title: FBXL19fl_ES_UNT_rep1_ChIP_H3K27ac

data_processing:
Paired-end reads were aligned to the genome sequence of concatenated mouse and spike-in genomes (mm10+dm6) using Bowtie 2 with the “--no-mixed” and “--no-discordant” options specified. Reads that were mapped more than once were discarded, followed by removal of PCR duplicates with SAMTools for native cChIP-seq or Sambamba for cross-linked cChIP-seq.
To internally calibrated cChIP-seq experiments, we spiked-in a fixed number of control cells (Drosophila SG4 cells) to each experimental sample. For annotation of genomic intervals and data visualisation, mm10 reads were randomly subsampled using factors that reflected the total number of dm6 reads in each sample. To account for any variation in spike-in cell mixing in different biological replicates, the downsampling factors were additionally corrected using the ratio of dm6/mm10 total read counts in corresponding Input samples.
For each condition, biological replicates were merged for downstream applications. Genome coverage tracks were generated using the pileup function from MACS2 (Zhang et al. 2008).
Metaprofile visualization was carried out using the Deeptools (Ramirez et al., 2016) software and the commands i) computeMatrix reference-point with the option --referencePoint center and ii) plotHeatmap.
cChIP-seq enrichments were quantified from bedgraph files using the annotatePeaks.pl script from HOMER (Heinz et al., 2010). Log2 fold changes between samples were calculated following the addition of a pseudocount of 1.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files representing genome coverage for merged replicates of spike-in normalised cChIP-seq profiles


title: Person 8 VeinEndothelialCells Normal

status: Public on Jan 21 2020

type: genomic

city: Los Angeles

first: Steve

last: Horvath

state: CA

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

country: USA

institute: University of California, Los Angeles

hyb_protocol: Next the samples were loaded onto the Infinium Human MethylationEPIC BeadChip

scan_protocol: GenomeStudio

data_processing: R function preprocessQuantile in the minfi R package.

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Person 8 VeinEndothelialCells Normal

label_protocol: Bisulfite conversion was performed on 500 ng of DNA using the llumina Infinium Methylation Assay protocol in the EZ DNA Methylation kit (Zymo Research).

extract_protocol: Genomic DNA of whole blood samples

treatment_protocol: Transient on-integrative reprogramming protocol optimized based on a cocktail of mRNAs expressing OCT4, SOX2, KLF4, c-MYC, LIN28 and NANOG (OSKMLN). This protocol consistently produces induced pluripotent stem cell (iPSC) colonies, regardless of age of the donors, after 12-15 daily transfections. Here we adopted a transient reprogramming protocol where OSKMLN were daily transfected for only four consecutive days.

tag: individual

tag: age

tag: cell type

value: vein endothelial cells

tag: treatmentstatus

value: Normal

tag: Sex

value: Female

tag: dnamage

tag: dnamageskinbloodclock


title: C2_Sample_32

type: SRA

city: Odense M

first: Tobias

last: Frisch

address: Campusvej 55

country: Denmark

institute: University of Southern Denmark

description: processed data file: countMatrix.txt

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed with trimmomatic: (TRIM:2:30:10 LEADING:20 TRAILING:20 SLIDING:4:20 TRAILING:20 MIN:17)
Mapping with STAR Aligner (version 2.5.3a).
Read counting with HTSeq-count (strict).
EdgeR was used to train generalized linear models to find differentially expressed genes while correcting for age, sex and sample distribution.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: countMatrix.txt contains read counts for every gene (row) and every sample (column).
Supplementary_files_format_and_content: Tab-separated text files with the results from EdgeR.

molecule: total RNA

extract_protocol:
miRNeasy Mini Kit (Qiagen).
TruSeq Stranded Total RNA library prep kit (Illumina).
Total RNA seq (deletion of ribosomal RNA).

tag: diagnosis

value: Control

tag: tissue

value: Brain

tag: lesion type

value: White matter (WM)


title: circRNA SS5

city: Beijing

first: lulu

last: wang

address: Malianwa

country: China

institute: China Agricultural University

data_processing:
Illumina Hiseq 4000 used for basecalling.
Reads containing adapter, poly-N, and low-quality bases at high proportion were removed to obtain clean reads
The reference genome (version: Gallus_gallus-5.0; GCA_000002315.3) was built using bowtie2 v2.2.8 and paired-end clean reads were aligned to the reference genome using Bowtie with default arguments
The circRNAs were detected by two softwares of find_circ and CIRI2
Genome_build: Gallus_gallus-5.0
Supplementary_files_format_and_content: tab-delimited text files include mapped_region for each Sample

organism: Gallus gallus

source_name: spleen

extract_protocol:
The total RNA was extracted from spleen tissues by Trizol (Invitrogen, CA) according to the manufacturer¡¯s instruction.A total of 5.0 ¦Ìg per sample RNA was used for library construction.
Firstly, ribosomal RNA was removed by Epicentre Ribo-zero? rRNA Removal Kit (Epicentre, USA) and ethanol precipitation was used to clean up residual rRNA. Secondly, 3 U/¦Ìg of RNase R (Epicentre, USA) was used to digest the linear RNA. The sequencing libraries were generated by NEBNext? Ultra? Directional RNA Library Prep Kit for Illumina? (NEB, USA) following manufacturer¡¯s recommendations and library quality was assessed by the Agilent Bioanalyzer 2100 system. The libraries were sequenced on an Illumina Hiseq 4000 platform and 150 bp paired-end reads were generated.

value: female

tag: treatment

value: 2,000 plaque-forming units (PFU) of the MDV-GA strain

value: survivor


title: MS5_Sample_35

description: processed data file: countMatrix.txt

value: Multiple sclerosis

value: Normal appearing white matter (NAWM)


title: Person 7 VeinEndothelialCells Normal

source_name: Person 7 VeinEndothelialCells Normal


title: Conj. Mel 6

type: RNA

city: Copenhagen

first: Lauge Hjorth

last: Mikkelsen

address: Frederik V's Vej 11, 1st Floor

department: Pathology

institute: Copenhagen University Hospital

description: FFPE tissue

hyb_protocol: NanoString Standard protocol. 100 ng RNA greater than 200 nt length.

scan_protocol: NanoString nCounter SPRINT profiler

data_processing: NanoString nsolver ver. 4, Standard normalization

label: NanoString

source_name: Conj. Mel 6

label_protocol: NanoString Standard protocol

extract_protocol: miRNeasy FFPE Kit, Qiagen, Standard protocol

tag: disease

value: conjunctival melanomas


title: Low Responder_Ctrl_3 hrs [JFM_93E]

city: Guelph

first: Mehdi

last: Emam

state: ON

address: 419 Gordon St

department: Pathobiology

country: Canada

institute: University of Guelph

data_processing:
Sequencing reads were filtered for quality and removing the index (universal illumina index) using Trimmomatic in the pair-end mode. Nucleotides with quality of less than 30 (in Phred score) at the beginning or the end of the reads were removed. In addition, reads shorter than 100 bp or with quality of less than 20 (in Phred score) in 5 adjacent base pair were removed from the analysis. The quality of the reads was checked by FastQC (v. 0.11.5) before and after trimming.
Clean reads were mapped to the bovine reference genome (UMD 3.1, Release 94) by using Spliced Transcripts Alignment to a Reference (STAR) v. 2.7.0a
The quantity of expression per annotated genes was calculated by using RNA-Seq by Expectation Maximization (RSEM) package (v. 1.3)
The raw count data were imported by R’ Bioconductor package “tximport” (v 1.10.1) and analyzed by DESeq2 (v. 1.22.2) by employing negative binomial GLM fitting approach. Every sample was numbered within a phenotype and consisted of two reads files, treated and control. The model term in DESeq2 was designed to calculate the differential expression in fold change (FC) between the phenotypes in the treated group after accounting for the expression level of the respective control sample
Genome_build: UMD 3.1, Release 94
Supplementary_files_format_and_content: RSEM aboundance; Gene_ID,external_gene_name,baseMean,log2 FoldChange,lfcSE,stat,pvalue,padj

organism: Bos taurus

source_name: Low Responder_Ctrl_3 hrs

growth_protocol: Blood Mononuclear Cells (BMCs) were purified based on the gradient centrifuge separation method and cultured for 2 hours in Monocyte Attachment Medium at 37 °C. Non-adherent cells were removed and the medium was replaced with AIM V® Medium in the presence of 5 ng/ml recombinant bovine Granulocyte-macrophage colony-stimulating factor and 5% CO2 for 6 days.

extract_protocol:
Briefly, 1 ml of Trizol Reagent was used to extract total RNA from 0.4E6 MDMs based on company’s recommendation.
Library construction was performed using the TruSeq Stranded mRNA Libraries Prep kit (Illumina Inc. San Diego, CA). Adapters were ligated to the ends of double-stranded cDNA and PCR amplified to create libraries.

treatment_protocol: One well of each sample was assigned as the control and the other well was exposed to PFA inactivated E. coli (MOI: 5)

tag: breed

value: Holstein

tag: lactating status

value: Lactating

tag: response to e.coli

value: Low Responder

value: Ctrl

tag: time point

value: 3 hrs

value: monocyte-derived macrophages


title: Low Responder_Exposed to E. coli_18 hrs [JFM_94F]

source_name: Low Responder_Exposed to E. coli_18 hrs

value: Exposed to E. coli

value: 18 hrs


title: Person 6 VeinEndothelialCells Treated

source_name: Person 6 VeinEndothelialCells Treated

value: vein endothelial cells

value: Treated

value: Female


title: Low Responder_Exposed to E. coli_3 hrs [JFM_91B]

source_name: Low Responder_Exposed to E. coli_3 hrs


title: Low Responder_Ctrl_18 hrs [JFM_94E]

source_name: Low Responder_Ctrl_18 hrs


title: MS4_Sample_29

description: processed data file: countMatrix.txt

value: Brain

value: Chronic active (CA)


title: circRNA SS4

value: male

value: 2,000 plaque-forming units (PFU) of the MDV-GA strain

value: survivor


title: C4_Sample_28

description: processed data file: countMatrix.txt

value: Control

value: White matter (WM)


title: Low Responder_Exposed to E. coli_18 hrs [JFM_92B]

value: Holstein

value: Lactating


title: MS3_Sample_27

description: processed data file: countMatrix.txt

value: Multiple sclerosis

value: Normal appearing white matter (NAWM)


title: Conj. Mel 4

description: FFPE tissue

source_name: Conj. Mel 4

value: conjunctival melanomas


title: circRNA SS3

value: female


title: Person 5 VeinEndothelialCells Normal

source_name: Person 5 VeinEndothelialCells Normal

value: Normal


title: Low Responder_Ctrl_18 hrs [JFM_92A]

value: Low Responder

value: Ctrl

value: 18 hrs

value: monocyte-derived macrophages


title: C3_Sample_26

description: processed data file: countMatrix.txt

value: Brain


title: Person 6 VeinEndothelialCells Normal

source_name: Person 6 VeinEndothelialCells Normal

value: vein endothelial cells

value: Female


title: Person 5 VeinEndothelialCells Treated

source_name: Person 5 VeinEndothelialCells Treated

value: Treated


title: Low Responder_Exposed to E. coli_3 hrs [JFM_92J]

value: Exposed to E. coli

value: 3 hrs


title: circRNA SS1

value: 2,000 plaque-forming units (PFU) of the MDV-GA strain

value: survivor


title: Conj. Mel 3

description: FFPE tissue

source_name: Conj. Mel 3


title: Conj. Mel 7

description: FFPE tissue

source_name: Conj. Mel 7


title: Low Responder_Ctrl_3 hrs [JFM_92I]

value: Holstein

value: Lactating


title: Conj. Mel 5

description: FFPE tissue

source_name: Conj. Mel 5

value: conjunctival melanomas


title: Conj. Mel 1

description: FFPE tissue

source_name: Conj. Mel 1


title: C1_Sample_24

description: processed data file: countMatrix.txt

value: Control

value: White matter (WM)


title: circRNA NS5

value: male

value: the same volume of diluent (0.2 mL)


title: C5_Sample_25

description: processed data file: countMatrix.txt


title: circRNA NS4

value: female


title: Person 4 SkinFibroblasts Treated

source_name: Person 4 SkinFibroblasts Treated

value: skin fibroblasts


title: Low Responder_Exposed to E. coli_18 hrs [JFM_91J]

value: Low Responder

value: 18 hrs

value: monocyte-derived macrophages


title: LTH_24h_3

city: Wuhan

first: Dong

last: Chen

state: Hubei

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

department: Center for Genome Analysis

institute: ABLife, Inc.

description: Mixed biological repeat 1 and biological repeat 2 in bench 1 for LTH at 24 hpi with M.oryzae infection

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniquely mapped reads were remained. One more reads with the same start and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2  and Qvalue <= 0.05
Reads were mapped using BWA
SAM files were then used to identify circRNAs with CIRI2
Reads were mapped to circRNAs using NovoAlign for calculating back-spliced reads
Genome_build: IRGSP v5.0
Supplementary_files_format_and_content: tab-delimited text files include gene FPKM values for each Sample

organism: Oryza sativa

source_name: leaves of three-week-old seedlings

growth_protocol: All rice plants were grown at 26 ± 2 ℃ and 70% relative humidity under 12 h light : 12 darkness. M. oryzae strains (NC-24, NC-34, B9, Zhong8-10-14, 97-95-1, F1, NC-14, B13 and E37) were cultured in complete media at 28 ℃ under 12 h light : 12 darkness for two weeks

extract_protocol:
Total RNA of each sample was isolated using TRIzol (Ambion) according to the manufacturer’s instructions.
For each sample, 25 µg of total RNA was used for circRNA-seq library preparation. Total RNA was depleted for ribosomal RNAs using the RiboMinus kit. The remaining RNAs were iron fragmented at 95℃ followed by end repair and 5' adaptor ligation. Then reverse transcription was performed with RT primer harboring 3' adaptor sequence and randomized hexamer. The cDNAs were purified and subjected to PCR amplification. PCR products corresponding to 300-500 bp were purified and quantified, and then stored at -80 ℃ until used for sequencing

treatment_protocol: Spores of each strain were mixed as the inoculum, and sprayed onto three-week-old seedlings of LTH and IR25. Leaves were collected at 0, 12, 24 hour post inoculation (hpi), immediately frozen in liquid nitrogen and stored at -80 ℃ until use

tag: cultivar

value: LTH

tag: genotype/variation

value: blast-susceptible

tag: developmental stage

value: three-week-old seedlings

value: leaf tissue


title: Person 3 SkinFibroblasts Treated

source_name: Person 3 SkinFibroblasts Treated

tag: individual

tag: age

tag: cell type

value: Treated

value: Male


title: Person 4 SkinFibroblasts Normal

source_name: Person 4 SkinFibroblasts Normal

tag: treatmentstatus

value: Normal

tag: Sex

value: Female

tag: dnamage


title: Low Responder_Ctrl_3 hrs [JFM_91A]

source_name: Low Responder_Ctrl_3 hrs

value: Holstein

value: Lactating

value: Ctrl

value: 3 hrs


title: MS4_Sample_22

description: processed data file: countMatrix.txt

tag: diagnosis

value: Multiple sclerosis

tag: tissue

value: Brain

value: Chronic active (CA)


title: Low Responder_Ctrl_18 hrs [JFM_91I]

value: Low Responder

tag: treatment

value: 18 hrs


title: Person 1 SkinFibroblasts Normal

source_name: Person 1 SkinFibroblasts Normal

value: skin fibroblasts

tag: dnamageskinbloodclock


title: circRNA NS2

source_name: spleen

value: female

value: the same volume of diluent (0.2 mL)


title: MS1_Sample_23

description: processed data file: countMatrix.txt

tag: lesion type

value: Normal appearing white matter (NAWM)


title: LTH_0h_3

description: Mixed biological repeat 1 and biological repeat 2 in bench 1 for LTH witout M.oryzae infection

value: LTH

value: blast-susceptible

value: three-week-old seedlings

value: leaf tissue


title: circRNA NS1


title: MS4_Sample_21

description: processed data file: countMatrix.txt


title: Conj. Mel 2

description: FFPE tissue

source_name: Conj. Mel 2

tag: disease

value: conjunctival melanomas


title: IR25_24h_3

description: Mixed biological repeat 1 and biological repeat 2 in bench 1 for IR25 at 24 hpi with M.oryzae infection

value: blast-resistant


title: Person 3 SkinFibroblasts Normal

source_name: Person 3 SkinFibroblasts Normal

value: Normal

value: Male


title: LTH_12h_3

description: Mixed biological repeat 1 and biological repeat 2 in bench 1 for LTH at 12 hpi with M.oryzae infection


title: MS8_Sample_20

description: processed data file: countMatrix.txt

value: Multiple sclerosis


title: High Responder_Exposed to E. coli_18 hrs [JFM_94B]

tag: breed

value: Holstein

value: Female

tag: lactating status

value: Lactating

tag: response to e.coli

value: High Responder

value: Exposed to E. coli

value: monocyte-derived macrophages


title: C4_Sample_19

description: processed data file: countMatrix.txt

value: Control

value: Brain

value: White matter (WM)


title: High Responder_Ctrl_3 hrs [JFM_93A]

source_name: High Responder_Ctrl_3 hrs

value: Ctrl

tag: time point

value: 3 hrs


title: circRNA TS4

value: female

value: 2,000 plaque-forming units (PFU) of the MDV-GA strain

value: tumorous


title: Person 1 SkinFibroblasts Treated

source_name: Person 1 SkinFibroblasts Treated

value: skin fibroblasts

value: Treated


title: IR25_12h_3

description: Mixed biological repeat 1 and biological repeat 2 in bench 1 for IR25 at 12 hpi with M.oryzae infection

tag: cultivar

tag: genotype/variation

value: blast-resistant

tag: developmental stage

value: three-week-old seedlings

value: leaf tissue


title: circRNA NS3

value: the same volume of diluent (0.2 mL)


title: circRNA TS3


title: IR25_0h_3

description: Mixed biological repeat 1 and biological repeat 2 in bench 1 for IR25 witout M.oryzae infection


title: High Responder_Ctrl_18 hrs [JFM_94A]

source_name: High Responder_Ctrl_18 hrs

value: Holstein

value: Female

value: Lactating

value: High Responder

value: 18 hrs

tag: cell type


title: C2_Sample_18

description: processed data file: countMatrix.txt

value: Control

value: Brain

value: White matter (WM)

tag: individual


title: Person 2 SkinFibroblasts Treated

source_name: Person 2 SkinFibroblasts Treated

tag: age

tag: treatmentstatus

tag: Sex

value: Male


title: circRNA TS2

value: female

value: 2,000 plaque-forming units (PFU) of the MDV-GA strain


title: High Responder_Exposed to E. coli_3 hrs [JFM_94J]

source_name: High Responder_Exposed to E. coli_3 hrs

value: Exposed to E. coli

value: 3 hrs

value: monocyte-derived macrophages


title: MS3_Sample_17

description: processed data file: countMatrix.txt

tag: diagnosis

value: Multiple sclerosis

tag: tissue

value: Chronic active (CA)


title: Person 2 SkinFibroblasts Normal

source_name: Person 2 SkinFibroblasts Normal

value: skin fibroblasts

value: Normal

tag: dnamage

tag: dnamageskinbloodclock


title: circRNA TS1

tag: treatment

value: tumorous


title: High Responder_Exposed to E. coli_3 hrs [JFM_93B]

tag: breed

value: Holstein

value: Female

value: Lactating


title: C4_Sample_16

description: processed data file: countMatrix.txt

value: Control

tag: lesion type


title: High Responder_Exposed to E. coli_18 hrs [JFM_93J]

tag: lactating status

tag: response to e.coli

value: High Responder

value: 18 hrs


title: rRNAdep_s3_rep2

city: Nanchang

last: Wang

state: JiangXi

address: Hong Gu Tan New Road, No. 999

institute: Nanchang University

description: stranded paired-end RNA-seq

data_processing:
Illumina Casava1.7 software used for basecalling.
Low quality and adaptor sequences in raw reads were trimmed using Trim_galore (v0.4.2, Babraham Bioinformatics) with the following parameters: --stringency 6 --paired. Then cleaned reads were aligned to the reference genome (Fragaria_vesca_v4.0) using STAR_2.5.4b with the following parameters: --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --seedSearchStartLmax 30 –quantMode GeneCounts or using TopHat (v2.1.2) with the following parameters: -N 5 --read-edit-dist 5 --library-type fr-firststrand -a 6 --microexon-search -m 2. Genome guided transcriptome assembly was performed using scallp (v0.10.2) with default settings.
Genome_build: https://www.rosaceae.org/species/fragaria/fragaria_vesca  Fragaria_vesca_v4.0 (ftp://ftp.bioinfo.wsu.edu/species/Fragaria_vesca/Fvesca-genome.v4.0.a1/)
Supplementary_files_format_and_content: Genomic coordinates file (GTF), including all genome guided transcriptome assembly from all polyA depleted and rRNA depleted samples
Supplementary_files_format_and_content: Tab-deliminated text file including raw count of all Fragaria_vesca_v4.0 reference genes and lncRNAs in polyA depleted and rRNA depleted samples

organism: Fragaria vesca

source_name: mature fruits with brown achenes_rRNA depleted RNA

growth_protocol: Strawberry plants including F.vesca (Hawaii4) and Falandi (Fragaria × ananassa Duch.) were grown at 20 °C-25 °C in a greenhouse (70–85% relative humidity, 12-h light, 12-h dark cycle). Fruits of them were collected, then immediately frozen in liquid nitrogen and stored at −80 °C.

extract_protocol:
Total RNA was extracted from strawberry fruit tissues using TRIzol (Invitrogen, USA) according to manufacturer's instruction.
RNA-seq libraries from rRNA-depleted RNA and poly(A)-depleted RNA were prepared as previously (Lu et al., 2015), then were sequenced by the Illumina HiSeq 2500 platform. F.vesca fruit tissues from at least five independent plants were combined to form one biological replicate, and all experiments were carried out with three biological replicates.

value: mature fruits with brown achenes

value: fruit

tag: molecule subtype

value: rRNA depleted RNA


title: rRNAdep_s3_rep1

description: stranded paired-end RNA-seq


title: High Responder_Ctrl_3 hrs [JFM_94I]

value: Ctrl

tag: time point


title: rRNAdep_s3_rep3

description: stranded paired-end RNA-seq

tag: developmental stage


title: rRNAdep_s2_rep3

description: stranded paired-end RNA-seq

source_name: mature fruits with yellow achenes_rRNA depleted RNA

value: mature fruits with yellow achenes


title: MS8_Sample_30

description: processed data file: countMatrix.txt

value: Brain

value: Normal appearing white matter (NAWM)


title: MS5_Sample_15

description: processed data file: countMatrix.txt

value: Multiple sclerosis


title: High Responder_Ctrl_18 hrs [JFM_93I]

tag: cell type

value: monocyte-derived macrophages


title: rRNAdep_s2_rep1

description: stranded paired-end RNA-seq


title: 3028-WT-OBEH

city: Uppsala

first: Bengt

last: Westermark

address: Dag Hammarskjölds väg 20

country: Sweden

institute: Uppsala University

data_processing:
Sequencing alignment using HISAT2  (Galaxy Version 2.1.0).
Read counts for each gene were determined with featureCounts (Galaxy Version 1.6.3).
Differential expression analysis was performed using the EdgeR package (version 3.22.5) within the R software version 3.5.0
Genome_build: Homo sapiens (hg19 with mtDNA replaced with rCRS, and containing pUC18 and phiX174)
Supplementary_files_format_and_content: .tabular file reports abundance measurements

source_name: glioblastoma cell culture

growth_protocol: Human glioma cell lines were cultured adherently on Primaria dishes coated with mouse laminin in Neurobasal and DMEM/F12 media (1:1) supplemented with N2 and B27 and human recombinant FGF2 and EGF, 10 ng/ml. Media was replaced three times each week.

extract_protocol:
RNA extraction with the RNeasy mini kit (Qiagen)
The sequencing library was prepared using TruSeq stranded total RNA library preparation kit (Illumina Hayward, CA) with ribosomal depletion using RiboZero Gold (Epicentre, Madison, WI) following the instructions of the manufacturers.

treatment_protocol: New media with or without BMP4 (10 ng/µl) was given to the cells every Monday, Wednesday and Friday for 14 days.

tag: cell line

tag: lentiviral vector


title: 3019-WT-OBEH


title: High Responder_Exposed to E. coli_3 hrs [JFM_92N]

value: Exposed to E. coli

value: 3 hrs


title: C5_Sample_13

description: processed data file: countMatrix.txt

value: White matter (WM)

tag: individual


title: circRNA SS2

tag: Sex

value: female

value: 2,000 plaque-forming units (PFU) of the MDV-GA strain

value: survivor


title: 3017-WT-OBEH


title: High Responder_Ctrl_3 hrs [JFM_92M]

value: Holstein

value: Female

value: Lactating

value: High Responder


title: 3065-WT-OBEH


title: rRNAdep_s2_rep2

description: stranded paired-end RNA-seq

value: fruit

value: rRNA depleted RNA


title: MS3_Sample_12

description: processed data file: countMatrix.txt

tag: diagnosis

value: Chronic active (CA)


title: High Responder_Exposed to E. coli_18 hrs [JFM_91N]

value: 18 hrs


title: MS3_Sample_11

description: processed data file: countMatrix.txt

tag: tissue

value: Brain

value: Normal appearing white matter (NAWM)


title: 3028-CTRL-OBEH

value: Control vector


title: rRNAdep_s1_rep3

description: stranded paired-end RNA-seq

source_name: immature fruits with green achenes_rRNA depleted RNA

value: immature fruits with green achenes


title: High Responder_Ctrl_18 hrs [JFM_91M]

value: Ctrl

value: monocyte-derived macrophages


title: C5_Sample_10

description: processed data file: countMatrix.txt

value: Control

value: White matter (WM)


title: 3017-SOX2-OBEH

value: Sox2 vector


title: rRNAdep_s1_rep2

description: stranded paired-end RNA-seq


title: C5_Sample_8

description: processed data file: countMatrix.txt


title: MS8_Sample_9

description: processed data file: countMatrix.txt

value: Multiple sclerosis


title: 3019-WT-BMP4

value: BMP4 10 ng/µl


title: MS8_Sample_6

description: processed data file: countMatrix.txt


title: rRNAdep_s1_rep1

description: stranded paired-end RNA-seq


title: polyAdep_s3_rep1

description: stranded paired-end RNA-seq

source_name: mature fruits with brown achenes_polyA depleted RNA

value: mature fruits with brown achenes

value: polyA depleted RNA


title: polyAdep_s3_rep2

description: stranded paired-end RNA-seq

value: fruit


title: 3028-SOX2-OBEH


title: polyAdep_s2_rep3

description: stranded paired-end RNA-seq

source_name: mature fruits with yellow achenes_polyA depleted RNA

value: mature fruits with yellow achenes


title: 3065-WT-BMP4


title: MS10_Sample_7

description: processed data file: countMatrix.txt

value: Remyelinating (RL)


title: 3017-CTRL-OBEH


title: 3017-WT-BMP4


title: polyAdep_s3_rep3

description: stranded paired-end RNA-seq


title: polyAdep_s2_rep1

description: stranded paired-end RNA-seq


title: MS4_Sample_4

description: processed data file: countMatrix.txt

value: Chronic active (CA)


title: MS6_Sample_3

description: processed data file: countMatrix.txt

value: Brain


title: MS7_Sample_2

description: processed data file: countMatrix.txt


title: 3017-SOX2-BMP4


title: 3028-CTRL-BMP4


title: C3_Sample_1

description: processed data file: countMatrix.txt


title: polyAdep_s1_rep3

description: stranded paired-end RNA-seq

source_name: immature fruits with green achenes_polyA depleted RNA


title: 3028-WT-BMP4


title: polyAdep_s1_rep2

description: stranded paired-end RNA-seq


title: MS8_Sample_5

description: processed data file: countMatrix.txt


title: polyAdep_s1_rep1

description: stranded paired-end RNA-seq


title: polyAdep_s2_rep2

description: stranded paired-end RNA-seq


title: 3028-SOX2-BMP4


title: 123-2-C11-KOsema3fb-tbx18-1_reseq

status: Public on Jan 20 2020

city: Oxford

first: Paul

middle: Richard

last: Riley

address: IMS-Tetsuya Nakamura Building, Old Road Campus

country: United Kingdom

institute: University of Oxford

description: Re-sequencing

data_processing:
Alignment to GRCz10-91 with STAR (v2.4.2a) outSJfilterCountUniqueMin -1 -1 -1 -1 --outSJfilterCountTotalMin 30 10 10 10 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical
BAM files with samtools (v1.3) view -bS
Sorting of BAM files with samtools (v1.3) sort
Removal of PCR duplicates from BAM files with samtools (v1.3) rmdup
Read counting with featureCounts (v1.4.5-p1) -p -B -a -t exon -g gene_id
Genome_build: GRCz10-91
Supplementary_files_format_and_content: Tab-delimited text files of raw counts on gene level
Supplementary_files_format_and_content: featureCounts_KOsema3fb.txt: Tab delimited text file (raw counts before QC), Column 1 = Ensembl gene ID, column 2 = gene length in basepairs, column 3 = gene name, columns 4-151 = counts for each cell, colnames = gene_id, gene_length, gene_name, cell names 1-151
Supplementary_files_format_and_content: featureCounts_KOsema3fb_reseq.txt: Tab delimited text file of resequenced samples (raw counts before QC)

molecule: polyA RNA

organism: Danio rerio

source_name: Heart

extract_protocol:
Larvae were physically disrupted, hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS.
Smartseq2, Illumina Nextera XT

tag: transgenic reporter

tag: cell fluorescence

value: myr-Citrine

tag: age

value: 5 days post fertilisation


title: 109-2-B08-KOsema3fb-tbx18-1_reseq

description: Re-sequencing


title: 143-2-E07-KOcxcl12a-1_reseq

description: Re-sequencing


title: 140-2-E04-KOcxcl12a-ctr-1_reseq

description: Re-sequencing


title: 130-2-D06-KOsema3fb-tbx18-1_reseq

description: Re-sequencing


title: 142-2-E06-KOcxcl12a-ctr-3_reseq

description: Re-sequencing


title: 147-2-E11-KOcxcl12a-5_reseq

description: Re-sequencing


title: 148-2-E12-KOcxcl12a-6_reseq

description: Re-sequencing


title: 146-2-E10-KOcxcl12a-4_reseq

description: Re-sequencing


title: 141-2-E05-KOcxcl12a-ctr-2_reseq

description: Re-sequencing


title: 144-2-E08-KOcxcl12a-2_reseq

description: Re-sequencing


title: 124-2-C12-KOsema3fb-tbx18-1_reseq

description: Re-sequencing


title: 106-2-B05-KOsema3fb-tbx18-1_reseq

description: Re-sequencing


title: 102-2-B01-KOsema3fb-tbx18-1_reseq

description: Re-sequencing


title: 099-2-A10-KOsema3fb-tbx18-1_reseq

description: Re-sequencing


title: 094-2-A04-KOsema3fb-tbx18-1_reseq

description: Re-sequencing


title: 088-1-H10-KOsema3fb-tbx18-1_reseq

description: Re-sequencing


title: 3017-CTRL-BMP4

value: Control vector

tag: treatment


title: 089-1-H11-KOsema3fb-tbx18-1_reseq

description: Re-sequencing


title: 083-1-H05-KOsema3fb-tbx18-1_reseq

description: Re-sequencing


title: 145-2-E09-KOcxcl12a-3_reseq

description: Re-sequencing


title: 091-2-A01-KOsema3fb-tbx18-1_reseq

description: Re-sequencing


title: 119-2-C07-KOsema3fb-tbx18-1_reseq

description: Re-sequencing


title: 113-2-C01-KOsema3fb-tbx18-1_reseq

description: Re-sequencing


title: 080-1-H02-KOsema3fb-tbx18-1_reseq

description: Re-sequencing


title: 075-1-G09-KOsema3fb-tbx18-1_reseq

description: Re-sequencing


title: 071-1-G05-KOsema3fb-tbx18-1_reseq

description: Re-sequencing


title: 070-1-G04-KOsema3fb-tbx18-1_reseq

description: Re-sequencing


title: 063-1-F09-KOsema3fb-tbx18-1_reseq

description: Re-sequencing


title: 085-1-H07-KOsema3fb-tbx18-1_reseq

description: Re-sequencing


title: 054-1-E12-KOsema3fb-tbx18-1_reseq

description: Re-sequencing


title: 038-1-D06-KOsema3fb-tbx18-1_reseq

description: Re-sequencing


title: 042-1-D11-KOsema3fb-tbx18-1_reseq

description: Re-sequencing


title: 045-1-E02-KOsema3fb-tbx18-1_reseq

description: Re-sequencing


title: 027-1-C06-KOsema3fb-tbx18-1_reseq

description: Re-sequencing


title: 058-1-F04-KOsema3fb-tbx18-1_reseq

description: Re-sequencing


title: 046-1-E03-KOsema3fb-tbx18-1_reseq

description: Re-sequencing


title: 053-1-E11-KOsema3fb-tbx18-1_reseq

description: Re-sequencing


title: 026-1-C05-KOsema3fb-tbx18-1_reseq

description: Re-sequencing


title: 021-1-B12-KOsema3fb-tbx18-1_reseq

description: Re-sequencing


title: 008-1-A10-KOsema3fb-tbx18-1_reseq

description: Re-sequencing


title: 009-1-A11-KOsema3fb-tbx18-1_reseq

description: Re-sequencing


title: 033-1-D01-KOsema3fb-tbx18-1_reseq

description: Re-sequencing


title: 143-2-E07-KOcxcl12a-1


title: 001-1-A03-KOsema3fb-tbx18-1_reseq

description: Re-sequencing


title: 147-2-E11-KOcxcl12a-5


title: 145-2-E09-KOcxcl12a-3


title: 146-2-E10-KOcxcl12a-4


title: 052-1-E10-KOsema3fb-tbx18-1_reseq

description: Re-sequencing


title: 144-2-E08-KOcxcl12a-2


title: 031-1-C11-KOsema3fb-tbx18-1_reseq

description: Re-sequencing


title: 059-1-F05-KOsema3fb-tbx18-1_reseq

description: Re-sequencing


title: 142-2-E06-KOcxcl12a-ctr-3


title: 138-2-E02-KOtgm2b-5


title: 140-2-E04-KOcxcl12a-ctr-1


title: 139-2-E03-KOtgm2b-6


title: 023-1-C02-KOsema3fb-tbx18-1_reseq

description: Re-sequencing


title: 137-2-E01-KOtgm2b-4


title: 141-2-E05-KOcxcl12a-ctr-2


title: 131-2-D07-KOtgm2b-ctr-1


title: 133-2-D09-KOtgm2b-ctr-3


title: 134-2-D10-KOtgm2b-1


title: 135-2-D11-KOtgm2b-2


title: 003-1-A05-KOsema3fb-tbx18-1_reseq

description: Re-sequencing


title: 128-2-D04-KOsema3fb-tbx18-1


title: 127-2-D03-KOsema3fb-tbx18-1


title: 013-1-B03-KOsema3fb-tbx18-1_reseq

description: Re-sequencing


title: 129-2-D05-KOsema3fb-tbx18-1


title: 148-2-E12-KOcxcl12a-6


title: 136-2-D12-KOtgm2b-3


title: 123-2-C11-KOsema3fb-tbx18-1


title: 126-2-D02-KOsema3fb-tbx18-1


title: 124-2-C12-KOsema3fb-tbx18-1


title: 125-2-D01-KOsema3fb-tbx18-1


title: 119-2-C07-KOsema3fb-tbx18-1


title: 116-2-C04-KOsema3fb-tbx18-1


title: 121-2-C09-KOsema3fb-tbx18-1


title: 120-2-C08-KOsema3fb-tbx18-1


title: 117-2-C05-KOsema3fb-tbx18-1


title: 118-2-C06-KOsema3fb-tbx18-1


title: 122-2-C10-KOsema3fb-tbx18-1


title: 132-2-D08-KOtgm2b-ctr-2


title: 113-2-C01-KOsema3fb-tbx18-1


title: 130-2-D06-KOsema3fb-tbx18-1


title: 111-2-B11-KOsema3fb-tbx18-1


title: 115-2-C03-KOsema3fb-tbx18-1


title: 108-2-B07-KOsema3fb-tbx18-1


title: 107-2-B06-KOsema3fb-tbx18-1


title: 109-2-B08-KOsema3fb-tbx18-1


title: 110-2-B09-KOsema3fb-tbx18-1


title: 106-2-B05-KOsema3fb-tbx18-1


title: 102-2-B01-KOsema3fb-tbx18-1


title: 104-2-B03-KOsema3fb-tbx18-1


title: 103-2-B02-KOsema3fb-tbx18-1


title: 101-2-A12-KOsema3fb-tbx18-1


title: 105-2-B04-KOsema3fb-tbx18-1


title: 100-2-A11-KOsema3fb-tbx18-1


title: 099-2-A10-KOsema3fb-tbx18-1


title: 114-2-C02-KOsema3fb-tbx18-1


title: 112-2-B12-KOsema3fb-tbx18-1


title: 097-2-A08-KOsema3fb-tbx18-1


title: 096-2-A06-KOsema3fb-tbx18-1


title: 098-2-A09-KOsema3fb-tbx18-1


title: 088-1-H10-KOsema3fb-tbx18-1


title: 093-2-A03-KOsema3fb-tbx18-1


title: 086-1-H08-KOsema3fb-tbx18-1


title: 091-2-A01-KOsema3fb-tbx18-1


title: 085-1-H07-KOsema3fb-tbx18-1


title: 092-2-A02-KOsema3fb-tbx18-1


title: 083-1-H05-KOsema3fb-tbx18-1


title: 089-1-H11-KOsema3fb-tbx18-1


title: 090-1-H12-KOsema3fb-tbx18-1


title: 095-2-A05-KOsema3fb-tbx18-1


title: 081-1-H03-KOsema3fb-tbx18-1


title: 077-1-G11-KOsema3fb-tbx18-1


title: 084-1-H06-KOsema3fb-tbx18-1


title: 078-1-G12-KOsema3fb-tbx18-1


title: 094-2-A04-KOsema3fb-tbx18-1


title: 087-1-H09-KOsema3fb-tbx18-1


title: 079-1-H01-KOsema3fb-tbx18-1


title: 076-1-G10-KOsema3fb-tbx18-1


title: 075-1-G09-KOsema3fb-tbx18-1


title: 074-1-G08-KOsema3fb-tbx18-1


title: MS4_Sample_14

description: processed data file: countMatrix.txt

tag: lesion type


title: 073-1-G07-KOsema3fb-tbx18-1


title: 071-1-G05-KOsema3fb-tbx18-1


title: 070-1-G04-KOsema3fb-tbx18-1


title: 072-1-G06-KOsema3fb-tbx18-1


title: 082-1-H04-KOsema3fb-tbx18-1


title: 080-1-H02-KOsema3fb-tbx18-1


title: 069-1-G03-KOsema3fb-tbx18-1


title: 068-1-G02-KOsema3fb-tbx18-1


title: 065-1-F11-KOsema3fb-tbx18-1


title: 067-1-G01-KOsema3fb-tbx18-1


title: 066-1-F12-KOsema3fb-tbx18-1


title: 062-1-F08-KOsema3fb-tbx18-1


title: 064-1-F10-KOsema3fb-tbx18-1


title: 063-1-F09-KOsema3fb-tbx18-1


title: 059-1-F05-KOsema3fb-tbx18-1


title: 058-1-F04-KOsema3fb-tbx18-1


title: 057-1-F03-KOsema3fb-tbx18-1


title: 051-1-E09-KOsema3fb-tbx18-1


title: 055-1-F01-KOsema3fb-tbx18-1


title: 049-1-E07-KOsema3fb-tbx18-1


title: 060-1-F06-KOsema3fb-tbx18-1


title: 052-1-E10-KOsema3fb-tbx18-1


title: 061-1-F07-KOsema3fb-tbx18-1


title: 054-1-E12-KOsema3fb-tbx18-1


title: 053-1-E11-KOsema3fb-tbx18-1


title: 046-1-E03-KOsema3fb-tbx18-1


title: 048-1-E06-KOsema3fb-tbx18-1


title: 056-1-F02-KOsema3fb-tbx18-1


title: 050-1-E08-KOsema3fb-tbx18-1


title: 047-1-E04-KOsema3fb-tbx18-1


title: 045-1-E02-KOsema3fb-tbx18-1


title: 044-1-E01-KOsema3fb-tbx18-1


title: 043-1-D12-KOsema3fb-tbx18-1


title: 042-1-D11-KOsema3fb-tbx18-1


title: 041-1-D10-KOsema3fb-tbx18-1


title: 040-1-D08-KOsema3fb-tbx18-1


title: 039-1-D07-KOsema3fb-tbx18-1


title: 038-1-D06-KOsema3fb-tbx18-1


title: 037-1-D05-KOsema3fb-tbx18-1


title: 036-1-D04-KOsema3fb-tbx18-1


title: 031-1-C11-KOsema3fb-tbx18-1


title: 034-1-D02-KOsema3fb-tbx18-1


title: 032-1-C12-KOsema3fb-tbx18-1


title: 033-1-D01-KOsema3fb-tbx18-1


title: 028-1-C07-KOsema3fb-tbx18-1


title: 022-1-C01-KOsema3fb-tbx18-1


title: 023-1-C02-KOsema3fb-tbx18-1


title: 030-1-C10-KOsema3fb-tbx18-1


title: 021-1-B12-KOsema3fb-tbx18-1


title: 018-1-B09-KOsema3fb-tbx18-1


title: 020-1-B11-KOsema3fb-tbx18-1


title: 016-1-B06-KOsema3fb-tbx18-1


title: 035-1-D03-KOsema3fb-tbx18-1


title: 024-1-C03-KOsema3fb-tbx18-1


title: 026-1-C05-KOsema3fb-tbx18-1


title: 014-1-B04-KOsema3fb-tbx18-1


title: 015-1-B05-KOsema3fb-tbx18-1


title: 013-1-B03-KOsema3fb-tbx18-1


title: 011-1-B01-KOsema3fb-tbx18-1


title: 012-1-B02-KOsema3fb-tbx18-1


title: 010-1-A12-KOsema3fb-tbx18-1


title: 009-1-A11-KOsema3fb-tbx18-1


title: 027-1-C06-KOsema3fb-tbx18-1


title: 007-1-A09-KOsema3fb-tbx18-1


title: 008-1-A10-KOsema3fb-tbx18-1


title: 025-1-C04-KOsema3fb-tbx18-1


title: 029-1-C09-KOsema3fb-tbx18-1


title: 006-1-A08-KOsema3fb-tbx18-1


title: 004-1-A06-KOsema3fb-tbx18-1


title: 019-1-B10-KOsema3fb-tbx18-1


title: 002-1-A04-KOsema3fb-tbx18-1


title: 003-1-A05-KOsema3fb-tbx18-1


title: 005-1-A07-KOsema3fb-tbx18-1


title: WGBS_sp7ne0dpa_rep2

city: St. Louis

first: Hyung Joo

last: Lee

state: MO

address: 4515 McKinley Avenue

department: Department of Genetics

institute: Washington University School of Medicine

description: sp7- cells in the uninjured fin (0 dpa)

library_source: genomic

data_processing:
Basecalls were performed by the Edison Family Center for Genome Sciences & Systems Biology Sequencing Center using bcl2fastq
The Illumina adapter sequences were trimmed from the raw sequencing reads using Trim Galore! Version 0.4.1 with the following parameters: --clip_R1 6 --clip_R2 6 --paired --retain_unpaired -r1 21 -r2 21.
Trimmed reads were mapped to in sillico bisulfite-converted zebrafish genome reference by using Bismark version 0.16.1 with the following parameters: -I 0 -X 2000 --un --ambiguous --bowtie2 -N 1 -L 28 --dovetail --score_min L,0,0.6.
Unpaired or unmapped reads 1 were then mapped as single read mode by using Bismark with the following parameters: --bowtie2 -N 1 -L 28 --score_min L,0,-0.6. Unpaired or unmapped reads 2 were also mapped as single read mode by using Bismark with the following parameters: --pbat --bowtie2 -N 1 -L 28 --score_min L,0,-0.6.
The PCR redundant reads were removed and methylation levels of each C nucleotide were exracted by using Bismark with the following two commands: bismark_methylation_extractor --paired-end --no_overlap --comprehensive --report --gzip for paired-end mapped reads and bismark_methylation_extractor --single-end --comprehensive --report --no_header --gzip for reads mapped with single end mode.
After merging paired-end and single end report files, Bismark command coverage2cytosine and custom script was used to calculate total read counts and methylation read counts per each CpG.
Genome_build: GRCz10
Supplementary_files_format_and_content: column 1 - chr: chromosome; column 2 - pos: coordinate for CpG on chromosome (0-based); column 3 - N: total number of reads at that position; column 4 - X: number of reads supporting a methylation.

source_name: zebrafish fin

extract_protocol:
The genomic DNA was extracted by incubating the cells in genomic DNA extraction buffer (50 mM Tris, 1 mM EDTA, 0.5% SDS, 1 mg/mL Proteinase K) followed by phenol-chloroform extraction.
The genomic DNA was treated with bisulfite and WGBS libraries were generated by using the TruSeq DNA Methylation Kit (Illumina).

tag: strain

value: sp7- cells

tag: passages

value: 0 dpa


title: 001-1-A03-KOsema3fb-tbx18-1


title: WGBS_sp7ne0dpa_rep1

description: sp7- cells in the uninjured fin (0 dpa)


title: WGBS_sp7ne4dpa_rep1

description: sp7- cells in the regenerating blastema (4 dpa)

value: 4 dpa


title: WGBS_sp7ne4dpa_rep2


title: WGBS_4dpa_rep1

description: regenerating blastema (4 dpa)

value: blastema


title: WGBS_sp7po4dpa_rep1

description: sp7+ cells in the regenerating blastema (4 dpa)

value: sp7+ cells


title: WGBS_sp7po4dpa_rep2


title: WGBS_4dpa_rep2

description: regenerating blastema (4 dpa)


title: WGBS_2dpa_rep1

description: regenerating blastema (2 dpa)

value: 2 dpa


title: WGBS_2dpa_rep2

description: regenerating blastema (2 dpa)


title: WGBS_1dpa_rep2

description: regenerating blastema (1 dpa)

value: 1 dpa


title: WGBS_sp7po0dpa_rep2

description: sp7+ cells in the uninjured fin (0 dpa)


title: WGBS_1dpa_rep1

description: regenerating blastema (1 dpa)


title: WGBS_0dpa_rep2

description: Uninjured fin (0 dpa)

value: fin


title: RNA_fosl1aKO_4dpa_rep2

description:
fosl1a KO regenerating blastema (4 dpa)
RNA_finRegen_fosl1aKO_featureCounts.txt.gz

data_processing:
Basecalls were performed by the Edison Family Center for Genome Sciences & Systems Biology Sequencing Center using bcl2fastq
The raw sequence reads were aligned to zebrafish transcriptome (Ensembl release 85) and the zebrafish genome assembly (GRCz10) by using STAR aligner version 2.5.2a with the following parameters: --sjdbScore 1 --clip3pAdapterSeq AGATCGGAAGAGC --outWigStrand Unstranded --outFilterType BySJout --outFilterMultimapNmax 1.
The total number of reads overlapping each gene were counted using featureCounts v.1.5.0 with Ensembl release 85 gtf file and the following parameters: -F GTF -t exon -g gene_id -O -s 0 --primary -p.
Genome_build: GRCz10
Supplementary_files_format_and_content: TXT

extract_protocol:
The total RNA was extracted by using TRIzol solution (Ambion), according to the manufacturer’s instructions with minor modifications.
RNA-seq libraries were generated by using TruSeq RNA Library Prep Kit v2 (Illumina), according to the manufacturer’s instructions.

tag: days post amputation

tag: genotype/variation

value: fosl1a KO


title: WGBS_0dpa_rep1

description: Uninjured fin (0 dpa)


title: RNA_fosl1aKO_1dpa_rep1

description:
fosl1a KO regenerating blastema (1 dpa)
RNA_finRegen_fosl1aKO_featureCounts.txt.gz


title: RNA_fosl1aKO_1dpa_rep2


title: RNA_fosl1aKO_0dpa_rep2

description:
fosl1a KO uninjured fin (0 dpa)
RNA_finRegen_fosl1aKO_featureCounts.txt.gz


title: RNA_fosl1aKO_4dpa_rep1


title: RNA_fosl1aWT_4dpa_rep2

description:
fosl1a WT regenerating blastema (4 dpa)
RNA_finRegen_fosl1aKO_featureCounts.txt.gz

value: fosl1a WT


title: RNA_fosl1aKO_0dpa_rep1


title: RNA_fosl1aWT_1dpa_rep2

description:
fosl1a WT regenerating blastema (1 dpa)
RNA_finRegen_fosl1aKO_featureCounts.txt.gz


title: WGBS_sp7po0dpa_rep1

description: sp7+ cells in the uninjured fin (0 dpa)


title: RNA_fosl1aWT_1dpa_rep1


title: RNA_fosl1aWT_0dpa_rep2

description:
fosl1a WT uninjured fin (0 dpa)
RNA_finRegen_fosl1aKO_featureCounts.txt.gz


title: RNA_fosl1aWT_0dpa_rep1


title: RNA_sp7po4dpa_rep2

description:
sp7+ cells in the regenerating blastema (4 dpa)
RNA_finRegen_featureCounts.txt.gz


title: RNA_sp7po4dpa_rep1


title: RNA_sp7po0dpa_rep2

description:
sp7+ cells in the uninjured fin (0 dpa)
RNA_finRegen_featureCounts.txt.gz


title: RNA_sp7ne4dpa_rep1

description:
sp7- cells in the regenerating blastema (4 dpa)
RNA_finRegen_featureCounts.txt.gz


title: RNA_sp7po0dpa_rep1


title: RNA_sp7ne0dpa_rep1

description:
sp7- cells in the uninjured fin (0 dpa)
RNA_finRegen_featureCounts.txt.gz


title: ATAC_sp7po4dpa_rep1

data_processing:
Basecalls were performed by the Edison Family Center for Genome Sciences & Systems Biology Sequencing Center using bcl2fastq
The Illumina adapter sequences were trimmed from the raw sequencing reads using cutadapt v.1.11 paired-end mode.
The trimmed reads were mapped to the zebrafish genome sequence by using bowtie2 version 2.3.3.1 with the following parameters: --local -k 4 -X 2000 --mm.
The ATAC peaks per replicate were identified from these insertion sites by using MACS2 version 2.1.1 callpeak function with the following parameters: -g 1.34e9 --keep-dup all -B --SPMR --nomodel --extsize 73 --shift -37 -p 0.01 --call-summits.
The ATAC signal bigWig tracks were converted from the bedGraph files generated by MACS2 version 2.1.1 bdgcmp function with the following parameter: -m FE.
Genome_build: GRCz10
Supplementary_files_format_and_content: bigWig

extract_protocol:
70,000 cells were washed with 50 µL of cold PBS buffer, lysed in 50 µL of cold lysis buffer (10 mM Tris, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630), and incubated with TDE1 enzyme (from Nextera DNA Sample Preparation Kit, Illumina) for 30 minutes at 37 ºC for transposition. Transposed DNA fragments were immediately purified by using MinElute PCR Purification Kit (Qiagen)
ATAC-seq libraries were amplified by using eleven cycles of PCR amplification with the initial 5-minute extension at 72 ºC, and purified by using the AMPure XP Beads (Beckrman Coulter). The purified libraries were eluted with 20 µL of nuclease-free water.


title: ATAC_sp7po0dpa_rep2

description: sp7+ cells in the uninjured fin (0 dpa)


title: ATAC_sp7po4dpa_rep2


title: ATAC_sp7po0dpa_rep1

description: sp7+ cells in the uninjured fin (0 dpa)


title: ATAC_sp7ne4dpa_rep2


title: 017-1-B07-KOsema3fb-tbx18-1


title: ATAC_sp7ne0dpa_rep1

description: sp7- cells in the uninjured fin (0 dpa)


title: ATAC_sp7ne4dpa_rep1


title: 464_5_H12_tcf21-4

data_processing:
Alignment to GRCz10-91 with STAR (v2.4.2a) outSJfilterCountUniqueMin -1 -1 -1 -1 --outSJfilterCountTotalMin 30 10 10 10 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical
BAM files with samtools (v1.3) view -bS
Sorting of BAM files with samtools (v1.3) sort
Removal of PCR duplicates from BAM files with samtools (v1.3) rmdup
Read counting with featureCounts (v1.4.5-p1) -p -B -a -t exon -g gene_id
Quality control on cells and genes with scater R package (v1.6.3)
Genome_build: GRCz10-91
Supplementary_files_format_and_content: Tab-delimited text files of raw counts on gene level before and after QC
Supplementary_files_format_and_content: featureCounts_all_data.txt: Tab delimited text file (raw counts before QC)
Supplementary_files_format_and_content: featureCounts_all_data.txt: Column 1 = Ensembl gene ID, column 2 = gene length in basepairs, column 3 = gene name, columns 4-467 = counts for each cell, colnames = gene_id, gene_length, gene_name, cell names 1-464
Supplementary_files_format_and_content: featureCounts_all_data.txt: Rows 1-35080 = nuclear genes, rows 35081-35117 = mitochondrial genes, rows 35118-35209 = ERCC spike-in sequences, rows 35210-35218 = fluorophore/tag sequences, rownames = gene names
Supplementary_files_format_and_content: featureCounts_count_data_QC.txt: Tab delimited text file (raw counts after QC)
Supplementary_files_format_and_content: featureCounts_count_data_QC.txt: Columns 1-366 = counts for each cell, colnames = cell names 1-366
Supplementary_files_format_and_content: featureCounts_count_data_QC.txt: Rows 1-21801 = nuclear genes, rows 21802-21885 = ERCC spike-in sequences, rows 21886-21891 = fluorophore/tag sequences, rownames = gene names

value: Heart

value: larval cardiac cells


title: RNA_fosl1aWT_4dpa_rep1


title: ATAC_sp7ne0dpa_rep2

description: sp7- cells in the uninjured fin (0 dpa)


title: 460_5_H08_tcf21-4


title: 458_5_H06_tcf21-4


title: 459_5_H07_tcf21-4


title: 463_5_H11_tcf21-4


title: 457_5_H05_tcf21-4


title: RNA_sp7ne4dpa_rep2


title: RNA_sp7ne0dpa_rep2


title: 449_5_G09_ref-myo-1

value: eGFP


title: 454_5_H02_ref-myo-1


title: 448_5_G08_ref-myo-1


title: 450_5_G10_ref-myo-1


title: 452_5_G12_ref-myo-1


title: 453_5_H01_ref-myo-1


title: 456_5_H04_ref-blank-1

source_name: Empty well

value: Empty well


title: 447_5_G07_ref-myo-1


title: 462_5_H10_tcf21-4


title: 444_5_G04_tcf21-4


title: 461_5_H09_tcf21-4


title: 443_5_G03_tcf21-4


title: 446_5_G06_tcf21-4


title: 445_5_G05_tcf21-4


title: 442_5_G02_tcf21-4


title: 455_5_H03_ref-blank-1


title: 441_5_G01_tcf21-4


title: 440_5_F12_ref-endo-1

value: kdrl:GFP, gata1a:dsRed

value: GFP


title: 439_5_F11_ref-endo-1

value: 5 days post fertilisation


title: 437_5_F09_ref-endo-1


title: 436_5_F08_ref-endo-1


title: 438_5_F10_ref-endo-1


title: 434_5_F06_ref-endo-1


title: 435_5_F07_ref-endo-1


title: 429_5_F01_tcf21-4


title: 431_5_F03_tcf21-4


title: 433_5_F05_tcf21-3


title: 425_5_E09_tcf21-4


title: 427_5_E11_tcf21-4


title: 428_5_E12_tcf21-4


title: 424_5_E08_tcf21-4


title: 432_5_F04_ref-endo-1


title: 423_5_E07_tcf21-4


title: 422_5_E06_ctr-1

value: Wildtype


title: 426_5_E10_tcf21-4


title: 430_5_F02_tcf21-4


title: 420_5_E04_tbx18-1


title: 421_5_E05_tbx18-1


title: 417_5_E01_tbx18-1


title: 418_5_E02_tbx18-1


title: 415_5_D11_tbx18-1


title: 414_5_D10_tbx18-1


title: 413_5_D09_tbx18-1


title: 412_5_D08_tbx18-1


title: 411_5_D07_tbx18-1


title: 410_5_D06_tbx18-1


title: 409_5_D05_tmkg-1

value: tcf21:dsRed, myl7:eGFP, kdrl:GFP, gata1a:dsRed


title: 406_5_D02_tbx18-1


title: 407_5_D03_tbx18-1


title: 405_5_D01_tbx18-1


title: 416_5_D12_tbx18-1


title: 403_5_C11_tbx18-1


title: 401_5_C09_tbx18-1


title: 404_5_C12_tbx18-1


title: 396_5_C04_tbx18-1


title: 399_5_C07_tbx18-1


title: 419_5_E03_tbx18-1


title: 393_5_C01_tbx18-1


title: 395_5_C03_tbx18-1


title: 451_5_G11_ref-myo-1


title: 394_5_C02_tbx18-1


title: 392_5_B12_wt1b-1


title: 389_5_B09_wt1b-1


title: 397_5_C05_tbx18-1


title: 386_5_B06_wt1b-1


title: 408_5_D04_tbx18-1


title: 390_5_B10_wt1b-1


title: 387_5_B07_wt1b-1


title: 388_5_B08_wt1b-1


title: 385_5_B05_wt1b-1


title: 402_5_C10_tbx18-1


title: 381_5_B01_wt1b-1


title: 400_5_C08_tbx18-1


title: 383_5_B03_wt1b-1


title: 380_5_A12_wt1b-1


title: 382_5_B02_wt1b-1


title: 398_5_C06_tbx18-1


title: 379_5_A11_wt1b-1


title: 378_5_A10_wt1b-1


title: 375_5_A07_wt1b-1


title: 376_5_A08_wt1b-1


title: 377_5_A09_wt1b-1


title: 391_5_B11_wt1b-1


title: 373_5_A05_wt1b-1


title: 372_5_A04_tbx18-1


title: 369_5_A01_wt1b-1


title: 371_5_A03_wt1b-1


title: 384_5_B04_wt1b-1


title: 367_4_H11_tcf21-4


title: 370_5_A02_wt1b-1


title: 366_4_H10_tcf21-4


title: 364_4_H08_tcf21-4


title: 360_4_H04_tcf21-4


title: 362_4_H06_tcf21-4


title: 361_4_H05_ref-blank-1


title: 363_4_H07_tcf21-4


title: 358_4_H02_tcf21-4


title: 355_4_G11_tcf21-4


title: 357_4_H01_tcf21-4


title: 352_4_G08_tcf21-4


title: 353_4_G09_tcf21-4


title: 374_5_A06_wt1b-1


title: 359_4_H03_tcf21-4


title: 348_4_G04_ref-myo-1


title: 354_4_G10_tcf21-4


title: 356_4_G12_tcf21-4


title: 349_4_G05_ref-myo-1


title: 368_4_H12_tcf21-4


title: 351_4_G07_tcf21-4


title: 365_4_H09_tcf21-4


title: 350_4_G06_ref-myo-1


title: 346_4_G02_ref-myo-1


title: 343_4_F11_tcf21-4


title: 347_4_G03_ref-myo-1


title: 342_4_F10_tcf21-4


title: 344_4_F12_tcf21-4


title: 339_4_F07_tcf21-4


title: 337_4_F05_tcf21-4


title: 338_4_F06_tcf21-4


title: 335_4_F03_ref-endo-1


title: 333_4_F01_ref-endo-1


title: 341_4_F09_ctr-1


title: 336_4_F04_tcf21-4


title: 332_4_E12_ref-endo-1


title: 331_4_E11_ref-endo-1


title: 345_4_G01_ref-myo-1


title: 340_4_F08_tcf21-4


title: 328_4_E08_ref-blood-1

value: dsRed


title: 324_4_E04_tcf21-4


title: 327_4_E07_ref-blood-1


title: 329_4_E09_ref-endo-1


title: 321_4_E01_wt1b-1


title: 326_4_E06_tcf21-4


title: 320_4_D12_wt1b-1


title: 319_4_D11_wt1b-1


title: 323_4_E03_wt1b-1


title: 322_4_E02_wt1b-1


title: 317_4_D09_wt1b-1


title: 316_4_D08_wt1b-1


title: 313_4_D05_wt1b-1


title: 334_4_F02_ref-endo-1


title: 312_4_D04_wt1b-1


title: 310_4_D02_wt1b-1


title: 305_4_C09_wt1b-1


title: 307_4_C11_wt1b-1


title: 308_4_C12_wt1b-1


title: 330_4_E10_ref-endo-1


title: 325_4_E05_tcf21-4


title: 303_4_C07_wt1b-1


title: 314_4_D06_wt1b-1


title: 318_4_D10_wt1b-1


title: 299_4_C03_wt1b-1


title: 301_4_C05_wt1b-1


title: 300_4_C04_wt1b-1


title: 302_4_C06_wt1b-1


title: 304_4_C08_wt1b-1


title: 298_4_C02_wt1b-1


title: 297_4_C01_wt1b-1


title: 296_4_B12_tbx18-1


title: 309_4_D01_wt1b-1


title: 311_4_D03_wt1b-1


title: 293_4_B09_tbx18-1


title: 291_4_B07_tbx18-1


title: 294_4_B10_tbx18-1


title: 292_4_B08_tbx18-1


title: 295_4_B11_tbx18-1


title: 289_4_B05_tbx18-1


title: 306_4_C10_wt1b-1


title: 288_4_B04_tbx18-1


title: 286_4_B02_tbx18-1


title: 287_4_B03_tbx18-1


title: 285_4_B01_tbx18-1


title: 284_4_A12_tbx18-1


title: 282_4_A10_tbx18-1


title: 283_4_A11_tbx18-1


title: 280_4_A08_tbx18-1


title: 281_4_A09_tbx18-1


title: 279_4_A07_tbx18-1


title: 278_4_A06_tbx18-1


title: 277_4_A05_tbx18-1


title: 276_4_A04_tmkg-1


title: 290_4_B06_tbx18-1


title: 274_4_A02_tbx18-1


title: 271_3_H11_ctr-1


title: 267_3_H07_ctr-1


title: 269_3_H09_ctr-1


title: 268_3_H08_ctr-1


title: 263_3_H03_ctr-1


title: 261_3_H01_ctr-1


title: 265_3_H05_ctr-1


title: 262_3_H02_ctr-1


title: 260_3_G12_ctr-1


title: 266_3_H06_ctr-1


title: 264_3_H04_ctr-1


title: 315_4_D07_wt1b-1


title: 259_3_G11_ctr-1


title: 258_3_G10_ctr-1


title: 257_3_G09_ctr-1


title: 255_3_G07_ctr-1


title: 256_3_G08_ctr-1


title: 253_3_G05_ctr-1


title: 254_3_G06_ctr-1


title: 252_3_G04_ctr-1


title: 275_4_A03_tbx18-1


title: 250_3_G02_ctr-1


title: 249_3_G01_ctr-1


title: 273_4_A01_tbx18-1


title: 251_3_G03_ctr-1


title: 270_3_H10_ctr-1


title: 247_3_F11_ctr-1


title: 246_3_F10_ctr-1


title: 248_3_F12_ctr-1


title: 245_3_F09_ctr-1


title: 243_3_F07_ctr-1


title: 244_3_F08_ctr-1


title: 240_3_F04_ctr-1


title: 236_3_E12_ctr-1


title: 239_3_F03_ctr-1


title: 237_3_F01_ctr-1


title: 242_3_F06_ctr-1


title: 235_3_E11_ctr-1


title: 241_3_F05_ctr-1


title: 234_3_E10_ctr-1


title: 238_3_F02_ctr-1


title: 233_3_E09_ctr-1


title: 231_3_E07_ctr-1


title: 230_3_E06_ctr-1


title: 229_3_E05_ctr-1


title: 232_3_E08_ctr-1


title: 226_3_E02_ctr-1


title: 225_3_E01_ctr-1


title: 228_3_E04_ctr-1


title: 227_3_E03_ctr-1


title: 221_3_D09_tmkg-1


title: 222_3_D10_tmkg-1


title: 223_3_D11_ctr-1


title: 224_3_D12_ctr-1


title: 220_3_D08_tmkg-1


title: 219_3_D07_tmkg-1


title: 218_3_D06_tmkg-1


title: 217_3_D05_tmkg-1


title: 216_3_D04_tmkg-1


title: 214_3_D02_tmkg-1


title: 213_3_D01_tmkg-1


title: 211_3_C11_tmkg-1


title: 215_3_D03_tmkg-1


title: 272_3_H12_ctr-1


title: 210_3_C10_tmkg-1


title: 208_3_C08_tmkg-1


title: 209_3_C09_tmkg-1


title: 212_3_C12_tmkg-1


title: 205_3_C05_tmkg-1


title: 203_3_C03_tmkg-1


title: 206_3_C06_tmkg-1


title: 198_3_B10_tmkg-1


title: 202_3_C02_tmkg-1


title: 200_3_B12_tmkg-1


title: 201_3_C01_tmkg-1


title: 196_3_B08_tmkg-1


title: 194_3_B06_tmkg-1


title: 199_3_B11_tmkg-1


title: 193_3_B05_tmkg-1


title: 191_3_B03_tmkg-1


title: 192_3_B04_tmkg-1


title: 190_3_B02_tmkg-1


title: 195_3_B07_tmkg-1


title: 188_3_A12_tmkg-1


title: 197_3_B09_tmkg-1


title: 187_3_A11_tmkg-1


title: 185_3_A09_tmkg-1


title: 207_3_C07_tmkg-1


title: 186_3_A10_tmkg-1


title: 184_3_A08_tmkg-1


title: 183_3_A07_tmkg-1


title: 189_3_B01_tmkg-1


title: 182_3_A06_tmkg-1


title: 178_3_A02_tmkg-1


title: 179_3_A03_tmkg-1


title: 181_3_A05_tmkg-1


title: 180_3_A04_tmkg-1


title: 177_3_A01_tmkg-1


title: 204_3_C04_tmkg-1


title: 175_2_H11_tcf21-2


title: 176_2_H12_tcf21-2


title: 174_2_H10_tcf21-2


title: 173_2_H9_tcf21-2


title: 169_2_H5_tcf21-2


title: 171_2_H7_tcf21-2


title: 168_2_H4_tcf21-2


title: 167_2_H3_tcf21-2


title: 170_2_H6_tcf21-2


title: 166_2_H2_tcf21-2


title: 165_2_H1_tcf21-2


title: 164_2_G8_tcf21-2


title: 163_2_G7_tcf21-2


title: 160_2_G4_tcf21-2


title: 161_2_G5_tcf21-2


title: 159_2_G3_tcf21-2


title: 156_2_F12_tcf21-2


title: 157_2_G1_tcf21-2


title: 158_2_G2_tcf21-2


title: 154_2_F10_tcf21-2


title: 172_2_H8_tcf21-2


title: 155_2_F11_tcf21-2


title: 151_2_F7_tcf21-2


title: 149_2_F5_tcf21-2


title: 150_2_F6_tcf21-2


title: 162_2_G6_tcf21-2


title: 147_2_F3_tcf21-2


title: 152_2_F8_tcf21-2


title: 146_2_F2_tcf21-2


title: 145_2_F1_tcf21-2


title: 144_2_E12_tcf21-2


title: 142_2_E9_tcf21-2


title: 148_2_F4_tcf21-2


title: 143_2_E11_tcf21-2


title: 141_2_E8_tcf21-2


title: 140_2_E7_tcf21-2


title: 139_2_E6_tcf21-2


title: 138_2_E5_tcf21-2


title: 153_2_F9_tcf21-2


title: 137_2_E4_tcf21-2


title: 136_2_E1_tcf21-2


title: 135_2_D12_tcf21-2


title: 134_2_D11_tcf21-2


title: PROG_200

city: Lund

first: Gottfrid

last: Sjodahl

address: Medicon Village

department: Department of Translational Medicine

institute: Lund Univeristy

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials â€¢ Heat cocktails at 99Â° for 5 minutes, then 42Â° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). â€¢ Transfer 200Î¼l of hyb solution to each array, then tape holes and parafilm. â€¢ Hybridize 16 hours at 45Â° at 60rpmâ€¢ Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using Bioconductor R package Affy. Probe intensities were normalized in labeling batches using RMA.
The file Processed_data_supplement.txt is available on the series record and contains the full dataset of 200 CEL files. These CEL files were normalized using RMA by labeling batches. Batches were combined and RMA normalized. The data was filtered for probes with signal intensity less than the median of negative control probes for >80% of the values. Gene symbols and EntrezID were appended using Bioconductor (hugene10stprobeset.db Version 8.6.0). Probes not mapping to a gene symbol were removed. The probes were median merged by gene symbol and log-transformed. Batch correction was performed using ComBat, and the final data set was median centered.

label: biotin

source_name: FFPE tissue specimen

label_protocol: SensationPlus FFPE Amplification and WT labeling kit

extract_protocol: High Pure FFPET RNA isolation kit (Roche)

value: bladder cancer

tag: tissue preparation

value: FFPE

tag: labeling batch

tag: patient identifier

tag: tumor number

tag: primary, recurrence, or progression

value: prog

tag: tumor stage

tag: grade (who1999)

tag: molecular subtype

value: GU


title: PROG_199

tag: tissue

value: Mes


title: PROG_198

value: rec


title: PROG_197

value: UroB


title: 133_2_D10_tcf21-2

value: Heart

tag: cell type

tag: transgenic reporter

tag: cell fluorescence


title: PROG_196

value: Ta

value: UroA-Prog


title: 131_2_D8_tcf21-2

value: larval cardiac cells

tag: age


title: PROG_195


title: Genomic DNA from OPSCC sample [MPC_T81]

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

country: Japan

institute: Chiba University

description: SAMPLE 22

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC Beadchip Kit using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting.

data_processing: BeadStudio software v3.2.

label_protocol: Standard Illumina Protocol.

extract_protocol: Genomic DNA was extracted and purified from clinical samples using QIAquick DNA mini kit according to standard instructions.

tag: disease state

value: oropharyngeal squamous carcinoma (OPSCC)

value: oropharyngeal cancer

tag: gender

value: male


title: 132_2_D9_tcf21-2

value: 5 days post fertilisation


title: 129_2_D6_tcf21-2


title: 130_2_D7_tcf21-2


title: PROG_194

value: primary


title: PROG_193

tag: re-analysis of sample in gse83586

value: Re-analysis of GSM2212982


title: Genomic DNA from OPSCC sample [MPC_T82]

description: SAMPLE 23


title: Genomic DNA from OPSCC sample [MPC_T84]

description: SAMPLE 25


title: Genomic DNA from OPSCC sample [MPC_T79]

description: SAMPLE 20


title: Genomic DNA from OPSCC sample [MPC_T77]

description: SAMPLE 18


title: 127_2_D4_tcf21-2


title: 126_2_D3_tcf21-2


title: PROG_192

value: bladder cancer

value: UroC


title: Genomic DNA from OPSCC sample [MPC_T14]

description: SAMPLE 1


title: 125_2_D2_tcf21-2


title: Genomic DNA from OPSCC sample [MPC_T80]

description: SAMPLE 21

value: female


title: Genomic DNA from OPSCC sample [MPC_T67]

description: SAMPLE 8


title: Genomic DNA from OPSCC sample [MPC_T74]

description: SAMPLE 15


title: Genomic DNA from OPSCC sample [MPC_T76]

description: SAMPLE 17


title: Genomic DNA from OPSCC sample [MPC_T75]

description: SAMPLE 16


title: Genomic DNA from OPSCC sample [MPC_T66]

description: SAMPLE 7


title: Genomic DNA from OPSCC sample [MPC_T68]

description: SAMPLE 9


title: PROG_188

value: FFPE


title: 124_2_D1_tcf21-2


title: Genomic DNA from OPSCC sample [MPC_T34]

description: SAMPLE 5


title: Genomic DNA from OPSCC sample [MPC_T59]

description: SAMPLE 6


title: Genomic DNA from OPSCC sample [MPC_T71]

description: SAMPLE 12


title: PROG_189


title: Genomic DNA from OPSCC sample [MPC_T73]

description: SAMPLE 14


title: PROG_190


title: Genomic DNA from OPSCC sample [MPC_T72]

description: SAMPLE 13


title: 123_2_C12_tcf21-2


title: 121_2_C9_tcf21-2


title: Genomic DNA from OPSCC sample [MPC_T78]

description: SAMPLE 19


title: 122_2_C11_tcf21-2


title: Genomic DNA from OPSCC sample [MPC_T33]

description: SAMPLE 4


title: Genomic DNA from OPSCC sample [MPC_T32]

description: SAMPLE 3


title: 120_2_C8_tcf21-2


title: 119_2_C5_tcf21-2


title: Genomic DNA from OPSCC sample [MPC_T69]

description: SAMPLE 10


title: PROG_186

value: GU


title: 118_2_C4_tcf21-2


title: 117_2_C1_tcf21-2


title: PROG_187

value: Re-analysis of GSM2212946

value: rec


title: Genomic DNA from OPSCC sample [MPC_T70]

description: SAMPLE 11


title: PROG_185


title: 115_2_B10_tcf21-2

value: Heart


title: 128_2_D5_tcf21-2


title: Genomic DNA from OPSCC sample [MPC_T31]

description: SAMPLE 2


title: 114_2_B9_tcf21-2


title: PROG_183


title: Genomic DNA from OPSCC sample [MPC_T83]

description: SAMPLE 24


title: PROG_184

value: Ta


title: 112_2_B7_tcf21-2


title: 110_2_B3_tcf21-2


title: 116_2_B12_tcf21-2


title: 109_2_B2_tcf21-2


title: 111_2_B5_tcf21-2


title: PROG_181

value: UroA-Prog


title: PROG_182


title: 106_2_A11_tcf21-2

value: larval cardiac cells


title: 107_2_A12_tcf21-2


title: PROG_179


title: PROG_180


title: 104_2_A9_tcf21-2


title: PROG_178


title: PROG_177


title: 103_2_A7_tcf21-2


title: PROG_174


title: PROG_176


title: 108_2_B1_tcf21-2


title: 113_2_B8_tcf21-2


title: 102_2_A6_tcf21-2


title: PROG_175

value: prog

value: UroB


title: PROG_173


title: PROG_191


title: PROG_172


title: PROG_169


title: PROG_171


title: 100_2_A4_tcf21-2


title: 101_2_A5_tcf21-2


title: PROG_170

value: Re-analysis of GSM2212984


title: 99_2_A3_tcf21-2

value: 5 days post fertilisation


title: 98_2_A2_tcf21-2


title: 97_2_A1_tcf21-2


title: PROG_168

value: Mes


title: 96_1_H12_tcf21-1


title: 95_1_H11_tcf21-1


title: 94_1_H10_tcf21-1


title: 93_1_H9_tcf21-1


title: 91_1_H7_tcf21-1


title: PROG_164


title: 105_2_A10_tcf21-2


title: 92_1_H8_tcf21-1


title: PROG_166

value: primary


title: 90_1_H6_tcf21-1


title: 87_1_H3_tcf21-1


title: 88_1_H4_tcf21-1


title: 89_1_H5_tcf21-1


title: PROG_162

value: bladder cancer


title: PROG_167


title: PROG_163


title: 86_1_H2_tcf21-1


title: PROG_157


title: PROG_152

value: ScNE


title: PROG_155


title: PROG_159


title: 85_1_H1_tcf21-1


title: 84_1_G12_tcf21-1


title: PROG_161

value: UroC


title: PROG_154

value: Re-analysis of GSM2213025

value: FFPE


title: PROG_160


title: 82_1_G10_tcf21-1


title: PROG_158

value: Re-analysis of GSM2213106


title: PROG_153

value: rec


title: PROG_156


title: PROG_151

value: Metastasis


title: PROG_165

value: Ba/Sq


title: 81_1_G9_tcf21-1

value: Heart


title: 80_1_G8_tcf21-1

value: larval cardiac cells


title: PROG_150


title: PROG_147

value: UroA-Prog


title: PROG_148

value: prog


title: PROG_146


title: 78_1_G6_tcf21-1


title: 77_1_G5_tcf21-1


title: 76_1_G4_tcf21-1


title: 83_1_G11_tcf21-1


title: 75_1_G3_tcf21-1


title: 74_1_G2_tcf21-1


title: 71_1_F11_tcf21-1


title: 70_1_F10_tcf21-1


title: 69_1_F9_tcf21-1


title: 79_1_G7_tcf21-1


title: 68_1_F8_tcf21-1


title: 67_1_F7_tcf21-1


title: PROG_149


title: PROG_145

value: Re-analysis of GSM2213166


title: 66_1_F6_tcf21-1

value: 5 days post fertilisation


title: 65_1_F5_tcf21-1


title: 73_1_G1_tcf21-1


title: 72_1_F12_tcf21-1


title: PROG_141

value: Re-analysis of GSM2213202


title: PROG_143

value: Ta


title: 64_1_F4_tcf21-1


title: PROG_144

value: bladder cancer


title: PROG_140


title: PROG_142

value: primary


title: 63_1_F3_tcf21-1


title: PROG_137

value: GU


title: 62_1_F2_tcf21-1


title: PROG_139


title: 61_1_F1_tcf21-1


title: PROG_135

value: Mes


title: 60_1_E12_tcf21-1


title: 58_1_E10_tcf21-1


title: 57_1_E9_tcf21-1


title: 59_1_E11_tcf21-1


title: 56_1_E8_tcf21-1


title: PROG_136

value: FFPE


title: 54_1_E6_tcf21-1


title: 55_1_E7_tcf21-1


title: 53_1_E5_tcf21-1


title: PROG_134


title: Genomic DNA from OPSCC sample [MPC_T89]

description: SAMPLE 69

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol.

label: Not provided

value: oropharyngeal squamous carcinoma (OPSCC)

value: oropharyngeal cancer

value: male


title: PROG_131


title: 51_1_E3_tcf21-1


title: PROG_132

value: rec


title: 48_1_D12_tcf21-1

value: Heart


title: Genomic DNA from OPSCC sample [MPC_T88]

description: SAMPLE 68


title: Genomic DNA from OPSCC sample [MPC_T86]

description: SAMPLE 66


title: PROG_129

value: UroC


title: Genomic DNA from OPSCC sample [MPC_T87]

description: SAMPLE 67


title: 52_1_E4_tcf21-1

value: larval cardiac cells


title: Genomic DNA from OPSCC sample [MPC_T85]

description: SAMPLE 65


title: PROG_130

value: prog


title: PROG_127


title: 49_1_E1_tcf21-1


title: 47_1_D11_tcf21-1


title: Genomic DNA from OPSCC sample [MPC_T62]

description: SAMPLE 61


title: PROG_128


title: 45_1_D9_tcf21-1


title: 44_1_D8_tcf21-1


title: 43_1_D7_tcf21-1


title: 42_1_D6_tcf21-1


title: PROG_126

value: cis


title: 46_1_D10_tcf21-1

value: 5 days post fertilisation


title: 40_1_D4_tcf21-1


title: Genomic DNA from OPSCC sample [MPC_T64]

description: SAMPLE 63


title: PROG_138


title: Genomic DNA from OPSCC sample [MPC_T57]

description: SAMPLE 57


title: PROG_123


title: Genomic DNA from OPSCC sample [MPC_T61]

description: SAMPLE 60


title: Genomic DNA from OPSCC sample [MPC_T55]

description: SAMPLE 55

value: female


title: Genomic DNA from OPSCC sample [MPC_T58]

description: SAMPLE 58


title: Genomic DNA from OPSCC sample [MPC_T56]

description: SAMPLE 56


title: 39_1_D3_tcf21-1


title: 38_1_D2_tcf21-1


title: 36_1_C12_tcf21-1


title: 35_1_C11_tcf21-1


title: Genomic DNA from OPSCC sample [MPC_T63]

description: SAMPLE 62


title: 41_1_D5_tcf21-1


title: PROG_124

value: ScNE


title: 37_1_D1_tcf21-1


title: Genomic DNA from OPSCC sample [MPC_T60]

description: SAMPLE 59


title: PROG_122

value: bladder cancer

value: Ta

value: UroA-Prog


title: PROG_133

value: Mes


title: 33_1_C9_tcf21-1


title: 34_1_C10_tcf21-1


title: Genomic DNA from OPSCC sample [MPC_T53]

description: SAMPLE 53


title: PROG_121

value: FFPE

value: UroB


title: 32_1_C8_tcf21-1


title: 31_1_C7_tcf21-1


title: PROG_120


title: 30_1_C6_tcf21-1


title: 29_1_C5_tcf21-1


title: 28_1_C4_tcf21-1


title: Genomic DNA from OPSCC sample [MPC_T52]

description: SAMPLE 52

value: oropharyngeal squamous carcinoma (OPSCC)

value: oropharyngeal cancer


title: 27_1_C3_tcf21-1


title: 50_1_E2_tcf21-1


title: 26_1_C2_tcf21-1


title: PROG_118

value: primary


title: PROG_117

value: rec


title: Genomic DNA from OPSCC sample [MPC_T51]

description: SAMPLE 51


title: 24_1_B12_tcf21-1

value: Heart


title: 23_1_B11_tcf21-1

value: larval cardiac cells


title: PROG_116


title: PROG_115


title: 21_1_B9_tcf21-1


title: 22_1_B10_tcf21-1


title: PROG_119


title: Genomic DNA from OPSCC sample [MPC_T49]

description: SAMPLE 49


title: Genomic DNA from OPSCC sample [MPC_T50]

description: SAMPLE 50

value: male


title: 20_1_B8_tcf21-1


title: Genomic DNA from OPSCC sample [MPC_T48]

description: SAMPLE 48


title: Genomic DNA from OPSCC sample [MPC_T65]

description: SAMPLE 64


title: 18_1_B6_tcf21-1


title: 19_1_B7_tcf21-1


title: 17_1_B5_tcf21-1


title: PROG_114


title: PROG_113

value: prog

value: Ba/Sq


title: 15_1_B3_tcf21-1

value: 5 days post fertilisation


title: Genomic DNA from OPSCC sample [MPC_T47]

description: SAMPLE 47


title: 14_1_B2_tcf21-1


title: 13_1_B1_tcf21-1


title: PROG_112


title: 12_1_A12_tcf21-1


title: 16_1_B4_tcf21-1


title: PROG_111


title: Genomic DNA from OPSCC sample [MPC_T45]

description: SAMPLE 45


title: 11_1_A11_tcf21-1


title: 9_1_A9_tcf21-1


title: 10_1_A10_tcf21-1


title: Genomic DNA from OPSCC sample [MPC_T46]

description: SAMPLE 46


title: Genomic DNA from OPSCC sample [MPC_T44]

description: SAMPLE 44


title: 8_1_A8_tcf21-1


title: PROG_109


title: PROG_107


title: PROG_110


title: 7_1_A7_tcf21-1


title: PROG_125

value: Re-analysis of GSM2212935

value: ScNE


title: Genomic DNA from OPSCC sample [MPC_T41]

description: SAMPLE 41

value: female


title: Genomic DNA from OPSCC sample [MPC_T40]

description: SAMPLE 40


title: Genomic DNA from OPSCC sample [MPC_T42]

description: SAMPLE 42


title: PROG_108

value: bladder cancer

value: Ta

value: UroA-Prog


title: 5_1_A5_tcf21-1


title: 4_1_A4_tcf21-1


title: 3_1_A3_tcf21-1


title: Genomic DNA from OPSCC sample [MPC_T54]

description: SAMPLE 54


title: pMo ATAC-seq DBA2J rep2

city: La Jolla

first: Eniko

last: Sajti

address: 9500 Gilman Drive

department: Pediatrics

institute: UCSD

data_processing:
For ATAC-Seq and RNA-Seq samples, reads were aligned to the mm10 genome of the corresponding inbred strain using default parameter for bowtie (RNA-Star, respectively). Aligned read files were analyzed with HOMER (http://biowhat.ucsd.edu/homer/) to find peaks, calculate TPM from the gene bodies of RefSeq genes, perform motif-  and  other analyses in the study. Genetic variation analyses were performed using custom R scripts.
Genome_build: mm10, and DBA/2J from mm10 using published variants (Keane, T. M. et al., Nature 477, 289-294 (2011))
Supplementary_files_format_and_content: Processed files include BED-like files (ATAC-Seq peak positions), expression text files (RNA-Seq expression data, using default HOMER parameters).  All genomic coordinates are relative to mm10 (NCBI 38) mouse assembly.

organism: Mus musculus

source_name: patrolling macrophages

extract_protocol:
Lungs were incubated at 37oC for 15 minutes while on a rotator. Red blood cells were lysed using RBC lysis buffer (eBioscience) for a 5 minute incubation. The obtained cell suspension was filtered using a 70 micron filter, washed and cells were resuspended in PBS. Cells were then incubated with anti-Fc blocking mAb (anti CD16/32, clone 93, BioLegend) and viability dye Zombie Aqua (Biolegend) for 10 min. After this, cells where stained with an antibody cocktail containing APC Cy7-conjugated CD45, PE-conjugated F4/80, BV605-conjugated CD11c, v450-conjugated CD11b, PE Cy7-conjugated CD64, AF700-conjufgated Ly6c, FITC-conjugated Ly6g, AF647-conjugated SiglecF mAb for 30 minutes. All labeled cells were passed through a FACS Aria II flow cytometer (BD Biosciences) and after proper gating 4 subsets of lung MP were sorted
RNA-seq: PolyA enriched mRNA was fragmented, in 2x Superscript III first-strand buffer with 10mM DTT (Invitrogen), by incubation at 94°C for 9 minutes, then immediately chilled on ice before the next step. The 10 µL of fragmented mRNA, 0.5 µL of Random primer (Invitrogen), 0.5 µL of Oligo dT primer (Invitrogen), 0.5 µL of SUPERase-In (Ambion), 1 µL of dNTPs (10 mM) and 1 µL of DTT (10 mM) were heated at 50°C for three minutes. At the end of incubation, 5.8 µL of water, 1 µL of DTT (100 mM), 0.1 µL Actinomycin D (2 µg/µL), 0.2 µL of 1% Tween-20 (Sigma) and 0.2 µL of Superscript III (Invitrogen) were added and incubated in a PCR machine using the following conditions: 25°C for 10 minutes, 50°C for 50 minutes, and a 4°C hold. The product was then purified with RNAClean XP beads according to manufacture’s instruction and eluted with 10 µL nuclease-free water. The RNA/cDNA double-stranded hybrid was then added to 1.5 µL of Blue Buffer (Enzymatics), 1.1 µL of dUTP mix (10 mM dATP, dCTP, dGTP and 20 mM dUTP), 0.2 µL of RNAse H (5 U/µL), 1.05 µL of water, 1 µL of DNA polymerase I (Enzymatics) and 0.15 µL of 1% Tween-20. The mixture was incubated at 16°C for 1 hour. The resulting dUTP-marked dsDNA was purified using 28 µL of Sera-Mag Speedbeads (Thermo Fisher Scientific), diluted with 20% PEG8000, 2.5M NaCl to final of 13% PEG, eluted with 40 µL EB buffer (10 mM Tris-Cl, pH 8.5) and frozen -80°C. The purified dsDNA (40 µL) underwent end repair by blunting, A-tailing and adapter ligation as previously described44 using barcoded adapters (NextFlex, Bioo Scientific). Libraries were PCR-amplified for 14-16 cycles, size selected using 10% PAGE/TBE gels, eluted and quantified with Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific),
ATAC-seq: Sorted cells in FACS Buffer were pelleted by centrifugation at 400 RCF for 6 minutes at 4oC in a pre-cooled fixed-angle microfuge. Supernatant was carefully removed and cell pellet was resuspend in 47.5 ul lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630), 2.5ul of TDE1 (Cat# FC-121-1030, Illumina) by pipetting. Transposition reactions were incubated at 37°C for 30 minutes. Transposed DNA was purified using a Zymo ChIP DNA Clean & Concentrator kit (Cat# D5205) and purified DNA was eluted in 10 ul elution buffer (10 mM Tris-HCl, pH 8). Transposed fragments were amplified and purified as described previously (Buenostro et al) with modified primers.

treatment_protocol: no treatment

tag: strain


title: 2_1_A2_tcf21-1


title: 1_1_A1_tcf21-1


title: Genomic DNA from OPSCC sample [MPC_T43]

description: SAMPLE 43


title: Genomic DNA from OPSCC sample [MPC_T38]

description: SAMPLE 38


title: 25_1_C1_tcf21-1


title: PROG_105

tag: tissue preparation

value: FFPE

value: GU


title: PROG_104

tag: labeling batch

value: UroC


title: iMo ATAC-seq DBA2J rep2

source_name: inflammatory macrophages


title: pMo ATAC-seq DBA2J rep1


title: Genomic DNA from OPSCC sample [MPC_T35]

description: SAMPLE 35

value: oropharyngeal squamous carcinoma (OPSCC)

value: oropharyngeal cancer


title: iMo ATAC-seq DBA2J rep1


title: Genomic DNA from OPSCC sample [MPC_T39]

description: SAMPLE 39


title: Genomic DNA from OPSCC sample [MPC_T37]

description: SAMPLE 37


title: PROG_102

tag: patient identifier

value: rec


title: EXOSOMES WT5

city: Madrid

first: Manuel

middle: J

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

data_processing:
Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline.
Sequencing adaptor contaminations were removed using CUTADAPT (Marcel Martin). The resulting reads were aligned with BWA against a miRNA sequence reference consisting in the mature Mus musculus component of miRBase21, and quantified using RSEM v1.17 (Li and Dewey, 2011).
Genome_build: miRBase21
Supplementary_files_format_and_content: TMM normalized counts per million (CPM) table, with miRNAs as rows and samples as columns

source_name: T cells blasts from C57BL/6 mice-derived EVs

growth_protocol: Total splenocytes were isolated from spleens of 8-to-12-week old WT C57BL/6 mice. After erythrocyte lysis, cells were cultured in RPMI supplemented with 10% FBS, 50µM β-mercaptoethanol, 1mM sodium pyruvate, and 2 ug ml-1 concanavalin A. After 36h, cells were washed and cultured in RPMI supplemented with 10% EXO-free FBS and 50 U ml-1 mrIL-2. Medium was refreshed every 2 days. EVs were isolated from supernatants of 6-day lymphoblast cultures by serial ultracentrifugation

extract_protocol:
Total RNA was isolated using the miRNeasy mini kit (QIAGEN)
The RNA sequencing library was prepared with the SmallRNA NEBNext Library Prep Set (New England Biolabs) following the manufacturer’s recommendations. The quality, quantity and the size distribution of the Illumina libraries were determined using the Small RNA Kit (Agilent Bioanalyzer).
Libraries were sequenced (single-end mode and length of 75 bp) on the Illumina HiSeq 2500 system using the standard RNA sequencing protocol for Small RNA NEBNext Library Prep Set

treatment_protocol: T cell blasts were pelleted and the supernatant centrifuged at 2000 × g for 20 min. The collected supernatant was subsequently ultracentrifuged at 10,000 × g for 40 min at 4 °C (Beckman Coulter Optima L-100 XP, Beckman Coulter), followed by a final ultracentrifugation at 100,000 × g for 1h at 4 °C. Both cells and EV pellets were resuspended in QIAZOL lysis buffer for RNA extraction.

tag: phenotype

value: C57BL/6 mice


title: Genomic DNA from OPSCC sample [MPC_T36]

description: SAMPLE 36

value: male


title: Genomic DNA from OPSCC sample [MPC_T30]

description: SAMPLE 34


title: Mle29c

first: ting

last: Xie

address: 127 San Vicente Blvd

department: Pulmonary

institute: Cedars-Sinai Medical Center

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse Genome 430 2.0 Array.

scan_protocol: GeneChips were scaned by GenePix 4000B scanner

data_processing: data were normalized by MAS5, all genelists were selected with a 10 fold change cutoff on a filtered gene list (expression filter of raw value >=30, in 1 out of x sample)

source_name: Mle29c cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Mlesico and Mle29c cells were grown in DMEM+10% FBS medium.

extract_protocol: Total RNA were extracted by Trizol

tag: cell line

value: Mle29c epithelial cell line


title: PROG_103

tag: tumor number

tag: primary, recurrence, or progression

value: prog

tag: tumor stage


title: EXOSOMES WT2


title: iMo ATAC-seq C57BL6J rep2


title: IM ATAC-seq DBA2J rep1

source_name: interstital macrophages


title: IM ATAC-seq DBA2J rep2


title: Mlesico

source_name: Mlesico cells

value: Mlesico epithelial cell line


title: PROG_099

tag: tissue

value: primary

tag: grade (who1999)

tag: molecular subtype


title: EXOSOMES WT1


title: PROG_106


title: PROG_100


title: iMo ATAC-seq C57BL6J rep1


title: Genomic DNA from OPSCC sample [MPC_T29]

description: SAMPLE 33


title: CELLS WT5

source_name: T cells blasts from C57BL/6 mice


title: PROG_098


title: Genomic DNA from OPSCC sample [MPC_T28]

description: SAMPLE 32


title: IM ATAC-seq C57BL6J rep2


title: Genomic DNA from OPSCC sample [MPC_T27]

description: SAMPLE 31


title: CELLS WT2


title: PROG_097


title: IM ATAC-seq C57BL6J rep1


title: CELLS WT1


title: pMo RNA-seq DBA2J rep2

description: DBA_RNA_pMo_rep2 TPM


title: Genomic DNA from OPSCC sample [MPC_T26]

description: SAMPLE 30


title: Genomic DNA from OPSCC sample [MPC_T24]

description: SAMPLE 28


title: Genomic DNA from OPSCC sample [MPC_T25]

description: SAMPLE 29


title: PROG_096


title: pMo RNA-seq DBA2J rep1

description: DBA_RNA_pMo_rep1 TPM


title: mES_diff_24h

city: Toronto

first: Jennifer

last: Mitchell

state: Ontario

address: 25 Harbord Street

department: Cell and Systems Biology

institute: University of Toronto

description: ES cells after 24 hours of differentiation

data_processing:
Reads were trimmed using BBDuk tool in BBMap for quality trimming and filtering
Reads were aligned to mm10 using Tophat2 running Bowtie2.
BedGraphs were generated using bedtools v2.22.0 genomecov script with standard settings.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph

source_name: embryonic stem cells

growth_protocol: ES cells were maintained on gelatin-coated plates in ES base media supplemented with LIF and two inhibitors (2i, CHIR99021 and PD0325901).

extract_protocol:
RNA was isolated using Trizol (Life Technologies) and DNase treated prior to library construction.
NEBNext mRNA Library Prep Reagent Set for Illumina

treatment_protocol: ES media was removed and replaced with ES base media lacking LIF and 2i

tag: media

value: ES base media without LIF and 2i

tag: time

value: 24 hours


title: PROG_095

value: bladder cancer


title: PROG_094

value: Ta


title: iMo RNA-seq DBA2J rep2

description: DBA_RNA_IMo_rep2 TPM


title: PROG_093


title: Genomic DNA from OPSCC sample [MPC_T21]

description: SAMPLE 25

tag: disease state


title: Genomic DNA from OPSCC sample [MPC_T23]

description: SAMPLE 27

tag: gender


title: mES_diff_6h

description: ES cells after 6 hours of differentiation

value: 6 hours


title: 6_1_A6_tcf21-1

value: Heart

tag: cell type

value: larval cardiac cells

tag: transgenic reporter

tag: cell fluorescence

tag: age

value: 5 days post fertilisation


title: PROG_091

tag: tissue preparation

value: FFPE

tag: labeling batch

tag: patient identifier

value: UroA-Prog


title: mES

description: ES cells maintained in the naïve state

tag: strain

value: ES base media with LIF and 2i


title: PROG_092

tag: tumor number

tag: primary, recurrence, or progression


title: AM RNA-seq DBA2J rep1

description: DBA_RNA_AM_rep1 TPM

source_name: alveolar macrophages


title: 8285

city: Salt Lake City

first: Diane

middle: M

last: Ward

state: UT

address: 15 N Medical Dr Suite 1100

department: Pathology Department - School of Medicine

institute: University of Utah

description: knock out replicate 5

data_processing:
Fastq reads were aligned to genome index containing known splice junctions using Novocraft Novoalign (v2.8). Splice junctions were generated using USeq MakeTranscriptome (v8.8) and UCSC EnsGene annotation.
Spliced alignments were converted back to genomic coordinates using USeq SamTranscriptomeParser (v8.8).
Differential expression was performed using USeq DefinedRegionDifferentialSeq and DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file containing the raw counts, regularized log2 counts, FPKM counts, and DESeq2 log2 ratio and -10log10 transformed adjusted P-value from DESeq2.

source_name: Liver

growth_protocol: Mice were maintained on a standard rodent chow (Harland, Teklad).

extract_protocol:
Liver tissues were homogenized in Trizol and flash frozen in liquid nitrogen.  mRNA was extracted using a Zymo Research kit with DNAseI treatment. QC was done on an Agilent tapestation RNA assay.
TruSEq Stranded total RNA sample prep kit with ribo-zero gold treatment

tag: genotype

value: Alb-cre Mfrn1-/- Mfrn2 -/-


title: pMo RNA-seq C57BL6J rep2

description: C57_RNA_pMo_rep2 TPM


title: AM RNA-seq DBA2J rep2

description: DBA_RNA_AM_rep2 TPM


title: 8580

description: knock out replicate 3


title: pMo RNA-seq C57BL6J rep1

description: C57_RNA_pMo_rep1 TPM


title: Genomic DNA from OPSCC sample [MPC_T20]

description: SAMPLE 24

value: oropharyngeal squamous carcinoma (OPSCC)

tag: tissue

value: oropharyngeal cancer

value: male


title: PROG_088

tag: tumor stage

tag: grade (who1999)

tag: molecular subtype


title: PROG_090

value: rec


title: 8274

description: knock out replicate 4


title: Genomic DNA from OPSCC sample [MPC_T19]

description: SAMPLE 23

tag: disease state

value: female


title: Genomic DNA from OPSCC sample [MPC_T22]

description: SAMPLE 26

tag: gender


title: PROG_101

value: UroC


title: PROG_089


title: 8574

description: knock out replicate 2


title: iMo RNA-seq C57BL6J rep2

description: C57_RNA_IMo_rep2 TPM


title: PROG_087

value: Mes


title: Genomic DNA from OPSCC sample [MPC_T18]

description: SAMPLE 22


title: PROG_086

value: bladder cancer

value: primary

value: GU


title: 8575

description: knock out replicate 1


title: iMo RNA-seq C57BL6J rep1

description: C57_RNA_IMo_rep1 TPM


title: Genomic DNA from OPSCC sample [MPC_T16]

description: SAMPLE 20


title: 8271

description: wildtype replicate 3

value: WT


title: IM RNA-seq C57BL6J rep2

description: C57_RNA_IM_rep2 TPM


title: Genomic DNA from OPSCC sample [MPC_T17]

description: SAMPLE 21


title: 8268

description: wildtype replicate 2


title: Genomic DNA from OPSCC sample [MPC_T15]

description: SAMPLE 19


title: IM RNA-seq C57BL6J rep1

description: C57_RNA_IM_rep1 TPM


title: AM RNA-seq C57BL6J rep2

description: C57_RNA_AM_rep2 TPM


title: PROG_085


title: iMo RNA-seq DBA2J rep1

description: DBA_RNA_IMo_rep1 TPM


title: AM RNA-seq C57BL6J rep1

description: C57_RNA_AM_rep1 TPM


title: Genomic DNA from OPSCC sample [MPC_T13]

description: SAMPLE 18


title: COCULTUREOVA3

data_processing:
Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline.
Sequencing adaptor contaminations were removed using CUTADAPT (Marcel Martin). The resulting reads were aligned with bowtie against a miRNA sequence reference consisting in the mature Mus musculus component of miRBase21, and quantified using RSEM v1.17 (Li and Dewey, 2011).
Genome_build: miRBase21
Supplementary_files_format_and_content: TMM normalized counts per million (CPM) table, with miRNAs as rows and samples as columns

source_name: B cells from CD19Cre/Ki DICERfl/fl mice spleens

growth_protocol: Spleens from CD19Cre/Ki DICERfl/fl mice were harvested, homogenized to get a cell suspension and B cells isolated after RBC lysis (Miltenyi Biotec) were activated 16h with LPS and IL4. Splenocytes and lymph nodes from OTII mice were  homogenized to get a cell suspension and after RBC lysis cultured for 16h with OVA peptide. Thereafter, OTII-CD4+T cells were isolated (Miltenyi Biotec) and cocultured 16h with previosuly isolated CD19Cre/Ki DICERfl/fl B cells either in the presence or absence of OVA peptide

extract_protocol:
Total RNA was isolated using the miRNeasy mini kit (QIAGEN)
The RNA sequencing library was prepared with the SmallRNA NEBNext Library Prep Set (New England Biolabs) following the manufacturer’s recommendations. The quality, quantity and the size distribution of the Illumina libraries were determined using the Small RNA Kit (Agilent Bioanalyzer).
Libraries were sequenced (single-end mode and length of 61 bp) on the Illumina HiSeq 2500 system using the standard RNA sequencing protocol for Small RNA NEBNext Library Prep Set

treatment_protocol: B cells from CD19Cre/Ki DICERfl/fl mice were cultured alone or cocultured with OTII CD4+ T cells either in the presence or absence of OVA peptide. After 16h culture, B cells were sorted and RNA isolated for small RNA sequencing analysis

tag: phenotype

value: CD19Cre/Ki DICERfl/fl


title: Genomic DNA from OPSCC sample [MPC_T11]

description: SAMPLE 16


title: Genomic DNA from OPSCC sample [MPC_T12]

description: SAMPLE 17


title: Genomic DNA from OPSCC sample [MPC_T10]

description: SAMPLE 15


title: PROG_083


title: PROG_082

value: prog

value: UroB


title: COCULTURENOOVA3


title: IMo_LPS20h_nasalB171227

data_processing:
Preprocessing: FASTQ files from sequencing experiments were mapped to the mouse mm10 genome. STAR with default parameters was used to map RNA-seq experiments (Dobin et al., 2013). HOMER was used to convert aligned reads into “tag directories” for further analysis (Heinz et al., 2010).
Each experiment was quantified using the “analyzeRepeats” script of HOMER. To generate a table of TPM values, the parameters -condenseGenes -count exons  -tpm were used which extract only one transcript (most aboundace) for a gene. And the smaller genes (<250bp) were removed from downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited text file: Table of TPM values for RNA-Seq

extract_protocol:
Total RNA was isolated from in vitro culture cells and purified using a Direct-zol RNA MicroPrep Kit (Zymo Research) according to the manufacturer’s instructions (Zymo Research). FACS purified cells were pelleted and put into 150 μl lysis/Oligo d(T) Magnetic Beads binding buffer (100mM Tris-HCl pH7.5, 500mM LiCl, 10mM EDTA pH8.0, 1% LiDS, 5mM DTT) and stored at –80°C until processing. mRNAs were enriched by incubation with Oligo d(T) Magnetic Beads (NEB, S1419S).
Sequencing libraries were prepared according to the Smart-seq2 method45 with some modifications. 500-5000 FACS isolated cells in Trizol (Thermo Fisher) were used as starting material. RNA was extracted with the Direct-zol MicroPrep kit (Zymo Research) with on-column DNAseI treatment. 10 µL purified RNA was mixed with 5.5 µL of SMARTScribe 5X First-Strand Buffer (Clontech), 1 µL polyT-RT primer (2.5 µM, 5’-AAGCAGTGGTATCAACGCAGAGTAC(T30)VN, 0.5 µL SUPERase-IN (Ambion), 4 µL dNTP mix (10 mM, Invitrogen), 0.5 µL DTT (20 mM, Clontech) and 2 µL Betaine solution (5 M, Sigma), incubated 50C 3 min. 3.9 µL of first strand mix, containing 0.2 µL 1% Tween-20, 0.32 µL MgCl2 (500 mM), 0.88 µL Betaine solution (5 M, Sigma), 0.5 µL (5 M, Sigma) SUPERase-IN (Ambion) and 2 µL SMARTScribe Reverse Transcriptase (100 U/µL Clontech) was added and incubated one cycle 25C 3 min., 42C 60 min. 1.62 µL template switch (TS) reaction mix containing 0.8 µL biotin-TS oligo (10 µM, Biotin-5’-AAGCAGTGGTATCAACGCAGAGTACATrGrG+G-3’), 0.5 µL SMARTScribe Reverse Transcriptase (100 U/µL Clontech) and 0.32 µL SMARTScribe 5X First-Strand Buffer (Clontech) was added, then incubated at 50C 2 min., 42C 80 min., 70C 10 min. 14.8 µL second strand synthesis, pre-amplification mix containing 1 µL pre-amp oligo (10 µM, 5’AAGCAGTGGTATCAACGCAGAGT-3’), 8.8 µL KAPA HiFi Fidelity Buffer (5X, KAPA Biosystems), 3.5 µL dNTP mix (10 mM, Invitrogen) and 1.5 µL KAPA HiFi HotStart DNA Polymerase (1U/µL, KAPA Biosystems), was added,  then amplified by PCR: 95C 3 min., 8 cycles 98C 20 seconds, 67C 15 sec and 72C 6 min, final extension 72C 5 min.  The synthesized dsDNA was purified using Sera-Mag Speedbeads (Thermo Fisher Scientific) with final 8.4% PEG8000, 1.1M NaCl, then eluted with 13 µL UltraPure water (Invitrogen). The product was quantified by Qubit dsDNA High Sensitivity Assay Kit (Invitrogen) and libraries were prepared using the Nextera DNA Sample Preparation kit (Illumina). Tagmentation mix containing 11 µL 2X Tagment DNA Buffer and 1 µL Tagment DNA Enzyme was added to 10 µL purified DNA, then incubated at 55C 15 min. 6 µL Nextera Resuspension Buffer (Illumina) was added and incubated at room temperature for 5 min. Tagmented DNA was purified using Sera-Mag Speedbeads (Thermo Fisher Scientific) with final 7.8% PEG8000, 0.98M NaCl, then eluted with 25 µL UltraPure water (Invitrogen). Final enrichment amplification was performed with Nextera primers,  adding 1 µL  Ad1 (100 µM, universal no barcode), 1 µL unique Ad2.n (100 µM, N7xx) barcoding primers and 27 µL NEBNext High-Fidelity 2X PCR Master Mix (New England BioLabs), then amplified by PCR: 72C 5 min., 98C 30 sec., 8-13 cycles 98C 10 seconds, 63C 30 sec., and 72C 1 min. Libraries were purified using 1.5 volumes of SpeedBeads in 2.5M NaCl, 20% PEG8000, further size selected using 10% PAGE/TBE gels, eluted and quantified with Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific), pooled and sequenced on a NextSeq 500 (Illumina) for 76 cycles at a depth of 25 to 30 million single end reads per sample.

tag: treatment

value: nasal LPS

tag: treatment time

value: lung

tag: cell type

value: inflammatory monocytes (iMo)


title: IMo_LPS20h_nasalA171227


title: ALONEOVA3


title: ALONENOVA3


title: PROG_084

tag: tissue preparation

value: FFPE


title: PROG_081

tag: labeling batch

value: Ta


title: Genomic DNA from OPSCC sample [MPC_T9]

description: SAMPLE 14

value: oropharyngeal squamous carcinoma (OPSCC)

value: oropharyngeal cancer

value: male


title: IMo_LPS06h_nasalB171227


title: mES_diff_12h

description: ES cells after 12 hours of differentiation

tag: media

value: ES base media without LIF and 2i

tag: time

value: 12 hours


title: COCULTUREOVA2


title: IMo_LPS06h_nasalA171227

tag: strain


title: COCULTURENOOVA2


title: IMo_LPS02h_nasalB171227


title: PROG_080

value: bladder cancer

tag: patient identifier

tag: tumor number

tag: primary, recurrence, or progression

value: rec


title: ALONEOVA2


title: ALONENOVA2


title: Genomic DNA from OPSCC sample [MPC_T7]

description: SAMPLE 12

tag: tissue


title: PROG_079

tag: tumor stage

tag: grade (who1999)


title: COCULTUREOVA1


title: IMo_LPS02h_nasalA171227


title: IM_LPS20h_nasalB171227

value: interstitial macrophages (IM)


title: PROG_078

value: primary

tag: molecular subtype

value: UroA-Prog


title: PROG_077

value: prog


title: Genomic DNA from OPSCC sample [MPC_T6]

description: SAMPLE 11

tag: disease state

tag: gender

value: female


title: Genomic DNA from OPSCC sample [MPC_T8]

description: SAMPLE 13


title: COCULTURENOOVA1

tag: phenotype

value: CD19Cre/Ki DICERfl/fl


title: Genomic DNA from OPSCC sample [MPC_T5]

description: SAMPLE 10


title: PROG_074


title: PROG_076


title: PROG_075


title: IM_LPS06h_nasalB171227

tag: treatment

value: nasal LPS

tag: treatment time

value: lung


title: Genomic DNA from OPSCC sample [MPC_T3]

description: SAMPLE 8


title: PROG_073

tag: tissue preparation

value: FFPE

value: UroC


title: Genomic DNA from OPSCC sample [MPC_T4]

description: SAMPLE 9

value: oropharyngeal squamous carcinoma (OPSCC)


title: ALONEOVA1


title: IM_LPS20h_nasalA171227

tag: cell type


title: JZ190120

city: Orange

first: Matthew

last: Simon

state: CT

address: West Campus, 100 West Campus Drive, Ste MIC312A

department: MBB

institute: Yale University

description: Reads filtered for number of T-to-C mutations (0-5+) and strandedness (min/pos)

data_processing:
Reads were filtered for unique sequences using FastUniq
Reads were trimmed using cutadapt (--minimum-length=20)
Reads were aligned to the GRCm38 genome using HISAT2 aligned with default parameters and --mp 4,2 .
Reads were processed using Picard tools, including FixMateInformation, SortSam and BuildBamIndex
Reads were filtered for those that aligned uniquely (flag: 83/163, 99/147), with MAPQ ≥ 2, and without insertions.
HTSeq-count was used to identify mapped reads in UCSC transcripts (union mode)
T-to-C mutations were identified using Rsamtools and a custom R script (available upon request). Only mutations at positions with a base quality score of greater than 45 that were at least three nt from the end of the read were counted. Reads were excluded where there were greater than five T-to-C mutations and these mutations did not account for at least one third of the observed mutations (NM tag).
SNP sites were filtered from our data in two ways: 1, bcftools was used to identify T-to-C SNP sites in control samples, and these sites were excluded from analysis; 2, sites exhibiting high T-to-C mutation rates in non-s4U treated controls were excluded from analysis.
To examine the distribution of reads with each minimum number of T-to-C mutations, bam files were filtered using Picard tools.
STAR aligner was used to make genome-coverage tracks (inputAlignmentsFromBam mode, outWigType bedGraph), and tracks were normalized using DESeq2 (estimateSizeFactors).
Tracks were converted to binary format using IGVtools (toTDF).
Genome_build: GRCm38
Supplementary_files_format_and_content: bedgraph

source_name: Mouse lung adenocarcinoma (K-rasLA2-G12D/+; p53LSL/LSL; Rosa26-CreERT2+, KPR) cells

growth_protocol: KPR cells, previously infected with with an sgRNA targeting the PVT1 p53RE or a nontargeting control, were grown in Dulbecco’s Modified Essential Media supplemented with 10% fetal bovine serum (Gibco), 0.1 mM nonessential amino acids, 2 mM L-glutamine, and Pen/Strep (50 U/ml). All cell cultures were maintained at 37℃ in a humidified incubator with 5% carbon dioxide.

extract_protocol:
RNA was harvested with Trizol reagent, followed by chloroform extraction and ethanol precipitation.   Genomic DNA was depleted using Turbo DNAse, followed by cleanup with RNAclean beads. RNA for transient-transciptome RNA-seq was enriched with MTS-biotin and all RNA was treated with oxidative-nucleophilic-aromatic-substitution chemistry as described in Schofield et al. Nature Methods 2018.
Libraries were generated following standard protocols using the SMARTer Stranded Total RNA-Seq Kit-Pico Input Mammalian, V2 (Takara Bio USA, cat. 634413).

treatment_protocol: Tamoxifen-treated cells had media spiked to a final concentration of 0.5 µM tamoxifen and untreated (no tamoxifen) cells had media spiked with vehicle control.  s4U-treated cells had their media spiked with s4U to a final concentration of 100 µM for total RNA-seq or 1 mM for transient-transcriptome RNA-seq. Untreated (no s4U) cells had their media left unsupplemented. Cells were incubated with s4U for 1h or 5m for total RNA-seq or transient-transcriptome RNA-seq, respectively.

tag: infected with

value: sgRNA targeting the Pvt1 p53RE (gΔRE)

value: +Tamoxifen

tag: s4u feed

value: No


title: Genomic DNA from OPSCC sample [MPC_T2]

description: SAMPLE 7

value: oropharyngeal cancer


title: ALONENOOVA1


title: IM_LPS02h_nasalB171227

tag: strain


title: PROG_072

value: bladder cancer

tag: labeling batch

tag: patient identifier


title: JZ190118

description:
s4U nascent
Reads filtered for number of T-to-C mutations (0-5+) and strandedness (min/pos)

value: lung adenocarcinoma (K-rasLA2-G12D/+; p53LSL/LSL; Rosa26-CreERT2+, KPR) cells

value: Yes