title: WT_IL-4+IL13_2_days_1

city: Baltimore

first: Immunometabolism

last: Department

state: Maryland

address: 1650 Orleans Street

department: Immunometabolism

institute: Johns Hopkins University

data_processing:
Sequenced libraries were processed with deepTools, using STAR, for trimming and mapping, and feature Counts to quantify mapped reads.
Raw mapped reads were processed in R (Lucent Technologies) with DESeq2 to generate normalized read counts to visualize as heatmaps using Morpheus (Broad Institute) and determine differentially expressed genes with greater than 2 fold change and lower than 0.05 adjusted P value.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data is a matrix with raw counts for features in samples, obtained with featureCounts.

source_name: Bone marrow

growth_protocol: To generate BMDMs, bone marrow cells were seeded in non-coated 10 cm dishes in DMEM cell culture medium supplemented with 10% fetal calf serum, 100 U/mL Penicillin, 0.1 mg/mL Streptomycin, 2 mM glutamine (all Sigma-Aldrich), and M-CSF (20 ng/mL, Peprotech). Growth medium was exchanged every 3 days

extract_protocol:
Cells were washed twice in PBS (4°C) and lysed in RLT lysis buffer (Qiagen). Total RNA was isolated using the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s instructions.
Libraries were prepared using the Illumina® Stranded TruSeq® RNA sample preparation Kit.

treatment_protocol: BMDMs form WT and Dars2 KO animals were seeded in 12-well plates (Sigma-Aldrich) in a density of 250,000 cells/cm2 in growth medium. Cells were stimulated with IL-4 + IL-13 (50 ng/mL each) or vehicle for 2 days or 12 days out of the 14 day culture.

tag: strain

tag: cell type

value: Bone marrow derived macrophage

tag: genotype

value: WT

tag: length of treatment

value: 2 days


title: Exp.1

status: Public on Oct 28 2021

type: SRA

country: USA

description: 4 and 12 dpw. Exp 1

library_source: transcriptomic

data_processing:
Raw reads were mapped to the mouse genome (GRCm38) and splice-site information from Ensembl release 87 with gsnap v.2018-07-04. Uniquely mapped reads and gene annotations from Ensembl release 87 were used as input for featureCounts v. 1.6.2 to create counts per gene and cell.
Samples were processed and analyzed in R (3.6.0) using Seurat (v4). Cells with less than 40% fragments mapped to genes were excluded from final data.
Genome_build: mm10
Supplementary_files_format_and_content: Rdata object containing metadata annotation of each cell (Well position, flow cytometry parameters, plate, experiment date) plus matrix of processed read counts per cell (column) and per gene (row).

molecule: total RNA

organism: Mus musculus

source_name: Skin

extract_protocol:
Single macrophages from wounded skin were index-sorted (BD FACS Aria II SORP) into 384 well plates containing 0.5 µl of nuclease free water with 0.2% Triton-X 100 and 4 U murine RNase Inhibitor (NEB), spun down and frozen at −80°C. Libraries were prepared following the Smart-seq2 workflo. Briefly, after thawing, 0.5 µl of a primer mix were added (5 mM dNTP (Invitrogen), 0.5 µM dT-primer (C6-aminolinker-AAGCAGTGGTATCAACGCAGAGTCGACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTVN), 1 U RNase Inhibitor (NEB)). RNA was denatured for 3 minutes at 72°C and the reverse transcription (RT) was performed at 42°C for 90 min after filling up to 10 µl with RT buffer mix for a final concentration of 1x superscript II buffer (Invitrogen), 1 M betaine, 5 mM DTT, 6 mM MgCl2, 1 µM TSO-primer (AAGCAGTGGTATCAACGCAGAGTACATrGrGrG), 9 U RNase Inhibitor and 90 U Superscript II. After synthesis, the reverse transcriptase was inactivated at 70°C for 15 min. The cDNA was amplified using Kapa HiFi HotStart Readymix (Peqlab) at a final 1x concentration and 0.1 µM UP-primer (AAGCAGTGGTATCAACGCAGAGT) under following cycling conditions: initial denaturation at 98°C for 3 min, 23 cycles [98°C 20 sec, 67°C 15 sec, 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA was purified using 1x volume of hydrophobic Sera-Mag SpeedBeads (GE Healthcare) resuspended in a buffer consisting of 10 mM Tris, 20 mM EDTA, 18.5 % (w/v) PEG 8000 and 2 M sodium chloride solution. The cDNA was eluted in 12 µl nuclease free water and the concentration of the samples was measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates (Corning) using AccuBlue Broad range chemistry (Biotium).
For library preparation up to 700 pg cDNA was desiccated and rehydrated in 1 µl Tagmentation mix (1x TruePrep Tagment Buffer L, 0.1 µl TruePrep Tagment Enzyme V50; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme) and tagmented at 55°C for 5 min. Subsequently, Illumina indices were added during PCR (72°C 3 min, 98°C 30 sec, 13 cycles [98°C 10 sec, 63°C 20 sec, 72°C 1 min], 72°C 5 min) with 1x concentrated KAPA Hifi HotStart Ready Mix and 300 nM dual indexing primers. After PCR, libraries were quantified with AccuBlue Broad range chemistry, equimolarly pooled and purified twice with 1x volume Sera-Mag SpeedBeads. This was followed by Illumina 50 bp paired-end sequencing on a Novaseq6000 aiming at an average sequencing depth of 0.5 mio reads per cell.
Single Cell RNA seq

treatment_protocol: Mice were anesthetized by i.p. injection of Ketanest/Rompun. Back skin was shaved and full-thickness excisional wounds were created using a standard biopsy puncher. Mice were housed individually during the entire time course of healing. Monocytes from female B6.RFP mice were isolated from B6.RFP mice via Immuno-magnetic depletion of whole bone marrow, counted and then 3x10^6 cells were adoptively transferred into each previously wounded C57/BL6 recipient via intravenous injection, either 2 or 12 days after injury. Wounds were excised 4 or 14 days after injury. Wounds from several mice were pooled in two separate experiments (2 biological replicates of several mice each).

value: Macrophage

tag: treatment

value: 4 and 12 dpw


title: WT_IL-4+IL13_2_days_2


title: S32_C_W8

city: Montreal

first: Gustavo

last: Turecki

state: Quebec

address: 6875 Boulevard LaSalle

department: Psychiatry

country: Canada

institute: McGill University

description:
exosome encapsulated RNA
32_W8

data_processing:
Removed adapter sequences with cutadapt (v.1.9.1) Discarded reads that do not have adapters as these fragments are too long for a small RNA library.
cutadapt -a TGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC --discard-untrimmed
Trimmed the first 4 and last 4 bases of the reads
Reads were aligned to the human genome (hg38) and features were quantified with Genboree's exceRpt pipeline v4.6.2
Genome_build: hg38
Supplementary_files_format_and_content: Tab-separated raw-count matrix, where rows are genes (miRNAs) and columns are samples. The file is a plain-text .tsv

organism: Homo sapiens

source_name: Neuronal-derived exosomes from plasma

extract_protocol:
Exosomes were extracted from 2mL of plasma using size exclusion chromatography, and further enriched for those of neuronal origin using an immunoassay. Small non-coding RNA was isolated using miRNeasy kit
Librarys were constructed using the 4N library prep protocol from the Galas lab. (Giraldez et al., 2018) First, degenerative adapters are added to the miRNA. These adapters are used to eliminate the problem of bias in small RNA library construction. The product is then reverse transcribed and amplified.

tag: tissue

value: Neuronal-derived exosomes from plasma

tag: disease state

value: Control

tag: patient id

tag: week

tag: treatment response

tag: age

tag: Sex

value: M

tag: sequencing batch


title: Dars2_KO_IL-4+IL13_2_days_2

value: Dars2 KO


title: S34_C_W0

description:
exosome encapsulated RNA
34_W0

value: F


title: s010302

city: Beijing

first: Ping

last: Lu

address: 5 Yiheyuan Road

country: China

institute: Peking University

description: polyA RNA

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
UMI-tools was used to extract and add the 8bp cell barcode sequence and unique molecular identifiers (UMIs) to read name of sequencing read pairs.
Subsequently we trimmed template switch oligo (TSO) sequence and ployA tail sequence in read1 and removed low-quality bases using costumed script and seqtk tool.
The clean read1 reads were aligned to mm10 reference genome using STAR.
Then, genomic features were added to reads using featureCounts of subread in order to count uniquely aligned reads with genes.
Finally, we used "count" tool in UMI-tools to obtain UMI counts.
Genome_build: mm10
Supplementary_files_format_and_content: A  comma-separated values (csv) file include UMI counts for each single cell RNA samples

source_name: mouse germ cells

extract_protocol:
Cells were randomly selected into precooled lysate. Then, the lysate were shocked at 72℃ for 3min to release RNA and Initial denaturation.
We used an improved Smart seq2 method. In brief, single-cell suspension is firstly prepared, and then single cells are selected into a PCR tube containing oligo(dT) primers and lysates through a suction tube.After cDNA amplification, the single cells labeled with different barcodes can be pooled together for subsequent library construction and sequencing. We add biotin in our indexed primers which can pair with 3’ cDNA primers, so after additional amplifying of pooled cDNAs following shearing to about 300bp , we use Dynabeads® MyOne™ Streptavidin C1 beads to enrich for the 3’ terminal of cDNAs. Then the library was constructed by using Kapa Hyper Prep Kit(Thermo Fither) and run on illumina Hiseq X Ten for 150bp pair-end reads.

treatment_protocol: BVSC transgenic mice were used in our study. Adult female C57BL/6 mice in natural estrus were cooped up with male BVSC mice at a ratio of 2:1. The mating status of mice was checked in the morning of the next day, and the female mice with vaginal suppository were retained. At noon of the day, the embryonic period was set at 0.5 days (E0.5).Germ cells are collected from E6.5 and collection methods for E6.5 and E7.5 were referenced in the published protocols. The germ cells from E8.5 to E18.5 were collected through flow sorting, and the whole embryo was digested directly from E8.5 to E10.5 to separate the BVSC+ cells. Gonads were separated from E11.5 to E18.5, and BVSC+ and negative cells were separated after digestion. Among them, E11.5 identified the Sry gene to distinguish male from female, and E13.5 to E16.5 divided the male gonads into three segments, defined as proximal, central and distal, according to their relative positions to mesonephroi.From E14.5 to E18.5, BV signal was gradually down-regulated, and SC+ positive cells were collected as germ cells. After flow cytometry enrichment, the samples before birth were examined by fluorescence microscopy for fluorescence signal, and then were selected into the 8-row PCR tube containing lysate. The day of birth was defined as P0. After mechanical and trypsin digestion of the gonads (testes), cells were transferred into 1% HSA.

tag: library


title: Exp.2

description: 4 and 12 dpw. Exp 2


title: TN-13

first: Yi

last: Feng

address: No.11,Xizhimen South Street, Xicheng District

department: Department of Anesthesiology

institute: Peking university people's hospital

data_processing:
Illumina RtaVersion v3.4.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using tophat2 software,tophat2 -a 8 -m 0 -i 50 -I 500000 -N 2 --read-gap-length 2 --read-edit-dist 2 -g --library-type fr-unstranded -p 8 -G -r 50 --microexon-search;For FPKM valuse analysis using RSEM software,RSEM --paired-end  --bowtie2 -p 8 --bowtie2-path.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample .

source_name: Whole blood cells in patients with trigeminal neuralgia

extract_protocol:
total RNA were extracted for using PAXgene Blood RNA Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Whole blood

tag: gender

value: Male

tag: condition

value: trigeminal neuralgia


title: S32_C_W0

description:
exosome encapsulated RNA
32_W0


title: TN-9


title: Control Lgr5+ ISC rep 1

city: Stony Brook

first: Vincent

last: Yang

state: New York

address: 101 Nicolls Rd., HSC T17-090

department: Medicine

institute: Stony Brook University

data_processing:
The reads were aligned with STAR (version 2.5.2a).
Genes annotated in Gencode vM16 were quantified with featureCounts (v1.4.3-p1).
Normalization and differential expression was done with the Bioconductor package DESeq2 (v1.18.1).
Genome_build: Mm10
Supplementary_files_format_and_content: tab-delimited text files include gene ID (in ENSEMBL), coordinates, strand, length of the transcripts, and counts (=number of reads mapping to the exons of the gene).

source_name: Control mouse intestinal stem cells

extract_protocol:
Proximal 1/3 of small intestine were resected, and crypts were isolated by villi scraping and 5mM EDTA incubation. Cells were dissociated with 4x TrpLE in DMEM for 45 minutes, and Lgr5-EGFPhi cells were sorted by flow cytometry. Total RNA was isolated using RNeasy Mini Kit (Qiagen) in combination with on-column DNase treatment.
Library was prepared using the KAPA Stranded RNA-Seq kit with RiboErase (Kapa Biosystems) according to the manufacturer's instructions.

treatment_protocol: Mice were injected with tamoxifen (1mg in 0.1 mL corn oil per injection) for 5 consecutive days to activate Cre recombinase for initating lineage-tracing, and to delete Klf5 in Klf5-KO mice

value: Adult small intestinal stem cell; proximal 1/3 of intestine


title: Dars2_KO_IL-4+IL13_2_days_1


title: S31_C_W8

description:
exosome encapsulated RNA
31_W8


title: TN-10

value: Female


title: C5AR1_KO_Mono

city: Bethesda

first: Jack

last: Bibby

address: 10 Center Drive

institute: National Institutes of Health

data_processing:
Trimgalore (v0.6.5) was used to filter adapters and low quality sequences using default parameters except “--stringency 3 --nextseq=20 --paired”
Alignment was performed using STAR (120) (v2.7.8a) under default parameters apart from “-- sjdbOverhang 50 --readFilesCommand zcat”
featureCounts (v2.0.2) was used to quantify gene expression under default parameters apart from “-p--countReadPairs”
Downstream analysis was performed in R (v4.1.0) using edgeR (v3.34) for filtering, normalization, and differential expression
Genome_build: mm10
Supplementary_files_format_and_content: "raw_count_matrix.txt." contains the raw output from featureCounts
Supplementary_files_format_and_content: "normalised_count_matrix.csv." contains normalised counts from edgeR. Data were TMM adjusted and extracted as counts per million values using the cpm() function in edgeR.

molecule: polyA RNA

source_name: Kidney derived cells

extract_protocol:
Total RNA was isolated using QIAzol (Qiagen) and chloroform extraction followed by purification on Direct-zol RNA miniprep kit (Zymo Research) and then quantified using Nanodrop 2000 UV-visible spectrometry
RNA sequencing libraries were generated using SENSE mRNA-Seq library prep kit according to manufacturer’s instructions (Lexogen GmbH, Vienna, Austria). In brief, up to 200 ng of total RNA was prepared and incubated with magnetic beads coated with oligo-dT, then all other RNAs except mRNA were removed by washing. Library preparation was then initiated by random hybridization of starter/stopper heterodimers to the poly(A) RNA still bound to the magnetic beads. These starter/stopper heterodimers contain Illumina-compatible linker sequences. A single-tube reverse transcription and ligation reaction extends the starter to the next hybridized heterodimer, where the newly synthesized cDNA insert was ligated to the stopper. Second-strand synthesis was performed to release the library from the beads. The resulting double-stranded library was purified and amplified (15 PCR cycles) after adding the adaptors and indexes. Finally, libraries were quantitated by qPCR using KAPA Library Quantification Kit (Kapa Biosystems, Inc., MA, USA) and validated using Agilent High Sensitivity DNA Kit on a Bioanalyzer (Agilent Technologies, CA, USA)

tag: background

value: C5ar1fl/fl LyzMcre

value: Kidney derived cells

tag: cell subtype

value: Monocyte


title: WT_Control_2_days_2

tag: strain

tag: cell type

value: Bone marrow derived macrophage

value: WT


title: TN-7


title: C5AR1_KO_Mac

tag: genotype

value: Macrophage


title: S31_C_W0

description:
exosome encapsulated RNA
31_W0


title: TN-11


title: C5AR1_WT_Mono

value: Wild type


title: WT_Control_2_days_1

tag: treatment

tag: length of treatment

value: 2 days


title: TN-4

tag: tissue


title: C5AR1_WT_Mac


title: S30_C_W8

description:
exosome encapsulated RNA
30_W8

value: Neuronal-derived exosomes from plasma

tag: disease state

value: Control

tag: patient id


title: TN-3


title: Dars2_KO_Control_2_days_1

value: Dars2 KO


title: C5_KO_Mac

value: C5fl/fl LyzMcre


title: S29_RES_W8

description:
exosome encapsulated RNA
29_W8

value: depressed

tag: week

tag: treatment response

value: Responder

value: F

tag: madrs score at week 0

tag: madrs score at week 8


title: S30_C_W0

description:
exosome encapsulated RNA
30_W0

tag: age

tag: Sex

tag: sequencing batch


title: WT_IL-4+IL13_12_days_2

value: 12 days


title: TN-2

value: Whole blood

tag: gender

value: Female

tag: condition

value: trigeminal neuralgia


title: Dars2_KO_Control_2_days_2

tag: strain


title: Control-10

source_name: Whole blood cells in pain-free comparisons

value: Male

value: control


title: S29_RES_W0

description:
exosome encapsulated RNA
29_W0


title: WT_IL-4+IL13_12_days_1

tag: cell type

value: Bone marrow derived macrophage

value: WT


title: C5_KO_Mono

tag: background

tag: genotype

value: Kidney derived cells

tag: cell subtype

value: Monocyte


title: C5_WT_Mono

value: Wild type


title: C5_WT_Mac

value: Macrophage


title: Control-9

tag: tissue


title: S28_NRES_W0

description:
exosome encapsulated RNA
28_W0

value: Neuronal-derived exosomes from plasma

tag: disease state

value: Non-responder

value: M


title: S28_NRES_W8

description:
exosome encapsulated RNA
28_W8

value: depressed

tag: patient id


title: Dars2_KO_IL-4+IL13_12_days_2

value: Dars2 KO

tag: treatment

tag: length of treatment


title: Control-8


title: Dars2_KO_IL-4+IL13_12_days_1

value: 12 days


title: WT_Control_12_days_2

value: Control


title: S27_NRES_W8

description:
exosome encapsulated RNA
27_W8

tag: week

tag: treatment response

value: F

tag: madrs score at week 0


title: Control-7

value: Whole blood

value: Female


title: Control-6

value: control


title: S27_NRES_W0

description:
exosome encapsulated RNA
27_W0

tag: age

tag: Sex

tag: madrs score at week 8


title: Dars2_KO_Control_12_days_2

value: Bone marrow derived macrophage


title: Control-4

tag: gender

tag: condition


title: Control-3

value: Male


title: WT_Control_12_days_1

tag: strain

tag: cell type

value: WT


title: S26_RES_W8

description:
exosome encapsulated RNA
26_W8

value: Responder

tag: sequencing batch

value: not measured


title: S26_RES_W0

description:
exosome encapsulated RNA
26_W0


title: X33D4

city: Utrecht

first: Floris

last: Valentijn

address: Heidelberglaan 100

country: Netherlands

institute: University Medical Center Utrecht

data_processing:
Illumina NextSeq500 software was used for basecalling
RNA-seq reads were aligned to the reference genome GRCm38 using STAR version2.4.2a
Read groups were added to the BAM files with Picard's AddOrReplaceReadGroups (v1.98).
The BAM files are sorted with Sambamba v0.4.5 and transcript abundances are quantified with HTSeq-count version 0.6.1p1 using the union mode
Reads per kilobase of transcript per million mapped reads (RPKM’s) were calculated with edgeR's RPKM function
Genome_build: GRCm38
Supplementary_files_format_and_content: excel file include RPKM values for each sample

source_name: kidney cortex

extract_protocol:
Kidneys were harvested and frozen at -80C. RNA was isolated using NEXTflex Poly(A) Beads (Bioo scientific, Austin, TX). Libraries were prepared using the Rapid Directional RNA-Seq Kit (NEXTflex)
RNA libraries were prepared for sequencing using the Rapid Directional RNA-Seq Kit (NEXTflex), looped in equimolarly and sequenced on Illumina NextSeq500 to produce single-end 75 base long reads

tag: genotype

value: CCN2 knockout

tag: injury state

value: IRI


title: X33D6


title: X33B4

value: SHAM


title: X33D5


title: X33D3


title: Control-2

tag: tissue


title: Control-5


title: S25_NRES_W8

description:
exosome encapsulated RNA
25_W8

value: Neuronal-derived exosomes from plasma

tag: disease state

tag: patient id

value: Non-responder

value: M


title: Dars2_KO_Control_12_days_1

value: Dars2 KO

tag: treatment

tag: length of treatment

value: 12 days


title: X33B3


title: S24_RES_W0

description:
exosome encapsulated RNA
24_W0

value: depressed

tag: week

tag: treatment response


title: S24_RES_W8

description:
exosome encapsulated RNA
24_W8

tag: age

tag: madrs score at week 0


title: X32B5


title: Control-1

value: Whole blood


title: X33C4

value: wild type


title: X32B4


title: VCaP_AU_4h_H3K27Ac (HiChIP-seq)

city: Ann Arbor

first: Pushpinder

middle: Singh

last: Bawa

state: Michigan

address: 1500 East Medical Center Drive

department: Pathology

institute: University of Michigan

library_source: genomic

data_processing:
Library strategy: HiChIP-seq
Raw fastq files were aligned using BWA mem with the -5SP options with an index containing only the main chromosome from the human genome release hg38 (available from the UCSC genome).
The aligned paired reads were annotated with pairtools parse (https://github.com/open2c/pairtools) with the following options --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 and the --chroms-path file corresponding to the size of the chromosome used for the alignment index.
The paired reads were further processed to remove duplicated reads, sorted with unaligned reads removed with the pairtools sort and the pairtools dedup tools with the basic option to produce an alignment file in the bam format as well as the location of the valid pair.
The valid pairs were finally converted to the .cool and .mcool format using the cooler cload and cooler zoomify tools and to the .hic format using the juicer tool.
Genome_build: hg38
Supplementary_files_format_and_content: .hic Hi-ChIP matrix

molecule: genomic DNA

source_name: VCaP

growth_protocol: All cell lines were purchased from ATCC and were grown in ATCC-suggested culture media. They were bimonthly tested for mycoplasma contamination, including within a week of NGS-experiments.

extract_protocol:
Intact cells were crosslinked using with 3mM DSG and 1% formaldehyde and processed as described in the Dovetail MNase HiChIP kit (Cat No. 21007) protocol.
HiChIP assay was performed on 5 million DMSO or AU-15330 treated (1uM for 4h) VCaP cells. Frozen cells were resuspended in 1X PBS and crosslinked with 3mM DSG and 1% formaldehyde. Washed cells were digested with 0.5 uL MNase in 100 uL of Nuclease digest buffer with MgCl2. Cells were lysed with 1X RIPA and clarified lysate (approximately 1400 ng) was used for ChIP. The antibody amount used per ChIP and vendor information are as follows: CTCF – 1.14 μg of Cell Signaling, Cat. 3418; H3K4me3 – 3.4 μg of Cell Signaling, Cat. 9751; H3K27ac – 0.4 μg of Cell Signaling, Cat. 8173. The Protein A/G bead pulldown, proximity ligation, and libraries were prepared as described in the Dovetail protocol (Dovetail™ HiChIP MNase Kit).
Crosslinked DNA was fragmented using an MNase cocktail and immunoprecipitated using 5-10ug of target antibody from 5M cells per HiChIP.

treatment_protocol: Cell were plated at 70-80% confluence in a 150mm culture plate and treated with AU-15330 dissolved in DMSO at 1uM concentration for 4h.

tag: cell line

value: VCaP

tag: dosage & duration

value: 1uM for 4h

tag: cancer type

value: prostate cancer


title: S25_NRES_W0

description:
exosome encapsulated RNA
25_W0

tag: Sex

tag: madrs score at week 8


title: S23_RES_W8

description:
exosome encapsulated RNA
23_W8

tag: sequencing batch


title: S23_RES_W0

description:
exosome encapsulated RNA
23_W0


title: S22_NRES_W8

description:
exosome encapsulated RNA
22_W8


title: X33D2

tag: strain

tag: genotype


title: DKO2_WGBS

city: La Jolla

first: Anjana

last: Rao

state: California

address: 9420 Athena Cir

department: Signaling and Gene Expression

institute: La Jolla Institute for Allergy and Immunology

data_processing:
WGBS reads were mapped to both the mouse genome mm10 GRCm38 (Dec. 2011) from UCSC and the phage lambda genome.
Bisulfite conversion efficiency was estimated based on cytosine methylation in all contexts.
Duplicated reads caused by PCR amplification were removed by PICARD’s MarkDuplicates.
CpG DNA methylation at both DNA strands was called by methratio.py script, from BSMAP (v2.90) (-g - i "correct" -x CG,CHG,CHH).
To identify differentially methylated cytosines and regions (DMCs and DMRs, with at least 3 CpGs) we used RADmeth methpipe-3.4.2 (adjust -bins 1:100:1 ; merge -p 0.05).
Genome_build: mouse genome mm10 GRCm38 (Dec. 2011) from UCSC
Supplementary_files_format_and_content: Tab separated file with the methylated C and total C in pairs per samples

source_name: Spleen

growth_protocol: Primary YFP+ CD19 DKO B cells or CD19+ YFP- control B cells were isolated using flow sorting.

extract_protocol:
Briefly, 1 ug of genomic DNA was spiked-in with unmethylated lambda-phage DNA (1:200) and sonicated using Bioruptor (9 cycles 30 seconds on, 30 seconds off).
The sonicated DNA fragments were end repaired, A-tailed and ligated with methylated adaptors (all using NEB kits). The adaptor ligated fragments were then treated with sodium bisulfite using the Methylcode kit (Invitrogen) for a total of 4 hours according to manufacturer’s protocol. The bisulfite converted, adaptor ligated fragments were then amplified with Kapa Hifi Hotstart Uracil+ PCR mix with NEB universal dual indexing primers. The libraries were then sequenced on an Illumina NovaSeq (150 bp paired-end reads)
Whole genome bisulfite sequencing

tag: tissue

value: Spleen

tag: cell type

value: B cells

value: 10 weeks of age

value: CD19 DKO


title: S22_NRES_W0

description:
exosome encapsulated RNA
22_W0

tag: disease state

tag: patient id


title: VCaP_DMSO_4h_H3K4me3 (HiChIP-seq)

tag: treatment

value: vehicle control


title: S21_RES_W8

description:
exosome encapsulated RNA
21_W8

tag: week

value: Responder


title: S21_RES_W0

description:
exosome encapsulated RNA
21_W0

value: Neuronal-derived exosomes from plasma

tag: treatment response


title: VCaP_AU_4h_H3K4me4 (HiChIP-seq)


title: VCaP_AU_4h_CTCF (HiChIP-seq)


title: Dfl1_WGBS

tag: age

value: Dfl


title: VCaP_DMSO_4h_H3K27Ac (HiChIP-seq)


title: DKO1_WGBS


title: X33C2

tag: injury state

value: IRI


title: X33A2

value: SHAM


title: VCaP_DMSO_4h_CTCF (HiChIP-seq)

tag: cell line


title: S20_RES_W8

description:
exosome encapsulated RNA
20_W8

value: M

tag: madrs score at week 0


title: X33A1


title: Organoids Day 30, wild-type, 12uM CHIR Repeat #1 - RNA-seq

city: Rehovot

first: Orly

last: Reiner

address: 234, Herzl Street,

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

description:
counts_chir_RNAseq.txt
CHIR41_S0_L009

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh37/hg38 whole genome using Cutadapt  -a $adapter -q 20 fastqf  ($adapter= sequence of adapter Fastqf= fastqfile) and STAR.
Raw counts were processed, and normalized reads were obtained by DESeq2.
Genome_build: GRCh37/hg38
Supplementary_files_format_and_content: tab-delimited text files include read values for each sample.

source_name: WIBR3 hESC Choroid plexus Organoids

extract_protocol:
Total RNA was extracted from samples using RNEASY mini-kit (Qiagen)
RNA libraries were prepared for sequencing using bulk MARS-seq protocol [Jaitin, D. A. et al. Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types Science 343, 776–9 (2014).] and TruSeq stranded mRNA library kit.

tag: developmental stage

value: Organoids Day 30

value: Wild type

value: 12uM CHIR


title: Organoids Day 30, wild-type, 12uM CHIR Repeat #3 - RNA-seq

description:
counts_chir_RNAseq.txt
CHIR43_S84_L002


title: X32A1

value: wild type


title: X32A2


title: S20_RES_W0

description:
exosome encapsulated RNA
20_W0

value: depressed

tag: Sex


title: X33C3


title: Dfl2_WGBS


title: S19_RES_W0.1

description:
exosome encapsulated RNA
19_W0.1

tag: madrs score at week 8


title: Organoids Day 30, wild-type, Repeat #1 - RNA-seq

description:
counts_chir_RNAseq.txt
CHIR11_S79_L002

value: 3uM CHIR


title: Organoids Day 30, wild-type, 12uM CHIR Repeat #2 - RNA-seq

description:
counts_chir_RNAseq.txt
CHIR42_S83_L002


title: HT29 CWP232228 1.5uM #2

city: Ottawa

first: Yannick

middle: D.

last: Benoit

state: Ontario

address: 451 Smyth road

institute: University of Ottawa

data_processing:
Processed raw sequences with fastp to perform automatic adapter trimming, and default sequence quality filtering (>60% of bases with Q≥15, and no more than 5 'N' basecalls)
Quantified transcripts from GENCODE v35 with salmon v1.3.0 using --gcBias flag and genomic decoys in index
Performed fold change analysis using DESeq2 as follows
Read transcript quantification data with tximport library and summarized to gene level quantification
Filtered to retain genes with at least 5 reads assigned in at least two samples
Constructed DESeqDataSet object with eight samples (two replicates of four conditions), using the model ~condition (cell type/treatment)
Calculated fold changes using the lfcShrink() function with the apeglm method.
Genome_build: GRCh38
Supplementary_files_format_and_content: salmon transcript quantification: Quantifrication of GENCODE v35 transcripts using salmon v1.3.0
Supplementary_files_format_and_content: DESeq2 fold change results: Results from the DESeq2 lfcShrink() function comparing two conditions, including results for all genes retained after filtering

source_name: Colorectal cancer cell line

extract_protocol:
RNA was extracted using the total RNA purification kit by Norgen Biotech Corp, following the manufacturer's guidelines. Quantification of total RNA samples was performed with a Qubit HS RNA assay (ThermoFisher Scientific) and fragment size was evaluated with a Fragment Analyzer HS NGS assay (AATI). A RNA Quality Number (RQN) of 8.0 or higher was considered satisf.txtactory for library construction. Library construction was performed with a Truseq RNA v2 (Illumina) with unique barcodes compatible with the Illumina NextSeq 500 platform.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Colorectal adenocarcinoma


title: HT29 YB-0158 0.3uM #1


title: BS65_2

city: Stanford

first: Robert

middle: A

last: Saxton

state: CA

address: 279 Campus Drive, Beckman Center, Room B173

department: Department of Molecular & Cellular Physiology

institute: Stanford University

data_processing:
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly.
Indexes of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5) (Dobin et. al., 2013).
The FPKM of each gene was calculated based on the length of the gene and reads count mapped to the gene and used to quantify relative gene expression levels (Mortazavi et. al., 2008).
Genome_build: Homo Sapiens(GRCh38/hg38)
Supplementary_files_format_and_content: raw or FPKM values for each Sample

source_name: human CD8+ T cells_10-DE

extract_protocol:
Cells were isolated by centrifugation at 300 g, and washed once in ice cold PBS. RNA was isolated using RNAeasy plus mini kit (Qiagen).
cDNA libraries were constructed using NEBnext® UltraTM II RNA Library Prep Kit for Illumina®, using 0.2 µg RNA input, and the mRNA enrichment method

treatment_protocol: 10 nM IL-10 for 24 hours

value: PBMC

tag: cell subtype

value: CD8+ T cell


title: HT29 ICG-001 10uM #2

value: 49 hours 10uM ICG-001


title: BS45_1

source_name: human CD8+ T cells_super-10


title: X33C1

tag: strain


title: S19_RES_W0.2

description:
exosome encapsulated RNA
19_W0.2

tag: sequencing batch


title: S16_NRES_W8

description:
exosome encapsulated RNA
16_W8

tag: tissue

value: Non-responder


title: S18_NRES_W0

description:
exosome encapsulated RNA
18_W0

value: F


title: BS45_2

tag: cell type


title: HT29 YB-0158 0.3uM #2


title: S16_NRES_W0

description:
exosome encapsulated RNA
16_W0

value: Neuronal-derived exosomes from plasma

tag: disease state


title: HT29 DMSO #1

value: 48 hours DMSO 0.1%


title: HT29 CWP232228 1.5uM #1


title: BS65_1


title: Organoids Day 30, wild-type, Repeat #2 - RNA-seq

description:
counts_chir_RNAseq.txt
CHIR12_S80_L002

tag: genotype


title: Organoids Day 30, wild-type, Repeat #3 - RNA-seq

description:
counts_chir_RNAseq.txt
CHIR13_S81_L002

tag: treatment


title: S18_NRES_W8

description:
exosome encapsulated RNA
18_W8

tag: patient id

tag: week


title: Unt_2

source_name: human CD8+ T cells_PBS

value: PBS


title: BS30_1

source_name: human CD8+ T cells_WT IL-10

value: WT IL-10


title: S17_NRES_W8

description:
exosome encapsulated RNA
17_W8

tag: treatment response

tag: age

value: M


title: HT29 DMSO #2

tag: cell line


title: S17_NRES_W0

description:
exosome encapsulated RNA
17_W0

tag: madrs score at week 0


title: BS30_2


title: Organoids Day 30, wild-type, Repeat #2 - MARS-seq

description:
counts_tp_Mars-seq.txt
CP_WT_organoids_D30_2

tag: developmental stage

value: Organoids Day 30


title: HT29 ICG-001 10uM #1

value: 48 hours 10uM ICG-001


title: Organoids Day 30, wild-type, Repeat #3 - MARS-seq

description:
counts_tp_Mars-seq.txt
CP_WT_organoids_D30_3

value: Wild type


title: Organoids Day 30, wild-type, Repeat #1 - MARS-seq

description:
counts_tp_Mars-seq.txt
CP_WT_organoids_D30_1


title: S19_RES_W8

description:
exosome encapsulated RNA
19_W8

value: Responder

tag: Sex


title: Organoids Day 18, wild-type, Repeat #2 - MARS-seq

description:
counts_tp_Mars-seq.txt
CP_WT_organoids_D18_2

value: Organoids Day 18


title: S14_NRES_W8

description:
exosome encapsulated RNA
14_W8

value: depressed

tag: madrs score at week 8


title: lacIF2_JS26_40

city: Dunedin

first: Peter

middle: Charles

last: Fineran

state: Otago

address: 720 Cumberland Street

department: Department of Microbiology and Immunology

country: New Zealand

institute: University of Otago

description: RNA extraction with Rneasy kit, Ribo-depleted (Ribo-zero bacteria) and library performed with TruSeq library

data_processing:
The reads were trimmed using Trimmomatic and their quality evaluated through FASTQC analysis.
Raw sequence reads were aligned to Serratia (accession number CP025085) and JS26 (accession number MN505213.1) genomes using Bowtie2 with default parameters.
The alignment was converted to BAM files format using SAMtools.
The differential expression between the uninfected controls (timepoint 0) and the infected samples (5, 20 and 40 mpi) was evaluated using the DESeq2  R/Bioconductor package (3.5.2) with a Wald test, followed by a Benjamini and Hochberg procedure. All sets were defined by a false discovery rate of 10%.
Genome_build: Serratia (accession number CP025085) and JS26 (accession number MN505213.1)
Supplementary_files_format_and_content: normalized counts.csv

organism: Prodigiosinella confusarubida

source_name: Serratia sp. ATCC 39006 cells

growth_protocol: Serratia WT, Serratia I-E BIM and Serratia I-F BIM were grown to exponential phase (OD600=0.3) in 25 ml LB at 30°C and in shaking conditions 160 (rpm).

extract_protocol:
Total RNA was extracted using the RNeasy kit (QIAGEN). Briefly, samples resuspended in RNAlater were harvested by centrifugation (17,000 g for 1 min at 4ºC) and resuspended in 250 µl of 10 mM Tris-HCl (pH 8.0). The resuspended pellet was transferred to a pre-chilled bead beater tube containing 350 ml of RLT buffer (lysis buffer) and b-mercaptoethanol. Cell lysis was performed with a bead beater, using three 10 sec pulses interspaced by a 1 min incubation in ice. The samples were chilled for 3 min on ice and cellular debris was removed by centrifugation (17,000 g for 1 min at 4ºC). The homogenate was transferred into a clean Eppendorf and 1.5 X volume of 100% ethanol was added and mixed by vortexing. The sample was transferred into the RNeasy mini spin column centrifuged (>8,000 g for 15 sec) and the flow through discarded. Next, the column was washed twice with 500 µl of Buffer RPE (washing buffer) followed by a centrifugation (>8,000 g for 15 sec). RNA was eluted by adding 50 µl of RNase free water followed by a centrifugation step (>8,000 g for 1 min). The sample was treated with TURBO DNase (Invitrogen) following the manufacturer’s instructions. Finally, impurities were removed by centrifugation (>8,000 g for 1 min) and the RNA samples were transferred to a new tube and stored at -20ºC.
RNA concentration was estimated using the nanodrop and the quality assessed by an RNA nano chip on the Bioanalyzer (Agilent). The total RNA samples were ribo-depleted using Ribo-zero rRNA removal kit (epicentre) and directional cDNA libraries were prepared with the TruSeq stranded mRNA library preparation kit (Illumina) following manufacturer’s instructions.
RNA-seq using Illumina HiSeq 2500 v4 Rapid single-read sequencing, with ~10 million reads (101 bp) generated per sample.

treatment_protocol: Cultures were infected at an moi=50 and 2 ml samples were taken at 0 (prior to phage infection), 5, 20 and 40 minutes post infection. Immediately after extraction, the samples were centrifuged (17,000 g for 1 min at 4ºC) to remove the free phage and the bacterial pellet was resuspended in 2 ml of RNAlater (invitrogen) and stored at -20ºC.

tag: replicate

value: Replicate 2

tag: agent

tag: time point

value: I-F BIM


title: Unt_1

value: PBMC

tag: cell subtype

value: CD8+ T cell


title: S13_NRES_W8

description:
exosome encapsulated RNA
13_W8

tag: tissue

value: Non-responder

tag: sequencing batch


title: DKO2 (G4-seq)

data_processing:
Library strategy: G4-seq
Paired-end (50bp) reads were mapped to the mouse genome mm10 GRCm38 (Dec. 2011) indexed with spiked-in G4 sequences, using Bowtie (V 1.1.2).
Reads that mapped to spike-ins were filtered out with samtools view; remaining reads in sam format were sorted and PCR duplicates were marked and removed with Picard (V 2.7.1).
Peaks were calculated with MACS2 (callpeak –keep-dup all -g mm -p 0.0001), using input as control.
Peaks from the replicates from same condition were merged with mergePeaks from HOMER and kept only those that intersected between the replicates.
Intersected peaks from the replicates were merged between the conditions to create the total number of peaks.
Tag directories were created and replicates were merged with makeTagDirectory from HOMER (-genome mm10);  makeMultiWigHub.pl was used to generate tracks
Genome_build: mouse genome mm10 GRCm38 (Dec. 2011)
Supplementary_files_format_and_content: Comma separated file with the rpkm normalized BG4 signal in G4 and Rloops union peaks

growth_protocol: Primary B cells were isolated using EasySep Mouse Pan B cell isolation kit (#19844 Stem Cell Technology, Canada).

extract_protocol:
Briefly, ~10 million cells were fixed with 1% formaldehyde at room temperature with nutation for 10 minutes mins at 1x106 cell/mL in media, quenched with 125 mM glycine, washed twice with ice cold PBS. Cells were pelleted, snap-frozen with liquid nitrogen, and stored at -80°C until use. Cell pellets were then lyzed using the Chromatrap ChIP hypotonic solution (800 ul) and lysis buffer (150ul) supplemented with protease inhibitor cocktail (invitrogen) on ice according to manufacturer’s instructions. The nuclei suspension was then sonicated using the bioruptor pico sonicator (Diagenode), 16 cycles 30 seconds on / 30seconds off and the lysates were then cleared by centrifugation at >12000g for 10 minutes. The lysates were diluted 1:10 times in intracellular buffer (25 mM HEPES pH 7.5, 10.5 mM NaCl, 110 mM KCl, 130 nM CaCl2, 1 mM MgCl2) (total 200 ul) then treated with 1mg/ml RNASE A (AM2269; Ambion, 1:100 dilution) for 20 minutes at 37C. Chromatin lysates were then incubated with BG4-Ig antibody (Ab00174-1.1, 1mg/ml; Absolute Antibody) (1:100) for 1.5 hours at 16 C followed by incubation with protein G magnetic dynabeads (Invitrogen). The beads were then washed 5 times with 1 ml wash buffer (intracellular buffer with 0.05% tween 20). The beads were re-suspended in elution buffer (100 mM NaHCO3, 1% SDS, 1 mg/mL RNaseA; Qiagen) treated with RNASE A (1:100, 100mg/ml) at 37 C for 30 minutes and proteinase K (1:40, 20mg/ml; Ambion) at 65 C for 2 hours to overnight. DNA was purified with Zymo ChIP DNA Clean & Concentrator-Capped Column (Zymo Research, Irvine, CA).
Library was prepared with NEB Ultra II library prep kit (NEB) following manufacturer’s instruction and was sequenced on an Illumina NovaSeq (50 bp paired-end reads).

tag: strain

value: Spleen

tag: cell type

value: B cells

value: 10 weeks of age

tag: genotype

value: CD19 DKO

tag: antibody

value: Ig-BG4 antibody (Ab00174-1.1; Absolute Antibody)


title: Organoids Day 18, wild-type, Repeat #3 - MARS-seq

description:
counts_tp_Mars-seq.txt
CP_WT_organoids_D18_3


title: DKO1 (G4-seq)


title: lacIF3_JS26_40

value: Replicate 3


title: S15_NRES_W0

description:
exosome encapsulated RNA
15_W0

value: Neuronal-derived exosomes from plasma

tag: disease state

tag: patient id

tag: week

tag: treatment response

value: F


title: lacIF3_JS26_20


title: DKO1_Input (G4-seq)

tag: age

value: none (input)


title: Organoids Day 18, wild-type, Repeat #1 - MARS-seq

description:
counts_tp_Mars-seq.txt
CP_WT_organoids_D18_1

tag: developmental stage

value: Wild type

tag: cell line


title: S14_NRES_W0

description:
exosome encapsulated RNA
14_W0

tag: Sex

tag: madrs score at week 0

tag: madrs score at week 8


title: Dflx2 (G4-seq)

value: Dfl


title: S13_NRES_W0

description:
exosome encapsulated RNA
13_W0

value: depressed


title: lacIF2_JS26_20

tag: replicate

value: Replicate 2

tag: agent

tag: time point


title: S12_NRES_W8

description:
exosome encapsulated RNA
12_W8

tag: tissue

value: M

tag: sequencing batch


title: S15_NRES_W8

description:
exosome encapsulated RNA
15_W8


title: Dflx1_Input (G4-seq)

tag: strain

tag: cell type

tag: genotype


title: Dflx1 (G4-seq)

tag: antibody


title: lacIF1_JS26_40

value: Replicate 1

value: I-F BIM


title: Doxorubicin 2mg/kg

city: Daejeon

first: Yee-Jin

last: Yun

address: 291 Daehak-ro, Yuseong-gu

country: South Korea

institute: Korea Advanced Institute of Science and Technology

description: T-Dox

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to GRCh37 whole genome by using HISAT2 version 2.1.0 with parameter -p 20 -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated by using StringTie version 2.1.3b, with parameter --rf -p 20 -l -o -G -A -C -e
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include FPKM, count, TPM values for each Sample

source_name: Tumor (xenografted MDA-MB-231 cells)

extract_protocol:
Tumors were removed, flash frozen on dry ice, and RNA was harvested. TruSeq stranded mRNA kit was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were injected s.c. with 9×106 stable pool of MDA-MB-231 cells at day 0. Day 7, mice were randomly divided into six different groups: Control, Rh2 (20mg/kg), Rh2 (30mg/kg), Rh2 (20mg/kg) + Dox (2mg/kg), Rh2 (30mg/kg) + Dox (2mg/kg), and Dox (2mg/kg). then BALB/c nude mice were received injections of Dox dissolved in 0.9% saline every other day with cumulative dose of 22 mg/kg body weight. Rh2 dissolved in PBS + Tween 80 was injected every day during the treatment course (3 weeks).

value: BALB/c nude (CAnN.Cg-Foxn1nu/Crl)

value: 6 weeks

value: Doxorubicin 2mg/kg


title: lacIF1_JS26_20


title: S12_NRES_W0

description:
exosome encapsulated RNA
12_W0

source_name: Neuronal-derived exosomes from plasma

tag: disease state

tag: patient id

tag: week

value: Non-responder


title: mHComb3 IL-22+CBLB treated hepatocytes

city: Bern

first: Daniel

last: Sanchez-Taltavull

address: Murtenstrasse 35

department: Department of BioMedical Research

country: Switzerland

institute: University of Bern

description: data.csv

data_processing:
fastq files were aligned to the mouse reference genome with Hisat
sam files were sorted and converted to bam files with SAMtools
reads were counted with featureCounts
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with read per sample

source_name: Isolated hepaocyte

growth_protocol: hepatocytes were isolated following the protocol of Seglin et al. method. Cells were resuspended in DMEM suplemented with 10% serum, penicillin and streptomycin, then plated at a density of 5x104 cells per cm2 on rat tail collagen coated 10cm diameter dishes. Four hours after plating the media was changed to arginine-free Williams E media supplemented with 40mM ornithine, 100iU/ml insulin, 2mg/ml hydrocortisone, penicillin and streptomycin, the culture media was then changed every second day.

extract_protocol:
RNA was extracted from snap-frozen tissue with RNeasy Micro Kit (Qiagen; 74004)
The library was prepared without size exclusion with the TruSeq Stranded mRNA kit (Illumina, 20020594)

treatment_protocol: 24h after plating, the hepatocytes were treated with CBLB (4ng/ml Cleveland BioLabs) or IL-22 (1ng/ml; PeproTech, #210-22) or the combination of the two.

tag: hepatocyte isolation number

tag: treatement concentration

value: 1ng/ml + 4ng/ml


title: Rh2-30 mg/kg + Doxorubicin 2mg/kg

tag: age

value: Rh2-30 mg/kg + Doxorubicin 2mg/kg


title: lacIF2_JS26_5


title: S11_RES_W8

description:
exosome encapsulated RNA
11_W8

tag: treatment response

value: Responder

tag: Sex

tag: madrs score at week 0


title: Rh2-20 mg/kg + Doxorubicin 2mg/kg

tag: agent

value: Rh2-20 mg/kg + Doxorubicin 2mg/kg


title: mHComb2 IL-22+CBLB treated hepatocytes

description: data.csv


title: Rh2-30 mg/kg

value: Rh2-30 mg/kg


title: lacIF3_JS26_5

tag: replicate

value: Replicate 3

tag: time point


title: lacIF1_JS26_5


title: S11_RES_W0

description:
exosome encapsulated RNA
11_W0

tag: tissue

value: Neuronal-derived exosomes from plasma

value: F

tag: sequencing batch

tag: madrs score at week 8


title: mHCBLB3 CBLB treated hepatocyte

description: data.csv

tag: strain


title: S10_RES_W8

description:
exosome encapsulated RNA
10_W8

value: depressed


title: mHComb1 IL-22+CBLB treated hepatocytes

description: data.csv


title: Rh2-20 mg/kg

value: Rh2-20 mg/kg


title: Control

description: T-Control

value: Control


title: S10_RES_W0

description:
exosome encapsulated RNA
10_W0

value: M


title: mHCBLB2 CBLB treated hepatocyte

description: data.csv


title: S9_RES_W8

description:
exosome encapsulated RNA
9_W8


title: lacIF2_JS26_0

value: Replicate 2

tag: genotype

value: I-F BIM


title: VCaP_AU-15330_1 uM_2h_2

description: Total RNA was extracted and sequencing using the polyA capture approach.

data_processing:
Strand-specific paired-end reads were then inspected for sequencing and data quality (for example, insert size, sequencing adaptor contamination, rRNA content, sequencing error rate).
Libraries passing quality control were trimmed of sequencing adaptors and aligned to the human reference genome, GRCh38. Sample were demultiplexed into paired end reads using Illumina's bcl2fastq conversion software v2.20.
Reads were mapped onto hg38 human reference genome using STAR. First the reference genome was indexed using STAR generate index.
Aligned file was used to compute read count for each gene using HTSeq count.
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw read count

extract_protocol:
Total RNA was isolated from cells using the Direct-zol kit (Zymo, Irvine, CA) and qualuty checked using the Bioanalyzer machine (only samples with RIN>9 was passed for sequencing).
RNA-seq libraries were prepared using 200–1,000 ng of total RNA. PolyA+ RNA isolation, cDNA synthesis, end-repair, A-base addition, and ligation of the Illumina indexed adapters were performed according to the TruSeq RNA protocol (Illumina). Libraries were size selected for 250–300 bp cDNA fragments on a 3% Nusieve 3:1 (Lonza) gel, recovered using QIAEX II reagents (QIAGEN), and PCR amplified using Phusion DNA polymerase (New England Biolabs). Library quality was measured on an Agilent 2100 Bioanalyzer for product size and concentration. Paired-end libraries were sequenced with the Illumina HiSeq 2500, (2×100 nucleotide read length) with sequence coverage to 15-20M paired reads.

treatment_protocol: Cell were plated at 70-80% confluence in a 6-well plate and treated with AU-15330 dissolved in DMSO at indicated concentrations (0.1 - 1uM) and for labeled durations (4-24h).

tag: treatment

tag: dosage

value: 1uM for 2h

tag: cancer type

value: prostate cancer


title: lacIF3_JS26_0


title: mHCBLB1 CBLB treated hepatocyte

description: data.csv

tag: hepatocyte isolation number


title: S9_RES_W0

description:
exosome encapsulated RNA
9_W0

tag: disease state

tag: patient id

tag: week


title: VCaP_AU-15330_1 uM_2h_1


title: VCaP_AU-15330_1 uM_1h_2

value: 1uM for 1h


title: mHIL223 IL-22 treated hepatocyte

description: data.csv

tag: treatement concentration


title: lacIE3_JS26_40

value: I-E BIM


title: VCaP_AU-15330_1 uM_1h_1


title: lacIF1_JS26_0

value: Replicate 1


title: mHIL221 IL-22 treated hepatocyte

description: data.csv


title: VCaP_AU-15330_1 uM_0.5h_2

value: 1uM for 0.5h


title: S7_NRES_W8

description:
exosome encapsulated RNA
7_W8

tag: treatment response

value: Non-responder

tag: age

tag: Sex

tag: madrs score at week 0


title: lacIE1_JS26_40

tag: replicate

tag: agent

tag: time point


title: lacIE3_JS26_20


title: VCaP_AU-15330_1 uM_0.5h_1


title: S6_NRES_W8

description:
exosome encapsulated RNA
6_W8

tag: tissue

tag: sequencing batch

tag: madrs score at week 8


title: mHCtrl3 Control hepatocyte

description: data.csv

tag: strain


title: mHCtrl1 Control hepatocyte

description: data.csv


title: S8_NRES_W8

description:
exosome encapsulated RNA
8_W8


title: mHIL222 IL-22 treated hepatocyte

description: data.csv


title: VCaP_DMSO_2h_2

tag: treatment

value: DMSO

tag: dosage

value: vehicle control

tag: cancer type


title: lacIE2_JS26_20

tag: genotype


title: lacIE2_JS26_40


title: S5_NRES_W8

description:
exosome encapsulated RNA
5_W8

value: Neuronal-derived exosomes from plasma

tag: disease state

tag: patient id

tag: week


title: VCaP_DMSO_2h_1


title: LAPC4_AU_R2_24h_1uM (RNA-seq)

extract_protocol:
Total RNA was isolated from cells using the Direct-zol kit (Zymo, Irvine, CA) and qualuty checked using the Bioanalyzer machine (only samples with RIN>9 was passed for sequencing).
RNA-seq libraries were prepared using 200–1,000 ng of total RNA. PolyA+ RNA isolation, cDNA synthesis, end-repair, A-base addition, and ligation of the Illumina indexed adapters were performed according to the TruSeq RNA protocol (Illumina). Libraries were size selected for 250–300 bp cDNA fragments on a 3% Nusieve 3:1 (Lonza) gel, recovered using QIAEX II reagents (QIAGEN), and PCR amplified using Phusion DNA polymerase (New England Biolabs). Library quality was measured on an Agilent 2100 Bioanalyzer for product size and concentration. Paired-end libraries were sequenced with the Illumina HiSeq 2500, (2×100 nucleotide read length) with sequence coverage to 15-20M paired reads.
PolyA RNA-seq

tag: cell line

value: 1uM for 24h


title: lacIE1_JS26_20


title: lacIE2_JS26_5


title: S6_NRES_W0

description:
exosome encapsulated RNA
6_W0

extract_protocol:
Exosomes were extracted from 2mL of plasma using size exclusion chromatography, and further enriched for those of neuronal origin using an immunoassay. Small non-coding RNA was isolated using miRNeasy kit
Librarys were constructed using the 4N library prep protocol from the Galas lab. (Giraldez et al., 2018) First, degenerative adapters are added to the miRNA. These adapters are used to eliminate the problem of bias in small RNA library construction. The product is then reverse transcribed and amplified.

value: depressed

tag: treatment response

tag: age

tag: Sex


title: S8_NRES_W0

description:
exosome encapsulated RNA
8_W0

value: F

tag: madrs score at week 0


title: S5_NRES_W0

description:
exosome encapsulated RNA
5_W0


title: S7_NRES_W0

description:
exosome encapsulated RNA
7_W0


title: mHCtrl2 Control hepatocyte

description: data.csv

tag: hepatocyte isolation number

tag: treatement concentration


title: LAPC4_AU_R2_24h_0.1uM (RNA-seq)

value: 0.1uM for 24h


title: lacIE1_JS26_5

tag: replicate

tag: agent

tag: time point


title: S4_RES_W8

description:
exosome encapsulated RNA
4_W8

tag: tissue

value: Responder

tag: sequencing batch

tag: madrs score at week 8


title: S4_RES_W0

description:
exosome encapsulated RNA
4_W0


title: LAPC4_AU_R1_24h_0.1uM (RNA-seq)

tag: treatment

tag: dosage

tag: cancer type


title: lacIE2_JS26_0

value: Replicate 2

tag: genotype


title: LAPC4_DMSO_R2_24h (RNA-seq)

tag: cell line


title: lacIE3_JS26_0

value: Replicate 3


title: lacIE3_JS26_5


title: S3_RES_W8

description:
exosome encapsulated RNA
3_W8

tag: disease state

tag: patient id

tag: week

tag: treatment response


title: S3_RES_W0

description:
exosome encapsulated RNA
3_W0

tag: age

tag: Sex

tag: madrs score at week 0


title: S2_RES_W8

description:
exosome encapsulated RNA
2_W8


title: lacIE1_JS26_0

tag: replicate

tag: agent


title: LAPC4_AU_R1_24h_1uM (RNA-seq)


title: lacwt3_JS26_40

tag: time point

value: WT


title: lacwt2_JS26_40


title: LAPC4_DMSO_R1_24h (RNA-seq)

value: prostate cancer


title: S2_RES_W0

description:
exosome encapsulated RNA
2_W0

tag: tissue

tag: sequencing batch


title: S1_RES_W8

description:
exosome encapsulated RNA
1_W8

tag: madrs score at week 8


title: LNCaP_AU_R2_24h (RNA-seq)

source_name: LNCaP

value: LNCaP

tag: treatment

tag: dosage


title: LNCaP_AU_R1_24h (RNA-seq)

tag: cancer type


title: lacwt1_JS26_40

tag: genotype


title: LNCaP_AU_R2_12h (RNA-seq)

tag: cell line

value: 1uM for 12h


title: lacwt3_JS26_20


title: S1_RES_W0

description:
exosome encapsulated RNA
1_W0

tag: disease state

tag: patient id


title: LNCaP_DMSO_R2_24h (RNA-seq)


title: lacwt2_JS26_20


title: LNCaP_AU_R1_12h (RNA-seq)


title: LNCaP_DMSO_R1_24h (RNA-seq)


title: VCaP_ZBC260_R2_24h (RNA-seq)

value: VCaP

value: ZBC-260 (BRD4 degrader)

value: 10nM for 24h


title: VCaP_ZBC260_R1_24h (RNA-seq)


title: VCaP_ZBC260_R2_8h (RNA-seq)

value: 10nM for 8h


title: SC, CCI-3

first: Dan

last: Wu

address: No. 16, Nei Nanxiao Street, Dongzhimen, Dongcheng District

institute: Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences

description: spinal cord on postoperative day 10

data_processing:
Illumina Casava1.7 software used for basecalling.
The clustering of the index-coded samples was performed on a cBot Cluster  Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to  the manufacturer’s instructions. After cluster generation, the library preparations  were sequenced on an Illumina Hiseq platform and 125 bp/150 bp paired-end reads  were generated.
Raw data (raw reads) of fastq format were firstly processed through in-house perl  scripts. In this step, clean data (clean reads) were obtained by removing reads  containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All  the downstream analyses were based on the clean data with high quality.
Differential expression analysis of two groups (four biological replicates per condition) was performed using the DESeq2 R package (1.16.1).
Genome_build: rn4
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Rattus norvegicus

source_name: SC, CCI

growth_protocol: Adult male Sprague-Dawley rats (180-200 g)  were housed with a fixed light/dark cycle (12/12 h), a room temperature of 21–22 ℃, and ad libitum access to food and water. CCI rat model was established as previously described. Briefly, the left common sciatic nerve in each rat was exposed at the mid-thigh level. The area proximal to the sciatic nerve’s trifurcation was freed of adhering tissue, and four ligatures were tied loosely around it with approximately 1 mm between each ligature. The sciatic nerve was exposed but not ligated in sham group animals.

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Sequencing libraries were generated using NEBNextUltra RNA Library Prep Set for Illumina (NEB, USA.) following manufacturer’s recommendations.

treatment_protocol: SC tissues (L4-L6) collected from the rats in the Sham and CCI groups on postoperative day 10 were immersed in TRIzol(Invitrogen, CA, USA) , and immediately frozen in liquid nitrogen for the high-throughput RNA-seq.

tag: strain

value: Sprague-Dawley

tag: developmental stage

value: adult

value: male

value: CCI

tag: time

value: postoperative day 10

value: Lumbar spinal cord (L4-L6)


title: SC, CCI-1

description: spinal cord on postoperative day 10

tag: Sex


title: SC, CCI-4

description: spinal cord on postoperative day 10


title: SC, CCI-2

description: spinal cord on postoperative day 10


title: lacwt1_JS26_20

tag: replicate

value: Replicate 1


title: lacwt2_JS26_5

value: Replicate 2

tag: agent


title: lacwt1_JS26_5

tag: time point


title: lacwt3_JS26_5

value: Replicate 3


title: SC, Sham-4

description: spinal cord on postoperative day 10

source_name: SC, Sham

value: Sham

tag: tissue


title: lacwt3_0

value: WT


title: VCaP_ZBC260_R1_8h (RNA-seq)

value: prostate cancer


title: VCaP_AU_R2_24h (RNA-seq)

value: 1uM for 24h


title: DNA methylation of normal esophagus tissues [B797N]

type: genomic

city: Shantou

first: Yang

last: Chen

address: Department of Biochemistry and Molecular Biology, Shantou University Medical College, 22 Xinling Road, Shantou

institute: Shantou University Medical College

description: normal esophagus tissue

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: GenomeStudio Methylation Module v1.8

label: Cy5 and Cy3

source_name: esophagus tissue

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified according to standard instructions in Illumina

tag: gender

value: Male

value: normal esophagus tissue

tag: tissue status

value: normal


title: VCaP_AU_R1_24h (RNA-seq)

value: VCaP

tag: treatment


title: SC, Sham-2

description: spinal cord on postoperative day 10

value: Sprague-Dawley


title: SC, Sham-1

description: spinal cord on postoperative day 10

value: adult


title: SC, Sham-3

description: spinal cord on postoperative day 10

value: male


title: VCaP_AU_R2_12h (RNA-seq)

tag: dosage

value: 1uM for 12h


title: DNA methylation of ESCC tissues [B797T]

description: ESCC tissue

value: ESCC tissue

value: tumor


title: DNA methylation of normal esophagus tissues [C200N]

description: normal esophagus tissue

value: Female


title: DNA methylation of ESCC tissues [C200T]

description: ESCC tissue


title: Pythium myriotylum self-confrontation replicate 3

city: Nanjing

first: Paul

last: Daly

state: Jiangsu

address: 50 Zhongling St

institute: Jiangsu Academy of Agricultural Sciences

data_processing:
Raw data (raw reads) were processed using Trimmomatic (Bolger, Lohse et al. 2014). The reads containing poly-N and the low quality reads were removed to obtain the clean reads.
Downstream analysis of the cleaned reads was performed using the following software tool in UseGalaxy.eu (Afgan, Baker et al. 2018)
For all samples, reads that passed the filters were mapped using HISAT2 Galaxy Version 2.1.0 (Kim, Paggi et al. 2019) onto a composite reference genome that consisted of the genomes of both species. The composite genome was made by concatenating into a single file those Fasta files made of the sequences for the scaffolds of the genomes (see genome build).
Uniquely mapped read counts (at the MAPQ10 threshold) for each gene were calculated using HTSeq-count Galaxy version 0.9.1 (http://www-huber.embl.de/users/anders/HTSeq/doc/count.html) (Anders, Pyl et al. 2015).
FPKM normalised read counts were defined originally by (Mortazavi, Williams et al. 2008). In our study, an FPKM value for a gene from a sample is the number of uniquely mapped (to the composite genome) fragments (counts) per kilobase of gene model per million uniquely mapped (to the composite genome) fragments (counts) onto gene models from that species.
Genome_build: For P. myriotylum, JAAS_PmSWQ7_1_0_assembly.fsa (PRJNA692555) was used, and for P. oligandrum the ATCC 38472 strain genome (GCA_005966545.1_ASM596654v1) (Faure, Veyssiere et al. 2020) was used.
Supplementary_files_format_and_content: tab-delimited text files include read counts and FPKM values for each sample

organism: Pythium myriotylum

source_name: mycelia

growth_protocol: Precultures were grown on 10 % V8 juice agar at 25°C.

extract_protocol:
The sample was mixed with 1 mL of Trizol before the addition of 200 µl chloroform: isoamyl alcohol (24:1). The RNA was precipitated by mixing 0.8 volume of isopropanol with the aqueous phase from the previous step and the resulting pellet was washed once with 70% EtOH before resuspension in DEPC-treated water. The RNA was then cleaned-up using a Tiangen Plant RNA extraction kit which included an on-column DNase treatment. RNA integrity was visualised using an agarose gel and a Bioanalyzer, and RNA quantity and purity using a nanodrop spectrophotometer.
A paired library 2x150 bp was prepared using the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina).

treatment_protocol: From the edge of the colony of P. myriotylum SWQ7 or P. oligandrum GAQ1, 0.5 cm mycelial plugs were transferred to 10 % V8 juice agar covered with a 14.2 cm diameter polycarbonate membrane with a 0.1 µm pore size (GVS filter technology, Cat. no. 1215304) in a 14 cm Petri dish. The mycelial plugs were placed equidistant from each other and from the edge of the Petri dish. The Petri dishes were inoculated with either two plugs of the same species (self-confrontation) or with one plug from each species (mixed species confrontation). The cultures were incubated at 25°C in the dark and mycelia from the confrontation zone was sampled. The mycelium was flash frozen in liquid nitrogen before being ground using a Tissue Lyser.

tag: isolate


title: DNA methylation of ESCC tissues [B786T]

description: ESCC tissue


title: Pythium myriotylum and Pythium oligandrum confrontation replicate 3

organism:
Pythium oligandrum
Pythium myriotylum

value: SWQ7 and GAQ1


title: DNA methylation of normal esophagus tissues [B788N]

description: normal esophagus tissue


title: DNA methylation of normal esophagus tissues [B786N]

description: normal esophagus tissue


title: DNA methylation of ESCC tissues [B785T]

description: ESCC tissue


title: VCaP_AU_R1_12h (RNA-seq)

source_name: VCaP

tag: cancer type


title: Pythium myriotylum self-confrontation replicate 2


title: VCaP_AU_R2_8h (RNA-seq)

tag: cell line

value: 1uM for 8h


title: Pythium myriotylum self-confrontation replicate 1


title: DNA methylation of ESCC tissues [B788T]

description: ESCC tissue


title: lacwt2_0

value: Replicate 2

tag: genotype


title: uba2c_repeat2

first: xinjian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

data_processing:
Zebracall software used for basecalling.
FastQC was used to perform quality control on RNAseq sequencing data, and the qualified data was mapped to the Arabidopsis tair10 genome using the default parameters of HISAT2.
Samtools (version 1.9) was used to convert the mapped reads from SAM to BAM format, and then the featureCounts program with default parameters was applied for genomic quantification on the sequencing data.
The Fold Change > 2 and FDR <0.05 parameters of the R package edgeR was the standard for differentially expressed genes identified in mutants.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited text file include normalized reads for each sample.

organism: Arabidopsis thaliana

source_name: Arabidopsis seedlings

growth_protocol: Arabidopsis seedlings were grown on MS (Murashige and Skoog) medium plates with a long-day (LD) photoperiod (23℃, 16 h light/ 22℃, 8 h darkness).

extract_protocol:
Total RNA was isolated with Trizol reagent from two-week-old seedlings grown on MS plates in LD.
Sequencing libraries were built for RNA-seq (the single-ended 50-bp strategy).

tag: growth conditions

value: long day (16 h light, 8 h dark)

value: seedlings


title: Pythium myriotylum and Pythium oligandrum confrontation replicate 1


title: VCaP_AU_R1_8h (RNA-seq)

value: prostate cancer


title: DNA methylation of ESCC tissues [B804T]

description: ESCC tissue

value: Male


title: Pythium myriotylum and Pythium oligandrum confrontation replicate 2


title: DNA methylation of normal esophagus tissues [B783N]

description: normal esophagus tissue

value: normal esophagus tissue


title: PBS1_2_fpkm

city: Kaifeng

first: Haigang

last: wu

state: Henan province

address: dongjing Road

department: School of Life Sciences

institute: Henan University

data_processing:
Illumina Casava1.7 software used for basecalling
Sequenced reads were trimed for adaptor sequence, and masked for low-complexity or low quality sequence, then mapped to the mm8 hole genome using bowtie v0.12.2 with parameters set as defaults.
Reads for kilobased of exon per megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: mm8

organism: Mustela putorius furo

source_name: ferret epithelial cells NBL-7

growth_protocol: The cells were cultured in the DMEM/FBS medium

extract_protocol:
Cells tissue samples were lyzed and harvested using Trizol reagent. THe purification of RNA was performed using protocol provided by extracting kits (Total RNA Extraction Kit, Cat. R1200, Solarbio life science, China).
RNA library were prepared for sequencnig using standard illumina protocols

treatment_protocol: As paper discription

tag: cell type

value: ferret epithelial cells NBL-7

value: treated with particulate matter wit500 ug/mL


title: PBS1_3_fpkm

value: treated with particulate matter with500 ug/mL


title: VCaP_AU_R2_4h (RNA-seq)

value: VCaP

value: 1uM for 4h


title: DNA methylation of ESCC tissues [B800T]

description: ESCC tissue


title: DNA methylation of ESCC tissues [B783T]

description: ESCC tissue


title: DNA methylation of normal esophagus tissues [B804N]

description: normal esophagus tissue

value: normal


title: uba2c_repeat1


title: Col-0_repeat2

value: wild type


title: DNA methylation of ESCC tissues [B799T]

description: ESCC tissue

value: ESCC tissue

value: tumor


title: DNA methylation of normal esophagus tissues [B785N]

description: normal esophagus tissue


title: Col-0_repeat1


title: PBS1_1_fpkm

value: treated with particulate matter with 500 ug/mL


title: VCaP_DMSO_R1_24h (RNA-seq)

value: DMSO

value: vehicle control


title: Ep2_1_fpkmfpkm

value: treated with particulate matter with 250 ug/mL


title: VCaP_DMSO_R2_24h (RNA-seq)


title: DNA methylation of normal esophagus tissues [B800N]

description: normal esophagus tissue


title: DNA methylation of ESCC tissues [B798T]

description: ESCC tissue


title: Ep1_3_fpkmfpkm

value: untreated


title: DNA methylation of normal esophagus tissues [B799N]

description: normal esophagus tissue

value: Female


title: VCaP_AU_R1_4h (RNA-seq)

value: prostate cancer


title: Ep2_2_fpkmfpkm


title: DKO2 (HTGTS)

data_processing:
Library strategy: HTGTS
Analysis was done following HTGTS pipeline (https://github.com/robinmeyers/transloc_pipeline)
paired-end reads were trimmed with TranslocPreprocess.pl
full analysis was performed with TranslocWrapper.pl
Post filter analysis was done using TranslocFilter.pl with default parameters
Unique hits were selected from the prey coordinates from each sample
Genome_build: mm10
Supplementary_files_format_and_content: HTGTS-DFL-1_result.tlx.gz,HTGTS-DFL-2_result.tlx.gz,HTGTS-DKO-1_result.tlx.gz,HTGTS-DKO-2_result.tlx.gz, postfilter hits from HTGTS pipeline

source_name: Spleen

extract_protocol:
Genomic DNA was sonicated with 2 pulses of 5 secs and and 1 minute off using the Bioruptor pico sonicator (Diagenode).
LAM-PCR was performed using Phusion High-Fidelity DNA Polymerase (Thermo Fisher) and Sμ 5’ biotinylated bait (TAGTAAGCGAGGCTCTAAAAAGCA). 4 independent PCRs were run with ~2.5 μg of sonicated DNA each, with 90 cycles of primer elongation. The biotinylated DNA fragments were purified using Dynabeads T1 streptavidin beads (Invitrogen) at room temperature, on a rotisserie, overnight. On bead ligation was performed with T4 DNA ligase (NEB) and annealed bridge adaptors (GCGACTATAGGGCACGCGTGGNNNNNN-NH2 and 5’P-CCACGCGTGCCCTATAGTCGC-NH2) for 1h at 25°C, 2h at 22°C, and overnight at 16°C. 15 cycles of nested PCR were performed on the DNA-bead complexes using an Sμ nested primer (ACACTCTTTCCCTACACGACGCTCTTCCGATCT-GGTAAGCAAAGCTGGGCTTG) and a reverse universal primer I7 (GACTGGAGTTCAGACGTGTGCTCTTCCGATCT-GACTATAGGGCACGCGTGG). The bold regions represent the complementary regions to the genomic sequence in the Sμ nested primer and the bridge adaptor for I7 primer. PCR products were cleaned with the QIAquick Gel Extraction Kit (Qiagen) and the final barcoding/indexing PCR was performed using the P5-I5 and P7-I7 universal dual indexing primers (NEB) for 15 cycles and purified using Ampure beads purification with a cutoff of 200 bp. Library quality was evaluated by Bioanalyzer (Agilent) and sequencing performed using the Illumina Miseq Reagent Kit v2 (600 cycles) following the manufacturer’s instructions. DNA junctions from 2 independent experiments were combined for analyses.

tag: strain

value: Spleen

value: B cells

tag: age

value: 12 weeks of age

value: CD19 DKO


title: uba2c_H3K27me3_repeat2

data_processing:
Basecalls performed using bcl2fastq version 2.16.
FastQC was used for the quality control of high-throughput sequencing data.
The -k1 -N1 parameters of Bowtie2 (version 2.3.5.1) were used for data mapping to the Arabidopsis tair10 genome, and the format conversion of the mapped reads was realized through the default parameters of SAMtools (version 1.9) and BEDtools.
The -egf 0.85 -fdr df 0.01 -e 100 -g 200 -w 200 parameters of the sicer_df subroutine of the SICER2 were used to identify the ChIP-enriched regions of the sequencing data.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig files were generated using bamCoverage.

extract_protocol:
Chromatin isolated from 12-day-old seedlings in LD were subjected to sonication and immunoprecipitation with the anti-H3K27me3 antibody.
Libraries were built for ChIP-seq (Illumina HiSeq X Ten; 150-bp pair-end sequencing)

value: seedlings

value: long day (16 h light, 8 h dark)

tag: chip antibody

value: Millipore, 07-449


title: Ep2_3_fpkmfpkm

value: ferret epithelial cells NBL-7


title: DNA methylation of normal esophagus tissues [B798N]

description: normal esophagus tissue

value: Male

value: normal esophagus tissue

value: normal


title: Col-0_H3K27me3_repeat2

value: wild type


title: uba2c_H3K27me3_repeat1


title: Dfl1 (HTGTS)

value: Dfl


title: DKO1 (HTGTS)


title: Col-0_H3K27me3_repeat1


title: Dfl2 (HTGTS)


title: DNA methylation of normal esophagus tissues [B794N]

description: normal esophagus tissue


title: DNA methylation of ESCC tissues [B801T]

description: ESCC tissue

value: ESCC tissue

value: tumor


title: lacwt1_0

tag: replicate

value: Replicate 1

value: WT


title: DNA methylation of normal esophagus tissues [B801N]

description: normal esophagus tissue

value: Female


title: DNA methylation of ESCC tissues [C199T]

description: ESCC tissue


title: cell line U-2-OS

status: Public on Oct 27 2021

type: RNA

city: Freiburg

last: Vuaroqueaux

address: Am Flughafen 14

department: Bioinformatics

country: Germany

institute: 4HF Biotec

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: RMA preprocessing

label: biotin

source_name: cell line

label_protocol: Standard Affymetrix protocol

growth_protocol: Patient-derived xenografts were passaged from mouse to mouse until RNA extraction. Cell lines were used at low passages and checked by STR analysis to confirm their identity before preparing stock cryovials.

extract_protocol: RNA were extracted either from cells cultured in Petri dishes (in vitro cell culture) or from pieces of snap frozen tumor xenografts from four individual tumors of the same tumor model in the same or different passages using the mirVana kit (Ambion) according to the manufacturer’s instructions. A DNAse digest was performed. Each RNA preparation was subjected to quality control using NanoDrop 2000 to control for purity and Bioanalyzer (Agilent) to control for RNA integrity. Only  the RNA samples with an integrity number (RIN)  between 6.5 and 10  and a ratio between 28s and 18 sRNA between 1.0 and 2.0, and the RNA was pure (260/280 nm and 260/230 nm close to 2.0), were used for the microarray analysis.


title: cell line U-937


title: Ep1_1_fpkmfpkm

value: untreated


title: cell line VCAP

value: VCAP


title: cell line THP-1


title: cell line SW756


title: cell line T24


title: cell line UXF_1138


title: cell line T47D


title: Ep1_2_fpkmfpkm


title: cell line WSU-DLCL2


title: cell line TT2609-C02


title: cell line SXFS_1301


title: cell line SXFO_678


title: cell line SW620


title: DNA methylation of ESCC tissues [B791T]

description: ESCC tissue


title: DNA methylation of normal esophagus tissues [C199N]

description: normal esophagus tissue


title: DNA methylation of normal esophagus tissues [B791N]

description: normal esophagus tissue


title: DNA methylation of ESCC tissues [B782T]

description: ESCC tissue


title: cell line SU-DHL-4


title: cell line SW579


title: cell line SU-DHL-1


title: cell line SNU-899


title: cell line SNU-878


title: DNA methylation of ESCC tissues [B794T]

description: ESCC tissue


title: cell line SW1710


title: DNA methylation of normal esophagus tissues [B782N]

description: normal esophagus tissue


title: cell line SNU-449


title: cell line SNU-398


title: cell line SNU-16


title: cell line SNB-19


title: cell line SNU-423


title: cell line SNU-761


title: cell line SNU-475


title: cell line U-251MG


title: cell line SNU-1076


title: cell line SN12C


title: cell line SK-MES-1


title: cell line RXF_393


title: cell line RXF_2282


title: cell line SF268


title: cell line SF295


title: cell line SK-BR-3


title: cell line RXF_2516


title: cell line SK-HEP-1


title: cell line RXF_1220


title: cell line SNB-75


title: cell line SCLC-21H


title: cell line RXF_486


title: cell line SK-OV-3


title: cell line RPMI-2650


title: cell line SK-LMS-1


title: RNA-seq, iWAT adipocytes, rep 2

city: Odense M

first: Anne

last: Loft

address: Campusvej 55

department: Biochemistry & Molecular Biology

country: Denmark

institute: University of Southern Denmark

data_processing:
Sequencing reads were aligned to the mouse reference genome (version mm9) using STAR (Dobin et al. 2013, Bioinformatics; 29(1):15-21) with default parameters.
The number of exon reads for all RefSeq genes were counted and differential gene expression analyses (paired samples) were performed using iRNA-seq (Madsen et al. 2015, Nucleic Acids Res.;43(6):e40).
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files containing non-normalized tag counts for each sample as well as differential gene expression analyses for each comparison including normalized tag counts (output from iRNA-seq)

source_name: iWAT-derived primary adipocytes

growth_protocol: Brown adipose tissue (pooled interscapular, cervical, and axillary depots) as well as the epididymal (eWAT) and inguinal (iWAT) adipose tissue were optained from 4-5wk old male NMRI mice.  Adipose tissues were carefully minced and treated with collagenase (type II; Sigma) to separate the SVF from mature adipocytes.

extract_protocol:
Total RNA from primary adipocytes was purified using TRIzol (Invitrogen) according to the manufacturer’s instructions. RNA was treated with Ribo-ZeroTM rRNA removal kit (Epicentre) and subjected to fragmentation and cDNA-synthesis using the TruSeq2 RNA kit (Illumina).
cDNA-seq libraries were constructed according to the manufacturer's instructions (Illumina) as described in (Nielsen R, Mandrup S, 2014 Genome-Wide Profiling of Transcription Factor Binding and Epigenetic Marks in Adipocytes by ChIP-seq. Methods in Enzymology 2014, Vol. 537, pp. 261-279).

treatment_protocol: The isolated SVF cells were cultured under differentiation-inducing conditions in a medium consisting of DMEM (Sigma), 10% newborn calf serum (NCS) (HyClone), 30 nM insulin, 25 μg/ml sodium ascorbate, 10 mM HEPES, pH 7.4, at 37°C, 4 mM l-glutamine (Invitrogen), 100 μg/ml streptomycin, 62.5 μg/ml penicillin, and 1 μM rosiglitazone (Novo Nordisk). The cultures were harvested 8 days after plating and for comparison between the in vitro differentiated adipocytes, only cultures with a >50% degree of differentiation were used.

value: Primary in vitro differentiated SVF cells

tag: adipose depot

value: iWAT


title: RNA-seq, BAT adipocytes, rep 2

source_name: BAT-derived primary adipocytes

value: BAT


title: RNA-seq, iWAT adipocytes, rep 1


title: RNA-seq, BAT adipocytes, rep 1


title: RNA-seq, eWAT adipocytes rep 1

source_name: eWAT-derived primary adipocytes

value: eWAT


title: RNA-seq, eWAT adipocytes, rep 2


title: cell line RXF_1183

first: Vincent


title: cell line RH-41


title: cell line RXF_1781


title: cell line RT112


title: cell line RPMI-8226


title: cell line RH-30


title: cell line PXF_1752


title: cell line RD-ES

value: RD-ES


title: cell line RCH-ACV

value: RCH-ACV


title: MDA-MB-231 tumorigenic BC cells treated with a small molecules CtBP2 inhibitor named HIPP - replicate5

city: Cefalù

first: Valentina

last: Bravatà

address: Contrada Pietrapollastra Pisciotto

country: Italy

institute: IBSBC CNR

description: Biological replicate 5 of 5

hyb_protocol: The microarrays (Agilent Whole Human Genome, 4x44k) were hybridazed according to an established protocol by Agilent Technologies (Santa Clara, CA, USA). Two-channel arrays were hybridized using Cy3 and Cy5 and quantified using Feature Extraction v9.5 software. The Agilent Whole Human Genome Array (4x44K) was used for competitive hybridization and the slides were washed, dried, and scanned in an Agilent microarray scanner (Agilent Technologies, Palo Alto, CA, USA).

scan_protocol: Images were scanned using Agilent scanner, G2505B (Agilent Technologies, Palo Alto, CA, USA).

data_processing: Agilent Data Processing Protocol Calculation Method: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software. FeatureExtractor_Version: 9.5.3.1. Protocol_Name: GE2-v5_95_Feb07.

source_name: Human breast cancer MDA-MB-231 cell line

label_protocol: 500 ng of total RNA was amplified according to the manufacturer’s instructions by double strand cDNA synthesis, followed by T7-based in vitro transcription. MDA-MB-231 untreated cells were used as a control. Amplified complementary RNA (cRNA) was labeled with cyanine 5 (Cy5)-conjugated dUTP, whereas cRNA of the chosen control, was labeled with cyanine 3 (Cy3)-conjugated dUTP.

growth_protocol: shCtBP2, HIPP and P4 MDA-MB-231 BC cell lines treated, all compared to control sample represented by untreated MDA-MB-231 BC cell line, were collected after 24 hours post treatments.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: original tissue

value: Breast cancer

value: HIPP

source_name: untreated human breast cancer MDA-MB-231 cell line


title: cell line RKO

value: RKO


title: MDA-MB-231 tumorigenic BC cells treated with a small molecules CtBP2 inhibitor named P4 - replicate4

description: Biological replicate 4 of 5


title: cell line PXF_698


title: cell line PC-3M


title: cell line PL-21


title: cell line PXF_1118


title: cell line PAXF_2059


title: cell line PAXF_546


title: MDA-MB-231 tumorigenic BC cells treated with a small molecules CtBP2 inhibitor named P4 - replicate1

description: Biological replicate 1 of 5


title: cell line RAJI

value: RAJI


title: cell line PAXF_1998


title: cell line PAXF_2005


title: cell line PAXF_1986


title: cell line PAXF_1657


title: MDA-MB-231 tumorigenic BC cells treated with a small molecules CtBP2 inhibitor named P4 - replicate5

description: Biological replicate 5 of 5


title: MDA-MB-231 tumorigenic BC cells with stable RNA interference of CtBP2 - replicate5

description: Biological replicate 5 of 5


title: MDA-MB-231 tumorigenic BC cells with stable RNA interference of CtBP2 - replicate3

description: Biological replicate 3 of 5


title: MDA-MB-231 tumorigenic BC cells treated with a small molecules CtBP2 inhibitor named P4 - replicate2

description: Biological replicate 2 of 5


title: MDA-MB-231 tumorigenic BC cells treated with a small molecules CtBP2 inhibitor named HIPP - replicate4

description: Biological replicate 4 of 5


title: MDA-MB-231 tumorigenic BC cells treated with a small molecules CtBP2 inhibitor named P4 - replicate3

description: Biological replicate 3 of 5


title: MDA-MB-231 tumorigenic BC cells with stable RNA interference of CtBP2 - replicate4

description: Biological replicate 4 of 5


title: cell line PAXF_1997


title: MDA-MB-231 tumorigenic BC cells treated with a small molecules CtBP2 inhibitor named HIPP - replicate3

description: Biological replicate 3 of 5


title: MDA-MB-231 tumorigenic BC cells treated with a small molecules CtBP2 inhibitor named HIPP - replicate2

description: Biological replicate 2 of 5


title: MDA-MB-231 tumorigenic BC cells treated with a small molecules CtBP2 inhibitor named HIPP - replicate1

description: Biological replicate 1 of 5


title: cell line PAXF_2035


title: cell line PA-TU-8902


title: cell line OVXF_899


title: cell line OVXF_1023


title: cell line PANC-1


title: MDA-MB-231 tumorigenic BC cells with stable RNA interference of CtBP2 - replicate1

description: Biological replicate 1 of 5


title: cell line OVCAR-8


title: MDA-MB-231 tumorigenic BC cells with stable RNA interference of CtBP2 - replicate2

description: Biological replicate 2 of 5


title: LB31 BLNK YF 3 (BLNK2)

city: Tokyo

first: Takuro

last: Nakamura

address: 3-8-31 Ariake, Koto-ku

department: The Cancer Institute

country: Japan

institute: Japanese Foundation for Cancer Research

description: Gene expression data from mouse preB-ALL cells

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430_2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: preB-ALL cell established from Blnk KO mouse introduced with loss-of-function mutant Blnk cDNA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: B220-positive mouse bone marrow cells were fractionated by cell sorter. LB31 mouse preB-ALL cells were cultured in RPMI1640 supplemented with 10% FBS and 5 ng/ml IL7-.

extract_protocol: Total RNA was purified using RNA Easy kit (QIAGEN) according to the manufacturer's protocol

treatment_protocol: LB31 cells were transduced with pMY retroviral vectors with or without Blnk or Blnk mutant cDNAs.

value: preB-ALL cell line LB31

tag: transduced with

value: retrovirus vector containing mutant Blnk cDNA


title: cell line OVCAR-5


title: LB31 BLNK 3 (BLNK2)

source_name: preB-ALL cell established from Blnk KO mouse introduced with Blnk cDNA

value: retrovirus vector containing Blnk cDNA


title: LB31 BLNK YF 2 (BLNK2)


title: cell line OVCAR-4


title: LB31 BLNK 1 (BLNK2)


title: cell line OE21


title: cell line OPM-2


title: LB31 BLNK 2 (BLNK2)


title: LB31 pMY 3 (BLNK2)

source_name: preB-ALL cell established from Blnk KO mouse introduced with empty vector

value: empty vector


title: cell line OCI-AML3


title: cell line OCUM-1


title: LAP tg/BLNK KO BM 3 (BLNK2)

description: Gene expression data from mouse bone marrow

source_name: mouse B220-positive bone marrow cells

value: bone marrow B-lymphocytes

tag: derived from

value: Blnk KO/LAP tg mice


title: LB31 pMY 2 (BLNK2)


title: cell line OCI-AML2


title: LAP tg/BLNK KO BM 2 (BLNK2)


title: cell line NOMO-1


title: LB31 pMY 1 (BLNK2)


title: cell line NUGC-4


title: Blnk KO BM 2 (BLNK2)

value: Blnk KO mice


title: cell line NCI-H69


title: cell line NCI-H929


title: cell line NCI-H727


title: LAP tg BM 2 (BLNK2)

value: Cebpb LAP transgenic mice


title: LAP tg BM 3 (BLNK2)


title: LAP tg/BLNK KO BM 1 (BLNK2)


title: High Arsenic exposed subject  KW93

city: Maastricht

first: Danyel

last: Jennen

address: Universiteitssingel 40

department: Toxicogenomics

institute: Maastricht University

hyb_protocol: For analysis of DNA methylation levels, the Human DNA Methylation 2.1M Deluxe Promoter Array (Roche NimbleGen) was used. This array has a density of 2.1 million probes (50-75 oligonucleotides long, median probe spacing 100 bp) that represent all annotated human promoters (~ 26,210), 27,867 CpG islands, and 750 miRNA promoters per slide. The promoters and CpG islands largely overlap with transcription start sites of well characterized RefSeq genes, covering, on average, 8 kb upstream and 3 kb downstream. Labeling and hybridization of arrays was performed according to the manufactures’ protocol. In brief, 1 µg of Input DNA and 1 µg of MeDIP DNA were labeled with Cy3 and Cy5 respectively by random priming using the Dual Color DNA labeling kit (Roche NimbleGen). The labeled samples were precipitated using isopropanol and quantified spectrophotometrically using the NanoDrop 1000. 34 µg of Cy3 Input and 34 µg of Cy5 MeDIP DNA were pooled and completely dried by using a speed vac. The pellet was dissolved in hybridization solution using the NimbleGen Hybridization kit. After denaturing, the probe was hybridized overnight on the 2.1M Deluxe Promoter Arrays using the HX1 mixers and the NimbleGen Hybridization system 4. Slides were washed using the NimbleGen wash buffer kit and scanned using the 2 µm high resolution NimbleGen MS 200 micro array scanner.

scan_protocol: Slides were scanned using the 2 µm high resolution NimbleGen MS 200 micro array scanner per manufacturer's protocol.

data_processing:
Signal intensity data was extracted from the scanned images of each array using NimbleScan v2.6 software and quantile normalized on a per channel basis. Log2 ratios of the intensities were computed (ratio of MeDIP signal / Input signal) and for each array, centering was performed by subtracting the global array bi-weight mean of the log2 ratios such that the computed log2 ratios were centered around 0. Identiﬁcation of methylated regions was performed using the Probe Sliding Window-ANOVA algorithm (PSW-ANOVA). PSW-ANOVA was implemented in the R statistical programming environment (v2.15.3) (http://www.r-project.org) as a custom script and was provided by Roche NimbleGen. PSW-ANOVA (sliding window of 750 bp comprising 7 probes without selection of a cutoff p-value) was used to identify methylated regions.  Peaks were identified in the methylated regions by searching for regions containing at least 8 consecutive probes.   Peaks were mapped to promoter regions (from 3 kb upstream to 1 kb downstream of the transcription start site (20) and CpG islands of genes using the NimbleScan v2.6 software.
[CpG_sites_arsenic_Pakistan.txt]  Scaled, log2 (medip/Input) ratio for demethylated regions

source_name: input DNA from human buffy coat

label_protocol: Genomic DNA was sonicated to obtain fragments ranging from 200 bp to 600 bp. MeDIP was performed using the MagMeDIP kit (Diagenode, Liège, Belgium) according to the manufacturer’s protocol. In brief, IP incubation mix (containing magbuffer A, magbuffer B, 1.5 µg methylated DNA positive control, 1.5 µg non-methylated DNA negative control) was added to 10 µg of sonicated sample and denatured at 95 °C. 10% of this was kept aside as Input sample and stored at 4°C. Beads were washed 3 times with ice-cold diluted magbuffer A and collected in 20 µl of diluted magbuffer A. The remaining sample was immunoprecipitated using 5µl of antibodymix (containing an antibody against 5’-methylcytidine (provided in the kit) magbuffer A and magbuffer C) and 20 µl of magnetic beads solution. Immunoprecipitation was performed overnight at 4 °C on a rotating wheel. The following day, magnetic beads were washed twice with wash buffer 1 and once with wash buffer 2 and kept on ice. Next, DNA elution was performed using the IPure kit (Diagenode, Liège, Belgium). 50 µl of elution buffer was added to the MeDIP-bead pellet and 92.5 µl to the Input sample and incubated for 15 min at room temperature on a rotating wheel. Supernatant was transferred to a new Eppendorf tube using a magnetic rack at room temperature. Samples were subsequently incubated with 2 µl of glycogen carrier, 100 µl of 100% isopropanol and 15 µl of magnetic beads and incubated for 1 hour at room temperature on a rotating wheel. Magnetic beads were washed using wash buffer 1 and wash buffer 2 for 5 minutes. The DNA was eluted twice by using 75 µl of buffer C and incubated for 15 min at room temperature on a rotating wheel. All the samples were precipitated with sodium acetate and ethanol with glycogen as a carrier for 30 min at -80 °C and centrifuged at max speed for 30 min at 4°C. The cell pellet was washed using 70% ethanol and after air drying suspended in 20µl MQ. 20 ng of both Input and MeDIP samples were used for amplification by whole genome amplification (WGA) using the WGA2 and WGA3 kit (Sigma Aldrich) following the manufacturer’s instruction, without performing the fragmentation step. WGA reactions were cleaned up using silica columns (Sigma Aldrich) and eluted in water. Methylation enrichment in the paired samples MeDIP/Input was derived from qPCR data by calculating the ratio positive control/negative control, applying the ΔΔCq method using the primers included in the kit.

extract_protocol: DNA used for MeDIP-Chip analyses was isolated from buffy coats using standard phenol-chloroform method. The total amount was at least 10 µg DNA, the 260/280 ratio ranged between 1.7-1.9, and the 260/230 ratio appeared higher than 1.6. A total of 57 DNA samples were prepared for the MeDIP-Chip experiments.

tag: exposure

value: High Arsenic exposed

tag: tissue

value: buffy coat

source_name: medip DNA from human buffy coat

value: monoclonal antibody against 5’-methylcytidine


title: cell line NCI-H522


title: LAP tg BM 1 (BLNK2)


title: High Arsenic exposed subject  KW89


title: cell line PA-TU-8988T


title: cell line NCI-H441


title: cell line NCI-H460


title: High Arsenic exposed subject  KW85


title: High Arsenic exposed subject  KP169


title: cell line NCI-H345


title: cell line NCI-H2171


title: cell line NCI-H82


title: wt BM 2 (BLNK2)

value: wild type mice


title: cell line NCI-H1299


title: High Arsenic exposed subject  KW81


title: wt BM 1 (BLNK2)


title: High Arsenic exposed subject  KW80


title: cell line NCI-H1975


title: wt BM 3 (BLNK2)


title: Blnk KO BM 1 (BLNK2)


title: cell line NCI-H1184


title: High Arsenic exposed subject  BD176


title: High Arsenic exposed subject  KP148


title: High Arsenic exposed subject  KP158


title: High Arsenic exposed subject  KW87


title: High Arsenic exposed subject  KM43


title: cell line MV4-11


title: High Arsenic exposed subject  SC39


title: High Arsenic exposed subject  BD191


title: cell line MOLT-4


title: cell line MOLP-2


title: cell line MOLM-6


title: LB31 BLNK YF 1 (BLNK2)


title: cell line MKN45


title: cell line MSTO-211H


title: High Arsenic exposed subject  GR132


title: cell line MOLM-13


title: cell line MM.1S


title: High Arsenic exposed subject  GR134


title: High Arsenic exposed subject  GR126


title: cell line MKN7


title: Medium Arsenic exposed subject  BD178

value: Medium Arsenic exposed


title: High Arsenic exposed subject  SM12


title: cell line MKN1


title: High Arsenic exposed subject  KW84


title: High Arsenic exposed subject  SC34


title: Medium Arsenic exposed subject  KP173


title: cell line MINO

value: MINO


title: cell line MEXF_622


title: cell line MIA-PaCa-2


title: cell line MEXF_535


title: cell line MEXF_520


title: cell line MEXF_462


title: cell line MEXF_394


title: Medium Arsenic exposed subject  KP160


title: High Arsenic exposed subject  GR115


title: cell line MFE-319


title: Medium Arsenic exposed subject  KP156


title: Medium Arsenic exposed subject  KP151


title: Medium Arsenic exposed subject  GR112


title: Medium Arsenic exposed subject  GR135


title: Medium Arsenic exposed subject  KW78


title: Medium Arsenic exposed subject  KW76


title: Medium Arsenic exposed subject  CF74


title: Medium Arsenic exposed subject  KM59


title: cell line MEXF_2090


title: cell line MEXF_1341


title: cell line MEXF_1829


title: Medium Arsenic exposed subject  KM46


title: Medium Arsenic exposed subject  SM20


title: cell line MEXF_276


title: cell line MEG-01


title: cell line MEC-1


title: cell line MDA-MB-468


title: Medium Arsenic exposed subject  KW83


title: cell line MDA-MB-231


title: cell line MDA-MB-453


title: Medium Arsenic exposed subject  SC33


title: Medium Arsenic exposed subject  SM8


title: Medium Arsenic exposed subject  SM17


title: cell line MAXF_401


title: Medium Arsenic exposed subject  SM7


title: cell line MCF7


title: Medium Arsenic exposed subject  KM54


title: Low Arsenic exposed subject  BD193

value: Low Arsenic exposed


title: cell line LXFL_1674


title: cell line LXFL_430


title: Low Arsenic exposed subject  BD174


title: Low Arsenic exposed subject  KM47


title: Low Arsenic exposed subject  BD190


title: cell line M059K


title: Low Arsenic exposed subject  GR140


title: cell line LXFL_529


title: Low Arsenic exposed subject  SC29


title: Low Arsenic exposed subject  SC26


title: Low Arsenic exposed subject  AK201


title: Low Arsenic exposed subject  BD195


title: cell line LXFL_1121


title: Blnk KO BM 3 (BLNK2)


title: cell line LXFL_1072


title: cell line LXFA_983


title: Low Arsenic exposed subject  BD187


title: Low Arsenic exposed subject  BD192