title: 43208

tag: height (inches)

tag: race

tag: debulking

value: Optimal

tag: patient survival


title: MDA-MB-231_shSMYD3_rep2

status: Public on Jun 30 2020

type: SRA

city: Seoul

first: Gu

last: Kong

address: 17 Haengdang-dong, Seongdong-gu

department: Department of Pathology

country: South Korea

institute: College of Medicine, Hanyang University

description: Total RNA were isolated from SMYD3-knockdown MDA-MB-231 tumors from the mammary glands of orthotopic xenograft NOD/SCID mice and analyzed by RNA-sequencing.

library_source: transcriptomic

data_processing:
Illumina bcl2fastq2 v2.17 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using STAR v2.6.
Fragments per kilobase of transcript per million mapped reads (FPKM) were calculated using Cufflinks v2.2.1. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file includes FPKM values for all samples

molecule: total RNA

organism: Homo sapiens

source_name: MDA-MB-231 is a cell line that was isolated from a pleural effusion of a 51-year-old caucasian female.

extract_protocol:
Total RNA was extracted from control and SMYD3 knockdown MDA-MB-231 tumors from the mammary glands of orthotopic xenograft NOD/SCID mice using TRIzol® RNA Isolation Reagents (Life technologies, Carlsbad, CA). RNA integrity was confirmed by a bioanalyzer using an Agilent RNA 6000 Pico Kit (Agilent, Santa Clara, CA). The isolated total RNA was processed for preparing mRNA sequencing library using TruSeq stranded mRNA sample preparation kit (illumina, San Diego, CA) according to manufacturer’s instruction. Simply, mRNAs were isolated from 400 ng total RNA by RNA purification bead using polyA capture, and followed by enzyme shearing.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

tag: tissue

value: mammary gland, breast; derived from metastatic site:pleural effusion

tag: Sex

value: female

tag: disease

value: adenocarcinoma


title: EMORY Subject D Day 01

city: Rockville

first: Johannes

last: Goll

state: MD

address: 401 N Washington St

department: Bioinformatics Service Group

country: USA

institute: The Emmes Company

data_processing:
Reads were mapped against the human reference using the STAR splice-aware read aligner (Version 2.5.2a). Gene expression quantification was carried out using the featureCounts function as implemented in the  Subread software (Version 1.5.0-p2). Options for featureCounts were set to count reads that were successfully mapped to a gene. For strand-specific RNA-sequencing data generated by Emory University,  the strand mapping option of feature counts was set to count the antisense strand (-s 2). For Saint  Louis University which did not use a strand-specific protocol, the option was set to count both sense  and antisense strands (-s 0). Reads that overlapped with multiple genes or had multiple mapping locations on the reference genome were excluded.
Genome_build: GRCh38 [ENSEMBL (Version 84, March 2016)]: The genomic reference was built by merging all  human chromosomes except X and Y chromosomes (to avoid gender-specific effects).
Supplementary_files_format_and_content: Feature counts matrix: columns=samples [EMO denotes samples sequenced at Emory University, and SLU indicates samples sequenced at Saint Louis University]; rows=features [genes].

molecule: polyA RNA

source_name: Peripheral Blood Mononuclear Cells

extract_protocol:
Total RNA was extracted using the miRNeasy Mini kit (Qiagen, CA).
250 ng of total RNA was used for library preparation. For Emory Univerity samples, Libraries were prepared using the  Illumina TruSeq mRNA stranded kit as per manufacturer’s instructions. For Saint Louis University samples, Libraries were prepared using the Illumina TruSeq v2 RNA library kit as per manufacturer’s instruction.

tag: cell type

value: Peripheral Blood Mononuclear Cells

tag: day

tag: subject

value: Subject D

tag: sequencing core

value: Emory University


title: MDA-MB-231_shSMYD3_rep1


title: 40976

city: Los Angeles

first: Sandra

last: Orsulic

state: CA

address: 10833 Le Conte Ave

department: Obstetrics and Gynecology

institute: David Geffen School of Medicine at UCLA

data_processing:
Sequencing was performed using the Illumina HiSeqX platform
Alignment using STAR (2.4.1) aligner
The raw read counts were estimated using HTSeq-0.6.1
Read count data were normalized using DESeq2
Hierarchical clustering analysis is performed for normalized counts of all the protein coding genes for all the samples
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: xlsx files for Raw.Read.Count and Normalized.Read.Count(using DESeq2 for normalization)

source_name: human omental metastasis

extract_protocol:
Total RNA was isolated using the miRNeasy FFPE kit (cat # 217504) according to the manufacturer's instructions (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols (SMARTer® Stranded Total RNA-Seq Kit v2)

treatment_protocol: FFPE tissue was collected at the time of surgery. FFPE blocks were sectioned onto uncharged glass slides. One 4 µm section was used for H&E  staining and delineating tumor areas by a pathologist. Depending on the tumor size, 1 to 3 unstained 10 µm sections were macrodissected (removal of non-tumor areas based on the H&E template) with a clean razor blade.

value: metastatic ovarian cancer

tag: organ site

value: omentum

tag: age at diagnosis

tag: weight (pounds)

tag: bmi

value: CAUCASIAN

tag: ethnicity

value: NON-HISPANIC

tag: cancer stage

value: IIIC

tag: tumor grade

tag: assumed progression free survival (months)

tag: assumed overall survival (months)

value: DWD-Died with Disease


title: EMORY Subject C Day 14

value: Subject C


title: MDA-MB-231_shCon_rep2

description: Total RNA were isolated from control MDA-MB-231 tumors from the mammary glands of orthotopic xenograft NOD/SCID mice and analyzed by RNA-sequencing.

tag: cell line


title: 40928

tag: tissue

tag: height (inches)

tag: race

value: ASIAN

tag: brca mutation status

value: WT

tag: brca mutation description

value: WT - No Mut

tag: debulking

tag: patient survival

value: Alive


title: EMORY Subject E Day 14

tag: cell type

tag: day

tag: subject

value: Subject E

tag: sequencing core


title: MDA-MB-231_shCon_rep1

value: mammary gland, breast; derived from metastatic site:pleural effusion

tag: Sex

value: female

tag: disease


title: EMORY Subject E Day 02

value: Peripheral Blood Mononuclear Cells


title: 40812

tag: organ site

tag: age at diagnosis

tag: weight (pounds)

tag: bmi

tag: ethnicity

value: Optimal

tag: cancer stage

tag: tumor grade


title: 24 h SFN treatment CCD-841 cell line 3

city: Norwich

first: Tamas

last: Dalmay

address: Earlham Road

department: School of Biological Sciences

country: United Kingdom

institute: University of East Anglia

description: sRNA

data_processing:
the original fastq files were converted to fasta format and reads without Ns were kept for further analysis
the 3' adapter and HD signatures [Sorefan et al 2012] were trimmed and the files were converted from redundant to non-redundant format
the reads were mapped to the reference genome, allowing 0 mis-matches and 0 gaps using PatMaN [Pruffer et al 2008]
the reads were mapped to mature miRNAs and miRNA hairpins, retrieved from miRbase, release 21
Genome_build: GRCh38
Supplementary_files_format_and_content: csv, expression levels

source_name: CCD-841 cell line

growth_protocol: Cells were maintained in adherent culture in DMEM supplemented with FBS, L-glutamine and Penicillin-Streptomycin. Caco-2 cells were not allowed to grow beyond 80% confluence, in order to avoid their differentiation. Prior to cell treatment, cells were allowed to grow to 70% confluence.

extract_protocol:
Total RNA was extracted using TRIZol Reagent according to manufacturers instructions, then purified using the Zymo RNA Clean & Commentator kit. RNA integrity was verified by agarose gel electrophoresis to visualise 28S and 18S bands.
Small RNA libraries prepared as described in Xu et al. 2015.

treatment_protocol: Cells were treated when 70% confluent, thus in the logarithmic growth phase, by adding DMSO-dissolved SFN or DMSO (control) to culture medium, then extracting RNA at 8 or 24 h.

value: healthy colon cells


title: EMORY Subject C Day 02

value: Emory University


title: EMORY Subject D Day 07

value: Subject D


title: 24 h SFN treatment CCD-841 cell line 2

description: sRNA


title: EMORY Subject C Day 00


title: 24 h SFN treatment CCD-841 cell line 1

description: sRNA


title: 37306

tag: tissue

value: metastatic ovarian cancer

value: omentum

tag: height (inches)

tag: race

value: CAUCASIAN

tag: brca mutation status

tag: assumed progression free survival (months)

tag: assumed overall survival (months)


title: 43026

value: NON-HISPANIC

tag: debulking

value: IIIC

tag: patient survival


title: 39021

value: ASIAN

tag: brca mutation description

value: IV

value: DWD-Died with Disease


title: NAE 18:3 R2

city: Denton

first: Ashley

middle: Elisabeth

last: Cannon

state: TX

address: 1155 Union Circle #305220

department: Biological Sciences

institute: The University of North Texas

data_processing:
Reads were mapped to the reference using STAR and the default settings
Expression analysis was completed using DESeq2
Supplementary_files_format_and_content: "counttable.txt" files are output from STAR; "normalized_countstable.csv" are output normalized counts from DESeq2

organism: Arabidopsis thaliana

source_name: Roots

growth_protocol: Arabidopsis seeds were surface sterilized by treatment with 70% ethanol for 3 min followed by 20% bleach (5.25 % sodium hypochlorite, Clorox) with 0.01% Triton X-100 (Sigma-Aldrich) for 5 min and then rinsed five times with sterile ddH2O. After the final rinse, Arabidopsis seeds were maintained in 1 mL of sterile ddH2O, wrapped in two layers of aluminum foil, and placed in the dark at 4°C for three days. After three days, the seedlings were sown in 50 mL of ½ Murashige and Skoog (Sigma-Aldrich) media, pH 5.7 with 1% sucrose (Fisher Scientific) in a 250 mL sterile Erlenmeyer flask. The seeds were grown at 21°C, 80 -110 µmoles/m2s, on a shaker (Bellco Biotechnologies) set at speed level 3.

extract_protocol:
Each Arabidopsis organ or seedling sample was ground to a fine powder and 500 µL of Hot Borate Buffer (200mM sodium tetraborate decahydrate - Sigma-Aldrich, 30 mM EGTA - Sigma-Aldrich, 1% SDS - Fisher, 1% deoxycholic acid - Sigma-Aldrich, 2% polyvinylpyrrolidone (PVP) 40K  - Sigma-Aldrich, 0.5% IGEPAL CA-630 - Sigma-Aldrich, 10 mM DTT - Sigma-Aldrich) and 17.5 µL of 20 mg/mL Proteinase K (ThermoFisher) were added. After mixing, the sample and buffer solution was added to a lilac shredder column from a RNeasy Plant Mini Kit (Qiagen). The manufacturer's protocol from the RNeasy Plant Mini Kit was followed for the remainder of the extraction.
Poly(A) enrichment and library preparation were performed using the TruSeq Stranded mRNA prep kit (Illumina). Libraries were quantified by fluorometry, immobilized, and processed onto a flow cell, followed by 2 x 75 bp sequencing-by-synthesis on a Next-Seq 500 system (Illumina) with two mid-output cassettes (Illumina). Library construction and RNA sequencing were performed by the UNT Genomics Center (http://untgenomicscenter.squarespace.com/).

treatment_protocol: After three days, the seedlings were separated into groups of 50 using sterile toothpicks and moved to 25 mL of ½ Murashige and Skoog in a petri dish (100 x 25 mm, Fisher Scientific). The seedlings were treated with 0.2% DMSO (Sigma-Aldrich), 40 µM NAE 18:2 (Cayman Chemical), or 70 µM NAE 18:3 (Cayman Chemical) for 1 h. After 1 h, whole seedlings, roots, and cotyledons were collected from each treatment group, flash frozen, and stored at -80°C.

tag: ecotype

value: Col-O

tag: organ

value: Roots

tag: age

value: 3 day-old

tag: agent


title: EMORY Subject B Day 14

tag: cell type

tag: day

tag: subject

value: Subject B

tag: sequencing core


title: Control CCD-841 cell line 2

description: sRNA


title: Control CCD-841 cell line 3

description: sRNA


title: NAE 18:3 R1


title: 35623

tag: tissue

tag: organ site

tag: age at diagnosis

tag: weight (pounds)

tag: bmi

tag: ethnicity

tag: cancer stage

tag: tumor grade

value: No recurrence to date

value: Alive


title: EMORY Subject D Day 00

value: Peripheral Blood Mononuclear Cells


title: 32761

tag: height (inches)

tag: race

tag: brca mutation status

value: WT

tag: brca mutation description

value: WT - No Mut

tag: debulking

value: Optimal

tag: assumed progression free survival (months)

tag: assumed overall survival (months)

tag: patient survival


title: EMORY Subject B Day 07

tag: cell type

tag: day

tag: subject

tag: sequencing core

value: Emory University


title: NAE 18:3 C3

source_name: Cotyledons

tag: ecotype

tag: organ

value: Cotyledons

tag: age

tag: agent


title: EMORY Subject B Day 02


title: EMORY Subject C Day 07

value: Subject C


title: Control CCD-841 cell line 1

description: sRNA

value: healthy colon cells


title: 32342

tag: tissue

value: metastatic ovarian cancer

tag: organ site

value: omentum

tag: age at diagnosis

tag: weight (pounds)

tag: bmi

value: CAUCASIAN

tag: ethnicity

value: NON-HISPANIC

value: Suboptimal

tag: cancer stage

value: IIIC

tag: tumor grade


title: NAE 18:3 C2

value: Col-O

value: 3 day-old


title: 8 h SFN treatment CCD-841 cell line

description: sRNA


title: EMORY Subject B Day 01

value: Subject B


title: EMORY Subject C Day 01

value: Peripheral Blood Mononuclear Cells


title: 40421

tag: height (inches)

tag: race

tag: brca mutation status

value: WT

tag: brca mutation description

tag: debulking

tag: assumed progression free survival (months)

tag: assumed overall survival (months)

tag: patient survival

value: Alive


title: NAE 18:3 R3

tag: ecotype

tag: organ

value: Roots

tag: age

tag: agent


title: NAE 18:3 C1


title: 31981

tag: tissue

tag: organ site

tag: age at diagnosis

tag: weight (pounds)

value: Mut

value: Optimal

value: No recurrence to date


title: EMORY Subject B Day 00

tag: cell type

tag: day

tag: subject

tag: sequencing core

value: Emory University


title: NAE 18:3 WS3

source_name: Seedlngs

value: Whole Seedlngs


title: 29764

value: metastatic ovarian cancer

value: omentum

tag: height (inches)

tag: bmi

tag: race

tag: ethnicity

tag: brca mutation status

tag: brca mutation description

value: WT - No Mut

tag: cancer stage

tag: tumor grade

value: DWD-Died with Disease


title: EMORY Subject A Day 14

value: Subject A


title: 24 h SFN treatment Caco-2 cell line 2

description: sRNA

source_name: Caco-2 cell line

value: colorectal adenocarcinoma cells


title: 29083

value: CAUCASIAN

value: NON-HISPANIC

tag: debulking

value: IIIC

tag: assumed progression free survival (months)

value: Unknown

tag: assumed overall survival (months)

tag: patient survival


title: NAE 18:3 WS2

tag: ecotype

value: Col-O

tag: organ

tag: age

value: 3 day-old

tag: agent


title: 24 h SFN treatment Caco-2 cell line 1

description: sRNA

tag: cell type


title: EMORY Subject A Day 07

value: Peripheral Blood Mononuclear Cells

tag: day

tag: subject

tag: sequencing core


title: EMORY Subject A Day 02


title: Control Caco-2 cell line 3

description: sRNA


title: 28601

tag: tissue

tag: organ site

tag: age at diagnosis

tag: height (inches)

tag: weight (pounds)

tag: bmi

tag: race

tag: ethnicity

value: Mut

value: Optimal


title: NAE 18:3 WS1


title: EMORY Subject A Day 01

value: Emory University


title: 28461

tag: debulking

tag: cancer stage

tag: tumor grade

tag: assumed progression free survival (months)

tag: assumed overall survival (months)

tag: patient survival


title: EMORY Subject A Day 00

tag: cell type

tag: day


title: NAE 18:2 R2

tag: ecotype

tag: organ

value: Roots

tag: age

tag: agent


title: 27910

tag: tissue

value: metastatic ovarian cancer

tag: organ site

tag: age at diagnosis

tag: brca mutation status

value: WT

tag: brca mutation description

value: IV

value: Alive


title: Control Caco-2 cell line 1

description: sRNA


title: 27521

value: omentum

tag: height (inches)

tag: weight (pounds)

tag: bmi

tag: race

value: ASIAN

tag: ethnicity

value: WT - No Mut

tag: debulking

value: DWD-Died with Disease


title: 24 h SFN treatment Caco-2 cell line 3

description: sRNA

tag: cell type

value: colorectal adenocarcinoma cells


title: NAE 18:2 C3

value: Cotyledons


title: NAE 18:2 R1

value: Col-O


title: 8 h SFN treatment Caco-2 cell line 2

description: sRNA


title: NAE 18:2 C2

value: 3 day-old


title: 8 h SFN treatment  Caco-2 cell line 1

description: sRNA


title: 28701

value: NON-HISPANIC

tag: cancer stage

tag: tumor grade

tag: assumed progression free survival (months)

tag: assumed overall survival (months)

tag: patient survival


title: 26062

tag: tissue

value: CAUCASIAN

value: IIIC


title: NAE 18:2 WS2

tag: ecotype

tag: organ

value: Whole Seedlngs

tag: age

tag: agent


title: RNASEQ001.1_G9a_siRNA_control_1

city: Stockholm

first: Anita

last: Göndör

address: Nobels väg 16, KI Solna Campus, Karolinska Institutet, Box 280

department: MTC

country: Sweden

institute: Karolinska Institutet

description: Control for G9a siRNA (Sequencing Replicate)

data_processing:
map with STAR v2.3.0e aligner
Convert to sorted/index bam files with Samtools v0.1.19
Run cufflinks with --library-type fr-firststrand
Genome_build: HG19
Supplementary_files_format_and_content: Cufflinks FPKM gene counts (no normalization)

source_name: HCT116, Control for G9a siRNA

growth_protocol: Human colon cancer cells (HCT116) and the foreskin fibroblast cells (CRL2429,ATCC) were seeded for 48hrs on an 8 well Lab-Tek II Chamber slides (154534, Lab Tek), fixed with 3% monomeric formaldehyde for 15 minutes at room temperature1 and then stored in 70% ethanol at -20Â°C until use.

extract_protocol: The RNA-Seq library was prepared under the instruction of TruSeq Stranded Total RNA Sample Prep Kit (illumine, RS-122-2201), and the sequencing was done on HiSeq-2000 in SciLife (Stockholm, Sweden)

treatment_protocol: HCT 116 cells and the foreskin fibroblast cells were grown on Lab-Tek II Chamber Slide system with low density and treated with 0.5 Î¼M BIX 01294 trihydrochloride hydrate (B9311, Sigma-Aldrich) for 72 hrs. 10 nM of G9a siRNA (sc-43777, Santa Cruz) was transfected in HCT 116 using LipofectamineTM RNAiMAX Transfection Reagent (13778-075, Invitrogen) and maintained for 72 hrs according to the provided protocol on both 6-well plates and Lab-Tek II Chamber Slide.

tag: cell line

value: colon cancer


title: RNASEQ001.1_G9a_siRNA_control_2


title: 8 h SFN treatment Caco-2 cell line 3

description: sRNA


title: NAE 18:2 R3

value: Roots


title: NAE 18:2 C1


title: NAE 18:2 WS3


title: 25258

value: metastatic ovarian cancer

tag: organ site

tag: age at diagnosis

tag: height (inches)

tag: weight (pounds)

tag: brca mutation status

value: Mut

tag: brca mutation description

value: BRCA 1 and 2

value: Optimal


title: Control Caco-2 cell line 2

description: sRNA

tag: cell type


title: 25147

value: omentum

tag: bmi

tag: race

tag: ethnicity

tag: debulking

tag: cancer stage

tag: tumor grade


title: NAE 18:2 WS1

tag: ecotype

tag: organ


title: DMSO R3

tag: age

tag: agent

value: DMSO


title: DMSO R2


title: 25038

tag: tissue

tag: organ site

value: WT

value: WT - No Mut

value: Suboptimal

tag: assumed progression free survival (months)

value: Unknown

tag: assumed overall survival (months)

tag: patient survival

value: DWD-Died with Disease


title: 26645

tag: age at diagnosis

tag: height (inches)

tag: weight (pounds)

value: NON-HISPANIC


title: RNASEQ001.1_G9a_inhibitor_1

description: Treated with G9a inhibitor (Sequencing Replicate)

source_name: HCT116, Treated with G9a inhibitor

tag: cell line

tag: cell type


title: RNASEQ001.1_G9a_inhibitor_2


title: 24894

tag: bmi

tag: race

value: CAUCASIAN

tag: ethnicity

tag: brca mutation status

tag: brca mutation description

tag: debulking


title: DMSO R1

tag: ecotype

value: Col-O

tag: organ

tag: age

value: 3 day-old

tag: agent


title: RNASEQ001.1_G9a_control_2

description: Control for G9a inhibitor (Sequencing Replicate)

source_name: HCT116, Control for G9a inhibitor

value: colon cancer


title: 24877

tag: tissue

tag: organ site

tag: cancer stage

value: IIIC

tag: tumor grade

tag: assumed progression free survival (months)

tag: assumed overall survival (months)


title: 25562

value: metastatic ovarian cancer

tag: age at diagnosis

tag: height (inches)

tag: weight (pounds)

value: III

tag: patient survival


title: 25315

tag: bmi

tag: race

tag: ethnicity

tag: brca mutation status

value: Mut


title: DMSO C3

tag: ecotype

tag: organ

value: Cotyledons


title: RNASEQ001.1_G9a_control_1

tag: cell line

tag: cell type


title: 24733

tag: tissue

tag: organ site

value: omentum

value: BLACK

tag: debulking


title: DMSO C2

tag: age

tag: agent

value: DMSO


title: RNASEQ001_G9a_siRNA_control_2

description: Control for G9a siRNA


title: 24693

tag: age at diagnosis

tag: brca mutation description

value: Optimal

tag: cancer stage

tag: tumor grade

tag: assumed progression free survival (months)

tag: assumed overall survival (months)


title: DMSO C1


title: RNASEQ001_G9a_siRNA_control_1

description: Control for G9a siRNA


title: 24601

tag: height (inches)

tag: weight (pounds)

tag: bmi

tag: race

tag: ethnicity

tag: patient survival


title: DMSO WS3

tag: ecotype

tag: organ

value: Whole Seedlngs


title: 24477

tag: tissue

tag: organ site

tag: brca mutation status

value: WT

value: WT - No Mut

tag: debulking

value: Suboptimal

value: IV


title: RNASEQ001.1_G9a_siRNA_1

description: Treated with G9a siRNA  (Sequencing Replicate)

source_name: HCT116, Treated with G9a siRNA

tag: cell line

tag: cell type


title: RNASEQ001.1_G9a_siRNA_2


title: RNASEQ001_G9a_siRNA_2

description: Treated with G9a siRNA


title: D6

city: La Jolla

first: Tina

last: Wang

address: 9500 Gilman Dr

institute: University of California, San Diego

description:
Dog_MethylationFractions.txt
Dog_mapped_human_MethylationFractions.txt

library_source: genomic

data_processing:
Basecalling Illumina HCS v3.3.x
reads were trimmed using TrimGalore, aligned to ensembl CanFam 3.1 with bismark (v0.14.3) using bowtie2 (2.1.0) with parameters -score_min L,0,-0.2
Data was filtered such that each CpG was covered at least 5x reads, present in 97% of samples and samples were that were missing > 30% CpGs were removed
Orthologous CpGs were determined by using liftOver from dog to human with CpG probes extended 50bp and intersected. CpGs within a mapped regions were merged by taking the average methylation value.
Genome_build: canFam3.1
Supplementary_files_format_and_content: tab-delimited files sample x CpG where CpGs are encoded by the chr:start:stop in canFam3 coordinates or mapped to human450K probes;

molecule: genomic DNA

organism: Canis lupus familiaris

source_name: blood

extract_protocol:
DNA extracted from whole blood using DNAeasy kit or phenol chloroform
Samples were sheared with covaris, a-tail extension, sequencing adapter ligation, amplified, bisulfite converted, amplified, qc-ed on bioanalyzer according to Roche SeqCap Epi Protocol

tag: age (years)

tag: gender (null if unknown)

value: M

value: whole blood


title: RNASEQ001_G9a_siRNA_1

description: Treated with G9a siRNA

value: colon cancer


title: DMSO WS2

value: Col-O

tag: age

value: 3 day-old

tag: agent


title: D5

value: F


title: D4-capture-2


title: DMSO WS1


title: RNASEQ001_G9a_inhibitor_2

description: Treated with G9a inhibitor


title: 24459

value: metastatic ovarian cancer

tag: age at diagnosis

tag: height (inches)

tag: weight (pounds)

value: CAUCASIAN

value: HISPANIC

tag: cancer stage

value: IIIB

tag: tumor grade

tag: assumed progression free survival (months)

tag: assumed overall survival (months)

value: DWD-Died with Disease


title: 24450

tag: tissue

value: omentum

tag: bmi

tag: race

tag: ethnicity

value: III

value: Unknown

tag: patient survival

value: Alive


title: D4-capture-1


title: 24209

tag: organ site

value: NON-HISPANIC

tag: debulking

value: Suboptimal

value: IIIC


title: RNASEQ001_G9a_inhibitor_1

description: Treated with G9a inhibitor

tag: cell line

tag: cell type


title: D3

tag: age (years)

tag: gender (null if unknown)

value: whole blood


title: RNASEQ001_G9a_control_2

description: Control for G9a inhibitor

value: colon cancer


title: 24150

tag: age at diagnosis

tag: height (inches)

tag: brca mutation status

value: WT

tag: brca mutation description

value: WT - No Mut

value: Optimal

value: IV


title: D2-capture-1

value: M


title: D2-capture-2


title: 24197

value: metastatic ovarian cancer

tag: weight (pounds)

value: CAUCASIAN

tag: cancer stage

tag: tumor grade

tag: assumed progression free survival (months)

value: Progressive disease


title: RNASEQ001_G9a_control_1

description: Control for G9a inhibitor


title: 24112

tag: tissue

value: omentum

tag: bmi

tag: race

tag: assumed overall survival (months)

value: DWD-Died with Disease


title: D1-capture-2

value: F


title: 33203


title: 22859

tag: organ site

tag: ethnicity

tag: debulking

value: IIIB

tag: patient survival


title: cmt3_Rep1_RNAseq

city: Beijing

first: Xin-Jian

last: He

address: No. 7, zhongguancun life science park road, changping district

country: China

institute: National Institute of Biological Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR10 whole genome using HISAT-2.1.0 with default parameters
Normalized reads were calculated using edgeR R package
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include normalized reads for each Sample

source_name: Arabidopsis seedlings

growth_protocol: Arabidopsis seedlings were grown on MS medium plates with a 16 h light/8 h dark photoperiod at 22ºC

extract_protocol:
Total RNA was extracted from 1 g samples of 2-week-old Arabidopsis seedlings with TRIzol reagent (Invitrogen)
libraries were prepared for mRNA-seq

value: seedlings

tag: genotype


title: tcx5/6;cmt3_Rep2_RNAseq


title: 23099

tag: age at diagnosis

value: NON-HISPANIC


title: tcx5/6;cmt3_Rep1_RNAseq


title: cmt3_Rep2_RNAseq


title: 22820

tag: height (inches)

value: IIIC


title: 31117

tag: age (years)

value: whole blood


title: 22359

tag: brca mutation status

tag: brca mutation description


title: 31279


title: 25293


title: 30379


title: 25415


title: 21819

tag: weight (pounds)

value: BLACK

tag: cancer stage


title: tcx5/6-SAM_Rep2_RNAseq

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR10 whole genome using HISAT-2.1.0 with default parameters
Normalized reads were calculated using edgeR R package
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted from 1 g samples of 2-week-old Arabidopsis seedlings, one-month-old leaf and SAM (shoot apical meristem) with TRIzol reagent (Invitrogen)
libraries were prepared for mRNA-seq

value: Arabidopsis seedlings


title: 14233

tag: tumor grade

tag: assumed progression free survival (months)


title: 23855

tag: tissue


title: 20879

tag: bmi

tag: race

value: UNKNOWN


title: tcx5/6-SAM_Rep1_RNAseq


title: 23852


title: 20098

tag: organ site

value: WT

value: WT - No Mut

value: Optimal

value: No recurrence to date

tag: assumed overall survival (months)

value: Alive


title: WT-SAM_Rep1_RNAseq

value: wild type


title: 23848


title: WT-SAM_Rep2_RNAseq


title: D1-capture-1

tag: gender (null if unknown)


title: 19638

value: metastatic ovarian cancer

value: omentum

value: CAUCASIAN

tag: ethnicity

value: Mut

tag: debulking

tag: patient survival


title: 19395

tag: age at diagnosis

tag: height (inches)


title: 23840

tag: age (years)


title: 18915

tag: brca mutation status

tag: brca mutation description

value: Suboptimal

value: DWD-Died with Disease


title: tcx5/6-leaf_Rep2_RNAseq

tag: genotype


title: 23820


title: 21979

tag: weight (pounds)

tag: cancer stage

value: IIIC

tag: tumor grade


title: 18856

tag: tissue

tag: bmi

value: NON-HISPANIC

value: N

value: IV

tag: assumed progression free survival (months)


title: 23826

value: whole blood


title: WT-leaf_Rep2_RNAseq

value: Arabidopsis seedlings


title: 18935

tag: organ site

tag: race

tag: assumed overall survival (months)


title: tcx5/6-leaf_Rep1_RNAseq


title: 23824


title: 23800


title: WT-leaf_Rep1_RNAseq


title: 18572

tag: ethnicity

value: WT

value: WT - No Mut

tag: debulking


title: 17856

tag: age at diagnosis

value: Optimal

tag: patient survival


title: 23792

tag: age (years)


title: 17836

tag: height (inches)

tag: brca mutation status


title: 22211


title: 23796


title: 22139


title: 17834

tag: brca mutation description


title: 17133

tag: weight (pounds)


title: 16073

value: ASIAN

tag: cancer stage


title: 13295


title: 16075

tag: tumor grade


title: 9137

tag: tissue


title: 17816


title: 9127


title: 7725


title: 16059

tag: bmi


title: 6529-capture-2

tag: gender (null if unknown)

value: F


title: 16035

value: metastatic ovarian cancer

tag: organ site

tag: assumed progression free survival (months)


title: 16011

value: omentum

tag: race

tag: assumed overall survival (months)


title: 2650-capture-2


title: 2650-capture-1


title: 16008

value: CAUCASIAN

tag: ethnicity

tag: debulking

value: Progressive disease


title: 16014

tag: age at diagnosis

tag: patient survival


title: RNA-seq_tcx5/6;ddm1 Rep2

description: Expression.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR10 whole genome using HISAT-2.1.0 with default parameters
Fragments  Per Kilobase of exon per Megabase of library size (FPKM) were calculated using edgeR R package
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

value: seedlings

tag: genotype


title: 2623-capture-2

tag: age (years)


title: 6529-capture-1


title: RNA-seq_tcx5/6;ddm1 Rep1

description: Expression.txt


title: 2623-capture-1

description:
Dog_Capture2_MethylationFraction.txt
only used for replicate capture analysis, is a capture1 experiment, but added to the capture 2 file


title: 15813

value: Unknown

value: DWD-Died with Disease


title: 16001

tag: height (inches)

value: NON-HISPANIC

value: IIIC


title: RNA-seq_ddm1 Rep2

description: Expression.txt


title: RNA-seq_ddm1 Rep1

description: Expression.txt


title: 7936

description: removed from process filed due to low coverage

value: M


title: 15749


title: RNA-seq_tcx5/6 Rep2

description: Expression.txt


title: 15661


title: 7335

value: whole blood


title: RNA-seq_tcx5/6 Rep1

description: Expression.txt


title: 15636


title: RNA-seq_WT Rep2

description: Expression.txt

value: wild type


title: 7328


title: 15597

value: Suboptimal


title: 7295


title: 7153


title: 15520


title: RNA-seq_WT Rep1

description: Expression.txt


title: 15490

tag: brca mutation status

value: Mut

tag: brca mutation description


title: 7046


title: 15442

tag: cancer stage

tag: tumor grade


title: 7008

tag: tissue


title: 15407

value: Optimal


title: 15335


title: 15370

value: HISPANIC


title: 7007

tag: gender (null if unknown)

value: F


title: 6537


title: 15094

value: metastatic ovarian cancer

tag: organ site


title: 7935


title: 6750


title: 15078

value: omentum

value: IV

tag: assumed progression free survival (months)


title: 15030

tag: race

value: CAUCASIAN

value: UNKNOWN

value: WT

value: WT - No Mut

value: Progressive disease


title: 3696


title: 14964

value: NON-HISPANIC

tag: assumed overall survival (months)

value: DWD-Died with Disease


title: 5856

value: whole blood


title: 5866

value: M


title: 14959

value: Suboptimal

value: IIIC

value: Unknown


title: 3654


title: 3592


title: 14919

tag: ethnicity

value: Optimal


title: 3589


title: 3591

value: F


title: 3539


title: 14952

value: metastatic ovarian cancer

tag: debulking


title: 14577

value: omentum

tag: age at diagnosis

value: No recurrence to date

value: Alive


title: 3436


title: 14549

tag: weight (pounds)

tag: bmi

value: CAUCASIAN

value: IIC

tag: patient survival


title: 3328

tag: age (years)


title: 13294

tag: height (inches)

value: IIA


title: 13201

value: HISPANIC


title: 3352


title: 12955

value: BLACK

value: UNKNOWN

value: Progressive disease


title: 13121

value: NON-HISPANIC

tag: brca mutation status

value: WT

tag: brca mutation description

value: WT - No Mut


title: 3255

value: whole blood


title: 3220


title: 12760

value: Optimal

tag: cancer stage

value: IIIC

tag: tumor grade

value: DWD-Died with Disease


title: 12261

tag: tissue

value: metastatic ovarian cancer

value: omentum

value: ASIAN

value: Died during surgical procedure


title: 3151

tag: gender (null if unknown)

value: M


title: 3209


title: 12309

tag: organ site

value: CAUCASIAN

value: Mut

tag: assumed progression free survival (months)


title: 3054

value: F


title: 3073


title: 12190

tag: race

tag: assumed overall survival (months)


title: 3033


title: 12126

tag: ethnicity

tag: debulking

value: No recurrence to date

value: Alive


title: 2967


title: 12051

tag: age at diagnosis

tag: weight (pounds)

value: NON-HISPANIC


title: 3018


title: 896

value: IV

value: Unknown

tag: patient survival


title: 2928

tag: age (years)

value: whole blood


title: 2916


title: 12019

value: Optimal


title: 13629

value: UNKNOWN

value: WT

value: WT - No Mut

value: IIIC


title: 3274


title: 2927


title: 2862


title: 2849


title: 2810


title: 2776


title: 2755


title: 2888


title: 12245

value: metastatic ovarian cancer

value: omentum

value: DWD-Died with Disease


title: 2747

value: M


title: 2665


title: 2661


title: 2664


title: 2714


title: 2640


title: 2649


title: 2625


title: 2903


title: 2638


title: 2624


title: 2604


title: 2616


title: 2583


title: 2668


title: 2619


title: RIFA_40

city: Gimcheon

first: Mohammad

last: Vatanparast

address: 167, Yongjeon-ro

department: Plant quarantine technology center

institute: Animal and Plant Quarantine Agency

data_processing:
HiSeq 4000 System (Illumina, San Diego, USA) used for basecalling.
Quality-filtered and adapter-trimmed using Trimmomatic v0.38. FastQC v0.11.7 was used to check data quality before and after trimming. de novo transcriptome assembly was performed using Trinity version trinity rnaseq r20140717, bowtie 1.1.2. Trinity groups transcripts into clusters based on shared sequence content. For assembled genes, longest contigs of the assembled contigs are filtered and clustered into the non-redundant transcripts using CD-HIT version 4.6. ORF prediction for unigenes was performed using TransDecoder version 3.0.1. For the differentially expressed gene analysis, the abundances of unigenes across samples were estimated into read count as an expression measure by RSEM algorithm (RSEM version v1.2.29, bowtie 1.1.2.
Unigenes were searched against Kyoto Encyclopedia of Genes and Genomes (KEGG) v20190104 (http://www.genome.jp/kegg/ko.html), NCBI Nucleotide (NT) v20180116 (https://www.ncbi.nlm.nih.gov/nucleotide/), Pfam v20160316 (https://pfam.xfam.org/), Gene ontology (GO) v20180319 (http://www.geneontology.org/),  NCBI non-redundant Protein (NR) v20180503 (https://www.ncbi.nlm.nih.gov/protein/), UniProt v20180116 (http://www.uniprot.org/), and EggNOG (http://eggnogdb.embl.de/) using BLASTN of NCBI BLAST and BLASTX of DIAMOND version 0.9.21 (https://github.com/bbuchfink/diamond) with an E-value default cutoff of E-value 10-5.
Significant unigene results were analyzed as Up and Down-regulated count by log2FC ≥ 5, ≤ -5 and ≥10, distribution of expression level between two groups was plotted as Volcano plot and simple bar plots.
The twenty genes in response to cold treatment (T10) were chosen for validation using qRT-PCR. To do that, S. invicta adults were incubated at 10 and 30°C in two separated group including 10 ants, for 24 h.
Genome_build: de novo transcriptome
Supplementary_files_format_and_content: read counts, FPKM and folde change data

organism: Solenopsis invicta

source_name: RIFA

growth_protocol: Ant colonies were maintained at 25±1℃. Each test colony plastic trays were placed in larger holding trays. Talcum powder was dusted on 10 cm top edge of the trays and in the bottom of the larger holding trays so that any ants escaping would not happen and would not interfered other test colonies. Ants were fed with 20% sucrose solution and mealworm (Tenebrio molitor larvae) and an artificial diet

extract_protocol:
RNAs samples were extracted from whole body of S. invicta adults using Trizol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's instruction. After RNA extraction, it was resuspended in nuclease-free water and quantified using a spectrophotometer (NanoDrop, Thermo Scientific, Wilmington, DE, USA). cDNA was then synthesized from RNA (1 μg) using RT PreMix (Intron Biotechnology, Seoul, Korea) containing oligo dT primer according to the manufacturer's instruction. After RNA extraction, it was resuspended in nuclease-free water and quantified using a spectrophotometer (NanoDrop, Thermo Scientific, Wilmington, DE, USA). cDNA was then synthesized from RNA (1 μg) using RT PreMix (Intron Biotechnology, Seoul, Korea) containing oligo dT primer according to the manufacturer's instruction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: To perform transcriptomic analysis medium workers were incubated at 10, 20, 30 and 40℃ for 24 h as the temperature treatment groups. Incubated ants at 30℃ were considered as control group.

tag: strain

value: RIFA

tag: genotype

value: Wild type

tag: age

value: Adult ant

value: Whole body

tag: treatment


title: RIFA_10


title: RIFA_20


title: 2597


title: 2542


title: 2554


title: 2564


title: 2667

value: F


title: IF_neg_7

city: Cambridge

first: Fiona

last: Gribble

state: Cambridgeshire

address: Box 289 Addenbrooke's Hospital, Hills Road

department: Medical Research Laboratories

institute: University of Cambridge

description: Human ileal organoids Venus- in IF medium, sample 7

data_processing:
Sequenced reads were trimmed for adapter sequence and mapped to the primary human genome (GRCh38) using BBMap, and raw counts generated with featureCounts.
Differential gene expression modelling and normalised counts per million were generated using DESeq2.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text file includes raw count values for all samples.

source_name: Ileal organoids

growth_protocol: Organoids were routinely replated into BME domes (~20 ul) on uncoated plastic, and grown in IF medium supplemented with 50 ng/ml EGF until large organoids had formed (14-21 days). EGF was removed from culture medium, and organoids allowed to differentiate (10-14 days).

extract_protocol:
hGLU-Venus organoid samples showing Venus expression were dissociated to single cells, and stained with DAPI and DRAQ5. Live cells (DAPI-, and DRAQ5+) were FACS sorted into 2x populations (Venus+, and Venus-). RNA extraction and isolation were performed using RNAeasy Micro Plus kit (Qiagen). RNA concentration and quality (RIN 6-9) were assessed using RNA6000 Pico Kit and Bioanalyser 2100 (Agilent).
The library was constructed with 2 ng of input RNA using the SMARTer Stranded Total RNA-Seq v2 Pico Input Mammalian kit (Takara Bio).

treatment_protocol: For accelerated endocrine differentiation, organoid growth medium was changed to IF* for 3-5 days (Wnt3A conditioned medium reduced to 10%, plus addition of 10 uM DAPT and 100 nM PD0325901).

value: Ileal organoids

tag: growth medium

value: IF

tag: facs population

value: Venus-

tag: sample number


title: IF_Venus_7

description: Human ileal organoids Venus+ in IF medium, sample 7

tag: tissue

value: Venus+


title: IF_Venus_8

description: Human ileal organoids Venus+ in IF medium, sample 8


title: IF_neg_8

description: Human ileal organoids Venus- in IF medium, sample 8


title: 2500

tag: gender (null if unknown)

value: whole blood


title: 2489


title: 2519


title: IF_Venus_6

description: Human ileal organoids Venus+ in IF medium, sample 6


title: 2538


title: HC_Bruseq

city: Leiden

first: Pietro

last: Spitali

state: Zuid Holland

address: Postzone S4-P, Albinusdreef 2

department: Human Genetics

country: Netherlands

institute: Leiden University Medical Center

description: globin reduced

data_processing:
Library strategy: Bru-seq
alignment with bowtie2
unmapped reads follow a second alignment with STAR
Genome_build: hg38
Supplementary_files_format_and_content: BED format (alignment and expression file)

source_name: Bru-seq data

growth_protocol: Healthy control and DMD immortalized myoblasts were plated on 0.5% gelatin coated Petri dishes. Once the cells were 90% confluent, they were rinsed once with HBSS and induced to differentiate to myotubes.

extract_protocol:
Total RNA was isolated using TriPure reagent . Bru-labeled RNA was immunopurified using anti-BrdU antibodies conjugated to magnetic beads for 1h at room temperature
Truseq single end sequencing

treatment_protocol: After 3 days of differentiation, bromouridine was added to the medium [final concentration of 2 mM] at 37°C for 30 min.

tag: disease state

value: Healthy control

value: immortalized myotubes


title: DMD_Bruseq

description: globin reduced

value: Duchenne


title: 2613


title: 2569


title: RIFA_30


title: IF_neg_5

description: Human ileal organoids Venus- in IF medium, sample 5


title: IF_neg_6

description: Human ileal organoids Venus- in IF medium, sample 6


title: 2266


title: CT20

city: Chicago

first: Catherine

middle: Genevieve

last: Triandafillou

state: IL

address: 929 E 57th St

institute: University of Chicago

data_processing:
each sample was quantified with kallisto (version 0.43.0) using paired-end mode, 100 rounds of bootstrapping
output abundances were merged and tidied using R into final file 20-04-15_processed-bootstrapped-revisionseq-data.tsv
Genome_build: S288C transcriptome: kallisto index built from this transcriptome is file scer-r64-merged-transcripts.index. FASTA is included.
Supplementary_files_format_and_content: tab-separated value format; each row is a gene, each column is an experiment, both raw counts and transcripts per million are included for each sample

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae

growth_protocol: Cells were grown in liquid culture at 30 C with shaking until in mid-log (OD 0.3)

extract_protocol:
Cells were harvested by brief spin (3000 g for 1 min) and then flash-freezing. Total RNA was extracted using the Direct-zol kit from Zymo, with additional DNA removal by treatment with Turbo Dnase
Illumina TruSeq with no poly-A selection

tag: biological replicate

tag: translation state

value: blocked

tag: translation additive

value: 0% glucose

tag: media ph

tag: temperature


title: 2270


title: CT22

value: allowed

value: 2% glucose

value: unshocked


title: 2557


title: pH 7.4 shock rep2

data_processing:
data were de-multiplexed using the script SplitRNATagSeqFastQ.py allowing for a maximum of 1 nucleotide mismatch in barcodes
each sample was quantified with kallisto using the following command (items in <> braces represent local variables): kallisto quant -i scer-r64-merged-transcripts.index --single -b 100 -o <outfile name> -l 380 -s 100 -t 4 <fastq input file (sample)>
output abundances were merged and tidied using R into final file 17-11-09_processed-mRNAseq-data.tsv
Genome_build: S288C transcriptome: kallisto index built from this transcriptome is file scer-r64-merged-transcripts.index
Supplementary_files_format_and_content: 17-11-09_processed-mRNAseq-data.tsv; tab-separated value format; each row is a gene, each column is an experiment, both raw counts and transcripts per million are included for each sample

growth_protocol: Cells were grown in liquid culture at 30 C with shaking until in mid-log (OD 0.4)

extract_protocol:
Cells were harvested by filtration and flash-freezing. Samples were cryogenically lysed using steel balls; lysate was thawed and total RNA was extracted using ammonium acetate preciptation
RNA TagSeq (Shishkin 2015); see http://drummondlab.org/protocols/protocol/rnatagseq-library-prep for full protocol

tag: ph during stress

tag: ionophore treated

value: yes

tag: taqseq barcode

value: AAGTGCCG


title: IF_Venus_4

description: Human ileal organoids Venus+ in IF medium, sample 4


title: CT21


title: CT19

value: 2% glucose, 200 ug/mL cycloheximide


title: pH 6.8 shock rep2

value: AGAGGACC


title: IF_neg_4

description: Human ileal organoids Venus- in IF medium, sample 4

value: Ileal organoids


title: IF*_Venus_3

description: Human ileal organoids Venus+ in IF* medium, sample 3

value: IF*


title: IF*_neg_3

description: Human ileal organoids Venus- in IF* medium, sample 3

value: Venus-


title: 2477

tag: age (years)

value: M


title: unshocked rep2

value: no

value: CACGATGA


title: pH 7.4 shock rep1

value: CGATCCAG


title: IF*_neg_2

description: Human ileal organoids Venus- in IF* medium, sample 2


title: CT16


title: CT17


title: CT15


title: IF_Venus_5

description: Human ileal organoids Venus+ in IF medium, sample 5

value: IF

value: Venus+


title: IF*_Venus_1

description: Human ileal organoids Venus+ in IF* medium, sample 1


title: shocked rep1

value: GGCCGGTA


title: IF*_neg_1

description: Human ileal organoids Venus- in IF* medium, sample 1


title: unshocked rep1

value: GTTAGAAA


title: CT12

value: allowed

value: 2% glucose


title: CAR20_2

first: Tong

last: Chuan

state: Beijing

address: No. 28 Fuxing Road

department: Molecular Biology and Immunology

institute: Chinese PLA General Hospital

description: CD20 CAR_24h2

data_processing:
Read quality was checked for each sample using FastQC v0.11.3.
High-quality reads were then imported into TopHat v2.1.0 for alignment into BAM files.
Calculate gene expression levels using cufflinks  v2.2.1
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count or FPKM values for each Sample.

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were collected from patients by leukapheresis. Primary T cells derived from the PBMCs were activated using Dynabeads Human T-Activator CD3/CD28 magnetic beads (Invitrogen) at a 1:1 bead:cell ratio and cultured in X-VIVO 15 medium (Lonza) supplemented with 300 U/ml recombinant human IL-2 (PeproTech). After 2 days, RetroNectin-coated plates (Takara) were loaded with viral supernatants by centrifuging the plates at 2,000 g for 2 h at 32 °C. Activated T cells were added to the plates and centrifuged at 800 g for 10 min, and Polybrene (Sigma) was added to increase infection efficiency. The following day, the transduced cells were collected and transferred to new flasks for further expansion. The Dynabeads were magnetically removed 2 days after initiating T cell transduction, and the cells were cultured at 106 cells per ml in X-VIVO 15 medium supplemented with 300 IU/mL IL-2, with fresh IL-2-containing medium added every 2 days until the cells were harvested on days 8-10.

extract_protocol:
T cells were resuspended in 250ul PBS and placed in 750ul TRIzol LS (Invitrogen). RNA was extracted using the RNeasy Mini Kit (QIAGEN) according to the manufacturer’s protocol. Total RNA integrity was checked using the Bioptic Qsep100 (BIOptic) and quantified using a Synergy H1 (BioTek).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: CD19 CAR, CD20 CAR, and TanCAR7 T cells were cocultured with Raji cells for 24 h, followed by magnetic selection of CD3+ cells (Miltenyi Biotec).

tag: cell type

value: T cell

tag: genotype

value: T cells expressing CD20 CAR


title: CAR20_1

description: CD20 CAR_24h1


title: CT18

value: blocked

value: 2% glucose, 200 ug/mL cycloheximide


title: shocked rep2

value: ATGTTGTA


title: CAR19_2

description: CD19 CAR_24h2

value: T cells expressing CD19 CAR


title: CT11

value: unshocked


title: Hearts, M36_2

city: shanghai

first: Xuelian

last: Shao

address: yangpu district, songhu road

department: School of life science

institute: Fudan university

description: gene fpkm heart of 36-month-zebrafish

data_processing:
Illumina Casava 1.8 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCz11 whole genome using Hisat2 v2.0.5
Genome_build: GRCz11
Supplementary_files_format_and_content: excel files include FPKM values for each Sample

organism: Danio rerio

source_name: Heart

growth_protocol: Zebrafish were raised and maintained under standard conditions

extract_protocol:
Hearts were removed from zebrafish, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: heart

tag: age

value: 36 months


title: CT10

value: 0% glucose


title: Hearts, M36_1

description: gene fpkm heart of 36-month-zebrafish


title: IF*_Venus_2

description: Human ileal organoids Venus+ in IF* medium, sample 2

value: Ileal organoids

tag: growth medium

value: IF*

tag: facs population


title: CT9


title: Hearts, M24_3

description: gene fpkm heart of 24-month-zebrafish

tag: tissue

value: 24 months


title: CAR19_1

description: CD19 CAR_24h1


title: Tancar7_2

value: T cells expressing TanCAR7


title: CT8


title: pH 6.8 shock rep1

value: yes

value: CTTGGGCC


title: CT14


title: Hearts, M24_2

description: gene fpkm heart of 24-month-zebrafish


title: CT13

value: allowed

value: 2% glucose


title: CT6


title: Tancar7_1

value: T cell


title: CT7

value: blocked


title: Hearts, M24_1

description: gene fpkm heart of 24-month-zebrafish


title: Hearts, M12_2

description: gene fpkm heart of 12-month-zebrafish

value: 12 months


title: CT5


title: Hearts, M12_3

description: gene fpkm heart of 12-month-zebrafish


title: CT3

value: 2% glucose, 200 ug/mL cycloheximide


title: CT4


title: Hearts, M36_3

description: gene fpkm heart of 36-month-zebrafish


title: Hearts, M6_3

description: gene fpkm heart of 6-month-zebrafish

value: 6 months


title: Hearts, M12_1

description: gene fpkm heart of 12-month-zebrafish


title: CT2


title: Hearts, M6_2

description: gene fpkm heart of 6-month-zebrafish


title: CT1


title: RNA-WT-2_H5YLWDSXX_L1_1.fq.gz

status: Public on Jun 29 2020

first: Zunpeng

last: Liu

address: Beichen West Road

department: Institute of Zoology, Chinese Academy of Sciences

institute: State Key Laboratory of Stem Cell and Reproductive Biology

description:
RNA-seq of WT hMSCs.
RNA-seq of WT hMSCs.
RNA-WT-2.count.txt

data_processing:
Reads were trimmed to remove the adapter sequences and low quality bases.
Clean reads were aligned to hg19 human refference genome using bowtie2 or histat2 software.
Genome_build: hg19
Supplementary_files_format_and_content: Txt file of read count for RNA-seq. bw file fof RPKM normalized read cout for each 10 bp bin size for others sequencing data.

source_name: Mesenchymal stem cell

growth_protocol: Human MSCs (hMSCs) were cultured in MEMa (Thermo Fisher Scientific) medium supplemented with 10% fetal bovine serum (FBS, Thermo Fisher Scientific (Cat:10099-141, Lot:1616964)), 0.1 mM non-essential amino acids (Thermo Fisher Scientific), 1% penicillin/streptomycin (Thermo Fisher Scientific), and 1 ng/ml bFGF (Joint Protein Central, Incheon, Korea).

extract_protocol:
For DamID-seq, genomic DNA were isolated using DNeasy Blood & Tissue Kit (Qiagen). For ChIP-seq, DNA was isolated sing phenol-chloroform-isoamylalcohol extraction and ethanol precipitation. For RNA-seq, total RNA was extracted in TRIzol (Thermo Fisher Scientific) and genomic DNA was removed using a DNA-free kit (Thermo Fisher Scientific)
For ATAC-seq, library amplified and purified using TruePrep DNA Library Prep Kit V2 for Illumina(Vazyme Biotech). For DamID-seq, the DNA library was constructed using aNEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. For ChIP-seq, the enriched fragments were constructed into libraries without the incorporation of spike-in controls via KAPA Hyper Prep Kits with PCR Library Ampli?cation/Illumina series (KK8504) following the manufacturer’s instructions. For RNA-seq, sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.
DamID-seq, ATAC-seq, ChIP-seq, and RNA-seq

value: Mesenchymal stem cell

value: WT hMSCs

tag: passage


title: RNA-WT-3_H5YLWDSXX_L1_1.fq.gz

description:
RNA-seq of WT hMSCs.
RNA-seq of WT hMSCs.
RNA-WT-3.count.txt


title: RNA-SIRT7_KO-2_H5YLWDSXX_L1_1.fq.gz

description:
RNA-seq of SIRT7 deficient hMSCs.
RNA-seq of SIRT7 deficient hMSCs.
RNA-SIRT7_KO-2.count.txt

value: SIRT7 defecient hMSCs


title: RNA-SIRT7_KO-3_H5YLWDSXX_L1_1.fq.gz

description:
RNA-seq of SIRT7 deficient hMSCs.
RNA-seq of SIRT7 deficient hMSCs.
RNA-SIRT7_KO-3.count.txt


title: RNA-SIRT7_KO-1_H5YLWDSXX_L1_1.fq.gz

description:
RNA-seq of SIRT7 deficient hMSCs.
RNA-seq of SIRT7 deficient hMSCs.
RNA-SIRT7_KO-1.count.txt


title: ATAC-WT_rep3

description:
ATAC sequencing of WT hMSCs.
ATAC sequencing of WT hMSCs.


title: ATAC-WT_rep2


title: ATAC-WT_rep4_FKDL171553714-1A_1.fq.gz


title: ATAC-SIRT7_KO_rep_3_FKDL171553717-1A_1.fq.gz

description:
ATAC sequencing of SIRT7 deficient hMSCs.
ATAC sequencing of SIRT7 deficient hMSCs.


title: ATAC-SIRT7_KO_rep_4_FKDL171553718-1A_1.fq.gz


title: ATAC-SIRT7_KO_rep_2_FKDL171553716-1A_1.fq.gz


title: Input-WT_FKDL190746010-1a_1.fq.gz

description:
Input file corresponding to H3K9me4 ChIP-seq data of WT hMSCs.
Input file corresponding to H3K9me3 ChIP-seq data of WT hMSCs.
Input-WT.bw


title: ATAC-SIRT7_KO_rep_1_FKDL171553715-1A_1.fq.gz

description:
ATAC sequencing of SIRT7 deficient hMSCs.
ATAC sequencing of SIRT7 deficient hMSCs.
ATAC-SIRT7_KO.bw


title: H3K9me3_ChIP-WT_rep3

description:
H3K9me3 ChIP-seq of WT hMSCs.
H3K9me3 ChIP-seq of WT hMSCs.


title: H3K9me3_ChIP-SIRT7_KO_rep2

description:
H3K9me3 ChIP-seq of SIRT7 deficient hMSCs.
H3K9me3 ChIP-seq of SIRT7 deficient hMSCs.


title: H3K9me3_ChIP-WT_rep1

description:
H3K9me3 ChIP-seq of WT hMSCs.
H3K9me3 ChIP-seq of WT hMSCs.
H3K9me3_ChIP-WT.bw


title: H3K9me3_ChIP-SIRT7_KO_rep3


title: RNA-WT-1_H5YLWDSXX_L1_1.fq.gz

description:
RNA-seq of WT hMSCs.
RNA-seq of WT hMSCs.
RNA-WT-1.count.txt


title: Hearts, M6_1

description: gene fpkm heart of 6-month-zebrafish

value: heart


title: H3K9me3_ChIP-SIRT7_KO_rep1

description:
H3K9me3 ChIP-seq of SIRT7 deficient hMSCs.
H3K9me3 ChIP-seq of SIRT7 deficient hMSCs.
H3K9me3_ChIP-SIRT7_KO.bw


title: PCB1_IP

city: Woods Hole

first: Neelakanteswar

last: Aluru

state: MA

address: 45 Water Street

department: Biology

institute: Woods Hole Oceanographic Institution

data_processing:
Pre-processing using Trimmomatic
Remving ribosomal reads using bbduk
Mapping the reads using STAR aligner
Peak calling using macs14
Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis
Genome_build: Danio_rerio.GRCz11.96
Supplementary_files_format_and_content: tdf

source_name: 78 hpf embryos

extract_protocol: AB strain of zebrafish embryos were exposed to 10 nM PCB126 (3,3',4,4',5-pentachlorobiphenyl, 99.2% purity; UltraScientific, RI, USA) or DMSO (solvent control; 0.01%) starting at 72 hours post-fertilization (hpf) for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression after 6 hour exposure. In addition, short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution (pH 7.2). At the end of the exposure, embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.

tag: agent

tag: strain

value: AB

tag: fraction

value: m6A-immunoprecipitated sample

tag: antibody

value: m6A antibody - Synaptic Systems, catalog#202 003; RRID:AB_2279214


title: PCB3_IP

value: m6A antibody - Synaptic Systems, catalog#202 003; RRID:AB_2279216


title: PCB4_Input

value: input control


title: PCB3_Input


title: PCB2_Input


title: DMSO4_IP

value: DMSO control

value: m6A antibody - Synaptic Systems, catalog#202 003; RRID:AB_2279217


title: PCB1_Input


title: ATAC-WT_rep1

description:
ATAC sequencing of WT hMSCs.
ATAC sequencing of WT hMSCs.
ATAC-WT.bw


title: DMSO3_IP


title: DMSO1_IP


title: DMSO3_Input


title: DMSO4_Input


title: H3K9me3_ChIP-WT_rep2


title: DMSO1_Input


title: Input-SIRT7_KO_FKDL190746011-1a_1.fq.gz

description:
Input file corresponding to H3K9me3 ChIP-seq data of SIRT7 deficient hMSCs.
Input file corresponding to H3K9me3 ChIP-seq data of SIRT7 deficient hMSCs.
Input-SIRT7_KO.bw


title: CD4+ T cells, WT-72h-4

city: New Haven

first: Clara

last: Abraham

state: CT

address: 333 Cedar Street, 1080 LMP

institute: Yale University

description:
WT72h_0_treat_pileup.bw (bigwig file from MACS2 after merging bioreps)
WT72h_0_peaks.txt (MACS2 peak calling after merging bioreps)
WT72h_finalPeaks.txt (Final peaks for each condition)

data_processing:
ATAC-seq paired-end reads were trimmed using the Trim Galore (v0.5.0; http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)
The trimmed reads were then aligned to the mm10 reference genome using bowtie2 (v2.2.9, for samples of 100bp read length) (Langmead et al. 2009, Langmead et al. 2012).
Peaks were called using MACS2 for each biological replicate and the pool of biological replicates.
Peaks were annotated using HOMER (v4.10.4).
Genome_build: mm10
Supplementary_files_format_and_content: MACS2 peak calling results and bigwig file from MACS2

organism: Mus musculus

source_name: T cells

extract_protocol:
Nuclei were incubated in transposition mix (TD reaction buffer, Nextera Tn5 Transposase [Illumina] at 37oC for 30min and then purified with MinElute PCR purification (Qiagen)
Libraries were prepared with the Nextera XT DNA Library Preparation Kit (cat# FC-131-1001) according to manufacturer instructions and then purified with MinElute PCR purification (Qiagen).

tag: treatment

value: 72 hour activated


title: CD4+ T cells, WT-72h-3


title: PCB2_IP

value: m6A antibody - Synaptic Systems, catalog#202 003; RRID:AB_2279215


title: CD4+ T cells, WT-72h-2


title: CD4+ T cells, WT-0h-4

description:
WT0h_0_treat_pileup.bw (bigwig file from MACS2 after merging bioreps)
WT0h_0_peaks.txt (MACS2 peak calling after merging bioreps)
WT0h_finalPeaks.txt (Final peaks for each condition)

value: Untreated


title: PCB4_IP


title: CD4+ T cells, WT-0h-3


title: CD4+ T cells, WT-0h-1


title: CD4+ T cells, WT-72h-1


title: CD4+ T cells, WT-0h-2


title: CD4+ T cells, KO-72h-3

description:
KO72h_0_treat_pileup.bw (bigwig file from MACS2 after merging bioreps)
KO72h_0_peaks.txt (MACS2 peak calling after merging bioreps)
KO72h_finalPeaks.txt (Final peaks for each condition)


title: CD4+ T cells, KO-72h-2


title: CD4+ T cells, KO-72h-4


title: CD4+ T cells, KO-0h-4

description:
KO0h_0_treat_pileup.bw (bigwig file from MACS2 after merging bioreps)
KO0h_0_peaks.txt (MACS2 peak calling after merging bioreps)
KO0h_finalPeaks.txt (Final peaks for each condition)


title: DMSO2_IP


title: CD4+ T cells, KO-72h-1


title: CD4+ T cells, KO-0h-3


title: B16F0_Ribotag_RNASeq_rep1

city: New York

first: Bernardo

last: Tavora

state: NY

address: 1230 York Ave

institute: The Rockefeller University

description:
012914F2F0_CAGATC_L002_R1_001
ribosome-bound mRNA from B16F0 tumors
F10_F0_Ribotag_filtered_logFC
F10_F0_count_table.txt
F10_F0_count_table_norm.txt

data_processing:
trimming of adapter sequences with cutadapt v1.16
read alignment to mm10 mouse genome using STAR v2.2.1
generation of count files using featureCounts v1.6.0
differential gene expression with EdgeR in R v3.3.2
Genome_build: mm10

source_name: endothelial cells of B16F0 tumours

growth_protocol: Tumors were grown s.c. in Rpl22fl/flHA;Cdh5(PAC)-CreERT2 C57BL/6 mice for 12 days

extract_protocol:
Ribosome-bound mRNAs were isolated according to Sanz et al. (PNAS 2009)
RNA libraries were prepared using the ScriptSeq library preparation kit (Epicentre)

treatment_protocol: Mice were treated with Tamoxifen to activate Cre recombinase in endothelial cells

value: syngeneic tumour

tag: phenotype

value: poorly metastatic


title: B16F0_Ribotag_RNASeq_rep3

description:
041814MF0_GCCAAT_L001_R1_001
ribosome-bound mRNA from B16F0 tumors
F10_F0_Ribotag_filtered_logFC
F10_F0_count_table.txt
F10_F0_count_table_norm.txt


title: B16F0_Ribotag_RNASeq_rep4

description:
F0-1_TGACCA_L006_R1_001
ribosome-bound mRNA from B16F0 tumors
F10_F0_Ribotag_filtered_logFC
F10_F0_count_table.txt
F10_F0_count_table_norm.txt


title: B16F0_Ribotag_RNASeq_rep5

description:
F0-2_ACAGTG_L006_R1_001
ribosome-bound mRNA from B16F0 tumors
F10_F0_Ribotag_filtered_logFC
F10_F0_count_table.txt
F10_F0_count_table_norm.txt


title: DMSO2_Input


title: CD4+ T cells, KO-0h-1


title: B16F0_Ribotag_RNASeq_rep2

description:
030414FF0_TGACCA_L001_R1_001
ribosome-bound mRNA from B16F0 tumors
F10_F0_Ribotag_filtered_logFC
F10_F0_count_table.txt
F10_F0_count_table_norm.txt

growth_protocol: Tumors were grown s.c. in Rpl22/fl/flHA;Cdh5(PAC)-CreERT2 C57BL/6 mice for 12 days


title: B16F10_Ribotag_RNASeq_rep5

description:
F10-1_GCCAAT_L006_R1_001
ribosome-bound mRNA from B16F10 tumors
F10_F0_Ribotag_filtered_logFC
F10_F0_count_table.txt
F10_F0_count_table_norm.txt

source_name: endothelial cells of B16F10 tumours

growth_protocol: Tumors were grown s.c. in Rpl22fl/flHA;Cdh5(PAC)-CreERT2 C57BL/6 mice for 12 days.

extract_protocol:
Tibosome-bound mRNAs were isolated according to Sanz et al. (PNAS 2009)
RNA libraries were prepared using the ScriptSeq library preparation kit (Epicentre)

value: highly metastatic


title: B16F10_Ribotag_RNASeq_rep6

description:
F10-2_CAGATC_L006_R1_001
ribosome-bound mRNA from B16F10 tumors
F10_F0_Ribotag_filtered_logFC
F10_F0_count_table.txt
F10_F0_count_table_norm.txt

extract_protocol:
ribosome-bound mRNAs were isolated according to Sanz et al. (PNAS 2009)
RNA libraries were prepared using the ScriptSeq library preparation kit (Epicentre)


title: B16F10_Ribotag_RNASeq_rep4

description:
041814FF10_CAGATC_L001_R1_001
ribosome-bound mRNA from B16F10 tumors
F10_F0_Ribotag_filtered_logFC
F10_F0_count_table.txt
F10_F0_count_table_norm.txt

extract_protocol:
Ribosome-bound mRNAs were isolated according to Sanz et al. (PNAS 2009)
RNA libraries were prepared using the ScriptSeq library preparation kit (Epicentre).

treatment_protocol: Mice were treated with Tamoxifen to activate Cre recombinase in endothelial cells.


title: B16F10_Ribotag_RNASeq_rep7

description:
F10-3_GGCTAC_L006_R1
ribosome-bound mRNA from B16F10 tumors
F10_F0_Ribotag_filtered_logFC
F10_F0_count_table.txt
F10_F0_count_table_norm.txt


title: B16F10_Ribotag_RNASeq_rep3

description:
030414FF10_ACAGTG_L001_R1_001
ribosome-bound mRNA from B16F10 tumors
F10_F0_Ribotag_filtered_logFC
F10_F0_count_table.txt
F10_F0_count_table_norm.txt


title: B16F10_Ribotag_RNASeq_rep2

description:
012014MF10_TGACCA_L002_R1_001
ribosome-bound mRNA from B16F10 tumors
F10_F0_Ribotag_filtered_logFC
F10_F0_count_table.txt
F10_F0_count_table_norm.txt

treatment_protocol: Mice were treated with tamoxifen to activate Cre recombinase in endothelial cells


title: B16F10_Ribotag_RNASeq_rep1

description:
012014FF10_ACAGTG_L002_R1_001
ribosome-bound mRNA from B16F10 tumors
F10_F0_Ribotag_filtered_logFC
F10_F0_count_table.txt
F10_F0_count_table_norm.txt


title: Sample_NB_TET2_WT4

city: Farmington

first: Sheng

last: Li

address: 10 Discovery Drive

institute: The Jackson Laboratory

data_processing:
Raw reads were trimmed for truseq R1 adapter sequences using Flexbar.
Trimmed reads were mapped to the GRCm38.p3 reference genome using STAR (version 2.3.0e_r291) with the default parameters.
Read Counts per gene were computed using featureCounts (v1.5.1) tool from Subread package with the following parameters: -t "exon", -g "gene_name". GRCm38 Gencode was used as a reference gene annotation.
Genome_build: GRCm38
Supplementary_files_format_and_content: nbgcb.genecounts.txt file contain raw read counts per gene.

source_name: Naïve B-cells

growth_protocol: Cells were isolated from mouse spleens

extract_protocol:
RNA was extracted using Trizol and Qiagen Rneasy kit
Illumina's RNA-seq-TruSeq-stranded-mRNA

treatment_protocol: Not applicable

value: naive B-cells

value: spleen

value: TET2 Wild-Type


title: Sample_NB_TET2_WT3


title: Sample_NB_TET2_KO3

value: TET2 Knock-Out


title: Sample_NB_TET2_WT2


title: Sample_NB_TET2_KO2


title: Sample_NB_TET2_KO4


title: CpG+MPL lo 2

city: Saranac Lake

first: Deborah

last: Brown

state: New York

address: 154 Algonquin Ave

institute: Trudeau Institute

data_processing:
samples were demultiplexed to produce FASTQ files. The original FASTQ format reads were trimmed by fqtrim tool (https://ccb.jhu.edu/software/fqtrim) to remove adapters, terminal unknown bases (Ns) and low quality 3’ regions (Phred score < 30).
The trimmed fastq files were processed by our newly developed standard pipelines utilizing STAR as the aligner and RSEM as the tool for annotation and quantification at both gene and isoform levels.
Trimmed FASTQ files were then aligned to the Mus musculus reference genome and normalized expression levels in transcripts per kilobase million (TPM) for all available genes. Benjamini-Hochberg (BH)  adjusted p values were also provided to adjust for multiple-testing false discovery rate (FDR).
Genome_build: GRCm38.p6

source_name: bone marrow derived dendritic cells

growth_protocol: Femurs were flushed with PBS and resulting cells were cultured in 5 ml for 7-8 days in the presence 5 ng/ml granulocyte-macrophage colony-stimulating factor (GM-CSF). On days 3, 5, and 7 bone marrow cultures were fed by removing half of the media and replacing with fresh media containing 5 ng/ml GM-CSF. BMDC were treated on day 7 after culture. Cells were collected from 6 well plates by gentle washing, counted, and re-plated in 12 well plates at 2x106 cells in 1 ml total.

extract_protocol:
RNA was purified using the RNeasy mini kit
Sequencing libraries were generated by the UNMC Next Generation Sequencing Core beginning with 1 µg of total RNA from each sample using the TruSeq V2 RNA sequencing library kit from Illumina following recommended procedures
libraries were assessed for size of insert by analysis of an aliquot of each library on a Bioanalyzer instrument. Multiplexed libraries (15 samples per pool) were sequenced on a single NextSeq HighOutput Flowcell V2 75 cycle using the NextSeq500 DNA Analyzer (Illumina) to generate a total of approximately 37 million 75 bp single reads for each sample.

treatment_protocol: BMDC cultures at d7 were cultured with media alone (control), CpG at 0.2 µg/ml, MPL at 0.01 µg/ml, combination CpG+MPL at 0.2 µg/ml and 0.01 µg/ml (high dose) or 0.1 µg/ml and 0.005 µg/ml (low dose), respectively for 24 h

value: BALB/c

value: bone marrow

value: dendritic cell

value: CpG+MPL at 0.1 µg/ml + 0.005 µg/ml (CpG+MPL low)


title: CpG+MPL lo 1


title: CpG+MPL lo 3


title: MPL 3

value: MPL at 0.01 µg/ml


title: CpG+MPL hi 3

value: CpG+MPL at 0.2 µg/ml and 0.01 µg/ml (CpG+MPL hi)


title: MPL 1


title: CpG3

value: CpG at 0.2 µg/ml


title: MPL 2


title: CpG 1


title: CpG 2


title: CpG+MPL hi 1


title: Control 2

value: control


title: Control 3


title: AB5309

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description:
paired-end (read2 used to read cell and molecule barcodes only)
Note: Second read contained only cell and molecule barcodes. This information was appended to the fastq entry header

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

source_name: Lung metastases

growth_protocol: 8 to 13 weeks-old mice housed at the Weizmann Institute animal facility under specific pathogen-free conditions.

extract_protocol:
Normal mammary fat pad: Tissue was minced using scissors and placed and disrupted for 25 min at 37oC in a gentleMACS C tube using gentleMACS dissociator, in the presence of enzymatic digestion solution containing 1 mg ml-1 collagenase II, 1 mg ml-1collagenase IV and 70 unit ml-1 DNase. Primary tumor: Tissue was minced using scissors and treated with enzymatic digestion solution containing 3 mg ml-1 collagenase A and 70 unit ml-1 DNase in RPMI 1640 for 20 min at 37oC, with pipetting every 3 min. Lung metastases: Metastases bearing lungs were harvested and placed in gentleMACS C tubes with an enzymatic digestion solution containing collagenase A 1.5 mg ml-1, dispase II 2.5 unit ml-1 and DNase I 70 unit ml-1 in RPMI 1640. The tissue was disrupted for 30 min at 37oC using gentleMACS dissociator. Following dissociation, all tissues were washed, filtered through a 70 μm cell strainer and pelleted by centrifugation at 350 g, 5min, 4°C.
Single-cell RNA-seq libraries were prepared as previously described {Jaitin, 2014}. In brief, mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline. The pooled sample was linearly amplified by T7 in vitro transcription, and the resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during ligation, RT, and PCR. Each pool of cells was tested for library quality and concentration as described previously {Jaitin, 2014}

treatment_protocol: BALB/c females were injected under anaesthesia with 100,000 4T1-luc cells suspended in PBS, directly into the lower left mammary fat pad. To obtain CAFs from primary tumors, mice were sacrificed and tumors were immediately excised post mortem. To obtain CAFs from lung metastases, primary tumors were surgically removed under anesthesia 2 weeks after the injection. 2-3 weeks post primary tumor removal the animals were sacrificed, metastases bearing lungs were immediately excised and metastases were isolated from the lungs.

tag: Sex

value: female

value: Lung metastases

value: Non-immune stromal cells

tag: selection marker

value: Ter119- CD45- EpCAM-

value: Orthotopic breast injection of 4T1-luc cells; surgical removal of primary tumor

tag: time point

value: Five weeks after injection

tag: replicate id

value: Met rep. 2

tag: mouse age

value: 13 weeks


title: AB5308

tag: cell type


title: AB5109

value: Met rep. 1


title: AB5312

value: BALB/c

value: Met rep. 3


title: AB5310


title: AB5313


title: AB5311


title: Control 1A

value: bone marrow

value: dendritic cell


title: AB5108


title: AB4570

source_name: Breast tumor

value: Breast tumor

value: Orthotopic breast injection of 4T1-luc cells

value: four weeks after injection

value: 4W rep. 6

value: 12 weeks


title: AB5110

value: female

value: Lung metastases


title: AB4571

value: Non-immune stromal cells

value: Ter119- CD45- EpCAM-


title: AB4569


title: AB4566

value: 4W rep. 5


title: AB4567


title: CpG+MPL hi 2

value: CpG+MPL at 0.2 µg/ml and 0.01 µg/ml (CpG+MPL hi)


title: AB4564


title: AB4556

value: 4W rep .4


title: AB4565


title: AB4554

value: 4W rep. 3


title: AB4555

value: BALB/c


title: AB4553


title: AB3846

value: 4W rep .2


title: AB4551


title: AB3845


title: AB4552


title: AB3844


title: AB3842


title: AB3843


title: AB2677

value: 4W rep. 1


title: AB4563

value: two weeks after injection

value: 2W rep. 3

value: 10 weeks


title: AB2675

value: Breast tumor

value: Orthotopic breast injection of 4T1-luc cells

value: four weeks after injection


title: AB3841

value: female

value: 12 weeks


title: AB2676

value: Non-immune stromal cells


title: AB2674

value: Ter119- CD45- EpCAM-


title: AB2673


title: AB4561

value: 2W rep. 2


title: AB4568

value: 4W rep. 6


title: AB4558

value: 2W rep. 1


title: AB5083

source_name: Normal mammary fat pad

value: Normal mammary fat pad

value: Time zero

value: NMF rep. 3

value: 8 weeks


title: AB4560

value: BALB/c

value: two weeks after injection


title: AB4559

value: 10 weeks


title: AB4557

value: Breast tumor


title: AB5082


title: AB4562

value: Orthotopic breast injection of 4T1-luc cells

value: 2W rep. 3


title: AB5084

value: female


title: AB5081

value: NMF rep. 2


title: AB5079

value: Non-immune stromal cells


title: AB5076

value: Ter119- CD45- EpCAM-

value: NMF rep. 1


title: AB5077


title: AB5080


title: AB5078


title: sample.18_GFPnegEpCAMneg

description: Single end protocol R2 used for 8N UMI

data_processing:
Illumina bcl2fastq software used for basecalling.
Reads were trimmed using cutadapt (DOI: 10.14806/ej.17.1.200) (parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a “A{10}” –times 2 -u 3 -u -3 -q 20 -m 25).
Reads were mapped to genome/shareDB/iGenomes/Mus_musculus/UCSC/mm10/Sequence/STAR_index/ using STAR (DOI: 10.1093/bioinformatics/bts635) v2.4.2a (parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic, –alignSoftClipAtReferenceEnds No).
Read count was performed with HTSeq-count (DOI: 10.1093/bioinformatics/btu638) in union mode.
Further analysis is done for genes having minimum 5 read in at least one sample.
Normalization of the counts and differential expression analysis was performed using DESeq2 (DOI: 10.1186/s13059-014-0550-8) with the parameters: betaPrior=True, cooksCutoff=FALSE, independentFiltering=FALSE. Raw P values were adjusted for multiple testing using the procedure of Benjamini and Hochberg.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

source_name: GFP- EpCAM- tumor derived cells (from 4T1-GFP tumors)

extract_protocol:
Primary tumor was minced using scissors and treated with enzymatic digestion solution containing 3 mg ml-1 collagenase A and 70 unit ml-1 DNase in RPMI 1640 for 20 min at 37oC, with pipetting every 3 min. Lung metastases: Metastases bearing lungs were harvested and placed in gentleMACS C tubes with an enzymatic digestion solution containing collagenase A 1.5 mg ml-1, dispase II 2.5 unit ml-1 and DNase I 70 unit ml-1 in RPMI 1640. The tissue was disrupted for 30 min at 37oC using gentleMACS dissociator. Following dissociation, all tissues were washed, filtered through a 70 μm cell strainer and pelleted by centrifugation at 350 g, 5min, 4°C.
3' end mRNA libraries were prepared for sequencing using a method developed at Dr. Ido Amit's lab, Weizmann Institute of Science

treatment_protocol: 8 weeks old BALB/c females were injected under anaesthesia with 100,000 4T1-luc or 4T1-GFP cells suspended in PBS, directly into the lower left mammary fat pad. To obtain CAFs from primary tumors, mice were sacrificed and tumors were immediately excised post mortem.

value: Non-immune cells derived from primary tumor

value: Ter119- CD45- GFP- EpCAM-

value: Orthotopic breast injection of 4T1-GFP cells

value: four weeks after injection

value: 12 weeks


title: sample.21_GFPposEpCAMpos

description: Single end protocol R2 used for 8N UMI

source_name: GFP+ EpCAM+ tumor derived cells (from 4T1-GFP tumors)

value: Ter119- CD45- GFP+ EpCAM+


title: sample.19_GFPnegEpCAMpos

description: Single end protocol R2 used for 8N UMI

source_name: GFP- EpCAM+ tumor derived cells (from 4T1-GFP tumors)

value: BALB/c

value: Ter119- CD45- GFP- EpCAM+


title: sample.20_GFPposEpCAMneg

description: Single end protocol R2 used for 8N UMI

source_name: GFP+ EpCAM- tumor derived cells (from 4T1-GFP tumors)

value: Ter119- CD45- GFP+ EpCAM-


title: sCAF

description: Single end protocol R2 used for 7N barcode + 8N UMI concatenated to R1 header

source_name: PDPN- CAFs (from 4T1-luc tumors)

extract_protocol:
Normal mammary fat pad: Tissue was minced using scissors and placed and disrupted for 25 min at 37oC in a gentleMACS C tube using gentleMACS dissociator, in the presence of enzymatic digestion solution containing 1 mg ml-1 collagenase II, 1 mg ml-1collagenase IV and 70 unit ml-1 DNase. Primary tumor: Tissue was minced using scissors and treated with enzymatic digestion solution containing 3 mg ml-1 collagenase A and 70 unit ml-1 DNase in RPMI 1640 for 20 min at 37oC, with pipetting every 3 min. Lung metastases: Metastases bearing lungs were harvested and placed in gentleMACS C tubes with an enzymatic digestion solution containing collagenase A 1.5 mg ml-1, dispase II 2.5 unit ml-1 and DNase I 70 unit ml-1 in RPMI 1640. The tissue was disrupted for 30 min at 37oC using gentleMACS dissociator. Following dissociation, all tissues were washed, filtered through a 70 μm cell strainer and pelleted by centrifugation at 350 g, 5min, 4°C.
3' end mRNA libraries were prepared for sequencing using a method developed at Dr. Ido Amit's lab, Weizmann Institute of Science

value: Breast tumor

value: Ter119- CD45- EpCAM- PDPN-


title: 4T1_RNASeq_J2_pulldown_rep1

description:
RNA pulled down from cell line lysate with monoclonal dsRNA-specific J2 antibody
ERV_count_4T1_J2_pulldown.txt

data_processing:
quality trimming and adapter removal with cutadapt v2.3
read alignment to mm10 mouse genome using BWA v0.7
aligned reads were filtered: (i) number of clipped positions over the length of the read, and (ii) the edit distance over the number of matching positions (both ratios were required to be <2%)
filtered reads were assigned to mm10 ERVs annotations downloaded from UCSC (ERVs were filtered from the RepeatMasker track of the Variation and Repeats group using the repName filter) using featureCounts v1.6.0
differential gene expression with DESeq2 v1.22
Genome_build: mm10

source_name: cell line

growth_protocol: Standard tissue culture protocol with D10F medium

extract_protocol: RNA libraries were prepared using the NEBNext Ultra II Directional RNA Library Kit with the NEBNext rRNA Depletion Kit (Human/Mouse/Rat) (New England Biolabs)

tag: extraction protocol

value: cells were lysed with NP-40 Lysis Buffer supplemented with cOmplete EDTA-free protease inhibitor, passed through a G26 needle before centrifugation at 20,000 g at 4 C for 10 min. The rest of supernatant was diluted 5-fold using NET-2 buffer supplemented with 10 u of Turbo DNase (Ambion) and 10 mM of MgCl2. Protein A Dynabeads that were coupled with J2 or mouse IgG2a isotype-specific control antibody were added to the supernatant and rotated at 4°C for 2 hours. Beads were washed twice with NET-2 buffer,  twice with HSWB and another two times with NET-2 buffer. After all liquids were drained from the beads, RNAs were isolated from the beads using TRIzol and RNA Clean & Concentrator-5 (Zymo Research)

tag: sample type

value: pulled-down RNA

tag: molecule

value: immunoprecipitated RNA


title: 4T1_RNASeq_J2_pulldown_rep2


title: 4T1_RNASeq_input_rep1

description:
isolated from cell line lysate
ERV_count_4T1_J2_pulldown.txt

value: cells were lysed with NP-40 Lysis Buffer supplemented with cOmplete EDTA-free protease inhibitor, passed through a G26 needle before centrifugation at 20,000 g at 4 C for 10 min. RNA from 10% of supernatant (input) was set aside for RNA isolation using TRIzol-LS and Direct-zol Miniprep kit (Zymo Research)

value: input control

value: total RNA


title: 67NR_cellfreeRNASeq_ERV_rep3

description:
cell-free RNA isolated from poorly metastatic 67NR cell line
ERV_count-table_cfRNA
ERV_count-table_DE2-norm_cfRNA
4T0v67NR_cfRNA_ERV_logFC.txt
4T1v67NR_cfRNA_ERV_logFC.txt

data_processing:
quality trimming and adapter removal with cutadapt v2.3
read alignment to mm10 mouse genome using BWA v0.7
aligned reads were filtered: (i) number of clipped positions over the length of the read, and (ii) the edit distance over the number of matching positions (both ratios were required to be <2%)
filtered reads were assigned to mm10 ERVs downloaded from UCSC using featureCounts v1.6.0
differential gene expression with DESeq2 v1.22

source_name: conditioned media from cell culture

extract_protocol:
Cell-free RNA from conditioned meia was concentrated using a 10kDa Amicon Ultra-15 filter and subsequently isolated using the Norgen Biotek Plasma/Serum RNA Purification Mini Kit
RNA libraries were prepared using the TruSeq Stranded Total RNA Human/Mouse/Rat kit (Illumina)

tag: phenotype in vivo

value: poorly metastatic

value: cells were starved overnight in Opti-MEM prior to cell free RNA isolation


title: pCAF

source_name: PDPN+ CAFs (from 4T1-luc tumors)

value: female

tag: tissue

value: Non-immune stromal cells

value: Ter119- CD45- EpCAM- PDPN+

value: Orthotopic breast injection of 4T1-luc cells


title: 67NR_cellfreeRNASeq_ERV_rep1


title: 4T07_cellfreeRNASeq_ERV_rep3

description:
cell-free RNA isolated from poorly metastatic 4T07 cell line
ERV_count-table_cfRNA
ERV_count-table_DE2-norm_cfRNA
4T0v67NR_cfRNA_ERV_logFC.txt
4T1v4T0_cfRNA_ERV_logFC.txt


title: 4T1_RNASeq_input_rep2


title: 67NR_cellfreeRNASeq_ERV_rep2


title: 4T07_cellfreeRNASeq_ERV_rep2


title: B16F10_RNASeq_ERV_rep3

description:
total RNA isolated from highly metastatic B16F10 cell line
ERV_count-table_F0_F10
F10vF0_ERV_logFC.txt
ERV_count-table_DE2-norm_F0_F10

extract_protocol:
Total RNA isolation was performed with Norgen Biotek Total RNA isolation kit.
RNA libraries were prepared using the TruSeq Stranded Total RNA Human/Mouse/Rat kit (Illumina)

value: highly metastatic


title: 4T1_cellfreeRNASeq_ERV_rep2

description:
cell-free RNA isolated from highly metastatic 4T1 cell line
ERV_count-table_cfRNA
ERV_count-table_DE2-norm_cfRNA
4T1v67NR_cfRNA_ERV_logFC.txt
4T1v4T0_cfRNA_ERV_logFC.txt


title: 4T07_cellfreeRNASeq_ERV_rep1


title: 4T1_cellfreeRNASeq_ERV_rep1


title: 4T1_cellfreeRNASeq_ERV_rep3


title: NMF

value: BALB/c

value: Normal mammary fat pad

value: Ter119- CD45- EpCAM-

value: Time zero

value: 8 weeks


title: B16F10_RNASeq_ERV_rep2


title: B16F0_RNASeq_ERV_rep2

description:
total RNA isolated from poorly metastatic B16F0 cell line
ERV_count-table_F0_F10
F10vF0_ERV_logFC.txt
ERV_count-table_DE2-norm_F0_F10


title: B16F10_RNASeq_ERV_rep1


title: B16F0_RNASeq_ERV_rep1


title: 67NR_RNASeq_ERV_rep3

description:
total RNA isolated from poorly metastatic 67NR cell line
ERV_count-table_4T1_4T07_67NR
4T1v67NR_ERV_logFC.txt
4T0v67NR_ERV_logFC.txt
ERV_count-table_DE2-norm_4T1_4T07_67NR


title: 67NR_RNASeq_ERV_rep2


title: 4T1_RNASeq_ERV_rep1

description:
total RNA isolated from highly metastatic 4T1 cell line
ERV_count-table_4T1_4T07_67NR
4T1v4T0_ERV_logFC.txt
4T1v67NR_ERV_logFC.txt
ERV_count-table_DE2-norm_4T1_4T07_67NR


title: 67NR_RNASeq_ERV_rep1


title: 4T07_RNASeq_ERV_rep1

description:
total RNA isolated from poorly metastatic 4T07 cell line
ERV_count-table_4T1_4T07_67NR
4T1v4T0_ERV_logFC.txt
4T0v67NR_ERV_logFC.txt
ERV_count-table_DE2-norm_4T1_4T07_67NR


title: 4T1_RNASeq_ERV_rep2


title: 4T1_RNASeq_ERV_rep3


title: 4T07_RNASeq_ERV_rep3


title: 4T07_RNASeq_ERV_rep2


title: ECCITE-seq Arrayed GDO LENTI: THP-1

first: Efthymia

last: Papalexi

address: 101 avenue of americas

institute: New York Genome Center

data_processing:
library strategy:  ECCITE-seq (Expanded CRISPR-compatible CITE-seq)
CITE-seq and ECCITE-seq RNA reads were mapped to the human genome (hg19). Transcripts were quanitfied using CellRanger v2.1.0
ADT, HTO and GDO counts were quantified using CITE-seq-count (https://github.com/Hoohm/CITE-seq-Count)
Cells were demultiplexed into their experimental conditions after normalization (centered log ratio transformation, margin = 2) using the HTOdemux or MULTISeqDemux function in Seurat.
gRNA identitied were assigned using HTODemux unless otherwise specified in the methods section of the manuscript.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data provided as a TSV expression matrix where the rows correspond to genes (protein or guide names accordingly) and the columns to single cells.

source_name: Acute Myeloid Leukemia cell line THP-1

growth_protocol: For all scRNA-seq experiments: THP-1 cells were grown in RPMI +10% FBS media. Cells were spun down and resuspended in PBS 1X. Cell  viability was quantified using trypan blue.

extract_protocol: For the scRNA/CITE/ECCITE-seq experiment: a panel of antibodies (ADTs) was used to stain the cells according to the CITE/ECCITE-seq protocol. To identify cell doublets. and keep track of experimental conditions, we split cells into aliquots and stained each aliquot with a unique hashing (HTOs) antibody.  Samples were washed and recombined and loaded on a 10X genomics chip. 5prime 10X genomics was ran and the manufacturers protocols was followed for cDNA library generation. To recover HTOs, ADTs and GDOs we followed the CITE/ECCITE-seq protocol found here: https://cite-seq.com/protocol/.

treatment_protocol: To induce the expression of various immune checkpoint proteins cells were treated with Decitabine (Sigma-Aldrich A3656, 0.25μM) for three days, TGFβ1 for two days (Thermo Fisher Scientific PHG9204, 2.5ng/ml) and IFNγ for one day (R&D systems 284-IF-100, 10ng/ml).

tag: cell line

value: Acute Myeloid Leukemia cell line

tag: experiment type

value: ECCITE-seq Arrayed GDO LENTI


title: ECCITE-seq Arrayed ADT: THP-1

value: ECCITE-seq Arrayed ADT


title: ECCITE-seq Arrayed HTO1: THP-1

value: ECCITE-seq Arrayed HTO


title: ECCITE-seq Arrayed GDO CITE03: THP-1

value: ECCITE-seq Arrayed GDO CITE03


title: ECCITE-seq Arrayed HTO2: THP-1


title: ECCITE-seq Arrayed cDNA: THP-1

value: ECCITE-seq Arrayed cDNA


title: B16F0_RNASeq_ERV_rep3

value: poorly metastatic


title: VUB04-3-24h

city: Gent

first: Laurentijn

last: Tilleman

address: Ottergemsesteenweg 460

country: Belgium

institute: Ghent University

data_processing:
Adequate sequencing quality was confirmed using FastQC version 0.11.7 (Andrews, 2010).
To remove the “QuantSEQ FWD” adaptor sequence, the reads were trimmed using cutadapt version 1.15.
The trimmed reads were mapped to the human reference genome using the STAR aligning software v 2.5.3a.
The RSEM software, version v1.3.0, was used to generate count tables.
Genome_build: Homo sapiens GRCh38.89
Supplementary_files_format_and_content: tab-delimited text files include gene_id, transcirpt_id(s), gene length, effective_length, expected_counts, TPM an FPKM for each sample

source_name: hESC

growth_protocol: hESC cultured on Laminin-521 in Nutristem medium. Fed daily, passaged once a week in a 1:10 - 1:20 ratio. For mesendoderm differentiation, hESC treated with CHIR99021 and Activin A for 24h.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) with on-column DNase digest.
Illumina mRNA sequencing libraries were made from 500 ng total RNA of each sample using the QuantSeq 3' mRNA-Seq Library Prep Kit (Lexogen, Vienna, Austria) according to manufacturer's protocol. Fiveteen PCR cycles were used during the enrichment PCR. The size distribution, purity (absence of free adaptors) and quantity of the resulting libraries were measured using a High Sensitivity DNA chip (Agilent Technologies, Santa Clara, CA, US). The libraries were equimolarly pooled and sequenced in an Illumina Nextseq 500 high throughput flow cell, generating single-end 75bp reads.

value: hESC

tag: developmental stage

value: differentiated to mesendoderm for 24h


title: VUB04-5

value: undifferentiated


title: VUB04-2-24h


title: VUB04-5-24h


title: VUB04-2


title: VUB02-1-24h


title: VUB04-4


title: VUB02-3-24h


title: VUB04-1-24h


title: VUB04-3


title: VUB02-2-24h


title: VUB01-1-24h


title: VUB04-4-24h


title: VUB01-2-24h


title: VUB03-5


title: VUB01-2


title: VUB02-1


title: VUB02-2


title: VUB03-1


title: VUB03-3


title: VUB03-4


title: VUB04-1


title: HeLa_siZFC3H1_rep1_SLICCAGE

city: Copenhagen

first: Mengjun

last: Wu

address: Ole Maaløes Vej 5

country: Denmark

institute: University of Copenhagen

data_processing:
Library strategy: SLICCAGE
CAGE reads were trimmed to remove linker sequences at 5’ ends and incorrect ‘G’ calls at 3’ ends using cutadapt (version 1.14) with parameters -u 5 -m 30 --nextseq-trim=30 -l 70. Trimmed reads were filtered so that only reads with minimum sequence quality of 30 in at least 50% of the bases were kept. rRNAs were further removed using rRNAdust
Remaining reads were mapped to the human genome (hg19) using bwa (version 0.7.16a-r1181) with default settings.
The number of 5’ ends of CAGE reads were counted at each genomic position to give a unit of CAGE tag start site (CTSS), at single-base resolution. The raw counts were normalized to tags per million mapped reads (TPM) for subsequent quantification.
SLICCAGE bigwig files were generated using  UCSC Genome Browser Utility ‘bedGraphToBigWig’, the score represents strand-specific per-base genome coverage which was normalized to the library size
Genome_build: hg19

source_name: epitheloid cervix carcinoma cells

growth_protocol: HeLa Kyoto cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin

extract_protocol:
SLIC-CAGE preparation was performed as described in [47] with an input of 2000 ng of total RNA as starting material. Individually prepared SLIC-CAGE libraries with unique barcodes were pooled (8 per lane). The following 8 barcodes were used: # 1 (ACC), #2 (CAC), # 3 (AGT), # 4 (GCG), # 5 (ATG), # 6 (TAC), # 7 (ACG) and #8 (GCT). All used primers and adaptors were purchased from Integrated DNA technologies (IDT).
RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.

treatment_protocol: siRNA transfections (for SLIC-CAGE and TIF-seq) were carried out using lipofectamine 2000 (Invitrogen) according to the manufacturer’s protocol. Cells were treated with 20 nM siRNA for 4 days, including a re-transfection 2 days after the initial transfection.

value: HeLa Kyoto

tag: transfection


title: HeLa_siZFC3H1_rep2_SLICCAGE


title: HeLa_siZFC3H1_rep3_SLICCAGE


title: HeLa_siZCCHC8_rep1_SLICCAGE


title: HeLa_siZCCHC8_rep2_SLICCAGE


title: VUB03-2


title: HeLa_EGFP_rep1_TIFseq

data_processing:
Library strategy: TIFSEQ2
Sequencing reads were converted by using bcf2fastq and demultiplexed according to the indexes, allowing two mismatches in index 1 and one mismatch in index 2. TIF-seq2 sequencing primer and Illumina TruSeq adapter were removed using cutadapt. Then, 8-bp unique molecular identifiers (UMIs) were extracted with UMI-tools from the 5’ ends and extra adenine stretches in the 3’ ends were removed with cutadapt.
STAR were employed for aligning 5’-end reads and 3’-end reads separately to the human reference genome hg38, allowing maximum intron length as 1 Mb. A customised script adapted from UMI-tools was employed to remove PCR duplicates from uniquely mapped read pairs on the same chromosome, allowing 1-bp shifting in the 5’ ends. The hg38 genome coordinates were converted to hg19 using UCSC liftOver tool.
Paired 5' end and 3' end reads located on the same chromosome and opposite strand were used to form 5’-to-3' end TIF transcripts. To avoid 3' ends produced by spurious internal poly A priming by the oligo(dT) primer, the sequence immediately downstream of the 3' end of each TIF transcript was further examined. If the downstream sequence started with five or more contiguous adenines, or had seven or more adenines in the first 10 bp, the corresponding TIF transcript was removed from this analysis. To remove artificially long TIF transcripts, GENCODE v19 genes were merged into transcription units using merge from bedtools (v2.23.0)[56] with parameter -s, TIF transcripts overlapped with more than one transcription units were removed.
TIF-seq bed files were obtained by pairing 5' end and 3' end reads located on the same chromosome and opposite strand
Genome_build: hg19

extract_protocol:
We took 2.5 µg total RNA per sample as input. Input RNA was incubated with Turbo Dnase to prevent genomic DNA contamination. 5’ phosphomonoesters of RNA degradation intermediate was dephosphorylated by Alkaline Phosphatase, Calf Intestinal. The 5’Cap of mature RNA was removed by incubating with Cap-Clip(0.125U/µl)  to allow for ligation to RNA adaptor. Mature RNA was ligated overnight with single strand DNA_RNA chimeric adaptor and was purified with 1.8X Ampure XP beads. Purified mature RNA worked as the template for reverse transcription(RT) to generate the first-strand cDNA with custom barcoded oligo dT primers. RNA template was then removed by RNase H and RNase cocktail mixture. The first-strand cDNA then worked as the template for PCR amplification with TERA(Takara). PCR products from different samples are then pooled together with equal mass. The pooled PCR products were then subjected to NOT1 HF (NEB) endonuclease digestion. To favour intramolecular ligation, the PCR products with sticky ends were highly diluted to a final concentration less than 1ng/µl and ligated with a high concentration of T4 DNA ligase at 16 ˚C for at least 16 hours. To remove the unligated linear PRC products, plasmid-safe were added. The self-circularized cDNA was purified with phenol-chloroform. Circularized cDNA was fragmented by Covaris ME220 sonicator (Duration 240s, peak power 30, duty factor 10, Avg Power(W) 6). The fragments were then purified with 1X Ampure XP beads according to manufacturer instruction. As the fragment of 5’ and 3’ docking site are labelled with biotin, these specific fragments are selected via streptavidin beads by incubating with M280 streptavidin beads. The fragments of docking site were then subjected to end repair, dA tailing and ligation of the barcoded partially forked adaptor with a common sequence to anneal to each other and the grafting part to anchor to Illumina sequencer flowcells. After final amplification using Phusion High Fidelity Master Mix with PCR graft P5 and P7 as primers for 11 cycles, the library was ready to load onto the sequencer. The library is ready to load onto sequencer after purification with 1X Ampure beads according to manufacturer instruction. We used four custom sequencing oligos. We added 15Ts to illumine read1 sequencing oligo and named it as SeqR1+15T. The sequencing oligos for index1, index2 and read2(SeqR2) are exactly the same as Illumina oligos. We diluted the oligos according to manufacturer instruction. We made two mixtures of sequencing oligos. Mixture 1 was composed of SeqR1+15T and SeqR2 in a 1:1 ratio. Mixture 2 was composed of index1 and index2 sequencing primer in 1:1 ratio. The mixture 1 was loaded into both positions for both custom read1 and read2 primers on Illumina sequencing kit. The mixture2 was loaded on custom index primer position on sequencing kit. TIFSEQ2 library was denatured, diluted and loaded according to manufacturer instruction. We used the stand-alone configuration of the NextSeq 500 sequencing instrument. We checked read1, index1, index2 and read2 as custom sequencing oligos. For paired-end sequencing, we set as read1 76bp, read2 76bp, index1 6bp, index2 6bp.
RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.

value: GFP


title: HeLa_siRRP40_rep2_TIFseq


title: HeLa_EGFP_rep2_SLICCAGE


title: HeLa_EGFP_rep2_TIFseq


title: HeLa_EGFP_rep1_SLICCAGE


title: 1782163197_C87_G4

city: Stanford

first: Wanxin

last: Wang

address: James H Clark Center, 318 Campus Drive, room E300

institute: Stanford Univeristy

data_processing:
bcl2fastq v2.17.1.14 was used for demultiplexing and generating *.fastq.
Raw reads in the *.fastq files were trimmed to 75bp using fastqx,
duplicate-removed using picard MarkDuplicates, and
aligned to reference using STAR with default parameters.
Aligned reads were converted to counts using HTSeq.
Genome_build: Ensembl human reference genome GRCh38.87 (dna.primary_assembly)
Supplementary_files_format_and_content: comma separated file including HTSeq count for each cell

source_name: endometrium biopsy

extract_protocol:
Single cells were lysed using the reagents (Takara/Clontech) and default protocol for Fluidigm C1 mRNA Seq
RNA libraries were prepared for sequencing using Illumina Nextera-XT protocols for single cells

tag: time in menstrual cycle

value: endometrium biopsy

tag: donor condition

value: fertile healthy

tag: gender

value: female


title: 1782163197_C95_H11


title: 1782163197_C96_H10


title: 1782163197_C78_E10


title: 1782163197_C92_H5


title: 1782163197_C86_G5


title: 1782163197_C82_F12


title: 1782163197_C88_G12


title: HeLa_siRRP40_rep1_TIFseq


title: 1782163197_C83_F11


title: 1782163197_C90_G10


title: 1782163197_C76_E12


title: VUB01-1


title: HeLa_siZCCHC8_rep3_SLICCAGE


title: HeLa_EGFP_rep3_SLICCAGE


title: 1782163197_C68_D5


title: 1782163197_C73_E6


title: 1782163197_C94_H12


title: 1782163197_C74_E5


title: 1782163197_C70_D10


title: 1782163197_C93_H4


title: 1782163197_C67_D4


title: 1782163197_C91_H6


title: 1782163197_C75_E4


title: 1782163197_C63_C6


title: 1782163197_C61_C4


title: 1782163197_C60_B12


title: 1782163197_C59_B11


title: 1782163197_C56_B5


title: 1782163197_C54_A12


title: 1782163197_C52_A10


title: 1782163197_C53_A11


title: 1782163197_C50_A5


title: 1782163197_C45_H3


title: 1782163197_C47_H8