title: SW480  - TP53 knock-out cells + R273H over expression - six hours post seeding_rep2

city: DVIRA

first: Ori

last: Hassin

state: HADAROM (SOUTHERN)

address: DVIRA 91

department: MCB

country: Israel

institute: Weizmann

description:
IRES-EGFP P53R273H
6h-system_Deseq_all_results.txt

data_processing:
Bcl files were converted into fastq by bcl2fastq. Demultiplexing is done using the sample barcode found on R2, the UMI found on R2 is inserted in the read name (in R1 fastq).  R1 Fastq data submitted.
MARS-seq analysis was done using the UTAP transcriptome analysis pipeline (Kohen et al., 2019). Reads were trimmed using Cutadapt (parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a “A{10}” –times 2 -u 3 -u -3 -q 20 -m 25) and mapped to the Mus_musculus genome using STAR v2.4.2a (parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic, –alignSoftClipAtReferenceEnds No).
The pipeline quantifies the 3’ of Gencode annotated genes (The 3’ region contains 1,000 bases upstream of the 3’ end and 100 bases downstream). Counting was done using htseq-count (union mode). Genes having minimum 5 UMI-corrected reads in at least one sample, were considered. Normalization of the counts and differential expression analysis was performed using DESeq2 package. Differentially expressed genes were defined as genes that had a significant adjusted p value of less than 0.05 and at least 2-fold change.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

source_name: SW480 cell line

growth_protocol: Cells were grown in normal condition (DMEM + 10% FBS + 1% Pen-Strep)

extract_protocol:
Cells were seeded and after 24 hours RNA was extracted using NucleoSpin kit (Macherey Nagel)
MARS-seq was used as described in Jaitin et al, 2014.
RNA sequencing 3' end

treatment_protocol: No treatment

value: colorectal cell line


title: small RNA KS21_2

status: Public on Sep 01 2021

type: SRA

city: Kanagawa

first: Manami

last: Tanaka

address: 2-22-9 Hiratsuka, Kanagawa 259-1211, Japan

country: Japan

institute: Bradeion Institute of Medical Sciences

description:
blood sample- 30 days after taking Huaier
healrthy control with Huaier uptake

library_source: transcriptomic

data_processing:
RNA: Alignment:Hisat2 and Bowtie2
RNA: Expression of genes by RSEM
Call DEGs by PossionDis method
Predicted novel transcripts by StringTie and call SNP by GATK
hg38
Genome_build: TXT, FA

molecule: total RNA

organism: Homo sapiens

source_name: blood

growth_protocol: The samples (4ml blood) in PAXgene Blood RNA tube was handled and kept at –80 C until shipping to BGI Shenzhen by dry-ice cargo.  The RNA extraction, quality check for sequencing were performed in BGI Shenzhen according to the BGI protocols.

extract_protocol:
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).
Library was prepared with 1 μg total RNA for each sample. Total RNA was purified by electrophoretic separation on a 15% urea denaturing polyacrylamide gel electrophoresis (PAGE) gel and small RNA regions corresponding to the 18–30 nt bands in the marker lane (14-30 ssRNA Ladder Marker, TAKARA) were excised and recovered. Then the 18–30 nt small RNAs were ligated to a 5′-adaptor and a 3′-adaptor. The adapter-ligated small RNAs were subsequently transcribed into cDNA by SuperScript II Reverse Transcriptase (Invitrogen, USA) and then several rounds of PCR amplification with PCR Primer Cocktail and PCR Mix were performed to enrich the cDNA fragments. The PCR products were selected by agarose gel electrophoresis with target fragments 100~120 bp, and then purified by QIAquick Gel Extraction Kit (QIAGEN, Valencia, CA).

treatment_protocol: Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA), according to the manual instructions. For tissue samples, grind about 60mg with liquid nitrogen into powder and transfer the powder samples into the 2ml tube contains 1.5ml Trizol reagent. The mix was centrifuge at 12000×g for 5min at 4°C. The supernatant was transferred to a new 2.0ml tube which was added 0.3ml of Chloroform/isoamyl alcohol (24:1) per 1.5ml of Trizol reagent. After the mix was centrifuged at 12000×g for 10min at 4°C, the aqueous phase was transferred to a new 1.5mL tube which was add equal volume of supernatant of isopropyl alcohol. The mix was centrifuged at 12000×g for 20min at 4°C and then removed the supernatant. After washed with 1ml 75% ethanol, the RNA pellet was air-dried in the biosafety cabinet and then dissolved by add 25μL~100μL of DEPC-treated water. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA)

tag: tumor origin

value: healthy control (Japanese male)


title: melanoma tissue 3

type: RNA

city: Xuzhou

first: Suwei

last: Dong

address: NO.32 Meijian RD

country: China

institute: The Second Affiliated Hospital of Xuzhou Medical University

description: gene expression

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila 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: 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: melanoma tissue 3

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: The MagMAX FFPE DNA/RNA Ultra (Thermofisher, USA) was used to extract RNA from paraffin-embedded specimens.

tag: tissue

value: melanoma

tag: gender

value: male


title: SW480  - shp53 + R273H over expression_rep2

description:
shp53 3' UTR  + IRES-EGFP P53R273H
sh-system_Deseq_all_results.txt

tag: cell type


title: melanoma tissue 4

description: gene expression

source_name: melanoma tissue 4

value: female


title: nevus tissue 1

description: gene expression

source_name: nevus tissue 1

value: nevus


title: melanoma tissue 5

description: gene expression

source_name: melanoma tissue 5


title: CSW18 transition stageEndosperm replicate-1

city: Saskatoon

first: Peng

last: Gao

state: Saskatchewan

address: 107 Science Place

country: Canada

institute: Agriculture and Agri-Food Canada

description:
replicate-1
Rawcount.xlsx

data_processing:
Illumina Casava software used for basecalling.
Trimming the adaptor sequences, filtering low-quality reads  and eliminating short reads using Trimmomatic.
Filtered reads were mapped to the IWGSC RefSeq v2.0 assembly wheat genome using STAR.
Read counting was carried out with FeatureCounts.
Genome_build: IWGSC RefSeq v2.0 assembly wheat genome
Supplementary_files_format_and_content: Matrix table files include raw counts for each sample

organism: Triticum aestivum

source_name: transition stageEndosperm

growth_protocol: Plants were grown in growth chambers under long-day conditions of 16 h light, 22°C and 8 h dark, 20 °C; light intensity was set to 100 to 120 μmol m−2 s−1 for whole life cycle.

extract_protocol:
Embryo, endosperm and pericarp tissue isolation procedure were precisely performed as described in Xiang et al., 2019.
For RNA-seq profile analysis, Illumina mRNA-seq libraries were constructed using the TruSeq RNA kit (version 1, rev A).

treatment_protocol: Flowers were emasculated and pollinated at the flower stage, to ensure sufficient and developmentally coordinated seed production for embryo isolation.

value: Endosperm

tag: Stage

value: transition stage

tag: ecotype

value: Chinese Spring


title: nevus tissue 2

description: gene expression

source_name: nevus tissue 2


title: VA_WT_L2_1

city: Nashville

first: Sierra

middle: D

last: Palumbos

state: TN

address: 2201 West End Ave, Nashville

department: Cell and Developmental Biology

country: USA

institute: Vanderbilt University

description: 2983-DMM-33_1_sequence (paired) (GE).clc

data_processing:
Reads were mapped and analyzed using CLC Genomics Workbench Version 21. Mapping done with CLC Genomics Workbench reference genome for C. elegans
The Differential Gene Expression tool was used to analyze differential expression between WT VA and L2 reference groups and WT vs. unc-4 VA groups.
Each gene is modeled by a separate Generalized Linear Model (see CLC Genomics Workbench Vesion 21 description).
A Principle Component Analysis was performed on all datasets to verify quality of RNA seq data and to determine variability between groups.
Genome_build: C. elegans WBcel235 reference genome
Supplementary_files_format_and_content: excel file includes TPM for VA enriched genes and unc-4 regulated genes

organism: Caenorhabditis elegans

source_name: Isolated L2 wild type VA neurons

growth_protocol: L2 larva were synchronized by hypochlorite treatment of adult hermaphrodites were allowed to hatch overnight in M9

extract_protocol:
Dissociated larval cells were generated as described (Spencer et al., PLoS ONE, 2014) cDNA synthesis was prepared using Clonetech Smart-Seq V3 Ultra Low Input RNA Kit
RNA libraries were prepared for sequencing using standard Illumina HiSeq 2500

treatment_protocol: A transectional labeling strategy was used to isolate VAs. VA and AVF neurons were captured by red only expression (pUnc-4::mCherry, pUnc-4C::GFP). VA neurons were isolated by FACS and collected in Trizol

tag: strain

value: pUnc-4::mCherry; pUnc-4C::GFP

tag: age

value: L2 synchronized animals

tag: cell isolation strategy

value: FACS sorting to isolate VA


title: nevus tissue 4

description: gene expression

source_name: nevus tissue 4


title: nevus tissue 3

description: gene expression

source_name: nevus tissue 3


title: small RNA KS2_1

description:
blood sample-before taking Huaier
stage IV, multiple metastasis

value: pancreas cancer


title: CSW17 mature stageEmbryo replicate-1

description:
replicate-1
Rawcount.xlsx

source_name: mature stageEmbryo

value: Embryo

value: mature stage


title: small RNA KS20_3

description:
blood sample- Huaier-free control
Huaier-free control

value: colorectal adenoma (benign)


title: T-cell-mROI-3

city: Boston,

first: Ajit Johnson

last: Nirmal

state: MA

address: 200 Longwood Avenue

department: Harvard Program in Therapeutic Science

institute: Harvard Medical School

data_processing:
The FASTQ files were processed using the bcbio pipeline v.1.2.1 software
The reads were mapped to the GRCh38 human reference genome using HISAT2 and Salmon
Length scaled transcripts per million (TPM) derived from Salmon was used for analysis.
Genome_build: hg38
Supplementary_files_format_and_content: Length-scaled transcript per million (TPM) CSV file

molecule: polyA RNA

source_name: T-cell zone

extract_protocol:
40 μm regions of interest were extracted using a mechanical picker from 5 μm tissue section. Tissue microregions were deposited with 2 µl PBS into PCR tubes containing 18 µl of lysis buffer: 1:16 mix of Proteinase K solution (QIAGEN) in PKD buffer (QIAGEN), with 0.1% RNasin Plus. After deposit, tubes were immediately placed in dry ice and stored at -80°C until ready for downstream RNA-seq workflow.
PCR tubes containing tissue microregions in the lysis buffer were removed from the freezer, allowed to thaw at room temperature for 5 min, and incubated at 56°C for 1 hr. Tubes were briefly vortexed, spun down, and placed on ice. Dynabeads Oligo(dT)25 beads (ThermoFisher) were washed three times with ice-cold 1X hybridization buffer (NorthernMax buffer (ThermoFisher) with 0.05% Tween 20 and 0.0025% RNasin Plus), and resuspended in original bead volume with ice-cold 2x hybridization buffer (NorthernMax buffer with 0.1% Tween 20 and 0.005% RNasin Plus). A volume of 20 µl of washed beads was added to each lysed sample, mixed by pipette, and incubated at 56°C for 1 min followed by room temperature incubation for 10 min. Samples were placed on a magnet and washed twice with an ice-cold 1X hybridization buffer, then once with ice-cold 1X PBS with 0.0025% RNasin Plus. Supernatant was removed, and the pellet was resuspended in 10.5 µl nuclease-free water. Samples were incubated at 80°C for 2 min and immediately placed on a magnet. Supernatant was transferred to new PCR tubes or plates, and placed on ice for subsequent whole transcriptome amplification or stored at -80°C. Reverse transcription and cDNA amplification were performed using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio, Kusatsu, Shiga, Japan). Resulting amplified cDNA libraries were assessed for DNA concentration using the Qubit dsDNA HS Assay Kit (ThermoFisher) and for fragment size distribution using the BioAnalyzer 2100 High Sensitivity DNA Kit (Agilent). Tonsil tissue microregion samples underwent Nextera XT library preparation (Illumina). Resulting libraries were characterized by using the Qubit dsDNA HS Assay Kit and BioAnalyzer 2100 High Sensitivity DNA Kit, pooled at equimolar ratios, and sequenced using a MiSeq (Illumina).

value: T cells


title: SW480  - TP53 knock-out cells + R273H over expression - six hours post seeding_rep1

value: colorectal cell line


title: T-cell-mROI-4


title: Control_DAY185

city: Gyeongsan-Si

first: Jintae

last: Lee

state: Gyeongsangbuk-Do

address: 214-1 Daedong

department: Chemical engineering

country: South Korea

institute: Yeungnam University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to Candida_albicans_SC5314 whole genome using Tophat
Read count extraction and nomalization were performed using edgeR.
Genome_build: Candida_albicans_SC5314 (NCBI)
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

organism: Candida albicans

source_name: Whole cell_control

growth_protocol: 25 ml of C. albicans DAY185 at an initial turbidity of 0.1 at OD600 was inoculated into PDB broth in 250 ml Erlenmeyer flasks and incubated for 4 h at 37ºC with agitation (250 rpm)

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using Clontech SMARTer Stranded RNA-Seq Kit standard protocols.

treatment_protocol: Cells were incubated for 4 h at 37ºC with agitation (250 rpm) in the presence or absence of Nepodin (10 µg/ml)


title: small RNA KS19_2

description:
blood sample- 30 days after taking Huaier
stage IIb, metastasis to lympy nodes

value: colorectal cancer (adenocarcinoma)


title: small RNA KS20_1


title: SW480  - shp53 + R273H over expression_rep3


title: T-cell-mROI-5


title: CSW11 two cell stageEmbryo replicate-1

description:
replicate-1
Rawcount.xlsx

source_name: two cell stageEmbryo

value: two cell stage


title: melanoma tissue 2

description: gene expression

source_name: melanoma tissue 2

value: melanoma

value: male


title: T-cell-mROI-1


title: SW480  - TP53 knock-out cells - six hours post seeding_rep1

description:
No over expression
6h-system_Deseq_all_results.txt


title: small RNA KS20_2


title: small RNA KS19_3

description:
blood sample- 90 days after taking Huaier
stage IIb, metastasis to lympy nodes


title: SW480  - shp53 + R273H over expression_rep1


title: SW480  - TP53 knock-out cells - six hours post seeding_rep2


title: small RNA KS18_3

description:
blood sample- 90 days after taking Huaier
stage 0,with prostate hyperploasia

value: lung cancer suspected by CT


title: small RNA KS19_1

description:
blood sample-before taking Huaier
stage IIb, metastasis to lympy nodes


title: SW480  - TP53 knock-out cells + R273H over expression_rep3

description:
IRES-EGFP P53R273H
6h-system_Deseq_all_results.txt
ko-system_Deseq_all_results.txt


title: T-cell-mROI-2


title: small RNA KS17_2

description:
blood sample- 30 days after taking Huaier
stage IV,with strong anemia

value: stomach cancer (adenocarcinoma)


title: Breast cancer_normal 108N

city: New Taipei

first: Chih-Cheng

last: Chien

address: No 2, Ln 59, Jian-Cheng Rd, Sijhih Dist

country: Taiwan

institute: Sijhih Cathay General Hospital

description: Gene expression data from breast cancer tissues.

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45 °C on GeneChip® Human Genome U133 Plus 2.0 expression arrays (Affymetrix, Inc., Santa Clara, CA).

scan_protocol: GeneChips were scanned using a GeneChip Scanner 3000.

data_processing: Scanned images processed by GeneChip® Operating Software and Affymetrix’s Microarray Suite software to generate detection p values. The Robust Multichip Average (RMA) algorithm, which consisted three steps of background adjustment, quantile normalization, and final summarization, was applied for perfect match probe signals within the study.

label: biotin

source_name: Breast cancer tumor tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA.

extract_protocol: Total RNA was extracted from frozen specimens using TRIzol® reagent (Invitrogen, Carlsbad, CA). RNA was purified using RNeasy® mini kits (Qiagen, Valencia, CA) and RNA integration was checked by gel electrophoresis.

treatment_protocol: Breast cancer samples were prospectively collected during surgery. Cancerous breast tissues were snap-frozen and stored in liquid nitrogen at -80 °C with RNAlaterTM reagent (Qiagen, Germantown, MD) within 30 minutes after surgery. Frozen samples were cut into 1~2-mm thick slices, and slices with more than 90% of cancer content were selected for microarray experiment.

value: Breast

tag: ihc

tag: grade

tag: alive

value: Alive

tag: relapse status

value: non-relapse

tag: overall survival (years)

tag: relapse free survival (years)


title: Breast cancer_Breast Cancer 119T [re-analysis]

description: re-analysis of GSM4393021

value: Lum-A


title: B-cell-mROI-2

source_name: B-cell follice A

value: B cells


title: Breast cancer_BH0533-3 [re-analysis]

description: re-analysis of GSM4393015

value: Basal


title: Breast cancer_Breast Cancer 121T [re-analysis]

description: re-analysis of GSM4393023


title: small RNA KS18_2

description:
blood sample- 30 days after taking Huaier
stage 0,with prostate hyperploasia

source_name: blood


title: small RNA KS17_1

description:
blood sample-before taking Huaier
stage IV,with strong anemia


title: Breast cancer_BH0533-5 [re-analysis]

description: re-analysis of GSM4393018

value: Normal


title: B-cell-mROI-5

source_name: B-cell follice B


title: small RNA KS18_1

description:
blood sample-before taking Huaier
stage 0,with prostate hyperploasia


title: SW480  - shp53 + R175H over expression_rep3

description:
shp53 3' UTR  + IRES-EGFP P53R175H
sh-system_Deseq_all_results.txt

source_name: SW480 cell line


title: SW480  - shp53 + R175H over expression_rep2


title: melanoma tissue 1

description: gene expression

source_name: melanoma tissue 1


title: B-cell-mROI-1


title: small RNA KS16_3

description:
blood sample- 90 days after taking Huaier
with liveer dysfunction

value: prostate cancer in situ(biopsy)


title: Breast cancer_Breast Cancer 108T [re-analysis]

description: re-analysis of GSM4393020


title: Breast cancer_BH0533-4 [re-analysis]

description: re-analysis of GSM4393017

value: Lum-B


title: SW480  - TP53 knock-out cells_rep3

description:
No over expression
6h-system_Deseq_all_results.txt
ko-system_Deseq_all_results.txt


title: B-cell-mROI-4


title: Breast cancer_BH0505-9 [re-analysis]

description: re-analysis of GSM4393011

value: relapse


title: small RNA KS17_3

description:
blood sample- 90 days after taking Huaier
stage IV,with strong anemia


title: SW480  - TP53 knock-out cells + R175H over expression_rep3

description:
IRES-EGFP P53R175H
ko-system_Deseq_all_results.txt

value: colorectal cell line


title: Breast cancer_BH0533-2 [re-analysis]

description: re-analysis of GSM4393014

value: Death


title: SW480  - shp53_rep3

description:
shp53 3' UTR
sh-system_Deseq_all_results.txt


title: B-cell-mROI-3


title: Tumor mROI 5

source_name: Tumor

extract_protocol:
40 μm regions of interest were extracted using a mechanical picker from 5 μm tissue section. Tissue microregions were deposited with 2 µl PBS into PCR tubes containing 18 µl of lysis buffer: 1:16 mix of Proteinase K solution (QIAGEN) in PKD buffer (QIAGEN), with 0.1% RNasin Plus. After deposit, tubes were immediately placed in dry ice and stored at -80°C until ready for downstream RNA-seq workflow.
PCR tubes containing tissue microregions in the lysis buffer were removed from the freezer, allowed to thaw at room temperature for 5 min, and incubated at 56°C for 1 hr. Tubes were briefly vortexed, spun down, and placed on ice. Dynabeads Oligo(dT)25 beads (ThermoFisher) were washed three times with ice-cold 1X hybridization buffer (NorthernMax buffer (ThermoFisher) with 0.05% Tween 20 and 0.0025% RNasin Plus), and resuspended in original bead volume with ice-cold 2x hybridization buffer (NorthernMax buffer with 0.1% Tween 20 and 0.005% RNasin Plus). A volume of 20 µl of washed beads was added to each lysed sample, mixed by pipette, and incubated at 56°C for 1 min followed by room temperature incubation for 10 min. Samples were placed on a magnet and washed twice with an ice-cold 1X hybridization buffer, then once with ice-cold 1X PBS with 0.0025% RNasin Plus. Supernatant was removed, and the pellet was resuspended in 10.5 µl nuclease-free water. Samples were incubated at 80°C for 2 min and immediately placed on a magnet. Supernatant was transferred to new PCR tubes or plates, and placed on ice for subsequent whole transcriptome amplification or stored at -80°C. Reverse transcription and cDNA amplification were performed using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio, Kusatsu, Shiga, Japan). Resulting amplified cDNA libraries were assessed for DNA concentration using the Qubit dsDNA HS Assay Kit (ThermoFisher) and for fragment size distribution using the BioAnalyzer 2100 High Sensitivity DNA Kit (Agilent). Breast cancer tissue microregion samples underwent Nextera XT library preparation (Illumina). Resulting libraries were characterized by using the Qubit dsDNA HS Assay Kit and BioAnalyzer 2100 High Sensitivity DNA Kit, pooled at equimolar ratios, and sequenced using a MiSeq (Illumina).

value: Tumor


title: Tumor mROI 3


title: SW480  - shp53 + R175H over expression_rep1


title: SW480  - shp53_rep2


title: Tumor mROI 4


title: small RNA KS16_2

description:
blood sample- 30 days after taking Huaier
with liveer dysfunction


title: small RNA KS15_2


title: small RNA KS16_1

description:
blood sample-before taking Huaier
with liveer dysfunction


title: SW480  - TP53 knock-out cells + R175H over expression_rep2


title: Tumor mROI 1


title: Breast cancer_BH0505-5 [re-analysis]

description: re-analysis of GSM4393008


title: SW480  - TP53 knock-out cells_rep2


title: Breast cancer_BH0533-1 [re-analysis]

description: re-analysis of GSM4393012


title: small RNA KS14_3

description:
blood sample- 90 days after taking Huaier
endoscopic polyp dissection after 90days of Huaier treatment

value: colorectal adenoma (benign)


title: small RNA KS15_3


title: SW480  - TP53 knock-out cells + R273H over expression_rep2


title: Tumor mROI 2


title: Breast cancer_BH0505-8 [re-analysis]

description: re-analysis of GSM4393010


title: Breast cancer_BH0485-8 [re-analysis]

description: re-analysis of GSM4393002


title: TIL mROI 5

source_name: Tumor and T cells

value: Tumor and T cells


title: Breast cancer_BH0485-9 [re-analysis]

description: re-analysis of GSM4393004


title: SW480  - TP53 knock-out cells + R273H over expression_rep1


title: small RNA KS15_1


title: small RNA KS14_1

description:
blood sample-before taking Huaier
endoscopic polyp dissection after 90days of Huaier treatment


title: TIL mROI 3


title: SW480  - shp53_rep1


title: Breast cancer_BH0505-3 [re-analysis]

description: re-analysis of GSM4393007


title: TIL mROI 2


title: small RNA KS1_3

description:
blood sample- 90 days after taking Huaier
stage IV, multiple metastasis

value: lung cancer (small cell carciinoma)


title: SW480  - TP53 knock-out cells + R175H over expression_rep1


title: small RNA KS13_3

description:
blood sample- 30 days after taking Huaier
endoscopic polyp dissection after 90days of Huaier treatment


title: small RNA KS14_2


title: Breast cancer_BH0485-7 [re-analysis]

description: re-analysis of GSM4393001


title: TIL mROI 4


title: small RNA KS13_2


title: ΔPus7 293T virion 6SG PA-Ψ-Seq

city: Taipei

first: Kevin

last: Tsai

address: 128 Sec. 2, Academia Rd. Nankang

department: Institute of Biomedical Sciences

institute: Academia Sinica

description:
Purified HIV virion RNA
Aligned to the HIV-1 NL4-3 genome, with one copy of LTR, U3 sequence on the 5' end, R-U5 on the 3' end

data_processing:
CASAVA 1.8.2
fastx toolkit: fastq_quality_filter -Q33| fastx_clipper -Q33 -v -a [index_sequence] -l 15 -c | fastq_to_fasta -Q33
Aligned to the human genome hg19 using Bowtie 0.12.7: bowtie -m 8 -a --best --strata --chunkmbs 10000
For hg19 alignments: tophat -N 1 --no-convert-bam --b2-N 1
hg19 non-aligning reads aligned to the HIV-1 NL4-3 genome using Bowtie 0.12.7: bowtie -m 3 -v 1 -a --best --strata --chunkmbs 10000
When comparing WT to Pus KO samples, the dataset with the higher read depth down sampled to match the one with the lower read depth using "macs2 randsample"
Filtered out all reads that lack a G>A or T>C mutation (for 6SG or 4SU-pulsed samples, respectively)
Peaks called with: "macs2 callpeak --nomodel -q $q --extsize 32 --shift 0 --keep-dup 5 -g hs" where $q is 0.0005 for WT samples, $q=0.05 for KO samples
Awk script to generate bed file, columns are "chromosome, start, end, score, strand"
For WT samples, peaks further screened with "awk '{if($1!="#" && $1!="chr" && $6>=3 && $8>=5) {print $1 "\t" $2-1 "\t" $3 "\t" $10 "\t" $6 "\t."}}' macs_called_peaks.xls > significant_peaks.bed" For KO samples, the if statement in the awk script is "if($1!="#" && $1!="chr" && $6>=1 && $8>=3)"
Genome_build: NL4-3 genome: 551-9626nt of GenBank AF324493.2
Genome_build: Human hg19
Genome_build: tRNA sequences from tRNAdb (Juhling Morl 2016)
Genome_build: rRNA: GenBank #U13369 nts 7935-12969, X03205, and U13369 nts 6623-6779
Genome_build: snRNA: NC_000001.11:c16514285-16514122, NC_000017.11:c43233977-43233790, NC_000012.12:c120293237-120293094, NC_000015.10:65296051-65296167, NC_000015.10:c67840045-67839940, NC_000001.11:28648600-28648734, NC_000022.11:42615244-42615393, NC_000002.12:121530880-121531009, NC_000009.12:c134164564-134164440, all from GRCh38.p13
Supplementary_files_format_and_content: bed files, aligned to hg19, HIV-1 NL4-3 genome, or tRNA, rRNA, snRNA sequences

source_name: ΔPus7 293T

extract_protocol:
PA-Ψ-seq or PA-m6A-seq (PAR-CLIP done with a pasudouridine or m6A RNA targeting antibody)
All samples were processed with the NEB Next small RNA-seq library prep kit for Illumina

tag: virus strain

value: HIV-1 NL4-3

tag: technique

value: PA-Psi-Seq

tag: pulldown antibody

value: anti-pseudouridine (anti-Psi) (MBL #347-3)


title: T cell mROI 3

source_name: T cell

value: T cell


title: T cell mROI 4


title: Cas9-control 293T virion 6SG PA-Ψ-Seq

source_name: ΔGFP 293T


title: Breast cancer_BH0485-6 [re-analysis]

description: re-analysis of GSM4392999

tag: tissue

value: Breast

value: Alive

value: non-relapse


title: T cell mROI 2


title: small RNA KS1_2

description:
blood sample- 30 days after taking Huaier
stage IV, multiple metastasis

tag: tumor origin


title: Breast cancer_BH0485-4 [re-analysis]

description: re-analysis of GSM4392996


title: T cell mROI 1

tag: cell type


title: TIL mROI 1


title: 293T cellular 4SU PA-Ψ-Seq_i3

description:
Cell extract polyA+ RNA
Aligned to hg19, single LTR HIV-1 NL4-3, rRNAs, tRNAs, and snRNAs


title: CEM cellular 4SU PA-Ψ-Seq

source_name: CEM


title: small RNA KS12_3

value: lung cancer (adenocarciinoma)


title: Breast cancer_BH0485-3 [re-analysis]

description: re-analysis of GSM4392995

tag: Stage


title: SW480  - TP53 knock-out cells_rep1


title: Breast cancer_BH0485-5 [re-analysis]

description: re-analysis of GSM4392998


title: small RNA KS13_1


title: Breast cancer_BH0485-10 [re-analysis]

description: re-analysis of GSM4393005


title: Breast cancer_BH0478-6 [re-analysis]

description: re-analysis of GSM4392993

value: Normal

value: Lum-A


title: small RNA KS12_2


title: small RNA KS12_1

description:
blood sample-before taking Huaier
stage IV, multiple metastasis


title: Breast cancer_BH0478-5 [re-analysis]

description: re-analysis of GSM4392992

value: Lum-B


title: Melanoma in situ mROI 9

source_name: Melanoma in situ + immune

extract_protocol:
40 μm regions of interest were extracted using a mechanical picker from 5 μm tissue section. Tissue microregions were deposited with 2 µl PBS into PCR tubes containing 18 µl of lysis buffer: 1:16 mix of Proteinase K solution (QIAGEN) in PKD buffer (QIAGEN), with 0.1% RNasin Plus. After deposit, tubes were immediately placed in dry ice and stored at -80°C until ready for downstream RNA-seq workflow.
PCR tubes containing tissue microregions in the lysis buffer were removed from the freezer, allowed to thaw at room temperature for 5 min, and incubated at 56°C for 1 hr. Tubes were briefly vortexed, spun down, and placed on ice. Dynabeads Oligo(dT)25 beads (ThermoFisher) were washed three times with ice-cold 1X hybridization buffer (NorthernMax buffer (ThermoFisher) with 0.05% Tween 20 and 0.0025% RNasin Plus), and resuspended in original bead volume with ice-cold 2x hybridization buffer (NorthernMax buffer with 0.1% Tween 20 and 0.005% RNasin Plus). A volume of 20 µl of washed beads was added to each lysed sample, mixed by pipette, and incubated at 56°C for 1 min followed by room temperature incubation for 10 min. Samples were placed on a magnet and washed twice with an ice-cold 1X hybridization buffer, then once with ice-cold 1X PBS with 0.0025% RNasin Plus. Supernatant was removed, and the pellet was resuspended in 10.5 µl nuclease-free water. Samples were incubated at 80°C for 2 min and immediately placed on a magnet. Supernatant was transferred to new PCR tubes or plates, and placed on ice for subsequent whole transcriptome amplification or stored at -80°C. Reverse transcription and cDNA amplification were performed using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio, Kusatsu, Shiga, Japan). Resulting amplified cDNA libraries were assessed for DNA concentration using the Qubit dsDNA HS Assay Kit (ThermoFisher) and for fragment size distribution using the BioAnalyzer 2100 High Sensitivity DNA Kit (Agilent). Melanoma tissue microregion libraries were prepared with ThruPLEX DNA-seq Kit (Takara Bio). Resulting libraries were characterized by using the Qubit dsDNA HS Assay Kit and BioAnalyzer 2100 High Sensitivity DNA Kit, pooled at equimolar ratios, and sequenced using a NextSeq (Illumina) sequencer.

value: Melanoma in situ + immune


title: Melanoma in situ mROI 8


title: small RNA KS1_1


title: CEM virion 4SU PA-Ψ-Seq


title: Breast cancer_BH0478-4 [re-analysis]

description: re-analysis of GSM4392990


title: small RNA KS11_3

description:
blood sample- 90 days after taking Huaier
surgical dissection before taking Huaier

value: oesophageal adenocarcinoma


title: Melanoma in situ mROI 7


title: small RNA KS11_2

description:
blood sample- 30 days after taking Huaier
surgical dissection before taking Huaier


title: Melanoma in situ mROI 5

source_name: Melanoma in situ

value: Melanoma in situ


title: small RNA KS11_1

description:
blood sample-before taking Huaier
surgical dissection before taking Huaier


title: Breast cancer_BH0478-3 [re-analysis]

description: re-analysis of GSM4392989

value: Basal


title: Melanoma in situ mROI 4


title: Breast cancer_BH0470-6 [re-analysis]

description: re-analysis of GSM4392987

value: relapse


title: small RNA KS10_6

description:
blood sample- 18 months after taking Huaier
surgical dissection at 6 weeks after taking Huaier

value: meningioma (benign)


title: Melanoma in situ mROI 6


title: Breast cancer_BH0470-3 [re-analysis]

description: re-analysis of GSM4392984


title: Melanoma in situ mROI 3


title: control-50

city: Solna

first: Estelle

last: Proux-Wéra

department: Department of Biochemistry and Biophysics

country: Sweden

institute: Science for Life laboratory

description: C57Bl/6 mice, 11-12 weeks old were acclimated to the swimming protocol by daily swim sessions, which gradually increased by 10 min over the course of 9 days. After the acclimatization period, the mice were made to swim for 3 weeks, twice per day, for 90 min, with 4 hours rest between the sessions. The first swimming session was at 9AM and the second at 3PM

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array 430 1.1. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: normalization:PLIER, expression analysis: LIMMA (R/Bioconductor)

organism: Mus musculus

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

value: Liver

tag: genotype

tag: treatment

value: control


title: Swimming-56

tag: age

value: Swimming


title: small RNA KS10_5

description:
blood sample- 14 months after taking Huaier
surgical dissection at 6 weeks after taking Huaier


title: Breast cancer_BH0470-2 [re-analysis]

description: re-analysis of GSM4392983


title: Swimming-53


title: control-52


title: Swimming-55


title: Melanoma in situ mROI 2


title: small RNA KS10_4

description:
blood sample- 9 months after taking Huaier
surgical dissection at 6 weeks after taking Huaier


title: Breast cancer_BH0434-1 [re-analysis]

description: re-analysis of GSM4392980

value: Death


title: Melanoma in situ mROI 28

source_name: Melanoma in situ resolved

value: Melanoma in situ resolved


title: Breast cancer_BH0470-5 [re-analysis]

description: re-analysis of GSM4392986

value: Breast

value: Alive


title: Breast cancer_BH0430-2 [re-analysis]

description: re-analysis of GSM4392979

value: non-relapse


title: Breast cancer_BH0470-1 [re-analysis]

description: re-analysis of GSM4392981


title: small RNA KS10_3

description:
blood sample- 90 days after taking Huaier
surgical dissection at 6 weeks after taking Huaier


title: Swimming-54


title: control-49


title: small RNA KS10_2

description:
blood sample- 30 days after taking Huaier
surgical dissection at 6 weeks after taking Huaier


title: Swimming-46

value: Skeletal muscle


title: Breast cancer_BH0396-7 [re-analysis]

description: re-analysis of GSM4392976

value: Lum-A


title: Breast cancer_BH0396-6 [re-analysis]

description: re-analysis of GSM4392974


title: Melanoma in situ mROI 27


title: Swimming-45


title: small RNA KS10_1

description:
blood sample-before taking Huaier
surgical dissection at 6 weeks after taking Huaier


title: Melanoma in situ mROI 26


title: Breast cancer_BH0396-5 [re-analysis]

description: re-analysis of GSM4392973

value: Lum-B


title: Melanoma in situ mROI 25


title: NB cell line SKNBE2C

city: HONG KONG

first: Zhihui

last: WENG

address: Lo Kwee-Seong Integrated Biomedical Sciences  Building, Area 39, The Chinese University of Hong  Kong

country: Hong Kong

institute: CUHK

data_processing:
BGISEQ-500 RS software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie2
Reads Per FPKM were calculated using a BGI protocol.
Supplementary_files_format_and_content: FPKMs

source_name: NB cell line

growth_protocol: ES cell–derived NCSC cells were routinely generated by NCSC differentiation medium.

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard BGI protocols

treatment_protocol: Doxycline is added into medium to induce MYCN overexpression

tag: cell line

value: NB cell line SKNBE2C

tag: passages


title: NB cell line SKNAS

value: NB cell line SKNAS


title: Melanoma in situ mROI 24


title: Breast cancer_BH0396-4 [re-analysis]

description: re-analysis of GSM4392971

tag: ihc

tag: grade


title: NB cell line MHH-NB-11

value: NB cell line MHH-NB-11


title: Swimming-47


title: Melanoma in situ mROI 23


title: Melanoma in situ mROI 22


title: NB cell line IMR-32

value: NB cell line IMR-32


title: control-43


title: control-42


title: control-41


title: MYCN-overexpression NCSC derived tumor 4

source_name: MYCN-overexpression NCSC derived tumor

value: NCSC derived tumor

value: MYCN overexpression


title: control-44


title: Melanoma in situ mROI 21


title: Breast cancer_BH0396-10 [re-analysis]

description: re-analysis of GSM4392977

source_name: Breast cancer tumor tissue

tag: alive

tag: relapse status

value: Normal


title: Breast cancer_BH0396-3 [re-analysis]

description: re-analysis of GSM4392970

tag: overall survival (years)

tag: relapse free survival (years)


title: Breast cancer_BH0394-9 [re-analysis]

description: re-analysis of GSM4392964


title: Melanoma in situ mROI 20

value: Melanoma in situ + immune


title: Melanoma in situ mROI 1

value: Melanoma in situ


title: MYCN-overexpression NCSC derived tumor 3


title: MYCN-overexpression NCSC derived tumor 2


title: Swimming-40

value: Brain

value: Swimming


title: MYCN-overexpression NCSC derived tumor 1


title: Melanoma in situ mROI 19


title: Melanoma in situ mROI 18


title: MYCN-overexpression NCSC replication 3

source_name: human ESC derived neural crest stem cells, with MYCN overexpression


title: Swimming-37


title: control-34

value: control


title: Swimming-39


title: Melanoma in situ mROI 17


title: Breast cancer_BH0394-8 [re-analysis]

description: re-analysis of GSM4392962

value: Breast

value: Alive


title: Breast cancer_BH0394-7 [re-analysis]

description: re-analysis of GSM4392961

value: non-relapse


title: Breast cancer_BH0396-1 [re-analysis]

description: re-analysis of GSM4392967


title: MYCN-overexpression NCSC replication 4

value: human ESC derived neural crest stem cells


title: MYCN-overexpression NCSC replication 2


title: MYCN-overexpression NCSC replication 1


title: Breast cancer_BH0394-6 [re-analysis]

description: re-analysis of GSM4392959

value: Lum-B


title: Swimming-38


title: Breast cancer_BH0394-5 [re-analysis]

description: re-analysis of GSM4392958

value: Lum-A


title: Melanoma in situ mROI 16


title: control-33


title: Breast cancer_BH0396-2 [re-analysis]

description: re-analysis of GSM4392968

value: Death


title: Breast cancer_BH0394-4 [re-analysis]

description: re-analysis of GSM4392956


title: control-36


title: control-35


title: Breast cancer_BH0394-3 [re-analysis]

description: re-analysis of GSM4392955


title: Breast cancer_BH0394-2 [re-analysis]

description: re-analysis of GSM4392954

value: Basal


title: Swimming-32

value: Spleen


title: Breast cancer_BH0394-1 [re-analysis]

description: re-analysis of GSM4392952


title: Melanoma in situ mROI 14


title: Breast cancer_BH0394-10 [re-analysis]

description: re-analysis of GSM4392965


title: control NCSC replication 4

source_name: human ESC derived neural crest stem cells


title: Swimming-31


title: Melanoma in situ mROI 15


title: Melanoma in situ mROI 13


title: control NCSC replication 3


title: Melanoma in situ mROI 10


title: control NCSC replication 2


title: Swimming-30


title: control NCSC replication 1


title: Melanoma in situ mROI 12


title: control-27


title: control-26


title: Invasive tumor mROI 9

source_name: Invasive tumor

value: Invasive tumor


title: control-28


title: Breast cancer_BH0344-9 [re-analysis]

description: re-analysis of GSM4392943


title: Breast cancer_BH0354-4 [re-analysis]

description: re-analysis of GSM4392951


title: Breast cancer_BH0354-1 [re-analysis]

description: re-analysis of GSM4392946


title: Breast cancer_BH0354-2 [re-analysis]

description: re-analysis of GSM4392948


title: Invasive tumor mROI 7


title: Invasive tumor mROI 6


title: Swimming-24

value: Subcutaneous white adipose tissue


title: Breast cancer_BH0354-3 [re-analysis]

description: re-analysis of GSM4392949


title: Melanoma in situ mROI 11


title: Breast cancer_BH0344-3 [re-analysis]

description: re-analysis of GSM4392939


title: control-25


title: Invasive tumor mROI 4


title: Swimming-29


title: Invasive tumor mROI 8


title: Breast cancer_BH0344-7 [re-analysis]

description: re-analysis of GSM4392942


title: Breast cancer_BH0344-4 [re-analysis]

description: re-analysis of GSM4392941


title: Swimming-23


title: Breast cancer_BH0344-2 [re-analysis]

description: re-analysis of GSM4392938


title: Invasive tumor mROI 3


title: Invasive tumor mROI 5


title: Swimming-22


title: Swimming-21


title: control-19


title: Invasive tumor mROI 2


title: control-20


title: Invasive tumor mROI 1


title: Breast cancer_BH0312-9 [re-analysis]

description: re-analysis of GSM4392930

value: Uncla


title: Invasive tumor mROI 13


title: Invasive tumor mROI 15


title: Breast cancer_BH0312-7 [re-analysis]

description: re-analysis of GSM4392928


title: Invasive tumor mROI 11


title: Invasive tumor mROI 14


title: Invasive tumor mROI 12


title: Invasive tumor mROI 16


title: control-17


title: control-09

value: Kidney


title: Swimming-16


title: Breast cancer_BH0312-4 [re-analysis]

description: re-analysis of GSM4392925

value: Normal


title: Breast cancer_BH0312-6 [re-analysis]

description: re-analysis of GSM4392926


title: Invasive tumor mROI 10


title: Breast cancer_BH0312-3 [re-analysis]

description: re-analysis of GSM4392923


title: Invasive margin mROI 9

source_name: Invasive margin

value: Invasive margin


title: Invasive margin mROI 8


title: Breast cancer_BH0312-8 [re-analysis]

description: re-analysis of GSM4392929


title: Swimming-15

value: Swimming


title: control-18

value: control


title: control-11


title: Invasive margin mROI 7


title: Swimming-14


title: Swimming-13


title: Breast cancer_BH0312-13 [re-analysis]

description: re-analysis of GSM4392936

value: Breast

value: relapse


title: Breast cancer_90T [re-analysis]

description: re-analysis of GSM4392902

value: Alive

value: non-relapse


title: Breast cancer_BH0312-10 [re-analysis]

description: re-analysis of GSM4392932


title: Breast cancer_BH0312-12 [re-analysis]

description: re-analysis of GSM4392935

value: Lum-B


title: Breast cancer_BH0312-11 [re-analysis]

description: re-analysis of GSM4392933

value: Lum-A


title: Breast cancer_BH0344-10 [re-analysis]

description: re-analysis of GSM4392945

value: Death


title: control-12


title: Invasive margin mROI 6


title: Swimming-07

value: Visceral white adipose tissue


title: Invasive margin mROI 5


title: Swimming-08


title: Breast cancer_9 normal

description: Gene expression data from breast cancer tissues.


title: Swimming-06


title: Swimming-05


title: Invasive margin mROI 4


title: Invasive margin mROI 2


title: Breast cancer_8 normal


title: control-10


title: Invasive margin mROI 3


title: Invasive margin mROI 11


title: control-04


title: Invasive margin mROI 12


title: Breast cancer_8 cancer [re-analysis]

description: re-analysis of GSM4392865


title: Breast cancer_75 normal


title: Breast cancer_78 cancer2 [re-analysis]

description: re-analysis of GSM4392900

value: Basal


title: Breast cancer_9 cancer [re-analysis]

description: re-analysis of GSM4392866


title: Breast cancer_76 normal


title: PK

city: St. Louis

first: Zhiyu

last: Dai

state: MO

address: 4960 Childrens Place

institute: Washington University in St. Louis

data_processing: The original sequencing data were trimmed using FASTX and aligned to the reference genome using TopHat2. The differential expression analysis was performed using Cuffdiff software

source_name: PK

extract_protocol:
Total RNA was isolated from left ventricular tissues with Trizol reagents (Invitrogen), followed by purification with the RNeasy Mini kit including DNase I digestion (Qiagen).
RNA sequencing was carried out by Novogene corporation on Illumina Hiseq platform

tag: strain

value: left ventricule

value: Egln1Tie2Cre mice


title: PH2

value: Egln1/Hif2aTie2Cre mice


title: PW

source_name: PW

value: Egln1 floxed mice


title: Invasive margin mROI 10


title: control-02


title: 19BBz_Scr_2

city: Philadelphia

first: Lexus

last: Johnson

state: Pennsylvania

address: 421 Curie Blvd, 532

department: Radiation Oncology

institute: University of Pennsylvania

description: 3' Poly-A mRNA

data_processing:
Orginal intensity file (.bcl) was transferred to fastq with tool cellranger mkfastq (bcl2fastq2 wrapper), which was subsequently subjected to cellranger count function for alignment.
Genome_build: mm10
Supplementary_files_format_and_content: .mtx

source_name: Immune cells

growth_protocol: B16-hCD19 tumors were implanted in flanks of B6 mice

extract_protocol:
Live/CD45.2+ endogenous immune cells were FACS sorted. 10X 3' v3.1 RNA processing/isolation kit used
Protocol for 10X 3' v2.0 kit utilized

treatment_protocol: Mice were treated i.v. (tail vein) with CAR-T cells of indicated genotype on day 5 and day 12

value: Sorted CD45.2+ endogenous immune cells

value: CD45.1+ 19BBz-Scr CAR-T cells


title: 19BBz_1

description: 3' Poly-A mRNA

value: CD45.1+ 19BBz CAR-T cells


title: Breast cancer_72 normal

value: Normal


title: Exophytic melanoma mROI 1

source_name: Exophytic tumor

value: Exophytic tumor


title: Breast cancer_75 cancer [re-analysis]

description: re-analysis of GSM4392897

value: Breast


title: Exophytic melanoma mROI 3


title: Exophytic melanoma mROI 2


title: 19BBz_2

description: 3' Poly-A mRNA


title: Breast cancer_76 cancer [re-analysis]

description: re-analysis of GSM4392899

value: Alive


title: Brisk TIL mROI 9

source_name: Brisk TIL

value: Brisk TIL


title: Breast cancer_70 cancer [re-analysis]

description: re-analysis of GSM4392893

value: non-relapse


title: 19BBz_Scr_1

description: 3' Poly-A mRNA


title: Breast cancer_72 cancer [re-analysis]

description: re-analysis of GSM4392895


title: Brisk TIL mROI 8


title: Brisk TIL mROI 6


title: 19BBz_7SL_1

description: 3' Poly-A mRNA

value: CD45.1+ 19BBz-7SL CAR-T cells


title: 19BBz_7SL_2

description: 3' Poly-A mRNA


title: PGCLC_100nM BPA_Rep3

city: Los Angeles

first: Steen

middle: Kian Thye

last: Ooi

state: CA

address: 621 Charles E. Young Drive S.

department: Institute for Society and Genetics

institute: UCLA

data_processing:
Data quality check was performed using Illumina Sequencing Analysis Viewer (SAV) software
Demultiplexing was performed with Illumina Bcl2fastq2 v 2.19.1.403 program
Fastq reads were checked for overall quality by FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Sequenced reads were trimmed for adaptor sequence then mapped to mm10 using STAR (Dobin, 2013) with parameters --runThreadN 20 --readFilesCommand zcat --runMode alignReads --outFilterMultimapNmax 1 --outSAMtype BAM Unsorted --quantMode GeneCounts --twopassMode Basic
Read counts were obtained using HTSeq (https://htseq.readthedocs.io/en/master/) using the following commands: htseq-count --mode=union --stranded=no --idattr=gene_id -r pos -f sam
Output files were filtered to remove genes with 9 or fewer read counts, Gene counts were normalized using the trimmed mean of M-values normalization (TMM) method (Robinson, 2010) before determining counts per million (cpm) values
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample.
Supplementary_files_format_and_content: BVSC_H18_d5_cpm_FC_FDR.xlsx: Analysis of RNA-seq data from day 5 BVSC-H18 PGC like cells (PGCLCs) derived from either untreated or 100nM Bisphenol A exposed epiblast like cells (EpiLCs). Table shows trimmed mean of M-values (TMM)-normalised counts per million (cpm) of genes indicated. Note, data set pre-filtered to remove genes with a low number of reads (< 10 reads). In addition, columns show log10 fold-change, p-value and Benjamini-Hochberg adjusted p-value (FDR).

source_name: PGCLC_100nM BPA

growth_protocol: BVSC ESCs were grown in 2i + LIF for 2-3 days, before harvesting and culturing in EpiLC Media. After 48 hours of culture, EpiLCs were harvested, counted and cultured in in U-bottom well plates in PGCLC media

extract_protocol:
For EpiLCs, cells were harvested using TrypLETM Select (ThermoFisher Scientific), before counting, pelleting and snap-freezing. For PGCLCs, Blimp1+Stella+ were FACS purified from TrypLETM Select dissociated aggregates.
Strand-specific RNA-seq libraries were prepared with Universal Plus mRNA-Seq kit (Nugen), according to the manufacturer’s protocol

treatment_protocol: For EpiLC exposure, 100nM BPA containing media was added 24 hours after seeding and cells were cultured for 24 hours.

value: in vitro derived PGCLC (d5)

value: Blimp1-mVenus; Stella-ECFP (BVSC)

value: 100nM BPA


title: Breast cancer_7 normal-1

value: Lum-A


title: control-03

value: Visceral white adipose tissue

value: control


title: Brisk TIL mROI 4


title: PGCLC_100nM BPA_Rep2


title: control-01


title: Brisk TIL mROI 5


title: PGCLC_100nM BPA_Rep1


title: Breast cancer_69 cancer [re-analysis]

description: re-analysis of GSM4392891

value: Basal


title: Breast cancer_7 cancer [re-analysis]

description: re-analysis of GSM4392863

value: Lum-B


title: Breast cancer_70 normal


title: Breast cancer_69 normal


title: Brisk TIL mROI 16


title: PGCLC_Untreated_Rep3

value: none (untreated)


title: PGCLC_Untreated_Rep2


title: Invasive margin mROI 1

value: Invasive margin


title: Breast cancer_64 normal

value: Death

value: Normal


title: Brisk TIL mROI 1


title: Breast cancer_65 cancer [re-analysis]

description: re-analysis of GSM4392888

value: Breast


title: EpiLC_100nM BPA_Rep3

description:
16-EpiLC-100nM-Rep3_S15_L001
16-EpiLC-100nM-Rep3_S15_L002
16-EpiLC-100nM-Rep3_S57_L004

source_name: EpiLC_100nM BPA

value: In vitro derived EpiLC


title: Breast cancer_64 cancer [re-analysis]

description: re-analysis of GSM4392886


title: Breast cancer_66 cancer [re-analysis]

description: re-analysis of GSM4392890

value: Alive


title: Brisk TIL mROI 3

value: Brisk TIL


title: Brisk TIL mROI 14


title: Brisk TIL mROI 7


title: Breast cancer_59 cancer [re-analysis]

description: re-analysis of GSM4392883

value: relapse


title: Breast cancer_65 normal

value: non-relapse


title: Brisk TIL mROI 12


title: Brisk TIL mROI 15


title: Brisk TIL mROI 11


title: EpiLC_100nM BPA_Rep2

description:
14-EpiLC-100nM-Rep2_S14_L001
14-EpiLC-100nM-Rep2_S14_L002
14-EpiLC-100nM-Rep2_S56_L004

value: Blimp1-mVenus; Stella-ECFP (BVSC)


title: Breast cancer_59 normal


title: Breast cancer_62 cancer [re-analysis]

description: re-analysis of GSM4392885


title: Breast cancer_58 cancer [re-analysis]

description: re-analysis of GSM4392882


title: PGCLC_Untreated_Rep1

value: in vitro derived PGCLC (d5)


title: RNA-seq 700 mOSM 15min Recovery 2h, Replicate 2

city: Hangzhou

first: Yuanhui

last: Mao

state: Zhejiang

address: 1369 West Wenyi Road

institute: Zhejiang University

data_processing:
The adaptor of all sequencing data was removed by Cutadapt.
For all Ribo-seq and RNA-seq except for Rep2, adaptor was removed by Cutadapt with parameters: -a CTGTAGGCACCATCAAT -m 15
For all Ribo-seq, the adaptor CTGTAGGCACCATCAAT was used. The trimmed reads with length <15 nt were excluded. The first SIX nucleotides (3 random nucleotides + 3-word barcode sequence) and the last FOUR nucleotides were removed (3 random nucleotides). The trimmed reads were aligned to transcriptome using bowtie with parameters: -a --best -m1 --strata -S --sam-nohead. PCR duplicates were removed. PCR duplicates were defined as the reads with exact same random sequences at both sides. More details can be found in PMID: 27450428
For RNA-seq, the adaptor AGATCGGAAGAG was used, and the last 90 nt were removed before adaptor trimming. The trimmed reads were aligned to transcriptome using STAR.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab separated RPKM (Ribo-seq) or FPKM (RNA-seq) value

source_name: Mouse embryonic fibroblasts cells

growth_protocol: MEFs (mouse embryonic fibroblasts) were grown in high glucose Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum, 1X Penicillin-Streptomycin-Glutamine at 37°C and 5% CO2.

extract_protocol:
After the indicated treatments cytoplasmic extracts were prepared and used to construct Ribo-seq and RNA-seq libraries
Three 15-cm plates of MEFs (80% confluency) were treated with the indicated intensity of hyperosmotic stress. Cells were washed three times with ice-cold PBS and scraped in 1 mL lysis buffer (10 mM HEPES pH 7.4, 5 mM MgCl2,100 mM KCl,1% Triton-X,100 μg/mL cycloheximide, 2 mM DTT, RNase inhibitor (NEB, 1:100 dilution), protease inhibitor (Roche, 1 tablet per 10 mL). The lysate was passed four times through a 26-gauge needle and centrifuged at 1300 x g for 10 min. Lysate (OD A260 = 10) was loaded on a linear 10%-50% sucrose gradient (gradient buffer was the same as the lysis buffer, lacking only Triton-X and Protease and RNase inhibitors) and centrifuged at 4°C at 31,000 rpm for 2 h and 20 min using an SW 32Ti rotor. The gradients were fractionated using a Teledyne ISCO fractionation system, and 12 fractions were collected. The fractions from (including) the 80S peak to the bottom of the gradient were combined. 300 μL of the combined fractions was digested with 5 μL RNase I (Ambion, AM2295) for 1 h at 4°C (slow rotation on the nutator). Immediately, Trizol LS (ThermoFisher Scientific, #10296010) was added, and RNA isolated according to the manufacturer’s instructions.
10 μg of total RNA isolated from the combined fractions was resolved by 15% TBE-Urea gel, and visualized with SYBR gold; bands from 28-30 nt were isolated. The RNA was eluted in 400 μL RNA elution buffer (EB) at 4°C overnigt (RNA EB: 0.3M sodium acetate (NaOAc, pH5.5), 1 mM EDTA, 0.4 U/μL murine RNase inhibitor). RNA was precipitated with 4 µL GlycoBlue™ Coprecipitant (ThermoFisher scientific, AM9515), 40 µL sodium acetate, and 1 mL ethanol overnight at -80°C. Recovered footprints were dephosphorylated in a 15 µL reaction mixture (1 µL T4 PNK (NEB, #M0201S), 10X T4 PNK buffer, 0.4 U/μL murine RNase inhibitor) at 37°C for 1 h followed by heat inactivation at 65°C for 10 min. Dephosphorylated RNA was precipitated as described above and recovered in 4 µl of water. Pre-adenylated DNA linker was ligated to the 3’-end of RNA in a 20 µl reaction (25% PEG8000, 1X T4 RNA ligase buffer, 1 mM DTT, 0.4 U/μL murine RNase inhibitor, 300 U T4 RNA ligase truncated KQ (M0373, NEB), 1 µM pre-adenylated DNA linker) for 6 h at 25°C followed by precipitation as described above. Ligated footprints were resolved on 10% TBE-urea PAGE gel, purified, eluted in the RNA EB at 4°C overnight, precipitated at -80°C as described above, and finally resuspended in 10.5 µl water. 1 µl of 2.5 µM RT primers were added and heated at 65°C for 5 min, cooled on ice, and incubated in RT mix (1.5 µL Superscript III, 1X RT buffer, 250 µM dNTPs, DTT) for 30 min at 55°C. RT product was precipitated with ethanol as described above, resuspended in 10 µl water and 2X loading dye, and resolved in 10% TBE urea PAGE gel. cDNA was isolated and eluted overnight in DNA elution buffer (DNA EB: 0.3 M NaCl, 1 mM EDTA), precipitated overnight, recovered, and used for PCR using NebNext Ultra II Q5 mastermix and NEBNext multiplex oligos for Illumina. Half of the cDNA was used to determine the optimal PCR cycle number. The PCR products were resolved on a native 8% TBE gel. The other half of the cDNA was amplified by the determined PCR cycle, resolved on native 8% TBE gel, and PCR products were cut, eluted in DNA EB, precipitated as described above, and recovered in 15 µl water. The quality and quantity of libraries were confirmed using an Advanced Analytical Fragment Analyzer (Agilent). Equal amounts of libraries were mixed and sequenced using NextSeq500 (aiming for 40 million reads per library).

treatment_protocol: MEFs ( about 80% confluency) were treated with the indicated intensity of hyperosmotic stress by addition of sorbitol to the growth media

value: MEFs (mouse embryonic fibroblasts)

tag: stress

value: 700 mOSM 15min Recovery 2h

tag: fraction

value: Cytoplasmic RNA


title: Brisk TIL mROI 2

tag: tissue


title: EpiLC_100nM BPA_Rep1

description:
13-EpiLC-100nM-Rep1_S13_L001
13-EpiLC-100nM-Rep1_S13_L002
13-EpiLC-100nM-Rep1_S55_L004

value: 100nM BPA


title: No Flow, Replicate 2

city: Szeged

first: Ana Raquel

last: Santa-Maria

address: Temesvári krt. 62

department: Biological Barriers Research Group

country: Hungary

institute: Biological Research Centre (BRC)

data_processing:
Illumina bcl2fastq2 v2.20 software used for basecalling and demultiplexing.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
PCR duplicates were cleaned using TrueQuant technology (UMI) and in-house GenXPro GmbH script.
Reads were aligned to the human reference genome (hg38) using the bowtie2 2.3.4.1 mapping tool.
Gene count data was normalized to account for differences in sequencing depth. Testing for differential gene expression was performed in the statistical programming platform R using the DeSeq2 R/Bioconductor package.
Genome_build: Genome Reference Consortium Human Build 38 (hg38)
Supplementary_files_format_and_content: Comma-delimited text file include raw counts for each sample

source_name: Hematopoietic stem cell-derived endothelial cells

growth_protocol: The in vitro BBB model, consisting of human endothelial cells in co-culture with bovine brain pericytes, was described by Cecchelli et al., 2014. Briefly, the hematopoietic stem cells were isolated from human cord blood and differentiated to endothelial cells (Cecchelli et al., 2014). These human endothelial cells (hEC) were seeded in 0.2% gelatin (type A from porcine skin) coated culture dishes and kept in endothelial cell culture medium (ECM, Sciencell, Carlsbad, CA, USA) supplemented with 5 % fetal bovine serum (FBS, heat inactivated), 1 % endothelial cell growth supplement (ECGS, Sciencell), and gentamycin (50 µg/ml). After reaching confluency, usually 2 days after seeding, hECs were gently trypsinized and 80 × 103 cells seeded into the porous polyester membrane of the lab-on-a-chip (LOC) device (Figure 1(b)). The membrane was coated with Matrigel (growth factor reduced BD Matrigel Matrix, BD Biosciences, Franklin Lakes, NJ, USA) at a dilution of 1:48. Bovine brain pericytes (PC) were isolated using the method described previously (Vandenhaute et al. 2011). PCs were cultured in 0.2% gelatin coated dishes in Dulbecco’s modified Eagle’s medium (DMEM, Life Technologies, Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 20% FBS, 1% Glutamax (Life Technologies) and gentamicin (50 µg/ml). Cells were kept in culture until reaching confluency. Then, PCs were trypsinized and 25 × 103 cells were added to the bottom compartment of the LOC device, wich was coated with 0.2% gelatin. The co-culture started when PCs were added (Figure 1(b)). In this in vitro non-contact human BBB co-culture model both compartments received hEC medium. And the LOC device with the cells was kept at 37°C in a humified atmosphere and 5% CO2.

extract_protocol:
After 24-hour static or dynamic condition, hECs were removed from the LOC devices by very fast and gentle trypsinization and RNA was isolated using RNeasy Plus Micro Kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions. Integrated gDNA eliminator spin column allows DNA depletion from RNA samples. RNA integrity (supplemental Figure 2) was checked using automated capillary electrophoresis (RNA Pico Sensitivity Assay, LabChip GX II Touch HT, Perkin Elmer, Waltham, MA, USA). RNA samples were stored at -80 °C until further analysis.
Genome-wide gene expression profiling was performed using massive analysis of cDNA ends (MACE-seq) with RNA extracted from hECs co-cultured with PCs in static and dynamic conditions (3 and 5 biological replicates, respectively). A total of 8 libraries were constructed using the Rapid MACE-Seq kit (GenXPro GmbH, Frankfurt, Germany), according to the manufacturer’s protocol. MACE-seq performs gene expression profiling by sequencing part of the 3’ end of mRNA transcipts. While synthetizing one cDNA molecule from each mRNA transcript, MACE-seq can accurately quantify transcribed polyadenylated transcripts. Briefly, samples with 100 ng of purified RNA were used for library preparation. RNA was fragmented using GenXPro Fragmentation Buffer. Synthesis of cDNA was performed by reverse transcription using barcoded oligo(dT) primers containing TrueQuant unique molecular identifiers, followed by template switching. Library amplification was done using polymerase chain reaction (PCR), purified by solid phase reversible immobilization beads (Agencourt AMPure XP, Beckman Coulter, Brea, CA, USA) and subsequent sequencing was performed using a NextSeq platform (Illumina Inc., San Diego, CA, USA).

treatment_protocol: To determine the importance of fluid flow on the human BBB model, the co-culture of hECs with PCs lasted for 6 days under static condition (supplemental Figure 1) then 24 hours under dynamic condition (Figure 1(c)), and compared with cells which were kept under static condition for 7 days. For the static condition, a 20 ml plastic disposable syringe with Luer cone (B. Braun, Melsungen, Germany) containing cell culture medium was placed in a syringe pump (Legato 110, KD Scientific, Holliston, MA, USA) and connected to the inlets/outlets of the LOC device via female Luer locks (Rotilabo, Carl Roth, Karlsruhe, Germany) using plastic tubes (1 mm inner, 3 mm outer diameter, Carl Roth). For the first six days of the dynamic condition and all the seven days of the static condition the syringe was programmed to change medium above the hEC monolayer every 8 hours at 500 µl/min flow rate. The medium in the lower compartment containing PCs was changed manually daily. Cell growth was monitored by phase contrast microscopy (MotiCam 1080, MoticEurope, Barcelona, Spain), since the transparency of the gold electrodes in the LOC device enables the visualization of the entire cell monolayer. TEER was measured every day. Upon reaching the 6th day, a constant circulation of culture medium was introduced by a peristaltic pump (Masterflex, Cole-Parmer, Vernon Hills, IL, USA) at 1ml/min flow rate for 24 hours for the model in dynamic conditions. Co-cultures in static conditions were kept as shown in supplemental Figure 1. Right after this 24-hour static and dynamic condition we performed integrity studies to determine the barrier properties of the human BBB model, did RNA extraction of hECs, stained the glycocalyx and measured the surface charge of hECs.

tag: culture

value: Static


title: Breast cancer_48 cancer [re-analysis]

description: re-analysis of GSM4392881

tag: Stage


title: RNA-seq 700 mOSM 2h Recovery 2h, Replicate 2

tag: cell type

value: 700 mOSM 2h Recovery 2h


title: RNA-seq 700 mOSM 15min Recovery 15min, Replicate 2

value: 700 mOSM 15min Recovery 15min


title: Breast cancer_45 normal

value: Death

value: Lum-A


title: RNA-seq 700 mOSM 2h Recovery 15min, Replicate 2

value: 700 mOSM 2h Recovery 15min


title: RNA-seq 700 mOSM 15min, Replicate 2

value: 700 mOSM 15min


title: Brisk TIL mROI 13


title: Breast cancer_58 normal

value: Breast

value: Alive

value: Normal


title: RNA-seq 700 mOSM 2h, Replicate 2

value: 700 mOSM 2h


title: Brisk TIL mROI 10

value: Brisk TIL


title: Breast cancer_48 normal

value: non-relapse

value: Lum-B


title: Flow, Replicate 2

value: Dinamic


title: No Flow, Replicate 1


title: RNA-seq 600 mOSM 2h, Replicate 2

value: MEFs (mouse embryonic fibroblasts)

value: 600 mOSM 2h

value: Cytoplasmic RNA


title: RNA-seq 500 mOSM 2h, Replicate 2

value: 500 mOSM 2h


title: RNA-seq 700 mOSM 2h, Replicate 1


title: A549-NLS3A-withDox-rep2

city: Wuerzburg

first: Carsten

middle: P

last: Ade

address: Am Hubland

department: Lehrstuhl Biochemie und Molekularbiologie

country: Germany

institute: University of Wuerzburg

data_processing:
Galaxy was used to analyze RNA-seq data (https://usegalaxy.org).
HISAT2 was used to align RNA-seq reads against hg19 (Kim et al., 2015).
FeatureCounts and limma were used to analyze differential expression (Liao et al., 2014; Law et al., 2014; Liu et al., 2015).
Metascape was used for identification of enriched pathways (Zhou et al., 2019).
Genome_build: hg19
Supplementary_files_format_and_content: A matrix file (txt format) containing Entrez gene ID and raw read counts for all genes of all samples.
Supplementary_files_format_and_content: Two separate differential expression files (tsv format) containing Entrez gene ID, gene symbol, Ensembl gene ID, logFC, average expression, p-value and q-value (FDR) for the comparisons of all genes. The first file shows the change in expression of genes after induction of wildtype-PRC1 expression, the second file shows the change in expression of genes after induction of the mutant-PRC1 allele.

source_name: A549 cells

growth_protocol: Lentiviral pInducer system (Meerbrey et al., 2011) was used to generate stable A549 lung cancer cell lines expressing doxycycline-inducible flag-tagged PRC1. To discriminate between nuclear functions of PRC1, we generated a cell line expressing PRC1 with mutations in the nuclear localization signals (PRC1-NLS3A). 1.25x105 cells were seeded in a 6-cm dish one day before inducing the expression constructs.

extract_protocol:
Total RNA was isolated by using the RNeasy Mini Kit (Qiagen). mRNA was isolated by using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs).
cDNA libraries were generated with 1 µg of purified mRNA by using NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs). The quality, quantity and the size of the cDNA libraries were determined with the Fragment Analyzer (Thermo Fisher Scientific, previously Advanced Analytical Technologies). Libraries were sequenced on a NextSeq500 System (Illumina).

treatment_protocol: Cells were treated with 250 ng/ml of doxycycline for 2 days to induce PRC1 or PRC1-NLS3A. Non-induced cells were used as controls.

value: lung epithelial carcinoma cells

tag: expression construct

value: induced


title: A549-NLS3A-withDox-rep3


title: No Flow, Replicate 3

value: Static


title: Breast cancer_28 camcer [re-analysis]

description: re-analysis of GSM4392878

tag: age

value: Lum-A


title: Breast cancer_22 normal


title: A549-NLS3A-withDox-rep1


title: Flow, Replicate 5


title: Breast cancer_45 cancer [re-analysis]

description: re-analysis of GSM4392879

value: Death

value: relapse


title: Breast cancer_28 normal

value: Breast

value: Alive


title: A549-NLS3A-noDox-rep3

value: non-induced


title: RNA-seq 700 mOSM 2h Recovery 2h, Replicate 1

value: 700 mOSM 2h Recovery 2h


title: Breast cancer_151T [re-analysis]

description: re-analysis of GSM4392919

value: non-relapse


title: Flow, Replicate 3


title: RNA-seq Normal Condition, Replicate 2

value: Normal Condition


title: RNA-seq 700 mOSM 2h Recovery 15min, Replicate 1

value: 700 mOSM 2h Recovery 15min


title: Flow, Replicate 4

value: Dinamic


title: Breast cancer_23 normal

value: Normal


title: RNA-seq 700 mOSM 15min Recovery 2h, Replicate 1

value: MEFs (mouse embryonic fibroblasts)

value: 700 mOSM 15min Recovery 2h

value: Cytoplasmic RNA


title: Flow, Replicate 1


title: Breast cancer_23 cancer [re-analysis]

description: re-analysis of GSM4392876


title: Breast cancer_15 normal


title: Breast cancer_15 cancer [re-analysis]

description: re-analysis of GSM4392873


title: Breast cancer_22 cancer [re-analysis]

description: re-analysis of GSM4392875

value: Basal


title: RNA-seq 700 mOSM 15min Recovery 15min, Replicate 1

value: 700 mOSM 15min Recovery 15min


title: RNA-seq 600 mOSM 2h, Replicate 1

value: 600 mOSM 2h


title: RNA-seq 500 mOSM 2h, Replicate 1

value: 500 mOSM 2h


title: Ribo-seq 700 mOSM 2h Recovery 2h, Replicate 2

data_processing:
Library strategy: Ribo-seq
The adaptor of all sequencing data was removed by Cutadapt.
For all Ribo-seq and RNA-seq except for Rep2, adaptor was removed by Cutadapt with parameters: -a CTGTAGGCACCATCAAT -m 15
For all Ribo-seq, the adaptor CTGTAGGCACCATCAAT was used. The trimmed reads with length <15 nt were excluded. The first SIX nucleotides (3 random nucleotides + 3-word barcode sequence) and the last FOUR nucleotides were removed (3 random nucleotides). The trimmed reads were aligned to transcriptome using bowtie with parameters: -a --best -m1 --strata -S --sam-nohead. PCR duplicates were removed. PCR duplicates were defined as the reads with exact same random sequences at both sides. More details can be found in PMID: 27450428
For RNA-seq, the adaptor AGATCGGAAGAG was used, and the last 90 nt were removed before adaptor trimming. The trimmed reads were aligned to transcriptome using STAR.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab separated RPKM (Ribo-seq) or FPKM (RNA-seq) value

value: Ribosome associated RNA


title: A549-NLS3A-noDox-rep1

value: lung epithelial carcinoma cells


title: A549-wt-withDox-rep2

value: wildtype

value: induced


title: RNA-seq Normal Condition, Replicate 1


title: A549-wt-withDox-rep3


title: A549-wt-withDox-rep1


title: Breast cancer_154T [re-analysis]

description: re-analysis of GSM4392922

value: Breast

value: Alive

value: Lum-B

value: Lum-A


title: Ribo-seq 700 mOSM 2h Recovery 15min, Replicate 2

value: 700 mOSM 2h Recovery 15min


title: Breast cancer_142T [re-analysis]

description: re-analysis of GSM4392917

value: non-relapse

value: Normal


title: A549-wt-noDox-rep3

value: non-induced


title: Ribo-seq 700 mOSM 2h, Replicate 2

value: MEFs (mouse embryonic fibroblasts)

value: 700 mOSM 2h


title: Ribo-seq 700 mOSM 15min Recovery 2h, Replicate 2

value: 700 mOSM 15min Recovery 2h


title: Ribo-seq 700 mOSM 15min Recovery 15min, Replicate 2

value: 700 mOSM 15min Recovery 15min


title: Ribo-seq 700 mOSM 15min, Replicate 2

value: 700 mOSM 15min


title: Breast cancer_140T [re-analysis]

description: re-analysis of GSM4392916

value: Basal


title: Breast cancer_153T [re-analysis]

description: re-analysis of GSM4392920


title: RNA-seq 700 mOSM 15min, Replicate 1

value: Cytoplasmic RNA


title: A549-wt-noDox-rep1

value: lung epithelial carcinoma cells

value: wildtype


title: A549-NLS3A-noDox-rep2


title: Breast cancer_136T [re-analysis]

description: re-analysis of GSM4392914

value: Breast


title: Breast cancer_14 cancer [re-analysis]

description: re-analysis of GSM4392872

value: Alive

value: relapse


title: Breast cancer_135N

value: Death

value: Lum-A


title: A549-wt-noDox-rep2


title: Ribo-seq 500 mOSM 2h, Replicate 2

value: 500 mOSM 2h

value: Ribosome associated RNA


title: Breast cancer_134T [re-analysis]

description: re-analysis of GSM4392911

value: non-relapse

value: Normal


title: Ribo-seq 600 mOSM 2h, Replicate 2

value: MEFs (mouse embryonic fibroblasts)

value: 600 mOSM 2h


title: Ribo-seq Normal Condition, Replicate 2

value: Normal Condition


title: Breast cancer_14 normal


title: Breast cancer_133T [re-analysis]

description: re-analysis of GSM4392910


title: Breast cancer_135T [re-analysis]

description: re-analysis of GSM4392913

value: Lum-B


title: E14.5 neocortex p300

city: Stanford

first: Gill

last: Bejerano

state: California

address: 279 Campus Drive West (MC 5329)

department: Developmental Biology

institute: Stanford University

library_source: genomic

data_processing:
ChIP-seq reads were mapped to the mouse genome (UCSC mm9 assembly, NCBI MGSCv37) using ELAND, retaining only reads that map uniquely with 2 or fewer mismatches
Peaks were called using MACS v1.4 with the p300 ChIP-seq reads as the treatment file, input DNA reads as the control file, and the parameters “--nomodel, --shiftsize = 100, -g mm”
Peaks overlapped by an exon, within 2.5 kb of a transcription start site, or suspected in non-unique read mapping were removed. Exon and transcription start site annotation was obtained from the UCSC knownGene track (build 5)
Reads were converted from ELANDEXPORT to FASTQ with the fq_all2std.pl script from maq v0.6.6 with the "export2std" option for uploading
Genome_build: mm9
Supplementary_files_format_and_content: peak text files

molecule: genomic DNA

source_name: E14.5 neocortex

growth_protocol: Embryos were harvested from timed pregnant embryonic day 14.5 (E14.5) Swiss Webster mice (Charles River). The dermis, skull mesenchyme, and bone primordia were removed and cortical caps were dissected with curved forceps and placed in PNGM (Lonza). The medial structures, cortical hem/hippocampus and choroid plexus were cut off in a secondary excision. Dissected dorsal cerebral wall tissue (0.15 g) was snap frozen in liquid nitrogen

extract_protocol:
Chromatin was isolated, sheared and immunoprecipitation was performed using 30 micrograms of chromatin and 4 micrograms of anti-p300 antibody, C-20 (Santa Cruz SC-585; Genpathway)
Library construction and sequencing was done using the Illumina GA II format (Illumina)

treatment_protocol: Tissue was fixed in 1% formaldehyde for 15 minutes

value: Neocortex

value: Swiss Webster (Charles River)

tag: chip antibody


title: Ribo-seq 700 mOSM 2h Recovery 15min, Replicate 1

value: 700 mOSM 2h Recovery 15min


title: Notch1-/- ES cells, d6, rep2

city: Lausanne

first: Frederic

last: Burdet

address: Quartier Sorge - Batiment Amphipole

country: Switzerland

institute: Swiss Institute of Bioinformatics

data_processing:
Base calling was with Illumina GAP Pipeline Software v1.90
Sequences were aligned to mm9 reference genome using Tophat 2.0.8 with option -g with mm9 reference GTF
Novel transcripts were predicted with Cufflinks 2.1.1
Novel transcripts predictions were merged with mm9 reference genome using Cuffmerge 2.1.1 with option -G with mm9 reference GTF
Counts were generated using htseq-count v0.5.4p3
Genome_build: mm9
Supplementary_files_format_and_content: Raw count data for genes were normalized to the relative size of each library using R/Bioconductor package DESeq, estimateSizeFactors function. Count data are provided in tab-delimited format
Supplementary_files_format_and_content: counts_genes_FPKM.: Normalized counts
Supplementary_files_format_and_content: htseq-count_summary: Raw counts

source_name: Notch1-/- ES cells, d6

growth_protocol: WT and Notch1-deleted mouse embryonic stem cells were were cultured on mouse embryonic fibroblasts feeders or on gelatinized plates in standard ES cell medium supplemented with 1000U/ml of LIF

extract_protocol:
Total RNA was isolated using Trizol (Invitrogen). RNA quantification and quality control were performed using a NanoDrop ND-1000 and Agilent 2100 Bioanalyzer, respectively
Sequencing libraries were prepared according to Illumina long RNA Seq library kit instructions with Poly(A) selection. Libraries were sequenced with the Illumina HiSeq2000 (2x100bp).

treatment_protocol: Cardiac differentiation of ES cells was induced by aggregating aliquots containing 1000 cells in hanging drops to form embryoid bodies. Differntiating cells were harvest 6 days following induction of differentiation.

tag: genotype


title: Ribo-seq 700 mOSM 2h Recovery 2h, Replicate 1

value: 700 mOSM 2h Recovery 2h


title: Notch1-/- ES cells, d0, rep2

source_name: Notch1-/- ES cells, d0


title: Notch1-/- ES cells, d6, rep3


title: E14.5 neocortex input

value: none (input)


title: Notch1-/- ES cells, d0, rep3


title: Notch1-/- ES cells, d0, rep1


title: Ribo-seq 700 mOSM 15min, Replicate 1

value: 700 mOSM 15min


title: Notch1-/- ES cells, d6, rep1


title: Ribo-seq 700 mOSM 15min Recovery 2h, Replicate 1

value: 700 mOSM 15min Recovery 2h


title: Ribo-seq 700 mOSM 2h, Replicate 1

value: 700 mOSM 2h


title: Breast cancer_13 cancer [re-analysis]

description: re-analysis of GSM4392870

source_name: Breast cancer tumor tissue

value: Breast

tag: ihc

value: Death

value: relapse

value: Basal


title: Ribo-seq 600 mOSM 2h, Replicate 1

value: Ribosome associated RNA


title: WT ES cells, d6, rep1

description:
Ebs2
TODO

source_name: WT ES cells, d6

value: WT


title: Breast cancer_120T [re-analysis]

description: re-analysis of GSM4392906

tag: grade

value: non-relapse


title: CD5TUMOR2

city: New York

first: Omar

last: Abdel-Wahab

state: NY

address: 1275 York Ave

department: HOPP

institute: MSKCC

data_processing:
Gene expression analysis was performed using the gene expression estimates computed by RSEM in units of transcripts per million (TPM). Those estimates were then further normalized using the TMM method (8), with a reference set of all protein-coding genes. Differentially expressed genes were defined as those with an associated Bayes factor ≥ 100 (computed using Wagenmakers’s Bayesian framework (9)) and an associated fold-change ≥ 1.5.
Supplementary_files_format_and_content: featureCounts RNA-seq quantification CD19 mice: CD19_annotated_combined.counts
Supplementary_files_format_and_content: featureCounts RNA-seq quantification MYC mice: MYC_annotated_combined.counts
Supplementary_files_format_and_content: featureCounts RNA-seq quantification BCL2 mice: BCL2_annotated_combined.counts
Genome_build: mm10

source_name: bone marrow

growth_protocol: Xpo1E571K/WT mice on a pure C57BL/6 background were crossed to B lineage CD19-cre mice (1), tamoxifen-inducible CAG-CreERT mice (2), and/or E-Myc (3) transgenic mice, each of which were also maintained on a pure C57BL/6 background. Eight-week-old female CD45.1 C57BL/6J mice (The Jackson Laboratory) were used as recipients for bone marrow transplantation assays and eight-week-old female NSG mice (The Jackson Laboratory) were used for cell line xenografting. Blood was collected by submandibular bleeding using heparinized microhematocrit capillary tubes (Thermo Fisher Scientific). For assessment of germinal center formation, age- and sex-matched C57BL/6J mice were immunized intraperitoneally at 8 to 12 weeks of age with 0.5 ml of a 2% sheep red blood cell (SRBC) suspension in PBS (Cocalico Biologicals) or PBS as control. Automated peripheral blood counts were obtained using a ProCyte Dx Hematology Analyzer (IDEXX). Primary patient samples Studies were approved by the Institutional Review Board of Memorial Sloan Kettering Cancer Center and conducted in accordance to the Declaration of Helsinki protocol. Patients provided samples after their informed consent and primary human de-identified CLL samples derived from whole peripheral blood or BM mononuclear cells were utilized.

extract_protocol:
RNA was extracted from sorted mouse cell populations using Qiagen RNeasy columns.
Poly(A)-selected, unstranded Illumina libraries were prepared with a modified TruSeq protocol. 0.5X AMPure XP beads were added to the sample library to select for fragments <400 bp, followed by 1X beads to select for fragments >100 bp. These fragments were then amplified with PCR (15 cycles) and separated by gel electrophoresis (2% agarose). 300 bp DNA fragments were isolated and sequenced on the Illumina HiSeq 2000 (100M 101 bp reads per sample)

treatment_protocol: Cells were incubated with antibodies in PBS/2% BSA (without Ca2+ and Mg2+) for 30 minutes on ice. For hematopoietic stem and progenitor cell analysis from adult mouse bone marrow, cells were stained with a lineage cocktail of monoclonal antibodies including B220 (RA3-6B2), CD19 (1D3), CD3 (17A2), CD4 (GK1.5), CD8a (53-6.7), CD11b (M1/70), Gr-1 (RB6-8C5), NK1.1 (PK136) and Ter119, allowing for mature lineage exclusion from the analysis. The composition of mature hematopoietic cell lineages in the bone marrow, spleen, thymus and peripheral blood was assessed using a combination of antibodies against B220, CD19, CD3, CD4, CD8a, CD11b, CD25 (PC61.5), CD44 (IM7), Gr-1, IgM (Il/41), CD43 (S11). All FACS sorting was performed on FACS Aria, and analysis was performed on an LSR Fortessa (BD Biosciences). Data analysis was performed using the FlowJo software.

tag: genotype/variation

value: CD19 XPO1 CD5tumor


title: WT ES cells, d6, rep2

description:
Ebs4
TODO


title: Breast cancer_12 normal

tag: alive

value: Alive

tag: relapse status

value: Normal

value: Lum-A


title: WT ES cells, d0, rep2

description:
3LL2
TODO

source_name: WT ES cells, d0


title: MYCXPO3

value: MYC XPO1 Mutant


title: WT ES cells, d0, rep1

description:
1LL2
TODO


title: Breast cancer_128T [re-analysis]

description: re-analysis of GSM4392907

tag: overall survival (years)

tag: relapse free survival (years)

value: Lum-B


title: Ribo-seq 700 mOSM 15min Recovery 15min, Replicate 1

tag: strain

value: MEFs (mouse embryonic fibroblasts)

tag: stress

value: 700 mOSM 15min Recovery 15min


title: Breast cancer_112T [re-analysis]

description: re-analysis of GSM4392904

tag: tissue


title: WT ES cells, d0, rep3

description:
4LL2
TODO


title: MYCXPO2


title: Breast cancer_10 normal


title: Breast cancer_129T [re-analysis]

description: re-analysis of GSM4392909


title: Ribo-seq Normal Condition, Replicate 1

value: Normal Condition

tag: fraction


title: MYCWT3

value: MYC XPO1 wildtype


title: Ribo-seq 500 mOSM 2h, Replicate 1

value: 500 mOSM 2h


title: WT ES cells, d6, rep3

description:
Ebs5
TODO


title: MYCXPO1


title: Breast cancer_111T [re-analysis]

description: re-analysis of GSM4392903

value: Breast

tag: Stage


title: PCLS_Media_UV-RV1B_72h_donor8_rep2

city: Stevenage

first: Ken

middle: A

last: Saunders

state: Hertfordshire

address: Gunnels Wood Road

country: United Kingdom

institute: GSK

description: Gene expression data precision cut lung slice

hyb_protocol: Labelled cDNA was hybridized onto human HG‐U133_Plus_2.0 microarrays (Affymetrix).

scan_protocol: Standard Affymentrix protocols

data_processing: Data was GCRMA normalized and quality control checked in Omicsoft Array Studio

label: Biotin

source_name: Precision cut lung slices treated with Media and UV-RV1B, for 72hr

label_protocol: FL-Ovation cDNA Biotin Module V2 kit (NuGen).

growth_protocol: Human lung lobes were obtained from male and female patients undergoing surgery. The average age of patients was 63 ± 8 years. Precision cut lung slices of approximately 300um each containing only small airways were obtained and cultured in DMEM

extract_protocol: PCLS were flash frozen after collection and total RNA was isolated from frozen samples

treatment_protocol: PCLS in 500 µl DMEM per well were infected with 1 x 10^6/ mL RV1b by inoculation for 2 h at 33 °C. As controls, PCLS were treated with UV-inactivated virus of the same batch or medium only. Supernatant was subsequently replaced by fresh medium and samples were post-incubated with infection medium until 1 day or 3 days post infection, in the presence or absence of 100nM rupintrivir or pleconaril.

tag: treatment

value: Media

tag: challenge

tag: replicate

tag: time

tag: individual

value: donor_ID 8

tag: date

value: Precision cut lung slices


title: PCLS_Media_Control_72h_donor8_rep1

source_name: Precision cut lung slices treated with Media only, for 72hr

value: Control


title: Breast cancer_13 normal

tag: age

tag: ihc

tag: grade

value: Death

value: relapse


title: MI_1

city: Cold Spring Harbor

first: Carlos

last: Martí-Gómez

email: carlos199m1@gmail.com, martigo@cshl.edu

state: New York

address: 1 Bungtown Rd

department: Quantitative Biology

institute: Cold Spring Harbor Laboratory

data_processing:
Read alignment: vast-tools v0.2.0
Gene expression quantification: vast-tools v0.2.0
AS events quantification: vast-tools v0.2.0
Genome_build: mm9
Supplementary_files_format_and_content: [raw_counts.csv]  Comma separated file containing raw counts for each sample. Genes are stored in rows and samples in columns
Supplementary_files_format_and_content: [AS_events.tsv]  File resulting from vast-tools combine. Includes AS event information and reads and PSI estimation for each sample

source_name: Remote area

extract_protocol:
Total RNA was purified from heart tissue using RNAesay (Qiagen)
A cDNA library was prepared according to Illumina recommendations and sequenced in a GAII analyzer using the single-end 50bp protocol

value: heart

tag: group

value: Infarcted


title: WT_2

value: Uninjured


title: CD19XPO3

tag: genotype/variation

value: CD19 XPO1 Mutant


title: Breast cancer_10 cancer [re-analysis]

description: re-analysis of GSM4392868

extract_protocol: Total RNA was extracted from frozen specimens using TRIzol® reagent (Invitrogen, Carlsbad, CA). RNA was purified using RNeasy® mini kits (Qiagen, Valencia, CA) and RNA integration was checked by gel electrophoresis.

tag: alive

value: Alive

tag: relapse status

value: non-relapse

tag: overall survival (years)

tag: relapse free survival (years)

value: Lum-A


title: MI_2

tag: strain

tag: tissue


title: WT_1


title: PCLS_Media_UV-RV1B_72h_donor8_rep1

tag: treatment


title: MYCWT2


title: Subject J, Pre-exercise, Ninth/Last session J_T9_1

city: Stockholm

first: Eric

last: Rullman

address: C1:82 Karolinska University Hospital, Huddinge

department: Laboratory Medicine

institute: Karolinska Institutet

data_processing:
The expression levels of each sample were normalized as Transcripts Per Kilobase Per Million (TPKM) by dividing the read count of each transcript model with its length and scaling the total per sample to one million using Kalisto V0.4.4. Quality control of raw and mapped reads was done using FastQC version 0.11.8.
Genome_build: Homo_sapiens.GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample
Supplementary_files_format_and_content: Matrix table with logCPM for every gene and every sample

source_name: Human skeletal muscle, Vastus lateralis

extract_protocol:
RNA was isolated from cleaned muscle specimens using Trizol and subsequent cleaning using RNAeasy columns. Libraries were prepared using standard Illumina TrueSeq prep-kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Vastus lateralis

tag: Sex

value: Male

tag: subject

value: J

value: Ninth/Last session

tag: exercise

value: Pre


title: MYCWT1

value: MYC XPO1 wildtype


title: PCLS_Pleconaril_RV1B_72h_donor8_rep1

source_name: Precision cut lung slices treated with Pleconaril and RV1B, for 72hr

value: Pleconaril

tag: challenge

tag: replicate

tag: time

tag: individual

value: donor_ID 8

value: Precision cut lung slices


title: PCLS_Rupintrivir_RV1B_72h_donor8_rep2

source_name: Precision cut lung slices treated with Rupintrivir and RV1B, for 72hr

value: Rupintrivir

tag: date


title: Subject K, Post-exercise, First session K_T1_2

description: Subject K, Post-exercise, First session

value: K

value: First session

value: Post


title: CD19WT2

value: CD19 XPO1 wildtype


title: PCLS_Media_Control_72h_donor8_rep2

value: Media

value: Control


title: Subject I, Pre-exercise, Ninth/Last session I_T9_1

value: I


title: CD19WT1


title: PCLS_Rupintrivir_RV1B_72h_donor8_rep1


title: PCLS_Pleconaril_RV1B_72h_donor8_rep2


title: Breast cancer_12 cancer [re-analysis]

description: re-analysis of GSM4392869

data_processing: Scanned images processed by GeneChip® Operating Software and Affymetrix’s Microarray Suite software to generate detection p values. The Robust Multichip Average (RMA) algorithm, which consisted three steps of background adjustment, quantile normalization, and final summarization, was applied for perfect match probe signals within the study.

value: Breast

tag: age

tag: Stage

tag: ihc

tag: grade

value: Alive

value: non-relapse

value: Normal

value: Lum-A


title: Subject J, Pre-exercise, First session J_T1_1

description: Subject J, Pre-exercise, First session

value: Vastus lateralis

value: Male

value: J

value: Pre


title: BCL2XPO2

tag: genotype/variation

value: BCL2 XPO1 Mutant


title: Subject K, Post-exercise, Ninth/Last session K_T9_2

value: K

value: Ninth/Last session


title: Subject J, Post-exercise, First session J_T1_2

description: Subject J, Post-exercise, First session

value: First session

value: Post


title: CD19XPO1

value: CD19 XPO1 Mutant


title: Subject K, Pre-exercise, Ninth/Last session K_T9_1


title: PCLS_Media_UV-RV1B_24h_donor8_rep1

source_name: Precision cut lung slices treated with Media and UV-RV1B, for 24hr

value: Media

value: donor_ID 8

value: Precision cut lung slices


title: PCLS_Media_Control_24h_donor8_rep1

source_name: Precision cut lung slices treated with Media only, for 24hr

value: Control


title: PCLS_Media_RV1B_72h_donor8_rep2

source_name: Precision cut lung slices treated with Media and RV1B, for 72hr


title: PCLS_Media_RV1B_72h_donor8_rep1


title: PCLS_Rupintrivir_RV1B_24h_donor8_rep2

source_name: Precision cut lung slices treated with Rupintrivir and RV1B, for 24hr

value: Rupintrivir


title: BCL2WT3

value: BCL2 XPO1 wildtype


title: Subject I, Post-exercise, Ninth/Last session I_T9_2

value: I


title: BCL2XPO1


title: BCL2WT2


title: PCLS_Rupintrivir_RV1B_24h_donor8_rep1


title: PCLS_Media_UV-RV1B_24h_donor8_rep2


title: BCL2XPO3


title: Subject H, Pre-exercise, Ninth/Last session H_T9_1

value: Vastus lateralis

value: H


title: Subject I, Pre-exercise, First session I_T1_1

description: Subject I, Pre-exercise, First session

value: Male


title: Subject H, Pre-exercise, First session H_T1_1

description: Subject H, Pre-exercise, First session

value: Pre


title: Subject H, Post-exercise, First session H_T1_2

description: Subject H, Post-exercise, First session


title: PCLS_Pleconaril_RV1B_24h_donor8_rep1

source_name: Precision cut lung slices treated with Pleconaril and RV1B, for 24hr

value: Pleconaril


title: Subject H, Post-exercise, Ninth/Last session H_T9_2


title: PCLS_Media_RV1B_24h_donor8_rep1

source_name: Precision cut lung slices treated with Media and RV1B, for 24hr


title: WT3_Pre_B

description:
WT3_Pre_B
murine_annotated_combined.counts

data_processing:
Gene expression analysis was performed using the gene expression estimates computed by RSEM in units of transcripts per million (TPM). Those estimates were then further normalized using the TMM method (8), with a reference set of all protein-coding genes. Differentially expressed genes were defined as those with an associated Bayes factor ≥ 100 (computed using Wagenmakers’s Bayesian framework (9)) and an associated fold-change ≥ 1.5.
Genome_build: GRCh37

source_name: XPO1 wild type Pre_B cell

growth_protocol: Xpo1E571K/WT mice on a pure C57BL/6 background were crossed to B lineage CD19-cre mice (1), tamoxifen-inducible CAG-CreERT mice (2), and/or E-Myc (3) transgenic mice, each of which were also maintained on a pure C57BL/6 background.   Eight-week-old female CD45.1 C57BL/6J mice (The Jackson Laboratory) were used as recipients for bone marrow transplantation assays and eight-week-old female NSG mice (The Jackson Laboratory) were used for cell line xenografting. Blood was collected by submandibular bleeding using heparinized microhematocrit capillary tubes (Thermo Fisher Scientific). For assessment of germinal center formation, age- and sex-matched C57BL/6J mice were immunized intraperitoneally at 8 to 12 weeks of age with 0.5 ml of a 2% sheep red blood cell (SRBC) suspension in PBS (Cocalico Biologicals) or PBS as control. Automated peripheral blood counts were obtained using a ProCyte Dx Hematology Analyzer (IDEXX). Primary patient samples  Studies were approved by the Institutional Review Board of Memorial Sloan Kettering Cancer Center and conducted in accordance to the Declaration of Helsinki protocol. Patients provided samples after their informed consent and primary human de-identified CLL samples derived from whole peripheral blood or BM mononuclear cells were utilized.

tag: cell type

value: Pre B cell

value: bone marrow

value: XPO1 wild type


title: Subject G, Post-exercise, Ninth/Last session G_T9_2

value: G

value: Ninth/Last session

value: Post


title: Subject I, Post-exercise, First session I_T1_2

description: Subject I, Post-exercise, First session

value: First session


title: WT3_mature_B

description:
WT3_mature_B
murine_annotated_combined.counts

source_name: XPO1 wild type mature _B cell

value: mature  B cell


title: PCLS_Media_RV1B_24h_donor8_rep2

value: Media

value: donor_ID 8

value: Precision cut lung slices


title: WT_Immature_B

description:
WT_Immature_B
murine_annotated_combined.counts

source_name: XPO1 wild type Immature _B cell

value: Immature  B cell


title: BCL2WT1

source_name: bone marrow

value: BCL2 XPO1 wildtype


title: Subject G, Pre-exercise, First session G_T1_1

description: Subject G, Pre-exercise, First session

value: Vastus lateralis


title: PCLS_Media_UV-RV1B_24h_donor7_rep2

value: donor_ID 7


title: PCLS_Media_Control_24h_donor8_rep2

value: Control


title: Subject F, Pre-exercise, Ninth/Last session F_T9_1

value: Male

value: F

value: Pre


title: WT2_Pro_B

description:
WT2_Pro_B
murine_annotated_combined.counts

source_name: XPO1 wild type Prp_B cell

value: Prp B cell

value: bone marrow

value: XPO1 wild type


title: Subject G, Post-exercise, First session G_T1_2

description: Subject G, Post-exercise, First session

value: G

value: Post


title: PCLS_Media_Control_24h_donor7_rep2


title: WT3_Pro_B

description:
WT3_Pro_B
murine_annotated_combined.counts

source_name: XPO1 wild type Pro_B cell

value: Pro B cell


title: WT1_Pro_B

description:
WT1_Pro_B
murine_annotated_combined.counts


title: Subject F, Post-exercise, Ninth/Last session F_T9_2

value: Ninth/Last session


title: WT1_Pre_B

description:
WT1_Pre_B
murine_annotated_combined.counts

value: Pre B cell


title: PCLS_Pleconaril_RV1B_24h_donor8_rep2

value: Pleconaril

value: donor_ID 8

value: Precision cut lung slices


title: PCLS_Rupintrivir_RV1B_24h_donor7_rep2

value: Rupintrivir


title: Subject E, Pre-exercise, Ninth/Last session E_T9_1

value: Vastus lateralis

value: E


title: E571K_Immature_B

description:
E571K_Immature_B
murine_annotated_combined.counts

source_name: XPO1-E571K mutant immature_B cell

value: immature B cell

value: XPO1-E571K mutant


title: E571K3_Pro_B

description:
E571K3_Pro_B
murine_annotated_combined.counts

source_name: XPO1-E571K mutant Pro_B cell


title: PCLS_Media_Control_24h_donor7_rep1

value: Media

value: Control

value: donor_ID 7


title: PCLS_Media_UV-RV1B_24h_donor7_rep1


title: E571K3_Pre_B

description:
E571K3_Pre_B
murine_annotated_combined.counts

source_name: XPO1-E571K mutant Pre_B cell

value: bone marrow


title: E571K3_mature_B

description:
E571K3_mature_B
murine_annotated_combined.counts

source_name: XPO1-E571K mutant mature_B cell

value: mature B cell


title: Subject F, Pre-exercise, First session F_T1_1

description: Subject F, Pre-exercise, First session

source_name: Human skeletal muscle, Vastus lateralis

value: Male

value: F

value: First session

value: Pre


title: WT2_Pre_B

description:
WT2_Pre_B
murine_annotated_combined.counts

value: Pre B cell

value: XPO1 wild type


title: Subject E, Post-exercise, First session E_T1_2

description: Subject E, Post-exercise, First session

value: Post


title: Subject F, Post-exercise, First session F_T1_2

description: Subject F, Post-exercise, First session


title: WT2_mature_B

description:
WT2_mature_B
murine_annotated_combined.counts

value: mature  B cell


title: PCLS_Rupintrivir_RV1B_24h_donor7_rep1

value: Rupintrivir

value: Precision cut lung slices


title: PCLS_Media_RV1B_24h_donor7_rep1


title: PCLS_Media_UV-RV1B_72h_donor6_rep2

source_name: Precision cut lung slices treated with Media and UV-RV1B, for 72hr

value: donor_ID 6


title: Subject E, Pre-exercise, First session E_T1_1

description: Subject E, Pre-exercise, First session

value: Vastus lateralis

value: E


title: Subject D, Post-exercise, Ninth/Last session D_T9_2

value: D

value: Ninth/Last session


title: E571K2_Pro_B

description:
E571K2_Pro_B
murine_annotated_combined.counts

value: Pro B cell

value: bone marrow

value: XPO1-E571K mutant


title: CD19XPO2

value: CD19 XPO1 Mutant


title: Subject D, Pre-exercise, Ninth/Last session D_T9_1

value: Male


title: E571K2_Pre_B

description:
E571K2_Pre_B
murine_annotated_combined.counts


title: WT1_mature_B

description:
WT1_mature_B
murine_annotated_combined.counts


title: PCLS_Pleconaril_RV1B_24h_donor7_rep2

description: Gene expression data precision cut lung slice

value: Pleconaril

value: donor_ID 7


title: PCLS_Media_Control_72h_donor6_rep1

source_name: Precision cut lung slices treated with Media only, for 72hr

value: Media

value: Control


title: Subject D, Pre-exercise, First session D_T1_1

description: Subject D, Pre-exercise, First session

value: First session

value: Pre


title: PCLS_Pleconaril_RV1B_24h_donor7_rep1

value: Precision cut lung slices


title: PCLS_Media_RV1B_24h_donor7_rep2


title: PCLS_Rupintrivir_RV1B_72h_donor6_rep2

source_name: Precision cut lung slices treated with Rupintrivir and RV1B, for 72hr

value: Rupintrivir

value: donor_ID 6


title: Subject E, Post-exercise, Ninth/Last session E_T9_2

value: Vastus lateralis

value: E

value: Post


title: Subject C, Post-exercise, First session C_T1_2

description: Subject C, Post-exercise, First session

value: C


title: Subject B, Pre-exercise, Ninth/Last session B_T9_1

value: B

value: Ninth/Last session


title: PCLS_Pleconaril_RV1B_72h_donor6_rep2

source_name: Precision cut lung slices treated with Pleconaril and RV1B, for 72hr