title: NES cells transduced with Control shRNA, biological replicate 3

city: Stockholm

first: Margareta

middle: T

last: Wilhelm

address: Solnavägen 9

department: MTC

country: Sweden

institute: Karolinska Institutet

description: Gene expression data from human NES cells stably expressing Control shRNA construct

hyb_protocol: 2.5ug of ss DNA target was hybridized to a Human Gene 2.1 ST Array Plate and washed and stained in the Gene Titan instrument according to the GeneChip WT Terminal Labeling and Hybridization User manual

scan_protocol: Array plates were scanned using a GeneTitan Multi-Channel (MC) Instrument.

data_processing: Scanner-generated probe cell intensity (CEL) files were imported into Expression Console Software, and expression levels were estimated using the RMA method.

source_name: NES cells transduced with Control shRNA

label_protocol: 150ng of total RNA was used to generate amplified sense strand DNA targets with Affymetrix WT Plus Reagent Kit followed by fragmentation and biotinylation with Affymetrix WT Plus Reagent Kit.

growth_protocol: Cells were maintained on 0.1 mg Poly-L-ornithine/1μg/ml laminin (Merck, P3655-100MG and L2020 respectively) coated plates in  NES culturing media (DMEM/F12+GlutaMax (ThermoFisher Scientific, 31331-028) with 1xN2 supplement (ThermoFisher Scientific, 17504-044), 0,1% B27 supplement (ThermoFisher Scientific, 17502-048), 10 ng/ml FGF2 (ThermoFisher Scientific, AA10-155), 10 ng/ml hEGF (PeproTech, AF100-15) and 1:100 Penicillin-Streptomycin (ThermoFisher Scientific, 15140-122) and puromycin (1ug/ml).

extract_protocol: Total RNA was extracted from using Quick-RNA™ MiniPrep (Zymo, R1050) according to manufacturers instructions

treatment_protocol: NES cells stably expressing either control or p53 shRNA were seeded at equal density and harvested at 80-90% Confluency

value: Human Neuroepithelial Stem Cell

value: control


title: R_CSE_Drug_Rep3

status: Public on Jan 28 2020

type: SRA

city: Waterloo

first: Jennifer

middle: A.

last: Aguiar

state: ON

address: 200 University Avenue East

department: Biology

country: Canada

institute: University of Waterloo

library_source: transcriptomic

data_processing:
Samples were sequenced on the Illumina HiSeq 2500 instrument with 125 bp paired-end reads to a minimum depth of 30 million reads per sample.
Reads were de-multiplexed and trimmed at The Centre for Applied Genomics and BCL files generated from the Illumina sequencer were converted to fastq files prior to our receivement of the reads.
Quality control was performed using FastQC (v.0.11.7) and Prinseq (v.0.20.4).
Sequences were aligned to the human reference genome (hg19) using HISAT2 (v.2.1.0)
Sequences were assembled into full transcriptomes using StringTie (v.1.3.3b). Samtools (v.1.9) was used to convert and sort HISAT2 output into sorted bam files for use by StringTie.
StringTie was also used to calculate transcript abundances for downstream differential expression analysis using the Ballgown package in R (v. 3.4.3.).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

molecule: total RNA

organism: Homo sapiens

source_name: cannabis smoke extract (CSE) with drug: formoterol/budesonide

growth_protocol: Calu-3 cells, an immortalized human lung adenocarcinoma cell line, were obtained from ATCC (HTB-55, Lot: 61449062) and maintained in Eagle’s Minimum Essential Medium (EMEM, Millipore Sigma) supplemented with 10mM HEPES (Millipore Sigma), 10% FBS (Millipore Sigma), and Antibiotic-Antimycotic (Gibco®, ThermoFisher Scientific). Calu-3 cells were cultured in vented 75cm^2 tissue culture flasks (Sarstedt) and used between passages 10-20. Calu-3 cells were seeded onto either 4.7cm^2 or 0.3cm^2 polyester Transwell® permeable supports with a pore size of 0.4μm (Corning) and grown for 20 days to allow the Calu-3 cells to semi-differentiate into a pseudo-stratified epithelium. BS was removed from Calu-3 cultures 24 hours prior to the start of the exposures.

extract_protocol:
Total RNA was extracted using a RNeasy Plus Kit (QIAGEN, Valencia, CA) according to the manufacturer's instructions.
cDNA was prepared at The Centre for Applied Genomics at the Hospital for Sick Children (Toronto, Ontario, Canada).

treatment_protocol: For exposures, fresh FBS free EMEM culture media was added to basal chambers and CSE or TSE media diluted with fresh FBS free EMEM culture media was added to the apical chambers for 24 hours. For intervention conditions, budesonide 100nM (Cayman Chemical) and formoterol 10nM (Cayman Chemical) was added to the exposure medias before being applied to Calu-3 cells for 24 hours.

tag: cell line

tag: cell type

value: Lung epithelium


title: NES cells transduced with p53 shRNA, biological replicate 1

type: RNA

description: Gene expression data from human NES cells stably expressing p53 shRNA construct

label: biotin

source_name: NES cells transduced with p53 shRNA

tag: genotype

value: p53 knockdown


title: NES cells transduced with p53 shRNA, biological replicate 3


title: NES cells transduced with p53 shRNA, biological replicate 2


title: NES cells transduced with Control shRNA, biological replicate 2


title: NES cells transduced with Control shRNA, biological replicate 1


title: CD4 for Patient EMG-EC-030

city: Cambridge

first: Ce

last: Gao

state: MA

address: 400 Technology Square

country: USA

institute: Ragon Institute of MGH, MIT and Harvard

description:
RNA-seq sample from a HIV-1 controller
rawcounts and TPM

data_processing:
FASTQ files were obtained by Illumina demultiplexing pipeline.
STAR and RSEM were used to align to HG38 and to calculate the raw counts for genes, respectively.
Genome_build: GRCh38
Supplementary_files_format_and_content: raw counts and TPM in csv

growth_protocol: ALL patient samples used for the RNAseq analysis were obtained ex vivo without any in vitro culture

extract_protocol:
Total RNA was extracted from the 4 cell populations using a commercial PicoPure RNA Isolation Kit
RNA-Seq libraries were generated as described in a previous study. Briefly, whole transcriptome amplification (WTA) and tagmentation-based library preparation was performed using SMART-seq2, followed by sequencing with a 75-cycle kit on a NextSeq 550 instrument (Illumina, CA). The quantification of transcript abundance was conducted using RSEM software (v1.2.22) supported by the STAR aligner software (STAR_2.4.2a). The raw reads were aligned to the GRCh38 human genome database.

treatment_protocol: There is no treatment for the patient samples used in the RNAseq study.

tag: tissue

value: peripheral blood

tag: cohort

value: Neut


title: CD4 for Patient EMG-EC-035


title: R_CSE_Drug_Rep2


title: R_TSE_Drug_Rep3

source_name: tobacco smoke extract (TSE) with drug: formoterol/budesonide


title: R_CSE_Drug_Rep1


title: CD4 for Patient EMG-EC-029

value: NonNeut


title: CD4 for Patient EMG-EC-031


title: CD4 for Patient EMG-EC-027


title: CD4 for Patient EMG-EC-034


title: CD4 for Patient EMG-EC-028


title: R_TSE_Drug_Rep2


title: R_TSE_Drug_Rep4


title: R_Control_Drug_Rep2

source_name: no smoke control with drug: formoterol/budesonide


title: R_TSE_Drug_Rep1


title: CD4 for Patient EMG-EC-026


title: R_Control_Drug_Rep1


title: R_Control_Drug_Rep3


title: R_CSE_Vehicle_Rep4

source_name: cannabis smoke extract (CSE) with vehicle


title: R_Control_Drug_Rep4


title: R_CSE_Vehicle_Rep3


title: CD4 for Patient EMG-EC-022


title: CD4 for Patient EMG-EC-017


title: CD4 for Patient EMG-EC-021


title: CD4 for Patient EMG-EC-020


title: CD4 for Patient EMG-EC-016


title: R_CSE_Vehicle_Rep2


title: CD4 for Patient EMG-EC-015


title: CD4 for Patient EMG-EC-019


title: CD4 for Patient EMG-EC-014


title: R_CSE_Vehicle_Rep1


title: R_TSE_Vehicle_Rep4

source_name: tobacco smoke extract (TSE) with vehicle


title: CD4 for Patient EMG-EC-012


title: CD4 for Patient EMG-EC-013


title: CD4 for Patient EMG-EC-011


title: R_Control_Vehicle_Rep4

source_name: no smoke vehicle control


title: R_TSE_Vehicle_Rep2


title: R_TSE_Vehicle_Rep3


title: CD4 for Patient EMG-EC-008


title: R_Control_Vehicle_Rep3


title: CD4 for Patient EMG-EC-007


title: R_Control_Vehicle_Rep2


title: CD4 for Patient EMG-EC-006


title: R_Control_Vehicle_Rep1


title: CD4 for Patient EMG-EC-003


title: CD4 for Patient EMG-EC-009


title: R_TSE_Vehicle_Rep1


title: CD4 for Patient EMG-EC-001


title: Bcells for Patient EMG-EC-060

source_name: Bcells


title: Bcells for Patient EMG-EC-058


title: Bcells for Patient EMG-EC-061


title: CLJ

city: Fuzhou

first: Xingrong

last: Lu

state: China

address: 29 Xinquan Road

department: Colorectal surgery

country: China

institute: Fujian medical university union hospital

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25 × Fragmentation Buffer, then the mixture was heated at 60°C for 30 min, finally, 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the lncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. Hybridized arrays were washed, fixed and scanned using the Agilent DNA Microarray Scanner (part number G2505B).

scan_protocol: Agilent Feature Extraction software (version 10.7.3.1) was used to analyze acquired array images.

data_processing: Quantile normalization and subsequent data processing were performed by using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, mRNAs that at least 1 out of 2 samples has flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.

source_name: primary colorectal cancer

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications.

extract_protocol: Total RNA was extracted from the tissue mentioned above using the Trizol reagents (Invitrogen), according to the manufacturer’s protocol. RNA quantity and quality were measured by NanoDrop ND-1000 and RNA integrity was assessed by standard denatured agarose gel electrophoresis.

value: primary colorectal cancer

tag: Sex

value: MALE

tag: response to the folfox

value: SD

tag: Stage

value: IV


title: ZJM

value: FEMALE

value: PD


title: ZXH


title: Bcells for Patient EMG-EC-057


title: WYY


title: CHP

value: PR


title: CBX


title: LZX


title: HGZ


title: CYY


title: LYH


title: CD4 for Patient EMG-EC-004


title: YCD


title: Bcells for Patient EMG-EC-055


title: Bcells for Patient EMG-EC-054


title: MEF

type: genomic

city: Beijing

first: Benyu

last: Liu

state: Beijing

address: 15, Datun Road, Chaoyang district

department: The CAS key Laboratory of Infection and Immunity, Institute of Biophysics

institute: Institute of Biophysics, CAS

description: MEF_MeDIP_ChIP array

hyb_protocol: The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Arrays were scanned on an Agilent Scanner G2505C scanner according to manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing:
Arrays were processed using Nimblegen's standard protocol for NimbleScan v2.5 ChIP data extraction.
scaled, log2 (ChIP/Input) ratio

molecule: genomic DNA

organism: Mus musculus

source_name: mouse embryonic fibroblasts

label_protocol: The purified DNA was quantified using a nanodrop ND-1000, labeled by the NimbleGen Dual-Color DNA labeling Kit and array hybridized according to the manufacturer’s protocol (Nimblegene Systems, Inc., Madison, WI, USA)

growth_protocol: Mouse embryonic fibroblasts (MEFs) were obtained at E14.5 embryos and supplied with Dulbecco’s modified Eagle’s medium (DMEM) (Invitrogen) with 15% FBS, 100 μg/ml streptomycin and 100 U/ml penicillin. Potential hematopoietic progenitor cells (CD45+CD41+CD31+c-Kit+) were negatively selected with Biotin labeled anti-CD45, anti-CD31, anti-CD41 and anti-c-Kit antibodies by magnetic beads.Hereafter, treated MEFs are referred to as 4neg MEFs for initiation of induction.

extract_protocol: DNA samples were sheared into 200-1000 bp fragments by Bioruptor sonicator (Diagenode). Sonicated genomic DNA was immunoprecipitated by anti-5-methylcytosine antibody (Diagenode) followed by purification using Qiagen MinElute columns.

treatment_protocol: 4neg MEFs were seeded on mitomycin (MMC)-treated MEFs as feeder cells and cultured in DMEM with 15% FBS, 100  μg/ml streptomycin, 100 U/ml penicillin, 2 mM L-glutamine, 0.1 mM non-essential amino acids.

value: MEFs

tag: agent

tag: anti-body

tag: strain

tag: chip antibody

value: none, input


title: YF4_OO: single cell RNA seq

city: Shanghai

first: Yuxuan

last: Zheng

address: 825 Zhangheng Rd.

institute: Fudan University

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Single-cell RNA-seq: The template switch oligo (TSO) and poly(A) tail sequences were trimmed from the raw single-cell RNA-seq data, and then the reads with adapters and low-quality bases were removed to obtain clean reads. The clean reads were mapped against the Ensembl Macaca fascicularis reference genome (version: Macaca_fascicularis_5.0) using Tophat (version: 2.0.12). Only the uniquely mapped reads according to UMI numbers were counted using HTSeq, i.e., reads with the same UMI sequence were counted only once.
Bulk RNA-seq: Raw RNA-seq sequencing data were removed adapters and low-quality bases to obtain the clean reads, and then clean reads were mapped against UCSC human reference hg19 using Tophat (version: 2.0.12), and uniquely mapped reads were counted using HTSeq. Gene expression levels were quantified with RPKM (reads per kilobase million).
Genome_build: Macaca_fascicularis_5.0
Genome_build: hg19
Supplementary_files_format_and_content: Single-cell RNA-seq: UMI_count.txt files include the UMI count values of Ensembl genes
Supplementary_files_format_and_content: Bulk RNA-seq: expression.txt files include the read count and RPKM

molecule: polyA RNA

organism: Macaca fascicularis

source_name: Ovary tissue cells

extract_protocol:
Single-cell RNA-seq: Single-cell RNA-seq libraries were constructed according to the STRT-seq protocol with modifications, as previously described. Briefly, individual oocytes or somatic cells were picked into lysis buffer by mouth pipetting. Then, the mRNA in lysates was reverse transcribed with SuperScript II reverse transcriptase (Thermo Fisher Scientific, 18064-071), and an 8 nt cell-specific barcode was added to the cDNA from each cell. Absolute counting of molecules was performed with the 8 nt unique molecular identifiers (UMIs). The synthesized cDNAs from cells with different barcodes were pooled together and amplified with 19-21 (somatic cells) or 13 (oocytes) cycles, followed by fragmentation with Covaris S2 (Thermo Fisher) and enrichment of fragments of interest via Dynabeads MyOne Streptavidin C1 beads (Thermo Fisher, 65001). The enriched fragments were constructed into libraries using a KAPA Hyper Prep Kit (KAPA, KK8504) and sequenced on an Illumina HiSeq 4000 platform with a 150-bp paired-end read length by Novogene.
Bulk RNA-seq: Total RNA was extracted from one million cells using TRIzol reagent (Invitrogen). 3 ug per sample were constructed into libraries through NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, E7530L) following manufacturer’s manuals. Sequencing data were generated via on Illumina HiSeq 4000 platform with 150-bp paired-end read length by Novogene.

value: Ovary

value: Oocytes

tag: individual

tag: age

tag: well

value: OO


title: Bcells for Patient EMG-EC-052


title: Bcells for Patient EMG-EC-053


title: Bcells for Patient EMG-EC-051


title: MDS-L KO LEN 3 72h

city: Vancouver

first: Aly

last: Karsan

state: BC

address: W10th Ave

department: Genome Sciences Centre

institute: BC Cancer Agency

hyb_protocol: hyb: 16 hr at 45°C; wash: Affymetrix fluidics station 450 Midi_euk2v3 protocol

scan_protocol: Scanning was performed on the GeneChip ® Scanner 3000 using the preset pixel value and resolution parameters defined in the scanner.

data_processing: RMA was performed using Affymetrix Expression Console (version 1.1) using HG-U219.na36.annot.csv annotations

source_name: MDS-L RUNX1-KO

label_protocol: Ambion IVT kit I; Biotin label

growth_protocol: MDS-L cells were grown in RPMI media, supplemented with 10% Fetal Bovine Serum, 1% Glutamine and 1% Penicillin/Streptomycin. Furthermore, 10ng/ml recombinant human IL-3 were added fresh at every passage. Cells were split every 2-3 days, and always kept at a confluence between 100,000-800,000 cells/ml.

extract_protocol: Cells were pelleted at 400xg for 5 min. Supernatant was removed and the pellet was resuspended in 1 ml of Trizol and RNA extracted per manufacturer directions.

treatment_protocol: MDS-L cells were seeded at 400,000 cells/ml (10ml final volume) in T75 flasks. Then, Lenalidomide (1µM Final concentration) or DMSO as control were added to the culture. Cells were then maintained at 37°C, 5% CO2 for 72h.

value: del(5q) MDS cell line

value: RUNX1-KO Clone 2G4KO

tag: treatment time (h)


title: YF4_OCS: single cell RNA seq

value: Somatic cells from ovarian cortex (small cells)

value: OCS


title: YF4_OCB2: single cell RNA seq

value: Somatic cells from ovarian cortex (big cells)


title: Bcells for Patient EMG-EC-050

value: peripheral blood

value: Neut


title: Bcells for Patient EMG-EC-048


title: MDS-L KO LEN 2 72h


title: YF4_OCB1: single cell RNA seq


title: Bcells for Patient EMG-EC-047

value: NonNeut


title: YF4_OM: single cell RNA seq

value: Somatic cells from ovarian medulla

value: OM


title: MDS-L KO DMSO1 72h


title: YF3_OO: single cell RNA seq


title: MDS-L KO DMSO2 72h


title: MDS-L KO LEN 1 72h


title: Bcells for Patient EMG-EC-046


title: YF3_OM: single cell RNA seq


title: YF3_OCS2: single cell RNA seq


title: YF3_OCS1: single cell RNA seq


title: Bcells for Patient EMG-EC-043


title: CD4 for Patient EMG-EC-002


title: YF3_OCB: single cell RNA seq

value: OCB


title: MDS-L KO DMSO3 72h


title: MDS-L WT LEN3 72h

source_name: MDS-L WT Control

value: WT Clone 1B2ct


title: Bcells for Patient EMG-EC-040


title: YF2_OM: single cell RNA seq


title: YF2_OO: single cell RNA seq


title: MDS-L WT DMSO3 72h


title: Bcells for Patient EMG-EC-038


title: Bcells for Patient EMG-EC-039


title: MDS-L WT LEN2 72h


title: Bcells for Patient EMG-EC-044


title: YF2_OCS1: single cell RNA seq


title: MDS-L WT LEN1 72h


title: YF2_OCS2: single cell RNA seq


title: MDS-L WT DMSO2 72h


title: YF2_OCB: single cell RNA seq


title: Bcells for Patient EMG-EC-035


title: Bcells for Patient EMG-EC-042


title: MDS-L KO LEN 1

source_name: MDS-L RUNX1-KO_LEN

treatment_protocol: MDS-L cells were seeded at 400,000 cells/ml (10ml final volume) in T75 flasks. Then, Lenalidomide (1µM Final concentration) or DMSO as control were added to the culture. Cells were then maintained at 37°C, 5% CO2 for 24h.

tag: treatment

value: 1 microMolar Lenalidomide for 24hrs


title: MDS-L KO LEN 3

tag: cell line


title: MDS-L KO LEN 2


title: YF1_OO: single cell RNA seq

tag: cell type


title: YF1_OM: single cell RNA seq


title: Bcells for Patient EMG-EC-034


title: MDS-L KO DMSO3

source_name: MDS-L RUNX1-KO_DMSO

tag: genotype

value: DMSO for 24hrs


title: YF1_OCS3: single cell RNA seq

tag: tissue

value: Ovary


title: Bcells for Patient EMG-EC-032

tag: cohort


title: Bcells for Patient EMG-EC-031


title: MDS-L KO DMSO2


title: Bcells for Patient EMG-EC-037


title: YF1_OCS2: single cell RNA seq


title: Bcells for Patient EMG-EC-030


title: YF1_OCS1: single cell RNA seq


title: Bcells for Patient EMG-EC-029


title: Bcells for Patient EMG-EC-028


title: Bcells for Patient EMG-EC-027


title: MDS-L WT LEN3

source_name: MDS-L WT Control_LEN


title: YF1_OCB: single cell RNA seq


title: OF4_OO: single cell RNA seq

value: Oocytes


title: Bcells for Patient EMG-EC-026


title: OF4_OM2: single cell RNA seq


title: Bcells for Patient EMG-EC-022


title: MDS-L WT LEN1


title: Bcells for Patient EMG-EC-021


title: MDS-L KO DMSO1


title: MDS-L WT LEN2


title: MDS-L WT DMSO3

source_name: MDS-L WT Control_DMSO


title: Bcells for Patient EMG-EC-020


title: OF4_OM1: single cell RNA seq


title: MDS-L WT DMSO2


title: MDS-L WT DMSO1


title: CD4 for Patient EMG-EC-032


title: OF4_OCB2: single cell RNA seq


title: OF4_OCB1: single cell RNA seq


title: OF4_OCS: single cell RNA seq


title: OF3_OO: single cell RNA seq

value: OO


title: Bcells for Patient EMG-EC-017


title: Bcells for Patient EMG-EC-019


title: OF3_OCS: single cell RNA seq


title: OF3_OCB2: single cell RNA seq


title: OF3_OCB1: single cell RNA seq


title: Bcells for Patient EMG-EC-014


title: Bcells for Patient EMG-EC-016


title: OF3_OM: single cell RNA seq


title: Bcells for Patient EMG-EC-015


title: OF2_OO: single cell RNA seq


title: Bcells for Patient EMG-EC-012


title: OF2_OM1: single cell RNA seq


title: Bcells for Patient EMG-EC-013


title: OF2_OM2: single cell RNA seq


title: OF2_OCS: single cell RNA seq


title: Bcells for Patient EMG-EC-011


title: Bcells for Patient EMG-EC-008


title: OF1_OO: single cell RNA seq


title: OF2_OCB1: single cell RNA seq


title: Bcells for Patient EMG-EC-006


title: Bcells for Patient EMG-EC-004


title: Bcells for Patient EMG-EC-007


title: OF1_OM: single cell RNA seq


title: Bcells for Patient EMG-EC-003


title: OF2_OCB2: single cell RNA seq


title: OF1_OCB2: single cell RNA seq


title: Bcells for Patient EMG-EC-001


title: OF1_OCB1: single cell RNA seq


title: OF1_OCS: single cell RNA seq


title: Bcells for Patient EMG-EC-009


title: Total_RNA_DKO_rep2

status: Public on Jan 27 2020

city: Toronto

first: Ulrich

last: Braunschweig

state: Ontario

address: 160 College Street

department: Donnelly Centre

institute: University of Toronto

description: Blencowe_Total_RNA_c_11_1_GATCAG_L005_R1_001

data_processing:
Fastqc assessment
Trimmomatic to remove adaptors
Bowtie to remove rRNA reads
Kallisto with pseudobam mapping to ensembl tsl1-3 mmu10 transcripts
Genome_build: Mmu10
Supplementary_files_format_and_content: rounded pseudoread count / tab format

source_name: Cortical glutamatergic neurons differentiated in vitro (DIV 8) from mES cells

growth_protocol:
Cell were differentiated into cortical glutamatergic neurons as described previously (Hubbart et al., F1000 Res 2013).
mESC-derived neurons DIV8 cultured in Neurobasal-A media supplemented with B27.

extract_protocol: ARTseq™ Ribosome Profiling Kit (Epicentre) following manufacturer's instructions.

treatment_protocol: Translation was blocked with 100 µg/ml cyclohexamide for 5 minutes.

value: Neurons (DIV 8) derived from CGR8 ES cells

value: Eif4g1/Eif4g3 double-knockout


title: Total_RNA_WT_rep2

description: Blencowe_Total_RNA_WT_5_TTAGGC_L005_R1_001

value: wildtype


title: Total_RNA_DKO_rep1

description: Blencowe_Total_RNA_c16_5_TAGCTT_L005_R1_001


title: Total_RNA_WT_rep1

description: Blencowe_Total_RNA_c_14_23_5_TGACCA_L005_R1_001


title: Ribo_DKO_rep2

description: Blencowe_RP_c_1_CHX_5_CTTGTA_L005_R1_001

data_processing:
Library strategy: Ribo-Seq
Fastqc assessment
Trimmomatic to remove adaptors
Bowtie to remove rRNA reads
Kallisto with pseudobam mapping to ensembl tsl1-3 mmu10 transcripts
Genome_build: Mmu10
Supplementary_files_format_and_content: rounded pseudoread count / tab format


title: iCLIP-seq of Flag-Srrm4 in in-vitro differentiated neurons, replicate 2

description:
Extracted RNA was reverse transcribed using primer Rt13clip: /5Phos/NNTCCGNNNAGATCGGAAGAGCGTCGTGgatcCTGAACCGC. Reads start with 5'-NNNCGGANN, where N are random bases.
Srrm4_meta-exon.pdf

data_processing:
51-nt or 58-nt raw reads that consisted of 3 random positions, a 4-nt multiplexing barcode, and another 2 random positions, followed by the actual read were initially trimmed to 45 nt from the 3'-end, and duplicates were discarded.
Reads were de-multiplexed (note that they are already de-multiplexed in this GEO record), and the random positions, barcode, and 3'-bases matching Illumina adaptors were removed.
Reads shorter than 25 nt were filtered out and remaining reads trimmed to 35 nt. These steps were carried out using Trimmomatic (Bolger et al., 2014). Surviving reads were mapped to the mouse genome/transcriptome (Ensembl annotation of NCBIm37) using tophat (Trapnell et al., 2009) with default settings. To prevent false assignments of reads from repetitive regions, any reads with a mapping quality < 3 were removed from further analysis.
Plots showing average crosslinking signal of events aligned to exon borders were generated as described previously for ChIP-seq data (Braunschweig et al., Genome Res (2014)), except that reads were first reduced to their first position, which is adjacent to the crosslink position, and no normalization against a control was performed. A 21-bp smoothing window average was used for display only.
Genome_build: mm9
Supplementary_files_format_and_content: PDF files contain figures showing the average (across represented exons) CLIP per million in the library, for each aligned base. Plots were generated directly from BAM files.

source_name: Cortical glutamatergic neurons differentiated in vitro from ES cells

extract_protocol:
Lysates generated from the crosslinked cells were treated with Turbo DNAse (Ambion) and diluted RNAse I (Ambion) for 5 minutes at 37°C to digest the genomic DNA and trim the RNA to short fragments of an optimal size range. RNA-protein complexes were immunoprecipitated using 100 μL of protein G Dynabeads (Life Technologies) and 10 μg of anti-Flag (Sigma) antibody. Following stringent high salt washes, the immunoprecipitated RNA was 3´ end dephosphorylated and a pre-adenylated adaptor was ligated at the 3´ end as previously described for the enhanced CLIP ligation method (Van Nostrand et al., Nat. Methods 2016) for adaptor ligation. After additional washes, the immunoprecipitated RNA was 5´ end-labeled using radioactive 32P isotopes. The immunoprecipitated complexes were separated with SDS-PAGE and transferred to a nitrocellulose membrane (Protran). RNA was recovered by digesting proteins using proteinase K.
RNA was reverse transcribed into cDNA using reverse transcription primers that include barcode sequences to enable multiplexing,  a unique molecular identifier, and a BamHI restriction site. The cDNA was size selected (low: 70 to 85 nt, middle: 85 to 110 nt, and high: 110 to 180 nt), circularized to add the adaptor to the 5′ end, digested at the internal BamHI site, and then PCR amplified using AccuPrime SuperMix I (Life Technologies). The final PCR libraries were purified by agarose gel electrophoresis using gel extraction columns (QIAGEN), eluted DNA was mixed at a ratio of 1:5:5 from the low, middle, and high fractions and submitted for sequencing.

treatment_protocol: Crosslinking (0.15 J/cm2) was done at 254 nm with a Stratalinker 1800.

value: Neurons derived from CGR8 ES cells

value: CGR8 ES cells were engineered to express Flag-tagged Srrm4 under the control of doxycyclin using the PiggyBac system, and single-cell subclones were derived. Cell were differentiated into cortical glutamatergic neurons as described previously (Hubbart et al., F1000 Res 2013). Neural precursor cells were dissociated and plated onto 15 cm plates coated with poly-D-Lysine and laminin (~20 million cells per plate). After 8 days Flag-Srrm4 expression was induced with 2 μg/ml doxycycline for 48 hours.

tag: antibody

value: Flag monoclonal antibody M2 (Sigma-Aldrich)


title: Bcells for Patient EMG-EC-059

value: peripheral blood

value: Neut


title: Ribo_WT_rep2


title: iCLIP-seq of Flag-Srrm4 in in-vitro differentiated neurons, replicate 1

description:
Extracted RNA was reverse transcribed using primer Rt9clip: /5Phos/NNGCCANNNAGATCGGAAGAGCGTCGTGgatcCTGAACCGC. Reads start with 5'-NNNTGGCNN, where N are random bases.
Srrm4_meta-exon.pdf

growth_protocol: Cell were differentiated into cortical glutamatergic neurons as described previously (Hubbart et al., F1000 Res 2013).


title: iCLIP-seq of Flag-Srrm3 in in-vitro differentiated neurons, replicate 3

description:
Extracted RNA was reverse transcribed using primer Rt14clip: /5Phos/NNTGCCNNNAGATCGGAAGAGCGTCGTGgatcCTGAACCGC. Reads start with 5'-NNNGGCANN, where N are random bases.
Srrm3_meta-exon.pdf

value: CGR8 ES cells were engineered to express Flag-tagged Srrm3 under the control of doxycyclin using the PiggyBac system, and single-cell subclones were derived. Cell were differentiated into cortical glutamatergic neurons as described previously (Hubbart et al., F1000 Res 2013). Neural precursor cells were dissociated and plated onto 15 cm plates coated with poly-D-Lysine and laminin (~20 million cells per plate). After 8 days Flag-Srrm3 expression was induced with 2 μg/ml doxycycline for 48 hours.


title: 36_Irf1_2_S46

city: La Jolla

first: Tatiana

last: Kisseleva

address: 9500 Gilman Dr

department: School of Medicine

institute: UCSD

data_processing:
For Chip-seq Basecalling, demultiplexing, and adapter trimming was performed using Illumina's bcl2fastq (v2.17.1.14).  For RNA-seq Base-calling was performed using Illumina Real Time Analysis RTA 1.18.64 with default parameters
ChIP-seq reads were aligned to the mouse (mm10) or human (hg38) genomes using bowtie2 (Langmead and Salzberg, 2012), keeping only reads that map to a single unique genomic location for further analysis (MAPQ > 10). ChIP-seq peaks were called using HOMER’s findPeaks program using “-mode histone” (histone marks, Pol II) using default parameters.  For RNA-seq Sequenced reads were mapped to the Mouse Genomes Project GRCm38_68.fa reference genome using STAR v2.5.1a with default parameters
For RNA-seq Read quantification was performed with RSEM v1.3.0 and Ensembl annotation Mus_musculus.GRCm38.68.gtf
Genome_build: Chip-seq hg38, mm10.  RNA-seq GRCm38.68
Supplementary_files_format_and_content: processed data is in supplementary file, which is a comma-separated text file containing a matrix of read counts for each gene accession number and sample

source_name: primary mouse HSCs

growth_protocol: Primary murine or human HSCs were cultured in Dulbecco’s modified Eagle’s medium (DMEM Life Technologies, 11965-092) supplemented with 10% FBS (Corning, 35-011-CV) and 1% Antibiotic-Antymycotic (Life Technologies #15240-062).

extract_protocol:
For Chip-seq Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody. Alternatively, DNA was phenol/chloroform-extracted from MNase-treated nuclei, and 134-154 bp long fragments were extractred from a 2% agarose gel. For RNA-seq Total RNA was isolated using Purelink RNA Mini Kit (Life Technologies)
For Chip-seq Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, ChIP DNA was PCR-amplified with Illumina primers for 12-16 cycles and library fragments of 200-300 bp (ChIP) (insert plus adaptor and PCR primer sequences) were isolated from a 2% agarose gel. For MNase-Seq, size-selected mononucleosome-derived DNA fragments were ligated to modified adapters that incorporate both the adapter sequence as well as the primer landing sites for the flow cell-conjugated primers. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer or Genome Analyzer II following the manufacturer's protocols. For RNA-seq Illumina Stranded Total RNA (Illumina 20020597)

treatment_protocol: shRNA-expressing lentiviral plasmids were co-transfected with plasmids pVSV-G and pCMVd8.2 dvpr into 293T cells. Viral containing media were collected 72 h later, filtered (0.22-μm pore size), concentrated by ultracentrifugation, and purified on a sucrose 20% gradient. Viral titers were measured using immunocapture p24-gag ELISA (Sequencing core facility, LJI). For viral transduction, lentiviral vectors at a multiplicity of infection (moi) of 30 + polybrene (10 μg/ml) were added to primary mHSCs (60-70% confluency, 24h after plating) for 36 hours, afterward fresh media containing ± puromycin (5 μg/ml) was added to infected cells for 48 hours. mHSCs were harvested, gene silencing was analyzed by qRT-PCR and RNA-Seq. Multiple shRNA hairpins were tested: ETS1 (n=5), ETS2 (n=10), NF1 (n=4), NF2 (n=5), GATA4 (n=5), GATA6 (n=5), IRF1 (n=7), IRF2 (n=10). A minimum of two target sequences with the least off-target knockdowns was selected for each gene (Suppl. Table 1), compared to non-coding hairpins. Infection with SHC-002 (CTRL1) was used as a control for targeting NF1/2, ETS1/2, GATA4/6 in mHSCs; SHC-202 (CTRL2) was used as a control for targeting IRF1/2 in mHSCs. CTRL1 (-) or CTRL2 (-) corresponds to SHC-002 (or SHC-202)-infected cells without purimycin treatment.

tag: strain background

value: Hepatic stellate cells isolated from mouse liver

tag: genotype/variation


title: iCLIP-seq of Flag-Srrm3 in in-vitro differentiated neurons, replicate 2

description:
Extracted RNA was reverse transcribed using primer Rt10clip: /5Phos/NNGACCNNNAGATCGGAAGAGCGTCGTGgatcCTGAACCGC. Reads start with 5'-NNNGGTCNN, where N are random bases.
Srrm3_meta-exon.pdf


title: Bcells for Patient EMG-EC-002


title: 32_Ets1_2_S42


title: 33_Gata4_6_S43


title: 22_Irf1_079_S32


title: 31_Ets1_2_S41


title: iCLIP-seq of Flag-Srrm3 in in-vitro differentiated neurons, replicate 1

description:
Extracted RNA was reverse transcribed using primer Rt9clip: /5Phos/NNGCCANNNAGATCGGAAGAGCGTCGTGgatcCTGAACCGC. Reads start with 5'-NNNTGGCNN, where N are random bases.
Srrm3_meta-exon.pdf


title: 23_Irf2_583_S33


title: 21_Irf1_079_S31


title: 20_Gata6_590_S30


title: Ribo_DKO_rep1

description: Blencowe_RP_c_16_CHX_5_ACTTGA_L005_R1_001


title: 19_Gata6_590_S28


title: 18_Gata4_214_S27


title: 12_Ets2_649_S21


title: 17_Gata4_214_S26


title: Ribo_WT_rep1

description: Blencowe_RP_c_14_23_CHX_5_GCCAAT_L005_R1_001


title: 11_Ets2_649_S20


title: 6_Ets1_640_S56


title: 5_Ets1_640_S55


title: 39_SHC202x2_S49

value: SHC-202x2 CTRL2


title: 34_Gata4_6_S44


title: 40_SHC202x2_S51


title: 38_SHC002x2_S48

value: SHC-002x2 CTRL1


title: 10_SHC202_pos_S19

value: SHC-202 CTRL2


title: 35_Irf1_2_S45


title: 4_SHC202_Pos_S54


title: 24_Irf2_583_S34


title: 8_SHC002_pos_S58

value: SHC-002 CTRL1


title: M2_rep2 (PE150)

city: Jena

first: Rainer

last: König

address: Am Klinikum 1

country: Germany

institute: University Hospital Jena

data_processing:
Sequenced reads were trimmed using Trimmomatic.
Remaining reads were mapped to the reference genome using TopHat2.
FeatureCounts was used to determine read counts.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read counts for each sample

source_name: peritoneal macrophages

extract_protocol:
Libraries for the validation experiment were constructed through Novogene using Illumina protocols
Qiagen RNeasy Plus Mini Kit according to manufacturer’s instructions


title: M2_rep1 (PE150)


title: M2_neg_siPool_rep2 (PE150)

value: negative siRNA pool


title: M2_rep3 (PE150)


title: M2_neg_siPool_rep3 (PE150)


title: M2_mock_rep3 (PE150)

value: mock


title: M2_mock_rep1 (PE150)


title: M2_siPool_Pparg_rep3 (PE150)

value: Pparg-siRNA pool


title: M2_siPool_Stat6_rep2 (PE150)

value: Stat6-siRNA pool


title: M2_siPool_Stat6_rep3 (PE150)


title: M2_siPool_Stat6_rep1 (PE150)


title: M2_siPool_Myc_rep3 (PE150)

value: Myc-siRNA pool


title: M2_siPool_Pparg_rep2 (PE150)


title: 37_SHC002x2_S47


title: M2_siPool_Myc_rep1 (PE150)


title: M2_siPool_Pparg_rep1 (PE150)


title: M2_siPool_E2f1_rep2 (PE150)

value: E2f1-siRNA pool


title: M2_siPool_E2f1_rep3 (PE150)


title: M2_siPool_combined_rep3 (PE150)

value: E2f1-Myc-Pparg-Stat6-siRNA pool


title: M2_siPool_combined_rep1 (PE150)


title: M1_mock_rep3 (PE150)


title: M2_neg_siPool_rep1 (PE150)


title: M2_siPool_combined_rep2 (PE150)


title: M1_mock_rep1 (PE150)


title: M2_siPool_E2f1_rep1 (PE150)


title: M1_rep3 (PE150)


title: M1_mock_rep2 (PE150)


title: M1_rep1 (PE150)


title: M0_mock_rep3 (PE150)


title: M0_rep3 (PE150)


title: M0_mock_rep2 (PE150)


title: M1_rep2 (PE150)


title: M0_mock_rep1 (PE150)


title: M2_siPool_Myc_rep2 (PE150)


title: M0_rep1 (PE150)


title: Ob

city: Guangzhou

first: Shiying

last: Dang

address: Institute of Biomedicine, Department of cellular Biology, Jinan University, 601 Huangpu Ave West, Guangzhou 510632, Guangdong, People’s Republic of china

institute: Institute of Biomedicine & Dept. Cellular Biology, Guangdong Province Key Lab of Bioengineering Medicine, Jinan University

description: total miRNA

data_processing:
Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts. In this step, clean datas(clean reads) were obtained by removing reads containing ploy-N, with 5’ adapter contaminants, without 3’ adapter or the insert tag, containing ploy A or T or G or C and low quality reads from raw data
The small RNA tags were mapped to reference sequence by Bowtie (Langmead et al., 2009) without mismatch to analyze their expression and distribution on the reference
Mapped small RNA tags were used to looking for known miRNA. miRBase20.0 was used as reference, modified software mirdeep2(Friedlander et al., 2011) and srna-tools-cli were used to obtain the potential miRNA and draw the secondary structures. Custom scripts were used to obtain the miRNA counts as well as base bias on the first position of identified miRNA with certain length and on each position of all identified miRNA respectively
To remove tags originating from protein-coding genes, repeat sequences, rRNA, tRNA, snRNA, and snoRNA, small RNA tags were mapped to RepeatMasker, Rfam database or those types of datas from the specified species itself.
miRNA expression levels were estimated by TPM (transcript per million) through the following criteria (Zhou et al., 2010):Normalization formula: Normalized expression = mapped readcount/Total reads*1000000
Genome_build: mm9
Supplementary_files_format_and_content: Excell files include TPM values for each Sample …

source_name: exosomes derived from adipose tissue

extract_protocol:
RNA was harvested using Trizol reagent.The amount of total RNA per sample was 3ug as the input material for the small RNA library.Small RNA Sample Pre Kit (NEB, USA) was used with 3 ug of total RNA for the construction of sequencing libraries.
small RNA libraries were prepared for sequencing using standard Illumina protocols

tag: diet

value: normal

tag: strain/genotype

value: B6 ob/ob

value: adipose tissue

value: 4 months-old


title: WT

description: total miRNA


title: M2_mock_rep2 (PE150)

tag: strain


title: M0_rep2 (PE150)


title: HFD

description: total miRNA

value: high-fat diets


title: PDA30364_tumor_11992_GEM+CD40-1

city: Heidelberg

first: Michael

last: Volkmar

state: BW

address: Im Neuenheimer Feld 280

department: D200 Molecular Oncology of Gastrointestinal Tumors

institute: German Cancer Research Center (DKFZ)

description: Gene expression data from tumor biopsy

hyb_protocol: After fragmentation, 11ug of cRNA were hybridized for 16h to the Affymetrix mouse 430 2.0 Gene Chip® array (GPL1261).

scan_protocol: GeneChips were scanned with the Affymetrix GeneChip Scanner 3000.

data_processing: Raw data was exported as cell intensity (CEL) files and analyzed using Chipster (Kallio et al., 2011; BMC Genomics 12, 507, doi:19.1186/1471-2164-12-507). After quality control, samples were normalized by applying the Robust Multichip Averaging (RMA) normalization method.

source_name: PDA30364 whole tumor, snap frozen, RNA isolated from tumor

label_protocol: Labeling was performed by the DKFZ's Genomics and Proteomics Core Facility using 200ng total RNA (RIN=>8.0) with  a GeneChip™ 3’IVT Plus Reagent Kit (Affymetrix).

growth_protocol: Murine tumor cell lines were passaged at least four times after thawing and grown as a monolayer with a maximal confluency of 70-80%. Cells were detached using 0.25% trypsin-EDTA solutions, centrifuged and washed once with cell culture medium. 0.5 x 10^6 PDA30364 tumor cells were injected in PBS/Matrigel (1:1, Corning) subcutaneously into the flank of six to twelve weeks old C57BL/6-Ly5.1 mice. Tumor growth was measured twice a week with a caliper. The tumor volume was calculated by multiplying length by width by height.

extract_protocol: Tumor material was homogenized in RLT buffer (Qiagen) supplemented with beta-mercaptoethanol with 2.8 mm steel beads (Precellys) using a tissue homogenizer (TissueLyzer sample disrupter, Qiagen) at 30 Hz, 30 sec for 3 times. Subsequent RNA extraction was performed using the RNeasy Mini kit (Qiagen) according to the manufacturer’s instructions with on-column DNase I digestion. Amount of isolated RNA was measured using a Nanodrop spectrophotometer, while RNA quality was determined using a Agilent 2100 Bioanalyzer.

treatment_protocol: Mice were treated with 120 mg/kg gemcitabine GEM/vehicle on treatment days 1, 5 and 12 and anti-CD40 Ab / isotype control antibody on days 3, 4, 6, and 14. Four mice per treatment group were sacrificed on days 22/23 after tumor inoculation and subjected to whole transcriptome analyses.

value: Whole tumor

tag: treatment groups

value: GEM+CD40 mIgG1


title: PDA30364_tumor_12043_GEM-1

description: Gene expression data from tumor biopsy

value: GEM+control IgG


title: PDA30364_tumor_11993_GEM+CD40-2

description: Gene expression data from tumor biopsy


title: PDA30364_tumor_12018_GEM+CD40-3

description: Gene expression data from tumor biopsy


title: PDA30364_tumor_11880_GEM-2

description: Gene expression data from tumor biopsy


title: PDA30364_tumor_11879_CD40-2

description: Gene expression data from tumor biopsy

value: Vehicle+CD40 mIgG1


title: PDA30364_tumor_11851_GEM-3

description: Gene expression data from tumor biopsy


title: PDA30364_tumor_12023_CD40-3

description: Gene expression data from tumor biopsy


title: PDA30364_tumor_11823_Ctrl-2

description: Gene expression data from tumor biopsy

value: Vehicle+control IgG


title: MDS-L WT DMSO1 72h

value: del(5q) MDS cell line

value: WT Clone 1B2ct


title: 1127 MAC 6 hr DEX 2

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression from Dexamethasone treated Macrophage cells (Mac 6hr Dex)

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner

data_processing: Data was obtained using the Agilent Feature Extraction software (v12), using the 1-color defaults for all parameters.

source_name: 6-hour Dexamethasone treated Macrophage cells (Mac 6hr Dex)

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced per manufacturer’s protocol.

growth_protocol: Human Monocyte cell line THP-1 were used for differentiation into macrophages with PMA during 3 hours and a time of recovery of 24 hours. Monocytes-THP-1 and macrophages-derived monocyte-THP-1 were maintained during 24 hours with charcoal medium before the Dex treatment for 6 hours.

extract_protocol: RNA samples from all treatments groups (Mono-THP-1 Vehicle and Dex and Macro-THP-1 vehicle and Dex) will be extracted using QIAshredder and RNeasy Mini kit with DNase treatment. The RNA concentration will be determined by Nanodrop and the quality using BioAnalyzer.

treatment_protocol: Monocytes-THP-1 and THP-1-derived macrophages were stimulated with vehicle or 100nM Dexamethasone during 6 hours in stripped medium.

tag: cell line source

value: Human Monocyte cell line

tag: cell subtype

value: Cell line diffferentited

value: Dex treatment


title: PDA30364_tumor_11848_CD40-1

description: Gene expression data from tumor biopsy


title: PDA30364_tumor_11882_Ctrl-1

description: Gene expression data from tumor biopsy


title: H3K9me3_KO_input

city: Copenhagen

first: Aditya

last: Sankar

email: cnj376@ku.dk, aditya.sankar@embl.de

address: Ole Maaloes Vej 5

department: Biotech Research and Innovation Centre

country: Denmark

institute: University of Copenhagen

library_source: genomic

data_processing:
Reads were trimmed using Trimmomatic and the settings ILLUMINACLIP:${ADAPTER_FASTA_FILE}:2:30:10 SLIDINGWINDOW:4:20 HEADCROP:5 CROP:125 MINLEN:30
ChIP-seq reads were aligned to the mm10 genome assembly using bowtie2 (Langmead B, Salzberg S. Nature Methods. 2012, 9:357-359.) and the settings --local -X 2000 and sorted using samtools (Li et al, Bioinformatics. 2009, 15;25(16):2078-9).
Mapped reads were imported into EaSeq (Lerdrup et al, Nature Structural & Molecular Biology, 2016, 23, 349–357, http://easeq.net) for subsequent analysis and generation of wig-files.
Genome_build: mm10
Supplementary_files_format_and_content: Gzip compressed wig files generated using EaSeq (see above); Scores represent fragments per kilobasepairs per million reads

source_name: 2-cell embryo

growth_protocol: MII oocytes and 2-cell embryos were isolated from, crosslinked and frozen for Chip according to previously published protocol (PMID: 27626377)

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Qiagene Ultra low input library preperation kit (180492) according to manufacturers instructions and quantified using KAPA library quantification kit from Roche (07960298001)

treatment_protocol: Antibodies

value: 2-cell embryo

tag: pooled numbers

tag: chip antibody

value: No antibody

value: Kdm4a KO


title: 1127 THP 6 hr CTL 1

description: Gene expression from vehicle treated THP-1 cells (THP 6hr Control)

source_name: 6-hour vehicle treated THP-1 cells (THP 6hr Control)

value: Cell line

tag: treatment

value: Vehicle


title: 1127 MAC 6 hr CTL 3

description: Gene expression from vehicle treated Macrophage cells (Mac 6hr Control)

source_name: 6-hour vehicle treated Macrophage cells (Mac 6hr Control)


title: 1127 THP 6 hr DEX 3

description: Gene expression from Dexamethasone treated THP-1 cells (THP 6hr Dex)

source_name: 6-hour Dexamethasone treated THP-1 cells (THP 6hr Dex)


title: 1127 MAC 6 hr DEX 1


title: 1127 MAC 6 hr CTL 1


title: 1127 MAC 6 hr DEX 3


title: 1127 THP 6 hr DEX 1


title: PDA30364_tumor_12016_GEM+CD40-4

description: Gene expression data from tumor biopsy


title: PDA30364_tumor_11851_GEM-4

description: Gene expression data from tumor biopsy


title: PDA30364_tumor_12878_CD40-4

description: Gene expression data from tumor biopsy


title: 1127 THP 6 hr CTL 2


title: PDA30364_tumor_11990_Ctrl-3

description: Gene expression data from tumor biopsy


title: 1127 THP 6 hr DEX 2


title: 1127 MAC 6 hr CTL 2


title: 1127 THP 6 hr CTL 3


title: PDA30364_tumor_12045_Ctrl-4

description: Gene expression data from tumor biopsy


title: H3K9me3_WT_input

value: WT


title: H3K9me3_KO

value: H3K9me3 (Pool of Abcam#ab8898, Lot GR153112-1 and Abcam#ab176916)


title: H3K36me3_KO_input

source_name: MII oocyte

value: MII oocyte


title: H3K9me3_WT


title: 2 cell embryo_KO rep4

data_processing:
Raw sequencing data was converted from bcl to fastq format and reads trimmed in BaseSpace.
Reads were trimmed with Trimmomatic v0.32 with settings: PE ILLUMINACLIP:TruSeq2-PE.fa:2:30:10:1:true HEADCROP:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:25
Reads were mapped and assigned repeat elements (RepeatMasker database; mm10,4.0.5,2014013) using RepEnrich2 (v0.1). The resulting abundance measurements (18,538 repeats) were analyzed in R using the statistical edgeR package
Genome_build: mm10
Supplementary_files_format_and_content: counts

source_name: 2 cell embryo_KO

growth_protocol: Wildtype or Kdm4a knockout oocytes were both fertilized with Kdm4a knockout sperm and observed for second polar body extrusion 6 hrs post fertilization. The following morning they were observed for successful completion of first cell division into 2 cell stage prior to sampling. Sampling was done simultaneously for wildtype and knockout embryos

extract_protocol:
Total RNA extraction, rRNA depletion and cDNA amplification was performed according to manufacturers instructions of the SMARTSeq Stranded kit from TakaraBio Catalog#634442
RNA libraries were prepared for sequencing using SMARTSeq Stranded kit for single cells using Takara Bio catalog#634442

treatment_protocol: 2 cell embryos were washed twice in clean M2 medium, twice in PBS and once in nuclease free water prior to tubing in individual tubes of a nuclease free 8-PCR strip prior to immediate lysis and cDNA amplification

value: preimplantation embryo

tag: age

value: 1.5 days post fertilization

value: Kdm4a knockout (m-/p-)


title: 2 cell embryo_KO rep5


title: 2 cell embryo_KO rep1


title: 2 cell embryo_KO rep3


title: H3K36me3_WT_input

tag: cell type


title: 2 cell embryo_WT rep2

source_name: 2 cell embryo_WT

tag: genotype


title: H3K36me3_KO


title: 8 cell embryo_8c_knockout_13

data_processing:
Raw sequencing data was converted from bcl to fastq format and reads trimmed in BaseSpace.
Reads were trimmed with Trimmomatic v0.32 with settings: PE ILLUMINACLIP:NexteraPE-PE.fa:2:30:10:1:true HEADCROP:15 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:25
Trimmed reads were mapped to mm10 genome assembly using STAR v2.5.1a in two-pass mode and guided by a RefSeq (UCSC,2018/08/05) gene annotation (settings: --sjdbOverhang 135  --twopassMode Basic --outSAMtype BAM SortedByCoordinate --outSAMattributes All --outSAMunmapped Within --outFilterMismatchNoverLmax 0.1 --outFilterMatchNmin 16 --outFilterMismatchNmax 5
The mapped reads were assigned to genes with featureCounts v1.5.1 with settings: --primary -p -B -O -M --fraction -s 0 -J
Genome_build: mm10
Supplementary_files_format_and_content: A single count table with counts for all 128 samples and 41,300 genes. The first 6 columns contain gene annotation.

source_name: 8 cell embryo_8c_knockout

growth_protocol: Wildtype or Kdm4a knockout MII oocytes (oocyte sampling was performed simulataneously here) were both fertilized with Kdm4a knockout sperm and observed for second polar body extrusion 6 hrs post fertilization. The following morning they were observed for successful completion of first cell division into 2 cell stage prior to sampling. Similarly, sampling was done for simultaneously for wildtype and knockout embryos 4-cell and 8-cell stage according to progression of the control embryos

extract_protocol:
RNA extraction and cDNA amplification was performed according to manufacturers instructions of the SMARTSeq Stranded kit from TakaraBio Catalog#634893
RNA libraries were prepared for sequencing using Nextera XT DNA library prepration kit with dual indexing from Illumina (Cat No FC-131-1024)

treatment_protocol: All samples were subjected to zona removal after washing in Tyrodes acid solution, and then washed thrice in clean M2 medium, twice in PBS and once in nuclease free water prior to tubing in individual tubes of a nuclease free 8-PCR strip prior to immediate lysis and cDNA amplification

tag: tissue

value: 3.5 days post fertilisation


title: 2 cell embryo_KO rep2


title: 8 cell embryo_8c_knockout_14


title: 2 cell embryo_WT rep6


title: 2 cell embryo_WT rep5


title: 2 cell embryo_WT rep4


title: 2 cell embryo_WT rep3


title: 8 cell embryo_8c_knockout_12


title: 8 cell embryo_8c_knockout_16


title: 8 cell embryo_8c_knockout_15


title: 2 cell embryo_KO rep6


title: H3K36me3_WT


title: 8 cell embryo_8c_knockout_11


title: 2 cell embryo_WT rep1


title: 8 cell embryo_8c_knockout_7


title: 8 cell embryo_8c_knockout_8


title: 8 cell embryo_8c_knockout_5


title: 8 cell embryo_8c_knockout_10


title: 8 cell embryo_8c_knockout_6


title: 8 cell embryo_8c_knockout_9


title: Sample_38_MH_ascites

city: Huntsville

first: Sara

last: Cooper

state: AL

address: 601 Genome Wau

institute: HudsonAlpha Institute

description:
replicate #1
3214-SJC-0229

data_processing:
adapter trimming using trimgalore v0.4.1
fastqc v0.10.1 for quality score assessment
star version v2,5,2b for alignment
ht-seq-gene v 0.5.3 to consoldiate reads to features
Genome_build: hg37
Supplementary_files_format_and_content: raw count table at the gene level for all samples

source_name: Ascites

extract_protocol:
RNA was extracted using Norgen Total RNA purification kit + DNase (cat #37500)
NEBNext Ultra RNA Library Prep Kit for Illumina (cat #E7530S) with polyA selection (cat# E7490S)

treatment_protocol: Patients were treated with platinum-based therapy or not as indicated

value: Ascites

tag: Stage

tag: patientid


title: Sample_31_DH_ascites

description:
replicate #1
3214-SJC-0223


title: Sample_34_JL_ascites

description:
replicate #1
3214-SJC-0225


title: Sample_35_MW_ascites

description:
replicate #1
3214-SJC-0226


title: Sample_36_NH_ascites

description:
replicate #1
3214-SJC-0227


title: Sample_37_ET_ascites

description:
replicate #1
3214-SJC-0228


title: 8 cell embryo_8c_knockout_3


title: Sample_20_JC_ascites

description:
replicate #1
3214-SJC-0220


title: Sample_21_MR_ascites

description:
replicate #1
3214-SJC-0221


title: 8 cell embryo_8c_knockout_4


title: 8 cell embryo_8c_knockout_2


title: 8 cell embryo_8c_wildtype_16

source_name: 8 cell embryo_8c_wildtype


title: Sample_18_BM_ascites

description:
replicate #1
3214-SJC-0219


title: Sample_16_MB_ascites

description:
replicate #1
3214-SJC-0217


title: Sample_17_SC_ascites

description:
replicate #1
3214-SJC-0218


title: 8 cell embryo_8c_knockout_1


title: Sample_15_MC_ascites

description:
replicate #1
3214-SJC-0216


title: 8 cell embryo_8c_wildtype_15


title: 8 cell embryo_8c_wildtype_14


title: Sample_39_CR_ascites

description:
replicate #1
3214-SJC-0230


title: Sample_33_SS_ascites

description:
replicate #1
3214-SJC-0224


title: Sample_14_HT_ascites

description:
replicate #1
3214-SJC-0215


title: Sample_27_FJ_ascites

description:
replicate #1
3214-SJC-0222


title: 8 cell embryo_8c_wildtype_13


title: Sample_12_GD_ascites

description:
replicate #1
3214-SJC-0213


title: Sample_13_TM_ascites

description:
replicate #1
3214-SJC-0214


title: 8 cell embryo_8c_wildtype_11


title: 8 cell embryo_8c_wildtype_12


title: Sample_09_RD_ascites

description:
replicate #1
3214-SJC-0211


title: Sample_07_SD_ascites

description:
replicate #1
3214-SJC-0209


title: Sample_05_CH_ascites

description:
replicate #1
3214-SJC-0207


title: 8 cell embryo_8c_wildtype_5


title: 8 cell embryo_8c_wildtype_6


title: 8 cell embryo_8c_wildtype_7


title: Sample_08_CD_ascites

description:
replicate #1
3214-SJC-0210


title: Sample_06_CC_ascites

description:
replicate #1
3214-SJC-0208


title: 8 cell embryo_8c_wildtype_4


title: Sample_03_IB_ascites

description:
replicate #1
3214-SJC-0205


title: 8 cell embryo_8c_wildtype_3


title: Sample_02_EE_ascites

description:
replicate #1
3214-SJC-0204


title: 8 cell embryo_8c_wildtype_1


title: Sample_83_MP_tumor

description:
replicate #1
3214-SJC-0248

source_name: Serous Ovarian Cancer Tumor

value: Serous Ovarian Cancer Tumor


title: 8 cell embryo_8c_wildtype_2


title: 4 cell embryo_4c_knockout_16

source_name: 4 cell embryo_4c_knockout

value: 2.5 days post fertilization


title: Sample_01_SM_ascites

description:
replicate #1
3214-SJC-0203


title: Sample_11_SK_ascites

description:
replicate #1
3214-SJC-0212


title: Sample_78_CS_tumor

description:
replicate #1
3214-SJC-0246


title: 8 cell embryo_8c_wildtype_10


title: Sample_82_LB09_tumor

description:
replicate #1
3214-SJC-0247


title: 8 cell embryo_8c_wildtype_9


title: 4 cell embryo_4c_knockout_15


title: 8 cell embryo_8c_wildtype_8


title: 4 cell embryo_4c_knockout_14


title: 4 cell embryo_4c_knockout_12


title: Sample_77_AR_tumor

description:
replicate #1
3214-SJC-0245


title: Sample_74_LB08_tumor

description:
replicate #1
3214-SJC-0244


title: Sample_04_JS_ascites

description:
replicate #1
3214-SJC-0206


title: 4 cell embryo_4c_knockout_9


title: 4 cell embryo_4c_knockout_10


title: 4 cell embryo_4c_knockout_13


title: Sample_82_LB09_ascites

description:
replicate #1
3214-SJC-0242


title: Sample_77_AR_ascites

description:
replicate #1
3214-SJC-0240


title: Sample_83_MP_ascites

description:
replicate #1
3214-SJC-0243


title: Sample_71KA

description:
replicate #1
3214-SJC-0131


title: Sample_74_LB08_ascites

description:
replicate #1
3214-SJC-0239


title: 4 cell embryo_4c_knockout_11


title: Sample_70LL

description:
replicate #1
3214-SJC-0130


title: 4 cell embryo_4c_knockout_7


title: 4 cell embryo_4c_knockout_6


title: 4 cell embryo_4c_knockout_5


title: 4 cell embryo_4c_knockout_3


title: Sample_68KC

description:
replicate #1
3214-SJC-0128


title: Sample_66WM

description:
replicate #1
3214-SJC-0126


title: Sample_67CB

description:
replicate #1
3214-SJC-0127


title: Sample_65LS

description:
replicate #1
3214-SJC-0125


title: 4 cell embryo_4c_wildtype_16

source_name: 4 cell embryo_4c_wildtype


title: 4 cell embryo_4c_knockout_1


title: Sample_63LB

description:
replicate #1
3214-SJC-0123


title: 4 cell embryo_4c_knockout_8


title: Sample_61JD

description:
replicate #1
3214-SJC-0121


title: 4 cell embryo_4c_wildtype_14


title: 4 cell embryo_4c_knockout_2


title: 4 cell embryo_4c_wildtype_13


title: Sample_39_CR

description:
replicate #1
3214-SJC-0119


title: Sample_37_ET

description:
replicate #1
3214-SJC-0117


title: 4 cell embryo_4c_wildtype_12


title: Sample_38_MH

description:
replicate #1
3214-SJC-0118


title: 4 cell embryo_4c_wildtype_11


title: 4 cell embryo_4c_wildtype_10


title: 4 cell embryo_4c_wildtype_9


title: Sample_69GA

description:
replicate #1
3214-SJC-0129


title: Sample_36_NH

description:
replicate #1
3214-SJC-0116


title: 4 cell embryo_4c_knockout_4


title: 4 cell embryo_4c_wildtype_6


title: Sample_34_JL

description:
replicate #1
3214-SJC-0114


title: 4 cell embryo_4c_wildtype_5


title: 4 cell embryo_4c_wildtype_7


title: Sample_64MM

description:
replicate #1
3214-SJC-0124


title: Sample_62LH

description:
replicate #1
3214-SJC-0122


title: Sample_33_SS

description:
replicate #1
3214-SJC-0113


title: 4 cell embryo_4c_wildtype_15


title: 4 cell embryo_4c_wildtype_4


title: Sample_32_JN

description:
replicate #1
3214-SJC-0112


title: 4 cell embryo_4c_wildtype_3


title: 4 cell embryo_4c_wildtype_2


title: Sample_29_JB

description:
replicate #1
3214-SJC-0109


title: Sample_31_DH

description:
replicate #1
3214-SJC-0111


title: Sample_28_EC

description:
replicate #1
3214-SJC-0108


title: 4 cell embryo_4c_wildtype_1


title: Sample_30_MD

description:
replicate #1
3214-SJC-0110


title: 2 cell embryo_2c_knockout_16

source_name: 2 cell embryo_2c_knockout

value: 1.5 days post fertilisation


title: Sample_27_FJ

description:
replicate #1
3214-SJC-0107


title: Sample_35_MW

description:
replicate #1
3214-SJC-0115


title: Sample_26_MH

description:
replicate #1
3214-SJC-0106


title: Sample_25_JC

description:
replicate #1
3214-SJC-0105


title: Sample_24_EE

description:
replicate #1
3214-SJC-0104


title: 2 cell embryo_2c_knockout_14


title: 2 cell embryo_2c_knockout_15


title: 2 cell embryo_2c_knockout_13


title: 4 cell embryo_4c_wildtype_8


title: 2 cell embryo_2c_knockout_12


title: Sample_23_AB

description:
replicate #1
3214-SJC-0103


title: Sample_22_EH

description:
replicate #1
3214-SJC-0102


title: 2 cell embryo_2c_knockout_10


title: Sample_21_MR

description:
replicate #1
3214-SJC-0101


title: Sample_20_JC

description:
replicate #1
3214-SJC-0100


title: Sample_18_BM

description:
replicate #1
3214-SJC-0098


title: 2 cell embryo_2c_knockout_9


title: Sample_16_MB

description:
replicate #1
3214-SJC-0096


title: Sample_19_AL

description:
replicate #1
3214-SJC-0099


title: 2 cell embryo_2c_knockout_6


title: 2 cell embryo_2c_knockout_8


title: Sample_14_HT

description:
replicate #1
3214-SJC-0094


title: 2 cell embryo_2c_knockout_5


title: 2 cell embryo_2c_knockout_7


title: 2 cell embryo_2c_knockout_4


title: Sample_15_MC

description:
replicate #1
3214-SJC-0095


title: Sample_13_TM

description:
replicate #1
3214-SJC-0093


title: Sample_17_SC

description:
replicate #1
3214-SJC-0097


title: 2 cell embryo_2c_knockout_3


title: 2 cell embryo_2c_knockout_2


title: Sample_11_SK

description:
replicate #1
3214-SJC-0091


title: Sample_12_GD

description:
replicate #1
3214-SJC-0092


title: 2 cell embryo_2c_wildtype_16

source_name: 2 cell embryo_2c_wildtype


title: Sample_10_JA

description:
replicate #1
3214-SJC-0090


title: 2 cell embryo_2c_wildtype_15


title: Sample_09_RD

description:
replicate #1
3214-SJC-0089


title: 2 cell embryo_2c_knockout_1


title: 2 cell embryo_2c_wildtype_14


title: 2 cell embryo_2c_wildtype_13


title: Sample_08_CD

description:
replicate #1
3214-SJC-0088


title: Sample_07_SD

description:
replicate #1
3214-SJC-0087


title: 2 cell embryo_2c_knockout_11


title: 2 cell embryo_2c_wildtype_12


title: Sample_06_CC

description:
replicate #1
3214-SJC-0086


title: Sample_05_CH

description:
replicate #1
3214-SJC-0085


title: 2 cell embryo_2c_wildtype_10


title: 2 cell embryo_2c_wildtype_11


title: Sample_04_JS

description:
replicate #1
3214-SJC-0084


title: Human HSC input

source_name: primary human HSCs

value: Hepatic stellate cells isolated from human liver

tag: disease stage

value: non-fibrotic


title: Human HSC H3K27ac donor 2

description: H3K27ac ChIP-seq in human (donor 2) HSCs

value: H3K27ac (Active Motif 39133)


title: Sample_03_IB

description:
replicate #1
3214-SJC-0083


title: Human HSC H3K4me2 donor 1

description: H3K4me2 ChIP-seq in human (donor 1) HSCs

value: H3K4me2 (Millipore, 07-030)


title: Human HSC H3K4me2 donor 2

description: H3K4me2 ChIP-seq in human (donor 2) HSCs


title: 2 cell embryo_2c_wildtype_9


title: 2 cell embryo_2c_wildtype_8


title: Sample_02_EE

description:
replicate #1
3214-SJC-0082


title: 2 cell embryo_2c_wildtype_7


title: CARD11K215M

first: Wei

last: Lv

address: 320 Yueyang Road

institute: Shang Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences

data_processing:
BGI software SOAPnuke was used for sequencing reads filtering to remove reads with adaptors, reads in which unknown bases (N) are more than 10%, and low quality reads (the percentage of base which quality is lesser than 15 is greater than 50% in a read). After data cleaning, the remaining data are stored in FASTQ format.
We use HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts) to do the mapping step.
We mapped clean reads to reference using Bowtie2, and then calculate the gene expression level with RESM. We detected DEG with PossionDis and hierarchical clustering for DEGs using pheatmap.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.gene.fpkm.txt: Tab-delimited text files include FPKM values for each Sample.

source_name: mouse spleen B cell

extract_protocol:
Cells used for RNA preparation come from mouse spleen cells stained with B220, CD93 and IgM to get sorted B cells (biolegend), and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: genotype/variation

value: Spleen B cells


title: Sample_12post_26

description:
replicate #1
3214-SJC-0190

value: Platinum


title: WT control for CARD11E134G comparison

value: Wild Type


title: 2 cell embryo_2c_wildtype_6


title: WT control for CARD11K215M comparison


title: Human HSC H3K27ac donor 1

description: H3K27ac ChIP-seq in human (donor 1) HSCs


title: CARD11E134G


title: 2 cell embryo_2c_wildtype_5


title: Mouse_3_M2_rep2 (SE50)

source_name: peritoneal macrophages

extract_protocol:
RNA libraries were prepared for sequencing using standard Illumina protocols
Qiagen RNeasy Plus Mini Kit according to manufacturer’s instructions


title: Sample_12pre_25

description:
replicate #1
3214-SJC-0189


title: 2 cell embryo_2c_wildtype_4


title: Mouse_3_M2_rep1 (SE50)


title: 2 cell embryo_2c_wildtype_3


title: Mouse_2_M2_rep2 (SE50)


title: Sample_11pre_23

description:
replicate #1
3214-SJC-0187


title: Sample_11post2_24

description:
replicate #1
3214-SJC-0188


title: 2 cell embryo_2c_wildtype_2


title: Sample_1post_20

description:
replicate #1
3214-SJC-0186


title: Mouse_1_M2_rep2 (SE50)


title: Mouse_1_M2_rep1 (SE50)


title: MII oocyte_MII_knockout_16

source_name: MII oocyte_MII_knockout

value: unfertilized oocyte


title: MM231-FGD5-cas9 3

first: Tingting

last: Zhang

address: Nanwei street

institute: Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College

hyb_protocol: Following fragmentation, 12 ug of cRNA were hybridized for 16 hr at 45℃ on GeneChip Human Genome Array. GeneChips were washed and stained in the  GeneChip® Fluidics Station 450.

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

data_processing: The data were analyzed with the Robust Multichip Analysis (RMA) algorithm using Affymetrix default analysis settings and global scaling as normalization method. And the analysis software is Expression Console.

source_name: tumor

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250ng total RNA (Expression Analysis Technical Manual, 2013-2015, Affymetrix).

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

value: breast cancer

tag: cell line

value: MDA-MB 231


title: MM231-FGD5-cas9 1


title: 2 cell embryo_2c_wildtype_1

value: preimplantation embryo


title: MM231-FGD5-cas9 2


title: Mouse_2_M2_rep1 (SE50)


title: MII oocyte_MII_knockout_14

value: MII oocyte

value: Kdm4a knockout (m-/p-)


title: Sample_110pre_17

description:
replicate #1
3214-SJC-0183


title: MM231 3


title: Sample_110post_18

description:
replicate #1
3214-SJC-0184


title: Mouse_3_M1_rep2 (SE50)

value: LPS+IFNg


title: MII oocyte_MII_knockout_15


title: Mouse_3_M1_rep1 (SE50)


title: MII oocyte_MII_knockout_13


title: MM231 2


title: Sample_109pre_15

description:
replicate #1
3214-SJC-0181

value: Serous Ovarian Cancer Tumor


title: MII oocyte_MII_knockout_12


title: MM231 1


title: Sample_1pre_19

description:
replicate #1
3214-SJC-0185


title: Sample_109post_16

description:
replicate #1
3214-SJC-0182


title: Mouse_2_M1_rep1 (SE50)


title: Mouse_2_M1_rep2 (SE50)


title: Sample_108post

description:
replicate #1
3214-SJC-0197


title: Mouse_1_M1_rep2 (SE50)


title: MII oocyte_MII_knockout_11


title: Sample_102post

description:
replicate #1
3214-SJC-0196


title: Sample_100post

description:
replicate #1
3214-SJC-0192


title: Mouse_3_M0_rep2 (SE50)


title: MII oocyte_MII_knockout_9


title: Sample_102pre

description:
replicate #1
3214-SJC-0195


title: Mouse_1_M1_rep1 (SE50)


title: R4 LPA

city: Allschwil

first: Axel

last: Klenk

address: Hegenheimermattweg 91

department: Research Informatics

country: Switzerland

institute: Idorsia Pharmaceuticals Ltd.

hyb_protocol: a pool of 300 ng of Cy3 labeled aRNA (examined sample) and 300 ng of Cy5 labeled aRNA rat reference (Agilent, Austin TX, USA) were hybridized using the Agilent Hybridization kit (Agilent, Austin TX, USA) according to the manufacturer's instructions. Hybridization was performed for 17 hours and washed according to Agilent's instructions.

scan_protocol: Scanned on an Agilent G2505B scanner using Agilent scan control (version 8.5.1) Images were quantified using Agilent Feature Extraction Software (version 11.5.5.1).

data_processing: BioConductor package vsn was used for variance-stabilizing normalization and glog transformation

label_protocol: 50 ng of totRNA were labeled using the Low Input Quick Amp Labeling kit (Agilent, Austin TX, USA) following the manufacturer's instructions.

extract_protocol: total RNA extracted  using MagMAX-96 for microarrays kit (Life technologies, Foster City CA, USA ) following the manufacturer's instructions

value: primary human skin fibroblasts

value: LPA

source_name: Stratagene Reference

value: Pool of 10 human cell lines


title: Mouse_3_M0_rep1 (SE50)


title: R3 TGFB

value: TGFB


title: R1 Vehicle

value: Vehicle


title: R4 LPA.TGFB


title: Sample_100pre

description:
replicate #1
3214-SJC-0191


title: MII oocyte_MII_knockout_7


title: Mouse_2_M0_rep2 (SE50)


title: Sample_107post_12

description:
replicate #1
3214-SJC-0178


title: MII oocyte_MII_knockout_10


title: MII oocyte_MII_knockout_6


title: R1 LPA


title: MII oocyte_MII_knockout_8


title: R2 LPA.TGFB


title: Mouse_1_M0_rep2 (SE50)


title: R3 Vehicle


title: Mouse_2_M0_rep1 (SE50)


title: MII oocyte_MII_knockout_5


title: Sample_105post_10

description:
replicate #1
3214-SJC-0176


title: MII oocyte_MII_knockout_4


title: R2 LPA


title: MII oocyte_MII_knockout_3


title: Sample_108pre_13

description:
replicate #1
3214-SJC-0179


title: MII oocyte_MII_knockout_2


title: Sample_22B22post

description:
replicate #1
3214-SJC-0202


title: R4 TGFB


title: R3 LPA.TGFB


title: Sample_107pre_11

description:
replicate #1
3214-SJC-0177


title: Sample_105pre_9

description:
replicate #1
3214-SJC-0175


title: MII oocyte_MII_knockout_1


title: Sample_14B22pre

description:
replicate #1
3214-SJC-0201


title: R1 TGFB


title: MII oocyte_MII_wildtype_16

source_name: MII oocyte_MII_wildtype


title: Sample_01_SM

description:
replicate #1
3214-SJC-0081


title: R1 LPA.TGFB


title: Sample_22B36post

description:
replicate #1
3214-SJC-0200


title: Sample_12B36pre

description:
replicate #1
3214-SJC-0199


title: MII oocyte_MII_wildtype_15


title: Sample_27post_32

description:
replicate #1
3214-SJC-0165


title: MII oocyte_MII_wildtype_14


title: R4 Vehicle


title: MII oocyte_MII_wildtype_13


title: Sample_27pre_31

description:
replicate #1
3214-SJC-0164


title: Mouse_1_M0_rep1 (SE50)


title: R2 Vehicle


title: Sample_14post2_28

description:
replicate #1
3214-SJC-0163


title: R2 TGFB


title: MII oocyte_MII_wildtype_12


title: MII oocyte_MII_wildtype_11


title: Sample_14pre_27

description:
replicate #1
3214-SJC-0162


title: Sample_24pre_29

description:
replicate #1
3214-SJC-0160


title: Sample_24postA_30

description:
replicate #1
3214-SJC-0198


title: MCF7 Nutlin3a, biological rep3

city: Solna

first: Gema

last: Sanz Santos

state: Stockholm

address: Nobels väg 16

institute: Karolinska Institutet

description:
NUTLIN_3
MCF7 treated with Nutlin 10µM

hyb_protocol: Following fragmentation, cRNA was hybridized on Human Genome U219 Arrays.

scan_protocol: GeneChips were scanned using a confocal scanner (Affymetrix).

data_processing: The data were analyzed with RMA method for background correction, normalization, and summarization.

source_name: MCF7 Nutlin3a

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

growth_protocol: MCF7 cells were maintained in Iscove's modified Dulbecco's medium supplemented with 10% fetal calf serum, penicillin/streptomycin (10 units/ml), and l-glutamine (2 mM.)

extract_protocol: Total RNA was isolated with the RNeasy Mini kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: MCF7 cells were treated with 1 μM RITA or 10 μM Nutlin3a for 8 hr.

value: Nutlin3a 10µM for 8 hr


title: R3 LPA


title: MCF7 Nutlin3a, biological rep1

description:
NUTLIN_1
MCF7 treated with Nutlin 10µM


title: MCF7 RITA, biological rep3

description:
RITA_3
MCF7 treated with RITA 1µM

source_name: MCF7 RITA

value: RITA 1µM for 8 hr


title: MCF7 Nutlin3a, biological rep2

description:
NUTLIN_2
MCF7 treated with Nutlin 10µM


title: MII oocyte_MII_wildtype_8


title: MCF7 control, biological rep3

description:
DMSO_3
MCF7 control

source_name: MCF7 control


title: MCF7 RITA, biological rep2

description:
RITA_2
MCF7 treated with RITA 1µM


title: Sample_3post_22

description:
replicate #1
3214-SJC-0159

value: Platinum


title: MII oocyte_MII_wildtype_7


title: MII oocyte_MII_wildtype_10


title: MCF7 control, biological rep2

description:
DMSO_2
MCF7 control


title: MCF7 RITA, biological rep1

description:
RITA_1
MCF7 treated with RITA 1µM


title: Sample_103post_8

description:
replicate #1
3214-SJC-0157


title: MII oocyte_MII_wildtype_6


title: MII oocyte_MII_wildtype_9


title: Sample_3pre_21

description:
replicate #1
3214-SJC-0158


title: MCF7 control, biological rep1

description:
DMSO_1
MCF7 control


title: Sample_103pre_7

description:
replicate #1
3214-SJC-0156


title: Sample_101post_4

description:
replicate #1
3214-SJC-0194


title: RNA_seq_Exd_V5_wt_brain_VNC_PE_rep3

city: New York City

first: Harmen

middle: J

last: Bussemaker

state: New York

address: 1212 Amsterdam Avenue, MC 2441

department: Biological Sciences

institute: Columbia University

data_processing:
SELEX-seq 16-bp libraries: Fastq files were reverse-complemented and both forward and reverse-complement read merged into one (fastx_reverse_complement -Q33 -z ; FASTX toolkit 0.0.12;Hannon lab). Next, fixed primer sites were trimmed using the following options: fastx_trimmer -Q33 -f 12 -l 41 –z (FASTX toolkit 0.0.12;Hannon lab). Kmer counting and relative affinity estimates were computed using the R package bioconductor.org/packages/SELEX. SELEX-seq 21-bp and 30bp libraries: Sequencing primer sequences were removed as part of the Illumina demultiplexing. For the 21-bp libraries both Hth-F and Hth-R Homothorax orientations are present in the same fastq and can be isolated by using the R package bioconductor.org/packages/SELEX and matching left an right barcode to either CTGTCA-21xN-CCCGGG (Hth-R) or TGACAG-21xN-CCCGGG (Hth-F).
ChIP-Seq: Deposited fastq files contain the merged and demultiplexed files from the four separate NextSeq 500 sequening lanes.
Files were aligned using bowtie-2 to the D. melanogaster genome version dm6.
Aligned sam files were next converted into bam files, sorted and cleared from duplicate reads using the samtools functions view, sort and rmdup. The sorted bam files containing unique reads were indexed (Samtools: index) and converted into bigwig files using the bamCoverage function from the Deeptools suite with parameters -bs 1 -e 125.
Peaks were called using the MACS2 function callpeak with input samples as control and parameters -g dm -q 0.01 --nomodel --extsize 125
ATAC-seq: like ChIP-seq but without removing duplicates.
RNA-seq: Raw, paired-end fastq files were aligned using hisat-2 to the D. melanogaster genome version dm6. Sam files were converted into bam files before loading into R for further processing.
Hi-C: Hi-C data were processed using the juicer toolbox provided by the Lieberman-Aiden lab (https://github.com/aidenlab/juicer). Cut files were generated in python using the D. melanogaster genome version dm6 and the restriction site for DpnII.
Genome_build: dm6
Supplementary_files_format_and_content: processed data files contain bigwig coverage tracks for all IP and input samples at 1 bp resolution with reads extended by 125bp. The wild-type Exd-V5 peak file used in the study is provided as a bed file containing the peak summit genome coordinates.  The output of the juicer tool program  is provides as a .hic file with resolution for 5000,100,50,25,10 and 5Kb resolution and MAPQ>30 cutoff.  No processed data are available for SELEX-seq or RNA-seq.

organism: Drosophila melanogaster

growth_protocol: ChIP-seq,ATAC-seq, wild-type RNA-seq & Hi-C: D. melanogaster larvae were grown at 25℃ on molasses food for 5-6 days.  DeGradFP RNA-seq: D. melanogaster larvae were grown at 18℃ on yeast food for 6-7 days, followed by 24 hours at 29℃.

extract_protocol:
SELEX-seq: All samples were assembled at RT for 30 mins. Procedures followed as described previously (Slattery, Cell, 2011; Kribelbauer, Cell Rep, 2017). ChIP-seq: Inverted larvae were cross-linked at room temperature (RT) for 10 min in 10 ml 1% formaldehyde solution buffered with 50mM HEPES (pH=8.0). Samples were quenched with 1 ml 2.5M Glycine and washed for 5 minutes in quench-solution (125 mM glycine, in 1X PBS and 0.01% Triton X-100). Inverted and cross-linked larvae were washed twice with Buffer A (10mM HEPES, pH=8.0; 10mM EDTA, pH=8.0, 0.5mM EGTA, pH=8.0; 0.025 % Triton-X) and twice with Buffer B (10mM HEPES, pH=8.0; 200mM NaCl, 1mM EDTA, pH=8.0; 0.5mM EGTA, 0.01 % Triton X-100). Wing discs were detached on ice in Buffer B and transferred into a final volume of 1 ml Buffer C (10mM HEPES, pH=8.0 ;1mM EDTA, pH=8.0; 0.5mM EGTA, pH=8.0). Chromatin was sheared into fragments by using a probe sonicator at 15 % amplitude (total time: 12 min with 15 seconds on and 40 second off intervals) and flash-frozen in liquid nitrogen for storage at -80℃ until further processing. Sheared chromatin was diluted in 5X RIPA dilution buffer (1x RIPA: 140mM NaCl; 10mM HEPES, pH=8.0; 1mM EDTA, pH=8.0; 1 % Glycerol; 1% Triton X-100; 0.1% DOC) and blocked with 10μg of the respective IgG-coated magnetic beads (Dynabeads, ThermoFisher) for 1h at 4℃. Beads were removed with a magnetic stand and supernatant was transferred into a new tube. 10 % of the sample was set aside to serve as an input control. Specific antibody and 1 % of Bovine Serum Albumine (BSA) was added to the remaining chromatin and incubated over night at 4℃. 30 μg of IgG-coated and pre-blocked (with 1 % BSA) Dynabeads were added to each chromatin antibody solution and incubated for another 2 hours. Antibody-bound TF-chromatin complexes were isolated by magnetic separation (5 min on a magnetic stand) and beads were washed twice with 1x RIPA, once with high salt RIPA (500mM NaCl), once with LiCl-Buffer and once with TE (10 mM Tris-Base, pH=8.0; 1mM EDTA, pH=8.0). Beads with chromatin and the input sample were redissolved in 0.5 ml Elution-Buffer (TE with 0.5 % Sodium Dodecyl Sulfate (SDS) and 50mM NaCl) and incubated for 30 min at 37℃ with RNase, followed by 2 hours at 55℃ with proteinase K (ThermoFisher). Remaining DNA-protein complexes were decrosslinked by incubating for 16 hours at 65℃. DNA was separated from the Dynabeads by magnetic separation and purified by phenol:chloroform extraction and DNA precipitation using 1x volume of isopropanol in 100mM ammonium acetate and 1 μl glycogen. Precipitated DNA was redissolved in 30 μl TE. ATAC-seq: Wing imaginal discs of third instar larvae were dissected from a lab stock of yw genotype in Phosphate-Buffered-Saline. Discs were washed in nuclear extraction buffer (NEB, 10nM HEPES pH. 7.5, 2.5mM MgCL2, 10mM KCl) and placed in a 1mL dounce homogenizer (Wheaton) on ice. Discs were treated with 15 strokes of the loose pestle, followed by a 10 minute incubation on ice, then 20 strokes of the tight pestle. Nuclei were counted using a hemocytometer, and 50,000 nuclei were transferred to a fresh Eppendorf containing 1mL of NEB buffer +0.1% tween-20. Following a brief mixing the nuclei were immediately pelleted for 10 min at a speed of 1000xg. The pellet was re-suspended in ATAC transposition buffer as in (Buenrostro et al., 2015) and tagmentation was carried out as previously described (Buenrostro et al., 2015). Amplified libraries were purified, and size-selected using  ampureXP (Beckman) beads for  a double-sided selection. RNA-seq: Discs were dissected on ice in BPS with 0.5% BSA and transferred to 350 μl of RLT buffer (Qiagen) with 1% β-mercaptoethanol (BME).   Discs were homogenized with a plastic pestle.  100 μl PBS and 250 μl Ethanol was added and RNA was purified using the Qiagen RNeasy mini kit. RNA was treated with DNaseI for 30 min at 37 ℃, followed by another column purification (Qiagen’s RNeasy micro kit).  Hi-C: Wing imaginal discs of third instar larva were dissected from the tub-exd-wt-V5 homozygous stock and incubated with 1 μg/ml of papain enzyme in 200 μl of Schneider’s medium for 15 min at RT to generate a single-cell suspension.  The dissociation reaction was quenched by adding 800 μl of Schneider’s medium with 10% Fetal Bovine Serum (FBS).   The cell suspension was pelleted at 600g (5 min at 4℃).  Immediately after the dissociation, cells were cross-linked in 1% methanol-free formaldehyde solution for 10 min at RT and processed further as described in Monahan et al. (PMID: 30626972).
Extrated SELEX-seq libraries were amplified using Illumina compatible amplification primers (Illumina small RNAseq or NEBNext Mulitplex Oligos). ChIP-seq and ATAC-seq libraries were constructed using the NEBNext Ultra DNA Library Prep Kit for Illumina with NEBNext Mulitplex Oligos (one separate index per sample) following standard instructions. Libraries were sequenced either at the NY Genome Center (HiSeq-2000) or at Columbia University (NextSeq 500, 75 bp kit). RNA-seq libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina Sequencing (NEB EE7760S) following the instruction for the use with the Poly(A) mRNA magnetic isolation module. Hi-C libraries were constructed using Nugen’s Ovation Ultralow System V2.Libraries were sequenced either at the NY Genome Center (HiSeq-2000) or at Columbia University (NextSeq 500, 75 or 150 (for paired-end samples) bp kit).

value: brain


title: MII oocyte_MII_wildtype_3

value: unfertilized oocyte


title: Sample_101pre_3

description:
replicate #1
3214-SJC-0193


title: MII oocyte_MII_wildtype_2


title: RNA_seq_Exd_V5_wt_brain_VNC_PE_rep2


title: LVC_rep2_l3

city: Bronx

first: Amit

last: Verma

state: NY

address: 1300 Morris Park Ave

department: Medicine

institute: Albert Einstein College of Medicine

data_processing:
Basecalls from Illumina HiSeq 2500 Sequencing System
Reads were mapped to hg19 reference with tophat (v2.0.13) with parameters: --no-coverage-search -p 3 -g 1
gene counts were generated with htseq (v0.6.1p1) using parameters: --strand=no
Genome_build: hg19
Supplementary_files_format_and_content: count files are tab delimited txt containing the number of reads mapped to each gene.

source_name: Ly1[b-cell lymphoma cellline]

extract_protocol:
Qiagen RNA Easy
RNA libraries were prepared for sequencing using standard Illumina Truseq protocols

value: ascorbic acid


title: RNA_seq_Exd_V5_wt_brain_VNC_PE_rep1


title: LVC_rep2_l2


title: RCMB020-E37NoMark

city: Uppsala

first: Fredrik

middle: Johansson

last: Swartling

address: Dag Hammarskjölds väg 20

department: Immunology, Genetics and Pathology

institute: Uppsala University

data_processing:
Base calling was performed using standard parameters in build-in software provided with the Ion Torrent Proton sequencer (Torrent suite ver.5.2.2).
Sequenced reads were mapped to hg19_AmpliSeq_Transcriptome_ERCC_v1 using standard parameters and build-in software provided with the Ion Torrent Proton sequencer  (Torrent suite ver.5.2.2).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file include gene symbol and raw counts.

source_name: PDX

extract_protocol:
RNA from fresh-frozen tumor biospy, alternatively from 10^6 cells, was extracted according to QUIAGEN RNEasy extraction protocol
Library was prepared according to Thermo Fisher Scientific protocol for AmpliSeq next generation sequencing application

tag: sample type


title: MII oocyte_MII_wildtype_1

tag: strain


title: MII oocyte_MII_wildtype_5


title: MII oocyte_MII_wildtype_4


title: H3K9me3_KO2_input

data_processing:
Reads were trimmed using Trimmomatic and the settings ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:20 HEADCROP:15 CROP:120 MINLEN:40 for H3K4me3 and SLIDINGWINDOW:4:20 HEADCROP:5 CROP:50 MINLEN:30 for H3K9me3 data
ChIP-seq reads were aligned to the mm10 genome assembly using bowtie2 (Langmead B, Salzberg S. Nature Methods. 2012, 9:357-359.) and the settings --local -X 2000 and sorted using samtools (Li et al, Bioinformatics. 2009, 15;25(16):2078-9).
Mapped reads were imported into EaSeq (Lerdrup et al, Nature Structural & Molecular Biology, 2016, 23, 349–357) for subsequent analysis and generation of wig-files.
Genome_build: mm10
Supplementary_files_format_and_content: Gzip compressed wig files generated using EaSeq (http://easeq.net); Scores represent fragments per kilobasepairs per million reads

source_name: MII oocytes

growth_protocol: MII oocytes were isolated from, crosslinked and frozen for Chip according to previously published protocol (PMID: 27626377)

value: MII oocytes


title: LVC_rep2_l1


title: LCO_rep2_l3

value: control


title: HB930_2

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina MethylationEPIC_v-1-0 DNA analysis BeadChip using standard Illumina protocol

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

data_processing: Illumina Genome Studio software; main result of the methylation assays is shown as a beta-value ranging from zero to one indicating 0 to 100% methylation for each interrogated locus

label: Cy3, Cy5

source_name: tumor biopsy

label_protocol: Standard Illumina protocol

extract_protocol: DNA from fresh-frozen tumor biospy, alternatively from 10^6 cells, was extracted according to QUIAGEN DNEasy Blood and Tissue extraction protocol

value: brain tumor biopsy


title: RCMB020-E371L


title: RNA_seq_Exd_V5_wt_wing_PE_rep1

value: wing imaginal disk


title: H3K9me3_WT2_input


title: RNA_seq_Exd_V5_R2AR5A_wing_deGradFP_PE_rep2

data_processing:
Library strategy: DeGradFP RNA-seq
SELEX-seq 16-bp libraries: Fastq files were reverse-complemented and both forward and reverse-complement read merged into one (fastx_reverse_complement -Q33 -z ; FASTX toolkit 0.0.12;Hannon lab). Next, fixed primer sites were trimmed using the following options: fastx_trimmer -Q33 -f 12 -l 41 –z (FASTX toolkit 0.0.12;Hannon lab). Kmer counting and relative affinity estimates were computed using the R package bioconductor.org/packages/SELEX. SELEX-seq 21-bp and 30bp libraries: Sequencing primer sequences were removed as part of the Illumina demultiplexing. For the 21-bp libraries both Hth-F and Hth-R Homothorax orientations are present in the same fastq and can be isolated by using the R package bioconductor.org/packages/SELEX and matching left an right barcode to either CTGTCA-21xN-CCCGGG (Hth-R) or TGACAG-21xN-CCCGGG (Hth-F).
ChIP-Seq: Deposited fastq files contain the merged and demultiplexed files from the four separate NextSeq 500 sequening lanes.
Files were aligned using bowtie-2 to the D. melanogaster genome version dm6.
Aligned sam files were next converted into bam files, sorted and cleared from duplicate reads using the samtools functions view, sort and rmdup. The sorted bam files containing unique reads were indexed (Samtools: index) and converted into bigwig files using the bamCoverage function from the Deeptools suite with parameters -bs 1 -e 125.
Peaks were called using the MACS2 function callpeak with input samples as control and parameters -g dm -q 0.01 --nomodel --extsize 125
ATAC-seq: like ChIP-seq but without removing duplicates.
RNA-seq: Raw, paired-end fastq files were aligned using hisat-2 to the D. melanogaster genome version dm6. Sam files were converted into bam files before loading into R for further processing.
Hi-C: Hi-C data were processed using the juicer toolbox provided by the Lieberman-Aiden lab (https://github.com/aidenlab/juicer). Cut files were generated in python using the D. melanogaster genome version dm6 and the restriction site for DpnII.
Genome_build: dm6
Supplementary_files_format_and_content: processed data files contain bigwig coverage tracks for all IP and input samples at 1 bp resolution with reads extended by 125bp. The wild-type Exd-V5 peak file used in the study is provided as a bed file containing the peak summit genome coordinates.  The output of the juicer tool program  is provides as a .hic file with resolution for 5000,100,50,25,10 and 5Kb resolution and MAPQ>30 cutoff.  No processed data are available for SELEX-seq or RNA-seq.

value: exd-GFP/y;Tub-GAL80-ts - UAS-DeGradFP/tub-exd-shapeMut-V5 ; headcase-GAL4/+


title: H3K9me3_WT1_input


title: DMB006-E34NoMark


title: LCO_rep2_l2


title: RNA_seq_Exd_V5_wt_wing_PE_rep3


title: H3K9me3_KO1_input

value: Kdm4a knockout (m-/p-)


title: LCO_rep2_l1


title: RNA_seq_Exd_V5_R2AR5A_wing_deGradFP_PE_rep1


title: A3-24-T


title: A6-11-T


title: DMB006-E342L


title: HB930


title: RNA_seq_Exd_V5_wt_wing_deGradFP_PE

value: exd-GFP/y;Tub-GAL80-ts - UAS-DeGradFP/tub-exd-WT-V5 ; headcase-GAL4/+


title: H3K9me3_KO1

value: H3K9me3 (Pool of Abcam#ab8898, Lot GR153112-1 and Abcam#ab176916)


title: LVC_rep1_l2


title: Hi-C_Exd_V5_wt_wing

description: chromatin contacts; DpnII


title: LVC_rep1_l3


title: A6-20-T


title: A6-10-T


title: RNA_seq_Exd_V5_wt_wing_PE_rep2


title: A3-33-T


title: H3K9me3_WT2


title: Sai2_2


title: RCMB028(11)-E311L


title: H3K9me3_KO2


title: RCMB028(11)-E311R


title: RCMB018(6?)-E641L

value: PDX-SHH


title: Sai2


title: LVC_rep1_l1


title: CTRL3_2


title: H3K9me3_WT1


title: DMB006(luc)-E181B


title: RCMB020-E372R


title: AF22


title: CTRL-10


title: LCO_rep1_l2


title: DMB006(luc)-E171R


title: H3K4me3_KO1_input


title: LCO_rep1_l1


title: A7-14-T

value: TUMOR hbNS (MYCN-T58A)


title: H3K4me3_WT2_input


title: Sai3


title: 4970_12_gTLE3_Enza_R3

city: Amsterdam

first: Sander

last: Palit

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
Deseq2 was used for RNA-seq data normalization.
The differential expression was based on the ratio of normalized read counts (FPKM, after library size correction).
An absolute fold-change threshold of 2 was used. Genes with a coverage <50 in both conditions were excluded from the analyses to prevent spurious results.
Genome_build: hg38
Supplementary_files_format_and_content: readcountfiles: tab-separated gene counts and gene annotation for all samples

source_name: LNCaP_sgTLE3 ENZ

growth_protocol: LNCaP cells harboring CRISPR constructs were cultured in RPMI (+10% FBS, +1% pen/strep) at 37C in 5% CO2.

extract_protocol:
RNA extraction using Trizol
Stranded RNA libraries were prepared for sequencing according to Illumina instructions

treatment_protocol: Cells were plated (500 000 cells / 10cm dish) in RPMI (+10% FBS, +1% pen/strep) at 37C in 5% CO2. Next day, enzalutamide (10 uM) or vehicle was added, and cells were cultured for 5 days (medium was refreshed daily) before harvesting using Trizol.

value: LNCaP

value: prostate cancer cell line

value: TLE3KO (sgTLE3)

value: 10 uM enzalutamide for 5 days


title: AF22_2


title: 4970_11_gTLE3_Enza_R2


title: H3K4me3_KO2

value: H3K4me3 (Pool of Millipore#04-745; Cell Signaling #9727 lot-2 and Cell Signaling #9751)


title: A7-11-T


title: H3K4me3_WT1_input


title: H3K4me3_KO1


title: T-43

value: TUMOR hbNS (MYCN-WT)


title: DMB012-E331R


title: T-38


title: 4970_9_gTLE3_UT_R3

source_name: LNCaP_sgTLE3 UT

value: vehicle for 5 days


title: T-40


title: H3K4me3_WT2

value: MII oocytes


title: A3-43T

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridized to Illumina MethylationEPIC_v-1-0 DNA analysis BeadChip using standard Illumina protocol

source_name: tumor biopsy (tumor)

extract_protocol: DNA from fresh-frozen tumor biopsy, alternatively from 10^6 cells, was extracted according to QUIAGEN DNEasy Blood and Tissue extraction protocol


title: H3K4me3_WT1


title: 4970_7_gTLE3_UT_R1


title: T-28

value: TUMOR hbNES (MYCN-WT)


title: 4970_6_gNT_Enza_R3

source_name: LNCaP_sgNT ENZ

value: control (sgNT)


title: T-30

value: TUMOR NES-2 (MYCN-WT)


title: A3-45T

value: brain tumor biopsy


title: A3-41T


title: 2LVC MspI (Ly1)

data_processing:
Library strategy: HELPGT
Images generated by the Illumina sequencer were analyzed by Illumina pipeline software (versions 1.3-1.4). Initial data processing was performed using the default read length of 36 bp, after which we isolated the sequences in which we found adapter-tags on the 3’-end, replaced the tag sequence with a poly(N) sequence of the same length), and re-ran the Illumina ELAND pipeline again on these sequences with the sequence length set at 27 bp (the 2-28 bp subsequence).
The data within the ELAND_extended.txt files were used for counting the number of aligned sequences adjacent to each CCGG (HpaII/MspI) site annotated in the hg19 freeze of the human genome at the UCSC genome browser. We permitted up to two mismatches in each sequence, and allowed a sequence to align to up to a maximum of 10 locations within the genome. For non-unique alignments, a sequence was assigned a partial count for each aligment location amounting to 1/n, where n represents the total number of aligned positions.
Genome_build: hg19
Supplementary_files_format_and_content: Hcount format; col1:  unique identifier for CCGG site;  col2: chromosome; col3: base position; col4: #reads mapped to this location on the forward strand; col5: #reads mapped to reverse strand; col6: #total reads mapped

extract_protocol: Genomic DNA from cell lines were isolated by Puregene Core Kit A (Qiagen) Two custom adapters were created for HELP-tagging, referred to as AE and AS. As well as an Illumina adapter sequence, adapter AE contains an EcoP15I recognition site and a T7 promoter sequence. Adapter AS contains an Illumina sequencing primer sequence. Five micrograms of genomic DNA were digested with HpaII and MspI in separate 200 μl reactions and purified by phenol/chloroform extraction followed by ethanol precipitation. The digested genomic DNA was ligated to adapter AE using an NEB Quick Ligation Kit (25 μl of 2x Quick ligase buffer, 3 μg of HpaII-digested DNA or 1 μg of MspI-digested DNA, 0.1 μl of Adapter AE (1 μM), 3 μl of Quick Ligase in a final volume of 50 μl). After AE ligation, the products were purified using AMpure (Agencort), then digested with EcoP15I (NEB). The restriction fragments were end-repaired to inhibit to dimerization of adapters, and tailed with a single dA, at the 3’ end. After the dA tailing reaction, adapter AS was ligated to the dA-tailed fragments using an NEB Quick Ligation Kit (25 μl of 2x Quick ligase buffer, 2.5 μl of Adapter AS (10 μM), 2.5 μl of Quick Ligase in a final volume 50 μl). After ligation, products were purified using the MinElute PCR purification kit (Qiagen) and in vitro-transcribed using MEGAshortscript (Ambion). Following in vitro transcription, products were purified with an RNeasy clean-up kit (Qiagen) before reverse transcription was performed using the SuperScript III kit (Invitrogen). The first strand cDNA produced was used as a template for PCR using the following conditions: 96°C for 2 minutes, then 18 cycles of 96°C for 15 seconds and 72°C for 15 seconds followed by 5 minutes at 72°C for the final extension. After PCR, the library was purified using a QIAQuick PCR clean-up kit (Qiagen).

tag: protocol

value: MspI

value: ascorbic acid

value: b-cell lymphoma


title: 2LVC HpaII (Ly1)

value: HpaII


title: 2LCO MspI (Ly1)

value: control


title: 4970_5_gNT_Enza_R2

value: LNCaP


title: LCO_rep1_l3


title: 4970_8_gTLE3_UT_R2

value: prostate cancer cell line


title: 4970_4_gNT_Enza_R1


title: 4970_3_gNT_UT_R3

source_name: LNCaP_sgNT UT


title: T-29


title: 1LVC MspI (Ly1)


title: T-22