title: LNCaP cells - AR-pS81_rep2

city: Boston

first: Shaoyong

last: Chen

address: 330 Brookline Avenue

institute: Beth Israel Deaconess Medical Center

data_processing:
Raw reads from the AR ChIP-seq experiment were aligned to the NBCI Build hg19 of the human genome with Bowtie v2.3.5 with default parameters. Only reads with a mapping quality >q5 were retained.
sam files are converted to bam with samtools v0.1.18
Peak calling was performed on datasets with MACS v2.2.6 software.
Top 5,000 peaks of enhancer and promoter were identified, and then analyzed for de novo motif discovery in ChIP-seq using HOMER
Genome_build: hg19
Supplementary_files_format_and_content: bed files in which the 4th column represents the fold enrichment

source_name: LNCaP cells

growth_protocol: LNCaP cells were cultured in androgen-depleted CDS medium

extract_protocol:
For crosslinking: the cells in media were fixed by adding formaldehyde (1%, final concentration) and incubation at room temperature for 10min, followed by quenching with glycine at a final concentration of 0.2M. Wash cells twice with pre-chilled PBS, and then harvest in PBS. The nuclear fraction is extracted by first re-suspending the pellet in 10ml of LB1 buffer (50mM Hepes-KOH, pH7.5; 140mM NaCl; 1mM EDTA; 10% glycerol; 0.5% NP-40; 0.25% Triton X-100) for 10min at 4°C . Cells were pelleted, re-suspended in 10ml of LB2 buffer (10mM Tris-HCl, pH8.0; 200mM NaCl; 1mM EDTA; 0.5mM EGTA) and mixed at 4°C  for 5min. Cells were then pelleted and re-suspended in 300µl of LB3 buffer (10mM Tris-HCl, pH8.0; 100mM NaCl; 1mM EDTA; 0.5mM EGTA; 0.1% Na-Deoxycholate; 0.5% N-lauroylsarcosine) and sonicated with a waterbath bioruptor (Diagenode). Then 30µl of 10% Triton-X100 was added and the lysate was centrifuged for 10min at 20,000 rcf to separate debris. The supernatant was then subjected to pre-clearing and ChIP analysis.
ChIPseq libraries were prepared using Swift S2 Acel reagents on a Beckman Coulter Biomek i7 liquid handling platform from approximately 1ng of DNA according to manufacturer’s protocol and 14 cycles of PCR amplification. Finished sequencing libraries were quantified by Qubit fluorometer and Agilent TapeStation 2200.  Library pooling and indexing was evaluated with shallow sequencing on an Illumina MiSeq. Subsequently, libraries were sequenced on a NovaSeq targeting 30 million 50bp read pairs by the Molecular Biology Core facilities at Dana-Farber Cancer Institute.

treatment_protocol: The DHT (10nM) treatment conditions are: A1 (AR, DHT for 4hrs); A2 (AR, DHT for 8hrs); S1 (pS81, DHT for 4hrs); S2 and S3 (pS81, DHT for 8hrs)

value: LNCaP

tag: chip-antibody

value: treated with DHT for 8hrs


title: LNCaP cells - AR-pS81_rep3

status: Public on Feb 05 2021

type: SRA

state: MA

country: USA

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell line

tag: treatment


title: Y_KO_660

city: San Diego

first: Pura

last: Muñoz-Cánoves

state: CA

address: 5510 Morehouse Dr

institute: Altos Labs

library_source: transcriptomic

data_processing:
Total RNA sequenced reads were pseudoaligned to the mm10 reference cDNA using Salmon v1.4.0.
Single Cell RNA sequenced reads were aligned to the mm10 reference genome using 10X Genomics Cell Ranger v5.0.0.
Genome_build: mm10
Supplementary_files_format_and_content: Tar files with the output of Salmon, including quant.sf containing the TPM values
Supplementary_files_format_and_content: Tar files with raw and filtered gene matrices, features, and barcodes

molecule: total RNA

organism: Mus musculus

source_name: myeloid biased HSC

extract_protocol:
Total RNA was extracted by using MagMax96 total RNA isolation kit (Ambion, AM1830) according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using Nextera XT DNA Library Preparation Kit

tag: strain

tag: cell type

value: myeloid biased HSC

tag: genotype

value: Igf2bp2 KO

tag: age

value: 3 Months


title: Ebf2-EGFP E15pos cells scRNA-seq rep3

city: Shanghai

first: Jia

last: Li

address: No.67 chifeng road, yangpu district

country: China

institute: Tongji University

description: single cell RNA

data_processing:
Samples were sequenced on Illumina HiSeq2500 platform using 150 base paired-end reads. Sequencing reads were analyzed by Cell Ranger (v2.0.0).
The gene expression datasets were analyzed by Seurat (v2.0) and Monocle package.
Genome_build: mm10
Supplementary_files_format_and_content: csv files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: cerebral cortex

extract_protocol:
Ebf2-EGFP positive cells at E15.5 were dissociated, resuspended and purified by FACS, about eight embryos from two timed-pregnant mice were used in the experiments.
Approximately 3000 cells were processed for downstream reverse transcription, cDNA synthesis and library preparation according to 10× Genomics Chromium Single Cell protocol.

value: cortical Ebf2-EGFP+ cells

tag: tissue

value: cerebral cortex

tag: developmental stage


title: O_WT_194

value: Igf2bp2 WT

value: 23 Months


title: Ebf2-EGFP E15pos cells scRNA-seq rep1

description: single cell RNA


title: LNCaP cells - AR-pS81_rep1

value: treated with DHT for 4hrs


title: H3K27me3 ChIP-seq Ebf2-EGFP E15 pos cells replicate2

data_processing:
ChIP-seq data were aligned to mouse genome mm10, performing Bowtie v. 1.1.2 on the Galaxy platform with the following options: -v 3 –M 1 -5 15.
Resulting output SAM files were converted to BAM format, and finally converted to BED files.
Peaks were called using MACS (Model-Based Analysis of ChIP-Seq), with a p-value cutting off of 1e-5.
Genome_build: mm10
Supplementary_files_format_and_content: BED files are peak files, including PeakCount, MeanPeakLength, MedianPeakLength.

extract_protocol:
ChIP assays were performed using mouse Ebf2-EGFP positive cells dissociated at E11.5, E13.5, E15.5 and Ebf2-EGFP negative cells at E11.5, with antibodies against H3K27ac (Ab4729, Abcam) and H3K27me3 (Ab6002, Abcam) as previously described (Shen X, et al., 2009).
ChIP-Seq libraries were prepared using NEB Next Ultra Ⅱ ChIP-Seq Library Prep Kit (Cat#E7645S & Cat#7335S, NEB) according to the manufacturer's instructions.

tag: antibody

value: Ebf2-EGFP positive cells


title: H3K27me3 ChIP-seq Ebf2-EGFP E15 pos cells replicate1


title: 515-Control 1

city: Beijing

first: Lihua

last: Ding

address: 27th Taiping Rd, Haidian District

institute: Beijing Institute of Biotechnology

description: Breast cancer tissue of 69 aged female

data_processing:
Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5
FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced
Feature Counts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: Hisat2 v2.0.5
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: MCF7 cells

extract_protocol:
Total RNA was extracted with Trizol
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Breast cancer tissue

value: Treated with hypoxia for 0 hours


title: LNCaP cells - AR_rep2

value: AR


title: H3K27me3 ChIP-seq Ebf2-EGFP E13 pos cells replicate1


title: O_WT_159


title: H3K27me3 ChIP-seq Ebf2-EGFP E11 neg cells replicate2

value: Ebf2-EGFP negative cells


title: H3K27me3 ChIP-seq Ebf2-EGFP E11 neg cells replicate1


title: LNCaP cells - AR_rep1


title: sgAMBRA1_3

city: Stanford

first: Andrea

middle: Christine

last: Chaikovsky

state: California

address: 265 Campus Drive

institute: Stanford University

data_processing:
RNA qunatification done by salmon version 0.8.2
Differential expression analysis with DESeq2 version 1.22.2
Genome_build: human GRCh38
Supplementary_files_format_and_content: Salmon-generated *quant.tar.gz

molecule: polyA RNA

source_name: Cell line

growth_protocol: U2OS cells were cultured in DMEM medium supplemented with 10% bovine growth serum and 1% penicillin-streptomycin-glutamine. Cells were plated at equal density and cultured for 48 hours prior to RNA extraction.

extract_protocol:
Cells were flash frozen on dry ice and sent to Novogene for total RNA isolation and quality control.
Library preparation and sequencing were performed by Novogene using Illumina’s sequencing platform.

tag: cancer type

value: osteosarcoma

value: AMBRA1 knockout


title: H3K27me3 ChIP-seq Ebf2-EGFP E11 pos cells replicate1


title: O_KO_577


title: O_WT_370

value: 26 Months


title: Ebf2-EGFP E15pos cells scRNA-seq rep2

description: single cell RNA


title: H3K27ac ChIP-seq Ebf2-EGFP E15 pos cells replicate2


title: H3K27ac ChIP-seq Ebf2-EGFP E15 pos cells replicate1


title: sgAMBRA1_2


title: sgAMBRA1_1


title: H3K27ac ChIP-seq Ebf2-EGFP E13 pos cells replicate2


title: H3K27ac ChIP-seq Ebf2-EGFP E13 pos cells replicate1


title: H3K27me3 ChIP-seq Ebf2-EGFP E13 pos cells replicate2


title: H3K27ac ChIP-seq Ebf2-EGFP E11 neg cells replicate1


title: H3K27ac ChIP-seq Ebf2-EGFP E11 pos cells replicate2


title: H3K27me3 ChIP-seq Ebf2-EGFP E11 pos cells replicate2


title: O_KO_564


title: O_KO_481


title: H3K27ac ChIP-seq Ebf2-EGFP E11 pos cells replicate1


title: O_WT_382


title: sgCtrl_3

value: wild-type


title: O_KO_480

value: myeloid biased HSC


title: sgCtrl_1


title: ChIP-seq Input Ebf2-EGFP E15 pos cells replicate2

description: E15posH3K27ac_peaks.bed & E15posH3K27me3_peaks.bed

value: input


title: luminal cell-100

city: Wuhan

first: Weizhen

state: Hubei

address: 115#, Donghu road

department: Medical Research Institute

institute: Wuhan University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Mus_musculus.GRCm38.94
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: mammary gland

growth_protocol: FACS-sorted cells were resuspended at a density of 4 × 105 cells per milliliter in chilled 100% growth factor-reduced Matrigel (BD Bioscience), and the mixture was allowed to polymerize before covering with culture medium. Culture medium was changed every 24 h.

extract_protocol:
The 3D culture of basal and luminal cells was harvested. Total RNA was extracted using RNAiso plus (Takara). mRNA was then enriched by oligo (dT) beads. RNA sequencing libraries were generated using the KAPA Stranded RNA-Seq Kit for illumina with multiplexing primers, according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Either DMSO or 100μM baicalin is added into the culture medium.

value: luminal cell

value: mammary gland

value: wild type

value: baicalin


title: Apo E4, male, 21 days post injury

city: New York

first: Jens

last: Hansen

state: NY

address: 1425 Madison Ave

department: Department of Pharmacological Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Random read removal to remove read imbalances between samples
Read alignment with Star 2.5.4b, bowtie2 2.1.10, samtools 0.1.7
Identification of DEGs using Cuffdiff 1.3.0

source_name: Incomplete spinal cord injury

extract_protocol:
TRIzol reagent (ThermoFisher)
TruSeq RNA Sample Prep Kit v2 protocol (Illumina),

treatment_protocol: Incomplete spical cord injury after induction of anesthesia by inhalation of 3% isoflurane (50 kdyne contusion spinal cord injury)

value: Human ApoE4 Targeted Replacement Mice


title: luminal cell-DMSO

value: DMSO


title: ChIP-seq Input Ebf2-EGFP E15 pos cells replicate1

value: Ebf2-EGFP positive cells

value: cerebral cortex


title: basal cell-100

value: basal cell


title: sgCtrl_2


title: ChIP-seq Input Ebf2-EGFP E13 pos cells replicate2

description: E13posH3K27ac_peaks.bed & E13posH3K27me3_peaks.bed


title: Sterile_MTD_Mek53S_3

city: Princeton

first: Stanislav

middle: Y

last: Shvartsman

state: NJ

address: Carl Icahn Lab, Washington Road

department: Chemical and Biological Engineering

institute: Princeton University/ Lewis-Sigler Institute for Integrative Genomics

data_processing:
Sample was sequenced on SN387 with HiSeq Rapid SBS Kit v2 recipe for 83 cycles. Image analysis and base-calling was performed with RTA version 1.18.64.0.
Adapter sequence was trimmed with 1 mismatch allowed. Salmon 0.8.2 was run with --seqBias and --gcBias flags
Number of reads is converted to transcripts per million (TMP) by Salmon
Genome_build: dm6
Supplementary_files_format_and_content: Table of gene level quantification output from Salmon

organism: Drosophila melanogaster

source_name: embryo

extract_protocol:
Embryos were collected and stored in RNA-later, transferred to TriReagent, homogenized and run through a Zymo Direct-Zol RNA column
RNA libraries were prepared for sequencing using standard Illumina protocols
directional RNA-seq

value: unfertilized embryo


title: ChIP-seq Input Ebf2-EGFP E11 neg cells replicate2

description: E11negH3K27ac_peaks.bed & E11negH3K27me3_peaks.bed

value: Ebf2-EGFP negative cells


title: ChIP-seq Input Ebf2-EGFP E11 neg cells replicate1


title: Sterile_MTD_Mek53S_2


title: basal cell-DMSO


title: Wounded for 9 hr, and then treated with cycloheximide for 3 hr

type: RNA

city: Minamiminowa

first: Shinpei

last: Katou

state: Kamiina, Nagano

department: Faculty of Agriculture

country: Japan

institute: Shinshu University

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 825 ng of the corresponding Cy3- and Cy5-labeled fragmented cRNA were combined and hybridized overnight (17 hours, 65 °C) to Agilent Whole Tobacco Genome Oligo Microarrays 4x44K using Agilent’s recommended hybridization chamber and oven.

scan_protocol: Fluorescence signals of the hybridized Agilent Oligo Microarrays were detected using Agilent’s DNA microarray scanner (Agilent Technologies).

data_processing: The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files.

organism: Nicotiana tabacum

source_name: Tobacco plants transformed with empty vector

label_protocol: 100 ng of total RNA were labeled using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol.

growth_protocol: Plants were grown in pots containing vermiculite in a chamber maintained at 25°C with 16 h of light.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: Leaves were wounded for 9 hr, and then treated with cycloheximide for 3, 4.5 and 6 hr

tag: agent

value: treated with cycloheximide after wounding

value: 6- to 7-week-old

value: Leaves

source_name: Tobacco plants in which expression of WIPK and SIPK is suppressed by RNAi


title: Wounded for 9 hr, and then treated with cycloheximide for 6 hr


title: Wounded for 9 hr, and then treated with cycloheximide for 4.5 hr


title: Sterile_MTD_Mek53S_1


title: NHS_NELFA_WT_REP1

city: Freiburg

first: Barbara

last: Hummel

address: Stübeweg 51

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

description: Slam-seq

data_processing:
Library strategy: Slam-seq
3'UTR annotations were taken from Gencode annotation release 31 and merged on a gene level. Adapters and polyA stretches were trimmed from raw reads using fastp. Trimmed reads were further processed with SlamDunk v0.3.4. "Slamdunk all" command was executed with default parameters except '-5 12 -n 100 -t 20 -m -rl 100 --skip-sam'.  Differential gene expression was done with DESeq2 using raw read counts with at least 2 T>C conversions. Size factors were calculated based on corresponding total read counts for global normalization.
Genome_build: hg38
Supplementary_files_format_and_content: slamdunk_mapped_filtered_tcount.tsv

source_name: HeLa

growth_protocol: HeLa cells were plated, and after 24 hours for experiment (1) NELF-A Wildtype was knocked down using Lipofectamine RNAiMAX with concurrent transfection with either NELF-A WT or NELF-A ΔIDR using Lipofectamine 3000, for experiment (2) scr siRNA and siZNF451 was used with Lipofectamine RNAiMAX all per manufacturers instructions. Media was changed 24 hours after transfection and/or knockdown.

extract_protocol:
RNA was extracted using Trizol per manufactures protocol, with addition of DTT, and protection from light during the procedure to prevent S-S cross-binding.
5 ug of RNA was used for SLAMseq modifications, as described in Herzog et. al. 2017. Briefly, Iodoacetamide (Sigma I1149) was conjugated to 4SU in a 50mM pH 8.0 phosphate buffer in DMSO/Water (1:1), the reaction was quenched with DTT and RNA was reprecipitated using Ethanol and NaOAc. Libraries were prepared using Quantseq 3’ mRNA-Seq Library Prep Kit (Lexogen).

treatment_protocol: Heat-shock and labeling was carried out 24 hours after the change of media (48 hours after transfection and/or knockdown) in the following manner: Cells were subject to heat shock at 43 degrees Celsius for 30 minutes, with labeling beginning 15 minutes into heat-shock with 200uM 4SU (Caymen Chemical 16373), after a total of thirty minutes of heat-shock, cells were returned to 37 degrees Celsius for 90 minutes of recovery. The total labeling time was 105 minutes.

value: HeLa

tag: condition

value: Non Heat-Shock


title: cb9-mycHEA_cl10_Myc

city: Milano

first: Mattia

last: Dalsass

state: MI

address: Via Adamello, 16

country: Italy

institute: IEO

data_processing:
Read filtering with fastx toolkit version 0.0.13.2: fastq_masker -Q33 -q 20 -r -N -v -i
Alignment to mm9 with bwa version 0.6.2; bwa aln -t 16 reffile -fastqfile| bwa samse -n 1 reffile - fastqfile | samtools view -q 1 -ut reffile - |samtools sort - bamfile
Removing duplicate reads: samtools rmdup -sS bamfile
Peak calling with MACS version 2.0.10; macs2 -t samplebam -c inputbam --mfold=7 30 -g mm -p 0.00001 or macs2 -t samplebam -c inputbam -f BAMPE --mfold=7 30 -g mm -p 0.00001
Genome_build: mm9
Supplementary_files_format_and_content: bed files with enriched regions

source_name: immortalized fibroblasts

growth_protocol: All the cell lines used in this work were grown in DMEM, supplemented with 10% fetal bovine serum, 2 mM L-glutamine and 1% penicillin/streptomycin. For the cb9Δmyc and the cb9-mycHEA cell lines, medium was also complemented with doxycycline (1 µg/ml) to keep the tet-Myc transgene expressed, unless otherwise specified.

extract_protocol:
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 250 bp were immunoprecipitated using different antibodies.
Libraries were prepared for Illumina sequencing using a standard protocol consisting in blunting, addition of dA overhangs, ligation of Illumina adapters, selection with AMPure beads and PCR with index primers.

value: cb9 fibroblastst

value: MYC HEA mutation (knock in)

value: OFF Dox for 24h

tag: chip antibody

value: c-Myc N262 (Santa Cruz sc764)


title: ChIP-seq Input Ebf2-EGFP E11 pos cells replicate2

description: E11posH3K27ac_peaks.bed & E11posH3K27me3_peaks.bed

value: input


title: ChIP-seq Input Ebf2-EGFP E11 pos cells replicate1


title: NHS_NELFA_WT_REP2

description: Slam-seq


title: NHS_NELFA_dIDR_REP2

description: Slam-seq


title: NHS_NELFA_dIDR_REP3

description: Slam-seq


title: Sterile_MTD_Dsor_2

value: MTD>MEK


title: HS_NELFA_WT_REP3

description: Slam-seq

value: Heat-Shock


title: Sterile_MTD_Dsor_3


title: NHS_NELFA_dIDR_REP1

description: Slam-seq


title: cb9-mycHEA_cl33_Myc


title: P1 cortex single cell RNA-seq

first: Guoping

last: Liu

address: 138 Yi Xue Yuan Road

institute: Fudan University

data_processing:
sc ATAC-seq: Cell ranger-ATAC pipeline software was used for base-calling, and alignment. SCALE pipeline was used for filtering, ZINBA software was used for peak calling
ScRNA-seq: Cell ranger pipeline was used for base-calling, aligment and filtering.
Seurat was used for further analyse.
Genome_build: mm10
Supplementary_files_format_and_content: matrix data containing raw counts for all cells in scRNA-seq
raw peaks for all single cells for scATAC-seq data

source_name: mouse cortex

extract_protocol:
Chromium single cell ATAC library and single cell RNA libraries were prepared for sequencing using standard 10X genomics protocols
single cell RNA-seq and single cell ATAC-seq

treatment_protocol: IS mouse were electroperated with pCAG-Cre plasmid and the cortex were harvested at P1 through FACS for scRNA-seq. For scATAC-seq, GFP+ cell were from FACS sorted E18.5 hGFAP-GFP cortex.

value: cortex


title: NHS_NELFA_WT_REP3

description: Slam-seq


title: ChIP-seq Input Ebf2-EGFP E13 pos cells replicate1

value: Ebf2-EGFP positive cells

value: cerebral cortex


title: 3721_9_EtBr_3

city: Amsterdam

first: Heinz

last: jacobs

address: Plesmanlaan 121

country: Netherlands

institute: NKI

data_processing:
The 65 bp single end reads were mapped to the aligned against the mouse reference genome (Ensembl build 38) using TopHat (version 2.1.0).
TopHat was supplied with a known set of gene models based on Ensembl GTF version 77 and was guided to use the first-strand as the library-type. As additional parameters --prefilter-multihits and –no coverage were used.
Genecounts were generated using a custom script, Itreecount (https://github.com/NKI-GCF/itreecount)
Genome_build: Ensembl GRCm38
Supplementary_files_format_and_content: Tab-separated file with number of reads per gene/sample.

source_name: DDT_lymphomas (p53-/- : pcnaK164R/delta WT): DOI: 10.18632/oncotarget.24785

growth_protocol: DNA damage tolerant (DDT) lymphomas were cultured in RPMI medium supplemented with 8% of Fetal Bovine Serum (FBS), 100 U/ml Penicillin, 100 µg/ml Streptomycin, 50 µM 2-Mercaptoethanol, 200 µM L-arginine (DOI: 10.18632/oncotarget.24777 ).

extract_protocol:
After the treatment, the cells were lysed in Trizol and frozen for subsequent processing. The complete procedure was repeated to generate three biological replicates.
Strand-specific cDNA libraries were generated using the TruSeq Stranded mRNA sample preparation kit (Illumina) according to the manufacturer’s protocol.

treatment_protocol: DDT lymphoma cells were plated (107 cells) in Petri dishes and treated with ABZ (400 nM), EtBr (400 nM) or mock treated for 12 hrs.

value: Thymic  lymphomas

value: Ethidium bromode (400 nM)


title: E18 cortex single cell ATAC-seq


title: Sterile_MTD_Dsor_1

value: unfertilized embryo


title: cb9-mycWT_cl10_Myc

value: WT


title: AML cell line_U937_sgILF3_rep3

first: Elizabeth

middle: Anne

last: Tindall

address: 10300 Campus Point Dr., Suite 100

institute: Bristol Myers Squibb

data_processing:
Fastq converted sequence files were adapter and quality trimmed using Cutadapt v1.15
mRNA reads were aligned to human genome version hg38using STAR v2.5
Aligned reads were annotated to a flattened exon file based on Gencode v24 annotation was prepared using the python script, “dexseq_prepare_annotation.py” provided with R package DEXSeq
The “featureCounts” function from Subread v1.6.2 package was used to generate exon bin counts
Genome_build: hg38
Supplementary_files_format_and_content: Read counts per non-overlapping exon region in text file format
Supplementary_files_format_and_content: tab separated list of Ensembl gene ID, chromosome, region start, region end, gene strand, region length, region raw read count

source_name: AML cancer cell line

growth_protocol: U937 cell lines were maintained in Roswell Park Memorial Institute (RPMI) 1640 tissue culture medium (Invitrogen) supplemented with 10% FBS, 1X sodium pyruvate, 1X non-essential amino acids, 100 U/mL penicillin, and 100 µg/mL streptomycin. U937 cells grown in flasks with agitation during the CRISPR screen were supplemented with 1X Pluronic F-68 Non-ionic surfactant (ThermoFisher). When applicable, Puromycin (Thermo Fisher), Blasticidin (Thermo Fisher) or Hygromycin (Thermo Fisher) was added to the cell culture medium at 1-2 μg/ml, 10-50 μg/ml, or 250-500 μg/ml, respectively.  All cell lines were cultured at 37ºC under an atmosphere of 5% CO2 in a humidified cell incubator.

extract_protocol:
Total RNA was extracted from cell pellets using the RNeasy Mini Kit, followed by mRNA isolation via poly-A selection.
Purified mRNAs were fragmented and converted to 1st strand cDNAs with reverse transcriptase. The resulting 1st strand cDNAs were converted to double stranded cDNAs, and subjected to end-repair, A-tailing, and adapter ligation. The libraries were amplified and sequenced using Illumina’s HiSeq 4000 (2x150bp configuration, single index, per lane).

treatment_protocol: U937 cell lines were transduced with plenti-EF1α-Cas9-P2A-Blast, followed by Blasticidin selection to establish Cas9-expressing cell lines. U937-Cas9 cells were transduced with plenti-H1TO-EF1a-HTLV-TetR-P2A-RFP-P2A-Puro vectors expressing non-targeting control sgRNA or gene-specific sgRNAs targeting ILF3 to generate stable, doxycycline-inducible sgRNA cell lines. U937-Cas9 cells expressing inducible sgNT-1 or sgILF3-2 were treated with or without 1 µg/ml of doxycycline in triplicate for 5 days.

value: human AML cancer cell line

tag: crispr guide target

tag: treatment group


title: cb9-mycWT_cl6_Myc


title: 3721_8_ABZ_3

source_name: DDT_lymphomas (p53-/- : pcnaK164R/delta WT): DOI: 10.18632/oncotarget.24784

value: Albendazole (400 nM)


title: sgAMBRA1#1 c1

data_processing:
RNA qunatification done by salmon version 0.8.2
Differential expression analysis with DESeq2 version 1.22.2
Genome_build: human GRCh38
Supplementary_files_format_and_content: quant.sf files are tab delimited text files

growth_protocol: U937 cells were cultured in RPMI-1640 medium supplemented with 10% bovine growth serum and 1% penicillin-streptomycin-glutamine. Cells were plated at equal density and cultured for 48 hours prior to RNA extraction.

value: lymphoma

value: AMBRA1 knockout


title: HS_NELFA_WT_REP1

description: Slam-seq

value: HeLa


title: AML cell line_U937_sgILF3_rep2


title: 3721_7_Control_3

description: DDT_Lymphomas_Control_treatment_Replicate3

source_name: DDT_lymphomas (p53-/- : pcnaK164R/delta WT): DOI: 10.18632/oncotarget.24783


title: cb9-mycHEA_cl10_input

value: cb9 fibroblastst

value: MYC HEA mutation (knock in)

value: OFF Dox for 24h


title: AML cell line_U937_sgILF3_rep1


title: HS_NELFA_dIDR_REP2

description: Slam-seq


title: cb9Δmyc_RA_Myc

value: infected with QCXIH-Myc RA

value: c-Myc N262 (Santa Cruz sc764)


title: 3721_6_EtBr_2

source_name: DDT_lymphomas (p53-/- : pcnaK164R/delta WT): DOI: 10.18632/oncotarget.24782


title: HS_NELFA_dIDR_REP1

description: Slam-seq

value: Heat-Shock


title: 3721_4_Control_2

description: DDT_Lymphomas_Control_treatment_Replicate2

source_name: DDT_lymphomas (p53-/- : pcnaK164R/delta WT): DOI: 10.18632/oncotarget.24780


title: AML cell line_U937_sgNT_rep3

value: Non Targeting (NT)

value: Control


title: mouse aorta crtl, biological rep2

city: Bad Nauheim

first: Thomas

last: Boettger

state: Hessen

address: Ludwigstr. 43

department: Cardiac Development

institute: MPI for Heart and Lung Research

description: Gene expression data from ctrl aorta

hyb_protocol: Nucleic acid hybridization was performed following Affymetrix instructions.

scan_protocol: Array scanning was performed using a GeneChip Scanner 3000 7G.

data_processing: Data were processed using the GeneChip™ Expression Console Software. Summarization and Normalization were performed using the RMA algorithm of Arraystar software.

label: biotin

source_name: aorta of mice

label_protocol: RNA was labelled using the Affymetrix GeneChip WT protocol following the manufacturer's instructions.

growth_protocol: Aorta was isolated from ANF-Cre positive / BMP10 loxP/loxP / BMP9-/- (BMP9/10 dKO) mice. ANF-Cre negative BMP10 loxP/loxP mice were used as controls.

extract_protocol: RNA was isolated using TRIZOL (Invitrogen) according to the manufacturer's protocol.

treatment_protocol: Aorta was dissected from animals immediately after killing.

value: Ctrl


title: mouse aorta BMP9/10 dKO, biological rep2

description: Gene expression data from BMP9/10 deficient aorta

value: BMP9/10 dKO


title: 3721_5_ABZ_2

source_name: DDT_lymphomas (p53-/- : pcnaK164R/delta WT): DOI: 10.18632/oncotarget.24781

value: Thymic  lymphomas


title: cb9Δmyc_HEA_Myc

value: infected with QCXIH-Myc HEA


title: 3721_3_EtBr_1

source_name: DDT_lymphomas (p53-/- : pcnaK164R/delta WT): DOI: 10.18632/oncotarget.24779

value: Ethidium bromode (400 nM)


title: mouse aorta crtl, biological rep1

description: Gene expression data from ctrl aorta


title: cb9Δmyc_WT_Myc

value: infected with QCXIH-Myc WT


title: HS_NELFA_WT_REP2

description: Slam-seq


title: cb9Δmyc_EV_Myc

value: infected with empty vector


title: AML cell line_U937_sgNT_rep1

value: human AML cancer cell line


title: mouse aorta BMP9/10 dKO, biological rep1


title: cb9Δmyc_EV_Dox_Myc

value: with DOX 1 µg/ml


title: cirrhosis liver ECs

city: New Haven

first: Yasuko

last: Iwakiri

state: CT

address: 300 Cedar street

department: Section of Digestive Diseases

institute: Yale University School of Medicine

description:
Barcoded cDNA
10X single-cell RNA seq

data_processing:
Preliminary standard analysis steps such as alignment and gene counting were performed based on Cell Ranger™ pipelines
Genome_build: mm10
Supplementary_files_format_and_content: csv file including count of each feature in each single cell

source_name: liver

extract_protocol:
Liver cell suspensions were obtained by collagenase perfusion and were spun down  to remove hepatocytes.  The supernatants were pelleted  and resuspended.  Isolated non-parenchymal cells (NPCs) were stained with SYTOX® Red to label dead cells and sent to FACS sorting.  Only live and GFP-positive cells were sorted with BD FACSAriaTM IIu .
Samples were prepared according to the instruction of 10x Genomics Single Cell 3, Reagent Kits v3. Single cell suspensions in RT Master Mix  were  loaded onto the 10x Genomics Single Cell A Chip to convert poly-adenylated mRNA into barcoded cDNA.  Barcoded cDNA was amplified by PCR to generate a sufficient mass for library construction.

treatment_protocol: Liver cirrhosis was induced by inhalation of vaporized carbon tetrachloride (CCl4) for 12 weeks.

value: liver

value: endothelial cells

tag: model

value: Liver cirrhosis

value: Cdh5-Cre+, mTmG +/+

value: 16 weeks


title: 3721_2_ABZ_1

source_name: DDT_lymphomas (p53-/- : pcnaK164R/delta WT): DOI: 10.18632/oncotarget.24778

value: Albendazole (400 nM)


title: AML cell line_U937_sgNT_rep2

value: Non Targeting (NT)


title: control liver ECs

description:
Barcoded cDNA
10X single-cell RNA seq

value: Control


title: cb9Δmyc_input

value: cb9 fibroblastst

value: OFF Dox for 24h


title: 3721_1_Control_1

description: DDT_Lymphomas_Control_treatment_Replicate1

source_name: DDT_lymphomas (p53-/- : pcnaK164R/delta WT): DOI: 10.18632/oncotarget.24777

value: Thymic  lymphomas


title: with DEX pretreatment, reoxygenation time is 24 h

city: Urayasu

first: Yui

last: Yamane

state: Chiba

address: 2-1-1 Tomioka

institute: Juntendo University Urayasu Hospital

description:
Gene expression data from human astrocytes with DEX pretreatment and reoxygenated for 24 h
HAD 24 h

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Gene Spring v14.9.1 (Agilent) using Affymetrix default analysis settings and global scaling as normalization method. A given gene was analyzed if its normalized intensity was more than 0.2.

source_name: human astrocytes after DEX pretreatment, OGD exposure and reoxygenation for 24h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: HA were  maintained in astrocyte medium (ScienCell Research), calculated the number and disseminated in 6 well plate with 5×103 cells/cm2 each well.

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

treatment_protocol: HA were incubated with or without 5 nM DEX for 1h. After washing with PBS, cells were resuspended in glucose-free DMEM and placed in an anaerobic chamber. Anoxia was initiated by transferring cell cultures to a modular incubator chamber  MIC-101 (Billups-Rothenberg) and flushing with a preanalysed gas mixture 95 % N2 / 5 % CO2 (Nippon Megacare Co.) for 15 min along with bubbling the cell culture with the same gas at a flow rate of 3 L/min. Then, the cells were further incubated in the anaerobic chamber for 4h at 37 ℃. After incubation, the cells were resuspended in the astrocyte medium, and further incubated in the normal atmosphere during 0, 2, 6, 12, 24 h. Total RNA was prepared from the HA by extraction with TRIzol reagent (Invitrogen)

value: astrocyte

value: brain


title: MYCN_only_2

status: Public on Feb 04 2021

city: Rochester

first: Hu

state: MN

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

institute: Mayo Clinic

data_processing:
Fastq files of pair-end RNA-Seq reads were aligned with Tophat 2.0.14  to the reference genome UCSC danRer10 using Bowtie2 2.2.6 with default parameters.
Gene level counts were obtained using featureCounts 1.4.6 from the subRead package with gene models from corresponding UCSC annotation packages.
Genome_build: danRer10
Supplementary_files_format_and_content: tab-delimited gene counts

organism: Danio rerio

source_name: zebrafish tumor

extract_protocol:
RNA was extracted from zebrafish tumors overexpressing MYCN alone or MYCN with knokcout of gas7. Total RNA was extracted using the Trizol reagent, as per manufacturer’s instructions. RNA integrity (RIN) was verified on an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and 100-200 ng of RNA (RIN ≥ 7.0) in a 5 μl volume was used for library preparation and RNA sequencing (RNAseq).
Paired-end sequencing libraries were prepared using the TruSeq Stranded Total Sample Preparation kit (Illumina) by the Mayo Clinic sequencing core facilities (Rochester, MN) followed by quality control, cluster generation and sequencing on the Illumina HiSeq 2000 platform. The reads were de-multiplexed and converted to FASTQ format using CASAVA software from Illumina (by the Mayo Clinic core).

value: peripheral sympathetic nervous system

value: MYCN overexpression only


title: NaCl_H3K9ac_ChIP_seq_Rep2

city: shanghai

first: yijing

last: zhang

address: 2005 Songhu Road

department: Biochemistry

data_processing:
Sequencing reads were cleaned with Trim Galore v0.4.4, Trimmomatic v0.36 and sickle, including removing bases with low quality score (<25) and irregular GC content, and cutting sequencing adaptors followed by filtering short reads.
The cleaned reads were mapped to International Wheat Genome Sequencing Consortium (IWGSC) RefSeq v1.0 using BWA 0.7.5a-r405  for ChIP-seq,  HISAT2 2.1.020 for RNA-seq data, all with default settings.
For ChIP-seq, MACS1.3.7 was used to identify read-enriched regions (peaks) with combined criteria: P value < 1e–5 and fold-change >32.  ChIP-seq data Target genes were defined as genes with a peak within or nearby the gene body (±2 kb).
For DAP-seq, MACS2.2.6 was used to identify protein binding sites (peaks). TF peaks which overlap with Halo peaks were removed. The top 6,000 peaks, ranked first by -log10(qvalue), then by fold enrichment, were used to discover novel DNA-binding motifs by MEME-ChIP in MEME software toolkit.
Genome_build: IWGSC RefSeq v1.0
Supplementary_files_format_and_content: In ChIP-seq, peak files were provided; In lncRNA-seq, read counts for genes (IWGSC RefSeq v1.0) were provided. In DAP-seq, peak files were provided.

organism: Triticum aestivum

source_name: Triticum aestivum 14-days-old seedlings

growth_protocol: 16h light, 8h dark, 22°C

extract_protocol:
Chromatin or RNA was extracted from 14-days-old seedlingss, using standard protocols. 2μg total RNA (rRNA depleted) were used to prepare lncRNA-seq，2.2 μg DNA extracted from the harvested seedlings were used to prepare ChIP-seq. For DAP-seq, genomic DNA was extracted from leaves (14-days-old). 5μg gDNA was used to prepare DAP-seq library.
Library construction and deep sequencing were performed by Genergy Biotechnology Co. Ltd. (Shanghai, China) using Illumina HiSeq 2000/2500 system (Illumina) to produce 150-bp paired-end reads.
For DAP-seq, genomic DNA was extracted from wheat leaves using Plant DNAzol Reagent (invitrogen) and fragmented. DNA was then end repaired using the End-It kit (Lucigen) and A-tailed using Klenow (3′–5′ exo-; NEB). Truncated Illumina Y-adapter was ligated to DNA using T4 DNA Ligase (Promega).

treatment_protocol: For hormone and NaCl treatments, germinated seeds were grown in Hoagland solution at 22 °C under long-days conditions for 7 days. The 7-day-old seedlings in Hoagland were treated with 100μm ABA, 100μm MeJA, 500μm SA and 150mM NaCl, respectively, followed by incubation for 7 days.

value: 14-days-old seedlings

tag: cultivar

value: Chinese Spring

tag: chip antibody manufacturer

value: Upstate

tag: chip antibody catalog #


title: Heat_H3K9ac_ChIP_seq_Rep2


title: Halo_DAP_seq

data_processing:
Library strategy: DAP-seq
Sequencing reads were cleaned with Trim Galore v0.4.4, Trimmomatic v0.36 and sickle, including removing bases with low quality score (<25) and irregular GC content, and cutting sequencing adaptors followed by filtering short reads.
The cleaned reads were mapped to International Wheat Genome Sequencing Consortium (IWGSC) RefSeq v1.0 using BWA 0.7.5a-r405  for ChIP-seq,  HISAT2 2.1.020 for RNA-seq data, all with default settings.
For ChIP-seq, MACS1.3.7 was used to identify read-enriched regions (peaks) with combined criteria: P value < 1e–5 and fold-change >32.  ChIP-seq data Target genes were defined as genes with a peak within or nearby the gene body (±2 kb).
For DAP-seq, MACS2.2.6 was used to identify protein binding sites (peaks). TF peaks which overlap with Halo peaks were removed. The top 6,000 peaks, ranked first by -log10(qvalue), then by fold enrichment, were used to discover novel DNA-binding motifs by MEME-ChIP in MEME software toolkit.
Genome_build: IWGSC RefSeq v1.0
Supplementary_files_format_and_content: In ChIP-seq, peak files were provided; In lncRNA-seq, read counts for genes (IWGSC RefSeq v1.0) were provided. In DAP-seq, peak files were provided.

source_name: Triticum aestivum leaves

value: leaves

value: Halo

value: Promega


title: MYCN_gas7mut_3

value: MYCN overexpression + gas7 knockout


title: MYCN_only_3


title: Dark_H3K9ac_ChIP_seq_Rep2


title: MeJA_H3K9ac_ChIP_seq_Rep2


title: MYCN_gas7mut_2


title: MYCN_gas7mut_1


title: MYCN_only_1


title: SA_H3K9ac_ChIP_seq_Rep2


title: Flood_H3K9ac_ChIP_seq_Rep2


title: Cold_H3K9ac_ChIP_seq_Rep2


title: S3 Small tumor

city: Houston

first: Richard

middle: Eric

last: Davis

state: TX

address: 7455 Fannin Street

institute: MD Anderson Cancer Center

description: replicate 3

hyb_protocol: Amplified cRNA was hybridized to Illumina mouse WG-6 version 2.0 mouse whole-genome arrays.

scan_protocol: As per Illumina instructions, with detection by Streptavidin-Cy3 conjugate.

data_processing: The non-normalized data were generated by GenomeStudio with background correction. The normalized data were generated from bead-level data by methods previously described (PMID: 20805315). In brief, bead-level values were quantile-normalized, adjusted by a model-based background correction method (PMID: 18450815), trimmed by the 3-MAD method employed by Illumina, and then averaged to give a single probe-level value. After this, the only probe results that are kept for the normalized matrix are those in which the detection p value is <0.05, in at least 25% of the samples.

source_name: B16 melanoma

label_protocol: 100 nanograms of total RNA was amplified and biotin-labeled through a two-round Eberwine procedure using MessageAmp II and Illumina TotalPrep RNA amplification kits (Ambion).

growth_protocol: C57BL/6 mice were inoculated with 400,000 cells of the syngeneic B16 melanoma cell line.

extract_protocol: Total RNA of dissected tumors was extracted using the RNAqueous kit (Ambion). The RNA quality was checked by using a Bioanalyzer 2100 instrument (Agilent).

treatment_protocol: After 8 days, mice developed tumors that were either small (10-20 mm2) or large (70-80 mm2). Tumors were excised and dissected free of surrounding normal tissue.

tag: cell line

value: B16 cell line

tag: strain

tag: tumor size


title: S1 Small tumor

description: replicate 1


title: L3 Large tumor

description: replicate 3


title: LD_Mut

city: Tianjin

first: Xuan

last: Ma

address: Binshui West Road

department: College of Life Sciences

institute: Tianjin Normal University

hyb_protocol: Affymetrix gene chip hybridization, washing, staining, and scanning were carried out according to manufacturer's instructions.

scan_protocol: GeneChips were scanned using Affymetrix Scanner 3000 with default settings.

data_processing: The microarray data were analyzed using MAS5 algorithm.

organism: Oryza sativa

source_name: hd1-3 mutant rice leaves,long day conditions

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

growth_protocol: 5-day-old seedlings of hd1-3 mutant and the wild-type Zhonghua11 after germination were grown in artificial climate chamber for 30 days. The growth conditions were set as 11.5 h light/ 12.5 h dark, 28℃ for short-day conditions and  15 h light/ 9 h dark, 28℃ for long-day conditions, respectively.

extract_protocol: Leaves of 35-day-old rice plants were collected. For short-day conditions, the samples were collected at 3 h after light; for long-day conditions, the samples were collected at 5 h after light. Total RNAs were extracted using TRIzol method and mRNAs were purified using mRNA purification kit.

tag: growth conditions

value: long day

tag: genotype

value: hd1-3 mutant


title: CS_stem_H3K9ac_ChIP_seq_Rep2

source_name: Triticum aestivum stems

tag: tissue

value: stems


title: LD_WT

source_name: wild-type rice leaves,long day conditions

value: wild type Zhonghua11


title: SD_Mut

source_name: hd1-3 mutant rice leaves,short day conditions

value: short day


title: L1 Large tumor

description: replicate 1


title: CS_spikelet(Feekes10)_H3K9ac_ChIP_seq_Rep2

source_name: Triticum aestivum booting spikelets

value: booting spikelets


title: L2 Large tumor

description: replicate 2


title: SD_WT

source_name: wild-type rice leaves,short day conditions


title: CS_Flag_H3K9ac_ChIP_seq_Rep2

source_name: Triticum aestivum flag leaves

value: flag leaves


title: NaCl_H3K4me3_ChIP_seq_Rep2

value: Abcam


title: MeJA_H3K4me3_ChIP_seq_Rep2


title: Heat_H3K4me3_ChIP_seq_Rep2


title: CS_leaf_H3K9ac_ChIP_seq_Rep2


title: S2 Small tumor

description: replicate 2


title: CS_flowering(Feekes10.5)_H3K9ac_ChIP_seq_Rep2

source_name: Triticum aestivum flowering spikelets

value: flowering spikelets


title: SA_H3K4me3_ChIP_seq_Rep2

value: 14-days-old seedlings


title: Dark_H3K27me3_ChIP_seq_Rep2

value: Chinese Spring


title: Cold_H3K27me3_ChIP_seq_Rep2

value: Upstate


title: CS_stem_H3K27me3_ChIP_seq_Rep2


title: Dark_H3K4me3_ChIP_seq_Rep2


title: Flood_H3K27me3_ChIP_seq_Rep2


title: NaCl_H3K27me3_ChIP_seq_Rep2


title: Heat_H3K27me3_ChIP_seq_Rep2


title: Cold_H3K4me3_ChIP_seq_Rep2


title: CS_flowering(Feekes10.5)_H3K27me3_ChIP_seq_Rep2


title: SA_H3K27me3_ChIP_seq_Rep2


title: Flood_H3K4me3_ChIP_seq_Rep2


title: CS_Flag_H3K4me3_ChIP_seq_Rep2


title: CS_spikelet(Feekes10)_H3K4me3_ChIP_seq_Rep2


title: CS_leaf_H3K4me3_ChIP_seq_Rep2

value: leaves


title: CS_flowering(Feekes10.5)_H3K4me3_ChIP_seq_Rep2


title: CS_stem_H3K4me3_ChIP_seq_Rep2


title: CS_leaf_H3K27me3_ChIP_seq_Rep2


title: CS_Flag_H3K27me3_ChIP_seq_Rep2


title: Heat_total_RNA_seq_Rep2


title: NaCl_total_RNA_seq_Rep2


title: MeJA_total_RNA_seq_Rep2


title: SA_total_RNA_seq_Rep2


title: Flood_total_RNA_seq_Rep2


title: Dark_total_RNA_seq_Rep2


title: CS_Stem_total_RNA_seq_Rep2


title: Cold_total_RNA_seq_Rep2


title: ABA_total_RNA_seq_Rep2


title: SA_H3K9ac_ChIP_seq_Rep1

extract_protocol:
Chromatin or RNA was extracted from 14-days-old seedlingss, using standard protocols. 2μg total RNA (rRNA depleted) were used to prepare lncRNA-seq，2.2 μg DNA extracted from the harvested seedlings were used to prepare ChIP-seq. For DAP-seq, genomic DNA was extracted from leaves (14-days-old). 5μg gDNA was used to prepare DAP-seq library.
Library construction and deep sequencing were performed by Genergy Biotechnology Co. Ltd. (Shanghai, China) using Illumina HiSeq 2000/2500 system (Illumina) to produce !Sample_extract_protocol_ch1 = For DAP-seq, genomic DNA was extracted from wheat leaves using Plant DNAzol Reagent (invitrogen) and fragmented. DNA was then end repaired using the End-It kit (Lucigen) and A-tailed using Klenow (3′–5′ exo-; NEB). Truncated Illumina Y-adapter was ligated to DNA using T4 DNA Ligase (Promega).


title: MeJA_H3K9ac_ChIP_seq_Rep1


title: Heat_H3K9ac_ChIP_seq_Rep1


title: NaCl_H3K9ac_ChIP_seq_Rep1


title: CS_Leaf_total_RNA_seq_Rep2


title: CS_Flag_total_RNA_seq_Rep2


title: CS_Sheath_total_RNA_seq_Rep2

source_name: Triticum aestivum sheaths

value: sheaths


title: CS_stem_H3K9ac_ChIP_seq_Rep1


title: ABA_H3K9ac_ChIP_seq_Rep1


title: Flood_H3K9ac_ChIP_seq_Rep1


title: Cold_H3K9ac_ChIP_seq_Rep1


title: ABA_H3K9ac_ChIP_seq_Rep2


title: Dark_H3K9ac_ChIP_seq_Rep1


title: CS_spikelet(Feekes10)_H3K9ac_ChIP_seq_Rep1


title: CS_flowering(Feekes10.5)_H3K9ac_ChIP_seq_Rep1


title: CS_sheath_H3K9ac_ChIP_seq_Rep1


title: CS_sheath_H3K9ac_ChIP_seq_Rep2


title: CS_leaf_H3K9ac_ChIP_seq_Rep1


title: CS_Flag_H3K9ac_ChIP_seq_Rep1


title: SA_H3K4me3_ChIP_seq_Rep1


title: NaCl_H3K4me3_ChIP_seq_Rep1


title: CS_flowering(Feekes10.5)_total_RNA_seq_Rep2


title: INA-6 replicate 2

type: genomic

city: Uppsala

first: Alba

last: Atienza-Párraga

state: Uppsala

address: Dag Hammarskjölds 20, Rudbecklaboratoriet-C11:3

department: Immunology, Genetics and Pathology

country: Sweden

institute: Uppsala University

description: untreated

hyb_protocol: The bisulfite converted DNA was eluted in 15μl according to the manufacturer´s protocol, evaporated to a volume of <4μl and and hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing: GenomeStudio 2.0

label: Cy3, Cy5

source_name: MM cell line

label_protocol: Standard Illumina labelling protocol

growth_protocol: The MM cell lines U1996 and INA-6 were cultured in RPMI-1640 AQmediaTM media (Sigma), with 1% GlutaMAX™-I X100 (Gibco) and antibiotics (streptomycin 50 mg/mL and penicillin 100 U/mL; Gibco). Cells were supplemented with IL-6. All cell lines were cultured at 37°C in a humidified 5% CO2 in-air atmosphere.

extract_protocol: Genomic DNA was extracted using the PureLink™ Genomic DNA Mini Kit (Invitrogen). Bisulphite conversion was performed using the EZ DNA MethylationTM Kit (Zymo Research #D5004) with 250 ng of DNA per sample.


title: MeJA_H3K4me3_ChIP_seq_Rep1


title: U1996 replicate 3

description: untreated


title: CS_flowering(Feekes10.5)_H3K4me3_ChIP_seq_Rep1


title: Flood_H3K4me3_ChIP_seq_Rep1


title: Heat_H3K4me3_ChIP_seq_Rep1


title: Cold_H3K4me3_ChIP_seq_Rep1


title: CS_stem_H3K4me3_ChIP_seq_Rep1


title: ABA_H3K4me3_ChIP_seq_Rep1


title: SA_H3K27me3_ChIP_seq_Rep1


title: CS_sheath_H3K4me3_ChIP_seq_Rep2


title: Dark_H3K4me3_ChIP_seq_Rep1


title: Flood_H3K27me3_ChIP_seq_Rep1


title: Heat_H3K27me3_ChIP_seq_Rep1


title: MeJA_H3K27me3_ChIP_seq_Rep1


title: MeJA_H3K27me3_ChIP_seq_Rep2


title: Dark_H3K27me3_ChIP_seq_Rep1


title: ABA_H3K4me3_ChIP_seq_Rep2


title: CS_spikelet(Feekes10)_H3K4me3_ChIP_seq_Rep1


title: NaCl_H3K27me3_ChIP_seq_Rep1


title: INA-6 replicate 3

description: untreated


title: U1996 replicate 1

description: untreated


title: CS_Flag_H3K4me3_ChIP_seq_Rep1


title: U1996 replicate 2

description: untreated


title: Cold_H3K27me3_ChIP_seq_Rep1


title: CS_stem_H3K27me3_ChIP_seq_Rep1


title: ABA_H3K27me3_ChIP_seq_Rep1


title: CS_leaf_H3K4me3_ChIP_seq_Rep1


title: CS_sheath_H3K27me3_ChIP_seq_Rep2


title: CS_spikelet(Feekes10)_H3K27me3_ChIP_seq_Rep1


title: CS_leaf_H3K27me3_ChIP_seq_Rep1


title: CS_Flag_H3K27me3_ChIP_seq_Rep1


title: INA-6 replicate 1

description: untreated


title: CS_sheath_H3K27me3_ChIP_seq_Rep1


title: CS_sheath_H3K4me3_ChIP_seq_Rep1


title: CS_seedlings_H3K27me3_ChIP_seq_Rep1


title: NaCl_total_RNA_seq_Rep1


title: Dark_total_RNA_seq_Rep1


title: MeJA_total_RNA_seq_Rep1


title: ABA_total_RNA_seq_Rep1


title: Cold_total_RNA_seq_Rep1


title: CS_flowering(Feekes10.5)_total_RNA_seq_Rep1


title: CS_Stem_total_RNA_seq_Rep1


title: CS_Spikelet(Feekes10)_total_RNA_seq_Rep1


title: CS_Spikelet(Feekes10)_total_RNA_seq_Rep2


title: CS_Leaf_total_RNA_seq_Rep1


title: ABA_H3K27me3_ChIP_seq_Rep2


title: CS_Sheath_total_RNA_seq_Rep1


title: CS_spikelet(Feekes10)_H3K27me3_ChIP_seq_Rep2


title: CS_Flag_total_RNA_seq_Rep1


title: CK_total_RNA_seq_Rep2


title: CS_flowering(Feekes10.5)_H3K27me3_ChIP_seq_Rep1


title: CK_total_RNA_seq_Rep1


title: SA_total_RNA_seq_Rep1


title: Heat_total_RNA_seq_Rep1


title: Flood_total_RNA_seq_Rep1


title: 20 Gy_24 h Case 3

city: Hefei

first: Lesha

last: Zhang

state: Anhui

address: 81 Meishan road

department: Physiology

institute: Anhui Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
The RNA sequencing (RNA-Seq) Fastq raw data were pruned using Trimmomatic to remove adaptors and lower mass reads. The quality of clean data was assessed using FastQC software. The quality-approved data were mapped to the reference genome of the rat (National Center for Biotechnology Information [NCBI] genome assembly, version Rnor_6.0) using HISAT2 (v2.0.13) and annotated with the annotation file (.gtf) NCBI Rnor_6.0.
The RNA-Seq quantification software Kallisto was used to obtain a count of known messenger RNAs (mRNAs) to compare the differences in transcript expression. Using the edgeR package software (http://bioconductor.org/packages/2.4/bioc/html/edgeR.html), the differences in the number of reads among samples were analyzed.
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text files include counts values for each Sample

organism: Rattus norvegicus

source_name: Brain microvascular endothelial cells

growth_protocol: The rats had free access to food and water and were house in a room with a 12-h light/dark cycle. The temperature of the room was maintained at 22–25 °C. Tissue attainment from the rats for the harvest of BMECs

extract_protocol:
A CLINIC600C linear accelerator (Varian, United States) was used to irradiate BMECs, at a rate of 2.5 Gy/min. Cells cultured to 60% confluence were irradiated with 5 Gy or 20 Gy. The x-ray source was 100 cm from the cells and had an irradiation range of 20 cm × 20 cm. The cells in the control group were not irradiated by x-rays, but received all other treatments that the x-ray–exposed group received. The primary cultured BMECs were divided into five groups: (1) unexposed controls; (2) 12 h after delivery of 5 Gy of radiation; (3) 24 h after delivery of 5 Gy of radiation; (4) 12 h after delivery of 20 Gy of radiation; and (5) 24 h after delivery of 20 Gy of radiation.
RNA was extracted using a commercially available kit (Vazyme Biotech Co., Ltd, Nanjing, China). BMECs with or without radiation exposure were digested and resuspended in lysis buffer RL1. The cell suspension was transferred to a genomic DNA filter column and centrifuged at 13000 × g for 2 min. The resulting supernatant was collected and buffer RL2 was added. The mixture was placed in an RNAPure column and centrifuged again. The precipitate was collected. Buffer RW1 and buffer RW2 were used to rinse the RNAPure columns. The columns were put into new RNase-free collection tubes. RNAase-free ddH2O (60 μL) was added to the central part of the columns. The columns remained at room temperature for 2 min to dissolve RNA, and were then centrifuged at 13000 × g for 1 min to elute RNA. A spectrophotometer was used to determine the purity and concentration of the extracted RNA. The optical density ratio of 260 nm to 280 nm was between 1.8 and 2.2, which met experimental requirements.

treatment_protocol: A gas mixture containing 100% oxygen and 2% isoflurane with the volume speed of 0.2 L/min was used to anesthetize rats. Then the rats were humanely killed by inhalation of excess carbon dioxide (CO2) and cleansed three times with 75% alcohol. All subsequent procedures were conducted under aseptic conditions. The brain and its cerebral hemispheres were removed and placed in a petri dish containing a sterile phosphate-buffered saline solution. The pia mater, surface blood vessels, and cerebral medulla were removed from the cerebral cortex. The harvested tissue was cut into pieces, homogenized into suspensions, and filtered through an 80-µm mesh screen. The resulting filtrate was then filtered through a 200-µm mesh screen. The oversize residue was collected and centrifuged at 1000 rpm for 5 min at 4 °C. The resulting precipitate was collected and digested with 0.2% type II collagenase (Sigma-Aldrich, St. Louis, MO, USA) in phosphate-buffered saline at 37 °C for 30 min and then centrifuged at 1000 rpm for 5 min at 4 °C. Finally, the obtained precipitate was resuspended in Endothelial Cell Medium containing 20% fetal bovine serum, 1% endothelial cell growth supplement, and 1% penicillin/streptomycin solution. The growth of other types of cells and impurities was reduced through the differential adhesion method, and the cell culture medium was replaced 4 h later. Cells were incubated at 37 °C in 5% CO2. The medium was replaced every 3 days.

tag: species

value: Spraque-Dawley

value: cerebral microvessels

tag: sample type

value: littermates, aged 2-3 weeks and weighing 10-43 g, sex in half

tag: model, treatment

value: 24 h cultured after radiation at dose of 20 Gy


title: 20 Gy_12 h Case 3

value: littermates, aged 2-3 weeks and weighing 10-31 g, sex in half

value: 12 h cultured after radiation at dose of 20 Gy


title: 5 Gy_24 h Case 1

value: littermates, aged 2-3 weeks and weighing 10-35 g, sex in half

value: 24 h cultured after radiation at dose of 5 Gy


title: 20 Gy_24 h Case 1

value: littermates, aged 2-3 weeks and weighing 10-41 g, sex in half


title: 20 Gy_24 h Case 2

value: littermates, aged 2-3 weeks and weighing 10-42 g, sex in half


title: 5 Gy_24 h Case 3

value: littermates, aged 2-3 weeks and weighing 10-37 g, sex in half


title: 5 Gy_12 h Case 2

value: littermates, aged 2-3 weeks and weighing 10-24 g, sex in half

value: 12 h cultured after radiation at dose of 5 Gy


title: 20 Gy_12 h Case 1

value: littermates, aged 2-3 weeks and weighing 10-29 g, sex in half


title: 5 Gy_12 h Case 1

value: littermates, aged 2-3 weeks and weighing 10-23 g, sex in half


title: Control 2

value: littermates, aged 2-3 weeks and weighing 10-21 g, sex in half

value: 12 h cultured without radiation


title: Control 1

value: Spraque-Dawley

value: littermates, aged 2-3 weeks and weighing 10-20 g, sex in half


title: AF_66W rep3

first: Xingyong

last: Chen

address: 130 Changjiangxilu

department: College of Animal Science and Technology

institute: Anhui Agricultural University

description:
3-A3_TTAGGC_L005
AF3_66W_FPKM

data_processing:
Raw data (raw reads) were processed using fastx(version:0.0.13). The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
Then the clean reads were mapped to reference genome using tophat(version:2.0.9).
FPKM value of each gene was calculated using cufflinks(version:2.1.1).
and the read counts of each gene were obtained.
DEGs were identified using the cufflinks Cuffdiff functions FoldChange and Fisher-test.
Genome_build: Anas_platyrhynchos.BGI_duck_1.0
Supplementary_files_format_and_content: FPKM values for each Sample with gene_id @ http://asia.ensembl.org/index.html

organism: Cairina moschata

source_name: abdominal fat_66 weeks

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany). Total RNA was quantified using a NanoDrop ND-2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: common name

value: Muscovy duck

tag: age

value: 66 weeks

value: abdominal fat


title: Control 3

value: cerebral microvessels

value: littermates, aged 2-3 weeks and weighing 10-22 g, sex in half


title: AF_35W rep1

description:
2-A1_CCGTCC_L004
AF1_35W_FPKM

source_name: abdominal fat_35 weeks

value: 35 weeks


title: AF_66W rep2

description:
3-A2_CGATGT_L005
AF2_66W_FPKM


title: AF_35W rep2

description:
2-A2_GTCCGC_L004
AF2_35W_FPKM


title: AF_35W rep3

description:
2-A3_GTGAAA_L004
AF3_35W_FPKM


title: AF_66W rep1

description:
3-A1_ATCACG_L005
AF1_66W_FPKM


title: AF_12W rep3

description:
1-A3_GATCAG_L003
AF3_12W_FPKM

source_name: abdominal fat_12 weeks

value: 12 weeks


title: AF_12W rep2

description:
1-A2_ACTTGA_L003
AF2_12W_FPKM


title: AF_12W rep1

description:
1-A1_CAGATC_L003
AF1_12W_FPKM


title: 5 Gy_24 h Case 2

value: littermates, aged 2-3 weeks and weighing 10-36 g, sex in half

value: 24 h cultured after radiation at dose of 5 Gy


title: 5 Gy_12 h Case 3

value: littermates, aged 2-3 weeks and weighing 10-25 g, sex in half


title: 20 Gy_12 h Case 2

value: littermates, aged 2-3 weeks and weighing 10-30 g, sex in half

value: 12 h cultured after radiation at dose of 20 Gy


title: In vivo grafted hESC-RPE and rabbit, rabbit 2

city: Lausanne

first: Gioele

last: La Manno

state: Vaud

address: Station 19

department: BMI

country: Switzerland

institute: EPFL

data_processing:
Cell Ranger 2.1.1 was used to convert Illumina base call files to FASTQ format.
Cell Ranger 3.1.0 was used to map FASTQ sequencing reads to the human GRCh38 reference transcriptome with the STAR aligner and to generate feature-barcode count matrices.
For cells isolated from rabbit retina were generated using a custom-built hybrid reference transcriptome combining both the human GRCh38 reference and the rabbit reference (Oryctolagus cuniculus 2.0.99, EMBL-EBI). FASTQ files were mapped to this hybrid reference with Cell Ranger 3.1.0 to generate count matrices. Reads were exclusively assigned either to a human or rabbit transcript.
The velocyto run10x command was used to produce loom files containing spliced and unspliced RNA count matrices
Downstream analyses, including dimensionality reduction and cell type annotation, were performed using both velocyto and scanpy in Python (version 3.7)
Genome_build: GRCh38 human reference, Oryctolagus cuniculus 2.0.99 EMBL-EBI rabbit reference
Supplementary_files_format_and_content: Processed data were stored in loom file format (http://loompy.org/) containing spliced and unspliced count matrices. For the human-rabbit cell mixture (rabbit1.tar.gz, rabbit2.tar.gz), processed data is provided as the 10X count matrices in mtx file format).

organism:
Homo sapiens
Oryctolagus cuniculus

source_name: In vitro hESC-derived culture grafted into albino rabbit retina, sorted

extract_protocol:
A rabbit eye with 30-day integrated hESC-RPE were enucleated and pigmented areas including neuroretina, choroid and RPE layer was dissected out, trimmed and mixed together in 500 uL of digestion buffer. Digestion buffer consisted of: 2mg/ml collagenase IV (ThermoFisher Scientific, 17104019), 120 U/μl DNase I (NEB, Sigma, 4536282001), and 1mg/ml papain (Sigma, 10108014001) in PBS. Eppendorfs containing the samples were rotated and incubated at 37°C on a thermocycler at 300g for 25 min until samples were homogenized. Samples were pipetted every 5 min to digest the tissue sample into single cells. Digestion was stopped by adding equivalent volume of 10% fetal bovine serum (ThermoFisher Scientific, 10082147) in PBS, the samples were filtered using a 30µm MACS Smart Strainer (Miltenyi, 130-098-458) followed by Dead Cell Removal kit (Miltenyi, 130-090-101) to remove dead cells and debris. The sample was stained with mouse anti-human HLA-ABC-FITC (1:20, BD Biosciences, 555552, clone [G46-2.6]), and anti-human HLA-ABC-positive cells were FACS-sorted as specified above, collected and resuspended to 1000 cells/uL in 1% BSA (Sigma, A1470-10g) in PBS for further scRNA-sequencing.
Cells were transported at 4°C to the Eukaryotic Single Cell Genomics Facility (ESCG, SciLifeLab, Stockholm, Sweden) where a 3’ cDNA library was prepared for single cell RNA sequencing (scRNA-seq) using the 10X Genomics platform and NovaSeq 6000 software.

tag: tissue/cell type


title: In vivo grafted hESC-RPE and rabbit, rabbit 1 [P13104_9002_S2_L002]

description:
P13104_9002_S2_L002
processed data file: rabbit1.tsv.mtx.tar.gz (linked to the *L001 sample records)

source_name: In vitro hESC-derived culture grafted into albino rabbit retina, unsorted

extract_protocol:
A rabbit eye with 30-day integrated hESC-RPE were enucleated and pigmented areas including neuroretina, choroid and RPE layer was dissected out, trimmed and mixed together in 500 uL of digestion buffer. Digestion buffer consisted of: 2mg/ml collagenase IV (ThermoFisher Scientific, 17104019), 120 U/μl DNase I (NEB, Sigma, 4536282001), and 1mg/ml papain (Sigma, 10108014001) in PBS. Eppendorfs containing the samples were rotated and incubated at 37°C on a thermocycler at 300g for 25 min until samples were homogenized. Samples were pipetted every 5 min to digest the tissue sample into single cells. Digestion was stopped by adding equivalent volume of 10% fetal bovine serum (ThermoFisher Scientific, 10082147) in PBS, the samples were filtered using a 30µm MACS Smart Strainer (Miltenyi, 130-098-458) followed by Dead Cell Removal kit (Miltenyi, 130-090-101) to remove dead cells and debris. Cells were finally resuspended to 1000 cells/uL in 1% BSA in PBS prior to scRNA-sequencing.
Cells were transported at 4°C to the Eukaryotic Single Cell Genomics Facility (ESCG, SciLifeLab, Stockholm, Sweden) where a 3’ cDNA library was prepared for single cell RNA sequencing (scRNA-seq) using the 10X Genomics platform and NovaSeq 6000 software.


title: In vivo grafted hESC-RPE and rabbit, rabbit 1 [P13104_9002_S2_L001]

value: In vitro hESC-derived culture grafted into albino rabbit retina, unsorted


title: AltRepop_24hr_1 [LH489_S21.R1.fastq.gz]

city: Irvine

first: Kim

last: Green

address: 3208 Biological Sciences 3

department: Neurobiology and Behavior

institute: University of California, Irvine

data_processing:
Illumina HiSeq 4000 was used to produce 50bp single-end reads.
Sequenced reads mapped to mm10 whole genome using STAR aligner.
featureCounts were calculated using function of the Rsubread package in R.
After filtering out low-count genes, count distributions were scaled using the calcNormFactors function of the edgeR package.
plotMDS function of the limma package in R was used to perform principal component analysis. Reads Per Kilobase of exon per Megabase of library size (RPKM)  were prepared and fitted to linear models using the voom and lmfit functions.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM values for all Samples

extract_protocol:
Brains were removed, microdissected into cortex, hippocampus, and thalamus/striatum, and flash frozen on dry ice.  RNA was extracted using Rneasy Mini Kit (Qiagen). cDNA synthesis, amplification, library construction and sequencing were performed by Novogene Inc. using Illumina NovaSeq and HiSeq platforms with paired-end 150 bp (PE 150) sequencing strategy.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: treatment

value: PLX

value: myeloid cells from whole hemispheres


title: AltRepop_24hr_3 [LH491_S23.R1.fastq.gz]


title: ControlAltRepop_24hr_3 [LH487_S19.R1.fastq.gz]

value: Vehicle


title: AltRepop_24hr_2 [LH490_S22.R1.fastq.gz]


title: AltRepop_24hr_4 [LH492_S24.R1.fastq.gz]


title: ControlAltRepop_24hr_4 [LH488_S20.R1.fastq.gz]


title: ControlAltRepop_24hr_2 [LH486_S18.R1.fastq.gz]


title: ControlAltRepop_24hr_1 [LH485_S17.R1.fastq.gz]


title: CR134aff7 Antagomir134

city: Dublin

first: Cristina

last: Reschke

address: 123 St Stephens Green, Dublin 2

country: Ireland

institute: Royal College of Surgeons in Ireland

description: Biological replicate 4 of 4. Mouse treated with Antagomir 134 for 24h after intra-amygdala kainic acid-induced status epilepticus

hyb_protocol: RNA amplifications and labeling were performed on an automated system (Caliper Life Sciences NV/SA, Belgium) with 3 ug total RNA from each sample.

scan_protocol: Hybridized slides were scanned on an Agilent scanner (G2565BA) at 100% laser power, 30% PMT. After automated data extraction using Imagene 8.0 (BioDiscovery), Loess normalization was performed (Yang et al., 2002) on mean spot-intensities. Gene-specific dye bias was corrected based on a within-set estimate as described in Margaritis et al 2009.

data_processing: Data was normalized on mean spot-intensity (by Loess) and gene-specifi dye bias was corrected based on a within-set estimate.

source_name: Brain

label_protocol: Microarray experiments were performed 8 times, of each samplegroup two samples were labeled with cy5 and co-hybridized with referencepool RNA labeled with cy3, and two samples were labeled and hybridized in the opposite way. Microarrays used were Mouse Whole Genome GE 4x44K v1  (Agilent Technologies, Belgium) representing 41174 M. musculus 60-mer probes in a 4x44K layout.

extract_protocol: Total RNA extracted using Trizol using per sample 800ul of Trizol, 200ul of chloroform, 450ul of isopropanol to precipitate the RNA, 75% of Ethanol for the  whashes and RNase-free water to resuspend the RNA.

treatment_protocol: Mice were treated with Antagomir-134 or Scramble (control) (intraperitoneal; 30mg/kg) for 24h after intra-amygdala kainic acid-induced status epilepticus

value: ipsilateral hippocampus

tag: gender

value: male

tag: life stage

value: Adult

value: Antagomir 134 for 24h

source_name: Reference pool


title: CR134aff6 Antagomir134

description: Biological replicate 3 of 4. Mouse treated with Antagomir 134 for 24h after intra-amygdala kainic acid-induced status epilepticus


title: CR134aff5 scramble (control)

description: Biological replicate 3 of 4. Mouse treated with Scramble for 24h after intra-amygdala kainic acid-induced status epilepticus

value: Scramble for 24h


title: CR134aff8 scramble (control)

description: Biological replicate 4 of 4. Mouse treated with Scramble for 24h after intra-amygdala kainic acid-induced status epilepticus

value: scramble for 24h


title: Cerebellum 266Q knock-in rep3

first: Pawel

middle: Michal

last: Switonski

address: 1001 Health Sciences Road

department: Department of Pathology & Laboratory Medicine

data_processing:
Model-based Analysis of ChIP-Seq (MACS)  algorithm used to call peaks:
The paired Input and ChIP FASTQ files were input to FASTQ Groomer, FASTQ Quality Trimmer (quality score >30)
Reads were mapped to mm10 using Bowtie2
Aligned reads were filtered for duplicates by RmDup
MACS was then run with  these paired files using an MFOLD high confidence threshold of 16, an estimate band size of 300 bp,  and a peak cutoff threshold of P <1e-05
Genome_build: mm10
Supplementary_files_format_and_content: Peak BED files
Supplementary_files_format_and_content: The bigWig format to display data in the Genome Browser as a graph

source_name: cerebellum

extract_protocol:
Tissue was fixed in 1% formaldehyde for 10 min at room temperature and quenched with 111 μl 1.25M glycine. Tissue was homogenized in nuclei isolation buffer (50mM Tris-HCl pH8, 60mM KCl, 0.5% NP-40), lysed in lysis buffer buffer (50mM Tris-HCl pH8, 10mM EDTA pH8, 0.5mM EGTA pH8, 0.5% SDS) and sonicated on a Pico Biorupter for  three 8x cycles of 30 sec on, 90 sec off at 4°C Chromatin was then diluted in dilution buffer (20mM Tris-HCl pH8, 2mM EDTA pH8, 150mM  NaCl, 1% Triton X100). After incubation with anti-H3K9ac coated magnetic beads, DNA waswashed,  treated with RNAse and proteinase K and cleaned up with g the Zymo ChIP DNA clean and concentrator kit (Zymo #D5201) following the  manufacturer’s protocol.
Library was prepared using standard UCSD Genomics core protocols to generate single ended  TruSeq adapters.  Library PCR amplification was performed at 15 cycles and agarose gel size  selection performed at the 300-600 bp range.  Samples were analyzed by Agilent Tapestation to  determine concentrations and loaded into the IGM Core’s Illumina HiSeq 4000.

value: 9 weeks

value: 266Q knock-in (heterozygous)

value: cerebellum

tag: chip antibody

value: Anti-acetyl-Histone H3 (Lys9), Millipore 07-352


title: AltRepop_6hr_4 [LH484_S16.R1.fastq.gz]


title: Cerebellum wild type rep3

value: wild type


title: Cerebellum 266Q knock-in rep2


title: AltRepop_6hr_2 [LH482_S14.R1.fastq.gz]


title: AltRepop_6hr_3 [LH483_S15.R1.fastq.gz]


title: Cerebellum 266Q knock-in rep1


title: Cerebellum 266Q knock-in rep4


title: CR134aff1 scramble (control)

description: Biological replicate 1 of 4. Mouse treated with Scramble for 24h after intra-amygdala kainic acid-induced status epilepticus


title: CR134aff3 Antagomir134

description: Biological replicate 1 of 4. Mouse treated with Antagomir 134 for 24h after intra-amygdala kainic acid-induced status epilepticus


title: CR134aff4 Antagomir134

description: Biological replicate 2 of 4. Mouse treated with Antagomir 134 for 24h after intra-amygdala kainic acid-induced status epilepticus


title: Cerebellum wild type rep2


title: Cerebellum wild type rep1


title: CR134aff2 scramble (control)

description: Biological replicate 2 of 4. Mouse treated with Scramble for 24h after intra-amygdala kainic acid-induced status epilepticus


title: AltRepop_6hr_1 [LH481_S13.R1.fastq.gz]


title: ControlAltRepop_6hr_4 [LH479_S11.R1.fastq.gz]


title: ControlAltRepop_6hr_5 [LH480_S12.R1.fastq.gz]


title: ControlAltRepop_6hr_3 [LH478_S10.R1.fastq.gz]


title: AltRepop_0hr_3 [LH475_S7.R1.fastq.gz]


title: AltRepop_0hr_4 [LH476_S8.R1.fastq.gz]


title: AltRepop_0hr_1 [LH473_S5.R1.fastq.gz]


title: ControlAltRepop_6hr_2 [LH477_S9.R1.fastq.gz]


title: ControlAltRepop_6hr_1 [LH472_S4.R1.fastq.gz]


title: AltRepop_0hr_2 [LH474_S6.R1.fastq.gz]


title: RepopSVZ_5 [SVZ15_S15]

source_name: RepopSVZ

value: subventricular zone


title: ControlAltRepop_0hr_1 [LH469_S1.R1.fastq.gz]


title: RepopSVZ_2 [SVZ12_S12]


title: ElimSVZ_3 [SVZ8_S8]

source_name: ElimSVZ


title: ElimSVZ_5 [SVZ10_S10]


title: ElimSVZ_4 [SVZ9_S9]


title: ElimSVZ_2 [SVZ7_S7]


title: Cerebellum wild type rep4


title: RepopSVZ_4 [SVZ14_S14]


title: ElimSVZ_1 [SVZ6_S6]


title: ControlAltRepop_0hr_2 [LH470_S2.R1.fastq.gz]


title: ControlSVZ_4 [SVZ4_S4]

source_name: ControlSVZ


title: RepopSVZ_3 [SVZ13_S13]


title: ControlSVZ_5 [SVZ5_S5]


title: ControlSVZ_3 [SVZ3_S3]


title: ControlSVZ_2 [SVZ2_S2]


title: ControlSVZ_1 [SVZ1_S1]


title: RegularRepop_3 [28d_REG_REPOP_3]

source_name: RegularRepop


title: RegularRepop_2 [28d_REG_REPOP_2]


title: RegularRepop_1 [28d_REG_REPOP_1]


title: ControlAltRepop_0hr_3 [LH471_S3.R1.fastq.gz]


title: ControlRegularRepop28d_4 [CON_4]


title: RepopSVZ_1 [SVZ11_S11]


title: BMM_d7_vavCre_3

city: Zürich

first: Manfred

last: Kopf

address: Otto-Stern-Weg 7

department: Biologie

institute: ETH Zürich

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 (Version25.06.2015) whole genome using STAR aligner.
differential expression analyses of read counts was perforemed using EdgeR
the read counts were scaled with the use of the trimmed mean of M-values (TMM) method proposed by Robinson and Oshlack (Robinson & Oshlack, 2010).
Supplementary_files_format_and_content: the text file (.txt), the processed data file includes Gene Identifier, gene name, description, normalized count (between-sample-normalization, TMM)

source_name: Bone marrow macrophage

extract_protocol:
Tissues were removed, cell were FACS sorted and 1000 cells were collected into lysis buffer. oligo-dT primers and dNTPs were added to lysed cells and hybridization of the primer to poly(A) tails
PCR products were purified with AMPure XP beads (Beckman Coulter) and 1 ng of the product was tagmented by using the Nextera XT DNA sample preparation kit (Illumina)

value: vavCre

value: bone marrow

tag: developmental stage

value: pup D7


title: ControlRegularRepop28d_1 [CON_1]

value: myeloid cells from whole hemispheres


title: ControlRegularRepop28d_2 [CON_2]

value: Vehicle


title: ControlRegularRepop28d_3 [CON_3]


title: BMM_d7_vavCre_2


title: BMM_d7_WT_2

value: WT


title: BMM_d7_vavCre_1


title: RPM_d7_WT_2

source_name: Red pulp macrophage

value: spleen


title: BMM_d7_WT_3


title: RPM_d7_WT_1


title: BMM_d7_WT_1


title: RPM_d7_WT_3


title: RPM_d7_vavCre_3


title: RPM_d7_vavCre_2


title: KLF12_OE_3

city: Nanjing

first: Yang

last: Liu

address: Hankou road 22

institute: Nanjing University

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then the clean reads were mapped to the reference genome using HISAT2 (v2.0.4).
FPKM were calculated using RSEM v1.2.8.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for all samples.

source_name: mouse fetus

extract_protocol:
9.0 dpc fetuses were removed and RNA was harvested using Trizol reagent.
Libraries were prepared for sequencing using standard Illumina protocols

value: fetus

value: 9.0 dpc

value: KLF12 overexpression


title: RPM_d7_vavCre_1


title: KLF12_OE_1


title: WT_3


title: KLF12_OE_2


title: Wnt1Cre Mutant #3

city: Philadelphia

first: Robert

middle: O

last: Heuckeroth

state: PENNSYLVANIA

address: 3615 Civic Center Blvd

department: Research Institute

institute: Children's Hospital of Philadelphia

data_processing:
Reads were aligned to remove repeat sequence and ribosomal RNA reads and then processed using RNA-Seq unified mapper (RUM) package. RUM files were visualized in the TessLA browser for subsequent analyses.
All processed data were summarized in one Excel file with the name "RNA SEQ_Processed Data". Comparison of gene expression levels between mutant and control ENCDC at either E11.5 or E13.5 were presented as log2 fold change between mutant and control, along with the false discovery rate for each comparison. Also included in the processed datasheet are both the actual read and log2 value of the actual read of the gene transcripts for each individual sample.

source_name: E11.5 stomach

extract_protocol:
ENCDC were isolated from individual E11.5 stomachs and E13.5 colons by incubating fetal organs with collagenase and dispase in Ham’s F12 media with 1% bovine serum albumin (37oC, 5% CO2 incubator, 20 minutes) and then triturating by pipetting up and down 15 times using a P1000 pipette tip before passing through a 30 μm strainer. Cells with TdTomato or EYFP fluorescence were purified by flow sorting (MoFlo Astrios high speed cell sorter, 100 μm nozzle), pelleted by centrifugation (500 x g), washed once with PBS, and frozen immediately at -80oC until analysis.
RNA isolation, library preparation, and RNA-SEQ analysis were performed by University of Pennsylvania Next-Generation Sequencing Core. The libraries were made using the combination of the Clontech (now Takara) SMART (cDNA synthesis and amplification) and Illumina Nextera XT (cDNA to library) kits. Libraries were then sequenced on an Illumina HiSeq 4000, using Sequencer Softwares RTA: 2.7.7 and HCS: HiSeqCS:HD 3.4.0.38. To obtain enough reads, each sample was sequenced twice, and the results were combined together.

value: Rar[alpha]DNLoxP/+; Wnt1Cre; ROSA26TdTomato (mutant)

value: Mixed background

value: Enteric neural crest-derived cells

value: embronic day 11.5

tag: barcode

value: TAGCGCTCCGTCTAAT


title: Wnt1Cre Mutant #2

tag: strain

value: ATGCGCAGCTAAGCCT


title: WT_1


title: Wnt1Cre Mutant #1

value: TACGCTGCAAGGAGTA


title: WT_2


title: Wnt1Cre Control #2

value: Wnt1Cre; ROSA26TdTomato (control)

value: GGAGCTACTATCCTCT


title: Wnt1Cre Mutant #4

value: ACTGAGCGTCTCTCCG


title: Wnt1Cre Control #4

value: CGGAGCCTACTGCATA


title: Wnt1Cre Control #1

value: ACTCGCTACTCTCTAT


title: RETCre Mutant #3

source_name: E13.5 colon

value: Rar[alpha]DNLoxP/+ ; RETCreERT2EYFPTandem (mutant)

value: embronic day 13.5

value: TCCTGAGCACTGCATA


title: RETCre Control #4

value: RETCreERT2-EYFPTandem (control)

value: CGAGGCTGTCTCTCCG


title: RETCre Control #3

value: CTCTCTACCGTCTAAT


title: RETCre Mutant #1

value: Mixed background

value: TAAGGCGACTCTCTAT


title: RETCre Control #2

value: Enteric neural crest-derived cells

value: TAGGCATGCTAAGCCT


title: RETCre Control #1

value: GGACTCCTAAGGAGTA


title: Wnt1Cre Control #3

value: embronic day 11.5

value: GCGTAGTAGTAAGGAG


title: R6/1-RGFP109_rep1

city: Berlin

first: Katharina

last: Hecklau

address: Charitéplatz 1, Virchowweg 6

institute: Charité-Universitätsmedizin Berlin

description:
RNAseq_Cuffdiff__WT-vehicle_vs_R6-1-RGFP109.txt
RNAseq_Cuffdiff__R6-1-vehicle_vs_R6-1-RGFP109.txt

data_processing:
Raw single-end reads of cDNA fragments were aligned to the mouse transcriptome (RefSeq, mm10) using the ‘RNA-Seq Alignment Workflow’ from BaseSpace, Illumina (version 1.1.0) with STAR aligner (version STAR_2.5.0b) for mapping.
Differential gene expression analysis was performed using ‘Cufflinks Assembly & DE Workflow' from BaseSpace, Illumina (version 2.1.0) with Cuffdiff 2 (Cufflinks, version 2.2.1).
Genome_build: mm10
Supplementary_files_format_and_content: *.txt: Tab-delimited text files contain cuffdiff output with columns: (1) tested id, (2) gene id, (3) gene, (4) locus, (5) sample 1, (6) sample 2, (7) test status, (8) FPKM of the gene in sample 1, (9) FPKM of the gene in sample 2, (10) log2(FPKM_2/FPKM_1), (11) test statistic, (12) p-value, (13) q-value, (14) significant (yes or no). WT=wild type, MUT=R6/1.

source_name: Striatum

extract_protocol:
Brain tissues were removed and flash frozen in liquid nitrogen. Flash-frozen tissues were homogenized in QIAzol Lysis Reagent (Qiagen) followed by RNA extraction using the miRNeasy Kit (Qiagen).
Illumina TruSeq RNA Sample Prep Kit was used with 380 ng of total RNA for the construction of sequencing libraries. Two pools with twelve libraries each were sequenced on a Illumina HiSeq 4000 instrument (1x51bp).

treatment_protocol: The HDAC1 and HDAC3 inhibitor RGFP109 (RG2833; CAS No. 1215493-56-3) was purchased from Selleckchem. RGFP109 was dissolved in dimethyl sulfoxide and diluted in 0.9% NaCl (1:2) directly before use (final concentration: 15 mg/ml). Mice were administered RGFP109 (30 mg/kg body weight) or an equal volume of vehicle solution by intraperitoneal injections five times a week for three weeks (total of 23 days) starting at the age of 11 to 14 weeks. Mice were deeply anesthetized using isoflurane and sacrificed by cervical dislocation 18 h after the final injection.

tag: model

value: Striatum


title: R6/1-RGFP109_rep2


title: R6/1-RGFP109_rep5


title: R6/1-RGFP109_rep7


title: R6/1-RGFP109_rep3


title: R6/1-RGFP109_rep6


title: R6/1-RGFP109_rep4


title: WT-RGFP109_rep6

description:
RNAseq_Cuffdiff__WT-vehicle_vs_WT-RGFP109.txt
RNAseq_Cuffdiff__R6-1-vehicle_vs_WT-RGFP109.txt

value: wild type


title: WT-RGFP109_rep5


title: WT-RGFP109_rep3


title: WT-RGFP109_rep4


title: WT-RGFP109_rep2


title: RETCre Mutant #2

value: CGTACTAGTATCCTCT


title: WT-RGFP109_rep1


title: R6/1-vehicle_rep6

description:
RNAseq_Cuffdiff__WT-vehicle_vs_R6-1-vehicle.txt
RNAseq_Cuffdiff__R6-1-vehicle_vs_R6-1-RGFP109.txt

value: vehicle


title: WT-vehicle_rep5

description:
RNAseq_Cuffdiff__WT-vehicle_vs_R6-1-vehicle.txt
RNAseq_Cuffdiff__WT-vehicle_vs_R6-1-RGFP109.txt


title: R6/1-vehicle_rep1


title: R6/1-vehicle_rep3


title: R6/1-vehicle_rep2


title: R6/1-vehicle_rep5


title: WT-vehicle_rep4


title: R6/1-vehicle_rep4


title: WT rep2 [WT_1695]

city: Fort Lauderdale

first: Lubov

last: Nathanson

state: Florida

address: 3321 College Ave.

department: INIM

institute: Nova Southeastern University

data_processing:
Sequenced reads were trimmed for adaptor sequence, reads containing N>10% were removed, reads with Q-score<=5 were removed.
Reads were mapped to GRCm38 using HISAT2
Mapped reads were quantified using HTSeq. For differential expression analysis only genes with counts > 0 in all samples in at least one group. Bioconductor/R package DESeq2 was used for normalization and differential gene expression analysis.
Genome_build: GRCm38
Supplementary_files_format_and_content: raw count values for each gene that had counts >0 for each sample in at least one group;  normalized counts

extract_protocol:
Livers were removed, and total RNA was extracted using Tri Reagent (Molecular Research Center, Cincinnati, OH).
rRNA was removed using the Ribo-Zero kit. Libraries were prepared using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina.

tag: strain background

tag: genotype/variation

value: 12 weeks

value: liver


title: WT rep3 [WT_1696]

tag: tissue


title: WT rep4 [WT_1700]


title: Inpp4b-/- rep3 [IN_1675]


title: WT-vehicle_rep1

tag: genotype


title: WT-vehicle_rep3


title: WT-vehicle_rep2


title: Patient tumor sample_45_on_treatment

city: Amsterdam

first: Tom

last: van den Ende

address: Meibergdreef 9

institute: Amsterdam UMC

data_processing:
The samples were sequenced on an Illumina HiSeq4000 with a single read consisting of 50bp and 100.000.000 reads per sample.
Data went through quality control using FastQC.
RNAseq reads were aligned to the human reference genome (NCBI37/hg19) using STAR v2.7.1, and annotated with Gencode v32.
Count files were converted into DESeq_vst values using DESeq2 in R Bioconductor.
DESeq libraries were used for differential expression analysis using the normalized counts in the R2 genome analysis and visualization platform (http://r2.amc.nl).
Genome_build: (NCBI37/hg19)
Supplementary_files_format_and_content: Table with gene counts for every gene and every sample

source_name: endoscopic tumor biopsy

extract_protocol:
Snap frozen tumor biopsies were cut into smaller pieces on the cryostat. One section was used for haematoxylin and eosin staining to determine the tumor cell percentage in the biopsy, which was performed by an experienced pathologist. Total RNA was isolated using the Qiagen AllPrep DNA/RNA/miRNA universal kit. The NanoDrop (Thermo Fisher) was used to measure RNA concentration (ng/ul). Biopsies were sent for bulk RNA sequencing in case the tumor % was ≥ 30% and RNA concentration was not lower than 20 ng/ul.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: esophageal adenocarcinoma

value: neoadjuvant chemoradiotherapy + atezolizumab

tag: response

value: non-responder


title: Patient tumor sample_44_on_treatment


title: Inpp4b-/- rep4 [IN_1678]


title: Inpp4b-/- rep2 [IN_1649]


title: WT rep1 [WT_1694]


title: Patient tumor sample_43_on_treatment


title: Patient tumor sample_43_baseline


title: Patient tumor sample_45_baseline


title: Patient tumor sample_44_baseline


title: Patient tumor sample_42_on_treatment

value: responder


title: SAMPLE 42

city: Santiago de Compostela

first: Sara

last: Pischedda

state: A Coruña

address: Avenida da Choupana s/n

department: Instituto de Investigación Sanitaria de Santiago de Compostela

country: Spain

institute: Hospital Clinico Universitario de Santiago de Compostela

hyb_protocol: Whole blood DNA was bisulfite converted using the EZ-96 DNA Bisulfite Zymo Research conversion protocol according to the manufacturer’s instructions.

scan_protocol: The array was imaged using the Illumina iScan system

data_processing: R software (minfi package)

source_name: blood clots

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from blood clots collected from the same participants at 12 and 24 months of age.

value: 24 months

value: f

value: blood


title: SAMPLE 40

value: m


title: SAMPLE 39


title: SAMPLE 46


title: Inpp4b-/- rep1 [IN_1648]


title: Patient tumor sample_42_baseline


title: Patient tumor sample_38_on_treatment


title: Patient tumor sample_41_baseline


title: Patient tumor sample_37_baseline


title: SAMPLE 48


title: SAMPLE 38


title: SAMPLE 41


title: SAMPLE 33


title: SAMPLE 43


title: SAMPLE 37


title: SAMPLE 35


title: Patient tumor sample_35_on_treatment


title: SAMPLE 47


title: Patient tumor sample_39_baseline


title: SAMPLE 34


title: Patient tumor sample_34_on_treatment


title: Patient tumor sample_40_baseline


title: SAMPLE 28


title: Patient tumor sample_33_resection

source_name: resection tumor biopsy


title: SAMPLE 31


title: SAMPLE 45


title: SAMPLE 44


title: SAMPLE 32


title: Patient tumor sample_33_on_treatment


title: SAMPLE 27


title: SAMPLE 29


title: SAMPLE 36


title: Patient tumor sample_36_on_treatment


title: SAMPLE 26


title: SAMPLE 30


title: SAMPLE 25


title: Patient tumor sample_31_resection


title: Patient tumor sample_34_resection


title: Patient tumor sample_35_baseline


title: Patient tumor sample_38_baseline


title: Patient tumor sample_31_on_treatment


title: Patient tumor sample_34_baseline


title: Patient tumor sample_30_baseline


title: Patient tumor sample_29_on_treatment


title: Patient tumor sample_33_baseline


title: Patient tumor sample_29_baseline


title: Patient tumor sample_32_resection


title: Patient tumor sample_31_baseline


title: Patient tumor sample_30_on_treatment


title: Patient tumor sample_28_on_treatment


title: Patient tumor sample_32_on_treatment


title: Patient tumor sample_26_on_treatment


title: Patient tumor sample_25_resection


title: Patient tumor sample_28_baseline


title: SAMPLE 21

value: 12 months


title: Patient tumor sample_26_baseline


title: Patient tumor sample_25_on_treatment


title: Patient tumor sample_24_baseline


title: Patient tumor sample_25_baseline


title: SAMPLE 24


title: Patient tumor sample_23_resection


title: Patient tumor sample_23_baseline


title: Patient tumor sample_22_on_treatment


title: Patient tumor sample_21_baseline


title: Patient tumor sample_22_baseline


title: Patient tumor sample_20_resection


title: Patient tumor sample_23_on_treatment


title: Patient tumor sample_20_on_treatment


title: Patient tumor sample_20_baseline


title: Patient tumor sample_19_on_treatment


title: Patient tumor sample_15_on_treatment


title: Patient tumor sample_17_baseline


title: Patient tumor sample_18_baseline


title: Patient tumor sample_18_on_treatment


title: Patient tumor sample_17_resection


title: Patient tumor sample_17_on_treatment


title: Patient tumor sample_15_baseline


title: Patient tumor sample_12_on_treatment


title: SAMPLE 20


title: SAMPLE 19


title: SAMPLE 14


title: SAMPLE 16


title: Patient tumor sample_12_baseline


title: Patient tumor sample_11_on_treatment


title: Patient tumor sample_10_on_treatment


title: SAMPLE 23


title: Patient tumor sample_11_baseline


title: Patient tumor sample_10_baseline


title: SAMPLE 22


title: Patient tumor sample_9_resection


title: SAMPLE 18


title: Patient tumor sample_9_on_treatment


title: SAMPLE 17


title: Patient tumor sample_8_baseline


title: SAMPLE 15


title: Patient tumor sample_7_baseline


title: Patient tumor sample_4_baseline


title: Patient tumor sample_6_baseline


title: Patient tumor sample_3_resection


title: Patient tumor sample_7_on_treatment


title: Gill tissue- normoxia [CON _3]

city: wuxi

first: Yi-Fan

last: Tao

state: jiangsu

address: 9 Shanshui East Road

institute: Freshwater Fisheries Research Center

description: Tachysurus fulvidraco ♀ × Pseudobagrus vachellii ♂

data_processing:
Raw data was first processing with cutadapt software (version 1.9) to remove reads that contain more than 5% N (N means base information cannot be determined) of all base; adaptor-polluted and low quality reads (more than 20% bases with a Q value<10).
Q20, Q30, GC-content of clean data were further calculated to verify sequence quality.
Then, we aligned clean reads to the tachysurus fulvidraco reference genome (https://www.ncbi.nlm.nih.gov/genome/?term=yellow+catfish) by using HISAT package to obtain annotation information
Genome_build: Tachysurus fulvidraco（ID:2648）
Supplementary_files_format_and_content: tab-delimited text files include FPKM and count values for each Sample

organism: Tachysurus vachellii

source_name: Gill

growth_protocol: The fish was acclimated in 450L cylindrical plastic tanks (DO: 6.5 ~ 7.0 mg/L, water temperature: 28 ± 1°C, pH 7.4 ± 0.2) under a natural photoperiod for one week. During the acclimation period, the fish was fed with a commercial feed (38% crude protein, 5% crude lipid) twice a day (8:00 and 16:00). Water quality was checked once a week. Ammonia, nitrate, and nitrite levels were kept lower than 0.1 mg/L. The fish was fasted for 24h before the beginning of the experiment.

extract_protocol:
Total RNA of gill tissues (n=9 per group) sampled at 96h was extracted by using TRIzol reagent (Invitrogen, USA). The RNA integrity and concentration were monitored by Agilent Bioanalyser 2100 (Agilent Technologies, USA) and NanoDrop Lite spectrophotometer (NanoDrop Technologies, USA). Then, equal amounts of extracted RNA from each group (hypoxia group, control group) were mixed (every three samples) for sequencing.
About 10 μg total RNA from these mixed sample was purified by using oligo-dT magnetic beads and then prepared for constructing RNA-seq libraries by mRNA-Seq Sample Preparation Kit (Illumina, USA) (Qiang et al., 2017). Transcriptome sequencing was performed by using Illumina Novaseq™ 6000 (LC Sciences, USA) that generated about 150bp double-ended (PE150) raw reads.

treatment_protocol: hypoxia treated for 96h

value: Normoxia

value: Gill


title: Patient tumor sample_3_on_treatment


title: Gill tissue- normoxia [CON _1]


title: Patient tumor sample_3_baseline


title: Patient tumor sample_2_on_treatment


title: SAMPLE 10


title: Gill tissue- normoxia [CON _2]


title: Gill tissue- hypoxia [STR _2]

value: Hypoxia


title: SAMPLE 11


title: SAMPLE 13


title: SAMPLE 4


title: SAMPLE 7


title: SAMPLE 9


title: SAMPLE 5


title: SAMPLE 3


title: Patient tumor sample_2_baseline


title: Gill tissue- hypoxia [STR _1]


title: Patient tumor sample_1_on_treatment


title: SAMPLE 12


title: Patient tumor sample_1_resection


title: C46

city: Cusano Milanino

first: Luciano

last: Calzari

address: Via Zucchi 18

institute: IRCCS Istituto Auxologico Italiano

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450K Beadchip using standard Illumina protocol

scan_protocol: Fluorescence intensities were captured by using the fluorescent scanner Illumina HiScan SQ (Illumina).

data_processing: Quality control, pre-processing and generation of β-values matrix were performed by using the ChAMP (release 2.8.9) package (Morris TJ et al., 2014) implemented R environment (version 3.6.2). ChAMP pre-processing module appears more suitable in preventing biases due to genetic variations in downstream analyses by filtering an increased number of probes. Sites with a detection p-value above 0.01 (n=4706) and a bead count <3 in at least 5% of samples (n=226) were removed. Moreover, also non-GpG probes (n=3025), potentially SNP affected probes (n=57699) (Zhou Wet al., 2017) probes aligning to multiple locations (n=11) (Nordlund J et al., 2013) and of X and Y chromosomes (n=9705) were filtered out. As a final outcome of the filtering procedures, a total of 410140 CpG sites were retained. Quantile normalization was performed through preprocessCore package (release 1.38.1).

label: Cy3 and Cy5

source_name: Control

label_protocol: Standard Illumina protocol

extract_protocol: DNA was extracted from peripheral blood lymphocytes of probands and their parents (Automated Extractor, Tecan Group Ltd. and Wizard Genomic DNA Purification Kit (Ref: A1125), Promega). Quality control and quantification of DNA was assessed by visualization of genomic DNA (gDNA) on 1% agarose gel electrophoresis and by using NanoPhotometer Pearl (Implen GmbH).

tag: disease state

value: control

value: Peripheral Blood

tag: Sex

value: female

tag: epigenetic age


title: SAMPLE 2

tag: age


title: SAMPLE 8


title: C47


title: SAMPLE 6


title: 1440322_Input_H2-D3

city: Memphis

first: Yong

last: Cheng

state: Tennessee

address: 262 Danny Thomas Place

department: Department of Hematology

institute: St. Jude Children’s Research Hospital

description: ChIP-seq

data_processing:
FASTQ files were mapped to hg19 by using BWA mem (v0.7.16a).
ChIP-seq peaks were called by using MACS2 (v2.1.1)
Genome_build: hg19
Supplementary_files_format_and_content: bigwiggle

growth_protocol: Approximately 2.5 × 107 cells were used for each immunoprecipitation. Cells were cross-linked with 1% formaldehyde for 10 min at room temperature with rotation, and the reaction was quenched with glycine at a final concentration of 125 mM. Cross-linked cells were then lysed and resuspended in 2 mL of RIPA buffer and sonicated for 12 cycles with a Branson 250 sonifier (10 s on/90 s off for a total of 2 min of pulses with 20% output from the micro-tip) to obtain fragments of chromatin approximately 200–300 bp in size. Supernatants were precleared by incubation with 200 µL of protein A/G agarose bead slurry (Thermo Fisher Scientific, cat. #15918014) overnight at 4°C with rotation. Meanwhile, 12.5 µg of IP antibody was incubated with 50 µL of protein A/G agarose bead slurry in 1 mL of PBS overnight at 4°C with rotation. Saved precleared chromatin (20 µL) was used as the input sample. Precleared chromatin was incubated with the antibody–bead complex for 7 h at 4°C with rotation. Cross-linking of DNA was reversed by incubation with RNase A (1 µg/µL), proteinase K (0.2 mg/mL), and 0.25 M NaCl overnight at 65°C.

extract_protocol:
Immunoprecipitated DNA was purified using the Qiagen PCR Extraction Kit and eluted with 20 µL of EB elution buffer. Sequencing libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit (NEB, cat. #E7645) with homemade TruSeq adaptors. Libraries were sequenced using an Illumina HiSeq 4000 system.
NA

tag: cell line

tag: antibody

value: Input


title: Gill tissue- hypoxia [STR _3]

tag: treatment


title: C41

description: Already submitted as GSM4602909(GSE152089)

value: male


title: 1440321_Input_H2-D3

description: ChIP-seq


title: C49


title: 1440320_H3K36me3_H2-D3

description: ChIP-seq


title: C48


title: C43

description: Already submitted as GSM4602911(GSE152089)


title: 1440319_H3K36me3_H2-D3

description: ChIP-seq


title: SAMPLE 1

tag: gender


title: C42

description: Already submitted as GSM4602910(GSE152089)


title: 1440317_H3K27ac_H2-D3

description: ChIP-seq


title: C44


title: 1440315_H3K27me3_H2-D3

description: ChIP-seq


title: 1440314_H3K9ac_H2-D3

description: ChIP-seq


title: 1440316_H3K27me3_H2-D3

description: ChIP-seq


title: C35

description: Already submitted as GSM4602903(GSE152089)


title: C40

description: Already submitted as GSM4602908(GSE152089)


title: 1440313_H3K9ac_H2-D3

description: ChIP-seq


title: WGBS-GV-CZ3

city: Hangzhou

first: Li

last: Shen

state: Zhejiang Province

address: 866 Yuhangtang Road

institute: Life Sciences Institute, Zhejiang University

data_processing:
ChIP-seq data analysis.ChIP-seq reads were trimmed to 50 bp and aligned to the mouse genome build mm9 using  bowtie2 (v2.3.4.1) with default parameters. All unmapped reads, non-uniquely mapped reads and PCR duplicates were removed. H3K4me3 peaks were called using MACS2 (v 2.1.1.20160309) with the parameters “--nomodel --nolambda --broad -B --SPMR -g mm” and signal tracks for each sample were generated with “wigToBigWig” from UCSC.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig
WGBS data analysis. Raw reads were trimmed using TrimGalore (v 0.4.4) with default parameters. Then the reads were mapped to converted mm9 reference using bismark (v0.19.0) with parameters “--bowtie2 --non_directional”. PCR duplicates were removed. The cytosine was distinguished as CpG, CHG and CHH and the methylation levels were calculated separately.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph

source_name: Cxxc1fl/fl;Gdf9-Cre mouse GV oocytes

growth_protocol: in vivo

extract_protocol: GV oocytes were collected from 3-week old WT and Cxxc1fl/fl;Gdf9-Cre mice. For each sample, 200 oocytes were picked into cell lysis buffer using mouth pipet. Then we performed scBS-seq protocol with slight modification.

treatment_protocol: 4 week mouse treated by  PMSG 44 h

tag: stain


title: C38

description: Already submitted as GSM4602906(GSE152089)


title: C30

description: Already submitted as GSM4602898(GSE152089)


title: 1440318_H3K27ac_H2-D3

description: ChIP-seq


title: 1440312_H3K9me3_H2-D3

description: ChIP-seq


title: WGBS-GV-CZ2


title: 1440311_H3K9me3_H2-D3

description: ChIP-seq


title: C45


title: WGBS-GV-CZ1


title: WGBS-GV-WT3

source_name: WT mouse GV oocytes


title: 1440310_H3K4me3_H2-D3

description: ChIP-seq


title: 1440309_H3K4me3_H2-D3

description: ChIP-seq


title: WGBS-GV-WT2


title: C27

description: Already submitted as GSM4602895(GSE152089)


title: C36

description: Already submitted as GSM4602904(GSE152089)


title: 1440308_H3K4me1_H2-D3

description: ChIP-seq


title: C31

description: Already submitted as GSM4602899(GSE152089)


title: WGBS-GV-WT1