title: Reference normalised MLL-N ChIP-seq in SEM cells following NT siRNA treatment

description:
ChIP-seq performed using MLL-N antibody in SEM cells following NT siRNA treatment
SEM_RUNX1-NT_MLL-N_peaks.txt


title: MS1 cells expressing TAZ 4A Rep 2

status: Public on May 23 2021

type: SRA

city: Dallas

first: Jordan

last: Driskill

state: TX

address: 5323 Harry Hines Blvd

department: Physiology

country: USA

institute: UT Southwestern

library_source: transcriptomic

data_processing:
Demultiplexing performed with bcl2fastq
Quality control assessed by FastQC
Sequencing reads mapped using STAR
Count data generated using featureCounts
EdgeR used for differential expression analysis
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text files with raw counts
Supplementary_files_format_and_content: tab-delimited text files with normalized transcripts per million

molecule: total RNA

organism: Mus musculus

source_name: Ms1 cell line (ATCC)

extract_protocol:
RNA extracted with RNAeasy plus mini kit. RNA was DNAse treated with the Invitrogen Turbo DNA-Free Kit
Libraries were prepared with the Illumina TruSeq Stranded Total RNA LT Sample Prep Kit. Poly-A RNA was purified and fragmented before cDNA synthesis. Adapters were ligated, and then samples were PCR amplified and purified with Ampure XP beads. Samples were normalized, pooled, and run on an Illumina HiSeq 2500 using SBS v3 reagents

tag: cell line

value: Ms1 cells

tag: cell type

value: endothelial cells (pancreas)

tag: lentiviral backbone used


title: MS1 cells expressing TAZ 4A Rep 1


title: THP-1 sgSCR LPS 4 hour replicate 2

city: Melbourne

first: Stephin

middle: J

last: Vervoort

address: 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

description:
SCR-LPS4h-2_S40
LPS_WT_vs_KO_normalizedcounts.csv
counts_LPS.txt

data_processing:
Sequenced reads were demultiplexed using bcl2fastq (v2.17.1.14)
Basic QC performed on fastq files using FASTQC (v0.11.6)
Sequencing reads were trimmed using cutadapt (v2.1) and aligned to the Hg19 or a combined Hg19/dm3 reference genome using HISAT 2 (v2.1.0)
Read counting across genomic regions was performed using the Subread (v2.0.0) featureCounts function and differential gene expression analysis was performed in Rstudio (v3.6.1) using Voom-Limma (v3.42.2)
Genome_build: Hg19 and dm3
Supplementary_files_format_and_content: Tag density files (TDF) of 3'UTR RNA coverage across the Hg19 genome;  text files of featureCounts counts; text file of normalized (voom) and normalized (voom and S2 spike-in) counts

organism: Homo sapiens

source_name: Acute myeloid leukemia cell line expressing Cas9 and non-targeting (Scramble) sgRNA

growth_protocol: Cells were cultured in RPMI-1640 supplemented with 10-20 percent heat-inactivated fetal bovine serum, 100U/mL penicillin, 100µg/mL streptomycin and 2mM GlutaMAX at 37 degrees celciuus and 5 percent carbon dioxide

extract_protocol:
Cells were lysed in TriZol reagent and total DNAse-treated RNA isolated using the Zymogen RNA mini-prep kit. For HT-29 cells, total RNA (5 percent) from Drosophila S2 cells was spiked into each human RNA sample.
RNA libraries were prepared using the Lexogen QuantSeq 3'-mRNA Seq Library Prep kit (015)

treatment_protocol: THP-1 cells were treated with LPS (1µg/mL) over a time-course and HT-29 cells were treated with CDK9i (AZ5576, 170nM, 2 hours), DBK-1154 (10µM, 2 hours 15 minutes) or a combination of both

value: THP-1 cell line

tag: genotype

tag: treatment

value: LPS 1µg/mL 4 hour


title: Reference normalised RUNX1 ChIP-seq in SEM cells following NT siRNA treatment

city: Oxford

first: Thomas

last: Milne

address: MRC MHU, WIMM, John Radcliffe Hospital

department: Radcliffe Department of Medicine

country: United Kingdom

institute: University of Oxford

description:
ChIP-seq performed using RUNX1 antibody in SEM cells following NT siRNA treatment
SEM_RUNX1-NT_RUNX1_peaks.txt

library_source: genomic

data_processing:
Alignment to the genome (Bowtie) maintaining strict read order
Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible)
Removal of PCR duplicates, parsing of informative reads using samtools rmdup
Genome_build: hg19
Supplementary_files_format_and_content: Peak calling using Homer v4.7

molecule: genomic DNA

source_name: Leukemia cell line (SEM)

growth_protocol: Cells were continuously grown in IMDM with 10% FBS, split when they reached a density of 1-2x10e6 cells/ml down to 5x10e5 cells/ml

extract_protocol:
Cells were washed with PBS and fixed in either 1% FA for 10 minutes (histones) or 2mM DSG for 30 minutes and 1% FA for 30 minutes (EZH2). For reference normalisation 10% S2 cells were spiked in prior to sonication. Cells were sonicated to give fragments of 100-300bp followed by IP.
DNA libraries were made using the NEBnext ultra DNA library preparation kit for Illumina (Cat no. E7370).

treatment_protocol: Cells were either untreated, or electroporated with non-targeting or RUNX1 targeting siRNA

value: Bone marrow aspirate from a 15-year old MLL-AF4 ALL patient

tag: chip antibody

value: Abcam ab23980

tag: sirna

value: non-targeting siRNA (Dharmacon D-001810-10-20)


title: THP-1 sgSCR LPS 4 hour replicate 1

description:
SCR-LPS4h-1_S35
LPS_WT_vs_KO_normalizedcounts.csv
counts_LPS.txt

value: expressing Cas9 and non-targeting (Scramble) sgRNA


title: Ctrl MS1 cells Rep 2

value: pCDH-puro


title: ChIP-seq input for RUNX1 in THP1 cell line

description:
ChIP-seq performed using RUNX1 antibody in THP1 cells
THP1_RUNX1_peaks.txt

source_name: Leukemia cell line (THP1)

value: Paediatric monocytic cell line derived from AML M5 with t(9;11)(q21;q23) translocation


title: Ctrl MS1 cells Rep 3


title: RUNX1 ChIP-seq in THP1 cells


title: Ctrl MS1 cells Rep 1


title: MS1 cells expressing TAZ-CAMTA1 Rep 2


title: AF4-C ChIP-seq in MLL-AF4 ALL patient blasts

description:
ChIP-seq performed using AF4-C antibody in MLL-AF4 ALL patient blast
ALL_blast_AF4_peaks.txt

source_name: MLL-AF4 ALL patient blasts

extract_protocol:
Cells were washed with PBS and fixed in either 1% FA for 10 minutes (histones) or 2mM DSG for 30 minutes and 1% FA for 30 minutes (EZH2). Cells were sonicated to give fragments of 100-300bp followed by IP.
DNA libraries were made using the NEBnext ultra DNA library preparation kit for Illumina (Cat no. E7370).

value: Abcam ab31812


title: MAZ ChIP-seq in SEM cells

description:
ChIP-seq performed using MAZ antibody in SEM cells
SEM_MAZ_peaks.txt

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

value: Bethyl A301-652A


title: ChIP-seq input for MLL-N and AF4-C in MLL-AF4 ALL patient blasts

description:
ChIP-seq performed using AF4-C antibody in MLL-AF4 ALL patient blast
ALL_blast_MLL_peaks.txt
ALL_blast_AF4_peaks.txt


title: H3K27ac-CTL1-HiChIP-seq

city: Nanjing

first: Jingping

last: Yang

state: Jiangsu

address: 22 Hankou Road

department: Medical School

country: China

institute: Nanjing University

description: DNA (HiChIP)

data_processing:
Library strategy: HiChIP
HiChIP-seq was processed using HiC-Pro on hg19.
Genome_build: hg19
Supplementary_files_format_and_content: .hic format

source_name: human podocyte

growth_protocol: human podocyte were grown in RPMI-1640 medium with 10% FBS, 1% insulin-transferrin-selenium (ITS) and 1% penicillin-streptomycin at 33. Podocyte began to differentiate at 37.

extract_protocol:
Cells were treated with 1uM DEX for 5 days.
libraries were constructed according to  the Illumina instruction

treatment_protocol: Differentiated human podocyte were treated with 1uM DEX for 5 days

value: Abcam, ab4729

tag: tissue

value: podocyte


title: THP-1 sgSCR untreated replicate 1

description:
SCR-UT-1_S32
LPS_WT_vs_KO_normalizedcounts.csv
counts_LPS.txt

value: Untreated control


title: GR-1h-ChIP-seq

data_processing:
ChIP-seq clean reads were aligned to hg19 or hg38 genome and call peaks use Macs2.
Genome_build: hg19,hg38
Supplementary_files_format_and_content: bed, bedgraph, hic

source_name: Podocyte

growth_protocol: The cells grew at 33°and differentiated at 37°

extract_protocol: libraries were constructed according to  the Illumina instruction

treatment_protocol: treat with 1uM DEX for 5 days or 1h

value: Santa Cruz Biotechnology, sc1003x

value: DEX 1h

value: Podocyte


title: H3K27ac-DEX2-HiChIP-seq

description:
DNA (HiChIP)
processed data file available on GSM3444788


title: MLL-N ChIP-seq in MLL-AF4 ALL patient blasts

description:
ChIP-seq performed using MLL-N antibody in MLL-AF4 ALL patient blast
ALL_blast_MLL_peaks.txt

value: Bethyl A300-086A


title: RNA-seq-CTL1

description: rRNAs depleted RNA

data_processing:
ChIP-seq reads were aligned using Bowtie2 on hg19. Peaks are called using MACS2
RNA-seq reads were aligned using HISAT2 on hg38. Aligned reads were assembled using StringTie and StringTie's output was processed by DESeq2.
HiChIP-seq was processed using HiC-Pro on hg19.
Genome_build: hg19, hg38


title: RNA-seq-DEX1

description: rRNAs depleted RNA


title: RNA-seq-DEX2

description: rRNAs depleted RNA


title: RNA-seq-CTL2

description: rRNAs depleted RNA


title: input

description: DNA


title: H3K27ac-CTL2-HiChIP-seq

description:
DNA (HiChIP)
processed data file available on GSM3444790


title: 6_WRKY14-RFP_ChIP_rep2

city: Sinagpore

first: Daisuke

last: Urano

address: 1 Research Link

country: Singapore

institute: Temasek Life Science Laboratory

data_processing:
1-5: STAR for genome mapping; 6: Botwie 2 for genome mapping
Genome_build: Arabidopisis: TAIR10; Marantica v3.1; Ricd: MSU7
Supplementary_files_format_and_content: 1-5: raw counts; 6: bigwig

organism: Marchantia polymorpha

source_name: gemmalings

growth_protocol: 1: 7-day-old Col-0  seedlings liquid grown in 1/2 MS, continuous light; 2: 7-day-old Tak1 gemma liquid grown in 1/2 B5, continuous light; 3: 7-day-old Col-0 and wrky25/33 ko mutant  seedlings liquid grown in 1/2 MS, continuous light; 4: 7-day-old NB seedlings grwon on 1/2 MS plates, 16/8 Light/Dark cycle; 5: 7-day-old Tak1 gemma liquid grown in 1/2 B5, continuous light; 6: 14-day-old Tak1 and respecitive WRKY 0E lines gemma liquid grown in 1/2 B5, continuous light

extract_protocol:
1-5: Plant samples were frozen in liquid nitrogen, and followed by RNA extraction using Rneasy Plant Mini Kit (Qiagen); 6: Nuclei was carried out by standard ChIP protocol, pull-down by tagRFP TRAP (Chromotek)
1-5: RNA libraries were prepared for sequencing using standard Illumina protocols; 6: Libraries were prepared according to Illumina's instructions

treatment_protocol: 1/2 Ms + 100 mM NaCl treatment for 0, 1, 3, 6, 12, 24, 48 and 72 hr

value: gemmalings

tag: day

value: MpWRKY14-tagRFP overexpression


title: 6_WRKY6-RFP_ChIP_rep2

value: MpWRKY6-tagRFP overexpression


title: 6_WRKY12-RFP_ChIP_rep2

value: MpWRKY12-tagRFP overexpression


title: 6_WRKY1-RFP_ChIP_rep2

value: MpWRKY1-tagRFP overexpression


title: 6_WRKY14-RFP_ChIP_rep1


title: 6_tak1_ChIP_rep2

value: Tak1, WT


title: 6_RFP_ChIP_rep2

value: tagRFP overexpression


title: GR-ChIP-seq

description: DNA

value: Santa Cruz,  sc1003


title: H3K27ac-DEX1-HiChIP-seq

description: DNA (HiChIP)


title: H3K27ac-DEX-ChIP-seq

description: DNA


title: H3K27ac-CTL-ChIP-seq

description: DNA


title: 6_WRKY6-RFP_ChIP_rep1


title: 6_WRKY12-RFP_ChIP_rep1


title: overexpression_control_rep_3

type: RNA

city: New York

first: Milad

last: Ibrahim

state: NY

address: 550 1st Avenue

department: Dermatology

institute: NYU Langone

hyb_protocol: cRNA were cleaned up, fragmented, and 5 µg cRNA were hybridized for 16 hours at 45C on affymetrix human gene 2.0 ST array GeneChip. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000 high resolution scanner (M10).

data_processing: The data were analyzed with affymetrix expression console using Multi-array Analysis (RMA) to obtain probeset expression value

label: biotin

source_name: A375 cell line overexpressing beta galactosidase

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 µg total RNA

growth_protocol: cells were cultured and routinely passaged to be maintained in the exponential phase in high glucose DMEM (Bio-Sera) supplemented with 10% Foetal Bovine Serum (Gibco), 100µg/ml primocin (Invivogen) and 300µg/m L-glutamine (Lab-tech). Cells were grown at 37°C in a 5% CO2 humidified atmoshphere

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

treatment_protocol: retroviral overexpression and lentiviral knockdown was maintained using G418 at 2µg/ml and puromycin at 2µg/ml respectively. Antibiotics were omitted 72 hours prior to RNA extraction

value: Human malignant melanoma cells

tag: genotype/variation

value: overexpressing beta galactosidase


title: knockdown_control_rep_3

source_name: A375 cell line scrambled shRNA control

value: scrambled shRNA control


title: 6_WRKY1-RFP_ChIP_rep1


title: TF ChIP-seq from HEK293 (ENCLB014YOP)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR348AGV/
***************
biological replicate number: 1
technical replicate number: 2
description: SETDB1 ChIP-seq on human HEK293
experiment encode accession: ENCSR348AGV
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR938LXW
encode release date: 2017-06-01
lab: Peggy Farnham, USC
library encode accession: ENCLB014YOP
fragmentation methods: see document

data_processing: See GSM*_README.txt supplementary file linked below

source_name: Homo sapiens HEK293 cell line

tag: antibody

tag: line

value: cell line

tag: description

value: Embryonic kidney, cells contain Adenovirus 5 DNA

tag: biosample encode accession

tag: Sex

value: female

tag: dev stage

value: embryonic

tag: age

value: unknown

tag: lab

value: Peggy Farnham, USC

tag: source

value: ATCC

tag: health state

tag: link

value: ENCBS253HIE at ENCODE; https://www.encodeproject.org/ENCBS253HIE/

value: Derived from ENCODE donor ENCDO000ABF; https://www.encodeproject.org/ENCDO000ABF/


title: 6_RFP_ChIP_rep1

value: gemmalings

tag: genotype


title: TF ChIP-seq from HEK293 (ENCLB656LGM)

description:
https://www.encodeproject.org/experiments/ENCSR348AGV/
***************
biological replicate number: 1
technical replicate number: 1
description: SETDB1 ChIP-seq on human HEK293
experiment encode accession: ENCSR348AGV
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR938LXW
encode release date: 2017-06-01
lab: Peggy Farnham, USC
library encode accession: ENCLB656LGM
fragmentation methods: see document


title: Control ChIP-seq from HEK293 (ENCLB204MWY)

description:
https://www.encodeproject.org/experiments/ENCSR938LXW/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on human HEK293
experiment encode accession: ENCSR938LXW
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2017-06-01
lab: Peggy Farnham, USC
library encode accession: ENCLB204MWY
fragmentation methods: see document


title: 6_tak1_ChIP_rep1


title: Control ChIP-seq from fibroblast of lung (ENCLB695AQF)

description:
https://www.encodeproject.org/experiments/ENCSR000AMZ/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq on human NHLF
experiment encode accession: ENCSR000AMZ
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2011-02-10
lab: Bradley Bernstein, Broad
library encode accession: ENCLB695AQF
fragmentation methods: see document

source_name: Homo sapiens female child (11 years) fibroblast of lung primary cell

value: fibroblast of lung

value: primary cell

value: child

value: 11 year

value: Bradley Bernstein, Broad

value: Lonza

value: ENCBS149EDI at ENCODE; https://www.encodeproject.org/ENCBS149EDI/

value: Derived from ENCODE donor ENCDO156MSV; https://www.encodeproject.org/ENCDO156MSV/


title: overexpression_control_rep_2

tag: cell line

tag: cell type

value: Human malignant melanoma cells

value: overexpressing beta galactosidase


title: IMR90_rep2_steadyState

city: Long Island City

first: Alyssa

last: Fronk

address: 30-02 48th Avenue, Suite 140

institute: Envisagenics

data_processing:
RNA-seq reads were aligned using STAR (v2.6.1b) to a custom genome containing both the human (hg19) and drosophila (dm3) genomes using the following parameters: outFilterMultimapNmax = 1, outFilterScoreMinOverLread = 0.51, outFilterMatchNminOverLread = 0.51, outFilterMismatchNmax = 4, alignIntronMax = 50000, twopassMode = basic.
MarkDuplicates (picard-tools v2.3.0) was used with the default parameters to mark PCR duplications within the mapped reads.
BigWig files were generated using deepTools (v3.3.0) bamCoverage (including the flag --ignoreDuplicates).
Genome_build: hg19, dm3
Supplementary_files_format_and_content: bigWig files were generated using deepTools (v3.3.0) bamCoverage using the default parameters

organism:
Drosophila melanogaster
Homo sapiens

source_name: IMR90 lung fibroblasts, S2 cells

growth_protocol: IMR90 primary human fetal lung fibroblast cells (ATCC) were cultured in MEM supplemented with 10% fetal bovine serum (FBS) and 1x Penicillin-Streptomycin (pen-strep) solution. A549 lung cancer cells (ATCC) were cultured in RPMI supplemented with 10% FBS and 1x pen-strep solution.

extract_protocol:
At each 5 minute time point, one plate of cells was removed from the incubator, washed once in ice cold 1x PBS, then 1mL of Cytoplasmic Lysis Buffer + S2 cells (CL+S2 buffer, 25mM Tris pH 7.9, 150mM NaCl, 0.1mM EDTA, 0.1% TritonX, 1mM DTT, 1x protease inhibitor cocktail, 1.3x10^6 S2 cells/mL) was added directly to the plate. Cells were collected by scraping and kept on ice until the end of the time course. After all samples were collected and incubated in CL+S2 buffer on ice for at least 10 min, the lysates were centrifugated at 3000 RPM for 5 min at 4C. The supernatant was removed and the pellet was washed in 1 mL CL buffer (without S2 cells) and re-centrifugated at the same speed. The pellet was then resuspended in 100μL Glycerol Resuspension Buffer (GR buffer, 20mM Tris pH 7.9, 75mM NaCl, 0.5mM EDTA, 50% glycerol, 0.85mM DTT), to which 1.1mL Nuclear Lysis Buffer (NL buffer, 20mM HEPES pH 7.6, 300mM NaCl, 7.5mM MgCl2, 1% NP-40, 1mM DTT, 1M Urea) was subsequently added. The resulting lysate was incubated on ice (with regular vortexing) for 15 min, then centrifugated at 16,000G for 10 min at 4C. The resulting chromatin pellet was resuspended in TRIzol (Invitrogen, 15596018) and RNA was extracted according to the manufacturer’s protocol. To ensure complete depletion of mRNA, the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490L) was used to capture and remove polyA mRNA. The manufacturer’s protocol was followed until the mRNA was bound to the beads. Following mRNA binding, the supernatant was removed from the beads and the nascent RNA was ethanol precipitated and resuspended in ddH2O. Nascent RNA was quantified on a Denovix QFX fluorometer using the Qubit RNA HS assay according to the manufacturer’s protocol. The quality of the RNA was assessed using an Aligent 2100 Expert Bioanalyzer instrument.
Sequencing libraries were generated using the KAPA Stranded RNA-seq Kit with RiboErase (HMR) (Roche 07962282001) according to the manufacturers protocol. Final libraries were also subjected to bioanalyzer runs to ensure proper fragment length distribution. All 9 libraries were barcoded and sequenced together on 2 lanes of an Illumina HiSeq (paired-end 150 bp reads).

treatment_protocol: Cells were treated with 100μM 5,6-Dichlorobenzimidazole 1-β-D-ribofuranoside (DRB) or DMSO as a vehicle control for 3 hours. After 3 hours, cells were washed twice in 37C 1x PBS and 37C fresh media was added to each plate, except the 0 minute time point, which was never washed out. Cells were immediately put back in the 37C incubator.

tag: human cell line

tag: time point

value: steadyState

tag: strain

value: S2 cells

tag: molecule subtype

value: nascent RNA


title: IMR90_rep2_0min

value: primary human fetal lung fibroblast cells


title: IMR90_rep2_25min


title: IMR90_rep2_35min


title: IMR90_rep2_5min


title: IMR90_rep2_30min


title: IMR90_rep2_15min


title: IMR90_rep2_20min


title: knockdown_rep_3

source_name: A375 cell line shRNA knockdown of Ambra1

tag: genotype/variation

value: shRNA knockdown of Ambra1


title: Control ChIP-seq from K562 (ENCLB775EPZ)

description:
https://www.encodeproject.org/experiments/ENCSR387OYT/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR387OYT
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-03-26
lab: Michael Snyder, Stanford
library encode accession: ENCLB775EPZ
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting ZNF281

tag: line

value: cell line

value: female

value: adult

value: 53 year

value: Michael Snyder, Stanford

value: Kevin White

value: chronic myelogenous leukemia (CML)

value: ENCBS352HHS at ENCODE; https://www.encodeproject.org/ENCBS352HHS/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: IMR90_rep1_25min


title: IMR90_rep2_10min


title: IMR90_rep1_20min


title: IMR90_rep1_steadyState


title: IMR90_rep1_30min


title: IMR90_rep1_0min


title: IMR90_rep1_5min


title: IMR90_rep1_35min


title: knockdown_rep_2


title: Control_4

city: Gottingen

first: Andre

last: Fischer

state: NS

address: Von Sieboldstr 3a

department: Epigenetic Mechanisms in Dementia

country: Germany

institute: German Center for Neurodegenerative Diseases (DZNE)

data_processing:
Base calling and fastq.gz conversion were performed using Illumina pipeline scripts.
Reads were mapped to mouse genome mm10.
Reads were counted using FeaturesCount.
Genome_build: mm10
Supplementary_files_format_and_content: Count files.

source_name: Postnatal cortex

extract_protocol:
RNA was isolated using TRIZOL from whole tissue.
Libraries for RNA-Seq were prepared using Illumina TruSeq RNA Sample Preparation v2 Kit.


title: knockdown_control_rep_2

value: scrambled shRNA control


title: Mutant_1


title: Control_1


title: Control_3


title: Mutant_3


title: Mutant_4


title: Control_2


title: Mutant_2


title: knockdown_control_rep_1

value: Human malignant melanoma cells


title: SSC_mouse_rep2

city: Shanghai

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

institute: Shanghai Jiao Tong University

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Illumina GenomeStudio

source_name: spermatogonial stem cells

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPre RNA Amplification kit (IL1791) for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit according to the prescribed protocol provided with the kit. Quality control was performed with nanodrop-1000 and electrophoresis.

value: spermatogonial stem cells


title: A549_rep2_30min

source_name: A549 lung adenocarcinoma cells, S2 cells

value: lung adenocarcinoma cells


title: A549_rep2_25min

value: S2 cells


title: A549_rep2_steadyState

value: steadyState

value: nascent RNA


title: IMR90_rep1_10min

value: primary human fetal lung fibroblast cells


title: A549_rep2_0min


title: IMR90_rep1_15min


title: A549_rep2_5min


title: overexpression_control_rep_1

value: overexpressing beta galactosidase


title: knockdown_rep_1

value: shRNA knockdown of Ambra1


title: SSC_mouse_rep1

description: replicate 1


title: 5_tak1_24h_rep3

tag: tissue

value: gemmalings

tag: day

value: Tak1, WT


title: 5_tak1_24h_rep2


title: 5_tak1_24h_rep1


title: Histone ChIP-seq from MCF-7 (ENCLB677PZB)

description:
https://www.encodeproject.org/experiments/ENCSR610IYQ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR610IYQ
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR768LHG
encode release date: 2017-01-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB677PZB
fragmentation methods: shearing (Covaris generic)
size range: 200-600

source_name: Homo sapiens MCF-7 immortalized cell line

tag: antibody

value: cell line

tag: description

value: mammary epithelium, doubling time ~ 29hoursATCC HTB-22

tag: biosample encode accession

value: 69 year

tag: dev stage

value: adult

tag: Sex

value: female

value: breast cancer (adenocarcinoma)

tag: passage number

value: Bradley Bernstein, Broad

value: ENCBS967MVZ at ENCODE; https://www.encodeproject.org/ENCBS967MVZ/

value: Derived from ENCODE donor ENCDO000AAE; https://www.encodeproject.org/ENCDO000AAE/

value: ENCODE dbxrefs Cellosaurus CVCL_0031; http://web.expasy.org/cellosaurus/CVCL_0031

value: ATCC sample source; http://www.atcc.org/products/all/HTB-22.aspx


title: 5_tak1_2h_rep2

tag: genotype


title: A549_rep2_15min

value: lung adenocarcinoma cells

value: S2 cells

value: nascent RNA


title: A549_rep1_steadyState

value: steadyState


title: 5_tak1_2h_rep3

value: gemmalings


title: A549_rep2_20min


title: A549_rep2_10min


title: overexpression_rep_3

source_name: A375 cell line overexpressing Ambra1

tag: cell line

value: Human malignant melanoma cells

value: overexpressing Ambra1


title: A549_rep1_25min

tag: cell type


title: ESC_R1/E_rep3

description: replicate 3

source_name: embryonic stem cells

value: embryonic stem cells


title: Control ChIP-seq from WTC11 (ENCLB777NYP)

description:
https://www.encodeproject.org/experiments/ENCSR764ZNN/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human WTC11
experiment encode accession: ENCSR764ZNN
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-03-26
lab: Michael Snyder, Stanford
library encode accession: ENCLB777NYP
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens WTC11 cell line

value: cell line

value: male

tag: age

value: 30 year

tag: lab

value: Michael Snyder, Stanford

tag: source

value: Richard Myers

tag: link

value: ENCBS224POW at ENCODE; https://www.encodeproject.org/ENCBS224POW/

value: Derived from ENCODE donor ENCDO882UJI; https://www.encodeproject.org/ENCDO882UJI/


title: A549_rep1_0min

tag: human cell line

tag: time point

tag: strain

tag: molecule subtype


title: A549_rep1_30min


title: 5_tak1_2h_rep1

tag: tissue

tag: day

value: Tak1, WT


title: A549_rep1_5min


title: SSC_mouse_rep3

description: replicate 3

value: spermatogonial stem cells


title: A549_rep1_20min

value: lung adenocarcinoma cells


title: overexpression_rep_1

tag: genotype/variation


title: overexpression_rep_2


title: ESC_R1/E_rep2

description: replicate 2


title: A549_rep1_15min

value: S2 cells


title: ESC_R1/E_rep1

description: replicate 1


title: A549_rep1_35min

value: nascent RNA


title: A549_rep1_10min


title: 5_tak1_0h_rep2


title: TF ChIP-seq from GM23338 (ENCLB457NCM)

description:
https://www.encodeproject.org/experiments/ENCSR591DTH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR591DTH
assay title: TF ChIP-seq
possible controls: ENCSR773IYZ
encode release date: 2018-02-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB457NCM
fragmentation methods: sonication (generic)
size range: 200-600
nucleic acid starting quantity: 20
nucleic acid starting quantity units: ng

source_name: Homo sapiens induced pluripotent stem cell line male adult (53 years) derived from fibroblast of arm

tag: antibody

tag: line

tag: description

value: These are induced pluripotent stem cells (iPSC) created from the PGP1 donor from the Personal Genome Project (PGP).

tag: biosample encode accession

value: 53 year

tag: dev stage

value: adult

value: Thomas Gingeras, CSHL

value: ENCBS368AAA at ENCODE; https://www.encodeproject.org/ENCBS368AAA/

value: Derived from ENCODE donor ENCDO336AAA; https://www.encodeproject.org/ENCDO336AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_F182; http://web.expasy.org/cellosaurus/CVCL_F182

value: Coriell sample source; http://www.ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM23338&PgId=166


title: 1_col-0_72h_rep2

organism: Arabidopsis thaliana

source_name: Seedlings

value: Seedlings

tag: genotype

value: col-0, WT


title: 5_tak1_0h_rep1

source_name: gemmalings

value: gemmalings


title: 1_col-0_72h_rep1


title: 2_tak1_72h_rep2


title: 1_col-0_24h_rep2


title: 1_col-0_48h_rep1


title: 2_tak1_72h_rep1


title: 2_tak1_48h_rep2


title: 1_col-0_48h_rep2


title: 2_tak1_24h_rep2


title: 1_col-0_6h_rep2


title: 1_col-0_12h_rep2


title: 1_col-0_12h_rep1


title: 2_tak1_12h_rep2


title: 1_col-0_24h_rep1


title: 2_tak1_24h_rep1


title: 2_tak1_6h_rep2


title: 5_tak1_0h_rep3


title: 1_col-0_3h_rep2


title: 2_tak1_6h_rep1


title: 1_col-0_3h_rep1


title: A549_DRB_rep3

data_processing:
Reads were aligned to the reference human genome (hg19) using STAR (v2.6.1b) with outFilterMultimapNmax = 1.
MarkDuplicates (picard-tools v2.3.0) was used with the default parameters to mark PCR duplications within the mapped reads.
Cufflinks (v2.2.1) was used to measure the Fragments Per Kilobase of transcript per Million mapped reads (FPKM) using the default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: Text files containing the FPKM values generated using Cufflinks (v2.2.1)

molecule: polyA RNA

source_name: A549 lung adenocarcinoma cells

growth_protocol: IMR90 primary human fetal lung fibroblast cells (ATCC) were cultured in MEM supplemented with 10% fetal bovine serum (FBS) and 1x Penicillin-Streptomycin (pen-strep) solution. A549 lung cancer cells (ATCC) were cultured in RPMI supplemented with 10% FBS and 1x pen-strep solution. Where noted, cells were treated with 25 μM  5,6-Dichlorobenzimidazole 1-β-D-ribofuranoside (DRB) or DMSO for 24 hours.

extract_protocol:
RNA was isolated using TRIzol according to the manufacturer’s protocol. mRNA was enriched using oligo(dT) beads.
Libraries were prepared by Novogene's standard unstranded mRNA library preparation protocol.

tag: cell line

tag: cell type

value: lung adenocarcinoma


title: 2_tak1_3h_rep2

value: Tak1, WT


title: 1_col-0_1h_rep2


title: A549_DRB_rep2


title: 2_tak1_3h_rep1


title: 1_col-0_1h_rep1


title: 2_tak1_48h_rep1


title: A549_DRB_rep1


title: 2_tak1_1h_rep1


title: 2_tak1_12h_rep1


title: 1_col-0_0h_rep2


title: 1_col-0_6h_rep1


title: IMR90_luc_rep3

value: primary human fetal lung fibroblast cells


title: 4_NB_24h_rep3

organism: Oryza sativa Japonica Group

source_name: seedlings

value: seedlings

value: NB, WT


title: 2_tak1_1h_rep2


title: IMR90_luc_rep4


title: 2_tak1_0h_rep1


title: IMR90_luc_rep1


title: S2 Cas9 sgINTS6E CDK9i RNAPII CTD4H8

data_processing:
Sequenced reads were demultiplexed using bcl2fastq (v2.17.1.14)
Basic QC performed on fastq files using FASTQC (v0.11.6)
Fastq files were aligned to a Hg19 or dm3 reference genome performed with Bowtie2 (v2.3.4.1) to generate SAM files
SAM files converted to BAM files using Samtools (v1.9) using view command. BAM files were sorted, indexed and potential PCR duplicates removed using rmdup function
bigWig files were generated from sorted, indexd BAM files using the Deeptools (v3.0.0) BamCoverage function (--normalize using CPM, --smoothLength 150 --binSize 50 -e 200 scaleFactor 1)
Average read density across defined genomic regions were defined using the Deeptools computeMatrix function and plotHeatmap function was used to generate chromatin occupancy heatmaps
Subread (v2.0.0) featureCounts function (-O -M -T 16 -F SAF) was used to count reads within TSS and gene body regions using bedtools (v2.27.1) slop function using UCSC Hg19 or dm3 chromosome sizes
Read density was calculated as RPKM in Rstudio (v3.6.1) using limma (v3.40.6) and edgeR (v.3.26.8) and visualized using ggplot2 (v3.3.1)
Genome_build: Hg19 or dm3
Supplementary_files_format_and_content: bigWig files of RNAPII, CDK9, INTS11, INTS6, BRD4 and RNAPII phospho-ser 2 occupancy across the genome in CPM

organism: Drosophila melanogaster

source_name: Drosophila fruit fly embryonic cell line expressing Cas9 and INTS6 targeting sgRNA

growth_protocol: THP-1 cells were cultured in RPMI-1640 supplemented with 10-20 percent heat-inactivated fetal bovine serum, 100U/mL penicillin, 100µg/mL streptomycin and 2mM GlutaMAX at 37 degrees celciuus and 5 percent carbon dioxide. S2 cells were cultured in Schneider's Drosophila medium supplemented with 10 percent heat-inactivated fetal bovine serum, 100U/mL penicillin, 100µg/mL streptomycin and 2mM GlutaMAX at room temperature and atmospheric carbon dioxide

extract_protocol:
Cells were cross-linked with formaldehyde solution, nuclei were extracted and sonicated using a Covaris. Protein-bound chromatin was isolated using indicated antibody and decrosslinked DNA was isolated using the Zymogen ChIP DNA Clean and Concentrator Kit
ChIP-seq librarys were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB E7645) and 200 - 500 base pair fragments were selected using a Pippin Prep (1.5% agarose, Sage Science)

treatment_protocol: Cells were treated with DMSO (untreated control), CDK9i (AZ5576, 100nM or 170nM 2 hours) or DBK-1154 (10µM 2 hours 15 minutes)

value: Schneiders Drosophila Line 2 (S2)

tag: chip antibody

value: RNA polymerase II, clone CTD4H8 (Millipore 05-623)

tag: treatment

value: CDK9i (AZ5576) 100nM 2 hours


title: IMR90_luc_rep2


title: 4_NB_24h_rep1


title: A549_DMSO_rep3

value: lung adenocarcinoma cells


title: 4_NB_24h_rep2


title: TF ChIP-seq from OCI-LY1 (ENCLB765NHN)

description:
https://www.encodeproject.org/experiments/ENCSR520VTO/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR520VTO
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR569IIN
encode release date: 2017-11-19
lab: Bradley Bernstein, Broad
library encode accession: ENCLB765NHN
fragmentation methods: none
size range: 200-600
nucleic acid starting quantity: 17
nucleic acid starting quantity units: ng

source_name: Homo sapiens OCI-LY1 immortalized cell line

value: cell line

value: established from the bone marrow of a 44-year-old man with B-cell Non-Hodgkin lymphoma (B-NHL; diffuse large cell), stage 4B at relapse in 1983

tag: age

value: 44 year

value: adult

tag: Sex

value: male

tag: health state

value: B cell lymphoma

tag: lab

value: Bradley Bernstein, Broad

tag: link

value: ENCBS397COL at ENCODE; https://www.encodeproject.org/ENCBS397COL/

value: Derived from ENCODE donor ENCDO350AAA; https://www.encodeproject.org/ENCDO350AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1879; http://web.expasy.org/cellosaurus/CVCL_1879


title: 4_NB_2h_rep3

tag: tissue

tag: day

tag: time point


title: A549_DMSO_rep2


title: S2 Cas9 sgINTS6E DMSO RNAPII CTD4H8

value: expressing Cas9 and INTS6 targeting sgRNA

value: DMSO (untreated control) 2 hours


title: 4_NB_2h_rep2

value: seedlings

value: NB, WT


title: S2 Cas9 sgINTS6D CDK9i RNAPII CTD4H8

value: Schneiders Drosophila Line 2 (S2)

value: RNA polymerase II, clone CTD4H8 (Millipore 05-623)


title: A549_rep2_35min

tag: human cell line

value: lung adenocarcinoma cells

tag: strain

value: S2 cells

tag: molecule subtype

value: nascent RNA


title: A549_DMSO_rep1


title: S2 sgINTS6D DMSO RNAPII CTD4H8


title: 4_NB_2h_rep1


title: 1_col-0_0h_rep1

value: Seedlings

value: col-0, WT


title: 2_tak1_0h_rep2

value: gemmalings

value: Tak1, WT


title: Control ChIP-seq from fibroblast of lung (ENCLB695AQE)

description:
https://www.encodeproject.org/experiments/ENCSR000AMZ/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on human NHLF
experiment encode accession: ENCSR000AMZ
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2011-02-10
lab: Bradley Bernstein, Broad
library encode accession: ENCLB695AQE
fragmentation methods: see document

source_name: Homo sapiens male adult (45 years) fibroblast of lung primary cell

value: fibroblast of lung

value: primary cell

tag: description

value: lung fibroblasts

tag: biosample encode accession

value: male

tag: dev stage

value: adult

value: 45 year

value: Bradley Bernstein, Broad

tag: source

value: Lonza

value: unknown

value: ENCBS339AAA at ENCODE; https://www.encodeproject.org/ENCBS339AAA/

value: Derived from ENCODE donor ENCDO269AAA; https://www.encodeproject.org/ENCDO269AAA/


title: human_normal_scar_sample1

city: GuangZhou

first: Hobart

last: Hu

state: GUangDong

address: Road LuJing

institute: Dermatology Hospital of Southern Medical University

data_processing:
The sequencing reads were examined by quality metrics, transcripts were mapped to a reference human genome (hg38) and assigned to individual cells of origin according to the cell specific barcodes, using the Cell Ranger pipeline (10X Genomics). To ensure that PCR amplified transcripts were counted only once, only single UMIs were counted for gene expression level [pmid:24363023]. In this way, cell-gene UMI counting matrices were generated for downstream analyses. From each sample, unwanted variations and low-quality cells were filtered by removing cells with high and low (>6000 and <200) UMI-counts. Meanwhile, to avoid the effects of doublets, cells thatwhich were identified as doublets using Doubletdetection (available from https://github.com/JonathanShor/DoubletDetection) were removed fromin our data.  Gene expression levels for each cell were normalized by the total expression, multiplied by a scale factor (10,000), and log-transformed. Batches were then regressed out, and scaled Z scored residuals of the model were used as normalized expression values. We defined the top 2000 most variable genes based on their average expression and dispersion as highly variable genes (HVG). We reduced the dimensionality of the data by performing principle component analysis (PCA) on HVG. To find cells subpopulations, clustering was performed on PCA scores using significant PCs assigned by a randomization approach proposed by Chung and Storey [pmid:25336500,26000488]. For those replicates (NS1, NS2, NS3 and KF1, KF2, KF3), the first 15 PCs were selected for clustering. To cluster cells, a K-nearest neighbor (KNN) graph constructed on a Euclidean distance matrix in PCA space was calculated and then converted to a shared nearest neighbor (SNN) graph, in order to find highly interconnected communities of cells[pmid:25805722]. Cells were then clustered using the Louvain method to maximize modularity[pmid:30914743]. To display data, the Unsupervised Uniform Manifold Approximation and Projection(UMAP) was applied to cell loadings of selected PCs, and the cluster assignments from the graph-based clustering were used. For cluster numbers higher than two, cluster-specific marker genes were identified by running the ‘find_all_markers’ Seurat function with parameters logfc.threshold = 0.5 and test.use = ’wilcox’. To identify differentially expressed genes between two clusters, we used the ‘find.markers’ Seurat function with logfc.threshold = 0.5 and test.use = ‘wilcox’. All analyses described in this section were performed using Seurat R package version 3.0.1.
Genome_build: hg38
Supplementary_files_format_and_content: count.Matrix.gz

source_name: all dermal cells

growth_protocol: This study was approved by the Medical and Ethics Committees ofDermatology Hospital, Southern Medical University, and each patientsigned an informed consent beforeenrolling in this study.Keloid tissues were harvested during plastic surgery from three patients confirmed to have clinical evidence of keloid (SupplementaryTable S1). No patient had received chemotherapy or radiotherapy prior to surgery. Normal scar tissues were obtained from two patients who underwent elective scar resection surgery(SupplementaryTable S1). Excised skin was immersed in physiological saline and then transferred to the lab immediately. The skin tissue was washed twice with PBS. After removal of the adipose tissue under the reticular dermis, the samples were cut into 5 mm diameter pieces and incubated withdispase II (Sigma)for 2 h at 37°C. The epidermis was peeled off and discarded and the dermis wasminced into small pieces and digested at 37°C for 2 hours using Collagenase IV (YEASEN, China). The resulting cell suspension was filtered through a 70μm cell strainer(BD Falcon), and centrifuged at1500 rpm for 10 min. The supernatant was removed and the pellet was washed oncewith PBS at 1500 rpm for 5 min. The pellet was then resuspended in PBS+1% FBS forflow cytometry.

extract_protocol: Single cell cDNA and library preparation and 3′-end single cell RNA-sequencing was wereperformed by Novogene (Beijing, China). For experiments using the 10×Genomics platform, the Chromium Single Cell 3’ Library & Gel Bead Kit v2 (PN-120237), Chromium Single Cell 3’ Chip kit v2 (PN-120236) and Chromium i7 Multiplex Kit (PN-120262) were usedaccording to the manufacturer’s instructions in the Chromium Single Cell 3’ Reagents Kits v2 User Guide. Thesinglecellsuspensionwaswashed twice with 1×PBS+ 0.04%BSA. The cell number and concentration was confirmed with TC20™ Automated Cell Counter  Approximately 8000 cells were subjected immediately onto the10× Genomics Chromium Controller machine for Gel Beads-in-Emulsion (GEM) generation.mRNA was preparedusing 10x Genomics Chromium Single Cell 3’ reagent kit (V2 chemistry).During this step, cells were partitioned into the GEMs along with Gel Beads coated with oligos.These oligos provide poly-dT sequences to capture mRNAs released after cell lysis inside thedroplets, as well as cell-specific and transcript-specific barcodes (16bp 10× Barcode and 10 bpUnique Molecular Identifier (UMI), respectively).   After RT-PCR, cDNAwas recovered, purified and amplified to generate sufficient quantitiesfor library preparation. Library qualityand concentration were assessed using Agilent Bioanalyzer 2100.  Libraries were run on the Hiseq X or Novaseq for Illumina PE150 sequencing. Post-processing and quality controlwere performed by Novogene using the 10× Cell Ranger package(v2.1.0, 10× Genomics).Reads were aligned to GRCh38 reference assembly (v2.2.0, 10× Genomics).

value: dermal

tag: cell type

value: all dermal cells

tag: sample type

value: normal scar


title: S2 sgSCR DMSO RNAPII CTD4H8

source_name: Drosophila fruit fly embryonic cell line expressing Cas9 and non-targeting (Scramble) sgRNA

tag: cell line

value: Schneiders Drosophila Line 2 (S2)

tag: genotype

tag: chip antibody

value: RNA polymerase II, clone CTD4H8 (Millipore 05-623)

tag: treatment

value: DMSO (untreated control) 2 hours


title: S2 sgSCR CDK9i RNAPII CTD4H8

value: expressing Cas9 and INTS6 targeting sgRNA

value: CDK9i (AZ5576) 100nM 2 hours


title: Histone ChIP-seq from HEK293 (ENCLB374EJC)

description:
https://www.encodeproject.org/experiments/ENCSR910LIE/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K36me3 ChIP-seq on human HEK293
experiment encode accession: ENCSR910LIE
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR938LXW
encode release date: 2017-06-01
lab: Peggy Farnham, USC
library encode accession: ENCLB374EJC
fragmentation methods: see document

source_name: Homo sapiens HEK293 cell line

tag: antibody

tag: line

value: cell line

value: Embryonic kidney, cells contain Adenovirus 5 DNA

tag: Sex

value: female

value: embryonic

tag: age

tag: lab

value: Peggy Farnham, USC

value: ATCC

tag: health state

tag: link

value: ENCBS253HIE at ENCODE; https://www.encodeproject.org/ENCBS253HIE/

value: Derived from ENCODE donor ENCDO000ABF; https://www.encodeproject.org/ENCDO000ABF/


title: human_keloid_sample2

tag: tissue

value: keloid


title: Histone ChIP-seq from HEK293 (ENCLB357IIW)

description:
https://www.encodeproject.org/experiments/ENCSR910LIE/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 ChIP-seq on human HEK293
experiment encode accession: ENCSR910LIE
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR938LXW
encode release date: 2017-06-01
lab: Peggy Farnham, USC
library encode accession: ENCLB357IIW
fragmentation methods: see document

tag: description

tag: biosample encode accession

value: unknown


title: human_keloid_sample3

value: dermal

value: all dermal cells


title: 4_NB_0h_rep1

value: seedlings

tag: day

value: NB, WT

tag: time point


title: human_normal_scar_sample3

tag: cell type

tag: sample type

value: normal scar


title: human_keloid_sample1


title: S2 sgSCR input DNA

tag: cell line

value: Schneiders Drosophila Line 2 (S2)

tag: genotype

value: expressing Cas9 and non-targeting (Scramble) sgRNA

value: RNA polymerase II, clone CTD4H8 (Millipore 05-623)

value: DMSO (untreated control) 2 hours


title: 4_NB_0h_rep2


title: human_normal_scar_sample2


title: 4_NB_0h_rep3


title: FAPP-NM05 Input ChIP-seq

status: Public on May 22 2021

city: Cambridge

first: Ayush

middle: T

last: Raman

state: MA

address: 75 Ames St

department: Epigenomics Program

institute: Broad Institute of MIT and Harvard

description:
FAPP-NM05_G
Input DNA

data_processing:
Raw fastq reads for all ChIP-seq experiments were processed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and aligned to the hg19 reference genome using Bowtie version 1.1.2 with the following criteria: -m 1 --best --strata. Duplicate reads were marked using SAMBLASTER before compression to BAM files. To directly compare FED and FASTED ChIP-seq samples, uniquely mapped reads for each mark were normalized by total reads per condition, sorted and indexed using samtools version 1.9.
Model based analysis of ChIP-seq (MACS) version 1.4.2 peak calling algorithm with a p-value threshold of 1e-5 to identify H3K9bhb, H4K12bhb and H3K27ac enrichment over “input” background.
deepTools version 1.5.11 was used to generate bigWig files by scaling the bam files to reads per kilobase per million (RPKM).
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: *_bed: Bed peak files

source_name: Normal

growth_protocol: Cells were cultured in DMEM, 10% Fetal Bovine Serum (FBS), 1% Penicillin/Streptomycin at 37c, 5% CO2.

extract_protocol:
Cells were crosslinked with both 0.75% formaldehyde and glycine. Chromatin was sheared to 300-700 bp using a Diagenode Bioruptor.
DNA were end-repaired, adapter-ligated using NEBNext Ultra II DNA library prep kit from Illumina and sequenced by Illumina HiSeq2000 at SR-50.

treatment_protocol: Cells did not undergo any treatment.

value: Normal colon

tag: chip-antibody

tag: patient


title: FAPP-NM05 H3K27ac ChIP-seq

description:
FAPP-NM05_C
ChIP-DNA

value: H3K27ac (Abcam ab4729)


title: FAPP-NM03 Input ChIP-seq

description:
FAPP-NM03_G
Input DNA


title: FAPP-NM04 H3K27ac ChIP-seq

description:
FAPP-NM04_C
ChIP-DNA


title: FAPP-NM01 H3K27ac ChIP-seq

description:
FAPP-NM01_C
ChIP-DNA


title: FAPP-NM01 Input ChIP-seq

description:
FAPP-NM01_G
Input DNA


title: FAPP-NM03 H3K27ac ChIP-seq

description:
FAPP-NM03_C
ChIP-DNA


title: FAPP-NM04 Input ChIP-seq

description:
FAPP-NM04_G
Input DNA


title: FAPP-AD03 H3K27ac ChIP-seq

description:
FAPP-AD03_C
ChIP-DNA

source_name: Adenoma

value: Colon adenoma


title: FAPP-AD03 Input ChIP-seq

description:
FAPP-AD03_G
Input DNA


title: FAPP-AD02 Input ChIP-seq

description:
FAPP-AD02_G
Input DNA


title: FAPP-AD02 H3K27ac ChIP-seq

description:
FAPP-AD02_C
ChIP-DNA


title: FAPP-AD01 H3K27ac ChIP-seq

description:
FAPP-AD01_C
ChIP-DNA


title: Noc4l KO BMDM cells + LPS 3

city: Beijing

first: Yongli

last: Qin

address: Yuanmingyuan Road 2

institute: China agricultural university

hyb_protocol: The labeled DNA was dissolved in the hybridization solution (2xgex hyb buffer (HI RPM), 25% formamide) and hybridized overnight at 45 ℃. At the end of hybridization, it was washed in the liquid containing 0.2% SDS and 2 × SSC at 42 ℃ for 5 min, and then washed in 0.2 × SSC at room temperature for 5 min. The slides can be used for scanning after being dried.

scan_protocol: The chip was scanned with Agilent g2565ca microarray scanner to get the hybrid image.

data_processing:
The chip image is analyzed by feature extraction image analysis software, and the image signal is transformed into digital signal.
The original data was input into geneprinting GX software, and the signal value is normalized by percentile shift method. Then the differential gene was screened by absolute fold change ≥ 2 and flag as detected.

source_name: Noc4l KO BMDM cells + LPS

label_protocol: The first strand cDNA was synthesized by cbcscript enzyme by using T7 oligo (DT) primer which contains T7 promoter sequence and starts with total RNA or mRNA. RNase H was used to cut the RNA in the heterozygous chain into short segments. DNA polymerase used RNA short segments as primers to extend, synthesize 2nd strand cDNA and purify double strand cDNA. Using cDNA as a template, the cDNA was synthesized by T7 enzyme mix, and then purified by RNA clean up kit (MN). 5ug of cRNA was reverse transcribe with CBCscript2 enzyme and random prime, and the reverse transcribed product was purified with PCR nucleospinextract II Kit (MN). The reverse transcripts were labeled with Klenow enzyme with random primer. The labeled products were purified with PCR nucleospinextract II Kit (MN).

growth_protocol: The mice were sacrificed by cervical dislocation, and both the femur and tibia were separated. After all muscle tissues were removed from the bones, the bones at both ends were cut, and the bone marrows were crushed with a 25-gauge needle attached to a 10 mL syringe. After washing three times with ice-cold PBS and centrifugation at 1,500 rpm for 5 min at 4 °C, the bone marrows were filtered through a 500 μm nylon mesh. The bone marrow-derived cells were centrifuged, resuspended in differentiation media (DMEM supplemented with 30% L929 supernatant, 10% FBS, 100 U·mL-1 penicillin, and 100 μg·mL-1streptomycin) and plated onto 10 cm cell culture plates. Fresh differentiation media were added to the cultured cells on Day 3 and Day 5. The medium was changed to fresh DMEM containing 10% FBS on Day 6, and BMDMs were attached to the bottom of the culture dishes.

extract_protocol: Using Trizol (Invitrogen, Gaithersburg, MD, USA) to extract total RNA from BMDM cells. The total RNA was further purified by using the nucleospin RNA clean up kit (marcherey-nagel, Germany). At last, the total RNA was quantified by spectrophotometer and inspected by formaldehyde denatured gel electrophoresis

treatment_protocol: BMDMs were treated with 100ng/ml LPS for 16h

tag: genotype/variation

value: Noc4l knockout

value: BMDM

tag: treatment

value: 100ng/ml LPS for 16h


title: Noc4l KO BMDM cells 1

source_name: Noc4l KO BMDM cells


title: Wild Type BMDM cells 3

source_name: Wild Type BMDM cells

value: wild type


title: COAD-T042 Input ChIP-seq

description:
COAD-T042_G
Input DNA

source_name: Tumor Sample

value: Colorectal tumor


title: Noc4l KO BMDM cells 2


title: Wild Type BMDM cells + LPS 3

source_name: Wild Type BMDM cells + LPS


title: Wild Type BMDM cells 2


title: Noc4l KO BMDM cells 3


title: Wild Type BMDM cells + LPS 1


title: Wild Type BMDM cells 1


title: COAD-T042 H3K27ac ChIP-seq

description:
COAD-T042_C
ChIP-DNA


title: Noc4l KO BMDM cells + LPS 2


title: Wild Type BMDM cells + LPS 2


title: Noc4l KO BMDM cells + LPS 1


title: FAPP-AD05 Input ChIP-seq

description:
FAPP-AD05_G
Input DNA


title: COAD-T036 H3K27ac ChIP-seq

description:
COAD-T036_C
ChIP-DNA


title: COAD-T036 Input ChIP-seq

description:
COAD-T036_G
Input DNA


title: COAD-T035 H3K27ac ChIP-seq

description:
COAD-T035_C
ChIP-DNA


title: COAD-T039 Input ChIP-seq

description:
COAD-T039_G
Input DNA


title: FAPP-AD01 Input ChIP-seq

description:
FAPP-AD01_G
Input DNA


title: COAD-T035 Input ChIP-seq

description:
COAD-T035_G
Input DNA


title: COAD-T038 Input ChIP-seq

description:
COAD-T038_G
Input DNA


title: COAD-T037 Input ChIP-seq

description:
COAD-T037_G
Input DNA


title: FAPP-AD05 H3K27ac ChIP-seq

description:
FAPP-AD05_C
ChIP-DNA


title: COAD-T040 Input ChIP-seq

description:
COAD-T040_G
Input DNA


title: COAD-T039 H3K27ac ChIP-seq

description:
COAD-T039_C
ChIP-DNA


title: COAD-T037 H3K27ac ChIP-seq

description:
COAD-T037_C
ChIP-DNA


title: COAD-T034 Input ChIP-seq

description:
COAD-T034_G
Input DNA


title: COAD-T034 H3K27ac ChIP-seq

description:
COAD-T034_C
ChIP-DNA


title: COAD-T032 Input ChIP-seq

description:
COAD-T032_G
Input DNA


title: COAD-T028 Input ChIP-seq

description:
COAD-T028_G
Input DNA


title: COAD-T032 H3K27ac ChIP-seq

description:
COAD-T032_C
ChIP-DNA


title: COAD-T027 Input ChIP-seq

description:
COAD-T027_G
Input DNA


title: COAD-T038 H3K27ac ChIP-seq

description:
COAD-T038_C
ChIP-DNA


title: COAD-T040 H3K27ac ChIP-seq

description:
COAD-T040_C
ChIP-DNA


title: COAD-T033 Input ChIP-seq

description:
COAD-T033_G
Input DNA


title: COAD-T026 Input ChIP-seq

description:
COAD-T026_G
Input DNA


title: COAD-T025 Input ChIP-seq

description:
COAD-T025_G
Input DNA


title: COAD-T026 H3K27ac ChIP-seq

description:
COAD-T026_C
ChIP-DNA


title: COAD-T027 H3K27ac ChIP-seq

description:
COAD-T027_C
ChIP-DNA


title: COAD-T025 H3K27ac ChIP-seq

description:
COAD-T025_C
ChIP-DNA


title: COAD-T024 Input ChIP-seq

description:
COAD-T024_G
Input DNA


title: COAD-T024 H3K27ac ChIP-seq

description:
COAD-T024_C
ChIP-DNA


title: COAD-T023 Input ChIP-seq

description:
COAD-T023_G
Input DNA


title: COAD-T021 Input ChIP-seq

description:
COAD-T021_G
Input DNA


title: COAD-T033 H3K27ac ChIP-seq

description:
COAD-T033_C
ChIP-DNA


title: COAD-T021 H3K27ac ChIP-seq

description:
COAD-T021_C
ChIP-DNA


title: COAD-T023 H3K27ac ChIP-seq

description:
COAD-T023_C
ChIP-DNA


title: COAD-T022 Input ChIP-seq

description:
COAD-T022_G
Input DNA


title: COAD-T028 H3K27ac ChIP-seq

description:
COAD-T028_C
ChIP-DNA


title: COAD-T018 H3K27me3 ChIP-seq

description:
COAD-T018_F
ChIP-DNA

value: H3K27me3 (Abcam ab6002)


title: COAD-T022 H3K27ac ChIP-seq

description:
COAD-T022_C
ChIP-DNA


title: COAD-T018 Input ChIP-seq

description:
COAD-T018_G
Input DNA


title: COAD-T018 H3K4me3 ChIP-seq

description:
COAD-T018_E
ChIP-DNA

value: H3K4me3 (Abcam ab8580)


title: COAD-T018 H3K4me1 ChIP-seq

description:
COAD-T018_A
ChIP-DNA

value: H3K4me1 (Abcam ab8895)


title: COAD-T018 H3K27ac ChIP-seq

description:
COAD-T018_C
ChIP-DNA


title: COAD-T018 H3K9me3 ChIP-seq

description:
COAD-T018_B
ChIP-DNA

value: H3K9me3 (Abcam ab8898)


title: COAD-T017 H3K79me2 ChIP-seq

description:
COAD-T017_D
ChIP-DNA

value: H3K79me2 (Abcam ab3594)


title: COAD-T017 H3K27ac ChIP-seq

description:
COAD-T017_C
ChIP-DNA


title: COAD-T017 H3K9me3 ChIP-seq

description:
COAD-T017_B
ChIP-DNA


title: COAD-T017 H3K27me3 ChIP-seq

description:
COAD-T017_F
ChIP-DNA


title: COAD-T017 H3K4me3 ChIP-seq

description:
COAD-T017_E
ChIP-DNA


title: COAD-T017 H3K4me1 ChIP-seq

description:
COAD-T017_A
ChIP-DNA


title: COAD-T016 Input ChIP-seq

description:
COAD-T016_G
Input DNA


title: COAD-T016 H3K4me3 ChIP-seq

description:
COAD-T016_E
ChIP-DNA


title: COAD-T017 Input ChIP-seq

description:
COAD-T017_G
Input DNA


title: COAD-T016 H3K9me3 ChIP-seq

description:
COAD-T016_B
ChIP-DNA


title: COAD-T016 H3K79me2 ChIP-seq

description:
COAD-T016_D
ChIP-DNA


title: COAD-T016 H3K27me3 ChIP-seq

description:
COAD-T016_F
ChIP-DNA


title: COAD-T015 Input ChIP-seq

description:
COAD-T015_G
Input DNA


title: COAD-T016 H3K4me1 ChIP-seq

description:
COAD-T016_A
ChIP-DNA


title: COAD-T016 H3K27ac ChIP-seq

description:
COAD-T016_C
ChIP-DNA


title: COAD-T015 H3K27me3 ChIP-seq

description:
COAD-T015_F
ChIP-DNA


title: COAD-T015 H3K4me3 ChIP-seq

description:
COAD-T015_E
ChIP-DNA


title: COAD-T015 H3K79me2 ChIP-seq

description:
COAD-T015_D
ChIP-DNA


title: COAD-T015 H3K27ac ChIP-seq

description:
COAD-T015_C
ChIP-DNA


title: COAD-T015 H3K9me3 ChIP-seq

description:
COAD-T015_B
ChIP-DNA


title: COAD-T014 Input ChIP-seq

description:
COAD-T014_G
Input DNA


title: COAD-T014 H3K27me3 ChIP-seq

description:
COAD-T014_F
ChIP-DNA


title: COAD-T014 H3K9me3 ChIP-seq

description:
COAD-T014_B
ChIP-DNA


title: COAD-T014 H3K27ac ChIP-seq

description:
COAD-T014_C
ChIP-DNA


title: COAD-T013 H3K27me3 ChIP-seq

description:
COAD-T013_F
ChIP-DNA


title: COAD-T013 Input ChIP-seq

description:
COAD-T013_G
Input DNA


title: COAD-T014 H3K4me1 ChIP-seq

description:
COAD-T014_A
ChIP-DNA


title: COAD-T013 H3K4me1 ChIP-seq

description:
COAD-T013_A
ChIP-DNA


title: COAD-T013 H3K4me3 ChIP-seq

description:
COAD-T013_E
ChIP-DNA


title: COAD-T012 H3K27ac ChIP-seq

description:
COAD-T012_C
ChIP-DNA


title: COAD-T012 H3K27me3 ChIP-seq

description:
COAD-T012_F
ChIP-DNA


title: COAD-T013 H3K27ac ChIP-seq

description:
COAD-T013_C
ChIP-DNA


title: COAD-T011 H3K27me3 ChIP-seq

description:
COAD-T011_F
ChIP-DNA


title: COAD-T011 Input ChIP-seq

description:
COAD-T011_G
Input DNA


title: COAD-T012 Input ChIP-seq

description:
COAD-T012_G
Input DNA


title: COAD-T012 H3K9me3 ChIP-seq

description:
COAD-T012_B
ChIP-DNA


title: COAD-T012 H3K4me3 ChIP-seq

description:
COAD-T012_E
ChIP-DNA


title: COAD-T011 H3K4me3 ChIP-seq

description:
COAD-T011_E
ChIP-DNA


title: COAD-T015 H3K4me1 ChIP-seq

description:
COAD-T015_A
ChIP-DNA


title: COAD-T011 H3K27ac ChIP-seq

description:
COAD-T011_C
ChIP-DNA


title: COAD-T014 H3K79me2 ChIP-seq

description:
COAD-T014_D
ChIP-DNA


title: COAD-T011 H3K9me3 ChIP-seq

description:
COAD-T011_B
ChIP-DNA


title: COAD-T011 H3K79me2 ChIP-seq

description:
COAD-T011_D
ChIP-DNA


title: COAD-T014 H3K4me3 ChIP-seq

description:
COAD-T014_E
ChIP-DNA


title: COAD-T011 H3K4me1 ChIP-seq

description:
COAD-T011_A
ChIP-DNA


title: COAD-T010 Input ChIP-seq

description:
COAD-T010_G
Input DNA


title: COAD-T010 H3K27me3 ChIP-seq

description:
COAD-T010_F
ChIP-DNA


title: COAD-T013 H3K79me2 ChIP-seq

description:
COAD-T013_D
ChIP-DNA


title: COAD-T010 H3K27ac ChIP-seq

description:
COAD-T010_C
ChIP-DNA


title: COAD-T010 H3K79me2 ChIP-seq

description:
COAD-T010_D
ChIP-DNA


title: COAD-T010 H3K4me3 ChIP-seq

description:
COAD-T010_E
ChIP-DNA


title: COAD-T008 Input ChIP-seq

description:
COAD-T008_G
Input DNA


title: COAD-T013 H3K9me3 ChIP-seq

description:
COAD-T013_B
ChIP-DNA


title: COAD-T008 H3K27me3 ChIP-seq

description:
COAD-T008_F
ChIP-DNA


title: COAD-T012 H3K4me1 ChIP-seq

description:
COAD-T012_A
ChIP-DNA


title: COAD-T010 H3K4me1 ChIP-seq

description:
COAD-T010_A
ChIP-DNA


title: COAD-T012 H3K79me2 ChIP-seq

description:
COAD-T012_D
ChIP-DNA


title: COAD-T008 H3K9me3 ChIP-seq

description:
COAD-T008_B
ChIP-DNA


title: COAD-T008 H3K4me3 ChIP-seq

description:
COAD-T008_E
ChIP-DNA


title: COAD-T007 Input ChIP-seq

description:
COAD-T007_G
Input DNA


title: COAD-T008 H3K79me2 ChIP-seq

description:
COAD-T008_D
ChIP-DNA


title: COAD-T007 H3K4me3 ChIP-seq

description:
COAD-T007_E
ChIP-DNA


title: COAD-T007 H3K27me3 ChIP-seq

description:
COAD-T007_F
ChIP-DNA


title: COAD-T008 H3K4me1 ChIP-seq

description:
COAD-T008_A
ChIP-DNA


title: COAD-T008 H3K27ac ChIP-seq

description:
COAD-T008_C
ChIP-DNA


title: COAD-T007 H3K27ac ChIP-seq

description:
COAD-T007_C
ChIP-DNA


title: COAD-T007 H3K79me2 ChIP-seq

description:
COAD-T007_D
ChIP-DNA


title: COAD-T007 H3K4me1 ChIP-seq

description:
COAD-T007_A
ChIP-DNA


title: COAD-T007 H3K9me3 ChIP-seq

description:
COAD-T007_B
ChIP-DNA


title: COAD-T006 Input ChIP-seq

description:
COAD-T006_G
Input DNA


title: COAD-T006 H3K27me3 ChIP-seq

description:
COAD-T006_F
ChIP-DNA


title: COAD-T006 H3K9me3 ChIP-seq

description:
COAD-T006_B
ChIP-DNA


title: COAD-T006 H3K4me3 ChIP-seq

description:
COAD-T006_E
ChIP-DNA


title: COAD-T006 H3K27ac ChIP-seq

description:
COAD-T006_C
ChIP-DNA


title: COAD-T006 H3K4me1 ChIP-seq

description:
COAD-T006_A
ChIP-DNA


title: COAD-T010 H3K9me3 ChIP-seq

description:
COAD-T010_B
ChIP-DNA


title: COAD-T005 H3K27me3 ChIP-seq

description:
COAD-T005_F
ChIP-DNA


title: COAD-T005 Input ChIP-seq

description:
COAD-T005_G
Input DNA


title: COAD-T005 H3K4me3 ChIP-seq

description:
COAD-T005_E
ChIP-DNA


title: COAD-T005 H3K79me2 ChIP-seq

description:
COAD-T005_D
ChIP-DNA


title: COAD-T005 H3K9me3 ChIP-seq

description:
COAD-T005_B
ChIP-DNA


title: COAD-T004 Input ChIP-seq

description:
COAD-T004_G
Input DNA


title: COAD-T005 H3K27ac ChIP-seq

description:
COAD-T005_C
ChIP-DNA


title: COAD-T004 H3K27ac ChIP-seq

description:
COAD-T004_C
ChIP-DNA


title: COAD-T004 H3K4me3 ChIP-seq

description:
COAD-T004_E
ChIP-DNA


title: COAD-T005 H3K4me1 ChIP-seq

description:
COAD-T005_A
ChIP-DNA


title: COAD-T004 H3K4me1 ChIP-seq

description:
COAD-T004_A
ChIP-DNA


title: COAD-T004 H3K9me3 ChIP-seq

description:
COAD-T004_B
ChIP-DNA


title: COAD-T004 H3K79me2 ChIP-seq

description:
COAD-T004_D
ChIP-DNA


title: COAD-T003 H3K27me3 ChIP-seq

description:
COAD-T003_F
ChIP-DNA


title: COAD-T003 H3K27ac ChIP-seq

description:
COAD-T003_C
ChIP-DNA


title: COAD-T003 H3K79me2 ChIP-seq

description:
COAD-T003_D
ChIP-DNA


title: COAD-T003 H3K4me1 ChIP-seq

description:
COAD-T003_A
ChIP-DNA


title: COAD-T003 H3K9me3 ChIP-seq

description:
COAD-T003_B
ChIP-DNA


title: COAD-T001 Input ChIP-seq

description:
COAD-T001_G
Input DNA


title: COAD-T003 H3K4me3 ChIP-seq

description:
COAD-T003_E
ChIP-DNA


title: COAD-T001 H3K27me3 ChIP-seq

description:
COAD-T001_F
ChIP-DNA


title: COAD-T001 H3K79me2 ChIP-seq

description:
COAD-T001_D
ChIP-DNA


title: COAD-T001 H3K9me3 ChIP-seq

description:
COAD-T001_B
ChIP-DNA


title: COAD-T001 H3K4me3 ChIP-seq

description:
COAD-T001_E
ChIP-DNA


title: COAD-T001 H3K4me1 ChIP-seq

description:
COAD-T001_A
ChIP-DNA


title: COAD-T001 H3K27ac ChIP-seq

description:
COAD-T001_C
ChIP-DNA


title: COAD-N020 Input ChIP-seq

description:
COAD-N020_G
Input DNA


title: COAD-N020 H3K27me3 ChIP-seq

description:
COAD-N020_F
ChIP-DNA


title: COAD-N020 H3K79me2 ChIP-seq

description:
COAD-N020_D
ChIP-DNA


title: COAD-N020 H3K4me3 ChIP-seq

description:
COAD-N020_E
ChIP-DNA


title: COAD-N020 H3K9me3 ChIP-seq

description:
COAD-N020_B
ChIP-DNA


title: COAD-N020 H3K4me1 ChIP-seq

description:
COAD-N020_A
ChIP-DNA


title: COAD-T003 Input ChIP-seq

description:
COAD-T003_G
Input DNA


title: COAD-N018 Input ChIP-seq

description:
COAD-N018_G
Input DNA


title: COAD-N018 H3K79me2 ChIP-seq

description:
COAD-N018_D
ChIP-DNA


title: COAD-N018 H3K4me3 ChIP-seq

description:
COAD-N018_E
ChIP-DNA


title: COAD-N018 H3K27ac ChIP-seq

description:
COAD-N018_C
ChIP-DNA


title: COAD-N018 H3K9me3 ChIP-seq

description:
COAD-N018_B
ChIP-DNA


title: Gx40%-2

city: Tianjin

first: Lixuejing

middle: huanglonghui

last: zhongcheng

address: 13th Street, Binhai New Area, Tianjin City

institute: Tianjin University of Science and Technology

data_processing:
Illumina Casava1.8 software used for basecalling.
Reference genome and gene model annotation files were downloaded from genome website directly. Both building index of reference genome and aligning clean reads to reference genome were used Bowtie2-2.2.3.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then 2 FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels .
Genome_build:  CP024644.1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Komagataeibacter xylinus

source_name: bacteria

extract_protocol:
Total RNA was used as input material for the RNA sample preparations. For prokaryotic samples, mRNA was purified from total RNA using probes to remove rRNA. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. And in the DNA polymerase I system, use dUTP to replace the dNTP of dTTP as the raw material to synthesize the second strand of cDNA. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. Then USER Enzyme was used to degrade the second strand of cDNA containing U, In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.

tag: strain

value: CGMCC 2955

value: control

tag: oxygen %


title: CK-2

city: Chengdu

first: Zhenyu

last: Bai

address: 211 Huimin Road, Wenjiang District

institute: Sichuan Agricultural University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads Vontaining adapter, reads Vontaining ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index  of  the  reference  genome  was  built  using  Bowtie  v2.0.6  and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to  this  gene, Vonsidering the effect of sequencing depth and gene length for the reads count at the same time(Mortazavi et al., 2008)
Genome_build: http://www.mbkbase.org/Pinku1/
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Chrysanthemum x morifolium

source_name: roots

growth_protocol: Chrysanthemum “jinba” grown in the greenhouse (16 h photoperiod, 23±2℃ temperature)

extract_protocol:
Chrysanthemums' roots were sampled, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 3 ug of total RNA for the Vonstruction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The control group  (CK-1, CK-2, CK-3) watered by purified water, the concentration of salt water in the experimental group was 100mM (T-1, T-2, T-3). The seedings were grown under the circumstance of 23±2℃, photoperiod of 16 hours, respectively moisty of 75%.The samples were collected from the root of white seedlings after 24 hours from processing.The roots samples were immediately frozen in liquid nitrogen and stored at -80°C.It’s three biological replicates per treatment for subsequent RNA extraction and analysis..

value: jinba

value: roots

tag: age


title: T-3


title: T-2


title: Gx40%-3


title: CK-3


title: T-1


title: Gx21%-3


title: CK-1


title: Gx40%-1


title: COAD-N017 Input ChIP-seq

description:
COAD-N017_G
Input DNA

value: Normal colon


title: COAD-N017 H3K4me3 ChIP-seq

description:
COAD-N017_E
ChIP-DNA


title: COAD-N017 H3K27me3 ChIP-seq

description:
COAD-N017_F
ChIP-DNA


title: Gx21%-1


title: Gx21%-2


title: COAD-N017 H3K79me2 ChIP-seq

description:
COAD-N017_D
ChIP-DNA


title: Gx15%-3


title: COAD-N020 H3K27ac ChIP-seq

description:
COAD-N020_C
ChIP-DNA

value: H3K27ac (Abcam ab4729)


title: COAD-N017 H3K27ac ChIP-seq

description:
COAD-N017_C
ChIP-DNA


title: Gx15%-2


title: arca40%-2

value: Arca


title: COAD-N017 H3K4me1 ChIP-seq

description:
COAD-N017_A
ChIP-DNA


title: COAD-N017 H3K9me3 ChIP-seq

description:
COAD-N017_B
ChIP-DNA


title: arca40%-3


title: Gx15%-1


title: COAD-N016 Input ChIP-seq

description:
COAD-N016_G
Input DNA


title: COAD-N018 H3K4me1 ChIP-seq

description:
COAD-N018_A
ChIP-DNA


title: COAD-N016 H3K4me3 ChIP-seq

description:
COAD-N016_E
ChIP-DNA


title: COAD-N016 H3K9me3 ChIP-seq

description:
COAD-N016_B
ChIP-DNA


title: COAD-N016 H3K27ac ChIP-seq

description:
COAD-N016_C
ChIP-DNA


title: COAD-N015 Input ChIP-seq

description:
COAD-N015_G
Input DNA


title: COAD-N015 H3K4me3 ChIP-seq

description:
COAD-N015_E
ChIP-DNA


title: arca21%-2


title: arca21%-1


title: arca21%-3


title: fnr40%-3

value: FNR


title: arca15%-1


title: arca15%-3


title: fnr40%-2


title: COAD-N015 H3K27me3 ChIP-seq

description:
COAD-N015_F
ChIP-DNA


title: fnr40%-1


title: arca15%-2


title: COAD-N015 H3K79me2 ChIP-seq

description:
COAD-N015_D
ChIP-DNA


title: arca40%-1


title: COAD-N016 H3K27me3 ChIP-seq

description:
COAD-N016_F
ChIP-DNA


title: fnr21%-3


title: COAD-N015 H3K27ac ChIP-seq

description:
COAD-N015_C
ChIP-DNA


title: COAD-N015 H3K9me3 ChIP-seq

description:
COAD-N015_B
ChIP-DNA


title: COAD-N016 H3K79me2 ChIP-seq

description:
COAD-N016_D
ChIP-DNA


title: fnr21%-2


title: COAD-N015 H3K4me1 ChIP-seq

description:
COAD-N015_A
ChIP-DNA


title: COAD-N014 H3K27me3 ChIP-seq

description:
COAD-N014_F
ChIP-DNA


title: COAD-N014 Input ChIP-seq

description:
COAD-N014_G
Input DNA


title: COAD-N016 H3K4me1 ChIP-seq

description:
COAD-N016_A
ChIP-DNA


title: fnr15%-3


title: fnr15%-2

value: CGMCC 2956


title: fnr21%-1


title: fnr15%-1


title: COAD-N014 H3K4me3 ChIP-seq

description:
COAD-N014_E
ChIP-DNA


title: COAD-N013 H3K4me3 ChIP-seq

description:
COAD-N013_E
ChIP-DNA


title: COAD-N013 H3K9me3 ChIP-seq

description:
COAD-N013_B
ChIP-DNA


title: COAD-N013 H3K79me2 ChIP-seq

description:
COAD-N013_D
ChIP-DNA


title: COAD-N013 H3K27ac ChIP-seq

description:
COAD-N013_C
ChIP-DNA


title: COAD-N013 Input ChIP-seq

description:
COAD-N013_G
Input DNA


title: COAD-N013 H3K4me1 ChIP-seq

description:
COAD-N013_A
ChIP-DNA


title: Control_02

city: Malaga

first: Cesar

last: Lobato-Fernandez

state: Malaga

address: Bulevar Louis Pasteur 21

department: Biochemistry and Biomolecular Biology

country: Spain

institute: University of Malaga

description: Direct RNA sequencing, gene expression and epitranscriptomic profile

data_processing:
Library strategy: DRS (Direct RNA Sequencing)
Basecalling was carried out with ONT Guppy software (https://community.nanoporetech.com). The resultant reads were filtered by quality (Q>8).
Read alignment was made with minimap2 software (Li, 2018. Bioinformatics 34: 3094–3100) using root transcriptome of maritime pine as reference. The alignment parameters were adjusted for DRS (-uf and -k14).
Differentially expressed (DE) transcripts were identified using the edgeR package for R, the transcripts were normalised by cpm and filtered (2 cpm in at least 2 samples) (Robinson et al., 2010. Bioinformatics 26: 139-140.). The transcripts with FDR < 0.05 were considered as differentially expressed.
Genome_build: Root transcriptome from maritime pine can be consulted at https://fmp.uma.es/sequenceserver/ or can also be obtained on demand from the contact author.
Supplementary_files_format_and_content: Tab-delimited text file includes CPM values for each sample.The column ID is the sequence identifier.

organism: Pinus pinaster

source_name: Water irrigated seedling roots

growth_protocol: Seeds from maritime pine (Pinus pinaster Ait.) from “Sierra Segura y Alcaraz” (Albacete, Spain) were provided by from the Área de Recursos Genéticos Forestales of the Spanish Ministerio de Agricultura, Pesca y Alimentación. Seeds were imbibed in distilled water for 24 h under continuous aeration and germinated in a plastic tray with vermiculite as a substrate. Seedlings were grown in vermiculite in plant growth chambers under 16 h light photoperiod, a luminal intensity of 100 μmol m−2 s−1, a constant temperature of 25 °C and watered twice a week with distilled water.

extract_protocol:
Total root RNA from maritime pine seedlings was isolated following the protocol described by Liao et al. (2004, Preparative Biochemistry & Biotechnology 34: 209–214) and modified by Canales et al. (2012, Frontiers in Plant Science 3: 100). The RNA concentration and purity were determined via spectrophotometry on a Nanodrop ND-1000 (Thermo Scientific, Waltham, MA, USA). Purity was determined through the 260/280 and 260/230 ratios. RNA quality was also determined in a Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA). The concentration was verified with a Qubit 4 Fluorometer (Invitrogen, Paisley, UK) and Qubit RNA BR, Broad-Range, Assay Kit (Invitrogen, Paisley, UK). Samples with a RIN value > 7 were selected to mRNA isolation. The polyA-RNA isolation was performed using Dynabeads™ mRNA Purification Kit (Invitrogen, Paisley, UK) following the manufacturer’s instructions. This process was carried out twice per sample to avoid rRNA contamination. polyA-RNA quality was determined in a Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA). The concentration was verified with a Qubit 4 Fluorometer (Invitrogen, Paisley, UK) and Qubit RNA HS, High Sensitivity, Assay Kit (Invitrogen, Paisley, UK).
Nanopore libraries for DRS were prepared from 1.65 up to 2.18 µg of isolated polyA-RNA using the nanopore Direct RNA Sequencing kit (SQK-RNA001, Oxford Nanopore Technologies, ONT, Oxford, UK) according to manufacturer’s instructions. The poly(T) adapter ligation to the polyA-RNA was performed using T4 DNA ligase (New England Biolabs, Ipswich, MA, USA) in the Quick Ligase reaction buffer (New England Biolabs) for 15 min at room temperature. First-strand cDNA synthesis was carried with SuperScript III Reverse Transcriptase (Thermo Fisher Scientific, Waltham, MA, USA) using the oligo(dT) adapter. The RNA-cDNA hybrid obtained was purified using Agencourt RNAClean XP magnetic beads (Beckman Coulter, Brea, CA, USA). The DRS adapter was ligated to polyA-RNA using T4 DNA ligase (New England Biolabs, Ipswich, MA, USA) in the Quick Ligase reaction buffer (New England Biolabs, Ipswich, MA, USA) for 15 min at room temperature followed by a second purification step using Agencourt beads (as described above). Finally, DRS libraries were loaded onto a R9.4 SpotON Flow Cells (Oxford Nanopore Technologies, Oxford, UK) and sequenced until complete nanopores depletion, around 24 hours of run time.

treatment_protocol: One-month old maritime pine seedlings were used for this experiment. Pine seedlings were randomly subdivided into two different groups, relocated into forestall seedbeds and watered with 80 mL distilled water. After three days of acclimation, the control group was irrigated with 80 mL of water (C) and the experimental group with 80 mL of 3 mM NH4Cl. Root samples were collected at 24 hours post-irrigation and immediately frozen in liquid N. This experiment was carried out three independent times.

value: Root

tag: developmental stage

value: One month-old seedling

tag: provenance

value: Sierra Segura-Alcaraz, Spain

value: water

tag: treatment time


title: Control_03

tag: tissue


title: Control_01


title: Ammonium_02

source_name: 3 mM NH4Cl irrigated seedling roots

value: 3 mM NH4Cl


title: COAD-N012 H3K27me3 ChIP-seq

description:
COAD-N012_F
ChIP-DNA

value: H3K27me3 (Abcam ab6002)


title: COAD-N012 Input ChIP-seq

description:
COAD-N012_G
Input DNA


title: Ammonium_01


title: COAD-N012 H3K4me3 ChIP-seq

description:
COAD-N012_E
ChIP-DNA

value: H3K4me3 (Abcam ab8580)


title: COAD-N012 H3K79me2 ChIP-seq

description:
COAD-N012_D
ChIP-DNA

value: H3K79me2 (Abcam ab3594)


title: COAD-N012 H3K27ac ChIP-seq

description:
COAD-N012_C
ChIP-DNA


title: UN_16_HTSeq

city: Madison

first: Alexandra

last: Linz

state: Wisconsin

address: 1552 University Ave

institute: University of Wisconsin-Madison

data_processing:
The paired-end FASTQ files were split into R1 and R2 files and R1 files were retained for further analysis as previous data contained only single-end reads.
Reads were trimmed using Trimmomatic version 0.3 with the default settings except for a HEADCROP of 5, LEADING of 3, TRAILING of 3,  SLIDINGWINDOW of 3:30, and MINLEN of 36.
After trimming the reads were aligned to the N. aromaticivorans genome sequence (GenBank accession NC_007794.1) using Bowtie2 version 2.2.2 with default settings except the number of mismatches was set to 1.
Aligned reads were mapped to gene locations using HTSeq version 0.6.0 using default settings except for the “reverse” strandedness argument was used.
edgeR version 3.26.8 was used to identify significantly differentially expressed genes from pairwise analyses, using Benjamini and Hochberg false discovery rate (FDR) less than 0.05 as a significance threshold.
Raw sequencing reads were normalized using the reads per kilobase per million mapped reads (RPKM).
Genome_build: NC_007794.1
Supplementary_files_format_and_content: Normalized RPKM read counts

organism: Novosphingobium aromaticivorans DSM 12444

source_name: Bacterial culture

growth_protocol: Cultures were inoculated from an overnight culture of SMB + 1 g/L glucose (2mL pelleted and washed with SMB). The cultures were 25mL of SMB plus the indicated substrates grown overnight. Prior to harvesting for RNA, we add an additional 25mL of media and waited 40 minutes to ensure logarithmic growth.

extract_protocol:
5.7mL of cold 95% ethanol + 5% acid phenol:chloroform was added to 40mL of culture to terminate growth. Cells were harvested by spinning each culture at 6000 rpm for 12 min at 4C. Pellets were resuspended in lysis buffer (20mL 10% sDS + 3.2mL 500mM EDTA + 76.8mL nuclease-free water) and incubated at 65C for 5min. RNA was extracted from the lysate using a Qiagen RNEasy Kit and on-column Qiagen DNAse digestion.
RNA-seq library preparation and sequencing was performed at the Joint Genome Institute. Libraries for sequencing were created using the Illumina TruSeq Stranded Total RNA kit following the standard protocol. Ribosomal RNA was depleted using the Illumina RiboZero bacterial kit. RNA-seq libraries were sequenced on an Illumina NextSeq in 2x151 reads using the standard protocol.

tag: medium

value: Standard Mineral Broth DSMZ Medium 1199

tag: substrates

value: 0.5 g/L glucose + 0.27 g/L GP-1


title: PCA_19_HTSeq

value: Standard Mineral Broth DSMZ Medium 1202

value: 0.5 g/L glucose + 0.37 g/L PCA


title: UN_17_HTSeq

value: Standard Mineral Broth DSMZ Medium 1200


title: GDK_15_HTSeq

value: Standard Mineral Broth DSMZ Medium 1198

value: 0.5 g/L glucose + 0.29 g/L G-diketone


title: Ammonium_03


title: UN_18_HTSeq

value: Standard Mineral Broth DSMZ Medium 1201


title: PCA_21_HTSeq

value: Standard Mineral Broth DSMZ Medium 1204


title: COAD-N012 H3K9me3 ChIP-seq

description:
COAD-N012_B
ChIP-DNA

value: Normal colon

value: H3K9me3 (Abcam ab8898)


title: COAD-N012 H3K4me1 ChIP-seq

description:
COAD-N012_A
ChIP-DNA

value: H3K4me1 (Abcam ab8895)


title: COAD-N011 Input ChIP-seq

description:
COAD-N011_G
Input DNA


title: COAD-N014 H3K79me2 ChIP-seq

description:
COAD-N014_D
ChIP-DNA


title: PCA_20_HTSeq

value: Standard Mineral Broth DSMZ Medium 1203


title: VA_12_HTSeq

value: Standard Mineral Broth DSMZ Medium 1195

value: 0.5 g/L glucose + 0.33 g/L vanillic acid


title: VA_11_HTSeq

value: Standard Mineral Broth DSMZ Medium 1194


title: COAD-N011 H3K4me3 ChIP-seq

description:
COAD-N011_E
ChIP-DNA

value: H3K4me3 (Abcam ab8580)


title: COAD-N011 H3K79me2 ChIP-seq

description:
COAD-N011_D
ChIP-DNA

value: H3K79me2 (Abcam ab3594)


title: COAD-N011 H3K27me3 ChIP-seq

description:
COAD-N011_F
ChIP-DNA

value: H3K27me3 (Abcam ab6002)


title: COAD-N011 H3K27ac ChIP-seq

description:
COAD-N011_C
ChIP-DNA

value: H3K27ac (Abcam ab4729)


title: VA_10_HTSeq

value: Standard Mineral Broth DSMZ Medium 1193


title: V_09_HTSeq

value: Standard Mineral Broth DSMZ Medium 1192

value: 0.5 g/L glucose + 0.28 g/L vanillin


title: FA_05_HTSeq

value: Standard Mineral Broth DSMZ Medium 1189

value: 0.5 g/L glucose + 0.29 g/L ferulic acid


title: COAD-N011 H3K4me1 ChIP-seq

description:
COAD-N011_A
ChIP-DNA


title: COAD-N011 H3K9me3 ChIP-seq

description:
COAD-N011_B
ChIP-DNA


title: GDK_14_HTSeq

value: Standard Mineral Broth DSMZ Medium 1197

value: 0.5 g/L glucose + 0.29 g/L G-diketone


title: V_08_HTSeq

value: Standard Mineral Broth DSMZ Medium 1191


title: FA_06_HTSeq

value: Standard Mineral Broth DSMZ Medium 1190


title: COAD-N010 H3K4me3 ChIP-seq

description:
COAD-N010_E
ChIP-DNA

value: Normal colon


title: GDK_13_HTSeq

value: Standard Mineral Broth DSMZ Medium 1196


title: COAD-N010 H3K79me2 ChIP-seq

description:
COAD-N010_D
ChIP-DNA


title: COAD-N010 Input ChIP-seq

description:
COAD-N010_G
Input DNA


title: Glu_01_HTSeq

value: Standard Mineral Broth DSMZ Medium 1185

value: 1 g/L glucose


title: COAD-N010 H3K4me1 ChIP-seq

description:
COAD-N010_A
ChIP-DNA

value: H3K4me1 (Abcam ab8895)


title: Glu_03_HTSeq

value: Standard Mineral Broth DSMZ Medium 1187


title: COAD-N008 H3K4me3 ChIP-seq

description:
COAD-N008_E
ChIP-DNA

value: H3K4me3 (Abcam ab8580)


title: COAD-N008 Input ChIP-seq

description:
COAD-N008_G
Input DNA


title: COAD-N008 H3K27ac ChIP-seq

description:
COAD-N008_C
ChIP-DNA

value: H3K27ac (Abcam ab4729)


title: COAD-N007 Input ChIP-seq

description:
COAD-N007_G
Input DNA


title: COAD-N008 H3K4me1 ChIP-seq

description:
COAD-N008_A
ChIP-DNA


title: FA_04_HTSeq

value: Standard Mineral Broth DSMZ Medium 1188


title: COAD-N007 H3K4me3 ChIP-seq

description:
COAD-N007_E
ChIP-DNA


title: COAD-N007 H3K27me3 ChIP-seq

description:
COAD-N007_F
ChIP-DNA

value: H3K27me3 (Abcam ab6002)


title: COAD-N007 H3K79me2 ChIP-seq

description:
COAD-N007_D
ChIP-DNA

value: H3K79me2 (Abcam ab3594)


title: COAD-N007 H3K27ac ChIP-seq

description:
COAD-N007_C
ChIP-DNA


title: COAD-N007 H3K9me3 ChIP-seq

description:
COAD-N007_B
ChIP-DNA

value: H3K9me3 (Abcam ab8898)


title: Glu_02_HTSeq

value: Standard Mineral Broth DSMZ Medium 1186


title: COAD-N008 H3K27me3 ChIP-seq

description:
COAD-N008_F
ChIP-DNA


title: COAD-N008 H3K79me2 ChIP-seq

description:
COAD-N008_D
ChIP-DNA


title: COAD-N007 H3K4me1 ChIP-seq

description:
COAD-N007_A
ChIP-DNA


title: COAD-N006 H3K27me3 ChIP-seq

description:
COAD-N006_F
ChIP-DNA


title: Valley Oak (SW.786) leaf RNA short read sequencing (illumina)

city: Los Angeles

first: Sorel

middle: Tanya

last: Fitz-Gibbon

state: CALIFORNIA

address: 961 Wellesley Ave

department: Ecology & Evolutionary Biology

institute: University of California, Los Angeles

data_processing:
Adapter-trimmed 101-101 nt paired end reads for each of the three tissues were aligned with STAR single pass (no a priori known splice junctions) on March 22 2019.
Data for all three tissues (bud, leaf and stem) were combined and a wiggle file produced where coverage is the sum of plus and minus strands including both unique and multimap reads.  Coverage units are reads per million
Genome_build: Valley Oak version 3.0
Supplementary_files_format_and_content: Wiggle format, all three tissues combined. Score is the sum of plus and minus strand coverage, including both unique and multimap reads.  Units are reads per million

organism: Quercus lobata

source_name: leaf

extract_protocol:
Plant tissues (100 mg each of leaves, buds and stems) were flash frozen in liquid nitrogen and ground with a mortar and pestle to a fine powder. RNA extractions were performed February 16, 2018. using a modified (see publication) version of the Conifer RNA prep protocol  from the Cronn Lab  (https://openwetware.org/wiki/Conifer_RNA_prep) and the Spectrum Plant Total RNA kit (Sigma, St. Louis, MO, USA).   RNA quality and quantity were assessed using the Agilent RNA ScreenTape System on the Agilent 2200 TapeStation system (Agilent Technologies, Santa Clara, CA, USA).
Total RNA was depleted of rRNA using the Ribo-Zero rRNA Removal Kit (Plant Leaf) (Illumina,San Diego, CA, USA). Total RNA input amounts were 5 ug for the leaf, 4.2 ug for the bud, and 4.1 ug for the stem.  Libraries were constructed using the TruSeq Stranded Total RNA protocol with a positive control (Illumina, San Diego, CA, USA). Libraries were analyzed using the Agilent D1000 Screen Tape System on the Agilent 2200 TapeStation (Agilent Technologies, Santa Clara, CA, USA). Fragments were found to be too small (~275bp) so an extra size selection step was performed with AMPure XP beads at a concentration of 0.65x, to yield fragments in the 400-700 bp range.

treatment_protocol: Bud, leaf and stem tissues from Quercus lobata SW786 were collected on October 28, 2017 at Sedgewick Reserve in Santa Barbara, CA and placed immediately on dry ice, then kept in the -80°C freezer until the day of extraction

value: USA:Santa Barbara


title: COAD-N006 Input ChIP-seq

description:
COAD-N006_G
Input DNA


title: COAD-N006 H3K4me3 ChIP-seq

description:
COAD-N006_E
ChIP-DNA


title: Valley Oak (SW.786) bud RNA short read sequencing (illumina)

source_name: bud


title: COAD-N006 H3K79me2 ChIP-seq

description:
COAD-N006_D
ChIP-DNA


title: Valley Oak (SW.786) stem RNA short read sequencing (illumina)

source_name: stem


title: 251486840567_1_2

city: Riverside

first: Juliet

last: Morrison

address: 900 University Avenue

department: Microbiology and Plant Pathology

institute: University of California, Riverside

description: DENV1, Day 1,  replicate 2

hyb_protocol: Probe labeling and microarray slide hybridization for each biological replicate was performed using the Mouse Whole Genome Microarray 4x44K Kit (Agilent Technologies) according to the manufacturer’s instructions

scan_protocol: Slides were scanned on an Agilent DNA microarray scanner (Model G2505B) using the XDR setting and raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1).

data_processing: Extracted raw data was partitioned into liver and spleen samples and separately background corrected using the “norm-exp” method with an offset of 1 and quantile normalized using the limma package in the R environment

source_name: DENV1, Day 1,  replicate 2

extract_protocol: RNA was extracted from tissues homogenized in Trizol (Invitrogen) according to the manufacturer's protocol.

treatment_protocol: Mice were infected with 1×106 plaque-forming units (pfu) of DENV1, 2, 3 or 4 strain by i.p. injection in 100μL of PBS. Drug-treated animals were given 0.6mg per mouse per day of ketotifen (Sigma) or an equivalent volume of saline by i.p. injection. The first dose was administered 1h after infection, with daily drug injections thereafter at 24h intervals.

value: Spleen


title: COAD-N008 H3K9me3 ChIP-seq

description:
COAD-N008_B
ChIP-DNA


title: 251486840587_1_2

description: DENV1, Day 1,  replicate 3

source_name: DENV1, Day 1,  replicate 3

label_protocol: Probe labeling and microarray slide hybridization for each biological replicate was performed using the Mouse Whole Genome Microarray 4x44K Kit (Agilent Technologies) according to the manufacturer’s instructions


title: 251486840579_1_2

description: DENV1, Day 3,  replicate 2

source_name: DENV1, Day 3,  replicate 2


title: 251486840568_1_4

description: DENV1, Day 3,  replicate 1

source_name: DENV1, Day 3,  replicate 1


title: 251486840583_1_1

description: DENV1, Day 3,  replicate 3

source_name: DENV1, Day 3,  replicate 3


title: COAD-N006 H3K27ac ChIP-seq

description:
COAD-N006_C
ChIP-DNA

source_name: Normal


title: 251486840573_1_3

description: DENV2, Day 3,  replicate 1

source_name: DENV2, Day 3,  replicate 1


title: COAD-N006 H3K9me3 ChIP-seq

description:
COAD-N006_B
ChIP-DNA


title: 251486840571_1_4

description: DENV2, Day 1,  replicate 3

source_name: DENV2, Day 1,  replicate 3


title: 251486840587_1_3

description: DENV2, Day 1,  replicate 2

source_name: DENV2, Day 1,  replicate 2


title: COAD-N005 Input ChIP-seq

description:
COAD-N005_G
Input DNA


title: COAD-N006 H3K4me1 ChIP-seq

description:
COAD-N006_A
ChIP-DNA


title: COAD-N005 H3K27me3 ChIP-seq

description:
COAD-N005_F
ChIP-DNA


title: COAD-N005 H3K4me3 ChIP-seq

description:
COAD-N005_E
ChIP-DNA


title: B73-B-Input

city: Wuhan

first: Handong

last: Su

state: Hubei

address: No.1,Shizishan Street · Hongshan District

institute: Huazhong Agricultural University

description: MNase-seq

data_processing:
Basecalls performed using Illumina CASAVA.
MNase-seq reads were mapped to maize B73 genome with BWA version 0.7.13 with the following configurations.
Only uniquely mapping reads were chosen for further analysis, and only a random one was picked for duplicates (reads mapped to the same location).
RPM values were calculated with 10 kb windows along the genome to make it comparable between different samples.
Genome_build:  B73 v4 genome
Supplementary_files_format_and_content: bedGraph files were generated using bedtools.

organism: Zea mays

source_name: maize

growth_protocol: Suitable materials were planted in the greenhouse or in the field for experiments.

extract_protocol: Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).180-400 bp fragments (contained the joint) were selected by gel extraction.

treatment_protocol: Extracted nuclei were digested with micrococcal nuclease (Sigma-Al drich) for experiments.

value: young leaves

value: control


title: Valley Oak (SW.786) bud whole genome bisulfite sequencing

description:
bisulfite treated DNA
YA055L3pf1-e1.bud

data_processing:
Adapter and quality trimmed reads were aligned using methylpy (Schultz et al. 2015)
Methylpy single-end-pipeline with --remove-clonal True --min-mapq 30 --min-base-quality 1 --trim-reads False --unmethylated-control "chrC" --binom-test True --min-cov 3
Genome_build: Valley Oak version 3.0
Supplementary_files_format_and_content: methylpy output table, headers: (1) chromosome (2) position (3) strand (4) sequence context (5) count of reads supporting methylation (6) read coverage (7) indicator of significant methylation

extract_protocol:
Total genomic DNA was extracted from frozen leaf tissue on August 24, 2017 using a prewash method (Li et al., 2007) followed by a modified CTAB protocol (Doyle and Doyle, 1987).
DNA was sonicated to 200-300 bp range. TruSeq Nano DNA Library Prep Kit (Illumina, San Diego, CA, USA) was used for end-repair, adapter ligation & purification.  Samples were then treated with bisulfite using the EpiTect kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol with one exception in that the bisulfite DNA conversion was performed twice for a total of 10 hours of incubation.

treatment_protocol: Samples were collected from Quercus lobata SW786 in 2017: bud (February), catkin (March) & young leaves (April)

value: February 2017


title: COAD-N005 H3K27ac ChIP-seq

description:
COAD-N005_C
ChIP-DNA

value: Normal colon


title: COAD-N005 H3K79me2 ChIP-seq

description:
COAD-N005_D
ChIP-DNA


title: COAD-N005 H3K9me3 ChIP-seq

description:
COAD-N005_B
ChIP-DNA


title: COAD-N005 H3K4me1 ChIP-seq

description:
COAD-N005_A
ChIP-DNA


title: COAD-N004 Input ChIP-seq

description:
COAD-N004_G
Input DNA


title: 251486840587_1_1

description: DENV1, Day 1,  replicate 4

source_name: DENV1, Day 1,  replicate 4


title: Valley Oak (SW.786) young leaf whole genome bisulfite sequencing

description:
bisulfite treated DNA
YA055L1pf1-e1.youngleaf

source_name: young leaf

value: April 2017


title: COAD-N004 H3K27me3 ChIP-seq

description:
COAD-N004_F
ChIP-DNA


title: COAD-N004 H3K4me3 ChIP-seq

description:
COAD-N004_E
ChIP-DNA


title: COAD-N004 H3K79me2 ChIP-seq

description:
COAD-N004_D
ChIP-DNA


title: Valley Oak (SW.786) catkin whole genome bisulfite sequencing

description:
bisulfite treated DNA
YA055L2pf1-e1.catkin

source_name: catkin

value: March 2017


title: COAD-N004 H3K27ac ChIP-seq

description:
COAD-N004_C
ChIP-DNA


title: COAD-N004 H3K9me3 ChIP-seq

description:
COAD-N004_B
ChIP-DNA


title: COAD-N004 H3K4me1 ChIP-seq

description:
COAD-N004_A
ChIP-DNA

value: H3K4me1 (Abcam ab8895)


title: COAD-N003 Input ChIP-seq

description:
COAD-N003_G
Input DNA


title: S34: 45D_WT_A

city: Bethesda

first: Edward

last: Giniger

state: MD

address: Bldg 35,Rm 1C-1002; 35 Convent Dr

department: NINDS

institute: NIH

hyb_protocol: Labeled cRNA were hybridized to the DroGene 1.0 ST GeneChip (Affymetrix, Santa Clara, CA) according to the manufacturer‚Äôs guidelines.

scan_protocol: The Affymetrix scanner 3000 was used in conjunction with Affymetrix GeneChip Operation Software to generate one .CEL file per hybridized cRNA.

data_processing: The Expression Console (Affymetrix) was used to summarize the data contained across all .CEL files and generate 16,322 RMA normalized probe expression values.

source_name: head

label_protocol: Extracted RNA were processed and labeled according to the manufacturer‚Äôs guidelines for use with the DroGene 1.0 ST GeneChip (Affymetrix, GeneChip Whole Transcript Sense Target Labeling).

growth_protocol: 25 male flies were aliquoted into a vial containing standard Nutri-Fly food (N) or Nutri Fly food with antibiotic (A); five sets of 10 vials were collected for each genotype and time point (each replicate consisted of 50 male flies).  Flies were maintained at 25C, 50% humidity with a 12 hr/12 hr light/dark cycle, and were transferred to fresh vials every three days.  Once at the appropriate age, flies were anesthetized under CO2, then flash frozen in liquid nitrogen; samples were stored at -80C until all time points were collected.

extract_protocol: Isolated tissue samples were stored at -80C prior to phenol-chloroform extraction using the TRIzol reagent.  Samples were homogenized in TRIzol, chloroform was added, and the resultant mixture centrifuged; RNA was precipitated from the upper aqueous layer using isopropanol.  Following ethanol washes, the purified RNA was resuspended in RNAse-free water and stored at -80C.

treatment_protocol: Axenic wild type fly line was generated by washing eggs with 70% ethanol, bleaching, rinsing with sterile water, and the transferring the sterilized eggs to sterile food supplemented with propionic acid (0.48%) + Pen/Strep (1:100 dilution). Axenic line was maintained as bacteria free on this food for > 3 generations before collection of flies for aging and RNA isolation.

value: head

value: 45 day old adult

tag: Sex

value: male

value: bacteria-free


title: S35: 45D_WT_A


title: COAD-N003 H3K27me3 ChIP-seq

description:
COAD-N003_F
ChIP-DNA

value: H3K27me3 (Abcam ab6002)


title: 251486840581_1_4

description: DENV2, Day 3,  replicate 3

source_name: DENV2, Day 3,  replicate 3


title: COAD-N003 H3K4me3 ChIP-seq

description:
COAD-N003_E
ChIP-DNA

value: H3K4me3 (Abcam ab8580)


title: S32: 45D_WT_A


title: COAD-N003 H3K79me2 ChIP-seq

description:
COAD-N003_D
ChIP-DNA

value: H3K79me2 (Abcam ab3594)


title: COAD-N003 H3K27ac ChIP-seq

description:
COAD-N003_C
ChIP-DNA

value: H3K27ac (Abcam ab4729)


title: 251486840569_1_4

description: DENV2&ketotifen, Day 3,  replicate 1

source_name: DENV2&ketotifen, Day 3,  replicate 1


title: COAD-N003 H3K9me3 ChIP-seq

description:
COAD-N003_B
ChIP-DNA

value: H3K9me3 (Abcam ab8898)


title: S33: 45D_WT_A


title: 251486840586_1_3

description: DENV2&ketotifen, Day 1,  replicate 2

source_name: DENV2&ketotifen, Day 1,  replicate 2

value: Spleen


title: COAD-N003 H3K4me1 ChIP-seq

description:
COAD-N003_A
ChIP-DNA


title: 251486840577_1_2

description: DENV2, Day 3,  replicate 2

source_name: DENV2, Day 3,  replicate 2


title: 251486840567_1_4

description: DENV2&ketotifen, Day 1,  replicate 1

source_name: DENV2&ketotifen, Day 1,  replicate 1


title: COAD-N001 Input ChIP-seq

description:
COAD-N001_G
Input DNA


title: S31: 45D_WT_A


title: S29: 30D_WT_A

value: 30 day old adult


title: 251486840569_1_3

description: DENV2&ketotifen, Day 1,  replicate 3

source_name: DENV2&ketotifen, Day 1,  replicate 3


title: COAD-N001 H3K27me3 ChIP-seq

description:
COAD-N001_F
ChIP-DNA


title: 251486840579_1_4

description: DENV2&ketotifen, Day 3,  replicate 2

source_name: DENV2&ketotifen, Day 3,  replicate 2


title: S30: 30D_WT_A


title: COAD-N001 H3K4me3 ChIP-seq

description:
COAD-N001_E
ChIP-DNA


title: 251486840584_1_4

description: DENV3, Day 1,  replicate 1

source_name: DENV3, Day 1,  replicate 1


title: 251486840573_1_4

description: DENV3, Day 1,  replicate 2

source_name: DENV3, Day 1,  replicate 2


title: S28: 30D_WT_A


title: COAD-N001 H3K79me2 ChIP-seq

description:
COAD-N001_D
ChIP-DNA

source_name: Normal


title: 251486840572_1_3

description: DENV2&ketotifen, Day 3,  replicate 3

source_name: DENV2&ketotifen, Day 3,  replicate 3


title: S27: 30D_WT_A


title: 251486840586_1_2

description: DENV3, Day 1,  replicate 3

source_name: DENV3, Day 1,  replicate 3


title: 251486840574_1_4

description: DENV3, Day 3,  replicate 1

source_name: DENV3, Day 3,  replicate 1


title: COAD-N001 H3K27ac ChIP-seq

description:
COAD-N001_C
ChIP-DNA


title: COAD-N001 H3K4me1 ChIP-seq

description:
COAD-N001_A
ChIP-DNA


title: SNU-C5 Cell line Input ChIP-seq

description:
COAD-C027_G
Input DNA

source_name: ATCC

value: Colon


title: SNU-C5 Cell line H3K27ac ChIP-seq

description:
COAD-C027_C
ChIP-DNA


title: RKO Cell line H3K27ac ChIP-seq

description:
COAD-C022_C
ChIP-DNA

value: RKO


title: RKO Cell line Input ChIP-seq

description:
COAD-C022_G
Input DNA


title: HCT15 Cell line Input ChIP-seq

description:
COAD-C021_G
Input DNA


title: S26: 30D_WT_A


title: S25: 10D_WT_A

value: 10 day old adult


title: CW2 Cell line H3K27ac ChIP-seq

description:
COAD-C020_C
ChIP-DNA


title: 251486840572_1_4

description: DENV3, Day 3,  replicate 2

source_name: DENV3, Day 3,  replicate 2


title: CW2 Cell line Input ChIP-seq

description:
COAD-C020_G
Input DNA


title: S24: 10D_WT_A


title: SW620 Cell line Input ChIP-seq

description:
COAD-C016_G
Input DNA


title: S23: 10D_WT_A


title: 251486840578_1_3

description: DENV3, Day 3,  replicate 3

source_name: DENV3, Day 3,  replicate 3


title: SW620 Cell line H3K27ac ChIP-seq

description:
COAD-C016_C
ChIP-DNA