title: MOLF PyMT 10061 PT  [WGS]

description: gDNA isolated from snap frozen tissue


title: Male Second Thoracic Segment Wing Right 4

status: Public on Apr 02 2020

type: SRA

city: Bloomington

first: David

middle: M

last: Linz

state: IN

address: Myers Hall 3rd Street

country: USA

institute: Indiana University

library_source: transcriptomic

data_processing:
Trimming: Trimmomatic v0.32 parameters: ‘2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:36’
Alignment: Bowtie2 v2.3.2
Counting: RSEM v1.3.0
DE Analysis: DESeq2
Genome_build: O. taurus NCBI Genome Assembly v2.0 (GCF_000648695.1)

molecule: polyA RNA

organism: Onthophagus taurus

source_name: Male Second Thoracic Segment Wing Right epithelium

extract_protocol:
Qiagen Rneasy Plus Micro Kit
Illumina TruSeq Stranded mRNA Sample Preparation Kit

tag: tissue

value: T2 wing

tag: developmental stage

value: Pre-pupae (larval stage)


title: Male Dorsal Head 5

source_name: Male Dorsal Head epithelium

value: Head epithelium


title: HCT116siERRa8_S5_L004

city: Omaha

first: Danielle

last: Frodyma

state: NE

address: Buffet Cancer Center 9.12.379

institute: University of Nebraska Medical Center

description: HCT116 cells treated with ERR𝛼 siRNA

data_processing:
Pipeline: XPRESSpipe v0.4.1
xpresspipe makeReference -o $REF -f $REF/genome_fastas -g $REF/transcripts.gtf --sjdbOverhang 75
xpresspipe peRNAseq -i $SCRDIR/input -o $SCRDIR/output -r $REF --gtf $REF/transcripts.gtf -e frodyma -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --sjdbOverhang 75 --quantification_method htseq
Trimming: fastp v0.20.0
Alignment: STAR 2.7.3a
Post-processing: Samtools v1.10
Read quantification: HTSeq 0.11.2
Differential expression analysis: DESeq2 v1.22.1
Quality control: MultiQC v1.8
Genome_build: Ensembl GRCh39 v99 (Homo sapiens)
Supplementary_files_format_and_content: .txt files (tab-delimited) with count data

molecule: total RNA

organism: Homo sapiens

source_name: Human colon tumor cells

growth_protocol: Cells were grown in 1X DMEM + 10% FBS growth media at 37degC and 5% CO2

extract_protocol:
RNA was extracted using QIAGEN Rneasy protocol
Illumina TrueSeq mRNA

treatment_protocol: Cells were treated with a final concentration of 20uM siRNA (Dharmacon) with either Control, PGC1β or ERRα  for 72 hours using the RNAiMax (BioRad) protocol

value: Human colon tumor cells

tag: cell type

tag: genotype/variation

value: HCT116 cells treated with ERR-alpha siRNA


title: HCT116siERRa8_S5_L003

description: HCT116 cells treated with ERR𝛼 siRNA


title: MOLF PyMT 10061 Lung met  [WGS]

city: Bethesda

first: Maxwell

last: Lee

state: MD

address: Building 37, Room 5120

department: CCR

institute: National Cancer Institute, NIH

description: gDNA isolated from snap frozen tissue

library_source: genomic

data_processing:
quantile normalized
Samples were trimmed of adapters using Trimmomatic software (0.39)
The trimmed reads were aligned to 316 the mm10 reference mouse genome using BWA (0.7.17) or Bowtie (2-2.3.5.1) mapping software
SAMtools (1.9) mpileup, 317 GATK (3.8-1) Mutect2, and Strelka (2.7.1) were used to identify potential variants and the variants were filtered for known 318 polymorphisms from mgp.v5 (ftp://ftp-mouse.sanger.ac.uk/current_snps /mgp.v5.merged.snps_ all.dbSNP142 .vcf.gz) and 319 variants with Phred-scaled quality score of < 30 were removed
Annotation was performed by Annovar (2018-04-16).
High probability SNVs were identified after reads were visualized in IGV and false positives were removed from the data. Select SNVs validated by Sanger sequencing performed by the CCR Genomics Core.
Genome_build: mouse mm10
Supplementary_files_format_and_content: vcf files include variants for each sample

molecule: genomic DNA

organism: Mus musculus

source_name: Lung met

extract_protocol:
Mice were bred and allowed to age until a humane endpoint was reached. Primary tumors and lung metastases were isolated and snap frozen in cryo vials using liquid nitrogen. Tissue was stored at -80 and gDNA was later isolated using the gDNA purification using ZR-Duet DNA/RNA MiniPrep kit from Zymo Research.  (cat.no. D7001)
Whole genome sequencing library preparation was performed using the TruSeq DNA Sample Prep kit FC-121-1001.  Samples were barcoded, pooled and sequenced on an Illumina HiSeq4000 to a depth of ~10x per sample. For RNA sequencing, the preparation of mRNA libraries and mRNA sequencing was performed by the Sequencing Facility using the HiSeq2500 instrument with Illumina TruSeq v4 chemistry.

treatment_protocol: genetically engineered mice were allowed to age until a humane endpoint was reached, no treatment was applied

value: Lung metastatic tumor

tag: oncogenic driver

value: PyMT

tag: model

value: Genetically engineered / Autochthonous

tag: strain

value: MOLF/EiJ x FVBn/J

tag: mouse id


title: Male Second Thoracic Segment Wing Left 4

source_name: Male Second Thoracic Segment Wing Left epithelium


title: MOLF PyMT 10055 Lung met  [WGS]

description: gDNA isolated from snap frozen tissue


title: HCT116siERRa8_S5_L002

description: HCT116 cells treated with ERR𝛼 siRNA


title: MOLF PyMT 10055 PT  [WGS]

description: gDNA isolated from snap frozen tissue

source_name: primary tumor

value: primary tumor


title: Male First Thoracic Segment Posterior Margin 4

source_name: Male First Thoracic Segment Posterior Margin epithelium

value: First Thoracic Segment epithelium


title: HCT116siERRa8_S5_L001

description: HCT116 cells treated with ERR𝛼 siRNA


title: BL6 PyMT 10109 Lung met gDNA

description: gDNA isolated from flash frozen tissue

data_processing:
Library strategy: DNA-seq
Samples were trimmed of adapters using Trimmomatic software (0.39)
The trimmed reads were aligned to 316 the mm10 reference mouse genome using BWA (0.7.17) or Bowtie (2-2.3.5.1) mapping software
SAMtools (1.9) mpileup, 317 GATK (3.8-1) Mutect2, and Strelka (2.7.1) were used to identify potential variants and the variants were filtered for known 318 polymorphisms from mgp.v5 (ftp://ftp-mouse.sanger.ac.uk/current_snps /mgp.v5.merged.snps_ all.dbSNP142 .vcf.gz) and 319 variants with Phred-scaled quality score of < 30 were removed
Annotation was performed by Annovar (2018-04-16).
High probability SNVs were identified after reads were visualized in IGV and false positives were removed from the data. Select SNVs validated by Sanger sequencing performed by the CCR Genomics Core.
Genome_build: mouse mm19
Supplementary_files_format_and_content: vcf files include variants for each sample

extract_protocol:
Mice were bred and allowed to age until a humane endpoint was reached. Primary tumors and lung metastases were isolated and snap frozen in cryo vials using liquid nitrogen. Tissue was stored at -80 and gDNA was later isolated using the gDNA purification using ZR-Duet DNA/RNA MiniPrep kit from Zymo Research.  (cat.no. D7001)
Exome libraries were prepared using an Agilent SureSelectXT Mouse All Exon Kit for target enrichment. Libraries were barcoded and pooled before sequencing on an Illumina HiSeq3000 or HiSeq4000 to an average depth of 40x.

value: C57BL/6J  x FVBn/J


title: Male First Thoracic Segment Horn 4

source_name: Male First Thoracic Segment Horn epithelium


title: Paternal age effects (10vs16m) on blastocysts transcriptome-rep2

type: RNA

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

country: Canada

institute: Université Laval

description: Biological replicates 2 of 4

hyb_protocol: The hybridization of microarray slides 4x44K printed with oligonucleotides by Agilent for all EmbryoGENE related projects using the expression array protocol.

scan_protocol: Scan on a PowerScanner (Tecan) using the autogain function. Images were quantified using ArrayPro version 6.3 (MediaCybernetics)

data_processing: Signal intensity data files were normalized and analyzed using the FlexArray 1.6.1 software (Genome Quebec, URL: http://genomequebec.mcgill.ca/FlexArray). The first step in the data processing was to remove the background of intensity files using a simple background subtraction. Data were then normalized for dye bias using a within-array loess and a between-array « quantile » normalization to minimize array effects. To calculate fold changes of probe intensity, normalized data were assessed using the e Bayes moderated t-test (LIMMA) included in the FlexArray software. A False Discovery Rate algorithm (Benjamini-Hochberg) was also applied.

organism: Bos taurus

source_name: blastocysts

label_protocol: The labelling aRNA was done using  the Universal Linkage System (ULS) by Kreatech for Gene Expression studies using microarray slides from Agilent. ULS is a non-enzymatic protocol that allows direct labeling of unmodified, amplified RNA. ULS will react with unmodified, amplified RNA and label it by formation of a coordinative bond on the N7 position of guanine. Fluorophore Cy3 and Cy5 are linked via a spacer to the ULS molecule.

growth_protocol: In vitro maturation, fertilization and culture of bovine embryos from slaughter ovaries. For more information, please refer to: Cagnone et al. 2012 Biol Reprod.

extract_protocol:
Total RNA and gDNA were extracted using the AllPrep DNA/RNA Micro Kit (Qiagen)
Amplification of RNA using the RiboAmpb HSPlus RNA Amplification kit (Thermo Fisher).

tag: sample type

value: IVF with sperm from a 10 months old bull

value: IVF with sperm from a 16 months old bull


title: BL6 PyMT 10113 Lung met gDNA

description: gDNA isolated from flash frozen tissue


title: Paternal age effects (12vs16m) on blastocysts transcriptome-rep1

description: Biological replicates 1 of 4

value: IVF with sperm from a 12 months old bull


title: HCT116siERRa7_S6_L004

description: HCT116 cells treated with ERR𝛼 siRNA


title: MOLF PyMT 10049 PT  [WGS]

description: gDNA isolated from snap frozen tissue


title: MOLF PyMT 10049 Lung met  [WGS]

description: gDNA isolated from snap frozen tissue


title: Male First Thoracic Segment Dorsal 4

source_name: Male First Thoracic Segment Dorsal epithelium


title: HCT116siERRa7_S6_L003

description: HCT116 cells treated with ERR𝛼 siRNA


title: BL6 PyMT 10111 Lung met gDNA

description: gDNA isolated from flash frozen tissue


title: MOLF PyMT 10048 PT  [WGS]

description: gDNA isolated from snap frozen tissue


title: BL6 PyMT 10113 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue

source_name: Primary tumor

value: Primary tumor


title: BL6 PyMT 10111 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue


title: HCT116siERRa7_S6_L002

description: HCT116 cells treated with ERR𝛼 siRNA


title: Male First Thoracic Segment Carinated Margin Left 4

source_name: Male First Thoracic Segment Carinated Margin Left epithelium


title: BL6 PyMT 10026 Lung met gDNA

description: gDNA isolated from flash frozen tissue


title: MOLF PyMT 10048 Lung met  [WGS]

description: gDNA isolated from snap frozen tissue


title: BL6 PyMT 10109 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue


title: HCT116siERRa7_S6_L001

description: HCT116 cells treated with ERR𝛼 siRNA


title: Male First Thoracic Segment Anterior Margin 4

source_name: Male First Thoracic Segment Anterior Margin epithelium


title: MOLF PyMT 10047 PT  [WGS]

description: gDNA isolated from snap frozen tissue


title: HCT116sipgc1b6_S3_L004

description: HCT116 cells treated with PGC1𝛽 siRNA

value: HCT116 cells treated with PGC1-beta siRNA


title: BL6 PyMT 10026 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue


title: HCT116sipgc1b6_S3_L003

description: HCT116 cells treated with PGC1𝛽 siRNA


title: MOLF PyMT 10047 Lung met  [WGS]

description: gDNA isolated from snap frozen tissue


title: Male Abdominal Pupal Support Structures 4

source_name: Male Abdominal Pupal Support Structures epithelium

value: Abdominal epithelium


title: BL6 PyMT 10025 Lung met gDNA

description: gDNA isolated from flash frozen tissue


title: Male Dorsal Head 4

value: Pre-pupae (larval stage)


title: MOLF PyMT 10000 PT  [WGS]

description: gDNA isolated from snap frozen tissue


title: BL6 PyMT 10025 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue


title: MOLF PyMT 10000 Lung met  [WGS]

description: gDNA isolated from snap frozen tissue


title: HCT116sipgc1b6_S3_L002

description: HCT116 cells treated with PGC1𝛽 siRNA


title: Male Second Thoracic Segment Wing Right 3

value: T2 wing


title: HCT116sipgc1b6_S3_L001

description: HCT116 cells treated with PGC1𝛽 siRNA

value: Human colon tumor cells


title: Male First Thoracic Segment Carinated Margin Right 4

source_name: Male First Thoracic Segment Carinated Margin Right epithelium


title: Male Second Thoracic Segment Wing Left 3


title: BL6 PyMT 9868 Lung met gDNA

description: gDNA isolated from flash frozen tissue


title: BL6 PyMT 9868 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue


title: HCT116sipgc1b2_S4_L004

description: HCT116 cells treated with PGC1𝛽 siRNA


title: Male First Thoracic Segment Posterior Margin 3


title: gfp_4

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

country: Germany

institute: Max Planck Institute for Heart and Lung Research

data_processing:
Read quality trimming was performed with Reaper version 15-065 to trim reads after a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads of at least 30 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Gencode mouse genome version mm10 (GRCm38, vM15) using STAR 2.5.3a with the parameters “--outFilterMismatchNoverLmax 0.1 --outFilterScoreMinOverLread 0.66 --outFilterMatchNminOverLread 0.66 --outFilterMatchNmin 20 --alignIntronMax 200000 --alignMatesGapMax 2000 --alignEndsProtrude 10 ConcordantPair”
Reads were counted per gene with featureCounts 1.5.3 from the Subread package using default parameters. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
The raw gene counts per sample were joined to a matrix and normalized with DESeq.
Genome_build: Mus musculus mm10
Supplementary_files_format_and_content: The tab-delimited text file (matrix.txt) contains DESeq normalized counts for all genes.

source_name: muscle

growth_protocol: FACS purifed MuSCs from Chd4LoxP/LoxP mice were allowed to expand in growth media containing DMEM GlutaMAX (Gibco) containing 20% FCS 1%, Penicillin/Streptomycin, and 5ng/ml bFGF. After a brief expansion of the MuSCs, Chd4 was efficiently floxed out using Adenoviral recombination.

extract_protocol:
Adenoviral treated cells were snap frozen in liquid nitrogen and RNA was extracted using RNA isolation kit
The library was created with the HiSeq Sequencing Kit Trueseq v3 following the stranded protocol.

treatment_protocol: Adenoviral infection of CRE recombinase; AdenoGFP serves as a control

tag: genotype

value: gfp


title: HCT116sipgc1b2_S4_L002

description: HCT116 cells treated with PGC1𝛽 siRNA


title: Male First Thoracic Segment Horn 3


title: MOLF PyMT 10000 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue


title: gfp_3


title: HCT116sipgc1b2_S4_L001

description: HCT116 cells treated with PGC1𝛽 siRNA


title: Male First Thoracic Segment Dorsal 3


title: gfp_2


title: HCT116siCONT2_S2_L004

description: HCT116 cells treated with Control siRNA

value: HCT116 cells treated with Control siRNA


title: Male First Thoracic Segment Carinated Margin Right 3


title: HCT116siCONT2_S2_L003

description: HCT116 cells treated with Control siRNA


title: Male First Thoracic Segment Carinated Margin Left 3


title: HCT116siCONT2_S2_L002

description: HCT116 cells treated with Control siRNA


title: Male First Thoracic Segment Anterior Margin 3


title: HCT116sipgc1b2_S4_L003

description: HCT116 cells treated with PGC1𝛽 siRNA


title: cre_3

value: cre


title: Male Abdominal Pupal Support Structures 3


title: HCT116siCONT2_S2_L001

description: HCT116 cells treated with Control siRNA


title: Male Dorsal Head 3

value: Head epithelium


title: cre_1


title: TMZ_MGMT-KO2 replicate 2

city: Tianjin

first: Bohan

last: Chen

address: NO.94 Weijin Road

country: China

institute: Nankai University

description: RNA-seq of TMZ-treated MGMT enhancer KO glioma cell line

data_processing:
Clean reads of RNA-seq were mapped to hg19 using HISAT2(2.1.0)
Expression levels of all genes were counted and expression profile matrix was constructed with HTSeq (0.9.1)
Differential expression analysis was calculated in R using DESeq2(1.18.1), with p value < 0.05 and fold change > 2 or < 1/2
Genome_build: hg19
Supplementary_files_format_and_content: Text files include genes counts values

source_name: U251_Cell line

growth_protocol: U251 cell line was cultured in DMEM supplemented with 10% fetal bovine serum (FBS)

extract_protocol:
RNA-seq:Total RNA was extracted using the Eastep® Super Total RNA Extraction Kit following the manufacturer’s instruction. Then, ribosomal RNA was deleted from 5 μg of total extracted RNA using the Ribo-Zero Gold Kit, using Illumina HiSeq-4000. Capture Hi-C: Cells were fixed in formalin for 10min and DNA was isolated and digested with Dpn II then sheared to 200-300bp fragments by sonication. Libraries were prepared using the NEBNext DNA library kit according to the manufacturer's instructions (New England BioLabs), using Illumina X Ten.
RNA ibraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: TMZ-treated groups were 1mM TMZ treated for 72h,and DMSO-treated groups were control groups for the same conditions

tag: treatment

value: tmz


title: HCT116siCONT1_S1_L004

description: HCT116 cells treated with Control siRNA


title: TMZ_MGMT-KO2 replicate 1


title: Male Second Thoracic Segment Wing Right 2

source_name: Male Second Thoracic Segment Wing Right epithelium


title: gfp_1


title: HCT116siCONT1_S1_L003

description: HCT116 cells treated with Control siRNA


title: cre_4


title: Male Second Thoracic Segment Wing Left 2


title: HeLa_Input control

last: Sturgill

state: MARYLAND

address: Building 41, Rm B622

department: NCI

institute: NIH

data_processing:
Circular Consensus Sequence (CCS) reads in fastq format were filtered to remove PacBio internal control (MG551957.1) by alignment with Bowtie v2.3.4
Filtered reads were converted to fasta, and sequence composition was examined using an in-house perl script.  Alignments to alpha-satellite subunits and HORs were performed with Bowtie v2.3.4 in sensitive-local mode
Genome_build: hg19
Supplementary_files_format_and_content: TXT files include sequence composition information (mono and dinucleotide counts) for IP samples

source_name: HeLa cells

growth_protocol: Human cell line HeLa were grown in DMEM (Invitrogen/ThermoFisher Cat #11965) supplemented with 10% FBS and 1X penicillin and streptomycin cocktail.

extract_protocol:
Libraries were constructed with the PacBio Standard Seq (v3) protocol.
After cells were grown to ~80% confluency, they were harvested as described here (Bui et al 2012; Bui et al 2017), but with a few modifications. In short, cells were harvested, washed with PBS and PBS containing 0.1% Tween 20 (Sigma-Aldrich cat #P7949). Nuclei were released with TM2 (20 mM Tris-HCl, pH 8.0; 2 mM MgCl2; 0.5 mM PMSF) with 0.5% Nonidet P-40 (Sigma-Aldrich cat #74385). Afterwards, nuclei were washed with TM2 and dissolved in a total volume of 2 mL of 0.1 M TE (10 mM Tris-HCl, pH 8.0; 0.2 mM EDTA, 100 mM NaCl). Subsequently, chromatin was digested for 6 minutes with 0.25 U MNase (Sigma-Aldrich cat #N3755-500UN) and supplemented with 1.5 mM CaCl2. MNase reaction was quenched with 10 mM EGTA. All centrifugations were done at 1000 rpm at 4ºC. The cell or nuclei pellet was only tapped once to facilitate breaking them up. Supernatant was removed, and chromatin extracted overnight in low salt solution (0.5X PBS; 0.1 mM EGTA supplemented with a protease inhibitor cocktail (Roche cat #05056489001)
N-ChIP chromatin bound to Protein G Sepharose beads (GE Healthcare cat #17-0618-02) were washed twice with ice cold 0.5X PBS and spun down for 1 minute at 4ºC at 800 rpm. The samples were used to prepare libraries for PacBio single-molecule sequencing as described in manufacturer’s protocol (PacBio, Menlo Park, CA). Libraries were produced and loaded on ZMW chip either by diffusion or following size selection of the inserts (> 1000 bp) for all four samples.

tag: cell line

value: HeLa

tag: chip antibody

value: Input


title: HeLa_Mock_IP

value: Mock IP


title: Control_MGMT-KO2 replicate 1

description: RNA-seq of DMSO-treated MGMT enhancer KO glioma cell line

value: control


title: HCT116siCONT1_S1_L002

description: HCT116 cells treated with Control siRNA

source_name: Human colon tumor cells


title: cre_2


title: HCT116siCONT1_S1_L001

description: HCT116 cells treated with Control siRNA


title: HeLa_CENP-C_IP

value: Anti-CENP-C (MBL international, PD030)


title: Male First Thoracic Segment Posterior Margin 2

value: First Thoracic Segment epithelium


title: HeLa_ACA_IP

value: α-ACA Serum (Centromere Ab Pos. Serum, BBI Solutions, SG140-2)


title: Male First Thoracic Segment Carinated Margin Left 2


title: Male First Thoracic Segment Horn 2


title: MC_T_1

city: Tai'an

first: Zhao

last: Sheng

state: Shandong

address: No.61 Daizong street

department: College of Horticultural Science and Engineering

institute: Shandong Agricultural University

description: 3225 rootstock has strong silicon absorption ability

data_processing:
Remove low quality reads, adaptor sequences, or unknown bases (N),which is greater than 10% from raw reads, and obtain “clean reads”
Reads mapping to the cucumber Genome (V2) and Sequencing quality assessment
Assess sequencing, Quantification of gene expression
 Expression pattern analysis of DEGs
Gene ontology enrichment analysis of DEGs
Draw Venn diagram, Go enrichment,and Cluster diagram
Each gene has unique gene ID, which is from  cucumber (Cucumis sativus L.) genome (http://www.icugi.org/cgi-bin/ICuGI/genome/index.cgi?organism=cucumber)
Genome_build: cucumber Chinese long genome V2
Supplementary_files_format_and_content: Excel 2003 in GeneDiffExp,GeneDiffExpFilter

organism: Cucumis sativus

source_name: Pericarp

growth_protocol: Seedlings were washed clean by tap-water, swathed around root and bottom stem using thin sponge and transplanted into a hole of 3cm thick cystosepiment. We used “Yamazaki cucumber nutrient solution formula” prepared by deionized water (with Si 8.7×10-4mM) as nutrient solution, aerated continuously and  refreshed solution every 4~5 days. Other cultural practices adopt cucumber routine management In flowering period, we added potassium silicate to keep the silicon concentrations to 1.7mM and collect pericarp in two hours.

extract_protocol:
Total RNA was isolated from each tissue using the TRIzol reagent according to the manufacturer’s protocol (Invitrogen, Burlington, ON, Canada). DNA was removed from RNA extracts by incubation with RNase-free DNase(New England Biolabs) for 30 min at 37°C. The RNA integrity and concentration was evaluated using an Agilent Technologies 2100 Bioanalyzer. Each sample had RNA Integrity Number (RIN) values greater than 7.5.
Poly(A) mRNA was isolated from total RNA using oligo(dT) magnetic beads (Invitrogen, Carlsbad, CA, USA). Fragmentation buffer was added to break the purified mRNA into short fragments. Using these short fragments as templates, first-strand cDNA synthesis was performed using random hexamer primers and reverse transcriptase (Invitrogen). Second-strand cDNA was synthesized using RNase H (Invitrogen), DNA polymerase I (New England Biolabs), dNTPs and buffer. Subsequently, the short fragments were purified using the QIAquick PCR extraction kit, eluted with EB buffer and end repaired. Poly(A) tails were added, and the fragments were ligated to sequencing adaptors. We then selected suitable fragments as templates for PCR amplification according to the results of agarose gel electrophoresis. The average insert size for the paired-end libraries was 200 bp (from 180 to 220 bp). Sixteen paired-end cDNA libraries were constructed, one for each sample. Finally, the cDNA libraries were loaded onto the flow cell channels of an Uon Proton platform for paired-end 140 bp×2 sequencing at the Beijing Genomics Institute (BGI), Shenzhen, China.

treatment_protocol: Grafted or not; 1.7mM silicon added or not

tag: code name

tag: grafted or not

value: cucumber grafted onto "3225" pumpkin rootstock

value: cultivated by deionized water nutrient solution with 1.7mM added-silicon for 2 hours

tag: phenotype

value: With dense bloom


title: ATP3013

city: New Orleans

first: Qinyan

last: Yin

state: Louisiana

address: 1430 Tulane Ave SL8509

department: Department of Medicine

institute: Tulane University

description:
non-Poly(A)-selected RNA
chrvirus_human_virus_database_ver4.txt.count2.xlsx
IPF_HERV_AnalysisMichaelQY.xlsx

data_processing:
Quality control for fastq files performed using FastQC
Reads were aligned to hg38 reference genome using STAR2.5.3a
Reads were aligned to hg38 reference transcriptome using RSEM
Differential expression testing of cellular genes performed using EBSeq
Virome screening perfomed using custom scripts
Genome_build: Hg38
Supplementary_files_format_and_content: Excel files with virus counts for 740 human viruses plus HERVs

source_name: Lung tissue

extract_protocol:
Lung tissues: 12 IPF patients and 5 controls, and encompassed patients underwent lung biopsies at the University of Alabama at Birmingham (UAB).
RNA extract protocol: Total RNA was prepared using Qiagen's RNeasy kit. Ribosomal RNA was removed from 1 µg total RNA for non-poly(A) selected RNA-seq.
RNA libraries were prepared for sequencing using using TruSeq stranded total RNA ribozero from Illumina.

value: lung

tag: diagnosis

value: Normal

tag: Sex

value: female

tag: age


title: ATP3014

tag: tissue


title: ATP3018


title: Control_MGMT-KO2 replicate 2


title: Control_MGMT-KO1 replicate 1


title: ATP3007

value: male


title: ATP3017


title: Male First Thoracic Segment Dorsal 2

tag: developmental stage

value: Pre-pupae (larval stage)


title: Control_MGMT-KO1 replicate 2


title: LC_T_2

description: 3212 rootstock has low silicon absorption ability

value: cucumber grafted onto "3212" pumpkin rootstock

value: With least bloom


title: Male First Thoracic Segment Carinated Margin Right 2


title: MC_C_2

value: cultivated by deionized water nutrient solution

value: With sparse bloom


title: MC_C_1


title: ATP2051

value: IPF


title: MC_T_2


title: TMZ_MGMT-KO1 replicate 1

value: tmz


title: LC_T_1


title: ATP2053


title: Male Dorsal Head 2

source_name: Male Dorsal Head epithelium

value: Head epithelium


title: Male Second Thoracic Segment Wing Right 1

value: T2 wing


title: C C3 (C)-Cy5

city: CÓRDOBA

first: Francisco

middle: Javier

last: Molina-Hidalgo

state: Cordoba

address: Edif. Severo Ochoa (C6.) Planta Baja-Ala Norte Campus de Rabanales

department: Biochemistry and molecular biology

country: Spain

institute: University of Cordoba

description:
FaPRE1 Control R3
raw data file: C.txt

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version 10.7).

data_processing: Agilent Feature Extraction Software (v 10.7) was used for background subtraction and LOWESS normalization.

organism: Fragaria x ananassa

source_name: Strawberry floral bud transformed with the empty vector Replicate 3

label_protocol: 4 µg of total RNA were label following the Two-color microarray-bases Gen Expression Analysis v. 6.5 (Agilent)

growth_protocol: Strawberry plants (F. x ananassa) used were grown in plant chamber at 25 ºC, 10.000 lux and 80% humidity and afterwards maintained in a greenhouse.

extract_protocol: Total RNA was isolated from independent strawberry floral buds, as stated by Asif et al. (2000). The total RNA obtained was treated with DNase I (RNase free) (Invitrogen), in accordance with the manufacturer's instructions, to remove genomic DNA contamination, after which it was purified by using the RNeasy Mini kit (Qiagen).

treatment_protocol: The A. tumefaciens strain AGL0 (Lazo et al., 1991), containing the pK7WG2-FaPRE1 was used to transform the strawberry explants (Fragaria × ananassa), according to Barceló et al. (1998). A total of 15-25 strawberry plants and 30-40 floral buds were analysed, respectively.

tag: genotype/variation

value: empty vector

value: floral bud


title: TMZ_MGMT-KO1 replicate 2


title: OX_PRE3 OX-PRE3-1 (A)-Cy3

description:
FaPRE1-OX R1
raw data file: A.txt

source_name: Strawberry floral bud transformed with the FaPRE1-OX construct Replicate 1

value: Elongated floral bud

value: FaPRE1 overexpression


title: ATP2049

value: lung


title: Blastocysts_12_months_rep1

type: genomic

description: Biological replicates 1 of 4

hyb_protocol: Hybridizations were performed according to the microarray manufacturer’s instructions (Agilent Technologies). Briefly, 1.4 μg of labeled sample (in 40 μL) was mixed with 158 μL of hybridization master mix containing 25 μL of Bovine Hybloc competitor DNA (1 mg/ml) , Applied Genetics Laboratories), 2.6 μL of Agilent 100x Blocking Agent and 130 μL of Agilent 2× HI-RPM Hybridization Buffer (Agilent Technologies). Samples were held at 95°C for 3 min and at 37°C for 30 min followed by addition of 65 μL of Agilent-CGHBlock (final volume 260 μL). The samples were loaded onto the microarray and hybridization was carried out in a hybridization oven (Shel Lab) for 40 h at 65°C and 20 rpm. Washing was carried out according to the microarray manufacturer’s instructions

scan_protocol: Scan on a PowerScanner (Tecan) at 2um using the autogain function. Images were quantified using ArrayPro version 6.3 (MediaCybernetics)

data_processing: The array data analysis methods and downstream analysis pipelines are described in detail in (Saadi et al., 2014). Briefly, after Loess normalization, quantile inter-array scale normalization was performed and fitted to a linear model and thus, Bayesian statistics of differential expression were obtained. Thus, differentially methylated probes were identified using linear models for microarray data (LIMMA).

source_name: Blastocysts

label_protocol: For each sample, 2 μg of DNA was labeled using the Universal Linkage System (ULS) labeling kit (Kreatech Biotechnology) according to the manufacturer’s instructions with minor modifications: 1 μL of Cy-ULS dye was added per 1 μg of genomic DNA adjusted with 10× labeling buffer. The labelling mixture was then held for 30 min at 85°C in a thermocycler, followed by 3 min on ice. Non-reacted ULS-Cy3/5 was removed by purification using a QIAquick PCR Purification Kit and samples were eluted in 23.5 μL nuclease-free water. A 1.5 μL aliquot was used to determine DNA concentration and dye incorporation using the ND- 1000 NanoDrop.

extract_protocol:
Total RNA and gDNA were extracted using the AllPrep DNA/RNA Micro Kit (Qiagen)
The methodology have been thoroughly describef in (Saadi et al., 2014). Briefly, 10ng of DNA sample and spike-in control were cut in ≈160bp fragment using MSEI restriction enzyme. MseLig 12 and MseLig 21 adapters were added to the fragmented gDNA sites. Sample were the digested using methyl sensitive restriction enzyme HpaII, HinP1I and AciI. Only unmethylated fragment have been targeted by those enzyme, leaving only one adapter on the cleaved fragment. Efficiency of the digestion was confirmed by analyzing the spike-in control added prior to the DNA fragmentation step. For the step, qPCR was performed by preparing a separate mixes containing forward and reverse primer targeting HpaII, HinP1I and AciI site. Undigested spike-in (1/1000 dilution) was used as a positive control and non-template controls were also added as negatives control. The amplification plot and the dissociation curve were evaluated for each primer set separately. The DNA fragmentation was considered successful when the threshold cycle (ct) was greater than 5 when compared to the undigested control.Fragment selection by ligation-mediated PCR After cleavage by methyl sensitive enzyme, the gDNA was purified by ethanol precipitation and dissolve in nuclease free water. Selective amplification of methylated fragments was performed using two rounds of ligation-mediated PCR (LM-PCR). The PCR products were resolved on 0.8% agarose gel to assess the quality. Then the previously added linker were removed.

tag: sample typ

value: IVF with sperm from a 12 months old bull

value: IVF with sperm from a 16 months old bull


title: Blastocysts_16_months_rep3 (12 vs. 16 m)

description: Biological replicates 3 of 4


title: Male Abdominal Pupal Support Structures 2

value: Abdominal epithelium


title: LC_C_1


title: OX_PRE3 OX-PRE3-3 (C)-Cy3

description:
FaPRE1-OX R3
raw data file: C.txt

source_name: Strawberry floral bud transformed with the FaPRE1-OX construct Replicate 3


title: ATP2048

value: female


title: Blastocysts_10_months_rep2

description: Biological replicates 2 of 4

value: IVF with sperm from a 10 months old bull


title: OX_PRE3 OX-PRE3-2 (B)-Cy5

description:
FaPRE1-OX R2
raw data file: B.txt

source_name: Strawberry floral bud transformed with the FaPRE1-OX construct Replicate 2


title: LC_C_2

value: cucumber grafted onto "3212" pumpkin rootstock


title: Blastocysts_12_months_rep2

description: Biological replicates 2 of 4


title: Male First Thoracic Segment Horn 1

source_name: Male First Thoracic Segment Horn epithelium

value: First Thoracic Segment epithelium

value: Pre-pupae (larval stage)


title: Blastocysts_16_months_rep4 (10 vs. 16 m)

description: Biological replicates 4 of 4


title: ATP2042

value: IPF

value: male


title: Male Second Thoracic Segment Wing Left 1

source_name: Male Second Thoracic Segment Wing Left epithelium


title: Blastocysts_10_months_rep1

description: Biological replicates 1 of 4


title: Blastocysts_16_months_rep4 (12 vs. 16 m)

description: Biological replicates 4 of 4


title: SW1990

city: Shatin

first: Yangchao

address: Shatin

country: Hong Kong

institute: The Chinese University of Hong Kong

data_processing:
The raw sequencing reads from each sample were first mapped to the reference human genome using TopHat2.
The unmapped reads were extracted and mapped to reference human genome using TopHat-Fusion. Reads were processed into two anchors from both end of the reads.
Anchors which were aligned into the same chromosome but in reversed orientation were considered as the potential back-spliced junction reads. Since the common back-spliced junction were GT/AG, GC/AG and AT/AC, back-spliced junction reads with these junctions were extracted.
Mapped reads (from TopHat2) and back-spliced reads (from TopHat-Fusion) were used to quantify the abundance of each circRNA candidate, denoted in RPM (Reads Per Million mapped reads).
Genome_build: hg19
Supplementary_files_format_and_content: expression in RPM; Output from Htseq

growth_protocol: HPDE cells were maintained in Keratinocyte Serum Free Medium (KSFM), supplemented with 0.2 ng/mL human recombinant epithelial growth factor, 30 μg/mL bovine pituitary extract and 3% antibiotic-antimycotic. PANC-1 and SW1990 cells were cultured in Dulbecco's modified Eagle's medium (DMEM), supplemented with 10 % fetal bovine serum (FBS) and 50 unit/ml penicillin-streptomycin.

extract_protocol:
RNA was extracted by TRIZOL according to the manufacturer's protocol
library was constructed using NEBNext® Ultra™ RNA Library Prep Kit for Illumina to the manufacturer's protocol. The library was quality controlled by Agilent 2200 TapeStation.

tag: cell type

value: pancreatic ductal adenocarcinoma cells (PDAC)


title: C C2 (B)-Cy3

description:
FaPRE1 Control R2
raw data file: B.txt

source_name: Strawberry floral bud transformed with the empty vector Replicate 2

value: Normal


title: Blastocysts_16_months_rep3 (10 vs. 16 m)

description: Biological replicates 3 of 4


title: C C1 (A)-Cy5

description:
FaPRE1 Control R1
raw data file: A.txt

source_name: Strawberry floral bud transformed with the empty vector Replicate 1

value: empty vector


title: PANC-1


title: Male First Thoracic Segment Dorsal 1

source_name: Male First Thoracic Segment Dorsal epithelium


title: ATP2041


title: Male First Thoracic Segment Anterior Margin 2

source_name: Male First Thoracic Segment Anterior Margin epithelium


title: ATP2032


title: ATP2025


title: HPDE

source_name: HPDE

value: HPDE

value: non-tumor human pancreatic ductal epithelial cells (HPDE)


title: Male First Thoracic Segment Carinated Margin Left 1

source_name: Male First Thoracic Segment Carinated Margin Left epithelium


title: CC_C_2

description: an inbred line cucumber with silicon absorption ability

value: self-grafted cucumber

value: cultivated by deionized water nutrient solution

value: With sparse bloom


title: ATP2024

value: lung


title: Male First Thoracic Segment Anterior Margin 1


title: Male First Thoracic Segment Carinated Margin Right 1

source_name: Male First Thoracic Segment Carinated Margin Right epithelium


title: C_T_2

source_name: Pericarp

value: non-grafted cucumber or own-rooted cucumber

value: cultivated by deionized water nutrient solution with 1.7mM added-silicon for 2 hours

value: With dense bloom


title: CC_T_2


title: CC_C_1


title: ATP2019

source_name: Lung tissue


title: C_C_2


title: Male Abdominal Pupal Support Structures 1

source_name: Male Abdominal Pupal Support Structures epithelium

value: Abdominal epithelium


title: Male Dorsal Head 1

source_name: Male Dorsal Head epithelium

value: Head epithelium


title: Male First Thoracic Segment Posterior Margin 1

source_name: Male First Thoracic Segment Posterior Margin epithelium

value: First Thoracic Segment epithelium

value: Pre-pupae (larval stage)


title: ATP2005

value: IPF

value: female


title: ATP2044

value: male


title: C_C_1


title: control_rep1

city: Stony Brook

first: Jonas

last: Nascimento Conde

state: NY

address: Life Sciences Building

institute: Stony Brook University

description: Gene expression data from human brain microvascular endothelial cells mock-transduced with empty lentiviral vector

hyb_protocol: Samples were hybridized to GeneChip Human Clariom S Arrays (Affymetrix) using the Hydridization, Wash and Stain kit (Affymetrix).

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix). Arrays were scanned at the Stony Brook Genomics Core Facility.

data_processing: Raw data was processed with the Expression Console software (Affymetrix) for background correction and normalization. Data analysis and statistical evaluations were performed with Transcriptome Analysis Console (TAC) Software (Affymetrix).

label: biotin

source_name: mock-transduced primary hBMECs

label_protocol: Fragmented and labeled single-stranded cDNA was generated from total RNA using the GeneChip WT PLUS Reagent Kit (Affymetrix).

growth_protocol: hBMECs (passage 3), derived from elutriation of dispase-dissociated normal human brain cortex tissue were purchased from Cell Biologics (H-6023), and were grown in endothelial cell basal medium-2 MV (EBM-2 MV; Lonza) supplemented with EGM-2 MV SingleQuots (Lonza) and incubation at 37°C and 5% CO2.

extract_protocol: Total RNA was purified using RNeasy (Qiagen) following the manufacturer protocol.

treatment_protocol: hBMECs were transduced using lentiviral vectors for the expression of ZIKV NS5 WT, ZIKV NS5 K252R and ZIKV NS5 NLS mutant. Cells were transduced for 6h at 37ºC and total RNA was extracted 48 h later. We used >95% of cells positive for analysis. Mock-transduced cells were used as control.

value: human brain microvascular endothelial cells (hBMECs)

value: mock

tag: method

value: lentivirus


title: ZVWT_rep1

description: Gene expression data from human brain microvascular endothelial cells constitutively expressing ZIKV NS5 WT via transduction with lentiviral vector

source_name: ZIKV NS5 WT-transduced primary hBMECs

value: ZIKV NS5 WT


title: ZVK252R_rep1

description: Gene expression data from human brain microvascular endothelial cells constitutively expressing ZIKV NS5 K252R via transduction with lentiviral vector

source_name: ZIKV NS5 K252R-transduced primary hBMECs

value: ZIKV NS5 K252R


title: C_T_1


title: ZVNLS_rep1

description: Gene expression data from human brain microvascular endothelial cells constitutively expressing ZIKV NS5 NLS mutant via transduction with lentiviral vector

source_name: ZIKV NS5 NLSmutant-transduced primary hBMECs

value: ZIKV NS5 NLS mutant


title: Recurrent, [225Ac]hu11B6 tx, LNCaP-AR s.c. tumor 3

status: Public on Apr 01 2020

city: New York

first: Robert

last: Klein

address: 1 Gustave L Levy Pl

institute: Icahn School of Medicine at Mount Sinai

description:
A3
lncap11b63_IGO_08595_B_9_S27

data_processing:
Quality Control of raw samples in .fastq format: FastQC with default parameters
Alignment of paired-end reads to reference genome: STAR; "--runThreadN 6 --outSAMType BAM SortedByCoordinate --outSAMUnmapped Within --outSAMAttributes Standard"
Sorting and indexing aligned reads: Samtools, default parameters
Conversion to read counts: HTSeq-count, default parameters
Normalisation of read counts: TMM method in R using edgeR, default parameters
Genome_build: GRCh37
Supplementary_files_format_and_content: Normalised read counts were analysed for differentially expressed gene profiles in R using edgeR

source_name: LNCaP-AR

growth_protocol: LNCaP/AR cell line was generated and maintained as previously described (Chen et al 2003). Cells were cultured at 37° C (5% CO2) in high-glucose RPMI medium supplemented with 10% fetal bovine serum (FBS), 1% HEPES, 1% Sodium Pyruvate, 1% penicillin-streptomycin and 1% L-Glutamine. In vivo xenograft experiments were done by subcutaneous injection of 2 × 1-5 x 106 LNCaP-AR cells (200 μl in 50% Matrigel [BD Biosciences, San Jose, CA] and 50% growth media) into the flanks of male athymic BALB/c nude mice (NU(NCr)-Foxn1nu (6-8 weeks old, 20-25 g) obtained from Charles River).

extract_protocol:
RNA from snap frozen LNCaP-AR tumors was extracted using the RNeasy Mini Kit (QIAGEN) according to the instructions provided by the manufacturer.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 500 ng of total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina (RS-122-2102, TruSeq Stranded mRNA LT Kit) with 8 cycles of PCR. Samples were barcoded and run on a HiSeq 4000 in a 50bp/50bp paired end run, using the HiSeq 3000/4000 SBS Kit (Illumina). An average of 44 million paired reads was generated per sample. Ribosomal reads represented maximally 1.2% of the reads generated and the percent of mRNA bases averaged 63%.

treatment_protocol: Samples A1, A2, A3 are extracted from LNCaP-AR s.c. that were harvested from mice treated with  Actinium-225 labelled hK2 targeting mAb hu11B6 (dose: 600nCi - tail vein injection). These tumors were initially visibly irradicated, but reappeared/progressed months after initial treatment. Samples C1, C2, C3 were untreated.

value: LNCaP-AR s.c. tumor

value: LNCaP-AR

value: 600nCi [225Ac]hu11B6 - (actinium-225 labelled hK2 targeting mAb

tag: tumor stage

value: irradiacated tumor (no visible mass) but recurrence approx 1 year after targeted alpha-tx


title: Recurrent, [225Ac]hu11B6 tx, LNCaP-AR s.c. tumor 1

description:
A1
lncap11b61_IGO_08595_B_7_S25


title: Recurrent, [225Ac]hu11B6 tx, LNCaP-AR s.c. tumor 2

description:
A2
lncap11b62_IGO_08595_B_8_S26


title: Untreated, LNCaP-AR s.c. tumor 3

description:
C3
lncapcon3_IGO_08595_B_3_S21

value: Expected/normal tumor growth pattern


title: unstimulated BDCA3 D5

city: Nijmegen

first: Jessie

middle: van

last: Buggenum

address: Heyendaalseweg 135

country: Netherlands

institute: Radboud University

description:
unstimulated BDCA3
Three donors were used for each treatment

data_processing:
After quality control, high quality reads were mapped to hg19
“edgeR”, version 3.16.5, in Bioconductor version 3.4 was used for whole-transcriptome principal coordinates analysis (using the “plotMDS” command), differential gene expression analysis, and GO term analysis
Differential expression was determined by fitting a generalized linear model using the “glmFit” command, and significance was determined using the likelihood ratio test provided by the “glmLRT” command
Genome_build: human genome version 19
Supplementary_files_format_and_content: txt

source_name: Blood

extract_protocol:
BDCA3 were purified from healthy donors and treated, RNA was harvested using Trizol (Invitrogen, MA, USA), following the standard protocol
Samples were send to BGI TECH SOLUTIONS (Hong Kong) for sequencing

value: purified BDCA3 cells

tag: donor


title: Untreated, LNCaP-AR s.c. tumor 2

description:
C2
lncapcon2_IGO_08595_B_2_S20

tag: treatment


title: Stimulus 2 BDCA3 D5

description:
Stimulus 2 BDCA3
Three donors were used for each treatment


title: Stimulus 1 BDCA3 D5

description:
Stimulus 1 BDCA3
Three donors were used for each treatment


title: Stimulus 2 BDCA3 D3


title: unstimulated BDCA3 D4


title: Combiantion BDCA3 D4

description:
Combiantion BDCA3
Three donors were used for each treatment


title: Stimulus 1 BDCA3 D4


title: Stimulus 2 BDCA3 D4


title: Combiantion BDCA3 D3


title: human week 14 kidney cortex single cell RNA-Seq, Kidney 2

city: Los Angeles

first: Guilherme

last: de Sena Brandine

state: CA

address: 1050 Child's Way

department: Quantitative and Computational Biology

institute: University of Southern California

description: Kidney 2 was stored for 16 hours at 4°C to test the gene expression effect of storage

data_processing:
Base call by bcl2fastq v. 2.17; adapter and index sequences were trimmed
Reads were mapped using STAR 2.5.1b and the Gencode GTF annotation (GRCh37.p19)
Count tables were generated from the FASTQ files using the Cell Ranger software version 2.0.2 with default parameters.
Read 1 is the Cell Barcode + UMI and read 2 is the actual RNA sequence
bam file contains cell barcode for each read at CR:Z tag
Genome_build: GRCh37.p19

source_name: human kidney cortex

extract_protocol:
single cell RNA-Seq of poly A selected mRNA;
10X Genomics: Chromium Single Cell 3’ v2

tag: developing stage

value: Week 14, Kidney 2


title: Combiantion BDCA3 D5


title: CC_T_1

value: self-grafted cucumber

value: cultivated by deionized water nutrient solution with 1.7mM added-silicon for 2 hours

value: With dense bloom


title: HEK293T-UCK2/NIH3T3 Enrichment, Replicate 3

city: Irvine

first: Whitney

last: England

address: 2403 Natural Sciences I

department: Pharmaceutical Sciences

institute: University of California Irvine

data_processing:
Reads were mapped to a combined human-mouse genome index built from GRCh38 (GENCODE annotations v30) and GRCm38 (GENCODE annotations vM21) reference genomes using STAR 2.6.0c.
Gene counts were quantified using STAR 2.6.0c.
Differential expression analysis of human and mouse genes was performed using DESeq2.
Genome_build: GRCh38/mm10
Supplementary_files_format_and_content: tsv: Normalized expression values.

source_name: HEK293T cells

growth_protocol: HEK293T expressing UCK2-GFP and wildtype NIH3T3 cells were grown in 10 cm co-cultures.

extract_protocol:
RNA was harvested from cells using 500uL Trizol.
Purified, biotin-enriched RNA along with input biotinylated RNA were carried through to library preparation using the Tru-seq Stranded total RNA library Prep Human/Mouse/Rat kit (Ilumina) with ribosome depletion. Superscript IV was used for first strand synthesis.

treatment_protocol: 2’AzUd was added at 100mM to complete culture medium from 200 mM DMSO stocks (final concentration of <1% DMSO). Following treatment, the media was decanted and the cells were washed briefly x2 with DPBS before treatment with Trizol reagent according to the manufacturer’s instructions. After precipitation, the RNA pellets were washed x2 with 70% ethanol followed by resuspension in 40 μL of nuclease free water. The RNA was treated with DNase TURBO (Thermo Fisher Scientific) for 30 min at 37 oC, followed by column cleanup using Zymo IIICG columns (Zymo Research) and resuspension to concentrations of 1-1.5 μg/μL. RNA was then subjected to biotinylation with DBCO biotin (Sigma Aldrich) as previously described in 150 μL reaction volumes. Enrichment was carried out using 50 – 100 μg of biotinylated RNA. MyOne Streptavidin C1 beads (Thermo Fisher Scientific) were washed x4 in bead binding buffer (1 M NaCl, 100 mM Tris-HCl pH 7.0, 10 mM EDTA, 0.2% (v/v) Tween-20) before resuspension in their original volume with bead binding buffer. Biotinylated RNA was added to the beads and incubated for 20 min at room temperature with end-over-end rotation to ensure that the beads were mixing. Following hybridization, beads were sequestered on the magnetic rack and the supernatant was removed. Beads bound with RNA were transferred to new tubes and were washed x4 with 42 oC high salt wash buffer (4 M NaCl, 100 mM Tris-HCl pH 7.0, 10 mM EDTA, 0.2% (v/v) Tween-20) followed by x3 washes with nuclease free water. Beads were then spun down and re-suspended in 100 μL of 95% formamide, 10 mM EDTA elution buffer, and was incubated at 90 oC for 5 min at 1000 RPM. Tubes were then cooled for 1 min on ice.

tag: cell line

value: human embryonic kidney

value: enriched


title: Stimulus 1 BDCA3 D3


title: HEK293T-UCK2/NIH3T3 Enrichment, Replicate 1


title: HEK293T-UCK2/NIH3T3 Enrichment, Replicate 2


title: human week 14 kidney cortex single cell RNA-Seq, Kidney 1

value: Week 14, Kidney 1


title: HEK293T-UCK2/NIH3T3 Input, Replicate 3

value: input


title: HEK293T-UCK2/NIH3T3 Input, Replicate 1


title: HEK293T-UCK2/NIH3T3 Input, Replicate 2


title: control LNCaP cells_LNCaP3

city: Dalals

first: zhi-ping

last: liu

state: TX

address: 6000 Harry Hines Blvd

department: internal medicine

institute: ut southwestern

description: control Lncap cells

data_processing:
We sequenced samples using Illumina Hiseq platform.
The sequencing reads which containing low-quality, adaptor-polluted and high content of unknown base(N) reads, are processed to remove this reads before downstream analyses
After reads filtering, we map clean reads to reference genome use HISAT
After genome mapping, we use StringTie to reconstruct transcripts. and with genome annotation information we identify novel transcripts exist in our samples use cuffcompare a tool of cufflinks;
we use rMATS to detect differentially splicing gene (DSG) between samples. DSG is regulated by alternative splicing(AS), which allows the production of a variety of different isofroms from one gene only.
Changes in relative abundance of isoforms, regardless of the expression change, indicate a splicing-related mechanism. We detect 5 types AS events, include Skipped Exon(SE), Alternative 5' Splicing Site(A5SS), Mutually exclusive exons(MXE) and Retained Intron(RI).
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: Counts, FPKMs

source_name: prostate cancer cell line

growth_protocol: prostate cancer cells were cultured in 10%FBS RPMI media

extract_protocol:
RNA extracted using Trizol (Invitrogen) following manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells are treated with 10%CFBS RPMI media for 3 days before harvest.

value: prostate cancer cell line LNCaP

tag: genotype

value: lncap cells with stable overexpression of plenti6 control plasmid


title: control LNCaP cells_LNCaP2

description: control Lncap cells


title: control LNCaP cells_LNCaP1

description: control Lncap cells


title: unstimulated BDCA3 D3


title: KDM4B-overexpression LNCaP cells_4b2_D6092

description: Lncap cells with stable overexpression of wild KDM4B

value: Lncap cells with stable overexpression of Flag-KDM4B


title: JM9

city: Buenos Aires

first: Florencia

middle: Paula

last: Madorsky Rowdo

address: Av. Patricias Argentinas 435

country: Argentina

institute: Fundación Instituto Leloir

data_processing:
Quality control of reads was performed with FASTX-Toolkit and FastQC
Reads were aligned to the latest human Hg38 reference genome using the STAR spliced read aligner
Fragment counts were derived using HTSeq package
Differentially expressed genes were identified by a ranking based on adjusted p-values ≤0.005 and a false discovery rate≤0.1 using the R/Bioconductor package edgeR
Genome_build: Hg38
Supplementary_files_format_and_content: excel file that includes FPKM values for each Sample and log fold change between samples

source_name: MEL-XY3 cells

growth_protocol: melanoma cells were grown in melanoma medium + 10% FCS

extract_protocol:
Cell samples were snap-freezed and RNA was extracted obtaining 0.2-0.4μg per sample, in a concentration  ≥20 ng/μl, RIN≥7.0, and 28S/18S≥1.0.
The total RNA samples are first treated with DNase I to degrade any possible DNA contamination. Then the mRNA is enriched by using the oligo(dT) magnetic beads. Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then the first strand of cDNA is synthesized by using random hexamer-primer. Buffer, dNTPs, RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End reparation and 3’-end single nucleotide A (adenine) addition is then performed. Finally, sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR amplification. During the QC step, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used to qualify and quantify of the sample library. The library products are ready for sequencing via Illumina HiSeq 4000

treatment_protocol: MEL-XY3 SUR cells were obtained in vitro after 5 week treatment with 10 µM PLX4032, changing media twice a week.

tag: tumor type

value: melanoma


title: KDM4B-overexpression LNCaP cells_4b1_D6092


title: JM7

source_name: MEL-XY3 SUR cells

value: 5 weeks with 10 uM PLX4032


title: KDM4B-overexpression LNCaP cells_4b4_D6092


title: HepG2_EPZ_H3K27ac_1

city: Chapel Hill

first: Jesse

last: Raab

address: 120 Mason Farm Rd

department: Genetics

institute: University of North Carolina Chapel Hill

description:
processed data file:
dtags_agg.csv

data_processing:
Align bowtie2 --sensitive
samtools rmdup
samtools merge
bamCoverage --binSize 10 --extendReads 150 --normalizeUsingRPKM --centerReads (For drug treated samples additionally --scaleFactor was used with the normalization factor derived as 1/#of tags mapped against reference drosophila genome in millions - file dtags_agg.csv
macs2 callpeak -q 0.001 --keep-dup all --shift 37 --nomodel --extsize 147 -g hs
peaks were filtered against blacklist (ENCODE) using bedtools and recursviely merged with other peaks within 500bp to yield final peak calls
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files = Reads per million (no treatment samples) or reference normalized reads per million (DMSO/EPZ64-38 treated) signal tracks
Supplementary_files_format_and_content: bed files = peaks called from merged replicates of bam files for INO80 subunits in Huh7 and HepG2
Supplementary_files_format_and_content: raw files ending in rmdup.dtags.bam  were aligned against dm3 to count the total number of non-duplicate uniquely mapping drosohpila reads in each IP sample and used for normalization - count values are in dtags_agg.csv

growth_protocol: Cells were grown in DMEM + 10% FBS + penicillin + streptomycin at 37 degrees in 5% C02. Experiments were performed on cells less than 10 passages.

extract_protocol:
Cells were fixed in 0.3% formaldehyde for 30 minutes at 4 degrees prior to processing for ChIP using protocol from Raab et al 2015.
Kapa Hyperprep kit using Illumina Truseq barcoded adapters

treatment_protocol: In experiments with drug treamtne (EPZ-6438 or DMSO at 1.0uM ) was added to cells for 120 hours prior to fixing for ChIP.

value: liver cancer cell line

tag: chip antibody

tag: chip antibody vendor

value: active motif

tag: chip antibody cat. #

tag: lot

tag: treated with

value: 1.0uM EPZ-6438 ( MedChemExpress, HY-13803)


title: HepG2_EPZ_H3K27ac_2

description:
processed data file:
dtags_agg.csv


title: HepG2_EPZ_Input_2

value: none (input)


title: HepG2_DMSO_H3K27ac_2

description:
processed data file:
dtags_agg.csv

value: DMSO


title: HepG2_DMSO_Input_2


title: HepG2_EPZ_Input_1


title: PH-T0-15-WT

city: Cambridge

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

country: United Kingdom

institute: University of Cambridge

description:
SLX-12919.D712_D505
processed data file: ph_raw_count.tsv

data_processing:
Reads are mapped using TopHat V2.0.11 to the mouse GRCm38 genome.
Gene-level counts were generated using htseq-count with Ensembl Transcript GTF V74.
Genome_build: GRCm38
Supplementary_files_format_and_content: ph_raw_count.tsv: Tab-delimited text file includes raw counts.

source_name: Whole Liver Tissue

extract_protocol:
Total RNA was isolated using STAT-60 (AMS biotechnology, CS-111)/chloroform (200 uL; Sigma, Cat 650471)/isopropanol (500 uL; Sigma, cat 33539)/75% ethanol (1ml) according to previously published protocol (PMID: 26679101). Samples were stored in aliquot at – 80 °C prior to use. All reagents, plastic ware, and supplies used were sterile, nuclease free, and of molecular biology grade. RNA purity (A260/A280>1.80) and concentration were determined using nanodrop spectrophotometer (Thermo Fisher scientific, Delaware USA). RNA integrity was studied using the 2100 Bioanalyzer System (Agilent) and RNA 6000 Nano Kit. An RNA Integrity Number (RIN) of 8 was considered the lowest cut-off for RNA Sequencing.
Sequencing libraries were constructed using Illumina mRNA library prep kit.

treatment_protocol: Liver tissues were snap-frozen and stored at -80*C until RNA extraction.

tag: strain

value: Wild Type

tag: Sex

value: Male

tag: tissue

value: Whole liver

value: Resected Liver - Baseline control

tag: time point

value: Day 0 (resected liver)


title: PH-T3-20-KO

description:
SLX-12919.D712_D507
processed data file: ph_raw_count.tsv

value: Bmp8b Knockout

value: Day 3 PH

value: 3 days after PH


title: PH-T3-19N-KO

description:
SLX-12919.D711_D507
processed data file: ph_raw_count.tsv


title: PH-T0-14-WT

description:
SLX-12919.D711_D505
processed data file: ph_raw_count.tsv


title: PH-T3-18-KO

description:
SLX-12919.D710_D507
processed data file: ph_raw_count.tsv


title: PH-T0-13-WT

description:
SLX-12919.D710_D505
processed data file: ph_raw_count.tsv


title: HepG2_DMSO_Input_1

tag: cell type


title: PH-T3-16-WT

description:
SLX-12919.D708_D507
processed data file: ph_raw_count.tsv


title: PH-T3-15-WT

description:
SLX-12919.D707_D507
processed data file: ph_raw_count.tsv


title: PH-T0-12N-WT

description:
SLX-12919.D709_D505
processed data file: ph_raw_count.tsv


title: PH-T0-16-WT

description:
SLX-12919.D701_D506
processed data file: ph_raw_count.tsv


title: PH-T3-12N-WT

description:
SLX-12919.D704_D507
processed data file: ph_raw_count.tsv


title: PH-T3-14N-WT

description:
SLX-12919.D706_D507
processed data file: ph_raw_count.tsv


title: PH-T3-13N-WT

description:
SLX-12919.D705_D507
processed data file: ph_raw_count.tsv


title: 2_months_WT_Rep4

first: Mo

last: Gou

address: China, Tianjin, Nankai University

description:
WT_young_promoter.bed
YWT4_1

data_processing:
Sequencing reads were trimmed to remove the low-quality reads and reads containing adapters. Sequencing reads were trimmed with default setting of Trimmomatic software (Bolger et al., 2014), to remove the adapters and low-quality reads.
Trimmed reads were aligned to mouse reference mm10 by using Bismark (v12.5) (Krueger and Andrews, 2011).
Genome_build: mm10
Supplementary_files_format_and_content: The bed files of 3 groups

source_name: mouse MII oocytes

extract_protocol:
Single MII oocyte was resuspended in PBS with 0.1% BSA (A3311-10g, SIGMA), picked up in 1 μl 0.1% BSA using a micropipette with an epT.I.P.S. pipette tip (0030000838, Eppendorf) under a dissecting microscope.
DNA methylation libraries of mice MII oocytes were constructed according to a previously reported method (Smallwood et al., 2014), with minor changes.
Low-input methylation sequencing


title: 2_months_WT_Rep3

description:
WT_young_promoter.bed
YWT3_1


title: 2_months_WT_Rep2

description:
WT_young_promoter.bed
YWT2_1


title: HepG2_DMSO_H3K27ac_1

description:
processed data file:
dtags_agg.csv


title: 2_months_Tet2KO_Rep3

description:
KO_young_promoter.bed
YKO3_R1


title: 2_months_WT_Rep1

description:
WT_young_promoter.bed
YWT1_1


title: 2_months_Tet2KO_Rep2

description:
KO_young_promoter.bed
YKO2_R1


title: 2_months_Tet2KO_Rep1

description:
KO_young_promoter.bed
YKO1_R1


title: 11_months_WT_Rep2

description:
WT_old_promoter.bed
OW2_R1


title: PH-T3-17-KO

description:
SLX-12919.D709_D507
processed data file: ph_raw_count.tsv


title: 11_months_WT_Rep1

description:
WT_old_promoter.bed
OWT1_R1


title: 11_months_WT_Rep3

description:
WT_old_promoter.bed
OW3_R1


title: ipsi_nerve_DP_wk10_F1

city: London

first: Franziska

last: Denk

address: Guy's Campus

department: Wolfson SPaRC

institute: King's College London

description: DP F2 ipsi D2 280110

data_processing:
Basic quality control was conducted in seqmonk on stampy bam files obtained from the sequencing facility.
Fastq files were trimmed by Trimmomatic (version-0.39) to eliminate reads with phred scores less than 33 and remove any residual adapters.
The reads were pseudo-aligned using kallisto (version 0.46.0).
Raw transcript counts were length and depth corrected by conversion to transcripts per million (TPM) using the R package tximport.
The R package sleuth was used for differential expression analysis (Wald test for twogroup comparisons, likelihood ratio test for multiple group comparisons).
Power simulations were conducted using the R package powsimR.
Genome_build: Ensembl v96 transcriptomes with genome assembly: GRCm38
Supplementary_files_format_and_content: Excels files include QC, TPM and sleuth analysis values for each sample

source_name: DoublePositive

extract_protocol:
The ligated sciatic nerve and its connected L3-L5 DRG were dissected, digested and stained for FACS. This process was repeated for the uninjured contralateral side. RNA from FACS collected samples was reverse transcribed into cDNA, amplified and purified in accordance with the Smart-seq2 method (Picelli et al. Nat Protocols)
SMARTer amplified cDNA was shipped to the Oxford Genomics Centre for batch-controlled library preparation using an Illumina NexteraXT kit (Illumina, Cat# FC-131-1096) and sequenced on an Illumina HiSeq 4000 (75 bp, paired-end reads).

treatment_protocol: Mice underwent partial sciatic nerve ligation surgery for 1 week and 10 weeks.

value: nerve

tag: condition

value: ipsilateral

tag: timepoint

value: 10 weeks after PSNL

tag: gender

value: female


title: ipsi_nerve_DP_wk10_M1

description: DP M2 ipsi D2 279122

value: male


title: contra_nerve_DN_wk10_M1

description: DN M1 contra D3 288109

source_name: DoubleNegative

value: contralateral


title: ipsi_nerve_MHC_wk10_F1

description: MHC F1 ipsi D2 270135

source_name: MHCII+


title: ipsi_nerve_MHC_wk10_F2

description: MHC F1 ipsi D3 277146


title: contra_nerve_MHC_wk10_M1

description: MHC M1 contra D3 274182


title: ipsi_nerve_MHC_wk10_M3

description: MHC M2 ipsi D3 275170


title: ipsi_nerve_Tcells_M3

description: T M2 ipsi D3 263124

source_name: T cells


title: ipsi_nerve_Tcells_M1

description: T M1 ipsi D2 257196


title: ipsi_nerve_Tcells_F3

description: T F2 ipsi D3 267171


title: ipsi_nerve_Tcells_F2

description: T F1 ipsi D3 265195


title: ipsi_nerve_Tcells_F1

description: T F1 ipsi D2 260160


title: contra_nerve_Tcells_M2

description: T M1 contra D3 262136


title: contra_nerve_Tcells_F3

description: T F2 contra D3 268159


title: contra_nerve_Tcells_M1

description: T M1 contra D2 258184


title: contra_nerve_Tcells_F1

description: T F2 contra D2 261148


title: contra_nerve_Tcells_F2

description: T F1 contra D3 266183


title: ipsi_DRG_DN_M2

value: DRG

value: 1 week after PSNL


title: ipsi_nerve_MHC_wk10_M1

description: MHC M2 ipsi D2 269147


title: ipsi_nerve_MHC_wk10_M2

description: MHC M1 ipsi D3 273194


title: ipsi_DRG_DN_M1


title: ipsi_nerve_DP_wk10_M2

description: DP M1 ipsi D3 281193


title: contra_nerve_MHC_wk10_F1

description: MHC F2 contra D2 272111


title: ipsi_DRG_DN_F1


title: contra_DRG_DN_F2


title: contra_DRG_DN_M1


title: ipsi_DRG_DN_F2


title: contra_DRG_DN_M2


title: ipsi_DRG_MHC_M2


title: ipsi_DRG_MHC_M1


title: ipsi_nerve_Tcells_M2

description: T M2 ipsi D2 259172


title: contra_DRG_DN_F1


title: ipsi_DRG_MHC_F1


title: ipsi_DRG_MHC_F2


title: contra_DRG_MHC_M2


title: contra_DRG_MHC_M1


title: contra_DRG_MHC_F1


title: ipsi_nerve_DN_M2


title: contra_DRG_MHC_F2


title: ipsi_nerve_DN_M1


title: contra_nerve_DN_M2


title: contra_nerve_DN_M1


title: contra_nerve_DN_F1


title: ipsi_nerve_DP_F1


title: ipsi_nerve_DP_M2


title: Untreated, LNCaP-AR s.c. tumor 1

description:
C1
lncapcon1_IGO_08595_B_1_S19

value: LNCaP-AR s.c. tumor

value: LNCaP-AR

tag: treatment

tag: tumor stage

value: Expected/normal tumor growth pattern


title: ipsi_nerve_MHC_M3


title: ipsi_nerve_MHC_M2


title: ipsi_nerve_DP_F2


title: ipsi_nerve_MHC_M4


title: ipsi_nerve_DP_M1


title: ipsi_nerve_MHC_M1


title: contra_nerve_MHC_F3


title: contra_nerve_MHC_F2


title: ipsi_nerve_MHC_F1


title: contra_nerve_MHC_M3


title: ipsi_nerve_MHC_F4


title: contra_nerve_MHC_M4


title: ipsi_nerve_MHC_F2


title: contra_nerve_MHC_M2


title: contra_nerve_MHC_M1


title: contra_nerve_MHC_F1


title: contra_nerve_MHC_F4


title: WT_82

first: Hanseul

last: Yang

address: 1230 York Avenue

institute: Rockefeller University

description: processed data file: WT_NFIBcKO_NFIXcKO_NFIBXdKO_TPM.txt

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse genome (mm10) using the Bowtie2 program (version 2.2.9).
The expression values of each gene were quantified as transcript per million (TPM) using RSEM (v1.2.30).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.genes.results.txt: Tab-delimited text files include TPM values for each Sample.
Supplementary_files_format_and_content: WT_NFIBcKO_NFIXcKO_NFIBXdKO_TPM.txt: Tab-delimited text file includes TPM values for each Sample.

source_name: Mouse back skin

extract_protocol:
Mouse hair follicle stem cells were purified from Sox9-CreER;NFIBfl/fl;NFIXfl/fl and WT littermate mice at P70 2nd telogen.
FACS-isolated cells were directly lysed into TRIzol LS (Invitrogen). Total RNA was purified using the Direct-zol RNA MiniPrep kit (Zymo Research) per manufacturer’s instructions. Quality of the RNA for sequencing was determined using an Agilent 2100 Bioanalyzer; all samples used had RNA integrity numbers >8. Library preparation using the Illumina TruSeq mRNA sample preparation kit was performed at the Weill Cornell Medical College Genomic Core facility (New York), and RNAs were paired-end sequenced on Illumina HiSeq 4000 or HiSeq 2500 machines.

value: Male

tag: age

value: Hair follicle stem cells

tag: sorting markers

value: DAPI (neg), Sca-1 (neg), integrina6 (pos), CD34 (pos)


title: NFIB-cKO_81

value: DAPI (neg), Sca-1 (neg), integrina6 (pos), CD34 (pos), YFP (pos)


title: NFIX-cKO_88


title: NFIB-cKO_85


title: ST2-Treg 2 (X11)

city: Indianapolis

first: Mark

middle: H

last: Kaplan

address: 635 Barnhill Dr. MS 420

department: Microbiology and Immunology

institute: Indiana University

data_processing:
Libraries were sequenced with 2×75bp paired-end configuration on HiSeq4000 (Illumina) using HiSeq 3000/4000 PE SBS Kit.
A Phred quality score (Q score) was used to measure the quality of sequencing. More than 90% of the sequencing reads reached Q30
The sequencing data were first assessed using FastQC (Babraham Bioinformatics) for quality control. All sequenced libraries were then mapped to the mouse genome (UCSC mm10) using STAR RNA-seq aligner
Uniquely mapped sequencing reads were assigned to mm10 refGene genes using featureCounts. Differential expression (DE) analyses were performed using edgeR v3.22.3 implemented in the Bioconductor package
Biological coefficients of variation between the samples were estimated using an empirical Bayes approach under the assumption that the data follows a negative binomial distribution.  We filtered out low expression transcripts based on percentage of samples (less than 50%) and CPM cutoff of 0.5. A total of 14,943 mRNAs remained after filtering and used in the differential expression analysis by edgeR.  Statistical significance was defined as FDR p-value £0.05 and a fold change (FC) ³2 of expression level between comparison of knockout mice and controls. The heat map and locus-by-locus volcano plot were performed using R package. Gene set enrichment analysis (GSEA) was used for the whole genome functional enrichment analysis, based on annotation files from Molecular Signatures Database (MSigDB) immunologic gene sets, to identify biological pathways that were significantly enriched after 3,000 times permutation
Genome_build: UCSC mm10
Supplementary_files_format_and_content: An xls file containing the CPM values and counts for each sample, generated using R package EdgeR v3.22.3

source_name: ST2-Treg cells

growth_protocol: ST2+ and ST2- Treg cells in lung of house dust mite extract challenged mice were sorted based on CD4, ST2 and YFP expression followed by RNA isolation.

extract_protocol:
RNeasy plus micro kit (Qiagen) was used to extract RNA from sorted ST2+/- Treg cells.
1 ng of RNA per sample were used to prepare cDNA library using Clontech SMART-Seq v4 Ultra Low Input RNA Kit

value: lung tissue

tag: treated

value: House dust mite extract


title: ST2+Treg 2 (X8)

source_name: ST2+Treg cells


title: ST2+Treg 1 (X7)


title: ipsi_nerve_MHC_F3

value: nerve


title: cLP_mac_wt_hh_S2

city: Oxford

first: Stephen

last: Sansom

state: Oxfordshire

address: Roosevelt Drive

department: NDORMS

institute: Kennedy Institute of Rheumatology

description:
featureCounts.counts.txt
salmon.tpms.txt

data_processing:
Sequence reads were aligned to the mouse genome with Hisat2 (version 2.1.0) using a “genome_trans” index built from the mm10 release of the mouse genome and Ensembl version 91 annotations (two-pass strategy to discover novel splice sites; with parameters: --dta and --score-min L,0.0,-0.2).
Mapped reads were counted using featureCounts (Subread version 1.6.3; Ensembl version 91 annotations; default parameters).
TPMs were estimated with salmon (version 0.11.3, with parameter "--gcBias") using a quasi index built from from the full set of Ensembl version 91 transcriptome annotations (parameters "--k=31 --keepDuplicates").
Genome_build: mm10
Supplementary_files_format_and_content: (1) "featureCounts.counts.txt" is a tab-delimited text file containing the table of gene-by-sample read counts computed with the featureCounts algorithm. (2) "salmon.tpms.txt" is a tab-delimited text file containing the table of gene-by-sample TPMs computed with Salmon.

source_name: colonic lamina propria

growth_protocol: Mice were bred and maintained under SPF conditions in accredited animal facilities at the University of Oxford. All procedures were conducted according to the Operations of Animals in Scientific Procedures Act (ASPA) of 1986 and approved by the Kennedy Institute of Rheumatology Ethics Committee. Animals were housed in individually ventilated cages at a constant temperature with food and water ad libitum. Mice were free of known intestinal pathogens and negative for Helicobacter species.

extract_protocol:
Colons and/or caeca were harvested from mice, washed in PBS/BSA and content flushed with forceps. Intestines were then opened longitudinally and washed once more before blotting to remove mucus. Gut tissue was then cut into 1 cm long pieces and placed in 50 mL centrifuge tube (Greiner) in ice cold PBS + 0.1% BSA. Colons were incubated 2 times at 200 rpm in 40 mL HBSS + 0.1% BSA + 1% Penicillin-Streptomycin (PS, Lonza) + 5mM EDTA (Sigma-Aldrich) at 37 °C for 10 min before the supernatant was aspirated. Tissue was placed in 40 mL PBS + 0.1% BSA + 1% PS for 5 min. Intestines were then incubated with 20 mL RPMI + 10% FCS +1% PS + 2.5 U/mL Collagenase VIII (Sigma-Aldrich) + 2 U/mL DNAse I (Roche), shaking at 200 rpm for 45 mins - 1 hour at 37 °C. Supernatant was filtered through a 70 μm cell strainer to which 30 mL of ice cold PBS + 0.1% BSA + 1% PS + 5 mM EDTA was added to ablate collagenase/DNase activity. Cells were washed in 30 mL PBS/BSA before filtering once more through a 40 μm cell strainer. The cells were then pelleted by centrifugation at 400 rcf for 10 minutes at 4 °C.  LPLs were isolated by resuspending cells in 4 mL P80 (80% P100 (9:1 percoll:10X PBS) + 20% RPMI) percoll in a 15 mL centrifuge tube (Greiner) before overlaying 4 mL P40 (40% P100 + 60% 1X PBS) layer. Cells were spun at 2000 rcf for 20 min at room temperature, slow acceleration, no brake. Mucus and cellular debris were aspirated from the surface of the P40 layer with a Pasteur pipette and pipetted into 40 mL of ice cold PBS + 0.1% BSA. Cells were pelleted by centrifugation at 400 rcf for 10 min and resuspended in 1 mL RPMI + 10% FCS + 1% PS before counting. Cells were sorted on a FACS ARIA II cell sorter (BD) using a 100 μm nozzle. For Bulk samples, cells were sorted directly into SmartSeq II lysis buffer (Picelli et al., 2013). For 10X samples submission, cells were sorted into 1.5 mL microcentrifuge tubes coated with FCS.
For each sample 100 cells were FACs sorted into 2ul of Smart-seq2 lysis buffer and cDNA prepared according to the Smart-seq2 protocol. RNA-seq libraries were prepared using Nextera XT kits (Illumina).

treatment_protocol: Mice were infected with 1x10^8 colony forming units (cfu) Hh in 200 μL sterile PBS on days 0 and 1 by oral gavage with a 22G curved, blunted needle (Popper & Sons). Mice were injected intraperitoneally once weekly starting on day 0 with 1 mg anti-IL10R blocking antibody (clone 1B1.2) in a volume of 200 μL. Infected mice were monitored weekly for colitis symptoms. Mice were culled by Schedule 1 method three weeks after day of infection, and organs were harvested for analysis.

value: C57BL/6 SJL

tag: genotype

tag: infection

value: Hh

value: mononuclear phagocytes FACs-isolated from the inflamed lamina propria

tag: facs  phenotype

value: CD45.1+ve, GFP+ve, CD11b+ve, Ly6c-lo, MHCII+ve, CD3-ve, CD19-ve, CD138-ve, NK1.1-ve, Ly6G-ve and Siglec F-ve

tag: replicate

value: chimera S2


title: cLP_mac_ko_hh_S2

tag: strain

value: CD45.2+ve, GFP+ve, CD11b+ve, Ly6c-lo, MHCII+ve, CD3-ve, CD19-ve, CD138-ve, NK1.1-ve, Ly6G-ve and Siglec F-ve


title: cLP_mac_ko_hh_S1

value: chimera S1


title: cLP_p2mono_ko_hh_S3

value: CD45.2+ve, GFP+ve, CD11b+ve, Ly6c-hi, MHCII+ve, CD3-ve, CD19-ve, CD138-ve, NK1.1-ve, Ly6G-ve and Siglec F-ve

value: chimera S3


title: cLP_p2mono_wt_hh_S3

value: CD45.1+ve, GFP+ve, CD11b+ve, Ly6c-hi, MHCII+ve, CD3-ve, CD19-ve, CD138-ve, NK1.1-ve, Ly6G-ve and Siglec F-ve


title: cLP_p2mono_ko_hh_S1


title: cLP_mac_wt_hh_S3


title: cLP_mac_wt_hh_S1


title: cLP_p1mono_ko_hh_S3

value: CD45.2+ve, GFP+ve, CD11b+ve, Ly6c-hi, MHCII-ve, CD3-ve, CD19-ve, CD138-ve, NK1.1-ve, Ly6G-ve and Siglec F-ve


title: ST2-Treg 1 (X10)


title: cLP_p2mono_ko_hh_S2


title: cLP_p2mono_wt_hh_S2


title: cLP_p1mono_wt_hh_S1

value: CD45.1, GFP+ve, CD11b+ve, Ly6c-hi, MHCII-ve, CD3-ve, CD19-ve, CD138-ve, NK1.1-ve, Ly6G-ve and Siglec F-ve


title: cLP_p1mono_ko_hh_S1


title: cLP_mph_wt

description:
matrix.mtx
barcodes.tsv
genes.tsv

data_processing:
Read mapping, quantitation and aggregation of sample count matrices was performed with the "cellranger count" and "cellranger aggr" (--normalize=none) tools as provided by the 10x Genomics Cell Ranger pipeline (version 2.1.1). For the "cellranger count" step, a custom reference was built using Ensembl annotations (version 91) for genes with the following biotypes: protein_coding, lincRNA, macro_lincRNA, IG_C_gene, IG_C_pseudogene, IG_D_gene, IG_D_pseudogene, IG_J_gene, IG_LV_gene, IG_V_gene, IG_V_pseudogene, IG_pseudogene, TR_C_gene, TR_D_gene, TR_J_gene, TR_J_pseudogene, TR_V_gene, TR_V_pseudogene, antisense_RNA, miRNA.
Cells with barcodes common to both samples were removed from the analysis to avoid issues associated with index hopping.
The aggregated count matrix was randomly down-sampled in order to normalize the median number of umis per-cell between the two samples ("downsampleMatrix" function from the DropletUtils R package).
Genome_build: mm10
Supplementary_files_format_and_content: The "matrix.mtx" MEX file contains the aggregated count matrix (cells in columns, genes in rows). The "barcodes.tsv" TSV file contains the cell barcodes (genotype is indicated in the cell barcode  with the suffixes "-wt" or "-ko"). The "genes.tsv" file contains the Ensembl gene identifiers and names. These files can be read with the "Read10X" function from the Seurat R package.

extract_protocol:
Colons and/or caeca were harvested from mice, washed in PBS/BSA and content flushed with forceps. Intestines were then opened longitudinally and washed once more before blotting to remove mucus. Gut tissue was then cut into 1 cm long pieces and placed in 50 mL centrifuge tube (Greiner) in ice cold PBS + 0.1% BSA. Colons were incubated 2 times at 200 rpm in 40 mL HBSS + 0.1% BSA + 1% Penicillin-Streptomycin (PS, Lonza) + 5mM EDTA (Sigma-Aldrich) at 37 °C for 10 min before the supernatant was aspirated. Tissue was placed in 40 mL PBS + 0.1% BSA + 1% PS for 5 min. Intestines were then incubated with 20 mL RPMI + 10% FCS +1% PS + 2.5 U/mL Collagenase VIII (Sigma-Aldrich) + 2 U/mL DNAse I (Roche), shaking at 200 rpm for 45 mins - 1 hour at 37 °C. Supernatant was filtered through a 70 μm cell strainer to which 30 mL of ice cold PBS + 0.1% BSA + 1% PS + 5 mM EDTA was added to ablate collagenase/DNase activity. Cells were washed in 30 mL PBS/BSA before filtering once more through a 40 μm cell strainer. The cells were then pelleted by centrifugation at 400 rcf for 10 minutes at 4 °C.  LPLs were isolated by resuspending cells in 4 mL P80 (80% P100 (9:1 percoll:10X PBS) + 20% RPMI) percoll in a 15 mL centrifuge tube (Greiner) before overlaying 4 mL P40 (40% P100 + 60% 1X PBS) layer. Cells were spun at 2000 rcf for 20 min at room temperature, slow acceleration, no brake. Mucus and cellular debris were aspirated from the surface of the P40 layer with a Pasteur pipette and pipetted into 40 mL of ice cold PBS + 0.1% BSA. Cells were pelleted by centrifugation at 400 rcf for 10 min and resuspended in 1 mL RPMI + 10% FCS + 1% PS before counting. Cells were sorted on a FACS ARIA II cell sorter (BD) using a 100 μm nozzle. For Bulk samples, cells were sorted directly into SmartSeq II lysis buffer (Picelli et al., 2013). For 10X samples submission, cells were sorted into 1.5 mL microcentrifuge tubes coated with FCS.
Libraries were generated using 10x Genomics Single Cell 3’ Solution (version 2) kit and subjected to Illumina sequencing (HiSeq 4000).

value: CD45.1+ve, GFP+ve, CD11b+ve, CD3-ve, CD19-ve, CD138-ve, NK1.1-ve, Ly6G-ve and Siglec F-ve

value: pool of cells from n=3 chimeras (S1,S2 and S3)


title: C 4 1 E4

city: Munich

first: Elias

middle: Rafael

last: Ruiz-Morales

state: Baviera

address: Marchioninistrasse 25

department: Institute of Epigenetics and Stem Cells

institute: Helmholtz Zentrum Muenchen

description: Kallisto abundance and counts file

data_processing:
Quality control of the sequencing: FastQC v0.11.7
Trimming of adapters: trimmomatic v0.38; ILLUMINACLIP:ADAPTERS_FILE:3:30:8:1:true LEADING:10 TRAILING:10 SLIDINGWINDOW:4:15 MINLEN:10
Quality control of the sequencing: FastQC v0.11.7
Indexing of the genome (transcripts): kallisto index  v0.44.0; kmer-size=31
Pseudoalignment with kallisto using the trimmed reads: kallisto quant  v0.44.0; Returns the abundance files
Genome_build: mm10 (vM19 GRCm38.p6)
Supplementary_files_format_and_content: Processed files are the output of the pseudoalignment using Kallisto quant. The format is a tab-separared values (.tsv) with five columns: target_id, length, eff_length, est_counts, tpm. Being the 'est_counts' the number of counts.  This table can be read by R using the package tximport with the parameter type = "kallisto".

source_name: mouse preimplantation embryo

growth_protocol: incubation KSOM

extract_protocol:
single embryo
Smartseq2

treatment_protocol: microinjection zygotes Suv39h1wt or mut mRNA

value: preimplantation embryo

tag: developmental stage

tag: injected with

tag: background strain

value: Hybrid crosses  (paternal DBA/ maternal F1:C57BL/6J × CBA/H)


title: cLP_p1mono_wt_hh_S3

tag: cell type


title: cLP_p2mono_wt_hh_S1


title: cLP_p1mono_ko_hh_S2


title: C 3 N E16b

description: Kallisto abundance and counts file

tag: tissue

value: non-injected


title: C 1 N E2a

description: Kallisto abundance and counts file

tag: timepoint


title: cLP_mac_ko_hh_S3

value: C57BL/6 SJL


title: cLP_p1mono_wt_hh_S2

value: Hh


title: A 2 2 E4

description: Kallisto abundance and counts file


title: C 4 1 E5-8 replicate

description: Kallisto abundance and counts file


title: B 2 N E4

description: Kallisto abundance and counts file


title: C 3 1 E5-8a

description: Kallisto abundance and counts file


title: D 3 2 E4b

description: Kallisto abundance and counts file


title: cLP_mph_ko

description:
matrix.mtx
barcodes.tsv
genes.tsv

value: mononuclear phagocytes FACs-isolated from the inflamed lamina propria

value: CD45.2+ve, GFP+ve, CD11b+ve, CD3-ve, CD19-ve, CD138-ve, NK1.1-ve, Ly6G-ve and Siglec F-ve


title: B 4 2 E16a

description: Kallisto abundance and counts file


title: D 2 1 E4a

description: Kallisto abundance and counts file


title: B 3 1 E4

description: Kallisto abundance and counts file


title: B 2 N E8

description: Kallisto abundance and counts file


title: A 2 1 E2

description: Kallisto abundance and counts file


title: A 1 1 E2b

description: Kallisto abundance and counts file


title: A 1 N E2b

description: Kallisto abundance and counts file


title: C 1 N E2b

description: Kallisto abundance and counts file


title: D 2 1 E4b

description: Kallisto abundance and counts file


title: B 3 1 E8

description: Kallisto abundance and counts file


title: B 4 2 E16b

description: Kallisto abundance and counts file


title: A 4 2 E16a

description: Kallisto abundance and counts file


title: C 1 N E2c

description: Kallisto abundance and counts file


title: D 4 1 E8

description: Kallisto abundance and counts file


title: C 2 N E5-8a

description: Kallisto abundance and counts file


title: D 2 2 E4a

description: Kallisto abundance and counts file


title: B 4 2 E16c

description: Kallisto abundance and counts file


title: D 3 2 E4a

description: Kallisto abundance and counts file


title: C 3 1 E5-8b

description: Kallisto abundance and counts file


title: B 3 2 E8-16a

description: Kallisto abundance and counts file


title: C 2 N E5-8c

description: Kallisto abundance and counts file


title: B 2 1 E4a

description: Kallisto abundance and counts file


title: B 1 N E2a

description: Kallisto abundance and counts file


title: A 3 N E8

description: Kallisto abundance and counts file


title: A 1 2 E2a

description: Kallisto abundance and counts file


title: C 2 N E5-8d

description: Kallisto abundance and counts file


title: D 2 2 E4b

description: Kallisto abundance and counts file


title: D 1 N E2a

description: Kallisto abundance and counts file


title: C 3 1 E8

description: Kallisto abundance and counts file


title: C 1 1 E2a

description: Kallisto abundance and counts file


title: C 2 2 E4b

description: Kallisto abundance and counts file


title: C 2 2 E3

description: Kallisto abundance and counts file


title: B 1 N E2b

description: Kallisto abundance and counts file


title: C 2 2 E4c

description: Kallisto abundance and counts file


title: A 3 N E16

description: Kallisto abundance and counts file


title: D 4 1 E5-8

description: Kallisto abundance and counts file


title: C 2 1 E2a

description: Kallisto abundance and counts file


title: C 4 N E16a

description: Kallisto abundance and counts file


title: B 2 1 E4b

description: Kallisto abundance and counts file


title: D 4 2 E5-8

description: Kallisto abundance and counts file


title: D 3 N E8

description: Kallisto abundance and counts file


title: B 4 N E16

description: Kallisto abundance and counts file


title: B 2 2 E4a

description: Kallisto abundance and counts file


title: A 3 1 E4

description: Kallisto abundance and counts file


title: B 1 1 E2c

description: Kallisto abundance and counts file


title: C 3 2 E4

description: Kallisto abundance and counts file


title: C 2 1 E2b

description: Kallisto abundance and counts file


title: C 1 2 E2a

description: Kallisto abundance and counts file


title: C 4 N E16b

description: Kallisto abundance and counts file


title: A 1 2 E2b

description: Kallisto abundance and counts file


title: B 3 2 E8-16b

description: Kallisto abundance and counts file


title: C 2 N E5-8b

description: Kallisto abundance and counts file


title: D 4 2 E8-16 replicate

description: Kallisto abundance and counts file


title: D 3 N M

description: Kallisto abundance and counts file

value: M


title: B 2 2 E4b

description: Kallisto abundance and counts file


title: A 3 2 E8

description: Kallisto abundance and counts file


title: D 1 1 E2b

description: Kallisto abundance and counts file


title: C 1 1 E2b

description: Kallisto abundance and counts file


title: A 2 N E4b

description: Kallisto abundance and counts file


title: B 1 2 E2a

description: Kallisto abundance and counts file


title: C 4 N B

description: Kallisto abundance and counts file

value: B


title: D 3 1 E4a

description: Kallisto abundance and counts file


title: D 1 1 E2

description: Kallisto abundance and counts file


title: C 3 2 E5-8a

description: Kallisto abundance and counts file


title: C 2 1 E4b

description: Kallisto abundance and counts file


title: D 1 2 E2a

description: Kallisto abundance and counts file


title: B 4 1 E8b

description: Kallisto abundance and counts file


title: A 2 N E4a

description: Kallisto abundance and counts file


title: A 2 1 E3

description: Kallisto abundance and counts file


title: A 4 N E16

description: Kallisto abundance and counts file


title: C 3 2 E5-8b

description: Kallisto abundance and counts file


title: C 4 1 E5-8

description: Kallisto abundance and counts file


title: B 1 2 E2b

description: Kallisto abundance and counts file


title: C 3 N E8

description: Kallisto abundance and counts file


title: B 4 1 E8a

description: Kallisto abundance and counts file


title: D 4 N E8-16

description: Kallisto abundance and counts file


title: B 3 N E8-16a

description: Kallisto abundance and counts file


title: D 2 N E4a

description: Kallisto abundance and counts file


title: D 3 1 E4b

description: Kallisto abundance and counts file


title: B 3 N E8-16b

description: Kallisto abundance and counts file


title: D 4 2 E8-16

description: Kallisto abundance and counts file


title: C 1 2 E2b

description: Kallisto abundance and counts file


title: C 1 2 E2c

description: Kallisto abundance and counts file


title: B 1 2 E2c

description: Kallisto abundance and counts file


title: B 4 1 E8c

description: Kallisto abundance and counts file


title: CCL4-09-KO

description:
SLX-12919_raw_counts.tsv
SLX-12919.D710_D503

data_processing:
Reads are mapped using TopHat V2.0.11 to the mouse GRCm38 genome
Gene-level counts where generated using htseq-count with Ensembl Transcript GTF V74
Genome_build: GRCm38
Supplementary_files_format_and_content: raw counts

extract_protocol:
Total RNA was isolated using STAT-60 (AMS biotechnology, CS-111)/chloroform (200 uL; Sigma, Cat 650471)/isopropanol (500 uL; Sigma, cat 33539)/75% ethanol (1ml) according to previously published protocol (PMID: 26679101).  Samples were stored in aliquot at – 80 °C prior to use. All reagents, plastic ware, and supplies used were sterile, nuclease free, and of molecular biology grade. RNA purity (A260/A280>1.80) and concentration were determined using nanodrop spectrophotometer (Thermo Fisher scientific, Delaware USA). RNA integrity was studied using the 2100 Bioanalyzer System (Agilent) and RNA 6000 Nano Kit. A RNA Integrity Number (RIN) of 8 was considered the lowest cut-off for RNA Sequencing.
Sequencing library were constructed using Illumina mRNA library prep kit

treatment_protocol: Liver tissues were snap-frozen and stored at -80*C until RNA extraction

value: Bmp8b Knockout

tag: Sex

value: Male

tag: diet

value: CCl4 - 2ul/g body weight CCl4:olive oil [1:1 (v/v)] mix

tag: time point

value: 3 days after IP


title: CCL4-07-WT

description:
SLX-12919_raw_counts.tsv
SLX-12919.D708_D503

value: Wild Type


title: CCL4-27-WT

description:
SLX-12919_raw_counts.tsv
SLX-12919.D712_D504

value: Control - Olive Oil IP Injection (2ul/g body weight)


title: A 2 2 E3

description: Kallisto abundance and counts file


title: CCL4-26-WT

description:
SLX-12919_raw_counts.tsv
SLX-12919.D711_D504


title: A 4 N B

description: Kallisto abundance and counts file


title: CCL4-08-KO

description:
SLX-12919_raw_counts.tsv
SLX-12919.D709_D503


title: CCL4-22-KO

description:
SLX-12919_raw_counts.tsv
SLX-12919.D709_D504


title: CCL4-35-KO

description:
SLX-12919_raw_counts.tsv
SLX-12919.D707_D505


title: CCL4-04-WT

description:
SLX-12919_raw_counts.tsv
SLX-12919.D706_D503


title: CCL4-30-WT

description:
SLX-12919_raw_counts.tsv
SLX-12919.D703_D505


title: CCL4-34-WT

description:
SLX-12919_raw_counts.tsv
SLX-12919.D706_D505


title: CCL4-02-KO

description:
SLX-12919_raw_counts.tsv
SLX-12919.D705_D503


title: WD35-KO

description:
SLX-13089_raw_counts.tsv
SLX-13089.D710_D502

value: Western Diet (Teklad, TD88137)

value: 32 weeks of diet


title: CCL4-05-WT

description:
SLX-12919_raw_counts.tsv
SLX-12919.D707_D503


title: WD34-WT

description:
SLX-13089_raw_counts.tsv
SLX-13089.D709_D502


title: CCL4-28-WT

description:
SLX-12919_raw_counts.tsv
SLX-12919.D701_D505


title: WD36-WT

description:
SLX-13089_raw_counts.tsv
SLX-13089.D711_D502


title: WD27-WT

description:
SLX-13089_raw_counts.tsv
SLX-13089.D706_D502

value: Low Fat Control Diet (Teklad, TD08485)


title: CCL4-29-WT

description:
SLX-12919_raw_counts.tsv
SLX-12919.D702_D505


title: CCL4-12-KO

description:
SLX-12919_raw_counts.tsv
SLX-12919.D712_D503


title: CCL4-24-WT

description:
SLX-12919_raw_counts.tsv
SLX-12919.D710_D504


title: WD25-WT

description:
SLX-13089_raw_counts.tsv
SLX-13089.D704_D502


title: WD32-WT

description:
SLX-13089_raw_counts.tsv
SLX-13089.D707_D502


title: WD23-WT

description:
SLX-13089_raw_counts.tsv
SLX-13089.D703_D502


title: WD20-WT

description:
SLX-13089_raw_counts.tsv
SLX-13089.D701_D502


title: WD21-WT

description:
SLX-13089_raw_counts.tsv
SLX-13089.D702_D502


title: WD19-WT

description:
SLX-13089_raw_counts.tsv
SLX-13089.D712_D501


title: WD18-WT

description:
SLX-13089_raw_counts.tsv
SLX-13089.D711_D501


title: WD15-KO

description:
SLX-13089_raw_counts.tsv
SLX-13089.D709_D501


title: WD12-WT

description:
SLX-13089_raw_counts.tsv
SLX-13089.D707_D501


title: WD14-WT

description:
SLX-13089_raw_counts.tsv
SLX-13089.D708_D501


title: WD06-KO

description:
SLX-13089_raw_counts.tsv
SLX-13089.D705_D501


title: WD07-WT

description:
SLX-13089_raw_counts.tsv
SLX-13089.D706_D501


title: WD02-KO

description:
SLX-13089_raw_counts.tsv
SLX-13089.D702_D501


title: WD04-KO

description:
SLX-13089_raw_counts.tsv
SLX-13089.D703_D501


title: WD05-WT

description:
SLX-13089_raw_counts.tsv
SLX-13089.D704_D501


title: WD01-KO

description:
SLX-13089_raw_counts.tsv
SLX-13089.D701_D501


title: WD33-KO

description:
SLX-13089_raw_counts.tsv
SLX-13089.D708_D502


title: WD26-WT

description:
SLX-13089_raw_counts.tsv
SLX-13089.D705_D502


title: SK145

city: Stanford

first: Seung

last: Kim

address: 279 Campus Dr B303

department: Developmental Biology

institute: Stanford University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to reference transcriptome using Salmon v0.11.3 with parameters salmon quant -i $salmon_index -l A \-1 $Input1 \-2 $Input2 \ p 8 -o quants/${Input1}_quant \ --gcBias –seqBias
Transcripts Per Million (TPM) were calculated using Salmon algorithm from Patro et al., Nat Methods, 2017.
Genome_build: Sus Scrofa reference transcriptome (Sscrofa 11.1, version 96)
Supplementary_files_format_and_content: "normalizedCounts_TPM" include TPM values for each Sample.

organism: Sus scrofa

source_name: pancreatic alpha cell

extract_protocol:
Cells were removed from pacreatic tissue, and RNA was harvested using RecoverAll Total Nucleic Acid Isolation kit. Takara SMARTer Stranded Total RNA-Seq Kit v2 (Cat# 634413) was used with total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using SMARTer Stranded Total RNA-Seq Kit protocol. Libraries were multiplexed and sequenced on NextSeq to generate 75bp PE reads.

tag: age

value: post natal day 8

value: pancreas

value: alpha cell


title: SK159

value: embryonic day 70


title: SK179

value: embryonic day 90


title: SK053


title: SK174

value: post natal day 22


title: SK164


title: SK058


title: SK184


title: SK141


title: SK169


title: SK113


title: SK112

source_name: pancreatic beta cell

value: beta cell


title: SK220

value: embryonic day 40


title: WD17-WT

description:
SLX-13089_raw_counts.tsv
SLX-13089.D710_D501


title: SK223


title: SK226


title: SK140


title: SK107


title: SK183


title: SK167


title: SK178


title: SK144


title: SK162


title: SK228


title: SK057


title: SK158


title: SK052


title: SK222


title: SK225


title: SK021


title: SK124


title: SK288

source_name: pancreatic delta cell

value: delta cell


title: SK279


title: SK275


title: SK283


title: SK219


title: SK317


title: SK030