title: S17-3

value: two-month-old

tag: period

value: early

tag: progress of activity

value: Free moving

tag: noise intensity and atmospheric pressure

value: 10dbA,normal atmospheric pressure

value: Hypothalamus


title: S13-3

status: Public on Dec 30 2020

type: SRA

city: Guangzhou

first: Gan

last: Xihui

address: School of Life Sciences Building 438, No. 132 Waihuan East Rd., Guangzhou University City, Panyu District

department: School of Life Sciences

country: China

institute: Sun Yat-sen University

library_source: transcriptomic

data_processing:
Illumina CASAVA 1.8 software used for basecalling.
Qualified reads were obtained after removing raw reads with adapters or of low quality and then aligned to the mouse genome by HISAT with default parameters.
RSeQC was used to measured gene expression abundance as reads per kilobase per million mapped reads (RPKM).
Differential expression analysis of two samples was performed using the previous statistics model. The resulting P-values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate. P-value <0.05 were assigned as differentially expressed gene.

molecule: total RNA

organism: Mus musculus

source_name: early_Free moving_10dbA_normal air pressure_hypothalamus cells

extract_protocol:
RNA was extracted with Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

tag: age

tag: tissue


title: Lung_Air_24hr_Rat84

type: RNA

city: Aberdeen Proving Ground

first: Heidi

last: Hoard-Fruchey

state: MD

address: 2900 Ricketts Point Rd

country: USA

institute: USAMRICD

description: Rat 84 24hr Air Lu

hyb_protocol: The complimentary RNA (cRNA) produced from the isolated total RNA was then fragmented and hybridized to GeneChip HT RG-230PM array plates (Affymetrix) according to the manufacturer’s instructions.

scan_protocol: The HT RG-230PM array plates were scanned using an Affymetrix GeneTitan system.

data_processing:
Raw data (CEL files) were imported into Partek Genomic suite v6.6 (Partek Incorporated, St. Louis, MO) and normalized using robust multiarray averaging (RMA)
affymetrix-algorithm-name = rma
affymetrix-algorithm-version = 1.0
affymetrix-array-type = HT_Rat230_PM
program-name = Expression Console
program-version = 1.4.1.46

label: Biotin

organism: Rattus norvegicus

label_protocol: The isolated RNA was amplified and biotinylated using the GeneChip 3’ in vitro transcription (IVT) Plus reagent kit (Affymetrix; Santa Clara, CA) according to the manufacturer’s instructions.

growth_protocol: Male Sprague-Dawley rats (300-400 g, Charles-River Laboratories, Wilmington, MA) were individually housed under standard conditions (12 hour light/dark cycle) with standard rodent chow and water provided ad libitum.

extract_protocol: Following eutanasia (ketamine (90 mg/kg) and xylazine (10 mg/kg)  by im followed by exsanguination), tissues were flash frozen in liquid nitrogen and stored at -80 until processing. Tissues were cryopulverized and total RNA isolated using RNeasy Plus mini kits (Qiagen; Germantown, MD) according to manufacturer's instructions with a DNase digestion step. Blood samples were collected via heart stick. RNA was isolated from collected blood samples and processed using the RNeasy Protect Animal Blood System (Qiagen) according to manufacturer’s instructions.

treatment_protocol: Whole-body PH3 inhalation exposures were conducted as described in Wong et al., 2017. PH3 concentrations was 15,480 ppm x minute (387 ppm x 40 minutes) and represents a “low” concentration Ct.

value: Sprague-Dawley

tag: Sex

value: male

value: adult

tag: treatment/exposure

value: Air

tag: treatment/exposure info

value: 0 ppm x 40 min (0 ppm x min)

tag: time point

value: 24 Hour

value: Lung


title: 6048_Follicular_2017-01-25 (batch 1)

city: Seattle

first: Sean

last: Hughes

state: WA

address: 850 Republican St

institute: University of Washington

hyb_protocol: standard as recommended by Illumina, except that hybridization was performed at 48C

scan_protocol: standard Illumina protocol using Illumina iScan system

data_processing: The data was preprocessed by Bioconductor lumi package (version 2.34.0). It was vst transformed and rsn normalized. Only probes with detection threshold < 0.05 in at least 10 samples were included in the analysis.

organism: Homo sapiens

source_name: Endocervical cytobrush from participant 6048 at the Follicular on 2017-01-25

label_protocol: Labeling was performed using 25 ng total RNA and the NuGEN Ovation PicoSL WTA System V2 and Encore BiotinIL kits.

extract_protocol: Total RNA was extracted using the Qiagen Rneasy Plus mini kit

tag: studyid

tag: date

tag: index

tag: rin

tag: enrollment

tag: status

value: Withdrawn

value: Positive

tag: progesterone

tag: bv

value: Y

tag: visit

value: Follicular

tag: drop

value: Don't drop

tag: batch


title: Brain_Air_24hr_Rat84

description: Rat 84 24hr Air Br

tag: strain

tag: age

value: Brain


title: 6020_NA_2016-08-25 (batch 1)

source_name: Endocervical cytobrush from participant 6020 at the NA on 2016-08-25

value: Drop for all:fourth visit


title: Brain_Air_24hr_Rat83

description: Rat 83 24hr Air Br

tag: Sex

tag: tissue


title: 6030_Luteal_2016-10-18 (batch 1)

source_name: Endocervical cytobrush from participant 6030 at the Luteal on 2016-10-18

value: LTFU

value: Atypical

value: N

value: Luteal

value: Drop for all:Hsv2 ambiguous


title: Lung_Air_24hr_Rat83

description: Rat 83 24hr Air Lu

value: Sprague-Dawley

value: male

value: adult

tag: treatment/exposure

tag: treatment/exposure info


title: 6022_Follicular_2016-07-05 (batch 1)

source_name: Endocervical cytobrush from participant 6022 at the Follicular on 2016-07-05

tag: studyid


title: 6017_Follicular_2016-05-24 (batch 1)

source_name: Endocervical cytobrush from participant 6017 at the Follicular on 2016-05-24

tag: date

value: Negative


title: met_rep2

city: Tel-Aviv

first: Katherine

last: Domb

address: Haim Levanon st.

department: Gray Faculty of Medical and Health Sciences

country: Israel

institute: Tel Aviv University

data_processing:
Adaptor and quality trimming using TrimGalore v0.6.0 with Cutadapt v1.15
Alignment to the reference genome and counting reads per gene/TE in the supplied annotation file, using STAR v2.7.0f
Genome_build: Ppatens v3.0
Supplementary_files_format_and_content: tab-delimited text file with raw read counts assigned to each of the annotated features (gene or transposable element), in each sample

organism: Physcomitrium patens

source_name: protonema

growth_protocol: 7 days on BCDAT media, 25 °C,  16-h light and 8-h dark regime

extract_protocol:
Total RNA was extracted from 7 days old protonema using SV Total RNA Isolation System (Promega, USA) and DNase treatment (Thermo Fisher Scientific, USA).
The polyA fraction (mRNA) was purified from 500 ng of total input RNA, followed by fragmentation and the generation of double-stranded cDNA. Then, Agencourt Ampure XP beads cleanup (Beckman Coulter), end repair, A base addition, adapter ligation and PCR amplification steps were performed. Libraries were quantified by Qubit (Thermo fisher scientific) and TapeStation (Agilent).

tag: genotype

value: met

tag: cultivar

value: Grandsen

value: 7 days


title: S5-2

source_name: early_Hind limb unloading_10dbA_normal air pressure_hypothalamus cells

value: two-month-old

tag: period

value: early

tag: progress of activity

value: Hind limb unloading

tag: noise intensity and atmospheric pressure

value: 10dbA,normal atmospheric pressure

value: Hypothalamus


title: 6020_Follicular_2016-06-17 (batch 1)

source_name: Endocervical cytobrush from participant 6020 at the Follicular on 2016-06-17

tag: index

tag: rin

tag: enrollment

tag: status

value: Complete

tag: progesterone

tag: bv

value: Follicular

value: Don't drop


title: 6007_Follicular_2016-04-26 (batch 1)

source_name: Endocervical cytobrush from participant 6007 at the Follicular on 2016-04-26

value: Withdrawn

value: Positive

value: N

tag: visit

tag: drop

value: Drop for microarray:PCA outlier

tag: batch


title: Lung_PH3_24Hr_Rat70

description: Rat 70 24hr PH3 Lu

tag: strain

value: Sprague-Dawley

tag: Sex

value: male

tag: age

value: adult

tag: treatment/exposure

tag: treatment/exposure info

value: 387 ppm  x 40 min (15,480 ppm x min)

tag: time point

value: 24 Hour

tag: tissue

value: Lung


title: 6022_Luteal_2016-07-19 (batch 1)

source_name: Endocervical cytobrush from participant 6022 at the Luteal on 2016-07-19

tag: studyid

tag: date

value: LTFU

value: Y

value: Luteal


title: Kidney_Air_24hr_Rat83

description: Rat 83 24hr Air K

value: Air

value: 0 ppm x 40 min (0 ppm x min)

value: Kidney


title: met_rep1

tag: genotype

value: met

tag: cultivar

value: Grandsen

value: 7 days


title: cmt_rep1

value: cmt


title: S1-2

value: two-month-old

tag: period

value: early

tag: progress of activity

value: Hind limb unloading

tag: noise intensity and atmospheric pressure

value: 10dbA,normal atmospheric pressure

value: Hypothalamus


title: drm12_rep2


title: S21-2


title: S9-3

value: Free moving


title: drm12_rep1


title: S17-2


title: 6007_Luteal_2016-04-06 (batch 1)

source_name: Endocervical cytobrush from participant 6007 at the Luteal on 2016-04-06

tag: index

tag: rin

tag: enrollment

tag: status

value: Withdrawn

value: Positive

tag: progesterone

tag: bv

value: N

tag: visit

value: Drop for microarray:PCA outlier


title: wt rep2

value: wt

tag: age


title: Brain_PH3_24Hr_Rat70

description: Rat 70 24hr PH3 Br

tag: strain

value: Sprague-Dawley

tag: Sex

value: male

value: adult

tag: treatment/exposure

tag: treatment/exposure info

value: 387 ppm  x 40 min (15,480 ppm x min)

tag: time point

value: 24 Hour

value: Brain


title: 6020_Ring_2016-09-22 (batch 1)

source_name: Endocervical cytobrush from participant 6020 at the Ring on 2016-09-22

tag: studyid

tag: date

value: Complete

value: Negative

value: Ring

tag: drop

value: Don't drop

tag: batch


title: S13-2

value: two-month-old

tag: period

value: early

tag: progress of activity

value: Hind limb unloading

tag: noise intensity and atmospheric pressure

value: 10dbA,normal atmospheric pressure

tag: tissue

value: Hypothalamus


title: Kidney_PH3_24Hr_Rat70

description: Rat 70 24hr PH3 K

value: Kidney


title: wt rep1

tag: genotype

value: wt

tag: cultivar

value: Grandsen

value: 7 days


title: Heart_PH3_24Hr_Rat70

description: Rat 70 24hr PH3 H

value: Sprague-Dawley

value: male

value: adult

value: Heart


title: S5-1

value: Free moving


title: S9-2


title: BIN67_Parent_BRG1_RNAseq_Rep4

city: Chapel Hill

first: Bernard

middle: E.

last: Weissman

state: NC

address: 450 West Drive

department: Pathology and Laboratory Medicine

institute: University of North Carolina at Chapel Hill

description:
BIN67 Parental cells, BRG1 transfected - Rep 4
BIN67_Parental_RNAseq_raw_gene_counts.txt

data_processing:
Fastq files were initially analyzed by fastqc (v0.11.5). Reads were aligned with STAR (v2.5.3a) to GENCODE v24 (hg38) using the 2-pass method.  Aligned reads were quantified by salmon (v0.8.2) for transcripts per million (TPM) counts. TPMs were summarized to gene level using tximport (v1.10.1) in R. Differentially expressed genes between BRG1 and Control samples using DESeq2 (v1.22.2).
IGV browser tracks (bigwig) were generated on the merged biological replicates by deeptools (v3.2.) bamCoverage with a binsize of 30 and normalized using RPKMs.
Genome_build: hg38 (GENCODE v24)
Supplementary_files_format_and_content: bigwig = normalized RPKM signal tracks of merged samples
Supplementary_files_format_and_content: raw counts = raw unnormalized counts summarized to gene level using tximport (countsFromAbundance = "no"). Matrix input for DESeq2 differential expression analysis
Supplementary_files_format_and_content: DESeq2 Results = excel file of DESeq2 results

source_name: Cell Line

growth_protocol: BIN67 cells were cultured in RPMI-1640 (Gibco #11875-093) supplemented with 10% FBS and maintained at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
RNA from frozen cell pellets was extracted using the Zymo Quick-RNA Miniprep Kit (Zymo cat# R1054).
Total RNA was prepared using the Illumina TruSeq mRNA v2 kit with an input of 500ng of RNA for each sample to produce unstranded RNA libraries following the manufacturer’s protocol. Final RNA libraries were quantified using the Qubit High Sense Reagent kit and Agilent Tapestation HSD1000 tapes. Libraries were equimolar pooled and paired end sequenced across three lanes of a HiSeq4000 (paired end x 78 bp).

treatment_protocol: BIN67 cells were co-transfected (FuGENE 6, Promega #E269A) with either control (pCMV-neo or pCDNA3-neo) or BRG1 (PBJ5-BRG1) plasmids at a 10:1 ratio to a plasmid containing puromycin resistance (pBABE-puro). Twenty-four hours after transfection, cells were placed on 2 µg/ml puromycin for 3 days and then harvested for RNA-seq analysis.

tag: cell line

tag: transfected vector


title: S1-1

tag: strain

tag: age


title: 6053_Luteal_2017-04-04 (batch 1)

source_name: Endocervical cytobrush from participant 6053 at the Luteal on 2017-04-04

tag: index

tag: rin

tag: enrollment

tag: status

value: Complete

value: Positive

tag: progesterone

tag: bv

value: N

tag: visit

value: Luteal


title: 6053_Ring_2017-06-15 (batch 1)

source_name: Endocervical cytobrush from participant 6053 at the Ring on 2017-06-15

tag: studyid

tag: date

value: Ring

tag: drop

value: Don't drop

tag: batch


title: S21-1

value: two-month-old

tag: period

value: early

tag: progress of activity

tag: noise intensity and atmospheric pressure

value: 10dbA,normal atmospheric pressure

tag: tissue


title: 6053_Follicular_2017-03-21 (batch 1)

source_name: Endocervical cytobrush from participant 6053 at the Follicular on 2017-03-21

value: Follicular


title: 6052_Luteal_2017-04-12 (batch 1)

source_name: Endocervical cytobrush from participant 6052 at the Luteal on 2017-04-12

value: Negative


title: 6020_Follicular_2016-06-30 (batch 1)

source_name: Endocervical cytobrush from participant 6020 at the Follicular on 2016-06-30

value: Don't drop:luteal changed to follicular


title: colo205_SF_rep.3

city: Daejeon

first: Seung Jin

last: Lee

address: 99 Daehak-ro, Yuseong-gu

department: College of pharmacy

country: South Korea

institute: Chungnam national university

description:
Gene expression data from the cells used as combination group treated for selumetinib followed by 5-FU (reverse sequence)
AF2

hyb_protocol: Following fragmentation, fragmented cDNA were hybridized for 16 hr at 45C on Affymetrix GeneChip® Human Gene 2.0 ST Array. The GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The Robust Multiarray Average (RMA) algorithm implemented in Affymetrix Expression Console software (version1.3.1) was used to normalize the raw data. Highly expressed genes that showed over 2-fold difference between the signal values of control and test samples were selected for further study.

label: biotin

source_name: colo205_selumetinib for 48 hr followed by 5-FU for 24 hr

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 300 ng total RNA (GeneChip® WT Terminal Labeling and Controls Kit P/N 901525 1, Affymetrix).

growth_protocol: Colo 205 cell line was maintained RPMI media containing 10% FBS at 37℃ in humidified atmosphere with 5% CO2

extract_protocol: Total RNA was extracted with Trizol reagent according to the manufacturer's instructions.

treatment_protocol:
V samples: colo205 cells were treated with DMSO for 48 hr, washed, and subsequently exposed to DMSO for another 24hr.
F samples: colo205 cells were treated with 3 uM 5-FU for 48 hr, washed, and subsequently exposed to DMSO for another 24hr.
S samples: colo205 cells were treated with 0.1 uM selumetinib for 48 hr, washed, and subsequently exposed to DMSO for another 24hr.
FS samples: colo205 cells were treated with 3 uM 5-FU for 48 hr, washed, and subsequently exposed to 0.1 uM selumetinib for another 24hr.
SF samples: colo205 cells were treated with 0.1 uM selumetinib for 48 hr, washed, and subsequently exposed to 3 uM 5-FU for another 24hr

tag: cell line

tag: tissue source

value: colorectal adenocarcinoma

tag: treated with


title: colo205_SF_rep.2

description:
Gene expression data from the cells used as combination group treated for selumetinib followed by 5-FU (reverse sequence)
AF1

value: selumetinib for 48 hr followed by 5-FU for 24 hr


title: 6052_Ring_2017-08-23 (batch 1)

source_name: Endocervical cytobrush from participant 6052 at the Ring on 2017-08-23

tag: index

tag: rin


title: 6052_Follicular_2017-03-28 (batch 1)

source_name: Endocervical cytobrush from participant 6052 at the Follicular on 2017-03-28

tag: enrollment

tag: status


title: colo205_FS_rep.1

description:
Gene expression data from the cells used as combination group treated for 5-FU followed by selumetinib
FA

source_name: colo205_5-FU for 48 h followed by selumetinib for 24 hr


title: BIN67_Parent_BRG1_RNAseq_Rep3

description:
BIN67 Parental cells, BRG1 transfected - Rep 3
BIN67_Parental_RNAseq_raw_gene_counts.txt

tag: transfected vector


title: 6047_Ring_2017-07-20 (batch 1)

source_name: Endocervical cytobrush from participant 6047 at the Ring on 2017-07-20

tag: progesterone

tag: bv

tag: visit


title: S17-1

source_name: early_Free moving_10dbA_normal air pressure_hypothalamus cells

tag: strain

tag: age

value: Hypothalamus


title: BIN67_Parent_Control_RNAseq_Rep4

description:
BIN67 Parental cells, control transfected - Rep 4
BIN67_Parental_RNAseq_raw_gene_counts.txt

value: Control


title: BIN67_Parent_BRG1_RNAseq_Rep2

description:
BIN67 Parental cells, BRG1 transfected - Rep 2
BIN67_Parental_RNAseq_raw_gene_counts.txt


title: BIN67_Parent_BRG1_RNAseq_Rep1

description:
BIN67 Parental cells, BRG1 transfected - Rep 1
BIN67_Parental_RNAseq_raw_gene_counts.txt


title: S13-1

tag: period

value: Free moving


title: colo205_Sv_rep.3

description:
Gene expression data from the cells used as selumetinib alone, paired control for FA-treated group
AX2

source_name: colo205_selumetinib for 48 hr followed by vehicle for 24 hr


title: colo205_SF_rep.1

description:
Gene expression data from the cells used as combination group treated for selumetinib followed by 5-FU (reverse sequence)
AF


title: 6047_Follicular_2017-02-22 (batch 1)

source_name: Endocervical cytobrush from participant 6047 at the Follicular on 2017-02-22

tag: studyid

tag: date

value: Complete

tag: drop

tag: batch


title: S9-1

tag: progress of activity

tag: noise intensity and atmospheric pressure

tag: tissue


title: BIN67_Parent_Control_RNAseq_Rep2

description:
BIN67 Parental cells, control transfected - Rep 2
BIN67_Parental_RNAseq_raw_gene_counts.txt

tag: cell line


title: RNAseq KI5

city: Gainesville

first: Rene

last: Opavsky

state: FL

address: 2033 Mowry rd, CGRC r..265

department: Anatomy and cell biology

institute: University of FLORIDA

description:
MYC;DNMT3bCI/CI
MTCLs_FPKM.txt

data_processing:
Quality check, trimming, filtering, and alignment of reads to the Mus musculus UCSC mm10 reference genome was performed at the ICBR Bioinformatics Core (UF, Florida). Methylation calling was performed with Methyldackel (v 0.3.0.1) using the mm10-CG index. Only CpG sites with a minimum sequencing depth 5x were included in analysis. Differentially methylated regions (DMRs) were determined by Metilene and defined based on average of minimum three consecutive differentially methylated cytosines (DMCs) with methylation change of ≥20% in the same direction with p values < 0.05 (as determined by MWU test). Maximal base pair cut-off for a distance between consecutive DMCs in DMR was set to 50 bp.
For RNA-seq, trimmed sequencing data were first aligned to reference genome using STAR aligner. RNA-seq data with minimum mapped quality 50 were quantitated using the RNA-seq quantitation pipeline in SeqMonk software. For differentially expressed genes, only genes with a fold change ≥ 2 and a p-value < 0.05 (by DeSeq2) were considered to be significant.
Genome_build: mm10 - Mus musculus, hg19 - Homo sapiens
Supplementary_files_format_and_content: Processed data files are bigwig files, they contain methylation value for CpG sites whith coverage ≥ 5x

source_name: MYC-induced lymphoma sample

extract_protocol:
For WGBS, genomic DNA was isolated from two independent Dnmt3b+/+, Dnmt3bD/D and Dnmt3bCI/CI MYC induced T-cell lymphoma samples using phenol/chloroform. For RNA-seq, total RNA was isolated using trizol.
The WGBS libraries were prepared and sequenced on an Illumina NovaSeq6000 sequencer using 150 bp long paired-end reads. The RNAseq libraries were generated and sequenced on NovaSeq6000 platform using paired-end 150 bp runs.

value: lymph node

value: FVB

tag: genotype


title: colo205_FS_rep.3

description:
Gene expression data from the cells used as combination group treated for 5-FU followed by selumetinib
FA2

source_name: colo205_5-FU  for 48 h followed by selumetinib for 24 hr

tag: tissue source

tag: treated with


title: colo205_FS_rep.2

description:
Gene expression data from the cells used as combination group treated for 5-FU followed by selumetinib
FA1

value: 5-FU  for 48 h followed by selumetinib for 24 hr


title: colo205_Sv_rep.2

description:
Gene expression data from the cells used as selumetinib alone, paired control for FA-treated group
AX1

value: selumetinib for 48 hr followed by vehicle for 24 hr


title: 6046_Ring_2017-04-26 (batch 1)

source_name: Endocervical cytobrush from participant 6046 at the Ring on 2017-04-26

tag: index

tag: rin

tag: enrollment

tag: status

tag: progesterone

value: N

value: Ring

value: Don't drop


title: colo205_Sv_rep.1

description:
Gene expression data from the cells used as selumetinib alone, paired control for FA-treated group
AX


title: colo205_Fv_rep.3

description:
Gene expression data from the cells used as 5-FU alone, paired control for FA-treated group
FX2

source_name: colo205_5-FU for 48 hr followed by vehicle for 24 hr


title: BIN67_Parent_Control_RNAseq_Rep1

description:
BIN67 Parental cells, control transfected - Rep 1
BIN67_Parental_RNAseq_raw_gene_counts.txt

source_name: Cell Line

tag: transfected vector


title: 6062_Follicular_2017-07-10 (batch 1)

source_name: Endocervical cytobrush from participant 6062 at the Follicular on 2017-07-10

tag: studyid

value: Active

tag: bv

tag: visit

value: Drop for microarray:rerun in batch 2


title: RNAseq KI4

description:
MYC;DNMT3bCI/CI
MTCLs_FPKM.txt

tag: strain


title: 6046_Follicular_2017-02-08 (batch 1)

source_name: Endocervical cytobrush from participant 6046 at the Follicular on 2017-02-08

tag: date

value: Negative

value: Follicular

tag: drop

tag: batch


title: 6047_Luteal_2017-04-06 (batch 1)

source_name: Endocervical cytobrush from participant 6047 at the Luteal on 2017-04-06

value: Positive

value: Luteal


title: colo205_Fv_rep.2

description:
Gene expression data from the cells used as 5-FU alone, paired control for FA-treated group
FX1

tag: cell line

value: colorectal adenocarcinoma

value: 5-FU for 48 hr followed by vehicle for 24 hr


title: RNAseq KI3

description:
MYC;DNMT3bCI/CI
MTCLs_FPKM.txt

tag: tissue

tag: genotype


title: 6045_Ring_2017-03-22 (batch 1)

source_name: Endocervical cytobrush from participant 6045 at the Ring on 2017-03-22

value: Withdrawn


title: 6046_Luteal_2017-01-25 (batch 1)

source_name: Endocervical cytobrush from participant 6046 at the Luteal on 2017-01-25

value: Complete


title: BIN67_BRG1_ChIPseq_IP_Rep3

description:
BIN67 +BRG1 Transfected ChIPseq BRG1 IP  - Rep 3
BIN67_BRG1_ChIPseq_IP_merged.bw

library_source: genomic

data_processing:
Reads were aligned to hg38 using bowtie2 using the --sensitive parameters, and duplicates were removed using samtools.
Peaks were called on the merged samples (samtools merge) using macs2 (v2.1.2) with the following parameters: Qval = 0.01 --keep-dup all --nomodel --extsize 150.
Peak calls were filtered the peaks against the ENCODE blacklist regions.
For visualization, bigwig tracks were generated on merged replicates using deeptools (v2.5.2) bamCoverage tool with a binsize of 40bp and extending fragments to 200bp.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig = normalized RPKM signal tracks of merged samples
Supplementary_files_format_and_content: narrowPeak = peaks called from merged replicate samples for IP (BRG1).

molecule: genomic DNA

extract_protocol:
ChIP-seq was performed as previously described (Raab JR et. al. (2017) Epigenetics Chromatin). Briefly, cells (5e6 cells) were fixed for 30 minutes at 4°C in 0.3% methanol free formaldehyde, quenched for 5 minutes with 125mM glycine, washed 3 times and snap frozen in liquid nitrogen and stored at -80°C. Frozen pellets were thawed for 30 minutes on ice, resuspended  in 1mL swelling buffer (25mM HEPES + 1.5mM MgCl2 + 10mM KCl + 0.1% Igepal containing 1mM PMSF and 1X protease inhibitor cocktail, Roche) and incubated 10 minutes at 4°C. Cells were dounced 20 strokes with a “B” pestle and then nuclei were pelleted at 2000 rpm for 7 minutes at 4°C. The nuclei were washed with 10mL MNase Digestion Buffer (15mM Hepes pH 7.9, 60mM KCl, 15mM NaCl, 0.32M Sucrose) and pelleted at 2000 RPM for 7 minutes at 4°C. The pellet was then resuspended in 1mL MNase Digestion Buffer per 4e7 cells + 3.3µL 1M CaCl2 per mL + PMSF (1mM) and Protease Inhibitor Cocktail (1X, Roche), then incubated for 5 minutes at 37°C to warm. We added MNase (NEB M0247S 2000U/µl) at 0.5µL/1e7 cells and incubated for 15 minutes at 37°C with agitation. Following digestion, the MNase was chelated using 1/50 volume 0.5M EGTA on ice for 5 minutes. We added 1 volume of 2X IP Buffer (20mM TrisCl pH 8, 200mM NaCl, 1mM EDTA, 0.5mM EGTA), then passed the sample through a 21G needle 5 times and added Triton X-100 to 1% final concentration. The sample was cleared at 13,000 RPM for 15 minutes at 4°C and chromatin was incubated with BRG1 antibody (abcam #ab110641) overnight at 4°C. Antibody/chromatin complexes were captured with protein A magnetic beads (Bio-Rad) for 2 hours at 4°C, washed 5 times with wash buffer (50mM Hepes pH 7.9/500mM LiCl/1mM EDTA/1% IGEPAL-ca-630/0.7% Na-Deoxycholate) and once with 10mM Tris/1mM EDTA/50mM NaCl. DNA was eluted at 65°C with agitation using 100µL freshly-prepared 1% SDS + 100mM NaHCO3. Crosslinks were reversed overnight by adding 5µL of 5M NaCl and incubating at 65°C. DNA was treated with 3µL RNaseA (30mg/mL) for 30 minutes at 37°C and then Proteinase K (20mg/mL) for 1 hours at 56°C and purified wit Zymo Clean and Concentrator ChIP Kit and quantified using Qubit before library preparation (Kapa Hyperprep). Libraries were sequenced on an Illumina NextSeq (Single End x 75 bp – 1 sample) and on an Illumina HiSeq4000 lane (Single End x 50 bp – 3 samples).
Libraries were prepared with the Kapa Hyperprep kit following standard protocols.

treatment_protocol: BIN67 cells were co-transfected (FuGENE 6, Promega #E269A) with either control (pCDNA3-neo) or BRG1 (PBJ5-BRG1) plasmids at a 10:1 ratio to a plasmid containing puromycin resistance (pBABE-puro). Twenty-four hours after transfection, cells were placed on 2 µg/ml puromycin for 3 days and then harvested for ChIP-seq studies.

tag: antibody

value: BRG1 abcam #ab110641


title: BIN67_Parent_Control_RNAseq_Rep3

description:
BIN67 Parental cells, control transfected - Rep 3
BIN67_Parental_RNAseq_raw_gene_counts.txt

value: Control


title: RNAseq KI2

description:
MYC;DNMT3bCI/CI
MTCLs_FPKM.txt

value: lymph node

value: FVB


title: colo205_Fv_rep.1

description:
Gene expression data from the cells used as 5-FU alone, paired control for FA-treated group
FX

tag: tissue source

tag: treated with


title: BIN67_BRG1_ChIPseq_IP_Rep2

description:
BIN67 +BRG1 Transfected ChIPseq BRG1 IP  - Rep 2
BIN67_BRG1_ChIPseq_IP_merged.bw


title: colo205_v_rep.3

description:
Gene expression data from the cells used as vehicle-treated control
V2

source_name: colo205_DMSO for 72 hr

value: DMSO for 72 hr


title: 6045_Follicular_2017-01-09 (batch 1)

source_name: Endocervical cytobrush from participant 6045 at the Follicular on 2017-01-09

tag: index

tag: rin

tag: enrollment

value: N


title: 6038_Ring_2017-01-11 (batch 1)

source_name: Endocervical cytobrush from participant 6038 at the Ring on 2017-01-11

tag: status

tag: progesterone

value: Ring

value: Don't drop


title: BIN67_BRG1_ChIPseq_Input_Rep3

description:
BIN67 +BRG1 Transfected ChIPseq Input  - Rep 3
BIN67_BRG1_ChIPseq_Input_merged.bw

tag: transfected vector

value: Input


title: BIN67_BRG1_ChIPseq_IP_Rep1

description:
BIN67 +BRG1 Transfected ChIPseq BRG1 IP  - Rep 1
BIN67_BRG1_ChIPseq_IP_merged.bw


title: colo205_v_rep.1

description:
Gene expression data from the cells used as vehicle-treated control
V


title: BIN67_BRG1_ChIPseq_Input_Rep2

description:
BIN67 +BRG1 Transfected ChIPseq Input  - Rep 2
BIN67_BRG1_ChIPseq_Input_merged.bw


title: RNAseq KO2

description:
MYC;DNMT3bD/D
MTCLs_FPKM.txt


title: 6045_Luteal_2017-01-25 (batch 1)

source_name: Endocervical cytobrush from participant 6045 at the Luteal on 2017-01-25

tag: studyid

value: Negative

tag: bv

tag: visit


title: colo205_v_rep.2

description:
Gene expression data from the cells used as vehicle-treated control
V1


title: T cell rep 1

city: Houston

first: David

last: Piwnica-Worms

state: TX

address: 1881 East Road, Unit 1907

department: Cancer Systems Imaging

institute: The University of Texas MD Anderson Cancer Center

data_processing:
Raw data QA and preprocessing (FastQC v0.11.8)
Sequence alignment and secondary QA (STAR 2.7.1a)
Data exploration and QA on gene expression (featureCounts 1.6.0)
Quantification of differential expression and exploratory analysis (DEseq2 1.22.2)
Downstream functional analysis (R 3.6)
Genome_build: Mm10
Supplementary_files_format_and_content: tab-delimited cvs files include p values
Supplementary_files_format_and_content: counts

growth_protocol: 1 x 10^6 B16F10 cells were seeded in a 100 mm cell culture plate for 4 days. CD8+ T cells were isolated from the spleens of adult C57BL/6 mice using a CD8a+ T cell isolation kit.

extract_protocol:
RNA was isolated from the B16F10 and CD8+ T cells incubated with and without HOCl using a RNeasy Mini Kit
RNA sequencing and analysis was performed by Admera Health conducted by Genohub using standard Illumina protocols

treatment_protocol: Cells were incubated in cell culture media with or without 600 µM HOCl for 5h and then processed for RNA.

tag: cell type

value: T cell

tag: strain


title: B16F10 HOCl rep 3

value: melanoma cell

tag: treatment

value: 600uM HOCl for 5h


title: T cell HOCl


title: BIN67_BRG1_ChIPseq_Input_Rep1

description:
BIN67 +BRG1 Transfected ChIPseq Input  - Rep 1
BIN67_BRG1_ChIPseq_Input_merged.bw

tag: cell line


title: B16F10 HOCl rep 2


title: RNAseq KO1

description:
MYC;DNMT3bD/D
MTCLs_FPKM.txt

tag: tissue

tag: genotype


title: 6038_Follicular_2016-10-20 (batch 1)

source_name: Endocervical cytobrush from participant 6038 at the Follicular on 2016-10-20

tag: date

value: Follicular

tag: drop

value: Don't drop:luteal changed to follicular

tag: batch


title: B16F10 HOCl rep 1


title: BIN67_Control_ChIPseq_IP_Rep2

description:
BIN67 Control Transfected ChIPseq BRG1 IP  - Rep 2
BIN67_Control_ChIPseq_IP_merged.bw

tag: antibody


title: 6038_Follicular_2016-10-27 (batch 1)

source_name: Endocervical cytobrush from participant 6038 at the Follicular on 2016-10-27

tag: index

tag: rin

tag: enrollment

value: Y


title: RNAseq WT4

description:
MYC;DNMT3b+/+
MTCLs_FPKM.txt


title: RNAseq WT3

description:
MYC;DNMT3b+/+
MTCLs_FPKM.txt


title: 6036_Ring_2017-01-19 (batch 1)

source_name: Endocervical cytobrush from participant 6036 at the Ring on 2017-01-19

tag: status

value: Complete

tag: progesterone


title: T cell rep 2


title: RNAseq KI1

description:
MYC;DNMT3bCI/CI
MTCLs_FPKM.txt

source_name: MYC-induced lymphoma sample


title: B16F10 rep 3


title: 6036_Luteal_2016-12-05 (batch 1)

source_name: Endocervical cytobrush from participant 6036 at the Luteal on 2016-12-05

tag: studyid

tag: bv

value: Luteal


title: RNAseq KO3

description:
MYC;DNMT3bD/D
MTCLs_FPKM.txt


title: B16F10 rep 2

tag: cell type


title: RNAseq WT2

description:
MYC;DNMT3b+/+
MTCLs_FPKM.txt

tag: strain


title: BIN67_Control_ChIPseq_Input_Rep3

description:
BIN67 Control Transfected ChIPseq Input  - Rep 3
BIN67_Control_ChIPseq_Input_merged.bw

tag: transfected vector

value: Control


title: WGBS KI2

value: lymph node


title: B16F10 rep 1


title: 6036_Follicular_2016-11-16 (batch 1)

source_name: Endocervical cytobrush from participant 6036 at the Follicular on 2016-11-16

tag: visit


title: 6034_Follicular_2016-11-16 (batch 1)

source_name: Endocervical cytobrush from participant 6034 at the Follicular on 2016-11-16


title: Terc-/-ESC PDL800times [scRNA-seq]

city: suwon

first: DAEUN

last: KIM

address: World cup-ro

institute: Ajou university

description: D800_20181210-YJ-telomere-scRNAseq_AA_L002

data_processing:
Library index were identified with Index2, cell barcode was inferred from Index1 and Read2, and aligned to the reference transcriptome using the inDrops pipeline
Mapped reads were quantified into barcode counts per gene
Using the Scanpy R package, count matrix was analyzed
Genome_build: mm10
Supplementary_files_format_and_content: tsv format of count matrix

source_name: mESC

growth_protocol: The Terc targeting construct (TR-10) was transfected into E14 mESC by electroporation to exchange the first Terc allele. The targeting plasmid included PGK-neo gene flanked by loxP sites. The transfected cells were selected with G418 (200 mg/ml) and Ganciclovir (1 mM). The resistant Terc+/- cells were picked after eight days. The neo gene was removed by infection with the adenovirus of Cre recombinase. The Terc+/- cells were re-targeted with TR-10. Two lines of Terc-/- ESC, DKO301 and DKO741 were recovered. Both of DKO301 and DKO741 produced survivors with rare frequencies. We got those ALT survivor cells at each PDL timing (PD100, PD350, PD400, PD450) with control (Terc+/+) cells. For mESC maintenance and stock preparation, mouse embryonic fibroblast (MEF) cells were used as feeder cells. Feeder-free mESCs were used for all experiments including nucleic acids extraction, protein extraction, immunostaining, and fluorescent in situ hybridization.

extract_protocol:
Cells were encapsulated with a custom inDrops microfluidic setup. In RT-lysis mix, Maxima H- RTase was used and additional oligos (RP-TSO, IDT) were added at concentration of 3 uM to faciliate template switching reaction within a droplet.
RNA libraries were constructed for sequencing following the Drop-seq protocol

treatment_protocol: Cells were longitudinally harvested at 100 and 800 passage

tag: genotype/variation

value: Terc knock-out

value: mouse Embryonic Stem Cell

tag: time point

value: 800 passage


title: WGBS KI1

tag: tissue

value: FVB

tag: genotype


title: BIN67_Control_ChIPseq_Input_Rep1

description:
BIN67 Control Transfected ChIPseq Input  - Rep 1
BIN67_Control_ChIPseq_Input_merged.bw

source_name: Cell Line

tag: cell line


title: 6034_Ring_2017-01-05 (batch 1)

source_name: Endocervical cytobrush from participant 6034 at the Ring on 2017-01-05

tag: date

value: N

value: Ring

tag: drop

value: Don't drop

tag: batch


title: BIN67_Control_ChIPseq_IP_Rep1

description:
BIN67 Control Transfected ChIPseq BRG1 IP  - Rep 1
BIN67_Control_ChIPseq_IP_merged.bw

tag: antibody

value: BRG1 abcam #ab110641


title: Salivary gland, BxlglRNAiRasV12_FM_3

city: Stockholm

first: Ulrich

last: Theopold

state: Stockholm

address: Svante Arrhenius väg 20C

department: Department of Molecular Biosciences, The Wenner-Gren Institute

country: Sweden

institute: Stockholm University

data_processing:
PE50-reads were pseudoaligned with kallisto (v0.44.0) to a transcriptome index derived from all Drosophila transcript sequences of the dmel release r6.19.
Transcript abundances was analysed in R with sleuth (v0.30.0).
Genome_build: dmel-all-transcript-r6.19.fasta.gz (transcriptome build)
Supplementary_files_format_and_content: Tab-delimited text file including est_counts and tpm values.

organism: Drosophila melanogaster

source_name: salivary gland

growth_protocol: All Drosophila crosses were reared on standard potatomash/molasses medium under tempered conditions in a 12h dark/12 h light-cycle. Virgins were collected for 3-7 d before setting crosses. Initially, crosses were kept on standard food without antibiotics for 48 h at 25°C. Eggs were collected for for 2 h at 25°C after precollections for 2 h at 25°C. Egg collections were incubated for 24 h at 29°C and batches of 24 hatched 1st instar larvae were afterwards transferred to vials with 3 ml standard food supplemented with Neomycin (0.1 mg·ml-1, Sigma-Aldrich, N1876), Vancomycin (0.1 mg·ml-1, Sigma-Aldrich, V2002), Metronidazol (0.1 mg·ml-1, Sigma-Aldrich, M3761) and Carbenicillin (0.1 mg·ml-1, Sigma-Aldrich, C1389). After incubation at 29°C for another 72 h (96 h AED), 3rd instar larvae were prepared for dissection.

extract_protocol:
Total RNA of dissected salivary glands was isolated with the RNAqueous-Micro Kit (ThermoFisher Scientific, AM1931) according to the instructors manual. Residual genomic DNA was digested with RNase-free DNaseI (ThermoFisher Scientific, EN0521) and cDNA reverse transcribed with SuperscriptIII (ThermoFisher Scientific, 18080-093) while using oligo(dT)16-primer (ThermoFisher Scientific, 8080128). Quality of all prepared totalRNA-extractions was evaluated on a 2100 Bioanalyzer Instrument (Agilent Technologies, 5067-1511).
Poly(A)-containing mRNA molecules from totalRNA-samples were purified with oligo(dT)-magnetic beads, subsequently fragmented and cDNA synthesised with random primers using the TruSeq RNA Sample Preparation Kit v2. Adapter ligation and PCR-amplification precede cluster formation with a cBot cluster generation system.

tag: strain information

value: ☿ w1118,BxGal4;;Drs-GFP x ♂ w1118;UAS-l(2)glRNAi;UAS-RasV12

tag: age

value: 96 h AED

value: salivary glands

tag: tissue part

value: posterior part


title: WGBS KO2


title: Terc-/-ESC PDL100times [scRNA-seq]

description: D100_20181210-YJ-telomere-scRNAseq_TA_L002

value: 100 passage


title: WGBS KO1


title: WGBS WT2


title: 6034_Luteal_2016-11-28 (batch 1)

source_name: Endocervical cytobrush from participant 6034 at the Luteal on 2016-11-28

tag: studyid

tag: index

tag: rin

tag: enrollment

tag: status

value: Complete

value: Negative

tag: progesterone

tag: bv

value: Don't drop:follicular changed to luteal


title: Salivary gland, BxlglRNAiRasV12_FM_2

tag: tissue


title: Salivary gland, BxlglRNAiRasV12_FM_1


title: 6032_Ring_2017-01-12 (batch 1)

source_name: Endocervical cytobrush from participant 6032 at the Ring on 2017-01-12

tag: visit


title: met/dnmt3b wgbs

data_processing:
Identical duplicate reads and low-quality reads were filtered out using Prinseq-lite software v0-20-4
Custom Perl scripts were used to convert all the Cs in the ‘forward’ reads and reference sequence to Ts, and all the Gs in the ‘reverse’ reads and reference sequence to As
Reads were aligned to the reference genome using Bowtie2.0
Custom Perl scripts were used to recover the original sequence information and, for each C (on either strand), to count the number of times it was sequenced as a C or a T.
For each sequence context (CG, CHG, CHH),  the genomic averaged fractional methylation as well as fractional methylation within a 50 bp sliding window that were used in downstream analyses were calculated.
Genome_build: Ppatens v3.0
Supplementary_files_format_and_content: Separate gff files for each methylation context (CG, CHG and CHH), each entry represents one citosine. Scores represent methylation level for each position, column 9 contains numbers of times each cytosine was sequenced as either C or T, as well as total reads coverage of the given citosine.
Supplementary_files_format_and_content: Separate gff files for each methylation context (CG, CHG and CHH), each entry represents 50-bp window. Scores represent methylation level for each window, column 9 contains numbers of times cytosines within the given window were sequenced as either C or T, as well as total reads coverage of citosines within the window.

source_name: protonema

extract_protocol:
Genomic DNA was extracted from 7 days old protonema using DNeasy Plant Mini Kit (Qaigen) according to manufacturer’s instructions
Genomic DNA was isolated from protonema, fragmented by sonication, end repaired, and ligated to custom synthesized methylated adaptors. Adaptor-ligated libraries were subjected to bisulfite conversion treatment using the Methylation-Gold kit (ZYMO) as outlined in the manufacturer’s instructions. The bisulfite-converted libraries were then amplified by PCR and gel purified (~350-400 bp size range) prior to quantification with a Bioanalyzer (Agilent).

tag: genotype

tag: cultivar

value: Grandsen

value: 7 days


title: 6032_Luteal_2016-09-29 (batch 1)

source_name: Endocervical cytobrush from participant 6032 at the Luteal on 2016-09-29

tag: date

value: Luteal

tag: drop


title: Salivary gland, BxlglRNAiRasV12_3

value: whole gland


title: ddcc_rep3

data_processing:
Adaptor and quality trimming using TrimGalore v0.6.0 with Cutadapt v1.15
Alignment to the reference genome and counting reads per gene/TE in the supplied annotation file, using STAR v2.7.0f
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text file with raw read counts assigned to each of the annotated features (gene or transposable element), in each sample

organism: Arabidopsis thaliana

source_name: leaves

growth_protocol: WT and ddcc seeds were sown on soil in pots, stratified at 4ºC for 48h and grown at 21ºC and under long day (16h light/8h darkness) regime

extract_protocol:
Total RNA was extracted from leaves tissue using RNeasy plant mini kit (Qiagen) according to manufacturer’s instructions
The polyA fraction (mRNA) was purified from 500 ng of total input RNA, followed by fragmentation and the generation of double-stranded cDNA. Then, Agencourt Ampure XP beads cleanup (Beckman Coulter), end repair, A base addition, adapter ligation and PCR amplification steps were performed. Libraries were quantified by Qubit (Thermo fisher scientific) and TapeStation (Agilent).

value: leaves

value: 28 days

value: ddcc (drm1drm2cmt2cmt3)


title: WGBS WT1

value: lymph node

tag: strain

value: FVB


title: BIN67_Control_ChIPseq_Input_Rep2

description:
BIN67 Control Transfected ChIPseq Input  - Rep 2
BIN67_Control_ChIPseq_Input_merged.bw

tag: cell line

tag: transfected vector

value: Control

tag: antibody

value: Input


title: ddcc_rep2

tag: age


title: 6028_Follicular_2016-09-13 (batch 1)

source_name: Endocervical cytobrush from participant 6028 at the Follicular on 2016-09-13

tag: studyid

tag: index

value: Positive

value: N

value: Follicular

value: Don't drop

tag: batch


title: 6028_Ring_2016-10-11 (batch 1)

source_name: Endocervical cytobrush from participant 6028 at the Ring on 2016-10-11

tag: rin

tag: enrollment

tag: status

value: Complete

value: Ring


title: 6032_Follicular_2016-10-18 (batch 1)

source_name: Endocervical cytobrush from participant 6032 at the Follicular on 2016-10-18

value: Negative

tag: progesterone

tag: bv


title: cmt/dnmt3b wgbs

tag: genotype

value: Grandsen

value: 7 days


title: Terc-/-ESC PDL450times

data_processing:
Library strategy: WGS
WGS reads were mapped to the mm10 reference genome using Burrows-Wheeler Aligner (BWA) MEM algorithm (version 0.7.17)
Duplicated reads were marked with Picard-Tools (version 1.96) and Samtools (version 1.9)
For visualizing mTALT reads on the UCSC genome browser (Kent et al., 2002), chr13: 119,891,001-120,300,000 region on the mm10 reference genome was masked with Ns and then all the reads were re-mapped onto the masked genome. Coverage of mapped reads was computed by bedtools genomecov (version v2.25.0)
Genome_build: mm10
Supplementary_files_format_and_content: bigwig format of genome coverage

extract_protocol:
Genomic DNA was extracted using DNeasy Blood & Tissue Kit (QIAGEN)
DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were longitudinally harvested at 100, 350, 450 and 800 passage

tag: cell type

value: mouse Embryonic Stem Cell


title: ddcc_rep1

tag: tissue

value: leaves

tag: cultivar


title: Terc-/-ESC PDL350times

tag: strain


title: 6028_Follicular_2016-08-04 (batch 1)

source_name: Endocervical cytobrush from participant 6028 at the Follicular on 2016-08-04

tag: date

tag: visit

tag: drop

value: Don't drop:luteal changed to follicular


title: Salivary gland, BxRasV12_3

tag: strain information

value: ☿ w1118,BxGal4;;Drs-GFP x ♂ w1118;;UAS-RasV12

tag: age

value: 96 h AED

value: salivary glands

tag: tissue part

value: whole gland


title: wt_rep3

value: 28 days

value: wild type


title: Salivary gland, BxRasV12_2


title: Terc-/-ESC PDL100times


title: wt_rep2


title: wt_rep1


title: Salivary gland, BxlglRNAiRasV12_2

value: ☿ w1118,BxGal4;;Drs-GFP x ♂ w1118;UAS-l(2)glRNAi;UAS-RasV12


title: Terc-/-ESC PDL800times-rep2

data_processing:
ATAC-seq reads were mapped to the mm10 reference genome using Burrows-Wheeler Aligner (BWA) MEM algorithm (version 0.7.17)
Duplicated reads were marked with Picard-Tools (version 1.96) and Samtools (version 1.9)
Peak-calling was performed using MACS2 (version 2.1.2) callpeak command.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig format of peak

extract_protocol:
50,000~75,000 cells were pelleted at 500 xg, 4°C for 5 min. I added 50 ul of cold RSB (10 mM Tris-Cl, pH 7.4, 10 mM NaCl, 3 mM MgCl2) containing 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin and pipetted 3 times. The cells were incubated on ice for 3min, and washed with 1ml of cold RSB containing 0.1% Tween-20 but no other detergents. The cells were pelleted and resuspended wiht 50 ul of transposition mixture (25 ul 2X TD buffer, 2.5 ul transposase, 16.5 ul PBS, 0.5 ul 1% digitonin, 0.5 ul 10% Tween-20, 5 ul H20) (2X TD buffer=20 mM Tris-Cl, pH 7.6, 10 mM MgCl2, 20% dimethyl formamide). The reaction was incubated at 37°C for 30 min with consistent shaking, and stop the reaction by adding 50 ul of tagmentation stop buffer (10 mM Tris-Cl, pH 8.0, 20 mM EDTA, pH 8.0). The reaction was cleaned with Zymo DNA clean and concentrator-5 kits. DNAs were eluted in 21 ul of elution buffer, and amplified for 5 cycles using NEBnext high-fidelity 2x PCR master mix.
DNA libraries were prepared for sequencing using standard Illumina protocols


title: Salivary gland, Bxw1118_3

value: ☿ w1118,BxGal4;;Drs-GFP x ♂ w1118


title: Salivary gland, Bxw1118_2


title: Terc-/-ESC PDL800times


title: Terc-/-ESC PDL450times-rep2


title: 6008_Follicular_2016-04-18 (batch 1)

source_name: Endocervical cytobrush from participant 6008 at the Follicular on 2016-04-18

tag: studyid

tag: index

value: Positive

value: N

value: Follicular

value: Don't drop

tag: batch


title: Salivary gland, BxlglRNAiRasV12_1


title: CCC-12_RNAseq

first: Su-Hyung

last: Park

address: 291 Daehak-ro

institute: Korea Advanced Institute of Science and Technology

data_processing:
Reads were trimmed based on sequencing quality using Sickle.
Poly-A tails and adaptor contents were removed using Cutadapt.
Trimmed reads were aligned on a human reference sequence (hg19) using Tophat2.
The number of mapped reads on the 3’ end of each gene was calculated using Bedtools.
Genome_build: hg19
Supplementary_files_format_and_content: Raw read count

molecule: polyA RNA

source_name: Cholangiocarcinoma tissue

extract_protocol:
Cells were cryopreserved in Trizol reagent and RNA extracted according to the manufacturer’s instructions.
Total RNA quality was assessed with the Agilent 2100 Bioanalyzer System. Extracted RNA samples were processed using the QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen, Vienna) and sequenced on an Illumina NextSeq 500. A median 2.0x107 (range 1.7x107 to 2.4x107) single-end reads with 75 bp were generated.

value: Cholangiocarcinoma tissue

value: Bulk tumor tissue

tag: gender

value: M

tag: phenotype

value: TRMhigh


title: 6027_Follicular_2016-09-19 (batch 1)

source_name: Endocervical cytobrush from participant 6027 at the Follicular on 2016-09-19

tag: rin

tag: enrollment

tag: status

value: Withdrawn

tag: progesterone

tag: bv


title: CCC-10_RNAseq

tag: tissue

tag: cell type

value: F

value: TRMlow


title: CCC-11_RNAseq


title: Salivary gland, Bxw1118_1

value: 96 h AED

value: salivary glands


title: Terc-/-ESC PDL800times-rep2

data_processing:
The reads were aligned to the mm10 reference genome using the STAR aligner (version 2.5.3a)
RSEM (v1.3.0) was used to calculate the expected read counts, FPKM and TMP for each sample from the corresponding bam files.
The read counts were processed using DESeq2 (v1.18.1) to identify differentailly expressed genes.
Genome_build: mm10

extract_protocol:
RNA was extracted using chloroform and isopropanol precipitation
RNA libraries were prepared for sequencing using standard Illumina protocols

value: mouse Embryonic Stem Cell

tag: strain


title: Terc-/-ESC PDL350times-rep2


title: Terc-/-ESC PDL450times-rep1


title: CCC-9_RNAseq


title: CCC-8_RNAseq


title: Terc-/-ESC PDL800times-rep1


title: Terc-/-ESC PDL100times-rep2


title: Terc-/-ESC PDL100times-rep2


title: Terc-/-ESC PDL350times-rep1


title: Terc-/-ESC PDL100times-rep1


title: 6008_Luteal_2016-03-30 (batch 1)

source_name: Endocervical cytobrush from participant 6008 at the Luteal on 2016-03-30

tag: date

value: Complete

tag: visit

value: Luteal

tag: drop

value: Drop for microarray:PCA outlier


title: Terc-/-ESC PDL100times-rep1

source_name: mESC


title: CCC-7_RNAseq

tag: age


title: CCC-6_RNAseq


title: 4OHT rep2

city: Iowa City

first: Ronald

last: Weigel

state: IA

address: 200 Hawkins Drive

department: Surgery

institute: University of Iowa

data_processing:
Basecalls were converted into .fastq files using the University of Iowa Genomics Division bcl2fastq software
10x Data was processed with the Cell Ranger pipeline, version 3.0.1
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited .tsv files for features, barcodes, single-cell expression matrices

source_name: Mammary epithelial cells

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were treated with daily injections of corn oil or 4OHT for 1 week.

value: FVB

value: post natal week 9

tag: genotype

value: Tfap2cfl/fl / Krt5-CreERT2

tag: treatment

value: 4OHT daily at 4 weeks for 5 days


title: 6008_Ring_2016-05-26 (batch 1)

source_name: Endocervical cytobrush from participant 6008 at the Ring on 2016-05-26

tag: studyid

tag: index

value: Positive

value: N

value: Ring

value: Don't drop

tag: batch


title: CCC-5_RNAseq

value: Cholangiocarcinoma tissue

value: Bulk tumor tissue

tag: gender

value: M

tag: phenotype

value: TRMhigh


title: CCC-4_RNAseq


title: CO rep2

value: Corn oil daily at 4 weeks for 5 days


title: 4OHT rep1


title: CCC-3_RNAseq

value: TRMlow


title: HSC  Zfp521-CKO chimeric rep3

city: Chongqing

first: Zhigang

last: Li

state: China

address: NO.30 GaotanYan  Street, Shapingba District

institute: Southwest Hospital, Army Medical University

data_processing:
The sequenced reads were aligned to the mouse genome (UCSC mm9) using Bowtie, with one mismatch allowed.
Sequencing results were normalized to ERCC spike-in, and differentially expressed genes were characterized using DESeq2 (Version 1.26.0).
Adjusted P-values were calculated by the Benjamini-Hochberg method. GSEA was performed with GSEA v2.0 software.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with FPKM for every gene and every sample

source_name: murine HSCs

extract_protocol:
Total RNA was purified from HSC isolated from Zfp521fl/fl or Zfp521-CKO mice with an RNeasy Micro Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: To generate a gene set upregulated in Zfp521-deficient HSCs,BM cells (2x106) from Zfp521fl/fland Zfp521-CKO CD45.2 mice were transplanted into lethally irradiated CD45.1 recipient mice.HSCs (CD150+CD48–LSK) were purified from recipient mice 2 months after transplantation, and were subjected to RNA-seq analysis.

value: HSC

tag: genotyping

value: Zfp521-CKO chimeric


title: HSC  Zfp521-CKO chimeric rep1


title: HSC  Zfp521fl/fl chimeric rep3

value: Zfp521fl/fl chimeric


title: CO rep1

value: FVB


title: HSC  Zfp521-CKO chimeric rep2


title: CCC-1_RNAseq


title: HSC  Zfp521fl/fl chimeric rep2


title: KO_3

city: beijing

first: Tongtong

last: Liu

address: Peking University Health Science Center, 38 Xueyuan Road, Haidian District, Beijing

institute: Peking University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome
Genome_build: mm10
Supplementary_files_format_and_content: txt files of normalized gene counts for each sample

source_name: Colon

extract_protocol:
colon tissue adjacent to tumors were removed, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 18 weeks


title: A375 inducible MELK shRNA #33 (+ doxycycline), replicate 3

city: Birmingham

first: Narendra

last: Wajapeyee

state: AL

address: 720 20th Street South, Kaul 540A

department: Department of Biochemistry and Molecular Genetics

institute: University of Alabama at Birmingham

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Signal intensities of probes were log2 transformed and quantile normalized (BeadArray package in R/Bioconductor).

source_name: A375 cell line, MELKshRNA.33, + Dox

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays.

growth_protocol: A375 inducible MELK shRNAs cell lines were grown in DMEM media with 10% fetal bovine serum and Penicillin and Streptomycin at 37 C under 5% CO2 condition.

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen) as per the instruction from the manufacturer and then purified using RNeasy mini columns (Qiagen) as per the manufacturer's instruction.

treatment_protocol: A375 cells that expressed inducible shRNA targeting MELK (#31, #33) were treated with doxycycline or vehicle for 3 days and subsequently were used for preparing the total RNA to perform gene expression array.

tag: cell line

value: melanoma cell line

tag: shRNA

value: doxycycline


title: A375 inducible MELK shRNA #31 (+ doxycycline), replicate 3

source_name: A375 cell line, MELKshRNA.31, + Dox


title: CCC-2_RNAseq

tag: tissue


title: A375 inducible MELK shRNA #33 (+ doxycycline), replicate 1

tag: cell type


title: A375 inducible MELK shRNA #31 (+ doxycycline), replicate 2


title: A375 inducible MELK shRNA #31 (+ doxycycline), replicate 1


title: A375 inducible MELK shRNA #31 (- doxycycline), replicate 3

source_name: A375 cell line, MELKshRNA.31, - Dox

value: vehicle


title: KO_2

tag: strain


title: A375 inducible MELK shRNA #31 (- doxycycline), replicate 2


title: A375 inducible MELK shRNA #33 (- doxycycline), replicate 3

source_name: A375 cell line, MELKshRNA.33, - Dox


title: HSC  Zfp521fl/fl chimeric rep1


title: A375 inducible MELK shRNA #33 (- doxycycline), replicate 1


title: KO_1


title: PD0_scRNA-seq

city: Qingdao

first: Jun-Jie

last: Wang

state: Shandong

address: Changcheng 700

department: Qingdao Agricultural University

institute: College of Life Sciences

description: 2x150 paired-end sequence reads

data_processing:
CellRanger count pipeline 2.2.0 is performed to generate the single cell information
Genome_build: mm10
Supplementary_files_format_and_content: The single cell expression matrix is stored as tab-delimited text files after normalization.

source_name: PD0 ovarian cells

extract_protocol:
The isolated ovaries were cut into pieces and transferred into digestive solution consist of 0.25 % trypsin/EDTA (Hyclone, USABeijing, China) and collagenase (Sigma-Aldrich, C5138, Shanghai, China) for 6 ~ 8 mins at 37 ℃. Following the termination of digestion, the single cell solution was obtained after filtration with 40 μm cell strainers (BD Falcon, 352340, USA) and two times wash with PBS containing 0.04 % BSA.
Single-cell RNA-seq libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V2 (10x Genomics Inc., 120237, Pleasanton, CA, USA) following the manufacture’s introduction.

value: Ovary

tag: developmental stage


title: Mel202_AZDDP_3

city: Bethesda

first: Robert

last: Robey

address: 37 Convent Drive Rm 2112

institute: NCI

description:
Combination replicate 3
12_Mel202_AZDDP_3_S12

data_processing:
Base calling was performed using Real-Time Analysis  software (RTA; version 1.18.64; Illumina)
Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt software (version 1.18) before alignment with the hg19 reference genome and the annotated transcripts using Spliced Transcripts Alignment to a Reference (STAR; version 2.6.1).
Gene expression quantification analysis was performed for all samples using STAR and RNA-Seq by Expectation Maximization (RSEM; version 1.2.3.1) tools.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each sample

extract_protocol:
Uveal melanoma cells were purchased from American Type Culture Collection. Cells were treated for 6 hours, harvested, and total RNA was isolated using a Qiagen RNeasy Plus Mini Kit.
Library was prepared for sequencing using TruSeqStranded mRNA Library Prep,

treatment_protocol: Uveal melanoma cell line Mel202 was either untreated or treated with 25 ng/mL romidepsin, 1 uM AZD-8055, or a combination of the two for 6 hours.

tag: tissue source

value: eye (uveal melanoma)

value: uveal melanoma cell line

value: 25 ng/mL romidepsin + 1 uM AZD-8055


title: PD3_scRNA-seq

description: 2x150 paired-end sequence reads

source_name: PD3 ovarian cells


title: MRL_lpr_3

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2, Qvalue < =0.05
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include gene FPKM  and raw count values for each Sample

source_name: kidney tissue from mouse with lupus nephritis

growth_protocol: Specific pathogen free (SPF) grade female Mrl/lpr and MRL/MpJ mice (weight 16-20 g and age 12 weeks) were purchased from Cloud-Clone Animal Inc. (Wuhan, China). The purchased animals were kept in SPF laboratory of Wuhan University Experimental Animal Center. All animals were fed the same feed and the experiment began after 2 weeks

extract_protocol:
Total RNA of each lung tissue sample was extracted using TRIzol Reagent (Ambion) according to the manufacturer’s instructions. To eliminate any DNA present, RQ1 DNase (Promega) was added to the extracted total RNA. The absorbance of the purified RNA was measured to determine the quality and concentration with a Smartspec plus (BioRad, Hercules, USA) at 260 nm/280 nm (A260/A280). Agarose gel electrophoresis (1.5%) was conducted to verify the integrity of the RNA
For RNA-seq library preparation, 10 μg of purified total RNA of each sample was purified and concentrated with oligo (dT)-conjugated magnetic beads (Invitrogen). Polyadenylated mRNAs were used for the construction of a directional RNA-seq library. Ion fragmentation of purified mRNAs was conducted at 95ºC following end repair and 5' adaptor ligation. The fragmented mRNAs were reverse-transcribed with RT primer, known 3' adaptors, and random hexamers. Then, purification and amplification of the cDNAs were conducted. The 200–500 bps of amplified cDNAs were collected. The cDNAs for each sample were quantified and stored at -80ºC until sequencing.

treatment_protocol: MRL/MpJ-Fas-lpr strain mice (Mrl/lpr), an established model of LN, were used in our study. Control MRL/MpJ mice without Fas-lpr mutation were used as healthy controls

value: kidney

tag: disease state

value: lupus nephritis

value: MRL/MpJ-Fas-lpr


title: WT_3

tag: age

value: wild type


title: Mel202_AZD_3

description:
AZD replicate 3
11_Mel202_AZD_3_S11


title: Mel202_Dp_3

description:
Romidepsin replicate 3
10_Mel202_Dp_3_S10

value: 25 ng/mL romidepsin


title: A375 inducible MELK shRNA #33 (+ doxycycline), replicate 2


title: MRL_lpr_2

tag: genotype


title: WT_2


title: A375 inducible MELK shRNA #33 (- doxycycline), replicate 2

tag: treatment


title: Mel202_c_3

description:
Control replicate 3
9_Mel202_c_3_S9

value: Untreated


title: MRL_lpr_1


title: A375 inducible MELK shRNA #31 (- doxycycline), replicate 1


title: WT_1


title: Ctrl_3

source_name: kidney tissue from healthy control mouse

value: healthy control

value: MRL/MpJ


title: Sesn3 KO liver 2

city: Indianapolis

first: Xiaocheng

middle: Charlie

last: Dong

state: IN

address: 635 Barnhill Drive, MS1021D

department: Biochemistry and Molecular Biology

institute: Indiana University School of Medicine

data_processing:
Sequencing was done on Illumina HiSeq 2000
The reads were mapped to the mouse genome using STAR (v2.5) RNA-seq aligner with the following parameter: “--outSAMmapqUnique 60”.
Uniquely mapped sequencing reads were assigned to mm10 genes using featureCounts (from subread v1.5.3) with the following parameters: “-s 2 –p –Q 10”.
The data was filtered using read count per million (CPM) > 0.5 in more than 4 of the samples, normalized using TMM (trimmed mean of M values) method and subjected to differential expression analysis using edgeR (v3.20.8).
Genome_build: mm10
Supplementary_files_format_and_content: Raw counts and analysis (excel) from edgeR

source_name: liver

extract_protocol:
Mouse livers were dissected and snap frozen in liquid nitrogen. Total RNAs were isolated using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Wild type (WT) and Sesn3 KO mice were intraperitoneally injected with DEN at a dose of 25 mg/kg at 2 weeks of age. At 4 weeks of age, the mice were fed with a choline-deficient high-fat diet (Research Diets #D05010402, containing 20 kcal% protein, 35.1 kcal% carbohydrate, and 44.9 kcal% fat) for 24 weeks.

value: liver

value: 6 months

value: Male


title: Ctrl_2


title: Sesn3 KO liver 1


title: Ctrl_1


title: Mel202_AZD_2

description:
AZD replicate 2
7_Mel202_AZD_2_S7


title: Mel202_Dp_2

description:
Romidepsin replicate 2
6_Mel202_Dp_2_S6


title: WT liver 3


title: Mel202_c_2

description:
Control replicate 2
5_Mel202_c_2_S5


title: WT liver 2


title: Ishikawa SF3B1 siRNA rep 3

city: ST LOUIS

first: RAMAKRISHNA

last: KOMMAGANI

state: Missouri

address: 425 S. Euclid Avenue, CB 8064

department: OB/GYN

institute: WASHINGTON UNIVERSITY

data_processing:
Basecalls and demultiplexing were performed with Illumina’s RTA version 1.9 and bcl2fastq2 software with a maximum of one mismatch in the indexing read.
RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.0.4b. Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5.  The counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust samples for differences in library size
Genes expressed less than one count-per-million in at least three sample were excluded from further analysis and new effective TMM size factors were recalculated. The rescaled matrix of counts were then imported into R/Bioconductor package Limma and weighted likelihoods based on the observed mean-variance relationship of every gene and sample were then calculated for all samples with the voomWithQualityWeights function.
Generalized linear models were then created to test for differential expression and the results were then filtered for Benjamini-Hochberg FDR adjusted p-values less than or equal to 0.01 and linear fold change≥ 2.5 fold-change.
Genome_build: Human Ensembl release 76

source_name: Ishikawa cells

extract_protocol:
Ishikawa cells were transfected with control or SF3B1 siRNA and then 48 hours later, total RNA was isolated using RNeasy total RNA isolation kit (Qiagen) for RNA-seq.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Ishikawa cells

value: SF3B1 siRNA


title: Mel202_AZDDP_1

description:
Combination replicate 1
4_Mel202_AZDDP_1_S4


title: Ishikawa SF3B1 siRNA rep 2


title: Mel202_AZDDP_2

description:
Combination replicate 2
8_Mel202_AZDDP_2_S8


title: Sesn3 KO liver 3


title: Ishikawa SF3B1 siRNA rep 1


title: Mel202_AZD_1

description:
AZD replicate 1
3_Mel202_AZD_1_S3


title: Mel202_Dp_1

description:
Romidepsin replicate 1
2_Mel202_Dp_1_S2


title: Ishikawa Control siRNA rep 3

value: Control siRNA


title: ThymusWT2_reused

city: Paris

first: Ludovic

last: Deriano

address: 25-28 Rue du Docteur Roux

department: Immunology

country: France

institute: Institut Pasteur

data_processing:
Basecalling was performed with Illumina RTA 1.18.64. Bcl conversions into Fastq were performed using bcl2fastq version 1.8.3.
Reads were mapped to mm10 genome with STAR version 2.4.0g1 using Ensembl annotation (GRCm38, release 78)
Duplicate reads were removed using the function MarkDuplicates from Picard tools and a filtering for uniquely mapped reads was performed.
We quantified read counts for all genes annotated in Ensembl release 78 with HTSeqcount version 0.6.1
Differential gene expression analysis was performed with the Bioconductor package DESeq2 version 1.6.3 and SARTools version 1.1.0
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file including differential expression results from DESeq2

source_name: Thymic lymphoma

extract_protocol:
RNA was prepared from single-cell suspensions of mouse tumor thymus using the RNeasy Mini Kit (Qiagen).
Libraries were generated according to the TruSeq Stranded mRNA Library Preparation kit protocol (Illumina)

value: thymus


title: ThymusWT3_reused


title: Ishikawa Control siRNA rep 2


title: Mel202_c_1

description:
Control replicate 1
1_Mel202_c_1_S1

value: eye (uveal melanoma)

value: uveal melanoma cell line


title: ThymusWT1_reused


title: PBMCs_con_rep4

city: Urumqi

first: Qi

last: Ma

address: No.91, Liyushan Road

institute: First Affiliated Hospital of Xinjiang Medical University

description: Gene expression in health control human peripheral blood mononuclear cells

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by percentile normalization.

source_name: Peripheral blood mononuclear cells, control, replicate 4

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

value: whole blood

value: male


title: PBMCs_con_rep3

source_name: Peripheral blood mononuclear cells, control, replicate 3

value: female


title: Ishikawa Control siRNA rep 1


title: PBMCs_con_rep5

source_name: Peripheral blood mononuclear cells, control, replicate 5


title: PBMCs_con_rep2

source_name: Peripheral blood mononuclear cells, control, replicate 2


title: BIN67_BRG1_ChIPseq_IP_Rep4

city: Chapel Hill

first: Bernard

last: Weissman

address: 450 West Drive

institute: University of North Carolina at Chapel Hill

description:
BIN67 +BRG1 Transfected ChIPseq BRG1 IP  - Rep 4
BIN67_BRG1_ChIPseq_IP_merged.bw

data_processing:
Reads were aligned to hg38 using bowtie2 using the --sensitive parameters, and duplicates were removed using samtools.
Peaks were called on the merged samples (samtools merge) using macs2 (v2.1.2) with the following parameters: Qval = 0.01 --keep-dup all --nomodel --extsize 150.
Peak calls were filtered the peaks against the ENCODE blacklist regions.
For visualization, bigwig tracks were generated on merged replicates using deeptools (v2.5.2) bamCoverage tool with a binsize of 40bp and extending fragments to 200bp.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig = normalized RPKM signal tracks of merged samples
Supplementary_files_format_and_content: narrowPeak = peaks called from merged replicate samples for IP (BRG1).

source_name: Cell Line

extract_protocol:
ChIP-seq was performed as previously described (Raab JR et. al. (2017) Epigenetics Chromatin). Briefly, cells (5e6 cells) were fixed for 30 minutes at 4°C in 0.3% methanol free formaldehyde, quenched for 5 minutes with 125mM glycine, washed 3 times and snap frozen in liquid nitrogen and stored at -80°C. Frozen pellets were thawed for 30 minutes on ice, resuspended  in 1mL swelling buffer (25mM HEPES + 1.5mM MgCl2 + 10mM KCl + 0.1% Igepal containing 1mM PMSF and 1X protease inhibitor cocktail, Roche) and incubated 10 minutes at 4°C. Cells were dounced 20 strokes with a “B” pestle and then nuclei were pelleted at 2000 rpm for 7 minutes at 4°C. The nuclei were washed with 10mL MNase Digestion Buffer (15mM Hepes pH 7.9, 60mM KCl, 15mM NaCl, 0.32M Sucrose) and pelleted at 2000 RPM for 7 minutes at 4°C. The pellet was then resuspended in 1mL MNase Digestion Buffer per 4e7 cells + 3.3µL 1M CaCl2 per mL + PMSF (1mM) and Protease Inhibitor Cocktail (1X, Roche), then incubated for 5 minutes at 37°C to warm. We added MNase (NEB M0247S 2000U/µl) at 0.5µL/1e7 cells and incubated for 15 minutes at 37°C with agitation. Following digestion, the MNase was chelated using 1/50 volume 0.5M EGTA on ice for 5 minutes. We added 1 volume of 2X IP Buffer (20mM TrisCl pH 8, 200mM NaCl, 1mM EDTA, 0.5mM EGTA), then passed the sample through a 21G needle 5 times and added Triton X-100 to 1% final concentration. The sample was cleared at 13,000 RPM for 15 minutes at 4°C and chromatin was incubated with BRG1 antibody (abcam #ab110641) overnight at 4°C. Antibody/chromatin complexes were captured with protein A magnetic beads (Bio-Rad) for 2 hours at 4°C, washed 5 times with wash buffer (50mM Hepes pH 7.9/500mM LiCl/1mM EDTA/1% IGEPAL-ca-630/0.7% Na-Deoxycholate) and once with 10mM Tris/1mM EDTA/50mM NaCl. DNA was eluted at 65°C with agitation using 100µL freshly-prepared 1% SDS + 100mM NaHCO3. Crosslinks were reversed overnight by adding 5µL of 5M NaCl and incubating at 65°C. DNA was treated with 3µL RNaseA (30mg/mL) for 30 minutes at 37°C and then Proteinase K (20mg/mL) for 1 hours at 56°C and purified wit Zymo Clean and Concentrator ChIP Kit and quantified using Qubit before library preparation (Kapa Hyperprep). Libraries were sequenced on an Illumina NextSeq (Single End x 75 bp – 1 sample) and on an Illumina HiSeq4000 lane (Single End x 50 bp – 3 samples).
Libraries were prepared with the Kapa Hyperprep kit following standard protocols.

tag: transfected vector

tag: antibody

value: BRG1 abcam #ab110641


title: PBMCs_T2D_rep5

description: Gene expression in T2D patient peripheral blood mononuclear cells

source_name: Peripheral blood mononuclear cells, T2D, replicate 5


title: 551T

value: mixed background C57BL/6 and 129S6/SvEv

value: Thymic lymphoma


title: BIN67_Control_ChIPseq_IP_Rep3

description:
BIN67 Control Transfected ChIPseq BRG1 IP  - Rep 3
BIN67_Control_ChIPseq_IP_merged.bw

value: Control


title: WT liver 1


title: 548T


title: 415T


title: 313T


title: IgG ChIPSeq

city: Madrid

first: Felipe

last: Cortés Ledesma

state: Madrid

address: Melchor Fernández Almagro 3

department: Molecular Oncology

country: Spain

institute: CNIO

data_processing:
Tags were aligned to human genome (hg19) using Bowtie (version 1.2.0).
For genome tracks, we used bamCoverage (deepTools) to convert aligned reads to signal tracks (bigwig) using RPKM normalization.
For peak calling, libraries were first subsampled so that both the test and the control samples had the same number of reads. Then, HOMER was called with parameter -style factor. Only peaks with a fold change over the control sample greater than 5 were retained.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files (bigWig) and peak files (bed)

source_name: MCF7 from ECACC

growth_protocol: MEM, 10% FSB, 2mM Glutamine, 1% Pen/Strep, 1% NEAA

extract_protocol:
To prepare chromatin, cells were fixed by adding formaldehyde to a final concentration of 1% and incubated at 37ºC for 10 min. Fixation was quenched by adding glycine to a final concentration of 125 mM. Cells were washed twice with cold PBS in the presence of complete protease inhibitor cocktail and PMSF. The cell pellet was lysed in two steps using 0.5% NP-40 buffer for nucleus isolation and SDS 1% lysis buffer for nuclear lysis. Sonication was performed using Bioruptor and chromatin was clarified by centrifugation (17000xg, 10 min, 4 ºC).  For IP, 50 μg chromatin and 4 μg antibody were incubated o/n in IP buffer at 4ºC, and then with 25 μL of Dynabeads protein A and Dynabeads protein G. Beads were then sequentially washed with IP buffer, IP buffer containing 500 mM NaCl and LiCl buffer. DNA was eluted by o/n incubation at 50 ºC in 100 μL elution buffer (1% SDS, 100 mM NaHCO3) with 200 mM NaCl and 10 μg of Proteinase K and purified.
Libraries were prepared by ChIPmentation as described by Schmidl et al. 2015 using NEBNext HF Polymerase and sequenced using Illumina NextSeq 500.

value: WT MCF7

tag: chip antibody

value: IgG (Sigma - I8140)


title: TOP2B ChIPSeq rep2

value: TOP2B (SIGMA – HPA024120)


title: 152T


title: Sch/T5_Ser2/5-P_ChIP Seq

city: Singapore

first: Mark

middle: Stephen

last: Featherstone

state: Singapore

address: 60, Nanyang Drive

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

data_processing:
Paired-end reads from ChIP-Seq and RNA-Seq were run through FastQC (Version 0.11.4) to generate quality reports, followed by quality and length trimming using trim_galore (Version 0.4.1).
Reads from ChIP and input DNA samples were mapped to PlasmoDbv9.0 using Bowtie2 (Version 2.2.6). RNA-Seq reads were mapped to the transcriptome of the same version using STAR-aligner (Version 2.5.1b).
Alignments with a MAPQ of 10 and properly paired were extracted using Samtools (Version 1.3). HTSeq-count (Version 0.6.1p1) and DESeq2 were used for read counting and normalization of RNA-Seq data.
Heatmap and profile plots were generated by deepTools (Version 2.3.4)
Peak calling was done using MACS2 (Version 2.1.1) with p = 0.05. Peak to gene annotation was done with bespoke scripts based on Bedtools (Version 2.25.0) suite
Genome_build: PlasmoDbv9.0
Supplementary_files_format_and_content: counts, bigwig, and peaks

organism: Plasmodium falciparum

source_name: Asexual stages

growth_protocol: P. falicparum was culture in RPMI at 2% haematocrit and sorbitol synchronized

extract_protocol:
RNA from each stage was isolated by Trizol method. Dnase treated RNA was used for preparing library for RNA Seq.Lysates were clarified from sonicated nuclei and RNAPII-DNA complexes were isolated with RNAPII antibodies.
Library preparation for RNA Seq was performed according to Illumina¹s Stranded  mRNA sample preparation protocol, following the manufacturer¹s recommendations.  Libraries for ChIP-Seq were prepared using NEBNext Ultra DNA library prep kit from Illumina

treatment_protocol: P. falciparum was formaldehyde cross-linked and 5x108 schizonts,1x109 trophozoites or 2x109 ring stage parasites were harvested for Chromatin immunoprecipitation.

value: Schizont stage

value: Anti-Ser2/5-P (Rai et al., 2014)


title: Sch/T5_Ser5-P_ChIP Seq

value: Anti-Ser5-P (Rai et al., 2014)


title: Sch/T5_CTD_ChIP Seq

value: Anti-CTD (Rai et al., 2014)


title: PBMCs_con_rep1

source_name: Peripheral blood mononuclear cells, control, replicate 1

tag: gender


title: PBMCs_T2D_rep4

source_name: Peripheral blood mononuclear cells, T2D, replicate 4


title: ANT-Plex 2d Muller glia

city: SEATTLE

first: THOMAS

middle: A

last: REH

address: 1959 NE PACIFIC STREET

department: BIOLOGICAL STRUCTURE

institute: UNIVERSITY OF WASHINGTON

data_processing:
Base calling and sample were demultiplexing preformed by cellranger mkfastq (version 3.0.2)
Sequences were alinged to genome and UMI counts were created using cellranger count (version 3.0.2)
Downstream analysis was preformed in R
Genome_build: mm10
Supplementary_files_format_and_content: Cellranger filtered output files, containing gene names, cellbarcodes, and expression matricies

source_name: Reprogramed Muller Glia

extract_protocol: 10x Chromium  Single Cell 3ʹ v3

value: ANT-plex

tag: days post-treatment

value: Reprogramed Muller Glia


title: PBMCs_T2D_rep3

source_name: Peripheral blood mononuclear cells, T2D, replicate 3


title: PBMCs_T2D_rep2

source_name: Peripheral blood mononuclear cells, T2D, replicate 2


title: PBMCs_T2D_rep1

source_name: Peripheral blood mononuclear cells, T2D, replicate 1


title: 756T

value: Atm-/-


title: Sch/T5_N20_ChIP Seq


title: Sch/T5_Input DNA


title: 737T


title: ANT-Plex 7d Muller glia


title: ANT 2d Muller glia

value: ANT


title: 411T


title: ANT 7d Muller Glia


title: ANT Cd45+/Cd11b+ cells

source_name: Retinal Immune cells

value: Retinal Immune cells


title: TOP2B ChIPSeq rep1


title: 410T


title: Troph_Ser5-P_ChIP Seq

value: Trohpozoite stage


title: 298T


title: Troph_CTD_ChIP Seq


title: Troph_N20_ChIP Seq


title: whole trachea digest, after polidocanol injury, Day_4

city: Boston

first: Carlos

last: Villacorta-Martin

state: MA

address: 670 Albany St

institute: Center for Regenerative Medicine at Boston University

data_processing:
The sample was processed using the standard Cellranger v.3 pipeline
Reads were mapped to GRCm38
Downstream analysis and QC done on Seurat
Differential expression using MAST models
Genome_build: GRCm38
Supplementary_files_format_and_content: the processed files are the standard output from the cellranger count pipeline: count matrices compressed in the HDF5  format

source_name: trachea explant

extract_protocol:
For scRNA-seq experiments the pulmonary vasculature was perfused via the right heart ventricle. Uninjured tracheas were peeled as previously described (Rock et al., 2009), in short, tracheas were dissected, cleaned, cut in smaller pieces and predigested in Dispase (15 U/mL, Sigma-Aldrich) for maximally 25 minutes and the epithelium was thereafter peeled from the mesenchyme. The epithelium was further digested in trypsin (0.25%) for 15 minutes. Whole tracheas, leftover mesenchyme and lung were digested with 1.5 mg/mL Collagenase A (Roche), 0.4 mg/mL DNase I (Roche), and 2 U/mL Dispase (Sigma–Aldrich) in RPMI base medium at 37 °C for 30-45  minutes. Reaction was stopped using FBS to a concentration of 10%.
Single cells were captured for sequencing library preparation using a 10X Chromium (10X Genomics, Pleasanton, CA) instrument at the BUMC Single Cell Core. Single-cell RNA-seq libraries were prepared according to the Single Cell 3’ v2 Reagent Kits User Guide (10X Genomics). Sequence libraries were constructed using the Chromium Single-Cell 3’ Library Kit (10X Genomics). Sequencing libraries were loaded on a NextSeq500 (Illumina) to obtain a sequencing depth of~200K reads per cell. 329 cells from the tracheal epithelium, 721 cells from the tracheal mesenchyme and 460 cells from whole lung parenchyma were captured and sequenced.

treatment_protocol: Polidocanol-induced injury was performed as previously described (Borthwick 2001). Mice were anesthetized in an Isoflurane chamber and delivered one dose of 15 μL freshly prepared, 2% Polidocanol or PBS sham control by oropharyngeal aspiration to induce injury. Tracheas were harvested 1-, 4- or 7-days following injury for scRNA-Seq,

value: trachea

tag: isolation method

value: Dissociated in Elastase, Dispase Collagenase, enriched for CD45 by FACS, post processing to obtain myeloid cells


title: whole trachea digest, after polidocanol injury, Day_7


title: Troph_Input DNA


title: Salivary gland, BxRasV12_1

city: Stockholm

first: Ulrich

last: Theopold

address: Svante Arrhenius väg 20C

institute: Stockholm University

data_processing:
PE50-reads were pseudoaligned with kallisto (v0.44.0) to a transcriptome index derived from all Drosophila transcript sequences of the dmel release r6.19.
Transcript abundances was analysed in R with sleuth (v0.30.0).
Genome_build: dmel-all-transcript-r6.19.fasta.gz (transcriptome build)
Supplementary_files_format_and_content: Tab-delimited text file including est_counts and tpm values.

source_name: salivary gland

extract_protocol:
Total RNA of dissected salivary glands was isolated with the RNAqueous-Micro Kit (ThermoFisher Scientific, AM1931) according to the instructors manual. Residual genomic DNA was digested with RNase-free DNaseI (ThermoFisher Scientific, EN0521) and cDNA reverse transcribed with SuperscriptIII (ThermoFisher Scientific, 18080-093) while using oligo(dT)16-primer (ThermoFisher Scientific, 8080128). Quality of all prepared totalRNA-extractions was evaluated on a 2100 Bioanalyzer Instrument (Agilent Technologies, 5067-1511).
Poly(A)-containing mRNA molecules from totalRNA-samples were purified with oligo(dT)-magnetic beads, subsequently fragmented and cDNA synthesised with random primers using the TruSeq RNA Sample Preparation Kit v2. Adapter ligation and PCR-amplification precede cluster formation with a cBot cluster generation system.

tag: strain information

value: ☿ w1118,BxGal4;;Drs-GFP x ♂ w1118;;UAS-RasV12

value: 96 h AED

value: salivary glands

tag: tissue part

value: whole gland


title: Ring/T2_Ser2/5-P_ChIP Seq

value: Ring stage


title: whole trachea digest, after polidocanol injury, Day_1

tag: tissue


title: Terc-/-ESC PDL800times-rep1

city: suwon

first: DAEUN

last: KIM

address: World cup-ro

institute: Ajou university

data_processing:
The reads were aligned to the mm10 reference genome using the STAR aligner (version 2.5.3a)
RSEM (v1.3.0) was used to calculate the expected read counts, FPKM and TMP for each sample from the corresponding bam files.
The read counts were processed using DESeq2 (v1.18.1) to identify differentailly expressed genes.
Genome_build: mm10

source_name: mESC

extract_protocol:
RNA was extracted using chloroform and isopropanol precipitation
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: mouse Embryonic Stem Cell


title: Trohp_Ser2/5-P_ChIP Seq

tag: strain

value: Anti-Ser2/5-P (Rai et al., 2014)


title: whole trachea digest


title: Ring/T2_Ser5-P_ChIP Seq

tag: developmental stage

value: Anti-Ser5-P (Rai et al., 2014)


title: Ring/T2_CTD_ChIP Seq

value: Anti-CTD  (Rai et al., 2014)


title: 044ACEDIL_sequence

city: San Francisco

first: Srilaxmi

last: Nerella

state: CA

address: HSE1355A, 513 Parnassus ave

department: Department of Medicine

institute: UCSF

description:
Messenger RNA from single cell preparations
Independent sample
044ACEDIL_sequence

data_processing:
UMI-based gene expression quantification, using Cell Ranger (Version 3.0, 10X Genomics, Pleasanton, CA)
Alignment to the hg38 human genome
Subsequent analyses using Seurat v3.0 in R
Genome_build: hg38 human genome
Supplementary_files_format_and_content: Cell Ranger output

source_name: Bronchial cells from human airway epithelial brushings

growth_protocol: Epithelial brushings were obtained at bronchoscopy

extract_protocol:
10X Chromium Controller
10X Chromium Next GEM Single Cell 3’GEM, Library & Gel Bead Kit (V3)

treatment_protocol: Epithelial brushings preparations were diaggregated using ACCUMAX. Cells were resuspended and stored resuspend in 50K aliquots using Fluidigm 10X freezing solution (minimum volume of 250 uL) at -80 in a cooling rack then transfer to liquid N2

value: Bronchial cells

tag: diagnosis

value: asthma

value: Post-Diluent Challenge


title: 043ACEAC_sequence

description:
Messenger RNA from single cell preparations
Independent sample
043ACEAC_sequence

value: Post-Allergen Challenge (house dust mite)


title: Ring/T2_Input DNA


title: NSRef-3_Uninf

city: Cambridge

first: Frank

last: Jiggins

address: Downing Street

country: United Kingdom

institute: Department of Genetics, University of Cambridge

description:
26 generations of selection for resistance to Leptopilina boulardi strain NSRef
integrated_rna_count_matrix.csv
integrated_scaled_hvg_matrix.csv
integrated_subcluster_scaled_hvg_matrix.csv
integrated_hemocytes.Robj
integrated_lamellocyte_subcluster.Robj

data_processing:
Fastq.gz files were generated from raw Illumina BCL files using bcl2fastq, Read 1: 26, Index read 1 (i7): 8, Read 2: 91
CellRanger v2 count, mapped to dm6, raw count matrix per sample provided
Seurat v3, keep cells expressing >250 or < 2500 features
Seurat v3, keep He+ or Srp+ cells
Seurat v3, replicate 2 excluded
Seurat v3, data integration (vst), normalisation (log-normal transform), 2000 highly variable feature (HVG) detection
Seurat v3, regress out number of features, UMI count and percent mitochondria
Seurat v3, PCA with 50 dimensions
Seurat v3, cluster all hemocytes (resolution = 0.3) and subcluster plasmatocyte progenitor cells and lamellocytes (resolution = 0.2)
Seurat v3, raw and scaled integrated count matrices provided
Seurat v3, R objects containing all hemocyte clustering and lamellocyte subclustering results provided
Genome_build: dm6
Supplementary_files_format_and_content: mtx files for CellRanger v2 cell count matrix for each sample
Supplementary_files_format_and_content: tsv files for CellRanger v2 barcode and genes metadata for cell count matrix for each sample
Supplementary_files_format_and_content: Robj for Seurat v3 R objects that contains all integrated and processed data and metadata including all clustering results
Supplementary_files_format_and_content: csv for integrated cell count matrix with cluster identities from Seurat v3

source_name: Larvae

growth_protocol: Hemocytes (cells) collected by dissecting third instar larvae, 96-111 hours post fertilization at 25C

extract_protocol:
Circulating hemocytes (cells) were collected in PBS and cleaned in OptiPrep solution (1.09g/ml)
10X Single Cell GEX v2 libraries were prepared from hemocyte cells

value: Hemocytes

value: Larvae

value: Outbred

tag: sample type

value: Selection, No Infection


title: 043ACEDIL_sequence

description:
Messenger RNA from single cell preparations
Independent sample
043ACEDIL_sequence


title: Peeled tracheal epithelium

value: trachea epithelium

value: peeled with dipase, dissocatied with trypsin, enriched for CD45 by FACS


title: RNA_Sch3 rep3

value: Schizont stage


title: RNAseq CD8_2

city: Gainesville

first: Rene

last: Opavsky

address: 2033 Mowry rd, CGRC r..265

institute: University of FLORIDA

data_processing:
Quality check, trimming, filtering, and alignment of reads to the Mus musculus UCSC mm10 reference genome was performed at the ICBR Bioinformatics Core (UF, Florida). Methylation calling was performed with Methyldackel (v 0.3.0.1) using the mm10-CG index. Only CpG sites with a minimum sequencing depth 5x were included in analysis. Differentially methylated regions (DMRs) were determined by Metilene and defined based on average of minimum three consecutive differentially methylated cytosines (DMCs) with methylation change of ≥20% in the same direction with p values < 0.05 (as determined by MWU test). Maximal base pair cut-off for a distance between consecutive DMCs in DMR was set to 50 bp.
For RNA-seq, trimmed sequencing data were first aligned to reference genome using STAR aligner. RNA-seq data with minimum mapped quality 50 were quantitated using the RNA-seq quantitation pipeline in SeqMonk software. For differentially expressed genes, only genes with a fold change ≥ 2 and a p-value < 0.05 (by DeSeq2) were considered to be significant.
Genome_build: mm10 - Mus musculus, hg19 - Homo sapiens
Supplementary_files_format_and_content: Processed data files are bigwig files, they contain methylation value for CpG sites whith coverage ≥ 5x

source_name: normal human CD8+ T-cells

extract_protocol:
For WGBS, genomic DNA was isolated from two independent Dnmt3b+/+, Dnmt3bD/D and Dnmt3bCI/CI MYC induced T-cell lymphoma samples using phenol/chloroform. For RNA-seq, total RNA was isolated using trizol.
The WGBS libraries were prepared and sequenced on an Illumina NovaSeq6000 sequencer using 150 bp long paired-end reads. The RNAseq libraries were generated and sequenced on NovaSeq6000 platform using paired-end 150 bp runs.

value: peripheral blood

value: normal human CD8+ T-cells


title: RNA_Sch2 rep2


title: NSRef-3_Inf

description:
Second instar larvae (48-63 hours post fertilization at 25C) infected with Leptopilina boulardi strain NSRef
26 generations of selection for resistance to Leptopilina boulardi strain NSRef
integrated_rna_count_matrix.csv
integrated_scaled_hvg_matrix.csv
integrated_subcluster_scaled_hvg_matrix.csv
integrated_hemocytes.Robj
integrated_lamellocyte_subcluster.Robj

tag: age

value: Selection, Infection


title: 6027_Luteal_2016-10-03 (batch 1)

city: Seattle

first: Sean

last: Hughes

address: 850 Republican St

institute: University of Washington

data_processing: The data was preprocessed by Bioconductor lumi package (version 2.34.0). It was vst transformed and rsn normalized. Only probes with detection threshold < 0.05 in at least 10 samples were included in the analysis.

source_name: Endocervical cytobrush from participant 6027 at the Luteal on 2016-10-03

extract_protocol: Total RNA was extracted using the Qiagen Rneasy Plus mini kit

tag: studyid

tag: date

tag: index

tag: rin

tag: enrollment

tag: status

value: Withdrawn

value: Positive

tag: progesterone

tag: bv

value: N

tag: visit

value: Luteal

tag: drop

value: Don't drop

tag: batch


title: HNSCC, treated, patient 8 rep 1

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

country: Italy

institute: University of Florence

hyb_protocol: Hybridization was performed according to specifications in One-Color Microarray-Based Gene Expression Analysis Protocol

scan_protocol: The data was extracted using Agilent Feature Extraction Software version 10.7.3.1 with default parameters of protocol GE1_107_Sep09.

data_processing: Data preprocessing was performed using R/Bioconductor (version 3.6)  limma (version 3.34.9) package. Briefly, raw Feature Extractor data was loaded into R and further background corrected (method=”minimum”), normalized (method=”quantile”) and filtered to remove control probes.

source_name: HNSCC

label_protocol: Labelling was performed with the one color (Cyanine 3-CTP) Low Input Quick Amp Labeling Kit (Agilent Technologies) accordinf to manufacturer protocol.

growth_protocol: Cells were kept in culture in DMEM medium supplemented with 10% FCS.

extract_protocol: RNA was extracted using RNeasy Micro Kit - QIAGEN following manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer

treatment_protocol: Cells were analyzed either resting either after 16 hours stimulation with IFNg and TNFa.

tag: cell type

value: mesenchymal stromal cells

tag: treatment

value: IFNG+TNFA

tag: tissue

value: HNSCC

tag: patient

tag: ChIP


title: HNSCC, untreated, patient 8 rep 2


title: RNAseq CD8


title: HNSCC, treated, patient 7 rep 2


title: whole lung digest

source_name: lung explant

tag: strain

value: lung

tag: isolation method

value: Dissociated in Elastase, Dispase Collagenase, enriched for CD45F480 by FACS


title: HNSCC, treated, patient 8 rep 2


title: NSRef-2_Uninf

value: Hemocytes

tag: age

value: Larvae

tag: genotype

value: Outbred

tag: sample type

value: Selection, No Infection


title: HNSCC, untreated, patient 7 rep 2


title: RNA_Sch1 rep1

source_name: Asexual stages

tag: developmental stage

value: Schizont stage


title: Peeled tracheal mesenchyme

value: trachea mesenchyme

value: epithelium peeled away with dispase, dissociated in Elastase, Dispase, Collagenase , enriched for CD45F480 by FACS


title: NSRef-2_Inf

value: Selection, Infection


title: Ring/T2_N20_ChIP Seq

value: Ring stage

tag: chip antibody


title: HNSCC, untreated, patient 8 rep 1


title: RNA_Troph3 rep3

value: Trohpozoite stage


title: HNSCC, treated, patient 7 rep 1


title: NSRef-1_Uninf


title: RNAseq CD4

source_name: normal human CD4+ T-cells

value: peripheral blood

value: normal human CD4+ T-cells


title: RNA_Troph2 rep2


title: RNAseq ori03

source_name: human peripheral T-cell lymphoma sample

value: lymph node

value: peripheral T-cell lymphoma


title: RNA_Troph rep1


title: NSRef-1_Inf


title: RNA_Ring rep3


title: RNAseq CD4_2


title: RNA_Ring rep2


title: RNAseq ori02


title: RNAseq ori01


title: Bone marrow, treated, patient 6 rep 2

source_name: BONE MARROW

value: mesenchymal stem cell line

value: IFNG+TNFA

value: BONE MARROW


title: C3_Uninf

description:
integrated_rna_count_matrix.csv
integrated_scaled_hvg_matrix.csv
integrated_subcluster_scaled_hvg_matrix.csv
integrated_hemocytes.Robj
integrated_lamellocyte_subcluster.Robj

value: Hemocytes

value: No Selection, No Infection


title: RNAseq hPTCL16


title: C2_Inf

description:
Second instar larvae (48-63 hours post fertilization at 25C) infected with Leptopilina boulardi strain NSRef
integrated_rna_count_matrix.csv
integrated_scaled_hvg_matrix.csv
integrated_subcluster_scaled_hvg_matrix.csv
integrated_hemocytes.Robj
integrated_lamellocyte_subcluster.Robj

value: Larvae

value: Outbred

value: No Selection, Infection


title: RNA_Ring rep1


title: C2_Uninf


title: HNSCC, untreated, patient 7 rep 1

value: mesenchymal stromal cells

value: HNSCC


title: Bone marrow, treated, patient 6 rep 1


title: C1_Uninf


title: E16_5_scRNA-seq

city: Qingdao

first: Jun-Jie

last: Wang

address: Changcheng 700

institute: College of Life Sciences

description: 2x150 paired-end sequence reads

data_processing:
CellRanger count pipeline 2.2.0 is performed to generate the single cell information
Genome_build: mm10
Supplementary_files_format_and_content: The single cell expression matrix is stored as tab-delimited text files after normalization.

source_name: E16.5 ovarian cells

extract_protocol:
The isolated ovaries were cut into pieces and transferred into digestive solution consist of 0.25 % trypsin/EDTA (Hyclone, USABeijing, China) and collagenase (Sigma-Aldrich, C5138, Shanghai, China) for 6 ~ 8 mins at 37 ℃. Following the termination of digestion, the single cell solution was obtained after filtration with 40 μm cell strainers (BD Falcon, 352340, USA) and two times wash with PBS containing 0.04 % BSA.
Single-cell RNA-seq libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V2 (10x Genomics Inc., 120237, Pleasanton, CA, USA) following the manufacture’s introduction.

value: Ovary


title: RNAseq hPTCL13


title: Bone marrow, untreated, patient 6 rep 2


title: Bone marrow, untreated, patient 6 rep 1


title: Bone marrow, treated, patient 5 rep 1


title: Bone marrow, treated, patient 4 rep 2


title: Bone marrow, untreated, patient 5 rep 1


title: C3_Inf


title: Bone marrow, untreated, patient 5 rep 2


title: C1_Inf


title: RNAseq hPTCL12


title: RNAseq hPTCL11


title: RNAseq hPTCL15


title: cmt/dnmt3b_rep2

city: Tel-Aviv

first: Katherine

last: Domb

address: Haim Levanon st.

department: Gray Faculty of Medical and Health Sciences

institute: Tel Aviv University

data_processing:
Adaptor and quality trimming using TrimGalore v0.6.0 with Cutadapt v1.15
Alignment to the reference genome and counting reads per gene/TE in the supplied annotation file, using STAR v2.7.0f
Genome_build: Ppatens v3.0
Supplementary_files_format_and_content: tab-delimited text file with raw read counts assigned to each of the annotated features (gene or transposable element), in each sample

source_name: protonema

extract_protocol:
Total RNA was extracted from 7 days old protonema using SV Total RNA Isolation System (Promega, USA) and DNase treatment (Thermo Fisher Scientific, USA).
The polyA fraction (mRNA) was purified from 500 ng of total input RNA, followed by fragmentation and the generation of double-stranded cDNA. Then, Agencourt Ampure XP beads cleanup (Beckman Coulter), end repair, A base addition, adapter ligation and PCR amplification steps were performed. Libraries were quantified by Qubit (Thermo fisher scientific) and TapeStation (Agilent).

tag: cultivar

value: Grandsen

value: 7 days


title: cmt/dnmt3b_rep1


title: cmt/dnmt3b_rep3


title: RNAseq hPTCL10


title: RNAseq hPTCL1


title: dnmt3b_rep3