title: FGG005_R013: AM2-null-unt

city: Belfast

first: Simon

middle: S

last: McDade

address: 97 Lisburn Road

department: CCRCB

country: United Kingdom

institute: Queen's University Belfast

data_processing:
FASTQ files were de-multiplexed, aligned to hg19 reference genome using Bowtie2 in using Basespace RNA-seq app (Illumina),
.bam files were mapped to RefSeq transcripts using Patek Genomics Suite (Partek) and gene-level RPKM normalized output used for differential gene expression analysis
Transcripts were filtered with an RPKM threshold of ≥0.5 in 50% of samples (12,411 genes) and significantly upregulated and downregulated transcripts identified using 3-way ANOVA with a mean RPKM fold-change threshold of ≥1.7x and False Discovery Rate (FDR) of 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file including RPKM values for each Sample ...

growth_protocol: HCT116 cell lines were cultured in McCoy's 5A Medium supplemented with 10% fetal bovine serum, 50U/ml penicillin, 0.1mg/ml streptomycin, 2mM L-glutamine and 1mM sodium pyruvate (all Gibco)

extract_protocol:
Cells were homogenised using TriPure Isolation Reagent (Roche) and total RNA was then extracted using the PureLink RNA Mini Kit (Ambion)
Total RNA was extracted as above, and 1μg of each RNA sample was used as a template to generate cDNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina), following the manufacturer's instructions for the low-sample (LS) protocol. These first-stranded cDNA samples were processed to barcoded cDNA libraries using an automated IP-Star (Diagenode),

treatment_protocol: Cells were treated with DMSO vehicle control, single agent Nutlin-3A (5uM), Entinostat (2.5uM) or combination of Nutlin-3A/Eninostat for 8 hours

value: colorectal cancer

tag: genotype

tag: treatment (8 hours)

value: DMSO

tag: replicate


title: WS_0013: WS patients 13

status: Public on Apr 25 2020

type: genomic

city: Kyoto

first: Ryo

last: Kimura

address: Yoshida-Konoe-cho

department: Anatomy and Developmental Biology

country: Japan

institute: Kyoto University Graduate School of Medicine

description: WS sample

hyb_protocol: Sandard Illumina protocol using bisulfite converted genomic DNA

scan_protocol: Standard protocol using the Illumina iScan system

data_processing: ChAMP analysis pipeline [ Y.Tian et al.,  Bioinformatics (2017)]

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Peripheral blood

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA was extracted from peripheral blood samples using the QIAamp DNA blood midi kit

tag: diagnosis

value: Williams syndrome (WS)

tag: gender

value: Female

tag: tissue

value: whole blood


title: dmsoBulk_1

type: SRA

city: Philadelphia

first: Eduardo

middle: A

last: Torre

state: PA

department: Bioengineering

country: USA

institute: University of Pennsylvania

library_source: transcriptomic

data_processing:
We aligned reads to hg19 and quantified reads per gene using STAR and HTSeq
Genome_build: hg19
Supplementary_files_format_and_content: .tsv files conain reads per gene (unnormalized)

molecule: polyA RNA

source_name: melanoma cells

growth_protocol: We grew these cells at 37°C in Tu2% media (78% MCDB, 20% Leibovitz’s L-15 media, 2% FBS, and 1.68mM CaCl2)

extract_protocol:
For each sample, we isolated mRNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module
We built the RNA sequencing libraries using the NEBNext Ultra RNA Library Prep Kit for Illumina
We sequenced the libraries via paired-end sequencing on a NextSeq 500

treatment_protocol: We either treated cells with 4uM EPZ5676 or with DMSO for seven days

tag: cell line

tag: cell type

value: melanoma

tag: treatment

value: Pre-treated with DMSO for 1 week

tag: cell population

value: Bulk population


title: WS_0004: WS patients 4

description: WS sample


title: RVC_02201

city: Tucson

first: Eugene

middle: H

last: Chang

state: AZ

address: 1501 N. Campbell Avenue

department: Department of Otolaryngology

institute: The University of Arizona

data_processing:
Data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq2 v 2.17 program.
The reads were mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15
We processed the discovery and validation data sets separately through making use of NOISeq library in order to filter out the genes with low count, specifically cpm <30 with method one. This procedure resulted in 7,474 and 7,905 unique genes, respectively, for discovery and validation cohorts.
We then utilized the function “ARSyNseq” (Nueda et al. 2012) implemented in R package NOISeq together with TMM normalization in order to remove the known batch effects in addition to other hidden and noisy systematic variation from each cohort separately.
Through the use of function “voomWithQualityWeights” (Ritchie et al. 2006, Law et al. 2014, Liu et al. 2015) from LIMMA package we further made the processed RNA count values ready for downstream statistical analysis with linear model implemented in LIMMA R library.
genome build: hg38
Supplementary_files_format_and_content:tab-delimited text file include rsem inferred count values for each Sample

molecule: total RNA

growth_protocol: We developed well-differentiated ciliated air-liquid interface (ALI) cultures from nasal tissues biopsied from thirty adults with physician-diagnosed asthma.

extract_protocol:
RNA was extracted from whole-cell lysates, mapped to the UCSC transcript set using Bowtie2 (v2.1.0) and the gene expression level was estimated using standard techniques.
Libraries for RNA-Seq were prepared with Kapa Stranded mRNA. The workflow consisted of mRNA enrichment, cDNA generation, and end repair to generate blunt ends, A-tailing, adaptor ligation and PCR amplification. Different adaptors were used for multiplexing samples in one lane.

treatment_protocol: We infected ALI cultures with common RV strains RV-A16 (1x105 RNA copies/well), RV-C15 (1x105 RNA copies/well, courtesy of Dr. James Gern), or DMEM/F12 media (control) for 4 hrs at 34°C, 5% CO2.

value: RVC

tag: clinical _w

value: Yes

tag: Sex

value: Male

value: NH

tag: race

value: W

tag: age

tag: cohort

value: validataion


title: ZS97_root_H3K4me1_rep1

city: Wuhan

first: Liang

last: Xie

state: Hubei

address: No.1,Shizishan Street

country: China

institute: Huazhong Agricultural University

library_source: genomic

data_processing:
Trimmomatic fitered the raw reads
ChIP-seq reads were aligned to the MSU.7.0/MH63 genome assembly using bwa mem
Data were filtered using the SAMTOOLS MAPQ30 and filter the  duplication reads
peaks were called using MACS.2.2.1 with narrow(H3K4me3,H3K27ac,PII)/broad(H3K27me3,H3K4me1,H3K9me2) parameters
Genome_build: MSU.7.0,MH63
Supplementary_files_format_and_content: bigWig by deepTools bamCoverage

organism: Oryza sativa

source_name: ZS97 root

growth_protocol: Germinating seeds were obtained by soaking dry seeds in water for 72 h at 37 °C. For roots and young leaves, the germinated seeds were grown in a phytotron with the day/night cycle set at 14 h/10 h and a temperature of 32 °C/28 °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 described34. 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. Mature leaves at the floral induction phase and young panicles 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)

treatment_protocol: Tissues were cross-linked with 1% formaldehyde for 10–15 min and quenched with 0.2 M glycine at room temperature.

value: root

tag: development stage

value: one-week old root after planting

tag: cultivar

tag: chip antibody


title: RVA_02201

value: RVA


title: FGG005_R015: AM2-null-N3A

value: colorectal cancer

tag: genotype

tag: treatment (8 hours)


title: Control_02201

value: Control


title: WS_0005: WS patients 5

description: WS sample

tag: diagnosis

value: Williams syndrome (WS)


title: WS_0023: WS patients 23

description: WS sample

tag: gender

value: Female


title: WS_0007: WS patients 7

description: WS sample

tag: tissue

value: whole blood


title: WS_0008: WS patients 8

description: WS sample


title: ZS97_root_H3K27me3_rep2


title: FGG005_R014: AM2-null-Ent

tag: cell line

value: Entinostat 2.5uM

tag: replicate


title: ZS97_mature_leaf_H3K27ac_rep2

source_name: ZS97 mature leaf

value: mature leaf

value: mature leaves were flag leaf at floral induction phase


title: WS_0002: WS patients 2

description: WS sample


title: ZS97_root_H3K27me3_rep1


title: WS_0021: WS patients 21

description: WS sample


title: WS_0018: WS patients 18

description: WS sample


title: RVC_88301

value: RVC

value: No


title: WS_0001: WS patients 1

description: WS sample

value: Male


title: FGG005_R016: AM2-null-Combo

tag: cell type

value: Combination


title: Control_88301

value: NH

value: W


title: ZS97_root_H3K27ac_rep2

value: root


title: RVA_73501

value: Yes

value: validataion


title: WS_0009: WS patients 9

description: WS sample


title: RVC_44401

value: NatAm


title: ZS97_root_H3K27ac_rep1

value: one-week old root after planting


title: ZS97_root_H3K4me3_rep2


title: RVA_44401

value: RVA


title: RVA_88301


title: Control_44401

value: Control


title: FGG005_R010: AM2-WT-Ent

value: colorectal cancer


title: RVC_73501


title: RVC_36001

value: Female


title: ZS97_root_H3K4me3_rep1


title: FGG005_R012: AM2-WT-Combo


title: FGG005_R009: AM2-WT-unt

value: DMSO


title: L24-RVC-1

value: H

value: Discovery


title: ZS97_panicle_RNAPII_rep2

source_name: ZS97 panicle

value: panicle

value: panicle (1.5-4.5 cm)

value: RNAPII


title: Pja2-pb rep2

city: Hefei

first: Kan

last: He

state: Anhui

address: 111 Jiulong Road

department: School of life sciences

institute: Anhui University

data_processing:
BGISEQ500 platform used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using HISAT software
Exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by Cufflinks
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include the expression values of this transcript  for each Sample ..

organism: Mus musculus

source_name: hippocampal cells

growth_protocol: HT-22 were routinely maintained in the conventional mouseEagle's medium

extract_protocol:
RNA was harvested using Trizol reagent.TruSeq® RNA LT Sample Prep Kit v2  was used with total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype/variation

value: Induced Pja2

value: hippocampal neuron

tag: strain

tag: passages

value: passage 21-24


title: ZS97_panicle_RNAPII_rep1


title: Control_36001

tag: clinical _w

value: No

tag: Sex

value: NH

tag: race

value: W


title: Pja2-pb rep1


title: ZS97_panicle_H3K9me2_rep2

tag: development stage


title: ZS97_panicle_H3K9me2_rep1

tag: cultivar


title: L24-Control-1

value: Male

tag: age

tag: cohort


title: FGG005_R007: AM1-null-N3A

tag: genotype

tag: treatment (8 hours)


title: C40-RVC-3

value: RVC


title: ZS97_panicle_H3K4me1_rep2

tag: chip antibody


title: L24-RVA-1

value: RVA


title: FGG005_R008: AM1-null-Combo

value: colorectal cancer

value: Combination


title: C40-RVA-3

value: Female


title: WT rep1

value: uninduced cells - control


title: FGG005_R011: AM2-WT-N3A


title: WT rep2


title: FGG005_R001: AM1-WT-unt

value: DMSO


title: RVA_36001

value: validataion


title: FGG005_R003: AM1-WT-N3A


title: ZS97_panicle_H3K4me1_rep1

tag: tissue

value: panicle

value: panicle (1.5-4.5 cm)


title: ZS97_panicle_H3K27me3_rep2


title: FGG005_R005: AM1-null-unt

tag: cell line


title: C20-RVC-2

value: Yes

value: H

value: Discovery


title: FGG005_R002: AM1-WT-Ent

value: Entinostat 2.5uM

tag: replicate


title: ZS97_panicle_H3K27me3_rep1


title: FGG005_R004: AM1-WT-Combo

tag: cell type


title: C20-RVA-1


title: FGG005_R006: AM1-null-Ent


title: ZS97_panicle_H3K27ac_rep2


title: C20-Control-1

value: Control


title: ZS97_panicle_H3K27ac_rep1


title: A59-RVC-3

value: No

value: NH

value: W


title: C40-Control-2


title: GT_18_5_RNAseq_rep2

city: Lausanne

first: Ana Rita

middle: Amandio

last: Lhopitallier

address: SV2842, Station 19

department: SV-ISREC-EPFL

country: Switzerland

institute: EPFL

data_processing:
Raw RNA-seq reads were aligned on the mouse mm10 genome assembly using TopHat 2.0.9 (Yates et al., 2016). Gene expression computations were performed using uniquely mapping reads extracted from TopHat alignments and genomic annotations from filtered gtf from Ensembl release 82 (Kim et al., 2013) as described in (Amândio et al., 2016).
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph

source_name: genital tubercule

extract_protocol:
Micro-dissected GT from different embryonic stages were stored individually at -80°C in RNAlater stabilization reagent (Ambion) before further sample processing. Total RNA was extracted from tissues using QIAGEN RNeasy Plus Micro Kit after disruption and homogenization. RNA quality was assessed using an Agilent 2100 Bioanalyser. Sequencing libraries were prepared according to TruSeq Stranded mRNA Illumina protocol, with polyA selection.
RNA-seq libraries were prepared with the Illumina TruSeq Stranded mRNA protocol and sequenced on an Illumina HiSeq 2500 sequencer. Single-end, 100bp reads were produced.

value: wildtype

tag: developmental stage

value: CBA / C57BL/6 mix


title: GT_18_5_RNAseq_rep1

tag: strain


title: A59-RVA-1

value: RVA


title: ZS97_panicle_H3K4me3_rep2


title: ZS97_panicle_H3K4me3_rep1


title: GT_16_5_RNAseq_rep2


title: GT_16_5_RNAseq_rep1


title: ZS97_young_leaf_RNAPII_rep2

source_name: ZS97 young leaf

value: young leaf

value: young leaves from two-week old seedlings

value: RNAPII


title: 962-RVC-1

value: RVC

value: Female


title: ZS97_young_leaf_RNAPII_rep1


title: 962-RVA-1


title: GT_E17_5_H3K27me3

data_processing:
ChIP-seq reads processing was done on the Duboule lab local Galaxy server (Afgan et al., 2016). Adapters and bad-quality bases were removed with Cutadapt version 1.16 (Martin, 2011) (options -m 15 -q 30 -a GATCGGAAGAGCACACGTCTGAACTCCAGTCAC). Reads were mapped to the mouse genome (mm10) using Bowtie2 (v2.3.4.1) (Langmead and Salzberg, 2012), with standard settings. The coverage was obtained as the output of MACS2 (v2.1.1.20160309) (Zhang et al., 2008). Peak calling in Figure 5 was done using MACS2 (v2.1.0.20160309) callpeak (--gsize 1870000000) using the corresponding input data as control BAM (-c).
Genome_build: mm10

extract_protocol:
Micro-dissected GT (35 to 40) or CR (70) were crosslinked in 1% formaldehyde/PBS for 20 min and stored at -80oC until further processing. Chromatin was sheared using a water-bath sonicator (Covaris E220 evolution ultra-sonicator). Immunoprecipitation was done using the following antibodies, anti-CTCF (Active Motif, 61311), anti- H3K27ac (Abcam, ab4729), and H3K27me3 (Merck Millipore, 07-449)
Libraries were prepared using the TruSeq protocol, and sequenced on the Illumina HiSeq system (100bp single-end reads) according to manufactures instructions.

value: genital tubercle

tag: antibody

value: wild type


title: 962-Control-1

tag: clinical _w


title: A59-Control-1

tag: Sex


title: GT_E17_5_H3K27ac


title: ZS97_young_leaf_H3K9me2_rep2


title: 952-RVC-1

value: Yes

value: Male

tag: race


title: 952-RVA-1

value: Discovery


title: GT_E13_5_H3K27me3


title: GT_E13_5_H3K27ac


title: GT_E13_5_Input


title: ZS97_young_leaf_H3K4me1_rep2

tag: development stage


title: ZS97_young_leaf_H3K4me1_rep1

tag: cultivar


title: GT_E17_5_WT_islandVVP

data_processing:
Library strategy: 4C-seq
4C-seq reads were demultiplexed, mapped on GRCm38/mm10 mouse assembly, and analyzed using the 4C-seq pipeline of the Bioinformatics and Biostatistics Core Facility (BBCF) HTSstation (http://htsstation.epfl.ch) (David et al., 2014) or using a local version of it using the facilities of the Scientific IT and Application Support Center of EPFL. Profiles were normalized to a 5Mb region surrounding the HoxD cluster and smoothened using a window size of 11 fragments
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph

extract_protocol:
Circular chromosome conformation capture (4C-seq) was performed as described in (Noordermeer et al., 2011). Briefly, tissues (20-40 GT or 40 cloaca) were isolated in PBS supplemented with 10% Fetal Calf Serum and dissociated to single cell by collagenase treatment.  Samples were fixed in 2% formaldehyde, lysed, and stored at −80°C. Samples were primarily digested with NlaIII (NEB, R0125L) followed by ligation under diluted conditions. After decrosslinking and DNA purification DpnII (NEB, R0543M) was used for the second restriction. All ligation steps were performed using highly concentrated T4 DNA ligase (Promega, M1794). For each viewpoint approximately 1μg of DNA was amplified by using 12 individual PCR reactions.
Libraries were constructed with inverse primers for different viewpoints (see Table 5) containing Illumina Solexa adapter sequences and sequenced on an Illumina HiSeq 2500 sequencer, as single-end reads (read length 100 base pairs or 80 base pairs). In some samples 4-bp barcodes were added between the adapter and each specific viewpoint to allow sample multiplexing.


title: ZS97_young_leaf_H3K27me3_rep2


title: Control_73501

value: Control

tag: age

value: validataion


title: GT_E17_5_WT_Hoxd13VP


title: 799-RVC-1

value: No

value: H

value: AfrAm

tag: cohort


title: ZS97_young_leaf_H3K27me3_rep1


title: 799-RVA-1


title: ZS97_young_leaf_H3K27ac_rep2


title: GT_E17_5_WT_GT2VP

tag: genotype

value: wildtype

value: CBA / C57BL/6 mix


title: 952-Control-1

value: NH

value: W


title: ZS97_young_leaf_H3K27ac_rep1

value: young leaf

value: young leaves from two-week old seedlings


title: GT_E15_5_WT_islandVVP


title: ZS97_young_leaf_H3K9me2_rep1


title: ZS97_young_leaf_H3K4me3_rep2


title: ZS97_root_H3K4me1_rep2

value: root

value: one-week old root after planting


title: 731-Control-1

value: Female


title: GT_E15_5_WT_Hoxd13VP


title: ZS97_young_leaf_H3K4me3_rep1


title: 731-RVC-1

value: RVC

value: Yes


title: GT_E13_5_delV_rep2_island_IVVP

description: average_GT_E13_5_delV_island_IVVP.bedGraph.gz

value: delV


title: GT_E15_5_WT_GT2VP


title: MH63_mature_leaf_RNAPII_rep2

source_name: MH63 mature leaf

value: mature leaf

value: mature leaves were flag leaf at floral induction phase

value: Minghui 63

value: RNAPII


title: 590-RVC-1

value: No

value: Male

value: Discovery


title: GT_E13_5_delV_rep1_island_IVVP

value: CBA / C57BL/6 mix


title: GT_E13_5_delV_rep2_Hoxd13VP

description: average_GT_E13_5_delV_Hoxd13VP.bedGraph.gz


title: 590-RVA-1

value: RVA

value: NH

value: W


title: 799-Control-1

value: Control

value: H

value: AfrAm


title: MH63_mature_leaf_RNAPII_rep1


title: 590-Control-1


title: MH63_mature_leaf_H3K9me2_rep2


title: 731-RVA-1

value: Female


title: GT_E13_5_delV_rep1_Hoxd13VP


title: MH63_mature_leaf_H3K9me2_rep1


title: 532-RVC-3

value: RVC

value: Yes


title: Colon cancer tissue 449T

city: Cheras

first: Nurul Syakima

last: Ab Mutalib

state: Kuala Lumpur

address: Jalan Yaacob Latiff

department: UKM Medical Molecular Biology Institute

country: Malaysia

institute: Universiti Kebangsaan Malaysia

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

scan_protocol: The beadchips were scanned using iScan

data_processing: GenomeStudio V1.9.0

label: Cy3, Cy5

source_name: Colon cancer tissue

label_protocol: Standard Illumina Protocol

extract_protocol: The tissues were subjected to nucleic acids extraction using Allprep DNA/RNA/miRNA Universal Kit (Qiagen, USA) according to the manufacturer’s recommendations.

tag: gender

tag: tumour stage

value: T3 N2 Mx

tag: tumour cellularity

value: Colon cancer tissue


title: GT_E13_5_delProx_rep2_Hoxd13VP

description: average_GT_E13_5_delProx_Hoxd13VP.bedGraph.gz

value: delProx


title: MH63_mature_leaf_H3K4me1_rep2

tag: tissue

value: mature leaf

value: mature leaves were flag leaf at floral induction phase

value: Minghui 63

tag: chip antibody


title: Colon cancer tissue 467T

value: T4b N1b Mx


title: Colon adjacent normal 449T

source_name: Colon adjacent normal 449T

value: Male

value: not applicable

value: Colon adjacent normal


title: 532-RVA-1

value: RVA

value: NH

value: W

value: Discovery


title: Colon cancer tissue 353T

value: T3 N3 Mx


title: MH63_mature_leaf_H3K4me1_rep1


title: Colon cancer tissue 456T

value: Female

value: T3 N1 Mx


title: Colon cancer tissue 469T

value: T3 N0 Mx


title: Colon adjacent normal 456T

source_name: Colon adjacent normal 456T


title: Colon adjacent normal 439T

source_name: Colon adjacent normal 439T


title: Colon adjacent normal 467T

source_name: Colon adjacent normal 467T


title: GT_E13_5_delGT2_rep1_Hoxd13VP

description: average_GT_E13_5_delGT2_Hoxd13VP.bedGraph.gz

value: CBA / C57BL/6 mix


title: GT_E13_5_delProx_rep1_Hoxd13VP

value: delProx


title: GT_E13_5_delGT2_rep2_Hoxd13VP


title: 532-Control-2

value: Control

value: Yes


title: Colon cancer tissue 398T

value: T4 N1 Mx

value: Colon cancer tissue


title: Tumor, mouse C2M3, metastatic tumor

type: RNA

city: Seattle

first: Kristin

middle: Gail

last: Anderson

state: WA

address: 1100 Fairview Ave N

department: Clinical Research Division

institute: Fred Hutchinson Cancer Research Center

description: Tumor, mouse C2M3, metastatic tumor

hyb_protocol: RNA samples were processed using the Clariom D Pico mouse Assay.

scan_protocol: not provided

data_processing: Arrays were analyzed using SST-RMA algorithm in the Affymetrix Transcriptome Analysis Console (TAC) Software. All samples passed the quality control criteria given by Affymetrix. Probes with less than two arrays above the 95th percentile of the antigenomic background probes were filtered out. Here, we provide the CHP files with the SST-RMA normalization.

label: biotin

label_protocol: not provided

extract_protocol: RNA was extracted from fresh frozen ID8VEGF tumors using the Qiagen RNeasy Plus Mini RNA isolation kit (cat: 74134).

value: Metastatic Tumor

tag: donor


title: Tumor, mouse C1M5, metastatic tumor

description: Tumor, mouse C1M5, metastatic tumor


title: MH63_mature_leaf_H3K27ac_rep2

value: mature leaf

value: mature leaves were flag leaf at floral induction phase

value: Minghui 63


title: MH63_mature_leaf_H3K27me3_rep1


title: MH63_mature_leaf_H3K27me3_rep2


title: 474-RVA-1

value: RVA

value: No

value: NH


title: GT_E13_5_WT_rep2_islandVVP

value: wildtype

tag: developmental stage


title: GT_E13_5_WT_rep2_island_IVVP

description: average_GT_E13_5_WT_island_IVVP.bedGraph.gz

tag: strain


title: Colon adjacent normal 501T

source_name: Colon adjacent normal 501T

value: Male

value: not applicable

value: Colon adjacent normal


title: MH63_mature_leaf_H3K27ac_rep1


title: 474-Control-1

value: Female

value: W

value: Discovery


title: Colon adjacent normal 361T

source_name: Colon adjacent normal 361T


title: Colon cancer tissue 361T

value: T2 N1 Mx


title: Colon adjacent normal 474T

source_name: Colon adjacent normal 474T


title: Tumor, mouse C1M3, metastatic tumor

description: Tumor, mouse C1M3, metastatic tumor


title: 409-RVC-1

value: RVC

value: H


title: GT_E13_5_WT_rep2_Hoxd13VP

description: average_GT_E13_5_WT_Hoxd13VP.bedGraph.gz

value: CBA / C57BL/6 mix


title: Tumor, mouse C2M3, primary tumor

description: Tumor, mouse C2M3, primary tumor

value: Primary Tumor


title: 409-RVA-1


title: GT_E13_5_WT_rep1_island_IVVP


title: MH63_mature_leaf_H3K4me3_rep1

value: mature leaf

value: mature leaves were flag leaf at floral induction phase


title: Tumor, mouse C1M5, primary tumor

description: Tumor, mouse C1M5, primary tumor


title: 409-Control-1

value: Control


title: 361-RVC-1

value: No


title: Colon cancer tissue 501T

value: T3 N0 Mx

value: Colon cancer tissue


title: Dimer_StreptavidinAP_Rep3

city: La Jolla

first: Neal

last: Devaraj

state: CA

address: 9500 Gilman Drive

department: Chemistry and Biochemistry

institute: UCSD

data_processing:
Sequencing adaptors were cut from raw sequencing data using Bowtie2 commands.
Sequencing reads were aligned using Bowtie2 (version 2.3.5) in end-to-end mapping mode with index built from hg38 and the transgene.
Salmon (version 1.1.0) was used to map RNA-seq reads to human transcriptome and quantify transcript expression.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files including sequencing reads for each sample; tab-delimited files containing TPM reads for each sample.

growth_protocol: Human HeLa-S3 cells were grown in complete DMEM media (Gibco) supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin. Cells were cultured at 37°C in a humidified incubator under 5% CO2.

extract_protocol:
Total RNA was extracted from the lysate upon the addition of 3 volumes of Trizol-LS (Invitrogen) and purification with the Zymo Direct-Zol kit (Zymo Scientific) according to manufacturer’s instructions.
Library preparation was conducted using TruSeq Stranded mRNA kit (Illumina), using a modified protocol. In lieu of polyA purification, 25 µL of washed Dynabeads MyOne C1 Streptavidin (Invitrogen) were incubated with 10 µg isolated total RNA sample in 1X RBW Buffer supplemented with 2 U/µL Murine RNAse inhibitor for 1 h at room temperature. Beads were washed 3 times in 1X RBW Buffer, followed by 2 washes with ultra-pure water. Subsequent to RNA binding and washing to the streptavidin beads, 19.5 μL of Fragment-Prime-Finish mix was added to each beads sample to elute and fragment the RNA. Library preparation was carried out in subsequent steps according to manufacturer’s protocol.

treatment_protocol: Stable HeLa cells expressing HDAC2-TAG, grown to ~80% confluency in a 10 cm plate, were lysed directly upon addition of 600 µL of Mammalian Protein Extraction Reagent (Thermo Scientific), supplemented with 2X HALT protease inhibitor (Thermo Scientific) and 1 U/µL Murine RNAse, according to manufacturer’s instructions. To this cell lysate, 1 µM preQ1-biotin, 100 nM E. Coli TGT or 500 nM obligate dimeric TGT (as noted), and 1 U/µL Murine RNAse inhibitor was added. Reactions were incubated for 2 h at room temperature prior to analysis.

tag: cell line background

value: Human HeLa-S3

tag: transgene

tag: rna-labelling condition


title: GT_E13_5_WT_rep1_Hoxd13VP

value: wildtype


title: 474-RVC-2

tag: clinical _w

tag: Sex

value: NH

tag: race


title: MH63_root_H3K9me2_rep2

source_name: MH63 root

value: root

tag: development stage

value: one-week old root after planting

tag: cultivar

value: Minghui 63


title: Dimer_StreptavidinAP_Rep2


title: Colon cancer tissue 474T

value: Female

tag: age


title: 361-RVA-1

value: RVA

value: Male

value: W

tag: cohort

value: Discovery


title: Colon adjacent normal 353T

source_name: Colon adjacent normal 353T

tag: gender

tag: tumour stage

value: not applicable

value: Colon adjacent normal


title: Tumor, mouse C1M3, primary tumor

description: Tumor, mouse C1M3, primary tumor

tag: tissue

value: Primary Tumor


title: Colon cancer tissue 439T

tag: tumour cellularity


title: Dimer_StreptavidinAP_Rep1


title: GT_E13_5_InvV_rep2_island_VVP

description: average_GT_E13_5_InvV_islandVVP.bedGraph.gz

tag: genotype

value: InvV

value: CBA / C57BL/6 mix


title: Colon cancer tissue 194T

value: T3 N0 Mx

value: Colon cancer tissue


title: TGT_StreptavidinAP_Rep2

value: Human HeLa-S3


title: MH63_root_H3K4me1_rep1

tag: chip antibody


title: Colon adjacent normal 466T

source_name: Colon adjacent normal 466T


title: 361-Control-1

value: Control

value: No

value: H


title: MH63_root_H3K27me3_rep1

value: root

value: one-week old root after planting

value: Minghui 63


title: 254-RVC-1

value: RVC

value: Male

value: NH


title: MH63_root_H3K27me3_rep2


title: 254-RVA-1

value: RVA

value: W

value: Discovery


title: 254-Control-3


title: MH63_root_H3K4me1_rep2


title: GT_E13_5_InvV_rep2_Hoxd13VP

description: average_GT_E13_5_InvV_Hoxd13VP.bedGraph.gz

value: InvV

tag: developmental stage

tag: strain


title: GT_E13_5_InvV_rep2_island_IVVP

description: average_GT_E13_5_InvV_island_IVVP.bedGraph.gz

value: CBA / C57BL/6 mix


title: GT_E13_5_InvV_rep1_island_VVP


title: GT_E13_5_WT_GT2VP

value: wildtype


title: TGT_StreptavidinAP_Rep1

tag: cell line background

tag: transgene


title: MH63_root_H3K27ac_rep2


title: Colon adjacent normal 469T

source_name: Colon adjacent normal 469T

value: not applicable

value: Colon adjacent normal


title: Colon cancer tissue 466T

value: Female

value: T3 N1 Mx

value: Colon cancer tissue


title: GT_E13_5_InvV_rep1_island_IVVP


title: 244-RVC-1

tag: clinical _w

value: Yes


title: 244-RVA-1

tag: Sex


title: MH63_root_H3K27ac_rep1

value: root

value: one-week old root after planting


title: GT_E13_5_InvV_rep1_Hoxd13VP


title: Colon adjacent normal 398T

source_name: Colon adjacent normal 398T


title: 244-Control-1

value: Control

tag: race


title: MH63_root_H3K4me3_rep2

tag: development stage

value: Minghui 63


title: GT_E12_5_WT_islandVVP


title: MH63_root_H3K4me3_rep1

tag: cultivar


title: MH63_panicle_RNAPII_rep2

source_name: MH63 panicle

value: panicle

value: panicle (1.5-4.5 cm)

value: RNAPII


title: GT_E12_5_WT_Hoxd13VP

source_name: genital tubercule


title: 217-RVC-1

value: RVC

value: No

value: NH

value: W

tag: age

value: Discovery


title: 217-RVA-1

value: RVA

tag: cohort


title: Colon adjacent normal 194T

source_name: Colon adjacent normal 194T

tag: gender

value: Female

value: not applicable

value: Colon adjacent normal


title: FB_E12_5_WT_islandVVP

source_name: forebrain

value: wildtype

value: CBA / C57BL/6 mix


title: MH63_panicle_RNAPII_rep1


title: 212-RVC-1

value: Male

value: H


title: MH63_panicle_H3K9me2_rep2

value: Minghui 63


title: LS174T Colon Cells LDHAB DKO + MPP Triplicate3

city: Tallahassee

first: Elizabeth

last: Mazzio

state: Florida

address: 1515 MLK Blvd

department: College of Pharmacy & Pharmaceutical Science

institute: Florida Agricultural & Mechanical University

description:
Aadenocarcinoma of the colon. 58 years Caucasian female Antigen Expression serologically defined colon cancer antigen 3; Homo sapiens, expressed HLA A2, B13, B67; Blood type O
Gene expression data from genetically modified LS174T cells grown under variable experimental treatment

hyb_protocol: Hybrization was conducted according to manufacturer's instructions as per the GeneChipTM WT PLUS Reagent Manual for Whole Transcript (WT) Expression Arrays. (Affymetrix, ThermoFisher Scientific), using GeneChip Human Gene 2.1 ST Array cartridges.

scan_protocol: Arrays were scanned with GeneAtlas Imaging station scanner (Affymetrix, ThermoFisher Scientific)

data_processing: The data was processed using Affymetrix expression console and evaluated by Affymetrix transcription console software (Affymetrix, ThermoFisher Scientific)

label: Biotin

source_name: LS174T Colon Cancer LDHAB Double Knock Out + MPP+

label_protocol: cDNA was labeled using according to manufacturer's instructions as per the GeneChipTM WT PLUS Reagent Manual for Whole Transcript (WT) Expression Arrays. (Affymetrix, ThermoFisher Scientific).

growth_protocol: LS174T Colon Cells were cultured in Dulbecco’s Modified Eagle’s Medium - high glucose with 4500 mg/L glucose, L-glutamine, sodium pyruvate, and sodium bicarbonate, supplemented with 6% FBS and 100 U/ml penicillin G sodium /100 μg/ml streptomycin sulfate. Cells were grown at 37°C with 95% air and 5% CO2 and sub-cultured every three to five days. Control Vectors were trypsinized once a week, and dispersed into a monolayer for reseeding

extract_protocol: After treatment, cells were washed three times in HBSS, rapidly frozen and stored at -80 C. Total RNA was isolated/ purified using the TRIzol/chloroform method, quality was assessed and concentration was equalized to 82ng/ul in nuclease free water

treatment_protocol: All three cell lines were treated ± MPP+ 231 microM prepared in HBSS with a pH of 7.4 , both at sub-lethal concentrations. For whole transcriptome microarray studies, after a 24 hour treatment, cells were rapidly washed in HBSS 3x, spun and frozen at -80C.

value: Aadenocarcinoma of the colon

value: 58 years

tag: ethnicity

value: Caucasian

value: female

tag: blood type

value: O


title: 212-RVA-1

value: No


title: LS174T Colon Cells G6PI + MPP KO Triplicate2

description:
Aadenocarcinoma of the colon. 58 years Caucasian female Antigen Expression serologically defined colon cancer antigen 3; Homo sapiens, expressed HLA A2, B13, B69; Blood type O
Gene expression data from genetically modified LS174T cells grown under variable experimental treatment

source_name: LS174T Colon Cancer G6PI Knock Out + MPP+

tag: tissue


title: LS174T Colon Cells LDHAB DKO + MPP Triplicate1

description:
Aadenocarcinoma of the colon. 58 years Caucasian female Antigen Expression serologically defined colon cancer antigen 3; Homo sapiens, expressed HLA A2, B13, B65; Blood type O
Gene expression data from genetically modified LS174T cells grown under variable experimental treatment


title: GT_E12_5_WT_GT2VP

tag: genotype


title: 212-Control-1

value: Control

value: W


title: LS174T Colon Cells G6PI + MPP KO Triplicate1

description:
Aadenocarcinoma of the colon. 58 years Caucasian female Antigen Expression serologically defined colon cancer antigen 3; Homo sapiens, expressed HLA A2, B13, B68; Blood type O
Gene expression data from genetically modified LS174T cells grown under variable experimental treatment


title: FB_E12_5_WT_GT2VP


title: MH63_panicle_H3K4me1_rep2

value: panicle

value: panicle (1.5-4.5 cm)

tag: chip antibody


title: MH63_panicle_H3K4me1_rep1


title: 203-RVC-1

value: RVC

value: NH

value: W/Asian

value: Discovery


title: LS174T Colon Cells Vector + MPP Triplicate2

description:
Aadenocarcinoma of the colon. 58 years Caucasian female Antigen Expression serologically defined colon cancer antigen 3; Homo sapiens, expressed HLA A2, B13, B63; Blood type O
Gene expression data from genetically modified LS174T cells grown under variable experimental treatment

source_name: LS174T Colon Cancer Vector Control + MPP+


title: FB_E12_5_WT_Hoxd13VP

value: wildtype

tag: developmental stage

value: CBA / C57BL/6 mix


title: 217-Control-3

value: Female


title: GT_E17_5_WT_ATAC_seq_rep2

description:
GT_E17_5_WT_ATAC_seq_rep2
processed data file: GT_E17_5_merge_WT_ATAC_seq.bedgraph.gz

data_processing:
ATAC-seq reads processing was done on the Duboule local Galaxy server (Afgan et al., 2016). Reads were mapped to the mouse genome (mm10) using Bowtie2 (v2.3.4.1) (Langmead and Salzberg, 2012), (-I 0 -X 2000 --fr --dovetail --very-sensitive-local). Reads with mapping quality below 30, mapping to mitochondria, or not properly paired were removed from the analysis. PCR duplicates were filtered using Picard (v1.56.0). Peak calling was done using MACS2 (v2.1.0.20151222) callpeak (--nomodel --shift -100 --extsize 200 --call-summits). The coverage was done using the center of the Tn5 insertion and extended on both sides by 20bp (script developed by L. Lopez-Delisle). When indicated, coverage profiles represent an average of the replicates, this was done by dividing each replicate by the number of million reads that fall within peaks in each sample (for normalization) and calculating the average coverage.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph

source_name: genital tubercle

extract_protocol:
ATAC–seq was performed as described in (Buenrostro et al., 2013). Micro-dissected tissues (a pool of 2 GT or 2 to 3 CR) were isolated in PBS supplemented with 10% Fetal Calf Serum and dissociated to single cell by collagenase treatment. After isolation, 50’000 cells were lysed in 50 μl of lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630), nuclei were carefully resuspended in 50μl transposition reaction mix (25μl TD buffer, 2.5μl Tn5 transposase and 22.5μl nuclease-free water) and incubated at 37 °C for 30min. DNA was isolated with a MinElute DNA Purification Kit (Qiagen).
Library amplification was performed by PCR (10 to 12 cycles) using NEBNext High-Fidelity 2x PCR Master Mix (NEB, M0541S). Library quality was checked on a fragment analyzer, and paired-end sequencing was performed on an Illumina NextSeq 500 instrument (read length 2 × 37 base pairs).

tag: strain background

tag: genotype/variation

value: genital tubercle


title: LS174T Colon Cells LDHAB DKO + MPP Triplicate2

description:
Aadenocarcinoma of the colon. 58 years Caucasian female Antigen Expression serologically defined colon cancer antigen 3; Homo sapiens, expressed HLA A2, B13, B66; Blood type O
Gene expression data from genetically modified LS174T cells grown under variable experimental treatment

value: Aadenocarcinoma of the colon

value: 58 years


title: MH63_panicle_H3K9me2_rep1

value: Minghui 63


title: MH63_mature_leaf_H3K4me3_rep2

source_name: MH63 mature leaf

value: mature leaf

value: mature leaves were flag leaf at floral induction phase


title: GT_E13_5_WT_rep1_islandVVP

tag: strain


title: CR_E10_5_WT_Hoxd13VP

source_name: cloaca region


title: LS174T Colon Cells G6PI KO Triplicate3

description:
Aadenocarcinoma of the colon. 58 years Caucasian female Antigen Expression serologically defined colon cancer antigen 3; Homo sapiens, expressed HLA A2, B13, B61; Blood type O
Gene expression data from genetically modified LS174T cells grown under variable experimental treatment

source_name: LS174T Colon Cancer G6PI Knock Out

value: Caucasian

value: female

value: O


title: LS174T Colon Cells Vector + MPP Triplicate1

description:
Aadenocarcinoma of the colon. 58 years Caucasian female Antigen Expression serologically defined colon cancer antigen 3; Homo sapiens, expressed HLA A2, B13, B62; Blood type O
Gene expression data from genetically modified LS174T cells grown under variable experimental treatment


title: LS174T Colon Cells G6PI KO Triplicate2

description:
Aadenocarcinoma of the colon. 58 years Caucasian female Antigen Expression serologically defined colon cancer antigen 3; Homo sapiens, expressed HLA A2, B13, B60; Blood type O
Gene expression data from genetically modified LS174T cells grown under variable experimental treatment


title: 203-RVA-1

value: RVA

tag: clinical _w

value: No

value: Male


title: MH63_panicle_H3K27me3_rep2

value: panicle

value: panicle (1.5-4.5 cm)


title: LS174T Colon Cells G6PI KO Triplicate1

description:
Aadenocarcinoma of the colon. 58 years Caucasian female Antigen Expression serologically defined colon cancer antigen 3; Homo sapiens, expressed HLA A2, B13, B59; Blood type O
Gene expression data from genetically modified LS174T cells grown under variable experimental treatment


title: GT_E17_5_WT_ATAC_seq_rep1

description:
GT_E17_5_WT_ATAC_seq_rep1
processed data file: GT_E17_5_merge_WT_ATAC_seq.bedgraph.gz

value: wildtype


title: LS174T Colon Cells LDHAB DKO Triplicate3

description:
Aadenocarcinoma of the colon. 58 years Caucasian female Antigen Expression serologically defined colon cancer antigen 3; Homo sapiens, expressed HLA A2, B13, B57; Blood type O
Gene expression data from genetically modified LS174T cells grown under variable experimental treatment

source_name: LS174T Colon Cancer LDHAB Double Knock Out


title: LS174T Colon Cells LDHAB DKO Triplicate1 Reprocessed

description:
Aadenocarcinoma of the colon. 58 years Caucasian female Antigen Expression serologically defined colon cancer antigen 3; Homo sapiens, expressed HLA A2, B13, B58; Blood type O
Gene expression data from genetically modified LS174T cells grown under variable experimental treatment


title: MH63_panicle_H3K27me3_rep1


title: GT_E13_5_invV_ATAC_seq_rep2

description: GT_E13_5_merge_invV_ATAC_seq.bedgraph.gz

data_processing:
ATAC-seq reads processing was done on the Duboule lab local Galaxy server (Afgan et al., 2016). Reads were mapped to the mouse genome (mm10) using Bowtie2 (v2.3.4.1) (Langmead and Salzberg, 2012), (-I 0 -X 2000 --fr --dovetail --very-sensitive-local). Reads with mapping quality below 30, mapping to mitochondria, or not properly paired were removed from the analysis. PCR duplicates were filtered using Picard (v1.56.0). Peak calling was done using MACS2 (v2.1.0.20151222) callpeak (--nomodel --shift -100 --extsize 200 --call-summits). The coverage was done using the center of the Tn5 insertion and extended on both sides by 20bp (script developed by Lucille Lopez-Delisle). When indicated, coverage profiles represent an average of the replicates, this was done by dividing each replicate by the number of million reads that fall within peaks in each sample (for normalization) and calculating the average coverage.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph, MACS2 bed

extract_protocol:
ATAC–seq was performed as described in (Buenrostro et al., 2013). Micro-dissected tissues (a pool of 2 GT or 2 to 3 CR) were isolated in PBS supplemented with 10% Fetal Calf Serum and dissociated to single cell by collagenase treatment. After isolation, 50,000 cells were lysed in 50 μl of lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630), nuclei were carefully resuspended in 50μl transposition reaction mix (25μl TD buffer, 2.5μl Tn5 transposase and 22.5μl nuclease-free water) and incubated at 37 °C for 30min. DNA was isolated with a MinElute DNA Purification Kit (Qiagen).
Library amplification was performed by PCR (10 to 12 cycles) using NEBNext High-Fidelity 2x PCR Master Mix (NEB, M0541S). Library quality was checked on a fragment analyzer, and paired-end sequencing was performed on an Illumina NextSeq 500 instrument (read length 2 × 37 base pairs).

value: inv(V)

value: CBA / C57BL/6 mix


title: MH63_panicle_H3K27ac_rep1


title: 176-RVA-1

tag: Sex

value: NH

value: W

value: Discovery


title: GT_E13_5_invV_ATAC_seq_rep1


title: MH63_panicle_H3K27ac_rep2

value: Minghui 63


title: GT_E13_5_delV_ATAC_seq_rep2

description: GT_E13_5_merge_delV_ATAC_seq.bedgraph.gz

value: del(V)


title: 176-RVC-1

value: RVC

tag: race


title: MH63_panicle_H3K4me3_rep2

tag: development stage


title: GT_E13_5_delV_ATAC_seq_rep1


title: MH63_panicle_H3K4me3_rep1

tag: cultivar


title: 113-RVC-3

tag: age


title: 176-Control-1

value: Control

tag: cohort


title: GT_E13_5_delProx_ATAC_seq_rep2

description: GT_E13_5_merge_delProx_ATAC_seq.bedgraph.gz

value: del(Prox)


title: 113-RVA-1


title: LS174T Colon Cells Vector Triplicate2 Reprocessed

description:
Aadenocarcinoma of the colon. 58 years Caucasian female Antigen Expression serologically defined colon cancer antigen 3; Homo sapiens, expressed HLA A2, B13, B54; Blood type O
Gene expression data from genetically modified LS174T cells grown under variable experimental treatment

source_name: LS174T Colon Cancer Vector Control

value: Aadenocarcinoma of the colon

value: 58 years

value: Caucasian

tag: gender

value: female

value: O


title: LS174T Colon Cells LDHAB DKO Triplicate1

description:
Aadenocarcinoma of the colon. 58 years Caucasian female Antigen Expression serologically defined colon cancer antigen 3; Homo sapiens, expressed HLA A2, B13, B55; Blood type O
Gene expression data from genetically modified LS174T cells grown under variable experimental treatment

tag: ethnicity


title: LS174T Colon Cells Vector Triplicate1 Reprocessed

description:
Aadenocarcinoma of the colon. 58 years Caucasian female Antigen Expression serologically defined colon cancer antigen 3; Homo sapiens, expressed HLA A2, B13, B53; Blood type O
Gene expression data from genetically modified LS174T cells grown under variable experimental treatment

tag: blood type


title: GT_E13_5_delProx_ATAC_seq_rep1


title: 203-Control-1

value: No

value: Male

value: W/Asian


title: LS174T Colon Cells LDHAB DKO Triplicate2

description:
Aadenocarcinoma of the colon. 58 years Caucasian female Antigen Expression serologically defined colon cancer antigen 3; Homo sapiens, expressed HLA A2, B13, B56; Blood type O
Gene expression data from genetically modified LS174T cells grown under variable experimental treatment

tag: tissue


title: MH63_young_leaf_RNAPII_rep2

source_name: MH63 young leaf

value: young leaf

value: young leaves from two-week old seedlings

value: RNAPII


title: MH63_young_leaf_RNAPII_rep1


title: GT_E13_5_delGT2_ATAC_seq_rep2

description: GT_E13_5_merge_delGT2_ATAC_seq.bedgraph.gz

tag: genotype

value: CBA / C57BL/6 mix


title: GT_E13_5_delGT2_ATAC_seq_rep1


title: MH63_young_leaf_H3K9me2_rep1

value: Minghui 63

tag: chip antibody


title: GT_E13_5_WT_ATAC_seq_rep3

value: wildtype

tag: developmental stage


title: MH63_young_leaf_H3K9me2_rep2


title: 083-RVA-1

value: RVA

value: Female

value: NH

value: W

value: Discovery


title: LS174T Colon Cells Vector Triplicate2

description:
Aadenocarcinoma of the colon. 58 years Caucasian female Antigen Expression serologically defined colon cancer antigen 3; Homo sapiens, expressed HLA A2, B13, B51; Blood type O
Gene expression data from genetically modified LS174T cells grown under variable experimental treatment

value: Aadenocarcinoma of the colon

value: 58 years

value: Caucasian


title: GT_E13_5_WT_ATAC_seq_rep2


title: LS174T Colon Cells Vector Triplicate3

description:
Aadenocarcinoma of the colon. 58 years Caucasian female Antigen Expression serologically defined colon cancer antigen 3; Homo sapiens, expressed HLA A2, B13, B52; Blood type O
Gene expression data from genetically modified LS174T cells grown under variable experimental treatment

value: female

value: O


title: MH63_young_leaf_H3K4me1_rep1


title: MH63_young_leaf_H3K4me1_rep2


title: 077-RVC-1

value: RVC

value: Yes

value: H


title: 083-Control-1

value: Control

value: No


title: 113-Control-1

value: Male


title: 083-RVC-1


title: GT_E13_5_WT_ATAC_seq_rep1

value: wildtype

value: CBA / C57BL/6 mix


title: MH63_young_leaf_H3K27me3_rep2

value: young leaf

value: young leaves from two-week old seedlings

value: Minghui 63


title: LS174T Colon Cells Vector Triplicate1

description:
Aadenocarcinoma of the colon. 58 years Caucasian female Antigen Expression serologically defined colon cancer antigen 3; Homo sapiens, expressed HLA A2, B13, B50; Blood type O
Gene expression data from genetically modified LS174T cells grown under variable experimental treatment


title: 077-RVA-1

value: RVA

value: Female

value: W

value: Discovery


title: CR_E10_5_WT_ATAC_seq_rep2


title: 077-Control-1


title: GT_E13_5_InvV_CnR_CTCF

data_processing:
Library strategy: CUT & RUN
CUT&RUN reads processing was done on the Duboule local Galaxy server (Afgan et al., 2016). Adapters and bad-quality bases were removed with Cutadapt version 1.16 (Martin, 2011). Reads were mapped to the mouse genome (mm10) using Bowtie2 (v2.3.4.1) (Langmead and Salzberg, 2012), (-I 0 -X 1000 --fr --dovetail --very-sensitive). Reads with mapping quality below 30 or not properly paired were removed from the analysis. The output BAM file was converted to BED using bamtobed bedtools v2.18.2 (Quinlan, 2014). The coverage was obtained as the output of MACS2 (v2.1.1.20160309) (Zhang et al., 2008) (--format BED --keep-dup 1 --bdg --nomodel --extsize 200 --shift -100).
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph

extract_protocol: CUT&RUN (Schmid et al., 2004; Skene and Henikoff, 2017) was performed as described in (Meers et al., 2019; Skene et al., 2018). Micro-dissected tissues were isolated in PBS supplemented with 10% fetal calf serum and dissociated to single cell by collagenase treatment. After isolation, 500’000 cells were washed and bound to concanavalin A-coated magnetic beads and permeabilized with wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, and Roche Complete protein inhibitor) containing 0.02% digitonin. Bound cells were incubated with primary antibody (anti-HOXA13, AbCam ab106503; anti-CTCF, Active Motif, 6131) for 2h at room temperature. After washes the samples were incubated with Protein A-MNase (pA-MN) for 1 hour at 4oC, then washed twice more with Wash Buffer. Samples were resuspended in low-salt rinse buffer (20 mM HEPES, pH7.5, 0.5 mM spermidine, and 0.125% Digitonin) and chilled to 0°C and the liquid was removed on a magnet stand. Ice-cold calcium incubation buffer (3.5 mM HEPES pH 7.5, 10 mM CaCl2, 0.05% Digitonin) was added and samples were incubated on an ice-cold block for 30 min. STOP buffer (270 mM NaCl, 20 mM EDTA, 4 mM EGTA ,0.02% Digitonin, 50 µg glycogen, 50 µg RNase A) was added and samples were incubated at 37°C for 30 min, replaced on a magnet stand and the liquid was removed to a fresh tube. DNA was extracted by Phenol-Chloroform extraction and ethanol precipitation. Libraries were prepared as described in (Skene et al., 2018). Library quality was checked on a fragment analyzer, and paired-end sequencing was performed on an Illumina NextSeq 500 instrument (read length 2 × 37 base pairs).

value: Inv(V)


title: Th17 cell Day 18 post activation

city: Charleston

first: Chrystal

last: Paulos

state: SC

address: 86 Jonathan Lucas St

department: Microbiology & Immunology

institute: Medical University of South Carolina

hyb_protocol: UofC Illumina Mouseref-8 hybridization protocol

scan_protocol: UofC Illumina Mouseref-8 scanning protocol

data_processing:
The data were normalised using quantile normalisation with IlluminaGUI in R
GSGX Version 1.9.0; CPaulos-JB-Nov20-14-M6v2_Quantile_Bkgd

source_name: Mouse CD4+ T cell

label_protocol: Biotinylated cRNA were prepared with the UofC MouseRef-8 Illumina protocol

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

value: RAG1- BW TRP-1 TCR

value: 6 weeks

tag: cell type

value: CD4+ T cell

tag: treatment

value: activated with TRP-1 peptide

tag: time point

value: day 18 post activation


title: MH63_young_leaf_H3K27ac_rep2


title: MH63_young_leaf_H3K27ac_rep1


title: MH63_young_leaf_H3K27me3_rep1


title: PTU_6hT3_WT_rep1_H3K27Ac

city: Odense

first: Lars

last: Grøntved

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

data_processing:
RNA-seq and ChIP-seq sequencing data was aligned to mm9 using STAR
Differential RNA expression, H3K27Ac and H3K9Ac were analysed by DESeq2
Bedgraph files were generated using HOMER
Nomilized tag counts were optained using HOMER
H3K27Ac and H3K9Ac domains were indentified using HOMER
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraphs, peak bed file and text file with RPKM

source_name: liver

extract_protocol:
Crosslinked sonicated chromatin was IP'ed antibody and protein A/G agarose beads. DNA was extracted by phenol/choloroform.
ChIP-seq were constructed using the NEBNext Library prep kit according to manufacturer´s (NEB) instructions.

value: liver

value: WT

value: H3K27Ac (Abcam, ab4729)


title: MH63_young_leaf_H3K4me3_rep1


title: CR_E10_5_WT_ATAC_seq_rep1

value: wildtype

tag: strain

value: CBA / C57BL/6 mix


title: AW_1

city: Nanjing

first: Rong

middle: Fang

last: Wei

state: Jiangsu

address: 138 Xianlin Road

institute: Nanjing Unveristy of Chinese Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Multiple myeloma cell

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Multiple myeloma cell

value: wild type

tag: cell line


title: AO_2

value: RFWD2 overexpression


title: CR_E10_5_WT_CnR_HoxA13


title: Th17 cell Day 4 post activation

value: day 4 post activation


title: PTU_6hT3_WT_rep2_H3K27Ac


title: MH63_young_leaf_H3K4me3_rep2

value: young leaf

value: young leaves from two-week old seedlings

value: Minghui 63


title: PTU_2hT3_WT_rep2_H3K27Ac


title: PTU_2hT3_WT_rep1_H3K27Ac


title: Th17 cell Day 12 post activation

value: RAG1- BW TRP-1 TCR

value: day 12 post activation


title: CD4 cell pre activation (Day 0)

value: 6 weeks

value: CD4+ T cell

value: pre activation (Day 0)


title: CMMP.WASP.d15.Y.2

status: Public on Apr 24 2020

city: Hannover

first: Adrian

last: Schwarzer

address: Carl-Neuberg-Str. 1

department: Experimental Hematology

country: Germany

institute: Hannover Medical School

description:
X5614
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498162

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried out as recommended in the ‘One-Color Microarray-Based Gene Expression Analysis Protocol V5.7’, except that 500 ng of each fluorescently labelled cRNA population were used for hybridization.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2565CA).

data_processing: Data extraction was performed with the ‘Feature Extraction Software V10.7.3.1’ by use of the extraction protocol file ‘GE1_107_Sep09.xml’. Data was analyzed using R/Bioconductor. The data was analyzed using R 3.5.1 and Bioconductor 3.741. Raw files were read in separately for each array design with the function “read.maimages” from the R package “limma”. A merged dataset was created by extracting all probes derived from the original Agilent Mouse Genome Oligo Microarray 4x44K v2 array (A_XX_PXXXXXX) from the four array platforms and combining them using the function “cbind.EList” from “limma”. The probe with the ID “A_55_P2337033“ interrogating the gene “2310065F04Rik” was manually excluded from the dataset since it strongly cross-reacted with the sequence of EGFP. The Raw data was log2-transformed and quantile-normalized using the ”limma” package. The four within-array replicates of each probe were collapsed using the “avereps” function from the R package “limma”. Batch correction between different SAGA assays was performed on quantile-normalized log2-values using the parametric ComBat algorithm as implemented in the R package “sva”.

label: Alexa Fluor 555

label_protocol: 100 ng of total RNA were used to prepare Aminoallyl-UTP-modified (aaUTP) cRNA (Amino Allyl MessageAmp™ II Kit; #AM1753; Thermo Fisher Scientific) applying one round of amplification as directed by the company, except for a twofold downscaling of all reaction volumes. Prior to the reverse transcription reaction, 1 µl of a 1:5000 dilution of Agilent’s One-Color spike-in Kit stock solution (#5188-5282, Agilent Technologies) was added to 100 ng of total RNA of each analysed sample. The labeling of aaUTP-cRNA was performed by use of Alexa Fluor 555 Reactive Dye (#A32756; Thermo Fisher Scientific) as recommended in the manual of the Amino Allyl MessageAmp™ II Kit (twofold downscaled reaction volumes).

growth_protocol: Lineage negative cells were isolated from 8-12 week old female C57BL/6J mice using the mouse lineage cell depletion kit (Miltenyi). After thawing, one aliquot per assay was cultured for 48 hours in StemSpan (STEMCELL Technologies) supplemented with 50 ng/ml rm-SCF, 100 ng/ml rh-Flt-3L, 100 ng/ml rh-IL-11, 20 ng/ml rm-IL-3 (Peprotech). For transduction, 250 µl of viral supernatant was preloaded on RetroNectin (TaKaRa)-coated 24-well plates. 1x105 cells were added and incubated overnight. The preloading procedure was repeated for the second round of transduction. Cells from the first transduction round were harvested and cells still bound to the RetroNectin were incubated with cell dissociation buffer (Gibco), pelleted and resuspended in 250 µl of fresh culture medium before being added to the suspension harvest. Subsequently, the 750 µl of cell suspension were added to the wells preloaded for the second transduction. Cells were incubated for 24 hours, harvested, mixed with 1.6 ml IMDM containing 10% FBS, 1% Penicillin/Streptomycin, 2 mM glutamine and cytokines as described above (IMDM+), and seeded onto 12-well suspension plates. On day 4 1.9 ml medium was added, cells were incubated for 48 hours on 6-well suspension plates, before adding another 2.2 ml of medium. On day 8 post-transduction samples were diluted (~ 1:10) by seeding 1 x106 cells in 4 ml of IMDM+ in 6-well suspension plates. On days 11 and 13 p.t., cells were given with 1.2 ml of IMDM+.

extract_protocol: RNAzol B (WAK-Chemie Medical) and Direct-Zol RNA MiniPrep Kit (Zymo Research) according to manufacturers instructions. RNA quality was assessed using the Agilent 2100 Bioanalyzer.

tag: facs

tag: immortalized

value: Yes

tag: vector

tag: assay batch id

tag: batch variable


title: LV.SF.d15.Y.3

description:
X5615
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498163


title: CMMP.WASP.d15.N.4

description:
X5613
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498161

value: No


title: CMMP.WASP.d15.Y.1

description:
X5612
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498160


title: AW_2


title: LV.EFS.d15.N17

description:
X5611
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498159


title: LV.EFS.d15.N16

description:
X5610
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498158


title: Th17 cell Day 7 post activation

tag: age

value: activated with TRP-1 peptide

value: day 7 post activation


title: Mock.d15.N.31

description:
X5607
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498154


title: RV.SF.d15.Y.28

description:
X5608
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498156


title: MFG.yc.d15.Y.2

description:
X5606
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498153


title: MFG.yc.d15.Y.1

description:
X5605
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498152


title: MFG.yc.d15.N.3

description:
X5604
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498150


title: LV.SF.d15.Y.4

description:
X5616
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498164


title: RV.SF.d15.Y.23

description:
X5603
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498149


title: Th17 cell Day 2 post activation

value: day 2 post activation


title: LV.EFS.d15.N14

description:
X5479
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498146


title: CMMP.WASP.d15.N.2

description:
X5476
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498142


title: Mock.d15.N.21

description:
X5473
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498139


title: MFG.yc.d15.N.2

description:
X5475
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498141


title: RV.SF.d15.Y.22

description:
X5474
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498140


title: LV.EFS.d15.N13

description:
X5477
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498143


title: CMMP.WASP.d15.N.1

description:
X5471
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498137


title: LV.EFS.d15.N12

description:
X5472
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498138


title: AO_1

value: Multiple myeloma cell


title: Mock.d15.N.22

description:
X5602
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498147


title: MFG.yc.d15.N.1

description:
X5470
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498136


title: CMMP.WASP.d15.N.3

description:
X5478
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498145


title: RV.SF.d15.Y.20

description:
X5410
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498133


title: Mock.d15.N.20

description:
X5468
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498134


title: Mock.d15.N.16

description:
X5407
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498130


title: Mock.d15.N.19

description:
X5409
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498132


title: RV.SF.d15.Y.17

description:
X5408
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498131


title: RV.SF.d15.Y.21

description:
X5469
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498135


title: Mock.d15.N.18

description:
X5405
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498128


title: LV.EFS.d15.N15

description:
X5609
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498157


title: RV.SF.d15.Y.19

description:
X5406
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498129


title: RV.SF.d15.Y.16

description:
X5404
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498127


title: Mock.d15.N.15

description:
X5403
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498126


title: RV.SF.d15.Y.18

description:
X5402
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498125


title: RV.SF.d15.Y.15

description:
X5400
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498123


title: Mock.d15.N.14

description:
X5399
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498122


title: LV.EFS.d15.N.5

description:
X5099
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498118


title: LV.EFS.d15.N.8

description:
X5268
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498120


title: RV.SF.d15.Y.6

description:
X5098
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498117


title: LV.EFS.d15.N.4

description:
X5096
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498115


title: Mock.d15.N.6

description:
X5097
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498116


title: RV.SF.d15.Y.5

description:
X5095
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498114


title: Mock.d15.N.11

description:
X5271
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498121


title: LV.EFS.d15.N.3

description:
X4997
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498112


title: LV.EFS.d15.N.2

description:
X4996
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498111


title: LV.SF.d15.Y.2

description:
X4994
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498109


title: LV.SF.d15.Y.1

description:
X4993
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498108


title: RV.SF.d15.Y.3

description:
X4991
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498106


title: MCI [SB_0105_M]

city: Yuseing-gu

first: JaeWoong

last: Min

state: Daejeon

address: 17 Techno 4-ro

country: South Korea

institute: Biorchestra

data_processing:
NGS was performed in the NovaSeq 6000 system (Illumina, https://www.illumina.com/) by the Chunlab (Seoul, Republic of Korea, http://www.chunlab.com/).
After, data was processed using 'Raw fastq' for miRNA sequencing.
We removed the adapter from each of the reads and performed a filtering operation that only left reads that were 15 to 30 nucleotides in length.
After mapping to GRCh38, miRNA’s read counts were derived by quantification with mirbase ver.22.
Since the total number of reads for each sample was different, normalization was performed by TMM method.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files include TPM and FPKM values for each Sample

source_name: MCI

extract_protocol:
Micro RNA was prepared with RNAeasy kit (Qiagen) and libraries were constructed using 600 ng of total RNA from each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols
Twelve whole blood samples were collected from three normal old (Sejong, Republic of Korea), five normal young (Biorchestra Co.), and four patients (Boramae Medical Center, Seoul, Republic of Korea).
The buffy coat layers were separated by centrifugation using ‘Histopaque’.
The isolated buffy coat was washed and then reacted with glycophorin A Micro Beads (MACS Co.) and CD45 Micro Beads (MACS Co.) to obtain pure platelets from which red blood cells and white blood cells were removed using MS Columns (MACS Co.).
RNA was collected through ethanol precipitation after dissolving platelets using Easy blue (IntRON) and Chloroform.
The concentration of RNA was confirmed by nanodrop and then confirmed rRNA Ratio [28s / 18s] through QC.

tag: subject status

value: mild cognitive impairment (MCI)

value: 76 year

value: Platelet

tag: molecule subtype

value: microRNA


title: MCI [SB_0104_M]

value: 73 year

tag: tissue


title: MCI [EX_0002_M]


title: Normal Old [SJ_0033_N]

source_name: Normal Old

value: Normal Old


title: Alzheimer's Disease [SB_0029_A]

source_name: Alzheimer's Disease

value: Alzheimer's Disease

value: 84 year


title: Normal Old [SJ_0032_N]

value: 62 year


title: Mock.d15.N.17

description:
X5401
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498124


title: Mock.d15.N.4

description:
X4990
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498105


title: Normal Old [SJ_0036_N]

value: 70 year


title: RV.SF.d15.Y.12

description:
X5265
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498119


title: Normal Young [BO_0005_N]

source_name: Normal Young

value: Normal Young

value: 36 year


title: Mock.d15.N.5

description:
X5094
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498113

value: No


title: Normal Young [BO_0004_N]

value: 40 year


title: Mock.d15.N.3

description:
X4909
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498104


title: Mock.d15.N.2

description:
X4908
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498103

value: Yes


title: Mock.d15.N.1

description:
X4907
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498102


title: RV.SF.d15.Y.2

description:
X4473
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498101


title: LV.EFS.d15.N.1

description:
X4995
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498110


title: Normal Young [BO_0003_N]

value: 46 year


title: Normal Young [BO_0001_N]


title: RV.SF.d15.Y.1

description:
X4469
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498099


title: RV.SF.d15.N.2

description:
X4471
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498100


title: RV.SF.d15.Y.4

description:
X4992
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498107


title: E12.0PG_RNAseq_rep2

city: Los Angeles

first: Neil

last: Segil

address: 1425 san pablo st, BCC 503K

department: BCC

institute: University of Southern California

data_processing:
The quality of the libraries was confirmed using a Bioanalyzer (Quick Biology Inc.). Reads were mapped to GRCm38/mm10 genome assembly using STAR.
For RNAseq, genes.results files provided for each sample contain length, effective length, and expected counts for each gene.
For ATAC and CUTnRUN libraries, Endcode pipeline was used; PCR duplicates were removed based on genomic coordinates for ATAC-seq, or by MIDs using UMI-tools for CUT&RUN.
Peaks were called by Model-based analysis of ChIP-Seq (MACS2) with FDR< 0.01 and the dynamic lambda (--nolambda) option for individual replicates.
NarrowPeak files provide the list of called peaks of significant signal enrichment.
Genome_build: GRCm38/mm10 genome
Supplementary_files_format_and_content: *.genes.results.txt
Supplementary_files_format_and_content: *.narrowPeak

source_name: Organ of Corti

extract_protocol:
Progenitors (Sox2-GFP+) were purified from E12 cochlea by FACS sorting. RNA was extracted using Quick RNA micro-kit (Zymo).
PolyA RNA were enriched and used for library with Illumina TruSeq RNA library kit.

value: Organ of Corti progenitor cells (Sox2-GFP+)

tag: antibody


title: RV.SF.d15.N.1

description:
X4467
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498098


title: E12.0PG_RNAseq_rep1


title: A+H-MP

city: Chengdu

first: Fangfang

last: Wang

address: Guoxuexiang NO.37

institute: West China Hospital, Sichuan University

data_processing:
Bcl2fastq (v2.17.1.14) software used for basecalling.
QC: Cutadapt V1.3 ; Gene expression: HTSEQ v0.6.1
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Trimmomatic (v0.30) to be high quality clean data.
In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include fpkm values for each Sample .

source_name: MV4-11 cells

extract_protocol:
Cell precipitation was collected , flash frozen on dry ice, and RNA was harvested using Trizol reagent. NEBNext® Ultra™ RNA Library Prep Kit for Illumina® was used with 1 ug of total RNA for the construction of sequencing libraries.
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol (NEBNext® Ultra™ RNA Library Prep Kit for Illumina®).

tag: sample type

value: AML cell line

tag: population

value: main


title: CTR-MP


title: WP3_WT Stress

city: Columbus

first: Damon

middle: Joseph

last: DiSabato

state: OH

address: 460 Medical Center Drive

institute: The Ohio State University

data_processing:
FASTQ files were aligned to the mouse mm10 genome using STAR Aligner
Data were normalized and differential expression testing was performed using DESeq2 in R
P-values below 0.05 were considered statistically significant
Genome_build: Mouse mm10 genome
Supplementary_files_format_and_content: Normalized data counts per subject

source_name: WT Stress_Hippocampus

extract_protocol:
Hippocampi were micro-dissected on ice and snap frozen in liquid nitrogen. RNA was isolated using the Tri-Reagent protocol (Sigma-Aldrich). RNA quality and integrity was determined using the Agilent 2200 TapeStation assay (Agilent Technologies)
RNA-Sequencing was performed on hippocampal RNA at Novogene Co., Ltd. Eukaryotic RNA-Seq libraries were prepared and were run on an Illumina sequencing instrument according to the protocols described by the manufacturer.

tag: strain background

tag: genotype/variation

value: WT

tag: treatemtn

value: stress

value: brain; hippocampus


title: WP5_WT Stress


title: CTR-SP

value: side

tag: treatment


title: WP6_WT Stress


title: WT_m2_d29 (Amplicon Bisulfite)

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

institute: Friedrich Miescher Institute for Biomedical Research

description: Mock-Cre transduction day 29

data_processing:
Alignment: For amplicon bisulfite samples, the last 100 base pairs were trimmed due to reduced sequencing quality using the preprocessReads function from the Bioconductor QuasR package with the truncateEndBases = 100 parameter.  Amplicon sequences were then aligned to the mm9 build using Rbowtie in the QuasR package and the following parameters: genome="BSgenome.Mmusculus.UCSC.mm9", paired="fr", bisulfite="undir".  For SureSelect samples, reads were aligned to the mm9 build using Rbowtie in the QuasR environment as for amplicon sequencing above except with the parameter bisulfie = "dir".
Methylation level determination: Methylation levels for CpGs in amplicons was determined using the AmpliconViews function from the R package AmpliconBiSeq with the parameters ‘conv = 80’ and exp.var = ‘90’. Methylation levels for SureSelect samples was calculated using the qMeth function in the QuasR package.  For the SureSelect methylation data (Supplemental_Table4), read counts for replicates of the same time points were added together before determining methylation levels. Coverage columns for Supplemental_Table4 reflect summed counts for the triplicate experiments.
Filtering: A minimum of 100x coverage was required for all methylation calls in the amplicon bisulfite data. If coverage did not reach this threshold for any time point, the respective methylation level was set to NA. We further removed all CpGs with NA at day 0 or with more than one NA during the time course across all replicates. In addition, we filtered out one amplicon (chr7:149767665-149767784) containing 9 CpGs due to high variability in methylation calls. From a total of 588 CpGs initially quantified, this filtering procedure resulted in 405 CpGs. For SureSelect, a minimum of 50x coverage in all time points and replicates was used to filter CpGs for further analysis.
Rate determination: For methylation and demethylation rate determination, please see text.
Genome_build: mm9
Supplementary_files_format_and_content: Table files with CpG coordinates, methylation level, coverage, rate of methylation, rate of demethylation and tet activity (SureSelect only). For sample identication in Supplemental tables, there are 4 elements in the sample name that reflect the sample composition. Taking the sample name 'TTKO_cre1_d4_methylation' as an example, the TTKO refers to 'Tet Triple Knock-Out', while the 'cre1' refers to 'Cre transduction, replicate 1', the element 'd4' refers to 'Day 4 post transduction' and finally 'methylation' is the percent methylated alleles at that CpG. Other acronyms used are 'WT' for 'Wild-type', 'coverage' for number of reads covering that particular CpG in the sample, and 'mock' refers to the negative control in cre transduction. More specifically, 'm' refers to 'mock' and indicates addition of DMSO to the cells instead of Cre protein. The column 'MLE_kMe' reflects the rate of methylation while 'MLE_kDe' reflects the rate of demethylation (described in detail in the manuscript). The confidence column reflects the confidence level of rate inferrence. Lastly, the 'tag' column in Supplemental Table 2 and 3 reflects whether the CpG resides in an LMR (Low Methylated Region), FMR (Fully Methylated Region), UMR (Unmethylated Region), metIsland (Methylated CpG Island), NP-specific (Neural Progenitor specific) and ES-specific (Embyonic Stem cell specific) region. The designation 'Constitutive' reflects that the CpG resides in regions with the methylation state of interest in different cell types. In Supplemental Table 2, 'inferredInWTandTET' indicates rates inferred in wild-type and TTKO timecourse, while 'kDeWT_predicted' indicates predicted demethylation rates in wild-type cells using TTKO time course information and wild-type steady state measurements.

source_name: Wild-type mESCs

extract_protocol: Approximately 2ug of extracted genomic DNA from days 0, 4, 8, 10, 13, 17 and 29 were first mixed with 3.2pg of both unmethylated Lambda bacteriophage and in vitro methylated T7 bacteriophage DNA. Addition of the bacteriophage DNA was used to control for bisulfite conversion efficiency. Samples were then bisulfite converted using the EpiTect kit from Qiagen per the manufacturer’s instructions. Primers designed to amplify UMRs, LMR and FMR regions (88 in total, Supplemental Table 1) were distributed in 96 well plates and amplification was carried out using Amplitaq gold using the following thermocycler settings (all temperatures are in celcius and all incubation times are 30” unless specified): 1 cycle of 95⁰ for 9’, 20 cycles of touchdown with 95⁰ melt, 55⁰-51⁰ annealing, and extension at 72⁰, followed by 36 cycles of 95⁰ melt, 51⁰ annealing and 72⁰ extension. The amplicon reactions were then mixed, run out on an agarose gel and DNA extracted. Libraries were then constructed using the NEBNext ChIP-seq Library Prep kit (#E6240) as per the manufacturers instructions, indexed, pooled and sequenced using the Illumina MiSeq platform in 250bp paired-end mode.

tag: strain

value: mESCs

value: Wild-type TET

value: Dnmt3a/3b intact

tag: timepoint

value: day 29

tag: replicate

value: replicate 2


title: Normal Young [BO_0002_N]

value: Normal Young

value: 41 year

value: Platelet

value: microRNA


title: WT_m3_d29 (Amplicon Bisulfite)

description: Mock-Cre transduction day 29

value: replicate 3


title: WP1_WT Stress


title: WP2_WT Stress


title: WC6_WT Control

source_name: WT Control_Hippocampus

value: Control


title: A+H-SP

value: AML cell line


title: WP4_WT Stress


title: WT_m3_d17 (Amplicon Bisulfite)

description: Mock-Cre transduction day 17

value: day 17


title: WT_m1_d17 (Amplicon Bisulfite)

description: Mock-Cre transduction day 17

value: replicate 1


title: WC5_WT Control

value: WT


title: WT_m1_d29 (Amplicon Bisulfite)

description: Mock-Cre transduction day 29


title: WT_m3_d13 (Amplicon Bisulfite)

description: Mock-Cre transduction day 13

value: day 13


title: WC4_WT Control

value: brain; hippocampus


title: WC3_WT Control


title: WC7_WT Control


title: WT_m2_d13 (Amplicon Bisulfite)

description: Mock-Cre transduction day 13

value: mESCs


title: VP5_IL-1R1 knockout Stress

source_name: IL-1R1 knockout Stress_Hippocampus

value: IL-1R1 knockout

value: stress


title: WC2_WT Control


title: WC1_WT Control


title: LV.SF.d15.N.2

description:
X5617
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498165

tag: facs

tag: immortalized

value: No

tag: vector


title: VP4_IL-1R1 knockout Stress


title: WT_m3_d10 (Amplicon Bisulfite)

description: Mock-Cre transduction day 10

value: Wild-type TET

value: Dnmt3a/3b intact

value: day 10


title: VP2 _IL-1R1 knockout Stress


title: WT_m1_d10 (Amplicon Bisulfite)

description: Mock-Cre transduction day 10


title: VP1_IL-1R1 knockout Stress


title: VC6_IL-1R1 knockout Control

source_name: IL-1R1 knockout Control_Hippocampus


title: WT_m3_d8 (Amplicon Bisulfite)

description: Mock-Cre transduction day 8

value: day 8


title: VP3_IL-1R1 knockout Stress


title: WT_m1_d8 (Amplicon Bisulfite)

description: Mock-Cre transduction day 8


title: VC5_IL-1R1 knockout Control


title: WT_m2_d8 (Amplicon Bisulfite)

description: Mock-Cre transduction day 8

value: replicate 2


title: WT_m2_d17 (Amplicon Bisulfite)

description: Mock-Cre transduction day 17


title: WT_m3_d4 (Amplicon Bisulfite)

description: Mock-Cre transduction day 4

value: day 4

value: replicate 3


title: VC4_IL-1R1 knockout Control

value: Control


title: VC3_IL-1R1 knockout Control


title: WT_m1_d4 (Amplicon Bisulfite)

description: Mock-Cre transduction day 4


title: VC1_IL-1R1 knockout Control


title: WT_m2_d4 (Amplicon Bisulfite)

description: Mock-Cre transduction day 4


title: VC2_IL-1R1 knockout Control


title: WT_m1_d13 (Amplicon Bisulfite)

description: Mock-Cre transduction day 13


title: WT_cre2_d29 (Amplicon Bisulfite)

description: Post-Cre transduction day 29

value: Dnmt3a/3b catalytic dead

value: day 29


title: WT_cre3_d29 (Amplicon Bisulfite)

description: Post-Cre transduction day 29


title: WT_cre1_d29 (Amplicon Bisulfite)

description: Post-Cre transduction day 29

value: replicate 1


title: WT_cre3_d17 (Amplicon Bisulfite)

description: Post-Cre transduction day 17

value: day 17


title: WT_cre2_d17 (Amplicon Bisulfite)

description: Post-Cre transduction day 17


title: WT_m2_d10 (Amplicon Bisulfite)

description: Mock-Cre transduction day 10


title: AE92 (spleen)

city: Newcastle Upon Tyne

first: Olaf

last: Heidenreich

address: Brewery Lane

department: Wolfson Childhood Cancer Research Centre

institute: Newcastle University

data_processing:
Sequencing data was analysed using a custom python script to extract barcode sequences and frequencies.Sequencing data was analysed using a python script (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5558874/bin/leu2017140x2.txt) to extract barcode sequences and frequencies.
Sequences which did not match the expected fixed triplets were processed to create a list of ‘rejected’ barcodes, which had the correct vector sequence leading up to the barcode, but contained mismatches or insertions/deletions within the barcode region.
Supplementary_files_format_and_content: Excel files providing barcode sequence and number of reads (1st tab) and 'rejected' barcodes not matching the correct fixed barcode sequence (2nd tab)

organism: synthetic construct

source_name: ALL primograft harvested from mouse

growth_protocol: ALL primograft samples were transduced with a lentiviral vector barcode library with an estimated complexity in excess of 100,000 barcodes and transplanted intrafemorally into NSG mice. Samples were collected from spleen, bone marrow and meninges, certain samples were transplanted into secondary and tertiary recipients.

extract_protocol:
Genomic DNA was extracted using a Qiagen Dneasy kit.
Barcode regions were amplified by PCR, and Illumina adaptors added by further cycles of PCR. Products were gel extracted, pooled and sequenced using a 50bp Illumina MiSeq run

value: secondary of AE9 spleen

tag: sample

tag: transduction

tag: cells transplanted


title: AE91 (spleen)


title: AE91 (meninges)


title: WT_cre1_d17 (Amplicon Bisulfite)

description: Post-Cre transduction day 17

tag: tissue

value: mESCs


title: WT_cre2_d13 (Amplicon Bisulfite)

description: Post-Cre transduction day 13

value: day 13


title: WT_cre3_d13 (Amplicon Bisulfite)

description: Post-Cre transduction day 13


title: AE89 (spleen)

value: tertiary of AE32 spleen


title: AE87 (right femur)


title: WT_cre3_d10 (Amplicon Bisulfite)

description: Post-Cre transduction day 10


title: AE87 (left femur)


title: AE88 (spleen)


title: AE87 (spleen)


title: WT_cre2_d10 (Amplicon Bisulfite)

description: Post-Cre transduction day 10


title: AE83 (spleen)

value: tertiary of AE61 spleen


title: AE82 (spleen)


title: KO2: Mettl3/14nKO Islets

city: Shanghai

first: Yanqiu

address: 197 Rui-jin 2nd Road, Shanghai 20025, CHINA.

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.

data_processing:
paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the reference genome (UCSC MM10) with hisat2 software (v2.0.4)
Guided by the Ensembl gtf gene annotation file, cuffdiff software (part of cufflinks) was used to get the gene level FPKM as the expression profiles of mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed mRNA were identified.
Genome_build: mm10

source_name: islet

extract_protocol:
Islet total RNA was extracted using a RNeasy Micro kit (Qiagen) following the manufacturer’s protocol.
RNA high throughput sequencing was performed by Cloud-Seq Biotech (Shanghai, China). Briefly, total RNA was used for removing the rRNAs with NEBNext rRNA Depletion Kit (New England Biolabs, Inc., Massachusetts, USA) following the manufacturer's instructions. RNA libraries were constructed by using NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Inc., Massachusetts,USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an illumina Hiseq instrument with 150bp paired end reads.

tag: age

value: Postnatal day 0

tag: genotype


title: WT1: Wild-Type Islets

value: Wild-Type


title: WT2: Wild-Type Islets


title: AE84 (spleen)

tag: sample type

value: tertiary of AE36 spleen


title: WT_cre1_d10 (Amplicon Bisulfite)

description: Post-Cre transduction day 10

value: Wild-type TET

value: day 10


title: KO1: Mettl3/14nKO Islets


title: AE79 (spleen)

value: tertiary of AE62 spleen


title: AE80 (spleen)


title: WT_cre3_d8 (Amplicon Bisulfite)

description: Post-Cre transduction day 8

value: day 8

value: replicate 3


title: AE62 (right femur)

value: secondary of AE26 spleen


title: AE90 (spleen)


title: WT_cre2_d8 (Amplicon Bisulfite)

description: Post-Cre transduction day 8

value: Dnmt3a/3b catalytic dead

value: replicate 2


title: WT_cre1_d13 (Amplicon Bisulfite)

description: Post-Cre transduction day 13

value: replicate 1


title: AE62 (left femur)


title: WT_cre1_d8 (Amplicon Bisulfite)

description: Post-Cre transduction day 8


title: AE62 (spleen)


title: AE61 (spleen)

value: secondary of AE27 spleen


title: AE60 (meninges)


title: WT_cre3_d4 (Amplicon Bisulfite)

description: Post-Cre transduction day 4

value: mESCs

value: day 4


title: AE59 (right femur)


title: WT_cre2_d4 (Amplicon Bisulfite)

description: Post-Cre transduction day 4


title: AE81 (spleen)


title: AE60 (spleen)


title: AE59 (left femur)


title: WT_cre1_d4 (Amplicon Bisulfite)

description: Post-Cre transduction day 4


title: AE59 (meninges)


title: NOT1_pollen, biological rep 2

city: Oeiras

first: Jorg

middle: D

last: Becker

address: Rua da Quinta Grande No 6

country: Portugal

institute: Instituto Gulbenkian de Ciencia

description: mature pollen grains isolated from Arabidopsis NOT1+/- flowers

hyb_protocol: 3.5µg of the amplified, fragmented and labeled ss-cDNA were prepared in a 150µl hybridization cocktail (containing hybridization controls) and 120µl were used for the hybridization. The array strips were subsequently washed and double-stained (Affymetrix GeneAtlas System).

scan_protocol: Array strips were scanned on an Affymetrix GeneAtlas System.

data_processing: Standard Quality Control for the data obtained in the arrays was performed using Expression Console software (Affymetrix). For subsequent analysis dChip software was used (https://sites.google.com/site/dchipsoft/)  (Li and Wong, 2001) . For normalization the array with the median CEL intensity of all arrays in analysis was used as baseline, and the Invariant Set method applied. Normalized CEL intensities were then used to compute model-based expression values employing as background subtraction the 5th percentile of region, for Perfect Match (PM)-only.

organism: Arabidopsis thaliana

source_name: Arabidopsis NOT1+/- mutant pollen

label_protocol: Total RNA was processed for hybridization onto Arabidopsis Gene 1.1 ST Array Strip (Affymetrix) using a GeneChip WT PLUS Reagent Kit (Affymetrix) and a GeneAtlas Hybridization, Wash and Stain Kit for WT Array Strips (Affymetrix) according to manufacturer’s instructions. Briefly, 100ng of total RNA containing spiked in Poly-A RNA controls (GeneChip Poly-A RNA Control Kit, Affymetrix) were reverse transcribed for synthesis of single-stranded cDNA. After second-strand synthesis, the double-stranded cDNA obtained was used as template for an in vitro transcription (IVT) reaction to generate amplified cRNA. Fifteen micrograms of purified cRNA were then used for a second cycle of single-strand cDNA synthesis, after which 5.5 μg of ss-cDNA was fragmented and end-labeled. During this process, checkpoints for purity as well as integrity and size distribution of cRNA and fragmented ss-cDNA were performed using NanoDrop 1000 Spectrophotometer and Bioanalyzer 2100, respectively

growth_protocol: Wild type and mutant seeds were surface sterilized by vapour-phase sterilization. Briefly, 1.5ml tubes containing seeds corresponding to a maximum volume of 30µl were placed in a desiccator jar, inside a fume hood, with chlorine gas (generated from the reaction of 94% bleach with 37% Chloridric acid) for 2-3 hours. The tubes containing the seeds were then transferred to a sterile laminar flow hood, for complete chlorine gas evaporation, during 30 min.   Seeds were plated into Petri dishes containing 4.3g/L Murashige and Skoog basal medium (Sigma) supplemented with 1x Gamborg’s B5 vitamins (Sigma), 1% Sucrose grade II (Sigma), 15 µg/ml of the fungicide Benomyl (Sigma) and the appropriate antibiotic. The medium was adjusted to pH 5.7 and solidified with 0.8% Plant agar (Duchefa). Seeds were stratified at 4ºC in the dark, for 3 days, and grown under long-day conditions (16 hours light at 22ºC and 8h dark at 18ºC) before seedlings were transferred to soil. Once in soil, vegetative growth was promoted by short-day growth conditions (12 hours light at 22ºC and 12h dark at 18ºC, with 65% humidity) until plants were transferred to long-day conditions (16 hours light at 22ºC and 8h dark at 18ºC, with 65% humidity) for flowering induction.

extract_protocol: Not1+/- mutant and Col-0 mature pollen samples were prepared in triplicate as follows. Open flowers were collected into 15ml tubes until around 5ml volume and processed in 7ml SE buffer for pollen release (Borges et al., Plant Physiology 148, 1168–1181)  The solution was then filtered through a Miracloth mesh (Calbiochem) to remove flower parts and centrifuged for 1min at 2600g to pellet the pollen. The pellet was resuspended in 1ml SE buffer, and hydrated and intact pollen grains were purified from the sample by Fluorescence-activated cell sorting (FACS), in a MoFlo high-speed cell sorter (Beckman Coulter) (Becker et al., Plant Physiology 133, 713–725). For each sample, approximately 300000 pollen grains were sorted into SE buffer.  Purified pollen was pelleted by 1min centrifugation at 800g and resuspended directly into TRI Reagent (Sigma). The sample was next grinded thoroughly with a mortar and pestle and processed for total RNA extraction with Direct-zol RNA MiniPrep Kit (Zymo Research), according to manufacturer’s instructions. Total RNA samples were cleaned up using an RNeasy Mini Kit, according to the manufacture’s procedures. RNA concentration and purity was determined in NanoDrop 1000 Spectrophotometer and RNA integrity was assessed by Bioanalyzer 2100, with a RNA 6000 Nano kit.

tag: ecotype

value: Columbia 0

value: NOT1+/- mutant

tag: cell type

value: pollen grain


title: TGT_StreptavidinAP_Rep3

data_processing:
Sequencing adaptors were cut from raw sequencing data using Bowtie2 commands.
Sequencing reads were aligned using Bowtie2 (version 2.3.5) in end-to-end mapping mode with index built from hg38 and the transgene.
Salmon (version 1.1.0) was used to map RNA-seq reads to human transcriptome and quantify transcript expression.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files including sequencing reads for each sample; tab-delimited files containing TPM reads for each sample.

extract_protocol:
Total RNA was extracted from the lysate upon the addition of 3 volumes of Trizol-LS (Invitrogen) and purification with the Zymo Direct-Zol kit (Zymo Scientific) according to manufacturer’s instructions.
Library preparation was conducted using TruSeq Stranded mRNA kit (Illumina), using a modified protocol. In lieu of polyA purification, 25 µL of washed Dynabeads MyOne C1 Streptavidin (Invitrogen) were incubated with 10 µg isolated total RNA sample in 1X RBW Buffer supplemented with 2 U/µL Murine RNAse inhibitor for 1 h at room temperature. Beads were washed 3 times in 1X RBW Buffer, followed by 2 washes with ultra-pure water. Subsequent to RNA binding and washing to the streptavidin beads, 19.5 μL of Fragment-Prime-Finish mix was added to each beads sample to elute and fragment the RNA. Library preparation was carried out in subsequent steps according to manufacturer’s protocol.

tag: cell line background

value: Human HeLa-S3

tag: transgene

tag: rna-labelling condition


title: WT_3_d0 (Amplicon Bisulfite)

description: Non-transduced

tag: strain

tag: genotype/variation

value: Dnmt3a/3b intact

tag: timepoint

value: day 0


title: AE62 (meninges)


title: AE57 (right femur)


title: NOT1_pollen, biological rep 3


title: AE59 (spleen)


title: AE57 (left femur)


title: WT_2_d0 (Amplicon Bisulfite)

description: Non-transduced

value: Wild-type TET

tag: replicate


title: AE57 (spleen)


title: AE45 (right femur)

value: secondary of AE12 spleen


title: WT_1_d0 (Amplicon Bisulfite)

description: Non-transduced


title: Wild_type_pollen, biological rep 2

description: mature pollen grains isolated from Arabidopsis wild type flowers

source_name: Arabidopsis WT pollen

value: wild type


title: AE45 (left femur)


title: Wild_type_pollen, biological rep 3


title: AE45 (meninges)


title: AE45 (spleen)


title: NOT1_pollen, biological rep 1


title: TTKO_m2_d29 (Amplicon Bisulfite)

description: Mock-Cre transduction day 29

source_name: TET triple knockout mESCs

value: TET triple knockout (TTKO)

value: day 29


title: AE44 (meninges)


title: AE58 (spleen)

value: secondary of AE26 spleen


title: Wild_type_pollen, biological rep 1


title: AE43 (left femur)