title: L150P, GC, Neu, Week7, RNA, S5 (total RNA)

status: Public on Jan 24 2023

data_processing:
instrument model: BGI DNBseq
Quality control with FastQC v0.11.5 and MutiQC v1.9
Pre-processing with Cutadapt v1.18 to remove adapter residues, reads with low quality, and reads excessively short after trimming (-q = 30, --pair-filter = any, min_length= "30")
Removal of residual rRNA annotated in SILVA v119.1 with BBDuk v38.22, minimum covered fraction = 0.5, kmer size = 31
Mapping with STAR v2.6.1d (1-pass)
StringTie v2.0 assembly and annotation extension (min tpm=1, min fpkm=1)
Gene quantification with featureCounts (subread v1.6.3), min overlap = 90 nt, min fraction overlap = 90%, fragment non-chimeric mapping. Merged GENCODE v33 and FANTOM-CAT annotations were provided, see supplementary file GENCODEv33-FANTOMCAT_merged_annotations.gtf.
Assembly: hg38
Supplementary files format and content: raw counts

source_name: hiPSC-derived glutamatergic cortical neurons

growth_protocol: Neural induction was initiated by changing the media into neural induction media containing 50% DMEM/F12 (Thermo Fisher Scientific, 11330057), 50% advanced neurobasal medium (Thermo Fisher Scientific, 21103049), 1% N2 (Thermo Fisher Scientific, 17502048), 1% B27 without retinoic acid (Thermo Fisher Scientific, 1258010), 1% Glutamax (Thermo Fisher Scientific, 35050061), 1% non-essential amino acid (NEAA, Thermo Fisher Scientific, 11140-050), 0,1% Pen/Strep (Sigma, P0781-100ML), supplemented with the inhibitors 10 μM SB431542 (SMAD inhibitor, SMS-gruppen, S1067) and 0,1 μM LDN193189 (Noggin analog, Sigma-Aldrich, SML0559).  The cells were maintained in induction media for 12 days with daily media change. On day 12 neural progenitor cells (NPCs) were passaged with Accutase (Thermo Fisher Scientific, A1110501) into neural expansion media containing growth factors 10 ng/ml FGF2 (ProSpec, CYT-557) and 10 ng/ml EGF (ProSpec, CYT-217) instead of the inhibitors. NPCs were expanded and banked. Following expansion, NPCs were plated onto Poly-L-Ornithine (PLO, Sigma-Aldrich, P4957)/laminin (Sigma-Aldrich, L2020- 1mg) coated dishes with a seeding density of 50 000 cells/cm2, and terminal neural differentiation was performed in neural maturation media, supplemented with 50 μM db-cAMP (Sigma Aldrich, D0627-100mg), 200 μM Ascorbic acid (Sigma Aldrich, A4403-100MG), 20 ng/ml BDNF (ProSpec, CYT-207) and 10 ng/ml GDNF (ProSpec, CYT-305).

extract_protocol:
RNeasy® Plus Mini Kit (Qiagen, 74134) according to the manufacturer’s protocol.
Library preparation and sequencing by BGI Hong Kong with DNBseq
PolyA and totalRNA-seq paired-end 2x100 nt, stranded

value: L150P - gene corrected

tag: development stage

value: 7 weeks

value: healthy


title: 17-CL1_shCTL_0hpi_3

status: Public on Mar 23 2023

type: SRA

city: DURHAM

first: ANKIT

last: GUPTA

address: TW 111 ALEXANDER DRIVE

department: RDBL

country: USA

institute: NIEHS

library_source: transcriptomic

data_processing:
Base calling was done with Guppy version 5.0.10.
Demultiplexing of barcoded oligos was done with Deeplexicon.
The alignment to the reference transcriptome was done with Minimap2 version 2.20.
The poly (A) tail length was determined with Nanopolish version 0.13.3.
Differential gene expression analysis was performed using DESeq2.
Supplementary files format and content: Comma separated value file wih polyA tail length, mapping transcript and replicate information for each read.

molecule: total RNA

organism: Mus musculus

source_name: 17-CL1 cells

growth_protocol: Mouse 17-CL1 cells were cultured in DMEM (Life Technologies) media supplemented with 10% Fetal Bovine Serum (FBS, Gemini Bio-Products), L-glutamine (Invitrogen), and Sodium pyruvate (Invitrogen). The 17-CL1 cells were cultured at 37ºC and in 5% CO2.

extract_protocol:
Total RNA was isolated with RNeasy Mini Kit (Cat. No. 74104, Qiagen)
5 µg of total RNA from 17-CL1 shCTL and shTUT4/7 knowckdown cells were used for each sample. Poly (A) containing mRNAs were enriched with Oligo(dT)25 Dynabead™ (61002, Thermo Fisher Scientific) and libraries were prepared using the Direct RNA Sequencing Kit (SQK-RNA002, Oxford Nanopore Technologies). All the libraries were multiplexed using the DeePlexiCon adapters, loaded to Nanopore R9 Flow Cells (FLO-MIN106D, Oxford Nanopore Technologies) and run on a MinION sequencer.

treatment_protocol: Cells were infected with 10 M.O.I. of MHV for different timepoints

tag: cell line

tag: genotype

value: shCTL

tag: treatment

value: Non-infected with mouse hepatitis virus

tag: viral strain

tag: duration

value: 0 hours


title: S1: MIX1441 day 1 (control)

status: Public on Feb 22 2023

city: Copenhagen

first: Christian

last: Anthon

address: Thorvaldsensvej 57

country: Denmark

institute: University of Copenhagen

description: MIX1441 day 1 (control)

data_processing:
QC with FastQC and trimmomatic
PCR bias reduction with Bbmap (first 7 bases of reads)
Mapping with segemehl
Identification of potential novel ncRNA with ANNOgesic + custom script
Expression analysis with featureCounts
Genome_build: (proprieatary genome sequence, part of bioproject)
Supplementary_files_format_and_content: DESeq2 normalized expressions

organism: Bacillus subtilis subsp. subtilis str. 168

growth_protocol: B. subtilis strain 168 ΔspoIIAC ΔamyE Δapr ΔnprE ΔsrfAC was maintained on LBPG medium at room temperature and not placed at 4 C. Two different substrains were generated, one with a codon-optimized α-amylase JE1 sequence (prsA+je1zyn), and one with the wild-type sequence (prsA+je1). The genomic sequences for both substrains were retrieved in a separate experiment by Novozymes A/S. If not indicated otherwise, strains were cultivated at 37 C in erythromycin (1 µg/ml)-supplemented triptone-yeast (TY) medium when appropriate. The bacterial enzyme production fermentations were conducted in duplicates in custom Novozymes made 5L tanks.

extract_protocol:
Samples were harvested by mixing 5 ml cell culture with 5 ml 100% ethanol, immediately storing on dry ice before transferring to -80°C. RNA was isolated using phenol-chloroform extraction.
Bacterial RNA library preparation was prepared from rRNA-depleted total RNA as described in https://doi.org/10.1002/cpnc.55
Single-end sequencing on an Illumina NextSeq 500. The read lengths were 76 bp.

tag: experimental group

value: control


title: L150P, GC, Neu, Week7, RNA, S4 (total RNA)

organism: Homo sapiens

tag: cell type

value: hiPSC-derived glutamatergic cortical neurons

tag: disease state


title: L150P, GC, Neu, Week7, RNA, S3 (total RNA)


title: L150P, GC, Neu, Week7, RNA, S2 (total RNA)


title: Indel-seq DIvA_4OHT_3

status: Public on Jul 03 2023

city: New York

first: Jaewon

last: Min

state: New York

address: 1130 St. Nicholas Ave

department: Pathology and Cell Biology (in the Institute for Cancer Genetics)

institute: Columbia University

library_source: genomic

data_processing:
The demultiplexing, barcoded processing
Assembly: hg19
Supplementary files format and content: bed
Supplementary files format and content: mcool
Library strategy: Indel-seq

molecule: genomic DNA

growth_protocol: U2OS cells were cultured in high-glucose DMEM supplemented with 10% FBS

extract_protocol:
gDNA extraction,Qiagen PureGene
Libraries were contructed using Indel-seq and Hi-C protocol

value: Cancer Cell line

value: WT


title: S2: MIX1442 day 1 (control)

description: MIX1442 day 1 (control)


title: L150P, Neu, Week7, RNA, S5 (total RNA)

value: L150P fAD

value: diseased


title: L150P, Neu, Week7, RNA, S4 (total RNA)


title: L150P, Neu, Week7, RNA, S3 (total RNA)


title: L150P, Neu, Week7, RNA, S1 (total RNA)


title: L150P, GC, Neu, Week7, RNA, S1 (total RNA)


title: A79V, GC, Neu, Week7, RNA, S4 (total RNA)

value: A79V - gene corrected


title: A79V, GC, Neu, Week7, RNA, S5 (total RNA)


title: A79V, GC, Neu, Week7, RNA, S3 (total RNA)


title: S7: MIX1443 day 3 (codon optimized)

description: MIX1443 day 3 (codon optimized)

value: codon optimized


title: S6: MIX1442 day 3 (control)

description: MIX1442 day 3 (control)


title: A79V, Neu, Week7, RNA, S5 (total RNA)

value: A79V fAD


title: A79V, GC, Neu, Week7, RNA, S2 (total RNA)


title: A79V, GC, Neu, Week7, RNA, S1 (total RNA)


title: A79V, Neu, Week7, RNA, S4 (total RNA)


title: A79V, Neu, Week7, RNA, S3 (total RNA)


title: L150P, GC, Neu, Week7, RNA, S5 (polyA RNA)

molecule: polyA RNA


title: L150P, GC, Neu, Week7, RNA, S3 (polyA RNA)


title: L150P, GC, Neu, Week7, RNA, S4 (polyA RNA)


title: A79V, Neu, Week7, RNA, S1 (total RNA)


title: L150P, GC, Neu, Week7, RNA, S2 (polyA RNA)


title: L150P, GC, Neu, Week7, RNA, S1 (polyA RNA)


title: L150P, Neu, Week7, RNA, S5 (polyA RNA)


title: L150P, Neu, Week7, RNA, S2 (polyA RNA)


title: A79V, GC, Neu, Week7, RNA, S5 (polyA RNA)


title: L150P, Neu, Week7, RNA, S1 (polyA RNA)


title: L150P, Neu, Week7, RNA, S2 (total RNA)


title: A79V, GC, Neu, Week7, RNA, S3 (polyA RNA)


title: A79V, GC, Neu, Week7, RNA, S4 (polyA RNA)


title: A79V, GC, Neu, Week7, RNA, S2 (polyA RNA)


title: A79V, Neu, Week7, RNA, S4 (polyA RNA)


title: A79V, Neu, Week7, RNA, S2 (polyA RNA)


title: A79V, Neu, Week7, RNA, S3 (polyA RNA)


title: A79V, GC, Neu, Week7, RNA, S1 (polyA RNA)


title: A79V, Neu, Week7, RNA, S1 (polyA RNA)


title: A79V, Neu, Week7, RNA, S2 (total RNA)


title: P864

status: Public on Jan 10 2023

city: La Jolla

first: Mariko

last: Horii

state: CA

address: 2880 Torrey Pines Scenic Dr

department: Pathology

institute: UCSD

data_processing:
Quality control was performed using FastQC (v. 0.11.3). Reads were mapped to GRCh38.89 (Ensembl) using STAR (v. 2.5.3a) (Dobin et al., 2013). The STAR parameters used were: --runThreadN 24 --sjdbOverhang 99 --genomeDir ref_ensembl_GRCh38_89/star_index --sjdbGTFtagExonParentGene gene_id --sjdbGTFfile ref_ensembl_GRCh38_89/Homo_sapiens.GRCh38.89.gtf --outSAMtype BAM Unsorted SortedByCoordinate --outReadsUnmapped Fastx --quantMode GeneCounts. Ensembl genes with at least 10 counts in 25% of samples were filtered for the analysis. Normalization and differential expression analysis were performed using R (v. 4.0.3) package DESeq2 (v. 1.30.1) (Love 2014). BiomaRt (v. 2.42.1) was used to convert Ensembl gene ID to HUGO gene names (Durinck 2009), and gene set enrichment analysis was done using R (v. 4.0.3) package FGSEA (v. 1.16.0).
Genome_build: GRCh38.89(Ensembl)
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample post filtering

source_name: Placental tissue

extract_protocol:
Total RNA was isolated using mirVana RNA Isolation Kit (ThermoFisher). RNA concentration was measured using Qubit RNA BR assay kit (ThermoFisher). RNA integrity was checked using RNA 6000 Nano chip read by Aligent 2100 bioanalyzer. All samples had a RIN above 7.0.
RNAseq libraries were prepared using the TruSeq Stranded Total RNA Sample preparation kit with Ribo-Zero Gold (Illumina).

tag: disease

value: Severe preeclampsia

tag: gender

value: Male

tag: sga

value: no


title: P1364

value: Non-hypertensive Control

value: yes


title: P1503


title: P1256


title: P1045

value: Female


title: P1430


title: L150P, Neu, Week7, RNA, S4 (polyA RNA)

value: 7 weeks


title: WT standard diet 1

status: Public on Nov 16 2022

city: Lausanne

first: David

last: Gatfield

address: Genopode building

department: Center for Integrative Genomics

country: Switzerland

institute: University of Lausanne

data_processing:
reads where trimmed from adapter sequence using cutadapt (ersion: 3.5; options: --match-read-wildcards --overlap 8 --discard-untrimmed --minimum-length 30) and quality filtered using faion: 0.0.14; options: -Q33 -q 30 -p 90)
UMIs were extracted from each read with UMItools (options: extract --extract-method string --bc-pattern NNNNNNNNCCCCC --3prime --filter-cell-barcode –error-correct-cell).
Reads where size-selected for single ribosome (monosomes; size 26 to 35). To estimate rRNA and tRNA contamination, reads were mapped to human and mouse rRNA and mouse tRNA databases using bowtie2 (options: -p 2 -L 15 -k 20 --trim5 2). Reads that failed to map to these, where then mapped to the mouse transcript database (Ensembl database v. 100).
Assembly: Ensembl transcript v100
Supplementary files format and content: Samples SGA files: tab delimited file reporting transcript ID, sample type, position, strand and read counts of predicted ribosome A sites.
Supplementary files format and content: codonCount.dat: tab delimited file with the following columns: Gene ID, transcript ID, codon position, read counts for each sample
Library strategy: Ribo-seq

source_name: liver

extract_protocol:
2 μg of RNA was separated and excised from a 15% urea-polyacrylamide gel. From the gel slices, RNA was extracted overnight at 4°C on a rotating wheel before precipitation in isopropanol during 3h at -20°C.
RNA3’-end repair was carried out with 2 U/μl of T4 PNK (Lucigen) prior to a 2h adaptor ligation at 25°C using 1.5 μl of ligase mix (3.3 U/μL of T4 RNA Ligase 1 (NEB), 66.6 U/μl of T4 RNA Ligase 2 Deletion Mutant (Lucigen) and 13.3 U/μL of riboguard (Lucigen)) and 1 uL of a 20 μM 5’-adenylated DNA adaptor (containing sample barcode and a 8N unique molecular identifiers (UMIs)). Adaptor removal was carried out by treating individual libraries with 2.7 U/μl of 5’deadenylase (NEB) and 5-5 U/μL of RecJ exonuclease (Lucigen) for 1h at 30°C and 1h at 37°C. Using Zymo Clean & Concentrator columns, samples were purified and pooled . Ribosomal RNA was depleted according to siTools Biotech rRNA depletion kit specifications with minor variations: 4 μl of a custom-made riboPOOL was used to deplete rRNA and the clean-up step was done using Zymo Clean & Concentrator columns

treatment_protocol: Standard and leucine-starved diets

tag: tissue

value: liver

value: Standard diet


title: WT Leucine deficient 1

value: Leucine deficient diet


title: L150P, Neu, Week7, RNA, S3 (polyA RNA)

value: hiPSC-derived glutamatergic cortical neurons


title: WT Leucine deficient 2

value: WT


title: WT standard diet 2


title: Input_Smchd1WT_MEF

status: Public on Jul 20 2022

city: Toyonaka

first: Koji

last: Nagao

state: Osaka

address: 1-1 Machikaneyama

department: Graduate School of Science

country: Japan

institute: Osaka University

data_processing:
Paired-end reads were trimmed to remove adaptor sequences using the cutadapt (Martin, 2011) and FLASH2 (Magoc and Salzberg, 2011) before mapping, and those with 50 bp were used as single-end reads for further analysis. The trimmed reads were mapped to B6-129S1/JF1 strain-specific diploid genome as described by Sakata et al. (Sakata et al., 2017) using bwa samse (Li and Durbin, 2009). Reads with low mapping quality (<20) were discarded to ensure that reads mapped to unique genomic positions were considered with confidence. Possible PCR duplicates were removed using samtools (Li et al., 2009). After inferring the haplotype for each cell line, we counted maternal-specific, paternal-specific, and all mapped reads separately in the ChIP and input samples in non-overlapping bins across the chromosome and expressed them as RPKM (reads per kilobase per million mapped reads). We calculated the enrichment ratio of the ChIP sample to the corresponding input defined as log2[(ChIP RPKM)/(input RPKM)]. Bins with RPKM < 0.1 for all mapped reads and RPKM < 0.02 for parental-specific reads were excluded as unmappable. Each profile of the ChIP enrichment was normalized to that of wild-type MEF so that the mode of the difference between the two autosomal profiles was 0. For each histone modification in each cell line, a single normalization factor was determined using the non-allelic profile of autosomal 50 kb bins and applied to any profiles regardless of a chromosome, bin size, or parental origin. The mode was estimated by the R package 'modeest.' To analyze the ChIP enrichment for each X-linked gene, we defined its gene body as a bin and excluded its length < 1 kb due to low read counts.
Assembly: mm9
Supplementary files format and content:
tab-delimited text file includes ChIP enrichment values defined as log2([ChIP RPKM]/[Input RPKM]) at each gene body on the inactive X chromosome for each sample.
bigWig file includes ChIP enrichment values defined as log2([ChIP RPKM]/[Input RPKM]).

source_name: MEF

extract_protocol:
ChIP was performed as described by Nozawa et al., (2013)
Libraries were generated using the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs) according to the manufacturer’s instructions. Size fractionation was carried out to enrich fragments of 100-300 bp from purified DNA for library preparation as well as the library around the size of 200 bp fragments after PCR amplification using AMPure XP (Beckman Coulter) magnetic beads.

tag: strain

value: C57BL6/J x (JF1 x C57BL6/J F1)

tag: developmental stage

value: MEF

value: Smchd1^+/+ Xist^deltaA/+

tag: Sex

value: female

tag: chip antibody


title: H3K9me3_Smchd1MD1_MEF

value: Smchd1^MD1/MD1 Xist^deltaA/+

value: H3K9me3 (mouse monoclonal; CMA318)


title: Input_Smchd1MD1_EpiSCs

source_name: EpiSCs

value: EpiSCs


title: H3K27me3_Smchd1WT_MEF

value: H3K27me3 (mouse monoclonal; CMA323)


title: A79V, Neu, Week7, RNA, S5 (polyA RNA)

value: A79V fAD

tag: development stage

value: diseased


title: H3K9me3_Smchd1WT_MEF


title: H3K27me3_Smchd1MD1_EpiSCs


title: Input_Smchd1WT_EpiSCs


title: H3K9me3_Smchd1MD1_EpiSCs


title: H3K27me3_Smchd1WT_EpiSCs


title: H3K9me3_Smchd1WT_EpiSCs


title: batch3-36_MIX1505_T5_je1zyn

status: Public on Jul 06 2022

data_processing:
Quality control with FastQC (version 0.11.8)
Pre-processing with trimmomatic (version 0.39) , 2 seed mismatch of BGI's adapter sequences, minimal 10bp overlap or 30bp palindormic overlap, sliding window 4bp PHRED quality 20, trailing quality 3 trimmed, minimal length 40 bp
Mapping against genomes with Segemehl (version 0.3.4, default settings)
Quanitfication with featureCounts (subread version 1.6.4, ≥50% overlaps).
Annotations from BSGatlas (version 1.1) and  additional putative ncNRAs (putative-ncRNA.bed)  from tiling-array study (Nicolas et al., 2012; Geissler et al., 2021)
Also include un-annotated regions (see file unannotated-regions.bed)
Genome_build: custom strain genomes (prsA-je1zyn.fna.gz and je1zyn.fna.gz)
Supplementary_files_format_and_content: uniquely_mapping-raw_counts

source_name: fed-batch fermentation

growth_protocol: Fed-batch AMY fermentation

extract_protocol:
phenol-chloroform RNA extraction
Library preparation and sequencing by BGI Hong Kong with DNBseq

value: control

tag: timepoint

value: timepoint 118h

tag: fermentation tank


title: batch3-35_MIX1504_T5_je1zyn

tag: genotype


title: batch3-34_MIX1503_T5_je1zyn


title: batch3-32_MIX1501_T5_prsA-je1zyn

value: PrsA over-expressing


title: batch3-33_MIX1502_T5_prsA-je1zyn


title: batch3-30_MIX1505_T4_je1zyn

value: timepoint 94h


title: batch3-28_MIX1503_T4_je1zyn


title: batch3-26_MIX1501_T4_prsA-je1zyn


title: batch3-31_MIX1500_T5_prsA-je1zyn


title: batch3-27_MIX1502_T4_prsA-je1zyn


title: batch3-29_MIX1504_T4_je1zyn


title: Input_Smchd1MD1_MEF


title: batch3-25_MIX1500_T4_prsA-je1zyn


title: batch2-23_MIX1504_T3_je1zyn

value: timepoint 71h


title: batch2-20_MIX1501_T3_prsA-je1zyn


title: H3K27me3_Smchd1MD1_MEF


title: batch2-22_MIX1503_T3_je1zyn


title: batch2-21_MIX1502_T3_prsA-je1zyn


title: batch2-19_MIX1500_T3_prsA-je1zyn


title: batch2-16_MIX1503_T2_je1zyn

value: timepoint 45h


title: batch2-15_MIX1502_T2_prsA-je1zyn


title: batch2-17_MIX1504_T2_je1zyn


title: batch2-18_MIX1505_T2_je1zyn


title: batch2-12_MIX1505_T1-2_je1zyn

value: timepoint 26h


title: batch2-14_MIX1501_T2_prsA-je1zyn


title: batch2-11_MIX1504_T1-2_je1zyn


title: batch2-10_MIX1503_T1-2_je1zyn


title: batch2-8_MIX1501_T1-2_prsA-je1zyn


title: batch2-7_MIX1500_T1-2_prsA-je1zyn


title: batch1-6b_MIX1505_T1-1_je1zyn

value: timepoint 21h


title: batch2-9_MIX1502_T1-2_prsA-je1zyn


title: batch2-13_MIX1500_T2_prsA-je1zyn


title: batch3-24_MIX1505_T3_je1zyn


title: batch1-5a_MIX1504_T1-1_je1zyn


title: batch1-4b_MIX1503_T1-1_je1zyn


title: batch1-2b_MIX1501_T1-1_prsA-je1zyn


title: batch1-3b_MIX1502_T1-1_prsA-je1zyn


title: batch1-2a_MIX1501_T1-1_prsA-je1zyn


title: batch1-5b_MIX1504_T1-1_je1zyn


title: batch1-6a_MIX1505_T1-1_je1zyn


title: subject7pre

status: Public on May 04 2022

city: Rochester

first: Yuanhang

last: Liu

state: MN

address: 200 1ST ST SW

institute: Mayo Clinic

data_processing:
After sequencing procedure, raw fastq files were processed through Mayo’s internal MAP-RSeq pipeline
Basically, the aligning and mapping of reads are performed using Star aligner against hg38 genome
The gene and exon counts are generated by FeatureCounts
Differential expression analysis was carried out using edgeR
Genome_build: hg38
Supplementary_files_format_and_content: norm_cpm.txt

source_name: skeletal muscle tissue

extract_protocol:
a percutaneous biopsy of the right vastus lateralis was performed under local anesthesia (2% lidocaine) using a modified Bergstrom needle. Muscle tissue was rapidly blotted with sterile gauze, weighed at the bedside, rapidly frozen in liquid nitrogen, and transferred to -80 freezer for storage
RNA was extracted from powdered muscle biopsy samples using the Qiagen RNeasy mRNA extraction kit

tag: subject

tag: group

value: obesepre


title: subject6pre


title: subject8pre


title: subject8post

value: obesepost


title: batch1-4a_MIX1503_T1-1_je1zyn


title: subject5pre


title: subject6post


title: subject7post


title: batch2-1_MIX1500_T1-1_prsA-je1zyn


title: subject5post


title: subject4pre

value: leanpre


title: subject1pre


title: subject3pre


title: subject4post

value: leanpost


title: subject3post


title: LuCaP_189.3_s2_ET1719_PDX_Tumor

status: Public on May 03 2022

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

data_processing:
Sequencing reads were mapped to the hg38 human genome and mm10 mouse genomes using STAR.v2.7.3a. Sequences aligning to the mouse genome deriving from potential contamination with mouse tissue were removed from the analysis using XenofilteR (v1.6).
Gene level abundance was quantitated using the GenomicAlignments summarizeOverlaps function using mode=IntersectionStrict, restricting to primary aligned reads, and counting reads mapping to the exonic regions of genes.
Assembly: hg38
Supplementary files format and content: Processed files are tab-delimited text files. Each file contains 7 columns: Entrez Gene ID, gene symbol, gene name, mRNA size, raw fragment count (by gene), FPM (fragments per million reads mapped) and FPKM (fragments per kilobase per million reads mapped).

source_name: LuCaP 189.3 PDX Tumor

growth_protocol: LuCaP xenograft lines were established from specimens acquired at either radical prostatectomy or at autopsy, implanted, and maintained by serial passage in intact immune compromised male mice (PMID: 28156002).

extract_protocol:
Total RNA was isolated from flash frozen LuCaP xenograft tissue with RNA STAT-60 (Tel-Test) followed by purification with RNeasy Mini Kit (Qiagen) utilizing the manufacturer’s recommended DNase digestion (Qiagen).
RNA-seq libraries were constructed from 1 ug total RNA using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit according to the manufacturer’s protocol.

value: male

value: prostate cancer

tag: molecular phenotype


title: batch1-3a_MIX1502_T1-1_prsA-je1zyn


title: LuCaP_189.4_s4_ET1650_PDX_Tumor

source_name: LuCaP 189.4 PDX Tumor

tag: cell type


title: LuCaP_189.4_s5_ET1825_PDX_Tumor


title: LuCaP_176_s5_ET1374_PDX_Tumor

source_name: LuCaP 176 PDX Tumor


title: LuCaP_174.1_s4_ET1549_PDX_Tumor

source_name: LuCaP 174.1 PDX Tumor


title: LuCaP_174.1_s4_ET1547_PDX_Tumor


title: LuCaP_173.2B_s9_ET2352_PDX_Tumor

source_name: LuCaP 173.2B PDX Tumor


title: LuCaP_189.3_s2_ET1603_PDX_Tumor


title: LuCaP_173.2_s2_ET292_PDX_Tumor

source_name: LuCaP 173.2 PDX Tumor


title: LuCaP_176_s5_ET1489_PDX_Tumor


title: LuCaP_173.2B_s11_ET2868_PDX_Tumor


title: LuCaP_173.1_s6_ET222_PDX_Tumor

source_name: LuCaP 173.1 PDX Tumor


title: LuCaP_173.2B_s12_ET3053_PDX_Tumor


title: LuCaP_173.2A_s12_ET2864_PDX_Tumor

source_name: LuCaP 173.2A PDX Tumor


title: LuCaP_173.2A_s9_ET2600_PDX_Tumor


title: LuCaP_173.2_s2_ET223_PDX_Tumor


title: subject2post


title: subject1post


title: LuCaP_170.2_s12_ET1999_PDX_Tumor

source_name: LuCaP 170.2 PDX Tumor


title: LuCaP_170.1_s5_ET2008_PDX_Tumor

source_name: LuCaP 170.1 PDX Tumor


title: LuCaP_167CR_s17_ET2791_PDX_Tumor

source_name: LuCaP 167CR PDX Tumor


title: LuCaP_173.1_s6_ET289_PDX_Tumor


title: LuCaP_170.3_s5_ET729_PDX_Tumor

source_name: LuCaP 170.3 PDX Tumor


title: subject2pre


title: LuCaP_167CR_s16_ET2551_PDX_Tumor


title: LuCaP_167_s16_ET1911_PDX_Tumor

source_name: LuCaP 167 PDX Tumor


title: LuCaP_147CR_s3_PDX_Tumor

source_name: LuCaP 147CR PDX Tumor


title: LuCaP_170.2_s9_ET1123_PDX_Tumor


title: LuCaP_170.1_s6_ET2317_PDX_Tumor


title: LuCaP_167_s8_PDX_Tumor


title: LuCaP_147CR_s23n2_ET2390_PDX_Tumor


title: LuCaP_147_p9s53n5_ET2061_PDX_Tumor

source_name: LuCaP 147 PDX Tumor


title: LuCaP_147_p9s37n4_PDX_Tumor


title: LuCaP_145.2_p9s25n3_PDX_Tumor

source_name: LuCaP 145.2 PDX Tumor


title: LuCaP_145.2_p9s26n3_PDX_Tumor


title: LuCaP_141_p2s44n4_PDX_Tumor

source_name: LuCaP 141 PDX Tumor


title: LuCaP_136CR_s4_2_PDX_Tumor

source_name: LuCaP 136CR PDX Tumor


title: LuCaP_141_p2s37n4_PDX_Tumor


title: LuCaP_105CR_s11_ET78_PDX_Tumor

source_name: LuCaP 105CR PDX Tumor


title: LuCaP_145.1_p2s18n5_PDX_Tumor

source_name: LuCaP 145.1 PDX Tumor


title: LuCaP_136_p8s42n8_ET783_PDX_Tumor

source_name: LuCaP 136 PDX Tumor


title: LuCaP_145.1_p25s19n5_PDX_Tumor


title: LuCaP_96CR_s41n1_ET2411_PDX_Tumor

source_name: LuCaP 96CR PDX Tumor


title: LuCaP_170.3_s10_ET2214_PDX_Tumor


title: LuCaP_105_s48n5_ET1755_PDX_Tumor

source_name: LuCaP 105 PDX Tumor


title: LuCaP_167CR_s15_ET2155_PDX_Tumor


title: LuCaP_105_s40n5_PDX_Tumor


title: LuCaP_105CR_s7_PDX_Tumor


title: LuCaP_96_p30s25n5_ET1110_PDX_Tumor

source_name: LuCaP 96 PDX Tumor


title: LuCaP_96_p18_PDX_Tumor


title: LuCaP_93_p39s22n6_PDX_Tumor

source_name: LuCaP 93 PDX Tumor


title: LuCaP_92_s64n12_ET2305_PDX_Tumor

source_name: LuCaP 92 PDX Tumor


title: LuCaP_96CR_s39n1_ET1173_PDX_Tumor


title: LuCaP_86.2CR_s3n1_PDX_Tumor

source_name: LuCaP 86.2CR PDX Tumor


title: LuCaP_92_s54n12_PDX_Tumor


title: LuCaP_86.2_s30_PDX_Tumor

source_name: LuCaP 86.2 PDX Tumor


title: LuCaP_86.2_s32n1_PDX_Tumor


title: LuCaP_136CR_s4_1_PDX_Tumor


title: LuCaP_86.2CR_s1_PDX_Tumor


title: LuCaP_136_p8s30n3_PDX_Tumor


title: LuCaP_81CR_s9_ET1092_PDX_Tumor

source_name: LuCaP 81CR PDX Tumor


title: LuCaP_81CR_s5_PDX_Tumor


title: LuCaP_81_s26n3_ET23_PDX_Tumor

source_name: LuCaP 81 PDX Tumor


title: LuCaP_81_s23n4_PDX_Tumor


title: LuCaP_78CR_s5_PDX_Tumor

source_name: LuCaP 78CR PDX Tumor


title: LuCaP_96CR_s40n1_ET1784_PDX_Tumor


title: LuCaP_78_p12s17n6_PDX_Tumor

source_name: LuCaP 78 PDX Tumor


title: LuCaP_77CR_s18n2_ET232_PDX_Tumor

source_name: LuCaP 77CR PDX Tumor


title: LuCaP_78CR_s2_PDX_Tumor


title: LuCaP_78_p12s23n6_ET1852_PDX_Tumor


title: LuCaP_77CR_s18n2_ET414_PDX_Tumor


title: LuCaP_93_p39s31n6_PDX_Tumor


title: LuCaP_77_p34s7_PDX_Tumor

source_name: LuCaP 77 PDX Tumor


title: LuCaP_73_p44s34n8_PDX_Tumor

source_name: LuCaP 73 PDX Tumor


title: LuCaP_77_p34s27n7_ET1177_PDX_Tumor


title: LuCaP_58_p54s40n9_ET1963_PDX_Tumor

source_name: LuCaP 58 PDX Tumor


title: LuCaP_70_p25s56n4_PDX_Tumor

source_name: LuCaP 70 PDX Tumor


title: LuCaP_73CR_s9n1_ET2068_PDX_Tumor

source_name: LuCaP 73CR PDX Tumor


title: LuCaP_70_p25s56n5_PDX_Tumor


title: LuCaP_35CR_s37_PDX_Tumor

source_name: LuCaP 35CR PDX Tumor


title: LuCaP_70CR_s6_PDX_Tumor

source_name: LuCaP 70CR PDX Tumor


title: LuCaP_35_p100s3_PDX_Tumor

source_name: LuCaP 35 PDX Tumor


title: LuCaP_73_p44s36n8_022213_PDX_Tumor


title: LuCaP_73CR_s4n1_020713_PDX_Tumor


title: LuCaP_35_P505s10_PDX_Tumor


title: LuCaP_70_p26s55n6_PDX_Tumor


title: LuCaP_70CR_s3_PDX_Tumor


title: LuCaP_58_p54s31n9_PDX_Tumor


title: LuCaP_35CR_s54_PDX_Tumor


title: LuCaP_35_p109s17n7_PDX_Tumor


title: LuCaP_49_p70s16n16_PDX_Tumor

source_name: LuCaP 49 PDX Tumor


title: S2_10

status: Public on Apr 13 2022

city: Tampa

first: Eric

last: Haura

state: FL

address: 12902 Magnolia Drive

institute: H. Lee Moffitt Cancer Center and Research Institute, Inc

data_processing:
The libraries were sequenced on the Illumina NextSeq 500 v2 sequencer with a 75-base paired-end run
Sequenced reads were trimmed for adaptor sequence with cutadapt, and mapped against reference genome hg19 using STAR v2.5.3a
Gene-level quantification was determined using HTSeq 0.6.1 by summation of raw counts of reads aligned to the region associated with each gene based on GENCODE v28.
Genome_build: hg19
Supplementary_files_format_and_content: CSV text files include normalized gene count for all samples.

source_name: Lung cancer cell line

growth_protocol: Cells were maintained in RPMI1640 media supplemented with 10% FBS and 1% antibiotic/antimycotic. Erlotinib-resistant cells were maintained in 100nM Erlotinib.

extract_protocol:
RNA was extracted using QIAGEN AllPrep RNA mini kit as per manufacturer’s protocol.
RNA-sequencing libraries were prepared using the NuGen FFPE RNA-Seq Multiplex System (Tecan US, Inc., Morrisville, NC). Briefly, 100 ng of DNase treated RNA was used to generate cDNA and a strand-specific library following the manufacturer’s protocol.Library molecules containing ribosomal RNA sequences were depleted using the NuGen AnyDeplete probe-based enzymatic process

tag: condition

value: Erlotinib resistant persister cell

value: Lung cancer cell line


title: LuCaP_23.1_p58s29n4_PDX_Tumor

source_name: LuCaP 23.1 PDX Tumor


title: LuCaP_23.1CR3_s9_ET2651_PDX_Tumor

source_name: LuCaP 23.1CR3 PDX Tumor


title: S1_34


title: Don3 PDAP1 IP

status: Public on Jan 10 2022

city: Bellinzona

first: Cristina

last: Leoni

state: Ticino

address: Via F. Chiesa 5

department: Molecular Immunology

institute: Institute for Research in Biomedicine

description: Total RNA

data_processing:
Quality control with using fastqc v. 0.11.5 and RSeQC v. 2.6.4
PCR duplicates were removed using UMI-Tools v1.1.1
Reads were mapped to the reference genome using HiSat2 v. 2.1.0
Counts generation by FeatureCounts v. 1.6.0
DE analysis DESeq2
Genome_build: Homo_sapiens.GRCh38.104

source_name: CD4+ human total memory

extract_protocol:
RNA extraction was performed using TRI reagent RT by MRC directly on agarose-streptavidin beads, followed by RNA column purification with Zymo spin kit from Zymo research.
RNA libraries were prepared for sequencing following CORALL Total RNA-Seq Library Prep Kit protocol.

value: Primary CD4 T cells

tag: treatment

value: Activated T cells

value: day 5 post-activation


title: S2_30


title: LuCaP_23.1_p58s26n7_PDX_Tumor

tag: gender


title: S2_17


title: LuCaP_23.1CR3_s10_ET2785_PDX_Tumor


title: PC9

value: parental cells


title: LuCaP_35CR_s59n1_PDX_Tumor


title: Don1 PDAP1 IP

description: Total RNA


title: Don2 PDAP1 IP

description: Total RNA


title: Don2 Input

description: Total RNA


title: Don3 Input

description: Total RNA


title: E08_MS273_218

status: Public on Nov 19 2021

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

institute: Kyoto University, Graduate school of medicine

description: Single cell transcriptome of amplified cDNA from cynomolgus monkey embryo at E08

data_processing:
All the reads were surveyed and the adaptor or the poly-A sequences were trimmed by cutadapt-1.3 with options "-e 0.1 -q 20 -n 2 -O 1 -m 30 -a CTCGAGGGCGCGCCGGATCC -g CTCGAGGGCGCGCCGGATCC -a AAAAAAAAAAAAAAAAAAAA -a TTTTTTTTTTTTTTTTTTTT". The trimmed reads with less than 30 bp were discarded.
Untrimmed and trimmed reads of 30 bp or longer were mapped onto the Cynomolgus monkey genome Macfac5.0 and the ERCC spike-in RNA sequences with tophat-1.4.1/bowtie1.0.1 with the “—no-coverage-search” option.
Mapped reads on the genome and the ERCC were separated, and the reads on the genome were converted into the expression levels by cufflinks-2.2.0 using the “—compatible-hits-norm”,  “—max-mle-iterations 50000", “—no-length-correction” and “—library-type fr-secondstrand” options and macfas5.0 reference gene annotations with extended TTSs. For the reference gene annotations used in cufflinks, we extended the TTSs of the reference genes up to 10 kb downstream to correctly estimate the expression levels of genes whose transcripts are longer than the reference toward the 3 prime.
Genome_build: Macaca fascicu;aris 5.0
Supplementary_files_format_and_content: tab-delimited text files *rpm.txt include RPM values (cufflinks) or *count.txt include Read counts (HTSeq) for each Sample

organism: Macaca fascicularis

source_name: Cynomolgus monkey embryo E08

growth_protocol: For cultivation of CMK6 and CMK9 cyESCs, they were cultured with conventional hESC medium [DMEM/F12 supplemented with 20% (vol/vol) of KSR, 1 mM of sodium pyruvate, 2 mM of GlutaMax, 0.1 mM of non-essential amino acids, 0.1 mM of 2-mercaptoethanol, 1000 U/ml of ESGRO mouse LIF, and 4 ng/ml of recombinant human bFGF] on mouse embryonic feeders (MEFs).

extract_protocol: For SC3-seq analysis, cDNA synthesis / amplification from single cells and library construction from the cDNAs were performed as described previously [Nakamura et al. 2015, NAR, 43, e60; Ishikura et al. 2016, Cell Reports, 17, 2789].

value: embryo

tag: sequencer

value: Nextseq550, High, 75 cycle


title: E08_MS273_204

tag: tissue


title: E08_MS273_214


title: E08_MS273_222


title: E08_MS273_215


title: Don1 Input

description: Total RNA


title: E08_MS273_220


title: E08_MS273_217


title: E08_MS273_202


title: E08_MS273_211


title: E08_MS273_212


title: E08_MS273_210


title: E08_MS273_206


title: LuCaP_23.1CR3_s7_ET1838_PDX_Tumor


title: E08_MS273_213


title: E08_MS273_203


title: E08_MS273_205


title: E07_MS257_217

description: Single cell transcriptome of amplified cDNA from cynomolgus monkey embryo at E07

source_name: Cynomolgus monkey embryo E07


title: E07_MS257_203


title: E07_MS257_216


title: E07_MS257_138


title: E07_MS257_135


title: E07_MS257_207


title: E07_MS257_204


title: E07_MS257_205


title: E08_MS273_219


title: E07_MS257_136


title: E08_MS273_201


title: E07_MS257_131


title: E07_MS257_130


title: E07_MS257_062


title: E07_MS257_051


title: E07_MS257_063


title: E07_MS257_049


title: E07_MS257_064


title: E07_MS257_068


title: E07_MS257_129


title: E07_MS257_060


title: E07_MS257_050


title: E07_MS257_048


title: E07_MS257_047


title: E07_MS257_046


title: E07_MS257_042


title: E07_MS257_134


title: E07_MS257_069


title: E07_MS257_026


title: E07_MS257_031


title: E07_MS257_030


title: E07_MS252_122


title: E07_MS257_029


title: E07_MS252_087


title: E07_MS257_028


title: E07_MS257_027


title: E07_MS257_035


title: E07_MS257_025


title: E07_MS252_127


title: E07_MS252_079


title: E07_MS252_082


title: E07_MS252_077


title: E07_MS252_085


title: E07_MS252_081


title: E07_MS257_033


title: E07_MS252_078


title: E07_MS252_061


title: E07_MS252_073


title: E07_MS252_058


title: E07_MS252_060


title: E07_MS252_063


title: E07_MS252_057


title: E09_MS099_025

description: Single cell transcriptome of amplified cDNA from cynomolgus monkey embryo at E09

data_processing:
All the reads were surveyed and the adaptor or the poly-A sequences were trimmed by cutadapt-1.3 with options "-e 0.1 -q 20 -n 2 -O 1 -m 30 -a CTCGAGGGCGCGCCGGATCC -g CTCGAGGGCGCGCCGGATCC -a AAAAAAAAAAAAAAAAAAAA -a TTTTTTTTTTTTTTTTTTTT". The trimmed reads with less than 30 bp were discarded.
Untrimmed and trimmed reads of 30 bp or longer were mapped onto the Cynomolgus monkey genome Macfac5.0 and the ERCC spike-in RNA sequences with tophat-1.4.1/bowtie1.0.1 with the “—no-coverage-search” option.
Mapped reads on the genome and the ERCC were separated, and the reads on the genome were converted into the expression levels (RPM) by cufflinks-2.2.0 using the “—compatible-hits-norm”,  “—max-mle-iterations 50000", “—no-length-correction” and “—library-type fr-secondstrand” options and macfas5.0 reference gene annotations with extended TTSs.
Mapped reads were also processed with HTSeq v0.11.0  to calculate number of read counts per gene.
For the reference gene annotations used in cufflinks and HTSeq, we extended the TTSs of the reference genes up to 10 kb downstream to correctly estimate the expression levels of genes whose transcripts are longer than the reference toward the 3 prime.
Genome_build: Macaca fascicu;aris 5.0
Supplementary_files_format_and_content: tab-delimited text files include RPM or raw count values for each Sample

source_name: Cynomolgus monkey embryo E09

extract_protocol:
For single cell isolation from cy pre-implantation embryos, a whole embryo was incubated with 0.25% trypsin/PBS  for around 10 min at 37℃, then dissociated into single cells by repeated pipetting, and dispersed in 0.1 mg/ml of PVA/PBS  for preparation of single-cell cDNAs.
For single cell isolation from cy post-implantation embryos, the implantation site was dissected out from the uterus and the embryonic fragment containing the epiblast (EPI), amnion, hypoblast, and yolk sac endoderm was isolated manually. The fragment was incubated with 0.25% trypsin/PBS for around 10 min at 37℃, then dissociated into single cells by repeated pipetting, and dispersed in 0.1 mg/ml of PVA/PBS.
For SC3-seq analysis, cDNA synthesis / amplification from single cells and library construction from the cDNAs were performed as described previously [Nakamura et al. 2015, NAR, 43, e60; Ishikura et al. 2016, Cell Reports, 17, 2789].


title: E08_MS219_098


title: E08_MS219_090


title: E08_MS219_089


title: E08_MS219_083


title: E08_MS219_082


title: E08_MS173_048


title: E07_MS252_083


title: E08_MS219_081


title: E08_MS173_049


title: E08_MS132_036


title: E08_MS130_073


title: E08_MS130_034


title: E08_MS130_030


title: E07_MS252_064


title: E08_MS130_037


title: E07_MS173_236


title: E08_MS130_029


title: Wild type Rep 2

status: Public on Oct 20 2021

city: Paris

first: Ashish

middle: Kumar

last: Singh

state: Ile-de-France

address: 25-28 Rue du Dr Roux

department: Development and Stem Cell Biology

country: France

institute: Institute Pasteur

data_processing:
Fastq files were demiltiplexed using Je demultiplex suite (Girardot et al., 2016).
For Mnase-Seq, paired-end reads were mapped to sacCer3 R64-1-1 genome using Bowtie2 ((Langmead and Salzberg, 2012) with default setting except -X 500, --no-discordant, --no-mixed options. For ATAC-Seq, default options were used.
Bam files were generated using samtools (Li et al., 2009). Mitochondrial and rDNA reads were removed from the bam files for MNase-Seq.
Nucleosome dyad coverage and bigWig files were generated using 140-160 bp reads and resizing to 50 bp at the dyad center for MNase-Seq.
Genome_build: R64-1-1 (sacCer3)
Supplementary_files_format_and_content: Signal intensity in bigWig file format

organism: Saccharomyces cerevisiae

growth_protocol: For anchor-away experiments, yeast strains were grown in YPAD media to OD 0.2-0.3 . For histone depletion experiments, cells were grown in SC + 2% galactose to OD 1.0. For deletion strains, cells were grown in YPAD to OD 1-0-2.0. For ATAC-seq, cells were grown to OD 0.4 in YPAD media.

extract_protocol:
Yeast nuclei was prepared according to (Almer and Horz, 1986). Cells were harvested  and incubated in 2 volume of preincubation solution (0.7 M ß-mercaptoethanol, 28 mM EDTA) for 25-30 mins. After washing with 1M sorbitol, cell wall was digested with Zymolyase. Spheroplasts were washed with 1M sorbitol and lysed with Ficoll buffer (18 % Ficoll, 20 mM KH2PO4 pH 6.8, 1 mM MgCl2, 0.25 mM EGTA, 0.25 mM EDTA). Nuclei was centrifuged and stored at -80 ̊C before use. For MNase digestion, nuclei was washed and dissolved in MNase digestion buffer (15 mM Tris-Cl pH 7.5, 50 mM NaCl, 1.4 mM CaCl2, 0.2 mM EGTA, 0.2 mM EDTA, 5 mM ß-mercaptoethanol). Equal volume of nuclei was digested with increasing amount of MNase for 20 mins at 37 ̊C. Reaction was stopped with 10 mM EDTA, 1% SDS and 50 mM Tris-Cl pH 8.5, followed by Proteinase K incubation for 30 mins at 37 ̊C. DNA was isolated by Phenol:Chloroform extraction and precipitation with 100% ethanol. Pellet was dissolved in TE buffer and RNA was removed with RNAse A incubation at 37 ̊C for 60 mins. DNA was precipitated with isopropanol, washed with 70% ethanol and dissolved in 50 μl TE. 25 μl DNA was loaded on 1.7% agarose gel and resolved for 4 hours at 2 V/cm. Appopriately digested sample with 70% mono-, 20% di- and 10% tri-nucleosome bands were used for library preparation without cutting mononucleosome band.
Libraries were prepared from whole MNase digested DNA. DNA fragments longer than 500 bp were removed using ampure size selection. 50 ng of size-selected DNA was used for library preparation with NEBNext Ultra II DNA Library Prep Kit, according to the manufacturer’s protocol. For PCR amplification step, 3 or 4 cycles were performed. Quality control on final libraries was performed using DNA 1000 Bioanalyzer and fragment length of ~270-280 bp was consistently observed, corresponding to ~150-160 bp insert length. Fro ATAC-seq, libraries were prepared using Nextera DNA Library Prep Kit in 25 ul reaction. Final fragment size of 100-600 bp were retained during Ampure purification.

treatment_protocol: For anchor-away background strains: Vehicle (90% ethanol, 10% Tween-20) or Rapamycin (1 μg/ml final concentration) dissolved in Vehicle. For histone depletion strain: Cells were washed with pre-warmed SC media and dissoved in SC media + 2% Galactose (control) or 2% Glucose (histone depletion).

tag: depletion or deletion

tag: protein tagged or deleted

tag: strain background

value: Wild type


title: Wild type Rep 1


title: E07_MS252_059

tag: developmental stage


title: RTT_ATACSeq_Rep2

status: Public on Jun 26 2021

city: Vienna

first: Anna

middle: Christina

last: Obenauf

address: Campus-Vienna-Biocenter 1

country: Austria

institute: Research Institute of Molecular Pathology

data_processing:
Adapters were trimmed (Trim Galore!), and trimmed reads aligned against mm10 using BWA.
Duplicates were marked (Picard) and normalized bigWig files scaled to 1 million mapped reads created (BEDTools, wigToBigWig)
Genome_build: mm10
Supplementary_files_format_and_content: BigWig file format with genome-wide ATACseq profiles.

source_name: RTT Braf/Pten tumor cells

growth_protocol: GFP+ Braf/Pten NTT and RTT celll lines  were injected into Rag2-/- mice. GFP+ cancer cells were sorted on Day 12 and immediately processed for ATAC-Seq library generation.

extract_protocol:
ATAC-seq was performed according to an adapted version adapted version of the Omni‐ATACseq protocol. Briefly, nuclei were isolated with nuclei isolation buffer (0.32 M sucrose, 3 mM CaCl2, 2 mM Mg Acetate, 0.1 mM EDTA, 10 mM Tris.HCl pH 8.0, 0.6% NP-40, 1mM DTT). After isolation, approximately 50,000 nuclei were resuspended in TD buffer with the Illumina Tn5 transposase (#15027865). The transposition reaction was performed at 37°C for 30 min. DNA fragments were purified from the reaction with the MinElute PCR purification Kit, Qiagen (# 28006) and amplified using the NEB Q5 High Fidelity PCR Mix (#M0492).
Library quality was assessed using a Fragment Analyzer system (Agilent). ATAC-seq libraries were quantified using a KAPA library quantification kit and sequenced on a NovaSeq instrument in 50 bp paired‐end mode.

tag: cell line name

value: Braf/Pten melanoma (YUMM1.7)

tag: drug


title: RTT_ATACSeq_Rep3


title: RTT_MEKi-128585.10184.LH14

description: Tumor cells were sorted in technical triplicates

data_processing:
Trimming was performed for QuantSeq 3' mRNA-Seq experiments (LH5, LH6, LH7, LH8, LH10, LH11, LH12) using BBDuk v36.92 (ref=polyA.fa.gz,truseq.fa.gz k=13 ktrim=r forcetrimleft=11 useshortkmers=t mink=5 qtrim=t trimq=10 minlength=30), and standard RNA-Seq experiments (LH1, LH2, LH4, LH14) using fastx-toolkit v0.0.13 (fastx_trimmer -f 13).
Reads mapping to mouse rRNA transcripts (refseq) were removed using bwa/0.7.12 alignment and samtools/1.3.1.
Remaining reads were aligned to mouse genome mm10 using TopHat v2.1.1 (GTF annotation file mm10, RefSeq from UCSC, 2015/01), and reads in genes were counted with htseq-count v0.6.1. Parameters for both tools were set dependent on the strandness of the experiments 1) for QuantSeq 3' mRNA-Seq experiments (LH5, LH6, LH7, LH8, LH10, LH11, LH12) tophat was run with parameter --library-type fr-secondstrand and htseq-count with -s yes 2) for RNA-Seq experiments (LH1, LH2, LH4) tophat was run with parameter --library-type fr-firststrand and htseq-count with -s reverse and 3) for SmartSeq libraries (LH9, LH13, LH14) tophat was run with parameter --library-type fr-unstranded and htseq-count with -s no
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_counts.txt: space-delimited text files with per gene read counts.

source_name: Braf/Pten RTT tumor cells

growth_protocol: Braf/Pten melanoma cells (NTT and RTT) were injected into Rag2-/- mice (CTRL group 3 days later). MEKi or control treatment was initiated and 72h after treatment start, size matched tumors were sorted.

extract_protocol:
Direct sorting into RNA lysis buffer.
Smart-seq2 protocol by Illumina, Nextera kit.
Illumina HiSeqV4 to obtain 50 bp single-end.

treatment_protocol: MEKi (0.5mg/kg Trametinib).

value: 72h MEKi

tag: tissue/cell type

value: Braf/Pten RTT tumor cells

tag: tumor cell label

value: GFP

tag: mouse number


title: RTT_MEKi-128583.10184.LH14


title: NTT_ATACSeq_Rep3

source_name: NTT Braf/Pten tumor cells


title: E08_MS219_086


title: NTT_ATACSeq_Rep2


title: RTT_MEKi-128584.10184.LH14


title: E08_MS173_038


title: RTT_MEKi-128582.10184.LH14


title: RTT_MEKi-128581.10184.LH14


title: RTT_MEKi-128580.10184.LH14


title: RTT_MEKi-128577.10184.LH14


title: RTT-128576.10184.LH14

value: CTRL


title: RTT_MEKi-128578.10184.LH14


title: RTT_MEKi-128579.10184.LH14


title: E08_MS130_035


title: RTT-128575.10184.LH14


title: RTT-128574.10184.LH14


title: RTT-128573.10184.LH14


title: RTT-128572.10184.LH14


title: RTT-128571.10184.LH14


title: NTT_MEKi-128566.10184.LH14

source_name: Braf/Pten NTT tumor cells

value: Braf/Pten NTT tumor cells


title: RTT_ATACSeq_Rep1


title: RTT-128568.10184.LH14


title: NTT_ATACSeq_Rep1


title: RTT-128570.10184.LH14


title: NTT_MEKi-128565.10184.LH14


title: NTT_MEKi-128564.10184.LH14


title: NTT_MEKi-128567.10184.LH14


title: NTT_MEKi-128563.10184.LH14


title: NTT_MEKi-128561.10184.LH14


title: NTT_MEKi-128559.10184.LH14


title: NTT_MEKi-128560.10184.LH14


title: NTT-128558.10184.LH14


title: NTT_MEKi-128562.10184.LH14


title: NTT-128556.10184.LH14


title: NTT-128557.10184.LH14


title: NTT-128554.10184.LH14


title: NTT-128555.10184.LH14


title: NTT-128553.10184.LH14


title: NTT-128551.10184.LH14


title: NTT-128550.10184.LH14


title: NTT-128552.10184.LH14


title: RTT-128569.10184.LH14


title: RTT_BrafPten_CTRL-99734.8494.LH12

data_processing:
Trimming was performed for QuantSeq 3' mRNA-Seq experiments (LH5, LH6, LH7, LH8, LH10, LH11, LH12) using BBDuk v36.92 (ref=polyA.fa.gz,truseq.fa.gz k=13 ktrim=r forcetrimleft=11 useshortkmers=t mink=5 qtrim=t trimq=10 minlength=30), and standard RNA-Seq experiments (LH1, LH2, LH4) using fastx-toolkit v0.0.13 (fastx_trimmer -f 13).
Reads mapping to mouse rRNA transcripts (refseq) were removed using bwa/0.7.12 alignment and samtools/1.3.1.
Remaining reads were aligned to mouse genome mm10 using TopHat v2.1.1 (GTF annotation file mm10, RefSeq from UCSC, 2015/01), and reads in genes were counted with htseq-count v0.6.1. Parameters for both tools were set dependent on the strandness of the experiments 1) for QuantSeq 3' mRNA-Seq experiments (LH5, LH6, LH7, LH8, LH10, LH11, LH12) tophat was run with parameter --library-type fr-secondstrand and htseq-count with -s yes 2) for RNA-Seq experiments (LH1, LH2, LH4) tophat was run with parameter --library-type fr-firststrand and htseq-count with -s reverse and 3) for SmartSeq libraries (LH9, LH13) tophat was run with parameter --library-type fr-unstranded and htseq-count with -s nomm10space-delimited text files with per gene read counts
Genome_build: mm10
Supplementary_files_format_and_content: space-delimited text files with per gene read counts

source_name: Sorted GFP+ tumor cells

extract_protocol:
For Quantseq and RNA-Seq RNA was isolated using the RNA-Easy Mini kit. For isolation from bulk tumors a trizol extraction step was included.
Libraries were generated using Quantseq and RNASeq library prep kits from Lexogen (Kit: Sense mRNA-Seq Library Prep kit, Quantseq 3' mRNA-Seq Library Kit), according to manufracturers instruction.

tag: sequencing type

value: Quantseq


title: RTT_BrafPten_MEKi-99739.8494.LH12

value: 1mg/kg Trametinib, 3d


title: RTT_BrafPten_CTRL-99735.8494.LH12


title: RTT_BrafPten_MEKi-99743.8494.LH12


title: RTT_BrafPten_MEKi-99742.8494.LH12


title: RTT_BrafPten_CTRL-99738.8494.LH12


title: RTT_BrafPten_CTRL-99737.8494.LH12


title: RTT_BrafPten_MEKi-99744.8494.LH12


title: RTT_BrafPten_CTRL-99736.8494.LH12


title: RTT_BrafPten_ACT_Tcell-99015.8443.LH13

description: Sorted 72h post transfer

source_name: Sorted CD3+ CD8+ T cells from tumour

value: Adoptive T cell transfer

value: Smartseq


title: RTT_BrafPten_ACT_Tcell-99012.8443.LH13

description: Sorted 72h post transfer


title: RTT_BrafPten_ACT_Tcell-99014.8443.LH13

description: Sorted 72h post transfer


title: RTT_BrafPten_ACT_Tcell-99009.8443.LH13

description: Sorted 72h post transfer


title: RTT_BrafPten_ACT_Tcell-99007.8443.LH13

description: Sorted 72h post transfer


title: RTT_BrafPten_ACT_Tcell-99005.8443.LH13

description: Sorted 72h post transfer


title: NTT_BrafPten_ACT_Tcell-99004.8443.LH13

description: Sorted 72h post transfer


title: NTT_BrafPten_ACT_Tcell-99002.8443.LH13

description: Sorted 72h post transfer


title: NTT_BrafPten_ACT_Tcell-99003.8443.LH13

description: Sorted 72h post transfer


title: NTT_BrafPten_ACT_Tcell-98999.8443.LH13

description: Sorted 72h post transfer


title: NTT_BrafPten_ACT_Tcell-99001.8443.LH13

description: Sorted 72h post transfer


title: NTT_BrafPten_ACT_Tcell-98997.8443.LH13

description: Sorted 72h post transfer


title: NTT_BrafPten_ACT_Tcell-99000.8443.LH13

description: Sorted 72h post transfer


title: NTT_BrafPten_ACT_Tcell-98998.8443.LH13

description: Sorted 72h post transfer


title: RTT_BrafPten_MEKi-99740.8494.LH12


title: RTT_BrafPten_MEKi-99741.8494.LH12


title: NTT_BrafPten_ACT_Tcell-98995.8443.LH13

description: Sorted 72h post transfer


title: RTT_BrafPten_ACT_Tcell-99016.8443.LH13

description: Sorted 72h post transfer


title: RTT_BrafPten_ACT_Tcell-99011.8443.LH13

description: Sorted 72h post transfer


title: NTT_BrafPten_ACT_Tcell-98994.8443.LH13

description: Sorted 72h post transfer


title: RTT_tumorBrafPten_vivo-73286.6659.LH10

value: Sorted GFP+ tumor cells


title: RTT.9dACT_tumorBrafPten_vivo-73299.6659.LH10


title: RTT_tumorBrafPten_vivo-73285.6659.LH10


title: RTT_BrafPten_ACT_Tcell-99006.8443.LH13

description: Sorted 72h post transfer


title: RTT.7dACT_tumorBrafPten_vivo-73291.6659.LH10


title: NTT_BrafPten_ACT_Tcell-98993.8443.LH13

description: Sorted 72h post transfer


title: RTT.9dACT_tumorBrafPten_vivo-73292.6659.LH10


title: RTT_tumorBrafPten_vivo-73287.6659.LH10


title: RTT.7dACT_tumorBrafPten_vivo-73298.6659.LH10


title: RTT.2.5dACT_tumorBrafPten_vivo-73290.6659.LH10


title: RTT.2.5dACT_tumorBrafPten_vivo-73288.6659.LH10


title: RTT.2.5dACT_tumorBrafPten_vivo-73289.6659.LH10


title: NTT_tumorBrafPten_vivo-73280.6659.LH10


title: NTT_tumorBrafPten_vivo-73281.6659.LH10


title: NTT.2.5dACT_tumorBrafPten_vivo-73284.6659.LH10


title: NTT_tumorBrafPten_vivo-73279.6659.LH10


title: NTT.2.5dACT_tumorBrafPten_vivo-73282.6659.LH10


title: NTT.2.5dACT_tumorBrafPten_vivo-73283.6659.LH10


title: RTT_immuneCD45_vivo-73296.6659.LH11

source_name: Sorted CD45+ cells from tumor

value: Sorted CD45+ cells from tumor


title: RTT_immuneCD45_vivo-73271.6659.LH11


title: RTT_immuneCD45_vivo-73272.6659.LH11


title: NTT_BrafPten_ACT_Tcell-98996.8443.LH13

description: Sorted 72h post transfer


title: RTT.9dACT_immuneCD45_vivo-73277.6659.LH11


title: RTT.7dACT_immuneCD45_vivo-73275.6659.LH11


title: RTT.9dACT_immuneCD45_vivo-73278.6659.LH11


title: RTT.7dACT_immuneCD45_vivo-73276.6659.LH11


title: RTT.2.5dACT_immuneCD45_vivo-73274.6659.LH11


title: RTT.2.5dACT_immuneCD45_vivo-73297.6659.LH11


title: RTT.2.5dACT_immuneCD45_vivo-73273.6659.LH11


title: NTT_immuneCD45_vivo-73266.6659.LH11


title: NTT_immuneCD45_vivo-73265.6659.LH11


title: NTT_immuneCD45_vivo-73267.6659.LH11


title: NTT.2.5dACT_immuneCD45_vivo-73270.6659.LH11


title: NTT.7dACT_immuneCD45_vivo-73294.6659.LH11


title: NTT.2.5dACT_immuneCD45_vivo-73269.6659.LH11


title: RTT_immuneCD103_vivo-85162.7622.LH9

source_name: Sorted CD11c+ CD103+ DCs from tumor

value: Sorted CD11c+ CD103+ DCs from tumor


title: NTT.7dACT_immuneCD45_vivo-73293.6659.LH11


title: RTT_immuneCD103_vivo-85151.7622.LH9


title: NTT.2.5dACT_immuneCD45_vivo-73268.6659.LH11


title: RTT_immuneCD103_vivo-85161.7622.LH9


title: RTT_immuneCD103_vivo-85153.7622.LH9


title: RTT_immuneCD103_vivo-85136.7622.LH9


title: RTT_immuneCD103_vivo-85160.7622.LH9


title: RTT.polyIC_immuneCD103_vivo-85158.7622.LH9

value: 50ug Poly I:C, 24h


title: RTT_immuneCD103_vivo-85145.7622.LH9


title: RTT_immuneCD103_vivo-85142.7622.LH9


title: RTT_immuneCD103_vivo-85152.7622.LH9


title: RTT_immuneCD103_vivo-85143.7622.LH9


title: RTT_immuneCD103_vivo-85138.7622.LH9


title: RTT_immuneCD103_vivo-85137.7622.LH9


title: RTT.polyIC_immuneCD103_vivo-85157.7622.LH9


title: RTT.polyIC_immuneCD103_vivo-85155.7622.LH9


title: RTT.polyIC_immuneCD103_vivo-85150.7622.LH9


title: RTT.polyIC_immuneCD103_vivo-85149.7622.LH9


title: NTT.7dACT_immuneCD45_vivo-73295.6659.LH11


title: RTT.polyIC_immuneCD103_vivo-85154.7622.LH9


title: RTT.polyIC_immuneCD103_vivo-85141.7622.LH9


title: RTT.polyIC_immuneCD103_vivo-85148.7622.LH9


title: RTT.polyIC_immuneCD103_vivo-85140.7622.LH9


title: NTT_immuneCD103_vivo-85132.7622.LH9


title: RTT.polyIC_immuneCD103_vivo-85139.7622.LH9


title: RTT_immuneCD103_vivo-85147.7622.LH9


title: RTT_immuneCD103_vivo-85146.7622.LH9


title: NTT_immuneCD103_vivo-85134.7622.LH9


title: NTT_immuneCD103_vivo-85131.7622.LH9


title: NTT_immuneCD103_vivo-85130.7622.LH9


title: NTT_immuneCD103_vivo-85127.7622.LH9


title: NTT_immuneCD103_vivo-85129.7622.LH9


title: NTT_immuneCD103_vivo-85128.7622.LH9


title: NTT_immuneCD103_vivo-85124.7622.LH9


title: NTT_immuneCD103_vivo-85126.7622.LH9


title: RTT_ct26_vitro-77791.6966.LH7

source_name: CT26 tumor cells in vitro

value: 10nM Trametinib

value: CT26 tumor cells in vitro


title: RTT_ct26_vitro-77792.6966.LH7


title: RTT_ct26_vitro-77790.6966.LH7


title: NTT_ct26_vitro-77786.6966.LH7


title: RTT.ifn_ct26_vitro-77793.6966.LH7

value: 10nM Trametinib, 10ng/ml IFN, 24h


title: RTT.ifn_ct26_vitro-77794.6966.LH7


title: NTT.ifn_ct26_vitro-77789.6966.LH7

value: 10ng/ml IFN, 24h


title: NTT_ct26_vitro-77784.6966.LH7


title: NTT_ct26_vitro-77785.6966.LH7


title: NTT_immuneCD103_vivo-85133.7622.LH9


title: NTT.ifn_ct26_vitro-77788.6966.LH7


title: RTT.ifn_ct26_vitro-77795.6966.LH7


title: NTT.ifn_ct26_vitro-77787.6966.LH7


title: NTT_immuneCD103_vivo-85135.7622.LH9


title: RTT_Braf/Pten_4SU_2h_MEKi3

data_processing:
3’ UTR annotations were assigned to Entrez GeneIDs and collapsed on a per-gene basis with the use of bedtools’ merge command. For genes lacking an annotated 3' UTR, Ensembl v84 3' UTRs were added (if available).
Adapters were trimmed from raw reads using cutadapt through the trim_galore (v0.3.7) wrapper tool with adapter overlaps set to 3bp for trimming.
Trimmed reads were further processed using SlamDunk v0.4.2, running the full analysis procedure (slamdunk all) and aligning against the mouse genome (GRCm38), trimming 12bp from the 5’ end, reporting up to 100 alignments for multi-mappers and activating the multi-mapper retention strategy, filtering for variants with a variant fraction of 0.2 and filtering for base-quality cutoff of ≥27. Remaining parameters were left to their defaults.
For gene-level analysis, raw reads mapped to different UTR annotations of the same gene were summed up by Entrez Gene ID
Genome_build: mm10
Supplementary_files_format_and_content: SlamDunk output containing UTR coordinates named by EntrezID, raw and normalized read counts, as well as T>C conversion statistics. For details see http://t-neumann.github.io/slamdunk/docs.html

source_name: RTT Braf/Pten cell lines

extract_protocol:
Fro SLAM-Seq cells were pre-treated with DMSO or MEKi for 30 min, then 4-SU was added and cells were harvested by snap-freezing cells after 90 min of labelling. RNA was extracted using RNAEasy mini kit (Qiagen), total RNA was alkylated and ethanol purified.
Libraries were generated using QuantSeq library prep kits from Lexogen (QuantSeq 3' mRNA-Seq Library Kit) using 500ng of RNA, according to manufracturers instruction.
QuantSeq

value: 100nM MEKi (2h) and 90 min 4-SU labelling

value: SlamSeq


title: RTT_ct26_vivo-77806.6966.LH8

source_name: CT26 bulk tumor

value: PBS

value: CT26 bulk tumor


title: RTT_ct26_vivo-77805.6966.LH8


title: NTT_ct26_vivo-77800.6966.LH8


title: NTT_ct26_vivo-77799.6966.LH8


title: RTT.polyIC_immuneCD103_vivo-85159.7622.LH9


title: RTT_Braf/Pten_4SU_2h_MEKi1


title: RTT_Braf/Pten_4SU_2h_DMSO3

value: DMSO and 90 min 4-SU labelling


title: RTT_ct26_vivo-77804.6966.LH8

value: Quantseq


title: NTT.on_ct26_vivo-77803.6966.LH8

value: 1mg/kg Trametinib, 3d


title: RTT_Braf/Pten_4SU_2h_DMSO1


title: RTT_Braf/Pten_4SU_2h_MEKi2


title: NTT.on_ct26_vivo-77802.6966.LH8


title: NTT_ct26_vivo-77798.6966.LH8


title: NTT_Braf/Pten_4SU_2h_MEKi2

source_name: NTT Braf/Pten cell lines


title: NTT.on_ct26_vivo-77801.6966.LH8


title: RTT_BrafPten_vitro-73.4503.LH1

source_name: Braf/Pten tumor cells in vitro

value: 100nM Dabrafenib

value: Braf/Pten tumor cells in vitro

value: RNASeq


title: NTT_Braf/Pten_4SU_2h_DMSO3


title: NTT_Braf/Pten_4SU_2h_MEKi1


title: NTT_Braf/Pten_4SU_2h_DMSO2


title: NTT_Braf/Pten_4SU_2h_DMSO1


title: RTT_BrafPten_vitro-59132.5569.LH2


title: RTT_BrafPten_vitro-02.4503.LH1


title: RTT_BrafPten_vitro-59136.5569.LH2


title: RTT_Braf/Pten_4SU_2h_DMSO2


title: NTT_BrafPten_vitro-59138.5569.LH2

value: DMSO, 48h


title: NTT_BrafPten_vitro-59130.5569.LH2


title: RTT.ifn_BrafPten_vitro-59137.5569.LH2

value: 100nM Dabrafenib, 10ng/ml IFN, 24h


title: NTT_BrafPten_vitro-25.4503.LH1


title: NTT.on_BrafPten_vitro-49.4503.LH1

value: 100nM Dabrafenib, 48h


title: RTT.ifn_BrafPten_vitro-59133.5569.LH2


title: NTT_Braf/Pten_4SU_2h_MEKi3


title: NTT.on_BrafPten_vitro-37.4503.LH1


title: NTT.ifn_BrafPten_vitro-59139.5569.LH2


title: NTT.ifn_BrafPten_vitro-59135.5569.LH2


title: NTT.on_BrafPten_vitro-61.4503.LH1


title: RTT.ifn_BrafPten_vitro-59141.5569.LH2


title: NTT_BrafPten_vitro-59134.5569.LH2


title: NTT.ifn_BrafPten_vitro-59131.5569.LH2


title: RTT_BrafPten_vitro-85.4503.LH1


title: NTT_BrafPten_vitro-01.4503.LH1


title: NTT_BrafPten_vitro-13.4503.LH1


title: RTT_BrafPten_vivo-52539.4954.LH4

source_name: Braf/Pten bulk tumor

value: Braf/Pten bulk tumor


title: RTT_BrafPten_vivo-52541.4954.LH4


title: RTT_BrafPten_vivo-52538.4954.LH4


title: NTT_BrafPten_vivo-305.4439.LH4


title: NTT_BrafPten_vivo-350.4439.LH4


title: NTT_BrafPten_vivo-304.4439.LH4


title: RTT_BrafPten_vitro-59140.5569.LH2


title: RTT_BrafPten_vivo-52540.4954.LH4


title: NTT.on_BrafPten_vivo-277.4439.LH4

value: Dabrafenib 30mg/kg 3d


title: NTT.on_BrafPten_vivo-74.4439.LH4


title: NTT.on_BrafPten_vivo-276.4439.LH4


title: NTT.ifn_Braf_vitro-77771.6966.LH5

source_name: Braf tumor cells in vitro

value: Braf tumor cells in vitro


title: RTT.ifn_Braf_vitro-77777.6966.LH5


title: NTT.ifn_Braf_vitro-77770.6966.LH5

value: 10ng/ml IFN, 24h


title: RTT.ifn.nsg_Braf_vitro-77783.6966.LH5

description: Derived from NSG mouse


title: NTT.ifn_Braf_vitro-77769.6966.LH5


title: RTT_Braf_vitro-77773.6966.LH5


title: RTT_Braf_vitro-77774.6966.LH5


title: RTT.nsg_Braf_vitro-77780.6966.LH5

description: Derived from NSG mouse


title: RTT.nsg_Braf_vitro-77778.6966.LH5

description: Derived from NSG mouse


title: RTT.ifn_Braf_vitro-77776.6966.LH5


title: RTT.nsg_Braf_vitro-77779.6966.LH5

description: Derived from NSG mouse


title: RTT_Braf_vitro-77772.6966.LH5


title: RTT.ifn.nsg_Braf_vitro-77782.6966.LH5

description: Derived from NSG mouse


title: RTT.ifn_Braf_vitro-77775.6966.LH5


title: RTT.ifn.nsg_Braf_vitro-77781.6966.LH5

description: Derived from NSG mouse


title: RTT_Braf_vivo-77813.6966.LH6

source_name: Braf bulk tumor

value: Braf bulk tumor


title: NTT_Braf_vitro-77767.6966.LH5


title: NTT_Braf_vitro-77766.6966.LH5


title: NTT_Braf_vivo-77808.6966.LH6


title: NTT_Braf_vivo-77807.6966.LH6


title: RTT_Braf_vivo-77797.6966.LH6


title: RTT_Braf_vivo-77796.6966.LH6


title: NTT.on_Braf_vivo-77812.6966.LH6


title: NTT_Braf_vivo-77809.6966.LH6


title: NTT.on_Braf_vivo-77811.6966.LH6


title: Y813140

status: Public on Jun 22 2021

city: Rockville

first: Tongwu

last: Zhang

state: MD

address: 9609 Medical Center Drive

department: Division of Cancer Epidemiology & Genetics

institute: National Cancer Institute

data_processing:
Illumina Casava1.7 software used for basecalling and The BCL (base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq
Sequenced reads were aligned using STAR(v2.7.3a) to human genomone (GATK resource bundle hg38)  with transcript annotation from GENCODE (release 35 based on GRCh38.p13). Quantification of transcripts was performed using RSEM(v1.3.2).
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: tab-delimited data matrix TPM quantified by RSEM for all samples,

source_name: Primary lung tumor

growth_protocol: mRNA was extracted from fresh frozen tumor tissues and correponding normal tissues.

extract_protocol:
Total RNA was isolated using a miRNeasy Mini kit (217004, Qiagen). To reduce melanin carryover, cell lysate in QIAzol reagent was heated at 65°C for 5 minutes before the addition of chloroform and phase separation.
Sequencing library was constructed following Illumina TruSeq Standard mRNA Library protocol for 151bp paired-end sequencing

value: lung

tag: tissue disease state

value: Primary lung tumor

tag: subject id

tag: patient diagnosis

value: lung cancer

tag: tumor subtype

value: Piano


title: Y813150

source_name: Normal lung tissue

value: Normal lung tissue


title: Y761150

value: Mezzo-forte


title: Y761140


title: Y719140


title: Y712150

value: Forte


title: Y719150


title: Y712140


title: Y695150


title: Y611150


title: Y695140


title: Y611140


title: Y591150


title: NTT_Braf_vitro-77768.6966.LH5

tag: treatment

value: Quantseq


title: Y600140


title: Y561140


title: Y591140


title: Y444150


title: Y561150


title: Y444140


title: Y408150


title: Y381140


title: NTT.on_Braf_vivo-77810.6966.LH6


title: Y345150


title: Y345140


title: Y408140


title: Y381150


title: Y339140


title: Y047150


title: Y105140


title: Y600150


title: Y018150


title: Y018140


title: Y105150


title: SC623144


title: SC623068


title: Y047140


title: SC623060


title: SC623136


title: SC623059


title: SC623049


title: SC623058


title: SC623027


title: SC623040


title: SC623067


title: Y339150


title: SC623035


title: SC623019


title: SC623011


title: SC623041


title: SC623018


title: SC623066


title: SC622996


title: SC622985


title: SC623004


title: SC622978


title: SC622977


title: CSP97544


title: GT01418-2003


title: CSP107359


title: CSP97513


title: CSP107355


title: SC623048


title: CSP107341


title: HPAEC si-FXN 5

status: Public on Apr 09 2021

city: Pittsburgh

first: Stephen

middle: Y

last: Chan

state: PA

address: 200 Lothrop Street

institute: University of Pittsburgh School of Medicine

data_processing:
Transcript alignment and quantification was performed using Salmon v1.4.0
Differential expression performed using DESeq2 v1.30.0
Genome_build: GRCh38
Supplementary_files_format_and_content: *.sf - tab delimited files for transcript quantification. Contains raw number of reads and TPM.

source_name: Lonza Primary Cells

growth_protocol: Pulmonary artery endothelial cells at passage 6 were plated in collagen-coated plastic 6-well plates and cultured to 70-80% confluency in endothelial growth media (Promocell).

extract_protocol:
Cells were lysed in Qiazol (Qiagen) and RNA extracted using Rneasy Mini Kit (Qiagen), according to the manufacturer’s instructions. Broad Range RNA Qubit quality control was also performed.
Total RNA sequencing (Paired-end read 75 cycles, 40-50M reads/sample) was run by the Health Sciences Sequencing Core (UPMC Children’s Hospital of Pittsburgh).

treatment_protocol: Transfection was performed using FXN-specific siRNA (40nM; sc-40580 Santa Cruz Biotechnology ) or scrambled negative control siRNA (40nM; sc-44236 Santa Cruz Biotechnology) with 1:500 Lipofectamine 2000 (Life Technologies) in one part OptiMEM (ThermoFisher) and three parts serum-starved endothelial growth media (PromoCell). Following 8 hours incubation, the transfection media was removed and replaced with full serum endothelial growth media. Experiment collection was performed 48 hours post-transfection.

tag: cell type

value: Primary human pulmonary artery endothelial cells

tag: passage

value: Passage 6

tag: Sex

value: Male

tag: age

value: 40nM FXN siRNA (sc-40580)


title: CSP107314

tag: tissue


title: HPAEC si-FXN 4


title: HPAEC si-FXN 6


title: SC623010


title: HPAEC si-NC 3

value: 40nM Negative control siRNA (sc-42236)


title: HPAEC si-NC 2


title: HPAEC si-NC 1


title: 8_GSK_100nM_d6_pig

status: Public on Sep 04 2020

data_processing:
library strategy: CUT&RUN
CUT&RUN data was analyzed utilizing the nf-core(Ewels et al. 2020) ChIPSeq pipeline(Wang et al. 2019) using the human genome hg38 and calling peaks in broad-peak mode.
Aligned reads of the individual replicates were merged using samtools v1.9(Li et al. 2009) and RPGC-normalized tracks were calculated and plotted as composite density plots using deeptools v3.1.2(Ramírez et al. 2016).
Genome_build: hg38
Supplementary_files_format_and_content: RPGC-normalized bigWig tracks

source_name: PeTa_GSK-LSD_guinea pig

growth_protocol: Cells were cultured as suspension cells in RPMI-1640 supplemented with 10% FBS, 2 mM L-glutamine, 50 U/mL penicillin and 50 mg/mL streptomycin.

extract_protocol:
CUT&RUN was performed according to the high-calcium/low-salt digestion protocol described previously (Meers et al. 2019).
The antibodies used in our CUT&RUN studies are anti-rabbit IgG isotype (ABIN101961, Antibodies online, 1:50), anti-H3K4me1 (C15410194, Diagenode, 1:50), anti-H3K27ac (ab4729, Abcam, 1:50) and anti-H3K27me3 (9733, CST, 1:50).
CUT&RUN libraries were prepared with the NEBNext® Ultra II DNA Library Prep Kit.

treatment_protocol: Cells were treated with 100 nM GSK-LSD1 for 6 days or DMSO.

value: PeTa

value: Merkel cell carcinoma cell line

value: GSK-LSD

tag: drug concentration

tag: antibody

value: guinea pig


title: H3K27ac_MNaseChIP_Villus

status: Public on Jan 16 2021

city: Piscataway

first: Michael

middle: P

last: Verzi

state: NJ

address: 145 Bevier Road

department: Genetics

institute: Rutgers, the State University of New Jersey

data_processing:
HiChIP-seq: Data were processed using the HiC-Pro pipeline, version 2.11.1.
HiChIP-seq: Reads were aligned to the mouse (mm9) genome assembly using bowtie2 (version 2.3.4.3) with mapping quality filter 15. HiC-Pro first performs global alignment using bowtie2 (--very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end –reorder) followed by local alignment (--very-sensitive -L 20 --score-min L,-0.6,-0.2 --end-to-end –reorder). Singleton, multi-mapped, and duplicate reads were removed. Reads were assigned to MboI restriction fragments using min and max size parameters of 100 and 100,000, respectively.
HiChIP-seq: HiC-Pro valid pairs were used as input for hichipper (version 0.7.0) to identify chromatin loops at regions known to contain active intestinal chromatin features, including promoter regions (identified by UCSC transcription start site +/- 2 kb). Active intestinal chromatin regions were defined from our data and public data sources of that empirically defined intestinal active chromatin regions, including ATAC-seq, DNase-seq, H3k4me3, H3K27ac and H3K4me3 ChIP-seq from intestinal stem, crypt, villus or intestinal epithelial cells.
MNase ChIP-seq: raw sequencing reads (fastq) were quality checked using fastQC (v0.11.3) and were further aligned to mouse (mm9) genomes using bowtie2 (v2.2.6) to obtain bam files.
MNase ChIP-seq: Deeptools bamCoverage (v2.4.2, duplicate reads ignored, RPKM normalized and extended reads) was used to generate bigwig files from bam files.
MNase ChIP-seq: Model-based Analysis of ChIP-Seq (MACS 1.4.1) was used for peak calling and to generate bed files from aligned reads.
ATAC-seq: Nextera transpose adapter reverse complement was removed from the 3’ end of the ATAC-seq reads using CutAdapt v1.9.1.
ATAC-seq: The trimmed FASTQ files were aligned to the mouse (mm9) genome using Bowtie2. The SAM files were converted into BAM files using the SAMtoBAM utility included in SAMtools v0.1.19. These BAM files were then sorted using the SortBAM utility included in SAMtools v0.1.19.
ATAC-seq: A BigWig file was generated for each sorted BAM file using the default parameters for the bamCoverage utility included in deeptools v2.4.2.
ATAC-seq:  A BED file was generated from each sorted BAM file using the BAMtoBED utility included in bedtools v2.17.0. The median insert size of each BED file was determined using the CollectInsertSizeMetrics utility included in the Picard v2.18.27 suite. Statistically significant enriched genomic regions (“peaks”) were identified from the BED files using MACS2 v2.1.0 with a 5’ shift of one-half the median insert length for each BED file.
Genome_build: mm9

source_name: WT adult jejunal villus cells

extract_protocol:
Freshly harvested jejunum was flushed with cold PBS, opened longitudinally, cut into 1 cm pieces, and then rotated in 3 mM EDTA in PBS for 5 mins, 10 mins and 40 mins at 4 °C (refresh EDTA/PBS every time). The tissue was then violently shaken to release the epithelium from underlying muscular tissue. The intestine pieces were discard and the supernatant was collected as whole epithelium fraction. 70-μm cell strainer was used to separate the villi and crypt fractions. Villi were collected from the top of a 70-μm cell strainer, while crypts passed through. Cells were pelleted by centrifugation at 170g at 4 °C, and followed by cold PBS wash. For Micrococcal nuclease (MNase) ChIP-seq, mouse villi and crypts were isolated as describe above, and resuspended in digestion buffer (50 mM Tris-HCl pH7.6, 1 mM CaCl2, 0.2% Triton X-100, 5 mM Na butyrate, and protease inhibitor cocktails) and treated with MNase for ChIP-seq, with histone H3K27Ac (Abcam ab4729) or H3K4Me2 (Millipore 07-030) antibodies.
NEB Next kit

value: Adult villus cells

value: jejunal epithelium

tag: genotype

value: WT


title: H3K4me2_MNaseChIP_Villus


title: SC622986

value: lung

value: Primary lung tumor

value: lung cancer


title: H3K4me2_MNaseChIP_Crypt

source_name: WT adult jejunal crypt cells

value: Adult crypt cells


title: H3K27ac_MNaseChIP_Crypt


title: 7.2_DMSO_d6_H3K27ac

description:
7.2_DMSO_d6_H3K27ac.bam.R1_val
processed data file: DMSO_d6_H3K27ac.bam.normalized.bw

tag: cell line name

tag: drug

value: DMSO


title: 6.2_DMSO_d6_H3K27me3

description:
6.2_DMSO_d6_H3K27me3.bam.R1_val
processed data file: DMSO_d6_H3K27me3.bam.normalized.bw


title: 6.1_DMSO_d6_H3K27me3

description:
6.1_DMSO_d6_H3K27me3.bam.R1_val
processed data file: DMSO_d6_H3K27me3.bam.normalized.bw


title: 2_GSK_100nM_d6_H3K27me3

description:
2_GSK_100nM_d6_H3K27me3.bam.R1_val
processed data file: GSK_d6_H3K27me3.bam.normalized.bw


title: GT01370-3103

value: Normal lung tissue

value: Forte


title: 4.2_DMSO_d6_H3K4me1

description:
4.2_DMSO_d6_H3K4me1.bam.R1_val
processed data file: DMSO_d6_H3K4me1.bam.normalized.bw


title: 4.1_DMSO_d6_H3K4me1

description:
4.1_DMSO_d6_H3K4me1.bam.R1_val
processed data file: DMSO_d6_H3K4me1.bam.normalized.bw


title: 14_GSK_100nM_d6_H3K27ac

description:
14_GSK_100nM_d6_H3K27ac.bam.R1_val
processed data file: GSK_d6_H3K27ac.bam.normalized.bw


title: 12_GSK_100nM_d6_H3K27ac

description:
12_GSK_100nM_d6_H3K27ac.bam.R1_val
processed data file: GSK_d6_H3K27ac.bam.normalized.bw


title: 1_GSK_100nM_d6_H3K4me1

description:
1_GSK_100nM_d6_H3K4me1.bam.R1_val
processed data file: GSK_d6_H3K4me1.bam.normalized.bw


title: CSP107338


title: 13_GSK_100nM_d6_H3K27me3

description:
13_GSK_100nM_d6_H3K27me3.bam.R1_val
processed data file: GSK_d6_H3K27me3.bam.normalized.bw


title: 1.1_DMSO_d6_pig

source_name: PeTa_DMSO_guinea pig


title: 1.2_DMSO_d6_pig


title: Total_skin_DAPI_neg_Rep1

data_processing:
Reads were aligned against the mouse genome (GRCm38) with STAR.
Aligned reads for each transcript were counted and collapsed to gene level using featureCounts.
Genome_build: GRCm38
Supplementary_files_format_and_content: featureCount output files of gene counts.

growth_protocol: 4-week old C57BL/6 mice

extract_protocol:
Mouse Merkel cells were stained with NCAM and 500 NCAM+/DAPI- cells were FACS sorted in triplicates.
The library was constructed according to SMART-seq2 library preparation protocol.

treatment_protocol: Epidermis was disscociated using the Miltenyi gentleMACS Dissociator with the Miltenyi Epidermis Dissociation Kit.

tag: strain

tag: tissue/cell type

value: total/bulk skin


title: Total_skin_DAPI_neg_Rep2


title: 7_GSK_100nM_d6_pig


title: NCAM_enriched_Rep3

value: Merkel cells


title: NCAM_enriched_Rep2


title: Total_skin_DAPI_neg_Rep3


title: PeTa_100nM_GSK_d6_R2 [ATACseq]

data_processing:
ATACseq data was analyzed using the nf-core/ATACseq pipeline (Patel et al, 2019) aligning against the human genome hg38 and calling peaks with MACS2 in narrow- and broad-peak mode. Aligned reads of the individual replicates were merged using samtools v1.9 (Li et al, 2009) and RPGC-normalized tracks were calculated and plotted as composite density plots using deeptools v3.1.2 (Ramírez et al, 2016).
Genome_build: hg38
Supplementary_files_format_and_content: BigWig file format with genome-wide ATACseq profiles.

extract_protocol:
100,000 viable cells were harvested and nuclei isolated for transposition reaction according to the Omni-ATACseq protocol.
Sequencing libraries were barcoded using Illumina Nextera Indexing

treatment_protocol: Cells were treated for 6 days with either 100nM GSK-LSD1 or DMSO.

tag: cell line


title: 7.1_DMSO_d6_H3K27ac

description:
7.1_DMSO_d6_H3K27ac.bam.R1_val
processed data file: DMSO_d6_H3K27ac.bam.normalized.bw


title: PeTa_100nM_GSK_d6_R1 [ATACseq]


title: scRNA_female_WBL_02

status: Public on Jun 29 2020

city: Bethesda

first: Kan

last: Jiang

address: 9000 Rockville Pike

institute: NIAMS/NIH

data_processing:
Raw sequencing data were processed with Cell Ranger software (version 3.0.0 or 3.0.2)
raw_feature_bc_matrix files were loaded to R/3.5.3 and analysis with Seurat v3.0
Genome_build: GrCh38

source_name: whole blood leukocytes

extract_protocol:
Whole blood leukocytes were isolated using a red blood cell depletion kit (Erythroclear Red Blood Cell Depletion Reagent kit; STEMCELL Technologies, cat. no. 01738)
Isolated whole blood leukocytes were encapsulated using microfluidics technology, and barcoded using a unique molecular identifier (UMI)
scRNAseq data were generated on Illumina HiSeq  3000 instruments according to the manufacturer's instructions

tag: gender

value: female

value: whole blood leukocytes

tag: description for exp id

tag: lab  data id


title: PeTa_DMSO_d6_R1 [ATACseq]

value: PeTa

value: Merkel cell carcinoma cell line

tag: treatment


title: PeTa_DMSO_d6_R2 [ATACseq]

tag: cell type


title: scRNA_female_WBL_04


title: scRNA_Male_WBL_01

value: Male


title: S13: mRNA_Female_Neu_06

data_processing:
Raw sequencing data were processed with bcl2fastq/2.17.1 to generate FastQ files. Reads of 50 bases were mapped to hg19 using TopHat 2.1.1
Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Partek6.6
Genome_build: hg19
Supplementary_files_format_and_content: excel for a RPKM file

source_name: neutrophils

extract_protocol:
Peripheral blood was collected in heparinized tubes after venipuncture. Neutrophils were isolated at room temperature by density gradient  followed by lysis method. For RNA purification, neutrophils were centrifuged at 1600rpm for 5 minutes and resuspended in 750 μL TRI reagent (Sigma, cat. no. 93289). RNA was isolated using Zymo Research Direct-zol RNA Miniprep kit (Zymo Research, cat. no. R2050)
cDNA libraries were prepared using the TruSeq® Stranded mRNA NeoPrep™ Kit (Illumina, cat. no. 20020594)
RNA seq data were generated on Illumina HiSeq 3000 instrument according to the manufacturer's instructions

value: neutrophils


title: S14: mRNA_Female_Neu_07


title: scRNA_female_WBL_01


title: scRNA_female_WBL_03


title: scRNA_Male_WBL_03


title: S11: mRNA_Female_Neu_04


title: S10: mRNA_Female_Neu_03


title: S09: mRNA_Female_Neu_02


title: S12: mRNA_Female_Neu_05


title: 10_GSK_100nM_d6_H3K4me1

description:
10_GSK_100nM_d6_H3K4me1.bam.R1_val
processed data file: GSK_d6_H3K4me1.bam.normalized.bw


title: S08: mRNA_Female_Neu_01


title: S06: mRNA_Male_Neu_06


title: S07: mRNA_Male_Neu_07


title: S03: mRNA_Male_Neu_03


title: NCAM_enriched_Rep1


title: S04: mRNA_Male_Neu_04


title: scRNA_Male_WBL_02


title: S01: mRNA_Male_Neu_01


title: CRPC_05-217I3_LN [re-analysis]

status: Public on Jun 01 2020

description:
05-217I3_LN
CRPC lymph node (LN) metastasis
05-217I3_LN

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18.X software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq Conversion Software v1.8.4
Reads were mapped to the hg38 human genome build using TopHat v2.X and bowtie2 v2.2.X.
Mean and standard deviation of fragment size were calculated with picard-tools v2.18.X
Transcript abundance was determined from the TopHat alignments in R using the Genomic Alignments Bioconductor package using the summarizeOverlaps function with mode=IntersectionStrict, counting reads mapping to the exonic regions of genes.
Genome_build: hg38
Supplementary_files_format_and_content: Processed files are tab-delimited text files. Each file contains 7 columns: Entrez Gene ID, gene symbol, gene name, mRNA size, raw fragment count (by gene), FPM (fragments per million reads mapped) and FPKM (fragments per kilobase per million reads mapped).

source_name: CRPC lymph node (LN) metastasis

extract_protocol:
Total RNA was isolated from 138 CRPC metastases frozen in Optimal Cutting Temperature compound (OCT; Tissue-Tek) from 72 patients with RNA STAT-60 (Tel-Test). Using an H&E stained slide for each metastatic site for orientation, one millimeter core punches of tumor were obtained, or where appropriate multiple sections enriched for tumor were cut using a Leica CM3050S cryostat. Total RNA was isolated from cell line samples using the RNeasy Mini Kit (Qiagen, cat#74134) with DNase digestion.
RNA-seq libraries were constructed from 1 ug total RNA using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit according to the manufacturer’s protocol.
Barcoded libraries were pooled and sequenced on the Illumina HiSeq 2500 generating 50-71 bp paired end reads.

value: male

value: prostate cancer

tag: tumor site

value: lymph node (LN)

tag: patient

tag: molecular phenotype


title: CRPC_06-131TT1_BONE [re-analysis]

description:
06-131TT1_BONE
CRPC bone metastasis
06-131TT1_BONE

source_name: CRPC bone metastasis

value: bone


title: CRPC_05-217F4_LN [re-analysis]

description:
05-217F4_LN
CRPC lymph node (LN) metastasis
05-217F4_LN


title: S02: mRNA_Male_Neu_02

tag: tissue


title: CRPC_00-010K6_LIVER

description:
00-010K6_LIVER
CRPC liver metastasis
00-010K6_LIVER

source_name: CRPC liver metastasis

value: liver


title: E09_MS155_128 (SingleCell196)

status: Public on Jan 29 2020

description: Cynomolgus Embryo at E09

data_processing:
library strategy: SC3-seq
Samples were sequenced on NextSeq and SOLiD sequencers with the read length are 76 and 50 bases.
All the reads were surveyed and the adaptor or the poly-A sequences were trimmed by cutadapt-1.3 with options "-e 0.1 -q 20 -n 2 -O 1 -m 30 -a CTCGAGGGCGCGCCGGATCC -g CTCGAGGGCGCGCCGGATCC -a AAAAAAAAAAAAAAAAAAAA -a TTTTTTTTTTTTTTTTTTTT". The trimmed reads with less than 30 bp were discarded.
Untrimmed and trimmed reads of 30 bp or longer were mapped onto the Cynomolgus monkey genome Macfac5.0 and the ERCC spike-in RNA sequences with tophat-1.4.1/bowtie1.0.1 with the “—no-coverage-search” option.
Mapped reads on the genome and the ERCC were separated, and the reads on the genome were converted into the expression levels by cufflinks-2.2.0 using the “—compatible-hits-norm”,  “—max-mle-iterations 50000", “—no-length-correction” and “—library-type fr-secondstrand” options and macfas5.0 reference gene annotations with extended TTSs. For the reference gene annotations used in cufflinks, we extended the TTSs of the reference genes up to 10 kb downstream to correctly estimate the expression levels of genes whose transcripts are longer than the reference toward the 3 prime.
Genome_build: macfas5.0
Supplementary_files_format_and_content: tab-delimited text file includes RPM values for each Sample

source_name: Cynomolgus Embryo at E09

growth_protocol:
For cultivation of CMK6 and CMK9 cyESCs, they were cultured with conventional hESC medium [DMEM/F12 supplemented with 20% (vol/vol) of KSR, 1 mM of sodium pyruvate, 2 mM of GlutaMax, 0.1 mM of non-essential amino acids, 0.1 mM of 2-mercaptoethanol, 1000 U/ml of ESGRO mouse LIF, and 4 ng/ml of recombinant human bFGF] on mouse embryonic feeders (MEFs).
For cultivation in 656BTAG42 cells under undifferentiated state, it was cultured in AITS medium containing 20ng/mL bFGF and 2.5nM IWR1

extract_protocol:
For single cell isolation from cy pre-implantation embryos, a whole embryo was incubated with 0.25% trypsin/PBS  for around 10 min at 37℃, then dissociated into single cells by repeated pipetting, and dispersed in 0.1 mg/ml of PVA/PBS  for preparation of single-cell cDNAs.
For single cell isolation from cy post-implantation embryos, the implantation site was dissected out from the uterus and the embryonic fragment containing the epiblast (EPI), amnion, hypoblast, and yolk sac endoderm was isolated manually. The fragment was incubated with 0.25% trypsin/PBS for around 10 min at 37℃, then dissociated into single cells by repeated pipetting, and dispersed in 0.1 mg/ml of PVA/PBS.
For single cell isolation from cyESCs, cells were first detached as clumps with CTK solution, incubated in 0.25% trypsin/PBS (Sigma-Aldrich) for around 10 min at 37℃, and dispersed into single cells in 1% (vol/vol) KSR/PBS containing 10 M of the ROCK inhibitor Y-27632. Cells under feeder-free condition were directly incubated in TrypLE Select for around 5 min at 37℃, and dispersed into single cells in 1% (vol/vol) KSR/PBS containing 10 uM of the ROCK inhibitor Y-27632.
For single cell isolation from cyPGCLCs, the cells dissociated with TryPLE select were collected by cell sorting.
For SC3-seq analysis, cDNA synthesis / amplification from single cells and library construction from the cDNAs were performed as described previously [Nakamura et al. 2015, NAR, 43, e60].

treatment_protocol: For cyPGCLCs, undifferentiated ESCs were dissociated and replated to low-adherent V-bottom plates to form aggregates with BMP4 (200 ng/ml), SCF (100 ng/ml), EGF (50 ng/ml), LIF(1000U/ml), and Y27632 (10µM) in GMEM containing 15% KSR or Advanced RPMI1640 containing B27, until the harvest day.

value: not applicable

value: embryo

tag: developmental stage


title: E09_MS155_127 (SingleCell195)

description: Cynomolgus Embryo at E09


title: CRPC_00-010M4_LN

description:
00-010M4_LN
CRPC lymph node (LN) metastasis
00-010M4_LN


title: E09_MS155_124 (SingleCell192)

description: Cynomolgus Embryo at E09


title: CRPC_05-144E6_LIVER [re-analysis]

description:
05-144E6_LIVER
CRPC liver metastasis
05-144E6_LIVER


title: CRPC_05-144V3_ADRENAL [re-analysis]

description:
05-144V3_ADRENAL
CRPC adrenal metastasis
05-144V3_ADRENAL

source_name: CRPC adrenal metastasis

value: adrenal


title: E16_MS133_046 (SingleCell500)

description: Cynomolgus Embryo at E16

source_name: Cynomolgus Embryo at E16


title: E09_MS155_125 (SingleCell193)

description: Cynomolgus Embryo at E09


title: E09_MS099_028 (SingleCell186)

description: Cynomolgus Embryo at E09


title: E09_MS099_054 (SingleCell190)

description: Cynomolgus Embryo at E09


title: E09_MS099_027 (SingleCell185)

description: Cynomolgus Embryo at E09


title: E09_MS099_024 (SingleCell183)

description: Cynomolgus Embryo at E09


title: E09_MS126_059 (SingleCell191)

description: Cynomolgus Embryo at E09


title: E09_MS099_026 (SingleCell184)

description: Cynomolgus Embryo at E09


title: E09_MS099_053 (SingleCell189)

description: Cynomolgus Embryo at E09


title: E08_MS133_044 (SingleCell178)

description: Cynomolgus Embryo at E08

source_name: Cynomolgus Embryo at E08


title: E08_MS133_043 (SingleCell177)

description: Cynomolgus Embryo at E08


title: S05: mRNA_Male_Neu_05


title: E08_MS133_041 (SingleCell175)

description: Cynomolgus Embryo at E08


title: E08_MS133_040 (SingleCell174)

description: Cynomolgus Embryo at E08


title: E08_MS133_042 (SingleCell176)

description: Cynomolgus Embryo at E08


title: E08_MS133_036 (SingleCell171)

description: Cynomolgus Embryo at E08


title: E09_MS155_126 (SingleCell194)

description: Cynomolgus Embryo at E09


title: E08_MS133_030 (SingleCell166)

description: Cynomolgus Embryo at E08


title: E08_MS133_031 (SingleCell167)

description: Cynomolgus Embryo at E08


title: E08_MS133_029 (SingleCell165)

description: Cynomolgus Embryo at E08


title: E08_MS133_034 (SingleCell170)

description: Cynomolgus Embryo at E08


title: E09_MS099_029 (SingleCell187)

description: Cynomolgus Embryo at E09


title: E08_MS133_028 (SingleCell164)

description: Cynomolgus Embryo at E08


title: E08_MS133_033 (SingleCell169)

description: Cynomolgus Embryo at E08


title: E08_MS151_035 (SingleCell180)

description: Cynomolgus Embryo at E08


title: E08_MS133_025 (SingleCell161)

description: Cynomolgus Embryo at E08


title: E08_MS133_023 (SingleCell159)

description: Cynomolgus Embryo at E08


title: E08_MS133_024 (SingleCell160)

description: Cynomolgus Embryo at E08


title: E08_MS133_022 (SingleCell158)

description: Cynomolgus Embryo at E08


title: E08_MS133_026 (SingleCell162)

description: Cynomolgus Embryo at E08


title: E08_MS133_020 (SingleCell156)

description: Cynomolgus Embryo at E08


title: E08_MS133_027 (SingleCell163)

description: Cynomolgus Embryo at E08


title: E08_MS133_021 (SingleCell157)

description: Cynomolgus Embryo at E08


title: E08_MS133_045 (SingleCell179)

description: Cynomolgus Embryo at E08


title: E08_MS133_019 (SingleCell155)

description: Cynomolgus Embryo at E08


title: E08_MS133_018 (SingleCell154)

description: Cynomolgus Embryo at E08


title: E08_MS133_017 (SingleCell153)

description: Cynomolgus Embryo at E08


title: E08_MS133_037 (SingleCell172)

description: Cynomolgus Embryo at E08


title: E08_MS133_032 (SingleCell168)

description: Cynomolgus Embryo at E08


title: E08_MS133_012 (SingleCell148)

description: Cynomolgus Embryo at E08


title: E08_MS133_014 (SingleCell150)

description: Cynomolgus Embryo at E08


title: E08_MS133_011 (SingleCell147)

description: Cynomolgus Embryo at E08


title: E08_MS133_013 (SingleCell149)

description: Cynomolgus Embryo at E08


title: E08_MS133_009 (SingleCell145)

description: Cynomolgus Embryo at E08


title: E08_MS133_016 (SingleCell152)

description: Cynomolgus Embryo at E08


title: E08_MS133_015 (SingleCell151)

description: Cynomolgus Embryo at E08


title: E08_MS133_007 (SingleCell143)

description: Cynomolgus Embryo at E08


title: E08_MS133_010 (SingleCell146)

description: Cynomolgus Embryo at E08


title: E08_MS133_008 (SingleCell144)

description: Cynomolgus Embryo at E08


title: E08_MS133_006 (SingleCell142)

description: Cynomolgus Embryo at E08


title: E08_MS133_004 (SingleCell140)

description: Cynomolgus Embryo at E08


title: E08_MS133_005 (SingleCell141)

description: Cynomolgus Embryo at E08


title: E08_MS133_001 (SingleCell137)

description: Cynomolgus Embryo at E08


title: E08_MS133_002 (SingleCell138)

description: Cynomolgus Embryo at E08


title: E08_MS132_005 (SingleCell131)

description: Cynomolgus Embryo at E08


title: E08_MS132_001 (SingleCell127)

description: Cynomolgus Embryo at E08


title: E08_MS132_006 (SingleCell132)

description: Cynomolgus Embryo at E08


title: E08_MS133_003 (SingleCell139)

description: Cynomolgus Embryo at E08


title: E08_MS132_008 (SingleCell134)

description: Cynomolgus Embryo at E08


title: E08_MS132_004 (SingleCell130)

description: Cynomolgus Embryo at E08


title: E08_MS126_063 (SingleCell126)

description: Cynomolgus Embryo at E08


title: E08_MS126_061 (SingleCell124)

description: Cynomolgus Embryo at E08


title: E08_MS132_207 (SingleCell136)

description: Cynomolgus Embryo at E08


title: E08_MS132_007 (SingleCell133)

description: Cynomolgus Embryo at E08


title: E08_MS132_003 (SingleCell129)

description: Cynomolgus Embryo at E08


title: E08_MS126_060 (SingleCell123)

description: Cynomolgus Embryo at E08


title: E08_MS126_044 (SingleCell114)

description: Cynomolgus Embryo at E08


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description: Cynomolgus Embryo at E08


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description: Cynomolgus Embryo at E08


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description: Cynomolgus Embryo at E08


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description: Cynomolgus Embryo at E08


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description: Cynomolgus Embryo at E08


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description: Cynomolgus Embryo at E08


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description: Cynomolgus Embryo at E08


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description: Cynomolgus Embryo at E08


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description: Cynomolgus Embryo at E08


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description: Cynomolgus Embryo at E08


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description: Cynomolgus Embryo at E08


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description: Cynomolgus Embryo at E08


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description: Cynomolgus Embryo at E08


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description: Cynomolgus Embryo at E08


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description: Cynomolgus Embryo at E08


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description: Cynomolgus Embryo at E08


title: E07_MS155_123 (SingleCell094)

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source_name: Cynomolgus Embryo at E07


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description: Cynomolgus Embryo at E07


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description: Cynomolgus Embryo at E07


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description: Cynomolgus Embryo at E07


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description: Cynomolgus Embryo at E07


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description: Cynomolgus Embryo at E07


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description: Cynomolgus Embryo at E08


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description: Cynomolgus Embryo at E07


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source_name: Cynomolgus Embryo at E06


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description: Cynomolgus Embryo at E06


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description: Cynomolgus Embryo at E06


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description: Cynomolgus Embryo at E06


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description: Cynomolgus Embryo at E06


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description: Cynomolgus Embryo at E08


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description: Cynomolgus Embryo at E06


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description: Cynomolgus Embryo at E06


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description: Cynomolgus Embryo at E06


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description: Cynomolgus Embryo at E06


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description: Cynomolgus Embryo at E06


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description: Cynomolgus Embryo at E07


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description: Cynomolgus Embryo at E06


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title: RRBS-seq of RNA from from pig-584

status: Public on Dec 05 2019

description:
metilene.5.Obese_Lean.3-3.out.tsv
metilene.5.Obese_Lean.5-5.out.tsv
RRBS-584

data_processing:
RRBS: The raw reads were cleaned for quality and adapters using and in-house tools removing TrueSeq adapters and clipping read tails of phred quality less than 20. The reads were mapped to the pig genome version 10.2 using bismark v 0.10 (Krueger and Andrews, 2011) with standard parameters except using bowtie 2 v2.1.0 for the mapping option of bismark (Langmead and Salzberg, 2012). The mapped reads were analyzed using Metilene v 0.2-7 requiring at least five pigs in both the obese and lean groups (–X 5 –Y 5)
mDNAcap:  The raw reads were trimmed for quality and adapters using trimmomatic V0.22 (Bolger et al., 2014) (quality trimming by phred quality of 20) The cleaned reads were mapped to the pig genome version 10.2 using segemehl V0.1.4 (Hoffmann et al., 2009) and the following parameters: accuracy 95%, and minimum mapping size 18. The mapped reads were analyzed with diffReps V1.55.4 using the G-test and default values for all remaining parameters
RNAseq: The raw reads were cleaned for quality and adapters using and in-house tools removing TrueSeq adapters and clipping read tails of phred quality less than 20 The reads were mapped to the pig transcriptome using the STAR aligner v2.3.1 (Dobin et al., 2013) with the following options and data: pig genome version 10.2, ensembl annotation version 70 and with intron-motifs [XS:A] tags in the SAM output. The aligned reads were assigned to transcripts of the ensembl version 70 annotation with cufflinks version 2.2.0 (Trapnell et al., 2013). The subsequent differential expression analysis was performed with cuffdiff from the cufflinks package and was based on the Ensembl v70 annotation. Standard options were used for the cufflinks programs in all cases. All further analysis was done using the annotation from ensemble v81.
Supplementary_files_format_and_content: [RNAseq]  fpkm_tracking.tsv, gene_exp.diff.tsv (1=obese, q2=lean)
Supplementary_files_format_and_content: [MeDIP-seq]  data_all.gt.Obese_lean.*.tsv (Treatment=obese, control=lean)
Supplementary_files_format_and_content: [RRBS-seq]  metilene.*.tsv

organism: Sus scrofa

source_name: Adipocytes

extract_protocol:
DNA was extracted from the mature adipocytes using the Epicenter kit (Illumina), and total RNA was isolated from the mature adipocytes according to the protocol described in (Cirera, 2013) using TriReagent and included a DNAse treatment step.
RNA libraries were prepared for sequencing using Truseq lib prep kit from Illumina together with RiboZero Gold  using 0.5ug of total RNA as input. mRRBS libraries were prepared as described in Boyle (2012) using 200ng DNA as input. MeDiP libraries were prepared from 1.1ug DNA, fragmented in a bioruptor and methylated DNA fragments were enriched using MethylMiner Methylated DNA Enrichment KIt (cat#ME10025). Sequencing libraries were generated according to the low Input TruSeq library preparation protocol.

treatment_protocol: Mature adipocytes were isolated from approx. 15 g of the retroperitoneal adipose tissue from each animal, treated with 0.2% collagenase and filtered through a 200-um nylon filter.

value: adipocyte

tag: Sex

value: M

tag: phenotype

value: obese


title: E06_MS099_059 (SingleCell049)

description: Cynomolgus Embryo at E06


title: RRBS-seq of RNA from from pig-577

description:
metilene.5.Obese_Lean.3-3.out.tsv
metilene.5.Obese_Lean.5-5.out.tsv
RRBS-577

value: lean


title: RRBS-seq of RNA from from pig-529

description:
metilene.5.Obese_Lean.3-3.out.tsv
metilene.5.Obese_Lean.5-5.out.tsv
RRBS-529


title: E07_MS099_047 (SingleCell081)

description: Cynomolgus Embryo at E07


title: RRBS-seq of RNA from from pig-524

description:
metilene.5.Obese_Lean.3-3.out.tsv
metilene.5.Obese_Lean.5-5.out.tsv
RRBS-524


title: RRBS-seq of RNA from from pig-522

description:
metilene.5.Obese_Lean.3-3.out.tsv
metilene.5.Obese_Lean.5-5.out.tsv
RRBS-522


title: RRBS-seq of RNA from from pig-473

description:
metilene.5.Obese_Lean.3-3.out.tsv
metilene.5.Obese_Lean.5-5.out.tsv
RRBS-473


title: RRBS-seq of RNA from from pig-503

description:
metilene.5.Obese_Lean.3-3.out.tsv
metilene.5.Obese_Lean.5-5.out.tsv
RRBS-503

value: F


title: RRBS-seq of RNA from from pig-525

description:
metilene.5.Obese_Lean.3-3.out.tsv
metilene.5.Obese_Lean.5-5.out.tsv
RRBS-525