title: OXA Replicate 3 - CITE-Seq

city: San Francisco

first: Jeffrey

middle: B

last: Cheng

state: CALIFORNIA

address: 1701 Divisadero St, 4th floor

department: Dermatology

institute: UCSF

description:
10X Genomics single-cell 3' RNA_seq (V3)
OXA3-barcodes.tsv.gz
OXA3-features.tsv.gz
OXA3-matrix.mtx.gz

data_processing:
Library strategy: CITE-seq
FASTQ files were initially processed using Cellranger version 3.1.0 to perform sample de-multiplexing, barcode processing, single-cell gene UMI-counting, and feature barcode (CITE-Seq) read-matching.
Seurat package (version 3.1.2) in R (version 3.6.1) were used for further quality control. Cells were filtered to include only cells displaying > 300 genes/cell and < 4000 genes/cell, and no more than 20% mitochondrial gene expression.
Genome_build: IMQ/IMQ-C transcripts were mapped to the mm10 reference genome while OXA/OXA-C transcripts were mapped to the mm10 + GRCh38 reference genome (as OXA/OXA-C samples contained spike-in human cells to assess for CITE-seq background staining levels).
Supplementary_files_format_and_content: filtered matrix files with 2 tsv files and 1 mtx file

source_name: Cutaneous immune cells

extract_protocol:
Mouse ears were minced and incubated in digestion media A (5 ml of RPMI 1640 supplemented with 10% FBS, 100uL of a 12.5 mg/ml stock of Liberase TL (Sigma 5401020001), and 50uL 0.1mg/ml of DNAse I (Sigma 10104159001)) for IMQ/IMQ-C samples or digestion buffer B (RPMI 1640 supplemented with 10% FBS, collagenase XI (2 mg/mL; Sigma c9407), and DNAse I (0.1 mg/mL; Sigma 10104159001) for OXA/OXA-C samples at 37 °C for 90 minutes with 200–250 rpm agitation. Cells were dispersed using a tissue dissociator (GentleMACS; Miltenyi Biotec – running program C) for 44s. Single cell suspensions were passed through 40-100 μm filters and washed with  FACS buffer (PBS with 2% FBS).
per 10x Single Cell 3’ Reagent Kit v2  and v3 manufacturer’s protocol ( v2 for sample IMQ-C and IMQ, v3 for sample OXA-C and OXA) and TotalSeq-A Antibodies Protocol with 10x Single Cell 3' Reagent Kit v2 (Biolegend) for OXA-C and OXA CITE-seq libraries

treatment_protocol:
For IMQ-induced skin inflammation, three mice received a daily topical thin coat of commercially available IMQ cream (5%) (Taro pharmaceuticals) on both ears for 7 consecutive days. Control mice were treated similarly with vehicle cream (Vanicream Moisturizing Skin Cream, Pharmaceutical Specialties, Inc.). Mouse ear skin samples were collected 24h after the last application.
For Oxazolone (OXA; Sigma-aldrich)-induced skin inflammation, OXA and control treated mice were sensitized by applying two 50uL treatments of 3% OXA in ethyl alcohol (EtOH) on shaved dorsal skin 24h apart. Nine days after sensitization, OXA treated mice were challenged with 10ul of 0.5% OXA in EtOH to the dorsal and ventral pinnae of both ears (40uL total per mouse) every other day for 3 challenges, while control mice were treated with 100% EtOH. Mouse ear skin samples were collected 24 hours following the final challenge.

value: Ear

value: Cutaneous immune cells

value: Wildtype

tag: mouse age

value: 10 weeks

tag: Sex

value: Male

value: OXA


title: OXA Replicate 2 - CITE-Seq

status: Public on Sep 26 2020

type: SRA

country: USA

description:
10X Genomics single-cell 3' RNA_seq (V3)
OXA2-barcodes.tsv.gz
OXA2-features.tsv.gz
OXA2-matrix.mtx.gz

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain

tag: tissue

tag: cell type

tag: genotype

tag: treatment


title: H460 2D

type: RNA

city: Jacksonville

first: Derek

middle: Charles

last: Radisky

state: Florida

address: 4500 San Pablo Road

department: Cancer Biology

institute: Mayo Clinic

description: Gene expression data

hyb_protocol: cRNA was hybridized onto chips for 18 h at 45 degrees C.  GeneChips were washed in the Affymetrix Fluidics Station 450 using the EukGE-WS2v4_450 wash protocol.

scan_protocol: Chips were scanned in an Affymetrix 3000 (7G) Confocal Scanner.

data_processing: The data were analyzed with Genespring GX 7.3.1 using Affymetrix default analysis settings and normalized to day1 control

label: biotin

organism: Homo sapiens

source_name: untreated H460 cells

label_protocol: This project used the Affymetrix Human Genome U133 Plus 2.0 GeneChip 200 ng of total RNA was used as input

growth_protocol: lung cancer cell lines were grown either on tissue culture plastic (2D) or in 3D culture on a thin layer of Matrigel covered with 2 % Matrigel dissolved in media (‘on top’ method).

extract_protocol: Phenol/cholorofom

treatment_protocol: grown on 2D or 3D

value: lung cancer cell

tag: cell line

tag: protocol

value: culture plastic (2D)


title: Omomyc 3hours, biological rep2

city: Nedlands

first: Pilar

last: Blancafort

state: WA

address: 6 Verdun Street

department: Cancer and Cell Biology

country: Australia

institute: Harry Perkins Institute of Medical Research

description: Expressing luciferase gene

data_processing:
Image analysis and base-calling was perfromed by the HiSeq Control Software (HCS) v2.2.68 and Real Time Analysis (RTA) v1.18.66.3. Sequence data are generated by bcl2fastq 2.17.1.14 pipeline.
Sequence data were aligned to the mm9(NCBIv37) genome build using STAR (v2.1.3)
Expression at the gene level (FPKM values) was estimated and normalized by Cufflinks (v2.2.1), Cuffmerge (v1.0.0) and Cuffnorm (v2.2.1).
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include average RPKM values for each replicate sample

growth_protocol: 150,000 cells were seeded in a p6-well plate in complete media (RPMI supplemented in 1% FBS and 1% antibiotic/antimicotic). Cells were allowed to grow for three days

extract_protocol:
Total RNA was extracted following the manufacturer´s kit, RNeasy Mini Kit from Qiagen. An additional step of genomic DNA elimination was included before the RNA elution using the RNase-Free DNase set (Qiagen). Eluted RNA samples were assayed with an absorbance at 260/280 nm between 1.8 and 2.0 and were subjected to a strict quality control at the Australian Genomic Research Facility (AGRF) in Perth before proceeding to library preparation and RNA Sequencing at the AGRF in Melbourne. All submitted samples had RNA integrity number (RIN) of 10.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with PBS, Omomyc, FPP-1746 and FPP-1746-Omomyc at 5µM for 3 and 6 hours.

tag: genotype/variation

value: Omomyc for 3 hours


title: FPP-1746-Omomyc 3hours, biological rep1

description: Expressing luciferase gene

value: FPP-1746-Omomyc for 3 hours


city: South San Francisco

first: Luz

middle: D

last: Orozco

state: CA

address: 1 DNA Way

department: Bioinformatics

institute: Genentech Inc.

description: SAM24331852 Female NSP4 KO GMP 3 Bone Marrow SAM24331852 NSP4 KO GMP 3 R3722 1,2,3,4,5,6,7,8 LIB339355 POOL8637 NXG422899 CGCTCATT D703 GGCTCTGA D504 NSP4.KO GMP 1.36842603544757

data_processing: Reads were aligned to the GRCm38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were from our internal database and available in the manuscript supplementary material. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supplementary files use Ensembl IDs, counts and nRPKM statistics.

source_name: bone marrow

extract_protocol: Cells were centrifuged at 2,600 rcf for 7 minutes (neurons) or 6,600 rcf for 7 minutes (other cell types) and the supernatant was discarded. RNA was extracted from the cell pellet using Qiagen RNeasy Plus Micro kit in a final volume of 25 μl. We typically obtained 200-300 ng RNA from neurons, 10-20 ng from microglia, and 2-5 ng from astrocytes. RNA quality was quantified using the Bioanalyzer.

tag: gender

value: Female

value: NSP4 KO GMP 3

value: Bone Marrow

value: SAM24331852 NSP4 KO GMP 3

value: CGCTCATT

value: GGCTCTGA

value: GMP


title: A427 3D

description: Gene expression data

source_name: A427 cells on Matrigel

value: matrigel (3D)


title: PBS 3hours, biological rep1

description: Expressing luciferase gene

value: PBS for 3 hrs


description: SAM24333388 Male NSP4 KO BMMC-P3 5 Bone Marrow SAM24333388 NSP4 KO BMMC-P3 5 R3812 1,2,3,4,5,6,7,8 LIB384448 POOL8816 NXG471557 TCCGGAGA D702 GGCTCTGA D504 NSP4.KO BMMC.P3 0.664107332824059

value: NSP4 KO BMMC-P3 5

value: SAM24333388 NSP4 KO BMMC-P3 5

value: TCCGGAGA


title: OXA-C Replicate 3 - CITE-Seq

description:
10X Genomics single-cell 3' RNA_seq (V3)
OXA-C3-barcodes.tsv.gz
OXA-C3-features.tsv.gz
OXA-C3-matrix.mtx.gz

value: Ear

value: Cutaneous immune cells

value: Wildtype

value: 10 weeks

value: Male

value: OXA-C


title: OXA Replicate 1 - CITE-Seq

description:
10X Genomics single-cell 3' RNA_seq (V3)
OXA1-barcodes.tsv.gz
OXA1-features.tsv.gz
OXA1-matrix.mtx.gz

value: OXA


title: H358 2D

description: Gene expression data

source_name: untreated H358 cells

value: lung cancer cell

value: culture plastic (2D)


description: SAM24333380 Male WT BMMC-P3 2 Bone Marrow SAM24333380 WT BMMC-P3 2 R3812 1,2,3,4,5,6,7,8 LIB384440 POOL8816 NXG471527 ATTACTCG D701 GGCTCTGA D504 WT BMMC.P3 0.54889935597658

value: WT BMMC-P3 2

value: Bone Marrow

value: ATTACTCG

value: WT


title: OXA-C Replicate 2 - CITE-Seq

description:
10X Genomics single-cell 3' RNA_seq (V3)
OXA-C2-barcodes.tsv.gz
OXA-C2-features.tsv.gz
OXA-C2-matrix.mtx.gz


description: SAM24331850 Female NSP4 KO GMP 1 Bone Marrow SAM24331850 NSP4 KO GMP 1 R3722 1,2,3,4,5,6,7,8 LIB339353 POOL8637 NXG422891 CGCTCATT D703 ATAGAGGC D502 NSP4.KO GMP 1.66727413309988

value: Female

value: NSP4 KO GMP 1

value: SAM24331850 NSP4 KO GMP 1

value: CGCTCATT

value: ATAGAGGC

value: GMP


title: H23 2D

description: Gene expression data

source_name: untreated H23 cells


title: OXA-C Replicate 1 - CITE-Seq

description:
10X Genomics single-cell 3' RNA_seq (V3)
OXA-C1-barcodes.tsv.gz
OXA-C1-features.tsv.gz
OXA-C1-matrix.mtx.gz

value: Ear

value: Cutaneous immune cells

value: Wildtype


description: SAM24331853 Female NSP4 KO GMP 4 Bone Marrow SAM24331853 NSP4 KO GMP 4 R3722 1,2,3,4,5,6,7,8 LIB339356 POOL8637 NXG422881 CGCTCATT D703 AGGCGAAG D505 NSP4.KO GMP 1.06620690964384

value: NSP4 KO GMP 4

value: SAM24331853 NSP4 KO GMP 4

value: AGGCGAAG


description: SAM24331848 Female NSP4 KO CMP 3 Bone Marrow SAM24331848 NSP4 KO CMP 3 R3722 1,2,3,4,5,6,7,8 LIB339351 POOL8637 NXG422886 TCCGGAGA D702 GTACTGAC D508 NSP4.KO CMP 1.80945164319909

value: NSP4 KO CMP 3

value: SAM24331848 NSP4 KO CMP 3

value: TCCGGAGA

value: GTACTGAC

value: CMP


title: OXA Replicate 3 - RNA-Seq

data_processing:
FASTQ files were initially processed using Cellranger version 3.1.0 to perform sample de-multiplexing, barcode processing, single-cell gene UMI-counting, and feature barcode (CITE-Seq) read-matching.
Seurat package (version 3.1.2) in R (version 3.6.1) were used for further quality control. Cells were filtered to include only cells displaying > 300 genes/cell and < 4000 genes/cell, and no more than 20% mitochondrial gene expression.
Genome_build: IMQ/IMQ-C transcripts were mapped to the mm10 reference genome while OXA/OXA-C transcripts were mapped to the mm10 + GRCh38 reference genome (as OXA/OXA-C samples contained spike-in human cells to assess for CITE-seq background staining levels).
Supplementary_files_format_and_content: filtered matrix files with 2 tsv files and 1 mtx file

value: 10 weeks

value: Male

value: OXA


title: OXA Replicate 2 - RNA-Seq


title: shHOIP_miRNA sequence

city: Shanghai

first: Jianxiu

last: Yu

address: Room 202, Building 7, 280 South Chongqing Road

department: Department of Biochemistry and Molecular Cell Biology

country: China

institute: Shanghai Jiao Tong University school of medicine

data_processing:
The raw data of RIP-Seq and RNA-Seq were trimmed by Cutadapt (version 1.9.3, https://cutadapt.readthedocs.io/en/stable/# ) and separately aligned to the human reference genome (UCSC hg19) by bowtie2 software (version 2.2.4, http://bowtie-bio.sourceforge.net/bowtie2/index.shtml ) and by hisat2 software (version 2.0.4, https://daehwankimlab.github.io/hisat2/ ) with default parameters, respectively.
The target binding regions of AGO2 were identified using MACS2 software (version 1.4.3), fold enrichment of each mRNA transcript matched to different MACS identified motifs were summed.
RNA-Seq high quality clean reads were guided by the Ensembl gtf gene annotation file, and measured by cuffdiff software (part of cufflinks) to get the gene level FPKM as the expression profiles of mRNA.
For miRNA-Seq, raw data were trimmed by cutadapt software (version 1.9.2) and then aligned to the merged human pre-miRNA databases (miRBase) using Novoalign software (version 3.02.12) with at most one mismatch.
The numbers of mature miRNA mapped tags were defined as the raw expression levels of that miRNA, the read counts were normalized by TPM approach. miRNA targets were performed by popular miRNA target prediction by using TargetMiner.
Genome_build: hg19 for RIP-Seq and RNA-Seq, miRBase for miRNA-Seq

source_name: HeLa cells

extract_protocol:
HeLa-Flag-AGO2 cells expressing HOIP/HOIL-1L and  HeLa cells knocking down HOIP were performed RIP-Seq separatly with anti-Flag and anti-AGO2 antibody, RNA-Seq and miRNA-Seq were also conducted in these two group stable cell lines.
RNA and miRNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HeLa cells expressing Flag-AGO2 were separately treated with normoxia (21% O2) and hypoxia (1% O2) for 24 h for following miRNA-Seq, RNA-Seq and RIP-Seq with anti-Flag antibody.

tag: cell lines

value: HeLa-shHOIP


title: pLKO.1_miRNA sequence


title: Control_miRNA sequence


title: HOIP+HOIL-1L_miRNA sequence


description: SAM24331846 Female NSP4 KO CMP 1 Bone Marrow SAM24331846 NSP4 KO CMP 1 R3722 1,2,3,4,5,6,7,8 LIB339349 POOL8637 NXG422887 TCCGGAGA D702 TAATCTTA D506 NSP4.KO CMP 1.80511305663137

value: Female

value: NSP4 KO CMP 1

value: Bone Marrow

value: SAM24331846 NSP4 KO CMP 1

value: TAATCTTA


title: hypoxia_miRNA sequence

value: Hypoxia (1% O2) 24h


title: normal_miRNA sequence

value: Normoxia (21% O2) 24h


title: OXA-C Replicate 3 - RNA-Seq

value: Ear

value: Cutaneous immune cells

value: Wildtype

value: OXA-C


title: OXA Replicate 1 - RNA-Seq


title: Control_RNA sequence

molecule: polyA RNA


title: A549 2D

description: Gene expression data

source_name: untreated A549 cells

value: lung cancer cell

value: culture plastic (2D)


title: OXA-C Replicate 2 - RNA-Seq

value: 10 weeks


title: SAM24331844 Female WT GMP 3 Bone Marrow

description: SAM24331844 Female WT GMP 3 Bone Marrow SAM24331844 WT GMP 3 R3722 1,2,3,4,5,6,7,8 LIB339347 POOL8637 NXG422895 TCCGGAGA D702 GGCTCTGA D504 WT GMP 1.40009732812703

value: WT GMP 3

value: TCCGGAGA

value: GGCTCTGA

value: WT

value: GMP


description: SAM24333379 Male WT BMMC-P3 1 Bone Marrow SAM24333379 WT BMMC-P3 1 R3812 1,2,3,4,5,6,7,8 LIB384439 POOL8816 NXG471547 ATTACTCG D701 CCTATCCT D503 WT BMMC.P3 0.581640958619756

value: Male

value: WT BMMC-P3 1

value: Bone Marrow

value: ATTACTCG

value: CCTATCCT


description: SAM24333387 Male NSP4 KO BMMC-P3 4 Bone Marrow SAM24333387 NSP4 KO BMMC-P3 4 R3812 1,2,3,4,5,6,7,8 LIB384447 POOL8816 NXG471525 TCCGGAGA D702 CCTATCCT D503 NSP4.KO BMMC.P3 0.774221716610769

value: NSP4 KO BMMC-P3 4

value: SAM24333387 NSP4 KO BMMC-P3 4


title: SAM24331840 Female WT CMP 3 Bone Marrow

description: SAM24331840 Female WT CMP 3 Bone Marrow SAM24331840 WT CMP 3 R3722 1,2,3,4,5,6,7,8 LIB339343 POOL8637 NXG422883 ATTACTCG D701 GTACTGAC D508 WT CMP 1.75011158926766

value: Female

value: WT CMP 3

value: GTACTGAC

value: CMP


title: A427 2D

description: Gene expression data

source_name: untreated A427 cells

value: lung cancer cell

value: culture plastic (2D)


title: IMQ Replicate 3 - RNA-Seq

description: 10X Genomics single-cell 3' RNA_seq (V2)

value: Ear

value: Cutaneous immune cells

value: Wildtype

value: 9 weeks

value: IMQ


description: SAM24333383 Male WT BMMC-P3 5 Bone Marrow SAM24333383 WT BMMC-P3 5 R3812 1,2,3,4,5,6,7,8 LIB384443 POOL8816 NXG471524 ATTACTCG D701 CAGGACGT D507 WT BMMC.P3 0.651627546201336

value: Male

value: WT BMMC-P3 5

value: CAGGACGT

value: WT


title: OXA-C Replicate 1 - RNA-Seq

value: 10 weeks

value: OXA-C


description: SAM24331849 Female NSP4 KO CMP 4 Bone Marrow SAM24331849 NSP4 KO CMP 4 R3722 1,2,3,4,5,6,7,8 LIB339352 POOL8637 NXG422893 CGCTCATT D703 TATAGCCT D501 NSP4.KO CMP 1.12425593905436

value: Female

value: NSP4 KO CMP 4

value: Bone Marrow

value: SAM24331849 NSP4 KO CMP 4

value: CGCTCATT

value: TATAGCCT


title: HOIP+HOIL-1L_RNA sequence


title: IMQ Replicate 2 - RNA-Seq

value: Ear


title: SAM24331839 Female WT CMP 2 Bone Marrow

description: SAM24331839 Female WT CMP 2 Bone Marrow SAM24331839 WT CMP 2 R3722 1,2,3,4,5,6,7,8 LIB339342 POOL8637 NXG422896 ATTACTCG D701 CAGGACGT D507 WT CMP 1.42061724694851

value: WT CMP 2

value: ATTACTCG

value: CMP


title: shHOIP-RIP_sequence

value: HeLa-shHOIP

tag: rip antibody


title: hypoxia_RNA sequence

value: Hypoxia (1% O2) 24h


title: normal_RNA sequence

value: Normoxia (21% O2) 24h


title: pLKO.1-RIP_sequence


title: IMQ-C Replicate 3 - RNA-Seq

value: Cutaneous immune cells

value: Wildtype

value: 9 weeks

value: Male

value: IMQ-C


title: IMQ Replicate 1 - RNA-Seq

value: IMQ


title: IMQ-C Replicate 2 - RNA-Seq


description: SAM24333384 Male NSP4 KO BMMC-P3 1 Bone Marrow SAM24333384 NSP4 KO BMMC-P3 1 R3812 1,2,3,4,5,6,7,8 LIB384444 POOL8816 NXG471536 ATTACTCG D701 GTACTGAC D508 NSP4.KO BMMC.P3 0.574617701059384

value: NSP4 KO BMMC-P3 1

value: Bone Marrow

value: SAM24333384 NSP4 KO BMMC-P3 1

value: GTACTGAC


title: shHOIP-Input_sequence


title: SAM24331841 Female WT CMP 4 Bone Marrow

description: SAM24331841 Female WT CMP 4 Bone Marrow SAM24331841 WT CMP 4 R3722 1,2,3,4,5,6,7,8 LIB339344 POOL8637 NXG422894 TCCGGAGA D702 TATAGCCT D501 WT CMP 1.12634246836935

value: Female

value: WT CMP 4

value: TCCGGAGA

value: TATAGCCT

value: WT


title: pLKO.1-Input_sequence


title: SAM24331838 Female WT CMP 1 Bone Marrow

description: SAM24331838 Female WT CMP 1 Bone Marrow SAM24331838 WT CMP 1 R3722 1,2,3,4,5,6,7,8 LIB339341 POOL8637 NXG422897 ATTACTCG D701 TAATCTTA D506 WT CMP 1.28819320942504

value: WT CMP 1

value: ATTACTCG

value: TAATCTTA

value: CMP


title: IMQ-C Replicate 1 - RNA-Seq

value: Ear

value: Cutaneous immune cells

value: Wildtype

value: 9 weeks


description: SAM24333386 Male NSP4 KO BMMC-P3 3 Bone Marrow SAM24333386 NSP4 KO BMMC-P3 3 R3812 1,2,3,4,5,6,7,8 LIB384446 POOL8816 NXG471568 TCCGGAGA D702 ATAGAGGC D502 NSP4.KO BMMC.P3 0.4728388030207

value: Male

value: NSP4 KO BMMC-P3 3

value: SAM24333386 NSP4 KO BMMC-P3 3

value: ATAGAGGC


title: Control-Input_sequence


description: SAM24333385 Male NSP4 KO BMMC-P3 2 Bone Marrow SAM24333385 NSP4 KO BMMC-P3 2 R3812 1,2,3,4,5,6,7,8 LIB384445 POOL8816 NXG471564 TCCGGAGA D702 TATAGCCT D501 NSP4.KO BMMC.P3 0.584563275359653

value: NSP4 KO BMMC-P3 2

value: Bone Marrow

value: SAM24333385 NSP4 KO BMMC-P3 2


description: SAM24333382 Male WT BMMC-P3 4 Bone Marrow SAM24333382 WT BMMC-P3 4 R3812 1,2,3,4,5,6,7,8 LIB384442 POOL8816 NXG471558 ATTACTCG D701 TAATCTTA D506 WT BMMC.P3 0.613742412776719

value: WT BMMC-P3 4


title: DRG-CPIP+EA rep3

city: Hangzhou

first: Chengyu

last: Yin

state: Zhejiang

address: 548 Binwen Road, Binjiang District, Hangzhou

department: The Third Clinical Medical College

institute: Zhejiang Chinese Medical University

description: EA_3 FPKM

data_processing:
The fragments were enriched by PCR amplification to construct a library ready for sequencing using BGISEQ-500 by BGI Group (Shenzhen, China).
Primary sequencing data produced by RNA-Seq (raw reads) were subjected to quality control (QC).
Raw reads were filtered into clean reads by internal software SOAPnuke (version 1.5.2), followed by: Remove reads in which unknown bases (N) are more than 10%; Remove reads with adaptors; Remove low quality reads (we define the low quality read as the percentage of base which quality is less than 15 and greater than 50% in a read).
QC of alignment was performed to determine if re-sequencing was needed. If the alignment result passed QC, downstream analysis including gene expression, differentially expressed genes, cluster analysis, Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, etc. was proceeded with
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Rattus norvegicus

source_name: Dorsal root ganglia

growth_protocol: Rats were randomly allocated, and 5 rats were housed per cage(12 hour light–dark cycles and 24 ± 2 ℃). Food and water were provided ad libitum.

extract_protocol:
At day 10, rats were deeply anesthetized with sodium pentobarbital (40 mg/kg) and were perfused transcardially with 200 mL 0.9% saline (4°C). After the perfusion, the right (ipsilateral) side L4-6 DRG segments were collected and were immediately preserved in the RNA later solution (Invitrogen, Carlsbad, USA). Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, USA) following the manufacturer’s instructions and treated with DNase I to degrade contaminating DNA. The purity and concentration of the samples was assessed by the Nanodrop Spectrophotometer (NanoDrop Products, CA, USA), and the RNA integrity was assessed by the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: EA treatment was conducted once daily for 10 consecutive days

value: Sprague Dawley

value: L4-6 DRG

value: CPIP+EA


title: Control-RIP_sequence

value: anti-Flag


description: SAM24331851 Female NSP4 KO GMP 2 Bone Marrow SAM24331851 NSP4 KO GMP 2 R3722 1,2,3,4,5,6,7,8 LIB339354 POOL8637 NXG422885 CGCTCATT D703 CCTATCCT D503 NSP4.KO GMP 1.45932581371255

value: Female

value: NSP4 KO GMP 2

value: SAM24331851 NSP4 KO GMP 2

value: CGCTCATT

value: CCTATCCT

value: GMP


title: DRG-CPIP+EA rep2

description: EA_2 FPKM


title: DRG-CPIP+EA rep1

description: EA_1 FPKM


title: SAM24331842 Female WT GMP 1 Bone Marrow

description: SAM24331842 Female WT GMP 1 Bone Marrow SAM24331842 WT GMP 1 R3722 1,2,3,4,5,6,7,8 LIB339345 POOL8637 NXG422889 TCCGGAGA D702 ATAGAGGC D502 WT GMP 1.30110654297563

value: WT GMP 1

value: TCCGGAGA

value: WT


title: normal-Input_sequence

value: Normoxia (21% O2) 24h


description: SAM24333381 Male WT BMMC-P3 3 Bone Marrow SAM24333381 WT BMMC-P3 3 R3812 1,2,3,4,5,6,7,8 LIB384441 POOL8816 NXG471522 ATTACTCG D701 AGGCGAAG D505 WT BMMC.P3 0.688391261182039

value: Male

value: WT BMMC-P3 3

value: Bone Marrow

value: ATTACTCG

value: AGGCGAAG


title: SAM24331845 Female WT GMP 4 Bone Marrow

description: SAM24331845 Female WT GMP 4 Bone Marrow SAM24331845 WT GMP 4 R3722 1,2,3,4,5,6,7,8 LIB339348 POOL8637 NXG422884 TCCGGAGA D702 AGGCGAAG D505 WT GMP 1.48152054508634

value: WT GMP 4


title: DRG-CPIP rep3

description: model_3 FPKM

value: Sprague Dawley

value: L4-6 DRG

value: CPIP


title: normal-RIP_sequence

value: anti-Flag


title: DRG-CPIP rep2

description: model_2 FPKM


title: OSK+tTA_VCS_recover rep6

type: genomic

city: Cambridge

first: Yuancheng Ryan

last: Lu

state: MA

address: 455 Main St

institute: Whitehead Institute for Biomedical Research

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

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

data_processing: Data were generated via the standard protocol of Illumina methylation assays, which quantifies methylation levels by the β value using the ratio of intensities between methylated and un-methylated alleles. Specifically, the β value was calculated from the intensity of the methylated (M corresponding to signal A) and un-methylated (U corresponding to signal B) alleles, as the ratio of fluorescent signals β = Max(M,0)/(Max(M,0)+ Max(U,0)+100). Thus, β values ranged from 0 (completely un-methylated) to 1 (completely methylated). Noob normalization was implemented using the minfi R package. The mathematical algorithm and available software underlying the skin & blood clock for in vitro studies (based on 391 CpGs) was previously published (Horvath, 2018, Aging).

label: cy3, cy5

molecule: genomic DNA

label_protocol: Standard Illumina Protocol

growth_protocol: SH-SY5Y neuroblastoma cells were obtained from the American Tissue Culture Collection (ATCC, CRL-2266) and maintained according to ATCC recommendations. Cells were cultured in a 1:1 mixture of Eagle’s Minimum Essential Medium (EMEM, ATCC, 30-2003) and F12 medium (ThermoFisher Scientific, 11765054) supplemented with 10% fetal bovine serum (FBS, Sigma, F0926) and 1X penicillin/streptomycin (ThermoFisher Scientific, 15140122). Cells were cultured at 37°C with 5% CO2 and 3% O2. Cells were passaged at ~80% confluency. SH-SY5Y cells were differentiated into neurons: Briefly, 1 day after plating, cell differentiation was induced for 3 days using EMEM/F12 medium (1:1) containing 2.5% FBS, 1× penicillin/streptomycin, and 10 µM all-trans retinoic acid (ATRA, Stemcell Technologies, 72264) (Differentiation Medium 1), followed by a 3 day incubation in EMEM/F12 (1:1) containing 1% FBS, 1 × penicillin/streptomycin, and 10 µM ATRA (Differentiation Medium 2). Cells were then split into 35 mm cell culture plates coated with poly-D-lysine (ThermoFisher Scientific, A3890401). A day after splitting, neurons were matured in serum-free neurobasal/B27 plus culture medium (ThermoFisher Scientific, A3653401) containing 1 × Glutamax (ThermoFisher Scientific, 35050061), 1 × penicillin/streptomycin, and 50 ng/ml BDNF (Alomone labs) (Differentiation Medium 3) for at least 5 days.

extract_protocol: DNA was extracted using the Zymo Quick DNA mini-prep plus kit (D4069) and DNA methylation levels were measured on Illumina 850 EPIC arrays.

treatment_protocol: Differentiated SH-SY5Y cells were transduced with AAV.DJ vectors at 106 genome copies/cell. Five days after transduction, vincristine (100 nM; Sigma, V8879) was added for 24 hrs to induce neurite degeneration. Neurons were then washed once with PBS and fresh Differentiation Medium 3 (see above) was added back to the plates.

value: Differentiated neurons from SH-SY5Y

tag: osk

value: yes

tag: status/time point

value: 9d post vincristine damage


title: OSK+tTA_VCS rep3

value: 1d vincristine damage


title: OSK+tTA_VCS_recover rep5


title: tTA_VCS_recover rep5

value: no


title: DRG-CPIP rep1

description: model_1 FPKM


title: hypoxia-Input_sequence

value: Hypoxia (1% O2) 24h


title: Mock treated sample, unstimulated B cell, biol rep 2

city: Espoo

first: Sini

last: Rautio

address: Konemiehentie 2

country: Finland

institute: Aalto University

description: Mock treated sample, unstimulated B cell, biological replicate 2

library_source: genomic

data_processing:
Library strategy: DREAM-Seq
Sequence reads were mapped with Bowtie2  (version 2.2.9) to the mm9 genome together with spike-in RNAs and synthetic R-loops. Only uniquely mapped reads were considered for further analysis. Duplicated reads were removed using Picard tool (version 1.77) and rRNA reads using split_bam.py script in RSeQC package (version 2.6.4).
We next applied DREAM-seq at a genome-wide level to primary mouse B cells, left unstimulated or stimulated with LPS and IL-4 to induce class switch recombination. We developed a computational analysis pipeline that consists of three main steps: 1) normalization of DREAM-seq data between RNaseH-treated and mock-treated samples for each biological replicate using the spike-ins, 2) identification of genomic regions with a strong DREAM-seq signal in mock-treated samples, relative to a genome-wide base (noise) level in the same mock-treated samples, that are reproducible across biological replicates, and 3) quantification of statistically significant decrease in normalized RNaseH-treated samples relative to mock-treated samples for the regions detected in step 2) (see Online Methods).
bigWig files were created by homer
Genome_build: mm9
Supplementary_files_format_and_content: bigWigs file contain normalized count per million values for reverse and forward strands separately.

source_name: Unstimulated B cell

growth_protocol: Splenic B cells were isolated with EasySep Mouse B cell isolation kit (Stem Cell Technology).

extract_protocol:
10^6 cells were washed twice with PBS1X, and incubated with 380uL of HLB buffer to strip the cytoplasmic membrane. Cells were incubated for 10 minutes with occasional flicking, then briefly vortexed, and spun at 1000G/4C/3 minutes. Nuclei were then washed three times with 1mL of HLB buffer, with spinning at 300G/4C/3 minutes. 4mL of TE low EDTA were added and 12.5uL of Proteinase K (20mG/mL). Then, 104uL of SDS 20% were added and the tubes were flipped a few times to allow homogenization. An overnight digestion at 37C allowed a complete lysis of the nuclei and subsequent release of genomic DNA. The next day, a Phenol-Chloroform extraction was performed with phase-lock tubes (5-prime). DNA was dried for 5 minutes at room temperature, resuspended in Tris-HCl 10mM pH8.0, and set to a concentration of 111.11nG/uL. Aliquots were flash-frozen in liquid nitrogen, and stored at -80C. 2.2uL of turbo DNA free buffer 10x were added to 2uG of nucleic acids in 18uL of Tris-HCl 10mM pH8.0. The reaction was spiked with 20pG of spike-in controls in 0.5uL (pool of 3ssRNAs and 1 DNA:RNA hybrid). The reaction was further divided in two x 10uL: tube “-“, and tube “+”. In tube -, DNA was incubated with 0.5uL of H2O, and in tube + with 0.5uL of RNaseH (2u/uL, ThermoFisher), at 37C. After 45 minutes, another 0.5uL of H2O or RNase H were added, and a second incubation of 45 minutes at 37C was performed. 11.25uL of Turbo DNA free buffer 1x containing 1.25uL of DNase mix were added, followed by an incubation at 37C for 45 minutes. Another 1.25uL of DNase Mix was added and the mixture incubated at 37C for 45 minutes. In order to inactivate the DNase, 0.2 volume of inactivation reagent was added and incubated for 5 minutes at room temperature, with occasional vortexings. The mixture was spun at maximum speed for 2 minutes at room temperature, and the supernatant was harvested, and heated at 65C for 10 minutes, then placed on ice. Finally, RNA was purified using RNA clean and concentrator (Zymo), eluted in 2x8uL of H2O, and used for subsequent sequencing experiment.
RNAs were speedvac’d to have a total of 9uL, then 1 uL of fragmentation buffer (ThermoFisher) was added, and the mixture incubated at 70C for 2.30’. Next, 1uL of stop solution + 40uL of TT buffer were quickly added and RNA fragments were purified with RNA clean and concentrator (Zymo), and eluted in 2x6uL of H2O. RNA was quantified with Qubit 2.0 (ThermoFisher) and solution was speedvac’d to a total of 5uL. Approximatively 30nG were used for library, using the TruSeq Stranded mRNA Sample Preparation kit from Illumina, starting with incubation of RFP on page 20 (catalog #15031047, RevE), and following the manufacturer’s instructions, with the exception of the amplification step. For PCR amplification, KAPA HiFi Hotstart real-time kit was used (Kapa Biosystems). Briefly, 20uL of purified dsDNA was incubated with 5uL of PCR primer cocktail (ref 15031748, Illumina), and 25uL of 2x Master Mix from KAPA HiFi (Kapa Biosystems). Standards were also added. DNA was amplified following these conditions: 98C/45 seconds, (98C/15 seconds, 60C/30 seconds, 72C/40 seconds) x real-time. A final amplification of 72C for 2 minutes was performed, and library was purified using AMPure XP beads from Agencourt. DNA was eluted in a LoBind tube (Eppendorf) in 15uL of Tris-HCl 10mM pH8.0, and 0.05% tween was added. Library was quantified using Qubit 2.0 (ThermoFisher) and fragment sizes by Bioanalyzer (Agilent). Library was sequenced on a HiSeq instrument (Illumina).

treatment_protocol: To induce IgG1 class switch recombination, B cells were stimulated with 25 ug/mL LPS (Sigma) and 10 ng/mL rmIL-4 (Peprotech) in RPMI1640 (ThermoFisher) supplemented with 10% FBS for 72 hours.

tag: stimulation status

value: unstimulated

value: Mock

value: B cells


title: tTA_VCS rep3


title: HOIP+HOIL-1L-Input_sequence


title: DRG-Con rep3

description: control_3 FPKM

value: Con


title: hypoxia-RIP_sequence


title: tTA_VCS_recover rep6


title: DRG-Con rep2

description: control_2 FPKM


title: RnaseH treated sample, unstimulated B cell, biol rep 2

description: RnaseH treated sample, unstimulated B cell, biological replicate 2

value: RnaseH


title: DRG-Con rep1

description: control_1 FPKM


title: Mock treated sample, unstimulated B cell, biol rep 1

description: Mock treated sample, unstimulated B cell, biological replicate 1


title: RnaseH treated sample, activated B cell, biol rep 3

description: RnaseH treated sample, activated B cell, biological replicate 3

source_name: Stimulated B cell

value: activated


title: PfCDP-KO_S3

city: Chennai

first: Arumugam

last: Rajavelu

state: Tamil Nadu

address: Adayar

country: India

institute: IITM

data_processing:
FastQ  files  were  generated  based  on  the  unique  dual  barcode  sequences
The sequencing quality was assessed using the FastQC software ver. 0.11.9. The adaptor sequences and low quality bases (phred quality cutoff set at 30) were trimmed from the reads using the Trim Galore tool ver. 0.6.5. The reads that survived quality check were aligned to the Plasmodium falciparum 3D7 isolate genome (ver. 46) using the Hisat2 read alignment tool.
The transcript abundance count data was generated using the HTSeq-count function (ver. 0.12.4). Differential gene expression analysis was performed using the DESeq2 package (ver. 3.11) in R programming environment. Genes were classified as deregulated on the basis of log2fold-change cutoff of +1 (for upregulation) and -1 (for downregulation) and p-value cutoff of 0.05.
The raw counts data estimated by the htseq-counts tool for each of the samples
Genome_build: Plasmodium falciparum 3D7 ver 46

organism: Plasmodium falciparum

source_name: Cells

extract_protocol:
The parasites were released from infected RBCs 0.15% saponin lysis and RNA was isolated from the control and PfΔCDP P. falciparum with Trizol solution followed by Qiagen RNA isolation kit. The quality of the RNA was analyzed on formaldehyde-denatured gel and the RNA stored at − 80 °C.
The libraries were prepared for sequencing using standard Illumina protocols

value: PfCDP KO


title: OSK+tTA_VCS_recover rep4


title: Control - Superficial temporal artery tissue2 [Q18033001N]

city: Fuzhou

first: Yi

last: Sun

address: Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Minhou County, Fuzhou, 350122, China

institute: Fujian Medical University

data_processing:
Basecalls performed using  Solexa pipeline v1.8
The trimmed reads (trimmed 5’,3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.0.5)software
The transcript abundances for each sample was estimated with StringTie（1.3.1c）
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.6.0)
The circRNA reads were aligned to reference genome using STAR(2.5.2b)detecting backesplicec junction reads with CIRCexplore2 (2.2.6)
Genome_build: hg19
Supplementary_files_format_and_content: FPKM

source_name: Control - Superficial temporal artery

extract_protocol:
RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis
Total RNA of each sample was used to prepare the RNA sequencing library 1)RNA fragment；2)Random primed first strand cDNA synthesis；3)dUTP based second strand cDNA synthesis;4)Adaptor ligation and PCR amplification.

tag: subject status

value: healthy control

value: Female

value: Arterial vessel


title: Whole body except venom gland 3

city: Goyang-si

first: Jungsuk

last: Sung

state: Gyeonggi-do

address: 32, Dongguk-ro, Ilsandong-gu

country: South Korea

institute: Life science

data_processing:
Paired end sequencing reads of cDNA libraries (101bp) generated from a NovaSeq6000 instrument were verified its sequence quality with FastQC v 0.10.0. For data preprocessing, low quality bases and adapter sequences in reads were trimmed using Trimmomatic v 0.32.
Trimmed reads were assembled using Trinity (strand specific option : --SS_lib_type RF). The Trinity program was utilized for de novo transcriptome assembly, combining read sequences of a certain length of overlap to form longer fragments without N gaps, called unigenes. These unigenes were further processed for read alignment and abundance estimation with Bowtie and RSEM.
The expression level of each unigenes was calculated using the Fragments Per kilo base of exon per Million mapped fragments (FPKM) method, which was able to exclude sequencing discrepancies in the calculation of gene expression and the influence of different gene lengths.
Genome_build: In order to build a reference for Callobius koreanus RNA-seq analysis, sequencing reads from this study were merged and assembled by Trinity.
Supplementary_files_format_and_content: Fasta files include assembled gene, unigenes, and predicted open read frame by trinity and transdecoder software.
Supplementary_files_format_and_content: TXT file include raw gene counts, TPM and FPKM values for every gene and every sample

organism: Callobius koreanus

source_name: whole body except venom gland

growth_protocol: The spider Callobius Koreanus was collected from Chungbuk, Korea. The venom glands of the spider were separated from the chelicerae and stored after washing in phosphate buffered saline.

extract_protocol:
TRIzol reagent (Life Technologies, Grand Island, NY, USA) was used for extracting total RNA and subsequent RNA sequencing using NGS method was followed (Theragen Etex Bio institute, Suwon, Korea). The sequencing was performed in triplicates for both venom gland and body, producing 6 data pools.
The sequencing library is prepared by random fragmentation of the DNA or cDNA sample, followed by 5' and 3' adapter ligation. Alternatively, "tagmentation" combines the fragmentation and ligation reactions into a single step that greatly increases the efficiency of the library preparation process. Adapter-ligated fragments are then PCR amplified and gel purified.

value: whole body except venom gland


title: PfCDP-KO_S2


title: HOIP+HOIL-1L-RIP_sequence

value: anti-Flag


title: Whole body except venom gland 2


title: OSK+tTA_VCS_recover rep3

value: Differentiated neurons from SH-SY5Y

value: yes


title: Mock treated sample, activated B cell, biol rep 3

description: Mock treated sample, activated B cell, biological replicate 3


title: RnaseH treated sample, activated B cell, biol rep 2

description: RnaseH treated sample, activated B cell, biological replicate 2


title: Control- Superficial temporal artery tissue1 [Q18022401N]

value: Male


title: OSK+tTA rep3

source_name: OSK+tTA

value: no vincristine damage


title: tTA_VCS rep2

value: no

value: 1d vincristine damage


title: Intracranial aneurysm - Intracranial aneurysm wall tissue4 [Q18030701AL]

value: patient with intracranial aneurysm


title: PfCDP-KO_S1


title: Whole body except venom gland 1


title: tTA_VCS_recover rep4

value: 9d post vincristine damage


title: Pf_Control_S3

value: Wild type


title: tTA_VCS_recover rep3


title: OSK+tTA_VCS_recover rep2


title: RnaseH treated sample, activated B cell, biol rep 1

description: RnaseH treated sample, activated B cell, biological replicate 1

value: RnaseH

value: B cells


title: RnaseH treated sample, unstimulated B cell, biol rep 1

description: RnaseH treated sample, unstimulated B cell, biological replicate 1

value: unstimulated


title: OSK+tTA rep2


title: Venom gland 1

source_name: venom gland

value: venom gland


title: OSK+tTA_VCS_recover rep1


title: tTA rep3

source_name: tTA


title: Intracranial aneurysm - Intracranial aneurysm wall tissue3 [Q18012201AL]

value: Female


title: Intracranial aneurysm - Intracranial aneurysm wall tissue1 [Q18022401AL]

value: Arterial vessel


title: Pf_Control_S2


title: Venom gland 2


title: Pf_Control_S1


title: Mock treated sample, activated B cell, biol rep 1

description: Mock treated sample, activated B cell, biological replicate 1

value: activated

value: Mock


title: Venom gland 3


title: OSK+tTA_VCS rep2

value: Differentiated neurons from SH-SY5Y


title: OSK+tTA_VCS rep1

value: yes


title: Control - Superficial temporal artery tissue4 [Q18012201N]

value: healthy control


title: D93-CTRL

status: Public on Sep 25 2020

city: Paris

first: Marc

last: Delord

address: Hopital Saint-Louis, 1 avenue Claude Vellefaux

department: Recherche clinique

country: France

institute: Centre hospitalier de Versailles

hyb_protocol: Each sample was hybridized onto Human Clariom D (ThermoFisher Scientific), washed, and stained with the Affymetrix® Fluidics Station 450.

scan_protocol: Array Scanning was performed with the Affymetrix® GeneChip Scanner 3000 7G using the Command Console software (ThermoFisher Scientific)

data_processing: Data summarized and normalized using the RMA routine as implemented in the oligo R library

label: Biotin

source_name: Hematopoietic Stem Cells

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix manual target preparation for expression array.

growth_protocol: CD34+ cells were further selected using Miltenyi Magnetically Activated Cell Sorting (MACS) columns (Miltenyi Biotech, Paris, France) according to the manufacturer’s instructions. CD34+ cells were then either put in culture or frozen at -80°C In IMDM medium (Gibco) supplemented with 10% Fetal bovine serum (FBS, REF) and 10% DMSO.

extract_protocol: RNA quantification and quality control was performed using the HT RNA Pico sensitivity LabChip Kit and the Caliper LabChip Microfluidics System (Perkin Elmer). Three nanogrammes of Total RNA was amplified, labeled, and fragmented using GeneChip WT Pico (ThermoFisher Scientific).

treatment_protocol: Cells were plated at a density of 40 000 cells/cm2 in 96-wells plates. Cells were cultured at 37◦C in a 5% CO2 humidified atmosphere using IMDM culture medium supplemented with antibiotics (Anti-anti, Sigma), 10% FBS, human IL-3 1ug/mL (Peprotech), SCF 10ug/mL (Peprotech) and G-CSF 10ug/mL (Peprotech). For figure 3,4 and 5, in addition to control non-treated cells, cells were treated either with Taxol (100nM), Blebbistatin (50µM), Nocodazole and Blebbistatin (2 and 50µM respectively), or Ciliobrevin (100µM).

tag: donor

value: CTRL

tag: cell subtype

value: CD34+ cells


title: D93-CILIO

value: CILIO


title: D92-TX

value: TX


title: OSK+tTA rep1

value: no vincristine damage


title: tTA_VCS_recover rep2

value: no

value: 9d post vincristine damage


title: tTA_VCS rep1

value: 1d vincristine damage


title: D92-CTRL


title: tTA_VCS_recover rep1


title: D19-CILIO


title: D19-CTRL


title: Intracranial aneurysm - Intracranial aneurysm wall tissue2 [Q18033001AL]

value: patient with intracranial aneurysm


title: Control - Superficial temporal artery tissue3 [Q18030701N]


title: Oropharyngeal tissue, Cancer, 31C

city: Shillong

first: Srimoyee

last: Ghosh

state: Meghalaya

address: Umshing-Mawkynroh

department: Zoology

institute: North Eastern Hill University

description: cancer oropharyngeal tissue sample

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

scan_protocol: The processed chips were scanned using an iScan reader (Illumina) and raw data were obtained in intensity Data Files (*.idat) format.

data_processing: The raw data were quality checked using the methylation module (v1.8.5) of GenomeStudio software v2010.3 (Illumina).

label: Cy5 and Cy3

source_name: Oropharyngeal tissue 43

extract_protocol: DNA sample was bisulfite converted using  EZ DNA methylation kit (Zymo Research) following the manufacturers protocol

tag: sample id

value: M

tag: sample type

value: Oropharyngeal tissue

tag: disease state

value: Cancer


title: Oropharyngeal tissue, Cancer, 32C

description: cancer oropharyngeal tissue sample

source_name: Oropharyngeal tissue 44


title: D92-CILIO


title: Oropharyngeal tissue, Cancer, 24C

description: cancer oropharyngeal tissue sample

source_name: Oropharyngeal tissue 35


title: D19-TX


title: Oropharyngeal tissue, Cancer, 22C

description: cancer oropharyngeal tissue sample

source_name: Oropharyngeal tissue 32


title: Mock treated sample, activated B cell, biol rep 2

description: Mock treated sample, activated B cell, biological replicate 2

value: activated

tag: cell type

value: B cells


title: Oropharyngeal tissue, Cancer, 28C

description: cancer oropharyngeal tissue sample

source_name: Oropharyngeal tissue 40


title: Oropharyngeal tissue, Normal, 21N

description: normal oropharyngeal tissue sample

source_name: Oropharyngeal tissue 29

value: Normal


title: Oropharyngeal tissue, Cancer, 30C

description: cancer oropharyngeal tissue sample

source_name: Oropharyngeal tissue 42

value: F


title: tTA rep1

value: Differentiated neurons from SH-SY5Y


title: Oropharyngeal tissue, Normal, 27N

description: normal oropharyngeal tissue sample

source_name: Oropharyngeal tissue 38


title: Oropharyngeal tissue, Normal, 22N

description: normal oropharyngeal tissue sample

source_name: Oropharyngeal tissue 31


title: Oropharyngeal tissue, Cancer, 27C

description: cancer oropharyngeal tissue sample

source_name: Oropharyngeal tissue 39


title: Oropharyngeal tissue, Cancer, 29C

description: cancer oropharyngeal tissue sample

source_name: Oropharyngeal tissue 41


title: Oropharyngeal tissue, Cancer, 21C

description: cancer oropharyngeal tissue sample

source_name: Oropharyngeal tissue 30


title: Oropharyngeal tissue, Normal, 23N

description: normal oropharyngeal tissue sample

source_name: Oropharyngeal tissue 33


title: Oropharyngeal tissue, Normal, 20N_R

description: normal oropharyngeal tissue sample

source_name: Oropharyngeal tissue 27


title: Oropharyngeal tissue, Cancer, 26C

description: cancer oropharyngeal tissue sample

source_name: Oropharyngeal tissue 37


title: Oropharyngeal tissue, Cancer, 23C

description: cancer oropharyngeal tissue sample

source_name: Oropharyngeal tissue 34


title: Oropharyngeal tissue, Cancer, 20C_R

description: cancer oropharyngeal tissue sample

source_name: Oropharyngeal tissue 28


title: Oropharyngeal tissue, Normal, 20N

description: normal oropharyngeal tissue sample

source_name: Oropharyngeal tissue 25


title: Oropharyngeal tissue, Cancer, 12C

description: cancer oropharyngeal tissue sample

source_name: Oropharyngeal tissue 24


title: D93-TX

source_name: Hematopoietic Stem Cells

tag: treatment


title: Oropharyngeal tissue, Cancer, 25C

description: cancer oropharyngeal tissue sample

source_name: Oropharyngeal tissue 36


title: Oropharyngeal tissue, Cancer, 20C

description: cancer oropharyngeal tissue sample

source_name: Oropharyngeal tissue 26


title: Oropharyngeal tissue, Cancer, 3C

description: cancer oropharyngeal tissue sample

source_name: Oropharyngeal tissue 23


title: Oropharyngeal tissue, Cancer, 19C

description: cancer oropharyngeal tissue sample

source_name: Oropharyngeal tissue 22


title: Oropharyngeal tissue, Normal, 18N

description: normal oropharyngeal tissue sample

source_name: Oropharyngeal tissue 19


title: ACC-9T

city: Copenhagen N

first: Thomas

last: Litman

state: Outside the US or Canada

address: Blegdamsvej 3C

department: ISIM

country: Denmark

institute: University of Copenhagen

hyb_protocol: Hybridization according to Affymetrix protocol.

scan_protocol: GeneArray scanner, according to Affymetrix protocol.

data_processing: RMA normalization method in Expression Console (Affymetrix TM). All intensity values vere log2 transformed before further analysis.

source_name: Adrenocortical carcinoma biopsy

label_protocol: Biotin labeling according to Affymetrix protocol.

extract_protocol: RNA was extracted from 50-100 mg of tumor using the Qiagen miRNeasy Kit.


title: Oropharyngeal tissue, Normal, 19N

description: normal oropharyngeal tissue sample

source_name: Oropharyngeal tissue 21


title: NA19

source_name: Normal adrenal biopsy


title: ACC-8T


title: Oropharyngeal tissue, Cancer, 18C

description: cancer oropharyngeal tissue sample

source_name: Oropharyngeal tissue 20


title: NA1


title: NA4


title: NA2


title: ACC-7T


title: Oropharyngeal tissue, Cancer, 9C

description: cancer oropharyngeal tissue sample

source_name: Oropharyngeal tissue 10


title: Oropharyngeal tissue, Cancer, 13C

description: cancer oropharyngeal tissue sample

source_name: Oropharyngeal tissue 12


title: Oropharyngeal tissue, Cancer, 17C

description: cancer oropharyngeal tissue sample

source_name: Oropharyngeal tissue 18


title: tTA rep2

source_name: tTA


title: Oropharyngeal tissue, Cancer, 14C

description: cancer oropharyngeal tissue sample

source_name: Oropharyngeal tissue 14


title: ACC-51T


title: Oropharyngeal tissue, Cancer, 8C

description: cancer oropharyngeal tissue sample

source_name: Oropharyngeal tissue 8


title: Oropharyngeal tissue, Normal, 16N

description: normal oropharyngeal tissue sample

source_name: Oropharyngeal tissue 15


title: ACC-4T4


title: Oropharyngeal tissue, Normal, 13N

description: normal oropharyngeal tissue sample

source_name: Oropharyngeal tissue 11


title: ACC-4T5


title: ACC-6T


title: Oropharyngeal tissue, Cancer, 16C

description: cancer oropharyngeal tissue sample

source_name: Oropharyngeal tissue 16


title: ACC-5T


title: ACC-50T


title: ACC-4T3


title: ACC-4T6


title: Oropharyngeal tissue, Normal, 6N

description: normal oropharyngeal tissue sample

source_name: Oropharyngeal tissue 5


title: ACC-4T2


title: Oropharyngeal tissue, Normal, 4N

description: normal oropharyngeal tissue sample

source_name: Oropharyngeal tissue 3


title: Oropharyngeal tissue, Normal, 9N

description: normal oropharyngeal tissue sample

source_name: Oropharyngeal tissue 9


title: ACC-52T


title: Oropharyngeal tissue, Cancer, 4C

description: cancer oropharyngeal tissue sample

source_name: Oropharyngeal tissue 4


title: Oropharyngeal tissue, Normal, 8N

description: normal oropharyngeal tissue sample

source_name: Oropharyngeal tissue 7


title: Oropharyngeal tissue, Cancer, 2C

description: cancer oropharyngeal tissue sample

source_name: Oropharyngeal tissue 2


title: Oropharyngeal tissue, Normal, 2N

description: normal oropharyngeal tissue sample

source_name: Oropharyngeal tissue 1


title: ACC-49T

source_name: Adrenocortical carcinoma biopsy


title: Oropharyngeal tissue, Normal, 17N

description: normal oropharyngeal tissue sample

source_name: Oropharyngeal tissue 17


title: ACC-47T


title: ACC-4T1


title: ACC-48T


title: Oropharyngeal tissue, Normal, 14N

description: normal oropharyngeal tissue sample

source_name: Oropharyngeal tissue 13


title: ACC-3T2


title: ACC-46T


title: ACC-35T1


title: ACC-36T


title: ACC-35T2


title: ACC-45T


title: ACC-42T


title: ACC-38T


title: ACC-34T


title: ACC-30T2


title: ACC-41T


title: ACC-3T1


title: NA18

source_name: Normal adrenal biopsy


title: ACC-32T


title: ACC-33T1


title: ACC-31T


title: ACC-29T2


title: ACC-2T


title: ACC-53T


title: ACC-21T


title: ACC-22T2


title: ACC-22T1


title: ACC-20T


title: ACC-1T


title: ACC-30T1


title: ACC-33T2


title: ACC-24T


title: ACC-29T1


title: ACC-19T


title: Oropharyngeal tissue, Cancer, 6C

description: cancer oropharyngeal tissue sample

source_name: Oropharyngeal tissue 6


title: ACC-23T


title: RNASeq of planctonic culture of Pseudomonas aeruginosa UCBPP-PA14 2

city: Braunschweig

first: Matthias

last: Preusse

address: Inhoffenstr. 7

country: Germany

institute: Helmholtz Centre for Infection Research

description:
PA14_wt_2
Wt_2
Processed data file: rpg_table_PA14_planctonic.csv

data_processing:
Mus musculus:
Reads were mapped using tophat2 version 2.1.0 (configurations: --no-novel-juncs --library-type fr-secondstrand. Attention, data from spermidine experiment are unstranded: fr-unstranded)
Files were converted into bam format using samtools version 1.9.
Reads per gene for RAW267.7 cells were extracted using the R package Rsubreads version 1.34.7.
Pseudomonas aeruginosa UCBPP-PA14:
Reads were mapped using bowtie2 version 2.2.6 (--no-1mm-upfront).
Files were converted into bam format using samtools version 1.9.
Reads per gene from Pseudomonas aeruginosa UCBPP-PA14 were extracted bedtools v2.29.0.
Supplementary_files_format_and_content: Semicolon separated csv file including reads per gene. Row names: gene Ids; column names: Treatment/bacterial strain (S/C: Spermidine/control; Wt: PA14 wild type, C: delta fliC, M: delta motABCD, K: delta flgK, U: uninfected).

organism: Pseudomonas aeruginosa UCBPP-PA14

growth_protocol:
DualSeq experiment: Bacteria: Bacterial subcultures were grown to mid-log phase (3.5 h) in liquid LB and the infection dose was adjusted to 5*10^5 bacteria (MOI 1). RAW264.7: Cells were cultured in DMEM Medium at 37°C , 5% CO2 and 75% Humidity. One day before infection, cells were isolated, counted and split into 24-well plates at a concentration of 2.5*10^5 cells per well.
Spermidine experiment: Cells were maintained as during the Dual-Seq Experiment.

extract_protocol:
DualSeq experiment: Medium was discarded. Cells were scratched off and resuspend in RNAprotect. RNA extraction was done as previously described (Kordes et al., 2018).
Spermidine experiment: Medium was discarded. Cells were scratched off and resuspend in RNA buffer. RNA extraction was done as previously described (Kordes et al., 2018).
DualSeq experiment: NEBNext Ultra II Directional RNA Library Prep.
Spermidine experiment: NEBNext® Single Cell/Low Input RNA Kit.

treatment_protocol:
DualSeq experiment: The bacterial concentration was adjusted to MOI 1 (5*10^5 per 100 µl) and 100 µl were used for the infection. The bacteria were centrifuged on top of the cells using 1200 rpm for 5 min. The infection was performed for 3 h at 37°C, 5% CO2 and 75% humidity.
Spermidine experiment: Cells were treated for 1 h with 10 µM spermidine at 37°C, 5% CO2 and 75% humidity. Triplicates were pooled to obtain one biological replicate.

tag: p. aeruginosa genotype

value: PA14 wt

tag: growth condition

value: Bacterial mid-log phase culture (4 h) in LB


title: RNASeq of planctonic culture of Pseudomonas aeruginosa UCBPP-PA14 delta motAB delta motCD 2

description:
PA14_dmotABCD_2
K_2
Processed data file: rpg_table_PA14_planctonic.csv

value: PA14 delta motABCD


title: RNASeq of planctonic culture of Pseudomonas aeruginosa UCBPP-PA14 1

description:
PA14_wt_1
Wt_1
Processed data file: rpg_table_PA14_planctonic.csv


title: RNASeq of planctonic culture of Pseudomonas aeruginosa UCBPP-PA14 delta fliC 1

description:
PA14_dfliC_1
C_1
Processed data file: rpg_table_PA14_planctonic.csv

value: PA14 delta fliC


title: RNASeq of planctonic culture of Pseudomonas aeruginosa UCBPP-PA14 delta flgK 2

description:
PA14_dflgK_2
M_2
Processed data file: rpg_table_PA14_planctonic.csv

value: PA14 delta flgK


title: RNASeq of planctonic culture of Pseudomonas aeruginosa UCBPP-PA14 delta fliC 2

description:
PA14_dfliC_2
C_2
Processed data file: rpg_table_PA14_planctonic.csv


title: RNASeq of planctonic culture of Pseudomonas aeruginosa UCBPP-PA14 delta flgK 1

description:
PA14_dflgK_1
M_1
Processed data file: rpg_table_PA14_planctonic.csv


title: RNASeq of RAW264.7 cells infected with Pseudomonas aeruginosa UCBPP-PA14 1

description:
RAW_PA14_wt_1
PA1
DualSeq
Processed data file: rpg_table_DualSeq_mm10.csv
Processed data file: rpg_table_DualSeq_PA14.csv

organism:
Mus musculus
Pseudomonas aeruginosa UCBPP-PA14

tag: mouse cell line

tag: infection

value: Infection dose:5*10^5 bacteria (MOI 1), Infection time:3 h

tag: spike-in

value: ERCC


title: RNASeq of RAW264.7 cells infected with Pseudomonas aeruginosa UCBPP-PA14 2

description:
RAW_PA14_wt_2
PA2
DualSeq
Processed data file: rpg_table_DualSeq_mm10.csv
Processed data file: rpg_table_DualSeq_PA14.csv


title: Cell line H295R

source_name: Adrenocortical tumor cell line

tag: gender

value: unknown


title: RNASeq of RAW264.7 cells infected with Pseudomonas aeruginosa UCBPP-PA14 delta motAB delta motCD 2

description:
RAW_PA14_dmotABCD_2
M2
DualSeq
Processed data file: rpg_table_DualSeq_mm10.csv
Processed data file: rpg_table_DualSeq_PA14.csv


title: RNASeq of RAW264.7 cells infected with Pseudomonas aeruginosa UCBPP-PA14 delta motAB delta motCD 1

description:
RAW_PA14_dmotABCD_1
M1
DualSeq
Processed data file: rpg_table_DualSeq_mm10.csv
Processed data file: rpg_table_DualSeq_PA14.csv


title: ACC-12T2


title: ACC-12T1


title: ACC-17T


title: ACC-13T1


title: ACC-12T4


title: ACC-14T


title: RNASeq of RAW264.7 cells infected with Pseudomonas aeruginosa UCBPP-PA14 delta flgK 2

description:
RAW_PA14_dflgK_2
K2
DualSeq
Processed data file: rpg_table_DualSeq_mm10.csv
Processed data file: rpg_table_DualSeq_PA14.csv


title: ACC-11T


title: ACC-10T


title: ACC-13T2


title: ACC-12T3


title: ACC-16T


title: RNASeq of RAW264.7 cells infected with Pseudomonas aeruginosa UCBPP-PA14 delta flgK 1

description:
RAW_PA14_dflgK_1
K1
DualSeq
Processed data file: rpg_table_DualSeq_mm10.csv
Processed data file: rpg_table_DualSeq_PA14.csv


title: RNASeq of RAW264.7 cells infected with Pseudomonas aeruginosa UCBPP-PA14 delta fliC 2

description:
RAW_PA14_dfliC_2
C2
DualSeq
Processed data file: rpg_table_DualSeq_mm10.csv
Processed data file: rpg_table_DualSeq_PA14.csv


title: RNASeq of RAW264.7 cells infected with Pseudomonas aeruginosa UCBPP-PA14 delta fliC 1

description:
RAW_PA14_dfliC_1
C1
DualSeq
Processed data file: rpg_table_DualSeq_mm10.csv
Processed data file: rpg_table_DualSeq_PA14.csv


title: Glyc_eco rep 2

city: Cuernavaca

first: Veronica

last: Jimenez-Jacinto

state: Morelos

address: Av. Universidad 2001. Col. chamilpa

department: Unidad Universitaria de Secuenciación Masiva y Bioinformática

country: Mexico

institute: Universidad Nacional Autonoma de Mexico

data_processing:
Base-calling with bcl2fastq2-2.15
alignment done with bowtie version 0.12.7
filter and manipulation with samtools 1.3
Frecuency count htseq-count version 0.6.0.
last filter bedtools v2.25.0
Genome_build: E. coli K-12 MG1655  and S. pombe 972 h-
Supplementary_files_format_and_content: raw counts of sequencing reads for the features of interest

organism: Escherichia coli

source_name: cells

growth_protocol: liquid culture were incubated to mid exponential growth

extract_protocol:
Cells were collected in log phase and RNA later added and harvested to 5000g for 5 min. Pellet were frozen on -80°C. RNA was harvested using Trizol reagent and precipitated with isopropyl alcohol, samples were treated with DNAses an concentrate with RNA cleaner kit. RRNA were removed with Ribominus bacteria /yeast kit and  Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: YE medium was used changed carbon source in each treatment : glucose 2% and  Glycerol : sodium acetate (10 :1) 2%(w/v)

tag: strain

tag: carbon source

value: Glycerol :sodium acetate (10 :1) 2%(w/v)

tag: age

value: mid exponential growth culture


title: Glyc_eco rep 1


title: Glyc_eco rep 3


title: Gluc_eco rep 3

value: Glucose 2%  (w/V)


title: Gluc_eco rep 1


title: MDCKII 3D-D3-1 RNA-seq

city: ATHENS

first: Shaying

last: Zhao

state: GA

address: B304B Life Sciences, 120 Green Street

institute: University of Georgia

data_processing:
Read pairs were aligned to the dog reference genome canFam3 with HISAT v2.1.0.
Cufflinks v2.2.1 was used to quantify gene expression in FPKM, guided by canine gene annotation CanFam3.1.84 downloaded from UCSC genome browser
Genome_build: canFam3
Supplementary_files_format_and_content: Tab-delimited files with expression values in FPKM for each sample

organism: Canis lupus familiaris

source_name: MDCKII cells

growth_protocol: MDCKII cells were maintained in Eagle’s minimal essential medium with 5% fetal bovine serum, 10 mM HEPES, 2 mM glutamine, 100 U/ml penicillin, 100 mg/ml streptomycin; For 3D cultures, cells were grown on top of matrigel. For 2D cultures, cells were seeded on transwell inserts grown until over-confluence. The cells for seeding were regarded as day0 samples.

extract_protocol:
Cysts grown for 24h, 3, 5, 8, 14 days, cells for seeding (day 0) and over-confluent cells were collected and RNA was extracted using the AllPrep DNA/RNA Mini Kit (Qiagen)
RNA-seq libraries were constructed using KAPA Stranded mRNA-Seq Kit

tag: cell line

value: MDCKII

tag: genotype

value: wildtype

tag: culturing time

value: day 3


title: MDCKII 2D-D4-1 RNA-seq

value: day 4


title: MDCKII D0-1 RNA-seq

data_processing:
Read pairs were aligned to the dog reference genome canFam3 with HISAT v2.1.0.
Cufflinks v2.2.1 was used to quantif
Read pairs were aligned to the dog reference genome canFam3 with HISAT v2.1.0.
Cufflinks v2.2.1 was used to quantify gene expression in FPKM, guided by canine gene annotation CanFam3.1.84 downloaded from UCSC genome browser
Genome_build: canFam3
Supplementary_files_format_and_content: Tab-delimited files with expression values in FPKM for each sample

extract_protocol:
Cysts grown for 24h, 3, 5, 8, 14 days, cells for seeding (day 0) and over-confluent cells were collected and RNA was extracted using the AllPrep DNA/RNA Mini Kit (Qiagen)
RNA-seq libraries were constructed using KAPA Stranded mRNA-Seq Kit
Cysts grown for 24h, 3, 5, 8, 14 days, cells for seeding (day 0) and over-confluent cells were collected and RNA was extracted using the AllPrep DNA/RNA Mini Kit (Qiagen)
RNA-seq libraries were constructed using KAPA Stranded mRNA-Seq Kit

value: day 0


title: RNASeq of RAW264.7 cells treated for 1 h with 10 µM spermidine 3

description:
RAW_Spermidine_3
S3
Unstranded
Processed data file: rpg_table_mm10_spermidine.csv

value: 10 µM Spermidine, 1 h incubation time


title: MDCKII 3D D14 RNA-seq

value: day 14


title: xrn1_A

city: Solna

first: Vicent

last: Pelechano

address: Nobels väg 16

department: MTC

country: Sweden

institute: ScilifeLab - Karolinska Institutet

data_processing:
Base-calling was performed using Illumina CASAVA pipeline and standard parameters (February 2011).
Filtering and trimming of adapters and low quality bases from reads wit Trimmomatic: 1) standard Illumina adapter removal and then removal of the barcodes at the 5’ end of reads (7 first bases), 2) removal of the P7 adapter in 3’ end after the polyA tail, 3) trimming of bases in 3’ that fall below a certain quality threshold (minumim quality).
Removal of polyA tails and downstream sequences with PRINSEQ and the options: min_gc 20, trim_right 16, min_len 20, trim_tail_right 5 out_format 3.
Mapping to the reference genome with Bowtie2, with default parameters.
Genome_build: Saccharomyces cerevisiae R64-1-1
Supplementary_files_format_and_content: Reads were collapsed to the last 3´nucleotide in bedGraph

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: Yeast cells were grown to mid-log phase (OD1) using either YPAD (1% yeast extract, 2% peptone, 1% glucose) or YPGal (1% yeast extract, 2% peptone, 1% galactose).

extract_protocol:
Total RNA was isolated by a standard hot phenol method and contaminant DNA was removed by DNase I treatment (as in PMID: 23295673).
Starting from total RNA, poly(A) RNA is reverse transcribed using a biotinylated adapter containing an anchored oligo-dT primer. After second strand synthesis, fragments are captured by streptavidin beads, end-repaired, adenylated, and ligated to a second adapter.  The library was prepared using  oligos that allows the sequencing into the poly(A) tail (from the body of the cDNA) (Internal protocol in  PMID: 23295673). Stringent library size selection (200bp was performed).

treatment_protocol: 2 independent biological replicates

tag: parental strain


title: xrn1_B


title: RNASeq of planctonic culture of Pseudomonas aeruginosa UCBPP-PA14 delta motAB delta motCD 1

description:
PA14_dmotABCD_1
K_1
Processed data file: rpg_table_PA14_planctonic.csv

value: Bacterial mid-log phase culture (4 h) in LB


title: RNASeq of RAW264.7 cells treated for 1 h with 10 µM spermidine 2

description:
RAW_Spermidine_2
S2
Unstranded
Processed data file: rpg_table_mm10_spermidine.csv


title: RNASeq of RAW264.7 cells treated for 1 h with 10 µM spermidine 1

description:
RAW_Spermidine_1
S1
Unstranded
Processed data file: rpg_table_mm10_spermidine.csv


title: RNASeq of untreated RAW264.7 cells (control for Spermidine treated cells) 3

description:
RAW_Control_3
C3
Unstranded
Processed data file: rpg_table_mm10_spermidine.csv

value: PBS treated


title: RNASeq of mock treated RAW264.7 cells 1

description:
RAW_untreated_1
U1
DualSeq
Processed data file: rpg_table_DualSeq_mm10.csv
Processed data file: rpg_table_DualSeq_PA14.csv

source_name: mock treated RAW264.7 cells


title: RNASeq of mock treated RAW264.7 cells 2

description:
RAW_untreated_2
U2
DualSeq
Processed data file: rpg_table_DualSeq_mm10.csv
Processed data file: rpg_table_DualSeq_PA14.csv


title: RNASeq of untreated RAW264.7 cells (control for Spermidine treated cells) 1

description:
RAW_Control_1
C1
Unstranded
Processed data file: rpg_table_mm10_spermidine.csv


title: RNASeq of untreated RAW264.7 cells (control for Spermidine treated cells) 2

description:
RAW_Control_2
C2
Unstranded
Processed data file: rpg_table_mm10_spermidine.csv


title: C20180629_normal cardiomyocyte-derived exosomes

first: Li

last: Zhang

address: Haowen Road no.5

institute: Fulgent Genetics

data_processing:
Illumina Casava1.7 software used for basecalling
Low quality reads are trimmed and filtered. Clean reads reads were aligned to the mm9 genome assembly using bowtie2
miRNA expression Analysis through RNAfold & miRDeep2
Gene expressiong difference analysis through DEGseq
Genome_build: GRCm38
Supplementary_files_format_and_content: TMP and counts values for each sample; DEG miRNA result

source_name: Normal cardiomyocytes

growth_protocol: The hearts of 1- to 2-day-old neonatal Wistar rats were minced and incubated in a solution with the addition of 1 mg/mL collagenase II and 0.12% trypsin at 37 °C. Following 10 min incubation, the first supernatant was discarded. The following supernatants were collected from several cycles of digesting with a mixture of collagenase II and trypsin enzyme until the tissue was homogenized. In each cycle, the fetal calf serum was added to stop homogenization. The dissociated cells were enriched for cardiomyocytes via differential adhesion for 60 min and were plated on a medium supplemented with 0.1 mM 5′-Bromo-2′-Deoxyuridine.

extract_protocol:
Total exosomal RNA was extracted with Trizol.
The Illumina TrueSeq small RNA library prep kit was then used to construct a small RNA library from exosomal RNA obtained. Adapters were directly, and specifically, ligated to the 3′ and 5′ end of the RNA. The ligated RNA molecule was reverse transcribed into single-stranded cDNA for PCR amplification. After that, sequencing was then performed on an Illumina HiSeq 2000 sequencer.

treatment_protocol: The primary neonatal rat cardiomyocytes were treated with or without 1 μmol/L Ang II for 48 h to stimulate hypertrophy.

value: Wistar rats

value: 1- to 2-day-old neonatal

tag: tissue

value: Heart

value: Normal cardiomyocytes

tag: molecule subtype

value: MicroRNA


title: E20180629_hypertrophic cardiomyocyte-derived exosomes

source_name: Hypertrophic cardiomyocytes

tag: cell type

value: Angiotensin II-induced hypertrophic cardiomyocytes


title: Gluc_eco rep 2

value: mid exponential growth culture


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H9_ad012

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: SSs

tag: Sex

value: male


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H9_ad008


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H9_ad007


title: MDCKII 3D-D8-1 RNA-seq

value: MDCKII

value: wildtype

value: day 8


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H9_ad001


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H9_ad002


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H8_ad002


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H8_ad008


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H8_ad006


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H8_ad007


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H7_ad012


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H8_ad012


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H7_ad010


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H7_ad001


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H7_ad006


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H7_ad007


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H9_ad004


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H7_ad002


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H7_ad004


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H7_ad008


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H6_ad007


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H6_ad004


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H6_ad006


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H5_ad012


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H6_ad002


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H5_ad001


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H8_ad004


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H8_ad010


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H6_ad010


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H5_ad006


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H5_ad004


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H5_ad002


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H5_ad010


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H4_ad012


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H5_ad007


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H5_ad008


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H4_ad006


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H4_ad002


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H4_ad010


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H4_ad004


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H4_ad007


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H4_ad008


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H2_ad012


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H2_ad010


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H2_ad006


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H2_ad004


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H2_ad008


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H2_ad002


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H12_ad010


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H12_ad002


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H11_ad012


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H12_ad007


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H11_ad007


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H11_ad004


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H11_ad008


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H12_ad008


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H12_ad004


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H12_ad006


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H10_ad008


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H11_ad002


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H11_ad001


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H10_ad010


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H11_ad006


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H2_ad007


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H10_ad007


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H10_ad004


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H10_ad001


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H10_ad006


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H1_ad012


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H10_ad002


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H4_ad001


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H1_ad007


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H1_ad010


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H1_ad002


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H1_ad004


title: CEMBA181210_5C_3_CEMBA181210_5C_4_H1_ad006


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