title: Mature_Mast_Cell_31

value: Live Lin- c-Kit+ FcεRI+ integrin β7low SSChi cells


title: RNASeq  ADAR1-p150OE_5-AZA-CdR_rep2

status: Public on Oct 20 2020

type: SRA

city: Toronto

first: Sajid

middle: A

last: Marhon

state: ON

address: 101 College Street

country: Canada

institute: Princess Margaret Cancer Centre

library_source: transcriptomic

data_processing:
RNAseq and MDA5-protection libraries have been aligned to the hg19 genome using the STAR aligner.
ADAR1 Editing had been called in the MDA5- protection library.
Inverted Repeats Alus have been detected in the MDA5-protected samples.
CUT&RUN library has been aligned to the hg19 genome using bowtie2 and normalized by the yeast (Saccharomyces cerevisiae)  spikein reads.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files for the RNASeq and MDA5-protection libraries are separated for the forward strand (Positive) and reverse strand (Negative).  Editing tables includes editing/mismatches within Alu repeats. Each table includes the editing in the two replicates of each genotype/treatment condition. It includes the depth of the reference and alternative nucleotide in each replicate and the total depth in the two replicates.  Inverted repeat tables are the tables for 5-AZA-CdR treatment-induced IR list, baseline IR list and the ADAR1KD Mock-treated-induced IR list. 5-AZA-CdR treatment-induced IR list are listed in two tables, one includes their expression in the ADAR1WT 5-AZA-CdR and the other includes their expression in the ADAR1WT Mock-treated sample. Baseline IR are listed in three tables which include their expression in the ADAR1WT Mock-treated, ADAR1WT 5-AZA-CdR, and the ADAR1KD Mock-treated samples. ADAR1KD Mock-treated-induced IR are listed in two tables which include their expression in the ADAR1WT Mock-treated and ADAR1KD Mock-treated samples.
Supplementary_files_format_and_content: githup_data.tar: Metadata for use with githup script.

molecule: total RNA

organism: Homo sapiens

source_name: RNASeq  ADAR1-p150OE_5-AZA-CdR_rep2

growth_protocol: Patient-derived colorectal cancer cells #92 were cultured in DMEM/F12 medium, supplemented with L-glutamine (1%), penicillin/streptomycin (1%), Fungizone, Non-essential amino acids (1X), Sodium Pyruvate (1mM), Heparin (4ug/ml Sigma),Neurocult SM1(STEMCELL), N2 supplement (STEMCELL), Lipids (0.2%, Sigma), EGF (20ng/ml, Reprokine) and basic FGF (10ng/ml,Reprokine).

extract_protocol:
Total RNA was extracted from 5-AZA-CdR or mock-treated samples using  QIAGEN RNeasy mini kit.  DNA was extracted for CUT&RUN using QIAGEN MinElute Kit.
For the MDA5 protection assay 100ng of RNA was used for the cDNA library construction using KAPA RNA Hyper-Prep with RiboErase library preparation kit from Roche.  For the RNA sequencing on total RNA, libraries were prepared using TruSeq Stranded Total RNA Kit (Illumina) and 200ng of RNA underwent ribosomal RNA depletion using Ribo-zero Gold rRNA beads. For DNA-sequencing, libraries were prepared using NEB Ultra II library Preparation kit

treatment_protocol: Patient-derived colorectal cancer cells#92  were seeded as 50,000 cells/mL 6-24hrs prior to treatment, then they were treated with 300nM of 5-AZA-CdR or mock-treated, they were kept in culture for 5days and then were collected

tag: cell type

value: Patient-derived colorectal cancer#92

tag: genotype

value: ADAR1 p150 OE

tag: time

tag: treatment


title: p20050_s005_7162_d10_BAL

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

country: USA

institute: Yerkes National Primate Research Center

description:
p20050_s005_7162_d10_BAL_S5
processed data file:
p20050_MacaM_RawCount.txt
p20050_MacaM_DESeq2_NormCount.txt

data_processing:
Illumina bcl2fastq v2.17.1.14 was used for demultiplexing.
Composite reference was generated by concatenating sequence (.fa) and annotation (.gtf) files for host and viral genome references
Reads were mapped to the Composite (MacaM MN985325.1)  genomic reference with STAR (v2.7.3a) with default alignment parameters.
Abundance estimation of raw read counts per transcript was done internally with STAR using the algorithm of htseq-count.
Normalized abundace was caluclated with DESeq2 R Package (version 1.26.0)
Genome_build: MacaM v7 (MacaM_Rhesus_Genome_v7.fasta,MacaM_Rhesus_Genome_Annotation_v7.8.2.gtf) (https://www.unmc.edu/rhesusgenechip/index.htm).
Genome_build: MN985325.1, SARS-CoV2 (strain MN985325.1) was downloaded from NCBI (https://www.ncbi.nlm.nih.gov/nuccore/MN985325)
Supplementary_files_format_and_content: tab delimited text file containing raw or normalized read counts for each sample (in columns) and each annotated transcript (in rows).

organism: Macaca mulatta

source_name: Group I_d10_BAL

extract_protocol:
RNA was extracted from PAXgene RNA Blood Tubes using the MagMAX for Stabilized Blood Tubes RNA Isolation Kit (ThermoFisher). RNA was extracted from BAL fluid stored in PAXgene RNA Blood Tubes using the PAXgene Blood RNA Kit IVD (Qiagen).
Globin transcripts in the blood RNA were blocked prior to library prep using the FastSelect Globin Reagent (Qiagen). Libraries were prepared using the Clontech SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio) in combination with the NexteraXT DNA Library Preparation kit (Illumina). Libraries were validated by capillary electrophoresis on an Agilent 4200 TapeStation, pooled at equimolar concentrations, and sequenced on an Illumina NovaSeq6000 at 100SR, yielding 25 million reads per sample.

tag: animalid

tag: timepoint

tag: group

tag: tissue

value: BAL


title: RNASeq  ADAR1-p150OE_5-AZA-CdR_rep1

source_name: RNASeq  ADAR1-p150OE_5-AZA-CdR_rep1


title: p20050_s052_7252_d7_BAL

description:
p20050_s052_7252_d7_BAL_S52
processed data file:
p20050_MacaM_RawCount.txt
p20050_MacaM_DESeq2_NormCount.txt

source_name: Group III_d7_BAL


title: p20050_s046_7250_d7_BAL

description:
p20050_s046_7250_d7_BAL_S46
processed data file:
p20050_MacaM_RawCount.txt
p20050_MacaM_DESeq2_NormCount.txt


title: RNASeq  ADAR1-p150OE_Mock-Treated_rep2

source_name: RNASeq  ADAR1-p150OE_Mock-Treated_rep2

value: Mock-Treated


title: RNASeq  ADAR1-p150OE_Mock-Treated_rep1

source_name: RNASeq  ADAR1-p150OE_Mock-Treated_rep1


title: Mature_Mast_Cell_30

city: Solna

first: Joakim

middle: S

last: Dahlin

address: CMM, Visionsgatan 18

department: Department of Medicine, Solna

country: Sweden

institute: Karolinska Institutet

data_processing:
RNA-seq reads were aligned to mm10 using GSNAP (version 2015-09-29) with parameters (-B 5 -t 24 -n 1 -Q -N 1).
Reads in features were counted with htseq-count (HTSeq version 0.5.3p3) with the parameter (-s no).
Genome_build: mm10
Supplementary_files_format_and_content: HTSeq counts(.txt)

molecule: polyA RNA

organism: Mus musculus

source_name: Peritoneal cells

extract_protocol:
189 single cells were index-sorted into 2 x 96-well PCR plates containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton per well), vortexed and frozen at -70 °C. Sample preparation for RNA-sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) with minor modifications. Following brief centrifugation at 2000 rpm for 2 minutes to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 50 U/reaction SmartScribe Reverse Transcriptase (Takara ClonTech, 639537) without Betaine and MgCl2, and amplified using 23 PCR cycles. ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882) using BioMek FXP Dual Span Liquid Handler. Single cell cDNA library was eluted in 22 µl volume of EB Buffer (Qiagen, 19086) and 20 µl volume collected to ensure minimal bead carryover.
Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set A and D (Illumina, FC-121-2001 and FC-121-2004 respectively), following the manufacturer’s protocol using ¼ of the recommended volumes and 1.26 µl cDNA library. Single cell libraries labelled with Index Kit A and D were pooled separately and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 32.0 µl EB Buffer and 30.0 µl volume collected to ensure minimal bead carryover. Quantification was performed with KAPA Library Quant Kit (Roche, 07960140001); index kit A pooled libraries were mixed with equimolar concentration of index kit D pooled libraries and sequenced in one lane on the Illumina HiSeq4000 system (50 bp single-end reads).

tag: strain

value: Mature mast cell

tag: sorting strategy

tag: gender

value: female


title: Mature_Mast_Cell_2


title: p20050_s040_7244_d7_BAL

description:
p20050_s040_7244_d7_BAL_S40
processed data file:
p20050_MacaM_RawCount.txt
p20050_MacaM_DESeq2_NormCount.txt


title: RNASeq  CTRL_5-AZA-CdR_rep1

source_name: RNASeq  CTRL_5-AZA-CdR_rep1

value: Wild type (LUC)


title: p20050_s034_7182_d7_BAL

description:
p20050_s034_7182_d7_BAL_S34
processed data file:
p20050_MacaM_RawCount.txt
p20050_MacaM_DESeq2_NormCount.txt

source_name: Group II_d7_BAL


title: p20050_s022_7173_d7_BAL

description:
p20050_s022_7173_d7_BAL_S22
processed data file:
p20050_MacaM_RawCount.txt
p20050_MacaM_DESeq2_NormCount.txt


title: RNASeq  CTRL_5-AZA-CdR_rep2

source_name: RNASeq  CTRL_5-AZA-CdR_rep2


title: RNASeq  CTRL-Mock-Treated_rep2

source_name: RNASeq  CTRL-Mock-Treated_rep2


title: p20050_s028_7174_d7_BAL

description:
p20050_s028_7174_d7_BAL_S28
processed data file:
p20050_MacaM_RawCount.txt
p20050_MacaM_DESeq2_NormCount.txt


title: Mature_Mast_Cell_26


title: CUT&RUN H3K27ac ADAR1WT_MockTreated_D5

description: CUTnRUN_ADAR1WT_Mock-treated_H3K27ac.hg19.bw

library_source: genomic

data_processing:
Library strategy: CUT&RUN
RNAseq and MDA5-protection libraries have been aligned to the hg19 genome using the STAR aligner.
ADAR1 Editing had been called in the MDA5- protection library.
Inverted Repeats Alus have been detected in the MDA5-protected samples.
CUT&RUN library has been aligned to the hg19 genome using bowtie2 and normalized by the yeast (Saccharomyces cerevisiae)  spikein reads.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files for the RNASeq and MDA5-protection libraries are separated for the forward strand (Positive) and reverse strand (Negative).  Editing tables includes editing/mismatches within Alu repeats. Each table includes the editing in the two replicates of each genotype/treatment condition. It includes the depth of the reference and alternative nucleotide in each replicate and the total depth in the two replicates.  Inverted repeat tables are the tables for 5-AZA-CdR treatment-induced IR list, baseline IR list and the ADAR1KD Mock-treated-induced IR list. 5-AZA-CdR treatment-induced IR list are listed in two tables, one includes their expression in the ADAR1WT 5-AZA-CdR and the other includes their expression in the ADAR1WT Mock-treated sample. Baseline IR are listed in three tables which include their expression in the ADAR1WT Mock-treated, ADAR1WT 5-AZA-CdR, and the ADAR1KD Mock-treated samples. ADAR1KD Mock-treated-induced IR are listed in two tables which include their expression in the ADAR1WT Mock-treated and ADAR1KD Mock-treated samples.
Supplementary_files_format_and_content: githup_data.tar: Metadata for use with githup script.

molecule: genomic DNA

source_name: CUT&RUN H3K27ac ADAR1WT_MockTreated_D5

value: Wild type (LACZ)


title: RNASeq  CTRL-Mock-Treated_rep1

source_name: RNASeq  CTRL-Mock-Treated_rep1


title: p20050_s016_7172_d7_BAL

description:
p20050_s016_7172_d7_BAL_S16
processed data file:
p20050_MacaM_RawCount.txt
p20050_MacaM_DESeq2_NormCount.txt

source_name: Group I_d7_BAL


title: Mature_Mast_Cell_28


title: Mature_Mast_Cell_27


title: RNASeq ADAR1KD_PIC_D24_rep2

description:
RNASeq_hg19_ADAR1KD_PIC_D24.Pos.bw
RNASeq_hg19_ADAR1KD_PIC_D24.Neg.bw

source_name: RNASeq ADAR1KD_PIC_D24_rep2

value: ADAR1 Knockdown


title: Mature_Mast_Cell_23


title: Mature_Mast_Cell_25


title: p20050_s004_7162_d7_BAL

description:
p20050_s004_7162_d7_BAL_S4
processed data file:
p20050_MacaM_RawCount.txt
p20050_MacaM_DESeq2_NormCount.txt


title: RNASeq ADAR1KD_PIC_D24_rep1

source_name: RNASeq ADAR1KD_PIC_D24_rep1


title: Mature_Mast_Cell_24


title: p20050_s010_7165_d7_BAL

description:
p20050_s010_7165_d7_BAL_S10
processed data file:
p20050_MacaM_RawCount.txt
p20050_MacaM_DESeq2_NormCount.txt


title: Mature_Mast_Cell_29


title: p20050_s051_7252_d4_BAL

description:
p20050_s051_7252_d4_BAL_S51
processed data file:
p20050_MacaM_RawCount.txt
p20050_MacaM_DESeq2_NormCount.txt

source_name: Group III_d4_BAL


title: RNASeq ADAR1KD_PIC_D14_rep2

description:
RNASeq_hg19_ADAR1KD_PIC_D14.Pos.bw
RNASeq_hg19_ADAR1KD_PIC_D14.Neg.bw

source_name: RNASeq ADAR1KD_PIC_D14_rep2


title: p20050_s045_7250_d4_BAL

description:
p20050_s045_7250_d4_BAL_S45
processed data file:
p20050_MacaM_RawCount.txt
p20050_MacaM_DESeq2_NormCount.txt


title: RNASeq ADAR1KD_PIC_D5_rep2

description:
RNASeq_hg19_ADAR1KD_PIC_D5.Pos.bw
RNASeq_hg19_ADAR1KD_PIC_D5.Neg.bw

source_name: RNASeq ADAR1KD_PIC_D5_rep2


title: p20050_s039_7244_d4_BAL

description:
p20050_s039_7244_d4_BAL_S39
processed data file:
p20050_MacaM_RawCount.txt
p20050_MacaM_DESeq2_NormCount.txt


title: Mature_Mast_Cell_22


title: Mature_Mast_Cell_21


title: Mature_Mast_Cell_20


title: RNASeq ADAR1KD_5-AZA-CdR_D24_rep2

description:
RNASeq_hg19_ADAR1KD_5-AZA-CdR_D24.Pos.bw
RNASeq_hg19_ADAR1KD_5-AZA-CdR_D24.Neg.bw

source_name: RNASeq ADAR1KD_5-AZA-CdR_D24_rep2


title: p20050_s027_7174_d4_BAL

description:
p20050_s027_7174_d4_BAL_S27
processed data file:
p20050_MacaM_RawCount.txt
p20050_MacaM_DESeq2_NormCount.txt

source_name: Group II_d4_BAL


title: RNASeq ADAR1KD_5-AZA-CdR_D24_rep1

source_name: RNASeq ADAR1KD_5-AZA-CdR_D24_rep1


title: p20050_s033_7182_d4_BAL

description:
p20050_s033_7182_d4_BAL_S33
processed data file:
p20050_MacaM_RawCount.txt
p20050_MacaM_DESeq2_NormCount.txt


title: p20050_s009_7165_d4_BAL

description:
p20050_s009_7165_d4_BAL_S9
processed data file:
p20050_MacaM_RawCount.txt
p20050_MacaM_DESeq2_NormCount.txt

source_name: Group I_d4_BAL


title: RNASeq ADAR1KD_5-AZA-CdR_D14_rep2

description:
RNASeq_hg19_ADAR1KD_5-AZA-CdR_D14.Pos.bw
RNASeq_hg19_ADAR1KD_5-AZA-CdR_D14.Neg.bw

source_name: RNASeq ADAR1KD_5-AZA-CdR_D14_rep2


title: RNASeq ADAR1KD_5-AZA-CdR_D14_rep1

source_name: RNASeq ADAR1KD_5-AZA-CdR_D14_rep1


title: RNASeq ADAR1KD_5-AZA-CdR_D5_rep2

description:
RNASeq_hg19_ADAR1KD_5-AZA-CdR_D5.Pos.bw
RNASeq_hg19_ADAR1KD_5-AZA-CdR_D5.Neg.bw

source_name: RNASeq ADAR1KD_5-AZA-CdR_D5_rep2


title: p20050_s003_7162_d4_BAL

description:
p20050_s003_7162_d4_BAL_S3
processed data file:
p20050_MacaM_RawCount.txt
p20050_MacaM_DESeq2_NormCount.txt


title: RNASeq ADAR1KD_5-AZA-CdR_D5_rep1

source_name: RNASeq ADAR1KD_5-AZA-CdR_D5_rep1


title: p20050_s050_7252_d2_BAL

description:
p20050_s050_7252_d2_BAL_S50
processed data file:
p20050_MacaM_RawCount.txt
p20050_MacaM_DESeq2_NormCount.txt

source_name: Group III_d2_BAL


title: RNASeq ADAR1KD_PIC_D14_rep1

source_name: RNASeq ADAR1KD_PIC_D14_rep1


title: RNASeq ADAR1KD_Mock-Treated_D24_rep2

description:
RNASeq_hg19_ADAR1KD_Mock-treated_D24.Pos.bw
RNASeq_hg19_ADAR1KD_Mock-treated_D24.Neg.bw

source_name: RNASeq ADAR1KD_Mock-Treated_D24_rep2


title: RNASeq ADAR1KD_PIC_D5_rep1

source_name: RNASeq ADAR1KD_PIC_D5_rep1


title: p20050_s044_7250_d2_BAL

description:
p20050_s044_7250_d2_BAL_S44
processed data file:
p20050_MacaM_RawCount.txt
p20050_MacaM_DESeq2_NormCount.txt


title: p20050_s021_7173_d4_BAL

description:
p20050_s021_7173_d4_BAL_S21
processed data file:
p20050_MacaM_RawCount.txt
p20050_MacaM_DESeq2_NormCount.txt


title: RNASeq ADAR1KD_Mock-Treated_D24_rep1

source_name: RNASeq ADAR1KD_Mock-Treated_D24_rep1


title: p20050_s015_7172_d4_BAL

description:
p20050_s015_7172_d4_BAL_S15
processed data file:
p20050_MacaM_RawCount.txt
p20050_MacaM_DESeq2_NormCount.txt


title: p20050_s038_7244_d2_BAL

description:
p20050_s038_7244_d2_BAL_S38
processed data file:
p20050_MacaM_RawCount.txt
p20050_MacaM_DESeq2_NormCount.txt


title: RNASeq ADAR1KD_Mock-Treated_D14_rep2

description:
RNASeq_hg19_ADAR1KD_Mock-treated_D14.Pos.bw
RNASeq_hg19_ADAR1KD_Mock-treated_D14.Neg.bw

source_name: RNASeq ADAR1KD_Mock-Treated_D14_rep2


title: RNASeq ADAR1KD_Mock-Treated_D14_rep1

source_name: RNASeq ADAR1KD_Mock-Treated_D14_rep1


title: ATACseq_serum_siTIP5_rep3

city: Zurich

first: Raffaella

last: Santoro

address: Winterthurerstrasse 190

department: Dep. of Molecular Mechanisms  of Disease

country: Switzerland

institute: University of Zurich

data_processing:
Raw sequencing reads were filtered for low-quality after adapter removal and aligned on mm10 using Bowtie2 with “-- very sensitive” mapping parameters. PCR duplicates were removed using Picard and only uniquely mapped reads were considered for further analysis. Due to very low transposition efficiency, Serum siCTRL replicate 2 was excluded from any further analysis. To call differentially open chromatin sites between the various conditions, the mapped reads of all conditions were merged into one alignment file. Peaks were called on the merged sample using MACS2 with --nomodel --shift -100 --extsize 200 --keep-dup all, to obtain a consensus peak set with equal contribution of each sample independent of the respective biological treatment (Lun and Smyth, 2014). The combined peak set was used to build a count matrix using the aligned reads of the individual samples. Differential peaks between sample groups were identified using edgeR (Robinson et al., 2010). For this, the count matrix was filtered for peaks with low coverage across all samples based on a average CPM value < -1, resulting in a final set of 128,253 peaks with p-values below 0.0034. The remaining counts were normalized using the total library size as well as edgeR’s TMM derived normalization factors. Between two sample groups, only regions with a log fold change above > 0.5 and a FDR value < 0.1 and group_CPM > -0.2 were considered as differentially accessible for further analysis.
Genome_build: GRCm38/mm10

source_name: mouse embryonic stem cells (ESCs)

growth_protocol: mouse embryonic stem cells (E14) were either cultured in N2B27 medium with LIF/2i or in medium containing 15% fetal bovine serum with LIF

extract_protocol:
ATAC-seq experiments were performed in biological triplicates of mES cells grown in 2i or serum conditions. Cell pellets from 50,000 cells for each condition were freshly harvested 72 h after transfection with siRNAs against TIP5 or a control sequence. The tagmentation reaction was performed as described in Buenrostro et al. (2013) with minor adjustments of the protocol, using the Nextera DNA Library Prep Kit (Illumina) together with the barcoded primers from the Nextera Index Kit (Illumina). In brief, an additional size selection step was performed after the first 5 cycles of library amplification. For this, the PCR reaction was incubated with 0.6 x volume of Ampure XP beads (Beckman Coulter) for 5 min to allow binding of high molecular weight fragments. Beads  containing long DNA fragments were separated on a magnet and the supernatant containing only small DNA fragments below roughly 800 bp were cleaned up using MinElute PCR purification columns (Qiagen).
All libraries were amplified for 12 cycles in total, visualized and quantified with a TapeStation2200 (Agilent), and sequenced on a Illumnina HiSeq4000 instrument obtaining 125 bp single-end reads.

treatment_protocol: ESCs were transfected with the indicated siRNAs and collected 3 days post transfection

value: ESC

tag: culture protocol

value: serum


title: RNASeq ADAR1KD_Mock-Treated_D5_rep2

description:
RNASeq_hg19_ADAR1KD_Mock-treated_D5.Pos.bw
RNASeq_hg19_ADAR1KD_Mock-treated_D5.Neg.bw

source_name: RNASeq ADAR1KD_Mock-Treated_D5_rep2


title: RNASeq ADAR1KD_Mock-Treated_D5_rep1

source_name: RNASeq ADAR1KD_Mock-Treated_D5_rep1


title: p20050_s026_7174_d2_BAL

description:
p20050_s026_7174_d2_BAL_S26
processed data file:
p20050_MacaM_RawCount.txt
p20050_MacaM_DESeq2_NormCount.txt

source_name: Group II_d2_BAL


title: p20050_s020_7173_d2_BAL

description:
p20050_s020_7173_d2_BAL_S20
processed data file:
p20050_MacaM_RawCount.txt
p20050_MacaM_DESeq2_NormCount.txt


title: p20050_s014_7172_d2_BAL

description:
p20050_s014_7172_d2_BAL_S14
processed data file:
p20050_MacaM_RawCount.txt
p20050_MacaM_DESeq2_NormCount.txt

source_name: Group I_d2_BAL


title: RNASeq ADAR1WT_PIC_D24_rep2

description:
RNASeq_hg19_ADAR1WT_PIC_D24.Pos.bw
RNASeq_hg19_ADAR1WT_PIC_D24.Neg.bw

source_name: RNASeq ADAR1WT_PIC_D24_rep2


title: p20050_s008_7165_d2_BAL

description:
p20050_s008_7165_d2_BAL_S8
processed data file:
p20050_MacaM_RawCount.txt
p20050_MacaM_DESeq2_NormCount.txt


title: p20050_s032_7182_d2_BAL

description:
p20050_s032_7182_d2_BAL_S32
processed data file:
p20050_MacaM_RawCount.txt
p20050_MacaM_DESeq2_NormCount.txt


title: RNASeq ADAR1WT_PIC_D24_rep1

source_name: RNASeq ADAR1WT_PIC_D24_rep1


title: sample_tissue_24A_R1_XX_uCG

city: Vilnius

first: Giedrius

last: Vilkaitis

address: Sauletekio av. 7

department: Department of Biological DNA Modification, Institute of Biotechnology

country: Lithuania

institute: Vilnius University

data_processing:
Select reads with length >= 80 nt
Select reads with 5' adapter and trim 3' adapter from the remaining reads
Align reads to a reference genome, minimum mapping quality 30
Remove PCR duplicates (used an in house script)
Calculate coverage per CG (used an in house script)
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files contain CG coverage for each sample

source_name: Chorionic villi tissue

extract_protocol:
Chorionic villi gDNA was purified using standard phenol-chloroform extraction. Cell-free DNA was isolated from blood plasma with "QIAamp MinElute ccfDNA kit" according to the manufacturer‘s instructions.
Libraries were constructed according to TOP-seq (Stasevskij et al., 2017) and hmTOP-seq (Gibas et al., 2020) protocols. Briefly, cfDNA and sonicated gDNA were labeled with azide moieties using Ado-6-azide (for uCG analysis) or UDP-6-azide-glucose (for 5hmCG analysis) cofactors. After ligation of adapters, the alkyne-bearing oligodeoxyribonucleotides (ODNs) with (5hmCG) or without (uCG) biotin were attached to the azide-modified DNA. Biotinylated DNA was enriched with streptavidin-coupled magnetic beads. Purified DNA after ODN conjugation (uCG) or biotin-enrichment (5hmC) was subsequently used in a DNA priming reaction. The products were amplified, size-selected and subjected to Ion Proton sequencing.

tag: sample type

value: Chorionic villi tissue sample

tag: dna modification

value: Unmodified CG sites


title: p20050_s049_7252_d1_BAL

description:
p20050_s049_7252_d1_BAL_S49
processed data file:
p20050_MacaM_RawCount.txt
p20050_MacaM_DESeq2_NormCount.txt

source_name: Group III_d1_BAL


title: p20050_s002_7162_d2_BAL

description:
p20050_s002_7162_d2_BAL_S2
processed data file:
p20050_MacaM_RawCount.txt
p20050_MacaM_DESeq2_NormCount.txt


title: RNASeq ADAR1WT_PIC_D14_rep2

description:
RNASeq_hg19_ADAR1WT_PIC_D14.Pos.bw
RNASeq_hg19_ADAR1WT_PIC_D14.Neg.bw

source_name: RNASeq ADAR1WT_PIC_D14_rep2


title: p20050_s043_7250_d1_BAL

description:
p20050_s043_7250_d1_BAL_S43
processed data file:
p20050_MacaM_RawCount.txt
p20050_MacaM_DESeq2_NormCount.txt


title: ATACseq_serum_siTIP5_rep2


title: ATACseq_serum_siCTRL_rep3

description:
EdgeR_Serum_siTIP5_vs_siCTRL_mm10.csv
EdgeR_2i_vs_serum_mm10.csv

value: siCTRL


title: ATACseq_serum_siTIP5_rep1


title: p20050_s037_7244_d1_BAL

description:
p20050_s037_7244_d1_BAL_S37
processed data file:
p20050_MacaM_RawCount.txt
p20050_MacaM_DESeq2_NormCount.txt


title: RNASeq ADAR1WT_PIC_D5_rep2

description:
RNASeq_hg19_ADAR1WT_PIC_D5.Pos.bw
RNASeq_hg19_ADAR1WT_PIC_D5.Neg.bw

source_name: RNASeq ADAR1WT_PIC_D5_rep2


title: ATACseq_2i_siTIP5_rep3


title: ATACseq_2i_siTIP5_rep2


title: ATACseq_serum_siCTRL_rep1


title: ATACseq_2i_siTIP5_rep1


title: RNASeq ADAR1WT_PIC_D5_rep1

source_name: RNASeq ADAR1WT_PIC_D5_rep1


title: p20050_s031_7182_d1_BAL

description:
p20050_s031_7182_d1_BAL_S31
processed data file:
p20050_MacaM_RawCount.txt
p20050_MacaM_DESeq2_NormCount.txt

source_name: Group II_d1_BAL


title: RNASeq ADAR1WT_5-AZA-CdR_D24_rep2

description:
RNASeq_hg19_ADAR1WT_5-AZA-CdR_D24.Pos.bw
RNASeq_hg19_ADAR1WT_5-AZA-CdR_D24.Neg.bw

source_name: RNASeq ADAR1WT_5-AZA-CdR_D24_rep2


title: p20050_s025_7174_d1_BAL

description:
p20050_s025_7174_d1_BAL_S25
processed data file:
p20050_MacaM_RawCount.txt
p20050_MacaM_DESeq2_NormCount.txt


title: ATACseq_2i_siCTRL_rep2

description:
EdgeR_2i_siTIP5_vs_siCTRL_mm10.csv
EdgeR_2i_vs_serum_mm10.csv


title: ATACseq_2i_siCTRL_rep3


title: RNASeq ADAR1WT_5-AZA-CdR_D24_rep1

source_name: RNASeq ADAR1WT_5-AZA-CdR_D24_rep1


title: RNASeq ADAR1WT_PIC_D14_rep1

source_name: RNASeq ADAR1WT_PIC_D14_rep1


title: ATACseq_2i_siCTRL_rep1


title: RNASeq ADAR1WT_5-AZA-CdR_D14_rep2

description:
RNASeq_hg19_ADAR1WT_5-AZA-CdR_D14.Pos.bw
RNASeq_hg19_ADAR1WT_5-AZA-CdR_D14.Neg.bw

source_name: RNASeq ADAR1WT_5-AZA-CdR_D14_rep2


title: Mature_Mast_Cell_11

source_name: Peritoneal cells


title: Mature_Mast_Cell_17


title: Mature_Mast_Cell_1


title: Mature_Mast_Cell_19


title: Mature_Mast_Cell_15


title: Mature_Mast_Cell_18


title: Mature_Mast_Cell_13


title: Mature_Mast_Cell_14


title: Mature_Mast_Cell_10


title: Mature_Mast_Cell_16


title: p20050_s007_7165_d1_BAL

description:
p20050_s007_7165_d1_BAL_S7
processed data file:
p20050_MacaM_RawCount.txt
p20050_MacaM_DESeq2_NormCount.txt

source_name: Group I_d1_BAL


title: p20050_s001_7162_d1_BAL

description:
p20050_s001_7162_d1_BAL_S1
processed data file:
p20050_MacaM_RawCount.txt
p20050_MacaM_DESeq2_NormCount.txt


title: RNAseq_serum_siTIP5_rep2

description:
raw_counts.csv
DEG_serum_siTIP5_vs_siCTRL.csv

data_processing:
Reads were aligned to the reference genome (ensembl version 82) with Subread (i.e. subjunc, version 1.4.6-p4; (Liao et al., 2013)) allowing up to 16 alignments per read (options: –trim5 10 –trim3 15 -n 20 -m 5 -B 16 -H –allJunctions). Count tables were generated with Rcount (Schmid and Grossniklaus, 2015) with an allocation distance of 100 bp for calculating the weights of the reads with multiple alignments, considering the strand information, and a minimal number of 5 hits. Variation in gene expression was analyzed with a general linear model in R with the package edgeR (version 3.12.0; (Robinson and Oshlack, 2010)) according to a crossed factorial design with two explanatory factors (i) siRNA against Tip5 and a mock sequence and (ii) ESCs grown on 2i or serum. Genes differentially expressed between specific conditions were identified with linear contrasts using trended dispersion estimates and Benjamini-Hochberg multiple testing corrections. For subsequent analyses only refseq transcripts were taken into account
Genome_build: GRCm38/mm10

source_name: mouse embryonic stem cells (ESCs)

extract_protocol:
Total RNA was purified with TRIzol reagent (Life Technologies)
The quality of the isolated RNA was determined with a Qubit® (1.0) Fluorometer (Life Technologies, California, USA) and a Bioanalyzer 2100 (Agilent, Waldbronn, Germany). Only those samples with a 260 nm/280 nm ratio between 1.8–2.1 and a 28S/18S ratio within 1.5–2 were further processed. The TruSeq RNA Sample Prep Kit v2 (Illumina, Inc, California, USA) was used in the succeeding steps. Briefly, total RNA samples (100-1000 ng) were poly A enriched and then reverse-transcribed into double-stranded cDNA. The cDNA samples was fragmented, end-repaired and polyadenylated before ligation of TruSeq adapters containing the index for multiplexing Fragments containing TruSeq adapters on both ends were selectively enriched with PCR. The quality and quantity of the enriched libraries were validated using Qubit® (1.0) Fluorometer and the Caliper GX LabChip® GX (Caliper Life Sciences, Inc., USA). The product is a smear with an average fragment size of approximately 260 bp. The libraries were normalized to 10nM in Tris-Cl 10 mM, pH8.5 with 0.1% Tween 20. The TruSeq SR Cluster Kit HS4000 (Illumina, Inc, California, USA) was used for cluster generation using 10 pM of pooled normalized libraries on the cBOT. Sequencing was performed on the Illumina HiSeq 4000 single end 100 bp using the TruSeq SBS Kit HS4000 (Illumina, Inc, California, USA).


title: RNAseq_serum_siTIP5_rep3


title: RNASeq ADAR1WT_5-AZA-CdR_D14_rep1

source_name: RNASeq ADAR1WT_5-AZA-CdR_D14_rep1


title: RNASeq ADAR1WT_5-AZA-CdR_D5_rep1

description:
RNASeq_hg19_ADAR1WT_5-AZA-CdR_D5.Pos.bw
RNASeq_hg19_ADAR1WT_5-AZA-CdR_D5.Neg.bw

source_name: RNASeq ADAR1WT_5-AZA-CdR_D5_rep1


title: Mature_Mast_Cell_12


title: RNASeq ADAR1WT_5-AZA-CdR_D5_rep2

source_name: RNASeq ADAR1WT_5-AZA-CdR_D5_rep2


title: p20050_s019_7173_d1_BAL

description:
p20050_s019_7173_d1_BAL_S19
processed data file:
p20050_MacaM_RawCount.txt
p20050_MacaM_DESeq2_NormCount.txt


title: p20050_s060_180264_Baseline_BAL

description:
p20050_s060_180264_Baseline_BAL_S60
processed data file:
p20050_MacaM_RawCount.txt
p20050_MacaM_DESeq2_NormCount.txt

source_name: No Inf_Baseline_BAL

value: Baseline

value: No Inf


title: RNASeq ADAR1WT_Mock-Treated_D24_rep2

description:
RNASeq_hg19_ADAR1WT_Mock-treated_D24.Pos.bw
RNASeq_hg19_ADAR1WT_Mock-treated_D24.Neg.bw

source_name: RNASeq ADAR1WT_Mock-Treated_D24_rep2


title: RNAseq_serum_siCTRL_rep3

description:
raw_counts.csv
DEG_serum_siTIP5_vs_siCTRL.csv
DEG_2i_vs_serum.csv


title: RNAseq_serum_siCTRL_rep2


title: RNAseq_serum_siTIP5_rep1


title: p20050_s013_7172_d1_BAL

description:
p20050_s013_7172_d1_BAL_S13
processed data file:
p20050_MacaM_RawCount.txt
p20050_MacaM_DESeq2_NormCount.txt


title: p20050_s058_180238_Baseline_BAL

description:
p20050_s058_180238_Baseline_BAL_S58
processed data file:
p20050_MacaM_RawCount.txt
p20050_MacaM_DESeq2_NormCount.txt


title: RNAseq_serum_siCTRL_rep1


title: RNASeq ADAR1WT_Mock-Treated_D5_rep1

description:
RNASeq_hg19_ADAR1WT_Mock-treated_D5.Pos.bw
RNASeq_hg19_ADAR1WT_Mock-treated_D5.Neg.bw

source_name: RNASeq ADAR1WT_Mock-Treated_D5_rep1


title: RNASeq ADAR1WT_Mock-Treated_D5_rep2

source_name: RNASeq ADAR1WT_Mock-Treated_D5_rep2


title: RNAseq_2i_siTIP5_rep1

description:
raw_counts.csv
DEG_2i_siTIP5_vs_siCTRL.csv


title: RNAseq_2i_siCTRL_rep3

description:
raw_counts.csv
DEG_2i_siTIP5_vs_siCTRL.csv
DEG_2i_vs_serum.csv


title: RNAseq_2i_siTIP5_rep2


title: VS047-L-CTRL_S22

city: Singapore

first: Eleonora

last: Adami

address: 8 College Road

department: CVMD

country: Singapore

institute: Duke-NUS Medical School

data_processing:
Sequenced libraries were demultiplexed using bcl2fastq v2.19.0.316 with the --no-lane-splitting option
Adapter sequences were then trimmed using trimmomatic6 v0.36 in paired end mode with the options MAXINFO:35:0.5 MINLEN:35. For reference, the adapter sequences are:  AGATCGGAAGAGCACACGTCTGAACTCCAGTCA (read 1) and AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT (read 2)
Trimmed reads were aligned to human genome hg38 using STAR v. 2.2.1 with the options --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 in paired end, single pass mode.
Only unique alignments were retained for counting. Counts were calculated at the gene level using the FeatureCounts module from subread v. 1.5.1, with the options -O -s 2 -J -T 8 -p -R -G.
Genome_build: Homo sapiens hg38 Ensembl release 92
Supplementary_files_format_and_content: Gene-level counts calculated by FeatureCounts (.txt)

source_name: Left Internal Mammary Artery

growth_protocol: normal human LIMA VSMCs (Passage 3-4) were stimulated with basal M231 medium for 24h

extract_protocol:
Total RNA was extracted from either aortic or arterial VSMCs lysate using Trizol (Invitrogen) followed by Purelink RNA mini kit (Invitrogen) purification.
Truseq Stranded mRNA (Poly A selection) kit

tag: patient id

value: vascular smooth muscle cells (VSMC)

value: Control

tag: rin


title: RNAseq_2i_siTIP5_rep3


title: VS047-L-TGFB_S23

growth_protocol: normal human LIMA VSMCs (Passage 3-4) were stimulated with 5 ng/ml of recombinant human TGFβ1 in basal M231 medium for 24h


title: VS045-L-TGFB_S20


title: RNAseq_2i_siCTRL_rep2


title: p20040_s042_7182_d14

description:
p20040_s042_7182_d14_S108
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt

source_name: Group II_d14_PBMC

value: PBMC


title: p20050_s057_171340_Baseline_BAL

description:
p20050_s057_171340_Baseline_BAL_S57
processed data file:
p20050_MacaM_RawCount.txt
p20050_MacaM_DESeq2_NormCount.txt

value: BAL


title: VS045-L-CTRL_S19


title: p20040_s056_7250_d14

description:
p20040_s056_7250_d14_S122
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt

source_name: Group III_d14_PBMC


title: RNAseq_2i_siCTRL_rep1


title: p20050_s055_171295_Baseline_BAL

description:
p20050_s055_171295_Baseline_BAL_S55
processed data file:
p20050_MacaM_RawCount.txt
p20050_MacaM_DESeq2_NormCount.txt


title: p20050_s059_180255_Baseline_BAL

description:
p20050_s059_180255_Baseline_BAL_S59
processed data file:
p20050_MacaM_RawCount.txt
p20050_MacaM_DESeq2_NormCount.txt


title: p20040_s028_7173_d14

description:
p20040_s028_7173_d14_S94
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt


title: RNASeq ADAR1WT_Mock-Treated_D24_rep1

source_name: RNASeq ADAR1WT_Mock-Treated_D24_rep1

value: Patient-derived colorectal cancer#92

value: Mock-Treated


title: p20050_s056_171332_Baseline_BAL

description:
p20050_s056_171332_Baseline_BAL_S56
processed data file:
p20050_MacaM_RawCount.txt
p20050_MacaM_DESeq2_NormCount.txt


title: p20040_s035_7174_d14

description:
p20040_s035_7174_d14_S101
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt


title: RNASeq ADAR1WT_Mock-Treated_D14_rep2

description:
RNASeq_hg19_ADAR1WT_Mock-treated_D14.Pos.bw
RNASeq_hg19_ADAR1WT_Mock-treated_D14.Neg.bw

source_name: RNASeq ADAR1WT_Mock-Treated_D14_rep2


title: p20040_s063_7252_d14

description:
p20040_s063_7252_d14_S129
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt


title: RNASeq ADAR1WT_Mock-Treated_D14_rep1

source_name: RNASeq ADAR1WT_Mock-Treated_D14_rep1


title: p20040_s049_7244_d14

description:
p20040_s049_7244_d14_S115
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt


title: p20040_s007_7162_d14

description:
p20040_s007_7162_d14_S73
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt

source_name: Group I_d14_PBMC


title: p20040_s021_7172_d14

description:
p20040_s021_7172_d14_S87
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt


title: p20040_s014_7165_d14

description:
p20040_s014_7165_d14_S80
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt


title: VS044-L-CTRL_S16


title: VS045-A-CTRL_S22

source_name: Aortic

growth_protocol: normal human aortic VSMCs (Passage 3-4) were stimulated with basal M231 medium for 24h


title: Human-EVs-26

city: Baltimore

first: Kenneth

middle: W.

last: Witwer

state: MD

address: 733 N. Broadway

department: Department of Molecular and Comparative Pathobiology

institute: Johns Hopkins University School of Medicine

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_035_rawlib.basecaller_A19_EV

data_processing:
FASTQC run before and after adapter trimming. The reads were aligned to the reference transcriptomes in a sequential manner.   First, all reads were mapped to RNA species with low sequence complexity and/or high number of repeats: rRNA, tRNA, RN7S, snRNA, snoRNA, scaRNA, VT-RNA, Y-RNA as well as mitochondrial chromosome (mtRNA). All reads that did not map to the above RNAs were aligned to premiRNA reference, then to protein coding mRNA transcripts (pc) and long non-coding RNAs (lncRNAs). Please note that some % of reads always overlaps between pc and lncRNAs. The reads which did not map to premiRNA, protein coding (pc) transcripts and lncRNAs were aligned to the remaining transcriptome [other ncRNAs containing mostly pseudogenes and non-protein coding parts of mRNAs]. Finally, all reads which did not map to human transcriptome were aligned to the hg38 genome reference (rest_hg38).
The mapping was performed with bowtie2 default settings for all references except premiRNA. PremiRNA were sequential mapping with bowtie using settings with: 0 mismatch tolerance, then 1 mismatch tolerance and finally 2 mismatches tolerance.
Genome_build: Hg38
Supplementary_files_format_and_content: Excel with raw counts

source_name: Brain

extract_protocol:
RNA was extracted by miRNeasy Mini Kit (Qiagen 217004) according to the manufacturer’s instructions.
Small RNA libraries were constructed using the Ion Total RNA-Seq Kit V2 (Life Technologies 4475936).

value: Temporal and inferior parietal cortex

value: EV fraction from 10,000 x g supernatant after SEC and ultracentrifugation

tag: disease state

value: Alzheimer's Disease

tag: apoe genotype


title: Human-EVs-27

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_036_rawlib.basecaller_A20_EV


title: Human-EVs-28

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_037_rawlib.basecaller_A21_EV


title: Human-EVs-29

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_038_rawlib.basecaller_A22_EV


title: Human-EVs-30

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_039_rawlib.basecaller_A23_EV


title: VS043-L-TGFB_S20


title: p20040_s062_7252_d10

description:
p20040_s062_7252_d10_S128
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt

source_name: Group III_d10_PBMC


title: Human-EVs-25

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_034_rawlib.basecaller_A18_EV


title: VS043-L-CTRL_S19


title: VS045-A-TGFB_S23

growth_protocol: normal human aortic VSMCs (Passage 3-4) were stimulated with 5 ng/ml of recombinant human TGFβ1 in basal M231 medium for 24h


title: Human-EVs-24

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_033_rawlib.basecaller_A17_EV


title: p20040_s055_7250_d10

description:
p20040_s055_7250_d10_S121
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt


title: p20040_s048_7244_d10

description:
p20040_s048_7244_d10_S114
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt


title: Human-EVs-23

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_032_rawlib.basecaller_A16_EV


title: VS042-L-CTRL_S16


title: VS042-L-TGFB_S17


title: Human-EVs-22

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_031_rawlib.basecaller_A15_EV


title: p20040_s041_7182_d10

description:
p20040_s041_7182_d10_S107
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt

source_name: Group II_d10_PBMC


title: Human-EVs-21

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_030_rawlib.basecaller_A14_EV


title: p20040_s034_7174_d10

description:
p20040_s034_7174_d10_S100
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt


title: VS044-L-TGFB_S17


title: VS042-A-TGFB_S14


title: Human-EVs-20

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_029_rawlib.basecaller_A13_EV


title: VS042-A-CTRL_S13


title: p20040_s027_7173_d10

description:
p20040_s027_7173_d10_S93
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt


title: VS041-L-TGFB_S14


title: VS039-L-TGFB_S16


title: Human-EVs-18

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_027_rawlib.basecaller_A11_EV


title: Human-EVs-15

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_024_rawlib.basecaller_A8_EV


title: p20040_s006_7162_d10

description:
p20040_s006_7162_d10_S72
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt

source_name: Group I_d10_PBMC


title: Human-EVs-19

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_028_rawlib.basecaller_A12_EV


title: p20040_s013_7165_d10

description:
p20040_s013_7165_d10_S79
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt


title: p20040_s054_7250_d7

description:
p20040_s054_7250_d7_S120
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt

source_name: Group III_d7_PBMC


title: p20040_s061_7252_d7

description:
p20040_s061_7252_d7_S127
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt


title: Human-EVs-17

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_026_rawlib.basecaller_A10_EV


title: Human-EVs-16

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_025_rawlib.basecaller_A9_EV


title: VS039-L-CTRL_S15


title: p20040_s020_7172_d10

description:
p20040_s020_7172_d10_S86
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt


title: VS039-A-CTRL_S12


title: VS039-A-TGFB_S13


title: Human-EVs-13

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_022_rawlib.basecaller_A6_EV


title: Human-EVs-14

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_023_rawlib.basecaller_A7_EV


title: Human-EVs-12

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_021_rawlib.basecaller_A5_EV


title: VS037-L-TGFB_S10


title: p20040_s040_7182_d7

description:
p20040_s040_7182_d7_S106
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt

source_name: Group II_d7_PBMC


title: VS037-L-CTRL_S9


title: p20040_s033_7174_d7

description:
p20040_s033_7174_d7_S99
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt


title: Human-EVs-11

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_020_rawlib.basecaller_A4_EV


title: p20040_s026_7173_d7

description:
p20040_s026_7173_d7_S92
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt


title: VS036-L-TGFB_S7


title: VS041-L-CTRL_S13


title: Human-EVs-10

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_019_rawlib.basecaller_A3_EV


title: VS036-L-CTRL_S6


title: Human-EVs-9

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_018_rawlib.basecaller_A2_EV


title: p20040_s019_7172_d7

description:
p20040_s019_7172_d7_S85
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt

source_name: Group I_d7_PBMC


title: p20040_s012_7165_d7

description:
p20040_s012_7165_d7_S78
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt


title: VS032-L-TGFB_S23


title: Human-EVs-8

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_017_rawlib.basecaller_A1_EV


title: VS032-L-CTRL_S22


title: Human-10K-30

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_039_rawlib.basecaller_A23_10K

value: 10,000 x g pellet from digested tissue


title: p20040_s047_7244_d7

description:
p20040_s047_7244_d7_S113
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt


title: VS031-L-TGFB_S20


title: p20040_s005_7162_d7

description:
p20040_s005_7162_d7_S71
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt


title: VS031-A-TGFB_S4


title: Human-10K-28

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_037_rawlib.basecaller_A21_10K


title: p20040_s053_7250_d4

description:
p20040_s053_7250_d4_S119
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt

source_name: Group III_d4_PBMC


title: VS031-L-CTRL_S19


title: Human-10K-27

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_035_rawlib.basecaller_A20_10K


title: VS027-L-TGFB_S17


title: p20040_s060_7252_d4

description:
p20040_s060_7252_d4_S126
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt


title: p20040_s046_7244_d4

description:
p20040_s046_7244_d4_S112
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt


title: p20040_s032_7174_d4

description:
p20040_s032_7174_d4_S98
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt

source_name: Group II_d4_PBMC


title: Human-10K-29

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_038_rawlib.basecaller_A22_10K


title: p20040_s025_7173_d4

description:
p20040_s025_7173_d4_S91
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt


title: Human-10K-25

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_034_rawlib.basecaller_A18_10K


title: VS031-A-CTRL_S3


title: Human-10K-26

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_036_rawlib.basecaller_A19_10K


title: p20040_s039_7182_d4

description:
p20040_s039_7182_d4_S105
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt


title: Human-10K-23

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_032_rawlib.basecaller_A16_10K


title: Human-10K-24

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_033_rawlib.basecaller_A17_10K


title: VS027-A-TGFB_S23


title: VS027-L-CTRL_S16

source_name: Left Internal Mammary Artery


title: VS027-A-CTRL_S22


title: p20040_s011_7165_d4

description:
p20040_s011_7165_d4_S77
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt

source_name: Group I_d4_PBMC


title: p20040_s018_7172_d4

description:
p20040_s018_7172_d4_S84
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt


title: Human-10K-21

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_030_rawlib.basecaller_A14_10K


title: VS026-L-TGFB_S13


title: VS026-L-CTRL_S12


title: Human-10K-20

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_029_rawlib.basecaller_A13_10K


title: p20040_s059_7252_d2

description:
p20040_s059_7252_d2_S125
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt

source_name: Group III_d2_PBMC


title: VS025-L-CTRL_S1


title: p20040_s052_7250_d2

description:
p20040_s052_7250_d2_S118
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt


title: VS024-L-TGFB_S9


title: p20040_s045_7244_d2

description:
p20040_s045_7244_d2_S111
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt


title: Human-10K-15

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_024_rawlib.basecaller_A8_10K


title: VS024-L-CTRL_S8


title: Human-10K-17

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_026_rawlib.basecaller_A10_10K


title: Human-10K-16

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_025_rawlib.basecaller_A9_10K


title: p20040_s024_7173_d2

description:
p20040_s024_7173_d2_S90
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt

source_name: Group II_d2_PBMC


title: VS024-A-TGFB_S20


title: Human-10K-19

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_028_rawlib.basecaller_A12_10K


title: p20040_s038_7182_d2

description:
p20040_s038_7182_d2_S104
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt


title: p20040_s017_7172_d2

description:
p20040_s017_7172_d2_S83
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt

source_name: Group I_d2_PBMC


title: p20040_s010_7165_d2

description:
p20040_s010_7165_d2_S76
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt


title: Human-10K-14

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_023_rawlib.basecaller_A7_10K


title: VS024-A-CTRL_S19


title: p20040_s004_7162_d4

description:
p20040_s004_7162_d4_S70
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt


title: VS023-L-TGFB_S5


title: Human-10K-13

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_022_rawlib.basecaller_A6_10K


title: VS023-L-CTRL_S4


title: Human-10K-22

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_031_rawlib.basecaller_A15_10K


title: p20040_s003_7162_d2

description:
p20040_s003_7162_d2_S69
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt


title: VS025-L-TGFB_S2


title: Human-10K-12

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_021_rawlib.basecaller_A5_10K


title: Human-10K-18

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_027_rawlib.basecaller_A11_10K


title: VS022-L-TGFB_S2


title: p20040_s058_7252_d1

description:
p20040_s058_7252_d1_S124
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt

source_name: Group III_d1_PBMC


title: p20040_s031_7174_d2

description:
p20040_s031_7174_d2_S97
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt


title: VS022-L-CTRL_S1


title: Human-10K-11

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_020_rawlib.basecaller_A4_10K


title: Human-10K-10

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_019_rawlib.basecaller_A3_10K


title: p20040_s051_7250_d1

description:
p20040_s051_7250_d1_S117
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt


title: VS018-L-TGFB_S23


title: Human-10K-9

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_018_rawlib.basecaller_A2_10K


title: VS018-L-CTRL_S22


title: p20040_s044_7244_d1

description:
p20040_s044_7244_d1_S110
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt


title: Human-10K-8

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_017_rawlib.basecaller_A1_10K


title: p20040_s030_7174_d1

description:
p20040_s030_7174_d1_S96
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt

source_name: Group II_d1_PBMC


title: Human-BH-28

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_037_rawlib.basecaller_A21_BH

value: Tissue homogenization


title: VS015-A-TGFB_S13

source_name: Aortic


title: VS015-A-CTRL_S12


title: VS017-L-CTRL_S19


title: VS014-L-TGFB_S5


title: p20040_s023_7173_d1

description:
p20040_s023_7173_d1_S89
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt


title: p20040_s009_7165_d1

description:
p20040_s009_7165_d1_S75
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt

source_name: Group I_d1_PBMC


title: Human-BH-29

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_038_rawlib.basecaller_A22_BH

source_name: Brain


title: p20040_s002_7162_d1

description:
p20040_s002_7162_d1_S68
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt


title: VS014-L-CTRL_S3


title: VS017-L-TGFB_S20


title: p20040_s016_7172_d1

description:
p20040_s016_7172_d1_S82
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt


title: Human-BH-27

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_036_rawlib.basecaller_A20_BH


title: Human-BH-26

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_035_rawlib.basecaller_A19_BH


title: VS011-L-TGFB_S21


title: p20040_s050_7250_baseline

description:
p20040_s050_7250_baseline_S116
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt

source_name: Group III_Baseline_PBMC


title: VS011-L-CTRL_S20


title: p20040_s057_7252_baseline

description:
p20040_s057_7252_baseline_S123
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt


title: p20040_s043_7244_baseline

description:
p20040_s043_7244_baseline_S109
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt


title: Human-BH-30

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_039_rawlib.basecaller_A23_BH


title: Human-BH-25

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_034_rawlib.basecaller_A18_BH


title: p20040_s037_7182_d1

description:
p20040_s037_7182_d1_S103
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt


title: Human-BH-24

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_033_rawlib.basecaller_A17_BH


title: p20040_s036_7182_baseline

description:
p20040_s036_7182_baseline_S102
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt

source_name: Group II_Baseline_PBMC


title: VS011-A-CTRL_S6


title: Human-BH-22

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_031_rawlib.basecaller_A15_BH


title: VS009-A-TGFB_S9


title: Human-BH-21

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_030_rawlib.basecaller_A14_BH


title: VS009-A-CTRL_S8


title: p20040_s022_7173_baseline

description:
p20040_s022_7173_baseline_S88
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt


title: VS007-L-CTRL_S1


title: Human-BH-20

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_029_rawlib.basecaller_A13-BH


title: p20040_s029_7174_baseline

description:
p20040_s029_7174_baseline_S95
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt


title: Human-BH-19

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_028_rawlib.basecaller_A12_BH


title: p20040_s015_7172_baseline

description:
p20040_s015_7172_baseline_S81
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt

source_name: Group I_Baseline_PBMC


title: VS007-A-CTRL_S16


title: VS007-A-TGFB_S17


title: p20040_s008_7165_baseline

description:
p20040_s008_7165_baseline_S74
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt


title: Human-BH-18

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_027_rawlib.basecaller_A11_BH


title: Human-BH-16

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_025_rawlib.basecaller_A9_BH


title: Input_HA_ChIP

city: Cleveland

first: Paul

last: Tesar

state: Ohio

address: 10900 Euclid Ave.

department: Genetics & Genome Sciences

institute: Case Western Reserve University

description: CRISPR-Control OPCs

data_processing:
Reads were quality and adapter trimmed using Trim Galore! Version 0.4.1.
Trimmed reads were alighed to mm10 with Bowtie2 version 2.3.2.
Duplicate reads (potential artifacts of PCR in library preparation) were removed using Picard MarkDuplicates.
Genome_build: mm10
Supplementary_files_format_and_content: bigWIG files were generated using Deeptools bamCoverage with reads per genome coverage normalization. BED files in a narrowPeaks format from MACS2.

source_name: Oligodendrocyte progenitor cells (OPCs)

growth_protocol: OPCs were grown in DMEM F12 supplemented with N2max and B27 and Fgf2 and Pdgfa.

extract_protocol:
Nuclei isolation and chromatin shearing were performed using the Covaris TruChIP protocol following manufacturer’s instructions for the “high-cell” format. In brief, 5-20 million cells were crosslinked in “Fixing buffer A” supplemented with 1% fresh formaldehyde for 10 minutes at room temperature with oscillation and quenched for 5 minutes with “Quench buffer E.” These cells were then washed with PBS and either snap frozen and stored at -80, or immediately continued to nuclei extraction and shearing per the manufacturer protocol. The samples were sonicated with the Covaris S2 using the following settings: 5% Duty factor 4 intensity for four 60-second cycles. Sheared chromatin was cleared and incubated overnight at 4 degrees with antibody that was pre-incubated with protein G magnetic DynaBeads (ThermoFisher).
Protein G dynabeads were then washed, eluted, reverse cross-linked and treated with RNase A followed by proteinase K. ChIP DNA was purified using Ampure XP beads (Aline Biosciences, C-1003-5) and then used to prepare illumina sequencing libraries.

treatment_protocol: Comparison of HA pulldown between control and HA-Ascl2 OPCs.

tag: cell type

value: epiblast stem cell derived OPCs

tag: antibody

value: input


title: p20040_s001_7162_baseline

description:
p20040_s001_7162_baseline_S67
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt


title: Human-BH-17

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_026_rawlib.basecaller_A10_BH

tag: treatment


title: P. falciparum 3D7 transcriptome at time point 25

first: Zbynek

last: Bozdech

state: Select if applicable

department: Molecular Genetics&Cell Biology

institute: Nanyang Technological University

data_processing:
Standard Illumina pipeline was used for base calling and demultiplexing
Sequenced reads were trimmed for adapter, primer and low quality bases from 3'-ends
Trimmed reads then mapped to Plasmodium falciparum 3D7 genome (genedb version 3) using STAR aligner with parameters --twopassMode Basic --outSAMstrandField intronMotif --alignIntronMin 60 --alignIntronMax 2500 --outFilterIntronMotifs RemoveNoncanonical --alignEndsType EndToEnd
Only uniquely mapped reads were extracted using samtools (version: 1.8) and raw count generated by bedtools (v2.27.1)
standard normalized count Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated, except gene length in the formula is replaced with mapped length
Genome_build: Plasmodium falciparum 3D7 geneDB version 3
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Plasmodium falciparum

source_name: infected erythrocytes culture in vitro

growth_protocol: P. falciparum strain 3D7 was obtained from BEI Resources (MRA-102) and cultured under standard conditions described before (William Trager, James B. Jensen, Human malaria parasites in continuous culture, Science, 193, 4254, 1976). Prior to time-point experiment, parasites were double-synchronized with 5% sorbitol solution to achieve a synchrony of +/- 6 hours and cultured under constant agitation. For sampling of highly synchronous parasites during the asexual life cycle, the first time point was considered as the TP1 (Time Point 1) when >95% of early ring stage parasites (approx. 4 hpi) were present in the culture. To ensure a sufficient amount of mRNA for subsequent analysis, parasites were cultured in 25 individual flasks in 25 mL of medium at 2% haematocrit and 8% parasitemia for each time point. Starting from TP1, parasites were collected every 2 hours for 25 successive time points. Parasite development was monitored by Giemsa staining and media change was performed once at 24 h time point to maintain parasite growth. The 9th time point was removed due to its big dissimilarity to all the other samples, and the total of 24 time points were used here to build an asexual reference transcriptome

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen) with chloroform supplemantaiton (Merck) and Direct-Zol-96 kit (Zymo) following manufacturers' instructions. All RNA samples were analyzed for integrity using Agilent Bioanalyzer 2100 platform. RNA 6000 Nano Chip (Cat. No.: 5067-1511, Agilent) was used for RNA samples according to manufacturer instructions.
Reverse transcription and cDNA synthesis were done following modifed Smart-Seq2 protocol using only oligo(d)T primers to enrich for mRNA transcripts (Picelli, S., Faridani, O., Björklund, Å. et al. Full-length RNA-seq from single cells using Smart-seq2. Nat Protoc 9, 171–181 (2014)). Purified amplicon (cDNA) was used to generate sequencing libraries using Illumina Nextera XT kit as described in manufacturer’s protocol. Libraries were analyzed on the Bioanalyser High-Sensitivity DNA chips (Agilent, Cat. No.: 5067-4626), subsequently pooled (24 samples per lane) and sequenced on Illumina HiSeq4000 platform generating 150 bp paired end reads with 110 Gb data output generated per lane.

value: intraerythorcytic P.falciparum


title: Human-BH-23

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_032_rawlib.basecaller_A16_BH


title: Human-BH-15

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_024_rawlib.basecaller_A8_BH


title: HA.Ascl2_HA_ChIP_B

description: HA-Ascl2 OPCs

value: HA (Cell Signaling Technologies, 3724S, 15ug)

tag: number of cells per chip

value: 60 million OPCs


title: Control_HA_ChIP_B

description: CRISPR-Control OPCs


title: P. falciparum 3D7 transcriptome at time point 23


title: P. falciparum 3D7 transcriptome at time point 22


title: Human-BH-13

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_022_rawlib.basecaller_A6_BH


title: Human-BH-14

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_023_rawlib.basecaller_A7_BH


title: P. falciparum 3D7 transcriptome at time point 24


title: P. falciparum 3D7 transcriptome at time point 21


title: Control_HA_ChIP_A

description: CRISPR-Control OPCs


title: HA.Ascl2_HA_ChIP_A

description: HA-Ascl2 OPCs


title: Vhl_HIF1b_ChIP_B

description: CRISPR-Vhl OPCs

extract_protocol: Nuclei isolation and chromatin shearing were performed using the Covaris TruChIP protocol following manufacturer’s instructions for the “high-cell” format. In brief, 5-20 million cells were crosslinked in “Fixing buffer A” supplemented with 1% fresh formaldehyde for 10 minutes at room temperature with oscillation and quenched for 5 minutes with “Quench buffer E.” These cells were then washed with PBS and either snap frozen and stored at -80, or immediately continued to nuclei extraction and shearing per the manufacturer protocol. The samples were sonicated with the Covaris S2 using the following settings: 5% Duty factor 4 intensity for four 60-second cycles. Sheared chromatin was cleared and incubated overnight at 4 degrees with antibody that was pre-incubated with protein G magnetic DynaBeads (ThermoFisher). Protein G dynabeads were then washed, eluted, reverse cross-linked and treated with RNase A followed by proteinase K. ChIP DNA was purified using Ampure XP beads (Aline Biosciences, C-1003-5) and then used to prepare illumina sequencing libraries.

treatment_protocol: Comparison between control and Vhl knockout OPCs.

value: epiblast stem cell derived oligodendrocyte progenitor cells (OPCs)

value: HIF1b (Cell Signaling Technlogies NB100-110, 25ug per ChIP)

value: 80 million OPCs


title: P. falciparum 3D7 transcriptome at time point 20


title: Control_HIF1b_ChIP_B

description: CRISPR-Control OPCs


title: Human-BH-11

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_020_rawlib.basecaller_A4_BH


title: Human-BH-12

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_021_rawlib.basecaller_A5_BH


title: Vhl_HIF1b_ChIP_A

description: CRISPR-Vhl OPCs


title: P. falciparum 3D7 transcriptome at time point 18


title: P. falciparum 3D7 transcriptome at time point 19


title: P. falciparum 3D7 transcriptome at time point 17


title: Human-BH-8

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_017_rawlib.basecaller_A1_BH


title: Human-BH-9

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_018_rawlib.basecaller_A2_BH


title: Vhl_Olig2_ChIP_B

description: CRISPR-Vhl OPCs

value: Olig2 (Millipore ab9610, 15ug per ChIP)

value: 20 million OPCs


title: Human-EVs-7

description:
Human_combined_raw_counts-CTRL.xlsx
IonXpressRNA_046_rawlib.basecaller_B7_EV

value: Control


title: Control_Olig2_ChIP_B

description: CRISPR-Control OPCs


title: P. falciparum 3D7 transcriptome at time point 16


title: Human-EVs-6

description:
Human_combined_raw_counts-CTRL.xlsx
IonXpressRNA_045_rawlib.basecaller_B6_EV


title: P. falciparum 3D7 transcriptome at time point 15


title: P. falciparum 3D7 transcriptome at time point 14


title: Uwt3

city: Grand Rapids

first: Ronald

middle: L.

last: Chandler

state: MI

department: Obstetrics, Gynecology and Reproductive Biology

institute: Michigan State University

description: Reanalyzed sample GSM3722003. RNA library. First flow cell. Cells from pooled mice.

data_processing:
Raw reads were trimmed with cutadapt and Trim Galore! followed by quality control analysis via FastQC.
Trimmed reads were aligned mm10 genome assembly, indexed to GENCODE (vM16) GFF3 annotation via STAR aligner with flag ‘--quantMode GeneCounts’ for feature counting.
STAR sample gene counts were concatenated for Stranded-Reverse (libtype), corresponding to column 4 of STAR output ReadsPerGene.out.tab file. Raw gene counts were combined with control cell data retrieved from GEO accession GSE129784.
Gene Ensembl IDs were converted to external gene names (symbols) via biomaRt. Low count genes were filtered (at least 1 count per sample on average) prior to normalization factor generation, dispersion estimation, negative binomial generalized linear model fitting, and hypothesis testing in DESeq2 for differential gene expression analysis. For linear modeling, the design matrix was constructed from a single “condition” variable with the inclusion of an intercept, in the form: ~ condition. Calculated differential gene expression probabilities were corrected for multiple testing by independent hypothesis weighting (IHW) for downstream analysis.
Genome_build: mm10 indexed to GENCODE (vM16) GFF3 annotation
Supplementary_files_format_and_content: Comma-separated values (CSV) and tab-separated values (TSV) tabular text files including per-sample gene counts (STAR output) and non-thresholded DESeq2 differential gene expression analysis.

source_name: endometrial epithelium

growth_protocol: Mice were housed at the Michigan State University Grand Rapids Research Center in accordance with protocols approved by Michigan State University.

extract_protocol:
Endometrial epithelial cells were magnetically sorted using EpCAM-PE and anti-PE microbeads. RNA was collected using the Arcturus PicoPure RNA Isolation Kit (ThermoFisher).
Directional mRNA-seq libraries were constructed from 500 ng of total RNA supplied to the KAPA mRNA HyperPrep kit (v4.17) (Kapa Biosystems). RNA was sheared to 300-400 bp. cDNA fragments were ligated to IDT for Illumina unique dual adapters (IDT DNA Inc.).

treatment_protocol: Mouse uteri were surgically removed and minced using scissors. Tissues were digested using the MACS Multi Tissue Dissociation Kit II (Miltenyi Biotec).

tag: genotype

value: Control wild-type


title: Human-BH-10

description:
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_019_rawlib.basecaller_A3_BH

value: Temporal and inferior parietal cortex


title: Uwt1

description: Reanalyzed sample GSM3722001. RNA library. First flow cell. Cells from pooled mice.


title: HiC_siCTRL_3

description: CTRL-merged.hic.gz

data_processing:
Library strategy: HiC
FastQ files were mapped to the mouse genome (mm10) using bwa-mem (Li and Durbin, 2010) and filtered and deduplicated using HiCUP v0.5.10 (Wingett et al., 2015). Chromosomal interaction matrices were generated using Juicer (Durand et al., 2016) at 500 Kb resolution and normalized by Knight and Ruiz’s matrix balancing algorithm. Biological replicates were first processed independently and inspected for clustering between Tip5 knockdown and control conditions by PCA. Next, replicates per condition were pooled to create merged contact maps that were used in the downstream analyses.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: HIC format. Merged files are available on the series record.

source_name: mouse embryonic stem cells (ESCs)

extract_protocol:
HiC experiments were performed in triplicates of ESC+2i treated with siRNA-control or siRNA-TIP5. Five million cells were pelleted and resuspended in PBS-10%FCS. PBS-10%FCS-4% formaldehyde was added to a final concentration of 2% formaldehyde (v/v). Samples were incubated at room temperature for 10 minutes with mixing. Ice-cold glycine solution was added to a final concentration of 0.2M and immediately centrifuged for 5 minutes at 300xg at 4°C.
Cells were washed in 1 ml of ice-cold PBS. Pellet was flash-frozen in liquid nitrogen. Pellet was taken up and washed in 1 ml ice cold lysis buffer1, resupended again in 1 ml of ice cold lysis buffer and incubated for 30 minutes at 4°C.  Sample was pelleted and washed in 0.5 ml 1.2x DpnII buffer, resuspended in 0.5 ml of DpnII buffer again and moved to a thermomixer at 37°C and 300 rpm. SDS was then carefully added to a concentration of 0.3%, slowly suspended with a pipet and incubated for an hour. Triton X-100 was added to a concentration of 2.6% and sample was incubated for another hour. To digest the sample, 200 units of DpnII enzyme were added for a 4 hour incubation in a thermomixer at 37°C and 900 rpm; another 200 units of DpnII were added for overnight incubation. From here on, we adopted the protocol described in (Rao et al., 2014) with some adjustments Cells were incubated for 20 minutes at 65°C to heat inactivate DpnII, pelleted and 300 ul of fill-in mastermix was added (218 μl of MilliQ, 30 μl of 10x NEB buffer 2, 15 μl of 10mM dCTP, 15 μl of 10mM dGTP, 15 μl of 10mM dTTP, 37.5 μl of 0.4mM biotin-14-dATP (Life Technologies, 19524-016), 10 μl of 5U/μl DNA Polymerase I, Large (Klenow) Fragment (NEB, M0210)). Sample was mixed by pipetting and incubated for 60 minutes @ 37°C shaking at 300 rpm and placed at 4°C afterwards. 900 ul of ligation mix was added (120 ul 10x ligase buffer, 50 units of T4 ligase (Roche) and 770 ul MilliQ) and mixed by inverting and incubated overnight at 16°C. Sample was pelleted for 5 minutes at 1000 x g and taken up in 500 µl 10 mM Tris. Protein was degraded by adding 50 μl of 20mg/ml proteinase K (NEB, P8102), 50 μl of 10% SDS and incubated at 55°C for 30 minutes. 57 μl of 5M of sodium chloride was then added and the sample was incubated at 68°C overnight or for at least 1.5 hours. Samples were cooled to room temperature and DNA was purified using NucleoMag P-Beads and taken up in 5mM Tris pH7.5. Samples were sheared to a size of 300-500 bp using a Covaris S2 focused-ultrasonicator. From here on, the protocol described in (Rao et al., 2014) was adopted.

value: siCTRL


title: Human-EVs-3

description:
Human_combined_raw_counts-CTRL.xlsx
IonXpressRNA_042_rawlib.basecaller_B3_EV

value: EV fraction from 10,000 x g supernatant after SEC and ultracentrifugation


title: Human-EVs-4

description:
Human_combined_raw_counts-CTRL.xlsx
IonXpressRNA_043_rawlib.basecaller_B4_EV


title: Human-EVs-2

description:
Human_combined_raw_counts-CTRL.xlsx
IonXpressRNA_041_rawlib.basecaller_B2_EV


title: Uwt2

description: Reanalyzed sample GSM3722002. RNA library. First flow cell. Cells from pooled mice.


title: P. falciparum 3D7 transcriptome at time point 12


title: P. falciparum 3D7 transcriptome at time point 13


title: Control_HIF1b_ChIP_A

description: CRISPR-Control OPCs


title: Human-EVs-1

description:
Human_combined_raw_counts-CTRL.xlsx
IonXpressRNA_040_rawlib.basecaller_B1_EV


title: P. falciparum 3D7 transcriptome at time point 8


title: P. falciparum 3D7 transcriptome at time point 11


title: Human-10K-7

description:
Human_combined_raw_counts-CTRL.xlsx
IonXpressRNA_046_rawlib.basecaller_B7_10K

value: 10,000 x g pellet from digested tissue


title: P. falciparum 3D7 transcriptome at time point 7


title: Human-10K-5

description:
Human_combined_raw_counts-CTRL.xlsx
IonXpressRNA_044_rawlib.basecaller_B5_10K


title: Human-EVs-5

description:
Human_combined_raw_counts-CTRL.xlsx
IonXpressRNA_044_rawlib.basecaller_B5_EV


title: P. falciparum 3D7 transcriptome at time point 5


title: P. falciparum 3D7 transcriptome at time point 6


title: HiC_siTIP5_1


title: Human-10K-6

description:
Human_combined_raw_counts-CTRL.xlsx
IonXpressRNA_045_rawlib.basecaller_B6_10K


title: HiC_siTIP5_3


title: P. falciparum 3D7 transcriptome at time point 4


title: P. falciparum 3D7 transcriptome at time point 3


title: Human-10K-4

description:
Human_combined_raw_counts-CTRL.xlsx
IonXpressRNA_043_rawlib.basecaller_B4_10K


title: P. falciparum 3D7 transcriptome at time point 10


title: Human-10K-3

description:
Human_combined_raw_counts-CTRL.xlsx
IonXpressRNA_042_rawlib.basecaller_B3_10K


title: SRSF6 rep2

city: Wuhan

first: Dong

last: Chen

state: Hubei

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

department: Center for Genome Analysis

country: China

institute: ABLife, Inc.

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2, Qvalue < =0.05
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include gene FPKM values for each Sample

source_name: hela cell

growth_protocol: The human HeLa cell line was purchased from the Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China. Cells were seeded into a petridish (100 mm) at a density of 1 × 105 cells/mL per well, and cultured at 37 ℃with 5% CO2 in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% fetal bovine serum (FBS) (Hyclone), penicillin (100 U/ml) and streptomycin (100 g/ml). ZFP36 overexpression plasmid transfection of HeLa cells was performed using Lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's instructions. Transfected cells were harvested after 48 h.

extract_protocol:
Total RNA was extracted by the TRIZOL (Ambion). The RNA was further purified with two phenol-chloroform treatments and then treated with RQ1 DNase (Promega) to remove DNA. The quality and quantity of the purified RNA were redetermined by measuring the absorbance at 260 nm/280 nm (A260/A280) using Smartspec Plus (BioRad). The integrity of RNA was further verified by 1.5% agarose gel electrophoresis.
For each sample, 1μg of total RNA was used for RNA-seq library preparation by VAHTS Stranded mRNA-seq Library Prep Kit (Vazyme). Polyadenylated mRNAs were purified and fragmented, and then converted into double strand cDNA. After the step of end repair and A tailing, the DNAs were ligated to VAHTS RNA Adapters (Vazyme). Purified ligation products corresponding to 200-500 bps were digested with heat-labile UDG, and the single strand cDNA was amplified, purified, quantified and stored at -80℃ before sequencing.
For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to Illumina HiSeq X Ten system for 150 nt paired-end sequencing.

treatment_protocol: OE_RNA against human SRSF6 transfection of HeLa cells was performed using lipofectAMINE 2000

value: SRSF6 overexpression in hela cell


title: HiC_siCTRL_2

description: CTRL-merged.hic.gz


title: Human-10K-2

description:
Human_combined_raw_counts-CTRL.xlsx
IonXpressRNA_041_rawlib.basecaller_B2_10K


title: HiC_siCTRL_1

description: CTRL-merged.hic.gz


title: P. falciparum 3D7 transcriptome at time point 2


title: Human-10K-1

description:
Human_combined_raw_counts-CTRL.xlsx
IonXpressRNA_040_rawlib.basecaller_B1_10K


title: P. falciparum 3D7 transcriptome at time point 1


title: Human-BH-7

description:
Human_combined_raw_counts-CTRL.xlsx
IonXpressRNA_046_rawlib.basecaller_B7_BH

value: Tissue homogenization


title: SRSF6 rep1


title: Human-BH-6

description:
Human_combined_raw_counts-CTRL.xlsx
IonXpressRNA_045_rawlib.basecaller_B6_BH


title: Ctrl rep2

value: hela cell (control plasmid)


title: cattle_adipose_3

city: Nanning

first: Huang

last: JiePing

address: Xixiangtang District

institute: Guangxi University

data_processing:
Low-quality reads and those containing adapters were removed to obtain clean reads using Trim Galore. High-quality data were used for the subsequent analysis. Each read was aligned to the reference genome using STAR. Mapped reads were assembled using Cufflinks v2.2.1. These assemblies were merged to the reference gene model annotation by Cuffmerge.
For mRNAs and lncRNAs, fragments per kilobase of transcript per million mapped reads (FPKM) was used as index to calculate the expression level of each transcript in every library using Cuffdiff program.
For circRNA prediction, the CIRCexplorer2 was employed to identify the back-spliced junction of circRNAs. To calculate the expression levels of circRNAs, back-spliced reads per million mapped reads (BSRP) was used.
Genome_build: UMD3.1
Supplementary_files_format_and_content: (1) Tab-delimited text files include FPKM  values (mRNAs and lncRNAs) or BSRP values (circRNAs) for each sample. (2) The .fa files include sequences of lncRNAs and circRNAs predicted in this study.

organism: Bos taurus

source_name: high IMF

growth_protocol: Three Xinyang buffalo and three Nanyang cattle were raised in the breeding farm of Xinyang Buffalo (Guangshan, Henan province, P.R. China) and the breeding center of Nanyang cattle (Nanyang, Henan province, P.R. China), respectively, with equivalent forage and feeding management conditions.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen, USA). The quality and concentration of total RNA were determined by the NanoDrop 2,000 (Nanodrop, Wilmington, DE) and 1% agarose gel.
Approximately 2 μg total RNA per sample was used for library construction according to protocol of the TruSeq® RNA LT Sample Prep Kit v2 (Illumina, USA).

treatment_protocol: Animals were weaned at three months of age, castrated at six months of age, started to fatten at 18 months of age, and slaughtered at 30 months of age.

tag: intramuscular fat

value: high IMF

value: adipose


title: Ctrl rep1


title: HiC_siTIP5_2


title: cattle_adipose_2

tag: tissue


title: Human-BH-5

description:
Human_combined_raw_counts-CTRL.xlsx
IonXpressRNA_044_rawlib.basecaller_B5_BH


title: cattle_adipose_1


title: OESTAU1_2nd

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2  Qvalue < =0.05
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include gene FPKM or read count values for each Sample

treatment_protocol: OE_RNA against human STAU1 transfection of HeLa cells was performed using lipofectAMINE 2000

tag: cell line

value: HeLa

tag: transfected with

value: STAU1 overexpression


title: OECtrl_2nd

value: control plasmid


title: cattle_muscle_3

value: muscle


title: OESTAU1_1st


title: Human-BH-4

description:
Human_combined_raw_counts-CTRL.xlsx
IonXpressRNA_043_rawlib.basecaller_B4_BH


title: Human-BH-2

description:
Human_combined_raw_counts-CTRL.xlsx
IonXpressRNA_041_rawlib.basecaller_B2_BH


title: cattle_muscle_2


title: Human-BH-1

description:
Human_combined_raw_counts-CTRL.xlsx
IonXpressRNA_040_rawlib.basecaller_B1_BH


title: OECtrl_1st


title: cattle_muscle_1


title: siBRG1_rep3

description:
RNA library from 12Z cells after 72 hours treatment with siRNA targeting SMARCA4/BRG1 (siBRG1)
12Z_RNA_siBRG1_rep3

data_processing:
Raw reads were trimmed with cutadapt and Trim Galore! followed by quality control analysis via FastQC.
Trimmed reads were aligned GRCh38.p12 genome assembly, indexed to GENCODE (v28) GFF3 annotation via STAR aligner with flag ‘--quantMode GeneCounts’ for feature counting.
STAR sample gene counts were concatenated for Stranded-Reverse (libtype), corresponding to column 4 of STAR output ReadsPerGene.out.tab file. Raw gene counts were combined with non-targeting siRNA (control) treated 12Z data retrieved from GEO accession GSE129782.
Gene Ensembl IDs were converted to external gene names (symbols) via biomaRt. Low count genes were filtered (at least 1 count per sample on average) prior to normalization factor generation, dispersion estimation, negative binomial generalized linear model fitting, and hypothesis testing in DESeq2 for differential gene expression analysis. For linear modeling, the design matrix was constructed from a single “condition” variable with the inclusion of an intercept, in the form: ~ condition. Calculated differential gene expression probabilities were corrected for multiple testing by independent hypothesis weighting (IHW) for downstream analysis.
Genome_build: GRCh38.p12 indexed to GENCODE (v28) GFF3 annotation
Supplementary_files_format_and_content: Comma-separated values (CSV) and tab-separated values (TSV) tabular text files including per-sample gene counts (STAR output) and non-thresholded DESeq2 differential gene expression analysis.

source_name: 12Z cell line

growth_protocol: 12Z cells were cultured in DMEM/F12 media supplemented with 10% FBS, 1% L-glutamine, and 1% Penicllin-Streptomycin.

extract_protocol:
72 hours following siRNA transfection and 48 hours following drug or vehicle treatment, RNA was extracted using the Quick-RNA Miniprep Kit (Zymo Research).
Directional mRNA-seq libraries were constructed from 500 ng of total RNA supplied to the KAPA mRNA HyperPrep kit (v4.17) (Kapa Biosystems). RNA was sheared to 300-400 bp. cDNA fragments were ligated to IDT for Illumina unique dual adapters (IDT DNA Inc.).

treatment_protocol: Cells were transfected in the absence of antibiotic with 50 nM siRNA (Dharmacon, ON-TARGETplus) via RNAiMax (ThermoFisher) lipofectamine reagent in OptiMEM (Gibco). 24 hours following transfection, growth media was replaced. 48 hours following transfection, growth media was replaced again with 0.5% FBS.

tag: condition


title: Human-BH-3

description:
Human_combined_raw_counts-CTRL.xlsx
IonXpressRNA_042_rawlib.basecaller_B3_BH


title: siBRG1_rep2

description:
RNA library from 12Z cells after 72 hours treatment with siRNA targeting SMARCA4/BRG1 (siBRG1)
12Z_RNA_siBRG1_rep2


title: siBRG1_rep1

description:
RNA library from 12Z cells after 72 hours treatment with siRNA targeting SMARCA4/BRG1 (siBRG1)
12Z_RNA_siBRG1_rep1


title: Ecs_melatonin_24h_rep3

type: RNA

city: Shenyang

first: Xiangshan

last: Xu

state: Liaoning

address: Fourth Chongshan Road, Huanggu District

institute: fourth affiliated hospital of China Medical University

description:
Umbilical cord
Gene expression after 24hr in ECs with melatonin treatment.

hyb_protocol: Array hybridization and wash were performed by GeneChip® Hybridization, Wash and Stain Kit (P/N900720, Affymetrix, Santa Clara, CA, US) and GeneChip Eukaryotic Hybridization Control Kit (P/N900454, Affymetrix, Santa Clara, CA, US) in Hybridization Oven 645 (P/N 00-0331 (220V), Affymetrix, Santa Clara, CA, US) and Fluidics Station 450 (P/N 00-0079, Affymetrix, Santa Clara, CA, US) according to the manufacturer’s instructions.

scan_protocol: Arrays were scanned by GeneChip® Scanner 7G (Affymetrix, Santa Clara, CA, US) and Command Console Software 3.2 (Affymetrix, Santa Clara, CA, US) with default settings.

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.

label: Biotin

source_name: ECs, melatonin

label_protocol: Total RNA was labeled and purified by FlashTag™ Biotin HSR RNA Labeling Kit (P/N 901911, Affymetrix) according to the manufacturer’s instructions to obtain biotin labeled miRNA.

growth_protocol: ECs monoculture subjected to low shear stress together with or without melatonin treatment.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: The supernatants of ECs were centrifuged at 300 × g for 10 min to remove cell components and collected the supernatants. Then the supernatants were further centrifuged at 2000 × g for 10 min and again centrifuged at 10,000 g for 60 min. After that, the supernatants were centrifuged with ultracentrifuge (Beckman, Optima XPN-100) at 110,000g × g for 70 min at 4 °C. The exosomes pellets were then washed with pre-cooling PBS followed by a second ultracentrifugation at 110,000× g for 70 min to precipitate the exosomes. Then the supernatants were discarded and the exosomes pellet was re-suspended in an appropriate amount of pre-cooling PBS and store at -80 °C for further study.

value: exosomes from endothelial cells

value: melatonin


title: Ecs_melatonin_24h_rep2


title: Ecs_melatonin_24h_rep1


title: 381e inoculated 12dpi 3rep. FW

city: Cercola

first: Ciro

middle: Gianmaria

last: Amoroso

address: Viale Giotto 15

department: Agricultural science

country: Italy

institute: university of Naples Federico II

description: Tolerant to ZYMV

data_processing:
SNP calling perfomerd with VCFtools, based on the two filtered .bam files, produced two VCF (Variant Call Format) files with the SNPs of each genotype in comparison to the genome.
reads (obtained after trimming) were analysed using the online platform AIR (www.transcriptomics.cloud) using the C. pepo genome sequence version 4.1
Genome_build: 4.1
Supplementary_files_format_and_content: include FPKM values, DEGs and Gene Ontology
Supplementary_files_format_and_content: Total expressed genes
Supplementary_files_format_and_content: Up regulated genes
Supplementary_files_format_and_content: Down regulated genes
Supplementary_files_format_and_content: Gene Ontology of tolerant cv. expressed genes
Supplementary_files_format_and_content: Gene Ontology of susceptible cv. expressed genes

organism: Cucurbita pepo

source_name: C.pepo 381e

extract_protocol:
Twelve days after treatment,leaves were removed from the plants, weighed and immediately frozen in liquid nitrogen and stored at −80°C. RNA was isolated from whole plants using the RNAeasy Plant Kit (Quiagen Valencia, USA).
Total purified RNA was converted to cDNA libraries and sequenced on Illumina HiSeq1500 platform

value: leaf

tag: Stage

value: 12 days post inoculation

tag: group

value: Tolerant to ZYMV


title: True French inoculated 12dpi 3rep. FW

description: Susceptible to ZYMV

source_name: C.pepo True French

value: Susceptible to ZYMV


title: Ecs_control_24h_rep3

description:
Umbilical cord
Gene expression after 24hr in ECs without melatonin treatment.

source_name: ECs, control

value: control


title: 381e inoculated 12dpi 2rep. FW

description: Tolerant to ZYMV


title: BRG1_rep2

description: BRG1 ChIP (replicate 2) library from wild-type 12Z cells

data_processing:
Raw reads for IPs and input were trimmed with cutadapt and Trim Galore!
Trimmed reads were aligned to GRCh38.p12 reference genome via Bowtie2 with flag `--very-sensitive`. Aligned reads were sorted and indexed with samtools.
Picard MarkDuplicates was used to remove PCR duplicates, followed by sorting and indexing.
MACS2 was used to call significant broad peaks (FDR < 0.05) on each ChIP replicate against the input control with otherwise default settings.
A naïve overlapping peak set, as defined by ENCODE, was constructed by calling peaks on pooled replicates followed by bedtools intersect to select for peaks of at least 50% overlap with each biological replicate.
The resulting peaks were repeat-masked by ENCODE blacklist filtering and filtered for non-standard contigs.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: Tabular peak set files including blacklist-filtered ChIP replicate broadPeaks (FDR < 0.05 MACS2 output) and naïve replicate-overlapping broadPeaks.

extract_protocol:
Cells were treated with 1% formaldehyde in fresh DMEM/F12 media for 10 min at room temp. Formaldehyde was quenched by the addition of 0.125 M Glycine, and cells were washed with PBS. 1x10^7 crosslinked cells were used per IP. Chromatin from crosslinked cells was fractionated by digestion with micrococcal nuclease using the SimpleChIP Enzymatic Chromatin IP Kit (Cell Signaling) per the manufacturers’ instructions, followed by 30 seconds of sonication. IPs were performed using the SimpleChIP Enzymatic Chromatin IP Kit per the manufacturers’ instructions with 1:100 anti-BRG1 antibody (ab110641, abcam). Crosslinks were reversed with 0.4 mg/mL Proteinase K (ThermoFisher) and 0.2 M NaCl at 65 C for 2 hours. DNA was purified using the ChIP DNA Clean & Concentrator Kit (Zymo).
Libraries for input and IP samples were prepared by the Van Andel Genomics Core from 10 ng of input and IP material when available, and all material when less than 10 ng available, using the KAPA Hyper Prep Kit (v5.16) (Kapa Biosystems). Prior to PCR amplification, end repaired and A-tailed DNA fragments were ligated to Bioo Scientific NEXTflex Adapters (Bioo Scientific).

value: Wild-type

tag: chip antibody

value: anti-BRG (ab110641, abcam)


title: Dclk1+ cells of PDAC 03

city: Kyoto

first: Takahisa

last: Maruno

state: Kyoto

address: 54 Syogoin-Kawahara-cho, Sakyo-ku

department: Gastroenterology and hepatology

country: Japan

institute: Kyoto university

description: mPDAC03 Dclk1+

hyb_protocol: 0.6ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE 8x60K Microarray Ver2.0 (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1(Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Data were normalized   on GeneSpring GX 14.5 (Agilent). Features flagged in Feature Extraction as not positive and significant or not above background were excluded.

source_name: Dclk1-positive PDACs cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 20ng Total RNA using the Pico WTA System(Ovation) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: RNA was prepared using the RNeasy Mini kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations.   RNA was quantified using a NanoDrop-2000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: strain

value: Dclk1CreERT2-IRES-EGFP/+; Pdx1-Flp; KrasFSF-G12D/+; Trp53frt/frt mice

value: FACS-sorted Dclk1+ PDAC


title: True French inoculated 12dpi 2rep. FW

description: Susceptible to ZYMV


title: Dclk1- cells of PDAC 03

description: mPDAC03 Dclk1-

source_name: Dclk1-negative PDACs cells

value: FACS-sorted Dclk1- PDAC


title: 381e inoculated 12dpi 1rep. FW

description: Tolerant to ZYMV


title: BRG1_rep1

description: BRG1 ChIP (replicate 1) library from wild-type 12Z cells


title: True French inoculated 12dpi 1rep. FW

description: Susceptible to ZYMV


title: whole cells, ITC

status: Public on Oct 19 2020

city: West Lafayette

first: Nadia

middle: Marie

last: Atallah

state: IN

address: 201 S. University St

department: Center for Cancer Research

institute: Purdue University

data_processing:
fastp was used to observe read quality
fastp was used to trim data
HISAT2  (v2.1)  to align reads to the reference genome
FeatureCounts  (v2.1) was used to count reads mapping to genes
edgeR Bioconductor package (v3.16.5) to identify differentially expressed genes
Genome_build: Cand_auris_B11221_V1
Supplementary_files_format_and_content: APR.RNAseq.genecounts.txt

organism: Candidozyma auris

source_name: whole cell

growth_protocol: Candida auris (AR0390) cells

extract_protocol:
Ambion Ribopure yeast kit
Illumina TruSeq kit
2x150 on a NovaSeq 6000

treatment_protocol: Exponential-phase cultures of C. auris AR0390 were treated with either DMSO (1%), aprepitant (10 µg/ml), itraconazole (1 µg/ml), or a combination of both drugs.

value: whole cell

value: Itraconazole 1 µg/ml


title: whole cells, ITC_APR

value: Itraconazole/Aprepitant combination (1/10 µg/ml)


title: whole cells, APR

value: Aprepitant 10 µg/ml


title: Dclk1- cells of PDAC 02

description: mPDAC02 Dclk1-


title: BJAB-rKSHV.219_kLANA_ChIP_I-BET_rep2

city: Hannover

first: Rishikesh

last: Lotke

state: Niedersachsen

address: Carl-Neuberg-Straße 1

department: Institut für Virologie

country: Germany

institute: Medizinische Hochschule Hannover

data_processing:
Basecalling was performed using the built-in Real-Time Analysis (RTA) software version 2.4.11.
All FASTQ sequence files were checked for quality using the FastQC tool. Reads exceeding 51 bp were trimmed from the 3’ end down to 51 bp using the FASTQ/A trimmer tool from the FASTX-toolkit.
We used Bowtie for aligning reads to the mouse (mm9) genome for mouse datasets, and human (hg19) genome for human datasets, using the default options with the following exceptions: --best, --strata and -m 1. For data from cells containing the KSHV genome, reads were also aligned to the HQ404500 sequence to which two copies of TRs were appended. Alignment of the reads to the long unique region (LUR) was performed with the aforementioned settings. All resulting SAM files were sorted, duplicates were removed and finally converted to BAM format.
Peak calling was performed using MACS using the default options with the following exceptions: --nomodel and --shiftsize value was set to half the size of mean fragment length of the ChIP-Seq library as determined by Agilent 2100 Bioanalyzer. For KSHV LUR, peak calling was performed with the aforementioned settings but with the genome size set to 137706 bp and using an additional option --nolambda. For alignment to the terminal repeat (TR) regions of the KSHV genome, reads were aligned using Bowtie with the aforementioned options for read alignment, except -m 1 was changed to -M 1. The SAM files were sorted and converted to BAM without removal of duplicates. No peak calling was performed for alignments for the TR. Instead, the aligned reads were extended to match the library fragment size using the igvtools ‘Count’ command from the Integrative Genomics Viewer (v2.3) with default settings, the window size set to 10 and the extension factor set depending on the average fragment size of the library.
Genome_build: hg19 (GRCh37) for human genome, HQ404500 appended with two copies of TRs for KSHV genome and mm9 (MGSCv37) for mouse genome.
Supplementary_files_format_and_content: wig files were generated during peak calling step using the MACS peak caller.

source_name: Human Burkitt lymphoma

growth_protocol: BCBL-1, BJAB-mCherry, BJAB-kLANA and BJAB-rKSHV.219 were cultured in RPMI 1640 (Gibco) with 20% (v/v) Foetal Calf Serum (FCS) (HyClone) whereas A20-GFP, A20-mLANA WT and A20-mLANA 3A mutant were cultured in RPMI 1640 with 10% (v/v) FCS. All cells were incubated in a humidified incubator with 5% CO2 at 37°C.

extract_protocol:
ChIP was performed as described in (Si, Verma, & Robertson, 2006; Günther & Grundhoff, 2010) with the following modifications. For kLANA and mLANA ChIP, the formaldehyde fixation time was 10 minutes, while for Brd2/4 it was 20 minutes. For the Brd2/4 ChIP experiments we used rabbit polyclonal antigen-affinity purified IgG antibodies (Bethyl laboratories, Inc. BRD2-A302-583A and BRD4-A301-958A100) at a concentration of 3 µg/mg of lysate. Antibodies were incubated with the lysates for 6 hours before adding protein G beads and then further incubated for 16 hours. For kLANA ChIP, we used an IgG2c rat monoclonal antibody (Advanced Biotechnologies Inc. 13-210-100) and prepared antibody-conjugated beads as previously described (Zhang et al., 2016), with the exception of the beads being washed and finally resuspended in ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris HCl - pH 8.0, 167 mM NaCl). Rabbit IgG Cell Signaling Technology® and Rat IgG Abcam were used as isotype controls in, respectively, the Brd2/4 and kLANA ChIP experiments. For the mLANA experiments, we used 50 µl of EZview™ Red anti-FLAG® M2 Affinity Gel (Sigma-Aldrich) per lysate derived from ~3 x 10^7 nuclei.
Libraries were prepared using the NEXTflex™ ChIP-Seq and NEXTflex™ ChIP-Seq Barcodes - 12 kits from BIOO Scientific Corp. according to the manufacturer’s instructions (NEXTflex™ ChIP-Seq kit Manual 5143-02) to prepare single-end DNA libraries from ChIP DNA using the gel-free protocol and libraries were size selected to be between 300-400 bp.

treatment_protocol: BCBL-1, BJAB-mCherry, BJAB-kLANA and BJAB-rKSHV.219 cells were plated in T-75 flasks at a cell density of 0.5 x 10^6 cells/ml and in the absence or presence of I-BET151 at a final concentration of 0.5 µM for 48 hours. For induction of A20-GFP, A20-mLANA WT or A20-mLANA 3A, cells were cultured in a T-75 flask at a density of 0.2 x 10^6 cells/ml supplemented with doxycycline at a final concentration of 1 µg/ml.

tag: modification to cells

value: BJAB cells latently infected with recombinant KSHV (rKSHV.219)

value: I-BET

value: IgG2c rat anti-KSHV LANA monoclonal (Advanced Biotechnologies Inc. 13-210-100)


title: BJAB-rKSHV.219_kLANA_ChIP_No_I-BET_rep2

value: No I-BET


title: Ecs_control_24h_rep2

value: exosomes from endothelial cells


title: whole cells, Untreated

value: Untreated control


title: Dclk1+ cells of PDAC 02

description: mPDAC02 Dclk1+


title: BJAB-rKSHV.219_kLANA_Input_No_I-BET_rep2


title: BJAB-rKSHV.219_kLANA_Input_I-BET_rep2


title: BJAB-rKSHV.219_kLANA_Input_I-BET_rep1


title: Ecs_control_24h_rep1


title: BJAB-rKSHV.219_kLANA_ChIP_No_I-BET_rep1


title: BJAB-kLANA_kLANA_ChIP_I-BET_rep2

value: BJAB-kLANA

value: BJAB cells transduced with lentivirus containing kLANA expression construct


title: BJAB-kLANA_kLANA_ChIP_No_I-BET_rep2


title: BJAB-kLANA_kLANA_Input_I-BET_rep2


title: Dclk1- cells of PDAC 01

description: mPDAC01 Dclk1-


title: BJAB-kLANA_kLANA_Input_No_I-BET_rep2


title: BJAB-rKSHV.219_kLANA_Input_No_I-BET_rep1


title: BJAB-rKSHV.219_kLANA_ChIP_I-BET_rep1


title: BJAB-kLANA_kLANA_ChIP_No_I-BET_rep1


title: BJAB-kLANA_kLANA_ChIP_I-BET_rep1


title: BJAB-kLANA_kLANA_Input_No_I-BET_rep1


title: BJAB-kLANA_kLANA_Input_I-BET_rep1