title: Genomic DNA from cord blood sample GDM.016

source_name: cord blood sample GDM.016


title: Genomic DNA from cord blood sample GDM.020

status: Public on Jan 31 2021

type: genomic

city: Toronto

first: Zain

last: Awamleh

address: 686 Bay street

country: Canada

institute: Sickkids

description: normal glucose tolerance pregnancy

hyb_protocol: bisulphite converted DNA was converted using EpiTect PLUS Bisulfite Kit, QIAGEN and hybridised to Illumina Infinium 450K Beadchip using standard Illumina protocol

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

data_processing: minfi Bioconductor package

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: cord blood sample GDM.020

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted using standard phenol-chloroform methods

tag: disease status

value: NGT


title: GFP at 0 hrs 1G donor 2 experiment 1 [CWRU003395_S35]

type: SRA

city: Cleveland

first: Mark

last: Cameron

state: OH

address: 10900 Euclid Ave

department: Population and Quantitative Health Sciences

country: USA

institute: Case Western Reserve University

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using skewer v0.2.2, then mapped to GRCh38 whole genome using Hisat2 v2.0.5
Read summarization was performed by the program featureCounts v1.5.0-p2 as part of the SubRead package.
Counts Per Million (CPM) values were generated through the edgeR Library v3.16.5 in R
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrices in CSV format containing raw as well as normalized Log2(n+0.25) CPM summarized reads

molecule: total RNA

source_name: GFP at 0 hours 1G

growth_protocol: The cells were cultured in DMEM/F12 (Life technologies) without phenol red, supplemented with 5% (w/v) horse serum, cholera toxin (Sigma), epidermal growth factor (Peprotech), hydrocortisone (Sigma), insulin (Sigma) and penicillin streptomycin (Life technologies). The cells were maintained at 37oC in a humidified, 5 % (v/v) CO2 incubating chamber. The inducible cells were trypsinized and seeded in fibronectin coated chamber flasks with 30% confluency and cultured for 24 h. To induce SUN1L-KDEL for LINC disruption and GFP-KDEL for control comparison, the media was supplemented  with 1 µg/ml doxycycline. These cells were cultured in doxycycline for 24 h before placing them on the 3-D clinostat.

extract_protocol:
RNA was extracted from 1 million PBMC using RNeasy Micro Kit from QIAGEN
RNA libraries were prepared for sequencing using the Truseq Stranded Total RNA HT Kit.

tag: cell line background

value: MCF 10A

tag: cell type

value: Mammary epithelial cells

tag: treatment

value: GFP

tag: gravity

tag: timepoint in hours

tag: donor id

tag: experiment


title: NA19131 cell line replicate 1

city: New York

first: Jeremiah

last: Li

state: NY

address: 430 E 29th St 14th Floor, 14th Floor

institute: Gencove

description: Genomic DNA extracted from B-lymphocytes by Coriell and genotyped using Infinium Global Screening Array (GSAMD-24v1-0_20011747_A1) beadchip (Illumina)

hyb_protocol: samples were incubated at 48C overnight before undergoing enzymatic base extension and fluorescent staining

scan_protocol: the beadchips were scanned using the iScan system (Illumina)

data_processing: genomic DNA was genotyped using the Infinium Global Screening Array (GSAMD-24v1-0_20011747_A1) beadchip (Illumina)

label: 2D barcodes

source_name: purified gDNA

label_protocol: sample vials containing gDNA extract were stored and individually labeled with unique 2D-barcodes

extract_protocol: an automated magnetic bead purification protocol (Hamilton Microlab STAR w/ Promega ReliaPrep Isolation system) was used to extract genomic DNA that was eluted in TE buffer (pH 8.0, 1mM EDTA)

tag: cell line


title: Genomic DNA from cord blood sample GDM.015

description: normal glucose tolerance pregnancy

source_name: cord blood sample GDM.015


title: Peruvian, NTL, Patient, 117

city: Toulouse

first: Juan Pablo

last: Cerapio

address: Av 2 Hubert Curien

country: France

institute: CRCT

description:
subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 117,Age: 44,Gender: Female,HBV: Negative,mtDNA haplotypes: B
NTLPER117

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

data_processing: Data were processed in R, normalized using Noob (normal-exponential out-of-band) normalization.

label: Cy3, Cy5

source_name: Peruvian NTL tissue from Patient 117

extract_protocol: Genomic DNA was extracted twice with phenol and once with chloroform, precipitated in ethanol, and resuspended in TE buffer (10 mM Tris; 0.1 mM EDTA; pH 8.0).

treatment_protocol: Sampling protocol: About 50 mg of HCC, as well as NTL from tumor-free margins of the resected surgical pieces, were harvested, flash-frozen in liquid nitrogen, and kept at -150°C for long-term storage.

tag: individual

value: Patient, 117

tag: nationality

value: Peruvian

tag: age

tag: gender

value: Female

tag: hbv

value: Negative

tag: mtdna haplotypes

value: B

tag: disease state

value: hepatocellular carcinoma (HCC)

tag: tissue

value: NTL


title: NA19119 cell line replicate 3


title: NA19131 cell line replicate 3


title: NA19131 cell line replicate 2


title: Genomic DNA from cord blood sample GDM.014

description: normal glucose tolerance pregnancy

source_name: cord blood sample GDM.014

tag: disease status


title: NA19119 cell line replicate 2


title: SUN1L at 20 hrs μg donor 1 experiment 2 [CWRU003428_S32]

source_name: SUN1L at 20 hours μg

tag: cell line background

value: μg


title: SUN1L at 20 hrs 1G donor 1 experiment 2 [CWRU003432_S33]

source_name: SUN1L at 20 hours 1G

tag: cell type


title: Peruvian, NTL, Patient, 101

description:
subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 101,Age: 24,Gender: Male,HBV: Positive,mtDNA haplotypes: C
NTLPER101

source_name: Peruvian NTL tissue from Patient 101

value: Patient, 101

value: Male

value: Positive

value: C


title: Genomic DNA from cord blood sample GDM.009

description: normal glucose tolerance pregnancy

source_name: cord blood sample GDM.009


title: Genomic DNA from cord blood sample GDM.012

description: normal glucose tolerance pregnancy

source_name: cord blood sample GDM.012


title: GFP at 20 hrs 1G donor 1 experiment 2 [CWRU003422_S34]

source_name: GFP at 20 hours 1G

tag: treatment


title: Genomic DNA from cord blood sample GDM.011

description: normal glucose tolerance pregnancy

source_name: cord blood sample GDM.011


title: Peruvian, NTL, Patient, 100

description:
subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 100,Age: 44,Gender: Female,HBV: Positive,mtDNA haplotypes: B
NTLPER100

source_name: Peruvian NTL tissue from Patient 100

value: Patient, 100


title: NA19119 cell line replicate 1


title: Peruvian, NTL, Patient, 109

description:
subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 109,Age: 38,Gender: Male,HBV: Negative,mtDNA haplotypes: B
NTLPER109

source_name: Peruvian NTL tissue from Patient 109

value: Patient, 109


title: Peruvian, NTL, Patient, 106

description:
subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 106,Age: 72,Gender: Male,HBV: Positive,mtDNA haplotypes: D
NTLPER106

source_name: Peruvian NTL tissue from Patient 106

value: Patient, 106

value: D


title: Genomic DNA from cord blood sample GDM.004

description: normal glucose tolerance pregnancy

source_name: cord blood sample GDM.004

value: NGT


title: SUN1L at 20 hrs 1G donor 2 experiment 2 [CWRU003433_S31]

value: MCF 10A

value: Mammary epithelial cells

tag: gravity


title: NA19041 cell line replicate 3


title: GFP at 2 hrs 1G donor 2 experiment 1 [CWRU003401_S29]

source_name: GFP at 2 hours 1G

value: GFP

tag: timepoint in hours


title: Genomic DNA from cord blood sample GDM.006

description: normal glucose tolerance pregnancy

source_name: cord blood sample GDM.006


title: Peruvian, NTL, Patient, 099

description:
subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 099,Age: 32,Gender: Female,HBV: Positive,mtDNA haplotypes: D
NTLPER099

source_name: Peruvian NTL tissue from Patient 099

value: Patient, 099

value: Peruvian

value: Female


title: Peruvian, NTL, Patient, 104

description:
subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 104,Age: 72,Gender: Male,HBV: Positive,mtDNA haplotypes: A
NTLPER104

source_name: Peruvian NTL tissue from Patient 104

value: Patient, 104

value: A

value: hepatocellular carcinoma (HCC)

value: NTL


title: NA19041 cell line replicate 2

source_name: purified gDNA


title: NA19041 cell line replicate 1


title: Genomic DNA from cord blood sample GDM.003

description: normal glucose tolerance pregnancy

source_name: cord blood sample GDM.003


title: Peruvian, NTL, Patient, 093

description:
subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 093,Age: 35,Gender: Male,HBV: Negative,mtDNA haplotypes: C
NTLPER093

source_name: Peruvian NTL tissue from Patient 093

value: Patient, 093

value: Male

value: Negative


title: GFP at 2 hrs μg donor 2 experiment 2 [CWRU003417_S28]

source_name: GFP at 2 hours μg

value: μg

tag: donor id


title: NA19017 cell line replicate 3


title: GFP at 2 hrs μg donor 1 experiment 2 [CWRU003416_S30]

tag: experiment


title: Peruvian, NTL, Patient, 095

description:
subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 095,Age: 30,Gender: Male,HBV: Positive,mtDNA haplotypes: A
NTLPER095

source_name: Peruvian NTL tissue from Patient 095

value: Patient, 095

value: Positive


title: SUN1L at 2 hrs 1G donor 1 experiment 1 [CWRU003410_S27]

source_name: SUN1L at 2 hours 1G


title: NA18912 cell line replicate 3

tag: cell line


title: Genomic DNA from cord blood sample GDM.013

description: normal glucose tolerance pregnancy

source_name: cord blood sample GDM.013

value: NGT


title: Genomic DNA from cord blood sample GDM.002

description: normal glucose tolerance pregnancy

source_name: cord blood sample GDM.002


title: NA19017 cell line replicate 1


title: Peruvian, NTL, Patient, 092

description:
subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 092,Age: 76,Gender: Male,HBV: Negative,mtDNA haplotypes: D
NTLPER092

source_name: Peruvian NTL tissue from Patient 092

tag: individual

value: Patient, 092

value: D


title: GFP at 20 hrs 1G donor 2 experiment 1 [CWRU003403_S24]

source_name: GFP at 20 hours 1G

value: MCF 10A

value: Mammary epithelial cells

value: GFP


title: SUN1L at 2 hrs 1G donor 2 experiment 1 [CWRU003411_S26]


title: NA18912 cell line replicate 2


title: GFP at 20 hrs μg donor 1 experiment 2 [CWRU003418_S23]

source_name: GFP at 20 hours μg


title: Genomic DNA from cord blood sample GDM.001

description: normal glucose tolerance pregnancy

source_name: cord blood sample GDM.001


title: Peruvian, NTL, Patient, 083

description:
subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 083,Age: 73,Gender: Male,HBV: Negative,mtDNA haplotypes: B
NTLPER083

source_name: Peruvian NTL tissue from Patient 083

value: Patient, 083

tag: nationality

value: Peruvian

value: B


title: SUN1L at 0 hrs 1G donor 1 experiment 2 [CWRU003424_S25]

source_name: SUN1L at 0 hours 1G


title: NA18912 cell line replicate 1


title: Peruvian, NTL, Patient, 091

description:
subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 091,Age: 65,Gender: Male,HBV: Negative,mtDNA haplotypes: A
NTLPER091

source_name: Peruvian NTL tissue from Patient 091

value: Patient, 091

tag: age

value: A

value: hepatocellular carcinoma (HCC)


title: Peruvian, NTL, Patient, 088

description:
subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 088,Age: 67,Gender: Male,HBV: Positive,mtDNA haplotypes: B
NTLPER088

source_name: Peruvian NTL tissue from Patient 088

value: Patient, 088

tag: gender

value: Male

value: NTL


title: Peruvian, HCC, Patient, 201

description:
subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 201,Age: 76,Gender: Male,HBV: Negative,mtDNA haplotypes: D
HCCPER201

source_name: Peruvian HCC tissue from Patient 201

value: Patient, 201

tag: hbv

value: Negative

value: HCC


title: NA18504 cell line replicate 3

source_name: purified gDNA


title: NA19017 cell line replicate 2


title: Peruvian, HCC, Patient, 191

description:
subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 191,Age: 67,Gender: Male,HBV: Negative,mtDNA haplotypes: A
HCCPER191

source_name: Peruvian HCC tissue from Patient 191

value: Patient, 191

tag: mtdna haplotypes


title: SUN1L at 20 hrs μg donor 2 experiment 2 [CWRU003429_S22]

source_name: SUN1L at 20 hours μg

value: μg


title: Peruvian, HCC, Patient, 190

description:
subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 190,Age: 46,Gender: Female,HBV: Positive,mtDNA haplotypes: A
HCCPER190

source_name: Peruvian HCC tissue from Patient 190

value: Patient, 190

value: Female

value: Positive

tag: disease state


title: NA18504 cell line replicate 2

description: Genomic DNA extracted from B-lymphocytes by Coriell and genotyped using Infinium Global Screening Array (GSAMD-24v1-0_20011747_A1) beadchip (Illumina)


title: SUN1L at 0 hrs 1G donor 2 experiment 2 [CWRU003425_S20]

value: MCF 10A

value: Mammary epithelial cells


title: NA18504 cell line replicate 1


title: SUN1L at 2 hrs μg donor 1 experiment 2 [CWRU003426_S19]

source_name: SUN1L at 2 hours μg


title: SUN1L at 2 hrs μg donor 2 experiment 1 [CWRU003407_S21]


title: Peruvian NTL tissue from Patient 074

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

data_processing: Noob (normal-exponential out-of-band) normalization

source_name: NTL tissue from Peruvian HCC patient

tag: subject id

value: Patient 074

tag: subject status

value: Peruvian patients with hepatocellular carcinoma (HCC)

value: B

tag: tissue

value: non-tumor liver (NTL) tissue


title: GFP at 2 hrs 1G donor 1 experiment 1 [CWRU003400_S18]

source_name: GFP at 2 hours 1G

tag: cell line background

tag: cell type

value: GFP


title: Peruvian, HCC, Patient, 179

description:
subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 179,Age: 33,Gender: Male,HBV: Positive,mtDNA haplotypes: C
HCCPER179

source_name: Peruvian HCC tissue from Patient 179

value: Patient, 179

value: Peruvian

value: Male

value: C

value: hepatocellular carcinoma (HCC)


title: Peruvian NTL tissue from Patient 077

value: Patient 077


title: NA12878 cell line replicate 2


title: NA12878 cell line replicate 3


title: Peruvian, HCC, Patient, 188

description:
subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 188,Age: 94,Gender: Female,HBV: Negative,mtDNA haplotypes: B
HCCPER188

source_name: Peruvian HCC tissue from Patient 188

value: Patient, 188

value: Negative

value: HCC


title: SUN1L at 20 hrs μg donor 1 experiment 1 [CWRU003408_S17]

tag: treatment

tag: gravity

value: μg


title: Peruvian NTL tissue from Patient 075

value: Patient 075

value: Positive


title: GFP at 20 hrs 1G donor 2 experiment 2 [CWRU003423_S16]

source_name: GFP at 20 hours 1G

value: MCF 10A

value: Mammary epithelial cells

tag: timepoint in hours

tag: donor id


title: Peruvian NTL tissue from Patient 073

value: Patient 073

value: Peruvian patients with hepatocellular carcinoma (HCC)

value: B


title: Peruvian NTL tissue from Patient 071

value: Patient 071

value: non-tumor liver (NTL) tissue


title: Peruvian, HCC, Patient, 180

description:
subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 180,Age: 34,Gender: Male,HBV: Positive,mtDNA haplotypes: B
HCCPER180

source_name: Peruvian HCC tissue from Patient 180

value: Patient, 180

value: Peruvian

value: Male


title: Peruvian, HCC, Patient, 120

description:
subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 120,Age: 20,Gender: Female,HBV: Positive,mtDNA haplotypes: B
HCCPER120

source_name: Peruvian HCC tissue from Patient 120

value: Patient, 120

value: Female

value: hepatocellular carcinoma (HCC)


title: NA12843 cell line replicate 3

tag: cell line


title: NA12878 cell line replicate 1


title: Peruvian, HCC, Patient, 121

description:
subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 121,Age: 82,Gender: Female,HBV: Negative,mtDNA haplotypes: B
HCCPER121

source_name: Peruvian HCC tissue from Patient 121

tag: individual

value: Patient, 121

value: Negative

value: HCC


title: GFP at 20 hrs μg donor 2 experiment 1 [CWRU003399_S14]

source_name: GFP at 20 hours μg

value: GFP

value: μg

tag: experiment


title: NA12843 cell line replicate 1


title: Peruvian NTL tissue from Patient 070

value: Patient 070

tag: age

value: Positive

value: C


title: NA12843 cell line replicate 2


title: SUN1L at 2 hrs 1G donor 2 experiment 2 [CWRU003431_S15]

source_name: SUN1L at 2 hours 1G

value: MCF 10A

value: Mammary epithelial cells


title: Peruvian NTL tissue from Patient 064

value: Patient 064

value: Peruvian patients with hepatocellular carcinoma (HCC)

tag: gender

value: B

value: non-tumor liver (NTL) tissue


title: Peruvian, HCC, Patient, 109

description:
subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 109,Age: 38,Gender: Male,HBV: Negative,mtDNA haplotypes: B
HCCPER109

source_name: Peruvian HCC tissue from Patient 109

value: Patient, 109

tag: nationality

value: Peruvian

value: Male

tag: hbv


title: SUN1L at 0 hrs 1G donor 2 experiment 1 [CWRU003405_S13]

source_name: SUN1L at 0 hours 1G


title: Peruvian NTL tissue from Patient 065

value: Patient 065

tag: mtdna haplotypes


title: NA12842 cell line replicate 3

source_name: purified gDNA


title: Peruvian NTL tissue from Patient 079

tag: subject id

value: Patient 079

value: Negative


title: ChIPseq sample 2: PAO1 RepC ChIPseq with pPf4r

city: Singapore

first: Muhammad Hafiz

last: Ismail

state: Singapore

address: Nanyang Technological University, 60 Nanyang Drive, SBS-01N-27

country: Singapore

institute: Nanyang Technological University / Singapore Centre for Environmental Life Sciences Engineering (SCELSE)

description: ChIPseq data

library_source: genomic

data_processing:
Raw reads were quality and adapter trimmed using bbduk
Reads were mapped to the reference genome using bowtie2 v 2.2.6 and output as bam files with these options: -p 6 --fr --non-deterministic
Peak calling was performed using the MACS2 callpeak function with these options: -f BAM -g 6264404 --bw 150 -B -q 0.05 --call-summits --fix-bimodal --extsize 200
Peaks were annotated using the ChIPseeker package in R
processed data files format and content: Bedgraph files generated using MACS2
processed data files format and content: Peak text and excel files
Genome_build: Pseudomonas aeruginosa PAO1 (NC_002516.2)

organism: Pseudomonas aeruginosa PAO1

source_name: Pseudomonas aeruginosa PAO1

growth_protocol: Cells were grown in lysogeny broth at 37°C to an OD600 of 0.3 before L-arabinose was added and allowed to grow for another hour

extract_protocol:
Cultures were treated with a final concentration of 1% formaldehyde before lysis with a sonicator. For each sample, 20 uL of antibodies and 20 uL of ChIP-Grade Protein A/G Magnetic beads were added to 800 uL of sample and incubated overnight at 4°C on a rotisserie
Libraries were prepared from purified immunoprecipitated DNA using the TruSeq ChIP Sample Preparation Kit as per manufacturer's instruction. The sequencing was done using the MiSeq Reagent Kit V3 175 cycles.

value: Bacteria culture

tag: genotype

value: pPf4r complemented

tag: chip antibody

value: His-Tag (D3I1O) XP® Rabbit mAb (Cell Signaling Technology, INC, Cat #12698BC)


title: SUN1L at 0 hrs 1G donor 1 experiment 1 [CWRU003404_S12]

tag: cell line background


title: Peruvian NTL tissue from Patient 068

value: Patient 068

tag: subject status

value: Female

value: Positive

tag: tissue


title: Peruvian NTL tissue from Patient 061

value: Patient 061

value: C


title: NA12842 cell line replicate 2


title: Peruvian NTL tissue from Patient 072

value: Patient 072

value: Peruvian patients with hepatocellular carcinoma (HCC)


title: SUN1L at 20 hrs μg donor 2 experiment 1 [CWRU003409_S11]

source_name: SUN1L at 20 hours μg

value: MCF 10A

tag: cell type

value: Mammary epithelial cells

tag: treatment

tag: gravity

value: μg


title: Peruvian, HCC, Patient, 117

description:
subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 117,Age: 44,Gender: Female,HBV: Negative,mtDNA haplotypes: B
HCCPER117

source_name: Peruvian HCC tissue from Patient 117

value: Patient, 117

value: Peruvian

value: B

tag: disease state

value: hepatocellular carcinoma (HCC)

value: HCC


title: Peruvian, HCC, Patient, 106

description:
subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 106,Age: 72,Gender: Male,HBV: Positive,mtDNA haplotypes: D
HCCPER106

source_name: Peruvian HCC tissue from Patient 106

tag: individual

value: Patient, 106

value: Male

value: D


title: Peruvian, HCC, Patient, 104

description:
subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 104,Age: 72,Gender: Male,HBV: Positive,mtDNA haplotypes: A
HCCPER104

source_name: Peruvian HCC tissue from Patient 104

value: Patient, 104

value: A


title: NA12842 cell line replicate 1

tag: cell line


title: GFP at 2 hrs μg donor 2 experiment 1 [CWRU003397_S10]

source_name: GFP at 2 hours μg

value: GFP

tag: timepoint in hours

tag: donor id

tag: experiment


title: NA12342 cell line replicate 3


title: S2y110 5

city: Mol

first: Mohamed

last: Mysara

state: Belgium

address: Boeretang 200

country: Belgium

institute: Belgian nuclear research center (SCK-CEN)

description:
Snap frozen, DNA extracted, bisulphite sequencing done, result of found DMRs
P0y110_vs_S2y110.txt
S1y110_vs_S2y110.txt
S2y0_vs_S2y110.txt
S2y30_vs_S2y110.txt

data_processing:
CLC Genomics Workbench 20.0, The paired reads were mapped to the reference genome (TAIR10.31) with “Map Bisulfite reads to reference” module, using non-directional approach (applying the default parameters).
Differentially methylated regions were assigned using “Call methylation level” module by doing all pairwise comparison within the same generation or within the same treatment dose (resulting in 18 sets of DMRs identified for the different comparisons). The default parameters were applied (while specifying the minimum high-confidence site-coverage = 5 and minimum number of samples = 3), reporting the methylation levels for CpG, CHG & CHH contexts separately.
The p-values produced from ANOVA statistical modelling where corrected using Benjamini Hochberg approach (using p.adjust in R v 3.5.0).
Annotation to the nearest genes was added to each of the DMRs using "Annotate by nearby gene" module, using reference genome’s genes set. Additionally, the annotation to the nearest transposable elements (TEs) was added with closest module in bedtools package, using the “TAIR10 transposable elements” data set (downloaded on 18/03/2020) from the TAIR website (www.arabidopsis.org).
The filtering criteria to find DMRs associated with either gene regions (promoter or gene body) or TEs, were a p-value≤0.05 and at least 20% difference in their methylation levels (referred to as methylation difference).
For the filtering in DMRs associated with promoter regions, we chose to filter for DMRs with a distance to the nearest gene of 2kbp ≤ X > 0. For those associated with gene bodies the filter was set at a distance of 0 to the nearest gene. DMRs associated with TEs were found by filtering for a distance of 0 to the nearest TE.
Genome_build: TAIR 10.31 &  TAIR10 transposable elements (www.arabidopsis.org)
Supplementary_files_format_and_content: Txt files containing information on the Differentially methylated regions (DMRs) in different columns, their methylation "context", location ("chromosome", DMR "Start" and "End"), methylation difference ("Case.methylation.level", "Control.methylation.level", "methylation difference"), "methylation status" (Hyper or Hypo),  "p value", "location in gene" (promoter or gene body), association with Transposable element ("TE")

organism: Arabidopsis thaliana

source_name: plant rosette

growth_protocol: seeds were vernalised at 4 C for 3 days, seeds grown on 0.6% agar hoagland solution in cut-off plugs in a hydroponic set-up (14 h photoperiod, Photosynthetically active radiation of 200 μmol m-2 s-1 at the leaf level, 65% humidity, day/night temperature 22C/18C)

extract_protocol:
Snap frozen plant rosettes were ground, DNA extraction was done using Zymo ZR Plant/Seed DNA microprep kit according to the manufactorer's protocol
Three different treatments (γ0 = control, γ30 = 30 mGy/h, γ110 = 110 mGy/h) per generation (P0, S1, S2) were selected for sequencing. This resulted in a total of nine different conditions with 5 biological replicates for each condition. Concentration of the extracted DNA was measured using the 'Quant-it Picogreen dsDNA assay kit' (Life Technologies, Grand Island, NY, USA). Subsequently, 400-600 ng of gDNA was fragmented to 300bp using the Covaris S2 focused-ultrasonicator (Covaris, Woburn, Massachusetts, USA). The size of the fragmented DNA was checked on a High sensitivity DNA chip (Agilent Technologies, Santa Clara, CA, USA). Library preparation with NEBNext Ultra II DNA library prep kit (New England Biolabs, Ipswich, MA, USA) was performed using methylated adapters, according to the manufacturer's protocol.

treatment_protocol: Three different generations (P0, S1, S2) of 14-day old plants were irradiated for two weeks with gamma radiation (CS-137 source) to different dose rates (γ30 = 30 mGy/h, γ60 = 60 mGy/h, γ110 = 110 mGy/h, or γ430 = 430 mGy/h)(P0 seeds originated from our standard seed stock and had never been irradiated, S1 seeds were harvested from the previously irradiated P0 plants and S2 seeds were harvested from previously irradiated S1 plants)

tag: sample type

value: plant rosette

tag: generation

value: Second generation (S2)

tag: dose rate

tag: replicate

value: 5/5 replicates


title: Peruvian, HCC, Patient, 116

description:
subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 116,Age: 77,Gender: Male,HBV: Negative,mtDNA haplotypes: B
HCCPER116

source_name: Peruvian HCC tissue from Patient 116

value: Patient, 116

tag: nationality

tag: age

tag: gender

tag: hbv

value: Negative

tag: mtdna haplotypes


title: NA12342 cell line replicate 2


title: SUN1L at 2 hrs μg donor 1 experiment 1 [CWRU003406_S8]

source_name: SUN1L at 2 hours μg

tag: cell line background

value: MCF 10A

tag: cell type

value: Mammary epithelial cells

tag: treatment

value: μg


title: S2y110 3

value: 3/5 replicates


title: Peruvian NTL tissue from Patient 058

source_name: NTL tissue from Peruvian HCC patient

tag: subject id

value: Patient 058

tag: subject status

value: Peruvian patients with hepatocellular carcinoma (HCC)

value: Positive

value: B

tag: tissue

value: non-tumor liver (NTL) tissue


title: S2y110 4

value: 4/5 replicates


title: GFP at 20 hrs μg donor 1 experiment 1 [CWRU003398_S9]

tag: gravity

tag: timepoint in hours

tag: donor id


title: Peruvian, HCC, Patient, 101

description:
subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 101,Age: 24,Gender: Male,HBV: Positive,mtDNA haplotypes: C
HCCPER101

source_name: Peruvian HCC tissue from Patient 101

tag: individual

value: Patient, 101

value: Peruvian

value: Male

value: C

tag: disease state

value: hepatocellular carcinoma (HCC)

value: HCC


title: Peruvian, HCC, Patient, 099

description:
subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 099,Age: 32,Gender: Female,HBV: Positive,mtDNA haplotypes: D
HCCPER099

source_name: Peruvian HCC tissue from Patient 099

value: Patient, 099

value: Female

value: D


title: Peruvian, HCC, Patient, 100

description:
subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 100,Age: 44,Gender: Female,HBV: Positive,mtDNA haplotypes: B
HCCPER100

source_name: Peruvian HCC tissue from Patient 100

value: Patient, 100


title: Peruvian NTL tissue from Patient 059

value: Patient 059


title: Peruvian, HCC, Patient, 095

description:
subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 095,Age: 30,Gender: Male,HBV: Positive,mtDNA haplotypes: A
HCCPER095

source_name: Peruvian HCC tissue from Patient 095

value: Patient, 095

value: A


title: S2y110 2

tag: sample type

value: plant rosette

tag: generation

value: Second generation (S2)

tag: dose rate

tag: replicate

value: 2/5 replicates


title: Peruvian, HCC, Patient, 200

description:
subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 200,Age: 42,Gender: Male,HBV: Positive,mtDNA haplotypes: D
HCCPER200

source_name: Peruvian HCC tissue from Patient 200

value: Patient, 200

tag: nationality

tag: age

tag: gender

tag: hbv

value: Positive


title: NA12342 cell line replicate 1

description: Genomic DNA extracted from B-lymphocytes by Coriell and genotyped using Infinium Global Screening Array (GSAMD-24v1-0_20011747_A1) beadchip (Illumina)

tag: cell line


title: GFP at 0 hrs 1G donor 2 experiment 2 [CWRU003415_S7]

source_name: GFP at 0 hours 1G

tag: cell line background

value: MCF 10A

tag: cell type

value: Mammary epithelial cells

tag: treatment

value: GFP

tag: experiment


title: Peruvian, HCC, Patient, 093

description:
subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 093,Age: 35,Gender: Male,HBV: Negative,mtDNA haplotypes: C
HCCPER093

source_name: Peruvian HCC tissue from Patient 093

value: Patient, 093

value: Peruvian

value: Male

value: Negative

tag: mtdna haplotypes

value: C

value: hepatocellular carcinoma (HCC)

tag: tissue


title: NA11930 cell line replicate 2

source_name: purified gDNA


title: S2y110 1

value: 1/5 replicates


title: NA11930 cell line replicate 3


title: Peruvian NTL tissue from Patient 055

tag: subject id

value: Patient 055

tag: subject status

value: Peruvian patients with hepatocellular carcinoma (HCC)

value: Female

value: B

value: non-tumor liver (NTL) tissue


title: SUN1L at 2 hrs 1G donor 1 experiment 2 [CWRU003430_S5]

source_name: SUN1L at 2 hours 1G

tag: gravity

tag: timepoint in hours

tag: donor id


title: ChIPseq sample 1: PAO1 RepC ChIPseq background control

description: ChIPseq data

source_name: Pseudomonas aeruginosa PAO1

value: Bacteria culture

tag: genotype

value: wild type

tag: chip antibody

value: His-Tag (D3I1O) XP® Rabbit mAb (Cell Signaling Technology, INC, Cat #12698BC)


title: Peruvian, HCC, Patient, 092

description:
subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 092,Age: 76,Gender: Male,HBV: Negative,mtDNA haplotypes: D
HCCPER092

source_name: Peruvian HCC tissue from Patient 092

tag: individual

value: Patient, 092

tag: nationality

tag: age

value: D

tag: disease state

value: HCC


title: GFP at 0 hrs 1G donor 1 experiment 1 [CWRU003394_S4]

tag: cell line background

value: MCF 10A

value: Mammary epithelial cells

value: GFP


title: S2y30 3

description:
Snap frozen, DNA extracted, bisulphite sequencing done, result of found DMRs
P0y30_vs_S2y30.txt
S1y30_vs_S2y30.txt
S2y0_vs_S2y30.txt
S2y30_vs_S2y110.txt

tag: sample type

value: plant rosette

tag: generation

value: Second generation (S2)

tag: dose rate

tag: replicate

value: 3/5 replicates


title: NA06985 cell line replicate 3

tag: cell line


title: NA11930 cell line replicate 1


title: S2y30 4

value: 4/5 replicates


title: S2y30 5

value: 5/5 replicates


title: NA06985 cell line replicate 2


title: GFP at 20 hrs 1G donor 1 experiment 1 [CWRU003402_S2]

source_name: GFP at 20 hours 1G

tag: cell type

tag: treatment

tag: experiment


title: S2y30 2

value: 2/5 replicates


title: NA06985 cell line replicate 1


title: S2y30 1

value: 1/5 replicates


title: Peruvian NTL tissue from Patient 052

tag: subject id

value: Patient 052

tag: subject status

value: Peruvian patients with hepatocellular carcinoma (HCC)

tag: gender

value: Male

tag: hbv

value: Positive

tag: mtdna haplotypes

value: A

tag: tissue

value: non-tumor liver (NTL) tissue


title: HG03521 cell line replicate 3


title: GFP at 2 hrs 1G donor 2 experiment 2 [CWRU003421_S6]

source_name: GFP at 2 hours 1G

tag: gravity

tag: timepoint in hours

tag: donor id


title: S2y0 5

description:
Snap frozen, DNA extracted, bisulphite sequencing done, result of found DMRs
P0y0_vs_S2y0.txt
S1y0_vs_S2y0.txt
S2y0_vs_S2y30.txt
S2y0_vs_S2y110.txt

source_name: plant rosette

tag: sample type

value: y0 (control group)(0 mGy/h)


title: Peruvian, HCC, Patient, 088

description:
subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 088,Age: 67,Gender: Male,HBV: Positive,mtDNA haplotypes: B
HCCPER088

source_name: Peruvian HCC tissue from Patient 088

tag: individual

value: Patient, 088

tag: nationality

value: Peruvian

tag: age

value: B

tag: disease state

value: hepatocellular carcinoma (HCC)

value: HCC


title: Peruvian, HCC, Patient, 083

description:
subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 083,Age: 73,Gender: Male,HBV: Negative,mtDNA haplotypes: B
HCCPER083

source_name: Peruvian HCC tissue from Patient 083

value: Patient, 083

value: Negative


title: mNET-seq_Pla-B1h_rep2

city: Göttingen

first: Sara

middle: Patricia

last: Monteiro Martins

address: Fassberg 11

department: Molecular Biology

country: Germany

institute: MPI for biophysical chemistry

description: Total Pol II-associated RNA

data_processing:
TT-seq and RNA-seq: Paired-end 75 and 150 bp reads with additional 6 bp of barcodes were obtained for each group of samples. Two replicates were treated with Pladienolide B (Pla-B) and two replicates treated with a control solvent (DMSO). Reads were aligned to the hg20/hg38 (GRCh38) genome assembly (Human Genome Reference Consortium) using STAR 2.6.0 (Dobin et al., 2013), with the following specifications: outFilterMismatchNmax 2, outFilterMultimapScoreRange 0 and alignIntronMax 500000. Bam files were filtered with Samtools (Li et al., 2009) to remove alignments with MAPQ smaller than 7 (-q 7) and only proper pairs (-f2) were selected. Read counts for different features were calculated with HTSeq (Anders et al., 2015). Further data processing was carried out using the R/Bioconductor environment. Expressed transcripts were defined as possessing more than 50 read counts per kilobase (RPK) in two summarized replicates of TT-seq solvent control (DMSO). Prior to quantification, data was normalized by using added RNA spike-in as described previously (Schwalb et al., 2016)
mNET-seq: Paired-end 42 bp reads with additional 6 bp of barcodes were obtained for each of the samples. Reads were trimmed for adapter content with Cutadapt (1.18, RRID:SCR_011841) (Martin, 2011) with -O 12 -m 25 -a TGGAATTCTCGG -A GATCGTCGGACT. mNET-seq data was normalized using S. cerevisiae RNA spike-ins. To this end, a combined genome was generated using the Ensemble genome assembly for both human hg38 (GRCh38) and S. cerevisiae (R64-1-1), against which the reads were mapped using STAR (2.6.0, RRID:SCR_015899) (Dobin et al., 2013). Around 80% and 20% of reads mapped to the human and S. cerevisiae genomes, respectively. Bam files were filtered with Samtools (1.3.1, RRID:SCR_002105) (Li et al., 2009) to remove alignments with MAPQ smaller than 7 (-q 7) and only proper pairs (-f2) were selected. Read counts for different features were calculated with HTSeq (0.6.1.p1, RRID:SCR_005514) (Anders et al., 2015). Further data processing was carried out using the R/Bioconductor environment. Antisense bias ratio was determined using positions in regions without antisense annotation with a coverage of at least 100 according to the defined major isoforms. Data was normalized using added S. cerevisiae RNA spike-ins. mNETs-seq coverage was normalized with a median of ratios method (Love et al., 2014) using the antisense corrected counts for S. cerevisiae transcripts with an RPK of 100 or higher in two summarized replicates of mNET-seq solvent control (DMSO).
ChIP-seq: Paired-end 42 or 75 bp reads with additional 6 bp of barcodes were obtained for each of the samples. Reads were aligned using Bowtie 2 (2.3.5, RRID:SCR_005476) (Langmead and Salzberg, 2012) to both human hg38 (GRCh38) and D. melanogaster (BDGP6.28). Bam files were filtered with Samtools (1.3.1, RRID:SCR_002105) (Li et al., 2009) to remove alignments with MAPQ smaller than 7 (-q 7) and only proper pairs (-f2) were selected. Further data processing was carried out using the R/Bioconductor environment. ChIP-seq coverages were obtained from piled-up counts for every genomic position, using physical coverage, that is, counting both sequenced bases covered by reads and unsequenced bases spanned between proper mate-pair reads. Data was normalized using added D. melanogaster RNA spike-ins. Normalization factors were obtained by dividing the total D. melanogaster read counts for each sample by the total read counts of the sample with the lowest read counts. ChIP-seq coverages were divided by the respective normalization factors.
Major isoform annotation: Salmon (0.13.1, RRID:SCR_017036) (Patro et al., 2017) was used in order to select the major isoforms present in our dataset. RNA-seq samples for 1 h DMSO or 1 uM Pla-B treatments were mapped against curated RefSeq annotated protein-coding isoforms (UCSC RefSeq GRCh38, downloaded in April 2019). For each gene, the major isoform was determined as the one with maximum mean Transcripts Per Million (TPM) value across all RNA-seq samples. Major isoforms were excluded from further analysis if they represented less than 70 % of the gene isoforms based on the calculated mean TPM value. Additionally, major isoforms associated with overlapping genes as well as isoforms located on chromosomes X, Y and M were discarded from further analysis. The final major isoform annotation includes 6,694 isoforms containing 65,976 exons and 59,282 introns.  A total of 5,535 major transcript isoforms of protein-coding genes with RPK >= 50 of TT-seq solvent control (DMSO) were included in the analysis.
Intronless genes annotation: Intronless genes were defined as RefSeq annotated genes comprising one single isoform with one single exon. To avoid effects from neighboring intron-containing genes, only intronless genes at least 1 kb distant from the neighboring intron-containing annotated transcripts (strand independent) were included in the analysis. Moreover, because a long 3Â´ UTR has been recently reported to be alternatively spliced in an intronless gene (FranÃ§ois et al., 2018), only intronless genes with UTRs <= 100 bp were included. A total of 51 expressed protein-coding intronless genes were included in the analysis.
Genome_build: hg20/hg38 (GRCh38) genome assembly (Human Genome Reference Consortium http://hgdownload.soe.ucsc.edu/downloads.html#human)
Supplementary_files_format_and_content: bigwig coverage files

source_name: K562 erythroleukemia cells

growth_protocol: Human K562 cells were obtained from DSMZ (DSMZ no.: ACC-10) and cultured in antibiotic-free RPMI 1640 medium (Thermo Fisher Scientific, 31870–074) supplemented with 10% heat-inactivated fetal bovine serum (Thermo Fisher Scientific, 10500–064) and 2 mM GlutaMAX (Thermo Fisher Scientific, 35050087) at 37 ̊C and 5% CO2. Cells were verified to be free of mycoplasma contamination using Plasmo Test Mycoplasma Detection Kit (InvivoGen, rep-pt1). K562 cells were authenticated at the DSMZ Identification Service according to standards for STR profiling (ASN-0002). Biological replicates were grown independently.

extract_protocol: TruSeq Small RNA Library Kit (Illumina)

treatment_protocol: Cells at a confluency of 300.000 cell/mL were treated with DMSO (1:20.000 dilution, Sigma, D2438) as solvent control or with 1 μM Pladienolide-B from a DMSO-resuspended 20 mM stock (1:20.000 dilution, Santa Cruz, sc-391691).

tag: method protocol

value: mNET-seq (Gressel et al., 2019;Nojima et al., 2015;Schlackow et al., 2017)

tag: treatment condition

value: 37 C, DMSO for 1h, 0.3% empigen BB, Total Pol II antibody (Diagenode, C15200004)


title: S2y0 4

value: plant rosette

tag: generation

value: Second generation (S2)

tag: dose rate

tag: replicate

value: 4/5 replicates


title: HG03521 cell line replicate 2

tag: cell line


title: mNET-seq_Pla-B1h_rep1

description: Total Pol II-associated RNA


title: Peruvian NTL tissue from Patient 050

source_name: NTL tissue from Peruvian HCC patient

tag: subject id

value: Patient 050

tag: subject status

value: Peruvian patients with hepatocellular carcinoma (HCC)

tag: gender

value: Female

tag: hbv


title: GFP at 20 hrs μg donor 2 experiment 2 [CWRU003419_S1]

source_name: GFP at 20 hours μg

tag: cell line background

value: MCF 10A

tag: cell type

value: Mammary epithelial cells

tag: treatment

value: GFP

tag: gravity

value: μg

tag: timepoint in hours

tag: experiment


title: HG03521 cell line replicate 1


title: S2y0 3

tag: sample type

value: y0 (control group)(0 mGy/h)

value: 3/5 replicates


title: HG03520 cell line replicate 3


title: Peruvian NTL tissue from Patient 047

value: Patient 047

tag: age

value: Positive

tag: mtdna haplotypes

value: D

tag: tissue

value: non-tumor liver (NTL) tissue


title: S2y0 2

tag: generation

tag: dose rate

value: 2/5 replicates


title: Peruvian NTL tissue from Patient 054

value: Patient 054

value: Male

value: C


title: SUN1L at 20 hrs 1G donor 1 experiment 1 [CWRU003412_S3]

source_name: SUN1L at 20 hours 1G

tag: donor id


title: Peruvian NTL tissue from Patient 044

tag: subject id

value: Patient 044

value: B


title: S2y0 1

value: plant rosette

value: Second generation (S2)

tag: replicate

value: 1/5 replicates


title: HG03520 cell line replicate 2

tag: cell line


title: Peruvian NTL tissue from Patient 049

value: Patient 049

tag: subject status

value: Peruvian patients with hepatocellular carcinoma (HCC)

tag: gender

tag: hbv


title: S1y110 5

description:
Snap frozen, DNA extracted, bisulphite sequencing done, result of found DMRs
P0Y110_vs_S1y110.txt
S1y0_vs_S1y110.txt
S1y30_vs_S1y110
S1y110_vs_S2y110.txt

value: First generation (S1)

value: 5/5 replicates


title: mNET-seq_DMSO1h_rep2

description: Total Pol II-associated RNA

tag: method protocol

value: mNET-seq (Gressel et al., 2019;Nojima et al., 2015;Schlackow et al., 2017)

tag: treatment condition

value: 37 C, DMSO for 1h, 0.3% empigen BB, Total Pol II antibody (Diagenode, C15200004)


title: Peruvian NTL tissue from Patient 043

value: Patient 043

value: Female

value: Positive


title: HG03382 cell line replicate 3


title: Peruvian NTL tissue from Patient 034

value: Patient 034

value: non-tumor liver (NTL) tissue


title: S1y110 4

value: 4/5 replicates


title: HG03382 cell line replicate 2


title: HG03382 cell line replicate 1


title: Peruvian NTL tissue from Patient 033

value: Patient 033

value: Male


title: S1y110 2

value: plant rosette

value: 2/5 replicates


title: B409_silique_RNA_rep2

city: WuHan

first: Guan

middle: Peng

last: Peng

state: HuBei

address: shizishan street

department: college of informatics

country: China

institute: Huazhong Agricultural University

data_processing:
Raw reads were filtered for adapter and low quality reads by Trimmomatic
Clean reads mapped to the reference genome with TopHat2
The FPKM was calculated by Cufflinks v2.1.1
Genome_build: Download the genome from www.genoscope.cns.fr/brassicanapus
Supplementary_files_format_and_content: tab-delimited text files include the FPKM value with echo gene for echo sample

organism: Brassica napus

source_name: B409 silique

growth_protocol: Germinating seeds were obtained by placed on moist paper for 7 d at 22 °C. For roots and young leaves, the germinated seeds were grown in a phytotron with the day/night cycle set at 16 h/8 h and a temperature of 22 °C/18 °C. Roots were obtained 7 d after planting on moist filter paper, and young leaves were obtained from 2-week-old plants cultured hydroponically as described. Approximately 20-d-old seedlings were transplanted to the field and managed under normal agricultural conditions on the experimental farm of Huazhong Agricultural University, Wuhan, China. Flower buds and siliques were harvested.

extract_protocol:
Total RNA was isolated from the indicated tissues using a RNeasy plant mini kit according to the manufacturer’s instructions (QIAGEN, 74904).
The RNA was used for library construction using an Illumina TruSeq RNA kit, according to the manufacturer’s recommendations.

treatment_protocol: Fresh samples are frozen using liquid nitrogen.

tag: cultivar

value: siliques (3–5 cm)

value: silique


title: B409_root_RNA_rep2

source_name: B409 root

value: one-week roots after planting

value: root


title: B409_silique_RNA_rep1


title: Peruvian, HCC, Patient, 091

description:
subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 091,Age: 65,Gender: Male,HBV: Negative,mtDNA haplotypes: A
HCCPER091

source_name: Peruvian HCC tissue from Patient 091

tag: individual

value: Patient, 091

tag: nationality

value: Peruvian

value: Negative

value: A

tag: disease state

value: hepatocellular carcinoma (HCC)

value: HCC


title: HG03298 cell line replicate 3


title: Peruvian NTL tissue from Patient 039

value: Patient 039

value: Peruvian patients with hepatocellular carcinoma (HCC)

tag: age

value: Female

value: Positive

tag: mtdna haplotypes

value: C


title: S1y110 1

tag: sample type

value: plant rosette

tag: generation

value: First generation (S1)

value: 1/5 replicates


title: B409_flower_bud_RNA_rep1

source_name: B409 flower bud

value: flower buds (≤ 2 mm)

tag: tissue

value: flower bud


title: S1y110 3

tag: dose rate

value: 3/5 replicates


title: B409_flower_bud_RNA_rep2


title: HG03298 cell line replicate 2

source_name: purified gDNA


title: Peruvian NTL tissue from Patient 045

tag: subject id

value: Patient 045

value: Male

value: B

value: non-tumor liver (NTL) tissue


title: Peruvian NTL tissue from Patient 038

value: Patient 038


title: B409_young_leaf_RNA_rep2

source_name: B409 young leaf

value: young leaves from two-week seedlings

value: young leaf


title: Peruvian NTL tissue from Patient 027

value: Patient 027

value: Peruvian patients with hepatocellular carcinoma (HCC)


title: S1y30 4

description:
Snap frozen, DNA extracted, bisulphite sequencing done, result of found DMRs
P0y30_vs_S1y30.txt
S1y0_vs_S1y30.txt
S1y30_vs_S1y110.txt
S1y30_vs_S2y30.txt

tag: replicate

value: 4/5 replicates


title: B409_young_leaf_RNA_rep1


title: HG03298 cell line replicate 1

tag: cell line


title: HG03202 cell line replicate 3


title: 2063A_root_RNA_rep2

source_name: 2063A root

value: one-week roots after planting

value: root


title: HG03202 cell line replicate 2


title: Peruvian NTL tissue from Patient 028

value: Patient 028

tag: subject status

tag: gender

value: Positive


title: S1y30 3

value: plant rosette

value: First generation (S1)


title: S1y30 2

value: 2/5 replicates


title: 2063A_root_RNA_rep1


title: Peruvian NTL tissue from Patient 022

value: Patient 022

tag: hbv

value: A


title: mNET-seq_DMSO1h_rep1

description: Total Pol II-associated RNA

tag: method protocol

value: mNET-seq (Gressel et al., 2019;Nojima et al., 2015;Schlackow et al., 2017)

tag: treatment condition

value: 37 C, DMSO for 1h, 0.3% empigen BB, Total Pol II antibody (Diagenode, C15200004)


title: 2063A_silique_RNA_rep2

source_name: 2063A silique

tag: cultivar

value: siliques (3–5 cm)

value: silique


title: S1y30 1

value: 1/5 replicates


title: HG03127 cell line replicate 3


title: Peruvian NTL tissue from Patient 023

value: Patient 023

value: Male

value: B

value: non-tumor liver (NTL) tissue


title: HG03127 cell line replicate 2


title: HG03202 cell line replicate 1


title: Peruvian NTL tissue from Patient 026

value: Patient 026

value: Peruvian patients with hepatocellular carcinoma (HCC)

value: D


title: S1y0 5

description:
Snap frozen, DNA extracted, bisulphite sequencing done, result of found DMRs
P0y0_vs_S1y0.txt
S1y0_vs_S1y30.txt
S1y0_vs_S1y30.txt
S1y0_vs_S2y0.txt

value: plant rosette

value: y0 (control group)(0 mGy/h)

value: 5/5 replicates


title: Peruvian NTL tissue from Patient 021

value: Patient 021

value: Positive


title: 2063A_silique_RNA_rep1


title: S1y0 4

value: First generation (S1)

value: 4/5 replicates


title: 2063A_flower_bud_RNA_rep2

source_name: 2063A flower bud

value: flower buds (≤ 2 mm)

value: flower bud


title: 2063A_flower_bud_RNA_rep1


title: HG03095 cell line replicate 3


title: Peruvian NTL tissue from Patient 025

value: Patient 025


title: 2063A_young_leaf_RNA_rep2

source_name: 2063A young leaf

value: young leaves from two-week seedlings

value: young leaf


title: HG03095 cell line replicate 2


title: Peruvian NTL tissue from Patient 019

value: Patient 019

value: Female

value: B


title: S1y0 1

source_name: plant rosette

value: 1/5 replicates


title: HG03095 cell line replicate 1


title: S1y0 2

value: 2/5 replicates


title: P0y110 5

description:
Snap frozen, DNA extracted, bisulphite sequencing done, result of found DMRs
P0y110_vs_S1y110.txt
P0y110_vs_S2y110.txt
P0y0_vs_P0y110.txt
P0y30_vs_P0y110.txt

value: plant rosette

value: Parent generation (P0)


title: 2063A_young_leaf_RNA_rep1


title: HG03127 cell line replicate 1


title: Peruvian NTL tissue from Patient 015

value: Patient 015

value: Peruvian patients with hepatocellular carcinoma (HCC)

value: non-tumor liver (NTL) tissue


title: B409_root_WGBS

data_processing:
Raw reads were filtered for adapter and low quality reads by Trimmomatic
Clean reads mapped to the reference genome with BatMeth2
The methylation level were calculated by BatMeth2
Genome_build: Download the genome from www.genoscope.cns.fr/brassicanapus
Supplementary_files_format_and_content: Show the echo site methylation level with detected

extract_protocol:
Genomic DNA was extracted using a DNeasy plant mini kit according to the manufacturer’s instructions (QIAGEN, 69104).
Bisulfite-treated DNA sequencing: Bisulfite conversion of DNA was conducted using the EZ DNA Methylation-GoldTM kit (ZYMO, D5005), and the bisulfite-treated DNA libraries were constructed using the Illumina TruSeq DNA sample prep kit, following the manufacturers’ instructions.

value: one-week roots after planting

tag: tissues

value: root


title: HG03082 cell line replicate 3


title: HG03520 cell line replicate 1


title: Peruvian NTL tissue from Patient 016

value: Patient 016

value: Positive


title: B409_root_RNA_rep1


title: B409_silique_WGBS

value: siliques (3–5 cm)

value: silique


title: P0y110 4

value: 4/5 replicates


title: HG03082 cell line replicate 2


title: P0y110 3

value: 3/5 replicates


title: B409_flower_bud_WGBS

value: flower buds (≤ 2 mm)

value: flower bud


title: HG03082 cell line replicate 1


title: B409_young_leaf_WGBS

value: young leaves from two-week seedlings

value: young leaf


title: P0y110 2

value: plant rosette

value: 2/5 replicates


title: Peruvian NTL tissue from Patient 012

value: Patient 012

value: Male

value: C


title: HG03077 cell line replicate 3


title: 2063A_root_WGBS

value: one-week roots after planting


title: S1y30 5

value: First generation (S1)

value: 5/5 replicates


title: P0y30 5

description:
Snap frozen, DNA extracted, bisulphite sequencing done, result of found DMRs
P0y30_vs_S1y30.txt
P0y30_vs_S2y30.txt
P0y0_vs_P0y30.txt
P0y30_vs_P0y110.txt

value: Parent generation (P0)


title: P0y110 1

value: 1/5 replicates


title: 2063A_silique_WGBS

value: siliques (3–5 cm)

value: silique


title: HG03077 cell line replicate 2


title: HG03077 cell line replicate 1


title: P0y30 4

value: 4/5 replicates


title: Peruvian NTL tissue from Patient 030

value: Patient 030

value: Peruvian patients with hepatocellular carcinoma (HCC)

value: Female

value: Positive

value: A

value: non-tumor liver (NTL) tissue


title: Peruvian NTL tissue from Patient 009

value: Patient 009


title: HG03063 cell line replicate 3


title: S1y0 3

value: plant rosette

value: y0 (control group)(0 mGy/h)

value: 3/5 replicates


title: 2063A_young_leaf_WGBS

value: young leaves from two-week seedlings

value: young leaf


title: HG03063 cell line replicate 2


title: 2063A_young_leaf_H3K27me3_H3K4me1_rep2

data_processing:
library strategy: ChIP-reChIP-seq
Raw reads were filtered for adapter and low quality reads by Trimmomatic
Clean reads mapped to the reference genome with bwa mem
The reads with mapping quality lower 30 and duplication were filtered by samtools
MACS2 were used to call the peak with -B --broad --broad-cutoff 0.01 -q 0.01 -g 8.6e8 --fe-cutoff 4.0 --nomode
Genome_build: Download the genome from www.genoscope.cns.fr/brassicanapus
Supplementary_files_format_and_content: bogWig file by deepTools bamCoverage

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody twice.
ChIP-reChIP-DNA was extracted with phenol:chloroform:isoamyl alcohol (Sigma–Aldrich, P3803), precipitated with ethanol, and resuspended in TE buffer. ChIP DNA libraries were prepared using an NEBNext® Ultra™ II DNA library prep kit for Illumina® (New England BioLabs, E7645). Briefly, ChIP DNA was end-repaired, ligated with an adaptor, and followed by 6–10 cycles of PCR amplification, per the manufacturer’s guidelines. Next, library fragments of 250–650 bp were selected using AMPure XP beads (Beckman, A63881). Finally, the DNA fragments were sequenced using an Illumina HiSeq X Ten system (paired-end 150-bp reads).

treatment_protocol: Tissues were cross-linked with 1% formaldehyde for 10 min and quenched with 0.2 M glycine at room temperature.

tag: development stage

tag: chip antibody


title: HG03063 cell line replicate 1


title: 2063A_young_leaf_H3K27me3_H3K4me1_rep1


title: HG03060 cell line replicate 3


title: Peruvian NTL tissue from Patient 004

value: Patient 004

tag: age

value: Male

tag: mtdna haplotypes

value: B


title: Peruvian NTL tissue from Patient 020

value: Patient 020


title: HG03060 cell line replicate 2


title: Peruvian NTL tissue from Patient 003

value: Patient 003

value: D


title: 2063A_young_leaf_H3K4me1_H3K27me3_rep2


title: Peruvian NTL tissue from Patient 013

value: Patient 013

value: Peruvian patients with hepatocellular carcinoma (HCC)


title: P0y0 5

description:
Snap frozen, DNA extracted, bisulphite sequencing done, result of found DMRs
P0y0_vs_S1y0.txt
P0y0_vs_S2y0.txt
P0y0_vs_P0y30.txt
P0y0_vs_P0y110.txt

tag: sample type

tag: generation

value: Parent generation (P0)

value: 5/5 replicates


title: P0y30 3

tag: dose rate


title: P0y30 1

value: 1/5 replicates


title: P0y0 4

value: 4/5 replicates


title: P0y30 2

value: plant rosette

value: 2/5 replicates


title: 2063A_young_leaf_H3K4me1_H3K27me3_rep1

tag: tissue


title: Peruvian HCC tissue from Patient 068

source_name: HCC tissue from Peruvian HCC patient

tag: subject id

value: Patient 068

value: Positive

value: C

value: HCC


title: HG03060 cell line replicate 1

tag: cell line


title: P0y0 3

value: y0 (control group)(0 mGy/h)

tag: replicate

value: 3/5 replicates


title: Peruvian HCC tissue from Patient 052

value: Patient 052

tag: subject status

tag: gender

value: Female

value: Negative

value: B


title: B409_input

data_processing:
Raw reads were filtered for adapter and low quality reads by Trimmomatic
Clean reads mapped to the reference genome with bwa mem
The reads with mapping quality lower 30 and duplication were filtered by samtools
MACS2 were used to call the peak
Genome_build: Download the genome from www.genoscope.cns.fr/brassicanapus
Supplementary_files_format_and_content: bogWig file by deepTools bamCoverage

growth_protocol: Germinating seeds were obtained by placed on moist paper for 7 d at 22 °C. For roots and young leaves, the germinated seeds were grown in a phytotron with the day/night cycle set at 16 h/8 h and a temperature of 22 °C/18 °C. Roots were obtained 7 d after planting on moist filter paper, and young leaves were obtained from 2-week-old plants cultured hydroponically as described. Approximately 20-d-old seedlings were transplanted to the field and managed under normal agricultural conditions on the experimental farm of Huazhong Agricultural University, Wuhan, China. flower bud buds and siliques were harvested.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
ChIP-DNA was extracted with phenol:chloroform:isoamyl alcohol (Sigma–Aldrich, P3803), precipitated with ethanol, and resuspended in TE buffer. ChIP DNA libraries were prepared using an NEBNext® Ultra™ II DNA library prep kit for Illumina® (New England BioLabs, E7645). Briefly, ChIP DNA was end-repaired, ligated with an adaptor, and followed by 6–10 cycles of PCR amplification, per the manufacturer’s guidelines. Next, library fragments of 250–650 bp were selected using AMPure XP beads (Beckman, A63881). Finally, the DNA fragments were sequenced using an Illumina HiSeq X Ten system (paired-end 150-bp reads).

tag: developmental stage

value: young leaves from two-week seedlings

value: young leaf


title: Peruvian HCC tissue from Patient 072

value: Patient 072

value: Peruvian patients with hepatocellular carcinoma (HCC)

value: Male

tag: hbv


title: HG03054 cell line replicate 2


title: Peruvian HCC tissue from Patient 038

value: Patient 038


title: P0y0 1

value: plant rosette

value: Parent generation (P0)

value: 1/5 replicates


title: 2063A_input_rep2

tag: cultivar


title: P0y0 2

value: 2/5 replicates


title: 2063A_input_rep1


title: Peruvian NTL tissue from Patient 006

value: Patient 006

value: Positive

value: non-tumor liver (NTL) tissue


title: HG03052 cell line replicate 3


title: HG03054 cell line replicate 1


title: Peruvian NTL tissue from Patient 010

value: Patient 010


title: B409_root_RNAPII_rep2

value: one-week roots after planting

value: root

value: RNAPII


title: B409_root_RNAPII_rep1


title: Peruvian HCC tissue from Patient 065

value: Patient 065

value: B

value: HCC


title: HG03052 cell line replicate 2


title: HG03052 cell line replicate 1


title: Peruvian HCC tissue from Patient 030

value: Patient 030

value: Peruvian patients with hepatocellular carcinoma (HCC)

value: C


title: B409_root_H3K9me2_rep2


title: B409_root_H3K9me2_rep1


title: HG02982 cell line replicate 3


title: Peruvian NTL tissue from Patient 011

value: Patient 011

value: Male


title: GDF11 3

city: S. Giovanni Rotondo (FG)

first: Tommaso

last: Mazza

address: Viale Cappuccini, 1

department: Bioinformatics

country: Italy

institute: IRCCS Casa Sollievo della Sofferenza

description:
RIN: 9.4
G3

data_processing:
Reads trimmed using Trimmomatic
Reads pseudo-aligned and counted with Salmon (ver. 1.2.1)
Normalization and comparisons performed using DESeq2
Genome_build: GRCh38 - gencode v34
Supplementary_files_format_and_content: Tab-delimited text files include variance-stabilized transformed values for each sample

growth_protocol: The human hepatic cancer cell lines HepG2 and Hep3B were purchased from American Type Culture Collection (ATCC, Manassas, VA) and were cultured in Nunc EasYFlasks in high glucose (4.5g/l) DMEM (1X) media supplemented with 10% fetal bovine serum (FBS) (Sigma-Aldrich, Czech Republic), 15 mM Hepes buffer (Biowest, France), Glutamine, 1% penicillin/streptomycin solution and 100 g/ml Normocin (InvivoGen, CA, USA). The medium was routinely changed every 2 days and the cells were sub-cultured using TrypLE Express enzyme (Gibco, Ireland) when reaching 90% confluence. For experiments, flasks with at least 60-70% confluence were treated with 100 ng/ml recombinant GDF11 protein for 24 hours.

extract_protocol:
Total RNA was extracted from at least three biological replicates of controls and GDF11 treated (100ng/ml, 24 h) HepG2 cells with TRIzol Reagent (Invitrogen, CA, US) and column separation using a DNeasy Blood & Tissue Kit (Qiagen, Germany), according to the manufacturer's instructions. RNA integrity was assessed using Agilent RNA 6000 Nano Kit and Agilent 2100 Bioanalyzer (both Agilent Technologies, CA, US). Samples with RIN≥8.5 were further processed for sequencing.
Indexed libraries were prepared from 250ng purified RNA using a NEB Next Ultra II Directional RNA Library Prep Kit (Illumina, UK), according to the manufacturer's instructions. The libraries were pooled in equimolar amounts(with a final concentration of 2 nmol/L), subjected to cluster generation and sequenced on an Illumina MiSeq System (Illumina) in a 1x75 format. Quality control was performed by FastQC and MultiQC. Short reads related to the sequencing of control and GDF11 treated HepG2 cells were aligned against the hg19 genome assembly, using STAR (ver. 2.6) with standard parameters.

treatment_protocol: For RNA-seq, the HepG2 cells were treated with 100 ng/ml recombinant GDF11 protein for 24 hours.

value: Hepatocellular carcinoma cells

tag: treatment

value: treatment with recombinant GDF11 protein


title: 2063A_flower_bud_WGBS

value: flower buds (≤ 2 mm)

tag: tissues

value: flower bud


title: GDF11 2

description:
RIN: 9.5
G2


title: B409_root_H3K4me1_rep1

tag: chip antibody


title: B409_root_H3K27me3_rep2


title: B409_root_H3K4me1_rep2


title: HG02982 cell line replicate 1


title: CTL 3

description:
RIN: 9.6
C3

value: control


title: HG02941 cell line replicate 3


title: B409_root_H3K27me3_rep1


title: CTL 2

description:
RIN: 9.9
C2


title: Peruvian HCC tissue from Patient 074

value: Patient 074

tag: age

value: Positive


title: B409_root_H3K27ac_rep2

value: one-week roots after planting

value: root


title: HG02941 cell line replicate 2


title: HG02941 cell line replicate 1


title: HG03054 cell line replicate 3


title: CTL 1

description:
RIN: 9.8
C1


title: Peruvian HCC tissue from Patient 075

value: Patient 075

tag: mtdna haplotypes


title: Peruvian HCC tissue from Patient 019

value: Patient 019


title: Peruvian HCC tissue from Patient 079

value: Patient 079

value: Female

value: HCC


title: B409_root_H3K27ac_rep1


title: Peruvian HCC tissue from Patient 073

value: Patient 073

value: Peruvian patients with hepatocellular carcinoma (HCC)

value: C


title: HG02982 cell line replicate 2


title: B409_root_H3K4me3_rep2


title: Peruvian HCC tissue from Patient 061

value: Patient 061

value: Male


title: HG02938 cell line replicate 3


title: GDF11 1

description:
RIN: 9.6
G1

value: Hepatocellular carcinoma cells

value: treatment with recombinant GDF11 protein


title: Peruvian HCC tissue from Patient 071

value: Patient 071

value: B


title: HG02938 cell line replicate 1


title: HG02938 cell line replicate 2


title: B409_silique_RNAPII_rep2

value: siliques (3-5 cm)

value: silique

value: RNAPII


title: Peruvian HCC tissue from Patient 064

value: Patient 064

value: Positive


title: HG02922 cell line replicate 3


title: right inferior colliculus from single-sided deaf group 2

type: RNA

city: Seongnam

first: So Young

last: Kim

address: Yatapro 59

country: South Korea

institute: CHA University

description: Gene expression data from hippocampus from noise group

hyb_protocol: One hundred and nine microliters of this mixture was injected into a GeneChip Rat Gene 2.0 ST Array (Affymetrix, Santa Clara, CA, USA) and placed in the Affymetrix GeneChip Hybridization Oven 640 at 45°C and 60 rpm for 16 hours overnight. Stain cocktails (stain cocktail 1 and stain cocktail 2 [GeneChip Hybridization, Wash, and Stain Kit]) cocktails (stain cocktail 1 and stain cocktail 2 [GeneChip Hybridization, Wash, and Stain Kit]) were added to amplify the signal intensities. The arrays were stained and washed in an Affymetrix GeneChip Fluidics Station 450 according to the FS450_0002 fluidics protocol.

scan_protocol: All arrays were scanned with the Affymetrix GeneChip Scanner 3000.

data_processing:
The raw analysis was performed with Transcriptome Analysis ConsoleTM (TAC) software.
Differential expression (DE) between rat exposed to SSD (experimental) and control rat (control) was predicted at the gene-level (probesets summarized into transcript clusters/genes).

label: biotin

organism: Rattus norvegicus

label_protocol: 5.5 μg of ss-cDNA was fragmented by uracil-DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease I (APE I) and labeled by terminal deoxynucleotidyl transferase (TDT) using the proprietary Affymetrix DNA labeling reagent.

growth_protocol: Right-side cochlear ablation surgery was performed on the rats in the SSD 2-week group. In the control group rats, a sham operation with a postauricular incision but without drilling the otic bulla was performed.

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

treatment_protocol: Within 4 hours, RNA was extracted from the IC tissues.

value: inferior colliculus tissue

tag: strain

value: SD


title: B409_root_H3K4me3_rep1

value: one-week roots after planting

value: root


title: right inferior colliculus from single-sided deaf group 3


title: B409_silique_RNAPII_rep1


title: Peruvian HCC tissue from Patient 077

value: Patient 077

value: Peruvian patients with hepatocellular carcinoma (HCC)

value: Female

value: HCC


title: HG02922 cell line replicate 2


title: Peruvian HCC tissue from Patient 070

value: Patient 070

value: Male


title: B409_silique_H3K9me2_rep2


title: B409_silique_H3K9me2_rep1


title: Peruvian HCC tissue from Patient 059

value: Patient 059

value: A


title: HG02922 cell line replicate 1


title: Peruvian HCC tissue from Patient 058

value: Patient 058

value: B


title: B409_silique_H3K4me1_rep2

value: siliques (3-5 cm)

value: silique


title: Peruvian HCC tissue from Patient 054

value: Patient 054

value: Positive

value: D


title: HG02882 cell line replicate 2


title: left inferior colliculus from single-sided deaf group 2

value: inferior colliculus tissue

value: SD


title: right inferior colliculus from control group 3

description: Gene expression data from hippocampus from control group


title: Peruvian HCC tissue from Patient 050

value: Patient 050


title: Peruvian HCC tissue from Patient 055

value: Patient 055

value: Peruvian patients with hepatocellular carcinoma (HCC)

value: C


title: left inferior colliculus from single-sided deaf group 3


title: Peruvian HCC tissue from Patient 047

value: Patient 047

value: Female

value: HCC


title: right inferior colliculus from single-sided deaf group 1


title: B409_silique_H3K4me1_rep1


title: Peruvian HCC tissue from Patient 045

value: Patient 045


title: HG02882 cell line replicate 1


title: B409_silique_H3K27me3_rep2


title: HG02881 cell line replicate 3


title: HG02882 cell line replicate 3


title: HG02881 cell line replicate 2


title: left inferior colliculus from single-sided deaf group 1


title: Peruvian HCC tissue from Patient 044

value: Patient 044


title: B409_silique_H3K27ac_rep2


title: B409_silique_H3K27me3_rep1


title: HG02881 cell line replicate 1


title: right inferior colliculus from control group 2


title: Peruvian HCC tissue from Patient 039

value: Patient 039

value: Male

value: B


title: right inferior colliculus from control group 1


title: B409_silique_H3K27ac_rep1

value: siliques (3-5 cm)

value: silique


title: Peruvian HCC tissue from Patient 034

value: Patient 034

value: Positive

value: A


title: HG02879 cell line replicate 3


title: Peruvian HCC tissue from Patient 049

value: Patient 049


title: B409_silique_H3K4me3_rep2


title: left inferior colliculus from control group 2

value: inferior colliculus tissue

value: SD


title: B409_flower_bud_RNAPII_rep2

value: flower buds (<= 2 mm)

value: flower bud

value: RNAPII


title: left inferior colliculus from control group 3


title: HG02879 cell line replicate 2


title: HG02878 cell line replicate 3


title: left inferior colliculus from control group 1


title: HG02878 cell line replicate 2


title: Peruvian HCC tissue from Patient 028

value: Patient 028

value: Peruvian patients with hepatocellular carcinoma (HCC)

value: Female

value: HCC


title: B409_flower_bud_H3K9me2_rep2


title: B409_flower_bud_H3K9me2_rep1


title: B409_flower_bud_RNAPII_rep1


title: HG02760 cell line replicate 3


title: B409_flower_bud_H3K4me1_rep2


title: HG02760 cell line replicate 2


title: Peruvian HCC tissue from Patient 023

value: Patient 023

value: Male


title: Peruvian HCC tissue from Patient 025

value: Patient 025

value: B


title: B409_flower_bud_H3K4me1_rep1


title: HG02878 cell line replicate 1


title: Peruvian HCC tissue from Patient 026

value: Patient 026


title: B409_flower_bud_H3K27me3_rep2


title: HG02759 cell line replicate 3


title: HG02760 cell line replicate 1


title: Peruvian HCC tissue from Patient 027

value: Patient 027

value: Positive

value: D


title: single-cell_injured_spinal_cord

city: St. Louis

first: Mayssa

last: Mokalled

state: MO

address: 4523 Clayton Ave CB 8103

department: Developmental Biology

institute: Washington University

data_processing:
Aligned reads were analyzed using the Seurat package v3.1.4 within R v3.6.3.
Cells that have unique number of genes between 200 to 4000 and a mitochondrial gene percentage less than five were filtered.
The “SCTransform” function was used for normalization, scaling and finding variable features. SCTransform returned 3000 highly variable features for downstream analysis.
Significant principal components were determined using “ElbowPlot” function.
Forty principal components were selected to create a Shared Nearest Neighbour (SNN) graph using the “FindNeighbours” function.
Clustering was performed by the Louvain algorithm using the function “FindClusters” and the resolution parameter was set to one.
Uniform Manifold Approximation and Reduction (UMAP) was used for non-linear dimensional reduction of the first 40 principle components and to visualize the data in two-dimensional space (“RunUMAP” function)
Differential gene expression for individual cluster was identified using Wilcoxon rank sum tests in the “FindAllMarkers” function.
Supplementary_files_format_and_content: RDS file

organism: Danio rerio

source_name: 5 days post injury spinal cord nuclear

extract_protocol:
gfap:EGFP transgenic animals were subjected to SCI and 2 mm SC tissue sections spanning the lesion site were collected at 1 wpi. Nuclei were isolated from 45 pooled SC tissues.
For single nuclear library preparation on the 10x Genomics platform, the Chromium Single Cell 3′ GEM Library and Gel Bead Kit v3 (cat# 1000092) and the Chromium Chip B Single Cell Kit (cat# 1000074) were used according to the manufacturer’s instructions in the Chromium Single Cell 3′ Reagents Kits V3 User Guide. The resulting cDNA libraries were quantified on an Agilent Tapestation and sequenced on Illumina HiSeq 3000.

treatment_protocol: Adult zebrafish were subjected to complete spinal cord transection.

value: spinal cord

tag: rna population

value: nuclear

tag: time point

value: 5 days post injury


title: Z_14_3_wpi_sc_2

description: Sample 11

data_processing:
Quality control and trimming of adapters and short sequences using Fastx
Sequence reads mapped to the zebrafish genome (Zv11) using Bowtie2
Sequence reads assembled and quantified using Cufflinks and Cuffdiff algorithms
Genome_build: Zv11

source_name: 21 days post injury (dpi) whole bulk spinal cord

extract_protocol:
For FACS-seq, animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted, resuspended, and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications.
TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single-end reads

treatment_protocol: Adult zebrafish were subjected to complete spinal cord transection or sham-injured (control).

tag: tissue

value: bulk spinal cord

tag: timepoint

value: 21 days post injury


title: HG02759 cell line replicate 2

tag: cell line


title: Peruvian HCC tissue from Patient 033

tag: subject id

value: Patient 033


title: HG02759 cell line replicate 1


title: Z_13_10_dpi_sc_2

description: Sample 9

source_name: 10 days post injury (dpi) whole bulk spinal cord

value: 10 days post injury


title: B409_flower_bud_H3K27ac_rep1

value: flower buds (<= 2 mm)

value: flower bud


title: B409_silique_H3K4me3_rep1

value: siliques (3-5 cm)

value: silique


title: Z_9_10_dpi_sc_1

description: Sample 8


title: B409_flower_bud_H3K4me3_rep2


title: HG02568 cell line replicate 3


title: Peruvian HCC tissue from Patient 022

value: Patient 022

tag: subject status

value: Peruvian patients with hepatocellular carcinoma (HCC)

value: Male

value: HCC


title: Z_12_5_dpi_sc_2

description: Sample 7

source_name: 5 days post injury (dpi) whole bulk spinal cord


title: HG02568 cell line replicate 1


title: B409_flower_bud_H3K4me3_rep1


title: Peruvian HCC tissue from Patient 016

value: Patient 016

tag: gender

value: Female

value: Positive

value: B


title: Z_8_5_dpi_sc_1

description: Sample 6

value: 5 days post injury


title: B409_young_leaf_RNAPII_rep2

tag: developmental stage

value: young leaves from two-week seedlings

value: young leaf

value: RNAPII


title: B409_flower_bud_H3K27ac_rep2


title: Z_11_uninjured_sc_2

description: Sample 5

source_name: Bulk uninjured spinal cord

value: bulk spinal cord

value: Uninjured


title: GTG_140_60: NCI-H1299

city: North Chicago

first: Xin

last: Lu

state: IL

address: 1 North Waukegan Rd

department: Oncology Discovery

institute: Abbvie

data_processing:
Illumina Casava1.8 software used for basecalling
Reads were aligned using the OmicSoft aligner and gene expression quantified based on UCSC gene model.
Differentially expressed genes between treatment conditions detected by DESeq2 with a statistical cut-off (FC>2, p<0.01)
Genome_build: B37

growth_protocol: Cell Lines were cultured in RPMI-1640 + 10% FBS

extract_protocol:
RNA was prepared by Qiazol extraction followed by RNeasy mini column (QIAGEN)
10 ug of total RNA was submitted to poly-A selection to remove ribosomal RNA and reverse transcribed to double-stranded cDNA. The cDNA was eblunt ended, adenylated, and ligated with Illumina indexes.

treatment_protocol: Cells were treated with DMSO or indicated inhibitors for 24 hr

tag: disease

value: non-small cell lung carcinoma

tag: dose


title: Peruvian HCC tissue from Patient 015

value: Patient 015

tag: hbv


title: Peruvian HCC tissue from Patient 043

value: Patient 043

value: C


title: HG02282 cell line replicate 3


title: Peruvian HCC tissue from Patient 013

value: Patient 013

value: Peruvian patients with hepatocellular carcinoma (HCC)


title: GTG_140_59: NCI-H1299

tag: treatment


title: B409_young_leaf_RNAPII_rep1

tag: cultivar

tag: chip antibody


title: HG02282 cell line replicate 2


title: Peruvian HCC tissue from Patient 021

value: Patient 021

tag: age

value: Male

tag: mtdna haplotypes

value: HCC


title: Z_7_uninjured_sc_1

description: Sample 4


title: Z_10_3_wpi_sc_1

description: Sample 10

value: 21 days post injury


title: GTG_140_58: NCI-H1299


title: HG02282 cell line replicate 1


title: Peruvian HCC tissue from Patient 010

value: Patient 010

value: Female

value: Positive

value: B


title: B409_young_leaf_H3K9me2_rep2

value: young leaves from two-week seedlings

value: young leaf


title: Z_3_gp_rp_rna_1

description: Sample 3

value: ctgfa:mCherry;gfap:EGFP cells

value: 5 days post injury


title: Peruvian HCC tissue from Patient 020

value: Patient 020


title: Peruvian HCC tissue from Patient 009

value: Patient 009


title: HG02215 cell line replicate 3


title: HG02879 cell line replicate 1


title: Peruvian HCC tissue from Patient 011

value: Patient 011


title: GTG_140_57: NCI-H1299

value: non-small cell lung carcinoma


title: Z_18_gp_rp_3

description: Sample 2


title: B409_young_leaf_H3K9me2_rep1


title: HG02215 cell line replicate 2


title: GTG_140_56: NCI-H1299

value: DMSO


title: Z_15_gp_rp_1

description: Sample 1


title: HG02568 cell line replicate 2


title: Peruvian HCC tissue from Patient 006

value: Patient 006

value: Peruvian patients with hepatocellular carcinoma (HCC)


title: Peruvian HCC tissue from Patient 012

value: Patient 012

value: Male

value: C

value: HCC


title: GTG_140_55: NCI-H1299


title: B409_young_leaf_H3K4me1_rep1


title: HG02215 cell line replicate 1


title: Mischocyttarus_Worker

city: London

first: Christopher

middle: Douglas Robert

last: Wyatt

address: Gower street

country: United Kingdom

institute: UCL

data_processing:
Trinity used to assemble a de novo transcriptome
RSEM used to calculate normalised gene counts per Trinity transcript
Supplementary_files_format_and_content: Trinity fasta transcriptome files (.fnn) and tab-delimited RSEM files for each queen/worker which include TPM/FPKM and expected count for each sample.

organism: Mischocyttarus basimacula

source_name: Whole brain

extract_protocol:
All wasps were collected directly from their nests during the daytime, placed immediately into RNAlater (Ambion, Invitrogen) and stored at -20°C until further use. Total RNA was extracted using the RNeasy Universal Plus Mini kit (Qiagen, #73404)
RNA libraries were prepared for sequencing using standard Illumina Truseq kit protocols

tag: caste

value: Worker

value: whole brain


title: B409_young_leaf_H3K4me1_rep2

value: young leaves from two-week seedlings


title: HG02107 cell line replicate 3


title: B409_young_leaf_H3K27me3_rep2

value: young leaf


title: GTG_140_36: Kasumi-1

value: acute myeloid leukemia


title: Mischocyttarus_Queen

value: Queen


title: Peruvian HCC tissue from Patient 003

value: Patient 003

value: Positive

value: D


title: HG02107 cell line replicate 2


title: B409_young_leaf_H3K27me3_rep1


title: GTG_140_35: Kasumi-1


title: Peruvian HCC tissue from Patient 004

value: Patient 004

value: B


title: BMWorker

organism: Brachygastra mellifica


title: GTG_140_34: Kasumi-1


title: B409_young_leaf_H3K27ac_rep2


title: HG02107 cell line replicate 1


title: HG02010 cell line replicate 3


title: BMQueen


title: B409_young_leaf_H3K4me3_rep2


title: HG02010 cell line replicate 2


title: B409_young_leaf_H3K27ac_rep1


title: B409_flower_bud_H3K27me3_rep1

value: flower buds (<= 2 mm)

value: flower bud


title: B409_young_leaf_H3K4me3_rep1


title: GTG_140_31: Kasumi-1

value: DMSO


title: HG02010 cell line replicate 1


title: 2063A_root_RNAPII_rep2

value: one-week roots after planting

value: root

value: RNAPII


title: GTG_140_24: MV-4-11


title: 2063A_root_RNAPII_rep1


title: HG02009 cell line replicate 2


title: HG02009 cell line replicate 3


title: T2_miRNA_3

city: Zhengzhou

first: Xingli

last: Ma

address: Wenhua Road 95

institute: Henan Agricultural University

description: Table S2.xlsx

data_processing:
The small RNA raw sequencing reads were subjected to the Illumina pipeline filter . The dataset was then further processed using an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, low complexity reads, common RNA families (rRNA, tRNA, snRNA, snoRNA), repeats in the NCBI GenBank , Repbase and Rfam  databases. The remaining non-annotated sequences were mapped to specific species precursors in miRBase 21.0 by BLAST searches to identify known miRNAs. All non-annotated reads with lengths of 18–25 nt were mapped to the peanut genome using the Bowtie package; only perfectly-matched sRNAs were used in further analyses.
Degradome raw sequencing reads were obtained following sequencing image analysis by Pipeline Firecrest Module and base-calling by Pipeline Bustard Module. The extracted sequencing reads were were then used in the standard data analysis.A Public software package, CleaveLand3.0 was used for analyzing sequencing data generated.
Normalization method: (1) Find a common set of sequences among all samples. (2) Construct a reference data set. Each data in the reference set is the copy number median value of a corresponding common sequence of all samples. (3) Perform 2-based logarithm transformation on copy numbers log2(copy#)of all samples and reference data set.   log2(copy#) (4) Calculate the log2(copy#) difference   log2(copy#) between individual sample and the reference data set. (5) Form a subset of sequences by selecting|  log2(copy#)|<2, which means less than 4 fold change from the reference set. (6) Perform linear regressions between individual samples and the reference set on the subset sequences to derive linear equations iy=aix+bi   where ia and ib are the slope and interception, respectively, of the derived line, log2(copy#)copy of the reference set, and y is the expected l log2(copy#)copy of sample i on a corresponding sequence. (7) Calculate the mid value xmid=(max(x)-min(x))/2 of the reference set. Calculate the corresponding expected log2(copy#)copy of sample i , yi,mid= aixmid+bi. Let yr,mid=xmid, let   yi, = yr,mid-yi,mid, which is the logarithmic correction factor of sample i. We then derive the arithmetic correction factor fi = 2  yi sample i. (8) Correct copy numbers of individual samples by multiplying corresponding arithmetic correction factor fi to original copy numbers.
Genome_build: https://peanutbase.org/files/genomes/Arachis_duranensis/assembly/ (Aradu_v1.0)
Supplementary_files_format_and_content: xlsx, expression data of small RNA and targets prediction results of small RNA.

organism: Arachis hypogaea

source_name: peanut seed

extract_protocol:
Fresh seeds were harvested from plants of both peanut RILs at 15 DAF and 35 DAF, and RNA was extracted using TRK-1001,TruSeq Small  RNA Sample Prep Kits was used with 1 ug of total RNA for the construction of sequencing libraries.
Total RNA was ligated to the RNA 3' and RNA 5' adapters and reverse transcription, followed by PCR, was performed to make cDNA constructs of the small RNAs. The small cDNA fractions that ranged from 22 nt to 30 nt in length were then isolated via 6% denaturing polyacrylamide gel electrophoresis. Finally, the cDNA constructs were purified, and the library was validated. We then performed single-end sequencing (50 bp) on an Illumina Hiseq2500 following the vendor’s recommended protocol.  Approximately 20 ug of total RNA were used to prepare Degradome library. (1) Approximately 150 ng of poly(A)+ RNA was used as input RNA and annealing with Biotinylated Random Primers. (2) Strapavidin capture of RNA fragments through Biotinylated Random Primers. (3)5' adaptor ligation to to only those RNAs containing 5'-monophosphates. (4) Reverse transcription and PCR (5) Libraries were sequenced using the 5'adapter only, resulting in the sequencing of the first 47 nucleotides of the inserts that represented the 5' ends of the original RNAs.

value: seed

tag: Stage

value: 35 days after flowering

tag: strain

tag: phenotype

value: a super-pod variety

tag: replicates


title: DS1_Degradome

description: Table S3.xlsx

data_processing:
Library strategy: Degradome-Seq
The small RNA raw sequencing reads were subjected to the Illumina pipeline filter . The dataset was then further processed using an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, low complexity reads, common RNA families (rRNA, tRNA, snRNA, snoRNA), repeats in the NCBI GenBank , Repbase and Rfam  databases. The remaining non-annotated sequences were mapped to specific species precursors in miRBase 21.0 by BLAST searches to identify known miRNAs. All non-annotated reads with lengths of 18–25 nt were mapped to the peanut genome using the Bowtie package; only perfectly-matched sRNAs were used in further analyses.
Degradome raw sequencing reads were obtained following sequencing image analysis by Pipeline Firecrest Module and base-calling by Pipeline Bustard Module. The extracted sequencing reads were were then used in the standard data analysis.A Public software package, CleaveLand3.0 was used for analyzing sequencing data generated.
Normalization method: (1) Find a common set of sequences among all samples. (2) Construct a reference data set. Each data in the reference set is the copy number median value of a corresponding common sequence of all samples. (3) Perform 2-based logarithm transformation on copy numbers log2(copy#)of all samples and reference data set.   log2(copy#) (4) Calculate the log2(copy#) difference   log2(copy#) between individual sample and the reference data set. (5) Form a subset of sequences by selecting|  log2(copy#)|<2, which means less than 4 fold change from the reference set. (6) Perform linear regressions between individual samples and the reference set on the subset sequences to derive linear equations iy=aix+bi   where ia and ib are the slope and interception, respectively, of the derived line, log2(copy#)copy of the reference set, and y is the expected l log2(copy#)copy of sample i on a corresponding sequence. (7) Calculate the mid value xmid=(max(x)-min(x))/2 of the reference set. Calculate the corresponding expected log2(copy#)copy of sample i , yi,mid= aixmid+bi. Let yr,mid=xmid, let   yi, = yr,mid-yi,mid, which is the logarithmic correction factor of sample i. We then derive the arithmetic correction factor fi = 2  yi sample i. (8) Correct copy numbers of individual samples by multiplying corresponding arithmetic correction factor fi to original copy numbers.
Genome_build: https://peanutbase.org/files/genomes/Arachis_duranensis/assembly/ (Aradu_v1.0)
Supplementary_files_format_and_content: xlsx, expression data of small RNA and targets prediction results of small RNA.

tag: tissue

value: 15 days after flowering and 35 days after flowering

value: a medium-pod variety


title: GTG_140_23: MV-4-11

tag: cell line

value: acute myeloid leukemia


title: 2063A_root_H3K9me2_rep2


title: T2_miRNA_1

description: Table S2.xlsx


title: C2_miRNA_3

description: Table S2.xlsx

value: 15 days after flowering


title: T2_miRNA_2

description: Table S2.xlsx


title: HG02009 cell line replicate 1

data_processing: genomic DNA was genotyped using the Infinium Global Screening Array (GSAMD-24v1-0_20011747_A1) beadchip (Illumina)


title: GTG_140_22: MV-4-11


title: 2063A_root_H3K9me2_rep1


title: GTG_140_33: Kasumi-1


title: DS2_Degradome

description: Table S3.xlsx


title: GTG_140_21: MV-4-11


title: GTG_140_32: Kasumi-1


title: 2063A_root_H3K4me1_rep2


title: HG01890 cell line replicate 3


title: HG01890 cell line replicate 2


title: C2_miRNA_1

description: Table S2.xlsx


title: 2063A_root_H3K4me1_rep1


title: GTG_140_19: MV-4-11


title: HG01890 cell line replicate 1


title: GTG_140_12: SKM-1


title: HG01889 cell line replicate 3


title: HG01889 cell line replicate 2


title: T1_miRNA_3

description: Table S2.xlsx


title: GTG_140_11: SKM-1


title: T1_miRNA_2

description: Table S2.xlsx


title: T1_miRNA_1

description: Table S2.xlsx


title: 2063A_root_H3K27me3_rep1


title: 2063A_root_H3K27ac_rep2


title: C2_miRNA_2

description: Table S2.xlsx


title: HG01886 cell line replicate 3


title: HG01889 cell line replicate 1


title: 2063A_root_H3K27ac_rep1


title: GTG_140_10: SKM-1


title: 2063A_root_H3K4me3_rep2


title: HG01886 cell line replicate 1


title: HG01886 cell line replicate 2


title: GTG_140_09: SKM-1


title: GTG_140_07: SKM-1


title: C1_miRNA_3

description: Table S2.xlsx


title: GTG_140_08: SKM-1


title: 2063A_silique_RNAPII_rep2

value: siliques (3-5 cm)

value: silique


title: P1A098LAC

city: Charlottesville

first: Matthew

last: Devall

state: Virginia

address: 1335 Lee Street

institute: University of Virginia

data_processing:
Base calls were generated in real-time on the NovaSeq6000 instrument (RTA 3.1.5); (2) demultiplexed, unaligned BAM files produced by Picard ExtractIlluminaBarcodes and IlluminaBasecallsToSam are converted to FASTQ format using SamTools bam2fq (v1.4); (3) sequence read and base quality are checked using the FASTX-toolkit (v0.0.13); (4) sequences are aligned to GRCh38 with reference transcriptome GENCODE release 29 using STAR (v2.6.1d
Briefly, 100bp paired-end reads were trimmed and aligned to the GENCODE reference transcriptome using STAR and reads were quantified using HT-Seq. Gene counts were generated for each sample and collated into a singular matrix for paired regression analysis in DESeq2.
Genome_build: GrCh38, GENCODE release 29
Supplementary_files_format_and_content: "Pheno.csv" contains sample metadata, "Asp_Counts.csv" contains raw counts, "SummaryStats.csv" contains the number and percentages of reads mapped for each samples

molecule: polyA RNA

source_name: Colon Organoid

growth_protocol: Normal 3D colon organoids included in the study were developed from biopsies of either distal or proximal colon using a modification of the method described by Sato et al. After isolation, colon crypts were embedded in Matrigel, and cell lines were established in growth media that included: advanced DMEM/F-12, 100U/ml penicillin, 100μg/ml streptomycin, 10mM Hepes, 1x N2, 1x B27, 2mM GlutaMAX, 1mM N-acetyl-cysteine, 10mM gastrin, 50% L-WRN conditioned media, 500nM A83-01, 10uM SB202190, 10mM nicotinamide, 50ng/ml EGF, 10μM Y27632. Colon organoids were grown and passaged as needed in 48-well culture plates.

extract_protocol:
For RNA isolation, media was gently removed and 200μl RNA lysis Solution RA1 with TCEP (Machery-Nagel; Cat No: 740902.50) was added to each well. The lysate was collected in a 1.5ml Eppendorf tube. Each tube was vortexed vigorously and placed on ice. Further steps were carried out according to manufacturer’s protocol of the Machel-Nagel RNA XS kit. RNA was checked for quality using the Agilent 4200 Tapestation. Samples with RIN > =8.5 were considered for library preparation and sequencing using the Illumina NovoSeq
Total RNA is normalized to 7.5ng/ul in a total volume of 50ul on the Perkin Elmer Janus Workstation (Perkin Elmer, Janus II).  Poly-A selection and cDNA synthesis are performed using the TruSeq Stranded mRNA kit as outlined by the manufacturer (Illumina, cat#RS-122-2103).  All steps are automated on the Perkin Elmer Sciclone NGSx Workstation to reduce batch to batch variability and to increase sample throughput.  Final RNASeq libraries are quantified using the Quant-it dsDNA High Sensitivity assay, and library insert size distribution is checked using a fragment analyzer (Advanced Analytical; kit ID DNF474).  Samples where adapter dimers constitute more than 4% of the electopherogram area are failed prior to sequencing.  Technical controls (K562,Thermo Fisher Scientific, cat# AM7832), are compared to expected results to ensure that batch to batch variability is minimized.  Successful libraries are normalized to 10nM for submission to sequencing.

treatment_protocol: Normal colon 3D organoid lines were thawed, grown and passaged as required in 48-well culture plates. Organoid lines were plated at a density of approximately 105 cells per well and allowed to grow for approximately 3 days prior to treatment with aspirin. Cells within the treatment group were treated with 0.5μL aspirin (100mM Sigma A5376) per 1mL complex media, equating to a 50μM dose of aspirin. Vehicle control samples were treated with an equal amount of 1M Tris pH7.2 with a final concentration of 50μM in complex media

tag: cell type

value: Colon Organoid

tag: Sex

value: M

value: CTL

tag: pair

value: L

tag: center

value: MGH

tag: smokingstatus

value: Never


title: GTG_140_20: MV-4-11

tag: disease

tag: treatment

value: DMSO

tag: dose


title: HG01879 cell line replicate 3

extract_protocol: an automated magnetic bead purification protocol (Hamilton Microlab STAR w/ Promega ReliaPrep Isolation system) was used to extract genomic DNA that was eluted in TE buffer (pH 8.0, 1mM EDTA)


title: C1_miRNA_1

description: Table S2.xlsx


title: 2063A_root_H3K27me3_rep2

tag: cultivar

tag: developmental stage

value: one-week roots after planting

value: root

tag: chip antibody


title: MYB+/+_CD43+ve_day6rep3

city: Guangzhou

first: ZAHIR

last: SHAH

state: Guangdong

address: 190 Kaiyuan avenue, Haungpu district, Guangzhou, China

department: Stem Cells and Regenerative Medicines

institute: GIBH,CAS, China

data_processing:
Samples were checked with FastQC software with no considerable issues found. Reads were trimmed and filtered with BBduk tool from the Bbmap package (used parameters: qtrim=rl trimq=20 maq=20 minlen=50). This procedure keeps 94.98-97.02% bases and 98.64-99.8% reads per sample.
Trimmed reads were mapped to the GRCh38 human genome with Gencode v.24 gene annotation (Harrow 2012) using the --quantMode GeneCounts option of the STAR v.2.5.3ab software (Dobin 2013). After removing of ~15,000 pseudogenes and 552 rRNA genes the STAR output tallies raw read per gene counts, that is total read counts for each of 46,214 transcripts, 19,844 of them representing protein-coding genes. According to the STAR manual, “with --quantMode GeneCounts option STAR will count number reads per gene while mapping. EdgeR was used to convert raw read per gene counts to CPM (counts per million reads) matrices.
Genome_build: GRCh38
Supplementary_files_format_and_content: mRNA expression raw counts
Supplementary_files_format_and_content: mRNA expression counts per million reads
Supplementary_files_format_and_content: description of genes_ntc_expression_raw_cpm_GEO.txt file

source_name: in vitro hematopoietic cells

growth_protocol: hESC cells–derived hematopoietic cells were routinely generated using EBs-based hematopoietci development in our established serum-free and cytokine-free hematopoietic system (un-published), with initial mesodermal patterning by BMP4 and VEGF supplimentations.

extract_protocol:
Differentiated cells were harvested at different time points, filtered and incubated with cell surface markers on ice. The washed cells were collected into Trizol reagent directly from Aria II-cell sorter.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: hESC-derived hematopoietic progenitors

tag: passage

tag: day of differentiation

value: Day 6

tag: genotype

value: MYB+/+


title: 2063A_silique_RNAPII_rep1

value: RNAPII


title: HG01879 cell line replicate 2

source_name: purified gDNA


title: P1A098LA

value: Case

tag: age


title: MYB+/+_CD43+ve_day6rep2


title: MYB+/+_CD43+ve_day6rep1


title: C1_miRNA_2

description: Table S2.xlsx

tag: tissue

value: seed

tag: Stage

value: 15 days after flowering

tag: strain

tag: phenotype

value: a medium-pod variety

tag: replicates


title: HG01879 cell line replicate 1

tag: cell line


title: 2063A_root_H3K4me3_rep1


title: P1A095LAC

tag: cell type

value: Colon Organoid

tag: Sex

value: F

tag: pair

tag: center

tag: smokingstatus

value: Former


title: P1A093LAC

value: M

tag: treatment

value: CTL

value: L


title: P1A095LA

value: MGH


title: 2063A_silique_H3K4me1_rep2

tag: cultivar

tag: developmental stage

value: siliques (3-5 cm)

value: silique

tag: chip antibody


title: 2063A_silique_H3K9me2_rep1


title: MYB+/+_CD43-ve_day6rep2

value: hESC-derived hematopoietic progenitors

tag: passage

tag: day of differentiation

tag: genotype


title: HG01784 cell line replicate 3


title: HG01784 cell line replicate 2


title: P1A093LA

tag: age

tag: tissue

value: Never


title: P1A074LAC

value: Current


title: HG01781 cell line replicate 3


title: HG01784 cell line replicate 1


title: P1A074LA


title: 2063A_silique_H3K27me3_rep2


title: MYB+/-YFP+ve_day12rep3

value: Day 12

value: MYB+/-


title: MYB+/-YFP+ve_day12rep2


title: 2063A_silique_H3K27me3_rep1


title: 2063A_silique_H3K9me2_rep2


title: MYB+/-YFP+ve_day12rep1


title: HG01781 cell line replicate 2


title: HG01781 cell line replicate 1


title: P1236RAC

value: R

value: UVA


title: P1236RA

value: Case


title: 2063A_silique_H3K27ac_rep2


title: 2063A_silique_H3K27ac_rep1


title: P1229LAC

value: Colon Organoid


title: HG01777 cell line replicate 3


title: 2063A_silique_H3K4me1_rep1


title: 2063A_silique_H3K4me3_rep2


title: P1229LA

value: F


title: MYB+/+_CD43-ve_day6rep1

value: Day 6

value: MYB+/+


title: 2063A_silique_H3K4me3_rep1


title: HG01777 cell line replicate 2


title: MYB+/+_CD43-ve_day6rep3


title: HG01777 cell line replicate 1


title: 2063A_flower_bud_RNAPII_rep2

value: flower buds (<= 2 mm)

value: flower bud

value: RNAPII


title: MYB+/-YFP+ve_day6rep1


title: MYB+/-YFP+ve_day6rep2


title: MYB+/-YFP-ve_day12rep1


title: HG01771 cell line replicate 3


title: P1225LA

value: L


title: P1225LAC

value: CTL


title: HG01771 cell line replicate 2


title: MYB+/-YFP-ve_day6rep2

value: hESC-derived hematopoietic progenitors


title: 2063A_flower_bud_RNAPII_rep1


title: P1212RAC

value: M

value: Never


title: 2063A_flower_bud_H3K9me2_rep2


title: MYB+/-YFP-ve_day12rep2

value: Day 12


title: MYB+/-YFP-ve_day6rep1

value: MYB+/-


title: HG01771 cell line replicate 1


title: P1212RA

value: R


title: 2063A_flower_bud_H3K9me2_rep1


title: P1210RAC

value: UVA


title: MYB-/-YFP+ve_day12rep3

value: MYB-/-


title: HG01770 cell line replicate 2


title: P1210RA

value: Colon Organoid

value: Case


title: MYB-/-YFP+ve_day12rep2


title: MYB-/-YFP+ve_day12rep1


title: HG01770 cell line replicate 1


title: 2063A_flower_bud_H3K4me1_rep1


title: 2063A_flower_bud_H3K4me1_rep2


title: 2063A_flower_bud_H3K27me3_rep2


title: HG01762 cell line replicate 3


title: 2063A_flower_bud_H3K27me3_rep1


title: P1208LA

value: F


title: MYB-/-YFP-ve_day12rep3


title: HG01762 cell line replicate 2


title: MYB-/-YFP-ve_day12rep1


title: P1183RAC

value: Current


title: HG01762 cell line replicate 1


title: HG01761 cell line replicate 3


title: 2063A_flower_bud_H3K27ac_rep1

value: flower buds (<= 2 mm)


title: P1179RAC