title: D9_H1CD43_positive3

city: Guangzhou

first: cuihua

last: wang

address: 190 Kaiyuan Avenue, Guangzhou Science Park, Luogang District, Guangzhou

institute: Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
Reads were aligned to the gencode (hg38_enst_v81) transcriptome using STAR (version 2.7)
The gene expression level was calculated by using  STAR
The RNA-seq data processing was performed as described45. To analyze the regular gene expression, the reads were aligned to the reference transcriptome by RSEM46 and bowtie2 (—bowtie2— bowtie2-sensitivity-level very_sensitive —no-bam-output —estimate -rspd) using the index built by RSEM with the human genome, hg38 and Ensembl gene annotation track v81
Genome_build: hg38

source_name: in vitro hematopoietic cells

growth_protocol: H1 hESCs were subjected to EB-primed planar differentiatiation in defined cell culture conditions and in the absence of exogenous hematopoietic cytokines

extract_protocol:
total RNA
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: BMP4 and VEGF were used to initiate mesodermal differentiation of hESCs, then, starting from Day 3 of differentiation, the only growth factor in the culture medium was VEGF

value: H1 human embryonic stem cells

value: hVEGF

value: hESC-derived cells

tag: cell subtype

tag: time


title: 0027-V05

status: Public on Oct 21 2020

type: SRA

city: Oxford

first: Daniel

last: O'Connor

state: Oxfordshire

address: Churchill Hospital

department: Paediatrics

country: United Kingdom

institute: University of Oxford

description:
Human infant whole blood RNA-sequencing data
ribosomal and globin RNA depleted

library_source: transcriptomic

data_processing:
Human RNA-sequencing alignment against Homo sapiens genome build GRCh38 (https://ccb.jhu.edu/software/hisat2/index.shtml), using HISAT2 version 2.0.5.
Gene counting was conducted using the HTSeq version 0.9.1, utilizing human gene annotation gtf (General Transfer Format) version GRCh38.88 (www.ensembl.org).
Computational depletion of ribosomal RNA using SortMeRNA (version 2.1).
The R (version 3.4.4) software environment for statistical computing was used. R packages: edgeR, used TMM  (version 3.20.9), limma used voom function (version 3.34.9)

molecule: total RNA

organism: Homo sapiens

source_name: Whole blood

extract_protocol:
Total RNA was extracted using the Blood RNA Kit (PreAnalytiX, Switzerland), using the automated protocol (QIAcube instrument, QIAGEN, Germany).
The ribodepleted and globin depleted fraction was selected from the total RNA using Ribo-ZeroTM Gold rRNA removal Kit (Illumina, USA). RNA was converted to cDNA, second-strand cDNA synthesis incorporated dUTP. The cDNA was end-repaired, A-tailed and adapter-ligated and prior to amplification, samples underwent uridine digestion (to ensure strand-specific sequencing)
The prepared libraries were size selected, multiplexed and quality controlled before 100bp paired-end sequencing (HiSeq4000). Sequencing was conducted at the Wellcome Trust Centre for Human Genetics (Oxford, UK).

treatment_protocol: Peripheral blood (up to 1.5ml) was collected into a reduced volume PAXgeneTM RNA stabilisation reagent (ratio of blood to PAXgene equivalent to manufacturer’s specifications).

tag: tissue

value: Whole blood

tag: vaccination status

tag: study group

value: Test

tag: Sex

value: Female

tag: post-vaccination log10 (menb sba titres)

tag: post-vaccination fever

value: Fever


title: Sample 94

type: RNA

city: Ottawa

first: Sabina

last: Halappanavar

state: Ontario

address: 251 Sir Frederick Banting Driveway, Building 22

country: Canada

institute: Health Canada

hyb_protocol: Equal amounts of Cy5-labeled experimental cRNA and Cy3-labeled reference RNA (200ng) were co-hybridized to Agilent Sureprint G3 Mouse GE 8x60K microarray slides, according to the instructions outlined in the Agilent Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) Protocol. Samples were hybridized for 17 hours at 65oC and 10 rpm.

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1). Non background subtracted median signal intensities were LOWESS normalized using the maanova library in R. Probes with technical replicates were averaged using the median.

organism: Mus musculus

source_name: Control day 90

label_protocol: Total RNA (200ng per array) was labeled using the Agilent Quick Amp Labeling Kit, Two-Color (Agilent Cat #: 5190-0444), according to the manufacturer's instructions. Control and experimental samples were labeled with Cyanine 5-CTP; whereas universal mouse reference RNA was labeled with Cyanine 3-CTP.

growth_protocol: Mice were housed in polypropylene cages with sawdust bedding and enrichment with a 12h light and 12h dark cycle. Temperature and humidity were maintained at 21 ± 1°C and 50 ± 10% respectively. Food (Altromin 1324) and tap water ad libitum were accessible to all mice.

extract_protocol: Mice were anaesthetized under isofluorane and murine lung, liver, and heart were collected, placed in cryovials and immediately snap frozen in liquid nitrogen. Tissues were stored at -80oC until RNA extraction was performed. Total RNA was extracted from random sections (n=5 per group) using Trizol reagent (Invitrogen) and further purified using the RNeasy Mini Kit (Qiagen) with an on-column DNase I digestion according to the manufacturer's instructions.Total RNA concentration and quality was determined using a Nanodrop 1000 Spectrophotometer and an Agilent 2100 Bioanalyzer, respectively. RNA samples used for gene expression microarray had A260/280 ratios > 2.0 and RINs > 7.0.

treatment_protocol: Seven weeks old C57BL/6J female mice were exposed to 0, 18, 54 and 162 ug/mouse of graphene oxide (GO) or reduced graphene oxide (rGO) or carbon black (CB) or vehicle control for 1 day, 28 days and 90 days.

tag: gender

value: female

value: Lung Tissue

tag: strain

tag: treatment

value: Control

tag: time point

value: day 90

tag: dose

value: 0 µg

source_name: Universal Mouse Reference RNA

tag: source

value: 11 mouse cell lines


title: Sample 92

source_name: CB 162 µg day 90

value: CB


title: Sample 93

source_name: rGO 18 µg day 1

value: rGO

value: day 1

value: 18 µg


title: D9_H1CD43_positive2

country: China

tag: cell line

value: H1 human embryonic stem cells

tag: cell type


title: Primary_biliary_cirrhosis_1 ML-1

city: Oslo

first: Trine

last: Folseraas

state: Oslo

address: Sognsvannsveien 7

department: Transplantation Medicine

country: Norway

institute: Oslo University Hospital Rikshospitalet

hyb_protocol: Standard Affymetrix GeneChip hybridization control protocol/kit

scan_protocol: Standard Affymetrix hybridization protocol

data_processing: Standard Affymetrix GeneChip protocol

label: biotin

source_name: Liver tissue

label_protocol: cRNA  were prepared with the  Affymetric GeneChip WT CDNA syntheis and amplification kit and  Terminal Labeling Kit

extract_protocol: Total RNA was extracted from frozen liver tissue samples  using the RNeasy Mini Kit or Micro Kit (Qiagen).

tag: condition

value: Primary biliary cirrhosis


title: 0026-V05


title: Primary_sclerosing_cholangitis_1_a PSC_1_a

value: Primary sclerosing cholangitis


title: Non_alcoholic_steatohepatitis_7 NASH_7

value: Non alcoholic steatohepatitis


title: Sample 91

source_name: Control day 28

value: day 28


title: D9_H1CD43_negative3

value: hVEGF

value: hESC-derived cells

tag: cell subtype


title: Non_alcoholic_steatohepatitis_6 NASH_6


title: D9_H1CD43_negative2

tag: time


title: 0023-V05

tag: tissue

value: Whole blood

value: Test

value: Female

value: Fever


title: D9_H1CD43_negative1


title: 0023-V03

tag: vaccination status

value: Pre-vaccination


title: D9_H1CD43_positive1


title: D6_H1CD43_positive3


title: 0022-V04

tag: study group


title: 0026-V04

tag: Sex


title: D6_H1CD43_positive2


title: 0020-V05

value: Control

value: Male

tag: post-vaccination log10 (menb sba titres)


title: D6_H1CD43_positive1


title: 0022-V05

tag: post-vaccination fever


title: 0020-V03


title: D6_H1CD43_negative3


title: 0019-V05


title: D6_H1CD43_negative2


title: Non_alcoholic_steatohepatitis_4 NASH_4


title: D6_H1CD43_negative1


title: Liver_tissue_healthy LTH_4

value: Liver tissue healthy


title: H1

value: no treatment

value: undifferentiated hESC


title: Non_alcoholic_steatohepatitis_3 NASH_3


title: Liver_tissue_healthy LTH_3


title: Non_alcoholic_steatohepatitis_5 NASH_5


title: Sample 81

source_name: rGO 162 µg day 90

tag: gender

value: female

value: Lung Tissue

value: rGO

value: day 90

value: 11 mouse cell lines


title: Non_alcoholic_steatohepatitis_2 NASH_2

value: Non alcoholic steatohepatitis


title: Sample 88

source_name: rGO 18 µg day 28

tag: strain

value: day 28

value: 18 µg


title: Sample 90

source_name: GO 18 µg day 90

tag: treatment

value: GO


title: Sample 86

tag: time point

value: 0 µg


title: Liver_tissue_healthy LTH_2


title: Sample 82

source_name: GO 54 µg day 90

tag: dose

value: 54 µg


title: Sample 84

source_name: rGO 54 µg day 90

tag: source


title: Sample 79


title: FLAG-NRF1-2

city: San Diego

first: Lara

last: Ibrahim

state: California

address: 10550 N Torrey Pines Rd

country: USA

institute: Scripps Research

data_processing:
Basescaling was performed by BGI
Single end, 50 bp-long reads from RNA Seq experiments were aligned to the GRCh37.p13 human genome reference assembly using SeqMan NGen 11.2.1 or 12.2.0 (DNAStar Inc.) using default parameters.
The assembly data were imported into ArrayStar 12.2 with Qseq (DNAStar Inc.) to quantify the gene expression levels. The sequence counts were normalized to reads per kilobase per million (RPKM) after filtering out non-mRNA sequence features.
Genome_build: GRCh37.p13 human genome reference assembly
Supplementary_files_format_and_content: XLSX file contains raw counts data for each sample

source_name: human embryonic kidney cells

growth_protocol: HEK293T cells were maintained in standard DMEM supplemented with 10%FBS and 1%PSQ at 37C and 5% CO2

extract_protocol:
Three independent experiments were performed. Cells were lysed and total RNA was collected (RNeasy mini kit, Qiagen)
Libraries were constructed using standard protocols at BGI

treatment_protocol: Cells were treated transfected with Fugene for 24 hr.

tag: cell line

value: transiently transfected with NRF1


title: Liver_tissue_healthy LTH_5


title: 0019-V03

value: Whole blood

value: Pre-vaccination

value: Test

value: Female


title: Non_alcoholic_steatohepatitis_1 NASH_1


title: Sample 80

source_name: rGO 18 µg day 90


title: Sample 85

value: CB


title: Liver_tissue_healthy LTH_6

value: Liver tissue healthy


title: PM365_endo_cs

type: genomic

city: Vancouver

first: Wendy

last: Robinson

state: BC

address: 950 W 28th Ave

department: Medical Genetics

institute: University of British Columbia

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

scan_protocol: Arrays were imaged using iSCAN using standard recommended Illumina scanner setting

data_processing: Beta value normalized with BMIQ and filtered for quality probes. See original publication for complete details.

label: Cy3, Cy5

molecule: genomic DNA

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted by standard salt method and purified using Qiagen DNeasy Kit according to standard instructions

tag: fetal sex

value: F

tag: trimester

value: Third

value: placenta

tag: cell type

value: Endothelial cs

tag: well


title: Sample 83

value: female

tag: tissue

value: Lung Tissue

value: day 90

value: 11 mouse cell lines


title: 0018-V04

tag: vaccination status

value: Control


title: TOP2B_TS543_ETO_chip-seq_2

city: New York

first: Junfei Zhao

last: Zhao

state: NY

address: 1130 St. Nicholas Ave

institute: Columbia University

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using bwa mem.
peaks were called using macs2 with the default setting.
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak files were generated using macs2.

source_name: Glioma cells

extract_protocol: Nuclear extracts were isolated, chromatin fragmented using Covaris sonicator in 1mL tubes for 1min. 10 ug of antibody (TOP2A Abcam TOP2B Abcam) wasc incubated overnight. Washes with RIPA Buffer 4 times and once of TE with 50mM NaCl. Reversed crosslink and DNA purified for sequencing using phenol:chloroform:isoamyl alcohol.

treatment_protocol: 50x10e6 cells were treated with etoposide or DMSO, crosslinked using formaldehyde 1%.

tag: chip antibody


title: 0016-V04

tag: study group

tag: Sex


title: FLAG-NRF2-2

value: transiently transfected with NRF2


title: ETO_TS543_Input_DNA_2

value: input


title: Liver_tissue_healthy LTH_1

tag: condition


title: S60-580338-TUMOR-RNA-Rag2+/-

city: Durham

first: David

last: Kirsch

state: NC

address: PO Box 96100

institute: Duke University

data_processing:
Base-calling was done on the instrument using RTA v3.3.3.
Demultiplexing was done using bcl2fatq v2.20.0.422
Sequenced reads were trimmed for adaptor sequence and low-quality sequence using Trimmomatic v0.36
Reads were mapped to mouse mm10 genome using STAR v5.5.4b and quantified to features using HT-Seq built in the STAR aligner.
Genome_build: mm10
Supplementary_files_format_and_content: text file with normalized counts by FPKM.UQNorm.LOG2

source_name: Tumor

growth_protocol: Primary p53/MCA sarcomas were generated in mice between 6-10 weeks old by intramuscular Adeno-sgp53-Cas9 injection into the gastrocnemius of Rag2-/- and Rag2+/- mice, followed by injection of 300 µg MCA (Sigma-Aldrich) resuspended in sesame oil (SigmaAldrich) at 6 µg/µl.

extract_protocol:
Tumor specimens and matched liver control were harvested and stored in RNALater at -80° until all samples were collected. RNA extractions from each sample were performed using AllPrep DNA/RNA Mini Kit (Qiagen).
RNA Library preparation was performed as indicated by the NEBNext Ultra II RNA Library Prep Kit for Illumina, and RNA sequencing was performed by Novogene on an Illumina Novoseq 6000 in 150 base pair, paired-end configuration.

treatment_protocol: Mice were not treated. Tumors were harvested from when volume reached ~70-150 mm3.

value: Primary p53/MCA sarcoma

tag: genotype

tag: replicate group


title: S44-580218-TUMOR-RNA-Rag2-/-


title: 0015-V03

value: Whole blood

value: Pre-vaccination

tag: post-vaccination log10 (menb sba titres)

tag: post-vaccination fever


title: 0015-V05

value: Female


title: S41-580215-TUMOR-RNA-Rag2-/-


title: TOP2B_TS543_DMSO_chip-seq_2


title: DMSO_TS543_Input_DNA_2


title: S59-580317-TUMOR-RNA-Rag2+/-


title: S58-580245-TUMOR-RNA-Rag2+/-


title: Sample 87

tag: gender

tag: strain

tag: treatment

value: GO

tag: time point

tag: dose

value: 54 µg


title: S56-580205-TUMOR-RNA-Rag2+/-


title: TOP2B_SNB19_ETO_chip-seq_2


title: 0014-V03

value: Test

value: Fever


title: ETO_SNB19_Input_DNA_2


title: 0013-V05


title: S55-580252-TUMOR-RNA-Rag2+/-


title: 0014-V05


title: TOP2B_SNB19_DMSO_chip-seq_2


title: DMSO_SNB19_Input_DNA_2


title: 0013-V04


title: 0010-V05


title: TOP2B_BT142_ETO_chip-seq_2


title: Sample 78

tag: source


title: S53-580209-TUMOR-RNA-Rag2+/-


title: S52-580214-TUMOR-RNA-Rag2+/-


title: ETO_BT142_Input_DNA_2


title: Sample 76

source_name: rGO 54 µg day 1

value: rGO

value: day 1


title: Primary_sclerosing_cholangitis_2_a PSC_2_a

value: Primary sclerosing cholangitis


title: Sample 77

value: female

value: Lung Tissue

value: 18 µg


title: Sample 75

value: CB

value: day 90

value: 11 mouse cell lines


title: Sample 74


title: 0008-V05

source_name: Whole blood

value: Control


title: Sample 73


title: S51-580314-TUMOR-RNA-Rag2-/-

value: Primary p53/MCA sarcoma


title: Sample 72

source_name: rGO 162 µg day 1


title: TOP2B_BT142_DMSO_chip-seq_2


title: Sample 71

source_name: Universal Mouse Reference RNA


title: 0008-V04

value: Whole blood

value: Pre-vaccination


title: S50-580247-TUMOR-RNA-Rag2-/-


title: 0010-V04

value: Female


title: S49-580243-TUMOR-RNA-Rag2-/-


title: Sample 69

value: day 28


title: S54-580210-TUMOR-RNA-Rag2+/-


title: DMSO_BT142_Input_DNA_2

value: input


title: 0005-V05

value: Male


title: 0005-V04


title: S48-580250-TUMOR-RNA-Rag2-/-


title: TS543_ETO_T2B


title: TOP2B_1711_DMSO


title: 0003-V05


title: S47-580208-TUMOR-RNA-Rag2-/-


title: 0003-V03


title: Sample 70

value: rGO


title: TOP2B_1711PERI_ETO


title: S46-580206-TUMOR-RNA-Rag2-/-


title: 0002-V05


title: S43-580217-TUMOR-RNA-Rag2-/-


title: 0002-V03


title: S45-580219-TUMOR-RNA-Rag2-/-


title: Sample 68

source_name: GO 18 µg day 28

value: GO


title: TOP2B_1523_DMSO


title: 0001-V05

value: Fever


title: 0001-V04


title: S42-580216-TUMOR-RNA-Rag2-/-


title: TOP2B_1523_ETO


title: TOP2B_1536_ETO


title: CL0I-402230-T-RNA [S2]

data_processing:
Base-calling was done on the instrument using RTA v3.3.3.
Demultiplexing was done using bcl2fatq v2.20.0.422
Sequenced reads were trimmed for adaptor sequence and low-quality sequence using Trimmomatic v0.36
Reads were mapped to mouse mm10 genome using STAR v5.5.4b and quantified to features using HT-Seq built in the STAR aligner.
Genome_build: mm10
Supplementary_files_format_and_content: csv file with read counts per gene

growth_protocol: Primary p53/MCA sarcomas were generated in mice between 6-10 weeks old by  intramuscular Adeno-Cre injection into the gastrocnemius of p53FL/FL mice, followed by injection of 300 µg MCA (Sigma-Aldrich) resuspended in sesame oil (SigmaAldrich) at 6 µg/µl. Allograft p53/MCA sarcomas were generated by injecting 50,000 cells resuspended in 100 uL DMEM (Gibco) and Corning matrigel from cell line 402230 into the gastrocnemius muscle of syngeneic mice.

extract_protocol:
Tumor specimens and matched liver control were harvested and stored in RNALater at -80° until all samples were collected. DNA and RNA extractions from each sample were performed using AllPrep DNA/RNA Mini Kit (Qiagen). Extracted total RNA quality and concentration was assessed on a 2100 Bioanalyzer (Agilent Technologies) and Qubit 2.0 (ThermoFisher Scientific), respectively. Only extracts with RNA Integrity Number (RIN) greater than 7 were processed for sequencing. DNA extraction was followed by RNAse treatment (Qiagen). Genomic DNA samples were quantified using fluorometric quantitation on the Qubit 2.0 (ThermoFisher Scientific). For each sample, 200 ng of DNA was sheared using focused-ultrasonicators (Covaris) to generate DNA fragments of about 300 bp in length.
RNA-seq libraries were prepared using the commercially available KAPA Stranded mRNA-Seq Kit (Roche) following the manufacturer’s protocol. In brief, mRNA transcripts were first captured using magnetic oligo-dT beads, fragmented using heat and magnesium, and reverse transcribed using random priming. During the 2nd strand synthesis, the cDNA:RNA hybrid was converted into to double-stranded cDNA (dscDNA) and dUTP incorporated into the 2nd cDNA strand, effectively marking the second strand. Illumina sequencing adapters were then ligated to the dscDNA fragments and amplified to produce the final RNA-seq library. The strand marked with dUTP was not amplified, allowing strand-specificity sequencing.
Libraries were indexed using a dual indexing approach allowing for multiple libraries to be pooled and sequenced on the same sequencing Illumina sequencing flow cell.

treatment_protocol: Tumors were treated when volume reached ~150 mm3 and harvested 3 days later. Mice received  200 ug IP of either muDX400 (Merck, murine anti-PD-1) or isotype control followed immediately by 0 or 20 Gy radiation. For mice receiving radiation, the tumor-bearing hind limb of the mice was irradiated with 20 Gy using the X-RAD 225Cx small animal image-guided irradiator (Precision X-Ray). The irradiation field included the whole left hind limb and was defined using fluoroscopy with 40 kVp, 2.5 mA X-rays using a 2 mm Al filter. Irradiations were performed using parallel-opposed anterior and posterior fields with an average dose rate of 300 cGy/min prescribed to midplane with 225 kVp, 13 mA X-rays using a 0.3 mm Cu filter.

tag: barcode

value: ACGGTCCA

tag: tumor type

value: CellLine

tag: radiation dose

value: Isotype


title: Sample 67

source_name: rGO 162 µg day 28

value: female

tag: tissue

value: Lung Tissue


title: TOP2B_1416_ETO

tag: chip antibody


title: P0I-402230-T-RNA [S1]

value: CACTCAAT

value: Primary


title: Sample 89

value: day 90

value: 11 mouse cell lines


title: Sample 66

value: Control

value: 0 µg


title: Sample 65

value: 54 µg


title: Sample 63

source_name: rGO 54 µg day 28

value: day 28


title: Sample 64


title: P20P-405254A-T-RNA [S144]

value: TCCGCGAA+CCTATCCT


title: TOP2B_1416_DMSO


title: TOP2B_1417_ETO


title: Sample 60

source_name: GO 54 µg day 1

value: day 1


title: Sample 61

source_name: GO 162 µg day 1

value: GO


title: Sample 62


title: Sample 59

source_name: Control day 1


title: Sample 57

source_name: GO 18 µg day 90

value: 18 µg


title: P20P-405264-T-RNA [S143]

value: CGGCTATG+AGGCGAAG


title: 1536_INPUT_ETO

value: input


title: Sample 58

source_name: rGO 162 µg day 90

value: rGO


title: TOP2B_1417_DMSO


title: P20P-405241-T-RNA [S142]

value: CTGAAGCT+TATAGCCT


title: INPUT_TS543


title: P20P-405265-T-RNA [S141]

value: TCTCGCGC+ATAGAGGC


title: INPUT_BT142


title: P20P-405134-T-RNA [S140]

value: ATTCAGAA+GGCTCTGA


title: DMSO_1417_INPUT


title: BT142_ETO_T2B


title: 1711_INPUT


title: P20P-405122-T-RNA [S138]

value: ATTACTCG+TAATCTTA

value: Primary


title: P20P-405003-T-RNA [S137]

value: CGCTCATT+CAGGACGT


title: 0018-V05

value: Whole blood

tag: vaccination status

tag: study group

value: Control

tag: Sex

value: Female


title: P20P-405050-T-RNA [S139]

tag: replicate group

value: GAGATTCC+GTACTGAC


title: Human mDC CT 24h [Main]

city: Boston

first: Wayne

middle: G.

last: Shreffler

state: MA

address: 149 13th Street

institute: Massachusetts General Hospital

description:
Main_11_CT
Gene expression data from human mDC stimulated with CT for 24h.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Data analysis was performed using R software (version 3.6.1). Expression values were log-normalized using the RMA function from the package Affy (version 1.62.0).

source_name: Human mDC CT 24h

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

growth_protocol: The mDC were cultured for 8h or 24h in StemSpan serum-free expansion medium (Stemcell Technologies) with penicillin (100 U/ml) and streptomycin (100 µg/ml), in the absence or presence of the indicated stimuli.

extract_protocol: The mDC were lysed with Buffer RLT + 1% beta-mercapto-ethanol, and total RNA was isolated using the RNeasy Micro Kit from Qiagen, according to the manufacturer's instructions.

treatment_protocol: mDC were stimulated for 8h or 24h with peanut protein extract (PN), the positive controls lipopolysaccharide (LPS) or cholera toxin (CT), the purified peanut proteins Ara h 1 or Ara h 2, soybean protein extract (SB), cow's milk protein (CM), birch pollen extract (BP), cockroach allergen extract (CR), or cat dander extract (CD).

tag: cell type

value: Myeloid dendritic cells

value: CT for 24h


title: Human mDC CD 24h [Main]

description:
Main_9_CD
Gene expression data from human mDC stimulated with CD for 24h.

source_name: Human mDC CD 24h

value: CD for 24h


title: P20I-405208-T-RNA [S136]

value: AGCGATAG+AGGCGAAG

value: Isotype


title: Sample 55

value: female

value: Lung Tissue

value: day 28

value: 11 mouse cell lines


title: Human mDC CR 24h [Main]

description:
Main_8_CR
Gene expression data from human mDC stimulated with CR for 24h.

source_name: Human mDC CR 24h

value: CR for 24h


title: 1711PERI_INPUT

source_name: Glioma cells

value: input


title: Sample 56

source_name: GO 18 µg day 1

value: GO

value: day 1

value: 18 µg


title: Human mDC LPS 24h [Main]

description:
Main_10_LPS
Gene expression data from human mDC stimulated with LPS for 24h.

source_name: Human mDC LPS 24h

value: LPS for 24h


title: Human mDC Arah2 24h [Main]

description:
Main_4_Arah2
Gene expression data from human mDC stimulated with Ara h 2 for 24h.

source_name: Human mDC Arah2 24h

value: Ara h 2 for 24h


title: DMSO_1416_INPUT


title: Human mDC CM 24h [Main]

description:
Main_6_CM
Gene expression data from human mDC stimulated with CM for 24h.

source_name: Human mDC CM 24h

value: CM for 24h


title: Sample 54

value: 54 µg

source_name: Universal Mouse Reference RNA


title: Sample 53

source_name: rGO 18 µg day 28

value: rGO


title: P20I-405223-T-RNA [S135]

source_name: Tumor

value: TAATGCGC+CCTATCCT

value: Primary


title: Human mDC Arah1 24h [Main]

description:
Main_3_Arah1
Gene expression data from human mDC stimulated with Ara h 1 for 24h.

source_name: Human mDC Arah1 24h

value: Myeloid dendritic cells

value: Ara h 1 for 24h


title: Human mDC BP 24h [Main]

description:
Main_7_BP
Gene expression data from human mDC stimulated with BP for 24h.

source_name: Human mDC BP 24h

value: BP for 24h


title: Sample 50

source_name: rGO 54 µg day 28

value: female

value: Lung Tissue

value: day 28


title: Human mDC Unstim 24h [Main]

description:
Main_1_Unstim
Gene expression data from human mDC cultured for 24h without stimulation.

source_name: Human mDC Unstim 24h

value: 24h without stimulation


title: Human mDC PN 24h [Main]

description:
Main_2_PN
Gene expression data from human mDC stimulated with PN for 24h.

source_name: Human mDC PN 24h

value: PN for 24h


title: Sample 48

source_name: Control day 90

value: Control

value: day 90

value: 0 µg

value: 11 mouse cell lines


title: 1523_INPUT

value: input


title: Sample 52

value: GO

value: day 1

value: 18 µg


title: Sample 49

source_name: GO 18 µg day 28


title: SMART_ChIP_R1881_rep4

first: Zhong

last: Chen

address: 905 S. LaSalle Street

department: Pathology

description:
Biological replicate 4
R-SMRT.ucsc.bw

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie-2.1 with default parameters. And only uniquely mapped reads were remained for further analysis.
peaks were called using Homer (v4.10.4) with default parameters
Genome_build: hg19
Supplementary_files_format_and_content: For ChIP-seq, bedgraph files were generated using bedtools, scores represent peaks genomic coverage.

source_name: human esophagus

growth_protocol: The human ESCC cell lines (KYSE series) were maintained in RPMI 1640 supplemented with 10% fetal bovine serum.

extract_protocol:
For ChIP-seq, cells were crosslinked with 1% formaldehyde for 10 min on horizontal rotator at room temperature and cell pellets were collected and subjected to sonication. The sheared chromatin was then diluted and immunoprecipitated with 4 µg of specific antibodies at 4°C overnight. After washing, chromatin complexes were eluted with elution buffer and crosslinking was reversed at 65°C overnight. DNA fragments were purified with the QIAquick PCR purification kit. For RNA-seq, total RNA was isolated using an RNeasy kit (QIAGEN). Next, mRNA was enriched using NEBNext Poly(A) mRNA Magnetic Isolation Module. After two rounds of processes, the  mRNA was recovered for library generation.
For ChIP-seq, the eluted ChIP DNA was used for library preparation with NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina according to the manufacturer’s protocol. The library was ampliﬁed with 12 PCR cycles and prepared with gel-based size selection. For RNA-seq, the library preparation was performed with NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina following the manufacturer’s instructions. The cDNA molecules were amplified by 8 cycles of PCR. Non-size selection libraries were then sequenced for using Illumina HiSeq 4000 at the Duke sequencing core.

treatment_protocol: For ChIP or RNA-seq experiments, ESCC cells were maintained in phenol red-free RPMI 1640 medium with 5% charcoal-stripped FBS for 3 days, and then treated with vehicle and AR ligands for the indicated time.

tag: cell line

value: ESCC cell line KYSE410

tag: disease state

value: esophageal squamous cell carcinoma

value: Anti-NCOR2/SMRT antibody  (ab24551) from abcam


title: Sample 51

source_name: GO 162 µg day 1

tag: gender

tag: strain


title: SMART_ChIP_R1881_rep3

description:
Biological replicate 3
R-SMRT.ucsc.bw

tag: treatment


title: P20I-405312-T-RNA [S132]

value: GAATTCGT+GTACTGAC

value: Primary

value: Isotype


title: P20I-405242-T-RNA [S133]

value: CGGCTATG+TATAGCCT


title: P20I-405319-T-RNA [S134]

value: TCCGCGAA+ATAGAGGC


title: SMART_ChIP_R1881_rep2

description:
Biological replicate 2
R-SMRT.ucsc.bw


title: Human mDC SB 24h [Main]

description:
Main_5_SB
Gene expression data from human mDC stimulated with SB for 24h.

source_name: Human mDC SB 24h

value: Myeloid dendritic cells

value: SB for 24h


title: SMART_ChIP_R1881_rep1

description:
Biological replicate 1
R-SMRT.ucsc.bw


title: D12_H1CD43_positive3

source_name: in vitro hematopoietic cells

value: H1 human embryonic stem cells

value: hVEGF

value: hESC-derived cells

tag: cell subtype

tag: time


title: P20I-405226-T-RNA [S131]

tag: barcode

value: TCCGGAGA+GGCTCTGA


title: SMART_ChIP_vehicle_rep4

description:
Biological replicate 4
V-SMRT.ucsc.bw

value: Vehicle


title: P20I-520063-T-RNA [S130]

value: ATTCAGAA+CAGGACGT

tag: tumor type


title: D12_H1CD43_positive2


title: P20I-405140-T-RNA [S129]

value: GAGATTCC+TAATCTTA

tag: radiation dose


title: Sample 47

source_name: rGO 162 µg day 90

value: female

tag: tissue

value: Lung Tissue

value: rGO

tag: time point

value: day 90

tag: dose

tag: source

value: 11 mouse cell lines


title: Human mDC PN 24h [Pilot]

description:
Pilot_4_PN_24h
Gene expression data from human mDC stimulated with PN for 24h.

value: PN for 24h


title: D12_H1CD43_positive1


title: SMART_ChIP_vehicle_rep3

description:
Biological replicate 3
V-SMRT.ucsc.bw

value: ESCC cell line KYSE410

value: esophageal squamous cell carcinoma

tag: chip antibody

value: Anti-NCOR2/SMRT antibody  (ab24551) from abcam


title: Sample 46

source_name: rGO 18 µg day 1

value: day 1

value: 18 µg


title: SMART_ChIP_vehicle_rep2

description:
Biological replicate 2
V-SMRT.ucsc.bw


title: P0P-520068-T-RNA [S127]

tag: replicate group

value: CTGAAGCT+ATAGAGGC

value: Primary


title: SMART_ChIP_vehicle_rep1

description:
Biological replicate 1
V-SMRT.ucsc.bw


title: D12_H1CD43_negative3

value: H1 human embryonic stem cells

value: hVEGF

tag: cell type

value: hESC-derived cells


title: P0P-405310-T-RNA [S128]

value: TCTCGCGC+TATAGCCT


title: P0P-405309-T-RNA [S126]

value: AGCGATAG+GGCTCTGA


title: Human mDC Unstim 24h [Pilot]

description:
Pilot_3_Unstim_24h
Gene expression data from human mDC cultured for 24h without stimulation.

value: Myeloid dendritic cells

value: 24h without stimulation


title: D12_H1CD43_negative1

tag: cell line


title: Human mDC Unstim 8h [Pilot]

description:
Pilot_1_Unstim_8h
Gene expression data from human mDC cultured for 8h without stimulation.

source_name: Human mDC Unstim 8h

value: 8h without stimulation


title: HDAC3_ChIP_R1881_rep4

description:
Biological replicate 4
R-HDAC3.ucsc.bw

tag: disease state

value: HDAC3 Polyclonal Antibody (PA5-85378) from Invitrogen


title: Human mDC PN 8h [Pilot]

description:
Pilot_2_PN_8h
Gene expression data from human mDC stimulated with PN for 8h.

source_name: Human mDC PN 8h

value: PN for 8h


title: CT star FUS Input RNA-Seq

city: London

first: Marc-David

last: Ruepp

address: 5 Cutcombe Road

department: Dementia Research Institute

institute: King's College

description: CT star FUS Input RNA-Seq

data_processing:
From the raw sequences, the adapter was trimmed using cutadapt version 1.14 with the aditional parameter –minimum-length 18
Trimmed reads were mapped to the Ensembl human genome assembly GRCh38.90 with STAR version 2.5.3a
Filtering the alignments to remove duplicates was done by applying utilities from the samtools suite version 1.8.3 (by applying three utilities f)
With an in-house python script the deletion sites indicative for bona fide CLIP binding sites were inferred while ensuring that the deletion does not overlap with a known SNP
Deletion sites were only kept when multiple reads overlap the according genomic position and not all of them possess the deletion with respect to the genome assembly
Genome_build: GRCh38.90
Supplementary_files_format_and_content: the identified binding sites inferred from crosslink-induced deletion sites

source_name: neuroblastoma cells

growth_protocol: SH-SY5Y cells were cultivated in DMEM supplemented with 10% fetal calf serum (FCS), penicillin (100 μg/mL), and streptomycin (100 μg/mL) and grown at 37°C and 5% CO2

extract_protocol: Library preparation of the RNA fragments derived from CLIP experiments was performed using the TruSeq small RNA sample preparation kit (Illumina). For Input RNA-Seq, total RNA was subjected to ribo-depletion using RiboCop (Lexogen) and library preparation was performed using the TruSeq stranded mRNA library preparation kit (Illumina). Sequencing was performed on a HiSeq 2500 platform (Illumina).

treatment_protocol: After 254nm cross-linking, cells were lysed in RIPA buffer and FUS-RNA complexes were purified using Streptactin-coated magnetic beads upon limited Rnase1 digestion. Following SDS-PAGE and western blot, RNA fragments were retrieved from the membrane by proteinase K treatment

value: neuroblastoma cells

tag: protein tag

value: Twin-Strep

tag: protocol

value: RNA-Seq


title: P0P-405206-T-RNA [S124]

source_name: Tumor

tag: strain

value: CGCTCATT+TAATCTTA

tag: treatment


title: Sample 44

source_name: rGO 54 µg day 1

tag: gender

value: female

value: Lung Tissue

value: rGO

value: day 1

value: 54 µg

source_name: Universal Mouse Reference RNA

value: 11 mouse cell lines


title: CT FUS Input RNA-Seq

description: CT FUS Input RNA-Seq


title: D12_H1CD43_negative2

value: H1 human embryonic stem cells

value: hVEGF

value: hESC-derived cells

tag: cell subtype

tag: time


title: HDAC3_ChIP_R1881_rep2

description:
Biological replicate 2
R-HDAC3.ucsc.bw

value: ESCC cell line KYSE410

value: esophageal squamous cell carcinoma


title: HDAC3_ChIP_R1881_rep1

description:
Biological replicate 1
R-HDAC3.ucsc.bw

value: HDAC3 Polyclonal Antibody (PA5-85378) from Invitrogen


title: P0P-405156-T-RNA [S122]

tag: barcode

value: GAATTCGT+CCTATCCT

tag: tumor type

value: Primary

tag: radiation dose


title: HDAC3_ChIP_vehicle_rep4

description:
Biological replicate 4
V-HDAC3.ucsc.bw

value: Vehicle


title: CT star FUS CLIP-Seq rep 3

description: CT star FUS CLIP-Seq rep 3

value: neuroblastoma cells

value: Twin-Strep

value: HITS-CLIP


title: P0P-405253-T-RNA [S125]

value: TAATGCGC+GTACTGAC


title: P0P-405077-T-RNA [S121]

value: TCCGGAGA+AGGCGAAG


title: HDAC3_ChIP_R1881_rep3

description:
Biological replicate 3
R-HDAC3.ucsc.bw


title: P0I-405263-T-RNA [S120]

value: TAATGCGC+ATAGAGGC

value: Isotype


title: Sample 42

source_name: rGO 54 µg day 90

value: female

tag: tissue

value: Lung Tissue

value: rGO

tag: time point

value: day 90

tag: dose

value: 54 µg

value: 11 mouse cell lines


title: HDAC3_ChIP_vehicle_rep3

description:
Biological replicate 3
V-HDAC3.ucsc.bw

value: ESCC cell line KYSE410

value: esophageal squamous cell carcinoma

tag: chip antibody

value: HDAC3 Polyclonal Antibody (PA5-85378) from Invitrogen


title: HDAC3_ChIP_vehicle_rep2

description:
Biological replicate 2
V-HDAC3.ucsc.bw

value: Vehicle


title: P0P-405227-T-RNA [S123]

tag: replicate group

value: ATTACTCG+CAGGACGT

value: Primary


title: CT star FUS CLIP-Seq rep 2

description: CT star FUS CLIP-Seq rep 2

tag: cell line

tag: cell type

value: neuroblastoma cells

value: Twin-Strep

value: HITS-CLIP


title: FL FUS Input RNA-Seq

description: FL FUS Input RNA-Seq

tag: protein tag

value: RNA-Seq


title: Sample 45

source_name: rGO 18 µg day 90

value: 18 µg

tag: source


title: Sample 41

source_name: Control day 1

value: female

tag: strain

value: Control

value: day 1

value: 0 µg


title: P0I-405204-T-RNA [S119]

value: AGCGATAG+TATAGCCT

tag: treatment

value: Isotype


title: CT star FUS CLIP-Seq rep 1

description: CT star FUS CLIP-Seq rep 1

tag: protocol


title: Sample 43

source_name: rGO 162 µg day 1

tag: gender

value: Lung Tissue

value: rGO

value: 11 mouse cell lines


title: CT FUS CLIP-Seq rep 3

description: CT FUS CLIP-Seq rep 3


title: HDAC3_ChIP_vehicle_rep1

description:
Biological replicate 1
V-HDAC3.ucsc.bw

value: ESCC cell line KYSE410

tag: disease state

value: esophageal squamous cell carcinoma

value: Vehicle

value: HDAC3 Polyclonal Antibody (PA5-85378) from Invitrogen


title: Sample 39

source_name: Control day 28

value: day 28


title: P0I-405313-T-RNA [S118]

tag: barcode

value: GAGATTCC+AGGCGAAG

value: Primary


title: CT FUS CLIP-Seq rep 2

description: CT FUS CLIP-Seq rep 2

value: neuroblastoma cells

value: Twin-Strep

value: HITS-CLIP


title: Sample 40

source_name: rGO 162 µg day 28

value: female

value: GO


title: P0I-405251-T-RNA [S117]

value: CTGAAGCT+GGCTCTGA

tag: tumor type


title: MERS_2S_mRNA

city: cambridge

first: Jonathan

middle: Lewis

last: Price

address: The Sanger Building Tennis Court Road

department: Biochemistry

institute: University of Cambridge

data_processing:
Trim reads - Cutadapt
Merge Reads - Pear - https://cme.h-its.org/exelixis/web/software/pear/
Merge UMI - https://gitlab.com/tdido/tstk
Hyb - 10.1016/j.ymeth.2013.10.015
Genome_build: hg38 and Vervet-AGM (ChlSab1.1)

source_name: MERS sgmRNAs

growth_protocol: Infection experiments were performed under biosafety level 3 conditions. Independent biological replicates were performed using 90-120 million cells each. Cells were cultivated in Dulbecco’s modified Eagles medium (DMEM) supplemented with 10% fetal bovine serum. Titration of virus stocks was conducted using Vero E6 cells. For SARS-CoV-2 infection, VeroE6/TMPRSS2 cells (PMID: 32165541) were inoculated with SARS-CoV-2 strain München-1.2/2020/984 at MOI=2 pfu/cell for 20 hours. For MERS infection, HuH7 cells were inoculated with MERS-CoV strain EMC/2012 (GenBank: JX869059.2; PMID: 23170002) at MOI=2 pfu/cell for 20 hours. Following inoculation cells were washed 3 times by PBS and were incubated for 20 minutes with 0.4 mg/ml Psoralen-triethylene glycol azide (psoralen-TEG azide, Berry & Associates) diluted in PBS and supplemented with OptiMEM I with no phenol-red (Gibco). Cells were subsequently irradiated on ice with 50 KJ/m2 365 nm UV using a CL-1000 crosslinker (UVP). Cell lysis was performed by RNeasy lysis buffer (Qiagen) supplemented with DTT. Proteins were degraded using proteinase K (NEB) and RNA was purified using RNeasy maxi kit (Qiagen). All cell lines were cultured in a humidified CO2 incubator at 37 °C and were regularly examined to exclude mycoplasma contamination.

extract_protocol:
The COMRADES assay was performed as described previously (Ziv et al., 2018). In brief, RNA was fragmented using RNase III (Ambion) and biotin was attached to crosslinked RNA duplexes using Click-IT Biotin sDIBO Alkyne (Life technologies). Biotinylated RNA duplexes were enriched using Dynabeads MyOne Streptavidin C1(Invitrogen) at the following reaction conditions: 100 mM Tris-Cl pH 7.5, 10 mM EDTA, 1 M NaCl, 0.1% Tween-20, 0.5 unit/µl Superase-In. Beads were washed 5 times on a magnet with 100 mM Tris-HCl pH 7.5, 10 mM EDTA, 3.5M NaCl, 0.1% Tween-20. RNA was eluted by adding 95% Formamide, 10 mM EDTA solution preheated to 65oC and purified using RNA Clean & Concentrator (Zymo Research). Each RNA sample was divided in two: one half was used for proximity ligation and then crosslink reversal (i.e. COMRADES sample), while in the other half, crosslink reversal was done before proximity ligation (i.e. control sample). Prior to proximity ligation, RNA was denatured by briefly heating to 95 °C. Proximity ligation was done under the following conditions: 1 unit/µl RNA ligase 1 (New England Biolabs), 1x RNA ligase buffer, 50 mM ATP, 1 unit/µl Superase-in (Invitrogen), final volume: 200 µl. Reaction was incubated for 16 hours at 16 °C and was terminated by cleaning with RNA Clean & Concentrator (Zymo Research). Crosslink reversal was done by irradiating the RNA on ice with 2.5KJ/m2 UVC.
Library preparation was done as described in(Ziv et al., 2018), using 6N unique molecular identifiers to eliminate PCR biases. Pre-adenylated adapters were used and all ligation reactions were carried without ATP to reduce ligation artefacts. All libraries and controls went through 13 PCR cycles using KAPA HiFi HotStart Ready Mix (KAPA Biosystems). PCR products were size-selected on a 1.8% agarose gel before loading on a Novaseq (Illumina) for paired-end 150 bp runs. Total of 1.6 billion sequences were achieved for this study.

value: Huh-7 cells

tag: viralrna

value: sgmRNAs


title: CT FUS CLIP-Seq rep 1

description: CT FUS CLIP-Seq rep 1


title: P0I-404905-T-RNA [S116]

value: TCCGGAGA+CAGGACGT

tag: radiation dose

value: Isotype


title: Sample 37

source_name: rGO 54 µg day 28

tag: tissue

value: Lung Tissue

value: rGO

tag: time point

value: 54 µg

value: 11 mouse cell lines


title: Sample 35

value: day 1

tag: dose


title: Sample 38

value: 18 µg


title: MERS_2C_mRNA


title: FL FUS CLIP-Seq rep 3

description: FL FUS CLIP-Seq rep 3


title: MERS_1S_mRNA


title: Sample 34

source_name: rGO 18 µg day 28

value: day 28


title: Sample 36

source_name: GO 18 µg day 28


title: Sample 33

source_name: CB 162 µg day 90

value: CB

value: day 90


title: Sample 32

source_name: GO 162 µg day 1


title: Sample 31

value: Control

value: 0 µg


title: Sample 29

source_name: GO 54 µg day 1

value: female

value: GO


title: FL FUS CLIP-Seq rep 2

description: FL FUS CLIP-Seq rep 2

source_name: neuroblastoma cells

value: neuroblastoma cells

value: Twin-Strep

value: HITS-CLIP


title: P0I-405137-T-RNA [S115]

source_name: Tumor

tag: replicate group

value: GAATTCGT+TAATCTTA

value: Primary

value: Isotype


title: P0I-404904-T-RNA [S114]

value: CGCTCATT+AGGCGAAG


title: FL FUS CLIP-Seq rep 1

description: FL FUS CLIP-Seq rep 1

tag: cell line


title: A20P-500591-T-RNA [S112]

value: CGGCTATG+GGCTCTGA

value: Allograft


title: P0I-405123-T-RNA [S113]

value: ATTACTCG+CCTATCCT


title: MERS_1C_mRNA

value: Huh-7 cells

value: sgmRNAs


title: MERS_1S

source_name: MERS genomic

value: genomic


title: MERS_2C


title: A20P-500589-T-RNA [S111]

value: TCCGCGAA+GTACTGAC


title: MERS_2S


title: MERS_1C


title: A20P-500615-T-RNA [S110]

value: ATTACTCG+TATAGCCT


title: A20P-405222-T-RNA [S109]

value: AGCGATAG+CAGGACGT


title: Subject 10

city: Denver

first: Camille

last: Moore

state: CO

address: 1400 Jackson St.

institute: National Jewish Health

description: Bronchoalveolar lavage cells from healthy adult

data_processing:
Initial pre-processing of the 10 subjects’ 10X scRNA-seq data, including demultiplexing, alignment to the hg38 human genome, and UMI-based gene expression quantification, was performed using Cell Ranger (version 3.0, 10X Genomics)
Genome_build: hg38
Supplementary_files_format_and_content: comma separated (.csv) matrix of raw counts.  Rows are features and columns are cells.

source_name: Bronchoalveolar lavage

extract_protocol:
Enrolled subjects underwent flexible fiberoptic bronchoscopy and bronchoalveolar lavage with serial installation and aspiration of normal saline. Lavage fluid was centrifuged to pellet cells. Cell pellet was resuspended  at 1x10^6 cells per ml in PBS containing 0.04% bovine serum albumin.
Single cells were captured using The Chromium Box (10x Genomics, Pleasanton, CA). The Chromium Single Cell 3’ GEM, library, and gel bead kit PN-1000075 were used along with Bead Chip B PN-1000092 for cell capture and library construction. Libraries were sequenced with the Illumina NovaSEQ 6000 sequencer (Illumina, Inc., San Diego, CA) using an S4 flow cell.

tag: Sex

value: M

tag: age

tag: cell type

value: Bronchoalveolar lavage cells

tag: diagnosis

value: healthy


title: Subject 9


title: A20I-405292-T-RNA [S108]

tag: strain

value: GAGATTCC+CCTATCCT

tag: treatment


title: Subject 7

value: F


title: A20I-405246-T-RNA [S107]

value: ATTCAGAA+AGGCGAAG


title: Subject 8


title: A20I-500610-T-RNA [S106]

value: TCCGGAGA+TATAGCCT

value: Isotype


title: Sample 30

source_name: GO 18 µg day 1

tag: gender

value: female

value: Lung Tissue

value: GO

value: day 1

value: 18 µg

source_name: Universal Mouse Reference RNA

tag: source

value: 11 mouse cell lines


title: Sample 26

source_name: GO 18 µg day 90

value: day 90


title: Sample 28

source_name: GO 54 µg day 90

value: 54 µg


title: Sample 24

value: rGO

value: day 28


title: Subject 6

value: M

value: Bronchoalveolar lavage cells


title: Sample 22


title: Sample 27

source_name: Control day 90

value: Control

value: 0 µg


title: A20I-405225-T-RNA [S105]

tag: barcode

value: GAATTCGT+ATAGAGGC

value: Allograft


title: Subject 5

value: F

value: healthy


title: Sample 23

value: female

value: Lung Tissue


title: Sample 25

source_name: rGO 162 µg day 28


title: A0P-520232-T-RNA [S104]

value: CTGAAGCT+GTACTGAC

tag: tumor type


title: Subject 4


title: Sample 21

value: GO

value: 18 µg


title: Sample 18

source_name: Control day 28

value: 11 mouse cell lines


title: Sample 20

source_name: rGO 54 µg day 28

value: 54 µg


title: A0P-500550-T-RNA [S103]

value: TCTCGCGC+GGCTCTGA


title: Sample 19

value: day 1


title: Subject 3

value: M


title: A0P-405173-T-RNA [S102]

value: CGGCTATG+CAGGACGT


title: Subject 2

value: Bronchoalveolar lavage cells


title: Sample 16

source_name: rGO 54 µg day 1

value: rGO


title: A0P-500553-T-RNA [S101]

value: TCCGCGAA+TAATCTTA


title: Subject 1


title: A0I-500596-T-RNA [S100]

value: ATTACTCG+AGGCGAAG

value: Allograft

value: Isotype


title: A0I-500551-T-RNA [S99]

value: CGCTCATT+CCTATCCT


title: Sample 14

source_name: rGO 18 µg day 90

value: female

value: Lung Tissue

value: day 90


title: SARS_1C_mRNA

organism: Chlorocebus pygerythrus

source_name: SARS-CoV-2 sgmRNAs

value: Vero Cells

tag: viralrna

value: sgmRNAs


title: Sample 15

source_name: rGO 54 µg day 90

value: 54 µg

value: 11 mouse cell lines


title: A0I-500545-T-RNA [S98]

value: GAGATTCC+ATAGAGGC

tag: radiation dose


title: Sample 17

source_name: rGO 162 µg day 1

tag: tissue

value: day 1


title: Sample 13

source_name: rGO 18 µg day 1

tag: time point

value: 18 µg


title: SARS_2S

source_name: SARS-CoV-2 genomic

value: genomic


title: Sample 12

source_name: Control day 1

value: Control

tag: dose

value: 0 µg


title: Sample 11

source_name: GO 18 µg day 28

value: GO

value: day 28


title: SARS_1S


title: A0I-500595-T-RNA [S97]

source_name: Tumor

tag: replicate group

value: ATTCAGAA+TATAGCCT

value: Allograft

value: Isotype


title: Sample 9

value: female

value: Lung Tissue

value: rGO

source_name: Universal Mouse Reference RNA


title: SARS_1C

tag: cell line

value: Vero Cells


title: Sample 10


title: SARS_2S_mRNA

value: sgmRNAs


title: SARS_2C_mRNA


title: MS2

city: TAMPA

first: Daria

last: Miroshnychenko

state: FL

address: 12902 USF Magnolia Drive

department: Cancer Physiology

institute: Moffitt Cancer Center

hyb_protocol: As per manufacturer  (Illumina)

scan_protocol: As per manufacturer  (Illumina)

data_processing: Genome Studio 2.0 ( Illumina), cnvPartition 3.2.0 plugin

label: C-Bio and A-DNP

source_name: hybrid between MDA-MB-231 and SUM159PT, subclone 2

label_protocol: As per manufacturer  (Illumina)

growth_protocol: Cell were grown in the corresponding media in standard conditions

extract_protocol: Quiagen DNAeasy

value: hybrid between MDA-MB-231 and SUM159PT

value: cell line

tag: sample group


title: MCFSUM

source_name: hybrid between MCFDCIS and SUM159

value: hybrid between MCFDCIS and SUM159


title: MS3

source_name: hybrid between MDA-MB-231 and SUM159PT, subclone 3


title: Sample 8

value: day 1

value: 11 mouse cell lines


title: Sample 6

value: 54 µg


title: MCF

source_name: MCFDCIS

value: MCFDCIS


title: MS1

source_name: hybrid between MDA-MB-231 and SUM159PT, subclone 1


title: SARS_2C

value: genomic


title: AML cells, Trib1 null 4

city: Tokyo

first: Takuro

last: Nakamura

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

department: The Cancer Institute

country: Japan

institute: Japanese Foundation for Cancer Research

description: Gene expression data from mouse AML

hyb_protocol: Following fragmentation, 7.5 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 PM Array. GeneChips were washed and stained in the Affymetrix GeneAtlas Fluidics Station.

scan_protocol: GeneChips were scanned using the Affymetrix GeneAtlas Imaging Station.

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

source_name: AML cell line expressing Hoxa9

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

growth_protocol: Trib1 hi and null cells were grown in IMDM supplemented with 10% fetal bovine serum, and 5 ng/ml IL-3. Mouse AML cells developed in the Trib1 homozygous knock-out mouse.

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

treatment_protocol: No treatment was provided.

value: AML cell line

tag: genotype


title: AML cells, Trib1 null 3

description: Gene expression data from mouse AML


title: AML cells, Trib1 null 1

description: Gene expression data from mouse AML


title: AML cells, Trib1 null 2

description: Gene expression data from mouse AML


title: Sample 7

source_name: Control day 28

value: Control

value: day 28

value: 0 µg


title: Sample 5

source_name: GO 18 µg day 90

value: female

value: GO

value: day 90

value: 18 µg


title: SM1

source_name: hybrid between SUM159PT and MDA-MB-231, subclone 1

value: hybrid between SUM159PT and MDA-MB-231

tag: cell type


title: MDA2

source_name: MDA-MB-231, replicate 2


title: AML cells, Trib1 hi 3

description: Gene expression data from mouse AML

source_name: AML cell line expressing Hoxa9 and Trib1

value: Hoxa9 and Trib1


title: AML cells, Trib1 hi 4

description: Gene expression data from mouse AML


title: SM2

source_name: hybrid between SUM159PT and MDA-MB-231, subclone 2

value: cell line


title: SM3

source_name: hybrid between SUM159PT and MDA-MB-231, subclone 3


title: SUM2

source_name: SUM159PT, replicate 2


title: Sample 4

source_name: CB 162 µg day 90

value: Lung Tissue

value: CB


title: SUM1

source_name: SUM159PT, replicate 1


title: Sample 2

source_name: GO 18 µg day 1

value: day 1

source_name: Universal Mouse Reference RNA

value: 11 mouse cell lines


title: AML cells, Trib1 hi 2

description: Gene expression data from mouse AML


title: Sample 3

source_name: GO 162 µg day 1


title: Sample 1

source_name: GO 54 µg day 1

value: 54 µg


title: AML cells, Trib1 hi 1

description: Gene expression data from mouse AML


title: MDA1

source_name: MDA-MB-231, replicate 1


title: Mtb_150_2

status: Public on Oct 20 2020

city: San Antonio

first: Joanne

last: Turner

state: TX

address: 8715 W Military Dr

institute: Texas Biomedical Research Institute

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using average normalization with BeadStudio

source_name: total RNA (globin reduced)

label_protocol: Biotinylated cRNA were prepared using the Illumina Totalprep-96 Amplification Kit with 250ng input

extract_protocol: RNA was extracted from Applied Biosystems Tempus Blood RNA Tubes using Applied Biosystems RNA Isolation kits. Globin message reduction was conducted using the Ambion GLOBINclear Mouse/Rat kit. Quality control was performed with Agilent Bioanalyser.

tag: infection status

value: Mtb

tag: time point days

value: Whole Blood


title: p3

source_name: hybrid between MDA231-MB-231 and SUM159PT, passage 3 bulk


title: p8

source_name: hybrid between MDA231-MB-231 and SUM159PT, passage 8 bulk


title: SARS_1S_mRNA

source_name: SARS-CoV-2 sgmRNAs

value: Vero Cells

value: sgmRNAs


title: Mtb_120_4

tag: strain


title: Mtb_120_2

tag: gender


title: B2

source_name: hybrid between MDA231-MB-231 and SUM159PT, subclone B2


title: Mtb_150_1


title: Mtb_120_1


title: Mtb_90_2


title: MDA231


title: Mtb_90_3


title: Mtb_120_3


title: Mtb_60_2


title: Mtb_150_3


title: Mtb_90_1


title: SUM159


title: Mtb_60_4


title: Mtb_90_4


title: Mtb_60_3


title: Mtb_150_4


title: A9

source_name: hybrid between MDA231-MB-231 and SUM159PT, subclone A9


title: Naive_150_2

value: Naive


title: Mtb_30_3

value: female


title: B1

source_name: hybrid between MDA231-MB-231 and SUM159PT, subclone B1


title: Mtb_60_1


title: Mtb_30_1


title: Naive_90_1


title: Naive_60_1


title: A2

source_name: hybrid between MDA231-MB-231 and SUM159PT, subclone A2


title: MCF-DCIS miR545 B2

city: Oklahoma City

first: Julio

middle: Cesar

last: Morales

state: OK

department: Department of Neurosurgery

institute: University of Oklahoma Health Science Center

description:
biological replicate 4
8962917086_I

hyb_protocol: Direct Hybridization Assay Protocols in Illumina Whole-Genome Gene Expression Direct Hybridization Assay Guide

scan_protocol: illumina HiScan¬ÆSQ System User Guide

data_processing: Raw data were generated by GenomeStudioTM Gene Expression Module v1.0 without background subtraction and normalization

source_name: Cell line

label_protocol: Ambion Illumina TotalPrep RNA Amplification Kit protocol

growth_protocol: Cells were grown in recommended growth media at 37 degrees Celsius supplemented with 5% CO2 for 72 hours.

extract_protocol: Total RNA was extracted following manufacturer's protocol for Qiagen Rneasy Plus, Cat. No. 74134, Appendix D: Purification of Total RNA containing small RNAs from cells

treatment_protocol: Cells were reverse transfected with 10 nM of miRNA mimics or mock transfected for 72 hours.  Cells were approximately 70% confluent before lysis and total RNA extraction

tag: motility

value: non-motile


title: MCF-DCIS miR34c-5p A

description:
biological replicate 1
8962917086_H


title: Naive_120_1


title: MCF-DCIS miR34c-5p B

description:
biological replicate 2
8962917086_L


title: A11

source_name: hybrid between MDA231-MB-231 and SUM159PT, subclone A11


title: MCF-DCIS miR205 A

description:
biological replicate 1
8962917086_F

value: motile


title: MCF-DCIS miR1276 B

description:
biological replicate 2
8962917086_C


title: A1

source_name: hybrid between MDA231-MB-231 and SUM159PT, subclone A1


title: MCF-DCIS miR205 B

description:
biological replicate 2
8962917086_J


title: MCF-DCIS miR614 B

description:
biological replicate 2
8691758096_L


title: MCF-DCIS miR191 B

description:
biological replicate 2
8962917086_K


title: Naive_30_1


title: MCF-DCIS miR545 A2

description:
biological replicate 3
8962917086_E


title: Naive_150_1


title: MCF-DCIS miR591 B

description:
biological replicate 2
8962917086_D


title: MCF-DCIS miR191 A

description:
biological replicate 1
8962917086_G


title: MCF-DCIS miR591 A

description:
biological replicate 1
8962917086_B


title: MCF-DCIS miR1276 A

description:
biological replicate 1
8962917086_A


title: A4

source_name: hybrid between MDA231-MB-231 and SUM159PT, subclone A4


title: MCF-DCIS mock B

description:
biological replicate 2
8691758096_J


title: MDA-MB-231 mock B

description:
biological replicate 2
8691758096_G


title: MCF-DCIS miR545 B1

description:
biological replicate 2
8691758096_K


title: MDA-MB-231 miR545 B

description:
biological replicate 2
8691758096_H


title: Mtb_30_4


title: MCF-DCIS miR545 A1

description:
biological replicate 1
8691758096_E


title: MCF-DCIS miR614 A

description:
biological replicate 1
8691758096_F


title: KO3 IP: P24 TRAP-Seq - cKO 3 IP

city: St Louis

first: Sarah

last: Smith

address: 660 S. Euclid Ave

institute: Washington University in St Louis School of Medicine

data_processing:
Library strategy: TRAP-seq
Read mapping was performed in Galaxy with RNA STAR using the MM10 reference genome and gene differential expression was estimated with EdgeR in R.
The Benjamini-Hochberg false discovery rate (FDR) was calculated for all genes; fold change and Z scores were calculated based on counts per million (CPM). Gene ontology (GO) was performed using PANTHER 41, Biological Process (Slim) unless otherwise specified.
Genome_build: mm10
Supplementary_files_format_and_content: Counts are provided in a column for each sample

source_name: IP Fraction after Translating Ribosome Affinity Purification

extract_protocol: For Bulk RNA-Seq, RNA was extracted from flash-frozen cerebral cortex of sex-matched littermate mice using Trizol (Thermo Fisher) followed by RNeasy Mini Kit (Qiagen) according to the manufacturers’ instructions. For sequencing, RNA was reverse-transcribed with oligo-dT priming, and the cDNA was sequenced on an Illumina HiSeq 2000. For TRAP-Seq, the brain was homogenized in 2 ml homogenization buffer (20mM Hepes-KOH, 150mM Kcl, 10mM Mgcl2) with RNase inhibitor, and 10% NP40 and 300mM DHPC (Avanti Polar Lipids) was added to the supernatant. After spinning down, 10% of the supernatant was used as for the input fraction with the rest being subjected to immunoprecipitation. GFP-ribosome positive ribosomes were pulled down by incubation with affinity antibody matrix (19C8 and 19F7, Memorial Sloan-Kettering Monoclonal antibody facility) at 4C overnight. RNA was collected by Qiagen miRNA kit. RNA quality and concentration were assessed using high sensitivity RNA ChiP on the Agilent BioAnalyzer. Intact RNA (RIN>8) was used for the library using NEBNext UltraRNA library preparation kit (E7530) as described 45,46. Briefly RNA was purified by oligdT beads and cDNA was synthesized by reverse transcriptase. After DNA fragmentation, end repair, adaptor ligation and PCR amplification, libraries were used for Illumina deep sequencing.

value: Cortex

value: cKO

tag: age


title: KO1 IP: P24 TRAP-Seq - cKO 1 IP


title: KO2 IP: P24 TRAP-Seq - cKO 2 IP


title: MDA-MB-231 miR545 A

description:
biological replicate 1
8691758096_B


title: MDA-MB-231 mock A

description:
biological replicate 1
8691758096_A


title: WT3 IP: P24 TRAP-Seq - Ctrl 3 IP

value: Ctrl


title: MDA-MB-231 miR614 B

description:
biological replicate 2
8691758096_I


title: MDA-MB-231 miR614 A

description:
biological replicate 1
8691758096_C


title: WT2 IP: P24 TRAP-Seq - Ctrl 2 IP


title: A3

source_name: hybrid between MDA231-MB-231 and SUM159PT, subclone A3

value: cell line


title: KO3 Input: P24 TRAP-Seq - cKO 3 Input

source_name: Input Fraction after Translating Ribosome Affinity Purification


title: KO2 Input: P24 TRAP-Seq - cKO 2 Input


title: 1051_200778090004_I.

city: Heidelberg

first: Obada

middle: Taleb

last: Alhalabi

address: Im Neuenheimer Feld 580 - TP3

department: Brain Tumor Translational Targets

country: Germany

institute: German Cancer Research Center DKFZ

hyb_protocol: Standard Illumina Hybridisation Protocol , (Whole-Genome Gene Expression  Direct Hybridization Assay Guide), 750 ng of cRNA were hybridized for 17 hr at 58°C on Illumina Human HT-12-Microarray.

scan_protocol: Gene Expression Microarrays were scanned using the Illumina iScan-Scanner according to Standard Illumina Scanning Protocol  (Whole-Genome Gene Expression  Direct Hybridization Assay Guide)

data_processing: The raw data were Quantile normalised with R using the Bioconductor package preprocessCore.

label: Biotin

source_name: Glioblastoma stem-like cells (GSCs)

label_protocol: The Illumina TotalPrep RNA Amplification Kit (life technologies) is used to generate single-stranded cRNA from input amounts of 200ng total RNA Label: Biotin, Cy3-Streptavidin

growth_protocol: Tissues were enzymatically dissociated and cells were cultivated as floating neurospheres in serum-free DMEM/F-12:Ham medium, supplemented with 2% B27-admixture (PeloBiotech) and basal fibroblast growth factor (Biomol), epidermal growth factor (Life Technologies) at 20 ng/ml each and heparin at 5 ng/ml, in addition to 1% penicillin/streptomycin. Passaging and seeding was carried out by dissociation with accutase (Sigma-Aldrich). Cells were regularly checked for mycoplasma contamination as per the recommendations of the German Collection of Microorganisms and Cells (Germany). Glioblastoma cell lines were authenticated using single nucleotide polymorphism profiling.

extract_protocol: RNA was extracted from GSCs using the RNAeasy MiniKit (Qiagen) according to the manufacturer’s protocol and examined for integrity using an Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: No treatment involved

value: Brain


title: MCF-DCIS mock A

description:
biological replicate 1
8691758096_D


title: 1037_200778090004_H.


title: 1079_200778090004_G.


title: 1005_200778090004_E.


title: NCH 711_200778090004_D.


title: NCH 421k_200778090004_A.


title: NCH 705_200778090004_C.


title: 1027_200778090004_F.


title: NCH 644_200778090004_B.


title: WT3 Input: P24 TRAP-Seq - Ctrl 3 Input


title: cKO2: P17 Bulk RNA-Seq - cKO Rep 2

data_processing:
Read mapping was performed in Galaxy with RNA STAR using the MM10 reference genome and gene differential expression was estimated with EdgeR in R.
The Benjamini-Hochberg false discovery rate (FDR) was calculated for all genes; fold change and Z scores were calculated based on counts per million (CPM). Gene ontology (GO) was performed using PANTHER 41, Biological Process (Slim) unless otherwise specified.
Genome_build: mm10
Supplementary_files_format_and_content: Counts are provided in a column for each sample

source_name: Bulk Cortex


title: cKO3: P17 Bulk RNA-Seq - cKO Rep 3


title: cKO4: P17 Bulk RNA-Seq - cKO Rep 4


title: WT1 Input: P24 TRAP-Seq - Ctrl 1 Input


title: WT2 Input: P24 TRAP-Seq - Ctrl 2 Input


title: cKO1: P17 Bulk RNA-Seq - cKO Rep 1


title: WT3: P17 Bulk RNA-Seq - Ctrl Rep 3


title: WT4: P17 Bulk RNA-Seq - Ctrl Rep 4


title: WT1: P17 Bulk RNA-Seq - Ctrl Rep 1


title: cKO1: P24 Bulk RNA-Seq - cKO Rep 1


title: KO1 Input: P24 TRAP-Seq - cKO 1 Input


title: cKO4: P24 Bulk RNA-Seq - cKO Rep 4


title: cKO3: P24 Bulk RNA-Seq - cKO Rep 3


title: cKO2: P24 Bulk RNA-Seq - cKO Rep 2


title: WT4: P24 Bulk RNA-Seq - Ctrl Rep 4


title: WT3: P24 Bulk RNA-Seq - Ctrl Rep 3


title: WT2: P24 Bulk RNA-Seq - Ctrl Rep 2


title: WT2: P17 Bulk RNA-Seq - Ctrl Rep 2


title: WT1: P24 Bulk RNA-Seq - Ctrl Rep 1


title: CE12-RV

city: Shanghai

first: Yuxuan

last: Zheng

address: 825 Zhangheng Rd.

institute: Fudan University

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Sequencing adapters, low quality sequences and amplification primers were trimmed from the raw sequencing reads.
For RNA-seq data, trimmed clean reads were aligned to Macaca fascicularis reference genome (Macaca_fascicularis_5.0) using TopHat (v 2.0.12) -pass mapping steps.
Genome_build: Macaca_fascicularis_5.0
Supplementary_files_format_and_content: UMI_count.txt files include the UMI count values of RefSeq genes

molecule: polyA RNA

organism: Macaca fascicularis

source_name: Retina tissue cells

extract_protocol: Single cell was randomly picked with mouth pipette, then washed by 1mg/ml HSA and transferred into prepared lysis buffer. The cells can store at -80℃ or do it immediately. We used a modified SMART-seq2 protocol to lysis for release all RNA, reverse transcription for capture the cDNA of mRNA and pre-amplification for increase yields of cDNAs. The resulting cDNAs from single cells were barcoded, and then pooled together with different barcode. Followed by 4 cycles, the index of sequence with biotin modified was added at 3’ end.

tag: individual

tag: position

value: Ventral

value: Retina

value: Retina tissue cells


title: Mtb_30_2

source_name: total RNA (globin reduced)


title: CE09-RV


title: CE09-RT

value: Temporal


title: CE04-RPE

value: Pigment epithelium


title: CE04-RN

value: Nasal


title: CE04-RD

value: Dorsal


title: CE03-RV


title: CE03-RPE


title: CE01-RV


title: CE01-RN


title: CE03-RT


title: CE03-RN


title: CE03-RD


title: CE01-RT


title: CE15-RPE


title: CE01-RPE


title: CE15-RN


title: CE14-RV


title: CE15-RD


title: CE14-RN


title: CE15-RV


title: CE14-RPE


title: CE14-RT


title: CE14-RD


title: CE15-RT


title: CE13-RV


title: CE13-RT


title: CE13-RD


title: CE12-RPE


title: CE11-RV


title: CE12-RD


title: CE11-RT


title: CE01-RD


title: CE11-RPE


title: CE10-RV


title: CE10-RN


title: CE10-RPE


title: CE11-RD


title: CE11-RN


title: CE07-RPE


title: CE08-RV


title: CE08-RT


title: CE09-RD


title: CE09-RPE


title: CE10-RT


title: CE07-RN


title: CE08-RPE


title: CE08-RN


title: CE08-RD


title: CE17-RV

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Sequencing adapters, low quality sequences and amplification primers were trimmed from the raw sequencing reads.
For RNA-seq data, trimmed clean reads were aligned to Macaca fascicularis reference genome (Macaca_fascicularis_5.0) using TopHat (v 2.0.12) -pass mapping steps.
Genome_build: Macaca_fascicularis_5.0
Supplementary_files_format_and_content: UMI_count.xls files include the UMI count values of RefSeq genes


title: CE17-RT


title: CE17-RN


title: CE12-RN


title: CE17-RPE


title: CE16-RT


title: CE17-RD


title: CE16-RV


title: CE16-RD


title: CE12-RT


title: CE16-RN


title: CE10-RD


title: CE16-RPE


title: CE09-RN


title: CE13-RPE


title: CE13-RN


title: CE06-RV


title: CE07-RD


title: CE07-RT


title: CE06-RPE


title: CE06-RD


title: CE06-RN


title: CE05-RPE


title: CE05-RV


title: CE06-RT


title: CE05-RT2


title: CE05-RD


title: CE05-RT1


title: CE05-RN


title: CE04-RV


title: WG0283681-DNA_H08_CS401123

city: Titusville

first: Qingqin

middle: S

last: Li

state: NJ

address: 1125 Trenton-Harbourton Road

institute: Janssen R&D, LLC

hyb_protocol: Infinium® HD Assay Methylation Protocol

scan_protocol: Infinium® HD Assay Methylation Protocol

data_processing:
Illumina® GenomeStudio
normalized (dasen) Average Beta
Unmethylated and methylated signal intensities

label: Cy3 and Cy5

source_name: ND, STG

label_protocol: Not provided

extract_protocol: AllPrep DNA/RNA/miRNA Universal Kit (QIAGEN Inc., Germantown, MD, USA)

tag: donorid

value: Male

tag: age at death

tag: pmi

value: STG

tag: dx

value: ND

value: possible AD

value: II

value: criteria not met

tag: array

tag: slide

tag: basename


title: WG0283681-DNA_G11_CS401126

value: Female

value: Criteria not met

value: IV


title: WG0283683-DNA_G12_CS401851

value: not AD

value: III


title: WG0283683-DNA_G11_CS401892


title: WG0283681-DNA_G10_CS401142


title: WG0283681-DNA_H09_CS401127


title: WG0283681-DNA_G12_CS401853


title: WG0283683-DNA_G10_CS401139


title: WG0283683-DNA_G09_CS401125

value: I


title: CE07-RV

tag: tissue

value: Retina

value: Retina tissue cells

value: Ventral


title: WG0283683-DNA_H07_CS401857


title: WG0283681-DNA_H07_CS401891


title: WG0283683-DNA_G08_CS401837


title: WG0283681-DNA_G08_CS401839


title: WG0283683-DNA_H05_CS401131


title: WG0283683-DNA_H06_CS401136


title: WG0283683-DNA_G07_CS401838


title: WG0283683-DNA_H04_CS401858


title: WG0283681-DNA_H04_CS401888


title: WG0283681-DNA_G07_CS401900


title: WG0283681-DNA_H05_CS401840


title: WG0283683-DNA_H01_CS401893


title: WG0283683-DNA_H02_CS401854


title: CE04-RT

tag: cell type

value: Temporal


title: WG0283683-DNA_G05_CS401134


title: WG0283681-DNA_H02_CS401140


title: WG0283681-DNA_G06_CS401144


title: WG0283681-DNA_F12_CS401137


title: WG0283683-DNA_G04_CS401130


title: WG0283681-DNA_H01_CS401841


title: WG0283681-DNA_G05_CS401859


title: WG0283683-DNA_F12_CS401856


title: WG0283683-DNA_F10_CS401898


title: WG0283683-DNA_F11_CS401129


title: WG0283681-DNA_G04_CS401138


title: WG0283681-DNA_F10_CS401846


title: WG0283681-DNA_F11_CS401855


title: WT1 IP: P24 TRAP-Seq - Ctrl 1 IP

value: Cortex

tag: genotype

value: Ctrl


title: WG0283683-DNA_G06_CS401890

value: STG


title: WG0283681-DNA_H06_CS401848

value: Male

value: ND


title: WG0283681-DNA_F09_CS401844

value: II


title: WG0283683-DNA_F07_CS401141

value: criteria not met


title: WG0283683-DNA_G03_CS401133

value: Female

value: possible AD


title: WG0283683-DNA_G02_CS401128


title: WG0283683-DNA_F09_CS401897


title: WG0283681-DNA_F08_CS401852


title: WG0283681-DNA_F07_CS401836


title: WG0283681-DNA_F06_CS401842


title: WG0283681-DNA_G03_CS401847


title: WG0283681-DNA_G02_CS401889


title: WG0283683-DNA_F05_CS401849


title: WG0283683-DNA_F03_CS401145


title: WG0283681-DNA_F05_CS401843


title: WG0283683-DNA_F04_CS401124


title: WG0283683-DNA_G01_CS401894


title: WG0283681-DNA_F03_CS401845


title: WG0283683-DNA_F02_CS401895


title: WG0283681-DNA_F02_CS401850


title: WG0283681-DNA_G01_CS401132


title: WG0283681-DNA_F01_CS401143


title: WG0283683-DNA_F01_CS401896


title: WG0283681-DNA_E04_CS405837

source_name: AD, STG

value: AD

value: definite AD

value: V

value: high


title: WG0283683-DNA_D10_CS405839


title: WG0283683-DNA_F08_CS401899

value: not AD

value: I


title: WG0283681-DNA_D10_CS405926


title: WG0283683-DNA_E04_CS403784

value: III

value: intermediate


title: WG0283683-DNA_E05_CS405921

value: IV


title: WG0283683-DNA_D09_CS405910


title: WG0283683-DNA_D07_CS405958


title: WG0283681-DNA_D09_CS405869

value: VI


title: WG0283683-DNA_E02_CS403782

value: STG


title: WG0283683-DNA_D08_CS403786

value: Male


title: WG0283683-DNA_D06_CS405923


title: WG0283683-DNA_F06_CS401135

value: ND


title: WG0283681-DNA_E03_CS405959


title: WG0283683-DNA_E01_CS405962


title: WG0283681-DNA_E01_CS405954


title: WG0283683-DNA_D03_CS403781


title: WG0283681-DNA_D04_CS403770

value: probable AD


title: WG0283683-DNA_D05_CS405973


title: WG0283681-DNA_E02_CS405927


title: WG0283681-DNA_C12_CS405970


title: WG0283681-DNA_E05_CS405916


title: WG0283683-DNA_D04_CS405914


title: WG0283681-DNA_D07_CS403788


title: WG0283681-DNA_D05_CS405961

value: II

value: low


title: WG0283683-DNA_E03_CS405909

value: Female


title: WG0283681-DNA_D02_CS405870

value: AD


title: WG0283683-DNA_D01_CS405919

value: definite AD


title: WG0283683-DNA_C10_CS403790


title: WG0283683-DNA_D02_CS405969


title: WG0283683-DNA_C09_CS400925


title: WG0283681-DNA_D01_CS405972

value: V


title: WG0283681-DNA_B12_CS405875

value: high


title: WG0283683-DNA_B09_CS405964


title: WG0283681-DNA_C08_CS400923


title: WG0283683-DNA_B10_CS405968


title: WG0283683-DNA_B11_CS405957


title: WG0283683-DNA_B08_CS405966


title: WG0283681-DNA_C07_CS403776


title: WG0283681-DNA_B08_CS405956


title: WG0283681-DNA_C11_CS405841


title: WG0283683-DNA_B12_CS403791


title: WG0283681-DNA_B07_CS405872


title: WG0283681-DNA_C06_CS405878


title: WG0283683-DNA_C06_CS405908


title: WG0283683-DNA_B07_CS403777


title: WG0283683-DNA_C05_CS405924


title: WG0283681-DNA_C10_CS405836


title: WG0283683-DNA_B05_CS405953


title: WG0283681-DNA_B05_CS405975


title: WG0283683-DNA_B03_CS405876


title: WG0283681-DNA_B04_CS403779


title: WG0283683-DNA_B04_CS401122


title: WG0283681-DNA_C05_CS405963


title: WG0283681-DNA_B10_CS405960


title: WG0283681-DNA_C04_CS405974


title: WG0283683-DNA_B02_CS403785


title: WG0283681-DNA_B02_CS405904


title: WG0283681-DNA_B11_CS405920


title: WG0283683-DNA_C03_CS403775


title: WG0283683-DNA_C04_CS405918


title: WG0283683-DNA_B01_CS405906


title: WG0284610-DNA_F07_CS419283

source_name: ND, IFG

value: IFG

value: possible AD

value: criteria not met


title: WG0283683-DNA_B06_CS405922


title: WG0283681-DNA_B06_CS405911

value: intermediate


title: WG0284610-DNA_B07_CS420455

value: not AD

value: III


title: WG0283683-DNA_C01_CS405905

value: STG

value: VI


title: WG0283681-DNA_B01_CS405877

value: Male


title: WG0284610-DNA_F06_CS420595

value: ND

value: IV


title: WG0284610-DNA_D03_CS416268


title: WG0284610-DNA_D02_CS420727

value: I


title: WG0284610-DNA_B02_CS416131

source_name: AD, IFG


title: WG0284610-DNA_D01_CS419602

value: Female


title: WG0284610-DNA_D06_CS420735


title: WG0284609-DNA_F06_CS419656


title: WG0284609-DNA_F07_CS420594

value: II


title: WG0284609-DNA_D08_CS420472

value: Criteria not met


title: WG0284609-DNA_B06_CS416276


title: WG0284609-DNA_B02_CS419289


title: WG0284610-DNA_F08_CS419598


title: WG0284610-DNA_D08_CS416140


title: WG0283683-DNA_C02_CS405913

value: AD

value: definite AD


title: WG0284610-DNA_B05_CS420588

value: IFG


title: WG0284610-DNA_D04_CS416535

value: possible AD


title: WG0284610-DNA_B08_CS416135

value: criteria not met


title: WG0284610-DNA_F03_CS416539


title: WG0284610-DNA_F02_CS420587


title: WG0284610-DNA_B01_CS420734


title: WG0283681-DNA_C02_CS405965

value: high


title: WG0284610-DNA_F01_CS416541

value: not AD


title: WG0284609-DNA_D11_CS419597


title: WG0284609-DNA_B12_CS419611

value: III


title: WG0284610-DNA_F04_CS419661


title: WG0284610-DNA_D05_CS419295


title: WG0284609-DNA_D12_CS420600


title: WG0284609-DNA_D09_CS419292


title: WG0284609-DNA_D10_CS420469


title: WG0284609-DNA_F08_CS416537


title: WG0284609-DNA_B08_CS416279


title: WG0284609-DNA_B07_CS420585


title: WG0284609-DNA_B05_CS420462


title: WG0284609-DNA_D06_CS416277


title: WG0284609-DNA_F05_CS416126


title: WG0284609-DNA_D04_CS420465


title: WG0284609-DNA_F02_CS416282


title: WG0284609-DNA_B03_CS420725


title: WG0284609-DNA_D02_CS420586


title: WG0284609-DNA_F01_CS416533


title: WG0284609-DNA_B01_CS416530


title: WG0284609-DNA_D01_CS420460


title: WG0284610-DNA_D07_CS419294


title: WG0284610-DNA_B06_CS416289


title: WG0284610-DNA_F05_CS416141


title: WG0284609-DNA_D03_CS419663


title: WG0284609-DNA_B09_CS419284


title: WG0284609-DNA_B10_CS416523


title: WG0284610-DNA_B03_CS416129


title: WG0284609-DNA_D07_CS416544


title: WG0284609-DNA_B04_CS420453


title: WG0284610-DNA_B04_CS416529


title: WG0284609-DNA_F03_CS416133


title: WG0284609-DNA_B11_CS420463


title: WG0284610-DNA_H04_CS416285


title: WG0284609-DNA_C11_CS416532

value: V


title: WG0284609-DNA_F04_CS416137

value: VI


title: WG0284609-DNA_D05_CS420450


title: WG0284610-DNA_E01_CS420724

value: Male


title: WG0284609-DNA_E03_CS420722


title: WG0284610-DNA_E03_CS419285


title: WG0284610-DNA_C06_CS416546

value: probable AD

value: intermediate


title: WG0284610-DNA_C05_CS416281


title: WG0284610-DNA_A06_CS419286


title: WG0284610-DNA_H05_CS416287


title: WG0284610-DNA_E04_CS416538

value: IV


title: WG0284610-DNA_A05_CS420730


title: WG0284610-DNA_E02_CS420584


title: WG0284610-DNA_H01_CS419303

value: Female


title: WG0284610-DNA_A02_CS419658


title: WG0284610-DNA_A01_CS416271


title: WG0284609-DNA_C12_CS419300


title: WG0284609-DNA_E11_CS416146


title: WG0284609-DNA_A11_CS420721


title: WG0284609-DNA_C09_CS419290


title: WG0284609-DNA_A09_CS416540


title: WG0284609-DNA_H05_CS420459


title: WG0284609-DNA_A08_CS420457


title: WG0284609-DNA_A07_CS419603

value: II

value: low


title: WG0284609-DNA_A05_CS416144

value: ND


title: WG0284609-DNA_C03_CS419601

value: AD

value: definite AD


title: WG0284610-DNA_A07_CS416290

value: IFG


title: WG0284609-DNA_A04_CS416124


title: WG0283683-DNA_C08_CS405838

value: STG


title: WG0284609-DNA_H03_CS416272


title: WG0284610-DNA_C08_CS420449

value: high


title: WG0284610-DNA_E08_CS419301


title: WG0284609-DNA_A02_CS420589


title: WG0284609-DNA_E02_CS420593


title: WG0284610-DNA_E06_CS419282


title: WG0284610-DNA_C01_CS416531


title: WG0284610-DNA_A03_CS420456


title: WG0284610-DNA_C04_CS419659


title: WG0284609-DNA_C10_CS416274


title: WG0284610-DNA_C07_CS416128


title: WG0284610-DNA_E07_CS416534


title: WG0284610-DNA_E05_CS416138


title: WG0284609-DNA_E07_CS416543


title: WG0284609-DNA_E09_CS420732


title: WG0284609-DNA_E08_CS420464


title: WG0284609-DNA_C07_CS416536


title: WG0284609-DNA_C06_CS420583


title: WG0284609-DNA_E06_CS416524


title: WG0284609-DNA_C05_CS420731


title: WG0284609-DNA_A01_CS420728


title: WG0284609-DNA_H06_CS420461


title: WG0284609-DNA_A06_CS420592


title: WG0284609-DNA_H04_CS416134

value: possible AD

value: criteria not met


title: WG0284609-DNA_H01_CS416527

value: V


title: WG0284609-DNA_C04_CS420720

value: VI


title: WG0284609-DNA_H02_CS419600


title: WG0284609-DNA_A03_CS420741

value: Male


title: WG0284609-DNA_E04_CS416288

value: probable AD

value: III


title: WG0284610-DNA_A04_CS416284

value: IV

value: intermediate


title: WG0284609-DNA_E05_CS416136

value: not AD


title: WG0284610-DNA_C03_CS419660

value: Female


title: cdk12as2_RI

city: Namur

first: Carlo

last: Yague-Sanz

address: 61 rue de Bruxelles

department: Medecine

country: Belgium

institute: Namur University

data_processing:
Reads were quality- and adaptor-trimmed using trimmomatic with options PE ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 HEADCROP:1 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36.
Reads that mapped on OP50 genome (the bacteria used to feed the worms in recovery condition) were discarded and the remaining reads were mapped on C.elegans genome using hisat2.
Mapped reads were summarized at the gene level using featurecounts while unmapped reads were re-analized in SL-quant in sensitive mode to quantify SL-transplicing events.
Differential gene expression analysis was performed using DESeq2 with the following multifactorial glm model: expression~strain+food+DMSO+inhibitor+strain:inhibitor.
Genome_build: ce10
Supplementary_files_format_and_content: Strand-specific genome coverage files (bigWig) were generated using deeptools v3.2 bamCoverage with options -bs 2 --scalefactor [1/(DESEQ2 sizefactor)]  --filterRNAstrand [forward, reverse] and a pseudocount of 1 was added to ease log-tranformation. Tracks for the individual replicates are available here, and merged tracks can be viewed on http://epigenomegateway.wustl.edu/legacy/?genome=ce10&session=qNwYUnhblv&statusId=1211040396 .

organism: Caenorhabditis elegans

source_name: L1-arrest C.elegans larvae

growth_protocol: Embryos were collected by bleaching treatment and resuspended in S-Medium (no food) at 10 embryos per μl. Embryos were incubated at 20°C for at least 12h to obtained synchronized starved L1s (S0).

extract_protocol:
A L1 liquid culture of 40 ml was pelleted, 2 minutes at 2000 rpm, 4°C and washed 3 times with 50 ml of M9. 1 ml of Tri Reagent was added and the tube was mixed by vortexing 30 seconds followed by snap freeze. Upon thawing in 42°C bath, 200 μl of Chloroform was added and the tube was mixed by vortexing 30 seconds, incubated 3 minutes at RT and centrifuged 15 minutes at 12000 rpm, 4°C. The aqueous phase was transferred (500 μl) and 500 μl of isopropanol was added, incubated 1h at - 20°C and centrifuged 15 minutes at 12000 rpm, 4°C. The supernatant was discarded and 1 ml of EtOH 70% was added, centrifuged 5 minutes, 7500 rpm, 4°C and the pellet was dried out at RT and dissolved in 100 μl of nuclease free water by heating 5 minutes at 65 °C.
After ribodepletion using the Ribominus eukaryote kit V2,RNA-seq library preparation was made using the Illumina TruSeq stranded total RNA library preparation kit following the instructions of the manufacturer with the notable exception that the quantity of AMPure XP beads used for clean ups was scaled up by a ratio of 1.1 in order to retrieve smaller RNA species such as tRNAs. The reads were sequenced on an illumina HiSEQ apparatus in paired-end mode.

treatment_protocol: The L1-synchronized culture (S0) was then split into three conditions during 4h: Starvation (S) where DMSO added to a final concentration of 0.1 ; Recovery (R) with DMSO added to a final concentration of 0.1% along with a 50ml pellet of OP50 bacteria (food) ; Recovery plus inhibitor (R+I) with 3MB-PP1 (CDK12-as inhibitor in DMSO) at 1uM and a 50ml pellet of OP50 bacteria (food).

tag: condition

value: starved + 4h recovery in (food + cdk12-as inhibitor)

tag: replicate

value: L1-arrest C.elegans larvae


title: WG0284609-DNA_A12_CS420723

tag: gender

value: AD

value: definite AD


title: cdk12as2_S

value: starved + 4h in DMSO


title: cdk12as2_R

value: starved + 4h recovery in (food + DMSO)


title: WT2_RI

value: N2 wild-type


title: WT2_R


title: cdk12as2_0

value: starved


title: WG0284609-DNA_C02_CS420729

value: IFG

value: high


title: WT2_S


title: WT1_S


title: WT1_RI


title: cdk12as1_0


title: WT1_R


title: cdk12as1_R


title: cdk12as1_S


title: cdk12as_1_RI_input

data_processing:
Reads were mapped onto C. elegans genome using bowtie2 with the option --no-unal
Normalized strand-specific genome coverage files (bigWig) were generated using the BEADS v1.1 algorithm.
Meta-gene matrixes were computed using deeptools ComputeMatrix in scale-region mode. Plots were generated in R.
Genome_build: ce10
Supplementary_files_format_and_content: Strand-specific genome coverage files in bigWig format.

growth_protocol: Embryos were collected by bleaching treatment and resuspended in S-Medium (no food) at 10 embryos per μl. Embryos were incubated at 20°C for at least 12h to obtained synchronized starved L1s.

extract_protocol:
L1s were pelleted 1 minute at 1200 rpm and washed 3 times with M9 before crosslinking in formaldehyde 2% during 30 mintues at 20 °C. Glycine was added to a 125 mM final concentration to quench the reaction. The worms were pelleted and washed with Tris pH8.0 20 mM (4°C) and snap freezed. The pellet was thawed on ice and washed with FA/SDS/PI (Hepes-KOH pH7.5 50 mM, NaCl 150 mM, EDTA 1 mM, Na deoxycholate 0.1%, Triton X-100 1%, SDS 0.1%, PMSF 1 mM), resuspended in 1.6 ml of FA/SDS/PI and incubated 15 minutes on ice. The sample was sonicated with a BioRuptor (Diagenode) (cycles of 30 seconds ON, 60 seconds OFF, 21 minutes). After transfer to 1.5 ml microcentrifuge tube and centrifugation for 30 minutes,14000 rpm, 4°C, the supernatant was transferred to a new tube. For each immunoprecipitation, an extract volume containing the equivalent of 400000 L1 (around 750 μl, 10% left as total extract at -20°C) was used. 3μl of the appropriate antibody (anti-Pol II 8WG16 (ab817), anti-S2P 3E10) was added overnight at 4°C. Per IP, 50μl of appropriate magnetic beads (Dynal/Invitrogen) were washed 4 times with PBS BSA (1mg/ml) and resuspended in PBS BSA (10 mg/ml) and then added to each IP and incubated 4h at 21°C. The beads were washed 3 times with 1ml of FA/SDS+NaCl 500mM, 1 time with 500 μl of IP Buffer and 1 time with 500 μl of TE and resuspended in 125 μl of Pronase Buffer 1X and incubated 20 minutes at 65°C. The total extract (100 μl) was similarly treated by adding 25 μl of Pronase Buffer 5x, 6.25 μl of Pronase and incubated 1h at 37°C, then overnight at 65°C. RNAse A was added 1h at 37°C and the DNA sample were purified on Rapace columns.
Illumina TruSeq ChIP-seq library preparation protocol according to the manufacturer instructions.

treatment_protocol: The L1-synchronized culture was then split into two conditions during 4h: Recovery (R) with DMSO added to a final concentration of 0.1% along with a 50ml pellet of OP50 bacteria (food) ; and Recovery plus inhibitor (R+I) with 3MB-PP1 (CDK12-as inhibitor in DMSO) at 1uM and a 50ml pellet of OP50 bacteria (food).

tag: ip

value: input


title: WT2_0


title: cdk12as_1_R_input


title: cdk12as_2_R_input


title: cdk12as_2_RI_input


title: WT1_0


title: cdk12as_2_RI_Cstf64

value: Cstf-64 antibody


title: cdk12as_2_RI_S2P

value: S2P (3E10 antibody)


title: cdk12as_2_R_Cstf64


title: cdk12as_2_R_S2P


title: cdk12as1_RI


title: cdk12as_1_RI_Cstf64


title: cdk12as_2_R_ama1

value: ama1 (Q2358 antibody)


title: cdk12as_2_RI_ama1


title: MDA5-Protected ADAR1KD_5-AZA-CdR_rep2

city: Toronto

first: Sajid

middle: A

last: Marhon

state: ON

address: 101 College Street

institute: Princess Margaret Cancer Centre

description:
CytoRNA
MDA5-protected_ADAR1KD_5-AZA-CdR.hg19.Pos.bw
MDA5-protected_ADAR1KD_5-AZA-CdR.hg19.Neg.bw

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.

source_name: MDA5-Protected ADAR1KD_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

value: Patient-derived colorectal cancer#92

value: ADAR1 Knockdown

tag: time

tag: treatment


title: cdk12as_1_R_ama1


title: cdk12as_1_R_S2P


title: cdk12as_1_R_Cstf64


title: cdk12as_1_RI_ama1


title: cdk12as_1_RI_S2P


title: MDA5-Protected ADAR1KD_5-AZA-CdR_rep1

source_name: MDA5-Protected ADAR1KD_5-AZA-CdR_rep1


title: MDA5-Protected ADAR1KD_Mock-Treated_rep2

description:
CytoRNA
MDA5-protected_ADAR1KD_Mock-treated.hg19.Pos.bw
MDA5-protected_ADAR1KD_Mock-treated.hg19.Neg.bw

value: Mock-Treated


title: MDA5-Protected ADAR1KD_MockTreated_rep1

source_name: MDA5-Protected ADAR1KD_MockTreated_rep1


title: Total CytoRNA ADAR1KD_5-AZA-CdR_rep2

description:
CytoRNA
Total-CytoRNA_ADAR1KD_5-AZA-CdR.hg19.Pos.bw
Total-CytoRNA_ADAR1KD_5-AZA-CdR.hg19.Neg.bw

source_name: Total CytoRNA ADAR1KD_5-AZA-CdR_rep2


title: Total CytoRNA ADAR1KD_Mock-Treated_rep2

description:
CytoRNA
Total-CytoRNA_ADAR1KD_Mock-treated.hg19.Pos.bw
Total-CytoRNA_ADAR1KD_Mock-treated.hg19.Neg.bw

source_name: Total CytoRNA ADAR1KD_Mock-Treated_rep2


title: Total CytoRNA ADAR1KD_5-AZA-CdR_rep1

source_name: Total CytoRNA ADAR1KD_5-AZA-CdR_rep1


title: MDA5-Protected ADAR1WT_5-AZA-CdR_rep2

description:
CytoRNA
MDA5-protected_ADAR1WT_5-AZA-CdR.hg19.Pos.bw
MDA5-protected_ADAR1WT_5-AZA-CdR.hg19.Neg.bw

source_name: MDA5-Protected ADAR1WT_5-AZA-CdR_rep2

value: Wild type (LACZ)


title: Total CytoRNA ADAR1KD_Mock-Treated_rep1

source_name: Total CytoRNA ADAR1KD_Mock-Treated_rep1


title: MDA5-Protected ADAR1WT_Mock-Treated_rep2

description:
CytoRNA
MDA5-protected_ADAR1WT_Mock-treated.hg19.Pos.bw
MDA5-protected_ADAR1WT_Mock-treated.hg19.Neg.bw


title: MDA5-Protected ADAR1WT_MockTreated_rep1

source_name: MDA5-Protected ADAR1WT_MockTreated_rep1


title: Total CytoRNA ADAR1WT_Mock-Treated_rep2

description:
CytoRNA
Total-CytoRNA_ADAR1WT_Mock-treated.hg19.Pos.bw
Total-CytoRNA_ADAR1WT_Mock-treated.hg19.Neg.bw

source_name: Total CytoRNA ADAR1WT_Mock-Treated_rep2


title: Total CytoRNA ADAR1WT_5-AZA-CdR_rep1

description:
CytoRNA
Total-CytoRNA_ADAR1WT_5-AZA-CdR.hg19.Pos.bw
Total-CytoRNA_ADAR1WT_5-AZA-CdR.hg19.Neg.bw

source_name: Total CytoRNA ADAR1WT_5-AZA-CdR_rep1


title: Total CytoRNA ADAR1WT_Mock-Treated_rep1

source_name: Total CytoRNA ADAR1WT_Mock-Treated_rep1


title: Total CytoRNA ADAR1WT_5-AZA-CdR_rep2

source_name: Total CytoRNA ADAR1WT_5-AZA-CdR_rep2


title: SSc

city: Serdang

first: Siti Nor Ani

last: Azaman

state: Selangor

address: Jalan UPM

country: Malaysia

institute: Universiti Putra Malaysia

data_processing:
CLC genomic workbench 6.0
de-novo assembly by Trinity (version 2.0.6)
Sequence alignment using Burrows-Wheeler Aligner (BWA)
Gene predictions and protein coding potential of the de novo assembly transcripts were determined using AUGUSTUS (version 2.5.5)
differential expression analysis using DESeq2
Genome_build: The fasta file of transcript sequences is available on the series record.
Supplementary_files_format_and_content: Excel files xlsx containing expression values (counts) and statistical analysis of nomal and stress C. sorokiniana

organism: Chlorella sorokiniana

source_name: C. sorokiniana stress sample (replicate 3)_with_high_light_condition_and_glucose

growth_protocol: The cells were first cultivated in Bold’s Basal Medium (BBM) at 27°C under continuous light at a light intensity about 10 µmol photons m-1 s-1 with a shaking speed of 30 rpm.

extract_protocol:
Total RNA was extracted using TRIzol method.
RNA libraries were prepared for sequencing using standard Illumina protocols with NEBNext Ultra Directional RNA Library for Illumina

treatment_protocol: stress was induced at mid log phase of culture by increasing the light intensity than the normal condition (100 µmol photons m-1 s-1) and the addition of 2% of glucose

tag: strain


title: control

city: 赣州

first: yunlong

last: meng

state: 江西

address: 江西省赣州市

institute: 赣南师范大学

data_processing:
Illumina Casava1.7 software used for basecalling.
Index of the reference genome was built using Hisat2(v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2(v2.0.5).
HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the DEGSeq R package (1.20.0). The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.005 and log2(Fold change) of 1 were set as the threshold for significantly differential expression.
Genome_build: ftp://ftp.ensembl.org/pub/release-93/fasta/danio_rerio/
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Danio rerio

source_name: tail fin

extract_protocol:
RNA was harvested using Trizol reagent.A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: time point

value: control

value: tail fin


title: ACE_72h

value: 72 hpa (hours post amputation)

tag: sample group

value: anterior cut edge (ACE)


title: PCE_72h

value: posterior cut edge (PCE)


title: TETp_4h_+dox_vs_-dox_rep2

city: Paris

first: Sadri

last: ZNAIDI

address: 25 rue du Docteur Roux

department: Mycology Department

country: France

institute: Institut Pasteur

description: Sample 20

hyb_protocol: Gene Expression Hybridization Kit (Cat# 5188-5242) from Agilent Technologies was used to prepare 50 µl of purified labeled samples as recommended by the manufacturer, followed by hybridization to the Agilent-026869 array.

scan_protocol: Images of Cy5 and Cy3 fluorescence were generated by scanning the expression arrays using an Axon Autoloader 4200AL scanner (Molecular Devices, Downington, PA). Images were analyzed with the GenePix Pro 6.1.0.2 software (Molecular Devices, Downington, PA).

data_processing: GenePix Results (GPR) files were imported into the Arraypipe 2.0 for spot filtering, background subtraction (limma normexp BG correction) and Lowess global normalization of signal intensities

organism: Candida albicans

source_name: Untreated control, grown in YPD medium during 4h

label_protocol: First-strand cDNA synthesis and Cy5/Cy3 labeling from 20 µg total RNA was performed using the Superscript III indirect cDNA labeling system (Invitrogen).

growth_protocol: For the CRZ2_2h, CRZ2_4h and TETp microarray experiments (Samples 1-6 and 19-22), total RNA was extracted from 3 independently-generated crz2Δ/crz2Δ strains carrying the PTET-CRZ2 fusion (samples 1-6) or the PTET empty vector (samples 19-22), pre-grown overnight in 10 ml YPD at 30ºC then diluted in fresh YPD medium supplemented or not with 40 µg.mL−1 doxycycline to an OD600 nm of 0.3 and re-grown for 2 (samples 1-3) and 4 (samples 4-6 and 19-22) hours. For the WT vs. crz2Δ/Δ and the Norm > Hyp shift microarray experiments (samples 7-12 and 13-18, respectively), strains CEC369 (wild-type) and C90 (crz2Δ/Δ) were grown overnight in 10 ml YPD at 30ºC, then diluted to an OD600 nm of 0.16 in 250-ml flasks containing 50 ml of YPD medium. The flasks were incubated in a BBL GasPak anaerobic jar at 37°C for 24 h without shaking (Hypoxia 37ºC) or in a 30ºC-incubator for 24h under vigorous shaking (Normoxia, 30ºC).

extract_protocol: Total RNA was extracted using the hot phenol method as described in Znaidi et al. (2013) PLoS Pathogens 9: e1003519.

treatment_protocol: See growth protocol

tag: genotype/variation

value: C. albicans strain carrying an empty vector control

value: Untreated control

source_name: Dox-treated at a concentration of 40 µg/mL in YPD medium for 4h

value: doxycycline


title: ACE_48h

value: 48 hpa (hours post amputation)


title: TETp_4h_+dox_vs_-dox_rep4

description: Sample 22


title: ACE_24h

value: 24 hpa (hours post amputation)


title: SSa

source_name: C. sorokiniana stress sample (replicate 1)_with_high_light_condition_and_glucose


title: NSc

source_name: C. sorokiniana normal sample (replicate 3)


title: NSb

source_name: C. sorokiniana normal sample (replicate 2)


title: MDA5-Protected ADAR1WT_5-AZA-CdR_rep1

source_name: MDA5-Protected ADAR1WT_5-AZA-CdR_rep1


title: PCE_24h


title: PCE_48h


title: SSb

source_name: C. sorokiniana stress sample (replicate 2)_with_high_light_condition_and_glucose


title: NSa

source_name: C. sorokiniana normal sample (replicate 1)


title: Macrophages, without stimulation + S. sendtneri, donor 858-5

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description: Gene expression data from human unstimulated macrophages cultured for 6 days with S. sendtneri

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of human Hugene-2_0-type from Affymetrix. A Custom CDF Version 19 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

source_name: Buffy coat, donor 858-5

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Macrophages were cultured in Macrophage Serum Free Medium at a concentration of 1x10^6 cells/ml, supplemented with 5ng/ml M-CSF, 10^-8M Dexamethasone for 6 days

extract_protocol: RNA was extracted using E.Z.N.A. total RNA Kit I according to manufacturer´s instructions.

treatment_protocol: Macrophages were stimulated at day 0 either with  IFNgamma (100ng/ml) or left untreated as control and cultured with extracts of either S. roemeri (1:500) or S. sendtneri (1:500) or with 70% EtOH (1:500) as control.

value: PBMC derived monocytes

tag: sample

tag: stimulation

value: Ns

tag: plant extract

value: Ss


title: TETp_4h_+dox_vs_-dox_rep1

description: Sample 19


title: TETp_4h_+dox_vs_-dox_rep3

description: Sample 21


title: Macrophages, without stimulation + S. sendtneri, donor 858-4

source_name: Buffy coat, donor 858-4


title: Macrophages, without stimulation + S. roemeri, donor 858-3

description: Gene expression data from human unstimulated macrophages cultured for 6 days with S. roemeri

source_name: Buffy coat, donor 858-3

value: Sr


title: Macrophages, without stimulation + EtOH 70%, donor 858-5

description: Gene expression data from human unstimulated macrophages cultured for 6 days with 70% EtOH

value: Ctrl


title: Macrophages, without stimulation + EtOH 70%, donor 858-4


title: Macrophages, without stimulation + S. sendtneri, donor 858-2

source_name: Buffy coat, donor 858-2