title: ACBM002_pCLP_5hmC

description:
5hmC pulldown sequencing data
ACBM002_pCLP


title: ACBM001_pGMP_5hmC

status: Public on May 01 2022

type: SRA

city: Stanford

first: Ravindra

last: Majeti

state: CA

address: 875 Blake Wilbur Dr Clinic F

country: USA

institute: Stanford University

description:
5hmC pulldown sequencing data
ACBM001_pGMP

library_source: genomic

data_processing:
Library strategy: 5hmC-seq
Seventy-five base-pair, paired-end DNA sequencing was completed using a NextSeq550 instrument with NovaSeq Hi Output version 2.5 reagent kits (Illumina, San Diego, CA, USA).
Raw data processing and demultiplexing to sample-specific FASTQ output was performed using the Illumina BaseSpace Sequence Hub.
Sequencing reads were aligned to the hg19 reference genome using default parameters of BWA-MEM.
Duplicate reads were marked and removed using Picard MarkDuplicates.
Assembly: hg19
Supplementary files format and content: Raw reads in peaks or reads in gene bodies data across all samples, RNA kallisto output normalized counts matrix

molecule: genomic DNA

organism: Homo sapiens

source_name: Human Bone Marrow HSPCs

growth_protocol:
Healthy hematopoietic cells were sorted and enriched
Cord blood cells were CD34 enriched, edited, and subjected to engraftment or other assays.

extract_protocol:
All the samples were collected into 1.5 mL microcentrifuge tubes and snap-freezed until further processing. Genomic DNA was extracted using the DNeasy Blood & Tissue Kit (QIAGEN, Germany) according to manufacturer’s instructions. Genomic DNA eluates were quantified using the Qubit dsDNA High Sensitivity assay (Thermo Fisher Scientific, Waltham, MA, USA) and stored at -20C until further processing. Prior to sequencing library construction, genomic DNA was fragmented to a modal 150 base pair size using an ME220 focused ultrasonicator (Covaris, Inc., Woburn, MA, USA). Modal fragmented DNA sizes were verified using the TapeStation 2200 dsDNA high sensitivity assay (Agilent Technologies, Santa Clara, CA, USA) and quantified as described above prior to commencing library construction.
Preparation of 5hmC enriched sequencing libraries was performed as described previously24. For each sample, two libraries were generated: a library derived from 5hmC enriched reads, and a library derived from input unenriched DNA. Fragmented DNA was normalized to 20 ng total input for each assay and ligated to sequencing adapters. Adapter ligated products were either prepared for whole genome sequencing using the KAPA Hyper Prep kit (Roche, Switzerland) according to manufacturer's instructions, or 5hmC bases were biotinylated via a two-step chemistry and subsequently enriched by binding to Dynabeads M270 Streptavidin (Thermo Fisher Scientific). All libraries were quantified using a Qubit dsDNA High Sensitivity Assay (Thermo Fisher Scientific) and normalized in preparation for sequencing. Fragment size profiles of sequencing libraries were verified with the Bioanalyzer dsDNA High Sensitivity assay (Agilent Technologies) prior to sequencing.

treatment_protocol: For TET2 edited and control samples, cells were grown in steady state or drug treated conditions before being assayed using the 5hmC sequencing protocol. See sample descriptioins for specific treatment conditions.

tag: source

value: Human Bone Marrow HSPCs

tag: cell type

value: GMP


title: ACBM001_pCMP_5hmC

description:
5hmC pulldown sequencing data
ACBM001_pCMP

value: CMP


title: CTRL 3

city: Stockholm

first: Malin

last: Wickström

address: Tomtebodavägen 18a

department: Department of Women's and Children's health

country: Sweden

institute: Karolinska institutet

library_source: transcriptomic

data_processing:
fastq files were aligned to the GRCh38 genome using the STAR 2-pass approach (v2.7.2a). A genome index was generated using --runMode genomeGenerate with annotations and the option --sjdbOverhang set to (read length - 1). First-pass alignment was performed using basic options only. A new index was then generated for each sample using the SJ.out.tab file from the first-pass alignment and --sjdbOverhang set to (read length - 1). Finally, a second alignment was performed.
Aligned reads were quantified using htseq-count version 0.9.0 with the --stranded=reverse, --type=exon, and --id=gene_id options
Genome_build: GRCh38
Supplementary_files_format_and_content: csv file with raw read counts for every gene and every sample

molecule: polyA RNA

organism: Mus musculus

source_name: DAOY xenograft tumor tissue

extract_protocol:
The core facility for Bioinformatics and Expression Analysis at Karolinska Institutet performed the lysis of tumor tissue, RNA extraction and sequencing. Qiagen RNeasy mini kit (Qiagen) was used for RNA extraction from the tumor lysates. Quality control of total RNA was performed with Agilent Tapestation.
Library constructs was prepared according to the Illumina TruSeq Stranded mRNA sample preparation protocol. Single-end reads of 75 bp generated using Illumina Nextseq 550. For each sample approximately 11,8 million reads were obtained.

value: DAOY xenograft tumor tissue

tag: treatment

value: CTRL

tag: Sex

value: f

tag: days of treatment


title: FO 4

value: Fish-oil


title: OIL 2

value: DHA-oil


title: FO 3


title: CTRL 1


title: OIL 1


title: CTRL 2


title: FO 2


title: FO 1


title: ACBM001_pMEP_5hmC

description:
5hmC pulldown sequencing data
ACBM001_pMEP

value: MEP


title: OIL 3


title: ACBM001_pCLP_5hmC

description:
5hmC pulldown sequencing data
ACBM001_pCLP

value: CLP


title: NSCLC Plasma_Exo-miRNA_rep 1 [1300194]

type: RNA

city: Genova

first: simona

last: coco

address: L.go R. Benzi, 10

country: Italy

institute: IRCCS Ospedale Policlinico San Martino

description: miRNA profiling

hyb_protocol: After adding Hyb Spike-In, each sample was hybridized at 55°C for 20 hours on G4872A-070156 Human miRNA Microarray, Release 21.0, 8 x 60K (Agilent Technologies). The supplement of a commercial synthetic DNA poly-A oligonucleotide 3’ labeled pCp-Cy3, was added to the final hybridization mix. The 30-mer synthetic oligonucleotide (HPLC purified) was synthesized by TIB Molbiol s.r.l. (Genova, Italy). The lyophilized oligonucleotide was resuspended at a final concentration of 100 pmol/μL. Before use, an aliquot was taken and through serial dilutions brought to two final concentrations of 50 and 5 amol/μL.

scan_protocol: Microarrays were scanned (3 microns, 20 bit) on an Agilent microarray scanner (part number G2505C) and data extracted using Agilent feature extraction v.12.0.0.7. QC metrics from feature extraction were used to evaluate the success of the labeling and hybridization.

data_processing: Pre-processing, filtering and differential expression analysis were carried out using the Limma package, available within Bioconductor. Background correction and between array normalization were carried out using the normexp method, with an offset = 20, and the scale method, respectively. Replicated probes were then averaged.

label: Cyanine 3-pCp

molecule: total RNA

source_name: NSCLC Plasma exosomes

label_protocol: Exosomal total RNA samples were processed using the Agilent miRNA complete labeling and hybridization kit (part number 5190-0456) and Agilent miRNA spike-in kit (part number 5190-1934). The Agilent miRNA microarray system was followed except 8 μL of purified total RNA samples at unknown concentration were used as input amount, instead of the recommended 100 ng of total RNA.

extract_protocol: Exosomal total RNA  samples were purified from 0.5 mL of plasma using the  exoRNeasy Serum/Plasma Midi kit (Qiagen, Hilden, Germany)  according to manufacturer instructions.

tag: tissue

value: plasma exosomes

tag: patient diagnosis

value: NSCLC

tag: age

tag: histotype

value: Scc

tag: Stage

value: IIB

tag: gender

value: male

value: Resection

tag: event (pd)

value: yes

tag: dfs (months)

tag: death

value: no

tag: os (months)


title: NSCLC Plasma_Exo-miRNA_rep 1 [1300161]

description: miRNA profiling

value: Adk


title: NSCLC Plasma_Exo-miRNA_rep 1 [1300256]

description: miRNA profiling


title: NSCLC Plasma_Exo-miRNA_rep 1 [1300218]

description: miRNA profiling

value: IB


title: NSCLC Plasma_Exo-miRNA_rep 1 [1300115]

description: miRNA profiling

value: IIA


title: NSCLC Plasma_Exo-miRNA_rep 1 [1200376]

description: miRNA profiling

value: IA


title: NSCLC Plasma_Exo-miRNA_rep 1 [1200391]

description: miRNA profiling


title: NSCLC Plasma_Exo-miRNA_rep 1 [1300029]

description: miRNA profiling

value: female


title: NSCLC Plasma_Exo-miRNA_rep 1 [1200277]

description: miRNA profiling


title: NSCLC Plasma_Exo-miRNA_rep 1 [1200279]

description: miRNA profiling


title: NSCLC Plasma_Exo-miRNA_rep 1 [1200362]

description: miRNA profiling


title: NSCLC Plasma_Exo-miRNA_rep 1 [1200268]

description: miRNA profiling


title: NSCLC Plasma_Exo-miRNA_rep 1 [1200166]

description: miRNA profiling


title: NSCLC Plasma_Exo-miRNA_rep 1 [1200230]

description: miRNA profiling


title: NSCLC Plasma_Exo-miRNA_rep 1 [1200075]

description: miRNA profiling


title: NSCLC Plasma_Exo-miRNA_rep 1 [1200130]

description: miRNA profiling


title: NSCLC Plasma_Exo-miRNA_rep 1 [1200142]

description: miRNA profiling


title: NSCLC Plasma_Exo-miRNA_rep 1 [1100331]

description: miRNA profiling


title: NSCLC Plasma_Exo-miRNA_rep 1 [1200210]

description: miRNA profiling


title: NSCLC Plasma_Exo-miRNA_rep 1 [1200062]

description: miRNA profiling

value: IIIA


title: NSCLC Plasma_Exo-miRNA_rep 1 [1200180]

description: miRNA profiling


title: NSCLC Plasma_Exo-miRNA_rep 1 [1200070]

description: miRNA profiling


title: NSCLC Plasma_Exo-miRNA_rep 1 [1200033]

description: miRNA profiling


title: NSCLC Plasma_Exo-miRNA_rep 1 [1100320]

description: miRNA profiling


title: NSCLC Plasma_Exo-miRNA_rep 1 [1200163]

description: miRNA profiling


title: NSCLC Plasma_Exo-miRNA_rep 1 [1100314]

description: miRNA profiling


title: NSCLC Plasma_Exo-miRNA_rep 1 [1200106]

description: miRNA profiling


title: NSCLC Plasma_Exo-miRNA_rep 1 [1100304]

description: miRNA profiling


title: NSCLC Plasma_Exo-miRNA_rep 1 [1100398]

description: miRNA profiling


title: NSCLC Plasma_Exo-miRNA_rep 1 [1100288]

description: miRNA profiling


title: NSCLC Plasma_Exo-miRNA_rep 1 [1100294]

description: miRNA profiling


title: NSCLC Plasma_Exo-miRNA_rep 1 [1100295]

description: miRNA profiling


title: NSCLC Plasma_Exo-miRNA_rep 1 [1100287]

description: miRNA profiling


title: NSCLC Plasma_Exo-miRNA_rep 1 [1100283]

description: miRNA profiling


title: NSCLC Plasma_Exo-miRNA_rep 1 [1100260]

description: miRNA profiling


title: NSCLC Plasma_Exo-miRNA_rep 1 [1000569]

description: miRNA profiling


title: NSCLC Plasma_Exo-miRNA_rep 1 [1000512]

description: miRNA profiling


title: NSCLC Plasma_Exo-miRNA_rep 1 [1000637]

description: miRNA profiling


title: NSCLC Plasma_Exo-miRNA_rep 1 [1000556]

description: miRNA profiling


title: NSCLC Plasma_Exo-miRNA_rep 1 [1000369]

description: miRNA profiling


title: NSCLC Plasma_Exo-miRNA_rep 1 [1000281]

description: miRNA profiling


title: NSCLC Plasma_Exo-miRNA_rep 1 [1000249]

description: miRNA profiling


title: NSCLC Plasma_Exo-miRNA_rep 1 [1000651]

description: miRNA profiling


title: NSCLC Plasma_Exo-miRNA_rep 1 [1000270]

description: miRNA profiling


title: NSCLC Plasma_Exo-miRNA_rep 1 [1000287]

description: miRNA profiling


title: NSCLC Plasma_Exo-miRNA_rep 1 [1000346]

description: miRNA profiling

value: ADK + Scc


title: NSCLC Plasma_Exo-miRNA_rep 1 [1000278]

description: miRNA profiling


title: NSCLC Plasma_Exo-miRNA_rep 1 [1100062]

description: miRNA profiling


title: NSCLC Plasma_Exo-miRNA_rep 1 [1000153]

description: miRNA profiling


title: NSCLC Plasma_Exo-miRNA_rep 1 [1000195]

description: miRNA profiling


title: NSCLC Plasma_Exo-miRNA_rep 1 [1000357]

description: miRNA profiling


title: NSCLC Plasma_Exo-miRNA_rep 1 [1000220]

description: miRNA profiling


title: NSCLC Plasma_Exo-miRNA_rep 1 [1000644]

description: miRNA profiling


title: NSCLC Plasma_Exo-miRNA_rep 1 [1000223]

description: miRNA profiling


title: Chronic epididymitis_small RNA_rep3

city: Hong Kong

first: Jianlin

last: Li

address: L 7-08, Department of Obstetrics and Gynecology  Laboratory block, 21th Sassoon Road, Hong Kong

country: Hong Kong

institute: The University of Hong Kong

description: small RNA

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38 whole genome using Hisat2
DEGs and DEMs were analyzed through DESeq2
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include reads count values for each Sample ...

source_name: epididymis

extract_protocol:
Illumina TruSeq RNA Sample Prep Kit and TruSeq Small RNA Sample Prep Kit were respectively used for mRNA and small RNA extraction, with 1-10 ug of total RNA for each sample in the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: segment

value: Corpus

tag: physiological conditions

value: Inflammation


title: NSCLC Plasma_Exo-miRNA_rep 1 [800138]

description: miRNA profiling

value: plasma exosomes


title: Chronic epididymitis_small RNA_rep4

description: small RNA

value: Caput


title: Chronic epididymitis_small RNA_rep1

description: small RNA


title: Control_small RNA_rep1

description: small RNA

value: Normal


title: Control_small RNA_rep4

description: small RNA


title: NSCLC Plasma_Exo-miRNA_rep 1 [1000065]

description: miRNA profiling

value: NSCLC

value: IIIB


title: NSCLC Plasma_Exo-miRNA_rep 1 [1000039]

description: miRNA profiling

value: Scc

value: male

value: Resection


title: Chronic epididymitis_small RNA_rep2

description: small RNA


title: NSCLC Plasma_Exo-miRNA_rep 1 [1000048]

description: miRNA profiling

value: Adk

value: no


title: NSCLC Plasma_Exo-miRNA_rep 1 [1000030]

description: miRNA profiling


title: NSCLC Plasma_Exo-miRNA_rep 1 [900330]

description: miRNA profiling

value: IIA


title: Chronic epididymitis_small RNA_rep5

description: small RNA


title: Control_small RNA_rep5

description: small RNA


title: Control_small RNA_rep2

description: small RNA

value: Cauda


title: NSCLC Plasma_Exo-miRNA_rep 1 [1000116]

description: miRNA profiling

value: IA

value: yes


title: Control_small RNA_rep3

description: small RNA


title: NSCLC Plasma_Exo-miRNA_rep 1 [900272]

description: miRNA profiling

value: IIIA


title: NSCLC Plasma_Exo-miRNA_rep 1 [1000070]

description: miRNA profiling

value: IIB


title: Control_mRNA_rep1

description: mRNA


title: NSCLC Plasma_Exo-miRNA_rep 1 [800160]

description: miRNA profiling


title: NSCLC Plasma_Exo-miRNA_rep 1 [800132]

description: miRNA profiling


title: Control_mRNA_rep5

description: mRNA


title: Control_mRNA_rep2

description: mRNA


title: NSCLC Plasma_Exo-miRNA_rep 1 [900321]

description: miRNA profiling

value: IB


title: Control_mRNA_rep4

description: mRNA


title: Chronic epididymitis_mRNA_rep4

description: mRNA

value: Inflammation


title: Control_mRNA_rep3

description: mRNA

value: Corpus


title: Chronic epididymitis_mRNA_rep3

description: mRNA


title: T_9511_2

city: Shanghai

first: Zhichao

last: Wang

address: 639 Zhizaoju Road, Shanghai 200011, P.R. China

department: Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine

country: China

institute: Department of Plastic and Reconstructive Surgery

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters.
Reads Oer Kilobase of exon per Megabase of libarary size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimitied text files include RPKM values for each Sample.

source_name: TAK-resistant ipNF9511.bc

growth_protocol: All cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Gibco), supplemented with 10% fetal bovine serum (FBS, Gibco), glutamine and 1 x penicillin/streptomycin (Gibco) at 37℃ in a ddH2O humidified atmosphere with 5% CO2.

extract_protocol:
Cells were flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina  Truseq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: To establish a TAK-733 resistant PNFs cell subline, ipNF05.5 and 9511.bc cells were incubated in 1/6 IC50 of TAK-733 for 2 weeks at first. After cells stably growing, the drug concentration elevated gradually over 6 months to a final dose of 5 times of the previous IC50 concentration and withdrawn for 2 passages before functional studies.

value: plexiform neurofibroma cell line

tag: cell line

tag: phenotype

value: TAK-733 resistant


title: T_055_1

source_name: TAK-resistant ipNF05.5

tag: cell type


title: Chronic epididymitis_mRNA_rep2

description: mRNA

value: Caput


title: sh-G9a-con

city: Hangzhou

first: Hongxiao

last: wang

state: zhejiang

address: kaixuan road

institute: Zhejiang University

data_processing:
PE150 was used for sequencing strategy.
Reads of samples were aligned to Homo_sapiens.GRCh38.94.chr (ftp://ftp.ensembl.org/pub/release-94/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz) .
Genome_build: GRCh38.94.chr
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: cancer cell Kyse510

extract_protocol:
Cell populations were directly homogenized into Trizol LS reagent (Invitrogen). Total RNA was immediately extracted .
Library construction started from fragmented cDNA, and then the paired-end sequencing was performed by Illumina and the sequencing strategy was PE150.

value: esophagus

value: esophageal cancer cell

tag: transfection

tag: treatment

value: untreated


title: sh-LSD1+DOX

tag: tissue

value: treated with doxycycline for 2 days


title: sh-LSD1-con


title: UNC0642

value: treated with UNC0642 for 2 days


title: Chronic epididymitis_mRNA_rep5

description: mRNA


title: C_9511_3

source_name: TAK non-resistant ipNF9511.bc

value: control


title: T_055_3


title: T_9511_1


title: SP2509

value: treated with SP2509 for 2 days


title: NSCLC Plasma_Exo-miRNA_rep 1 [1000313]

description: miRNA profiling

value: plasma exosomes

tag: patient diagnosis

value: NSCLC

value: Adk

value: IA

value: female

value: Resection

value: no


title: T_9511_3

value: plexiform neurofibroma cell line


title: T_055_2

value: TAK-733 resistant


title: sh-G9a+Dox


title: SP+UNC

value: treated with SP2509 and UNC0642 for 2 days


title: DMSO-con

value: esophagus


title: C_055_2

source_name: TAK non-resistant ipNF05.5


title: C_9511_2


title: C_9511_1


title: C_055_1


title: C_055_3


title: RNA-seq_NC_rep2

city: Kanazawa

first: Yusuke

last: Miyanari

address: Kakuma

department: NanoLSI

country: Japan

institute: Kanazawa University

data_processing:
RNA-seq libraries were trimmed for adaptor sequences and low-quality bases using trimmomatic and mapped to hybrid reference genome (hg38 and dm6) by hisat2 [Kim.NatBio.2019].
The mapped reads were splitted to hg38 and dm6 with sambamba.
Read counts were computed with featureCounts
Genome_build: hg38
Supplementary_files_format_and_content: Read counts were analyzed using RVUseq (Risso, Nat.Biotech.2014), EDAseq (Risso,BMCBio.2011), and edgeR by taking into account spike-in normalization.

source_name: human haploid eHAP cells

growth_protocol: eHAP cells (Horizon Discovery) (Essletzbichler et al., 2014) grown in Iscove’s Modified Dulbecco’s Medium (IMDM, Wako) supplemented with 10% FBS (Sigma) and penicillin/streptomycin (Wako).

extract_protocol:
5x10^5 eHAP cells and 1x104 S2 cells were mixed in a tube. RNA was extracted from 5x105 eHAP cells using RNeasy Mini Kit. Genomic DNA was removed by TURBO DNase. mRNA was purified using polyA magnetic beads (NEB).
A Library for sequencing was prepared using NEBNext UltraII RNA Library Prep Kit for Illumina (NEB) and sequenced on HiSeq4000. Three biological replicates were analyzed for each experimental condition.

treatment_protocol: Cas9-expressing eHAP cells were transfected with a plasmid expressing sgRNAs against indicated gene and puromycin-resistance gene using FuGENE HD (Promega), and selected with puromycin from 24 hrs post-transfection to 72 hrs. On 5 days post-transfection, cells were used for RNA-seq assays.

value: eHAP

tag: genotype

value: wild-type

tag: knockout gene


title: RNA-seq_TFDP1_rep3

value: knockout


title: CRISPR_screen_day5_7low_rep3

description: "Low" fraction, day7, replicate3

data_processing:
Library strategy: CRISPR screen
Adaptor sequences were trimmed by using cutadapt
Bowtie2 with the parameter “-N 1 -X 2000 --no-mixed --no-discordant” mapped ATAC-seq reads to the hybrid reference genome (hg38 and dm6).
MAGeCK-RRA in MAGeCK-VISPR v0.5.3 [Li 2015 Genome Biology] was used to analyze the data
Supplementary_files_format_and_content: MAGeCK-VISPR output

source_name: CRISPR lentivirus sgRNA library (Brunello)

extract_protocol:
In one batch of screen, a series of these processes was repeated five times to collect ~ 2.2 x 106 cells in total for each population. Three batches of screen was independently performed to collect three biological replicates. Genomic DNA was extracted from the sorted cells by phenol chloroform extraction
Integrated lentivirus genome encoding sgRNA was sequenced with illumina HiSeq2500 as described previously (Doench et al., 2016)[Doench, 2016 Nat Biotech]

treatment_protocol: Cas9 expressing eHAP cells were transduced with human sgRNA lentivirus library (Doench, 2016 Nature biotech, Addgene, #73178). The cells were selected with 1 µg/ml of puromycin for 2 days, and then used for ATAC-see at 5 and 7 days post-transduction, respectively. Cells in the G2 phase were specifically gated to sort th 5% of the cells with the highest and lowest ATAC-see signal intensity(“high” or “low” population) . The sgRNA enrichment in each population was analysed by high-throughput sequencing and computationally compared by using the MAGeCK program (Li et al., Genome Biology 2014).

tag: replicate

tag: day af transduction

value: day 7


title: RNA-seq_TFDP1_rep1


title: RNA-seq_NC_rep3


title: RNA-seq_NC_rep1


title: RNA-seq_TFDP1_rep2


title: CRISPR_screen_day5_high_rep3

description: "High" fraction, day5, replicate3

value: day 5


title: CRISPR_screen_day7_high_rep2

description: "High" fraction, day7, replicate2


title: CRISPR_screen_day7_all_rep2

description: "All" fraction, day7, replicate2


title: CRISPR_screen_day5_7low_rep2

description: "Low" fraction, day7, replicate2


title: CRISPR_screen_day5_7low_rep1

description: "Low" fraction, day7, replicate1


title: CRISPR_screen_day7_high_rep1

description: "High" fraction, day7, replicate1


title: CRISPR_screen_day5_low_rep3

description: "Low" fraction, day5, replicate3


title: CRISPR_screen_day5_all_rep2

description: "All" fraction, day5, replicate2


title: CRISPR_screen_day5_all_rep3

description: "All" fraction, day5, replicate3


title: CRISPR_screen_day5_high_rep2

description: "High" fraction, day5, replicate2


title: CRISPR_screen_day7_all_rep1

description: "All" fraction, day7, replicate1


title: CRISPR_screen_day5_all_rep1

description: "All" fraction, day5, replicate1


title: ATAC-seq_Group1_NC1_rep2

data_processing:
The sequenced reads were quality controlled by Trimmomatic with the option “ILLUMINACLIP:adapter_file:2:30:10 LEADING:20 TRAILING:20 MINLEN:36”.
Bowtie2 with the parameter “-N 1 -X 2000 --no-mixed --no-discordant” mapped ATAC-seq reads to the hybrid reference genome (hg38 and dm6).
The reads mapped to multiple positions, chrY, chrM, and blacklisted regions were removed by Samtools (http://www.htslib.org/), and the duplicated reads were filtered by Picard MarkDuplicates.
The positions of HG38-mapped reads were corrected by shifting + 4 bp for (+) strand or -5 bp for (-) strand and were used for detecting peak regions.
The scaling factors were calculated by using total mapped read counts for hg38 and dm3, and were used for spike-in normalization.
Genome_build: hg38
Supplementary_files_format_and_content: BigWig files for each replicate were generated by using deeptools bamCoverage with option --sclaeFactor and subsequently merged into one file by calculating mean enrichment.

extract_protocol:
ATAC-seq was performed as described previously (Buenrostro et al., 2013; Corces et al., 2017) with some modifications. To quantitatively analyze ATAC-seq data between experimental conditions, we used a fixed number of Drosophila S2 cells as a spike-in control for each sample. The read counts for the spike-in were used to internally calibrate ATAC-seq data, as described previously (Bonhoure et al., 2014; Hu et al., 2015; Orlando et al., 2014). In brief, 1x104 (for group1) or 2.5x103 S2 cells (for group2) were first mixed with 1x105 eHAP cells in a tube, washed with cold PBS, and centrifuged at 935 x g for 5 min. Cells were permeabilized with cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Then cells were transposed using Tn5 complex with MEAB34 adaptors in TAPS-DMF buffer at 37 ˚C for 30 min. Genomic DNA was purified with Monarch PCR & DNA Cleanup Kit (NEB).
After amplification of transposed DNA using Q5 High-Fidelity 2X Master Mix (NEB), DNA was size-selected using SPRI beads to produce libraries with fragments between 150 and 600 bp. To reduce a contamination of mitochondrial DNA, the libraries for group2 were treated with an anti-mitochondrial DNA CRISPR/Cas9 library to specifically digest mitochondrial DNA as described previously (Montefiori et al., 2017). The libraries were sequenced on HiSeq3000 or HiSeq2500 for 100 bp or 50 bp paired-end reads, respectively. Two biological replicates were analyzed for each experimental condition.

treatment_protocol: Cas9-expressing eHAP cells were transfected with a plasmid expressing sgRNAs against indicated gene and puromycin-resistance gene using FuGENE HD (Promega), and selected with puromycin from 24 hrs post-transfection to 72 hrs. On 5 days post-transfection, cells were used for ATAC-seq assays.

tag: group

value: a control for Group1


title: ATAC-seq_Group1_TFDP1KO_rep2


title: CRISPR_screen_day7_high_rep3

description: "High" fraction, day7, replicate3


title: CRISPR_screen_day5_high_rep1

description: "High" fraction, day5, replicate1


title: ATAC-seq_Group1_TFDP1KO_rep1


title: CRISPR_screen_day5_low_rep2

description: "Low" fraction, day5, replicate2


title: PBS_1

city: Los Angeles

first: Julie

middle: E

last: Lang

address: 1510 San Pablo Street, Suite 412

department: Deparment of Surgery

institute: University of Southern California

description: negative control for carry forward or amplification bias. Buffer only. This sample contained no cells.

data_processing:
Fastq files have been created using bcl2fastq-1.8.3 from Illumina
Trimmomatic ver. 0.36. was used to remove adaptor sequences and to trim the reads based on quality, using the following parameters: ILLUMINACLIP:my_TrueSeq_list.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36    The file my_TrueSeq_list.fa contains the adaptor sequences, and it is different from the default file provided by Trimmomatic. Available upon request.
Reads were aligned to the human genome ver. GRCh38.p7 using STAR 2.5.0a, with the only   additional option: --chimSegmentMin 20
Read counts for every feature in the genome were obtained by adding --quantMode GeneCounts to the STAR 2.5.0a command line, and using the gencode.v25.annotation.gtf file
Genome_build: GRCh38.p7
Supplementary_files_format_and_content: Text files with read counts for features as described above

extract_protocol:
PBS processed with ANGLE Parsortix and subjected to RNA amplification/libarary prep
Ovation RNA Seq System V2 and Ovation Ultralow Library System V2 (both NuGEN Technologies, San Carlos, CA)

treatment_protocol: Not applicable.  All samples were prior to treatment.

tag: biopsy source tissue

value: n/a (buffer only)


title: PBS_3

source_name: PBS processed with ANGLE Parsortix and subjected to RNA amplification/libarary prep


title: PBS_2


title: Chronic epididymitis_mRNA_rep1

description: mRNA

value: Caput

value: Inflammation


title: 36541_PB_FollowUp

source_name: peripheral blood

growth_protocol: Not applicable

extract_protocol:
Blood: 200μL of PB was placed in 600μL of RNAlater then later RNA was extracted with the RiboPure blood RNA kit (ThermoFisher, Waltham, MA),  CTC were sorted into Prelude Direct Lysis Module (NuGEN, San Carlos, CA); Metastases were extracted using Trizol (Thermo Fisher Scientific).
Ovation RNA Seq System V2 and Ovation Ultralow Library System V2 (both NuGEN Technologies, San Carlos, CA)
RNA-Seq with poly-A isolation

tag: subject id

tag: gender

tag: subject status

value: breast cancer patient

tag: tumor stage

value: stage IV

value: peripheral blood; normal leukocyte population

value: Peripheral blood


title: CRISPR_screen_day5_low_rep1

description: "Low" fraction, day5, replicate1

tag: cell line


title: 101738_PB_FollowUp

value: female


title: 19065_PB_FollowUp


title: 81103_PB


title: 79556_PB


title: 80541_PB


title: 36978_PB_FollowUp


title: ATAC-seq_Group1_NC1_rep1


title: 78534_PB


title: 79412_PB


title: ATAC-seq_Group1_PARP1KO_rep2


title: 79388_PB


title: 113166_PB


title: 113488_PB


title: 78908_PB


title: 78536_PB


title: 79412_2nd_PB


title: 28089_PB


title: 111956_PB


title: 113457_PB


title: 36541_PB


title: 36978_PB


title: 111961_PB


title: 111958_PB


title: 112165_PB


title: 111951_PB


title: 19065_MET2

source_name: metastases

value: fresh metastatic tissue biopsies

value: Ascites


title: 68185_PB


title: 113059_PB


title: 81103_MET1

value: Pleural effusion


title: 112370_PB


title: 79644_MET1

value: CSF


title: 101738_PB


title: 80541_MET1

value: Skin


title: 79644_PB


title: 79556_MET1


title: 79412_2nd_MET


title: 112165_MET2

value: Lung


title: CRISPR_screen_day7_all_rep3

description: "All" fraction, day7, replicate3

value: eHAP

value: day 7


title: 112370_MET2

value: Brain


title: 36978_MET2

value: Breast


title: 36541_MET1


title: 113166_MET1

value: Liver


title: 79555_MET1


title: 113457_MET1


title: 113059_MET1


title: 78536_MET1

value: Bone


title: 101738_MET1

value: breast cancer patient


title: 79412_MET1

value: stage IV

value: Pericardial effusion


title: 28089_MET1


title: 112370_MET1


title: ATAC-seq_Group1_PARP1KO_rep1

value: knockout


title: 113488_MET1

value: female


title: 36978_CTC_FollowUp

source_name: circulating tumor cells sorted from peripheral blood

value: Peripheral blood


title: 19065_MET1

value: fresh metastatic tissue biopsies

value: Ascites


title: 112165_MET1

value: Lymph node


title: 79412_CTC_FollowUp

value: circulating tumor cells sorted from peripheral blood


title: 79388_MET1


title: 68185_MET1

value: CSF


title: 19065_CTC_FollowUp


title: 36541_CTC_FollowUp


title: 36978_MET1


title: 81103_CTC


title: 78908_MET1


title: 80541_CTC


title: 101738_CTC_FollowUp


title: 79412_2nd_CTC


title: 79644_CTC


title: 79556_CTC


title: 79555_CTC


title: 79412_CTC


title: 36978_CTC


title: 36541_CTC


title: 68185_CTC


title: 28089_CTC


title: 79388_CTC


title: 19065_CTC


title: 78908_CTC


title: 113488_CTC


title: 79555_PB

value: peripheral blood; normal leukocyte population


title: 113059_CTC


title: 101738_CTC


title: 113166_CTC


title: 112370_CTC


title: 112165_CTC


title: RBL-2H3 Ctrl-rep2

city: Shenzhen

first: Hui

state: Guangdong

address: Taoyuanjiedao

institute: Shenzhen University

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36)
low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKMs were calculated
Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1)
Gene ontology (GO) analysis and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis for differentially expressed genes were both implemented by KOBAS software (version: 2.1.1) with a pvalue cutoff of 0.05 to judge statistically significant enrichment.
Genome_build: Rattus_norvegicus.Rnor_6.0
Supplementary_files_format_and_content: ab-delimited text files include RPKM values of each sample

organism: Rattus norvegicus

source_name: Rat basophilic leukemia 2H3 cells

growth_protocol: RBL-2H3 cells were cultured in complete Dulbecco’s modifed eagle medium with 4.0  mM  l-glutamine with sodium pyruvate penicillin (100 U/ml), 100 μg/ml streptomycin, non-essential amino acids, and 10% fetal bovine serum in a humidifed incubator at 37 °C, 5% CO2

extract_protocol:
RNA was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: RBL-2H3 cells  were sensitized with 50ng/ml anti-DNP IgE for 12h, washed with Tyrode's buffer, and stimulated with 100ng/ml DNP-HSA  for 4h.

value: Blood corpuscle


title: RBL-2H3 Ctrl-rep1


title: 19065_PB


title: RBL-2H3 DHC-rep2

value: DHC


title: RBL-2H3 DHC-rep3


title: RBL-2H3 DHC-rep1


title: 113457_CTC


title: Female_Myofibroblast_3

city: Boulder

first: Kristi

last: Anseth

state: CO- COLORADO

address: 3415 Colorado Ave, 596 UCB

institute: University of Colorado - Boulder

description: Female VICs cultured on plastic (myofibroblast)

data_processing:
Samples were sequenced on the NextSeq 500 (Illumina) using a high-output 75-cycle kit (single read, 1x75 bp).
Read quality, in fastq format, was evaluated using FastQC (V0.11.5)
Adapter sequences were removed from fastq files using Trimmomatic (V0.36)
Trimmed fastq read files were aligned to the sus scrofa genome (GCF_000003025.6_Sscrofa11.1_genomic.gff, obtained from NCBI) using the hierarchical indexing for spliced alignment of transcripts software known as HISAT2 (V2.1.0)
After converting aligned read sam files to bam files using Samtools (V1.3.1), transcript alignment was performed using the Rsubread and featureCounts
Counts were obtained using Rsubread (V1.30.9)
Genome_build: SusScrofa 11.1
Supplementary_files_format_and_content: The processed data file (ProcessedDataFile.xlsx) contains CPM values.

organism: Sus scrofa

source_name: Aortic valve leaflets

growth_protocol: Male and female porcine VICs were isolated, seeded on PEG-norbornene hydrogels (elastic modulus ~5.8 kPa) or tissue culture plastic, and cultured in Media 199 (Life Technologies) supplemented with 1% fetal bovine serum, 50 U/mL penicillin, 50 μg/mL streptomycin, and 1 μg/mL amphotericin B for 48 hours.

extract_protocol:
mRNA was isolated using an RNeasy Micro Kit (Qiagen) according to the manufacturer’s protocol.
RNA quality was assessed using an Agilent 2100 Bioanalyzer prior to library construction. RNA libraries were constructed using the mRNA KAPA Hyperprep kit (Kapa Biosystems).

value: Valvular Interstitial Cell

value: Female

tag: age

value: 5-6 months

tag: culture

value: plastic


title: Female_Fibroblast_3

description: Female VICs cultured on gel (fibroblast)

tag: cell type

value: gel


title: Female_Fibroblast_1


title: sequencing of D04 cells, treated for 72 hours with TRASH targeting ASOs 2

city: San Francisco

first: Valentin

last: Feichtenschlager

address: 2340 Sutter Street

department: Dermatology

institute: UCSF

description:
Lipofectamine 3000 was used as transfection reagent
Sample 10

data_processing:
Evaluate sequence quality
trim reads
map reads to genome
generate hit counts for genes/exons
compare hit counts
Genome_build: hg19, GRCh38
Supplementary_files_format_and_content: xlsx files with identifiers and gene expression values

source_name: skin

growth_protocol: cells were cultivated in cell culture media at 37 celsius and 5% C02

extract_protocol:
Total RNA was isolated using the RNeasy® mini-Kit (QIAGEN N.V.) following the manufacturer’s protocol. Followed by ribosomal RNA depletion, RNA Fragmentation and Random Priming, First and second strand cDNA synthesis, end repair, 5'phosphorylation and dA-Tailing, Adaptor Ligation, PCR Enrichment
Samples 1-5: Sequence reads were aligned to the human genome (hg19) using TopHat (Version 2.0.11). Samples 6-11: Sequence reads were aligned to the GRCh38 reference genome.

treatment_protocol: 6-11 were treated with Antisense Oligonucleotides (50nmol) and Lipofectamine 3000 (2ul/ml)

value: melanoma

tag: treatment

value: no vector

tag: knockdown

value: TRASH targeting ASOs


title: RBL-2H3 Ctrl-rep3

tag: tissue

value: Peripheral blood


title: Male_Fibroblast_1

description: Male VICs cultured on gel (fibroblast)

value: Male


title: Female_Myofibroblast_1


title: Female_Fibroblast_4


title: 78536_CTC

value: female

value: breast cancer patient

value: stage IV


title: Female_Myofibroblast_2


title: Male_Fibroblast_3

description: Male VICs cultured on gel (fibroblast)


title: P36_S1_PD

city: Trondheim

first: Kristine

last: Misund

address: Prinsesse Kristinas gate 1

department: Department of Clinical and Molecular Medicine

country: Norway

institute: NTNU

data_processing:
Libraries were either; 1) normalized and pooled to 2.2/2.5 pM (flowcell 1/flowcell2) and subjected to clustering on two NextSeq 500 high output flowcells. Finally paired end read sequencing was performed for 75X2 cycles on a NextSeq 500 instrument (Illumina, Inc. San Diego, CA, USA), according to the manufacturer's instructions. Base calling were done on the NS500 instrument by RTA 2.4.6. or; 2) normalized and pooled to 2.3 pM and subject to clustering by a cBot Cluster Generation System on a HiSeq4000 flowcell (Illumina), according to manufacturers instructions. Finally paired end read sequencing was performed for 75X2 cycles performed on a Illumina HiSeq4000 instrument, in accordance with the manufacturer’s instructions. FASTQ files were created with bcl2fastq 2.17 (Illumina).
Transcript expression values were generated by quasi alignment using salmon (http://salmon.readthedocs.io/en/latest/index.html) and the Ensembl (Hg19) human genome.
Aggregation of transcript to gene expression was performed using tximport (http://bioconductor.org/packages/release/bioc/html/tximport.html) and normalized to transcripts per million (TPM) values.
Genome_build: Hg19
Supplementary_files_format_and_content: tab-delimited text file include gene counts for every gene and every sample
Supplementary_files_format_and_content: tab-delimited text file include TPM values for every gene and every sample

source_name: Multiple myeloma cells (CD138+)

extract_protocol:
CD138-positive tumor cells were isolated using RoboSep (StemCell Technologies, Grenoble, France). Tumor purity was subsequently determined by evaluation of MGG-stained cytopspin slides or by flow cytometry. Only samples with a tumor purity ≥80% were included in the study. Tumor  total RNA were extracted using All-Prep Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions
RNA Seq libraries were prepared using TruSeq Stranded mRNA kit (Illumina) according to the manufacturer's instructions. Briefly, 500 ng total RNA was used as starting material.

tag: Stage

value: Progressive Disease (PD)

tag: sample


title: Male_Myofibroblast_2

description: Male VICs cultured on plastic (myofibroblast)


title: sequencing of D04 cells, treated for 72 hours with non targeting control-ASOs 1

description:
Lipofectamine 3000 was used as transfection reagent
Sample 6

value: non targeting control-ASOs


title: Male_Fibroblast_2

description: Male VICs cultured on gel (fibroblast)


title: Male_Myofibroblast_4


title: P36_S2_PD


title: Female_Myofibroblast_4


title: sequencing of D04 cells, treated for 72 hours with non targeting control-ASOs 3

description:
Lipofectamine 3000 was used as transfection reagent
Sample 8


title: sequencing of D04 cells, treated for 72 hours with TRASH targeting ASOs 3

description:
Lipofectamine 3000 was used as transfection reagent
Sample 11


title: P35_S2_PD


title: sequencing of D04 cells, treated for 72 hours with non targeting control-ASOs 2

description:
Lipofectamine 3000 was used as transfection reagent
Sample 7


title: P35_S1_PD


title: P34_S4_PD


title: Female_Fibroblast_2


title: Male_Fibroblast_4

description: Male VICs cultured on gel (fibroblast)


title: Male_Myofibroblast_1


title: sequencing of D04 cells, treated for 72 hours with TRASH targeting ASOs 1

description:
Lipofectamine 3000 was used as transfection reagent
Sample 9


title: Male_Myofibroblast_3


title: P34_S3_PD


title: P34_S2_PD


title: P34_S1_PD


title: P32_S1_NDMM

value: Newly Diagnosed symptomatic MM (NDMM)


title: P33_S1_NDMM


title: P33_S2_PD


title: P31_S3_PD


title: P32_S2_PD


title: P29_S2_PD


title: P30_S1_NDMM


title: P31_S1_NDMM


title: P31_S2_PD


title: P30_S2_PD


title: P28_S1_NDMM


title: P26_S1_NDMM


title: P27_S1_NDMM


title: P25_S2_PD


title: P26_S3_PD


title: P29_S1_NDMM


title: P27_S3_PD


title: P24_S2_PD


title: P25_S1_NDMM


title: P23_S3_PD


title: P25_S3_PD


title: P23_S1_NDMM


title: P23_S2_PD


title: P18_S2_PD


title: P18_S1_NDMM


title: P18_S3_PD


title: P9_S2_PD


title: P26_S2_PD


title: P28_S2_PD


title: P27_S2_PD


title: 17NP

first: TAIWEI

last: ZHANG

address: 180 Fenglin Rd

institute: Zhongshan Hospital Fudan University

data_processing:
High-throughput sequencing service was provided by CloudSeq Biotech (Shanghai, China). Transcriptome high-throughput sequencing and subsequent bioinformatics analysis were all done by Cloud-Seq Biotech (Shanghai, China). Briefly, total RNA was used for removing the rRNAs using Ribo-Zero rRNA Removal Kits (Illumina, USA) following the manufacturer's instructions. RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, USA).
10 pM libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 150 cycles on Illumina HiSeq Sequencer according to the manufacturer’s instructions.
Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). The high quality trimmed reads were used to analyse mRNAs.
The high quality reads were aligned to the human reference genome (UCSC hg19) with hisat2 software (v2.0.4). Then, guided by the Ensembl gtf gene annotation file, cuffdiff software (v2.2.1, part of cufflinks) was used to get the FPKM as the expression profiles of mRNA, and fold change, p-value and FDR were calculated with DeSeq.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: mRNA_Expression_Profiling_upload.txt: Matrix table with raw gene counts for every gene and every sample.

source_name: Nucleus Pulposus

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

value: Nucleus Pulposus

tag: classification

value: Degeneration


title: 18NP


title: 14NP


title: 16NP


title: P24_S1_NDMM


title: P9_S1_NDMM


title: 5NP


title: NAFLD liver sample 1

city: Edinburgh

first: John

middle: Roger

last: Wilson-Kanamori

address: 47 Little France Crescent

department: Centre for Inflammation Research

country: United Kingdom

institute: University of Edinburgh

data_processing:
Demultiplexing, alignment (to a modified version of the GRCh38 reference counting intronic reads in addition to those aligned to exons), and estimation of cell-containing partitions and associated UMIs using Cell Ranger 3.1.0
Quality control, normalisation, data integration, and downstream analysis using Seurat 3.1.2
Supplementary_files_format_and_content: fastq: fastq files of individual samples; mtx: count matrix in sparse matrix format; barcodes: barcode ids per sample; features: feature ids per sample

source_name: NAFLD liver explant

extract_protocol:
TST nuclei digestion
10x Genomics single cell 3' gene expression v3

value: liver explant

tag: condition

value: NAFLD


title: 4NP


title: Healthy liver sample 2

description: 10x Genomics single cell 3' gene expression v3

source_name: Healthy liver explant

value: Healthy


title: 2NP

value: Control


title: Healthy liver sample 1


title: 20NP


title: 19NP


title: NAFLD liver sample 2


title: siCD81 1

city: Chicago

first: Priyam

last: Patel

state: IL

address: 750 North Lake Shore Drive, Rubloff 11-146

department: Quantitative Data Science Core

institute: Northwestern University

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned to mm10 using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited file with read counts per gene

growth_protocol: DMEM complete +10% FBS, 1% Pen-strep; in an incubator at 37 C and 5% CO2

extract_protocol:
Total RNA of MDA-MB-231 cells was isolated using Trizol, phase separated by chloroform, and extracted by alcohol
Illumina TruSeq Total RNA-Seq Library Prep

treatment_protocol: siRNA and Dharmafect transfection reagent diluted in 1 ml Opti-MEM media and 9 ml DMEM media

tag: genotype/variation


title: siCD81 3


title: siCD81 2


title: siCon 2

value: non-targeting siRNA (siCon)


title: siCon 3


title: MIA PaCa-2 LINC00901 KO Rep2

city: Jackson

first: Yin-Yuan

last: Mo

state: MS

address: 2500 N State Street, G652

institute: Univ of Mississippi Medical Center

data_processing:
Cutadapt and perl scripts were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases.
sequence quality was verified using FastQC
map the reads of each sample to the genome by HISAT2
the paired-end sequencing on an Illumina Hiseq 4000 at LC Sciences following the vendor's recommended protocol.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: pancreatic cancer cell line

growth_protocol: MIA PaCa-2LINC00901 or vector control cells were  cultured in DMEM medium (Gibco) supplemented with 10% FBS and 2.5% horse serum.

extract_protocol:
The total RNA were extracted by Direct-zol RNA Miniprep Plus (Zymo, CA,USA) followingthe manufacturer's procedure. RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: epithelial cell

tag: genotype

value: LINC00901 KO

value: MIA PaCa-2


title: MIA PaCa-2 LINC00901 KO Rep3


title: MIA PaCa-2 LINC00901 KO Rep1


title: MIA PaCa-2 LCV2 Rep2

value: Vector Control


title: MIA PaCa-2 LCV2 Rep3


title: MIA PaCa-2 LINC00901 OE Rep1

growth_protocol: MIA PaCa-2 overexpressed LINC00901 or vector control cells were  cultured in DMEM medium (Gibco) supplemented with 10% FBS and 2.5% horse serum.

value: LINC00901 overexpression


title: MIA PaCa-2 LCV2 Rep1


title: D61N3

city: Madison

last: Svaren

state: WI

address: 1500 Highland Ave.

department: Comparative Biosciences

institute: University of Wisconsin

data_processing:
Illumina Pipeline  Casava 1.9
Reads were aligned to GRCm38/mm10 genome using the STAR aligner
Data were analyzed using DEseq2
Genome_build: Genome_build: mm10
Supplementary_files_format_and_content: raw counts and DEseq2 analysis

source_name: sciatic nerve

growth_protocol: Mice were housed with a normal light/dark cycles and ad libitum access to chow and water. D61N mutation in MPZ was created by CRISPR mutagenesis

extract_protocol:
Total RNA was purified using Zymo RNA purification kit
Illumina, RNA with PolyA selection,
Illumina HiSeq 2x150bp, performed by Genewiz (South Plainfield, NJ)

value: sciatic nerve

value: 2 months

value: Mpz wt/D61N


title: MIA PaCa-2 LINC00901 OE Rep2


title: MIA PaCa-2 LINC00901 OE Rep3


title: D61N1


title: MIA PaCa-2 pCDH Rep3


title: MIA PaCa-2 pCDH Rep2


title: ctl2

value: Mpz wt/wt


title: D61N2


title: ctl1


title: ctl3


title: siCon 1


title: muscle_Treg_D3_VMNA_vs_Vehicle_Mafko_vs_Mafwt_scRNAseq

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

description: scRNA-seq of muscle Treg 3 days post CTX injury in vehicle- vs VMNA-treated mice and Maf-wt vs Maf-ko mice

data_processing:
fastq quality read filtering (>80% with Sanger Q>20)
cell barcode demultiplexing (custom script)
Cellranger mkfastq
Cellranger count
Genome_build: mm10
Supplementary_files_format_and_content: filtered read counts>400-1000 genes, <4000-10000 UMIs

growth_protocol: Tregs from hindlimb muscles and colons of Foxp3Gfp, Foxp3-cre x Maffl/fl (MafΔTreg)  and Foxp3-cre x Mafwt/wt (Maf-wt) were sorted by flow cytometry 3 days post CTX injury.

extract_protocol:
Muscle and colon were enzymatically dissociated and digested with collagenase II/dispase to single cell suspensions. Tregs from hindlimb muscles and colons of Foxp3-Gfp, Foxp3-cre x Maffl/fl (MafΔTreg)  and Foxp3-cre x Mafwt/wt (Maf-wt) were sorted by flow cytometry 3 days post CTX injury. Single cells were then encapsulated in nanodroplets according to the 10x Genomics protocol.
10X Genomics library prep (3' V2 or 5' V3) Library were sequenced using a HiSeq4000.

treatment_protocol: Mice were injected them with 0.03 mL per muscle of Naja mossambica cardiotoxon (0.03 mg/mL) in one or more hindlimb muscles. For antibiotics treatment, mice were treated with 0.5 mg/ml vancomycin, 1 mg/ml metronidazole, 1 mg/ml neomycin, 1 mg/ml ampicillin (VMNA) dissolved in drinking water for three weeks prior to muscle injury.

tag: strain

value: 3 days after cardiotoxin-induced hindlimb skeletal muscle injury

value: Skeletal muscle


title: fibroblasts late repeat 2

city: Pittsburgh

first: Hatice

middle: Ulku

last: Osmanbeyoglu

state: Pennsylvania

address: 5607 Baum Blvd

department: Biomedical Informatics

institute: University of Pittsburgh

data_processing:
Library strategy: repli-seq
Raw Repli-seq reads were trimmed and filtered for quality using Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Reads were aligned using bowtie2 (Langmead B & Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9(4):357-359.) against mm10.
Genome-wide replication timing (RT) profiles were constructed, scaled and pooled for analysis as previously described (Marchal C, et al. (2018) Genome-wide analysis of replication timing by next-generation sequencing with E/L Repli-seq. Nat Protoc
Briefly, Log2 ratios of early versus late read counts were calculated for 50kb non-overlapping windows, Loess smoothed at 300kb windows.
Genome_build: Genome_build: mm10
Supplementary_files_format_and_content: Supplementary_files_format_and_content: bedGraph Genome-wide replication timing (RT) profiles: Log2 ratios of early versus late read counts were calculated for 50kb non-overlapping windows, Loess smoothed at 300kb windows.

source_name: ears

growth_protocol: CD8+ T cells: RPMI supplemented with 10% FBS, pen/strep, 1 % NEAA, 1 % sodium pyruvate, 5 mM HEPES pH 8.0, and 50 µM βME. Fibroblasts: DMEM containing 15 % FBS, pen/strep, 1 % NEAA, 1 % sodium pyruvate, 2.5 mM HEPES pH 8.0, and 0.12 mM βME

extract_protocol:
cells were fixed with 75 % EtOH, stained with PI, sorted into "early" and "late" S-phase based on DNA content, genomic DNA was extracted, sonicated, BrdU-labeled fragments were immunoprecipitated with an antibody
NEBNext kit (NEB#7370S) was used according to manufacturer's instructions. BrdU IP was performed after the end processing step and before indexing.

treatment_protocol: CD8+ T cells and fibroblasts were treated with DMSO or 5uM AZD6738 for total of 1 h and labeled ongoing replication with 10uM BrdU for the last 30 min. of treatment.

value: fibroblasts

value: B6.Cg-Thy1a/Cy Tg(TcraTcrb)8Rest/J

value: 4-8 weeks old

value: DMSO for 1 h

tag: timing

value: Late


title: fibroblasts early repeat 1

value: Early


title: CD8+ T cells late ATRi

source_name: spleen and lymph nodes

value: CD8+ T cells

value: 5uM AZD6738 for 1 h


title: fibroblasts late repeat 1


title: CD8+ T cells control late repeat 4


title: fibroblasts early repeat 2


title: CD8+ T cells control late repeat 3


title: CD8+ T cells control early repeat 4


title: CD8+ T cells control early repeat 3


title: CD8+ T cells control late repeat 1


title: CD8+ T cells control early repeat 2


title: muscle_Treg_D3_scRNAseq_counts

description: scRNA-seq of muscle Treg 3 days post CTX injury

source_name: Muscle Treg D3 post CTX


title: CD8+ T cells control early repeat 1


title: Day6-2 (miRNA-seq)

city: Beijing

first: Yibin

last: Zhu

address: Tsinghua, Beijing, China

institute: Tsinghua University

data_processing:
Remove low quality tags
Remove tags with 5' primer contaminants
Remove tags without 3' primer
Remove tags without insertion
Remove tags with poly A
Remove tags shorter than 18nt
Genome_build: miRBase 22.1 and Rfam 14.4
Supplementary_files_format_and_content: Excel files include RPKM values, log2 ratio, P values, FDR, KEGG Orthology, and GO analysis for each Sample ...

organism: Aedes aegypti

source_name: whole body

growth_protocol: Aedes Aegypti was reared at 28℃ and 80% humidity.

extract_protocol:
The total mosquito RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
small RNA-Seq

treatment_protocol: 7 days old mosquitos were following a blood meal, then cultured after 1hr or 6 days

value: Rockefeller

value: whole body

tag: protocol

value: blood feeding

tag: blood from

value: human donor 2

tag: time

value: 6 days


title: S0

description: sugar feeding

data_processing:
Remove low quality tags
Remove tags with 5' primer contaminants
Remove tags without 3' primer
Remove tags without insertion
Remove tags with poly A
Remove tags shorter than 18nt
Genome_build: miRBase and Rfam; FASTA with novel sequences is available on the series record
Supplementary_files_format_and_content: txt files include RPKM values, log2 ratio, P values, FDR, KEGG Orthology, and GO analysis for each Sample ...

extract_protocol:
The total mosquito RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 7 days old mosquitos were following a blood meal, then cultured after 1hr

tag: time after sugar meal

value: 1 hr


title: Day6-4 (miRNA-seq)

value: human donor 4


title: Day6-1 (miRNA-seq)

value: human donor 1


title: muscle_colon_Treg_D3_scRNAseq_scTcr

description: scRNA-seq and scTcr-seq of muscle and colon Treg 3 days post CTX injury

value: 3 days after cardiotoxin-induced hindlimb skeletal muscle injury

value: Skeletal muscle and colon


title: CD8+ T cells early ATRi

value: B6.Cg-Thy1a/Cy Tg(TcraTcrb)8Rest/J

tag: age


title: Plus_By_Plus.5

first: Tanvi

last: Sinha

state: California

address: 555 Mission Bay blvd. S, Apt 1608

data_processing:
Trimming of known adapters and low-quality regions was performed using fastq-mcf
Sequence quality control was assessed using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and RSeQC
Alignment of the provided samples to the reference genome (mouse mm9) was performed using STAR 2.5.2a
Reads were assigned to genes using the featureCounts, part of the Subread suite (http://subread.sourceforge.net/, and gene-level counts were arrived at using Ensembl gene annotation in GTF format.
Genome_build: Mm9
Supplementary_files_format_and_content: logCPM counts and differential expression statistics

source_name: E8.5 Embryo

extract_protocol:
Embryos were harvested, yolk sac was removed and flash frozen in liquid nitrogen. Total RNA was extracted using RNAeasy Micro Plus kit from Qiagen.
10ng of RNA from each sample was used to prepare cDNA libraries using the Trio RNA-seq kit from Tecan Biosciences

value: Yolk sac

value: Mixed

tag: Sex

value: F


title: Plus_By_Plus.6


title: Day6-3 (miRNA-seq)

value: human donor 3


title: Day0-4 (miRNA-seq)


title: Plus_By_Plus.4


title: Day0-3 (miRNA-seq)


title: Plus_By_Plus.1


title: Plus_By_enhDelta.4

value: Etv2 +/enhdelta


title: Plus_By_Plus.3


title: MIA PaCa-2 pCDH Rep1

tag: cell type

value: epithelial cell

value: Vector Control

tag: cell line

value: MIA PaCa-2


title: Plus_By_Plus.2

tag: tissue

value: M


title: Plus_By_enhDelta.3


title: Day0-1 (miRNA-seq)

value: Rockefeller

value: whole body

value: blood feeding


title: Plus_By_enhDelta.2


title: CD8+ T cells control late repeat 2

value: CD8+ T cells

value: 4-8 weeks old

tag: treatment

value: DMSO for 1 h

value: Late


title: ind3hB

city: Tulln

first: Harald

last: Berger

state: NOE

address: Konrad-Lorenzstraße 43

department: DAGZ

country: Austria

institute: Universität f. Bodenkultur Wien

data_processing:
Illumina HiSeq v4
Reads were filtered using trimmomatic and mapped on the Aspergillus nidulans genome assembly (A_nidulans_FGSC_A4_version_s10-m03-r07). Mapping was performed using BWA  and reverse transcripts were counted using python script HTSeq and exons as annotation features.
Normalization and statistics were done using R/Bioconductor and the limma and edgeR packages, using mean-variance weighting (voom) and TMM normalisation
Genome_build: A_nidulans_FGSC_A4_version_s10-m03-r07
Supplementary_files_format_and_content: Matrix table with RPKM values for each experiment
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Aspergillus nidulans

growth_protocol: A spore density of 4E6 spores/mL was inoculated in 50 mL  liquid AMM in 100 mL  Erlenmeyer flasks, respectively, and the culture grown at 37 °C and 180 rpm. The time of cultivation was 18 hours.AMM was prepared containing  50 mM glucose and 10 mM nitrate.

extract_protocol: poly A enrichment, NEXTERA library prep kit

treatment_protocol: Following 18 hours growth the samples were treated with Polaramycin B for 0, 0.5 or 3 hours

value: Polaramycin B 3 hours

tag: replicate

value: Replicate 2


title: ind05hB

value: Polaramycin B 30 min


title: ind05hA

value: Replicate 1


title: ind0hB

value: untreated


title: Plus_By_enhDelta.1

value: Yolk sac

value: Mixed

value: Etv2 +/enhdelta


title: Day0-2 (miRNA-seq)

value: human donor 2

value: 1 hr


title: ind0hA


title: enhDelta_By_enhDelta.5

value: Etv2 enhdelta/enhdelta

value: M


title: enhDelta_By_enhDelta.4

value: F


title: 17_SG_Wills_07_DMSO_24hpa_Run02_S8_R

city: Seattle

first: Anneke

middle: Dixie

last: Kakebeen

state: WA

address: 5611 9th Ave NW

department: Biochemistry

institute: University of Washington

data_processing:
Adapters were trimmed from reads and short (<20bp) or low-quality (Phred < 33) sequences were removed using Trim Galore! v0.4.4_dev.
Reads were aligned to xenTro9 using Bowtie2 v2.3.4.1 (–-very-sensitive -X 2000)
Duplicate reads were marked using Picard v2.18.5 ‘MarkDuplicates’ and removed using SAMtools v1.8 (samtools view -q 20 -F 1804).
Peaks were called using MACS2 v2.1.1.20160309 (options: --nomodel --shift -100 --extsize 200 -g 1.7e9). Consensus peak set used for differential accessibility was generated by combining all peaks called in all samples, reducing to 400 bp windows centered on summits, and merging peaks overlapping by 201 bp or more (bedtools merge -d -201, bedtools v2.27.1)
A matrix of counts for all samples was generated using ‘featureCounts’ v1.6.2 in the Subread package  (options: -F SAF -p)] in consensus regions
Genome_build: UCSC xenTro9
Supplementary_files_format_and_content: Per-sample peak summits called by MACS2 provided as bed files. Consensus peak set provided as SAF file. FeatureCounts output provided as tab-delimited text file.

organism: Xenopus tropicalis

source_name: regenerated tail tissue

growth_protocol: Use of Xenopus tropicalis was carried out under the approval and oversight of the IACUC committee at UW, an AALAC-accredited institution. Ovulation of adult X. tropicalis and generation of embryos by in vitro fertilization according to published methods. Fertilized eggs were de-jellied in 3% cysteine in 1/9x modified frog ringer’s solution (MR) for 10-15 minutes. Embryos were reared in 1/9x modified frog ringer’s solution (MR), until reaching stage 41 as assesed by Nieuwkoop and Farber.

extract_protocol:
At each timepoint, regenerating tadpoles were anesthetized until non-responsive to touch. A scalpel was used to amputate to the regenerated tail tissue. Regenerated tail tips were collected and spun down at 1000xg. Media was taken off and ~60 tails were resuspended in 200 uL of 0.035 mg/ml liberase in PBS (Roche 05401119001). Tails were left to incubate for 20 min at room temperature. A p-200 was then used to pipet the tails up and down gently and break up tail tissue. Once no visible chunks were apparent, cells were spun down for 3 min at 1000xg. Supernatant was disposed and cells were washed with 180 uL of 1xPBS. Cells were spun down for 3 min at 1000xg and supernatant was discarded. Cells were resuspended in 15 uL of TN5 reaction mix using the TN5 enzyme, buffer, and water from the Nextera DNA Sample prep kit (Illumina 15028212). Cells were transposed for 1 hr at 37C. Post transposition, cells were removed from 37C and DNA was purified using the Qiagen MinElute kit (Qiagen 28206). DNA was eluted in 10 uL of buffer EB. Purified DNA was then amplified using the 2xNEB PCR Master Mix (NEB M0541L), a universal forward primer, and an indexed reverse primer from the i7 Illumina series
Initial amplification as follows: 72C:5 min, 98C:30 s, then 5 cycles of 98C:10 s, 63C:30 s, 72C:1 min. 5 uL of the initial PCR product was then used for a 15 µl side qPCR reaction to determine how many more cycles to run to stop amplification prior to saturation. The side reaction was carried out as follows: 98C:30 s, then 30 cycles of 98C:10 s, 63C:30 s, 72C:1 min. The number of cycles was determined by taking the range of the starting and ending CT values and dividing that number by 4, then identifying how many cycles the sample had gone through at the derived CT value. The initial PCR reactions were then run for the calculated number of extra cycles and removed from the thermo cycler. Amplified samples were purified with the Qiagen MinElute kit and eluted in 20 uL of buffer EB. 5 uL of purified PCR product were run out on a 5% acrylamide gel in 1xTBE at 100V for ~45 min. Gels were stained with Ethidium Bromide and imaged on the gel imager (BioRad). Samples with sufficient periodic bands, relating to length of DNA to wrap a mono-, di-, tri- nucleosome, were then run out on a bioanalyzer. Library concentrations were taken using the Qubit high sensitivity dsDNA assay. Libraries were pooled by normalizing library concentrations to the lowest concentration and adding equal volumes of libraries for a minimum of 5 ng of each library.
Libraries were sequenced on the Illumina Next-Seq platform across one NextSeq 500 High Output Kit v2.5 (150 cycles, Illumina CAT. 20024907) for TSA and respective controls and one Next-seq High output 150 cycle and one Next-seq Mid output 150 cycle kit (150 cycles, Illumina CAT.  20024904) Libraries were sequenced with, paired end, 75 bp reads at the Seattle Genomics facility.

treatment_protocol: X. tropicalis tadpoles were reared to stage 41. Tadpoles were anesthetized with 0.05% ms-222 in 1/9x MR and tested for touch prior to amputation. Once anesthetized a sterilized scalpel was used to amputate the most distal 1/3 of the tail. Tadpoles were transferred from anesthetic media into fresh 1/9xMR within 10 minutes post amputation and left to regenerate at a density not greater than 3 tadpoles per 1 mL of media.Tricostatin A (TSA, Sigma T8552) and 3-Deazaneplanocin (DZNep, Cayman chemical 13828) were suspended in DMSO as a vehicle. For experiments inhibitors were diluted to the following final concentrations in 1/9th MR; TSA 20nM, DZNep 15 uM, DMSO controls contained 1uL DMsO per 1 mL 1/9th MR.

tag: hours post amputation

value: DMSO


title: enhDelta_By_enhDelta.2


title: ind3hA


title: enhDelta_By_enhDelta.3


title: 16_SG_Wills_07_TSA_24hpa_Run02_S7_R

value: TSA


title: 15_SG_Wills_07_DMSO_6hpa_Run02_S6_R


title: enhDelta_By_enhDelta.1


title: Delta_By_Plus.6


title: Delta_By_Plus.5


title: 14_SG_Wills_07_TSA_6hpa_Run02_S5_R


title: 13_SG_Wills_07_DMSO_3hpa_Run02_S4_R


title: 09_SG_Wills_07_WT_Whole-Tail_24hpa_Run01_S9_R

source_name: Uninjured tail tip

value: uninjured


title: 12_SG_Wills_07_TSA_3hpa_Run02_S3_R


title: 11_SG_Wills_07_WT_0hpa_Run02_S2_R

source_name: tissue proximal to amputation


title: 10_SG_Wills_07_WT_Whole-Tail_0hpa_Run02_S1_R


title: 07_SG_Wills_07_TSA_24hpa_Run01_S7_R


title: Delta_By_Plus.4


title: 06_SG_Wills_07_DMSO_6hpa_Run01_S6_R


title: 08_SG_Wills_07_DMSO_24hpa_Run01_S8_R


title: 18_SG_Wills_07_WT_Whole-Tail_24hpa_Run02_S9_R

source_name: uninjured tail tip


title: Delta_By_Plus.3


title: 05_SG_Wills_07_TSA_6hpa_Run01_S5_R


title: 02_SG_Wills_07_WT_0hpa_Run01_S2_R


title: Delta_By_Plus.2


title: G017_SG_Wills_08_UNI24_S8_R


title: 01_SG_Wills_07_WT_Whole-Tail_0hpa_Run01_S1_R


title: G016_SG_Wills_08_DZnep24HPA_S7_R

value: DZNep


title: Mast cells_cyclic hypoxia_exp1

city: Mexico city

first: Monica

last: Lamas

state: Distrito Federal

address: Calzada de los Tenorios 235

department: Pharmacobiology

country: Mexico

institute: CINVESTAV

description: Experiment 1 of 1

hyb_protocol: Equal quantities of label cDNA were hybridized using hybridization solution UniHyb (TeleChem International INC) to the 22 thousand oligos mouse arrays for 14 h at 42°C.

scan_protocol: Array images were acquired and quantified on GenePix 4100-A reader using GenePix software (Molecular Devices, USA).

data_processing: Microarray data analysis was performed using the genArise free software package, developed in the Computing Unit of Cellular Physiology Institute of UNAM (http://www.ifc.unam.mx/genarise/). This software is a tool for dual-color microarray data implemented in the R language. It contains specific functions to perform an analysis of DNA microarrays data to select genes that are significantly differentially expressed under different conditions by calculating an intensity-dependent Z-score.

label: Cy3 (Alexa555)

source_name: Normoxic bone marrow-derived mast cells

label_protocol: 10 μg of pooled RNA were used for cDNA synthesis, incorporating dUTP-Alexa555 or dUTP-Alexa647. This was perform employing the First-Strand cDNA labeling kit from Invitrogen. The incorporation of the fluorophore was analyzed using the absorbance at 555 and 650 nm for Alexa555 and Alexa647, respectively.

growth_protocol: Bone marrow-derived mast cells (BMMCs) were differentiated in vitro by extracting the bone marrow from tibias of C57BL/6J mice four to six weeks old. BMMCs were maintained in culture medium RPMI supplemented with 20 ng/mL IL-3, 10% heat-inactivated fetal bovine serum, 25mM HEPES, 50 μM β-mercaptoethanol, 0.1 mM non-essential amino acids, 1mM pyruvate, 100 U/ml penicillin, and 100 μg/ml streptomycin. The culture medium was changed every 7 days.

extract_protocol: Total RNA was extracted using TRIzol according to the manufacturer's instructions

tag: primary cell culture age

value: 6-8 wk of age

value: BMMCs manteined at 21% oxygen for 2.5 hours

label: Cy5 (Alexa647)

source_name: Hypoxic bone marrow-derived mast cells

value: BMMCs exposed 1 hour at 1% oxygen, plus 30 minutes at 21% oxygen, plus 1 hour at 1% oxygen (H2)


title: Delta_By_enhDelta.5

value: Etv2 delta/enhdelta


title: G015_SG_Wills_08_Veh24HPA_S6_R


title: G011_SG_Wills_08_Veh3HPA_S2_R


title: Delta_By_Plus.1


title: G014_SG_Wills_08_DZnep6HPA_S5_R


title: 04_SG_Wills_07_DMSO_3hpa_Run01_S4_R


title: Delta_By_enhDelta.2


title: G007_SG_Wills_08_Veh24HPA_S7_R


title: Delta_By_enhDelta.3


title: G013_SG_Wills_08_Veh6HPA_S4_R


title: Delta_By_Delta.5


title: G009_SG_Wills_08_UNI24_S9_R


title: G004_SG_Wills_08_DZnep3HPA_S4_R


title: Delta_By_enhDelta.4


title: Delta_By_enhDelta.1


title: G005_SG_Wills_08_Veh6HPA_S5_R


title: G006_SG_Wills_08_DZnep6HPA_S6_R


title: G003_SG_Wills_08_Veh3HPA_S3_R


title: G012_SG_Wills_08_DZnep3HPA_S3_R


title: 03_SG_Wills_07_TSA_3hpa_Run01_S3_R


title: G008_SG_Wills_08_DZnep24HPA_S8_R


title: shCtrl mESC

city: Shanghai

first: Chenqi

last: Lu

address: Handan Road 220

department: school of lifescience

institute: Fudan University

description: Shctrl

data_processing:
Adapters and reads with lower mapping quility were trimed by trim_galore.
Reads were aligned to the mouse mm10 reference genomes using the Hisat2.
Raw counts were quantified against Ensemble transcript (GRCm38.83) and annotated by featureCount.
Differentially expressing genes were detected by nbinomTest in DESeq.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes raw count for each sample.

source_name: Mouse ESCs (46C)

growth_protocol: Mouse ESCs (46C) were cultured on feeders in mouse ESC medium containing 15% fetal bovine serum (FBS), 0.1 mM 2-mercaptoethanol, 2 mM L-glutamine, 0.1 mM nonessential amino acids (NEAA), 1 mM sodium pyruvate and LIF in DMEM. For differentiation without LIF, cells were cultivated in mouse ESC medium without LIF and then plated in 12-well low attachment plates. For commitment assays, mouse ESCs were cultured without LIF for 3 days, and then re-plated with 500 cells to further culture for five days with mouse ESC medium.

extract_protocol:
Mouse ESCs were harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For RNA interference, short hairpin RNA (shRNA) targets the transcript of linc1557 were used and cloned into the pLKO.1-TRC vector. After virus infection of mouse ESCs, we used 1 mg/ml puromycin to treat cells for two days, then picked out and obtained the stably infected clones for further analysis.

value: ESCs (46C)

value: control shRNA


title: sh1557 mESC

value: linc1557 knockdown


title: G002_SG_Wills_08_0HPA_S2_R


title: Delta_By_Delta.4

value: Yolk sac

value: Mixed


title: G010_SG_Wills_08_WhT41_S1_R


title: G001_SG_Wills_08_WhT41_S1_R


title: Delta_By_Delta.3


title: Delta_By_Delta.2


title: MNase-seq_TFDP1KO_rep1

city: Kanazawa

first: Yusuke

last: Miyanari

address: Kakuma

institute: Kanazawa University

data_processing:
The sequenced reads were quality controlled by Trimmomatic with the option “ILLUMINACLIP:adapter_file:2:30:10 LEADING:20 TRAILING:20 MINLEN:36”.
Bowtie2 with the parameter “-- very-sensitive --maxins 400” mapped MNase-seq reads to the hybrid reference genome (hg38 and dm6).
The reads mapped to multiple positions, chrY, chrM, and blacklisted regions were removed by Samtools (http://www.htslib.org/), and the duplicated reads were filtered by Picard MarkDuplicates.
The scaling factors were calculated by using total mapped read counts for hg38 and dm3, and were used for spike-in normalization.
Genome_build: hg38
Supplementary_files_format_and_content: The read coverage on hg38 were normalized with the scaling factors using bamCoverage with parameters “--binSize 1 --MNase --sclaeFactor”

source_name: human haploid eHAP cells

extract_protocol:
To analyze nucleosome occupancy quantitatively in control and TFDP1 knockout cells, We included Drosophila S2 cells as a spike-in control. After mixing 1x106 eHAP cells and 5x104 S2 cells, cells were washed with PBS containing 0.1% BSA and subsequently permeabilized with 0.5% IGEPAL CA-630 in RSB buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 1 mM CaCl2, 3 mM MgCl2 and 0.5 mM PMSF) for 20 min on ice. Nuclei were digested in RSB containing 2.5 U MNase (Takara) at 37 ˚C for 10 min. The reaction was terminated by adding EDTA, EGTA and Proteinase K. The extracted DNA was fractionated by agarose gel electrophoresis, and DNA fragments between 125 and 175 bp representing mono-nucleosome was purified with Monarch PCR & DNA Cleanup Kit followed by treatment with RNase.
Libraries for sequencing were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) and sequenced on Illumina HiSeq3000 for 100 bp paired-end reads. Two biological replicates were analyzed for each experimental condition.

treatment_protocol: Cas9-expressing eHAP cells were transfected with a plasmid expressing sgRNAs against indicated gene and puromycin-resistance gene using FuGENE HD (Promega), and selected with puromycin from 24 hrs post-transfection to 72 hrs. On 5 days post-transfection, cells were used for MNase-seq assays.

value: eHAP

value: knockout

tag: knockout gene


title: MNase-seq_NC_rep2

tag: genotype

value: wild-type


title: ChIP-seq_eHAP input gDNA

data_processing:
The sequenced reads were quality controlled by Trimmomatic with the option “ILLUMINACLIP:adapter_file:2:30:10 LEADING:20 TRAILING:20 MINLEN:36”.
Reads were mapped to human genome (hg38) using Bowtie2 with the parameter “-N 1”
Non-uniquely mapping reads were filtered out using XS tag.
PCR duplicates and reads mapped to ENCODE blacklisted regions (Amemiya,ScieRep,2019) were removed using Picard Tools
Genome_build: hg38
Supplementary_files_format_and_content: Read coverages for ChIP-seq were normalized against the input DNA library by using deeptools bamCompare with options “--scaleFactorsMethod SES --operation subtract --extendReads 150 --bin 30”

source_name: a control input DNA

extract_protocol:
Chromatin immunoprecipitation was conducted as described previously [Takahashi 2014 Nat Comm] with the following modifications. Chromatin samples were digested with MNase at 37 ˚C for 20 min followed by sonication with Bioruptor (On, 30 s; Off, 30 sec; Power, High; 2 cycles). After centrifugation at 15,000 rpm for 10 min at 4 °C, the supernatants were incubated with a Dynabeads-conjugated primary antibody at 4 °C overnight with gentle agitation. After washing with RIPA buffer (50 mM Hepes-KOH, pH 7.5, 500 mM LiCl, 1 mM EDTA, 1% IGEPAL CA-630 and 0.7% sodium deoxycholate), eluates were purified using Monarch PCR & DNA Cleanup Kit (NEB).
libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB)

tag: transgene

tag: chip antibody

value: none (input)


title: MNase-seq_NC_rep1


title: ChIP-seq_TFDP1-FL1

source_name: ChIP-seq for FLAG (TFDP1), rep1

value: anti-FLAG (Sigma, F1802)


title: Vhl; Tsc1 cDKO rep3 [72520_L_IGO_07112_D_41_S2]

city: New York

first: Jianing

last: Xu

state: NY

address: 1275 York Ave

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Sequenced reads were trimmed for adaptor sequence, and mapped to mm10 whole genome using STAR-2.5.3a (PARTEK Flow)
Aligned reads were quantified to mm10 - Ensembl Transcripts release 83 (PARTEK Flow)
Genome_build: mm10
Supplementary_files_format_and_content: CSV files containing gene raw counts for individual samples generated by Partek Flow

source_name: Vhl; Tsc1 cDKO_kidney cortices

extract_protocol:
Kidney cortices were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

tag: genotype/variation

value: Ksp-Cre; VhlF/F; Tsc1F/F

value: post natal 4 weeks

value: Kidney


title: ChIP-seq_H3K4me3-2

source_name: ChIP-seq for H3K4me3, rep2

value: anti-H3K4me3 (MAB Institute, MABI0304)


title: ChIP-seq_TFDP1-FL2

source_name: ChIP-seq for FLAG (TFDP1), rep2


title: ChIP-seq_H3K27me3-1

source_name: ChIP-seq for H3K27me3, rep1

value: anti-H3K27me3 (Cell Signaling Technology, 9733)


title: Vhl; Tsc1 cDKO rep4 [72520_R_IGO_07112_D_42_S43]


title: Vhl; Pbrm1 cDKO rep4 [75560_R_IGO_07112_D_20_S10]

source_name: Vhl; Pbrm1 cDKO_kidney cortices

value: Ksp-Cre; VhlF/F; Pbrm1F/F


title: Vhl; Tsc1 cDKO rep2 [72519_R_IGO_07112_D_40_S42]


title: Vhl; Tsc1 cDKO rep1 [72519_L_IGO_07112_D_39_S7]


title: ChIP-seq_H3K27ac-2

source_name: ChIP-seq for H3K27ac, rep2

value: anti-H3K27ac (MAB Institute, MABI0309)


title: ChIP-seq_H3K4me3-1

source_name: ChIP-seq for H3K4me3, rep1


title: Vhl; Pbrm1 cDKO rep3 [75560_L_IGO_07112_D_19_S9]


title: ChIP-seq_H3K27ac-1

source_name: ChIP-seq for H3K27ac, rep1


title: Vhl; Pbrm1 cDKO rep1 [68617_L_IGO_07112_D_17_S20]


title: Delta_By_Delta.1

source_name: E8.5 Embryo

tag: strain

value: M


title: Vhl; Pbrm1 cDKO rep2 [68621_L_IGO_07112_D_18_S17]


title: ATAC-seq_Group2_EIF3D_rep2

data_processing:
The sequenced reads were quality controlled by Trimmomatic with the option “ILLUMINACLIP:adapter_file:2:30:10 LEADING:20 TRAILING:20 MINLEN:36”.
Bowtie2 with the parameter “-N 1 -X 2000 --no-mixed --no-discordant” mapped ATAC-seq reads to the hybrid reference genome (hg38 and dm6).
The reads mapped to multiple positions, chrY, chrM, and blacklisted regions were removed by Samtools (http://www.htslib.org/), and the duplicated reads were filtered by Picard MarkDuplicates.
The positions of HG38-mapped reads were corrected by shifting + 4 bp for (+) strand or -5 bp for (-) strand and were used for detecting peak regions.
The scaling factors were calculated by using total mapped read counts for hg38 and dm3, and were used for spike-in normalization.
Genome_build: hg38
Supplementary_files_format_and_content: BigWig files for each replicate were generated by using deeptools bamCoverage with option --sclaeFactor and subsequently merged into one file by calculating mean enrichment.

extract_protocol:
ATAC-seq was performed as described previously (Buenrostro et al., 2013; Corces et al., 2017) with some modifications. To quantitatively analyze ATAC-seq data between experimental conditions, we used a fixed number of Drosophila S2 cells as a spike-in control for each sample. The read counts for the spike-in were used to internally calibrate ATAC-seq data, as described previously (Bonhoure et al., 2014; Hu et al., 2015; Orlando et al., 2014). In brief, 1x104 (for group1) or 2.5x103 S2 cells (for group2) were first mixed with 1x105 eHAP cells in a tube, washed with cold PBS, and centrifuged at 935 x g for 5 min. Cells were permeabilized with cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Then cells were transposed using Tn5 complex with MEAB34 adaptors in TAPS-DMF buffer at 37 ˚C for 30 min. Genomic DNA was purified with Monarch PCR & DNA Cleanup Kit (NEB).
After amplification of transposed DNA using Q5 High-Fidelity 2X Master Mix (NEB), DNA was size-selected using SPRI beads to produce libraries with fragments between 150 and 600 bp. To reduce a contamination of mitochondrial DNA, the libraries for group2 were treated with an anti-mitochondrial DNA CRISPR/Cas9 library to specifically digest mitochondrial DNA as described previously (Montefiori et al., 2017). The libraries were sequenced on HiSeq3000 or HiSeq2500 for 100 bp or 50 bp paired-end reads, respectively. Two biological replicates were analyzed for each experimental condition.

tag: group


title: Tsc1 cKO rep4 [72536_L_IGO_07112_D_38_S11]

source_name: Tsc1 cKO_kidney cortices

value: Ksp-Cre; Tsc1F/F

tag: age


title: ATAC-seq_Group2_THAP11_rep2


title: ChIP-seq_H3K27me3-2

source_name: ChIP-seq for H3K27me3, rep2


title: Tsc1 cKO rep2 [72534_R_IGO_07112_D_44_S6]


title: CAFs shControl replicate 1

first: Mark

middle: Adam

last: Eckert

address: 929 East 57th St, W107

department: OB/GYN

institute: University of Chicago

description: replicate 1 of shControl CAFs

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Illumina GenomeStudio GSGX 1.9.0

label: biotin

source_name: Human CAFs

label_protocol: Biotinylated cRNA were prepared with the Ambion Total Prep Kit.

extract_protocol: RNA was extracted from confluent 10 cm dishes using Qiagen RNeasy Mini kit using manufacturer's recommended protocol. Quality control was performed with Agilent Bioanalyser.

tag: shRNA construct

value: shControl

tag: vector backbone


title: Tsc1 cKO rep1 [72533_L_IGO_07112_D_43_S4]


title: ATAC-seq_Group2_THAP11_rep1

tag: cell line


title: MV (L.i.t.)

city: Houston

first: Ningbo

last: Zheng

state: Texas

address: 3455 Cullen Blvd

institute: University of Houston

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2
We used featureCounts to collect the raw gene count information with the following configurations -t exon -g gene_name.
Assembly: mm10
Supplementary files format and content: tab-delimited file with gene names in column one and counts in the second column.
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Melanoma cell line

growth_protocol: B6 mice were inoculated s.c with 1×106 B16 cells. Indicated treatments were administrated on day 7 when tumors reached ~7×6 mm.

extract_protocol:
Tumor tissues (~100 mg/mice, 12 days after ACT) were harvested. Total RNA was extracted from the tumor tissues for RNA-Seq (n=2).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Adjuvant CTX (i.p.) was administered to mice one day before ACT. In group 2 and 3, 5×106 TRP-1 T cells were i.v. injected. In group 3, free MV was intratumorally injected only into the left tumors [refers to ‘MV (L. i.t.)’], and right tumors did not receive intratumorally injection [refers to ‘remote tumor (no MV)’].  In group 4, 5×106 TRP-1 TMV cells were i.v. injected.

tag: tissue

value: Skin

tag: disease

value: Melanoma

value: MV was intratumorally injected only into the left tumors, TRP-1 T cells were i.v. injected.


title: CAFs shControl replicate 2

description: replicate 2 of shControl CAFs


title: CD10 positive  stromal cells_ectopic endometrium

city: hefei

first: xuxu

last: zhao

address: 81 Meishan Road

institute: Anhui Medical University

description: Gene expression in human ectopic endometrium CD10 positive stromal cells

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, limma packages in R.

source_name: CD10 positive  stromal cells,ectopicendometrium

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

growth_protocol: Fresh specimens were collected without contamination and transferred on ice on DMEM/F12 (Hyclone; USA).First, we minced all fresh sterile tissues into small pieces. Then we enzymatically digested them in DMEM/F12 with 5 mg/mL collagenase type IV (Sigma; USA) and 50U/ml deoxyribonuclease type I (DNase I; Sigma; USA) for 1 hour at 37℃. Epithelial cells and undigested tissue were removed from cell suspensions using a 70 μm strainer. After centrifuging for 10 min at 600×g to further remove leukocytes and erythrocytes, we washed stromal cells with 1% PBS. All stromal cells have finally been resuspended in 1% PBS for later use.

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

value: ectopic endometrium

tag: gender

value: female

tag: menstrual cycle

value: secretory phase


title: Pbrm1 cKO rep4 [75554_R_IGO_07112_D_28_S12]

source_name: Pbrm1 cKO_kidney cortices

value: Ksp-Cre; Pbrm1F/F


title: ATAC-seq_Group2_UBAP2L_rep2

source_name: human haploid eHAP cells

growth_protocol: eHAP cells (Horizon Discovery) (Essletzbichler et al., 2014) grown in Iscove’s Modified Dulbecco’s Medium (IMDM, Wako) supplemented with 10% FBS (Sigma) and penicillin/streptomycin (Wako).

value: eHAP

value: knockout


title: CTX

tag: treatment

value: PBS was intratumorally injected only into the left tumors


title: Pbrm1 cKO rep3 [73047_R_IGO_07112_D_27_S41]

value: post natal 4 weeks

value: Kidney


title: ATAC-seq_Group2_DCAF7_rep1

tag: knockout gene


title: CAFs shNNMT replicate 2

description: replicate 2 of shNNMT CAFs

value: shNNMT


title: ATAC-seq_Group2_DCAF7_rep2

tag: genotype


title: Pbrm1 cKO rep2 [73047_L_IGO_07112_D_26_S24]


title: Tsc1 cKO rep3 [72535_L_IGO_07112_D_37_S48]


title: monocytes sorted from spleen, high_GS_treated3

city: London

first: Jun

last: Wang

address: Charterhouse Square

institute: Barts Cancer Institute, Queen Mary, London

data_processing:
Illumina Casava1.9 software used for basecalling.
Raw reads were aligned to the reference genome (mm10) using Tophat2 or STAR aligner (for myeloid cells). Number of reads aligned to the exonic region of each gene were counted using the Rsamtools Bioconductor package based on the genome annotation from UCSC ‘ensGene’ table. Genes on the sex chromosomes were excluded from the following analysis.
Only genes that achieved at least two read count per million reads (CPM) in at least three samples were kept. Read counts were further normalized using the conditional quantile normalization (cqn) method accounting for gene length and GC content.
This generated normalized log2 RPKM values for each filtered gene across all samples. Differential expression analysis was performed using LIMMA, with the array quality weights function applied
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include log2 transformed RPKM values for each sample

source_name: monocytes sorted from spleen

extract_protocol:
Whole tumours were frozen in RNAlater and RNA was extracted using Qiagen RNeasy mini kit. The RNA library was prepared using TruSeq Stranded Total RNA library preparation with Ribozero Gold and quality measured on Agilent BioAnalyzer. The NGS was performed on HiSeq 2000 TM using V3 flow cells on one lane at 100bp paired-end. whole RNA was extracted from pellets of sorted myeloid cells using Qiagen RNeasy mini kit and stored in -80 until analysis. Libraries were made by using either IlluminaTrue Seq kits or Nugen Library Construction kits. Samples were multiplexed in 4 lanes and sequenced via the Illumina HiSeq2000 platform. 100 base-pair, paired-end data sequence data were then generated and subsequently analysed.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: KPC

value: myeloid cell

value: GS9820 treated

tag: days after treatment

value: 14 days


title: CAFs shNNMT replicate 1

description: replicate 1 of shNNMT CAFs


title: CD10 positive  stromal cells_normal endometrium

description: Gene expression in human normal endometrium CD10 positive stromal cells

source_name: CD10 positive  stromal cells,normal endometrium

value: normal endometrium


title: Remote tumor (no MV)

value: Skin

value: Melanoma


title: TRP-1MV

value: TRP-1MV cells were i.v. injected.


title: ATAC-seq_Group2_EIF3D_rep1


title: ATAC-seq_Group2_UBAP2L_rep1


title: monocytes sorted from spleen, high_GS_treated2


title: MNase-seq_TFDP1KO_rep2


title: monocytes sorted from spleen, high_GS_treated4


title: Vhl cKO rep4 [72799_R_IGO_07112_D_24_S5]

source_name: Vhl cKO_kidney cortices

value: Ksp-Cre; VhlF/F


title: ATAC-seq_Group2_NAA10_rep2


title: monocytes sorted from spleen, high_vehicle2

value: vehicle control


title: ATAC-seq_Group2_CNOT3_rep2


title: monocytes sorted from spleen, high_vehicle3


title: Vhl cKO rep2 [68705_L_IGO_07112_D_22_S37]


title: monocytes sorted from spleen, high_vehicle1


title: ATAC-seq_Group2_NAA10_rep1


title: ATAC-seq_Group2_EP400_rep2


title: Pbrm1 cKO rep1 [73046_R_IGO_07112_D_25_S46]

value: Ksp-Cre; Pbrm1F/F


title: ATAC-seq_Group2_EP400_rep1

value: eHAP


title: ATAC-seq_Group2_HNRNPU_rep2

value: knockout

value: HNRNPU


title: WT rep3 [68737_R_IGO_07112_D_9_S38]

source_name: WT_kidney cortices

value: Ksp-Cre

value: post natal 4 weeks


title: PMNs sorted from spleen, low_GS_treated3

source_name: PMNs sorted from spleen


title: PMNs sorted from spleen, low_GS_treated4


title: WT rep4 [75666_R_IGO_07112_D_10_S30]

value: Kidney


title: ATAC-seq_Group2_CNOT3_rep1


title: PMNs sorted from spleen, low_GS_treated2

value: KPC


title: Vhl cKO rep3 [72798_R_IGO_07112_D_23_S40]


title: ATAC-seq_Group2_HNRNPU_rep1


title: Vhl cKO rep1 [68702_L_IGO_07112_D_21_S15]


title: PMNs sorted from spleen, low_GS_treated1

value: myeloid cell


title: WT rep1 [68735_R_IGO_07112_D_1_S1]


title: ATAC-seq_Group2_NC2_rep2

value: wild-type

value: a control for Group2


title: WT rep2 [68736_R_IGO_07112_D_2_S49]


title: ATAC-seq_Group2_NC2_rep1


title: FibroblastSample4, EpithelialKrasG12DOncogene, p53flfl Fibroblasts

city: Charleston

first: Michael

middle: C

last: Ostrowski

state: SC

address: 86 Jonathon Lucas Street

department: Biochemistry & Molecular Biology

institute: Medical University of South Carolina

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials according to the manufacturers instructions

scan_protocol: Affymetrix Gene ChIP Scanner 3000

data_processing:
Raw signal intensity preprocessing from .CEL files was done using RMA. This consisted of background adjustment, quantile normalization, and median polish. R was used to form class comparisons to determine differentially expressed genes at P < 0.05 with the Student's t-test. For heat map construction, geometric means after RMA normalization from control samples was set as the reference, with the color (blue or red) corresponding to the ratio between the gene expression in mutant and reference samples. Functional gene annotation was done with DAVID.
MoEx-1_0-st-v1, Mm9
MoEx-1_0-st-v1 Annotations, Probeset, Mm9

source_name: Mammary fibroblasts

label_protocol: Samples were fragmented and  labeled using the GeneChip™ WT Terminal Labeling Kit

growth_protocol: Isolated mammary epithelia and fibroblasts grown in vitro

extract_protocol: Total RNA extraction using Trizol (Invitrogen) followed by purification with RNeasy (Qiagen)

treatment_protocol: None other than described genetic modification. Mice were treated with doxycycline for 9 weeks prior to epithelial and fibroblast isolation and cells maintained in doxycycline in vitro

tag: cell type

value: Mammary fibroblasts

tag: epithelia status

value: KrasG12D mutation

tag: fibroblast status

value: Wild-type p53


title: PMNs sorted from spleen, low_vehicle3

tag: strain


title: PMNs sorted from spleen, low_vehicle2


title: H3K9me2 ChIP seq

city: Berkeley

first: Jose

middle: A

last: Viscarra

state: Ca

address: 220 Morgan Hall

department: NST

institute: UC Berkeley

data_processing:
Adapters were removed using FASTQ Groomer v1.1.1
Reads were aligned to reference genome mm10 using Map with BWA v0.7.17.4
Peaks were called using MACS v1.0.1
bigwig files were generated using Wig/Bedgraph-to-bigwig converter v1.1.1
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig file is included for visualization of peaks using genome browser.

source_name: liver

growth_protocol: Mice were maintained on chow diet until 6 weeks of age.

extract_protocol:
Liver was crosslinked and minced, nuclei were isolated and sonicated.  Lysates were clarified and ChIP reactions were set up using H3K9me2 antibody.
NEBNext Ultra DNA library prep kit was used in preparation of libraries.  Manufacturers protocol was followed.

treatment_protocol: Mice were fasted overnight, then refed a high carbohydrate diet for 6 hours.

value: liver

tag: chip antibody

value: Histone H3 dimethyl K9 (ab1220)


title: FibroblastSample3, EpithelialKrasG12DOncogene, p53flfl Fibroblasts


title: Input DNA


title: FibroblastSample2, EpithelialKrasG12DOncogene, p53flfl Fibroblasts


title: KPC tumour, GS_treated4

source_name: KPC tumour

value: tumour

value: GS9820 treated

value: 14 days


title: FibroblastSample1, EpithelialKrasG12DOncogene, p53flfl Fibroblasts


title: KPC tumour, GS_treated3


title: KPC tumour, GS_treated5


title: FibroblastSample4, EpithelialKrasG12DOncogene, FspCrep53flfl Fibroblasts

value: p53 deletion


title: PMNs sorted from spleen, low_vehicle1

value: vehicle control


title: KPC tumour, vehicle5


title: FibroblastSample4, NoEpithelialOncogene, p53flfl Fibroblasts

value: Wild-type


title: KPC tumour, vehicle6


title: KPC tumour, GS_treated2


title: FibroblastSample3, EpithelialKrasG12DOncogene, FspCrep53flfl Fibroblasts


title: FibroblastSample2, EpithelialKrasG12DOncogene, FspCrep53flfl Fibroblasts


title: KPC tumour, GS_treated1


title: FibroblastSample3, NoEpithelialOncogene, p53flfl Fibroblasts


title: T3

city: yinchuan

first: yufei

last: zhang

state: ningxia

address: ningxia medicine university

institute: ningxia medicine university

description: TOLF group3

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions.  On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.   After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slices are scanned immediately after washing on an Agilent DNA microarray scanner (G2505C) using a color scan setting of 1x44K array slices (scan area 61x21.6 mm, scan resolution 10um, dye channel set to green, green PMT set to 100%)

data_processing: Feature extraction software 9.1 (Agilent) is used to analyze the scanned images with default parameters, and the signal strength after background subtraction and spatial de-trending is obtained.  Exclude features marked as feature non-uniform outliers in feature extraction.

source_name: TOLF group3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).   Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using Quick Amp Labeling Kit, one-color (Agilent P/N 5190-0442), as recommended by manufacturers.  Use GLOBINclear (Ambion Inc., Austin, TX) to further reduce globin information, specifically removing a- and B-globin.  The RNA was quantified using a nanodrop-1000 spectrophotometer and the quality was monitored using an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Peripheral blood of the experimental group and the control group was collected on an empty stomach and stored in AN EDTA anticoagulant tube. All the EDTA anticoagulant blood samples were centrifuged by a high-speed centrifuge within 30 minutes (3000rpm, 10min). After that, the upper plasma was collected and placed in a cryopreserved tube and frozen at -80 ℃ for use. Frozen plasma was frozen and crushed with liquid nitrogen using a biological grinder, and specimens were homogenized by adding TRIzol to a bead-mill tissue grinder.

tag: disease state

value: OLF

value: whole blood

tag: Sex

value: male

tag: age


title: T2

description: TOLF group2

source_name: TOLF group2


title: FibroblastSample1, NoEpithelialOncogene, p53flfl Fibroblasts


title: T1

description: TOLF group1

source_name: TOLF group1


title: C4

description: Control group4

source_name: Control group4

value: control

value: female


title: T4

description: TOLF group4

source_name: TOLF group4


title: FibroblastSample4, NoEpithelialOncogene, FspCrep53flfl Fibroblasts


title: T5

description: TOLF group5

source_name: TOLF group5


title: C1

description: Control group1

source_name: Control group1


title: KPC tumour, vehicle7

value: KPC


title: KPC tumour, vehicle3


title: KPC tumour, vehicle4


title: KPC tumour, vehicle1


title: FibroblastSample1, NoEpithelialOncogene, FspCrep53flfl Fibroblasts

value: Mammary fibroblasts


title: FibroblastSample1, EpithelialKrasG12DOncogene, FspCrep53flfl Fibroblasts

value: KrasG12D mutation


title: C2

description: Control group2

source_name: Control group2


title: FibroblastSample3, NoEpithelialOncogene, FspCrep53flfl Fibroblasts


title: KPC tumour, vehicle2


title: FibroblastSample2, NoEpithelialOncogene, p53flfl Fibroblasts

value: Wild-type p53


title: EpithelialSample3, EpithelialKrasG12DOncogene, p53flfl Fibroblasts

source_name: Mammary epithelia

value: Mammary epithelia


title: FibroblastSample2, NoEpithelialOncogene, FspCrep53flfl Fibroblasts