title: Patient 15 M013

city: Hatfield

first: Floryne

middle: Ottilie

last: Buishand

address: Hawkshead Lane

department: Clinical Science and Service

country: United Kingdom

institute: Royal Veterinary College

hyb_protocol: The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.1 software package (Agilent Technologies).

source_name: Adrenocortical carcinoma

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar).

extract_protocol: Total RNA was extracted from fresh frozen tissue samples using a Qiazol protocol (RNeasy Mini Kit, Qiagen) according to the manufacturer’s instructions. RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Englewood, CO, USA). Only samples with a minimum RNA integrity number of seven were included for analysis.

tag: clinical diagnosis

value: Hypercortisolism


title: A_LV_S104 ATACseq

status: Public on Jul 01 2019

type: SRA

city: Philadelphia

first: E

middle: JOHN

last: WHERRY

state: PA

address: 421 Curie Blvd,354 BRB II/III

department: Systems Pharmacology       and Translational Therapeutics,Institute for Immunology

country: USA

institute: University of Pennsylvania

library_source: genomic

data_processing:
Paired-end reads were mapped to the hg19 reference genome using Bowtie2
Only concordantly mapped pairs were kept for further analysis
Peak calling was performed using MACS v1.4 to identify areas of sequence tag enrichment
BedTools was used to find common intersection between identified peaks (1bp minimum overlap) and to create a merged peak list
ATAC-seq tag enrichment, DNA motif analysis across the merged peak list,and GO term assessment were computed using HOMER (homer.salk.edu)
Genome_build: hg19
Supplementary_files_format_and_content: bed files generated by peak calling

molecule: genomic DNA

organism: Homo sapiens

source_name: CD4 T cells

extract_protocol:
Mononuclear cells from mesenteric LN, TDL, and PBMC were thawed, rested overnight, and sorted in cell numbers of 5-25,000 into complete RPMI with 50% FBS. Nuclei from cell pellets (5,000-25,000 cells) were isolated using a lysis buffer and pelleted in low-bind 1.5mL tubes (Eppendorf).
Nuclei were resuspended in 25ml TD buffer with Tn transposase (Illumina). The transposition reaction was continued for 45 minutes at 37°C. The resulting DNA fragments were purified using the MinElute PCR purification Kit (Qiagen). Libraries were prepared using Nextera (Illumina) and sequenced by the Children’s Hospital of Philadelphia partnership with the Bejing Genomics Institute on two lanes of a Hiseq 4000 paired-end sequencing (100 bp read length).

tag: tissue

value: LymphNode

tag: cell type


title: Patient 16 M014

type: RNA

molecule: total RNA

value: Nonfunctional


title: Patient 18 M017


title: A_LV_S103 ATACseq


title: Patient 17 M016

value: Conn's Syndrome


title: Patient 19 M150448


title: Patient 12 6417

value: Cushing's Syndrome


title: Patient 10 6450

source_name: Adrenocortical adenoma

value: Ectopic Cushing's Syndrome


title: A_LV_S110 ATACseq


title: Patient 14 M012


title: Patient 20 M156691


title: Jurkat control2 replicate

city: Fukuoka

first: Yoshikane

last: Kikushige

address: 3-1-1 Maidashi, Higashiku

country: Japan

institute: Kyushu University

description: Jurkat cont4

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µL containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µL of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human Gene Expression 8x60K Microarrays (G4851B) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid: 039494_D_F_20120628) to obtain background subtracted and spatially detrended Processed Signal intensities. Raw expression data was imported and normalized by using GeneSpring GX software (Agilent Technologies). According to the guided workflow for Agilent single color experiment, normalization algorithm of 75-percentile shift was used, and the preprocessing baseline was adjusted to median of all samples.

source_name: Jurkat cells cultured in the control DMEM/F-12 medium +10%FBS for 10 days (experiment2 replicate)

label_protocol: Cyanine 3 (Cy3)-labeled cRNA was synthesized with Low Input Quick Amp Labeling kit, one-color (Agilent) according to the manufacturer's instructions. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted by using Isogen2 (NIPPON GENE) according to the manufacturer's instructions.

treatment_protocol: Jurkat cells were cultured in DMEM/F12 medium supplemented with 10% heat-inactivated fetal bovine serum (FBS) with or without BCAA for 8-10 days. Medium exchange was performed every 5 days.

tag: cell line

value: Jurkat

value: acute lymphoblastic leukemia cell line

tag: treatment

value: control


title: Patient 8 6435


title: Jurkat BCAA-free1

description: Jurkat BCAA free1

source_name: Jurkat cells cultured in the BCAA-free DMEM/F-12 medium +10%FBS for 8 days (experiment1)

value: without BCAA for 8-10 days


title: Patient 11 6466


title: Patient 13 6425


title: Jurkat BCAA-free2

description: Jurkat BCAA free3

source_name: Jurkat cells cultured in the BCAA-free DMEM/F-12 medium +10%FBS for 10 days (experiment2)


title: Jurkat BCAA-free1 replicate

description: Jurkat BCAA free2

source_name: Jurkat cells cultured in the BCAA-free DMEM/F-12 medium +10%FBS for 8 days (experiment1 replicate)


title: Patient 9 6447


title: Jurkat BCAA-free2 replicate

description: Jurkat BCAA free4

source_name: Jurkat cells cultured in the BCAA-free DMEM/F-12 medium +10%FBS for 10 days (experiment2 replicate)


title: Jurkat control1 replicate

description: Jurkat cont2

source_name: Jurkat cells cultured in the control DMEM/F-12 medium +10%FBS for 8 days (experiment1)


title: Jurkat control2

description: Jurkat cont3

source_name: Jurkat cells cultured in the control DMEM/F-12 medium +10%FBS for 10 days (experiment2)


title: HEK293T Cytosolic replicate 1

city: Rehovot

first: Miguel

middle: A.

last: Garcia-Campos

state: Center District

address: Herzl 234, Meyer Bldg., Room 1410

department: Molecular Genetics

country: Israel

institute: Weizmann Insitute of Science

library_source: transcriptomic

data_processing:
RNA-seq reads were aligned to the hg19 genome using STAR (V. 2.5.3a) and default parameters
Alignment files were processed using the mazter_mine pipeline as noted in publication
Genome_build: hg19
Supplementary_files_format_and_content: Tab separated text file with cleavage efficiencies at single-nucleotide resolution

molecule: polyA RNA

extract_protocol:
Nucleozol RNA extraction.
Fragmentation, 3' adapter ligation, cDNA synthesis, second adapter ligation and enrichment

tag: genotype

value: WT


title: HEK293T Cytosolic replicate 2


title: Patient 5 6392


title: HEK293T FTO OE replicate 2

value: FTO OE


title: Patient 6 6394


title: HEK293T FTO OE replicate 1


title: Patient 7 6402


title: Patient 1 6357


title: kclz1

city: Boulder

first: Lynn

last: Sanford

state: CO

address: UCB 596

department: Biochemistry

institute: University of Colorado Boulder

description:
S7_KCl_Zn_01
processed data file:
gene_level_counts.txt
gene_level_count_annotations.txt
all_samples_TPM.txt
DESeq2_gene_kclz_kclo.txt
DESeq2_gene_kclz_kclt.txt

data_processing:
The first ten bases of all reads were trimmed from each separate fastq file in a single-end fashion with trimmomatic (v0.32)
Trimmed fastq files were mapped in a paired-end fashion with tophat2 (v2.0.6, bowtie2 v2.0.2) with the parameters --b2-very-sensitive -r 110 --mate-std-dev 180, as well as including the rn6 genes GTF file. Resultant BAM files were indexed with samtools (v0.1.18)
The featureCounts function within the R package Rsubread (v1.24.2, R v3.3.0) was used to generate gene-level read counts, with the following parameters: GTF.featureType=”exon”, GTP.attrType=”gene_id”, useMetaFeatures=TRUE, allowMultiOverlap=FALSE, largestOverlap=FALSE, strandSpecific=2, isPairedEnd=TRUE, requireBothEndsMapped=TRUE, checkFragLength=TRUE, minFragLength=50, maxFragLength=60000, countChimericFragments=FALSE.
Differential expression analysis was performed pairwise between conditions with the R package DESeq2 (v1.14.1). All gene-level counts for all samples were loaded into a dds object, then analyzed. Pairwise comparisons were then extracted.
Genome_build: rn6 (fasta and gtf files were downloaded from Illumina iGenomes (https://support.illumina.com/sequencing/sequencing_software/igenome.html) on 7/31/2017)
Supplementary_files_format_and_content: For the following files, column headers or filename abbreviations match sample titles (i.e. kclo1 = KCl only treatment, replicate 1; kclz2 = KCl/ZnCl2 treatment, replicate 2, etc.).
Supplementary_files_format_and_content: gene_level_counts.txt is a tab-delimited text file of gene-level counts as determined by featureCounts. All samples are included, one sample per column. File was output from an R object, so column headers are offset 1 column in text file, but will read into R correctly.
Supplementary_files_format_and_content: gene_level_count_annotations.txt is a tab-delimited text file containing the annotation information extracted by featureCounts. This includes a portion of the gene GTF file input, including gene name, chromosomal positions of features (in this case exons), strand, and total gene length (used to calculate TPM).
Supplementary_files_format_and_content: all_samples_TPM.txt is a tab-delimited text file containing transcripts per million (TPM) values for all genes and all samples, as calculated with the counts and gene length output by featureCounts in the previous two files.

organism: Rattus norvegicus

growth_protocol: Cells were extracted from microdissected embryonic (E18) rat hippocampi, with tissue pooled from 10 embryos prior to dissociation. Cells were grown for 14 days in Neurobasal medium supplemented with 2% B27 supplement and 0.3x GlutaMAX. Cultures were treated with 4 µM cytosine arabinoside from DIV3-6.

extract_protocol:
Cells were lysed and RNA extracted according to the Promega Maxwell RSC simplyRNA isolation kit
Libraries were generated from RNA samples according to the Bioo NextFlex Dir RNA kit

treatment_protocol: Cultures were placed at room temperature. Media was removed and neurons incubated in a high-potassium buffer solution (98 mM NaCl, 50 mM KCl, 1.5 mM CaCl2, 1 mM MgCl2, 10 mM HEPES, 10 mM glucose, pH 7.4) for 10 seconds, with and without the addition of 10 µM ZnCl2 or 10 µM tris(2-pyridylmethyl)amine (TPA). Each of the three conditions (Stimulation, stimulation + ZnCl2, stimulation + TPA) was performed in triplicate. After treatment, samples were placed back in the removed neuron culture media and incubated for 90 minutes at 37 °C and 5% CO2 before cell lysis and RNA isolation.

tag: strain

value: Sprague Dawley

tag: age

value: Embryonic day 18

value: Dissociated hippocampal culture

tag: day in vitro

value: DIV 14


title: kclz3

description:
S9_KCl_Zn_03
processed data file:
gene_level_counts.txt
gene_level_count_annotations.txt
all_samples_TPM.txt
DESeq2_gene_kclz_kclo.txt
DESeq2_gene_kclz_kclt.txt


title: kclt3

description:
S6_KCl_TPA_03
processed data file:
gene_level_counts.txt
gene_level_count_annotations.txt
all_samples_TPM.txt
DESeq2_gene_kclz_kclt.txt
DESeq2_gene_kclt_kclo.txt

source_name: dissociated hippocampal culture_KCl/TPA

value: KCl/TPA


title: Patient 4 6390


title: Control 5 7064

source_name: Normal adrenal cortex


title: HEK293T Control OE replicate 3

value: Control OE


title: kclt2

description:
S5_KCl_TPA_02
processed data file:
gene_level_counts.txt
gene_level_count_annotations.txt
all_samples_TPM.txt
DESeq2_gene_kclz_kclt.txt
DESeq2_gene_kclt_kclo.txt


title: Patient 2 6358


title: HEK293T Control OE replicate 2


title: Control 4 7062


title: Control 2 7047


title: Jurkat control1

description: Jurkat cont1


title: Kasumi9 BCAA free2 replicate

description: Gene expression of THP1 cells in BCAA-free medium (BCAA-free DMEM/F12+ 10% FBS)

source_name: Kasumi9 cells cultured in the BCAA-free DMEM/F-12 medium+10%FBS for 10 days (experiment2 replicate)

treatment_protocol: Kasumi9 cells were cultured in DMEM/F12 medium supplemented with 10% heat-inactivated fetal bovine serum (FBS) for 8-10 days with or without BCAA. Medium exchange was performed every 7 days.


title: Patient 3 6361


title: Control 1 7046


title: HEK293T Control OE replicate 1


title: kclo2

description:
S2_KCl_02
processed data file:
gene_level_counts.txt
gene_level_count_annotations.txt
all_samples_TPM.txt
DESeq2_gene_kclz_kclo.txt
DESeq2_gene_kclt_kclo.txt

source_name: dissociated hippocampal culture_KCl

value: KCl


title: kclz2

description:
S8_KCl_Zn_02
processed data file:
gene_level_counts.txt
gene_level_count_annotations.txt
all_samples_TPM.txt
DESeq2_gene_kclz_kclo.txt
DESeq2_gene_kclz_kclt.txt


title: Control 3 7065


title: Kasumi9 BCAA free1

source_name: Kasumi9 cells cultured in the BCAA-free DMEM/F-12 medium+10%FBS for 8 days (experiment1)


title: kclo1

description:
S1_KCl_01
processed data file:
gene_level_counts.txt
gene_level_count_annotations.txt
all_samples_TPM.txt
DESeq2_gene_kclz_kclo.txt
DESeq2_gene_kclt_kclo.txt


title: Kasumi9 control2

description: Gene expression of THP1 cells in control medium (DMEM/F12+ 10% FBS)

source_name: Kasumi9 cells cultured in the control DMEM/F-12 medium+10%FBS for 10 days (experiment2)


title: Kasumi9 control2 replicate

source_name: Kasumi9 cells cultured in the control DMEM/F-12 medium+10%FBS for 10 days (experiment2 replicate)


title: Kasumi9 BCAA free2

source_name: Kasumi9 cells cultured in the BCAA-free DMEM/F-12 medium+10%FBS for 10 days (experiment2)


title: OSCC1_VH_DNA 0911-6020

type: genomic

city: Taoyuan

first: Ji-Dung

last: Luo

address: No. 259, Wen-Hua 1st road

department: Graduate Institute of Biomedical Sciences

country: Taiwan

institute: Chang Gung University

hyb_protocol: Follow the manufecturer's porcedure.

scan_protocol: Follow the manufecturer's porcedure.

data_processing:
Analysis with Illumina GenomeStudio.
GenomeStudio computed normalized signal intensitie

label: biotin

source_name: FFPE

label_protocol: Follow the manufecturer's porcedure.

growth_protocol: OPMD and cacner tissues were obtained from two oral cancer patients during surgery. The peripheral blood samples from the two patients were also collected.

extract_protocol: Tissue and blood DNA were extracted by QIAGEN DNA FFPE Tissue Kit and QIAGEN QIAMP blood mini kit, respectively.

treatment_protocol: tumor tissues were fixed in formaldehyde and embedded in paffarine. Peripheral blood samples were collected in evacuated blood tube with EDTA.

tag: patient

value: verrucous hyperplasia


title: Kasumi9 BCAA free1 replicate

source_name: Kasumi9 cells cultured in the BCAA-free DMEM/F-12 medium+10%FBS for 8 days (experiment1 replicate)


title: kclt1

description:
S4_KCl_TPA_01
processed data file:
gene_level_counts.txt
gene_level_count_annotations.txt
all_samples_TPM.txt
DESeq2_gene_kclz_kclt.txt
DESeq2_gene_kclt_kclo.txt


title: HEK293T AlkBH5 OE replicate 2

value: AlkBH5 OE


title: OSCC2_Tumor_DNA_Duplicate 1303-6353-0d

description: Duplicate of 1303-6353-0

value: tumor


title: OSCC2_VH_DNA 1005-6780


title: OSCC2_VH_DNA_duplicate 1005-6780d

description: Duplicate of 1005-6780


title: hESC WT replicate 3

source_name: human embryonic stem cells

value: human embryonic stem cells


title: HEK293T AlkBH5 OE replicate 1


title: OSCC1_Tumor_DNA 1008-6763


title: Wctr4C26

city: Aurora

first: Lauren

last: Jillson

state: Colorado

address: 12801 E 17th Avenue, Room L18-6213, Mail stop 8303

department: Pharmacology

institute: University of Colorado Anschutz Medical Campus

data_processing:
PE150 reads were generated at an estimated 20 million reads per sample
Raw reads (fastq files) were mapped to the Ensembl v90 transcriptome of the Mus musculus genome build GRCm38 using Bowtie2 with the parameter settings ‘--sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 --no-mixed --no-discordant’; transcripts were quantified using the rsem-calculate-expression function in RSEM v1.3.1
Genes that had an average count of less than 5 across all replicates were removed.
The log-fold change was calculated for each gene using the voom workflow in the limma R package (voom pipeline)
Genome_build: GRCm38
Supplementary_files_format_and_content: The raw transcript counts (WFU3_compiled_raw) and RSEM-normalized values (WFU3_compiled_normalized)  below contain compiled data for each cell type delineated by column headers.

organism: Mus musculus

source_name: prostate epithelial stem cell (WFU3 cell line)

growth_protocol: WFU3 cells are maintained in uncoated culture dishes in complete 50:50 Dulbecco’s modified Eagle’s medium (DMEM)/Ham’s F-12 medium (F12) (full list of supplements are cited above).

extract_protocol:
1.5 million shControl, shChd1, shMap3k7 or shDouble WFU3 cells were plated onto 10cm dishes in complete growth medium. Twenty-four hours later RNA was isolated using 5prime Perfect RNA Cell kit (Fischer Scientific) according to the manufacturer’s protocol.
After quality control, RNA samples were enriched for mRNA using oligo(dT) beads, fragmented for a 250-300 bp target range, then cDNA synthesis using random hexamer primers, second strand synthesis is performed using dNTPs, RNAas H and DNA polymerase I in Illumina synthesis buffer, Illumina sequencing adapters, then the double-stranded cDNA library is size selected and PCR enriched.

treatment_protocol: Knockdown of Map3k7(TAK1) in WFU3 cells was generated by lentiviral transfection of either shMap3k7 or non-targeting shControl plasmids cloned into a modified LentLox3.7 lentivirus vector. EGFP expression determined infection efficiency. Individual clones (Clones 1 and 7 with shMap3k7, and clones 4 and 5 with shControl) were isolated using cloning cylinders after cells were grown at clonogenic density. These clones were then transfected with shChd1 (construct 96526 or 96528) or shControl constructs in a pLKO.1-puromycin plasmid using lentiviral transfection. Puromycin resistance was used to determine successful transfection.

value: WFU3 prostate epithelial stem cell line

value: sh Ctrl  4 GFP -shCHD1 96526 Puro

tag: passage


title: Wctr4C28

value: sh Ctrl  4 GFP -shCHD1 96528 Puro


title: OSCC2_Tumor_DNA 1303-6353-0


title: hESC WT replicate 2


title: kclo3

description:
S3_KCl_03
processed data file:
gene_level_counts.txt
gene_level_count_annotations.txt
all_samples_TPM.txt
DESeq2_gene_kclz_kclo.txt
DESeq2_gene_kclt_kclo.txt


title: WT1ctrlp

value: shTak1 GFP CLONE 1 sh Ctrl puro


title: HEK293T AlkBH5 OE replicate 3


title: hESC WT replicate 1

value: WT


title: OSCC1_Blood_DNA O00229-7

source_name: whole blood

value: blood


title: hESC FTO KO replicate 3

value: FTO KO


title: WT7C28

value: shTak1 GFP CLONE7 shChd1 96528 puro


title: WT7C26

value: shTak1 GFP CLONE7 shChd1 96526 puro


title: hESC FTO KO replicate 2


title: OSCC2_Blood_DNA O0106-11


title: WT7ctrlp

value: shTak1 GFP CLONE 7 sh Ctrl puro


title: WT1C28

value: shTak1 GFP CLONE 1 shChd1 96528 puro


title: WT1C26

value: shTak1 GFP CLONE 1 shChd1 96526 puro


title: Wctrl5

value: sh Ctrl 5 GFP -shCtrl puro


title: Wctrl4

value: sh Ctrl  4 GFP -shCtrl puro


title: THP-1 cell BCAA-free exp3

description: THP-1 BCAA free3

source_name: THP-1 cells culture in the BCAA-free DMEM/F-12 medium+10%FBS for 5 days (experiment3)

treatment_protocol: THP-1 cells were cultured in DMEM/F12 medium supplemented with 10% heat-inactivated fetal bovine serum (FBS) for 3-5 days with or without BCAA.

value: acute lymphoblastic leukemia cell line

value: without BCAA for 8-10 days


title: Kasumi9 control1

source_name: Kasumi9 cells cultured in the control DMEM/F-12 medium+10%FBS for 8 days (experiment1)

value: control


title: Kasumi9 control1 replicate

source_name: Kasumi9 cells cultured in the control DMEM/F-12 medium+10%FBS for 8 days (experiment1 replicate)


title: THP-1 cell BCAA-free exp4

description: THP-1 BCAA free4

source_name: THP-1 cells culture in the BCAA-free DMEM/F-12 medium+10%FBS for 3 days (experiment4)


title: hESC FTO KO replicate 1

value: human embryonic stem cells


title: Wctrlpn

value: WFU3 prostate epithelial stem cell line

value: sh Ctrl puro- shCtrl neo


title: THP-1 cell BCAA-free exp1

description: THP-1 BCAA free1

source_name: THP-1 cells culture in the BCAA-free DMEM/F-12 medium+10%FBS for 4 days (experiment1)


title: THP-1 cell BCAA-free exp2

description: THP-1 BCAA free2

source_name: THP-1 cells culture in the BCAA-free DMEM/F-12 medium+10%FBS for 4 days (experiment2)


title: PcDC2 rep2

city: Seoul

first: Chae Gyu

last: Park

state: Seoul

address: 50-1 Yonsei-ro

department: Severance Biomedical Science Institute

country: South Korea

institute: Yonsei University College of Medicine

description:
Normalized_FPKM.txt
sample name in processed data file:
66

data_processing:
bcl2fastq v1.8.4 package was used for basecalling.
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence with Trimmomatic0.32.
To estimate expression levels, the RNA-Seq reads were mapped to the genome of Mus musculus using HISAT2 2.1.0, which is capable of reporting split-read alignments across splice junctions and determined using StringTie 1.3.4d software in default options.
The reference genome sequence of Mus musculus (mm10) and annotation data were downloaded from UCSC. The transcript counts in isoform level were calculated, and the relative transcript abundances were measured in FPKM (Fragments Per Kilobase of exon per Million fragments mapped) using Cufflinks.
Raw data (the reads for each transcript) were normalized by FPKM (Fragments Per Kilobase of exon model per Millon mapped fragments).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values for each Sample

source_name: Peritoneal myeloid mononuclear cell

extract_protocol:
Peritoneal cells were isolated by flushing peritoneal cavity with PBS containing 3% FBS. 5ml of ice-cold isolation buffer were injected into peritoneal cavity. Then peritoneal cavity was gently massaged to dislodge the attached immune cells. Suspended peritoneal cells were harvested.
Reverse transcription of mRNA and generation of cDNA libraries were carried out with SMARTer Ultra low input RNA library kit and sequencing with Illumina NovaSeq

value: Peritoneal cavity

value: myeloid mononuclear cell

tag: cell subtype

value: peritoneal type 2 dendritic cells

tag: cell markers

value: mouse MHCII+ CD11c+ CD115-

value: post natal week 8


title: THP-1 cell control exp4

description: THP-1 cont4

source_name: THP-1 cells culture in the control DMEM/F-12 medium+10%FBS for 3 days (experiment4)


title: THP-1 cell control exp1

description: THP-1 cont1

source_name: THP-1 cells culture in the control DMEM/F-12 medium+10%FBS for 4 days (experiment1)


title: ARPC 2+LPS

city: Bari

first: Fabio

last: Sallustio

state: Bari

address: Piazza G. Cesare N°11

country: Italy

institute: University of Bari

description:
Gene expression after LPS stimulation and 24 hours culture
257236314287_S01_GE1_107_Sep09_2_4

hyb_protocol: Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 °C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software v 10.7.3 (Agilent) using default parameters  to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: RNA ARPC + LPS 24 h culture

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Low Input Quick Amp Labeling (LIQA) kit (Agilent Technologies)  according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: ARPC were growth in EGM-MV with 20% FCS and incubated at 37°C with 5.0% CO2

extract_protocol: Total RNA extraction was performed by means of RNeasy Mini kit (Qiagen) according to the manufacturer’s protocol. DNase treatment was carried out to remove any contaminating DNA (RNase-Free DNase Set, Qiagen). The RNA concentration was determined with NanoDrop Spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).

treatment_protocol: ARPC were growth without LPS (basal condition) or were stimulated in vitro with LPS (4μg/ml) for 24h

value: adult renal stem/progenitor cells (ARPC)

tag: stimulated with

value: LPS (4μg/ml) for 24h

tag: time point

value: 24 h culture


title: THP-1 cell control exp2

description: THP-1 cont2

source_name: THP-1 cells culture in the control DMEM/F-12 medium+10%FBS for 4 days (experiment2)


title: Control (Pol IV rdr2 mutant)

city: Bloomington

first: Craig

middle: S.

last: Pikaard

state: Indiana

address: 915 E. Third Street

department: Department of Biology and Department of Molecular and Cellular Biochemistry

institute: Howard Hughes Medical Institute, Indiana University

data_processing:
Raw reads were subject to adapter trimming and read merging by an in-house script 'PE_trimadapter.py'.
Remaining reads were aligned to the Arabidopsis TAIR10 genome assembly and Sf9 draft genome assembly, allowing 0 mismatches, to remove non-M13 contaminant RNAs present in enzyme fractions.
Remaining reads were aligned to the bacteriophage M13 genome (M13mp18) allowing up to 3 mismatches.
Genome_build: M13mp18 (Bayou Labs)
Supplementary_files_format_and_content: Tab-delimited txt file with read sequences, read length and strandedness

organism: synthetic construct

source_name: in vitro reaction with M13 as template

extract_protocol:
RNA transcripts were precipitated with isopropanol after in vitro transcription
RNA transcripts were prepared according to Illumina's instructions accompanying the TruSeq small RNA Prep Kit. Briefly, for precursors produced by Pol IV and RDR2 and siRNAs produced by DCL3 dicing of the precursors, 80 cycles of paired-end sequencing was performed. A replicate precursor sample produced by Pol IV-RDR2 and a control sample produced by Pol IV extracted from Pol IV rdr2 mutant background were subjected to 73 cycles of single-end sequencing.

tag: template

value: M13mp18 (+) strand DNA template

tag: product


title: PcDC2 rep1

description:
Normalized_FPKM.txt
sample name in processed data file:
52


title: Precursors (rep2)

value: siRNA precursors (produced by in vitro activities of Pol IV-RDR2)


title: PcDC1

description:
Normalized_FPKM.txt
sample name in processed data file:
51

value: peritoneal type 1 dendritic cells


title: 12A1_RNA

city: Grand Rapids

first: Ronald

middle: L.

last: Chandler

state: MI

department: Obstetrics, Gynecology and Reproductive Biology

institute: Michigan State University

description: RNA library from 12Z cells after siARID1A treatment

data_processing:
Raw reads were trimmed with cutadapt and Trim Galore! followed by quality control analysis via FastQC.
Trimmed reads were aligned GRCh38.p12 genome assembly, indexed to GENCODE (v28) GFF3 annotation via STAR aligner with flag ‘--quantMode GeneCounts’ for feature counting.
STAR sample gene counts were concatenated for Stranded-Reverse (libtype), corresponding to column 4 of STAR output ReadsPerGene.out.tab file.
Low count genes were filtered prior to DESeq2 count normalization (at least 1 count per sample on average) and subsequent differential-expression analysis comparisons within flow cells (i.e. respective wild-type samples were used). Calculated differential-expression probabilities were corrected for multiple testing by independent hypothesis weighting (IHW) for downstream analysis.
Genome_build: GRCh38.p12 indexed to GENCODE (v28) GFF3 annotation
Supplementary_files_format_and_content: Comma-separated values (CSV) and tab-separated values (TSV) tabular text files including gene counts (STAR output) and non-thresholded DESeq2 differential-expression analysis.

source_name: 12Z cell line

growth_protocol: 12Z cells were grown in DMEM/F12 + 10% FBS, 1% pen/strep, 1% L-glutamine

extract_protocol:
72 hours after siRNA transfection, RNA was prepared using the Quick-RNA Miniprep Kit (Zymo Research).
RNA-seq libraries were prepared using the KAPA Stranded mRNA-seq Kit from 500 ng of total RNA material.

treatment_protocol: Cells were transfected with siRNAs using Lipofectamine RNAiMax reagent, and media was replaced after 24 hours.

value: 12Z endometriotic epithelial cells

tag: condition

value: siARID1A knockdown


title: 12A3_RNA


title: 12A2_RNA


title: P-IV.I rep2

description:
Normalized_FPKM.txt
sample name in processed data file:
49

tag: tissue

value: peritoneal dendritic cells

value: mouse MHCII+ CD11c+ CD115+


title: siRNAs

value: mature siRNAs (produced by DCL3)


title: P-IV.I rep1

description:
Normalized_FPKM.txt
sample name in processed data file:
45

tag: cell type


title: P-IV.II rep2

description:
Normalized_FPKM.txt
sample name in processed data file:
57

value: small peritoneal macrophages


title: UPF1-silenced rep3

city: Godollo

first: Daniel

last: Silhavy

state: US and Canada only

address: Szent-Gyorgyi 4

department: Agricultural Biotechnology Intsitute

country: Hungary

institute: National Agricultural Research and Innovation Cen.

description: Sample 6

data_processing:
Read alignment (TopHat v2.1.1)
Differential Gene Expression (Cufflinks suite v2.2.1)
Genome_build: Solgenomics Niben v1.0.1

organism: Nicotiana benthamiana

growth_protocol: Seeds of wild type Nicotiana benthamiana plants were germinated directly on Jiffy pellets (Jiffy-7 44mmm; Jiffy International AS, Norway), and then seedling were transferred to soil. Tobacco plants were grown in a greenhouse. After VIGS-treatment N. benthamiana plants were kept in a growth chamber at 23°C under 14/10 h light/dark conditions.

extract_protocol:
Total RNA was extracted from 100 mg of leaf tissue (White and Kaper, 1989). Briefly, the homogenized plant materials were resuspended in 600 μL of extraction buffer (0.1 M glycine-NaOH, pH 9.0, 100 mM NaCl, 10 mM EDTA, 2% SDS, and 1% sodium lauroylsarcosine) and mixed with an equal volume of phenol. The aqueous phase was treated with equal volumes of phenol and chloroform, precipitated with ethanol, and resuspended in sterile water.
Libraries were prepared from total RNA samples with Illumina TruSeq RNA Sample Preparation Kit.

treatment_protocol: Virus-induced gene silencing (VIGS) was used to transiently silence UPF1. N. benthamiana plants were infected with Tobacco Rattle Virus VIGS vector containing a segment from the UPF1 or from the PDS gene (called UPF1 and control silenced plants, respectively).

tag: genotype/variation

value: leaf


title: Precursors (rep1)


title: ARPC 2

description:
Gene expression after 24 hours culture
257236314287_S01_GE1_107_Sep09_2_3

source_name: RNA ARPC 24 h culture


title: N350_ATAC

description: ATAC library from 12Z cells after non-targeting siRNA control treatment

data_processing:
Raw reads from technical replicates were concatenated (forward-forward and reverse-reverse) then trimmed with cutadapt and Trim Galore! followed by quality control analysis via FastQC.
Trimmed reads were aligned to GRCh38.p12 reference genome via Bowtie2 with flags ‘--very-sensitive’ and ‘-X 1000’ in concordance with the library size-selection step.
Mitochondrial reads were then discarded from BAMs, via Harvard ATACseq module removeChrom, and subsequently filtered for only properly-paired mates by samtools view with flags '-f 3'.
Library complexity was estimated with ATACseqQC and normalized by subsampling to lowest complexity based on interpolation estimates calculated from preseqR.
PCR duplicates were removed with Picard MarkDuplicates.
Final BAM files were converted to BEDPE format with bedtools bamtobed with flag ‘-bedpe’, and coordinates were shifted 4 and 5 bp to correct for TN5 transposase integration. BEDPE files were then re-written to minimal BEDPE format as defined by MACS2.
MACS2 was used to call broad peaks from final “minimal” BEDPE fragment coordinates with FDR < 0.05 threshold and no control input, and resulting peaks were repeat-masked by filtering to ENCODE hg38 blacklist..
In csaw, reads were counted in replicate-overlapping regions defined by MACS2, windows greater than 1 kb in width and low count windows were filtered (logCPM < -3), then trended biases were removed by lowess-normalization. Differential-accessibility was calculated by edgeR in csaw, and proximal windows (within 500 bp) were merged.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: Comma-separated values (CSV) and tab-separated values (TSV) tabular text files including blacklist-filtered broadPeaks (MACS2 output) and non-thresholded differential-accessibility results (lowess-normalized csaw output).

extract_protocol:
48 hours after siRNA transfection, nuclei were isolated in cold lysis buffer (10mM Tris-HCL [pH 7.4], 10 mM NaCl, 3mM MgCl2, 0.1% NP-40) by centrifugation at 500Xg for 10 min.
ATAC-seq libraries were prepared using the Nextera DNA Library Prep Kit, puified using the Qiagen MinElute Reaction Cleanup Kit, amplified by PCR and purified using Kapa Pure Beads.

tag: cell line

value: non-targeting siRNA control

value: Control


title: 12Z_ChIP_ARID1A_IP2

description: ARID1A ChIP (replicate 2) library from wild-type 12Z cells

data_processing:
Raw reads from technical replicates were concatenated then trimmed with cutadapt and Trim Galore! followed by quality control analysis via FastQC.
Trimmed reads were aligned to GRCh38.p12 reference genome via Bowtie2 with flag â€˜--very-sensitiveâ€™.
PCR duplicates were removed with Picard MarkDuplicates.
MACS2 was used to call broad peaks from final BAM files for each IP replicate against input control with FDR < 0.05 threshold, and resulting peaks were repeat-masked by filtering to ENCODE hg38 blacklist.
NaÃ¯ve overlapping peaks were calculated by combining replicates on pooled BAM files and selecting for peaks of at least 50% overlap with each biological replicate.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: Blacklist-filtered replicate broadPeaks (MACS2 output) and naïve overlapping broadPeaks.

extract_protocol:
Cells were scraped in PBS, and 1x10^7 cells were used per IP. Crosslinked chromatin was digested with MNase using the SimpleChIP Enzymatic Chromatin IP Kit (Cell Signaling) followed by 30 seconds of sonication. ChIP was performed with the SimpleChIP Enzymatic Chromatin IP Kit with 1:100 anti-ARID1A (12354, Cell Signaling). DNA was purified using the ChIP DNA Clean & Concentrator Kit (Zymo).
Libraries were prepared from 10 ng of input material and all IP material using the KAPA Hyper Prep Kit (v5.16) (Kapa Biosystems). Libraries were pooled and sequenced to 75 bp single-end reads on an Illumina NextSeq 500.

treatment_protocol: Wild-type 12Z cell were treated with 1% formaldehyde in DMEM/F12 media for 10 minutes followed by quenching with 0.125 M Glycine.

tag: genotype

value: wild-type

tag: chip antibody

value: ARID1A antibody


title: 12Z_ChIP_Input

description: Input library from wild-type 12Z cells


title: ARPC 1+LPS

description:
Gene expression after LPS stimulation and 24 hours culture
257236314287_S01_GE1_107_Sep09_2_2

value: adult renal stem/progenitor cells (ARPC)


title: P-IV.II rep1

description:
Normalized_FPKM.txt
sample name in processed data file:
50

tag: strain

value: Peritoneal cavity

value: myeloid mononuclear cell

tag: age

value: post natal week 8


title: ARPC 1

description:
Gene expression after 24 hours culture
257236314287_S01_GE1_107_Sep09_2_1

value: 24 h culture


title: UPF1-silenced rep2

description: Sample 5


title: N150_ATAC


title: SPM rep2

description:
Normalized_FPKM.txt
sample name in processed data file:
55

value: mouse MHCII+ CD11c- CD115+


title: THP-1 cell control exp3

description: THP-1 cont3

source_name: THP-1 cells culture in the control DMEM/F-12 medium+10%FBS for 5 days (experiment3)

value: acute lymphoblastic leukemia cell line

tag: treatment

value: control


title: UPF1-silenced rep1

description: Sample 4


title: A250_ATAC

description: ATAC library from 12Z cells after siARID1A treatment

value: 12Z endometriotic epithelial cells

value: siARID1A knockdown


title: SPM rep1

description:
Normalized_FPKM.txt
sample name in processed data file:
48


title: A150_ATAC


title: B_3

city: La Jolla

first: David

middle: D

last: Schlaepfer

state: CA

address: 3855 Health Sciences Dr.

department: Moores Cancer Center

institute: UCSD

description: KT13 plus active beta-catenin [replicate 3]

data_processing:
Sequencing, and bioinformatic analyses were performed by Novogene, Inc.
Illumina CASAVA 1.8 software was used for basecalling.
Following adapter trimming, reads with adapter sequences, low quality, or with N>10% were removed.
Clean reads were mapped to the mm10 genome assembly using STAR v2.5, mismatch =2.
Differential expression analysis was performed using the DESeq2 R package 2_1.6.3. The resulting P-values were adjusted using Benjamini and Hochberg's approach for controlling the False Disovery Rate (FDR). Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized abundance measurements from DESeq2.

source_name: KMF ovarian cancer cells

growth_protocol: Independent samples of RNA were isolated from KMF cells grown in 3D PromoCell XF media as anchorage-independent tumorsperes for 5 days. RNA sequencing was performed by Novogene (Beijing, China)

extract_protocol:
Total RNA was extracted using a PureLink RNA Mini Kit (Thermo).
Library preparation was performed by Novogene, Inc., using at least 1 ug high-quality total RNA input per sample. mRNA enrichment was performed with poly-T oligo-attached magnetic beads. Libraries were constructed using NEBNext Ultra RNA Library Prep Kit for Illumina as per manufacturer's instructions.

treatment_protocol: [None] Cells growing as tumorspheres in PromoCell XF media for 5 days

value: Derived from ID8 cells passaged in-vivo

value: FAK-/- [KT13] re-expressing active beta-catenin


title: 12Z_ChIP_ARID1A_IP1

description: ARID1A ChIP (replicate 1) library from wild-type 12Z cells


title: control-silenced rep2

description: Sample 2

value: control-silenced

value: leaf


title: B_2

description: KT13 plus active beta-catenin [replicate 2]


title: AP3_RNA

description: RNA library from 12Z cells after siARID1A and pBabe-PIK3CA*H1047R treatment

treatment_protocol: Cells were transfected with siRNAs using Lipofectamine RNAiMax reagent. 24 hours after siRNA transfection, cells were transfected with pBabe vector containing PIK3CA*H1047R or pBabe empty vector using the FuGene HD transfection reagent (Promega). Media was replaced after 4 hours.


title: control-silenced rep1

description: Sample 1


title: control-silenced rep3

description: Sample 3


title: B_1

description: KT13 plus active beta-catenin [replicate 1]


title: AP1_RNA


title: R_2

description: KT13 plus GFP-FAK-R454 [replicate 2]

value: FAK-/- [KT13] re-expressing GFP-FAK-R454


title: NP2_RNA

description: RNA library from 12Z cells after non-targeting siRNA control and pBabe-PIK3CA*H1047R treatment

value: Control


title: HEK293T FTO OE replicate 3

value: FTO OE


title: G_3

description: KT13 plus GFP-FAK wildtype [replicate 3]

value: FAK-/- [KT13] re-expressing lentiviral GFP-FAK


title: R_1

description: KT13 plus GFP-FAK-R454 [replicate 1]


title: IMX-101, Control, Rep 5

city: Vicksburg

first: Kurt

middle: A

last: Gust

state: MS

address: 3909 Halls Ferry Rd.

department: Environmental Laboratory

institute: US Army ERDC

hyb_protocol: The Agilent 8 x 60K, 2µm feature size microarray platform (Custom Array G4102A, AMADID 365741) was used for transcript expression assays (Agilent Technologies).  Samples from the five exposure replicates were hybridized to microarrays in a completely randomized design using a random number generator.  The microarray experiments included the following exposure concentrations of IMX-101 at 0 (control), 6.2, 12.6, 25.2 and 50.9 mg/L (DNAN nominal + NTO measured + NQ measured).   Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the custom-designed Agilent test array for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed at room temperature with GE Wash Buffer 1 (Agilent) and with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: An Agilent Surescan Microarray Scanner (G2505 C, Agilent Technologies Inc.) was used to scan microarrays at 2 μm resolution.

data_processing: Data were extracted from microarray images using Agilent Feature Extraction software, version 10.7.3.1 (Agilent Technologies).  Microarray data were normalized to the 75th percentile within each array followed by median scaling among all exposures using GeneSpring Software version GX14.9 (Agilent Technologies). GeneSpring was also used to conduct statistical analyses to identify differentially expressed transcripts (DET) among treatments. A moderated t-test with fold change cutoff of ≥ 1.5 was conducted to identify differentially expressed transcripts relative to the control.

organism: Pimephales promelas

source_name: whole testes

label_protocol: The Agilent Low Input One-Color Microarray Hybridization protocol (Agilent Technologies) was utilized for microarray hybridizations following manufacturer’s recommendations where 80 ng of total RNA was used as the starting material for each exposure replicate.

growth_protocol: Exposures were performed in 7.6 L glass fish tanks with a test solution volume of 6.0 L following ASTM general guidance (ASTM 2014).  Partial water renewals were conducted thrice weekly on Mondays, Wednesdays and Fridays by removing and replacing 3.0 L of exposure solution.  Fish were fed Tetramin (Tetra U.S., Blacksburg, VA) fish food daily.  On water renewal days, food was added after renewals were performed.

extract_protocol: Each testis was homogenized in lysis buffer using a Kimble™ Kontes™ Pellet Pestle™ (DWK Life Sciences, Rockwood, TN)  before RNA isolation with RNeasy kits (Qiagen, Valencia, CA). Total RNA concentrations were measured using a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The integrity of total RNA was assessed on an Agilent 2100 Bioanalyzer (Palo Alto, CA).  Criteria for acceptable RNA integrity included a RNA integrity number > 8.0 from the Agilent 2100 Bioanalyzer and a 260/280 spectrophotometric reading > 2.0.  If two samples were available that met RNA integrity standards within each exposure replicate, the samples were pooled.  Otherwise, RNA from a single fish contributed to the exposure replicate.  Overall, 24 of the 31 exposure replicates contained RNA from two individual testes samples, the rest contained RNA from a single testis sample.

treatment_protocol: Two fish were exposed in each tank to IMX-101 at 0 (control), 6.2, 12.6, 25.2 and 50.9 mg/L (DNAN nominal + NTO measured + NQ measured) where each experimental treatment included 5 replicate tanks.  All fish surviving until the conclusion of the 21d assay were euthanized by immersion in an overdose solution of MS-222 (300 mg/L) for at least 10 minutes after cessation of movement.  After euthanasia, each fish was weighed (g) and then necropsied where one testis was fixed in 10% neutral-buffered formalin for histopathological evaluation and the other fixed for transcriptomics by flash freezing in liquid nitrogen.

value: adult

tag: gender

value: male


title: IMX-101, Control, Rep 4


title: IMX-101, Control, Rep 3


title: G_2

description: KT13 plus GFP-FAK wildtype [replicate 2]


title: NP1_RNA


title: NP3_RNA


title: AP2_RNA


title: G_1

description: KT13 plus GFP-FAK wildtype [replicate 1]


title: AE3_RNA

description: RNA library from 12Z cells after siARID1A and pBabe empty vector treatment


title: IMX-101, Control, Rep 2


title: IMX-101, Control, Rep 1


title: AE2_RNA


title: K_3

description: KMF FAK knockout KO clone KT13 [replicate 3]

value: KMF FAK-/- [clone KT13]


title: AE1_RNA


title: IMX-101, 12.6mg/L, Rep 5


title: K_2

description: KMF FAK knockout KO clone KT13 [replicate 2]


title: Normal Fallopian tube control, FT13b

city: Iowa City

first: Henry

last: Reyes

state: Iowa

address: 200 Hawkins Drive

department: OBGYN

institute: University of Iowa

description: Tube

hyb_protocol: According to MethylationEPIC protocols

scan_protocol: Methylation intensity is measured with the Illumina iScan

data_processing: Results were reported as DNA methylation ratios (proportion of methylated/ unmethylated) referred to as Beta and processed using the Minfi R package

label: Cy5 and Cy3

source_name: Normal Fallopian tube control, FT13b

label_protocol: Zymo EZ DNA methylation kit was used with 500 ng of total gDNA for bisulfite conversion. Infinium Illumina methylationEPIC arrays were used with Illumina Iscan to interrogate and measure methylation eintensity patterns.

extract_protocol: Samples and controls were collected and flash frozen. Genomic DNA was collected via Qiagen DNEasy blood and tissue kit.

value: Normal Fallopian tube control


title: NE3_RNA

description: RNA library from 12Z cells after non-targeting siRNA control and pBabe empty vector treatment


title: K_1

description: KMF FAK knockout KO clone KT13 [replicate 1]


title: NE2_RNA


title: High grade serous ovarian cancer, Patient23b

description: Primary

value: High grade serous ovarian cancer


title: IMX-101, 12.6mg/L, Rep 3


title: IMX-101, 12.6mg/L, Rep 2


title: P_3

description: KMF wildtype [replicate 3]

value: KMF wildtype


title: Normal Fallopian tube control, FT17b

description: Tube

source_name: Normal Fallopian tube control, FT17b


title: High grade serous ovarian cancer, Patient24b

description: Primary


title: IMX-101, 12.6mg/L, Rep 4


title: High grade serous ovarian cancer, Patient115

description: Primary

tag: clinical outcomes

value: dead

tag: fu (months)


title: Normal Fallopian tube control, FT15b

description: Tube

source_name: Normal Fallopian tube control, FT15b


title: P_2

description: KMF wildtype [replicate 2]


title: Pbld17

city: Chengdu

first: xiaomeng

last: liu

address: No.55,Section 4,South Renmin Road

country: Colombia

institute: Sichuan Cancer Hospital & Institute, Sichuan Cancer Center

description:
ccfDNA
s107
PB10_TFC_RJ_cmp166_m2-5

data_processing:
library strategy: MCTA-Seq
(1) Illumina CASAVA version 1.8 were used to the basecalling.
(2) Sequencing adapters, low quality sequences and amplification primers were trimmed from the raw sequencing reads.
(3) Whole or any subsets of adaptor sequences were trimmed at 3'- end of the reads.
(4) The MCTA-Seq primer sequences including 6 bp at the 5'- end and 12 bp at the 3'- end of reads were trimmed.
(5) Low-quality reads, as > 10% bases being N, or Phred quality of > 50% bases being <5 or having  > 3 unmethylated CHs, were discarded.
(6) Cytosines in a read were computationally replaced with thymines and then mapped to computationally converted hg19 references using the Bismark and Bowtie programs.
(7) The reads were discarded if there was < 2 genomic CpG sites ± 3 bp surrounding the position corresponding to the 5'- end of the aligned reads.
(8) For a certain CpG site following a certain CGCGCGG, the methylation value is calculated as the number of fully methylated reads, i.e., all CpGs from the CGCGCGG site to the CpG site on the read were methylated, normalized by the total number of reads uniquely mapped to the whole human genome and expressed as methylated alleles per million mapped reads (MePM).
(9) For all of the amplicons from the 9,513 CGIs with no CGCGCGGs, the duplication rates were calculated by dividing the reads by the "HHHHH" unique molecule identifiers (UMIs) on primer A.
(10) When duplication rate of plasma sample was larger than that of paired white blood cell (WBC) samples, then plasma sample data were normalized to a duplication rate which similar to WBC by random extraction.
Genome_build: hg19
Supplementary_files_format_and_content: All_samples_sumT_mepm.txt.gz file include the MePM (methylated alleles per million mapped reads) value of each CGCGCGG sites which was processed by step 1-8.
Supplementary_files_format_and_content: nor_samples.txt.gz file include the MePM (methylated alleles per million mapped reads) value of each CGCGCGG sites which was processed by step 1-10.

source_name: plasma

extract_protocol:
Genomic DNAs were extracted using the Dneasy Blood & Tissue Kit (Qiagen) according to the manufacturer's protocol.
The plasma cell-free DNAs were extracted using the QIAamp DNA Blood Midi Kit (Qiagen) according to the manufacturer's protocol.
Library were constructed following the MCTA-Seq library preparation protocol.

tag: disease state

value: benign liver disease patient

value: plasma


title: High grade serous ovarian cancer, Patient83b

description: Primary


title: High grade serous ovarian cancer, Patient25b

description: Primary


title: Pbld16

description:
ccfDNA
s106
PB10_TFC_RJ_cmp166_m2-4


title: HuH7 SD-70 rep3

city: Derqui

first: Juan

last: Bayo

state: Buenos Aires

address: Av Peron 1500

department: IIMT

country: Argentina

institute: Universidad Austral-Conciet

data_processing:
Basecalls were performed using CASAVA (v. 1.8.1)
Reads were aligned to hg19 geneome assembly and transcript assembly was performed using tophat (v.2.0.12)
CPM calculation and differential expression analysis was performed using edgeR (v.3.16.5)
Genome_build: hg19
Supplementary_files_format_and_content: Supplementary_files_format_and_content: tab-delimited text files include CPM values for each Sample

source_name: Huh-7 Cell Line

growth_protocol: HuH7 cell line was maintained in DMEM (Life Technologies Inc.) with 10% FBS.

extract_protocol:
Total RNA was extracted using RNeasy Plus Mini kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: 4x10^6 HuH-7  cells were seeded in P150 dishes. Next day cells were treated with the different JumonjiC inhibitors or DMSO as control during 24 h.

tag: histology

value: Hepatocellular carcinoma

value: M

tag: race

value: Japanese


title: Normal Fallopian tube control, FT18b

description: Tube

source_name: Normal Fallopian tube control, FT18b


title: High grade serous ovarian cancer, Patient113

description: Primary

value: alive


title: IMX-101, 12.6mg/L, Rep 1


title: HuH7 SD-70 rep2


title: High grade serous ovarian cancer, Patient111

description: Primary


title: High grade serous ovarian cancer, Patient22b

description: Primary


title: id8ip3

data_processing:
Sequencing, and bioinformatic analyses were performed by Novogene, Inc.
Illumina CASAVA 1.8 software was used for basecalling.
Following adapter trimming, reads with adapter sequences, low quality, or with N>10% were removed.
Clean reads were mapped to the mm10 genome assembly using STAR v2.5, mismatch =2.
Differential expression analysis was performed using the DESeq2 R package 2_1.6.3. The resulting P-values were adjusted using Benjamini and Hochberg's approach for controlling the False Disovery Rate (FDR). Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file; output from DESeq2. Include readcount for three replicates per group, log2FoldChange, pval, padj, and FPKM values for each gene.

source_name: ID8-IP / KMF ovarian cancer cells

growth_protocol: Three independent samples of RNA were isolated from ID8 or KMF cells grown in 3D PromoCell XF media as tumorsperes for 5 days at various cell passages. RNA sequencing was performed by Novogene (Beijing, China)

value: Derived from ID8 cells passaged in-vivo

tag: cell passages

value: passage 22


title: Pbld15

description:
ccfDNA
s105
PB10_TFC_RJ_cmp166_m2-3


title: HuH7 SD-70 rep1


title: P_1

description: KMF wildtype [replicate 1]


title: id8ip2

value: passage 17


title: High grade serous ovarian cancer, Patient105

description: Primary


title: High grade serous ovarian cancer, Patient114

description: Primary


title: Pbld14

description:
ccfDNA
s104
PB10_TFC_RJ_cmp166_m2-1


title: HuH7 GSK-J4 rep3

value: 24 h with GSK-J4 (6.2 mM)


title: Pbld13

description:
ccfDNA
s103
PB10_TFC_RJ_cmp166_m1-6


title: HuH7 GSK-J4 rep2


title: id8ip1

value: passage 14


title: High grade serous ovarian cancer, Patient106

description: Primary


title: id83

source_name: ID8 ovarian cancer cells

value: Derived from transformed mouse ovarian epithelial cells

value: passage 35


title: High grade serous ovarian cancer, Patient102

description: Primary


title: HuH7 GSK-J4 rep1


title: id82

value: passage 24


title: Pbld11

description:
ccfDNA
s101
PB10_TFC_RJ_cmp166_m1-3


title: Pbld12

description:
ccfDNA
s102
PB10_TFC_RJ_cmp166_m1-4


title: HuH7 JIB-04 rep3

value: 24 h with JIB-04 (1mM)


title: id81

value: passage 23


title: High grade serous ovarian cancer, Patient110

description: Primary

value: High grade serous ovarian cancer

value: dead


title: HuH7 JIB-04 rep2


title: NE1_RNA

value: 12Z endometriotic epithelial cells

tag: condition

value: Control


title: Pbld10

description:
ccfDNA
s100
PB10_TFC_RJ_cmp166_m1-2

value: benign liver disease patient

tag: tissue

value: plasma


title: PTU_NCORdeltaID_rep2_HDAC3

city: Odense

first: Lars

last: Grøntved

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

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

source_name: liver

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

value: liver

value: L-NCORdeltaID

value: PTU

value: HDAC3 (Santa Cruz, sc-11417)


title: Pbld9

description:
ccfDNA
s99
PB10_TFC_RJ_cmp166_m1-1


title: High grade serous ovarian cancer, Patient103

description: Primary


title: HuH7 JIB-04 rep1

value: Hepatocellular carcinoma

value: M

value: Japanese


title: HuH7 DMSO rep3

value: 24 h with DMSO


title: High grade serous ovarian cancer, Patient108


title: Input_rep2

city: Philadelphia

first: Yana

last: Kamberov

address: Curie bvld

institute: University of Pennsylvannia

data_processing:
Bioinformatics analysis was done using Galaxy platform at usegalaxy.org
ChIP-seq reads from two run of Illumina HiSeq 2500 were merged into one file to each experiment for later analysis
Merged ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2, later MAPQ was used to remove multi-mapping reads and RmDup was used to remove PCR duplicates
peaks were called using MACS2 and default parameters at galaxy plataform
Genome_build: hg19
Supplementary_files_format_and_content: wig files were generated using Wig/BedGraph-to-bigWig converter (Galaxy Version 1.1.1); Scores represent Deaf1 enrichment

growth_protocol: Human keratinocytes were maintained as previously described (PMID: 10504454)

extract_protocol:
Confluent cells were fixed using formaldehyde (1% final concentration) for 10 minutes at room temperature and the EZ-Magma ChIP HiSens kit (EMD Millipore) was used to perform the chromatin inmunoprecipitation
library construction was done using NEBNext DNA Ultra II DNA library prep kit for Illumina (New England Biolabs)

tag: cell type

value: Keratinocytes cell


title: PTU_WT_rep2_HDAC3

description: WT mice match with L-NCORdeltaID

value: WT


title: High grade serous ovarian cancer, Patient100

description: Primary

value: alive


title: PTU_NCORdeltaID_rep1_HDAC3


title: sh-YTHDC2_RNA_seq_rep2

city: Hangzhou

first: Yuanhui

last: Mao

state: Zhejiang

address: 1369 West Wenyi Road

country: China

institute: Zhejiang University

description: RNA-seq of YTHDC2 knockdown in HEK293 cells, rep2

data_processing:
For all Ribo-seq and RNA-seq except for Rep2, adaptor was removed by Cutadapt with parameters: -a CTGTAGGCACCATCAAT -m 15
For all Ribo-seq and RNA-seq except for Rep2, the first SIX nucleotides (3 randome nucleotides + 3-word barcode sequence). The last FOUR nucleotides were removed (3 random nucleotides)
The trimmed reads were aligned to transcriptome using bowtie with parameters: -a --best -m1 --strata -S --sam-nohead
PCR duplicates were removed. PCR duplicates were defined as the reads with exact same random sequences at both sides. More details can be found in PMID: 27450428
For YTHDC2 RNA-seq and Ribo-seq rep2, the adaptor AAAAAAAAA was removed by Cutadapt with parameters: -a AAAAAAAAA -m 15. The trimmed reads were firstly aligned to rRNA, the remaining unmapped reads were then aligned to transcriptome using bowtie with parameters: -a --best -m1 --strata -S --sam-nohead
Genome_build: GRCh38 for human, mm10 for Mouse
Supplementary_files_format_and_content: Tab separated RPKM value

source_name: Human embryonic kidney 293

growth_protocol: 293T cells were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) with 10% fetal bovine serum (FBS).

extract_protocol:
293T sh-Scramble and sh-YTHDC2 Cells were lysed in lysis buffer (10 mM HEPES, pH 7.4, 100 mM KCl, 5 mM MgCl2, 1% Triton X-100) containing CHX (100 µg ml-1),The supernatant was collected and subjected to sucrose gradient sedimentation.
For RNA-seq, 12 µg Trizol extracted total RNAs were fragmentated by using freshly prepared RNA fragmentation buffer (10 mM Tris-HCl, pH 7.0, 10 mM ZnCl2) and heating at 94°C for 5 min, followed by adding 1 µl 0.5 M EDTA to  terminate. For Ribo-seq, *E. coli* RNase I (Ambion) was added into the pooled fractions from ribosome profiling (100 U per 100 µl) and incubated at 4 °C for 1 hr to convert the polysome into monosome. RNase I digested RNA extracts (Ribo-seq) and fragmented RNAs (RNA-seq) were dephosphorylated  for 1 hr at 37 °C in a 15 µl reaction (1× T4 polynucleotide kinase buffer, 10 U SUPERase_In and 20 U T4 polynucleotide kinase). The products were separated on a 15% polyacrylamide TBE-urea gel (Invitrogen) and visualized using SYBR Gold (Invitrogen). Selected regions in the gel corresponding to 40-60 nt (for RNA-seq) or 25-35 nt (for Ribo-seq) were excised. RNA fragments were dissolved by soaking overnight in 400 μl RNA elution buffer  (300 mM NaOAc, pH 5.5, 1 mM EDTA, 0.1 U ml-1 SUPERase_In). The gel debris  was removed using a Spin-X column (Corning), followed by ethanol precipitation. Purified RNA fragments were re-suspended in nuclease-free water. 0.15 μg linker was added to the RNA fragments, heated at 70°C for 90  s and then cooled to room temperature, followed by ligation for 3 hrs at at 22°C in a 20 µl reaction (1× T4 Rnl2 reaction buffer, 10 U SUPERase_In, 15%  PEG8000 and 20 U T4 RNA ligase 2 truncated). The reaction was heat inactivated at 80 °C for 10 min and the products were separated on a 10% polyacrylamide TBE-urea gel and selected regions in the gel corresponding to 65-85 nt (for RNA-seq) or 50-70 nt (for Ribo-seq) were excised. RNA  fragments were dissolved by soaking overnight in 400 μl RNA elution buffer,  purified RNA fragments were re-suspended in nuclease-free water. The linker  ligated RNA sample was mixed with 0.5 mM dNTP and 2.5 mM synthesized primer and incubated at 75°C for 5 min, followed by incubation on ice for 3 min. The reaction mix was then added with 20 mM Tris (pH 8.4), 50 mM KCl, 5 mM MgCl2, 10 mM DTT, 40 U RNaseOUT and 200 U SuperScript III. Reverse transcription reaction was performed according to the manufacturer’s instruction. Reverse transcription products were separated on a 10% polyacrylamide TBE-urea gel as described earlier. The extended first-strand product band was expected to be approximately 200 nt, and the  corresponding region was excised. The cDNA was recovered by  gel elution buffer (300 mM NaCl, 1 mM EDTA). First-strand cDNA was circularized in 20 μl of reaction containing 1× CircLigase buffer, 2.5 mM MnCl2, 1M Betaine and 100 U CircLigase II (Epicentre). Circularization was performed at 60 °C for 1 hr, and the reaction was heat inactivated at 80 °C for 10 min, then was precipitated by ethanol. Circular template was amplified by PCR by using the Phusion high-fidelity (HF) enzyme (NEB) according to the manufacturer’s instructions. PCR products were separated on a nondenaturing 8% polyacrylamide TBE gel as described earlier. Expected DNA at 180 bp was excised and recovered as described earlier. After quantification by Agilent BioAnalyzer DNA 1000 assay, equal amounts of barcoded samples were pooled into one sample. Approximately 5 pM mixed DNA samples were used for cluster generation followed by sequencing by using sequencing primer 5’-CGACAGGTTCAGAGTTCTACAGTCCGACGATC-3’ (Illumina HiSeq).

treatment_protocol: YTHDC2 was knocked down in 293T cells using lentiviral shRNA (target sequence:GCCCACAGATTGGCTTATTTA).

value: Human embryonic kidney

tag: knockdown


title: High grade serous ovarian cancer, Patient96

description: Primary

value: High grade serous ovarian cancer


title: HuH7 DMSO rep2


title: Deaf1_ChIP-seq_rep2

tag: cell line


title: HuH7 DMSO rep1


title: sh-Scram_RNA_seq_rep2

description: RNA-seq of scramble HEK293 cells, rep2

value: shScram


title: PTU_T3_WT_rep2_HDAC3

description: WT mice match with L-NCORdeltaID

tag: genotype


title: PTU_WT_rep1_HDAC3

description: WT mice match with L-NCORdeltaID

tag: chip antibody


title: Single cell RNAseq of human ILCs

city: Gaithersburg

first: Jingya

last: Wang

state: Maryland

address: 1 Medimmune Way

department: Early respiratory and immunology

institute: Astrazeneca

data_processing:
No demultiplexing was performed and analysis was done for cell mixtures.
Sequencing reads were aligned to GRCh38 human genome using CellRanger software (v2.0, 10X Genomics) with raw gene count table as the output file.
ILC_count table was generate using the Seurat package with parameters of min.cells = 4, min.genes = 200
Quality check was performed based on the correlation between UMI and gene number at single-cell level.
Genome_build: GRCh38 human genome
Supplementary_files_format_and_content: ILC_count.csv reports counts; column names are 16nt cellbarcode

source_name: human ILCs in peripheral blood

extract_protocol: The Chromium Single Cell Gene Expression Solution from 10X Genomics

value: healthy

value: peripheral blood

value: mixed sample (non-demultiplexed)

tag: mixed sample details

value: ILC2s, ILC3s, CD56high NK cells

tag: cell state

value: naïve/primary


title: High grade serous ovarian cancer, Patient97

description: Primary

value: dead


title: High grade serous ovarian cancer, Patient98

description: Primary


title: Donor2 RNA-seq Rep3

city: Boston

first: Hufeng

last: Zhou

address: 181 Longwood Ave,

department: Department of Microbiology and Molecular Genetics

institute: Harvard Medical School

data_processing:
The data was generated using standard protocol, describe in this paper,
http://www.nature.com/nprot/journal/v7/n3/abs/nprot.2012.016.html

The software used in mapping is Tophat, with default parameter, and transcription quantification is using Cufflinks, with default parameter.

source_name: peripheral blood mononuclear cells from healthy anonymous platelet donor

extract_protocol:
Total RNA extraction was performed using PureLink RNA mini kit (Ambion) and 1 ug of RNA as used. Ribosomal RNA was depleted using the NEBNext rRNA Depletion kit (human/mouse/rat) (New England Biosciences),NEBNext Ultra RNA Library Prep Kit for Illumina (Cat#E7530S) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using NEBNext® Ultra RNA Library Prep Kit for Illumina protocols

value: PBMCs

value: Primary B cells


title: sh-Scram_RNA_seq_rep1

description: RNA-seq of scramble HEK293 cells, rep1


title: sh-YTHDC2_Ribo_seq_Rep3

description: Ribo-seq of YTHDC2 knockdown in HEK293 cells, rep3

data_processing:
Library strategy: Ribo-seq
For all Ribo-seq and RNA-seq except for Rep2, adaptor was removed by Cutadapt with parameters: -a CTGTAGGCACCATCAAT -m 15
For all Ribo-seq and RNA-seq except for Rep2, the first SIX nucleotides (3 randome nucleotides + 3-word barcode sequence). The last FOUR nucleotides were removed (3 random nucleotides)
The trimmed reads were aligned to transcriptome using bowtie with parameters: -a --best -m1 --strata -S --sam-nohead
PCR duplicates were removed. PCR duplicates were defined as the reads with exact same random sequences at both sides. More details can be found in PMID: 27450428
For YTHDC2 RNA-seq and Ribo-seq rep2, the adaptor AAAAAAAAA was removed by Cutadapt with parameters: -a AAAAAAAAA -m 15. The trimmed reads were firstly aligned to rRNA, the remaining unmapped reads were then aligned to transcriptome using bowtie with parameters: -a --best -m1 --strata -S --sam-nohead
Genome_build: GRCh38 for human, mm10 for Mouse
Supplementary_files_format_and_content: Tab separated RPKM value


title: Donor2 RNA-seq Rep2


title: Donor2 RNA-seq Rep1


title: sh-YTHDC2_Ribo_seq_Rep2

description: Ribo-seq of YTHDC2 knockdown in HEK293 cells, rep2


title: sample 2

city: Los Angeles

first: junjun

last: jing

address: 2250 Alcazar Street

institute: Center for Craniofacial Molecular Biology, University of Southern California

description: samplel 2

data_processing:
Reads were mapped to NCBI mouse reference genome (Genome Reference Consortium Mouse Build 38, Jan 2012) using Burrows-Wheeler Alignment (BWA) tool.
The aligned bam files were sorted using SAMtools followed by peak calling by MACS2-2.1.1 using broad calling with p< 0.005.
Filter to get unique mapped reads
peak calling by MACS2-2.1.1 using broad calling with p< 0.005.
Gencode M18 annotation was used to quantify the aligned reads to genes/transcripts using Partek E/M method.
Genome_build: mm10
Supplementary_files_format_and_content: broadPeak, gappedPeak

source_name: molar

growth_protocol: Mice were raised in animal facilities according to protocol.

extract_protocol:
Molars of three-day-old wildtype mice were dissected out. After removing the epithelial tissue, the mesenchymal tissue was collected for CHIP sequencing
CHIP DNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: molar

tag: age

value: post natal day 3

value: wildtype

tag: antibody


title: input 2

description: input 2


title: PTU_T3_WT_rep1_HDAC3

description: WT mice match with L-NCORdeltaID

value: liver

tag: treatment

value: HDAC3 (Santa Cruz, sc-11417)


title: sh-Scram_Ribo_seq_Rep2

description: Ribo-seq of scramble HEK293 cells, rep2


title: sh-Scram_Ribo_seq_Rep3

description: Ribo-seq of scramble HEK293 cells, rep3


title: High grade serous ovarian cancer, Patient21

description: Primary

tag: clinical outcomes

tag: fu (months)


title: sample

description: sample


title: negative control

description: negative control

value: IgG


title: sh-Scram_Ribo_seq_Rep1

description: Ribo-seq of scramble HEK293 cells, rep1

value: Human embryonic kidney


title: input

description: input


title: sh-YTHDC2_Ribo_seq_Rep1

description: Ribo-seq of YTHDC2 knockdown in HEK293 cells, rep1


title: D8 Cl13△CD4

first: E

last: WHERRY

address: 421 Curie Blvd,354 BRB II/III

institute: University of Pennsylvania

data_processing:
Sequenced reads were mapped to the mouse genome build mm10 using CellRanger
Cellranger counts was used separately on each sample to generate gene expression matrices
Cellranger aggr was used to aggregate the counts from individual samples using the "depth" normalization method
Genome_build: mm10
Supplementary_files_format_and_content: Cellranger aggr output files for all 4 samples together-cell barcodes,gene names and sparse expression matrix

source_name: P14 cells from D8 p.i. of LCMV-Clone13 infected recipient mice (5 mice pooled), pre-treated with GK1.5 antibody for CD4+ T cell depletion

extract_protocol:
CD8+ T cells are MACS isolated from splenocytes. P14+ cells are FACS sorted from purified CD8+ T cells.
10X Genomics instruction protocol, with 5000 targeted cells loading. Sequencing was performed on NextSeq 500 using High-throughput flow cell.

treatment_protocol: Naïve P14s are isolated and transferred into recipients, followed by LCMV-Armstrong infection,LCMV-Clone13 infection and LCMV-Clone13 infection with GK1.5 treatment.

value: Spleen

value: 7-9 weeks

value: P14 cells


title: CC36 shTM9_2

city: Geneva

first: Ariel

last: Ruiz i Altaba

address: 1 rue Michel Servet

department: GEDEV

country: Switzerland

institute: University of Geneva Medical School

data_processing:
The CC14 experiment samples (CC14 CTH, shTMED9 and shTMED3) and CC36 experiment samples (CC36 CTH and shTMED9) have been sequenced in two separate batches. For both of the experiments, the reads were mapped with the TopHat v.2 software to the UCSC hg38 reference. The table of counts with the number of reads mapping to each gene feature of UCSC reference was prepared with HTSeq v0.6p1 (htseq-count).
The normalizations and differential expression analyses were performed like this: for all the comparisons involving only CC14 samples, only the CC14 samples were normalized together and analyzed for DE genes. Next, for comparisons involving CC36 samples, all the CC14 and CC36 samples were normalized together and analyzed for DE Genes.
The differential expression analysis was performed with the statistical analysis R/Bioconductor package EdgeR v. 3.4.2, for the genes annotated in hg38. Briefly, the counts were normalized according to the library size and filtered. The genes having a count above 0.5 counts per million reads (cpm) in at least 3 samples were kept for the analysis. It corresponds to the 10 counts detection threshold usually used for RNAseq data. The differentially expressed genes tests were done with a GLM (generalized linear model), negative binomial distribution with a quasi-likelihood statistics. The P-values were corrected for multiple hypothesis testing using Benjamini-Hochberg (BH) method.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: CC14_FoldChanges_allgenes_shTMED9_vs_CTH_Vector_alone.xlsx : Differential Expression Matrix of CC14 shTMED9 vs. Control_Vector_alone cells.
Supplementary_files_format_and_content: CC14_FoldChanges_allgenes_shTMED3_vs_CTH_Vector_alone.xlsx : Differential Expression Matrix of CC14 shTMED3 vs. Control_Vector_alone cells.
Supplementary_files_format_and_content: CC14_FoldChanges_allgenes_shTMED3_vs_shTMED9.xlsx : Differential Expression Matrix of CC14 shTMED3 vs. shTMED9 cells.
Supplementary_files_format_and_content: CC14_Normalized_counts.xlsx : Normalized counts for all CC14 Samples (CTH, shTMED3 and shTMED9).
Supplementary_files_format_and_content: CC14_Raw_counts.xlsx : Raw counts for all CC14 samples (CTH, shTMED3 and shTMED9).
Supplementary_files_format_and_content: CC36_all_genes_fold_changes_shTMED9_vs_CTH_Vector_alone.xlsx : Differential Expression Matrix of CC36 shTMED9 vs. Control_Vector_alone cells.
Supplementary_files_format_and_content: CC36_and_CC14_Normalized_counts_cpm_all_samples.xlsx : Normalized counts for all CC14 (CTH, shTMED3 and shTMED9) and CC36 (CTH and shTMED9) samples together.
Supplementary_files_format_and_content: CC36_and_CC14_Raw_counts_all.xlsx : Raw counts for all CC14 (CTH, shTMED3 and shTMED9) and CC36 (CTH and shTMED9) samples together.

source_name: Primary colon cancer cells

growth_protocol: Primary colon cancer cells were maintained at a confluence of 70-75% in a 10cm diameter plate with 5% serum containing Gibco DMEMF12 medium.

extract_protocol:
TRIZOL (following the manufacturer's manual).
Illumina TruSeq protocol.

treatment_protocol: Cells were treated with control or shTMED3 or shTMED9 expressing lentivirus at MOI 2. Cells were FACS sorted and replated prior to RNA extraction.

tag: cell name

value: colon cancer

tag: grade

tag: shRNA


title: CC36 shTM9_3


title: D8 Cl13

department: Systems Pharmacology       and Translational Therapeutics,Institute for Immunology

source_name: P14 cells from D8 p.i. of LCMV-Clone13 infected recipient mice (5 mice pooled)

tag: tissue


title: sh-YTHDC2_RNA_seq_rep1

description: RNA-seq of YTHDC2 knockdown in HEK293 cells, rep1

tag: cell type


title: Normal Fallopian tube control, FT11

description: Tube

source_name: Normal Fallopian tube control, FT11

value: Normal Fallopian tube control


title: High grade serous ovarian cancer, Patient19

description: Primary

value: High grade serous ovarian cancer


title: High grade serous ovarian cancer, Patient14


title: High grade serous ovarian cancer, Patient107

description: Primary


title: High grade serous ovarian cancer, Patient16

description: Primary


title: High grade serous ovarian cancer, Patient17

description: Primary


title: High grade serous ovarian cancer, Patient15

description: Primary


title: CC36 CTH_3

value: control


title: High grade serous ovarian cancer, Patient18

description: Primary

value: dead


title: D8 Arm

source_name: P14 cells from D8 p.i. of LCMV-Armstrong infected recipient mice (5 mice pooled)


title: Normal Fallopian tube control, FT2

description: Tube

source_name: Normal Fallopian tube control, FT2


title: CC36 CTH_2


title: Naïve

source_name: P14 cells from Naïve P14+ mouse


title: ATAC-Seq NF-YA KD, Rep 2

city: RTP

first: Raja

last: Jothi

state: NC

address: 111 TW Alexander Drive; A314

department: National Institute of Environmental Health Sciences

institute: National Institutes of Health

description:
Tn5 Transposase digested DNA from ESCs transfected with NF-YA siRNA
KD_open_chromatin_51nt.bigWig
Processed data files represent merged data from 2 biological replicates

data_processing:
MNase-Seq and ChIP-Exo reads were aligned to the mouse genome (mm9) using the Bowtie algorithm. Those reads that mapped to unique locations were retained for further analysis.
Ribo-Seq read pairs were trimmed with cutadapt tool and fragments shorter than 23nt were discarded. The remaining pairs were aligned to the mouse genome (mm9) using CRAC and only read pairs that mapped to unique locations were retained for further analysis.
RNA-Seq reads were mapped to mouse (mm9) genome using TopHat v2.1.0. and only those reads that mapped to unique locations were retained for further analysis.
Start-Seq reads were trimmed for adapter sequence using cutadapt 1.2.1 and read pairs with either of the paired-end-read trimmed to less than 20nt were discarded.  A single additional nucleotide was removed from the 3’ end of each read to facilitate mapping of fully overlapping pairs. Remaining pairs were filtered for rRNA and tRNA by aligning to indices containing each using bowtie 0.12.8, with unmapped read pairs retained. Following this, a similar alignment was performed to an index containing the sequence of spike-in RNAs only, and finally, the remaining unmapped reads were aligned to mm9 utilizing the same parameters, retaining read pairs mapping to unique locations.
RNA-Seq: Paired end reads were mapped to the mouse genome (mm9) using STAR aligner and htseq-count was used to count reads per gene which were utilized in edgeR for differential expression analysis.
ATAC-Seq: Paired end reads were aligned to the mouse genome (mm9) using Bowtie algorithm after removal of low quality reads (mean Phred quality score < 20). Those reads that mapped to unique locations were retained for further analysis.
Genome_build: mm9

source_name: mouse Embryonic Stem Cells (ESCs)

growth_protocol: Mouse ES cells were routinely maintained on gelatin-coated plates in the ESGRO complete plus clonal grade medium (Millipore). For experiments,  passage 20-35 cells were cultured on gelatin-coated plates in M15 medium: DMEM (Invitrogen) supplemented with 15% FBS (vol/vol), 10 mM 2-mercaptoethanol, 0.1 mM nonessential amino acids (Invitrogen), 1× EmbryoMax nucleosides (Millipore), and 1U per ml of ESGRO mLIF (Millipore)

extract_protocol:
Mnase-Seq: DNA was extracted by phenol/chloroform extraction and mono/di-nucleosome fragments were gel-purified.  RNA-Seq: Total RNA was extracted from nuclei using Trizol (Invitrogen). Ribosomal RNA was removed prior to library construction by hybridizing to ribo-depletion beads that contain biotinylated capture probes (Ribo-Zero, Epicentre). RNA was then fragmented and libraries were prepared according to the TruSeq Stranded Total RNA Gold Kit (Illumina) using random hexamer priming.   Start-Seq: Total RNA was extracted from nuclei using Trizol (Invitrogen). Start-RNA libraries were prepared as described in (PMID:20007866) and size-selected (20-80 nt) to exclude full length snRNA species.  Ribo-Seq: Total RNA and ribosome-protected RNA from Cyclohexamide (CHX)-treated cells were isolated using the TruSeq Ribo Profile Mammalian Kit (Illumina) following the manufacturer’s intructions.  ATAC-Seq:  DNA fragments were purified with 2 successive rounds of AMPure XP beads (1:3 ratio of sample to beads).
MNase-Seq libraries were prepared using NuGen’s Ovation Ultralow Library System V2.  RNA-Seq libraries were prepared according to the TruSeq Stranded Total RNA Gold Kit (Illumina) using random hexamer priming.  Ribo-Seq libraries were prepared according to TruSeq Ribo Profile Mammalian Library Prep Kit (Illumina).  Start-Seq libraries were prepared according to the TruSeq Small RNA Kit (Illumina). Illumina Spike-ins were used for normalization.  ATAC-Seq libraries were prepared according to NuGen’s Ovation Ultralow Library System V2.

treatment_protocol: For transfections, ESCs (~25x103) were cultured in M15 medium and transfected with 50nM siRNA using Lipofectamine 2000 (Invitrogen) at day 0 and collected after 48h. Gene-specific siRNAs used: NF-YA (Invitrogen, MSS247473), non-targeting control (Dharmacon, D- 001810-02-50).

value: NF-YA siRNA (Invitrogen, MSS247473)

tag: passages


title: PTU_T3_WT_H3K4me1

value: WT

value: H3K4me1 (Abcam, ab8895)


title: High grade serous ovarian cancer, Patient20

description: Primary


title: PTU_WT_H3K4me1

value: PTU


title: CC14 shTM9_4


title: CC36 shTM9_1


title: Normal Fallopian tube control, FT2.1

description: Tube

source_name: Normal Fallopian tube control, FT2.1


title: Normal Fallopian tube control, FT9

description: Tube

source_name: Normal Fallopian tube control, FT9


title: CC14 shTM9_3


title: ATAC-Seq NF-YA KD, Rep 1

tag: cell line


title: Normal Fallopian tube control, FT4

description: Tube

source_name: Normal Fallopian tube control, FT4


title: High grade serous ovarian cancer, Patient12

description: Primary


title: ATAC-Seq Control KD, Rep 1

description:
Tn5 Transposase digested DNA from ESCs transfected with control siRNA
NT_open_chromatin_51nt.bigWig
Processed data files represent merged data from 2 biological replicates

value: non-targeting control siRNA (Dharmacon, D- 001810-02-50)


title: Normal Fallopian tube control, FT1

description: Tube

source_name: Normal Fallopian tube control, FT1


title: ATAC-Seq Control KD, Rep 2


title: PTU_WT_CBP

source_name: liver

value: liver

tag: genotype

value: CBP (Santa Cruz, sc-369)


title: CC14 shTM9_2


title: Normal Fallopian tube control, FT6

description: Tube

source_name: Normal Fallopian tube control, FT6


title: CC14 shTM3_3


title: WT_Ole_TG_390

city: Rehovot

first: Dena

last: Leshkowitz

department: Bioinformatics Unit, Life Sciences Core Facilities

institute: Weizmann Institute of Science

description:
Distal Forelimb Sox9+/Scx+ progenitors
WT_Ole_Sox9+/Scx+ #2

data_processing:
Bcl files were converted into fastq by bcl2fastq v2.17.1.14. Demultiplexing is done using the sample barcode found on R2, the UMI found on R2 is inserted in the read name (in R1 fastq).
Adapters and low quality bases were removed from the raw reads using cutadapt version 1.8.3 (parameters -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a "A{100}" -a "T{100}" --times 2 --cut 3 -q 20  -m 30 )
The remaining reads (raw data submitted)  were mapped to the Mus musculus genome (mm10) using tophat2.
Read counts per gene were calculated using HTSeq-count and a Refseq gtf file (downloaded from igenomes UCSC), which was modified to contain a window surrounding the 3' UTR. Duplicate reads were marked and filtered based on having the same UMI and mapping to the same gene, using a python script.
Genes were filtered out if their sum counts after UMI filter <=10 or  maximum value <= 5. Normalization and differential expression analysis was performed using the DESeq2 R-package (Bioconductor, https://bioconductor.org/packages/release/bioc/html/DESeq2.html). Differentially expressed genes were defined as genes that had a significant adjusted p value of less than 0.05 (after adjusment with fdrtools).
Genome_build: mm10
Supplementary_files_format_and_content: Excel containing Raw  and normalized UMI counts for 13158 genes (after filtering)

source_name: Sox9+/Scx+ progenitors FACS sorted from distal forelimb

growth_protocol: To extract cells from tissues, PBS was replaced with 1 ml heated 0.05% trypsin (0.25% dissolved in DMEM, 37˚C) and incubated for 15 min at 37˚C, gently agitated every 5 minutes. Tissues were then dissociated by vigorous pipetting using 1 ml tips. Next, 4 ml of DMEM supplemented with 10% FBS and 1% Pen Strep was added and cell suspensions were filtered into a 15 ml tube using a syringe and a 40 mm filter net. Finally, tubes were centrifuged at 1,000 rpm for 7 minutes, supernatant was removed and cells were resuspended in 1 ml of cold PBS and used immediately for FACS. 5*104 cells were sorted, added with 350 ul of Buffer RLT Plus(Qiagen), lysed and frozen at -80C.

extract_protocol:
Cell lysates were thawed and RNA was purified using RNeasy Plus Micro Kit (Qiagen) according to manufacture guidelines (Protocol: Purification of Total RNA from Animal and Human Tissues).
Purified RNA was stored at -80C. For library preparation RNA was used for the bulk MARS-seq  protocol (Jaitin et al. 2014 Science.343:776-9). MARS-seq libraries were sequenced using Illumina NextSeq 500 High Output v2 Kit (75 cycles).
Bulk Mars-Seq (3' end-RNA-seq)

value: Distal Forelimb

value: Embryonic Day 13.5

value: No treatment

value: wild-type


title: PTU_T3_WT_NCOR1

tag: chip antibody

value: NCOR1 (Abcam, ab24552)


title: WT_Ole_TG_393

description:
Distal Forelimb Sox9+/Scx+ progenitors
WT_Ole_Sox9+/Scx+ #3


title: PTU_WT_NCOR1


title: CC14 shTM3_2

value: colon cancer


title: WT_Ole_TG_389

description:
Distal Forelimb Sox9+/Scx+ progenitors
WT_Ole_Sox9+/Scx+ #1


title: PTU_T3_WT_MED1

value: MED1 (Santa Cruz, sc-8998)


title: CC14 shTM3_1


title: WT_DT_TG_393

description:
Proximal Forelimb Sox9+/Scx+ progenitors
WT_DT_Sox9+/Scx+ #3

source_name: Sox9+/Scx+ progenitors FACS sorted from Proximal forelimb

value: Proximal Forelimb


title: CC14 CTH_4

value: control


title: PTU_WT_MED1


title: Normal Fallopian tube control, FT8

description: Tube

source_name: Normal Fallopian tube control, FT8

value: Normal Fallopian tube control


title: WT_DT_TG_390

description:
Proximal Forelimb Sox9+/Scx+ progenitors
WT_DT_Sox9+/Scx+ #2


title: High grade serous ovarian cancer, Patient8

description: Primary

value: High grade serous ovarian cancer

value: dead


title: WT_DT_TG_389

description:
Proximal Forelimb Sox9+/Scx+ progenitors
WT_DT_Sox9+/Scx+ #1


title: PTU_T3_PV_rep2_Pvexp_H3K27Ac

value: TRbetaPV

value: H3K27Ac (Abcam, ab4729)


title: High grade serous ovarian cancer, Patient5

description: Primary


title: CC14 CTH_3


title: High grade serous ovarian cancer, Patient10

description: Primary


title: CC14 CTH_2


title: High grade serous ovarian cancer, Patient2

description: Primary


title: PTU_PV_rep2_PVexpH3K27Ac

value: PTU


title: OX8X: Old animal 8

city: Cambridge

first: Lee

last: Rubin

state: MA

address: 7 Divinity Ave

institute: Harvard University

description: 10x single cell data

data_processing:
Cell Ranger (version 1.2) (10X Genomics) was used to perform sample de-multiplexing, barcode processing and single cell gene unique molecular identifier (UMI) counting, while a digital expression matrix was obtained for each experiment with default parameters, mapped to the 10x reference for mm10, version 1.2.0.
After the initial sequencing, the samples in each pool were re-pooled based on the actual number of cells detected by Cell Ranger, aiming to sequence each sample to a similar depth (number of reads/cell) (median: 40,007). Multiple NextSeq runs were conducted to achieve over 70% sequencing saturation as determined again by Cell Ranger (median: 75%).
Basic processing and visualization of the scRNA-seq data were performed using the Seurat package (version 2.3) in R (version 3.3.4)
Meta data with cell types, nUMI, nGene, and lineage are in the additional meta data file within the processed data section.
Genome_build: mm9
Supplementary_files_format_and_content: There are 16 processed files that are txt files with matrices for each gene and each cell from that animal.  In addtion, there is a combined additional metadata file that has each cell as a row and meta data including the following parameters nGene, nUMI, cluster (e.g. cell type), animal_type (young or old), cell_class (immune_lin, olg_lin, etc), and a final variable combining cell type and age.

source_name: 10x of dissociated mouse brain - old 15

extract_protocol:
Brain cells were processed through all steps to generate stable cDNA libraries. Briefly, after dissociation, cells were diluted in ice-cold PBS containing 0.4% BSA at a density of 1,000 cells/ul.
For every sample, 17,400 cells were loaded into a Chromium Single Cell 3’ Chip (10x Genomics) and processed following the manufacturer’s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3’ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics). Libraries were pooled based on their molar concentrations. Pooled libraries were then loaded at 2.07 pM and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read1, 57 bases for read2 and 8 bases for Index1.

value: brain

value: 21-22 months

tag: cells


title: High grade serous ovarian cancer, Patient3

description: Primary


title: High grade serous ovarian cancer, Patient9

description: Primary


title: CC36 CTH_1

source_name: Primary colon cancer cells


title: erythroblast_neratinib

first: Melissa

last: Kinney

address: 1 Blackfan Circle

institute: Boston Children's Hospital

data_processing:
RNA-seq reads were analyzed with the Tuxedo Tools following a standard pipeline (rcbio 1.5) for Orchestra (Harvard Medical School's LSF based clusters). Reads were mapped with TopHat version 2.1.0 and Bowtie2 version 2.2.4 with default parameters against build hg19 of the human genome, and build hg19 of the RefSeq human genome annotation. Samples were quantified with the Cufflinks package version 2.2.1. Differential expression was performed using Cuffdiff with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: cufdiff output

source_name: Human bone marrow CD34-derived erythroblasts

growth_protocol: CD34+ progenitors derived from mobilized peripheral blood (AllCells) were expanded for 4 days in StemSpan SFEM (STEMCELL Technologies) with the addition of IL3 (10 ng/mL), IL6 (50 ng/mL), TPO (50 ng/mL), SCF (50 ng/mL) and Flt3 (50 ng/mL). Unless specified, all cytokines were from PeproTech. Erythroid differentiation was accomplished using a previously published, 3-stage protocol16. Briefly, All stages of differentiation consisted of a basal erythroid differentiation medium (EDM) comprised of: IMDM with 15% FBS, 1% BSA, 2 mM L-glutamine, 500 µg/mL holo-transferrin, and 10 µg/mL insulin. Stage 1 consists of EDM plus the addition of dexamethasone (1 µM), β-estradiol (1 µM), IL3 (5 ng/mL), SCF (100 ng/mL) and EPO (6U) for 5 days (days 0-5). Stage 2 consists of EDM plus the addition of SCF (50 ng/mL) and EPO (6U) for 4 days (days 5-9). Stage 3 consists of EDM plus the addition of EPO alone (2U) for 8 days (days 9-17). At all stages, cells are cultured in 24 well plates in 1 mL of media. Cell number seeded at the beginning of stages 1, 2, and 3 are: 105, 2x105, and 5x105/well.

extract_protocol: Libraries were constructed using the SMARTseq v4 kit with 10 ng input RNA

treatment_protocol: All inhibitors were added to cell cultures at 1 µM on days 9 and 13 of differentiation, corresponding to the beginning and middle of stage 3 (supplemented with EPO only, as described above). DMSO was used for a vehicle control in all cell culture studies. RNA was extracted after 24 hours of incubation with ERBB inhibitors (day 10 of erythroid differentiation).

value: Erythroid progenitors


title: PTU_PV_rep1_Pvexp_H3K27Ac

value: liver


title: High grade serous ovarian cancer, Patient4

description: Primary

data_processing: Results were reported as DNA methylation ratios (proportion of methylated/ unmethylated) referred to as Beta and processed using the Minfi R package


title: High grade serous ovarian cancer, Patient94

description: Primary


title: erythroblast_lapatinib


title: PTU_T3_WT_rep2_Pvexp_H3K27Ac

description: WT mice match with TRbetaPV

value: WT


title: PTU_T3_WT_rep1_Pvexp_H3K27Ac

description: WT mice match with TRbetaPV


title: High grade serous ovarian cancer, Patient1

description: Primary

value: alive


title: High grade serous ovarian cancer, Patient7

description: Primary


title: erythroblast_dacomitinib


title: OX5X: Old animal 5

description: 10x single cell data

source_name: 10x of dissociated mouse brain - old 12


title: erythroblast_afatinib


title: OX4X: Old animal 4

description: 10x single cell data

source_name: 10x of dissociated mouse brain - old 11


title: PTU_WT_rep2_PVexpH3K27Ac

description: WT mice match with TRbetaPV


title: erythroblast_DMSO


title: OX3X: Old animal 3

description: 10x single cell data

source_name: 10x of dissociated mouse brain - old 10


title: PTU_WT_rep1_Pvexp_H3K27Ac

description: WT mice match with TRbetaPV


title: OX6X: Old animal 6

description: 10x single cell data

source_name: 10x of dissociated mouse brain - old 13


title: DHX36-iso2 overexpression 2

city: Würzburg

first: Markus

last: Sauer

address: Am Hubland, Biozentrum - Lehrstuhl für Biochemie

country: Germany

institute: University of Würzburg

data_processing:
Illumina high-seq 2500 platform was used for sequencing
Basecalling was done using bcl2fastq V2.17.1
The reads were aligned to the hg19 genome using PARalyzer
normalized reads and clusters were combined in a csv file
Genome_build: hg19
Supplementary_files_format_and_content: PARalyzer output

source_name: DHX36-iso2 overexpression

growth_protocol: Stable overexpression HEK293 cells were grown and routinely passaged in DMEM supplemented with 10% FCS and 1% pen/strip as well as 100 µg/ml hygromycin B and 10 µg/ml blasticidin.

extract_protocol:
Cells were lysed in NP-40 lysis buffer and lysate was clarified by centrifugation. First RNase T1 was followed by immunoprecipitation with FLAG-M2 antibody After washing, second RNase T1 digestion was performed, 3´ends of the RNA fragments were dephosphorylated using CIP, and RNA was radioactively 5´end-labeled using l T4 PNK and 32P-γ-ATP. RNA-protein complexes were separated by SDS-PAGE and excised. After proteinase K treatment, small RNA cDNA library preparation was performed.
Preadenylated, barcoded 3´adapter oligonucleotide was ligated followed by ligation of a 5´adapter. Ligation products were reverse transcribed and amplified by PCR.

treatment_protocol: 15 h before cell harvesting, transgene expression was induced with 500 ng/ml tetracycline. Cells were crosslinked with 365 nm UV-light for 5 min

tag: genotype/variation

value: stably expressing Tetracycline-inducible HA-Flag-DHX36-iso2

tag: ip antibody

value: Monoclonal ANTI-FLAG® M2 antibody produced in mouse (Sigma-Aldrich)


title: DHX36-iso2 overexpression 1


title: PTU_T3_WT_CBP

value: CBP (Santa Cruz, sc-369)


title: PTU_NCORdeltaID_rep2_H3K9Ac

value: L-NCORdeltaID

value: H3K9Ac (Milipore, 06-942)


title: OX1X: Old animal 1

description: 10x single cell data

source_name: 10x of dissociated mouse brain - old 8

tag: age


title: PTU_T3_WT_rep2_H3K9Ac

description: WT mice match with L-NCORdeltaID


title: OX2X: Old animal 2

description: 10x single cell data

source_name: 10x of dissociated mouse brain - old 9


title: DHX36-iso1 E335A overexpression 2

source_name: DHX36-iso1 E335A overexpression

value: stably expressing Tetracycline-inducible HA-Flag-DHX36-iso1-E335A


title: PTU_WT_rep2_H3K9Ac

description: WT mice match with L-NCORdeltaID


title: DHX36-iso1 E335A overexpression 1


title: YX8L: Young animal 8

description: 10x single cell data

source_name: 10x of dissociated mouse brain - young 8

value: 2-3 months


title: YX7R: Young animal 7

description: 10x single cell data

source_name: 10x of dissociated mouse brain - young 7


title: YX6L: Young animal 6

description: 10x single cell data

source_name: 10x of dissociated mouse brain - young 6


title: PTU_NCORdeltaID_rep1_H3K9Ac

source_name: liver


title: High grade serous ovarian cancer, Patient11

description: Primary

value: High grade serous ovarian cancer


title: High grade serous ovarian cancer, Patient88

description: Primary

value: dead


title: High grade serous ovarian cancer, Patient85

description: Primary