title: 281T RNA

tag: disease

tag: gleason secondary

tag: gleason sum

tag: isup

tag: pt

tag: cm

tag: postop psa


title: 296T RNA

status: Public on Apr 23 2023

type: SRA

city: Moscow

first: Anastasiya

last: Kobelyatskaya

address: Vavilov str, 32

country: Russia

institute: Engelhardt Institute of Molecular Biology, RAS

library_source: transcriptomic

data_processing:
STAR+featureCounts - mRNA, miRge3.0 - miRNA (Hg37)
Assembly: Hg37
Supplementary files format and content: counts mRNA/miRNA in tsv files

molecule: total RNA

organism: Homo sapiens

source_name: primary tumor

extract_protocol:
MagNA Lyser device + MagNA Pure Compact System + MagNA Pure Compact RNA Kit
mRNA / miRNA libraries were prepared using the TruSeq Stranded mRNA Kit / NEBNext Small RNA Library Prep Set for Illumina according to the manufacturer’s protocol.Sequencing was performed on a NextSeq500 system (Illumina, San Diego, CA, USA) using a NextSeq 500/550 High Output Kit v2.5 (Illumina), read mode single.

tag: tissue

value: primary tumor

tag: cell type

value: prostate cancer

tag: Sex

value: male

tag: age

tag: risk group

value: high

tag: lapc

value: lapc

tag: gleason primary

tag: pn

tag: ln percent

tag: r residual_tumor

tag: preop psa

tag: biochemical recurrence

value: brf

tag: tmprss2 erg

value: NO

tag: treatment


title: 12A_M_1048

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq2

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

tag: strain


title: 279T RNA

tag: disease

tag: gleason secondary

tag: gleason sum

tag: isup

tag: pt

tag: cm

value: YES


title: 278T RNA

tag: tissue

tag: cell type

tag: Sex

tag: age

tag: risk group

value: intermediate

tag: lapc

value: lpc

tag: postop psa


title: 273T RNA

tag: gleason primary

tag: pn

tag: ln percent

tag: r residual_tumor

tag: tmprss2 erg


title: ACH0239 genomic DNA

type: genomic

city: Research Triangle Park

first: Xuting

last: Wang

state: NC

address: 111 TW Alexander Dr

institute: NIEHS/NIH

description: ACH0239 genomic DNA

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 and MethylationEPIC Beadchips using standard Illumina protocol

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

data_processing:
ChAMP
Matrix_processed: Average Beta (normalized using ChAMP)

label: Cy5 and Cy3

label_protocol: 500 ng of DNA was bisulfite converted using the EZ-DNA Methylation kit (Zymo Research)

extract_protocol: Nucleated DNA from whole blood was collected after sucrose-induced osmotic lysis of cells followed by phenol-chloroform extraction and DNA was stored in Tris-EDTA buffer at -20°C.

value: Female

value: whole blood


title: ACH0238 genomic DNA

description: ACH0238 genomic DNA


title: 12A_M_1047

tag: brain region

tag: strain


title: 27T RNA

tag: disease

tag: gleason secondary

tag: gleason sum

tag: isup

tag: preop psa

tag: biochemical recurrence

tag: treatment


title: 12A_M_1046

tag: age


title: 12A_M_1051


title: 272T RNA

tag: tissue

tag: cell type

tag: Sex

tag: risk group

tag: lapc

tag: pt

tag: cm


title: 310T RNA

tag: gleason primary

tag: pn

tag: ln percent

tag: r residual_tumor

tag: tmprss2 erg


title: 24T RNA

tag: disease

tag: gleason secondary

tag: gleason sum

tag: isup

value: bcr

tag: postop psa


title: ACH0244 genomic DNA

description: ACH0244 genomic DNA

tag: tissue


title: 12A_M_1045

tag: brain region

tag: age

tag: strain


title: 24N miRNA

source_name: normal prostate tissue

value: normal prostate tissue

tag: cell type

tag: Sex

tag: risk group

tag: lapc

tag: preop psa

tag: biochemical recurrence

tag: treatment


title: 240T RNA

tag: gleason primary

tag: pt

tag: pn

tag: cm

tag: ln percent

tag: r residual_tumor

tag: tmprss2 erg


title: ACH0237 genomic DNA

description: ACH0237 genomic DNA

tag: tissue


title: 12A_M_1044

tag: brain region

tag: age


title: ACH0236 genomic DNA

description: ACH0236 genomic DNA

value: Male


title: 239T RNA

tag: cell type

tag: disease

tag: postop psa


title: 237T RNA

tag: Sex

tag: risk group

tag: lapc

tag: gleason secondary

tag: gleason sum

tag: isup


title: 12A_M_1043

tag: strain


title: ACH0235 genomic DNA

description: ACH0235 genomic DNA


title: 236T RNA

tag: gleason primary

tag: pt

tag: pn

tag: cm

tag: biochemical recurrence

tag: treatment


title: 234T RNA

tag: tissue

tag: age

tag: ln percent

tag: r residual_tumor

tag: tmprss2 erg


title: 12A_M_1042

tag: brain region


title: 232T RNA

tag: cell type

tag: disease

tag: Sex

tag: risk group

tag: lapc

tag: postop psa


title: ACH0230 genomic DNA

description: ACH0230 genomic DNA


title: 228T RNA

tag: gleason primary

tag: gleason secondary

tag: gleason sum

tag: isup

tag: pt


title: ACH0224 genomic DNA

description: ACH0224 genomic DNA

tag: tissue


title: 223T RNA

tag: age

tag: pn

tag: cm

tag: treatment


title: 221T RNA

tag: ln percent

tag: r residual_tumor

tag: preop psa

tag: biochemical recurrence

tag: tmprss2 erg


title: 12A_M_1040

tag: brain region

tag: strain


title: 12A_M_1041


title: ACH0221 genomic DNA

description: ACH0221 genomic DNA

tag: Sex


title: 221N miRNA

tag: cell type

tag: disease

tag: risk group

tag: lapc

tag: gleason primary

tag: gleason secondary

tag: postop psa


title: 20T RNA

tag: tissue

tag: age

tag: gleason sum

tag: isup

tag: pt

tag: pn

tag: cm


title: 220T RNA

tag: ln percent

tag: r residual_tumor

tag: biochemical recurrence

tag: tmprss2 erg

tag: treatment


title: 12A_M_1039

tag: brain region

tag: strain


title: 20N miRNA

tag: cell type

tag: disease

tag: Sex

tag: risk group

tag: lapc

tag: gleason primary

tag: preop psa


title: 206T RNA

tag: tissue

tag: age

tag: gleason secondary

tag: gleason sum

tag: isup

tag: pt

tag: postop psa


title: ACH0215 genomic DNA

description: ACH0215 genomic DNA


title: 204T RNA

tag: pn

tag: cm

tag: ln percent

tag: r residual_tumor

tag: biochemical recurrence

tag: tmprss2 erg

tag: treatment


title: 12A_M_1038

tag: brain region

tag: strain


title: 203T RNA

tag: cell type

tag: disease

tag: Sex

tag: risk group

tag: lapc

tag: gleason primary

tag: preop psa


title: 202T RNA

tag: tissue

tag: age

tag: gleason secondary

tag: gleason sum

tag: isup

tag: pt

tag: postop psa


title: ACH0210 genomic DNA

description: ACH0210 genomic DNA


title: ACH0209 genomic DNA

description: ACH0209 genomic DNA


title: 12A_M_1037


title: 1T RNA

tag: pn

tag: cm

tag: ln percent

tag: r residual_tumor

tag: biochemical recurrence

tag: tmprss2 erg

tag: treatment


title: ACH0206 genomic DNA

description: ACH0206 genomic DNA

tag: Sex


title: 12A_M_1036

tag: brain region

tag: strain


title: 197T RNA

tag: tissue

tag: cell type

tag: disease

tag: risk group

tag: lapc

tag: gleason primary

tag: preop psa


title: ACH0223 genomic DNA

description: ACH0223 genomic DNA


title: 225T RNA

tag: age

tag: gleason secondary

tag: gleason sum

tag: isup

tag: pt

tag: pn


title: ACH0201 genomic DNA

description: ACH0201 genomic DNA


title: 12A_M_1035


title: 197N miRNA

tag: cm

tag: ln percent

tag: r residual_tumor

tag: biochemical recurrence

tag: postop psa

tag: tmprss2 erg

tag: treatment


title: 12A_M_104

tag: brain region

tag: strain


title: 196T RNA

tag: tissue

tag: cell type

tag: disease

tag: Sex

tag: risk group

tag: lapc

tag: gleason primary


title: 190T RNA

tag: age

tag: gleason secondary

tag: gleason sum

tag: isup

tag: pt

tag: pn

tag: preop psa


title: 18T RNA

tag: cm

tag: ln percent

tag: r residual_tumor

tag: biochemical recurrence

tag: postop psa

tag: tmprss2 erg

tag: treatment


title: ACH0197 genomic DNA

description: ACH0197 genomic DNA

tag: Sex

tag: tissue


title: ACH0196 genomic DNA

description: ACH0196 genomic DNA


title: 190N miRNA

tag: cell type

tag: disease

tag: risk group

tag: lapc

tag: gleason primary


title: 12A_M_1033

tag: brain region

tag: age

tag: strain


title: 186N miRNA

tag: gleason secondary

tag: gleason sum

tag: isup

tag: pt

tag: pn

value: Nx

tag: cm


title: 186T RNA

tag: r residual_tumor

tag: biochemical recurrence

tag: postop psa

tag: tmprss2 erg

tag: treatment


title: 12A_M_1031


title: 12A_M_1030


title: ACH0193 genomic DNA

description: ACH0193 genomic DNA

tag: Sex

tag: tissue


title: 185T RNA

tag: cell type

tag: disease

tag: risk group

tag: lapc

tag: gleason primary

tag: ln percent

tag: preop psa


title: 185N miRNA

tag: age

tag: gleason secondary

tag: gleason sum

tag: isup

tag: pt


title: 12A_M_103

tag: brain region

tag: strain


title: ACH0192 genomic DNA

description: ACH0192 genomic DNA


title: ACH0191 genomic DNA

description: ACH0191 genomic DNA


title: 182N miRNA

tag: pn

tag: cm

tag: r residual_tumor

tag: biochemical recurrence

tag: postop psa

tag: tmprss2 erg

tag: treatment


title: 17T RNA

tag: tissue

tag: cell type

tag: disease

tag: Sex

tag: risk group

tag: lapc

tag: gleason primary


title: 12A_M_1028

tag: age


title: 12A_M_1029

tag: brain region


title: ACH0190 genomic DNA

description: ACH0190 genomic DNA


title: ACH0189 genomic DNA

description: ACH0189 genomic DNA


title: 177T RNA

tag: gleason secondary

tag: gleason sum

tag: isup

tag: pt

tag: ln percent


title: 12A_M_1027

tag: strain


title: 179T RNA

tag: pn

tag: cm

tag: r residual_tumor

tag: preop psa

tag: biochemical recurrence

tag: postop psa

tag: tmprss2 erg


title: ACH0188 genomic DNA

description: ACH0188 genomic DNA

tag: Sex

tag: tissue


title: 175T RNA

tag: cell type

tag: disease

tag: age

tag: risk group

tag: lapc

tag: gleason primary

tag: treatment


title: 172T RNA

tag: gleason secondary

tag: gleason sum

tag: isup

tag: pt

tag: ln percent


title: 176T RNA

tag: pn

tag: cm

tag: r residual_tumor

tag: preop psa

tag: biochemical recurrence


title: 173T RNA

tag: tissue

tag: cell type

tag: Sex

tag: postop psa

tag: tmprss2 erg


title: 172N miRNA

tag: disease

tag: age

tag: risk group

tag: lapc

tag: gleason primary


title: 170T RNA

tag: gleason secondary

tag: gleason sum

tag: isup

tag: pt

tag: treatment


title: 170T RNA2

tag: pn

tag: cm

tag: ln percent

tag: r residual_tumor

tag: preop psa


title: 12A_M_1023

tag: brain region

tag: strain


title: ACH0186 genomic DNA

description: ACH0186 genomic DNA

tag: Sex

tag: tissue


title: 12A_M_1025

tag: age


title: ACH0185 genomic DNA

description: ACH0185 genomic DNA


title: 170N miRNA

tag: cell type

tag: disease

tag: risk group

tag: lapc

tag: biochemical recurrence

tag: postop psa

tag: tmprss2 erg


title: 12A_M_1022


title: 165T RNA

tag: gleason primary

tag: gleason secondary

tag: gleason sum

tag: isup

tag: pt

tag: pn

tag: treatment


title: 163T RNA

tag: Sex

tag: cm

tag: ln percent

tag: r residual_tumor

tag: preop psa


title: ACH0184 genomic DNA

description: ACH0184 genomic DNA

tag: tissue


title: 182T RNA

tag: cell type

tag: disease

tag: age

tag: risk group

tag: lapc


title: 162T RNA

tag: gleason primary

tag: gleason secondary

tag: tmprss2 erg


title: 12A_M_1021

tag: brain region

tag: strain


title: ACH0183 genomic DNA

description: ACH0183 genomic DNA


title: 15N miRNA

tag: gleason sum

tag: isup

tag: pt

tag: pn

tag: biochemical recurrence

tag: postop psa

tag: treatment


title: 12A_M_1026


title: ACH0180 genomic DNA

description: ACH0180 genomic DNA

tag: Sex

tag: tissue


title: 153T RNA

tag: cell type

tag: disease

tag: age

tag: cm

tag: ln percent

tag: r residual_tumor

tag: preop psa


title: 150T RNA

tag: risk group

tag: lapc

tag: gleason primary

tag: gleason secondary

tag: tmprss2 erg


title: 12A_M_102

tag: brain region

tag: strain


title: 150N miRNA

tag: gleason sum

tag: isup

tag: pt

tag: pn

tag: biochemical recurrence

tag: postop psa

tag: treatment


title: 144T RNA

tag: tissue

tag: cell type

tag: disease

tag: Sex

tag: age

tag: cm

tag: ln percent


title: ACH0178 genomic DNA

description: ACH0178 genomic DNA


title: ACH0177 genomic DNA

description: ACH0177 genomic DNA


title: ACH0176 genomic DNA

description: ACH0176 genomic DNA


title: 143T RNA

tag: risk group

tag: lapc

tag: gleason primary

tag: gleason secondary

tag: r residual_tumor

tag: preop psa

tag: tmprss2 erg


title: 140T RNA

tag: gleason sum

tag: isup

tag: pt

tag: pn

tag: biochemical recurrence


title: 143N miRNA

tag: tissue

tag: cell type

tag: disease

tag: postop psa

tag: treatment


title: 12A_M_1018

tag: brain region

tag: age

tag: strain


title: 12A_M_1017


title: 13T RNA

tag: Sex

tag: risk group

tag: lapc

tag: gleason primary

tag: gleason secondary

tag: cm

tag: ln percent


title: 144N miRNA

tag: gleason sum

tag: isup

tag: pt

tag: pn

tag: r residual_tumor

tag: preop psa

tag: tmprss2 erg


title: 12A_M_1016

tag: brain region


title: 138T RNA

tag: tissue

tag: cell type

tag: disease

tag: age

tag: biochemical recurrence

tag: postop psa

tag: treatment


title: 12T RNA

tag: Sex

tag: risk group

tag: lapc

tag: gleason primary

tag: gleason secondary

tag: cm


title: ACH0175 genomic DNA

description: ACH0175 genomic DNA


title: 138N miRNA

tag: gleason sum

tag: isup

tag: pt

tag: pn

tag: ln percent

tag: r residual_tumor


title: 12A_M_1015

tag: brain region

tag: strain


title: 12N miRNA

tag: tissue

tag: cell type

tag: disease

tag: age

tag: preop psa

tag: biochemical recurrence

tag: tmprss2 erg


title: ACH0171 genomic DNA

description: ACH0171 genomic DNA

tag: Sex


title: 15T RNA

tag: risk group

tag: lapc

tag: gleason primary

tag: gleason secondary

tag: cm

tag: postop psa

tag: treatment


title: 12A_M_1020

tag: brain region


title: 12A_M_1014

tag: strain


title: ACH0170 genomic DNA

description: ACH0170 genomic DNA

tag: tissue


title: 124T RNA

tag: cell type

tag: gleason sum

tag: isup

tag: pt

tag: pn

tag: ln percent

tag: r residual_tumor


title: 124N miRNA

tag: disease

tag: Sex

tag: age

tag: risk group

tag: biochemical recurrence

tag: tmprss2 erg


title: 12A_M_1013


title: 12A_M_1019


title: 12A_M_1012


title: 122T RNA

tag: lapc

tag: gleason primary

tag: gleason secondary

tag: cm

tag: preop psa

tag: postop psa

tag: treatment


title: 119T RNA

tag: tissue

tag: cell type

tag: gleason sum

tag: isup

tag: pt


title: ACH0167 genomic DNA

description: ACH0167 genomic DNA

tag: Sex


title: 117T RNA

tag: disease

tag: age

tag: pn

tag: ln percent

tag: r residual_tumor


title: 119N miRNA

tag: risk group

tag: lapc

tag: gleason primary

tag: biochemical recurrence

tag: tmprss2 erg


title: ACH0174 genomic DNA

description: ACH0174 genomic DNA


title: 115T RNA

tag: gleason secondary

tag: cm

tag: treatment


title: ACH0165 genomic DNA

description: ACH0165 genomic DNA

tag: tissue


title: ACH0166 genomic DNA

description: ACH0166 genomic DNA


title: 114T RNA2

tag: cell type

tag: gleason sum

tag: isup

tag: preop psa

tag: postop psa


title: 114T RNA

tag: disease

tag: Sex

tag: age

tag: pt

tag: pn


title: 12A_M_1011

tag: brain region

tag: strain


title: 12A_M_101


title: ACH0164 genomic DNA

description: ACH0164 genomic DNA


title: 12A_M_1009


title: 114N miRNA

tag: risk group

tag: lapc

tag: gleason primary

tag: ln percent

tag: r residual_tumor

tag: biochemical recurrence

tag: tmprss2 erg


title: 12A_M_1008


title: 110T RNA

tag: tissue

tag: cell type

tag: gleason secondary

tag: gleason sum

tag: isup

tag: cm

tag: treatment


title: 111T RNA

tag: disease

tag: Sex

tag: age

tag: pt

tag: pn

tag: postop psa


title: 125T RNA

tag: risk group

tag: lapc

tag: gleason primary

tag: ln percent

tag: preop psa


title: ACH0163 genomic DNA

description: ACH0163 genomic DNA

tag: tissue


title: 10T RNA

tag: cell type

tag: gleason secondary

tag: r residual_tumor

tag: biochemical recurrence

tag: tmprss2 erg


title: 126T RNA

tag: disease

tag: gleason sum

tag: isup

tag: cm

tag: treatment


title: 109N miRNA

tag: Sex

tag: age

tag: pt

tag: pn

tag: postop psa


title: 12A_M_1006

tag: brain region

tag: strain


title: 12A_M_1005


title: ACH0168 genomic DNA

description: ACH0168 genomic DNA

tag: tissue


title: 108T RNA

tag: cell type

tag: risk group

tag: lapc

tag: gleason primary

tag: gleason secondary

tag: ln percent


title: ACH0154 genomic DNA

description: ACH0154 genomic DNA


title: 108N miRNA

tag: disease

tag: gleason sum

tag: isup

tag: r residual_tumor

tag: tmprss2 erg


title: ACH0153 genomic DNA

description: ACH0153 genomic DNA

tag: Sex


title: 104T RNA

tag: age

tag: pt

tag: pn

tag: cm

tag: preop psa

tag: treatment


title: ACH0152 genomic DNA

description: ACH0152 genomic DNA

tag: tissue


title: 104N miRNA

tag: cell type

tag: risk group

tag: lapc


title: 102T RNA

tag: gleason primary

tag: gleason secondary

tag: ln percent

tag: biochemical recurrence

tag: postop psa


title: 12A_M_1003

tag: brain region

tag: strain


title: 12A_M_1002

tag: age


title: 102N miRNA

tag: disease

tag: Sex

tag: gleason sum

tag: isup

tag: pt

tag: r residual_tumor

tag: tmprss2 erg


title: ACH0151 genomic DNA

description: ACH0151 genomic DNA

tag: tissue


title: hTERT RPE-1, mCherry_4, H3K9me3, biol rep 2

first: Juliana

middle: S

last: Capitanio

state: California

address: 10010 N Torrey Pines Rd

department: molecular and call biology laboratory

institute: The Salk Institute for Biological Studies

data_processing:
fastq files were processed with nf-core/chipseq v1.2.2 pipeline (https://nf-co.re/chipseq/1.2.2/usage) using nextflow with -profile docker and the following genome parameters: --fasta /data/genomes/human/GRCh38.primary_assembly.genome.fa --gtf /data/genomes/human/gencode.v38.primary_assembly.annotation.gtf
obtained bam files were used for peak calling with epic2 (PMID: 30923821) using --bin-size 1000 --gaps-allowed 3 --false-discovery-rate-cutoff 0.001 and filtered for log2Fold change of at least 0.6 (1.5x above background).
Differential presence of H3K9me3 between samples was determined using the R package DiffBind (v 3.0.15) with normalization parameters normalize=DBA_NORM_LIB, spikein = TRUE, background=TRUE and analyze parameters bBlacklist=T, bGreylist = F, method = DBA_DESEQ2
Assembly: hg38
Supplementary files format and content: bed files resulting from epic2 peak caling.Columns are as follows: Chromosome Start End Pvalue Score Strand ChIPCount InputCount FDR log2FoldChange
Supplementary files format and content: bigwig tracks created with bamCoverage by nf-core/chipseq pipeline
Library strategy: Cut&Run

source_name: Eye; Pigmented epithelium; Retina

growth_protocol: hTERT RPE-1 cells were cultured in DMEM/F12 supplemented with 10% fetal bovine serum, 1% penicillin-streptomycin, and 0.01 mg/mL hygromycin B.

extract_protocol:
Cut&Run DNA was isolated using the EpiCypher CUTANA protocol with a H3K9me3 antibody (ab8898).
Cut&Run libraries were prepared using the NEBNext Ultra II Library Prep Kit for Illumina.

value: Eye; Pigmented epithelium; Retina

tag: cell line

value: hTERT RPE-1

tag: cell type

value: Epithelial cell

tag: genotype

value: mCherry overexpression

tag: treatment

value: 0.05 ug/mL doxycycline, 24 hours

tag: chip antibody

value: H3K9me3 (Abcam, ab8898)


title: 12A_M_1000


title: hTERT RPE-1, mCherry_4, H3K9me3, biol rep 1


title: ACH0150 genomic DNA

description: ACH0150 genomic DNA


title: hTERT RPE-1, mCherry_3, H3K9me3, biol rep 1


title: ACH0149 genomic DNA

description: ACH0149 genomic DNA


title: hTERT RPE-1, LmnB1_6, H3K9me3, biol rep 1

value: LmnB1 overexpression


title: hTERT RPE-1, LmnB1_6, H3K9me3, biol rep 2


title: 12A_M_1


title: 109T RNA

value: primary tumor

value: prostate cancer

value: male

tag: risk group

value: high

tag: lapc

value: lapc

tag: gleason primary

tag: gleason secondary

tag: pn

tag: cm

tag: ln percent

tag: preop psa

tag: biochemical recurrence

value: brf

tag: postop psa

value: NO


title: ACH0158 genomic DNA

description: ACH0158 genomic DNA

tag: Sex

value: Female

value: whole blood


title: ACH0148 genomic DNA

description: ACH0148 genomic DNA

tag: tissue


title: hTERT RPE-1, LmnB1_16, H3K9me3, biol rep 1

tag: cell line


title: hTERT RPE-1, LmnB1_16, H3K9me3, biol rep 2

tag: cell type


title: 12A_M_0

tag: brain region

tag: age

tag: strain


title: hTERT RPE-1, input

tag: genotype

value: WT

tag: treatment

tag: chip antibody


title: 12A_M_1004


title: ApoE -/- mouse aorta, Ad-FAM3A4

city: Beijing

first: Yuehong

last: Zheng

address: No. 1 Shuaifuyuan, Dongcheng District

department: Department of Vascular Surgery

country: China

institute: Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences

description: Sample10 Adv-FAM3A

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Aorta

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Aorta

value: ApoE knockout

value: Ang II released by a subcutaneous slow-release pump, FAM3A-overexpression vector adenovirus injected weekly from the caudal vein


title: ApoE -/- mouse aorta, Ad-FAM3A7

description: Sample13 Adv-FAM3A


title: ApoE -/- mouse aorta, Ad-FAM3A6

description: Sample12 Adv-FAM3A


title: ApoE -/- mouse aorta, Ad-FAM3A5

description: Sample11 Adv-FAM3A


title: ACH0143 genomic DNA

description: ACH0143 genomic DNA


title: ACH0142 genomic DNA

description: ACH0142 genomic DNA

value: Male


title: ApoE -/- mouse aorta, Ad-FAM3A1

description: Sample7 Adv-FAM3A


title: ApoE -/- mouse aorta, Ad-FAM3A2

description: Sample8 Adv-FAM3A


title: hTERT RPE-1, mCherry_3, H3K9me3, biol rep 2

value: Eye; Pigmented epithelium; Retina

value: hTERT RPE-1

value: Epithelial cell

value: mCherry overexpression

value: 0.05 ug/mL doxycycline, 24 hours


title: ACH0140 genomic DNA

description: ACH0140 genomic DNA


title: 12A_M_100


title: ApoE -/- mouse aorta, Ad-sham6

description: Sample6 Adv-sham

value: Ang II released by a subcutaneous slow-release pump, empty vector adenovirus injected weekly from the caudal vein


title: ApoE -/- mouse aorta, Ad-sham5

description: Sample5 Adv-sham


title: ApoE -/- mouse aorta, Ad-sham4

description: Sample4 Adv-sham


title: Ortho, rep2

first: Xiang

last: Lv

state: Beijing

address: No.5, Dongdan Santiao, Dongcheng District, Beijing

department: School of Basic Medicine

institute: Peking Union Medical College

data_processing:
Sequencing library was constructed following standard protocol and sequenced by Nova6000, and the sequencing files (fastq format) were analysised for further analysis.
Cutadapt and trimmomatic software were performed to remove linkers and low-quality sequences.
After data cleaning, hisat2 software was performed to align to the mouse genome mm10 to obtain a sam file, which was compressed it into a bam file using samtools.
FeatureCounts software was performed to obtain gene expression matrix (count file).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: BM

extract_protocol:
Total RNA was extracted from sorted cells using Trizol reagent (Life Technologies, CA, USA). Sodium acetate at a final concentration of 0.3 M and 1.5 µL of glycoblue coprecipitant (Thermo Fisher, AM 9516) were added to improve the recovery of RNA.
Libraries were prepared with NEBNext Ultra RNA Library Prep Kit for Illumina (NEB)

value: BM

value: Erythroblast


title: Ortho, rep1

value: orthochromatic erythroblasts


title: Ortho, rep3


title: Poly, rep2

value: polychromatic erythroblasts


title: ACH0137 genomic DNA

description: ACH0137 genomic DNA

value: Female


title: Poly, rep1


title: ApoE -/- mouse aorta, Ad-sham3

description: Sample3 Adv-sham


title: ACH0136 genomic DNA

description: ACH0136 genomic DNA

value: whole blood


title: ApoE -/- mouse aorta, Ad-sham1

description: Sample1 Adv-sham


title: ApoE -/- mouse aorta, Ad-sham2

description: Sample2 Adv-sham


title: Baso, rep3

value: basophilic erythroblasts

value: WT


title: ACH0144 genomic DNA

description: ACH0144 genomic DNA


title: ACH0135 genomic DNA

description: ACH0135 genomic DNA


title: Baso, rep2


title: ACH0134 genomic DNA

description: ACH0134 genomic DNA


title: ApoE -/- mouse aorta, Ad-FAM3A3

description: Sample9 Adv-FAM3A

value: Aorta

value: ApoE knockout


title: ACH0141 genomic DNA

description: ACH0141 genomic DNA

value: Male


title: Baso, rep1


title: ACH0133 genomic DNA

description: ACH0133 genomic DNA


title: Poly, rep3


title: Pro, rep3

value: proerythroblasts


title: ACH0132 genomic DNA

description: ACH0132 genomic DNA


title: Pro, rep2


title: patient 37c patent (control)

city: Poriya

first: Natalia

last: Volinsky

address: building 26

department: Research Institute

country: Israel

institute: Tzafon Medical Center

data_processing: Primary and secondary analysis of miRNA sequencing results was performed using a web resourceGene Globe Data Analysis Center (Qiagen). Read numbers were identified according to Unique Molecular Identifiers (UMI) for each species.

source_name: coronary serum

extract_protocol:
MiRNA libraries were prepared from RNA samples of 16 patent and 18 STEMI patients, using the QIAseq miRNA Library Kit (Qiagen).  Library concentrations were measured with Qubit dsDNA HS Assay Kit (Molecular Probes Life Technology) and the quality was assessed by Bioanalyzer and TapeStation systems (Agilent).
All miRNA libraries were sequenced using Nextseq 550 (Illumina) with a read length of 75 bp.

value: coronary serum

tag: diagnosis

value: healthy

value: male


title: patient 38c STEMI

value: ST-elevation myocardial infarction


title: patient 34c STEMI


title: preeclampsia rep 1

type: RNA

city: Changsha

first: MI

middle: CHUN

last: MEI

state: HuNan

address: 138 Tongzipo Road, Yuelu District

department: Department of Obstetrics and Gynecology

institute: The Third Xiangya Hospital, Central South University

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Phalanx Human OneArray Ver. 6 Release 1 for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: preeclampsia

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Placental Tissue samples were obtained immediately after delivery. Pieces of villous tissue (0.5×0.5×0.5 cm), approximately 2 cm beside the umbilical cord insertion, from the middle layer of placenta midway between maternal and fetal surfaces from different lobes were excised, excluding sites of haemorrhage , infarction, and fibrin deposition. To avoid RNA degradation, tissues were immediately stored in 1.0ml RNAstore Reagent (CWbiotech Company, China), and then stored at -80℃ until use.

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

tag: mean arterial pressure (mmhg)

tag: urine protein

tag: condition

value: placents from preeclamptic pregnancies


title: Pro, rep1

value: BM


title: ACH0130 genomic DNA

description: ACH0130 genomic DNA


title: patient 33c patent (control)


title: ACH0129 genomic DNA

description: ACH0129 genomic DNA


title: patient 35c STEMI


title: preeclampsia rep 3


title: preeclampsia rep 2


title: patient 36c patent (control)


title: normal rep 2

source_name: normal

value: normal placentas


title: normal rep 3


title: patient 32c patent (control)


title: patient 31c STEMI


title: ACH0128 genomic DNA

description: ACH0128 genomic DNA


title: patient 29c patent (control)


title: 3 month C57BL/6 mouse epididymal initial segment single cell RNA-seq

city: Guangzhou

first: Yun

last: Xie

state: China

address: No. 58 Zhongshan 2nd Road, Yuexiu District, 0080, China.

institute: sun yat-sen university

library_source: transcriptomic single cell

data_processing:
Cell Ranger was used for preprocessing raw sequence data from a 10X single cell sequencing experiment.
Seurat R-package was used for quality control, analysis, and exploration.
Assembly: mm10
Supplementary files format and content: .cloupe

source_name: epididymal initial segment

extract_protocol: Libraries were constructed using 10X Genomics platform.

value: epididymal initial segment

tag: developmental stage

value: Young


title: 21 month C57BL/6 mouse epididymal initial segment single cell RNA-seq

value: Old


title: ACH0127 genomic DNA

description: ACH0127 genomic DNA

value: Female

value: whole blood


title: patient 28c patent (control)


title: patient 27c STEMI


title: normal rep 1


title: patient 26c STEMI


title: ACH0131 genomic DNA

description: ACH0131 genomic DNA


title: ACH0126 genomic DNA

description: ACH0126 genomic DNA


title: Tumor tx FOLFIRINOX + Isotype Control [FOL_ISO]

city: Boston

first: Stephanie

last: Dougan

state: MA

address: 1 Jimmy Fund Way

department: Cancer Immunology & Virology

institute: Dana-Farber Cancer Institute

data_processing:
The 10x Cellranger pipeline (v6.1.0) was used to align reads to the mm10 reference genome and generate a single-cell feature count matrix for each library using default parameters.
Assembly: mm10
Supplementary files format and content: For each sample, a MEX sparse matrix (compressed) containing raw gene-level counts for all sequenced barcodes

source_name: Tumor

extract_protocol:
Single-cell suspensions were generated from the digested tumors and were enriched for fibroblasts using antibodies against CD31 and CD90, followed by positive selection with magnetic beads.
10X 5' v2 protocol

value: Tumor

value: KPCY 6694c2

value: FOLFIRINOX + Isotype Control


title: Tumor tx FOLFIRINOX + anti-TGFb [FOL_TGFB]

value: FOLFIRINOX + anti-TGFb


title: patient 25c patent (control)


title: patient 24c patent (control)


title: Tumor tx Gemcitabine + anti-TGFb [GEM_TGFB]

value: Gemcitabine + anti-TGFb


title: patient 23c STEMI

value: coronary serum


title: ACH0125 genomic DNA

description: ACH0125 genomic DNA


title: Tumor tx Gemcitabine + Isotype Control [GEM_ISO]

value: Gemcitabine + Isotype Control


title: ACH0123 genomic DNA

description: ACH0123 genomic DNA


title: patient 21c patent (control)

value: healthy

value: male


title: Tumor tx PBS + anti-TGFb [PBS_TGFB]

value: PBS + anti-TGFb


title: ACH0121 genomic DNA

description: ACH0121 genomic DNA


title: patient 20c patent (control)


title: patient 30c STEMI

value: ST-elevation myocardial infarction


title: patient 17c STEMI


title: ACH0120 genomic DNA

description: ACH0120 genomic DNA

value: Male


title: patient 18c STEMI


title: RNA-Em-E7.5-Dnmt1/3a/3b-TKO-4

first: Jiansen

last: Lu

address: No. 5 Yiheyuan Road, Haidian District

department: Biomedical Pioneering Innovation Center (BIOPIC)

institute: Peking University

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
7.5_DTKO_em4

data_processing:
For WGBS, trim_galore(v0.6.4) were used to remove low quality reads and adaptor sequence. Reads pass quality control were mapped to mm10 mouse genome using BitMapperBS(v1.0.2.2) in pair-end mode with parameters "--sensitive --pbat --unmapped_out" at first. Unmapped reads were output by samtools(v1.11) and mapped again using BitMapperBS's single-end mode. Aligned bam files were merged and sorted by samtools and the methylation information in MethylKit and bedGraph format were extracted by MethylDackel(v0.4.0) with default parameters. Bed format methylation files were generated by local scripts and BigWig files used in IGV were generated by UCSC binary tools bedGraphToBigWig(v4).
For RNA-seq, trim_galore(v0.6.4) were used to quality control for raw fastq data. After that, clean reads were mapped to mm10 genome by STAR(2.7.2b) with parameters “--quantMode TranscriptomeSAM GeneCounts” to output alignments translated into transcript coordinates in the bam files, and read counts of each genes, which were then used to calculate TPM (Transcript Per Milion).
Genome_build: mm10
Supplementary_files_format_and_content:
bed: Filtered six columns bed format methylation information. Six columns correspond to chromosome, start site, end site, methylation levels (%), counts of C, strand, counts of T. Only CpG site with coverage greater than 3 were remained.
methylkit: methylation call data used for R package methylkit(v1.12.0).
expression levels: raw counts and TPM values of each gene
expression matrix

source_name: embryo

extract_protocol:
For RNA-seq, the embryos (E6.5 and E7.5) of control, Dnmt1 knock-out, Dnmt3a/3b double knock-out and Dnmt1/3a/3b triple knock-out were carefully collected from mouse decidua. The epiblast (epi) and extraembryonic ectoderm (exe) of embryos were quickly separated by needle.  For WGBS, gDNA was extracted from the embryos (E6.5 and E7.5) by using TIANamp Micro DNA Kit (TIANGEN, Cat#DP316) according to the manufacturer's instructions.
For RNA-seq, the cDNA library experimental procedure was mainly according to reported protocol (Peng et al., 2019, Nature). Sequencing was performed on the Illumina Nova Seq 6000 at the Novogene Bioinformatics Institute, Beijing, China.  For WGBS, the DNA methylation library experimental procedure was mainly modified from previous published method (PMID 28182018; PMID 22649061). After extraction of mouse embryo genomic DNA, 10 ng of DNA was taken as the start material for DNA methylation library preparation. 0.1 ng lambda DNA for each sample was spiked into the sample to quantify the C-to-T conversion efficiency. The bisulfite treatment was performed using EZ-96 DNA Methylation-Direct MagPrep (Zymo cat#D5044) based on user instruction, and the sample was eluted in 19.5 μL H2O. To synthesize the first stand after bisulfite conversion, 2.5 μL 10× Blue buffer (TIANGEN), 2 μL 10 mM dNTP (TAKARA) and 1 μL 100 mM bio-P5-N6-Oligo 1 (/5Biosg/CTACACGACGCTCTTCCGATCTNNNNNN) were added to the sample and sample was incubated at 65°C for 3 min. Then 1μL Klenow exo–  (TIANGEN) was added and the sample was incubated at 4°C for 5 min, +1°C/15 sec to 37°C, 37°C for 30 min. The random priming was repeated 4 times and the free-primer was removed by treating with Exo I (NEB). The biotin-labelled fragments were enriched using Dynabeads M280 Streptavidin beads (Invitrogen) with rotation at room temperature for 45 min. The second strand was synthesized using P7-N9-oligo2 (AGACGTGTGCTCTTCCGATCTNNNNNN) and Klenow exo– (TIANGEN). The final PCR was performed using NEB pre-indexed primer, universal primer, and KAPA HiFi HotStart ReadyMix (KAPA) for 5 cycles. 300-800 bp PCR production was isolated using 2% agarose gel electrophoresis. Sequencing was performed on the Illumina Nova Seq 6000 at the Novogene Bioinformatics Institute, Beijing, China.

value: C57BL/6(male) X F1(female)

value: epiblast


title: ACH0119 genomic DNA

description: ACH0119 genomic DNA


title: patient 16c patent (control)


title: Tumor tx PBS + Isotype Control [PBS_ISO]

value: PBS + Isotype Control


title: patient 13c STEMI


title: ACH0118 genomic DNA

description: ACH0118 genomic DNA


title: patient 15c patent (control)


title: ACH0117 genomic DNA

description: ACH0117 genomic DNA

value: Female


title: patient 6c STEMI


title: RNA-Em-E7.5-Dnmt1/3a/3b-TKO-1

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
7.5_DTKO_em1


title: RNA-Em-E7.5-Dnmt1/3a/3b-TKO-2

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
7.5_DTKO_em2


title: patient 4c patent (control)


title: patient 5c STEMI


title: patient 3c patent (control)


title: patient 12c patent (control)


title: patient 22c STEMI


title: ACH0114 genomic DNA

description: ACH0114 genomic DNA

value: whole blood


title: RNA-Em-E7.5-Dnmt3a/3b-DKO-3

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
7.5_D3ab_em3


title: patient 1c STEMI


title: patient 2c STEMI


title: patient 19c patent (control)


title: ACH0116 genomic DNA

description: ACH0116 genomic DNA


title: ACH0113 genomic DNA

description: ACH0113 genomic DNA


title: ACH0115 genomic DNA

description: ACH0115 genomic DNA


title: RNA-Em-E7.5-Dnmt3a/3b-DKO-4

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
7.5_D3ab_em4


title: Tonsil dpi3 [Ton9]

city: Wanju-Gun

first: woncheoul

last: park

state: Iseo-Myeon

address: 1500 kongjwipatjwi-Ro

department: Animal genomics and Bioinformatics

country: South Korea

institute: National Institute of Animal Science

description:
Ton9
tonsil_count.csv

data_processing:
For base calling of Illumina sequencer produced raw pictures, real-time analysis (RTA) software was used and using the BCL to fastq Illumina software, the produced BCL image files were converted to FASTQ raw readings
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Sscrofa11.1 reference genome using Hisat2 v2.2.1 and FeatureCounts from the Subread package v2.0.1, the mapped reads were utilized to construct a count matrix
Differential expression (DE) analysis of lymphoma and non–lymphoma groups was performed using the DESeq2 package in R
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Sus scrofa

source_name: Tonsil

extract_protocol:
RNA sample using the Trizol/chloroform/isopropanol method according to the manufacturer's instructions (InvitrogenTM, Carlsbad, CA, USA)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: African swine fever virus infection in pig

value: Tonsil

tag: time point


title: Tonsil dpi3 [Ton8]

description:
Ton8
tonsil_count.csv


title: Tonsil dpi3 [Ton7]

description:
Ton7
tonsil_count.csv


title: ACH0112 genomic DNA

description: ACH0112 genomic DNA


title: Tonsil dpi1 [Ton5]

description:
Ton5
tonsil_count.csv


title: RNA-Em-E7.5-Dnmt3a/3b-DKO-1

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
7.5_D3ab_em1


title: RNA-Em-E7.5-Dnmt1/3a/3b-TKO-3

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
7.5_DTKO_em3


title: Tonsil dpi1 [Ton4]

description:
Ton4
tonsil_count.csv


title: RNA-Em--E7.5-Dnmt1-KO-4

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
7.5_DX1_em4


title: ACH0111 genomic DNA

description: ACH0111 genomic DNA


title: Tonsil dpi0 [Ton3]

description:
Ton3
tonsil_count.csv


title: patient 9c STEMI


title: RNA-Em--E7.5-Dnmt1-KO-3

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
7.5_DX1_em3


title: ACH0110 genomic DNA

description: ACH0110 genomic DNA


title: Tonsil dpi0 [Ton2]

description:
Ton2
tonsil_count.csv


title: Tonsil dpi0 [Ton1]

description:
Ton1
tonsil_count.csv


title: RNA-Em--E7.5-Dnmt1-KO-2

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
7.5_DX1_em2


title: Spleen dpi3 [Sp9]

description:
Sp9
spleen_count.csv

source_name: Spleen

value: Spleen


title: ACH0109 genomic DNA

description: ACH0109 genomic DNA


title: Spleen dpi3 [Sp7]

description:
Sp7
spleen_count.csv


title: RNA-Em--E7.5-Dnmt1-KO-1

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
7.5_DX1_em1


title: ACH0108 genomic DNA

description: ACH0108 genomic DNA


title: ACH0107 genomic DNA

description: ACH0107 genomic DNA


title: Spleen dpi1 [Sp5]

description:
Sp5
spleen_count.csv


title: RNA-Em-E7.5-control-4

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
7.5_ey_em4

value: wild type


title: Spleen dpi1 [Sp6]

description:
Sp6
spleen_count.csv


title: RNA-Em-E7.5-Dnmt3a/3b-DKO-2

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
7.5_D3ab_em2


title: Spleen dpi0 [Sp2]

description:
Sp2
spleen_count.csv


title: ACH0106 genomic DNA

description: ACH0106 genomic DNA


title: Spleen dpi1 [Sp4]

description:
Sp4
spleen_count.csv


title: RNA-Em-E7.5-control-3

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
7.5_ey_em3


title: Tonsil dpi1 [Ton6]

description:
Ton6
tonsil_count.csv


title: Spleen dpi0 [Sp1]

description:
Sp1
spleen_count.csv


title: Spleen dpi0 [Sp3]

description:
Sp3
spleen_count.csv


title: Muscle dpi3 [Mu9]

description:
Mu9
muscle_count.csv

source_name: Muscle

value: Muscle


title: ACH0105 genomic DNA

description: ACH0105 genomic DNA


title: RNA-Em-E7.5-control-1

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
7.5_ey_em1


title: RNA-Em-E7.5-control-2

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
7.5_ey_em2


title: Muscle dpi3 [Mu8]

description:
Mu8
muscle_count.csv


title: ACH0104 genomic DNA

description: ACH0104 genomic DNA


title: Muscle dpi3 [Mu7]

description:
Mu7
muscle_count.csv


title: ACH0103 genomic DNA

description: ACH0103 genomic DNA


title: Muscle dpi1 [Mu6]

description:
Mu6
muscle_count.csv


title: RNA-Ex-E7.5-Dnmt1/3a/3b-TKO-4

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
7.5_DTKO_ex4

value: extraembryonic ectoderm


title: RNA-Ex-E7.5-Dnmt1/3a/3b-TKO-3

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
7.5_DTKO_ex3


title: ACH0100 genomic DNA

description: ACH0100 genomic DNA


title: Muscle dpi1 [Mu4]

description:
Mu4
muscle_count.csv


title: Muscle dpi0 [Mu3]

description:
Mu3
muscle_count.csv


title: Spleen dpi3 [Sp8]

description:
Sp8
spleen_count.csv


title: RNA-Ex-E7.5-Dnmt1/3a/3b-TKO-2

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
7.5_DTKO_ex2


title: Muscle dpi0 [Mu2]

description:
Mu2
muscle_count.csv


title: RNA-Ex-E7.5-Dnmt1/3a/3b-TKO-1

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
7.5_DTKO_ex1


title: Muscle dpi0 [Mu1]

description:
Mu1
muscle_count.csv


title: ACH0098 genomic DNA

description: ACH0098 genomic DNA


title: Mesenteric dpi3 [Me9]

description:
Me9
mesentric_count.csv

source_name: Mesenteric

value: Mesenteric


title: Mesenteric dpi3 [Me8]

description:
Me8
mesentric_count.csv


title: RNA-Ex-E7.5-Dnmt3a/3b-DKO-4

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
7.5_D3ab_ex4


title: ACH0097 genomic DNA

description: ACH0097 genomic DNA


title: Mesenteric dpi3 [Me7]

description:
Me7
mesentric_count.csv


title: RNA-Ex-E7.5-Dnmt3a/3b-DKO-3

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
7.5_D3ab_ex3


title: INTS11FKBP_2h_mNET_seq_rep2

first: Hua

address: 38 Xueyuan Rd

data_processing:
library strategy: mNET-seq
Illumina bcl2fastq2 Conversion Software v2.20 used for basecalling.
Reads were demultiplexed, trimmed for adapter content with cutadapt and mapped with STAR to the GRCm38 (mm10) genome assembly.
Further data processing was carried out using the R/Bioconductor environment.
Assembly: mm10
Supplementary files format and content: All processed data is made available as supplementary files to the manuscript

source_name: mESCs

growth_protocol: E14 ESCs (129/Ola background) were maintained on 0.2% gelatin-coated plates in Glasgow Minimum Essential Medium (GMEM, Sigma-Aldrich, G5154) containing 15% fetal bovine serum (Gibco, 26140079), supplemented with 1× Pen-Strep (Thermofisher Scientific, 15140122), 2 mM Glutamax (Thermofisher Scientific, 35050061), 50 µM β-mercaptoethanol (Thermofisher Scientific, 21985023), 0.1 mM nonessential amino acids (Thermofisher Scientific, 11140050), 1 mM sodium pyruvate (Thermofisher Scientific, 11360070), and Leukemia Inhibitory Factor (LIF, 1000U/mL, Millipore).

extract_protocol:
Cells were seeded the day before the experiment to get 100 million cells per sample the following day. We randomly assigned flasks for each treatment and treated cells with DMSO only or Auxin ligand, before extracting the chromatin-bound RNA Pol II. The cells were first washed with ice-cold DPBS, resuspended in 4 mL ice-cold HLB+N buffer (10 mM Tris-HCl (pH 7.5), 10 mM NaCl, 2.5 mM MgCl2, 0.5% (vol/vol) NP-40 and 1× proteinase inhibitor) and incubated on ice for 5 minutes, then cells were scrapped to a 15-mL centrifugate tube.
Libraries were constructed using NEBNext Multiplex Small RNA Library Prep kit (NEB, NC0477293).

treatment_protocol: The sample was collected before the addition of QIAzol (Qiagen), which was used to stop the reaction at the desired time point.

value: mESCs


title: Mesenteric dpi1 [Me6]

description:
Me6
mesentric_count.csv


title: ACH0096 genomic DNA

description: ACH0096 genomic DNA


title: INTS11FKBP_2h_mNET_seq_rep1


title: RNA-Ex-E7.5-Dnmt3a/3b-DKO-2

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
7.5_D3ab_ex2


title: Mesenteric dpi1 [Me5]

description:
Me5
mesentric_count.csv


title: ACH0095 genomic DNA

description: ACH0095 genomic DNA


title: INTS11FKBP_0h_mNET_seq_rep2


title: Mesenteric dpi1 [Me4]

description:
Me4
mesentric_count.csv


title: ACH0094 genomic DNA

description: ACH0094 genomic DNA


title: RNA-Ex-E7.5-Dnmt3a/3b-DKO-1

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
7.5_D3ab_ex1


title: Muscle dpi1 [Mu5]

description:
Mu5
muscle_count.csv


title: Mesenteric dpi0 [Me3]

description:
Me3
mesentric_count.csv


title: ACH0093 genomic DNA

description: ACH0093 genomic DNA


title: INTS11FKBP_0h_mNET_seq_rep1


title: RNA-Ex--E7.5-Dnmt1-KO-4

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
7.5_DX1_ex4


title: RNA-Ex--E7.5-Dnmt1-KO-3

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
7.5_DX1_ex3


title: ACH0092 genomic DNA

description: ACH0092 genomic DNA


title: Mesenteric dpi0 [Me2]

description:
Me2
mesentric_count.csv


title: ACH0099 genomic DNA

description: ACH0099 genomic DNA


title: ACH0091 genomic DNA

description: ACH0091 genomic DNA


title: Mesenteric dpi0 [Me1]

description:
Me1
mesentric_count.csv


title: INTS11FKBP_2h_TT_seq_Rep2

data_processing:
Library strategy: TT-seq
Illumina bcl2fastq2 Conversion Software v2.20 used for basecalling.
Paired-end reads were demultiplexed by bcl2fastq. Raw reads were aligned to the mouse mm10 genome assembly using STAR.
Further data processing was carried out using the R/Bioconductor environment.
Assembly: mm10
Supplementary files format and content: All other processed data is made available as supplementary files to the manuscript

extract_protocol:
Following the specified treatment, we supplemented the treatment medium with 1 mM 4-thiouridine (4sU) and metabolically labeled the cells for 10 min. The cells were lysed in QIAzol (Qiagen, 79306) and total RNA was isolated according to the manufacturer’s instructions before the addition of 100 ng RNA spike-in mix together with QIAzol.
Libraries were constructed using TruSeq Stranded Total RNA kit (Illumina, 20020596).


title: Mandibular dpi3 [Ma9]

description:
Ma9
mandibular_count.csv

source_name: Mandibular

value: Mandibular


title: RNA-Ex--E7.5-Dnmt1-KO-2

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
7.5_DX1_ex2


title: RNA-Ex--E7.5-Dnmt1-KO-1

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
7.5_DX1_ex1


title: INTS11FKBP_2h_TT_seq_Rep1


title: ACH0089 genomic DNA

description: ACH0089 genomic DNA


title: Mandibular dpi3 [Ma8]

description:
Ma8
mandibular_count.csv


title: INTS11FKBP_0h_TT_seq_Rep2


title: INTS11FKBP_8h_TT_seq_Rep1


title: RNA-Ex-E7.5-control-4

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
7.5_ey_ex4


title: Mandibular dpi3 [Ma7]

description:
Ma7
mandibular_count.csv


title: ACH0087 genomic DNA

description: ACH0087 genomic DNA


title: ACH0090 genomic DNA

description: ACH0090 genomic DNA


title: INTS11FKBP_0h_TT_seq_Rep1


title: ACH0086 genomic DNA

description: ACH0086 genomic DNA


title: RNA-Ex-E7.5-control-2

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
7.5_ey_ex2


title: SLAM_seq_INTS11FKBP_8h_rep3

data_processing:
library strategy: Quant-seq
Illumina bcl2fastq2 Conversion Software v2.20 used for basecalling.
Gene and 3' UTR annotations were obtained from the UCSC table browser (https://genome.ucsc.edu/cgi-bin/hgTables, mm10 vM14 3' UTR). Adapters were trimmed from raw reads using cutadapt through the trim_galore wrapper tool with adapter overlaps set to 3bp for trimming.
SLAM-seq analysis was done similar to previously described by SlamDunk package.
For Quant-seq, concatenated fastq files were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using trim_galore, then mapped to mm10 whole genome using HISAT 2.2.1 with default parameters. The number of reads mapped to the 3' UTR of genes was determined with featureCounts. Raw reads were normalized to counts per million (CPM).
Assembly: mm10
Supplementary files format and content: All other processed data is made available as supplementary files to the manuscript

extract_protocol:
RNA (1 μg) was treated with 10 mM iodoacetamide in a 50-μl reaction volume at 50 °C for 15 min with 50 mM NaPO4 (pH 8.0), and 50% (v/v) DMSO followed by addition of 1 μl of 1 M DTT to stop the reaction. RNA was precipitated at -80 °C for 60 min with 1 μl of GlycoBlue (Thermofisher Scientific, AM9515), 5 μl of 3 M NaOAc (pH 5.2), and 180 μl of 100% ethanol. RNA was pelleted at 4 °C (12,000g, 30 min), washed with 1 mL of 80% ethanol, and centrifuged at 4 °C (12,000g, 30 min). The RNA pellet was dried at room temperature for 10 min and resuspended in 20 μl of nuclease-free H2O. RNA yield and quality were assessed using the 2200 TapeStation (Agilent).
Libraries were constructed using QuantSeq 3′-mRNA Seq Library Prep Kit FWD for Illumina (Lexogen, SKU: 015.96).

treatment_protocol: For SLAM-seq experiments, cells were incubated with 100 μM 4-thiouridine (4sU; Biosynth, NT06186) for 60 min before RNA isolation.

value: DPY30-mAID degron


title: Mandibular dpi1 [Ma6]

description:
Ma6
mandibular_count.csv


title: RNA-Ex-E7.5-control-1

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
7.5_ey_ex1


title: ACH0085 genomic DNA

description: ACH0085 genomic DNA


title: SLAM_seq_INTS11FKBP_8h_rep2


title: RNA-Em-E6.5-Dnmt1/3a/3b-TKO-4

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
6.5_DTKO_em4


title: Mandibular dpi1 [Ma4]

description:
Ma4
mandibular_count.csv


title: INTS11FKBP_8h_TT_seq_Rep2


title: SLAM_seq_INTS11FKBP_8h_rep1


title: ACH0083 genomic DNA

description: ACH0083 genomic DNA


title: RNA-Em-E6.5-Dnmt1/3a/3b-TKO-3

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
6.5_DTKO_em3


title: Mandibular dpi0 [Ma2]

description:
Ma2
mandibular_count.csv


title: RNA-Em-E6.5-Dnmt1/3a/3b-TKO-2

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
6.5_DTKO_em2


title: Mandibular dpi0 [Ma3]

description:
Ma3
mandibular_count.csv


title: ACH0081 genomic DNA

description: ACH0081 genomic DNA


title: SLAM_seq_INTS11FKBP_4h_rep3


title: SLAM_seq_INTS11FKBP_4h_rep2


title: ACH0080 genomic DNA

description: ACH0080 genomic DNA


title: RNA-Em-E6.5-Dnmt1/3a/3b-TKO-1

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
6.5_DTKO_em1


title: Mandibular dpi0 [Ma1]

description:
Ma1
mandibular_count.csv


title: RNA-Em-E6.5-Dnmt3a/3b-DKO-4

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
6.5_D3ab_em4


title: ACH0077 genomic DNA

description: ACH0077 genomic DNA


title: SLAM_seq_INTS11FKBP_4h_rep1


title: SLAM_seq_INTS11FKBP_48h_rep3


title: Lung dpi3 [Lu9]

description:
Lu9
lung_count.csv

source_name: Lung

value: Lung


title: Lung dpi3 [Lu8]

description:
Lu8
lung_count.csv


title: ACH0076 genomic DNA

description: ACH0076 genomic DNA


title: SLAM_seq_INTS11FKBP_48h_rep2


title: ACH0075 genomic DNA

description: ACH0075 genomic DNA


title: RNA-Em-E6.5-Dnmt3a/3b-DKO-3

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
6.5_D3ab_em3


title: RNA-Em-E6.5-Dnmt3a/3b-DKO-2

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
6.5_D3ab_em2


title: Lung dpi3 [Lu7]

description:
Lu7
lung_count.csv


title: Mandibular dpi1 [Ma5]

description:
Ma5
mandibular_count.csv


title: RNA-Em-E6.5-Dnmt3a/3b-DKO-1

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
6.5_D3ab_em1


title: Lung dpi1 [Lu6]

description:
Lu6
lung_count.csv


title: SLAM_seq_INTS11FKBP_48h_rep1


title: ACH0074 genomic DNA

description: ACH0074 genomic DNA


title: RNA-Em--E6.5-Dnmt1-KO-4

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
6.5_DX1_em4


title: SLAM_seq_INTS11FKBP_2h_rep3


title: Lung dpi1 [Lu5]

description:
Lu5
lung_count.csv


title: ACH0082 genomic DNA

description: ACH0082 genomic DNA


title: ACH0071 genomic DNA

description: ACH0071 genomic DNA


title: Lung dpi1 [Lu4]

description:
Lu4
lung_count.csv


title: Lung dpi0 [Lu3]

description:
Lu3
lung_count.csv


title: SLAM_seq_INTS11FKBP_2h_rep2


title: ACH0070 genomic DNA

description: ACH0070 genomic DNA


title: SLAM_seq_INTS11FKBP_24h_rep3


title: RNA-Em--E6.5-Dnmt1-KO-3

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
6.5_DX1_em3


title: RNA-Em--E6.5-Dnmt1-KO-2

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
6.5_DX1_em2


title: RNA-Em--E6.5-Dnmt1-KO-1

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
6.5_DX1_em1


title: Lung dpi0 [Lu2]

description:
Lu2
lung_count.csv


title: SLAM_seq_INTS11FKBP_24h_rep2


title: SLAM_seq_INTS11FKBP_24h_rep1


title: RNA-Em-E6.5-control-4

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
6.5_ey_em4


title: RNA-Em-E6.5-control-3

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
6.5_ey_em3


title: ACH0066 genomic DNA

description: ACH0066 genomic DNA


title: ACH0069 genomic DNA

description: ACH0069 genomic DNA


title: ACH0068 genomic DNA

description: ACH0068 genomic DNA


title: Lung dpi0 [Lu1]

description:
Lu1
lung_count.csv


title: ACH0065 genomic DNA

description: ACH0065 genomic DNA


title: Inguinal dpi3 [In8]

description:
In8
lnguinal_count.csv

source_name: Inguinal

value: Inguinal


title: RNA-Em-E6.5-control-2

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
6.5_ey_em2


title: RNA-Em-E6.5-control-1

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
6.5_ey_em1


title: SLAM_seq_INTS11FKBP_1h_rep2


title: Inguinal dpi3 [In7]

description:
In7
lnguinal_count.csv


title: ACH0064 genomic DNA

description: ACH0064 genomic DNA

value: Male


title: ACH0072 genomic DNA

description: ACH0072 genomic DNA


title: SLAM_seq_INTS11FKBP_1h_rep1


title: RNA-Ex-E6.5-Dnmt1/3a/3b-TKO-4

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
6.5_DTKO_ex4

value: C57BL/6(male) X F1(female)


title: ACH0063 genomic DNA

description: ACH0063 genomic DNA


title: Inguinal dpi1 [In6]

description:
In6
lnguinal_count.csv


title: SLAM_seq_INTS11FKBP_2h_rep1


title: SLAM_seq_INTS11FKBP_0p5h_rep3


title: ACH0062 genomic DNA

description: ACH0062 genomic DNA


title: SLAM_seq_INTS11FKBP_0p5h_rep2


title: ACH0060 genomic DNA

description: ACH0060 genomic DNA


title: ACH0061 genomic DNA

description: ACH0061 genomic DNA


title: Inguinal dpi3 [In9]

description:
In9
lnguinal_count.csv


title: RNA-Ex-E6.5-Dnmt1/3a/3b-TKO-2

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
6.5_DTKO_ex2


title: RNA-Ex-E6.5-Dnmt1/3a/3b-TKO-1

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
6.5_DTKO_ex1


title: Inguinal dpi0 [In3]

description:
In3
lnguinal_count.csv


title: Inguinal dpi1 [In4]

description:
In4
lnguinal_count.csv


title: Inguinal dpi0 [In2]

description:
In2
lnguinal_count.csv


title: SLAM_seq_INTS11FKBP_1h_rep3


title: SLAM_seq_INTS11FKBP_0h_rep2


title: ACH0059 genomic DNA

description: ACH0059 genomic DNA


title: SLAM_seq_INTS11FKBP_0p5h_rep1


title: ACH0058 genomic DNA

description: ACH0058 genomic DNA


title: RNA-Ex-E6.5-Dnmt3a/3b-DKO-3

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
6.5_D3ab_ex3


title: ACH0057 genomic DNA

description: ACH0057 genomic DNA


title: RNA-Ex-E6.5-Dnmt3a/3b-DKO-1

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
6.5_D3ab_ex1


title: ACH0056 genomic DNA

description: ACH0056 genomic DNA


title: RNA-Ex-E6.5-Dnmt3a/3b-DKO-2

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
6.5_D3ab_ex2


title: Liver dpi3 [Li8]

description:
Li8
liver_count.csv

source_name: Liver

value: Liver


title: SLAM_seq_INTS11FKBP_0h_rep1


title: Pol2_INTS11FKBP_2h

data_processing:
Illumina bcl2fastq2 Conversion Software v2.20 used for basecalling.
FASTQ reads were mapped to the GRCm38 (mm10) genome using Bowtie2 (v2.4.1) using the standard settings.
DeepTools (v3.3.0) was used to generate occupancy heat maps, and the resulting normalized occupancy matrix was used as input for custom R scripts to generate average profile plots and to calculate processivity indices.
Assembly: mm10
Supplementary files format and content: All other processed data is made available as supplementary files to the manuscript

extract_protocol:
ES cells were cross-linked by the addition of 1% formaldehyde (Sigma-Aldrich, 252549-1L) in the dish for 10 minutes at RT before quenching with 0.125 M glycine. The fixed cells were washed with PBS and resuspended in SDS buffer (100 mM NaCl, 50 mM Tris-HCl pH 8.0, 5 mM EDTA, 0.5% SDS, 1x protease inhibitor cocktail from Roche). The resulting nuclei were spin down, resuspended in the immunoprecipitation buffer at 1 mL per 16 million cells (SDS buffer and Triton Dilution buffer (100 mM NaCl, 100 mM Tris-HCl pH 8.0, 5 mM EDTA, 5% Triton X-100) mixed in 2:1 ratio with the addition of 1x protease inhibitor cocktail from Roche) and processed on a Bioruptor Plus Sonicator (Diagenode) to achieve an average fragment length of 200-300 bps.
Libraries were constructed using NEBNext Ultra II DNA Library prep kit (NEB, E7645L).

treatment_protocol: dTAG-13 was added at the indicated time point.

value: INTS11 dTAG degron

tag: time

tag: antibody

value: total Pol2


title: Inguinal dpi0 [In1]

description:
In1
lnguinal_count.csv

tag: tissue


title: RNA-Ex--E6.5-Dnmt1-KO-4

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
6.5_DX1_ex4


title: Pol2_INTS11FKBP_0h


title: RNA-Ex-E6.5-Dnmt1/3a/3b-TKO-3

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
6.5_DTKO_ex3


title: Inguinal dpi1 [In5]

description:
In5
lnguinal_count.csv


title: ACH0055 genomic DNA

description: ACH0055 genomic DNA

tag: Sex

value: Female

value: whole blood


title: RNA-Ex-E6.5-Dnmt3a/3b-DKO-4

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
6.5_D3ab_ex4


title: ACH0054 genomic DNA

description: ACH0054 genomic DNA


title: HA_INTS11_INTS11FKBP_2h

tag: cell type

value: HA (INST11)


title: RNA-Ex--E6.5-Dnmt1-KO-3

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
6.5_DX1_ex3


title: RNA-Ex--E6.5-Dnmt1-KO-2

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
6.5_DX1_ex2


title: Liver dpi1 [Li6]

description:
Li6
liver_count.csv


title: Liver dpi1 [Li5]

description:
Li5
liver_count.csv


title: HA_INTS11_INTS11FKBP_0h


title: RNA-Ex--E6.5-Dnmt1-KO-1

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
6.5_DX1_ex1


title: ACH0053 genomic DNA

description: ACH0053 genomic DNA


title: ACH0049 genomic DNA

description: ACH0049 genomic DNA


title: RNA-Ex-E6.5-control-4

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
6.5_ey_ex4

value: wild type


title: SLAM_seq_INTS11FKBP_0h_rep3


title: RNA-Ex-E6.5-control-3

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
6.5_ey_ex3


title: Liver dpi0 [Li2]

description:
Li2
liver_count.csv


title: COM-edm2 seedling

city: nanjing

first: la

middle: yu

last: mei

address: xuanwu

institute: njau

data_processing:
Bismark version v0.22.1.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Mapped to TAIR10 whole genome using bowtie2 version 2.3.5.
Deduplicated reads by bismark.
methylation extracting by bismark.
Assembly: TAIR10
Supplementary files format and content: Matrix table with wig file for every sample

organism: Arabidopsis thaliana

source_name: the whole plant

growth_protocol: soil,16 hour light, 8 hour dark cycle

extract_protocol:
14-day-old seedling of COM-edm2 plants were grown in soil
DNA libraries were prepared for sequencing using standard Illumina protocols

value: seedling

tag: line

value: Col-LUC

value: 14-day-old seedling


title: ACH0047 genomic DNA

description: ACH0047 genomic DNA


title: ACH0045 genomic DNA

description: ACH0045 genomic DNA


title: RNA-Ex-E7.5-control-3

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
7.5_ey_ex3

value: extraembryonic ectoderm


title: Liver dpi0 [Li1]

description:
Li1
liver_count.csv


title: Liver dpi3 [Li9]

description:
Li9
liver_count.csv


title: Sham5

city: hangzhou

first: kaicheng

last: deng

state: zhejiang

address: sandun

institute: zhejiang university

data_processing:
Fastp (version 0.19.7) was used to perform basic statistics on the quality of the raw reads.
Trimmed sequence reads were mapped to rn6 using Hisat2 (Default parameters).
Read count extraction and normalization were performed using featureCounts.
Assembly: rn6
Supplementary files format and content: gene_count_raw.csv: Comma-separated text file includes raw counts for each Sample.

organism: Rattus norvegicus

source_name: Left ventricle

extract_protocol:
The fresh heart MI regions were harvested from rat 1 d post-MI and patch implantation. Total RNA was extracted from heart tissues by Trizol.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: Left ventricle

value: Sham


title: Sham2


title: Sham3


title: Sham1


title: ACH0044 genomic DNA

description: ACH0044 genomic DNA


title: Liver dpi3 [Li7]

description:
Li7
liver_count.csv


title: Kidney dpi3 [K9]

description:
K9
kidney_count.csv

source_name: Kidney

value: Kidney


title: ACH0043 genomic DNA

description: ACH0043 genomic DNA


title: Kidney dpi3 [K8]

description:
K8
kidney_count.csv


title: iCarP+/Light+4

value: iCarP+/Light+


title: WGBS-Em-E7.5-Dnmt1/3a/3b-TKO-3

value: epiblast


title: RNA-Ex-E6.5-control-1

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
6.5_ey_ex1

value: C57BL/6(male) X F1(female)


title: Kidney dpi3 [K7]

description:
K7
kidney_count.csv


title: WGBS-Em-E7.5-Dnmt1/3a/3b-TKO-2


title: iCarP+/Light+2


title: WGBS-Em-E7.5-Dnmt1/3a/3b-TKO-1


title: Liver dpi1 [Li4]

description:
Li4
liver_count.csv

value: Liver


title: Kidney dpi1 [K6]

description:
K6
kidney_count.csv


title: ACH0041 genomic DNA

description: ACH0041 genomic DNA


title: ACH0042 genomic DNA

description: ACH0042 genomic DNA

value: Male


title: ACH0051 genomic DNA

description: ACH0051 genomic DNA


title: Liver dpi0 [Li3]

description:
Li3
liver_count.csv


title: iCarP+/Light+1


title: MI5

value: MI


title: ACH0040 genomic DNA

description: ACH0040 genomic DNA

value: Female


title: Kidney dpi1 [K5]

description:
K5
kidney_count.csv


title: WGBS-Em-E7.5-Dnmt3a/3b-DKO-3


title: ACH0039 genomic DNA

description: ACH0039 genomic DNA

value: whole blood


title: WGBS-Em-E7.5-Dnmt3a/3b-DKO-2


title: MI4


title: RNA-Ex-E6.5-control-2

description:
RNA_counts_filtered_matrix.csv and RNA_TPM_filtered_matrix.csv (the files only contains expression values for those samples that passed our quality control procedure and were used for analysis in our work)
6.5_ey_ex2


title: Kidney dpi1 [K4]

description:
K4
kidney_count.csv


title: WGBS-Em-E7.5-Dnmt3a/3b-DKO-1


title: Kidney dpi0 [K3]

description:
K3
kidney_count.csv


title: ACH0037 genomic DNA

description: ACH0037 genomic DNA


title: MI3


title: WGBS-Em--E7.5-Dnmt1-KO-3


title: MI1


title: Kidney dpi0 [K2]

description:
K2
kidney_count.csv


title: WGBS-Em--E7.5-Dnmt1-KO-2


title: iCarP+/Light+5


title: Kidney dpi0 [K1]

description:
K1
kidney_count.csv


title: ACH0033 genomic DNA

description: ACH0033 genomic DNA


title: WGBS-Em--E7.5-Dnmt1-KO-1


title: ACH0034 genomic DNA

description: ACH0034 genomic DNA


title: Heart dpi3 [H9]

description:
H9
heart_count.csv

source_name: Heart

value: Heart


title: ACH0032 genomic DNA

description: ACH0032 genomic DNA


title: WGBS-Em-E7.5-control-3

value: wild type


title: Brain, BDL_AAV_VEGFC2

city: New Haven

first: Chihao

last: Zhang

state: CT

address: 300 Cedar Street

department: Internal Medicine

institute: Yale University

data_processing:
Raw fastq files were assessed for quality before and after trimming adaptors using the FastQC software.  Using Trimmomatic 0.36, reads with a minimum length of 50 bp and a Phred quality score >30 were finally retained
Indexes were constructed for a genome file and the reads were aligned to the reference genome using HISAT2
The number of the fragments mapped to each gene was calculated using the featureCounts command
Genome_build: RGSC 6.0/rn6
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample

source_name: Brain

extract_protocol:
Brains were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 200 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The AAVs were prepared in phosphate-buffered saline (PBS) with a concentration of 1.5 x 1011 GC/rat in a total volume of 20 μl. A 30-gauge needle connected with a PE10 tube filled with AAV solution was inserted 3 mm deep into the cisterna magna.  A 20 μl of solution was injected into the cisterna magna at a rate of 1.6 μl/min (1.5 x 1011 GC/rat in both groups) by a 50 μl syringe (Hamilton Company, Reno, NV) using a syringe pump (Harvard Apparatus, Holliston, MA)

value: Sprague-Dawley

tag: age

value: post natal day 60

tag: protocol

value: bile duct ligation (BDL)

tag: bdl modeling time

value: 4 weeks

value: AAV-VEGFC

value: brain


title: Heart dpi3 [H8]

description:
H8
heart_count.csv


title: Brain, BDL_AAV_VEGFC1

tag: strain

tag: treatment


title: WGBS-Em-E7.5-control-2

tag: genotype


title: ACH0031 genomic DNA

description: ACH0031 genomic DNA

data_processing:
ChAMP
Matrix_processed: Average Beta (normalized using ChAMP)

extract_protocol: Nucleated DNA from whole blood was collected after sucrose-induced osmotic lysis of cells followed by phenol-chloroform extraction and DNA was stored in Tris-EDTA buffer at -20°C.


title: Brain, BDL_AAV_GFP3

value: AAV-GFP


title: WGBS-Em-E7.5-control-1


title: ACH0030 genomic DNA

description: ACH0030 genomic DNA


title: Brain, BDL_AAV_GFP2


title: Brain, BDL_AAV_VEGFC3


title: ACH0029 genomic DNA

description: ACH0029 genomic DNA


title: Heart dpi1 [H6]

description:
H6
heart_count.csv


title: Heart dpi1 [H4]

description:
H4
heart_count.csv


title: ACH0028 genomic DNA

description: ACH0028 genomic DNA


title: Heart dpi1 [H5]

description:
H5
heart_count.csv


title: Brain, BDL_AAV_GFP1


title: WGBS-Ex-E7.5-Dnmt1/3a/3b-TKO-2

value: extraembryonic ectoderm


title: ACH0036 genomic DNA

description: ACH0036 genomic DNA


title: ACH0027 genomic DNA

description: ACH0027 genomic DNA


title: Heart dpi0 [H3]

description:
H3
heart_count.csv


title: Brain, BDL2


title: ACH0026 genomic DNA

description: ACH0026 genomic DNA


title: Heart dpi0 [H2]

description:
H2
heart_count.csv


title: WGBS-Ex-E7.5-Dnmt3a/3b-DKO-3


title: WGBS-Ex-E7.5-Dnmt3a/3b-DKO-2


title: Heart dpi0 [H1]

description:
H1
heart_count.csv


title: ACH0025 genomic DNA

description: ACH0025 genomic DNA


title: Brain, Sham3

value: sham


title: WGBS-Ex-E7.5-Dnmt3a/3b-DKO-1

value: C57BL/6(male) X F1(female)


title: Brain, BDL1


title: WGBS-Ex-E7.5-Dnmt1/3a/3b-TKO-1


title: Heart dpi3 [H7]

description:
H7
heart_count.csv


title: Brain, Sham2


title: WGBS-Ex--E7.5-Dnmt1-KO-3


title: ChIPseq_input_Day8minus_rep1

city: Maebashi

first: Tetsuro

last: Komatsu

address: 3-39-15 Showa-machi

country: Japan

institute: Gunma University

description: 1percent-input-AD8-minus_S9.uniq.rmdup.merge.extend500.bw

data_processing:
Reads were aligned to the mm9 mouse genome using Bowtie 2 (version 2.2.9).
Mapped reads having <40 MAPQ were omitted (samtools view -bhS -F 0x4 -q 40 | samtools sort), and duplication removal was then carried out using the markdup -r function of samtools (version 1.11).
ChIP-seq signals around TSSs (-/+5 kb) were calculated using featureCounts (version v1.5.0-p2).
For visualization on IGV (Integrative Genomics Viewer, version 2.8.7), aligned reads (BAM files) for each replicate were merged with samtools (version 1.9) and then converted to bigWig files using the bamCoverage function of deepTools (normalized as CPM (Counts Per Million), version 3.5.0) with the following option in the bamCoverage function: -e 500.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: bigWig

source_name: 3T3-L1 preadipocyte cell line

growth_protocol: Cells were maintained in DMEM-HG (high glucose), 10% CS until reaching confluent. 2 days before differentiation induction, the medium was replaced with fresh DMEM-HG, 10% CS. On day of differentiation induction (Day 0), the medium was replaced with DMEM-HG, 10% FBS supplemented with 1.67 uM insulin, 1 uM dexamethasone, and 115 ug/mL of IBMX. On Day 2, the medium was replaced with DMEM-HG, 10% FBS supplemented with 1.67 uM insulin. On Days 4 and 6, the medium was replaced with DMEM-HG, 10% FBS.

extract_protocol:
Lysates were prepared from cells fixed with 0.5% formaldehyde and subjected to sonication to release protein-DNA complexes with 200-300 bp in length. Histone-DNA complexes were obtained by immunoprecipitation with specific histone methylation antibodies. After proteinase K treatment and reverse-crosslinking, DNA fragments were purified using QIAquick PCR Purification Kit (QIAGEN).
Library preparation was carried out using ThruPLEX DNA-Seq Kit (TAKARA BIO) according to the manufacturer's protocol.

treatment_protocol: In the first 2 days of differentiation, cells were cultured in the absence or presence of 100 uM deferoxamine.

tag: cell line

value: preadipocyte cell line

value: untreated

value: Day 8

tag: chip antibody

tag: replicate

value: replicate 1


title: Brain, Sham1


title: WGBS-Ex--E7.5-Dnmt1-KO-2

tag: developmental stage


title: WGBS-Ex-E7.5-Dnmt1/3a/3b-TKO-3


title: ACH0022 genomic DNA

description: ACH0022 genomic DNA

value: Female

value: whole blood


title: ChIPseq_input_Day2plus_rep1

description: 1percent-input-AD2-plus_S11.uniq.rmdup.merge.extend500.bw

value: DFO-treated

tag: time point

value: Day 2


title: WGBS-Ex--E7.5-Dnmt1-KO-1


title: Kc cell, sxl, rep3

city: Shanghai

first: Zhan

last: Ding

address: 300 Feng Lin Road

institute: CAS Center for Excellence in Molecular Plant Sciences

library_source: other

data_processing:
After the adapter sequences were removed from raw reads by cutadapt (version 1.15) for the R- and R+ samples, the pair-end reads were then merged using PEAR (version 0.9.5), and the merged reads were discard if <30nt.
The remaining merged reads and reads from the PolyA samples were mapped to the Drosophila genome (dm6) using STAR (version 2.6.1a), where the parameter "-chim_segment_min" was set to 10, and genes were annotated by a 6.88 version of the Ensembl database.
Transcripts were assembled by cufflinks, and the CIRCexplorer2 (19) was used for new transcript structure information to identify back-spliced junction (BSJ) from the fusion junction reads that were calculated by STAR. The abundance of each gene was calculated by stringtie(v2.0).
For PAR-CLIP sequenceing analysis, raw reads were filtered by CTK_v1.1.3, and their adaptor sequences were removed by cutadapt_v1.18 and extracted by umi_tools. Clean reads were then mapped to Drosophila genome dm6 by STAR and annotated by Ensembl v6.88, in which highly duplicated reads caused by PCR were removed by umi_tools. OmniCLIP was then applied for identification of the SXL-binding peaks, and CTK_v1.1.3 was used for searching T>C CIMS.
Assembly: dm6
Supplementary files format and content: tab-delimited text files include TPM values for mRNA samples, whole genome coverage files (bigWig) for other samples.

molecule: other

organism: Drosophila melanogaster

source_name: Kc cell

extract_protocol:
Total RNA samples were isolated by TRIzol (Sigma) and treated with DNase I (Takara), in which mRNAs (referred as ‘PolyA’ samples) were isolated using Dynabeads® mRNA Purification Kit (Ambion), and the rest of RNAs were recovered for further depletion of rRNA (referred as ‘R-’ samples). In order to deplete completely the rRNA, 42 additional probes targeting Drosophila specific rRNA sequences were designed and applied into the probe-pool in RiboMinus kit (Ambion) (Table Sx). To obtain enriched circular RNAs (referred as ‘R+’ samples), 2.5 ug of each R- sample was digested by 50 U of RNase R (Epicentre) at 37°C for 1 hour, followed by TRIzol purification and ethanol precipitation.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Kc cell

value: embryo cell

tag: rip antibody

value: Sxl


title: ACH0021 genomic DNA

description: ACH0021 genomic DNA


title: Brain, BDL3

value: Sprague-Dawley

value: post natal day 60

value: bile duct ligation (BDL)

value: 4 weeks


title: ChIPseq_input_Day2minus_rep1

description: 1percent-input-AD2-minus_S10.uniq.rmdup.merge.extend500.bw


title: ACH0020 genomic DNA

description: ACH0020 genomic DNA

value: Male


title: WGBS-Ex-E7.5-control-2

source_name: embryo

value: wild type

value: C57BL/6(male) X F1(female)

value: extraembryonic ectoderm


title: Kc cell, sxl, rep2


title: WGBS-Ex-E7.5-control-3


title: Kc cell, sxl, rep1


title: ACH0017 genomic DNA

description: ACH0017 genomic DNA


title: ChIPseq_input_Day0_rep1

description: 1percent-input-AD0_S9.uniq.rmdup.merge.extend500.bw

value: preadipocyte cell line

value: untreated

value: Day 0


title: ChIPseq_H3K27me3_Day8plus_rep2

description: H3K27me3-AD8-plus_S6.uniq.rmdup.merge.extend500.bw

value: Day 8

value: replicate 2


title: ChIPseq_input_Day8plus_rep1

description: 1percent-input-AD8-plus_S10.uniq.rmdup.merge.extend500.bw

value: DFO-treated

value: replicate 1


title: ChIPseq_H3K27me3_Day8minus_rep2

description: H3K27me3-AD8-minus_S5.uniq.rmdup.merge.extend500.bw


title: Kc cell, IgG, rep3

value: Kc cell

value: embryo cell

value: IgG


title: ACH0016 genomic DNA

description: ACH0016 genomic DNA

value: Female

value: whole blood


title: Kc cell, IgG, rep2


title: WGBS-Ex-E7.5-control-1


title: ACH0024 genomic DNA

description: ACH0024 genomic DNA


title: ChIPseq_H3K27me3_Day2minus_rep2

description: H3K27me3D2minus_uniq.rmdup.merge.extend500.bw

value: Day 2


title: ACH0015 genomic DNA

description: ACH0015 genomic DNA

value: Male


title: ACH0023 genomic DNA

description: ACH0023 genomic DNA


title: Kc cell, IgG, rep1


title: WGBS-Em-E6.5-Dnmt1/3a/3b-TKO-2

value: epiblast


title: WGBS-Em-E6.5-Dnmt1/3a/3b-TKO-3

value: C57BL/6(male) X F1(female)


title: Kc cell, sxl, rep4

value: Sxl


title: ACH0014 genomic DNA

description: ACH0014 genomic DNA


title: ChIPseq_H3K27me3_Day8plus_rep1

value: preadipocyte cell line


title: ChIPseq_H3K27me3_Day0_rep2

description: H3K27me3D0_uniq.rmdup.merge.extend500.bw

value: untreated


title: WGBS-Em-E6.5-Dnmt1/3a/3b-TKO-1


title: WGBS-Em-E6.5-Dnmt3a/3b-DKO-3


title: WGBS-Em-E6.5-Dnmt3a/3b-DKO-2


title: testis of male fly, polyA+, rep1

molecule: polyA RNA

source_name: testis

value: testis

value: Canton-S

value: male


title: testis of male fly, polyA+, rep2


title: ACH0013 genomic DNA

description: ACH0013 genomic DNA


title: head of male fly, polyA+, rep2

source_name: head

value: head


title: ChIPseq_H3K27me3_Day8minus_rep1

value: Day 8

value: replicate 1


title: ACH0011 genomic DNA

description: ACH0011 genomic DNA


title: WGBS-Em-E6.5-Dnmt3a/3b-DKO-1


title: ChIPseq_H3K27me3_Day2minus_rep1


title: ACH0010 genomic DNA

description: ACH0010 genomic DNA


title: ChIPseq_H3K27me3_Day2plus_rep1

description: H3K27me3D2plus_uniq.rmdup.merge.extend500.bw

value: DFO-treated


title: ChIPseq_H3K27me3_Day2plus_rep2

value: replicate 2


title: WGBS-Em--E6.5-Dnmt1-KO-3


title: ACH0007 genomic DNA

description: ACH0007 genomic DNA

value: Female


title: head of male fly, polyA+, rep1


title: ACH0018 genomic DNA

description: ACH0018 genomic DNA

value: whole blood


title: ACH0008 genomic DNA

description: ACH0008 genomic DNA


title: WGBS-Em--E6.5-Dnmt1-KO-2


title: ACH0006 genomic DNA

description: ACH0006 genomic DNA


title: ovary of female fly, polyA+, rep2

source_name: ovary

value: ovary

value: female


title: ChIPseq_H3K27me3_Day0_rep1

value: Day 0


title: body of male fly, polyA+, rep1

source_name: body

value: body


title: ACH0004 genomic DNA

description: ACH0004 genomic DNA


title: ovary of female fly, polyA+, rep1


title: ChIPseq_H3K9me3_Day8minus_rep2

description: H3K9me3-A-D8-minus_S5.uniq.rmdup.merge.extend500.bw


title: ChIPseq_H3K9me3_Day8plus_rep2

description: H3K9me3-A-D8-plus_S6.uniq.rmdup.merge.extend500.bw


title: WGBS-Em-E6.5-control-3

value: wild type

value: C57BL/6(male) X F1(female)

value: epiblast


title: head of female fly, polyA+, rep2


title: WGBS-Em-E6.5-control-2


title: ACH0002 genomic DNA

description: ACH0002 genomic DNA


title: WGBS-Em-E6.5-control-1


title: ChIPseq_H3K9me3_Day2minus_rep2

description: H3K9me3-A-D2minus_S8.uniq.rmdup.merge.extend500.bw

value: preadipocyte cell line

value: untreated

value: Day 2


title: head of female fly, polyA+, rep1

value: head

value: Canton-S


title: ACH0003 genomic DNA

description: ACH0003 genomic DNA


title: ChIPseq_H3K9me3_Day0_rep2

description: H3K9me3-A-D0_S7.uniq.rmdup.merge.extend500.bw


title: WGBS-Ex-E6.5-Dnmt1/3a/3b-TKO-3

value: extraembryonic ectoderm


title: body of female fly, polyA+, rep2


title: pycr-1(wrm22) replicate 4 Poly RNA

city: Koln

first: Jorge

last: Boucas

address: Joseph-Stelzmann-Str. 9b

department: Bioinformatics

country: Germany

institute: Max Planck Institute for Biology of Ageing

description:
geneexp_ALL.tsv
diff_sig_geneexp.xlsx

data_processing:
Quality check: FastQC 0.11.7
Alignment: Hisat version 2.1.0
Guided assembly: StringTie 1.3.4d; -p 18 -G ORIGINAL_GTF -f 0.99
Merging assemblies: Cuffmerge 2.2.1; --min-isoform-fraction 1.0
Quantification: Cuffquant 2.2.1
Differential analysis: Cuffdiff 2.2.1; --dispersion-method per-condition
Supplementary_files_format_and_content: tab-separated values or excel table of gene expression
Genome_build: WBcel235_RELEASE_96

organism: Caenorhabditis elegans

source_name: Polysomal fraction of total worm lysis

growth_protocol: Synchronized worms were grown on regular NGM plates seeded with OP50 until day 1 of adulthood at 20 degree Celsius and then collected.

extract_protocol:
Synchronized gravid day 1 adults were grown on NGM plated seeded with OP50. Per genotype and replicate, ~12000 worms were harvested and washed twice with M9, once with M9 supplemented with 1 mM cycloheximide (Sigma) and once with lysis buffer (20 mM Tris pH 8.5, 140 mM KCl, 1.5 mM MgCl2, 0.5 % Nonidet P40, 1 mM DTT, 1 mM cycloheximide). Worms were pelleted and resuspended in 350 µL cold lysis buffer supplemented with 1% sodiumdeoxycholate (DOC, Sigma). Resuspended worms were lysed using a chilled Dounce homogenizer. Ribonuclease inhibitor RNasin (Promega) was added to samples at a concentration of 0,4 U/µL. Samples were then mixed and incubated on ice for 30 min, followed by a centrifugation step (12000 g, 10 minutes, 4°C) for clearance. The pellet was discarded and the RNA concentration of the supernatant was estimated by absorbance measurement at 260 nm.  To prepare sucrose gradients, 15% (w/v) and 60% (w/v) sucrose solutions were prepared in basic lysis buffer (20mM Tris pH 8.5, 140 mM KCl, 1.5 mM MgCl2, 1mM DTT, 1mM cycloheximide). Linear sucrose gradients were produced using a Gradient Master (Biocomp). Equivalent amounts of sample (around 400 µg RNA) were loaded on the gradient and centrifuged at 39000 g for 3 h at 4°C, using an Optima L-100 XP Ultracentrifuge (Beckman Coulter) and the SW41Ti rotor. To analyze the sample on the gradient during fractionation, absorbance at 254 nm was measured and recorded (Econo UV monitor EM-1, Biorad) using the Gradient Profiler software (version 2.07). Gradient fractionation was performed from the top down using a Piston Gradient Fractionator (Biocomp) and a fraction collector (Model 2110, Biorad). For precise analysis of ribosomal fractions, they were collected by hand according to their absorbance profile; for RNAseq fractions containing 3 ribosomes per mRNA or more were collected per sample. RNA extraction from total lysates and from each fraction was performed using the Direct-zol RNA MicroPrep Kit (Zymo Research) according to the manufacturer´s recommendations.
RNA libraries were prepared for sequencing using standard Illumina protocols with a ribosomal RNA depletion method by Cologne Center for Genomics.

value: Day 1 adults


title: WGBS-Ex-E6.5-Dnmt1/3a/3b-TKO-2


title: body of female fly, polyA+, rep1


title: WGBS-Ex-E6.5-Dnmt1/3a/3b-TKO-1


title: pycr-1(wrm22) replicate 3 Poly RNA

description:
geneexp_ALL.tsv
diff_sig_geneexp.xlsx


title: ChIPseq_H3K9me3_Day8plus_rep1

value: DFO-treated

value: Day 8

value: replicate 1


title: testis of male fly, ribo-&polyA-, rep2

value: testis

value: male


title: pycr-1(wrm22) replicate 2 Poly RNA

description:
geneexp_ALL.tsv
diff_sig_geneexp.xlsx


title: body of male fly, polyA+, rep2


title: ChIPseq_H3K9me3_Day8minus_rep1


title: ChIPseq_H3K9me3_Day2plus_rep1

description: H3K9me3-A-D2plus_S9.uniq.rmdup.merge.extend500.bw


title: pycr-1(wrm22) replicate 1 Poly RNA

description:
geneexp_ALL.tsv
diff_sig_geneexp.xlsx


title: testis of male fly, ribo-&polyA-, rep1


title: WGBS-Em--E6.5-Dnmt1-KO-1


title: WGBS-Ex-E6.5-Dnmt3a/3b-DKO-3


title: ChIPseq_H3K9me3_Day2minus_rep1


title: WGBS-Ex-E6.5-Dnmt3a/3b-DKO-2


title: pycr-1(wrm22) replicate 4 Total RNA

description:
geneexp_ALL.tsv
diff_sig_geneexp.xlsx

source_name: Total worm lysis


title: WGBS-Ex-E6.5-Dnmt3a/3b-DKO-1


title: head of male fly, ribo-&polyA-, rep1


title: pycr-1(wrm22) replicate 3 Total RNA

description:
geneexp_ALL.tsv
diff_sig_geneexp.xlsx


title: ChIPseq_H3K9me3_Day0_rep1

value: Day 0


title: WGBS-Ex--E6.5-Dnmt1-KO-3


title: ChIPseq_H3K9me3_Day2plus_rep2

value: replicate 2


title: pycr-1(wrm22) replicate 2 Total RNA

description:
geneexp_ALL.tsv
diff_sig_geneexp.xlsx


title: ChIPseq_H3K9me2_Day8plus_rep2

description: H3K9me2-AD8-plus_S2.uniq.rmdup.merge.extend500.bw


title: body of male fly, ribo-&polyA-, rep2

value: body


title: WGBS-Ex--E6.5-Dnmt1-KO-2

value: C57BL/6(male) X F1(female)


title: body of male fly, ribo-&polyA-, rep1


title: ChIPseq_H3K9me2_Day8minus_rep2

description: H3K9me2-AD8-minus_S1.uniq.rmdup.merge.extend500.bw


title: pycr-1(wrm22) replicate 1 Total RNA

description:
geneexp_ALL.tsv
diff_sig_geneexp.xlsx


title: Wildtype replicate 3 Poly RNA

description:
geneexp_ALL.tsv
diff_sig_geneexp.xlsx

value: Wild type (Bristol N2)


title: WGBS-Ex--E6.5-Dnmt1-KO-1


title: ovary of female fly, ribo-&polyA-, rep2

value: ovary

value: female


title: ChIPseq_H3K9me2_Day2plus_rep2

description: H3K9me2-D2plus_uniq.rmdup.merge.extend500.bw

value: preadipocyte cell line

value: Day 2


title: Wildtype replicate 2 Poly RNA

description:
geneexp_ALL.tsv
diff_sig_geneexp.xlsx


title: WGBS-Ex-E6.5-control-3

value: wild type


title: ChIPseq_H3K9me2_Day2minus_rep2

description: H3K9me2-D2minus_uniq.rmdup.merge.extend500.bw

value: untreated


title: ChIPseq_H3K9me2_Day0_rep2

description: H3K9me2-D0_uniq.rmdup.merge.extend500.bw


title: WGBS-Ex-E6.5-control-2

value: extraembryonic ectoderm


title: Wildtype replicate 1 Poly RNA

description:
geneexp_ALL.tsv
diff_sig_geneexp.xlsx

value: Day 1 adults


title: ovary of female fly, ribo-&polyA-, rep1

value: Canton-S


title: head of female fly, ribo-&polyA-, rep2

value: head


title: WGBS-Ex-E6.5-control-1


title: head of female fly, ribo-&polyA-, rep1


title: Wildtype replicate 2 Total RNA

description:
geneexp_ALL.tsv
diff_sig_geneexp.xlsx


title: Wildtype replicate 3 Total RNA

description:
geneexp_ALL.tsv
diff_sig_geneexp.xlsx


title: ChIPseq_H3K9me2_Day8minus_rep1

value: Day 8

value: replicate 1


title: WGBS-E7.5-Tet1/2; Dnmt3a/3b-4KO-4

value: Tet1/2; Dnmt3a/3b-4KO

value: whole embryo


title: WGBS-E7.5-Tet1/2; Dnmt3a/3b-4KO-3


title: ChIPseq_H3K9me2_Day2plus_rep1

value: DFO-treated


title: head of male fly, ribo-&polyA-, rep2

value: male


title: Wildtype replicate 1 Total RNA

description:
geneexp_ALL.tsv
diff_sig_geneexp.xlsx

value: Wild type (Bristol N2)


title: body of female fly, ribo-&polyA-, rep1

value: body


title: WGBS-E7.5-Tet1/2; Dnmt3a/3b-4KO-2

value: C57BL/6(male) X F1(female)


title: testis of male fly, RNase R treatment

value: testis


title: WGBS-E7.5-Tet1/2; Dnmt3a/3b-4KO-1