutant


title: ICM_#2

description: single cell  RNA seq


title: ICM_#3

description: single cell  RNA seq


title: LateBlastocyst_#1_B

description: single cell  RNA seq

source_name: human late blastoycst

value: late blastoycst


title: LateBlastocyst_#1_A

description: single cell  RNA seq


title: LateBlastocyst_#2

description: single cell  RNA seq

value: late blastocyst


title: Sample 72

description: Column name in processed data:  q44_0

value: brain

value: Substantia nigra pars reticulata (SNr)

value: GTAGAGGA


title: MiddleBlastocyst_#2

description: single cell  RNA seq

source_name: human middle blastocyst

value: middle blastocyst


title: Sample 67

description: Column name in processed data:  q57_0

value: postnatal day 15

value: GFP positive

value: GFP-positive GABAergic SNr neurons

value: CTCTCTAC


title: MiddleBlastocyst_#1_B

description: single cell  RNA seq


title: MiddleBlastocyst_#1_A

description: single cell  RNA seq


title: Sample 63

description: Column name in processed data:  q23_0

value: AGGCAGAA


title: Sample 65

description: Column name in processed data:  q77_0

value: GGACTCCT


title: Sample 66

description: Column name in processed data:  q50_0

value: TAGGCATG


title: Sample 60

description: Column name in processed data:  q15_0

value: GGAAGGCC


title: Sample 64

description: Column name in processed data:  q66_0

value: TCCTGAGC

value: CGTTCATA


title: Sample 80

description: Column name in processed data:  q3_0

value: postnatal day 16

value: CAGAGAGG

value: ACGCCGGA


title: EarlyBlastocyst_#2

description: single cell  RNA seq

source_name: human early blastocsyt

value: early blastocsyt


title: Sample 59

description: Column name in processed data:  q28_0

value: brain

value: Substantia nigra pars reticulata (SNr)

value: AAGAGGCA


title: Sample 68

description: Column name in processed data:  q67_0

value: postnatal day 15

value: GFP negative

value: GFP-negative SNr cells


title: EarlyBlastocyst_#1_B

description: single cell  RNA seq


title: Sample 56

description: Column name in processed data:  q16_0

value: GFP positive

value: GFP-positive GABAergic SNr neurons


title: Sample 57

description: Column name in processed data:  q5_0

value: GCTACGCT


title: Sample 55

description: Column name in processed data:  q33_0

value: CTCTCTAC


title: 150DAF rep1

city: wuhan

first: jinqiu

last: wang

state: hubei

address: Shizishan Street

institute: College of Horticulture and Forestry, Huazhong Agricultural University

description: RNA-seq data of fruits peel at 150 day after flowering

data_processing:
Removal of low-quality reads was achieved by using the FASTQ quality filter of the FASTX-toolkit. All reads in which 80 % or less bases had a quality score of 20 or less were removed. The sequencing reads were mapped to sweet orange reference genomes
The Tophat and Cufflinks workflow were used for analysing RNA-seq data.Q value<0.005 and the absolute value of log2（foldchange）>1 were used as the threshold for significantly differential expression. InterPro and Swiss-prot were used to predict GO terms.
Genome_build: citrus sinensis whole genome
Supplementary_files_format_and_content: A file includes RPKM values of all the Samples

organism: Citrus sinensis

source_name: peel

extract_protocol:
Total RNA was extracted by Trizol method
20 mg total RNA was prepared to enrich mRNA by using the oligo (dT) magnetic beads. After adding fragmentation buffer, the mRNA was interrupted to short fragments (approximately 200 bp). The first strand cDNA was then synthesized with random hexamer-primer using the mRNA fragments as templates. Buffer, dNTPs, RNase H and DNA polymerase I were added to synthesize the second strand. The double-strand cDNA was purified with QiaQuick PCR extraction kit and washed with EB buffer for end repair and single nucleotide A (adenine) addition. Finally, sequencing adaptors were ligated to the fragments.

treatment_protocol: No treatment

tag: developmental stage

value: 150 day after flowering


title: Morula_#2

description: single cell  RNA seq

source_name: human morula

value: morula


title: 120DAF rep1

description: RNA-seq data of fruits peel at 120 day after flowering

value: 120 day after flowering


title: Sample 53

description: Column name in processed data:  q8_0

source_name: postnatal day 14_GFP positive

value: postnatal day 14

value: GGACTCCT

value: GGAAGGCC


title: Morula_#3

description: single cell  RNA seq


title: 120DAF rep2


title: 8cell_#4

description: single cell  RNA seq

source_name: human 8 cell

value: 8 cell


title: Morula_#1_A

description: single cell  RNA seq


title: Morula_#1_B

description: single cell  RNA seq


title: Sample 52

description: Column name in processed data:  q20_0

value: brain

value: TCCTGAGC


title: 8cell_#3

description: single cell  RNA seq


title: 8cell_#2

description: single cell  RNA seq


title: 4cell_#3

description: single cell  RNA seq

source_name: human 4 cell

value: 4 cell


title: 8cell_#1_A

description: single cell  RNA seq


title: Sample 47

description: Column name in processed data:  q18_0

source_name: postnatal day 14_GFP negative

value: Substantia nigra pars reticulata (SNr)

value: AAGAGGCA

value: ACCGAGAG


title: Sample 46

description: Column name in processed data:  q6_0

value: GFP positive

value: CGAGGCTG


title: 150DAF rep2


title: Sample 44

description: Column name in processed data:  q79_0

value: GFP negative

value: GFP-negative SNr cells

value: CAGAGAGG


title: 8cell_#1_B

description: single cell  RNA seq


title: Sample 45

description: Column name in processed data:  q68_0

value: GFP-positive GABAergic SNr neurons

value: GCTACGCT


title: 4cell_#2

description: single cell  RNA seq


title: Sample 43

description: Column name in processed data:  q52_0

value: postnatal day 14

value: CTCTCTAC


title: Sample 41

description: Column name in processed data:  q65_0

value: GGACTCCT


title: 4cell_#1_B

description: single cell  RNA seq


title: 4cell_#1_A

description: single cell  RNA seq


title: Sample 42

description: Column name in processed data:  q59_0

value: TAGGCATG


title: Sample 38

description: Column name in processed data:  q24_0

source_name: postnatal day 20_GFP positive

value: postnatal day 20

value: brain

value: CGTACTAG


title: Sample 51

description: Column name in processed data:  q62_0

value: Substantia nigra pars reticulata (SNr)

value: AGGCAGAA

value: GGAAGGCC


title: 2cell_#2

description: single cell  RNA seq

source_name: human 2 cell

value: 2 cell


title: Sample 48

description: Column name in processed data:  q27_0

value: GTAGAGGA

value: ACCGAGAG


title: 2cell_#1_B

description: single cell  RNA seq


title: Sample 40

description: Column name in processed data:  q76_0

value: GFP positive

value: TCCTGAGC


title: 2cell_#3

description: single cell  RNA seq


title: Zygote_#4

description: single cell  RNA seq

source_name: human zygote

value: zygote


title: Sample 36

description: Column name in processed data:  q75_0

value: GFP-positive GABAergic SNr neurons

value: GATCGGAG


title: Sample 37

description: Column name in processed data:  q35_0

value: TAAGGCGA


title: Sample 35

description: Column name in processed data:  q43_0

value: AAGAGGCA


title: Zygote_#3

description: single cell  RNA seq


title: Sample 31

description: Column name in processed data:  q17_0

value: CTCTCTAC


title: Zygote_#1_B

description: single cell  RNA seq


title: Zygote_#2

description: single cell  RNA seq


title: Zygote_#1_A

description: single cell  RNA seq


title: Sample 30

description: Column name in processed data:  q7_0

value: postnatal day 20

value: TAGGCATG


title: Oocyte_#3

description: single cell  RNA seq

source_name: human MII oocyte

value: MII oocyte


title: Sample 29

description: Column name in processed data:  q37_0

value: brain

value: Substantia nigra pars reticulata (SNr)

value: GGACTCCT


title: Sample 33

description: Column name in processed data:  q41_0

value: GCTACGCT


title: Sample 28

description: Column name in processed data:  q25_0


title: Oocyte_#2

description: single cell  RNA seq


title: Sample 25

description: Column name in processed data:  q71_0


title: 2cell_#1_A

description: single cell  RNA seq

value: 2 cell


title: Oocyte_#1_B

description: single cell  RNA seq


title: Oocyte_#1_A

description: single cell  RNA seq


title: Sample 24

description: Column name in processed data:  q46_0

source_name: postnatal day 16_GFP positive

value: postnatal day 16

value: GTAGAGGA

value: AAGTCCTG


title: Sample 23

description: Column name in processed data:  q73_0

value: GFP positive


title: EarlyBlastocyst_#1_A

description: single cell  RNA seq

value: early blastocsyt


title: Sample 26

description: Column name in processed data:  q49_0

value: GFP-positive GABAergic SNr neurons

value: CGTACTAG

value: GATCGGAG


title: Sample 21

description: Column name in processed data:  q58_0


title: Sample 19

description: Column name in processed data:  q80_0

value: CTCTCTAC


title: OMV replicate 2

data_processing:
Sequences were trimmed and aligned to the PA14 reference genome with CLC Genomics Workbench (Qiagen).
The RNA-Seq analysis was run with the following modifications from the standard parameters: a) use of 50 additional bases up- and downstream of annotated genes to capture sRNAs that align to intergenic regions, b) maximum number of mismatches = zero to eliminate unspecific alignment of yeast sequences from the LB medium and c) maximum number of hits for a read = 4.
Pileups of uniquely mapped reads as well as frequency tables for each unique sequence (generated with the CLC Small RNA Analysis tool) were exported for normalization and further analysis with the R software environment for statistical computing and graphics
Unique sequences were extracted with the CLC genomics small RNA tool
Normalization to account for differences in library size was performed using the R software
Supplementary_files_format_and_content: sRNA_unique.csv: csv file with PA14 and OMV log2 counts for each unique sequence
Supplementary_files_format_and_content: Top_Loci.csv: csv file with log2 counts for PA14 and OMV for the 68 top loci

organism: Pseudomonas aeruginosa PA14

source_name: outer membrane vesicle

growth_protocol: PA14 was grown in 30 ml LB medium for 16 h at 37°C and 225 rpm

extract_protocol:
RNA was extracted with the miRNeasy kit (Qiagen), followed by DNase digestion
TruSeq Small RNA Library Preparation Kit (Illumina)

treatment_protocol: OMVs were isolated by ultracentrifugation of filtered supernatant. For PA14 whole cells, the pellet from 1 ml of the culture was used.

tag: tissue type

value: outer membrane vesicles (OMVs)


title: OMV replicate 3


title: PA14 replicate 2

source_name: whole cell

value: whole cells


title: PA14 replicate 1


title: PA14 replicate 3


title: Sample 20

description: Column name in processed data:  q51_0

value: CAGAGAGG


title: OMV replicate 1


title: Sample 17

description: Column name in processed data:  q60_0

value: brain


title: Sample 13

description: Column name in processed data:  q22_0

value: Substantia nigra pars reticulata (SNr)

value: TAAGGCGA


title: Sample 14

description: Column name in processed data:  q34_0


title: Sample 15

description: Column name in processed data:  q42_0

value: AGGCAGAA


title: Sample 12

description: Column name in processed data:  q19_0

value: CGCGTCTT


title: Sample 11

description: Column name in processed data:  q26_0

source_name: postnatal day 15_GFP positive

value: postnatal day 15

value: AAGAGGCA


title: Sample 8

description: Column name in processed data:  q40_0


title: Sample 18

description: Column name in processed data:  q69_0

value: postnatal day 16

value: TAGGCATG

value: AAGTCCTG


title: Sample 7

description: Column name in processed data:  q2_0

value: GFP positive

value: GFP-positive GABAergic SNr neurons


title: Sample 6

description: Column name in processed data:  q11_0


title: Sample 3

description: Column name in processed data:  q47_0


title: Sample 2

description: Column name in processed data:  q55_0

value: CGTACTAG


title: Sample 1

description: Column name in processed data:  q64_0


title: Sample 16

description: Column name in processed data:  q53_0

value: TCCTGAGC


title: Sample 5

description: Column name in processed data:  q30_0

value: GGACTCCT


title: del_fpo1-1dak-2

city: Seoul

first: Hokyoung

last: Son

address: Daehak-dong, Gwanak-gu

department: Center for Food and Bioconvergence

country: South Korea

institute: Seoul National University

description: mRNAs from Fusarium graminearum wild-type strain fpo1 at 1 day after sexual induction

data_processing:
BWA software was used for basecalling and genome alignment.
Sequenced reads were mapped to MIPS FGDB_v32 genome (obtained from ftp://ftpmips.gsf.de/fungi/FGDB/v32/) using bwa with parameters aln -q 20 and paired-end results were generated by sampe option.
Reads within exon were counted by the HTSEQ package of Python.
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 was counted and normalized by the size of the meta-transcript and by the size of the library.
RPK100M = 100 x RPKM
Genome_build: FGDB_v32
Supplementary_files_format_and_content: tab-delimited text files include gene information and raw counts, RPK100M, RPKM values for each Sample …

organism: Fusarium graminearum

source_name: Fungi culture

growth_protocol: Fungal strain was grown at 25 ºC under near UV light for 1 day after sexual induction

extract_protocol: Illumina TruSeqTM RNA sample prep kit with standard low throughput (LT) protocol

tag: genotype/variation

value: fpo1 mutant


title: del_fpo1-1dak-1


title: del_abaA-1dak-3

description: mRNAs from Fusarium graminearum wild-type strain abaA at 1 day after sexual induction

value: abaA mutant


title: del_abaA-1dak-1


title: Z3639-1dak-2

description: mRNAs from Fusarium graminearum wild-type strain Z-3639 at 1 day after sexual induction

value: wild-type


title: Z3639-1dak-1


title: Z3639-1dak-3


title: Sample 10

description: Column name in processed data:  q36_0

value: brain

value: Substantia nigra pars reticulata (SNr)

value: CGAGGCTG


title: mRNAs from Fusarium graminearum wild-type strain Z-3639 after 15 min incubation in complete media at 37 ºC, rep1

growth_protocol: Fungal strain was grown in complete medium (CM)  for 15 min at 25 ºC and 37 ºC

tag: condition

value: high temperature


title: mRNAs from Fusarium graminearum wild-type strain Z-3639 after 15 min incubation in complete media at 37 ºC, rep3


title: ILC1_input

description: Input DNA

source_name: Tonsils

tag: markers


title: mRNAs from Fusarium graminearum wild-type strain Z-3639 after 15 min incubation in complete media at 37 ºC, rep2


title: ILC1_K27ac_rep3


title: mRNAs from Fusarium graminearum wild-type strain Z-3639 after 15 min incubation in complete media at 25 ºC, rep2

value: normal temperature


title: mRNAs from Fusarium graminearum wild-type strain Z-3639 after 15 min incubation in complete media at 25 ºC, rep3


title: mRNAs from Fusarium graminearum wild-type strain Z-3639 after 15 min incubation in complete media at 25 ºC, rep1


title: CFBE + OMV rep 3

description: Sample 12

data_processing:
Data analysis was performed with CLC Genomics Workbench.
Adaptors were trimmed and sequences were aligned to the PA14 reference genome.
Pileup tables of uniquely mapped reads were compiled for each sample.
Genome_build: Pseudomonas aeruginosa UCBPP-PA14, complete genome; NC_008463.1
Supplementary_files_format_and_content: Each speadsheet in the 'Unique reads.xls' contains the reads that uniquely mapped to PA14 reference for each sample. Each spreadsheet nubmer (e.g. 1,2,…11,12) correspond to the sample number indicated in the description field.

organism:
Pseudomonas aeruginosa
Homo sapiens

source_name: CFBE + OMV

tag: cell line

value: bronchial epithelial cells

tag: exposed to

value: PA14 outer membrane vesicle (OMV)


title: CFBE + OMV rep 2

description: Sample 10


title: del_fpo1-1dak-3


title: CysNO treatment: Treat_2

city: Daegu

first: Sang-Uk

last: Lee

address: 80 Daehakro, Bukgu

institute: Kyungpook National University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
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: tair10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Arabidopsis thaliana

source_name: Leaf

growth_protocol: Arabidopsis thaliana accession Col-0 seeds were grown under 16 hrs of light and 8 hrs of dark at 18oC.

extract_protocol:
RNA was extracted from triplicate leaf samples of treated and control plants using RNeasy® Plant Mini Kit (Qiagen) according to standard protocol provided by the manufacturer.
RNA was purified using miRNeasy Kit (Qiagen), following the manufacturer’s instructions. Quality of RNA was analyzed by Agilent 2100 Bioanalyzer QC and samples with RIN(RNA Integrity Number) 7 ≥ and 28s/18s ratio 1.0 ≥ were used for c DNA synthesis. Library was prepared using TruSeq RNA library prep kit (Illumina) for 100bp paired-end sequencing.  Briefly, poly A tailed transcript RNA was isolated using oligo(dT) selection from 2µg total RNA and ramdomly fragmented by Mg 2+  ion treatment. The fragmented mRNA was subjected to cDNA synthesis through random hexamer priming. End-repair, A-tailing and Adapter ligation was conducted for Blunt-end producing and Adapter genernation. After that c DNA was amplified by PCRcDNA libraries were quantified by KAPA library quantification kit (Illumina). Samples were sequenced using Hiseq-2500 sequencer (Illumina)

treatment_protocol: Rosette stage plants (about 4 weeks old) were infiltrated with 1mM CysNO (mixing equimolar HCL-dissolved L-Cysteine and sodium nitrite solution) at the abaxial side of the leaf and samples were collected after 6hrs in liquid nitrogen. Control plants were infiltrated with buffer (1mM HCl) only

tag: Stage

value: Leaf 7

value: wild type

tag: treatment

value: 1mM CysNO


title: CFBE + OMV rep 1

description: Sample 8


title: del_abaA-1dak-2


title: CysNO treatment: Treat_1


title: CysNO treatment: Control_3

value: buffer (1mM HCl)


title: CysNO treatment: Treat_3


title: primary HBE + OMV donor 1

description: Sample 2

source_name: primary HBE + OMV

value: primary human bronchial epithelial (HBE) cells


title: LIGR-Seq_no-AMT_no-Ligase_Rep2

status: Public on May 12 2016

city: Toronto

first: Timothy

last: Sterne-Weiler

state: Ontario

address: 160 College Street, Room 1030

department: The Donnelly Centre

country: Canada

institute: University of Toronto

description: Digested RNA

data_processing:
Single-end strand-specific LIGR-seq reads were trimmed of their 5´ random barcodes and aligned/analyzed using a custom software suite, aligater (available at http://github.com/timbitz/aligater), which is implemented in Julia (v0.4) and Perl (v5).
In the first alignment step `aligater align`, the reads are mapped via a samtools compatible wrapper to `bowtie2` in `--local --reorder` mode with `-k 50` under ‘very sensitive’ conditions `-R 3 -N 0 -L 16 -i S,1,0.50`.
In the chimera detection step `aligater detect`, sam/bam format alignments are read in blocks for each read and recursively chained following a stringent chaining penalty of `-48` which corresponds to the bowtie2 score of roughly 6 matches with perfect quality scores.
In order to ensure that chained alignments are ligation products rather artifacts caused by mis-mapping of spliced transcripts or repetitive and paralogous/pseudogene regions, we align the 40 nucleotides centered upon each ligation site to the NCBI BLAST databases (human_genomic, other_genomic, nt) using lenient parameters `-word_size 24 -perc_identity 75 -culling_limit 1 -num_alignments 5`.  This post-processing step `aligater post --blast` subsequently removed any chimeras with known BLAST hits that match at least 6 bp on both sides of the ligation site.
A sequence-specific library model of two 32 nt k-mers, one from each side of a ligation site, was trained through a two-pass algorithm `aligater reclass` (Figure S1E) which (a) first stored the most stringent classification for every pair of 32 nt windows sliding every 16 nt, and (b) second assigned the most stringent class by iterating through every set of two 32 nt windows for each putative ligation.
Genome_build: hg19
Supplementary_files_format_and_content: lig file (description at http://github.com/timbitz/aligater)

source_name: HEK293T Cells

growth_protocol: 293T cells were cultured in DMEM with 10% FBS and plated at 2.2x106 cells/10 cm plate. 72 hours after plating, cells were collected in ice cold PBS, washed twice in PBS, followed by a third wash in cold TS buffer (0.15 M NaCl/0.01 M Tris-HCl, pH 7.2). Cells were aliquoted into 2x107 cells/tube and pelleted. Each pellet was resuspended in 2 mL cold TS buffer and AMT was added to a final concentration of 20 μL/mL. Cells were incubated for 10 min on ice, mixing every few minutes, and transferred to an open 60 mm petri dish placed on ice.

extract_protocol:
Immediately after incubation, reactions were placed on ice and RNA was phenol-chloroform extracted. After washing in 70% ethanol, the RNA was resuspended in 20 μL of TS buffer. For crosslink reversal, RNA was resuspended in TS buffer in open eppendorf tubes were placed on ice. The RNA was irradiated for 5 min intervals for 10 min at 254 nm at a distance of ~ 15 cm from the UV bulb. AMT was removed from samples by ethanol precipitation and the RNA was resuspended in 10 μL of water.
The SMARTER strand library preparation kit (Clontech), which is well suited for low amounts of input, was used to prepare libraries from RNA samples according to the manufacturer’s instructions with a few modifications. Briefly, first strand cDNA synthesis was performed using a primer that adds a universal sequence to the 5´ end of the first strand, and using a reverse transcriptase that adds several nucleotides to the end of the cDNA. A universal forward primer was annealed to the added nucleotides for synthesis of the second cDNA strand. Primers specific to added sequences from the first and second strand cDNA synthesis were used for library amplification, where the reverse primer includes a barcode index allowing multiplexing during sequencing. Libraries were amplified for 20 cycles for replicate 1 and 17 cycles for replicate 2. For extraction and clean-up of nucleic acid from the RT reaction and PCR reaction with Solid Phase Reversible Immobilization (SPRI) AMPure beads, a 1:2 ratio of sample:beads was used to obtain fragments < 100 bp (the ratio of sample to beads preferentially selects an empirically determined size range of nucleic acid). Following library preparation, samples were separated on a 6% TBE 1.0 PAGE gel (Novex) at 150 V, 16 A. Products above 200 nt were excised and eluted overnight in 30 μL of H20 at 10oC. Size distribution was verified using a Bioanalyzer.

treatment_protocol: Cells were pelleted, resuspended in 500 μL TRI-reagent (Sigma) for RNA extraction as per the manufacturer’s instructions. DNAse I treatment was performed using 2 μL TURBO Dnase I (Ambion), 5 μL of 10x TURBO DNase I buffer in a final reaction volume of 50 μL. Ribosomal RNA was depleted from 4 μg of total RNA using the Ribozero Gold kit (Epicentre as per the manufacturer’s instructions and depletion was verified using a Bioanalyzer. To generate short, single-strand ends with 3´-hydroxl and 5´ phosphate ends for ligation, 400 ng of RNA was digested in a 20 μL reaction with 1 x S1 buffer and 2 μL  of 1:100 S1 enzyme (diluted in 1 x S1 buffer). The RNA was incubated with S1 nuclease for 30 min at room temperature. Reactions were stopped by phenol-chloroform extraction of the RNA. Ligation was perfomed using circRNA ligase (Epicenter, Illumina Inc.), which was selected due to its ability to favor ligation events between proximal RNA ends (as it is typically employed for intramolecular ligation) and the reduced level of in vitro RNA hybridizations due to the elevated reaction temperature. In 18 μL reaction volumes, 50 ng of S1-digested RNA was incubated with 2 μL 10x circRNA ligase buffer (Epicentre for 2 min at 85oC to denature RNA. The tube was immediately transferred to ice and 1 μL of 10 mM ATP and 1 μL of circRNA ligase was added. Ligation reaction was mixed thoroughly and incubated in a thermocycler for 1 hr at 60oC. 0.5 μL of RNaseR (Epicentre), 2.5 μL RNaseR buffer and 2 μL water were added to each ligation reaction in a total volume of 25 μL. The reaction was mixed and incubated for 10 min at 37oC.

value: 15-18 Passages


title: CysNO treatment: Control_2


title: CysNO treatment: Control_1


title: LIGR-Seq_no-AMT_Ligase_Rep2

description: Digested RNA


title: LIGR-Seq_AMT_no-Ligase_Rep2

description: Digested RNA


title: LIGR-Seq_AMT_Ligase_Rep1

description: Digested RNA


title: LIGR-Seq_AMT_Ligase_Rep2

description: Digested RNA


title: primary HBE + OMV donor 2

description: Sample 4

extract_protocol:
RNA was extracted with the miRNeasy kit (Qiagen)
TruSeq Small RNA Library Preparation Kit (Illumina)
50 bp single end RNA-Seq with Illumina HiSeq


title: RNA-Seq_MGG8a_13 [Sample 19]

city: Basel

first: Tommy

middle: Beat

last: Schlumpf

state: Basel-Stadt

address: Mattenstrasse 26

department: D-BSSE

country: Switzerland

institute: ETH Zürich

description: processed data: RNA_GBM_Diff.txt

data_processing:
Genomic alignment with TopHat 2.0.12, --b2-very-sensitive --library-type fr-firststrand --b2-N 1
Differential expression calling with edgeR 3.10.2 and R 3.2.0
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited textfile containing the raw readcounts, normalized cpm and gene fold-changes

source_name: MGH4 differentiated GSC

growth_protocol: Withdrawal of growth factors for 7 days in DMEM with 10% FCS on 100ug/mL poly-D-lysine (Sigma) and 15ug/mL laminin (Sigma) coated plates.

extract_protocol:
Total RNA extraction kit Exiqon, on colum DNASE treatment (Qiagen)
Illumina polyA stranded

value: Glioma cell line

tag: cell subtype

value: Differentiated cancer stem cells


title: RNA-Seq_MGG8a_10 [Sample 18]

description: processed data: RNA_GBM_Diff.txt

tag: cell type


title: RNA-Seq_MGG4a_9 [Sample 17]

description: processed data: RNA_GBM_Diff.txt


title: RNA-Seq_MGG4a_7 [Sample 15]

description: processed data: RNA_GBM_Diff.txt


title: RNA-Seq_MGG4s_4 [Sample 12]

description: processed data: RNA_GBM_Diff.txt

source_name: MGH4 Glioma stem-like cells

growth_protocol: Neurobasal medium (Invitrogen) supplemented with L-glutamine (Glutamax, Gibco), B27 supplement (Invitrogen), N2 supplement (Invitrogen), 20 ng/mL recombinant human EGF (R&D Systems), 20 ng/ml recombinant human FGF2 (R&D Systems).

value: Cancer stem-like cells


title: RNA-Seq_MGG4s_5 [Sample 13]

description: processed data: RNA_GBM_Diff.txt


title: RNA-Seq_MGG8s_6 [Sample 14]

description: processed data: RNA_GBM_Diff.txt


title: RNA-Seq_MGG8a_8 [Sample 16]

description: processed data: RNA_GBM_Diff.txt


title: LIGR-Seq_no-AMT_Ligase_Rep1

description: Digested RNA


title: RNA-Seq_MGG4s_2 [Sample 11]

description: processed data: RNA_GBM_Diff.txt


title: RNA-Seq_MGG8_OE [Sample 10]

description: processed data: RNA_IMP2a_OE.txt

source_name: MGH8 differentiated GSC

growth_protocol: DMEM + 10% FCS, puromycin selection for 5 days

treatment_protocol: MGH8 adherent cell line infected with lentiviral vector encoding Imp2

tag: infected with

value: lentiviral vector encoding Imp2

value: IMP2 overexpression


title: RNA-Seq_MGG4_OE [Sample 8]

description: processed data: RNA_IMP2a_OE.txt

treatment_protocol: MGH4 adherent cell line infected with lentiviral vector encoding Imp2


title: RNA-Seq_MGG8_KD [Sample 6]

description: processed data: RNA_IMP2s_KD.txt

source_name: MGH8 Glioma stem-like cells

growth_protocol: Neurobasal medium (Invitrogen) supplemented with L-glutamine (Glutamax, Gibco), B27 supplement (Invitrogen), N2 supplement (Invitrogen), 20 ng/mL recombinant human EGF (R&D Systems), 20 ng/ml recombinant human FGF2 (R&D Systems). Puromycin selection for 5 days

treatment_protocol: MGH8 cell line infected with shRNA sequence targeting Imp2

value: shRNA sequence targeting Imp2

value: IMP2 knockdown


title: RNA-Seq_MGG4_KD_ctrl [Sample 3]

description: processed data: RNA_IMP2s_KD.txt

data_processing:
Genomic alignment with TopHat 2.0.12, --b2-very-sensitive --library-type fr-firststrand --b2-N 1
Differential expression calling with edgeR 3.10.2 and R 3.2.0
Genome_build: hg19
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited textfile containing the raw readcounts, normalized cpm and gene fold-changes

treatment_protocol: MGH4 cell line infected with non-silencing control vector

value: non-silencing control vector

value: control for MP2 knockdown


title: RNA-Seq_MGG4_OE_ctrl [Sample 7]

description: processed data: RNA_IMP2a_OE.txt

treatment_protocol: MGH4 adherent cell line infected with lentiviral empty control vector

value: lentiviral empty control vector

value: control for IMP2 overexpression


title: RNA-Seq_MGG8_KD_ctrl [Sample 5]

description: processed data: RNA_IMP2s_KD.txt

treatment_protocol: MGH8 cell line infected with non-silencing control vector


title: LIGR-Seq_no-AMT_no-Ligase_Rep1

description: Digested RNA

tag: passages


title: RNA-Seq_MGG4_KD [Sample 4]

description: processed data: RNA_IMP2s_KD.txt

treatment_protocol: MGH4 cell line infected with shRNA sequence targeting Imp2


title: LIGR-Seq_AMT_no-Ligase_Rep1

description: Digested RNA


title: RNA-Seq_mm_P21_ctrl [Sample 22]

description: processed data: RNA_brain_IMP2_KO.txt

data_processing:
Genomic alignment with TopHat 2.0.12, --b2-very-sensitive --library-type fr-firststrand --b2-N 1
Differential expression calling with edgeR 3.10.2 and R 3.2.0
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited textfile containing the raw readcounts, normalized cpm and gene fold-changes

source_name: P21 IMP2fl/fl brain

growth_protocol: NeuroCult NSC Basal Medium (ref. 05700, Stemcell Technologies) supplemented with 10% Neurocult NSC Proliferation Supplement (ref. 05701, Stemcell Technologies) and 20ng/mL EGF

tag: strain background

tag: age

value: Postnatal week 15

value: C57BL6 bckgrnd mice with IMP2 floxed/floxed integrated but not crossed to Nestin Cre line

tag: tissue

value: brain


title: SVZ H3K27me3 ChIP-Seq

city: San Antonio

first: Chin-Hsing Annie

last: Lin

state: TX

address: One UTSA Circle

department: Biology

institute: University of Texas at San Antonio

data_processing:
Basecalls performed with Illumina RTA version 1.12.4.2
Reads were aligned to the Olive Baboon reference PapAnu2.0 with Bowtie version 1.1.1 using the following parameters: bowtie -p 8 --mm -S -m 1 --best --phred33-quals
Peaks were called with MACS2 v2.1.0.20140616 program: https://github.com/taoliu/MACS/ using the callpeak function with the following parameters: -m 2 50 (all data sets) and --broad (H3K27me3 only).
Genome_build: PapAnu2.0 build 78
Supplementary_files_format_and_content: bed file containing ChIP-Seq peak calls generated from MACS2

organism: Papio anubis

source_name: neural progenitors cells

extract_protocol:
We manually conjugated antibody against cell type markers, such as GFAP, Nestin, Vimentin, PSA-NCAM, or Doublecortin to Dynabeads. We then used the Dynabeads-conjugated antibody to purify cells dissociated from SVZ microdissection. Briefly, cells from fresh dissected baboon SVZ were immediately dissociated with Accutase, equilibrated in binding buffer containing phosphate-buffered saline (PBS), 0.05% TritonX-100 (or saponin, detergent choice depends upon antibody), and subsequently subjected to Dynabeads-conjugated antibody purification. After elution with high salt and pH-gradient buffer, the purified populations were crosslinked in 1.1% formaldehyde before chromatin shearing by Diagenode Bioruptor. The resulting sheared chromatin fragments in a size range between 200 to 500 base pairs were incubated with Protein A Dynabeads (Life Technology Dynabeads protein A) conjugated to H3K27me3 antibody (Active Motif #39155; 1:1000) or H4K20me3 antibody (Upstate #07-463; 1:1000) overnight. For normalization, the aliquot of sheared chromatin fragments were incubated with antibody against total histone 3-conjugated Protein A Dynabeads (unmodified H3 antibody, Millipore #05-499; 1:1000) or total H4 (Cell Signaling #2592; 1:1000). Enriched chromatin was eluted and de-crosslinked, prior to library preparation with TruSeq ChIP sample prep kit (Illumina #IP-202-2012 and #IP-202-1024) and deep sequencing to > 200 million tags on an Illumina HiSeq2000 sequencer.
Libraries were prepared according to instructions for Illumina Library Kit, Illumina  TruSeq v2. Total H3 reads are maintained in GEO Sample GSM1413005.

tag: region

value: subventricular zone

tag: chip antibody


title: RNA-Seq_mm_ED15_ctrl [Sample 20]

description: processed data: RNA_brain_IMP2_KO.txt

source_name: ED15 IMP2fl/fl brain

value: Embryonic day 15


title: RNA-Seq_mm_ED15_KO [Sample 21]

description: processed data: RNA_brain_IMP2_KO.txt

source_name: ED15 IMP2fl/fl nestin cre brain

value: IMP2 floxed/floxed but crossed to Nestin Cre (i.e part of IMP2 is removed from the genome in tissues with Nestin expression)


title: SVZ H4K20me3 ChIP-Seq

extract_protocol:
We manually conjugated antibody against cell type markers, such as GFAP, Nestin, Vimentin, PSA-NCAM, or Doublecortin to Dynabeads. We then used the Dynabeads-conjugated antibody to purify cells dissociated from SVZ microdissection. Briefly, cells from fresh dissected baboon SVZ were immediately dissociated with Accutase, equilibrated in binding buffer containing phosphate-buffered saline (PBS), 0.05% TritonX-100 (or saponin, detergent choice depends upon antibody), and subsequently subjected to Dynabeads-conjugated antibody purification. After elution with high salt and pH-gradient buffer, the purified populations were crosslinked in 1.1% formaldehyde before chromatin shearing by Diagenode Bioruptor. The resulting sheared chromatin fragments in a size range between 200 to 500 base pairs were incubated with Protein A Dynabeads (Life Technology Dynabeads protein A) conjugated to H3K27me3 antibody (Active Motif #39155; 1:1000) or H4K20me3 antibody (Upstate #07-463; 1:1000) overnight. For normalization, the aliquot of sheared chromatin fragments were incubated with antibody against total histone 3-conjugated Protein A Dynabeads (unmodified H3 antibody, Millipore #05-499; 1:1000) or total H4 (Cell Signaling #2592; 1:1000). Enriched chromatin was eluted and de-crosslinked, prior to library preparation with TruSeq ChIP sample prep kit (Illumina #IP-202-2012 and #IP-202-1024) and deep sequencing to > 200 million tags on an Illumina HiSeq2000 sequencer.
Libraries were prepared according to instructions for Illumina Library Kit, Illumina  TruSeq v2


title: shCOX2-3

city: Pittsburgh

first: Donald

middle: B

last: DeFranco

state: PA

address: 3501 Fifth Ave

department: Pharmacology and Chemical Biology

institute: University of Pittsburgh

description: BPH1 shCOX2 #3

data_processing:
The raw sequenced reads were aligned from FASTQ files to the human genome build GRCh37/hg19 and the UCSC reference transcriptome using TopHat and Bowtie2 with default parameters.
Samples were further processed with CuffLink to calculate transcript abundance represented by fragments per kilobase of exon per million mapped reads (FPKM)
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Excel file includes individual FPKM for each sample as well as log2 fold change comparing shCOX2 to scrambled control

source_name: prostate

growth_protocol: BPH1 scr and shCOX2 cells were grown in RPMI supplemented with 5% FBS and 1% P/S.

extract_protocol:
Total RNA was extracted using Trizol and chloroform.
Libraries were prepared using the Illumina Tru-seq Stranded Total RNA kit with Ribo-Zero Gold rRNA depletion according to manufacturer protocol.

value: BPH patient derived prostate epithelial cell

tag: lentiviral shrna


title: shCOX2-1

description: BPH1 shCOX2 #1


title: shCOX2-2

description: BPH1 shCOX2 #2


title: BPH1-3

description: BPH1 scrambled control #3

value: scrambled control


title: BPH1-2

description: BPH1 scrambled control #2


title: RNA-Seq_MGG8_OE_ctrl [Sample 9]

description: processed data: RNA_IMP2a_OE.txt

treatment_protocol: MGH8 adherent cell line infected with lentiviral empty control vector

value: Glioma cell line

value: Differentiated cancer stem cells

tag: genotype/variation


title: WT replicate 2

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

data_processing:
Sequencing, data quality, reads repartition (e.g., for potential ribosomal contamination), and insert size estimation were performed using FastQC, Picard-Tools, Samtools and rseqc
Reads were mapped using STARv2.4.0
Gene expression was estimated using Mouse FAST DB v2014_2 annotations (GenoSplice). Genes were considered as expressed if their rpkm value was greater than 97.5% compared to background rpkm value based on intergenic regions
Differential gene expression was compute using Deseq
Analyses at the exon/pattern levels were compute using GenoSplice pipeline based on Mouse FAST DB v2014_2 annotations
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file includes deseq normalized expression values for each gene and for each sample. Annotations from Mouse FAST DB v2014_2 were also provide

source_name: Hippocampus

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

tag: strain

value: Hippocampus

value: 8 weeks

value: WT


title: WT replicate 4


title: Slm2KO replicate 2


title: Slm2KO replicate 1


title: BPH1-1

description: BPH1 scrambled control #1


title: WT replicate 3


title: SVZ Total H4 ChIP-Seq

value: Cell Signaling #2592; 1:1000


title: Slm2KO replicate 4


title: RNA-Seq_mm_P21_KO [Sample 23]

description: processed data: RNA_brain_IMP2_KO.txt

source_name: P21 IMP2fl/fl nestin cre brain


title: Gfi1-KD sample 2 - H3 ChIP

city: Montreal

first: Möröy

last: Tarik

state: Quebec

address: 110 Pine avenue West

institute: Insititut de Recherches Cliniques

data_processing:
ChIP-Seq reads were aligned to mm10 using Bowtie2 v2.10
.bam files were converted into .sam files using samtools
The annotatePeaks.pl function of the Homer software was used to quantify read densities around gene Transcription Start Sites.
Genome_build: mm10
Supplementary_files_format_and_content: Each processed data file is the result of a call to annotatepeaks.pl in the Homer software and covers th eH3 and H3K9Ac ChIP for the 2 replicates of a given genotype. Each line in the file represents one ensembl transcript with each column representing a sinble bin of 25bp. The first column is the Ensembl Transcript ID, the next 101 match the H3 ChIP in replicate 1, the next 101 match the H3K9Ac ChIP in replicate 1, then H3 in replicate 2, then H3K9Ac in replicate 2. There is one output file for transcripts on the positive strand and one for transcripts on the negative strand. In the positive file, the genomic area covered is -500bp to +200bp relative to the TSS. In the negative file, the genomic area covered is -2000bp to +500bp relative to the TSS.

source_name: Leukemic cells

extract_protocol:
Cells were fixed with 1% formaldehyde. Cell lysis was performed using the following buffers: total cell lysis - 5mM PIPES pH 8, 85mM KCl, 0.5% NP-40, 1X protease inhibitor cocktail, 1mM PMSF, and nuclear lysis – 50mM Tris, 10mM EDTA, 1% SDS, 1X protease inhibitor cocktail, 1mM PMSF. After sonication (Covaris E220 sonicator), immunoprecipitation was performed using Protein A/G Dynabeads (Life Technologies)
Sequencing libraries were prepared from immunoprecipitated chromatin using the TruSeq DNA kit from Illumina according to the manufacturer’s instructions and sequenced using the TruSeq PE Clusterkit v3-cBot-HS

value: Leukemic cells

tag: genotype

value: Gfi1 KD/KD

tag: mouse strain

value: C57/BL6 NUP98-HOXD13

tag: antibodies

value: ab1791; Abcam


title: Gfi1-KD sample 2 - H3K9Ac ChIP

value: ab4441; Abcam


title: Gfi1 KD Leukemic cells Replicate 2

data_processing:
RNA-Seq reads were aligned to GRCm38 using Tophat v2.0.10
Reads were processed with Samtools.
For differential expression, countfiles were generated by mapping reads to Ensembl genes using HTSeq-count. Further analysis was carried out using the DESeq R package
Genome_build: GRCm38
Supplementary_files_format_and_content: txt files are tab-delimited text files containing counts on GRCm38 Ensembl genes

extract_protocol:
RNA was extracted using a MagMax-96 Total RNA Isolation kit (Ambion).
RNA-Seq, libraries were prepared from RNA extracts using the TruSeq Stranded mRNA kit from Illumina according to the manufacturer’s instructions and sequenced using using the TruSeq PE Clusterkit v3-cBot-HS.

value: homo


title: Gfi1 KI Leukemic cells Replicate 2

value: het


title: Gfi1 KI Leukemic cells Replicate 1


title: Gfi1-KI sample 2 - H3K9Ac ChIP

value: Gfi1 KI/wt


title: Gfi1-KI sample 2 - H3 ChIP


title: Gfi1-KI sample 1 - H3K9Ac ChIP


title: Gfi1-KI sample 1 - H3 ChIP


title: VHIP_Susceptible_48hr_2

city: New York

first: Immanuel

last: Purushothaman

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

description: processed data file = VHIP.Susceptible_vs_Control.cuffdiff.txt

data_processing:
Bowtie2, version 2.1.0, parameters: default
TopHat2, version 2.0.9, parameters: --no-novel-juncs --b2-very-sensitive
Cuffdiff, version 2.1.1, parameters: -b path_to/mm9.fa --multi-read-correct
Genome_build: NCBIM37
Supplementary_files_format_and_content: text and excel format with cuffdiff output. Supplementary files are available in a tar archive on the series record.

source_name: adult ventral hippocampus

extract_protocol:
Total RNA was isolated with TriZol reagent (Invitrogen) and purified with RNAeasy micro kits from Qiagen. All RNA samples were determined to have 260/280 and 260/230 values ≥1.8.
RNA integrity was assessed using either an Agilent 2100 Bioanalyzer with the RNA 6000 Nano assay or an Agilent 2200 TapeStation with the R6K ScreenTape (Agilent, Santa Clara, CA). Average RIN values were above 9. Libraries were prepared using the TruSeq RNA Sample Prep Kit v2 protocol (Illumina, San Diego, CA). Briefly, the cDNA was synthesized from poly-A-selected and then fragmented total RNA using random hexamers, followed by end-repair and ligation with sequencing adaptors. The libraries were then size selected and purified using AMPure XP beads (Beckman Coulter, Brea, CA). Barcode bases (6 bp) were introduced at one end of the adaptors during PCR amplification steps. Library size and concentration were measured by Bioanalyzer or Tape Station (Life Technologies, Grand Island, NY) before sequencing.

treatment_protocol: Please see "Experimental Procedures" from Bagot et al. "Circuit-wide transcriptional profiling reveals region specific gene co-expression networks regulating depression susceptibility " for detailed descriptions of sequencing experiments

value: brain

tag: brain region

value: adult ventral hippocampus

tag: timepoint

value: 48h post CSDS

tag: phenotype

value: susceptible


title: VHIP_Resilient_48hr_3

description: processed data file = VHIP.Resilient_vs_Control.cuffdiff.txt

value: resilient


title: Gfi1-KD sample 1 - H3 ChIP

tag: cell type


title: VHIP_Susceptible_48hr_3


title: VHIP_Susceptible_48hr_1


title: VHIP_Resilient_48hr_2


title: WT replicate 1

value: Hippocampus


title: VHIP_Resilient_48hr_1


title: PFC_Susceptible_48hr_3

description: processed data file = PFC.Susceptible_vs_Control.cuffdiff.txt

source_name: adult prefrontal cortex

value: adult prefrontal cortex


title: PFC_Susceptible_48hr_2


title: Gfi1 KD Leukemic cells Replicate 1


title: Slm2KO replicate 3

value: 8 weeks


title: PFC_Resilient_48hr_2

description: processed data file = PFC.Resilient_vs_Control.cuffdiff.txt


title: VHIP_Control_48hr_3

description: processed data file = VHIP.Resilient_vs_Control.cuffdiff.txt, VHIP.Susceptible_vs_Control.cuffdiff.txt

value: control


title: PFC_Susceptible_48hr_1


title: VHIP_Control_48hr_1

description: processed data file = VHIP.Resilient_vs_Control.cuffdiff.txt,VHIP.Susceptible_vs_Control.cuffdiff.txt


title: Gfi1-KD sample 1 - H3K9Ac ChIP

value: Leukemic cells


title: VHIP_Control_48hr_2


title: PFC_Resilient_48hr_1


title: PFC_Resilient_48hr_3


title: PFC_Control_48hr_3

description: processed data file = PFC.Resilient_vs_Control.cuffdiff.txt,PFC.Susceptible_vs_Control.cuffdiff.txt


title: PFC_Control_48hr_2

description: processed data file = PFC.Resilient_vs_Control.cuffdiff.txt, PFC.Susceptible_vs_Control.cuffdiff.txt


title: PFC_Control_48hr_1


title: Nac_Susceptible_48hr_3

description: processed data file = NAC.Susceptible_vs_Control.cuffdiff.txt

source_name: adult nucleus accumbens

value: adult nucleus accumbens


title: Nac_Susceptible_48hr_1


title: Nac_Resilient_48hr_3

description: processed data file = NAC.Resilient_vs_Control.cuffdiff.txt


title: Nac_Susceptible_48hr_2


title: Nac_Resilient_48hr_1


title: Nac_Resilient_48hr_2


title: Nac_Control_48hr_3

description: processed data file = NAC.Resilient_vs_Control.cuffdiff.txt,NAC.Susceptible_vs_Control.cuffdiff.txt


title: Nac_Control_48hr_2


title: AMY_Susceptible_48hr_2

description: processed data file = AMY.Susceptible_vs_Control.cuffdiff.txt

source_name: adult amygdala

value: adult amygdala


title: AMY_Susceptible_48hr_3


title: AMY_Control_48hr_3

description: processed data file = AMY.Resilient_vs_Control.cuffdiff.NB.txt, AMY.Susceptible_vs_Control.cuffdiff.txt


title: AMY_Control_48hr_2

description: processed data file = AMY.Resilient_vs_Control.cuffdiff.NB..txt, AMY.Susceptible_vs_Control.cuffdiff.txt


title: AMY_Resilient_48hr_3

description: processed data file = AMY.Resilient_vs_Control.cuffdiff.NB..txt


title: AMY_Resilient_48hr_2


title: VHIP_Susceptible_28d_1

description: processed data file = VHIP_control_vs_susceptible_28day.diff_list.xlsx

value: 28d post CSDS


title: VHIP_Susceptible_28d_2


title: VHIP_Susceptible_28d_4


title: AMY_Control_48hr_1


title: VHIP_Resilient_28d_3

description: processed data file = VHIP_control_vs_resilient_28day.diff_list.xlsx


title: VHIP_Susceptible_28d_3


title: VHIP_Resilient_28d_4


title: VHIP_Control_28d_4

description: processed data file = VHIP_control_vs_resilient_28day.diff_list.xlsx,VHIP_control_vs_susceptible_28day.diff_list.xlsx


title: VHIP_Resilient_28d_1


title: VHIP_Control_28d_1


title: VHIP_Control_28d_2


title: PFC_Susceptible_28d_3

description: processed data file = PFC_control_vs_susceptible_28day.diff_list.xlsx


title: VHIP_Control_28d_3


title: PFC_Susceptible_28d_2


title: PFC_Susceptible_28d_1


title: PFC_Susceptible_28d_4


title: PFC_Resilient_28d_3

description: processed data file = PFC_control_vs_resilient_28day.diff_list.xlsx


title: AMY_Susceptible_48hr_1


title: PFC_Resilient_28d_2


title: PFC_Resilient_28d_4


title: Nac_Control_48hr_1

description: processed data file = NAC.Resilient_vs_Control.cuffdiff.txt, NAC.Susceptible_vs_Control.cuffdiff.txt


title: PFC_Control_28d_3

description: processed data file = PFC_control_vs_resilient_28day.diff_list.xlsx,PFC_control_vs_susceptible_28day.diff_list.xlsx


title: AMY_Resilient_48hr_1


title: VHIP_Resilient_28d_2


title: PFC_Control_28d_2


title: PFC_Control_28d_4


title: Nac_Susceptible_28d_1

description: processed data file = NAC_control_vs_susceptible_28day.diff_list.xls


title: Nac_Susceptible_28d_4


title: Nac_Susceptible_28d_3


title: Nac_Resilient_28d_4

description: processed data file = NAC_control_vs_resilient_28day.diff_list.xlsx


title: Nac_Resilient_28d_3


title: Nac_Resilient_28d_2


title: Nac_Susceptible_28d_2


title: Nac_Control_28d_4

description: processed data file = NAC_control_vs_resilient_28day.diff_list.xlsx,NAC_control_vs_susceptible_28day.diff_list.xls


title: Nac_Control_28d_3


title: Nac_Resilient_28d_1


title: Nac_Control_28d_2


title: Nac_Control_28d_1


title: AMY_Susceptible_28d_4

description: processed data file = AMY_control_vs_susceptibl_28day.diff_list.xlsx


title: AMY_Susceptible_28d_3


title: AMY_Susceptible_28d_2


title: AMY_Resilient_28d_1

description: processed data file = AMY_control_vs_resilient_28day.diff_list.xls


title: AMY_Resilient_28d_3


title: AMY_Control_28d_4

description: processed data file = AMY_control_vs_resilient_28day.diff_list.xls,AMY_control_vs_susceptibl_28day.diff_list.xlsx


title: AMY_Control_28d_1


title: AMY_Resilient_28d_2


title: VHIP_Susceptible_28d1hstress_8

description: processed data file = VHIP_control_vs_susceptible_28day1hstress.diff_list.xlsx

value: 28d +1h stress post CSDS


title: PFC_Control_28d_1


title: VHIP_Susceptible_28d1hstress_6


title: VHIP_Resilient_28d1hstress_7

description: processed data file = VHIP_control_vs_resilient_28day1hstress.diff_list.xlsx


title: VHIP_Susceptible_28d1hstress_5


title: VHIP_Control_28d1hstress_8

description: processed data file = VHIP_control_vs_resilient_28day1hstress.diff_list.xlsx,VHIP_control_vs_susceptible_28day1hstress.diff_list.xlsx


title: VHIP_Resilient_28d1hstress_5


title: VHIP_Control_28d1hstress_7


title: VHIP_Resilient_28d1hstress_6


title: PFC_Resilient_28d_1


title: VHIP_Resilient_28d1hstress_8


title: PFC_Susceptible_28d1hstress_6

description: processed data file = PFC_control_vs_susceptible_28day1hstress.diff_list.xlsx


title: PFC_Susceptible_28d1hstress_5


title: AMY_Resilient_28d_4


title: AMY_Susceptible_28d_1


title: PFC_Resilient_28d1hstress_7

description: processed data file = PFC_control_vs_resilient_28day1hstress.diff_list.xlsx


title: PFC_Resilient_28d1hstress_5


title: PFC_Susceptible_28d1hstress_8


title: PFC_Control_28d1hstress_8

description: processed data file = PFC_control_vs_resilient_28day1hstress.diff_list.xlsx,PFC_control_vs_susceptible_28day1hstress.diff_list.xlsx


title: PFC_Susceptible_28d1hstress_7


title: PFC_Control_28d1hstress_7


title: PFC_Resilient_28d1hstress_6


title: PFC_Resilient_28d1hstress_8


title: VHIP_Control_28d1hstress_5


title: PFC_Control_28d1hstress_5


title: Nac_Susceptible_28d1hstress_8

description: processed data file = NAC_contorl_vs_susceptible_28day1hstress.diff_list.xls


title: PFC_Control_28d1hstress_6


title: AMY_Control_28d_2


title: Nac_Susceptible_28d1hstress_7


title: Nac_Susceptible_28d1hstress_6


title: Nac_Resilient_28d1hstress_8

description: processed data file = NAC_contorl_vs_resilient_28day1hstress.diff_list.xlsx


title: Nac_Susceptible_28d1hstress_5


title: Nac_Resilient_28d1hstress_7


title: Nac_Resilient_28d1hstress_6


title: Nac_Resilient_28d1hstress_5


title: Nac_Control_28d1hstress_7

description: processed data file = NAC_contorl_vs_resilient_28day1hstress.diff_list.xlsx,NAC_contorl_vs_susceptible_28day1hstress.diff_list.xls


title: Nac_Control_28d1hstress_8


title: AMY_Susceptible_28d1hstress_8

description: processed data file = AMY_control_vs_susceptible_28day1hstress.diff_list.xlsx


title: AMY_Susceptible_28d1hstress_5


title: AMY_Resilient_28d1hstress_7

description: processed data file = AMY_control_vs_resilient_28day1hstress.diff_list.xlsx


title: AMY_Resilient_28d1hstress_8


title: Nac_Control_28d1hstress_6


title: AMY_Control_28d1hstress_8

description: processed data file = AMY_control_vs_resilient_28day1hstress.diff_list.xlsx,AMY_control_vs_susceptible_28day1hstress.diff_list.xlsx


title: AMY_Resilient_28d1hstress_5


title: AMY_Control_28d1hstress_7


title: VHIP_GFP_5

description: processed data file = vhip_dkkl1_vs_gfp.txt

value: 24h post accelerated defeat

value: accelerated social defeat


title: VHIP_GFP_4


title: AMY_Control_28d_3


title: VHIP_GFP_3


title: AMY_Control_28d1hstress_5


title: AMY_Susceptible_28d1hstress_6


title: VHIP_GFP_2


title: VHIP_GFP_1


title: VHIP_DKKL1_3


title: VHIP_DKKL1_2


title: MAF9-iBET-1

city: Ann Arbor

first: Yali

last: Dou

state: MI

address: 1301 Catherine Street

department: Pathology Department

institute: University of Michigan

data_processing:
RNA-Seq reads were mapped to mm9 using TopHat2 with default parameters, only unique mapped reads used to subsequent analysis.
Read numbers for each gene was counted using Subread program.
Read counts were used to performed differentially gene expression analysis by DESeq program.
Genome_build: mm9
Supplementary_files_format_and_content: Read counts matrix table (tsv)

source_name: Bone marrow

growth_protocol: MAF9 (MLL-AF9-transduced mouse bone marrow) cells were cultured in Iscove’s modified Dulbecco’s medium (IMDM) + 15% fetal bovine serum (FBS) and supplemented with 10 ng/ml interleukin-3 (IL-3).

extract_protocol:
RNA isolation and DNase treatment were according to instructions of RNeasy Mini Kit, QIAGEN
RNA libraries were prepared with the Illumina TruSeq protocol according to the manufacturer’s protocol for RNA-seq libraries.

treatment_protocol: MAF9 cells were treated with MM-401, EPZ, MI-2, iBET inhibitors separately at its IC50 dose for 4 days. DMSO was used as a control treatment.

value: MLL-AF9  transduced mouse bone marrow cells

tag: agent

value: iBET


title: AMY_Resilient_28d1hstress_6

value: brain


title: Nac_Control_28d1hstress_5


title: MAF9-EPZ-2

value: EPZ


title: VHIP_DKKL1_1

value: adult ventral hippocampus


title: MAF9-MI-1

value: MI


title: AMY_Susceptible_28d1hstress_7

value: susceptible


title: MAF9-MM401-2


title: MAF9-MM401-1


title: MAF9-MI-2


title: MAF9-DMSO-1

value: DMSO


title: AMY_Control_28d1hstress_6


title: MAF9-DMSO-2


title: 4OHT-Input

data_processing:
Reads were mapped to mm9 using bowtie with default parameters, only unique mapped reads used to subsequent analysis.
Peaks were called using the Hpeak program
Genome_build: mm9
Supplementary_files_format_and_content: bigwig file for coverage and bed file for called peaks

extract_protocol:
ChIP experiments were performed using 1E8 cells and 15µl of antibodies per ChIP according to standard protocols.
Libraries were prepared with the Illumina TruSeq protocol according to the manufacturer’s protocol.

treatment_protocol: MAF9 cells were treated with MM-401 at 20µM for 2 days.DMSO was used as a control treatment; MLL1 flox/flox, ER-Cre+/- cells were treated with 4OHT(400nM) for 2 days. EtOH was used a control treatment.

tag: antibody

value: none, input


title: 4OHT-WDR5

value: MLL1 flox/flox, ER-cre+/-, MAF9 transduced mouse bone marrow cells

value: WDR5 (anti-rabbit antibody made by our lab)


title: EtOH-H3K4me2

value: EtOH


title: EtOH-Input


title: 4OHT-H3K4me2


title: EtOH-WDR5


title: MM401-WDR5


title: MAF9-MM401-Input


title: MM401-MLL1

value: MLL (anti-rabbit antibody made by our lab)


title: MAF9-EPZ-1


title: MAF9-iBET-2


title: DMSO-WDR5


title: DMSO-H3K4me2


title: DMSO-MLL1


title: MAF9-DMSO-Input