title: Esophageal mucosae with high risk2

description:
Cancer patients, with alcohol drinking, betel nuts chewing and cigarette smoking
SAMPLE 29


title: Esophageal mucosae with high risk9

status: Public on Mar 02 2018

type: genomic

city: Chuo-ku

first: Satoshi

last: Yamashita

state: Tokyo

address: Tsukiji 5-1-1

country: Japan

institute: National Cancer Center Research Institute

description:
Cancer patients, with alcohol drinking, betel nuts chewing and cigarette smoking
SAMPLE 36

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

scan_protocol: Arrays were imaged using Illumina iScan according to manufacturer's specifications (Illumina Inc.).

data_processing: Genome Studio software V2011.1 (Methylation module 1.9.0), was used.  Beta values were obtained after background correction and normalization to internal controls.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: biopsy, esophageal mucosa

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA samples were isolated using Phenol-chloroform extraction protocol.  The same amount of genomic DNA samples from 4 (or 8) individuals were pooled.

tag: gender

value: Male

tag: age


title: Esophageal mucosae with high risk6

description:
Cancer patients, with alcohol drinking, betel nuts chewing and cigarette smoking
SAMPLE 33


title: Esophageal mucosae with high risk1

description:
Cancer patients, with alcohol drinking, betel nuts chewing and cigarette smoking
SAMPLE 28


title: Esophageal mucosae with high risk3

description:
Cancer patients, with alcohol drinking, betel nuts chewing and cigarette smoking
SAMPLE 30


title: Esophageal mucosae with low risk5

description:
Non-cancer patients, no alcohol drinking, no betel nuts chewing, no cigarette smoking
SAMPLE 15


title: Esophageal mucosae with intermediate risk5

description:
Non-cancer patients, with alcohol drinking, betel nuts chewing and cigarette smoking
SAMPLE 22


title: genomic DNA from 200123470035_R02C02

city: Los Angeles

first: Ritz

last: Beate

state: California

address: 650 Charles E Young Dr. South

department: Epidemiology

country: USA

institute: UCLA Fielding School of Public Health

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

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

data_processing:
R software v3.4.2
GEOsubmit_PEGsaliva_450kMethylationDataBackgroundNormalized.txt contains normalized (background normalization method) data

label: cy3, cy5

extract_protocol: genomic DNA was extracted from saliva samples using the Qiagen Gentra Puregene Cell Kit according to standard instructions

tag: disease state

value: Parkinson's disease (PD)

value: Female

tag: ethnicity

value: Caucasian

tag: tissue

value: saliva


title: genomic DNA from 200123470035_R01C02

value: PD-free control (Ctrl)


title: Esophageal mucosae with intermediate risk2

description:
Non-cancer patients, with alcohol drinking, betel nuts chewing and cigarette smoking
SAMPLE 19


title: genomic DNA from 200123470035_R03C01


title: Esophageal mucosae with low risk3

description:
Non-cancer patients, no alcohol drinking, no betel nuts chewing, no cigarette smoking
SAMPLE 13


title: Esophageal mucosae with high risk7

description:
Cancer patients, with alcohol drinking, betel nuts chewing and cigarette smoking
SAMPLE 34


title: Esophageal mucosae with low risk7

description:
Non-cancer patients, no alcohol drinking, no betel nuts chewing, no cigarette smoking
SAMPLE 17


title: Esophageal mucosae with intermediate risk1

description:
Non-cancer patients, with alcohol drinking, betel nuts chewing and cigarette smoking
SAMPLE 18


title: Esophageal mucosae with intermediate risk7

description:
Non-cancer patients, with alcohol drinking, betel nuts chewing and cigarette smoking
SAMPLE 24


title: genomic DNA from 200123470008_R05C02

value: Hispanic


title: Esophageal mucosae with intermediate risk8

description:
Non-cancer patients, with alcohol drinking, betel nuts chewing and cigarette smoking
SAMPLE 25


title: genomic DNA from 200123470008_R05C01


title: genomic DNA from 200123470035_R01C01


title: Esophageal mucosae with intermediate risk6

description:
Non-cancer patients, with alcohol drinking, betel nuts chewing and cigarette smoking
SAMPLE 23


title: Esophageal mucosae with low risk2

description:
Non-cancer patients, no alcohol drinking, no betel nuts chewing, no cigarette smoking
SAMPLE 12


title: Esophageal mucosae with low risk1

description:
Non-cancer patients, no alcohol drinking, no betel nuts chewing, no cigarette smoking
SAMPLE 11


title: genomic DNA from 200123470008_R06C02


title: genomic DNA from 200123470035_R02C01


title: Esophageal mucosae with intermediate risk9

description:
Non-cancer patients, with alcohol drinking, betel nuts chewing and cigarette smoking
SAMPLE 26


title: genomic DNA from 200123470008_R06C01


title: Esophageal mucosae with intermediate risk4

description:
Non-cancer patients, with alcohol drinking, betel nuts chewing and cigarette smoking
SAMPLE 21


title: genomic DNA from 200123470008_R04C01


title: genomic DNA from 200123470008_R03C02


title: genomic DNA from 200123470008_R02C02


title: Esophageal mucosae with low risk6

description:
Non-cancer patients, no alcohol drinking, no betel nuts chewing, no cigarette smoking
SAMPLE 16


title: genomic DNA from 200123470008_R04C02


title: genomic DNA from 200123470008_R01C02


title: genomic DNA from 200123470008_R01C01


title: genomic DNA from 200123470008_R03C01


title: Esophageal mucosae with low risk4

description:
Non-cancer patients, no alcohol drinking, no betel nuts chewing, no cigarette smoking
SAMPLE 14


title: genomic DNA from 200123470008_R02C01


title: genomic DNA from 200091640111_R04C01


title: genomic DNA from 200091640111_R04C02


title: genomic DNA from 200091640111_R05C02


title: Esophageal mucosae with intermediate risk3

description:
Non-cancer patients, with alcohol drinking, betel nuts chewing and cigarette smoking
SAMPLE 20


title: genomic DNA from 200091640111_R03C01


title: genomic DNA from 200091640111_R02C02


title: genomic DNA from 200091640111_R03C02


title: genomic DNA from 200091640111_R02C01


title: genomic DNA from 200091640111_R01C02


title: genomic DNA from 200091640111_R05C01


title: genomic DNA from 200091640109_R06C01


title: genomic DNA from 200091640111_R01C01


title: genomic DNA from 200091640109_R03C01


title: genomic DNA from 200091640109_R04C01


title: genomic DNA from 200091640109_R05C02


title: genomic DNA from 200091640109_R04C02


title: genomic DNA from 200091640108_R06C02


title: genomic DNA from 200091640109_R01C02


title: genomic DNA from 200091640109_R01C01


title: genomic DNA from 200091640109_R02C01


title: genomic DNA from 200091640109_R06C02


title: genomic DNA from 200091640108_R06C01


title: genomic DNA from 200091640108_R05C01


title: genomic DNA from 200091640108_R04C02


title: genomic DNA from 200091640108_R03C02


title: genomic DNA from 200091640108_R02C01


title: genomic DNA from 200091640108_R02C02


title: genomic DNA from 200091640108_R03C01


title: genomic DNA from 200091640108_R05C02


title: genomic DNA from 200091640092_R06C01


title: genomic DNA from 200091640108_R01C01


title: genomic DNA from 200091640092_R06C02


title: genomic DNA from 200091640108_R04C01


title: genomic DNA from 200091640109_R03C02


title: genomic DNA from 200091640109_R02C02


title: genomic DNA from 200091640092_R03C01


title: genomic DNA from 200091640109_R05C01


title: genomic DNA from 200091640092_R03C02


title: genomic DNA from 200091640092_R04C02


title: genomic DNA from 200091640092_R05C01


title: genomic DNA from 200091640092_R02C01


title: genomic DNA from 200091640092_R01C02


title: genomic DNA from 200091640088_R05C02


title: genomic DNA from 200091640092_R04C01


title: genomic DNA from 200091640088_R04C02


title: genomic DNA from 200091640088_R06C01


title: genomic DNA from 200091640092_R02C02


title: genomic DNA from 200091640092_R01C01


title: genomic DNA from 200091640092_R05C02


title: genomic DNA from 200091640088_R02C02


title: genomic DNA from 200091640108_R01C02


title: genomic DNA from 200091640088_R05C01


title: genomic DNA from 200091640088_R04C01


title: genomic DNA from 200091640088_R03C01


title: genomic DNA from 200091640088_R01C02


title: genomic DNA from 200091640088_R03C02


title: genomic DNA from 200091640088_R01C01


title: genomic DNA from 200091640067_R05C02


title: genomic DNA from 200091640088_R02C01


title: genomic DNA from 200091640067_R06C02


title: genomic DNA from 200091640067_R06C01


title: genomic DNA from 200091640067_R04C02


title: genomic DNA from 200091640067_R05C01


title: genomic DNA from 200091640067_R04C01


title: genomic DNA from 200091640088_R06C02


title: genomic DNA from 200091640067_R03C02


title: genomic DNA from 200091640067_R03C01


title: genomic DNA from 200091640067_R02C02


title: genomic DNA from 200091640062_R06C02


title: genomic DNA from 200091640062_R06C01


title: genomic DNA from 200091640067_R01C02


title: genomic DNA from 200091640067_R01C01


title: genomic DNA from 200091640062_R04C01


title: genomic DNA from 200091640062_R03C01


title: genomic DNA from 200091640062_R05C02


title: genomic DNA from 200091640062_R04C02


title: genomic DNA from 200091640062_R03C02


title: genomic DNA from 200091640061_R06C02


title: genomic DNA from 200091640061_R06C01


title: Adipocyte guadecitabine 1

type: SRA

city: Bloomington

first: Kenneth

last: Nephew

state: IN

institute: Indiana University

library_source: transcriptomic

data_processing:
NextSeq read sequences were cleaned using Trimmomatic version 0.32 with the paramaters “2:20:5 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:17” to remove adapter sequences and perform quality trimming.
Custom perl scripts along with FASTX-Toolkit version 0.0.13.2 with the following parameters, “-l 17 -v -M 1 -i “ was also used to look for partial adapters within the read.
FASTX-Toolkit was then used to reverse complement the reads.
The resulting reads were mapped against GRCh38.p5 using TopHat2 version 2.1.1 with parameters “--b2-very-sensitive --read-edit-dist 2 --max-multihits 100”. Tophat uses Bowtie, which is based on the Burrows-Wheeler transform algorithm, for sequence alignment and allows for mapping across exon junctions
Read counts for each gene were created using custom perl scripts and Gencode v24 as the annotation
Custom perl scripts were used for estimation of transcript abundances based on Fragments Per Kilobase of exon per Million fragments mapped (FPKM).
Initial differential expression analysis was carried out using the DESeq2 package (version 1.12.4) in R/Bioconductor (R version 3.3.1).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited files include RPKM values for each sample

molecule: total RNA

source_name: Adipocytes (ATCC)

growth_protocol: Normal, human primary subcutaneous pre-adipocytes (ATCC PCS-210-010) were grown in fibroblast basal medium (ATCC PCS-201-030) supplemented with phenol red. Preadipocytes were differentiated following an adipogenic differentiation protocol (Fink T, Zachar V. Adipogenic differentiation of human mesenchymal stem cells. Mesenchymal Stem Cell Assays and Applications: Springer; 2011. p 243-51.). Briefly, preadipocytes were seeded at 18,000 cells/cm2. Initiation of adipogenesis was induced by replacing the fibroblast basal medium with adipogenic induction medium (AIM) for 15 days. Oil Red O staining was performed to confirm adipocyte differentiation.

extract_protocol:
On day 4, RNA was harvested from the adipocytes using the RNAEasy kit (Qiagen)
RNA-seq libraries were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina #RS-122-2101) according to manufacter's protocol.

treatment_protocol: In duplicate, subcutaneous, human, primary adipocytes (ATCC) were treated with DMSO control or guadecitabine (100nM, 3X daily).

tag: passages

value: Subcutaneous, primary

tag: treatment

value: guadecitabine (100nM, 3X daily)


title: Adipocyte DMSO Control 2

value: DMSO


title: genomic DNA from 200091640062_R02C02


title: genomic DNA from 200091640062_R01C01


title: Adipocyte DMSO Control 1


title: Adipocyte guadecitabine 2


title: genomic DNA from 200091640061_R05C02


title: genomic DNA from 200091640061_R04C02


title: genomic DNA from 200091640061_R05C01


title: genomic DNA from 200091640061_R03C02


title: genomic DNA from 200091640061_R03C01


title: genomic DNA from 200091640061_R01C02


title: genomic DNA from 200091640062_R01C02


title: genomic DNA from 200091640061_R04C01


title: genomic DNA from 200049730103_R06C01


title: genomic DNA from 200091640061_R02C02


title: genomic DNA from 200049730103_R04C02


title: genomic DNA from 200091640067_R02C01


title: genomic DNA from 200091640062_R02C01


title: genomic DNA from 200091640061_R01C01


title: genomic DNA from 200049730103_R02C02


title: genomic DNA from 200091640062_R05C01


title: genomic DNA from 200049730103_R03C01


title: genomic DNA from 200091640061_R02C01


title: genomic DNA from 200091640111_R06C02


title: genomic DNA from 200049730077_R06C02


title: genomic DNA from 200049730077_R05C01


title: genomic DNA from 200049730077_R04C02


title: genomic DNA from 200091640111_R06C01


title: genomic DNA from 200049730103_R01C02


title: genomic DNA from 200049730103_R01C01


title: genomic DNA from 200049730103_R03C02


title: genomic DNA from 200049730077_R05C02


title: genomic DNA from 200049730077_R03C01


title: genomic DNA from 200049730077_R03C02


title: genomic DNA from 200049730077_R02C01


title: genomic DNA from 200049730077_R04C01


title: genomic DNA from 200049730077_R01C01


title: genomic DNA from 200049730005_R06C02


title: genomic DNA from 200049730103_R04C01


title: genomic DNA from 200049730103_R06C02


title: genomic DNA from 200049730077_R02C02


title: genomic DNA from 200049730005_R05C01


title: genomic DNA from 200049730077_R01C02


title: genomic DNA from 200049730005_R04C02


title: genomic DNA from 200049730005_R06C01


title: genomic DNA from 200049730005_R03C02


title: genomic DNA from 200049730005_R03C01


title: genomic DNA from 200049730005_R04C01


title: genomic DNA from 200049730005_R05C02


title: genomic DNA from 200049730004_R06C02


title: genomic DNA from 200049730103_R02C01


title: genomic DNA from 200049730004_R05C02


title: genomic DNA from 200049730005_R02C01


title: genomic DNA from 200049730005_R02C02


title: genomic DNA from 200049730004_R04C02


title: genomic DNA from 200049730004_R03C01


title: genomic DNA from 200049730004_R04C01


title: genomic DNA from 200049730004_R03C02


title: genomic DNA from 200049730004_R06C01


title: genomic DNA from 200049730004_R05C01


title: genomic DNA from 200049730004_R02C02


title: genomic DNA from 200049730004_R01C01


title: genomic DNA from 100946230031_R06C02


title: genomic DNA from 200049730004_R02C01


title: genomic DNA from 200049730004_R01C02


title: genomic DNA from 100946230031_R05C01


title: genomic DNA from 100946230031_R05C02


title: genomic DNA from 100946230031_R06C01


title: sperm_WT_naive_1

city: Göttingen

first: Gaurav

last: Jain

state: Lower Saxony

address: Von-Siebold-Str. 3a, Office no: 2.212

country: Germany

institute: The German Center for Neurodegenerative Diseases (German: Deutsches Zentrum für Neurodegenerative Erkrankungen DZNE)

description: Small RNA

data_processing:
Base calling and fastq conversion were performed using Illumina pipeline scripts.
We trimmed the 3' adapters and filtered out the reads with the minimum length of 15 nucleotides using cutadapt 1.8.1 with Python 2.7.6.
Read alignment done using bowtie (v.1.1.2).
Read count distribution and visualization was generated using in-house python script with python version 2.7.10.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_mirnaCounts.txt: htseq_counts

organism: Mus musculus

source_name: sperm

extract_protocol:
RNA was isolated using Tri Reagent from Sigma-Aldrich.
Libraries for RNA-Seq were prepared using Illumina TruSeq RNA Sample Preparation v2 Kit.

tag: strain/background

tag: genotype/variation

value: wild-type

value: 3 months

value: Sperm


title: genomic DNA from 100946230031_R04C02


title: sperm_WT_naive_2

description: Small RNA


title: genomic DNA from 200049730005_R01C02


title: genomic DNA from 100946230031_R03C01


title: genomic DNA from 200049730005_R01C01


title: genomic DNA from 100946230031_R03C02


title: genomic DNA from 100946230031_R02C01


title: genomic DNA from 100946230031_R04C01


title: genomic DNA from 100946230031_R01C02


title: genomic DNA from 100946230030_R06C01


title: genomic DNA from 100946230031_R02C02


title: genomic DNA from 100946230030_R04C02


title: genomic DNA from 100946230031_R01C01


title: genomic DNA from 100946230030_R01C02


title: genomic DNA from 100946230030_R01C01


title: genomic DNA from 100946230030_R02C02


title: genomic DNA from 100946230030_R05C01


title: genomic DNA from 100946230030_R04C01


title: genomic DNA from 100946230030_R05C02


title: genomic DNA from 100946230030_R03C02


title: genomic DNA from 100946230030_R03C01


title: genomic DNA from 100946230024_R06C01


title: genomic DNA from 100946230024_R04C02


title: genomic DNA from 100946230030_R02C01


title: genomic DNA from 100946230024_R05C02


title: genomic DNA from 100946230024_R06C02


title: genomic DNA from 100946230024_R02C02


title: genomic DNA from 100946230024_R05C01


title: genomic DNA from 100946230024_R01C01


title: genomic DNA from 100946230024_R03C01


title: genomic DNA from 100946230024_R03C02


title: genomic DNA from 100946230024_R02C01


title: genomic DNA from 100946200165_R05C02


title: genomic DNA from 100946230024_R01C02


title: genomic DNA from 100946200165_R06C02


title: genomic DNA from 100946200165_R06C01


title: genomic DNA from 100946200165_R02C01


title: genomic DNA from 100946200165_R04C02


title: genomic DNA from 100946200165_R01C02


title: genomic DNA from 100946200152_R05C02


title: genomic DNA from 100946200152_R05C01


title: genomic DNA from 100946230024_R04C01


title: genomic DNA from 100946200152_R03C01


title: genomic DNA from 100946200152_R03C02


title: genomic DNA from 100946200165_R02C02


title: genomic DNA from 100946200165_R03C01


title: genomic DNA from 100946200152_R01C02


title: genomic DNA from 100946200165_R01C01


title: genomic DNA from 100946200152_R04C02


title: genomic DNA from 100946200152_R02C02


title: genomic DNA from 100946200151_R06C01


title: genomic DNA from 100946200151_R05C02


title: genomic DNA from 100946200152_R01C01


title: genomic DNA from 100946200151_R06C02


title: genomic DNA from 100946200152_R02C01


title: genomic DNA from 100946200151_R05C01


title: genomic DNA from 100946200165_R05C01


title: genomic DNA from 100946200151_R02C02


title: genomic DNA from 100946200151_R04C02


title: genomic DNA from 100946200165_R04C01


title: genomic DNA from 100946200165_R03C02


title: genomic DNA from 100946200151_R04C01


title: genomic DNA from 100946200126_R05C01


title: genomic DNA from 100946200126_R04C02


title: genomic DNA from 100946200151_R03C01


title: genomic DNA from 100946200152_R06C02


title: genomic DNA from 100946200152_R06C01


title: genomic DNA from 100946200126_R02C02


title: genomic DNA from 100946200151_R01C01


title: genomic DNA from 100946200126_R01C02


title: genomic DNA from 100946150004_R06C02


title: genomic DNA from 100946150004_R05C02


title: genomic DNA from 100946200126_R06C01


title: genomic DNA from 100946200151_R01C02


title: genomic DNA from 100946200151_R02C01


title: genomic DNA from 100946200126_R05C02


title: genomic DNA from 100946200126_R04C01


title: genomic DNA from 100946200126_R03C01


title: genomic DNA from 100946200126_R06C02


title: genomic DNA from 100946150004_R04C02


title: genomic DNA from 100946150004_R04C01


title: genomic DNA from 100946150004_R03C01


title: genomic DNA from 100946150004_R02C02


title: genomic DNA from 100946150004_R02C01


title: genomic DNA from 100946200126_R01C01


title: genomic DNA from 100946200126_R02C01


title: genomic DNA from 100946200151_R03C02


title: genomic DNA from 100946200126_R03C02


title: genomic DNA from 100946150004_R06C01


title: genomic DNA from 100946150004_R03C02


title: OrgR2-1

city: Brisbane

first: Stefan

last: Thor

state: QLD

address: Skerman Bldg (65) room 506  Faculty of Medicine

department: School of Biomedical Sciences

country: Australia

institute: The University of Queensland

description:
pool 200+ st14+15 whole embryos
OrgR-esc-linearRPKM-nofilter.csv

data_processing:
LaserGene suite v14-v15, DNASTAR SeqMan Ngen Qseq alignment (unpacked FASTQ)
Reference dmel genome, focus on CDS/mRNA/ncRNA
RPKM normalization
Data exported from Dnastar to .csv, linear RPKM values, no filtering
Genome_build: dm6 plus iso1 mt
Supplementary_files_format_and_content: .csv (genesymbol annotation with linear RPKM per sample, column 1: genesymbol, column 2-9 samples, row 1: headers, each subsequent row is a gene, values rounded to three decimal places).

organism: Drosophila melanogaster

source_name: pooled st14+15 whole embryo OrgR wt

growth_protocol: Flies were maintained under standard conditions

extract_protocol:
200+ whole embryos from stage 14 and 15 were pooled, then RNA extraction with Qiagen Rneasy kit
NEBNext Ultra RNA Library Prep Kit; RNA-seq Illumina HiSeq2500 ~40M reads PE 150bp unstranded

treatment_protocol: esc mutants were maternal zygotic mutants

value: whole embryos

tag: developmental stage

value: stage 14 and 15

tag: genotype

value: wt


title: esc1-2

source_name: pooled st14+15 whole embryo esc maternal zygotic mutant

value: esc


title: esc1-1


title: RNA_IBM1_rep3

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

description: mRNA ibm1 rep3

data_processing:
MethylC-seq: MethylC-seq analysis was performed as described in (Schmtiz et al. 2013)
TAB-seq: TAB-seq analysis was performed as described in (Schmtiz et al. 2013)
ChIP-seq: MethylC-seq was performed using bowtie1.1.1
RNA-seq: MethylC-seq was performed using TopHat v2.0.13 and Cufflinks v2.2.1
Genome_build: TAIR10 reference genome
Supplementary_files_format_and_content: tab delimited text file, see "allc_header_descriptions.txt", "ChIP_column_header_descriptions.txt" and "RNA_column_header_descriptions.txt" for column headers

organism: Arabidopsis thaliana

source_name: ibm1 rep3

growth_protocol: The hTET1-CD sequence in the pMDC32 vector was transformed into Agrobacterium tumefaciens strain C58C1 and plated on LB-agar supplemented with kanamycin (50 µg/mL). A single kanamycin resistant colony was selected and used to start a 250-mL culture in LB Broth Miller liquid media supplemented with gentamicin (25 µg/mL), kanamycin (50 µg/mL), and rifampicin (15 µg/mL), which was incubated for two days at 30˚C. Bacterial cells were pelleted by centrifugation at 4,000 RPM for 30 minutes and the supernatant decanted. The remaining bacterial pellet was re-suspended in 200 mL of 5% sucrose with 0.05% Silwet L77. Plant transformation was performed using the floral dip method described by (Clough and Bent. 1998). Seeds were harvested upon senescence and transgenic plants were identified via selection on ½ LS plates supplemented with Hygromycin B (15 µg/mL).

extract_protocol: Genomic DNA libraries were prepared following the MethylC-seq protocol without use of the bisulfite conversion step. MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). TAB-seq libraries were prepared as previously described in (Yu et al. 2012). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. ChIP library preparation. Leaves were treated with formaldehyde to covalently link protein to DNA, washed several times with distilled water, patted dry and ground into fine powder in liquid nitrogen. Chromatin was extracted with a series of extraction buffers and sonicated. The final chromatin solution was incubated overnight with anti-H3K9me2 antibody (Cell Signaling Technology, 9753S) coated Dynabeads protein A (Life Technologies, 10002D) to precipitate the immune complex. After a few washes, the immune complex was eluted and incubated at 65 degrees in the presence of a high concentration of NaCl in a water-bath overnight. After degrading the proteins with proteinase K, DNA was recovered by phenol/chloroform/isoamyl alcohol extraction followed by ethanol precipitation. The DNA pellet was then dissolved in 30µl of nuclease-free water.

tag: ecotype

value: leaf


title: genomic DNA from 100946150004_R01C02

value: Male


title: genomic DNA from 100946150004_R01C01

value: Parkinson's disease (PD)


title: RNA_IBM1_rep1

description: mRNA ibm1 rep1

source_name: ibm1 rep1


title: genomic DNA from 200049730103_R05C01

value: Female


title: Chip_35S_TET1_2T6

description: ChIP 35S:TET1-2T6

library_source: genomic


title: RNA_MET1

description: mRNA met1


title: TAB_seq_35S_TET1_3

description: TAB-seq 35S:TET1-3 rep1

data_processing:
Library strategy: TAB-Seq
MethylC-seq: MethylC-seq analysis was performed as described in (Schmtiz et al. 2013)
TAB-seq: TAB-seq analysis was performed as described in (Schmtiz et al. 2013)
ChIP-seq: MethylC-seq was performed using bowtie1.1.1
RNA-seq: MethylC-seq was performed using TopHat v2.0.13 and Cufflinks v2.2.1
Genome_build: TAIR10 reference genome
Supplementary_files_format_and_content: tab delimited text file, see "allc_header_descriptions.txt", "ChIP_column_header_descriptions.txt" and "RNA_column_header_descriptions.txt" for column headers


title: methylome_ACT2_TET1_4

description: methylome ACT2:TET1-4

data_processing:
Library strategy: MethylC–seq
MethylC-seq: MethylC-seq analysis was performed as described in (Schmtiz et al. 2013)
TAB-seq: TAB-seq analysis was performed as described in (Schmtiz et al. 2013)
ChIP-seq: MethylC-seq was performed using bowtie1.1.1
RNA-seq: MethylC-seq was performed using TopHat v2.0.13 and Cufflinks v2.2.1
Genome_build: TAIR10 reference genome
Supplementary_files_format_and_content: tab delimited text file, see "allc_header_descriptions.txt", "ChIP_column_header_descriptions.txt" and "RNA_column_header_descriptions.txt" for column headers


title: TAB_seq_Col_0_WT

description: TAB-seq Col-0 WT

source_name: Col-0 WT


title: Pdgfb_Trp53_ko_2

city: Madrid

first: Osvaldo

last: Graña

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Structural Biology

country: Spain

institute: CNIO

description:
Isolation of poly A+ RNA from total RNA.
Strand-specific RNA-Seq (dUTP).
processed data file: FPKM_table.txt

data_processing:
RNA-seq analysis:
RNA-seq data were analyzed with the nextpresso pipeline (http://bioinfo.cnio.es/nextpresso/), as follows: RNA-seq reads were aligned to the mouse genome (NCBI37/mm9) with TopHat-2.0.10 (using Bowtie 1.0.0 and Samtools 0.1.19), allowing three mismatches and twenty multihits. Transcripts assembly, estimation of their abundances were calculated with Cufflinks 2.2.1, using the mouse NCBI37/mm9 transcript annotations from https://ccb.jhu.edu/software/tophat/igenomes.shtml .
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: FPKM_table.txt: FPKM values calculated with Cuffnorm.

source_name: Trp53 gRNA PDGFB tumorspheres

growth_protocol: NeuroCult proliferation kit (Stem Cell Technologies, Cat. 05702), supplemented with 10 ng/ml recombinant human EGF (Gibco, Cat. PHG0313), 20 ng/ml basic-FGF (Sigma-Aldrich, Cat. F0291-25UG), and 1 mg/ml Heparin (Stem Cell Technologies, Cat. 07980).

extract_protocol:
TRIzol reagent (Invitrogen, Cat. 15596-026).
800 ng of total RNA from the samples was used. PolyA+ fraction was purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq Stranded mRNA LT Sample Prep Kit" (this kit incorporates dUTP during 2nd strand cDNA synthesis, which implies that only the cDNA strand generated during 1st strand synthesis is eventually sequenced). Adapter-ligated library was completed by PCR with Illumina PE primers. The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation and sequenced in paired-end format (Illumina NovaSeq 6000), leading to 101bp paired-end reads.

tag: strain

value: Ntv-a; Nes-Cre; LSL-Cas9

value: Ntv-a T/T; Nes-Cre +/T; LSL-Cas9 +/T

tag: cell type

value: Trp53 gRNA PDGFB tumorspheres


title: methylome_ACT2_TET1_1.2_TET1

description: methylome ACT2:TET1-1.2-TET1


title: methylome_ACT2_TET1_3

description: methylome ACT2:TET1-3


title: RNA_IBM1_rep2

description: mRNA ibm1 rep2

source_name: ibm1 rep2


title: methylome_ACT2_TET1_5

description: methylome ACT2:TET1-5


title: methylome_ACT2_TET1_1.1+TET1

description: methylome ACT2:TET1-1.1+TET1


title: methylome_ACT2_TET1_2

description: methylome ACT2:TET1-2


title: Pdgfb_Trp53_ko_1


title: hMSC_TERTs reactivated after G0 for 24hrs (R24), rep 1

type: RNA

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: Gene expression in hMSC-TERTs reactivated post G0 for 24 hrs.

hyb_protocol: 600ng of labeled cRNA sample were fragmented at 60º C and hybridized on the array using the Gene Expression Hybridization kit (Part Number 5190-0404; Agilent) in Sure hybridization Chambers (Agilent) at 65º C for 16 hours. Hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327).

scan_protocol: The hybridized and washed microarray slides were scanned on a G2600D scanner (Agilent Technologies) at 5micron resolution.

data_processing: Data was analyzed using GeneSpring GX Version 11.5 software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift (Percentile shift normalization)

source_name: hMSC_TERTs, 24 hrs reactivated post G0

label_protocol: The samples were labeled using Agilent Quick Amp Kit (Part number: 5190-0424). 500ng of total RNA was reverse transcribed using oligodT primer tagged to T7 promoter sequence. cDNA thus obtained was converted to double stranded cDNA in the same reaction. Further the cDNA was converted to cRNA in the in-vitro transcription step using T7 RNA polymerase enzyme and Cy3 dye was added into the reaction mix. During cRNA synthesis Cy3 dye was incorporated into the newly synthesized strands. cRNA obtained was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106). Concentration and amount of dye incorporated was determined using Nanodrop. Samples that pass the QC for specific activity were taken for hybridization.

growth_protocol: hMSC-TERTs were maintained and cultured in growth medium (MEM-alpha (Gibco),16% FBS (Gibco), 1% penicillin and streptomycin (Penstrep) (Gibco)). Proliferating cells were G0 arrested in suspension medium (2% methyl cellulose (Sigma Aldrich), 16% FBS (Gibco) and 1% Penstrep in MEM-alpha). For re-activation studies, G0 arrested MSCs were replated on adherent plastic dishes in growth medium for desired time periods.

extract_protocol: Total RNA was prepared using the GenElute Mammalian Total RNA miniprep kit (Sigma-Aldrich) following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: cell line

value: hMSC-TERTs


title: TAB_seq_35S_TET1_4

description: TAB-seq 35S:TET1-3 rep2


title: Pdgfb_Pten_ko_2

source_name: Pten gRNA PDGFB tumorspheres

value: Pten gRNA PDGFB tumorspheres


title: Pdgfb_Cdkn2a_ko_2

source_name: Cdkn2a gRNA PDGFB tumorspheres

value: Cdkn2a gRNA PDGFB tumorspheres


title: methylome_35S_TET1_1.5_TET1

description: methylome 35S:TET1-1.5-TET1


title: hMSC_TERTs reactivated after G0 for 24hrs (R24), rep 3


title: hMSC_TERTs reactivated after G0 for 1hr (R1), rep 2

description: Gene expression in hMSC-TERTs reactivated post G0 for 1 hr.

source_name: hMSC_TERTs, 1 hr reactivated post G0


title: methylome_35S_TET1_1.4_TET1

description: methylome 35S:TET1-1.4-TET1


title: Quiescent hMSC_TERTs,rep 1

description: Gene expression in G0 arrested hMSC-TERTs

source_name: hMSC_TERTs, G0 arrested


title: hMSC_TERTs reactivated after G0 for 3hrs (R3), rep 1

description: Gene expression in hMSC-TERTs reactivated post G0 for 3 hrs.

source_name: hMSC_TERTs, 3 hrs reactivated post G0


title: hMSC_TERTs reactivated after G0 for 1hr (R1), rep 3


title: hMSC_TERTs reactivated after G0 for 3hrs (R3), rep 2


title: hMSC_TERTs reactivated after G0 for 3hrs (R3), rep 3


title: hMSC_TERTs reactivated after G0 for 24hrs (R24), rep 2


title: Quiescent hMSC_TERTs,rep 3


title: Quiescent hMSC_TERTs,rep 2


title: hMSC_TERTs reactivated after G0 for 1hr (R1), rep 1


title: Base3

city: Xi'an

first: Jianhua

last: Qiu

state: Shaanxi

address: 127 West Changle Rd

department: Otolaryngology Head & Neck Surgery

country: China

institute: Xijing Hospital, Fourth Military Medical University

data_processing:
HCS v3.5.0 software for HiSeq X System was used for base calling
Clean data (clean reads) were obtained by removing reads containing adaptors, reads containing poly-N sequences and low-quality reads from the raw data.
Bowtie v2.2.3 was used to build the index of the reference genome, and TopHat v2.0.12 was used to align paired-end clean reads to the Rattus norvegicus reference genome
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Trapnell, Cole, et al., 2010).
Genome_build: Rattus norvegicus reference genome (ftp://ftp.ensembl.org/pub/release-89/fasta/rattus_norvegicus/dna/)
Supplementary_files_format_and_content: Excel file includes chromosome, strand, gene read count for each samples, fpkm, p-value, padj value, OG analysis results, associated gene name and description

organism: Rattus norvegicus

source_name: Inner Ear Cochlear Outer Hair Cells

extract_protocol:
cochlear basilar membrane were removed and divided into apical turn, middel turn and basal turn. Apical turn and basal turn were separately treated with 1 mg/ml Collagenase IV (Sigma) diluted in Leibovitz L-15 culture medium (Sigma) at room temperature for 10min enzymatic digestion. After gently trituration, isolated single outer hair cell could be identified under microscope. 30 outer hair cells for each sample were collected and RNA was harvested using Trizol reagent. NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB) was used with total of 3ug RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Sprague-Dawley (SD)

value: Postnatal day 9 (P9)

value: Wild type

tag: sub population

value: basal turn


title: Proliferating hMSC_TERTs, rep 2

description: Gene expression in proliferating hMSC_TERTs

source_name: hMSC_TERTs, Asynchronously growing


title: Proliferating hMSC_TERTs, rep 3


title: Proliferating hMSC_TERTs, rep 1


title: methylome_35S_TET1_1.3_TET1

description: methylome 35S:TET1-1.3-TET1


title: Pdgfb_Cdkn2a_ko_1


title: Base2


title: Base1


title: p53_ko_NSCs_1

source_name: Ctrl gRNA transduced NSCs

value: Gtv-a; hGFAP-Cre; LSL-Cas9; p53lox/lox

value: Gtv-a T/T; hGFAP-Cre +/T; LSL-Cas9 +/T; p53lox/lox

value: Ctrl gRNA transduced NSCs


title: Apex3

value: apical turn


title: Pdgfb_Pten_ko_1


title: Myb_Qk_1

source_name: Myb-Qk gRNA transduced NSCs

value: Myb-Qk gRNA transduced NSCs


title: Bcan_Ntrk_2

source_name: Bcan-Ntrk1 tumorspheres

value: Bcan-Ntrk1 tumorspheres


title: Apex1


title: methylome_35S_TET1_1.1+TET1

description: methylome 35S:TET1-1.1+TET1

value: leaf


title: Bcan_Ntrk_1


title: SCEC and corresponding normal tissue, replicate 2

city: Shanghai

first: Juan

last: Wang

address: No. 135 Guowei Road

institute: Shanghai Jiayin Biotechnology Co., Ltd.

description:
Biological replicate from SCEC patient 3
252206030966_1_3

hyb_protocol: Array hybridization was performed using Agilent Oligo aCGH Hybridization Kit in Hybridization Oven at 65℃, 20rpm for 24 hours.Array wash was performed using Agilent Oligo aCGH Wash Buffer 1 and 2 set in staining dishes follow the manufacturer's instructions.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version 10.7).

data_processing: Agilent data analysis using the agilent cytogenomics software which provides no normalized data on probe level. Therefore, the preliminary results from cytogenomics software are reported in matrix linked at the foot of the Series record.

source_name: SCEC, patient 2

label_protocol: Experimental sample and control sample were labeled with Cy5 NHS ester and Cy3 NHS ester respectively, using Agilent Genomic DNA Labeling Kit PLUS followed the manufacturer’s instructions. Labeled DNA fragments were purified using Amicon Ultra-0.5, Ultracel-30 Membrane, 30 kDa. Measured the absorbance at A260nm (DNA), A550nm(Cyanine 3), and A650nm(Cyanine 5)of purified DNA fragments to calculate the Specific Activity.

growth_protocol: A total of 3 SCEC tissues and matched adjacent noncancerous tissues were dissected from the surgical specimens and snap-frozen in liquid nitrogen, then stored at -80°C in the tissue bank of Fudan University Shanghai Cancer Center.

extract_protocol: Sample DNA was extracted using DNeasy Blood &Tissue Kit (Cat#69506, QIAGEN, GmBH, Germany), Use Nano Drop (Cat#ND-1000, ThermoFisher, Waltham, MA, US) and 1% agarose gel electrophoresis to check the quantity and quality of purified DNA.

treatment_protocol: Tissue sections were cut from frozen blocks and then stained with toluidine blue for genomic DNA (gDNA). Carcinoma cells or non-malignant cells were collected from cancerous or adjacent noncancerous tissue sections using LMD (Leica Microsystems, Wetzlar, Germany) by pathologists

value: middle thoracic SCEC with stage III

source_name: corresponding normal tissue, patient 2

value: control


title: methylome_35S_TET1_1

description: methylome 35S:TET1-1


title: Myb_Qk_2


title: Apex2


title: SCEC and corresponding normal tissue, replicate 3

description:
Biological replicate from SCEC patient 4
252206030966_1_4

source_name: SCEC, patient 3

source_name: corresponding normal tissue, patient 3


title: methylome_35S_TET1_3_rep2

description: methylome 35S:TET1-3 rep2


title: methylome_35S_TET1_3_rep1

description: methylome 35S:TET1-3 rep1


title: methylome_35S_TET1_2T6

description: methylome 35S:TET1-2T6


title: SCEC and corresponding normal tissue, replicate 1

description:
Biological replicate from SCEC patient 1
252206030966_1_1

source_name: SCEC, patient 1

source_name: corresponding normal tissue, patient 1


title: methylome_35S_TET1_2

description: methylome 35S:TET1-2


title: methylome_35S_TET1_2T5

description: methylome 35S:TET1-2T5


title: methylome_Col_0_WT_1

description: methylome Col-0 WT-1

source_name: Col-0 WT


title: methylome_Col_0_WT_2

description: methylome Col-0 WT-2


title: Healthy_20151116_H-miR-Shomron-13-24-16-11-15_01_05

city: Tel Aviv

first: Nir

last: Pillar

state: Israel

address: Faculty of Medicine (Room 303), Tel Aviv University

country: Israel

institute: Tel Aviv University

description: Nanostring human miRNA panel

hyb_protocol: Refer to the NanoString nCounter Assay System Manual

data_processing: Relative log expression normalization was conducted using R DEseq2 package and in house scripts,

label: labeled by manufacturer

source_name: PBMCs

extract_protocol: Total RNA was extracted form PBMCs using Trizol, 300ng were sent for Nanostring miRNA multiplexing

treatment_protocol: Affected individuals and their matched healthy controls

value: healthy

value: PBMCs


title: Healthy_20151116_H-miR-Shomron-13-24-16-11-15_01_07

description: Nanostring human miRNA panel

scan_protocol: Refer to the NanoString nCounter Assay System Manual


title: p53_ko_NSCs_2


title: methylome_35S_TET1_1.2+TET1

description: methylome 35S:TET1-1.2+TET1


title: Healthy_20151116_H-miR-Shomron-13-24-16-11-15_01_03

description: Nanostring human miRNA panel

label_protocol: Refer to the NanoString nCounter Assay System Manual


title: Healthy_20151116_H-miR-Shomron-13-24-16-11-15_01_02

description: Nanostring human miRNA panel


title: 16 ni vs. 16 P12 wt

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

hyb_protocol: Whole human genome 44k microarrays (Agilent-026652) were done according to the supplier's protocol (Agilent Technologies) using the SSC wash protocol.

scan_protocol: Scanning of microarrays was performed with 5 µm resolution and extended range (XDR) using a DNA microarray laser scanner (Agilent Technologies).

data_processing: Raw microarray image data were analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.11.5.1.1, Agilent). The extracted MAGE-ML files were analyzed with the Rosetta Resolver Biosoftware (Rosetta Biosoftware).

source_name: gastric epithelial cells, donor 16, uninfected

label_protocol: RNA labeling was performed with the Quick-Amp Labeling Kit (Agilent Technologies) according to supplier's instructions.

growth_protocol: Gastric primary epithelial cells were isolated from healthy stomach tissue (Schlaermann et al., 2014) and grown in Matrigel, generating 3D spheroids that can be maintained and passaged in long-lasting cultures. These spheroids were transferred to standard culture dishes generating 2D monolayers to study infection with H. pylori. Data were obtained from cells isolated from two independent donors (16 and 17).

extract_protocol: Total RNA was isolated by the Trizol (Invitrogen) method following the manufacturer's protocol.

treatment_protocol: H. pylori was grown on GC agar plates with vancomycin as described elsewhere (Wunder et al., 2006). For infection, bacteria were collected from plates and resuspended in RPMI 1640 (serum free). Primary cultures were grown to a confluency of 60%, washed twice with PBS and serum starved with RPMI 1640 for 16 h prior to experiment. The infection was carried out in RPMI 1640 under serum-starved conditions at 37 °C and 5% CO2 for 26.5 h and at an MOI of 20.

value: gastric epithelial cells

tag: donor

tag: infection

source_name: gastric epithelial cells, donor 16, infected with WT H. pylori P12

value: wildtype H. pylori P12


title: Healthy_20151116_H-miR-Shomron-13-24-16-11-15_01_04

description: Nanostring human miRNA panel


title: Tamoxifen treated MCF-7/c-Jun -Tet cells, biological rep2

city: Huddinge

first: Karin

last: Dahlman-Wright

address: Blickagången 16

department: Department of Biosciences and Nutrition

country: Sweden

institute: Karolinska Institutet

description: Gene expression data after Tamoxifen stimulation

hyb_protocol: Hybridization to Clariom™ D Assay_ human array catridge was carried out overnight with biotin-labeled cRNA according to the Affymetrix protocol.

scan_protocol: Array plates were scanned using a GeneTitan scanner.

data_processing: Preprocessing in Affymetrix Transcriptome Analysis Console (TAC) Software (v. 3.1) using the following methods: Summarization: PLIER, Background Correction: PM-GCBG, Normalization: Global Median.

label: biotin

source_name: MCF-7/c-Jun -Tet cells

label_protocol: Total RNA was converted to sense strand cDNA using Ambion WT Expression kit. For fragmentation and labeling WT GeneChip WT target Labeling kit was used.

growth_protocol: MCF-7/c-Jun +Tet cells were maintained in DMEM supplemented with 10% FBS containing media in presence of 2μg/ml tetracycline.MCF-7/c-Jun -Tet cells were maintained in 10% FBS containing media in absence of tetracycline.

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (Qiagen, Valencia, CA).

treatment_protocol: Cells were cultured in steroid depleted media for 72 h and treated with ethnaol, 10 nM 17β-estradiol or 1μM Tamoxifen for 24 h.

value: Tamoxifen


title: Tamoxifen treated MCF-7/c-Jun +Tet cells, biological rep3

source_name: MCF-7/c-Jun +Tet cells


title: Tamoxifen treated MCF-7/c-Jun -Tet cells, biological rep3


title: Tamoxifen treated MCF-7/c-Jun -Tet cells, biological rep1


title: 16 ni vs. 16 P12 d cagt

source_name: gastric epithelial cells, donor 16, infected with delta-cagT H. pylori P12

value: delta-cagT H. pylori P12


title: 17 P12 d cagt vs. 17 ni

source_name: gastric epithelial cells, donor 17, infected with delta-cagT H. pylori P12

source_name: gastric epithelial cells, donor 17, uninfected


title: Tamoxifen treated MCF-7/c-Jun +Tet cells, biological rep2


title: 17 P12 wt vs. 17 ni

source_name: gastric epithelial cells, donor 17, infected with WT H. pylori P12


title: Tamoxifen treated MCF-7/c-Jun +Tet cells, biological rep1


title: Healthy_20151116_H-miR-Shomron-13-24-16-11-15_01_06

description: Nanostring human miRNA panel


title: corresponding normal samples,patient3

description: gene expression data from corresponding normal tissue of SCEC patient3

hyb_protocol: Array hybridization and wash was performed using GeneChip Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: The gene chips were scanned using a confocal laser scanner (GeneArray Scanner 3000). The scanned image was converted into numerical values of the signal intensity by Command Console Software 3.1 (Affymetrix) with default settings.

data_processing: Raw data were subjected to Robust Multiarray Average quantile normalization analysis (RMA) algorithm by GeneSpring GX 12.5 Software (Agilent technology, Santa Clara, CA, US) to generate .CEL intensity files

source_name: SCEC Normal, patient3

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: A total of 3 SCEC tissues and matched adjacent noncancerous tissues were dissected from the surgical specimens and snap-frozen in liquid nitrogen, then stored at -80°C in the tissue bank of Fudan University Shanghai Cancer Center

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Tissue sections were cut from frozen blocks and then stained with cresyl violet for total RNA (Ambion, Austin, TX, USA). Carcinoma cells or non-malignant cells were collected from cancerous or adjacent noncancerous tissue sections using LMD (Leica Microsystems, Wetzlar, Germany) by pathologists


title: corresponding normal samples,patient2

description: gene expression data from corresponding normal tissue of SCEC patient2

source_name: SCEC Normal, patient2


title: SCEC, dissected from the surgical specimens, patient 3

description: gene expression data from SCEC patient3

source_name: SCEC Tumor, patient3


title: SCEC, dissected from the surgical specimens, patient 2

description: gene expression data from SCEC patient2

source_name: SCEC Tumor, patient2


title: E2 treated MCF-7/c-Jun +Tet cells, biological rep3

description: Gene expression data after E2 stimulation


title: Healthy_20151112_H-miR-Shomron-12-11-15_01_12

description: Nanostring human miRNA panel


title: E2 treated MCF-7/c-Jun -Tet cells, biological rep3


title: Healthy_20151116_H-miR-Shomron-13-24-16-11-15_01_01

description: Nanostring human miRNA panel


title: Healthy_20151112_H-miR-Shomron-12-11-15_01_11

description: Nanostring human miRNA panel


title: Affected_20151112_H-miR-Shomron-12-11-15_01_10

description: Nanostring human miRNA panel

value: affected


title: Affected_20151112_H-miR-Shomron-12-11-15_01_09

description: Nanostring human miRNA panel


title: Affected_20151112_H-miR-Shomron-12-11-15_01_07

description: Nanostring human miRNA panel


title: Affected_20151112_H-miR-Shomron-12-11-15_01_08

description: Nanostring human miRNA panel


title: E2 treated MCF-7/c-Jun +Tet cells, biological rep2


title: E2 treated MCF-7/c-Jun -Tet cells, biological rep2


title: corresponding normal samples,patient1

description: gene expression data from corresponding normal tissue of SCEC patient1

source_name: SCEC Normal, patient1


title: Affected_20151112_H-miR-Shomron-12-11-15_01_03

description: Nanostring human miRNA panel


title: Affected_20151112_H-miR-Shomron-12-11-15_01_05

description: Nanostring human miRNA panel


title: E2 treated MCF-7/c-Jun -Tet cells, biological rep1


title: vehicle treated MCF-7/c-Jun -Tet cells, biological rep3

description: Gene expression data using ethanol as vehicle control

value: vehicle


title: Affected_20151112_H-miR-Shomron-12-11-15_01_04

description: Nanostring human miRNA panel


title: 9_14631_170Weeks_Nugen

city: Atlanta

first: Gregory

middle: K

last: Tharp

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

hyb_protocol: Arrays were washed, stained and scanned as described in the Affymetrix GeneChip® Expression Analysis Technical Manual

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

data_processing: Data from .CEL files were analyzed using R Bioconductor.

organism: Chlorocebus sabaeus

source_name: whole blood

label_protocol: 4 µg of the amplified cDNA was fragmented, biotinylated, and hybridized to arrays using the NuGEN Ovation Encore Biotin Module, according to kit instructions.

extract_protocol: Total RNA extraction was performed using the Paxgene RNA IVD kit (QIAGEN, Hilden, Germany)

tag: gender

value: female

tag: sivagm used for experimental infection

value: whole blood

tag: serostatus simian retrovirus type d (before experimental infection)

value: negative

tag: serostatus siv (before experimental infection)

tag: serostatus stlv-1 (before experimental infection)


title: 7_14626_170Weeks_Nugen

tag: tissue


title: vehicle treated MCF-7/c-Jun -Tet cells, biological rep2

tag: treatment


title: SCEC, dissected from the surgical specimens, patient 1

description: gene expression data from SCEC patient1

source_name: SCEC Tumor, patient1


title: 6_14632_170Weeks_Nugen

value: GU


title: vehicle treated MCF-7/c-Jun -Tet cells, biological rep1


title: 10_14628_170Weeks_Nugen


title: vehicle treated MCF-7/c-Jun +Tet cells, biological rep3


title: 12_14634_170Weeks_Nugen


title: vehicle treated MCF-7/c-Jun +Tet cells, biological rep2


title: 4_14624_170Weeks_Nugen

value: positive


title: E2 treated MCF-7/c-Jun +Tet cells, biological rep1


title: 3_14629_170Weeks_Nugen

value: WT


title: Affected_20151112_H-miR-Shomron-12-11-15_01_06

description: Nanostring human miRNA panel

tag: disease state


title: Affected_20151112_H-miR-Shomron-12-11-15_01_02

description: Nanostring human miRNA panel


title: Affected_20151112_H-miR-Shomron-12-11-15_01_01

description: Nanostring human miRNA panel


title: 11_14633_170Weeks_Nugen


title: 8_14630_170Weeks_Nugen


title: Placenta_normal_rep4

status: Public on Mar 01 2018

city: Beijing

first: Zhenyu

last: Zhang

address: Gongtinanlu 8hao

institute: Beijing Chao-Yang Hospital,Capital Medical University

description: Different gene expression of basal plate of the placenta between normal and preeclampsia pregnancy

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit (Cat # 5190-0456, Agilent technologies, Santa Clara, CA, US) in hybridization Oven (Cat # G2545A, Agilent technologies, Santa Clara, CA, US) at 55°C，20 rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat # 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat #5188-5327, Agilent technologies, Santa Clara, CA, US)

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat # G2565CA, Agilent technologies, Santa Clara, CA, US)

data_processing: Data were extracted with  Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) with default settings. Raw data were normalized by Quantile algorithm, included in the R package AgiMicroRna(López-Romero, P. BMC Genomics. 2011.)

source_name: basal plate of the placenta, normal pregnancy

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit (Cat # 5190-0456, Agilent technologies, Santa Clara, CA, US) followed the manufacturer’s instructions, labeling section.

extract_protocol: Total RNA was extracted and purified using mirVana™ miRNA Isolation Kit (Cat#AM1561, Ambion, Austin, TX, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

tag: age

value: 33 years old


title: Placenta_normal_rep2

value: 31 years old


title: Placenta_normal_rep3

value: 28 years old


title: Warm white adipocyte H3K4me1 ChIP rep 2

city: Boston

first: Evan

last: Rosen

state: MA

address: 3 Blackfan Cir

department: Endocrinology

institute: Beth Israel Deconess Medical Center

description: biological replicate

data_processing:
ChIP-seq data were aligned to the mm10 mouse genome using Bowtie2 (Langmead and Salzberg, 2012).
Duplicates and low quality reads were removed by Picard (http://picard.sourceforge.net)
Reads were processed using samtools (Li et al., 2009)
Peaks were called by MACS2 (Zhang et al., 2008), and low peaks (4<fold higher coverage than whole cell extract (WCE)) were removed.
Reads were assigned to peaks, normalized and quantified using featureCounts and EdgeR. Low signal peaks (log2 CPM<2) were removed, and differential peaks were defined at log2 FC≥1 and log2 FDR≤0.05 (except H3K4me1 which used FDR≤0.25).
For ChIP-seq track visualization, reads were processed to the BigWig file format using bedtools (Quinlan and Hall, 2010) and bedGraphToBigWig (Kent et al., 2010).
Processed Bigwig files were viewed in WashU Epigenome Browser (Zhou and Wang, 2012).
ChIP-seq peak heatmaps and distribution plots were generated with the normalized BigWig files within 10kb genomic regions surrounding peaks by using deepTools2 (Ramirez et al., 2016).
Overlaps between H3K27ac and H3K4me1 were determined using bedtools. Peaks were assigned to genomic annotations and genes with HOMER (Heinz et al., 2010), and GO pathway analysis was performed by DAVID Bioinformatics Resources 6.8.
Motif enrichment analysis was conducted using FIMO from the MEME package (Grant et al., 2011) with the JASPAR database (Mathelier et al., 2014)
genome build: mm10
processed data files format and content: bigwig

source_name: inguinal WAT

growth_protocol: Mice were maintained on a standard chow diet (8664 Harlan Teklad, 6.4% w/w fat) under a regular 12h light/12h dark cycle at constant temperature (23°C).

extract_protocol:
Tissues were dounce homogenized, and cross-linked nuclei were isolated and sorted by BD FACS Aria II using mCherry fluorescence. Sorted nuclei were sheared by Covaris E220 and used for ChIP for overnight. Immunoprecipitates were washed and subjected to elution and reverse crosslinking. DNA was then extracted by AMPure XP beads according to the manufacturer’s manual.
Sequencing libraries were constructed using the “on-bead” preparation method as previously described (Roh et al., Cell Rep, 2017). ChIP-isolated DNA was subjected to end repair/phosphorylation using the End-It DNA End-Repair Kit (Epicentre), A-tailing using the Klenow Fragment and index adaptor ligation using Quick Ligase (NEB). AMPure XP beads were left in all the reactions to allow isolation of DNA using PEG (Polyethylene Glycol 8000)/NaCl solution, thus minimizing loss between reactions. After ligation, DNA was eluted and amplified by PCR for 14-16 cycles using the PfuUltra II Hotstart PCR Master Mix. DNA sized between 250 and 600bp was selected by gel electrophoresis and extraction using E-Gel EX Agarose Gels (Invitrogen) and MinElute Gel Extraction kits (Qiagen). Libraries were analyzed using the Qubit and Agilent Bioanalyzer, pooled at a final concentration of 12pM and sequenced on a HiSeq2500 or NextSeq500 system.

treatment_protocol: Mice were exposed to cold (4°C for 1 week (cold brown/beige adipocyte samples), and subsequently incubated at 30°C for 4 weeks (warm brown/beige adipocyte samples). Mice born and maintained at 30°C at all times used for warm white adipocyte samples.

value: adipose

tag: chip antibody

value: H3kK4me1 (Cell Signaling, 5326)


title: Placenta_ preeclampsia_rep3

source_name: basal plate of the placenta, preeclampsia patient

value: 30 years old


title: Warm white adipocyte H3K4me1 ChIP rep 1

description: biological replicate


title: Blood_AA4

first: Youyu

last: Sheng

address: 12 Middle Wulumuqi Road, Shanghai 200040, China.

institute: Huashan hospital

description: miRNA expression in blood of patient with alopecia areata

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5 μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 22.5 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human miRNA Microarray (8*60K) 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: The arrays were scanned with the Agilent Scanner G2505C (Agilent Technologies)

data_processing: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data. Next, Genespring software (version 12.5; Agilent Technologies) was employed to finish the basic analysis with the raw data. To begin with, the raw data was normalized with the quantile algorithm. The probes that at least 75.0 percent of samples in any 1 condition out of 2 conditions have flags in Detected were chosen for further data analysis. Differentially expressed miRNAs were then identified through fold change as well as P value calculated using t-test.

source_name: Peripheral Blood, Alopecia areata, replicate 4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg 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.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556) following the manufacturer’s instructions. Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific)and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).


title: Placenta_ preeclampsia_rep1

value: 32 years old


title: Placenta_ preeclampsia_rep2

value: 26 years old


title: Blood_C5

description: miRNA expression in blood of control

source_name: Peripheral Blood, Control, replicate 5


title: Blood_AA1

source_name: Peripheral Blood, Alopecia areata, replicate 1

value: male


title: Warm white adipocyte H3K4me1 ChIP rep 3

description: biological replicate


title: Blood_C2

description: miRNA expression in blood of control

source_name: Peripheral Blood, Control, replicate 2


title: Warm brown adipocyte H3K4me1 ChIP rep 7

description: technical replicate

source_name: interscapular BAT


title: Blood_C4

description: miRNA expression in blood of control

source_name: Peripheral Blood, Control, replicate 4


title: Warm beige adipocyte H3K4me1 ChIP rep 2

description: biological replicate


title: Blood_C1

description: miRNA expression in blood of control

source_name: Peripheral Blood, Control, replicate 1


title: Warm brown adipocyte H3K4me1 ChIP rep 6

description: biological replicate


title: Blood_AA2

source_name: Peripheral Blood, Alopecia areata, replicate 2


title: Blood_C3

description: miRNA expression in blood of control

source_name: Peripheral Blood, Control, replicate 3


title: Blood_AA5

source_name: Peripheral Blood, Alopecia areata, replicate 5


title: Warm beige adipocyte H3K4me1 ChIP rep 1

description: biological replicate


title: Warm brown adipocyte H3K4me1 ChIP rep 5

description: technical replicate


title: Warm brown adipocyte H3K4me1 ChIP rep 1

description: biological replicate


title: Warm brown adipocyte H3K4me1 ChIP rep 3

description: biological replicate


title: Warm brown adipocyte H3K4me1 ChIP rep 2

description: biological replicate


title: Placenta_normal_rep1

value: 29 years old


title: Warm brown adipocyte H3K4me1 ChIP rep 4

description: biological replicate


title: Cold brown adipocyte H3K4me1 ChIP rep 8

description: technical replicate


title: Cold brown adipocyte H3K4me1 ChIP rep 7

description: biological replicate


title: Cold beige adipocyte H3K4me1 ChIP rep 2

description: biological replicate


title: Cold beige adipocyte H3K4me1 ChIP rep 1

description: biological replicate


title: 1_14623_170Weeks_Nugen


title: 2_14625_170Weeks_Nugen


title: 5_14627_170Weeks_Nugen


title: TN DEN brown adipocyte H3K27ac ChIP rep 2

description: biological replicate

value: H3K27ac (Active Motif, 39133)


title: Cold brown adipocyte H3K4me1 ChIP rep 3

description: biological replicate


title: Cold brown adipocyte H3K4me1 ChIP rep 4

description: biological replicate


title: vehicle treated MCF-7/c-Jun +Tet cells, biological rep1

source_name: MCF-7/c-Jun +Tet cells

value: vehicle


title: Cold brown adipocyte H3K4me1 ChIP rep 2

description: biological replicate


title: Warm whiite adipocyte H3K27ac ChIP rep 2

description: biological replicate


title: Cold brown adipocyte H3K4me1 ChIP rep 6

description: technical replicate


title: TN Sham brown adipocyte H3K27ac ChIP rep 1

description: biological replicate


title: Cold brown adipocyte H3K4me1 ChIP rep 1

description: biological replicate


title: Cold brown adipocyte H3K4me1 ChIP rep 5

description: biological replicate


title: Cold brown adipocyte H3K27ac ChIP rep 2

description: biological replicate


title: Warm beige adipocyte H3K27ac ChIP rep 2

description: biological replicate


title: Warm brown adipocyte H3K27ac ChIP rep 2

description: biological replicate


title: Warm white adipocyte mRNA rep 1

description:
biological replicate
mRNA_NuTRAP_iWAT_white_rewarm_001_001_001

data_processing:
RNA-seq data were aligned to the mm10 mouse genome using HISAT2 (Kim et al., 2015).
Duplicates and low quality reads were removed by Picard (http://picard.sourceforge.net)
Reads were assigned to transcripts, normalized and quantified using featureCounts (Liao et al., 2014) and EdgeR (Robinson et al., 2010).
Low expressed genes (log2 CPM≥2) were filtered out, and differentially expressed genes were defined at log2 fold-change (FC) ≥1 and log2 false discovery rate (FDR)≤0.05
Gene set enrichment analysis was performed using DAVID Bioinformatics Resources 6.8 (Huang da et al., 2009) and summarized by REVIGO (Supek et al., 2011).
Genome_build: mm10
Supplementary_files_format_and_content: read counts with batch normalization

extract_protocol:
TRAP was performed as previously described (Roh et al., Cell Rep 2017). Adipose tissues were homogenized and processed to immunoprecipitation using anti-GFP antibody. Immunoprecipitates were washed and subjected to RNA extraction using Qiagen Micro RNeasy kit according to the manufacturer’s instructions. Isolated RNA was quantified by Qubit, and RNA integrity was analyzed by Agilent Bioanalyzer.
TRAP-isolated RNA (≤100ng) was treated with the Ribo-Zero rRNA removal kit (Epicentre) to deplete ribosomal RNA and converted into double stranded cDNA using NEBNext mRNA Second Strand Synthesis Module. cDNA was subsequently tagmented and amplified for 12 cycles by using Nextera XT DNA Library Preparation Kit. Sequencing libraries were analyzed Qubit and Agilent Bioanalyzer, pooled at a final concentration of 12pM, and sequenced on a HiSeq2500.


title: Warm brown adipocyte mRNA rep 5

description:
biological replicate
mRNA_NuTRAP_BAT_brown_rewarm_005_001_001


title: Warm white adipocyte mRNA rep 2

description:
biological replicate
mRNA_NuTRAP_iWAT_white_rewarm_002_001_001


title: Warm beige adipocyte mRNA rep 3

description:
biological replicate
mRNA_NuTRAP_iWAT_beige_rewarm_005_001_001


title: Warm white adipocyte mRNA rep 5

description:
biological replicate
mRNA_NuTRAP_iWAT_white_rewarm_005_001_001


title: Warm white adipocyte mRNA rep 3

description:
biological replicate
mRNA_NuTRAP_iWAT_white_rewarm_003_001_001


title: Warm white adipocyte mRNA rep 4

description:
biological replicate
mRNA_NuTRAP_iWAT_white_rewarm_004_001_001


title: Cold beige adipocyte mRNA rep 4

description:
biological replicate
mRNA_NuTRAP_iWAT_beige_cold_005_001_001


title: TN Sham brown adipocyte H3K27ac ChIP rep 2

description: biological replicate


title: TN DEN brown adipocyte H3K27ac ChIP rep 1

description: biological replicate


title: Cold beige adipocyte mRNA rep 2

description:
biological replicate
mRNA_NuTRAP_iWAT_beige_cold_003_001_001


title: Cold brown adipocyte mRNA rep 4

description:
biological replicate
mRNA_NuTRAP_BAT_brown_cold_004_001_001


title: Cold brown adipocyte mRNA rep 2

description:
biological replicate
mRNA_NuTRAP_BAT_brown_cold_002_001_001


title: Warm brown adipocyte mRNA rep 4

description:
biological replicate
mRNA_NuTRAP_BAT_brown_rewarm_004_001_001


title: Warm brown adipocyte mRNA rep 1

description:
biological replicate
mRNA_NuTRAP_BAT_brown_rewarm_001_001_001


title: Cold beige adipocyte H3K27ac ChIP rep 2

description: biological replicate


title: Warm beige adipocyte mRNA rep 1

description:
biological replicate
mRNA_NuTRAP_iWAT_beige_rewarm_003_001_001


title: Warm beige adipocyte mRNA rep 2

description:
biological replicate
mRNA_NuTRAP_iWAT_beige_rewarm_004_001_001


title: Warm brown adipocyte mRNA rep 3

description:
biological replicate
mRNA_NuTRAP_BAT_brown_rewarm_003_001_001


title: MOCK-14

city: Murcia

first: Livia

last: Donaire

state: Murcia

address: Campus de Espinardo

department: Plant Pathology

institute: Centro de Edafología y Biología Aplicada del Segura

data_processing:
Basecalls performed using CASAVA version 1.4
Adapters were trimmed and small RNAs were filtered by length (20 to 26 nts) using in-house Perl scripts
sRNAs were collapsed using in-house Perl scripts
Supplementary_files_format_and_content: tab delimited files containing sRNA sequences  and counts per each sRNA sequence

source_name: Leaves

growth_protocol: Arabidopsis plants were grown in chambers at 22-24 ºC and with a 16h photoperiod

extract_protocol:
Total RNA was extracted using Trizol according to manufacturer’s instructions
Libraries were prepaired according to Illumina TruSeq Small RNA Library Prep Kit

treatment_protocol: Rossette leaves were rub inoculated with buffer or with a TuMV-infected N. benthamiana extract

tag: ecotype

tag: agent

value: Healthy, none

value: 14 dpi


title: Cold brown adipocyte mRNA rep 1

description:
biological replicate
mRNA_NuTRAP_BAT_brown_cold_001_001_001

tag: strain


title: Cold beige adipocyte mRNA rep 3

description:
biological replicate
mRNA_NuTRAP_iWAT_beige_cold_004_001_001


title: Cold beige adipocyte mRNA rep 1

description:
biological replicate
mRNA_NuTRAP_iWAT_beige_cold_001_001_001


title: Warm brown adipocyte mRNA rep 2

description:
biological replicate
mRNA_NuTRAP_BAT_brown_rewarm_002_001_001


title: Cold brown adipocyte mRNA rep 5

description:
biological replicate
mRNA_NuTRAP_BAT_brown_cold_005_001_001


title: Cold brown adipocyte mRNA rep 3

description:
biological replicate
mRNA_NuTRAP_BAT_brown_cold_003_001_001


title: TuMV-14

value: Turnip mosaic virus


title: LUHMES undifferentiated ChIP-seq CTCF Sample 1

city: Grand Rapids

first: Gerry

middle: A.

last: Coetzee

state: MI

address: 333 Bostwick Ave NE

department: Center for Neurodegenerative Science

institute: Van Andel Research Institute

description:
sonicated fixed chromatin
processed data files:
merge_ctcf_luhU.bed
merged_luhmes_ctcf_040317.bed
ave_chip_ctcf_luhmes.bw

data_processing:
Two biological replicates with 2 technical replicates each were used for input and ChIP for both H3K27Ac and CTCF. Following sequencing, fastq files were aligned to the HG19 genome assembly using default setting for BWA v0.7.15 (Li and Durbin, 2009).
Aligned reads were merged with Samtools and peaks were called using MACS2 v2.1 using a liberal FDR cutoff of 0.1 (Zhang et al., 2008).
Narrowpeaks were aligned and an irreproducible discovery rate (IDR) of <0.01 was used for filtering (Li et al., 2011).
The R package ChIPseeker was used with TxDb.Hsapiens.UCSC.hg19.knownGene to define H3K27Ac peaks as proximal promoters if within 100 bp of a gene TSS or as enhancers if further than 2 kb from a TSS.
genome build: hg19
Supplementary_files_format_and_content: Table_S2_H3K27ac.xlsx: excel file with multiple tabs containing BED formatted genomic coordinates for LUHMES undifferentiated-only, intersection/both, and differentiated-only enhancers and promoters as determined by H3K27ac ChIP-seq.
.bw - bigWig files containing aligned sequence map densities.

source_name: Lund human mesencephalic cells (LUHMES)

growth_protocol: LUHMES cells were cultured essentially as done by (Scholz et al., 2011). Briefly, the cells were incubated in a humidified 37 °C, 5% CO2 incubator on flasks pre-coated with 50 mg/mL poly-L-ornithine (Sigma, Cat # P3655) and 1 mg/mL fibronectin (Sigma, Cat # F114) in water. The coated flasks were incubated at 37 °C overnight, rinsed with water, and allowed to dry before seeding cells. Cells were cultured in complete growth medium containing Advanced DMEM:F12 (Thermo Fisher, Cat # 12634-010) with 2mM L-glutamine (Thermo Fisher, Cat # 25030081), 1X N-2 supplement (Thermo Fisher, Cat # 17502-048), and 0.04 mg/mL bFGF (Stemgent, Cat # 03-0002). Cells were allowed to reach 80% confluency before passaging with 0.025% trypsin/EDTA.  For RNA-seq: the parental LUHMES cells were split into 6 separate flasks. These were grown to 80% confluence and then each one was passaged to new flasks using 3.5*10^6 cells.  RNA was taken from the remaining cells to give 6 undifferentiated RNA samples. The newly passaged cultures were switched to differentiation media 24 hours later and allowed to differentiate for 6 days before taking the 6 differentiated RNA samples. These (12) were the only RNA samples we had for this experiment. Samples 1-3 for each of undifferentiated and differentiated were re-sequenced for the paired end sequencing.

extract_protocol:
For ChIP experiments, we used previously published protocols (Rhie et al., 2014). Briefly, about 1 x 107 cells were fixed by adding fresh formaldehyde directly to the culture medium at a final concentration of 1%. The reaction was quenched with 10X (1.15 M) glycine for 5 min at room temperature. Chromatin from fixed cells was sonicated using a Bioruptor Pico (Diagenode, Cat # B01060001) with 30 seconds on and 30 seconds off cycles to produce fragments between 200 and 500 base pairs. For immunoprecipitation, 100 μg of sonicated chromatin was used and 10 μg (10%) was saved as an input control. To probe for active enhancers in both undifferentiated and differentiated cells, samples were incubated at 4 °C overnight with an H3K27ac primary antibody (Active Motif, Cat # 39133) or an IgG control (Sigma, Cat # R9133). For CTCF sites, CTCF(D31H2) XP (Cell Signaling Technology, cat # 3418) was used as primary antibody. For secondary antibody, A/G magnetic beads (Pierce, Cat # 88802) were added to the samples prior to an additional incubation for 2 h at 4 °C. The beads were then washed with a series of salt buffers before elution. The immunoprecipitated and input control DNA was purified using A QIAprep Spin Miniprep Kit (Qiagen, Cat # 27104).
Libraries for Input and IP samples were prepared by the Van Andel Genomics Core from 10 ng of input material and all available IP material using the KAPA Hyper Prep Kit (v5.16) (Kapa Biosystems, Wilmington, MA USA). Prior to PCR amplification, end-repaired and A-tailed DNA fragments were ligated to Bio Scientific NEXTflex Adapters (Bioo Scientific, Austin, TX, USA).  The quality and quantity of the finished libraries were assessed using a combination of Agilent DNA High Sensitivity chip (Agilent Technologies, Inc.), QuantiFluor dsDNA System (Promega Corp., Madison, WI, USA), and Kapa Illumina Library Quantification qPCR assays (Kapa Biosystems). Sequencing (75 bp, single end) was performed on an Illumina NextSeq 500 sequencer using a 75-bp sequencing kit (v2) (Illumina Inc., San Diego, CA, USA).  Base calling used Illumina NextSeq Control Software (NCS) v2.0, and the output of NCS was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v1.9.0.

treatment_protocol: Prior to differentiation, cells were seeded at 3.5 x 10^6 per T75 flask containing complete growth medium and incubated at 37 °C for 24 h. For induction of differentiation, culture medium was changed to freshly prepare DMEM:F12 with 2 mM L-glutamine, 1X N-2, 1 mM cAMP (Carbosynth, Cat # ND07996), 1 mg/mL tetracycline (Sigma, Cat # T7660), and 2 ng/mL glial cell line-derived neurotrophic factor (GDNF) (Sigma, Cat # G1777).

tag: cell line

value: Lund human mesencephalic cells (LUHMES)

tag: Stage

value: neural progenitor cells, undifferentiated

tag: Sex

value: female

tag: passages


title: LUHMES differentiated ChIP-seq H3k27ac Sample 1

description:
sonicated fixed chromatin
extraction 6 days post- differentiation protocol
processed data files:
Table_S2_H3K27ac.xlsx
chip_h3k27ac_luhd.bw

value: dopaminergic neurons, differentiated


title: LUHMES undifferentiated ChIP-seq CTCF Sample 2


title: LUHMES undifferentiated ChIP-seq H3k27ac Sample 1

description:
sonicated fixed chromatin
processed data files:
Table_S2_H3K27ac.xlsx
chip_h3k27ac_luhmes.bw

extract_protocol:
For ChIP experiments, we used previously published protocols (Rhie et al., 2014). Briefly, about 1 x 10^7 cells were fixed by adding fresh formaldehyde directly to the culture medium at a final concentration of 1%. The reaction was quenched with 10X (1.15 M) glycine for 5 min at room temperature. Chromatin from fixed cells was sonicated using a Bioruptor Pico (Diagenode, Cat # B01060001) with 30 seconds on and 30 seconds off cycles to produce fragments between 200 and 500 base pairs. For immunoprecipitation, 100 μg of sonicated chromatin was used and 10 μg (10%) was saved as an input control. To probe for active enhancers in both undifferentiated and differentiated cells, samples were incubated at 4 °C overnight with an H3K27ac primary antibody (Active Motif, Cat # 39133) or an IgG control (Sigma, Cat # R9133). For CTCF sites, CTCF(D31H2) XP (Cell Signaling Technology, cat # 3418) was used as primary antibody. For secondary antibody, A/G magnetic beads (Pierce, Cat # 88802) were added to the samples prior to an additional incubation for 2 h at 4 °C. The beads were then washed with a series of salt buffers before elution. The immunoprecipitated and input control DNA was purified using A QIAprep Spin Miniprep Kit (Qiagen, Cat # 27104).
Libraries for Input and IP samples were prepared by the Van Andel Genomics Core from 10 ng of input material and all available IP material using the KAPA Hyper Prep Kit (v5.16) (Kapa Biosystems, Wilmington, MA USA). Prior to PCR amplification, end-repaired and A-tailed DNA fragments were ligated to Bio Scientific NEXTflex Adapters (Bioo Scientific, Austin, TX, USA).  The quality and quantity of the finished libraries were assessed using a combination of Agilent DNA High Sensitivity chip (Agilent Technologies, Inc.), QuantiFluor dsDNA System (Promega Corp., Madison, WI, USA), and Kapa Illumina Library Quantification qPCR assays (Kapa Biosystems). Sequencing (75 bp, single end) was performed on an Illumina NextSeq 500 sequencer using a 75-bp sequencing kit (v2) (Illumina Inc., San Diego, CA, USA).  Base calling used Illumina NextSeq Control Software (NCS) v2.0, and the output of NCS was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v1.9.0.


title: LUHMES differentiated ChIP-seq CTCF Sample 2

description:
sonicated fixed chromatin
extraction 6 days post- differentiation protocol
processed data files:
luhd_ctcf_32517.bed
merged_luhmes_ctcf_040317.bed
ave_chip_ctcf_luhd.bw


title: LUHMES differentiated ChIP-seq CTCF Sample 1


title: LUHMES undifferentiated RNA-seq Sample 6

description:
sample name: LU6
processed data files:
Table_S1.xlsx
expressed_nochange.bed
de_neg.bed
de_pos.bed

data_processing:
Following sequencing, fastq files were trimmed using Trimmomatic V0.36 and the settings: ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50
Trimmed fastq files were aligned to HG19 using STAR v2.5 (Dobin and Gingeras, 2015).
Alignments (bam files) were converted to feature counts using HTSeq v0.6.0 referenced against the ENSEMBLE annotation of HG19: Homo_sapiens.GRCh37.87.gtf counting against the feature “exon”, grouped by “gene_id”, and using the strand parameter “reverse”.  This set included exon locations for 57,905 genomic entities including pseudogenes, lncRNAs, and 20,356 protein coding genes.
The resulting gene_id map counts were normalized using edgeR (TMM) and tested for significant differential expression with Limma and Voom, in R (v3.3.1) (Law et al., 2014; Ritchie et al., 2015; Robinson and Oshlack, 2010).
The normalized count data for all 18 datasets revealed, through principle component analysis (PCA), that there was very high similarity between paired-end and single-end mapping relative to differentiation status. Therefore, the datasets were combined for analysis. However, Voom weighted the single end sequencing counts more highly than paired-end data – meaning statistical significance is largely independent of the paired-end data sets. More complicated modeling designs, which treated the paired-end and single-end libraries as separate design variables, produced roughly the same end results. It should also be noted that Voom recommends an initial filtering out of low count genes prior to statistical modeling. We found that the significant DE results differed little between different pre-filtering conditions, only serving to alter the marginal DE cases and to reduce the gene set size, and so elected to jointly evaluate all 57,905 genes without a filtering step. The log2 FC and p-value for DE, as well as normalized log2CPM were derived for each gene. The processed data from both a unfiltered 1 batch and filtered 2-batch model are included.
genome build: hg19
Supplementary_files_format_and_content: Table_S1.xlsx: excel file with three tabs containing mapped exon RNA-seq counts, log2(normalized count per million) data and DE stats using design model 1, and log2(normalized count per million) data and DE stats using design model 2 (with count filter and 2 batch model).
.bed - tab delimited txt files in BED format containing genomic coordinates.

extract_protocol:
RNA extractions were done using the Qiagen RNeasy Mini Kit (Cat# 74104).
Libraries were prepared by the Van Andel Research Institute Genomics Core from 1 μg of material using the KAPA Stranded mRNA-seq Kit (v4.16) (Kapa Biosystems, Wilmington, MA USA). RNA was sheared to 250-300 bp. Prior to PCR amplification, cDNA fragments were ligated to Bio Scientific NEXTflex Adapters (Bioo Scientific, Austin, TX, USA). The quality and quantity of the finished libraries were assessed using a combination of Agilent DNA High Sensitivity chip (Agilent Technologies, Inc.), QuantiFluor dsDNA System (Promega Corp., Madison, WI, USA), and Kapa Illumina Library Quantification qPCR assays (Kapa Biosystems).


title: LUHMES differentiated RNA-seq Sample 2

description:
This sample was sequenced twice, once in single-end mode and once in paired-end mode. Thus, this sample is associated with two SRR, one for the single-end file and one for the paired-end files.
extraction 6 days post- differentiation protocol
sample name: LD2, LD8pe
processed data files:
Table_S1.xlsx
expressed_nochange.bed
de_neg.bed
de_pos.bed
ave_rnaseq_pe_20817_luhmes_dif.bw

data_processing:
Following sequencing, fastq files were trimmed using Trimmomatic V0.36 and the settings: ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50
Trimmed fastq files were aligned to HG19 using STAR v2.5 (Dobin and Gingeras, 2015).
Alignments (bam files) were converted to feature counts using HTSeq v0.6.0 referenced against the ENSEMBLE annotation of HG19: Homo_sapiens.GRCh37.87.gtf counting against the feature “exon”, grouped by “gene_id”, and using the strand parameter “reverse”.  This set included exon locations for 57,905 genomic entities including pseudogenes, lncRNAs, and 20,356 protein coding genes.
The resulting gene_id map counts were normalized using edgeR (TMM) and tested for significant differential expression with Limma and Voom, in R (v3.3.1) (Law et al., 2014; Ritchie et al., 2015; Robinson and Oshlack, 2010).
The normalized count data for all 18 datasets revealed, through principle component analysis (PCA), that there was very high similarity between paired-end and single-end mapping relative to differentiation status. Therefore, the datasets were combined for analysis. However, Voom weighted the single end sequencing counts more highly than paired-end data – meaning statistical significance is largely independent of the paired-end data sets. More complicated modeling designs, which treated the paired-end and single-end libraries as separate design variables, produced roughly the same end results. It should also be noted that Voom recommends an initial filtering out of low count genes prior to statistical modeling. We found that the significant DE results differed little between different pre-filtering conditions, only serving to alter the marginal DE cases and to reduce the gene set size, and so elected to jointly evaluate all 57,905 genes without a filtering step. The log2 FC and p-value for DE, as well as normalized log2CPM were derived for each gene. The processed data from both a unfiltered 1 batch and filtered 2-batch model are included.
genome build: hg19
Supplementary_files_format_and_content: Table_S1.xlsx: excel file with three tabs containing mapped exon RNA-seq counts, log2(normalized count per million) data and DE stats using design model 1, and log2(normalized count per million) data and DE stats using design model 2 (with count filter and 2 batch model).
.bed - tab delimited txt files in BED format containing genomic coordinates.
.bw - bigWig files containing aligned sequence map densities.


title: LUHMES undifferentiated RNA-seq Sample 2

description:
This sample was sequenced twice, once in single-end mode and once in paired-end mode. Thus, this sample is associated with two SRR, one for the single-end file and one for the paired-end files.
sample name: LU2, LU8pe
processed data files:
Table_S1.xlsx
expressed_nochange.bed
de_neg.bed
de_pos.bed
ave_rnaseq_pe_20817_luhmes_undiff.bw


title: LUHMES differentiated RNA-seq Sample 3

description:
This sample was sequenced twice, once in single-end mode and once in paired-end mode. Thus, this sample is associated with two SRR, one for the single-end file and one for the paired-end files.
extraction 6 days post- differentiation protocol
sample name: LD3, LD9pe
processed data files:
Table_S1.xlsx
expressed_nochange.bed
de_neg.bed
de_pos.bed
ave_rnaseq_pe_20817_luhmes_dif.bw


title: LUHMES undifferentiated RNA-seq Sample 3

description:
This sample was sequenced twice, once in single-end mode and once in paired-end mode. Thus, this sample is associated with two SRR, one for the single-end file and one for the paired-end files.
sample name: LU3, LU9pe
processed data files:
Table_S1.xlsx
expressed_nochange.bed
de_neg.bed
de_pos.bed
ave_rnaseq_pe_20817_luhmes_undiff.bw


title: LUHMES undifferentiated RNA-seq Sample 1

description:
This sample was sequenced twice, once in single-end mode and once in paired-end mode. Thus, this sample is associated with two SRR, one for the single-end file and one for the paired-end files.
sample name: LU1, LU7pe
processed data files:
Table_S1.xlsx
expressed_nochange.bed
de_neg.bed
de_pos.bed
ave_rnaseq_pe_20817_luhmes_undiff.bw


title: LUHMES differentiated RNA-seq Sample 1

description:
This sample was sequenced twice, once in single-end mode and once in paired-end mode. Thus, this sample is associated with two SRR, one for the single-end file and one for the paired-end files.
extraction 6 days post- differentiation protocol
sample name: LD1, LD7pe
processed data files:
Table_S1.xlsx
expressed_nochange.bed
de_neg.bed
de_pos.bed
ave_rnaseq_pe_20817_luhmes_dif.bw


title: LUHMES differentiated RNA-seq Sample 6

description:
extraction 6 days post- differentiation protocol
sample name: LD6
processed data files:
Table_S1.xlsx
expressed_nochange.bed
de_neg.bed
de_pos.bed


title: LUHMES differentiated RNA-seq Sample 5

description:
extraction 6 days post- differentiation protocol
sample name: LD5
processed data files:
Table_S1.xlsx
expressed_nochange.bed
de_neg.bed
de_pos.bed


title: LUHMES undifferentiated ChIP-seq H3k27ac Sample 2


title: Bel-7402_Baicalein_80uM_rep2

first: Zongfang

last: Li

address: 157 W 5th RD

department: the second affiliated hospital

institute: Xi’ an Jiaotong University

hyb_protocol: Labeled cDNA was hybridized to the array for 16 hours at 48 ℃ and 60 rpm in Hybridization Oven 645 and were then washed and stained using the GeneChip ® Hybridization Wash and Stain Kit in the 450 Fluidics Station according to the manufacturer's instructions.

scan_protocol: GeneChips were scaned by using Affymetrix GeneChip Command Console (AGCC) which installed in GeneChip Scanner 3000 7G.

data_processing: The raw data (CEL files) were extracted from the scanned images using the Affymetrix GeneChip Command Console. Expression data were generated by Affymetrix.

label: Biotin

source_name: Bel-7402 cell line treated with 80 uM  baicalein for 24h

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA by using Ambion WT Expression Kit and GeneChip WT Terminal Labeling and Controls Kit.

growth_protocol: Human  hepatocellular carcinoma cell lines Bel-7402 was cultured in Dulbecco’s modified Eagle’s medium (Hyclone, USA) supplemented with 10% fetal bovine serum (Gibco, USA), 1% penicillin-streptomycin (100 U/ml penicillin and 100 μg/ml streptomycin; Hyclone, USA) at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol: After a 24h incubation, the cell were harvested and the total RNA was extracted using TRIzol reagent (Invitrogen, USA) according to the manufacturers’ instructions.

treatment_protocol: The cell lines Bel-7402 was seeded in 6-well plate at a concentration of 2×105 per well and incubated overnight. Then the cells was treated with various concentration (0,40 and 80μM) of baicalein dissolved in DMSO (final DMSO concentration in growth media, 0.1%) for 24h.

value: Hepatocellular carcinoma


title: Bel-7402_Baicalein_80uM_rep1


title: Bel-7402_Baicalein_40uM_rep1

source_name: Bel-7402 cell line treated with 40 uM  baicalein for 24h


title: LUHMES differentiated ChIP-seq H3k27ac Sample 2


title: LUHMES undifferentiated RNA-seq Sample 5

description:
sample name: LU5
processed data files:
Table_S1.xlsx
expressed_nochange.bed
de_neg.bed
de_pos.bed


title: Bel-7402_Baicalein_40uM_rep3


title: Bel-7402_DMSO_rep3

source_name: Bel-7402 cell line treated with 0.1%  DMSO for 24h


title: Bel-7402_Baicalein_40uM_rep2


title: LUHMES differentiated RNA-seq Sample 4

description:
extraction 6 days post- differentiation protocol
sample name: LD4
processed data files:
Table_S1.xlsx
expressed_nochange.bed
de_neg.bed
de_pos.bed


title: LUHMES undifferentiated RNA-seq Sample 4

description:
sample name: LU4
processed data files:
Table_S1.xlsx
expressed_nochange.bed
de_neg.bed
de_pos.bed


title: Bel-7402_Baicalein_80uM_rep3


title: Bel-7402_DMSO_rep2


title: T21-0-2

city: Tartu

first: Hindrek

last: Teder

address: Tiigi 61b

country: Estonia

institute: The Competence Centre on Health Technologies

description:
acoustically sheared
counts_umi2.tsv

data_processing:
Library strategy: TAC-seq
BCLs were converted to FASTQs using Illumina's bcl2fastq2 (version 2.20) with --barcode-mismatches 1
Reads were converted to FASTA format, trimmed to 62 bp, shorter than 62 bp reads were removed using FASTX-Toolkit (version 0.0.14)
UMI subsequences were joined using AWK
Reads were demultiplexed by target sequence using FASTX-Toolkit with 6 mismatches
Target sequence (54 bp) were trimmed, reads with N nucleotide were removed using FASTX-Toolkit
Merge sequences by UMI using FASTX-Toolkit
Read and molecule counts were calculated per sample and target (UMI thresholds 1 and 2 were used)
Supplementary_files_format_and_content: tab-delimited text file containing targeted read and molecule counts of each sample at fixed UMI thresholds

extract_protocol:
Genomic DNAs from GM01359 and GM04616 cell lines (NIGMS Human Genetic Cell Repository at the Coriell Institute of Medical Research (USA)) were extracted using DNeasy Blood and Tissue kit (Qiagen). To mimic cfDNA, the genomic DNAs were fragmented to 150-200 bp using Covaris M220 Focused-ultrasonicator (Thermo Fisher) with following settings: 50 μl volume, 10% duty cycle, 75 W peak incident power, 200 cycles per burst and 360 s. Concentrations were quantified by Qubit dsDNA HS (Thermo Fisher).
10 ng of acoustically sheared (Covaris) cell-free like DNAs were combined to create excess rates of chromosome 21 above diploidy level, that mimic 5 to 30% fetal fraction. 100% fraction is the GM04616 cell line DNA with trisomy 21. Samples were pipetted into strip tubes, adding 1 μl of 5 µM TAC-seq probe mixture and 1 µl 10× hybridization buffer, containing 100 mM Tris-HCl (pH 7.5) (Sigma-Aldrich), 500 mM KCl (Sigma-Aldrich), 0.2% Tween-20 (Sigma-Aldrich) and 0.1 mM EDTA (Sigma-Aldrich). The final hybridization volume was 12 µl. The content was mixed on vortex and centrifuged briefly. Strip tubes were placed on thermocycler, denatured 2 min at 98°C and following 2 h at 60°C for hybridization. After hybridization, thermostable ligase reaction master mix was added on thermocycler, keeping constant (60°C) hybridization temperature. Following, 2.5 µl Taq DNA ligase mixture, containing 1.5 µl 10× Taq DNA ligation buffer (NEB) and 1 U Taq DNA ligase (NEB) was added to each individual reaction tube and mixed by pipetting. Ligation reaction was stopped after 20 min incubation by placing reaction tubes on ice. 25 μl of previously combined Dynabeads MyOne Carboxylic Acid beads (3 µl) (Thermo Fisher) and 22 µl of capture buffer was added to ice-cooled ligated sample. The content was mixed by vortex. The capture was carried out for 10 min at RT, and after that the samples were placed on DynaMag-96 Side Magnet (Thermo Fisher) holding 8-well strip tubes on VersiPlate Frame (Thermo Fisher). The clean supernatant was removed. The beads on magnet were washed once with 50 µl fresh 80% ethanol. Ethanol was removed by pipetting, and the clean pellet, without ethanol drops, was dried for 2 min. Once beads were dry, strip tubes were removed from the magnet and 18 µl of PCR master mix was added directly to beads. The master mix contained 1× proofreading HOT FIREPol Blend Master Mix (SolisBiodyne, Tartu, Estonia) and 250 nM TAC-seq Left primer. In addition to universal TAC-seq Left, 16 different TAC-seq barcode oligonucleotides were used to introduce a six-nucleotide barcode to each studied sample. For that, 2 µl of 5 µM TAC-seq Barcoded primers were added individually to each PCR reaction. Strip tubes were closed with clean domed caps, mixed on vortex until all beads were suspended. The ERCC spike-in reaction was incubated at 95°C for 12 min, followed by two cycles of 95°C for 20 s, 57°C for 60 s and 72°C for 20 s. In addition, 19 cycles of 95°C for 20 s, 65°C for 20 s and 72°C for 20 s with a final extension at 72°C for 1 min using the default ramp speed of the T100 cycler (Bio-Rad) were performed. PCR products were pooled together into 1.5 ml tube. The pooled tube was placed on magnet to remove carboxylated beads before the following column purification. Clear supernatant was purified with DNA Clean & Concentrator-5 column (Zymo Research) and eluted with 50 µl EB. The library was size-selected using AMPure XP beads (Beckman Coulter) in a single-step selection to reduce 81 bp linear PCR double-stranded by-product. 50 µl beads were added to 50 µl of the purified PCR product, incubated for 5 min at room temperature and captured by a magnet for 3 min. After incubation on magnet, the supernatant was discarded and the remaining beads were centrifuged at 500×g for 10 s. After centrifugation, the beads were placed again on the magnet and all remaining supernatant was removed. The beads were eluted directly without ethanol washing in 25 µl of EB and incubated for 1 min at RT. Finally, the eluted library was transferred to a clean tube after 1 min incubation on the magnet. The library (single 180 bp product) was visualized on a TapeStation High Sensitivity D1000 ScreenTape (Agilent Technologies) and quantified using KAPA Library Quantification Kit (Roche).
Library was analyzed by Illumina NextSeq500 instrument using custom LNA barcode primer, 1.8 pM loading concentration, 63 bp for read-1 and 6 bp for barcode read-2

tag: t21 cell line proportion

tag: t13 cell line

tag: t13 cell line proportion


title: T21-15-2

description:
acoustically sheared
counts_umi2.tsv

tag: t21 cell line


title: T21-10-1

description:
acoustically sheared
counts_umi2.tsv


title: T21-100-2

description:
acoustically sheared
counts_umi2.tsv


title: T21-0-1

description:
acoustically sheared
counts_umi2.tsv


title: T21-5-1

description:
acoustically sheared
counts_umi2.tsv


title: T21-30-1

description:
acoustically sheared
counts_umi2.tsv


title: T21-100-1

description:
acoustically sheared
counts_umi2.tsv


title: T21-20-2

description:
acoustically sheared
counts_umi2.tsv


title: T21-30-2

description:
acoustically sheared
counts_umi2.tsv


title: T21-25-2

description:
acoustically sheared
counts_umi2.tsv