title: r_017_pre

tag: timepoint

value: Pre

tag: pathotype

value: Lymphoid

tag: biologic

value: Certolizumab

tag: status

value: Responder

tag: bx rna conc. (ng/ul)

tag: bx rna volume (ul)

tag: bx rna yield (ng)

tag: rin

tag: ethnicity

value: Caucasian

tag: age

tag: gender

value: M

tag: smoking status (prev)

value: Yes

tag: smoking status (curr)

value: RA

tag: duration of disease (yrs)

tag: steroids (medication)

value: No

tag: location of joint biopsy

value: Wrist

tag: aggregational histological score

value: Grade 3

tag: inflammatory score

tag: swollen joint count (28)

tag: tender joint count (28)

tag: das28 score

tag: delta das28

tag: patient global assessment of pain (vas)

tag: patient global assessment of disease activity (vas)

tag: physician global assessment of disease activity (vas)

tag: haq-di score

tag: rf

tag: acpa (ccp)

tag: radiographic erosion


title: 5E 02032017

status: Public on Jun 06 2022

type: SRA

city: Boston

first: Ionita

middle: Calin

last: Ghiran

state: MA

address: 3 Blackfan Circle

department: Medicine

country: USA

institute: Beth Israel Deaconess Medical Center

library_source: transcriptomic

data_processing:
All FASTQ files were processed uniformly through the extra-cellular RNA processing toolkit (exceRpt), with an adapter sequence of [] and random barcode length [] (on []). Information about exceRpt is available at https://github.gersteinlab.org/exceRpt/.
Assembly: hg19
Supplementary files format and content: Each processed data file is a core results archive generated by exceRpt. The core results archive contains read counts for alignments to the different transcriptome libraries used by exceRpt (miRNA / piRNA / tRNA / GENCODE annotations / circRNA), taxonomy trees for exogenous rRNA and genomic reads aligned by exceRpt, and a variety of other files generated by exceRpt.

molecule: total RNA

organism: Homo sapiens

source_name: Plasma

extract_protocol:
RNA Isolation method was . RNA Isolation kit was miRcury biofluids (Exiqon).
Library construction kit was NEBNext small RNA library prep (NEB). Samples were not multiplexed. Type of Starting Material was total RNA.

tag: diagnosis

value: Healthy Subject

tag: anatomical location

value: Entire cardiovascular system

tag: tissue

value: Plasma

tag: rna source

value: total cell-free biofluid RNA

tag: rna isolation kit

value: miRcury biofluids (Exiqon)

tag: anticoagulant

value: EDTA


title: r_016_post

city: Worcester

first: Jing

last: Wang

address: 100 Research Drive

institute: AbbVie

data_processing:
RNA-seq reads were aligned to the Ensembl release 76 top-level assembly with STAR version 2.0.4b.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5.
Assembly: GRCh38.85
Supplementary files format and content: Raw count

source_name: Synovial Tissue

extract_protocol: Total RNA was extracted from synovial tissue using Trizol and Chloroform (ThermoFisher Scientific, Invitrogen Division, UK)

treatment_protocol: anti-TNF treatment (19 etanercept, 27 certolizumab pegol)

tag: timepoint

value: Post

tag: pathotype

tag: biologic

tag: status

tag: bx rna conc. (ng/ul)

tag: bx rna volume (ul)

tag: bx rna yield (ng)

tag: rin

tag: ethnicity

tag: age

tag: gender

value: F

tag: smoking status (prev)

tag: smoking status (curr)

tag: duration of disease (yrs)

tag: steroids (medication)

tag: location of joint biopsy

tag: aggregational histological score

value: Diffuse

tag: inflammatory score

tag: swollen joint count (28)

tag: crp

tag: esr


title: pilB::Tn5 Mutant (Btn5) in Fresh BG-11 Media on Day 1, Replicate #1

city: La Jolla

first: Ryan

last: Simkovsky

state: California

address: 9500 Gilman Drive

institute: University of California San Diego

description: Btn5_BG_D1 Replicate 1

data_processing:
FASTQ files were trimmed using trimmomatic and reverse complemented to match the published genome orientation prior to further analysis.
Analysis Pipeline 1: Analysis was performed using Rockhopper 2, using default parameters, to generate raw gene read counts and normalized read counts
Analysis Pipeline 2: Sequences were aligned to the reference genome using Bowtie2, file format conversation was performed using SAMtools and BEDTools,htseq-count was used to generate strand-specific raw gene counts, and the DeSeq2 R package was used to generate normalized counts.
Assembly: A combined file of NC_007604.1 (chromosome), NC_007595.1 (large plasmid), and NC_004990.1 (small plasmid)
Supplementary files format and content: Raw Count Files: tab-delimited text files include raw gene counts for each sample
Supplementary files format and content: Normalized Count Files: tab-delimited text files include normalized gene counts for each sample

organism: Synechococcus elongatus PCC 7942 = FACHB-805

source_name: Cyanobacterial cell

growth_protocol: Cultures were grown in bubbling tubes for one or four days, as previously describe by Parnasa, et al. (2016). For pilB::Tn5 samples on Day 4, biofilms had formed so that samples were taken from the planktonic superntant fraction and from the biofilm separately.

extract_protocol:
Total RNA was extracted using a modified phenol-chloroform, LiCl, and ethanol precipitation protocol from Tu, et al. (2004). DNA was removed via DNase treatment, and the RNA was repurified using a phenol-chloroform and ethanol precipitation procedure.
Total RNA was depleted of ribosomal RNA using the Bacteria Ribo-Zero rRNA Removal Kit (Epicentre) and purified using the RNeasy miniprep kit (Qiagen) according to the manufacturer's instructions. Sequencing libraries were prepared by The Scripps Research Institute Sequencing Core using a TruSeq Stranded Total RNA kit following the manufacturer's instructions.

tag: cell type

value: Cyanobacterial cell

tag: strain

tag: genotype

tag: treatment

value: Fresh BG-11

tag: time

value: Day 1

tag: fraction

value: Supernatant


title: pilB::Tn5 Mutant (Btn5) in Fresh BG-11 Media on Day 1, Replicate #2

description: Btn5_BG_D1 Replicate 2


title: r_018_pre

tag: timepoint

value: Pre

tag: pathotype

value: Lymphoid

tag: biologic

value: Certolizumab

tag: status

value: Responder

tag: bx rna conc. (ng/ul)

tag: bx rna volume (ul)

tag: bx rna yield (ng)

tag: rin

tag: ethnicity

value: Asian

tag: age

tag: gender

value: Yes

tag: diagnosis

value: RA

tag: tender joint count (28)

tag: das28 score

tag: delta das28

tag: patient global assessment of pain (vas)

tag: patient global assessment of disease activity (vas)

tag: physician global assessment of disease activity (vas)

tag: haq-di score

tag: rf

tag: acpa (ccp)

tag: radiographic erosion


title: 2C 02032017

value: Healthy Subject

tag: anatomical location

value: Entire cardiovascular system

tag: tissue

value: Plasma

tag: rna source

value: total cell-free biofluid RNA

tag: rna isolation kit

tag: anticoagulant

value: Citrate


title: r_015_post

tag: timepoint

value: Post

tag: pathotype

tag: biologic

tag: status

tag: bx rna conc. (ng/ul)

tag: bx rna volume (ul)

tag: bx rna yield (ng)

tag: rin

tag: ethnicity

value: Caucasian

tag: age

tag: gender

value: F

tag: smoking status (prev)

value: No

tag: smoking status (curr)

tag: duration of disease (yrs)

tag: steroids (medication)

tag: location of joint biopsy

value: Knee

tag: aggregational histological score

value: Grade 2

tag: inflammatory score

tag: swollen joint count (28)

tag: crp

tag: esr


title: Wild Type in Conditioned Media on Day 1, Replicate #3

description: WT_CM_D1 Replicate 3

tag: cell type

value: Cyanobacterial cell

tag: strain

tag: genotype

value: Wild Type

tag: treatment

value: Conditioned Media (CM)

tag: time

value: Day 1

tag: fraction

value: Supernatant


title: dry seed TDr-3_replicate 2

city: Valencia

first: Javier

last: Forment

state: Valencia

address: Ingeniero Fausto Elio, s/n

department: Biotecnología

country: Spain

institute: Instituto de Biología Molecular y Celular de Plantas, IBMCP (UPV-CSIC)

data_processing:
raw reads cleaning with cutadapt
clean reads mapping to TAIR10 Arabidopsis thaliana genome with HISAT2
read counting with htseq-count
differential expression analysis with DESeq2
Genome_build: TAIR10
Supplementary_files_format_and_content: TSV (tab-separated values) file with read counts per sample and Arabidopsis thaliana Araport11 gene

organism: Arabidopsis thaliana

source_name: dry seed

growth_protocol: Arabidopsis thaliana ecotypes were grown simultaneously to obtain fresh seeds in homogeneous conditions (16 hr light/8 hr dark, at 22°C and 70–75% RH) in pots containing a 1:2 vermiculite:soil mixture.

extract_protocol:
Dry seed total RNA extraction was performed according to Oñate-Sánchez and Vicente-Carbajosa (2008). DNA removal was performed with DNAse kit (E.Z.N.A).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: accession


title: GS832_NT

city: Rotterdam

first: Iris

last: Verploegh

address: Doctor Molewaterplein 40

country: Netherlands

institute: Erasmus MC

description: PolyA RNA

data_processing:
Preliminary sequencing results were converted to FAST! Files with Cell Ranger version 3.0.2. The CellRanger (10X Genomics) secondary analysis pipeline was used to generate a digital gene expression matrix.
QC, normalization and additional analysis were executed in the Seurat R package.
Genome_build: GRCh38
Supplementary_files_format_and_content: barcodes.tsv, features.tsv, matrix.mtx: the barcode, gene and expression matrix file of each sample.

source_name: Glioblastoma monolayer culture

growth_protocol: Cells were grown as a monolayer on ECM (1:100) under serum free conditions (+FGF and EGF).

extract_protocol:
We took our prepared solutions and created such concentration that was calculated to recover 10,000 cells. We used the 10x Genomics Chromium Single Cel 3' Reagents Kit v3. With the 10x protocol, we added the single cells, the Gel Beads and the oils onto the 10x Genomics single-cell-A chip and ran them on the machine. After the droplet generation, samples were transferred into a PCR tube and reverse transcription was performed. After the reverse transcription, cDNA was recovered using the Recovery Agent provided by 10x Genomics followed by a Silane DynaBead clean-up as outlined as described by the manufacturer. Purified cDNA was amplified for 12 cycles before being cleaned up by using SPRIselect beads. The samples were measured on an Agilent bioAnalyzer with a Highsense DNA chip machine to determine the cDNA concentration. The final qpcr library was quantified with the NEBnext library quant kit for Illumina on a Thermo Fast7500.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were seeded as a monolayer of 200,000 cells in a 6-wells plate well the day before treatment. The following day the cells were treated with 60 ng/ml of BMP4 or had their medium refreshed. 24 hours later cells were collected. Cells were kept in suspension with 1% dispase in PBS.

value: Glioblastoma

tag: passage

value: No treatment

tag: bmp4 sensitivity

value: Sensitive


title: dry seed TDr-3_replicate 1


title: Wild Type in Conditioned Media on Day 1, Replicate #2

description: WT_CM_D1 Replicate 2


title: 6C 02032017

tag: diagnosis

value: Healthy Subject

tag: anatomical location

value: Entire cardiovascular system

tag: tissue

value: Plasma

tag: rna source

tag: rna isolation kit

value: miRcury biofluids (Exiqon)

tag: anticoagulant


title: Wild Type in Conditioned Media on Day 1, Replicate #1

description: WT_CM_D1 Replicate 1


title: r_015_pre

tag: timepoint

value: Pre

tag: pathotype

value: Lymphoid

tag: biologic

value: Certolizumab

tag: status

value: Responder

tag: bx rna conc. (ng/ul)

tag: bx rna volume (ul)

tag: bx rna yield (ng)

tag: rin

tag: ethnicity

value: Caucasian

tag: age

tag: gender

tag: smoking status (prev)

tag: smoking status (curr)

value: RA

tag: duration of disease (yrs)

tag: steroids (medication)

tag: location of joint biopsy

tag: aggregational histological score

tag: inflammatory score

tag: swollen joint count (28)

tag: tender joint count (28)

tag: das28 score

tag: delta das28

tag: patient global assessment of pain (vas)

tag: patient global assessment of disease activity (vas)

tag: physician global assessment of disease activity (vas)

tag: haq-di score

tag: crp

tag: rf

tag: acpa (ccp)

tag: radiographic erosion


title: dry seed_Ren-1_replicate 2

tag: accession


title: 2S 02032017

source_name: Serum

tag: diagnosis

tag: anatomical location

tag: tissue

value: Serum

tag: rna source

value: total cell-free biofluid RNA

tag: rna isolation kit


title: r_014_post

tag: timepoint

value: Post

tag: pathotype

tag: biologic

tag: status

tag: bx rna conc. (ng/ul)

tag: bx rna volume (ul)

tag: bx rna yield (ng)

tag: rin

tag: ethnicity

tag: age

tag: gender

value: F

tag: smoking status (prev)

value: No

tag: smoking status (curr)

tag: duration of disease (yrs)

tag: steroids (medication)

tag: location of joint biopsy

value: MCP

tag: aggregational histological score

value: Grade 3

tag: inflammatory score

tag: swollen joint count (28)

tag: tender joint count (28)

tag: esr

value: Yes


title: dry seed_Ren-1_replicate 1

tag: accession


title: 3C 02032017

tag: diagnosis

value: Healthy Subject

tag: anatomical location

value: Entire cardiovascular system

tag: tissue

tag: rna source

tag: rna isolation kit

tag: anticoagulant

value: Citrate


title: r_013_post

tag: timepoint

tag: pathotype

tag: biologic

value: Etanercept

tag: status

tag: bx rna conc. (ng/ul)

tag: bx rna volume (ul)

tag: bx rna yield (ng)

tag: rin

tag: ethnicity

value: Asian

tag: age

tag: gender

value: M

tag: smoking status (prev)

value: Wrist

tag: das28 score

tag: delta das28

tag: patient global assessment of pain (vas)

tag: patient global assessment of disease activity (vas)

tag: physician global assessment of disease activity (vas)

tag: haq-di score

tag: crp

tag: rf

tag: acpa (ccp)

tag: radiographic erosion


title: 3S 02032017

tag: diagnosis

tag: anatomical location

tag: tissue

tag: rna source

tag: rna isolation kit

value: miRcury biofluids (Exiqon)


title: 6E 02032017

value: Plasma

tag: anticoagulant

value: EDTA


title: Wild Type in Fresh BG-11 Media on Day 1, Replicate #1

description: WT_BG_D1 Replicate 1

tag: cell type

value: Cyanobacterial cell

tag: strain

tag: genotype

value: Wild Type

tag: treatment

value: Fresh BG-11

tag: time

value: Day 1

tag: fraction

value: Supernatant


title: 4C 02032017

value: total cell-free biofluid RNA


title: dry seed_Pro-0_replicate 2

tag: accession


title: dry seed_Pro-0_replicate 3


title: Wild Type in Fresh BG-11 Media on Day 1, Replicate #2

description: WT_BG_D1 Replicate 2


title: Wild Type in Fresh BG-11 Media on Day 1, Replicate #3

description: WT_BG_D1 Replicate 3


title: r_014_pre

tag: timepoint

value: Pre

tag: pathotype

value: Lymphoid

tag: biologic

value: Certolizumab

tag: status

value: Responder

tag: bx rna conc. (ng/ul)

tag: bx rna volume (ul)

tag: bx rna yield (ng)

tag: rin

tag: ethnicity

value: Caucasian

tag: age

tag: gender

value: F

tag: smoking status (prev)

value: No

tag: smoking status (curr)

value: RA

tag: duration of disease (yrs)

tag: steroids (medication)

tag: location of joint biopsy

value: MCP

tag: aggregational histological score

value: Grade 3

tag: inflammatory score

tag: swollen joint count (28)

tag: tender joint count (28)

tag: das28 score

tag: delta das28

tag: patient global assessment of pain (vas)

tag: patient global assessment of disease activity (vas)

tag: physician global assessment of disease activity (vas)

tag: haq-di score

tag: crp

tag: esr

value: Yes


title: r_016_pre

tag: timepoint

tag: pathotype

tag: biologic

tag: status

tag: bx rna conc. (ng/ul)

tag: bx rna volume (ul)

tag: bx rna yield (ng)

tag: rin

tag: ethnicity

tag: age

tag: gender

tag: smoking status (prev)

tag: diagnosis

value: Wrist

value: Grade 2

tag: rf

tag: acpa (ccp)

tag: radiographic erosion


title: 4S 02032017

value: Healthy Subject

tag: anatomical location

value: Entire cardiovascular system

tag: tissue

value: Serum

tag: rna source

tag: rna isolation kit

value: miRcury biofluids (Exiqon)


title: r_013_pre

tag: timepoint

value: Pre

tag: pathotype

tag: biologic

value: Etanercept

tag: status

value: Asian

value: M

tag: smoking status (curr)

tag: duration of disease (yrs)

tag: steroids (medication)

tag: location of joint biopsy

tag: aggregational histological score

tag: inflammatory score

tag: swollen joint count (28)

tag: tender joint count (28)

tag: das28 score

tag: delta das28

tag: patient global assessment of pain (vas)

tag: patient global assessment of disease activity (vas)

tag: physician global assessment of disease activity (vas)

tag: haq-di score

tag: crp

tag: esr


title: dry seed_Pro-0_replicate 1

tag: accession


title: dry seed_PAR-4_replicate 3


title: Experiment #2 Flask Conditioned Media Biofilmers

library_source: genomic

data_processing:
FASTQ files were  analyzed using the scripts developed by Morgan Price and published as part of Wetmore, et al. (2015) to generate strain counts, gene counts, fitness scores, and T-values.
Assembly: A combined file of NC_007604.1 (chromosome), NC_007595.1 (large plasmid), and NC_004990.1 (small plasmid)
Supplementary files format and content: Raw Count Files: tab-delimited text files include raw barcode counts in each RB-TnSeq assessed gene for each sample
Library strategy: RB-TnSeq

molecule: genomic DNA

growth_protocol: The S. elongatus PCC 7942 RB-TnSeq library was revived from freeze stocks, grown in triplicate flasks, and then pooled. Aliquots of the pooled cultures were taken and frozen at -80°C to serve as Time 0 (T0) samples. The pooled libraries were used to inoculate bubbling tubes or flasks, in either fresh BG-11 media or Conditioned Media, for biofilm formation assays, depending upon the details of the experiment. After biofilm formation was visibly observed, planktonic cell samples were collected by decanting the supernatants of the cultures into sterile conical tubes. Each vessel was then gently washed once with water, which was decanted to a sterile conical tube to investigate settler cells. The remaining biofilms were resuspended in a water wash through physical scraping of the vessel and collected into a sterile conical tube. All samples were then centrifuged to generate cell pellets, which were frozen at -80°C prior to genomic DNA extraction.

extract_protocol:
Frozen cell pellets were thawed and genomic DNA was extracted using a phenol-chloroform and ethanol precipitation protocol, as previously described by Clerico, et al 2007.
Barcodes of transposon insertions in the pooled library were PCR amplified. Primers for this amplification contained adapters for Illumina sequencing, experiment-specific barcodes, and heterogenous spacers for enhanced length diversity, as described by Wetmore, et al. (2015). Amplicons were assessed by gel electrophoresis and purified using a PCR-purification kit (Zymo).

tag: cell type

value: Cyanobacterial cell

tag: strain

tag: genotype

value: RB-TnSeq Library 2.0

tag: growth vessel

value: flask

tag: treatment

value: Conditioned Media

tag: fraction

value: Biofilm


title: r_012_post

tag: timepoint

value: Post

tag: pathotype

value: Myeloid

tag: biologic

tag: status

value: Responder

tag: bx rna conc. (ng/ul)

tag: bx rna volume (ul)

tag: bx rna yield (ng)

tag: rin

tag: ethnicity

value: Caucasian

tag: age

tag: gender

tag: smoking status (prev)

tag: smoking status (curr)

value: No

tag: diagnosis

value: RA

tag: duration of disease (yrs)

tag: steroids (medication)

tag: location of joint biopsy

tag: aggregational histological score

value: Pauci-immune

tag: inflammatory score

tag: swollen joint count (28)

tag: rf

tag: acpa (ccp)

tag: radiographic erosion


title: Experiment #2 Flask Fresh BG-11 Biofilmers

tag: cell type

tag: strain

tag: genotype

tag: growth vessel

tag: treatment

value: Fresh BG-11

tag: fraction


title: r_012_pre

tag: timepoint

value: Pre

tag: pathotype

tag: biologic

tag: status

tag: bx rna conc. (ng/ul)

tag: bx rna volume (ul)

tag: bx rna yield (ng)

tag: rin

tag: ethnicity

tag: age

tag: gender

tag: smoking status (prev)

value: Yes

tag: smoking status (curr)

value: Wrist

value: Under QC Assessment

tag: tender joint count (28)

tag: das28 score

tag: delta das28

tag: patient global assessment of pain (vas)

tag: patient global assessment of disease activity (vas)

tag: physician global assessment of disease activity (vas)

tag: haq-di score

tag: crp

tag: esr


title: r_011_post

tag: timepoint

tag: pathotype

tag: biologic

value: Etanercept

tag: status

tag: bx rna conc. (ng/ul)

tag: bx rna volume (ul)

value: M

tag: diagnosis

tag: duration of disease (yrs)

tag: steroids (medication)

tag: location of joint biopsy

tag: aggregational histological score

tag: inflammatory score

tag: swollen joint count (28)

tag: rf

tag: acpa (ccp)

tag: radiographic erosion


title: 1H 02032017

value: Healthy Subject

tag: anatomical location

value: Entire cardiovascular system

tag: tissue

value: Plasma

tag: rna source

value: total cell-free biofluid RNA

tag: rna isolation kit

value: miRcury biofluids (Exiqon)

tag: anticoagulant

value: Heparin


title: dry seed_PAR-4_replicate 2

tag: accession


title: 2H 02032017


title: Experiment #2 Test Tube Conditioned Media Biofilmers

tag: cell type

value: Cyanobacterial cell

tag: strain

tag: genotype

value: RB-TnSeq Library 2.0

tag: growth vessel

value: bubbling tube

tag: treatment

value: Conditioned Media

tag: fraction

value: Biofilm


title: Experiment #2 Test Tube Conditioned Media Settlers

value: Settled Cells


title: dry seed_PAR-4_replicate 1


title: 6H 02032017

tag: diagnosis


title: r_011_pre

tag: timepoint

value: Pre

tag: pathotype

value: Myeloid

tag: biologic

tag: status

value: Responder

tag: bx rna conc. (ng/ul)

tag: bx rna volume (ul)

tag: bx rna yield (ng)

tag: rin

tag: ethnicity

value: Caucasian

tag: age

tag: gender

tag: smoking status (prev)

value: Yes

tag: smoking status (curr)

value: No

value: RA

tag: duration of disease (yrs)

tag: steroids (medication)

tag: location of joint biopsy

tag: aggregational histological score

value: Pauci immune

tag: inflammatory score

tag: swollen joint count (28)

tag: tender joint count (28)

tag: das28 score

tag: delta das28

tag: patient global assessment of pain (vas)

tag: patient global assessment of disease activity (vas)

tag: physician global assessment of disease activity (vas)

tag: haq-di score

tag: crp

tag: esr


title: dry seed_Ors-1_replicate 2

tag: accession


title: Experiment #2 Test Tube Fresh BG-11 Biofilmers

tag: cell type

tag: strain

tag: genotype

tag: growth vessel

tag: treatment

value: Fresh BG-11

tag: fraction


title: 3E 02032017

tag: diagnosis

value: Healthy Subject

tag: anatomical location

value: Entire cardiovascular system

tag: tissue

value: Plasma

tag: rna source

value: total cell-free biofluid RNA

tag: rna isolation kit

value: miRcury biofluids (Exiqon)

tag: anticoagulant

value: EDTA


title: r_010_post

tag: timepoint

value: Post

tag: pathotype

tag: biologic

value: Etanercept

tag: status

tag: bx rna conc. (ng/ul)

tag: bx rna volume (ul)

tag: bx rna yield (ng)

tag: rin

tag: ethnicity

tag: age

tag: gender

value: F

tag: smoking status (prev)

tag: smoking status (curr)

tag: duration of disease (yrs)

tag: steroids (medication)

tag: location of joint biopsy

value: Wrist

tag: aggregational histological score

value: Grade 1

tag: inflammatory score

tag: swollen joint count (28)

tag: tender joint count (28)

tag: das28 score

tag: delta das28

tag: patient global assessment of pain (vas)

tag: patient global assessment of disease activity (vas)

tag: physician global assessment of disease activity (vas)

tag: rf

tag: acpa (ccp)

tag: radiographic erosion


title: Experiment #2 Test Tube Fresh BG-11 Settlers

tag: cell type

value: Cyanobacterial cell

tag: strain

tag: genotype

value: RB-TnSeq Library 2.0

tag: growth vessel

value: bubbling tube

tag: treatment

tag: fraction

value: Settled Cells


title: 3H 02032017

tag: diagnosis

tag: anatomical location

tag: tissue

tag: rna source

tag: rna isolation kit

tag: anticoagulant

value: Heparin


title: dry seed_Ors-1_replicate 1

tag: accession


title: 5S 02032017

value: Serum


title: Experiment #2 Test Tube Fresh BG-11 Planktonic

value: Fresh BG-11

value: Supernatant


title: r_009_post

tag: timepoint

tag: pathotype

value: Myeloid

tag: biologic

tag: status

value: Responder

tag: bx rna conc. (ng/ul)

tag: bx rna volume (ul)

tag: bx rna yield (ng)

tag: rin

tag: ethnicity

value: Caucasian

tag: age

tag: gender

tag: smoking status (prev)

value: Yes

tag: smoking status (curr)

value: No

value: RA

tag: duration of disease (yrs)

tag: steroids (medication)

tag: location of joint biopsy

tag: aggregational histological score

value: Diffuse

tag: inflammatory score

tag: swollen joint count (28)

tag: tender joint count (28)

tag: das28 score

tag: delta das28

tag: patient global assessment of pain (vas)

tag: patient global assessment of disease activity (vas)

tag: physician global assessment of disease activity (vas)

tag: haq-di score

tag: crp

tag: esr


title: dry seed Fi-1_replicate 2

tag: accession


title: 4E 02032017

tag: diagnosis

value: Healthy Subject

tag: anatomical location

value: Entire cardiovascular system

tag: tissue

value: Plasma

tag: rna source

value: total cell-free biofluid RNA

tag: rna isolation kit

value: miRcury biofluids (Exiqon)

tag: anticoagulant

value: EDTA


title: dry seed Kelsherbach-4_replicate 1


title: r_009_pre

tag: timepoint

value: Pre

tag: pathotype

tag: biologic

value: Etanercept

tag: status

tag: bx rna conc. (ng/ul)

tag: bx rna volume (ul)

tag: bx rna yield (ng)

tag: rin

tag: ethnicity

tag: age

tag: gender

value: F

tag: smoking status (prev)

tag: smoking status (curr)

tag: duration of disease (yrs)

tag: steroids (medication)

tag: location of joint biopsy

value: Wrist

tag: aggregational histological score

tag: inflammatory score

tag: swollen joint count (28)

tag: rf

tag: acpa (ccp)

tag: radiographic erosion


title: Experiment #2 Time 0 #11

tag: cell type

value: Cyanobacterial cell

tag: strain

tag: genotype

value: RB-TnSeq Library 2.0

tag: growth vessel

value: flask

tag: treatment

value: Fresh BG-11

tag: fraction

value: Supernatant


title: r_008_post

tag: timepoint

value: Post

tag: pathotype

value: Myeloid

tag: biologic

tag: status

value: Responder

tag: bx rna conc. (ng/ul)

tag: bx rna volume (ul)

tag: bx rna yield (ng)

tag: rin

tag: ethnicity

value: Bangladeshi

tag: age

tag: gender

tag: smoking status (prev)

value: No

tag: diagnosis

value: RA

value: Yes

value: Grade 2

tag: tender joint count (28)

tag: das28 score

tag: delta das28

tag: patient global assessment of pain (vas)

tag: patient global assessment of disease activity (vas)

tag: physician global assessment of disease activity (vas)

tag: haq-di score

tag: crp

tag: esr


title: BW10s8_PANC1_R1_8-SIK3-100-4h1

city: REGENSBURG

first: Claudia

last: GEBHARD

address: FRANZ-JOSEF-STRAUSS ALLEE 11

country: Germany

institute: UNIVERSITY HOSPITAL REGENSBURG

data_processing:
Sequenced reads were trimmed for adaptor sequences using skewer v0.2.2
Reads were mapped to hg38 whole genome using bowtie2 v2.3.3 with the –very-sensitive parameter and a maximum insert size of 2000 bp
Duplicate and unpaired reads were removed using the sambamba (Tarasov et al., 2015) ‘markdup’ command, and reads with mapping quality >30 and alignment to the nuclear genome were kept.
Peak calling for each sample was performed using HOMER v4.10 (Heinz et al., 2010) with the following approach: Two different peak sets were called, once we used the options ‘-style factor -fragmentLength 150 -size 250 -minDist 250 –L 4 –fdr 0.0001’ parameters, to identify highly robust small regions of open chromatin, and in a second approach we used the parameters ‘-region -fragmentLength 150 -size 150 -minDist 250 -L 4 -fdr 0.0001’ to identify larger regions of open chromatin. The two peak sets were then merged using the mergePeaks function of HOMER to create the peak set that was used for downstream analysis.
For visualization purposes only, coverage files from filtered bam files were produced using bedtools (Quinlan and Hall, 2010) genomeCoverageBed, each position was normalized by dividing to the total library size and multiplying by 106, followed by conversion to a bigwig using the bedGraphToBigWig command from the UCSC genome browser tools.
Assembly: UCSC hg38
Supplementary files format and content: Processed data files contain bed files (peaks) and bigWig files (for genome browser visuaizations)

source_name: PANC1 cell line

growth_protocol: Human pancreatic ductal adenocarcinoma cell line PANC-1 (ATCC® CRL-1469™; source: male). were acquired from American Type Cell Culture (ATCC). PANC-1 were cultured under standard conditions in DMEM media supplemented with 10% fetal calf serum, 100 U/ml penicillin G and 100 µg/ml streptomycin at 37 °C in a humidified atmosphere under 5% CO2.

extract_protocol: Chromatin accessibility mapping on purified cell populations was performed using the ATAC-seq method as previously described (Buenrostro et al., 2013; Corces et al., 2017), with minor adaptations. Briefly, in each experiment 2,000 - 15,000 sorted cells were pelleted by centrifuging for 10 min at 4 °C at 500 x g. After centrifugation, the pellet was carefully lysed in 50 µl resuspension buffer supplemented with NP-40 (Sigma), Tween-20 and Digitonin (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1 % NP-40, 0.1 % Tween-20, 0.01 % Digitonin) and incubated for 3 minutes on ice. Then, 1 ml of ice-cold resuspension buffer supplemented with Tween-20 was added, and the sample was centrifuged at 4 °C at 500 x g for 10 minutes. The supernatant was discarded, and the cell pellet was carefully resuspended in the transposition reaction (25 µl 2 x TD buffer (Illumina), 2.5 µl TDE1 (Illumina), 16.5 µl PBS, 5 µl nuclease-free water, 0.5 µl 1% Digitonin (Promega), 0.5 µl 10% Tween-20 (Sigma)) for 30 min at 37 °C on a shaker at 1000 rpm. Following DNA purification with the Clean and Concentrator-5 kit (Zymo) eluting in 23 µl, 2 µl of the eluted DNA was used in a quantitative 10 µL PCR reaction (1.25 µM forward and reverse custom Nextera primers (Corces et al., 2017), 1x SYBR green final concentration) to estimate the optimum number of amplification cycles with the following program 72°C 5 min; 98°C 30 s; 25 cycles: 98°C 10 s, 63°C 30 s, 72°C 1 min; the final amplification of the library was carried out using the same PCR program and the number of cycles according to the Cq value of the qPCR. Library amplification using custom Nextera primers was followed by SPRI size selection with AmpureXP beads to exclude fragments larger than 1,200 bp. DNA concentration was measured with a Qubit fluorometer (Life Technologies). The libraries were sequenced using the Illumina HiSeq3000/4000 or NextSeq platforms.

treatment_protocol: PANC-1 cells were transfected either with Ctrl or SIK3 specific siRNA and treated with 100 ng/ml rHuTNF for 4 h or 24h or left untreated.

tag: cell line

tag: timepoint

tag: condition

value: 100 TNF

tag: knockdown


title: Experiment #2 Time 0 #10

tag: cell type

tag: strain

tag: genotype

tag: growth vessel

tag: treatment

tag: fraction


title: dry seed Fi-1_replicate 1

tag: accession


title: r_008_pre

value: Pre

tag: pathotype

tag: biologic

value: Etanercept

tag: status

tag: bx rna conc. (ng/ul)

tag: bx rna volume (ul)

tag: bx rna yield (ng)

tag: rin

tag: ethnicity

tag: age

tag: gender

tag: smoking status (prev)

tag: smoking status (curr)

tag: diagnosis

tag: duration of disease (yrs)

tag: steroids (medication)

tag: location of joint biopsy

tag: aggregational histological score

tag: inflammatory score

tag: swollen joint count (28)

tag: tender joint count (28)

tag: das28 score

tag: delta das28

tag: patient global assessment of pain (vas)

tag: rf

tag: acpa (ccp)

tag: radiographic erosion


title: dry seed Kelsherbach-4_replicate 2

tag: accession


title: r_007_post

tag: timepoint

tag: pathotype

tag: biologic

tag: status

tag: bx rna conc. (ng/ul)

tag: bx rna volume (ul)

tag: bx rna yield (ng)

tag: rin

tag: ethnicity

value: Caribbean

tag: age

tag: gender

value: F

tag: smoking status (prev)

value: Wrist

tag: patient global assessment of disease activity (vas)

tag: physician global assessment of disease activity (vas)

tag: haq-di score

tag: crp

tag: esr


title: Experiment #2 Time 0 #9

tag: cell type

value: Cyanobacterial cell

tag: strain

tag: genotype

value: RB-TnSeq Library 2.0

tag: growth vessel

value: flask

tag: treatment

tag: fraction


title: dry seed Da-0_replicate 3

tag: accession


title: r_007_pre

tag: timepoint

tag: pathotype

tag: biologic

tag: status

tag: bx rna conc. (ng/ul)

tag: bx rna volume (ul)

tag: bx rna yield (ng)

tag: rin

tag: smoking status (curr)

tag: diagnosis

tag: duration of disease (yrs)

tag: steroids (medication)

tag: location of joint biopsy

tag: aggregational histological score

value: Diffuse

tag: inflammatory score

tag: swollen joint count (28)

tag: tender joint count (28)

tag: das28 score

tag: delta das28

tag: patient global assessment of pain (vas)

tag: rf

tag: acpa (ccp)

tag: radiographic erosion


title: dry seed Da-0_replicate 2

tag: accession


title: r_010_pre

tag: timepoint

tag: pathotype

value: Myeloid

tag: biologic

tag: status

tag: bx rna conc. (ng/ul)

tag: bx rna volume (ul)

tag: bx rna yield (ng)

tag: rin

tag: ethnicity

value: Caucasian

tag: age

tag: gender

tag: smoking status (prev)

value: Grade 1

tag: patient global assessment of disease activity (vas)

tag: physician global assessment of disease activity (vas)

tag: haq-di score

tag: crp

tag: esr


title: BW10s5_PANC1_R1_5-Scr-0-4h1

tag: cell line

tag: timepoint

tag: condition

value: 0 TNF

tag: knockdown

value: scr


title: Experiment #2 Time 0 #12

tag: cell type

tag: strain

tag: genotype

tag: growth vessel

tag: treatment

value: Fresh BG-11

tag: fraction

value: Supernatant


title: Experiment #2 Time 0 #7


title: r_006_post

value: Post

tag: pathotype

tag: biologic

value: Certolizumab

tag: status

value: Responder

tag: bx rna conc. (ng/ul)

tag: bx rna volume (ul)

tag: bx rna yield (ng)

tag: rin

tag: ethnicity

tag: age

tag: gender

value: M

value: Yes

tag: smoking status (curr)

value: No

tag: diagnosis

value: RA

tag: duration of disease (yrs)

tag: steroids (medication)

tag: location of joint biopsy

tag: aggregational histological score

tag: inflammatory score

tag: swollen joint count (28)

tag: tender joint count (28)

tag: das28 score

tag: delta das28

tag: patient global assessment of pain (vas)

tag: rf

tag: acpa (ccp)

tag: radiographic erosion


title: dry seed Col-0_replicate 2

tag: accession


title: dry seed Da-0_replicate 1


title: Experiment #2 Time 0 #5

tag: cell type

value: Cyanobacterial cell

tag: strain

tag: genotype

value: RB-TnSeq Library 2.0

tag: growth vessel

tag: treatment

tag: fraction


title: Experiment #2 Time 0 #6

value: flask


title: BW10s4_PANC1_R1_4-SIK3-100-24h1

tag: cell line

tag: timepoint

tag: condition

value: 100 TNF

tag: knockdown


title: r_006_pre

value: Pre

tag: pathotype

value: Myeloid

tag: biologic

tag: status

tag: bx rna conc. (ng/ul)

tag: bx rna volume (ul)

tag: bx rna yield (ng)

tag: rin

tag: ethnicity

value: Caucasian

tag: age

tag: gender

tag: smoking status (prev)

tag: smoking status (curr)

tag: diagnosis

tag: duration of disease (yrs)

tag: steroids (medication)

tag: location of joint biopsy

value: Wrist

tag: aggregational histological score

value: Diffuse

tag: inflammatory score

tag: swollen joint count (28)

tag: tender joint count (28)

tag: das28 score

tag: patient global assessment of disease activity (vas)

tag: physician global assessment of disease activity (vas)

tag: haq-di score

tag: crp

tag: esr


title: BW10s3_PANC1_R1_3-SIK3-0-24h1

tag: cell line

tag: timepoint

tag: condition

value: 0 TNF

tag: knockdown


title: BW10s6_PANC1_R1_6-Scr-100-4h1

value: scr


title: BW10s23_PANC1_R3_SIK3-0-4h


title: Experiment #2 Time 0 #4

tag: cell type

tag: strain

tag: genotype

tag: growth vessel

tag: treatment

value: Fresh BG-11

tag: fraction

value: Supernatant


title: r_005_pre

tag: pathotype

tag: biologic

value: Certolizumab

tag: status

value: Responder

tag: bx rna conc. (ng/ul)

tag: bx rna volume (ul)

tag: bx rna yield (ng)

tag: rin

tag: ethnicity

tag: age

tag: gender

value: F

tag: smoking status (prev)

tag: smoking status (curr)

tag: diagnosis

tag: duration of disease (yrs)

tag: steroids (medication)

tag: location of joint biopsy

value: MCP

tag: aggregational histological score

value: Grade 1

tag: inflammatory score

tag: swollen joint count (28)

tag: tender joint count (28)

tag: delta das28

tag: patient global assessment of pain (vas)

tag: rf

tag: acpa (ccp)

tag: radiographic erosion


title: Experiment #2 Time 0 #8

tag: cell type

value: Cyanobacterial cell

tag: strain

tag: genotype

value: RB-TnSeq Library 2.0

tag: growth vessel

tag: treatment

tag: fraction


title: BW10s7_PANC1_R1_7-SIK3-0-4h1

tag: cell line

tag: timepoint

tag: condition

tag: knockdown


title: dry seed_Chat-1_replicate 2

tag: accession


title: Experiment #2 Time 0 #3

value: flask


title: dry seed_Chat-1_replicate 1


title: r_004_post

value: Post

tag: pathotype

tag: biologic

tag: status

tag: bx rna conc. (ng/ul)

tag: bx rna volume (ul)

tag: bx rna yield (ng)

tag: rin

tag: ethnicity

tag: age

tag: gender

tag: smoking status (prev)

value: Yes

tag: smoking status (curr)

value: No

tag: diagnosis

value: RA

tag: duration of disease (yrs)

tag: steroids (medication)

tag: location of joint biopsy

tag: aggregational histological score

value: Pauci-immune

tag: inflammatory score

tag: swollen joint count (28)

tag: tender joint count (28)

tag: das28 score

tag: patient global assessment of disease activity (vas)

tag: physician global assessment of disease activity (vas)

tag: haq-di score

tag: crp

tag: esr


title: BW10s22_PANC1_R3_Scr-100-4h

tag: cell line

tag: timepoint

tag: condition

value: 100 TNF

tag: knockdown


title: r_004_pre

value: Pre

tag: pathotype

value: Myeloid

tag: biologic

tag: status

tag: bx rna conc. (ng/ul)

tag: bx rna volume (ul)

tag: bx rna yield (ng)

tag: rin

tag: ethnicity

value: Caucasian

tag: age

tag: gender

tag: smoking status (prev)

tag: smoking status (curr)

tag: diagnosis

tag: duration of disease (yrs)

value: Wrist

value: Diffuse

tag: delta das28

tag: patient global assessment of pain (vas)

tag: rf

tag: acpa (ccp)

tag: radiographic erosion


title: BW10s21_PANC1_R3_Scr-0-4h

tag: cell line

tag: timepoint

tag: condition

value: 0 TNF

tag: knockdown

value: scr


title: Experiment #2 Time 0 #2

tag: cell type

tag: strain

tag: genotype

tag: growth vessel

tag: treatment

value: Fresh BG-11

tag: fraction

value: Supernatant


title: Experiment #2 Time 0 #1

value: Cyanobacterial cell

value: RB-TnSeq Library 2.0


title: dry seed_CAM16_replicate 1

tag: accession


title: BW10s24_PANC1_R3_SIK3-100-4h


title: Experiment #1 Test Tube Fresh BG-11 Settlers

value: RB-TnSeq Library 1.0

value: bubbling tube

value: Settled Cells


title: dry seed Col-0_replicate 1


title: dry seed_Bor-4_replicate 2


title: r_003_post

value: Post

tag: pathotype

value: Fibroid

tag: biologic

value: Etanercept

tag: status

value: Responder

tag: bx rna conc. (ng/ul)

tag: bx rna volume (ul)

tag: bx rna yield (ng)

tag: rin

tag: ethnicity

tag: age

tag: gender

value: F

tag: smoking status (prev)

value: No

tag: smoking status (curr)

tag: diagnosis

value: RA

tag: duration of disease (yrs)

tag: steroids (medication)

tag: location of joint biopsy

tag: aggregational histological score

tag: inflammatory score

tag: swollen joint count (28)

tag: tender joint count (28)

tag: das28 score

tag: patient global assessment of disease activity (vas)

tag: physician global assessment of disease activity (vas)

tag: haq-di score

tag: crp

tag: esr

value: Yes


title: r_005_post

tag: timepoint

tag: pathotype

value: Myeloid

tag: biologic

value: Certolizumab

tag: status

tag: bx rna conc. (ng/ul)

tag: bx rna volume (ul)

tag: bx rna yield (ng)

tag: rin

tag: ethnicity

value: Caucasian

tag: age

tag: gender

value: MCP

value: Diffuse

tag: delta das28

tag: patient global assessment of pain (vas)

tag: rf

tag: acpa (ccp)

tag: radiographic erosion


title: r_003_pre

value: Pre

tag: smoking status (prev)

tag: smoking status (curr)

tag: diagnosis

tag: duration of disease (yrs)

tag: steroids (medication)

tag: location of joint biopsy

value: Wrist

tag: aggregational histological score

value: Under QC Assessment

tag: inflammatory score

tag: swollen joint count (28)

tag: tender joint count (28)

tag: das28 score

tag: patient global assessment of disease activity (vas)

tag: physician global assessment of disease activity (vas)

tag: haq-di score

tag: crp

tag: esr


title: dry seed_Bor-4_replicate 1

tag: accession


title: Experiment #1 Test Tube Fresh BG-11 Biofilmers

tag: cell type

value: Cyanobacterial cell

tag: strain

tag: genotype

value: RB-TnSeq Library 1.0

tag: growth vessel

value: bubbling tube

tag: treatment

value: Fresh BG-11

tag: fraction

value: Biofilm


title: BW10s19_PANC1_R3_SIK3-0-24h

tag: cell line

tag: timepoint

tag: condition

value: 0 TNF

tag: knockdown


title: BW10s2_PANC1_R1_2-Scr-100-24h1

value: 100 TNF

value: scr


title: r_002_post

value: Post

tag: pathotype

value: Fibroid

tag: biologic

value: Etanercept

tag: status

value: Responder

tag: bx rna conc. (ng/ul)

tag: bx rna volume (ul)

tag: bx rna yield (ng)

tag: rin

tag: ethnicity

value: Asian

tag: age

tag: gender

value: M

tag: smoking status (prev)

value: No

tag: smoking status (curr)

value: Yes

tag: diagnosis

value: RA

tag: duration of disease (yrs)

tag: steroids (medication)

tag: location of joint biopsy

tag: aggregational histological score

value: Pauci-immune

tag: inflammatory score

tag: swollen joint count (28)

tag: tender joint count (28)

tag: das28 score

tag: delta das28

tag: patient global assessment of pain (vas)

tag: rf

tag: acpa (ccp)

tag: radiographic erosion


title: dry seed_UNKW06_replicate 3

tag: accession


title: Experiment #1 Time 0 #4

tag: cell type

value: Cyanobacterial cell

tag: strain

tag: genotype

value: RB-TnSeq Library 1.0

tag: growth vessel

value: flask

tag: treatment

tag: fraction

value: Supernatant


title: BW10s18_PANC1_R3_Scr-100-24h

tag: cell line

tag: timepoint

tag: condition

tag: knockdown


title: dry seed_UNKW06_replicate 2


title: r_002_pre

value: Pre

tag: pathotype

tag: biologic

tag: status

tag: bx rna conc. (ng/ul)

tag: bx rna volume (ul)

tag: bx rna yield (ng)

tag: rin

tag: ethnicity

tag: age

tag: gender

tag: smoking status (prev)

tag: smoking status (curr)

tag: diagnosis

tag: duration of disease (yrs)

tag: steroids (medication)

tag: location of joint biopsy

value: Wrist

tag: aggregational histological score

tag: inflammatory score

tag: swollen joint count (28)

tag: tender joint count (28)

tag: das28 score

tag: patient global assessment of disease activity (vas)

tag: physician global assessment of disease activity (vas)

tag: haq-di score

tag: crp

tag: esr


title: dry seed_CAM16_replicate 2

tag: accession


title: Experiment #1 Time 0 #3

tag: cell type

tag: strain

tag: genotype

tag: growth vessel

tag: treatment

value: Fresh BG-11

tag: fraction


title: BW10s17_PANC1_R3_Scr-0-24h

tag: cell line

tag: timepoint

tag: condition

value: 0 TNF

tag: knockdown

value: scr


title: Experiment #1 Time 0 #2


title: BW10s20_PANC1_R3_SIK3-100-24h

value: 100 TNF


title: dry seed_UNKW06_replicate 1


title: r_001_post

value: Post

tag: pathotype

value: Fibroid

tag: biologic

value: Certolizumab

tag: status

value: Responder

tag: bx rna conc. (ng/ul)

tag: bx rna volume (ul)

tag: bx rna yield (ng)

tag: rin

tag: ethnicity

value: Caucasian

tag: age

tag: gender

value: F

tag: smoking status (prev)

tag: smoking status (curr)

tag: diagnosis

tag: duration of disease (yrs)

tag: steroids (medication)

tag: location of joint biopsy

tag: aggregational histological score

tag: inflammatory score

tag: swollen joint count (28)

tag: tender joint count (28)

tag: das28 score

tag: delta das28

tag: patient global assessment of pain (vas)

tag: rf

tag: acpa (ccp)

tag: radiographic erosion


title: BW10s1_PANC1_R1_1-Scr-0-24h1

tag: cell line

tag: timepoint

tag: condition

tag: knockdown


title: Experiment #1 Time 0 #1

tag: cell type

tag: strain

tag: genotype

tag: growth vessel

tag: treatment

tag: fraction


title: MIFN4R

status: Public on Jun 05 2022

city: Houston

first: Ganiraju

last: Manyam

state: TX

address: 1515 Holcombe Blvd

institute: UT MD Anderson Cancer Center

description:
MB49 tumors in vivo were treated with lentiviral IFNαl (LV-IFNα)
MB49_in_vivo_IX_015

data_processing:
RNA-Seq libraries were prepared and sequencing was performed in house using Ion Gene Studio S5.
Primary analysis of RNA sequencing data was performed using AmpliseqRNA analysis plugin in the Torrent Suite software.
Raw reads were aligned with mouse reference genome Ampliseq_mouse_Trasncriptome_V1_Reference
The raw counts are normalized and normlized reads per gene [er millopn mapped reads (rpm) were generated and used for analysis.
Assembly: Ampliseq_mouse_Trasncriptome_V1_Reference
Supplementary files format and content: Gene-Level Read Count files

organism: Mus musculus

source_name: Bladder

extract_protocol:
Total RNA was isolated using miRVANA miRNA isolation kit (Thermo Fisher Scientific)
cDNA libraries were prepared using Ion Ampliseq transcriptome mouse gene expression chef-ready kit (A36412)

tag: tissue

value: Bladder

value: MB49 in vivo

value: Bladder cancer cell line

value: DMBA induced C57Bl/6


title: MLVC3R

description:
MB49 tumors in vivo were treated with lentiviral Ctrl (LV-Ctrl)
MB49_in_vivo_IX_012


title: MLVC2R

description:
MB49 tumors in vivo were treated with lentiviral Ctrl (LV-Ctrl)
MB49_in_vivo_IX_013


title: MSAL1R

description:
MB49 tumours in vivo were treated with vehicle alone Ctrl
MB49_in_vivo_IX_001


title: MIFN3-2R

description:
MB49 tumors in vivo were treated with lentiviral IFNαl (LV-IFNα)
MB49_in_vivo_IX_011


title: MSAL3R

description:
MB49 tumours in vivo were treated with vehicle alone Ctrl
MB49_in_vivo_IX_003


title: MIFN2R

description:
MB49 tumors in vivo were treated with lentiviral IFNαl (LV-IFNα)
MB49_in_vivo_IX_010


title: UPPLIFN1

description:
UPPL1541 cell line in vivo treated with LV-IFNα
UPPL1541_IX_034

value: UPII PTEN/p53 null


title: r_001_pre

value: Pre

tag: pathotype

tag: biologic

tag: status

tag: bx rna conc. (ng/ul)

tag: bx rna volume (ul)

tag: bx rna yield (ng)

tag: rin

tag: ethnicity

tag: age

tag: gender

tag: smoking status (prev)

value: Yes

tag: smoking status (curr)

tag: diagnosis

value: RA

tag: duration of disease (yrs)

tag: steroids (medication)

tag: location of joint biopsy

tag: aggregational histological score

value: Pauci-immune

tag: inflammatory score

tag: swollen joint count (28)

tag: tender joint count (28)

tag: das28 score

tag: patient global assessment of disease activity (vas)

tag: physician global assessment of disease activity (vas)

tag: haq-di score

tag: crp

tag: esr

value: No


title: UPPLLVC2

description:
UPPL1541 cell line in vitro treated with LV-Ctrl
UPPL1541_IX_032

tag: tissue

tag: cell line

tag: cell type

tag: genotype


title: CM49LVC2

description:
MB49 cell line in vitro treated with LV-Ctrl
MB49_IX_016


title: UPPLLVC3

description:
UPPL1541 cell line in vitro treated with LV-Ctrl
UPPL1541_IX_033


title: MLVC4R

description:
MB49 tumors in vivo were treated with lentiviral Ctrl (LV-Ctrl)
MB49_in_vivo_IX_009


title: UPPLsal1

description:
UPPL1541 cell line in vitro no treatement
UPPL1541_IX_025


title: HEK293_50k_cells_Input.rep1

city: Chicago

first: Ruitu

last: Lyu

state: IL

address: 929 E 57th Street

department: Chemistry

institute: The University of Chicago

data_processing:
library strategy: strand-specific KAS-seq
First, the trim-galore package was used to remove low-qualified bases and adapter-containing reads from raw spKAS-seq data. Trimmed reads shorter than length 30 bp were discarded, and the rest were aligned to the reference genome (hg19) using bowtie2 (v2.3.3.1) under default parameters.
Sam files were subsequently converted and sorted to bam files using samtools (v1.9). Duplicated mapped reads were removed using picard MarkDuplicates (v1.141).
For paired-end spKAS-seq data, SAMtoBED.py was used to combine “properly paired” alignments into a single BED interval. For single-end spKAS-seq data, deduplicated unique mapped reads were extended to 150 bp to match the average length of DNA fragments (awk command).
Bed files were converted to bedGraph files using bedtools. BedGraph files were then converted to bigWig files using bedgraphtobigwig from UCSC pre-compiled utilities.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig, spKAS-seq density on plus and minus strands.

source_name: Human embryonic kidney cells

growth_protocol: HEK293T and HepG2 cells were purchased from ATCC (CRL11268 for HEK293T, HB8065 for HepG2) and were cultured in DMEM (Gibco 11995) supplemented with 10% (v/v) fetal bovine serum (Gibco), 1% penicillin and streptomycin (Gibco 10378) and grown at 37 °C with 5% CO2. K562 cells were purchased from ATCC (CCL243) and were cultured in RPMI 1640 (Gibco 11875) supplemented with 10% (v/v) fetal bovine serum (Gibco), 1% penicillin and streptomycin (Gibco) and grown at 37 °C with 5% CO2. All cell lines were routinely checked to be free of mycoplasma.

extract_protocol:
After labeling, cells were harvested for genomic DNA isolation by using the PureLink Genomic DNA mini kit (Thermo, K182002). Around 2 µg genomic DNA was then diluted in 100 µL 1× PBS supplemented with 25 mM K3BO3 and 20 mM DBCO-PEG4-biotin (Sigma, 760749). The mixture was gently shacked at 37 °C for 1.5 h, after which 5 µL RNase A (Thermo, 12091039) was added, followed by another 5 min incubation at 37 °C. DNA was then purified from the reaction by using the DNA Clean & Concentrator-5 kit (Zymo, D4013) and was fragmented to 150-350 bp by sonicating 30 cycles at 30s-on/30s-off setting using Diagenode Bioruptor Pico. Save 5% of the sonicated DNA as input and use the rest for enrichment with 10 µL Dynabeads MyOne Streptavidin C1 (Thermo, 65001). The beads were washed by 1× B&W buffer (5 mM Tris-HCl pH 7.4, 0.5 mM EDTA, 1 M NaCl, 0.05% Tween-20), resuspended in 95 µL 2× B&W buffer, and mixed with sonicated DNA. The binding was performed at room temperature for 15 min. The beads were washed once in 1× B&W buffer and then washed twice with 100 mM NaOH solution to denature the dsDNA and remove the DNA strands that are not labeled by N3-kethoxal. A final wash with 1× B&W buffer was followed, and DNA was eluted in 10 µL H2O by heating the beads at 95 °C for 10 min.
Input and enriched DNA were used for library construction by using the Accel-NGS Methyl-seq DNA library kit (Swift, 30024). Libraries were sequenced on Illumina platforms with pair-end more with around 60 million reads per library.

treatment_protocol: Cells were treated with 5 mM N3-kethoxal dissolved in their culture media for 10 min at 37 °C, 5% CO2.

value: Human embryonic kidney cells

tag: treatment

value: untreated

value: wild type

tag: tag

value: Input


title: UPPL100U-3

description:
UPPL1541 cell line in vitro treated with 100U recombinant IFNα
UPPL1541_IX_030


title: CM49LVC1

description:
MB49 cell line in vitro treated with LV-Ctrl
MB49_IX_015


title: CM49100-3

description:
MB49 cell line in vitro treated with 100U recombinant IFNα
MB49_IX_014


title: UPPLsal3

description:
UPPL1541 cell line in vitro no treatement
UPPL1541_IX_027


title: Spinal cord contusion injury, 3 days, replicate 4

type: RNA

city: Hangzhou

first: Linlin

state: Zhejiang

address: Yuhangtang Road No.866

department: Department of Basic Medicine Sciences

country: China

institute: Zhejiang University

description: CircRNA, lncRNA and mRNA expression in injured spinal cord in mice at 6 days after spinal cord contusion injury

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, limma packages in R

source_name: Spinal cord contusion injury, 3 days

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp WT Labeling Kit (Cat.# 5190-2943, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted and purified using miRNeasy Mini Kit（Cat#217004，QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

tag: gender

value: female

tag: age

value: Spinal cord contusion injury

value: spinal cord


title: UPPLIFN3

description:
UPPL1541 cell line in vivo treated with LV-IFNα
UPPL1541_IX_036

value: Bladder


title: CM49SAL1

description:
MB49 cell line in vitro no treatement
MB49_IX_009


title: Spinal cord contusion injury, 3 days, replicate 3

description: CircRNA, lncRNA and mRNA expression in injured spinal cord in mice at 5 days after spinal cord contusion injury


title: Spinal cord contusion injury, 3 days, replicate 1

description: CircRNA, lncRNA and mRNA expression in injured spinal cord in mice at 3 days after spinal cord contusion injury


title: UPPL100U-2

description:
UPPL1541 cell line in vitro treated with 100U recombinant IFNα
UPPL1541_IX_029


title: CM49IFN1

description:
MB49 cell line in vivo treated with LV-IFNα
MB49_IX_002


title: BBNLVC3

description:
BBN cell line in vitro treated with LV-Ctrl
BBN975_IX_021

value: p53+/- treated with BBN


title: BBNIFN3

description:
BBN cell line in vivo treated with LV-IFNα
BBN975_IX_024

value: Bladder cancer cell line


title: CM49100-2

description:
MB49 cell line in vitro treated with 100U recombinant IFNα
MB49_IX_013

value: DMBA induced C57Bl/6


title: BBN100U-1

description:
BBN cell line in vitro treated with 100U recombinant IFNα
BBN975_IX_016


title: CD19 minigene library RNA-seq 01

city: Mainz

first: Julian

last: König

address: Ackermannweg 4

department: Biology

institute: Institute of Molecular Biology, Mainz

description: imb_koenig_2018_14_sub01_schulz_CD19_RNAseq_mut_S1f_L001

data_processing:
Quality trimming: trimmomatic (v0.36) with the following parameters: PE -threads 16 -phred33 -trimlog trimmomatic.log SLIDINGWINDOW:6:10 MINLEN:0
Demultiplexing: Custom scripts specified in README.txt
Adapter trimming: Cutadapt (v1.16) with parameters --adapter=TAGAGGTTCC --no-indels --minimum-length=244 --pair-filter=both
Mapping index generation: STAR (v2.6.1b) with parameter --genomeSAindexNbases 4
Mapping: STAR (v2.6.1b) with parameters --outFilterMultimapNmax 1 --outSAMattributes All --alignEndsType EndToEnd --sjdbGTFfile CUSTOM_GTF --sjdbOverhang 259
Sorting and indexing: SAMtools (v1.5)
Isoform reconstruction and filtering: Custom Perl scripts
Genome_build: Custom CD19 minigene variant sequence
Supplementary_files_format_and_content: Matrix table with read frequences of reconstructed isoforms

molecule: polyA RNA

source_name: NALM-6 cells

growth_protocol: NALM-6 cells were obtained from ATCC and cultured in RPMI medium (Life Technologies) with 10% foetal bovine serum (Life Technologies) and 1% l-glutamine (Life Technologies).

extract_protocol:
Cells were harvested after 24hrs of the electroporation and RNA was isolated via the RNeasy Mini Kit (Qiagen). 20 µg isolated RNA was poly-A-selected using Dynabeads Oligo (dT)25 beads (Invitrogen) according to manufacturer’s recommendations.
Reverse transcription was performed on 500 ng poly-A-selected RNA with RevertAid Reverse Transcriptase (Thermo Fisher Scientific) according to the manufacturer’s recommendations. To prevent chimeric amplicons, the RNA-seq libraries were amplified via emulsion PCR (Williams, 2006) using the Phusion DNA Polymerase (NEB). The following primers containing Illumina adapters were used in the PCR: 5’- CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCTNNNNNNNNNNGGAACCTCTAGTGGTGAAGG-3’ (fwd) 5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTNNNNNNNNNNCCGCCAGTGTGATGGATATC-3’ (rev) under following conditions: : 98 °C for 30 s, 25 cycles of [98 °C for 10 s, 63 °C for 20 s, 72 °C for 1 min] and final extension at 72 °C for 5 min. Amplicons were purified using Agencourt AMPure XP beads (Backman Coulter). Purified products were analysed on the TapeStation 2200 capillary gel electrophoresis instrument (Agilent) and quantified using the Qubit assay (Thermo Fisher Scientific).

treatment_protocol: Cells were twice washed in Dulbecco's phosphate buffered saline (DPBS, Gibco Thermo Fisher Scientific) and then collected in R buffer with a density of 2 x 107 cells / ml. For electroporation, we used 5 µg plasmid DNA (with a concentration of at least 1 µg/µl) to 2 x 106 cells in R buffer for a 100 µl NEON electroporation pipette tip (Thermo Fisher Scientific) at 1600 V for 30 ms and 1 pulse. Cells were harvested 24 h later.


title: CD19 minigene library RNA-seq 02

description: imb_koenig_2018_14_sub02_schulz_CD19_RNAseq_mut_S1_L001


title: CM49SAL2

description:
MB49 cell line in vitro no treatement
MB49_IX_010


title: BBN100U-3

description:
BBN cell line in vitro treated with 100U recombinant IFNα
BBN975_IX_018


title: BBNsal2

description:
BBN cell line in vitro no treatement
BBN975_IX_014


title: Control, replicate 3

description: CircRNA, lncRNA and mRNA expression in normal spinal cord in mice

source_name: Control

value: Control


title: Control, replicate 2


title: Control, replicate 4


title: Control, replicate 1


title: Patient 40 untreated

city: Atlanta

first: Milad

last: Rad

state: GA

address: 266 Ferst Dr NW

department: School of Electrical and Computer Engineering

institute: Georgia Institute of Technology

description: Patient derived neutrophils were incubated overnight with vehicle control in media.

hyb_protocol: The GeneFilters were prehybridized for 2 h at 51C with 0.5 mg/ml of poly-dA (Invitrogen) and 0.5 mg/ml Cot-1 DNA (Invitrogen) in 10 ml of AlkPhos DIRECT hybridization buffer (Amersham Bioscience) and then hybridized for 17 h at 51C with the denatured radi

scan_protocol: The Human Immunology v2 NanoString nCounter Gene Expression CodeSet was used (NanoString, Seattle, WA). All NanoString-based measurements were conducted at the Emory University Integrated Genomics Core facility using an amplification step for low abundant RNA applied to all samples as previously described.

data_processing: Digital images are processed within the nCounter instrument, and the Reporter Probe counts are tabulated in a comma separated value (CSV) format for convenient data analysis with Nanostring’s free nSolver Analysis Software.

label: biotin

source_name: neutrophils

label_protocol: Five mg of total RNA was reverse-transcribed using oligo-dT primers (Invitrogen) and SuperScript II reverse transcriptase (Invitrogen) in the presence of 100 mCi of [33P]dCTP (Amersham Bioscience, Piscataway, NJ) according to the instructions for the Gene

extract_protocol: RNA was isolated from neutrophils using the Nucleospin RNA II kit with on-column genomic DNA digestion according to the manufacturer’s protocol (Takara, Mountain View, CA). RNA sizing quantification and quality control was performed in the Emory Integrated Genomics Core on an Agilent 2100 bioanalyzer using Pico and Nano Agilent kits and a Tecan optical density plate reader to measure the concentration of the RNA.28 A low input RNA amplification kit was used. Only children with paired poly(I:C) gene expression data were used in the NanoString gene expression analysis.

value: Unstimulated

tag: cluster


title: Spinal cord contusion injury, 3 days, replicate 2

description: CircRNA, lncRNA and mRNA expression in injured spinal cord in mice at 4 days after spinal cord contusion injury


title: Patient 37 polyIC

description: Patient derived neutrophils were incubated overnight with LMW LyoVec-poly(I:C) in media.

value: Stimulated


title: Patient 39 untreated


title: Patient 37 untreated


title: Patient 39 polyIC


title: Patient 36 polyIC


title: Patient 36 untreated


title: Patient 32 polyIC


title: Patient 32 untreated


title: Patient 27 polyIC


title: Patient 25 polyIC


title: Patient 27 untreated


title: Patient 25 untreated


title: Patient 24 untreated


title: Patient 24 polyIC


title: Patient 23 polyIC


title: Patient 23 untreated


title: Patient 20 untreated


title: Patient 20 polyIC


title: Patient 22 untreated


title: Patient 19 untreated


title: Patient 17 polyIC


title: Patient 22 polyIC


title: Patient 18 untreated


title: BBNIFN2

description:
BBN cell line in vivo treated with LV-IFNα
BBN975_IX_023


title: Patient 16 untreated


title: Patient 16 polyIC


title: Patient 18 polyIC


title: Patient 19 polyIC


title: Patient 17 untreated


title: Patient 15 untreated


title: Patient 14 untreated


title: Patient 13 untreated


title: Patient 12 polyIC


title: Patient 12 untreated


title: Patient 10 polyIC


title: Patient 10 untreated


title: Patient 15 polyIC


title: Patient 7 polyIC


title: Patient 14 polyIC


title: Patient 6 polyIC


title: Patient 6 untreated


title: Patient 8 polyIC


title: Patient 7 untreated


title: Patient 13 polyIC


title: Patient 8 untreated


title: Patient 2 untreated


title: Patient 4 polyIC


title: Patient 64

description: Patient derived neutrophils


title: Patient 4 untreated


title: Patient 2 polyIC


title: Patient 5 polyIC


title: Patient 1 polyIC


title: Patient 61

description: Patient derived neutrophils


title: Patient 3 untreated


title: Patient 1 untreated


title: Patient 63

description: Patient derived neutrophils


title: Patient 62

description: Patient derived neutrophils


title: Patient 3 polyIC


title: Patient 39

description: Patient derived neutrophils


title: Patient 58

description: Patient derived neutrophils


title: Patient 57

description: Patient derived neutrophils


title: Patient 53

description: Patient derived neutrophils


title: CM49IFN2

description:
MB49 cell line in vivo treated with LV-IFNα
MB49_IX_003


title: Patient 46

description: Patient derived neutrophils


title: Patient 5 untreated


title: Patient 45

description: Patient derived neutrophils


title: Patient 60

description: Patient derived neutrophils


title: Patient 51

description: Patient derived neutrophils


title: Patient 49

description: Patient derived neutrophils


title: Patient 50

description: Patient derived neutrophils


title: Patient 48

description: Patient derived neutrophils


title: Patient 43

description: Patient derived neutrophils


title: Patient 52

description: Patient derived neutrophils


title: Patient 37

description: Patient derived neutrophils


title: Patient 42

description: Patient derived neutrophils


title: Patient 47

description: Patient derived neutrophils


title: Patient 41

description: Patient derived neutrophils


title: Patient 59

description: Patient derived neutrophils


title: Patient 40

description: Patient derived neutrophils


title: Patient 27

description: Patient derived neutrophils


title: Patient 36

description: Patient derived neutrophils


title: Patient 25

description: Patient derived neutrophils


title: Patient 20

description: Patient derived neutrophils


title: Patient 19

description: Patient derived neutrophils


title: Patient 32

description: Patient derived neutrophils


title: Patient 24

description: Patient derived neutrophils


title: Patient 18

description: Patient derived neutrophils


title: Patient 16

description: Patient derived neutrophils


title: BBNsal1

description:
BBN cell line in vitro no treatement
BBN975_IX_013


title: Patient 17

description: Patient derived neutrophils


title: Patient 23

description: Patient derived neutrophils


title: Patient 13

description: Patient derived neutrophils


title: Patient 10

description: Patient derived neutrophils


title: Patient 26

description: Patient derived neutrophils


title: Patient 12

description: Patient derived neutrophils


title: Patient 14

description: Patient derived neutrophils


title: Patient 3

description: Patient derived neutrophils


title: Patient 4

description: Patient derived neutrophils


title: BBNLVC2

description:
BBN cell line in vitro treated with LV-Ctrl
BBN975_IX_020


title: Patient 7

description: Patient derived neutrophils


title: Patient 2

description: Patient derived neutrophils


title: Patient 8

description: Patient derived neutrophils


title: Patient 5

description: Patient derived neutrophils


title: Patient 1

description: Patient derived neutrophils


title: Patient 64 untreated


title: Patient 63 polyIC


title: Patient 64 polyIC


title: Patient 15

description: Patient derived neutrophils


title: Patient 60 polyIC


title: Patient 63 untreated


title: Patient 60 untreated


title: Patient 62 polyIC


title: Patient 58 polyIC


title: Patient 57 polyIC


title: Patient 61 polyIC


title: Patient 62 untreated


title: Patient 51 polyIC


title: Patient 53 untreated


title: Patient 61 untreated


title: Patient 51 untreated


title: Patient 6

description: Patient derived neutrophils


title: Patient 59 untreated


title: Patient 49 polyIC


title: Patient 49 untreated


title: Patient 57 untreated


title: Patient 50 polyIC


title: Patient 53 polyIC


title: Patient 59 polyIC


title: Patient 58 untreated


title: Patient 52 polyIC


title: Patient 46 untreated


title: Patient 50 untreated


title: Patient 48 untreated


title: Patient 52 untreated


title: Patient 48 polyIC


title: Patient 47 polyIC


title: Patient 43 untreated


title: Patient 47 untreated


title: Patient 42 polyIC


title: Patient 46 polyIC


title: Patient 45 polyIC


title: CD19 minigene library DNA-seq 01

data_processing:
Quality contol: FastQC
Demultiplexing and adapter trimming: Custom scripts specified in README.txt
Mapping: BLASR (v5.1) with standard parameters
Variant Calling: GATK HaplotypeCaller (v4.0.10) with the parameters --kmer-size 10 --kmer-size 15 --kmer-size 25 --allow-non-unique-kmers-in-ref.  Barcodes with more than 25% variants of low penetrance (AF < 0.8) were discarded.
Genome_build: Custom CD19 minigene sequence specified in README.txt

extract_protocol:
The DNA-seq was performed on the PacBio SMRT sequencing platform at MPI-CBG Dresden. For this purpose, the minigene plasmid library was digested with EcoRI and HindIII (New England Biolabs) and run on an agarose gel. The desired band at the size of 1,301 nt was cut out and purified using QIAquick Gel Extraction Kit (Qiagen).
Standard library preparation for run on PacBio SMRT cell.

tag: molecule subtype

value: transfected DNA


title: Patient 42 untreated


title: Patient 43 polyIC


title: MAC_dXKR8_Clone2_mouse2

city: Pittsburgh

first: Jacob

last: Stewart-Ornstein

state: PA

address: UPMC Hillman Cancer Center, 5117 Centre Avenue

department: computational and systems biology

institute: University of Pittsburgh, School of Medicine

data_processing:
Align fastq file to MM10 transcriptome with Salmon 0.7.2
Sum counts from transcripts by gene symbol
Genome_build: mm10
Supplementary_files_format_and_content: TSV read counts

source_name: sorted macrophage

growth_protocol: subcu MC38 tumors grown on the C57BL6 mice for 16 days. Tumors were dissected and macrophages were isolated by FACS

extract_protocol:
By Invitrogen PureLink kit
Truseq (illumina) with rRNA depletion
mRNA library constructed from sorted macrophages

treatment_protocol: No further treatment

tag: genotype/variation

value: Xkr8 KO


title: MAC_dXKR8_Clone1_mouse2


title: Patient 41 polyIC


title: CD19 minigene library DNA-seq 02


title: Patient 41 untreated


title: Patient 40 polyIC


title: Patient 45 untreated


title: cD8 enriched splenocytes_s3ATAC

city: Portland

first: Andrew

last: Adey

state: OR

address: 3181 S.W. Sam Jackson Park Rd, RHH, L103

department: MMG

institute: Oregon Health & Science University

data_processing:
Demultiplexing performed using unidex (https://github.com/adeylab/unidex)
Alignment to mm10 genome using bwa mem
Conversion to fragment files using sinto
Assembly: mm10
Supplementary files format and content: tsv files for frgaments and sample annotation and bam file for alignment

source_name: cD8 enriched splenocytes

extract_protocol:
Nuclei were isolated and CD8 enriched
s3-ATAC-seq according to Mulqueen et. al. Nature Biotechnology 2021

value: multiplexed treated and untreated

tag: strain

tag: disease

value: AML


title: 21LP071

city: Chengdu

first: Hao

last: Xu

state: China

address: No.17 section3 renmin south road, chengdu

institute: Sichuan university

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the steps: (1)remove the Adaptors; (2) exclude low quality reads; (3) remove low quality basic group from 3'-end to 5' end; (4)evaluate original sequencing, Effective sequencing, Q30, GC values.
Assembly: hg19
Supplementary files format and content: txt,gene coiunts expression

source_name: oral mucosa

extract_protocol:
Total RNA was extracted from tissue by Trizol reagent (Invitrogen). The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequecncing using standard illumina protocols

tag: condition

value: oral lichen planus

value: oral mucosa

value: immunosuppressive therapy


title: MAC_dXKR8_Clone2_mouse1


title: MAC_dXKR8_Clone1_mouse1


title: WT-6dpf-4 [N047-04]

city: Gwangju

first: Yunju

last: Jo

address: 123, Cheomdangwagi-ro

country: South Korea

institute: Gwangju Institute of Science and Technology

data_processing:
Quantitative analysis was performed using 51bp of insert reads (Read2). Cell barcode and UMI in Read1 was extracted by using UMI-tools (ver.1.1.1). Four cell barcodes were mixed and used for all samples. Adaptor sequence and low quality sequence were removed and read length below 20bp were discarded by using Trim Galore (ver.0.6.7). Reads were mapped to the GRCz11 reference using HISAT2 (ver.2.2.1). Read counts for each gene were obtained by featureCounts (ver.2.0.1). UMI duplication was removed by UMI-tools.
Assembly: GRCz11
Supplementary files format and content: tab-delimited text files include TMM values for each Sample

organism: Danio rerio

source_name: liver

extract_protocol:
Total RNA was extracted by using Direct-zol RNA Kit (ZYMO RESEARCH) according to the manufacture’s instruction.
3’UTR RNA-seq was performed using the CEL-Seq2 protocol except that Second Strand Synthesis Module (NEB) was used for double-stranded cDNA synthesis and library was amplified by 9 cycles of PCR without any sample pooling.

value: liver

value: Wild type

value: fasted


title: WT-6dpf-1 [N047-01]


title: pex5KO-6dpf-2 [N047-06]

value: pex5 KO


title: 22RV1 cells, 2 µM Thal-SNS032, 24 hour, rep3 [E3]

city: Shanghai

first: Jiacheng

last: Li

state: Shanghai

address: 555 Zuchongzhi Road

department: Drug Discovery and Design Center

institute: Shanghai Institute of Materia Medica, Chinese Academy of Sciences

data_processing:
Illumina Casava1.7 software was used for basecalling.
The software fqtools-plus was used to remove adapter polluted reads(reads contain adapter more than 5bp),  low-quality reads(reads in which more than 15% bases with base calling quality Q≤19), and reads which contain N higher than 5%(For paired-end sequencing, both reads will be filtered if either end has N beyond the offset 5%)
The software STAR 2.5.3a was applied to map the sequencing reads to hg19 followed by gene annotation in GTF format (UCSC hg19) with parameters as follows: alignIntronMax INTRONMAX ; outFilterMultimapNmax 1; outReadsUnmapped Fastx; outSAMtype BAM SortedByCoordinate; twopassMode Basic.
The alignment files outputed from STAR 2.5.3a were used for quantification of gene expression by the software featureCounts 1.5.3. Reads count for each gene in each sample was counted by featureCounts with parameters as follows:"featureCounts -a $gtf -o $result -p ${fastq}  -T 40 > $log 2>&1 &".
Assembly: hg19
Supplementary files format and content: tab-delimited text files include reads count values for each sample.

growth_protocol: 22Rv1 cells were cultured inRPMI 1640 Medium (BasalMedia, Catalog# L210KJ) contained 10% fetal bovine serum, as well as 1% antibiotic & anti-mycoplasma Penicillin-Streptomycin-SaveIt (PSS) solution (Hanbio, Catalog# HB-PSS-100) in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
After three times washes with PBS, cells were collected after adding Trizol Reagent.
Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.

treatment_protocol: 22RV1 cells were exposed to DMSO, 2 µM SNS032, 2 µM LL-K9-3, and 2 µM Thal-SNS032 in biological triplicate for 24 hours

value: human prostate cancer (AR positive)

value: WT

value: 2 uM Thal-SNS032 for 24 hour


title: 22RV1 cells, 2 µM LL-K9-3, 24 hour, rep2 [D2]

value: 2 uM LL-K9-3 for 24 hour


title: MAC_WTb_mouse2

value: wild type


title: 21LP066


title: 22RV1 cells, 2 µM SNS032, 24 hour, rep3 [B3]

value: 2 uM SNS032 for 24 hour


title: 22RV1 cells, 2 µM Thal-SNS032, 24 hour, rep2 [E2]


title: 21LP062


title: MAC_WTb_mouse1


title: 22RV1 cells, 2 µM SNS032, 24 hour, rep2 [B2]


title: 21LP061


title: 21LP069


title: 21LP067


title: 22RV1 cells, 2 µM LL-K9-3, 24 hour, rep1 [D1]


title: 22RV1 cells, 2 µM SNS032, 24 hour, rep1 [B1]


title: 22RV1 cells, 2 µM LL-K9-3, 24 hour, rep3 [D3]


title: 22RV1 cells, DMSO, 24 hour, rep3 [A3]

value: 0.1% DMSO for 24 hour


title: 21LP056


title: 22RV1 cells, DMSO, 24 hour, rep2 [A2]


title: 21LP055


title: ZFM_Paracancerous

first: jin

last: wang

address: 2901 Caolang Road, Jinshan District,

institute: Shanghai Public Health Clinical Center, Fudan University,

description: Gene expression data from Paracancerous tissue lower than Kidney Malignancy with HIV tissue

data_processing:
The original sequencing data were fastQ format files (FQ files). After analysis and processing, they were sorted into the results of expression values at the transcription level, and the differential transcripts were calculated and displayed.
The original image data files obtained by high-throughput sequencing are converted into original sequencing sequences by CASAVA base recognition, and these sequence files are called RAW reads. The original data of this project is in fastQ format and stored in xxx.fq.gz file name format. The file is mainly used to store the original sequencing information and other software tools for use.
The original data obtained by sequencing are stored in fastQ format. Since this project is double-end sequencing, each sample contains two FASTQ files. For each individual FASTQ file, FastQC[1] software was used to evaluate the quality of the sequencing results.
Fastp software is used to filter the sequence
Hisat was used for sequence alignment. Its alignment algorithm is called Spliced Maping algorithm, which can partition and map the read that cannot be fully matched. It is suitable for the alignment of eukaryotic genomes containing introns.
Assembly: hg19
Supplementary files format and content: EdgeR software package was used to analyze differences in gene expression between samples and groups. After p-value is calculated, multiple hypothesis testing is performed and the threshold of p-value is determined by controlling the False Discovery Rate (FDR). The corrected p-value is called Q value. At the same time, the differential expression multiple (FOLD change, FC for short) was calculated according to FPKM value, which was often represented by LOG2 (FC). In general, the FPKM value of 0.1 or 1 is used as the threshold to judge whether a gene is expressed or not. Different literatures use different thresholds. By default, the results of any group whose FPKM>1 in the comparison group are retained in this differential gene analysis.

source_name: Paracancerous tissue7

growth_protocol: 7 IHIV-associated kidney cancer tissue during operation as well as its corresponding adjacent normal tissue.

extract_protocol:
Total RNA was extracted and purified using mirVana™ miRNA Isolation Kit (Cat#AM1561, Ambion, Austin, TX, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).
Paired-end libraries were synthesized by using the mRNA-seq Lib Prep Kit for Illumina  (ABclonal, China) following Sample Preparation Guide. Briefly, The poly-A containing mRNA   molecules were purified using poly-T oligo-attached magnetic beads.Following purification, the   mRNA is fragmented into small pieces using divalent cations under 94℃ for 8 min. The cleaved   RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers.   This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These   cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then   ligation of the adapters. The products are then purified and enriched with PCR to create the final   cDNA library

treatment_protocol: The fresh samples were extremely quick intensive chilling in liquid nitrogen within 5 minutes of excision to avoid degradation. Then frozen specimens were storage at -80 °C refrigerator.

value: Paracancerous tissue7

value: male


title: 22RV1 cells, DMSO, 24 hour, rep1 [A1]


title: LKQ_Tumor

source_name: Kidney Malignancy  with HIV tissue6

value: Kidney Malignancy  with HIV tissue6


title: ZFM_ Tumor

source_name: Kidney Malignancy  with HIV tissue7

value: Kidney Malignancy  with HIV tissue7


title: pex5KO-6dpf-1 [N047-05]


title: 21LP050

value: oral lichen planus

value: oral mucosa


title: 21LP047

value: immunosuppressive therapy


title: 21LP037


title: 21LP046


title: H2Aub-Usp16KO-GV

first: Li

last: Shen

state: Zhejiang Province

address: 866 Yuhangtang Road

institute: Life Sciences Institute, Zhejiang University

data_processing:
ChIP-seq reads were trimmed to 50 bp and aligned to the mouse genome build mm9 using  bowtie2 (v2.3.4.1) with default parameters. All unmapped reads, non-uniquely mapped reads and PCR duplicates were removed. H3K4me3 peaks were called using MACS2 (v 2.1.1.20160309) with the parameters -q 0.05 --nomodel --nolambda --broad --extsize 300 -B --SPMR -g mm and signal tracks for each sample were generated with chromstaR (v1.7.3) with parameter binsizes = 1000,stepsizes = 200.
Assembly: mm9
Supplementary files format and content: bigWig

source_name: Mouse GV Ooctye

growth_protocol: Female mice were injected with 5 IU of PMSG and humanely euthanized 44 h later. Oocytes at the GV stage were harvested from ovary in M2 medium. Female mice were injected with 5 IU of PMSG followed by hCG 44 h later. Oocytes and cumulus complexes were harvested from oviducts at 16 h after hCG injection. We could get oocytes at MII stage after digestion with 0.3% hyaluronidase. Superovulated females were crossed with fertile WT males and we could get zygotes the next day and 2-cell stage embryos the third day from oviducts.

extract_protocol:
ChIP-seq was performed following the previously reported carrier DNA assisted ChIP-seq (CATCH-Seq) protocol. For each immunoprecipitation assay, 200-500 oocytes, zygotes or 2-cell embryos, as well as one microgram of H2AK119ub1 antibody (8240, Cell Signaling Technology) was used.
The sequence libraries were generated using the NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645, New England Biolabs) following the manufacturer's instructions.

treatment_protocol: Zona pellucida-free oocytes and embryos were collected in 0.2% BSA in DPBS and then stored at -80℃.

tag: stain

value: Mouse GV Ooctye

tag: antibody


title: 21LP013


title: 21LP009


title: XC_ Tumor

source_name: Kidney Malignancy  with HIV tissue5

value: Kidney Malignancy  with HIV tissue5


title: 21LP025


title: 21LP034


title: LKQ_Paracancerous

source_name: Paracancerous tissue6

value: Paracancerous tissue6


title: 21LP058


title: H2Aub-WT-MII-2

data_processing:
ChIP-seq reads were trimmed to 50 bp and aligned to the mouse genome build mm9 using  bowtie2 (v2.3.4.1) with default parameters. All unmapped reads, non-uniquely mapped reads and PCR duplicates were removed. H3K4me3 peaks were called using MACS2 (v 2.1.1.20160309) with the parameters -q 0.05 --nomodel --nolambda --broad --extsize 300 -B --SPMR -g mm and signal tracks for each sample were generated with chromstaR (v1.7.3) with parameter binsizes = 1000,stepsizes = 200.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig

source_name: Mouse MII Ooctye

tag: developmental stage

value: MII Ooctye


title: H2Aub-WT-2-cell-1

source_name: Mouse 2-cell embryo

value: 2-cell embryo


title: 21LP012

tag: tissue


title: H2Aub-WT-Zygote-1

source_name: Mouse Zygote

value: Zygote


title: YHZ_Tumor

source_name: Kidney Malignancy  with HIV tissue4

value: Kidney Malignancy  with HIV tissue4


title: 21LP006


title: XC_Paracancerous

source_name: Paracancerous tissue5

value: Paracancerous tissue5


title: H2Aub-Usp16KO-MII

value: Mouse MII Ooctye


title: 22RV1 cells, 2 µM Thal-SNS032, 24 hour, rep1 [E1]

tag: cell line

value: human prostate cancer (AR positive)

value: WT

value: 2 uM Thal-SNS032 for 24 hour


title: YHZ Paracancerous

source_name: Paracancerous tissue4

value: Paracancerous tissue4

value: male


title: H2Aub-WT-GV-1

value: GV Ooctye


title: H2Aub-WT-MII-1


title: Liver_Nfkbiz_4w_rep3

city: Yakushiji Shimotsuke-shi

first: Morisada

last: Hayakawa

state: Tochigi

country: Japan

institute: Jichi Medical University

description: Gene expression data from the liver of nfkbiz-expressing AAV8 vector-treated mice fed a high-fat diet (CDAHFD) for 4 weeks.

hyb_protocol: Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45˚C on GeneChip Mouse Genome 430 2.0 Array. GeneChip array was washed and stained in the GeneChip Fluidics Station 450 (Thermo Fisher Scientific).

scan_protocol: GeneChip array was scanned using GeneChip Scanner 3000 7G.

data_processing: Single Array Analysis was calculated by Microarray Suite version 5.0 (MAS5.0) with Thermo Fisher Scientific default setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label: Biotin

source_name: Liver of nfkbiz-expressing AAV8 vector-treated mice fed a high-fat diet (CDAHFD) for 4 weeks

label_protocol: Biotinylated cRNA was synthesized by GeneChip 3' IVT PLUS Reagent Kit Thermo Fisher Scientific) from 100 ng total RNA according to the manufacturer's instructions. Biotinylated cRNA yield was checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: C57BL/6 mice were injected intravenously with AAV8 vector expressing luciferase or nfkbiz. Four weeks after vector injection, CDAHFD challenge was performed for 4 weeks.

extract_protocol: Total RNA was isolated from liver cells using an RNeasy Plus Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Mice anesthetized with isoflurane were intracardially perfused with PBS to remove blood, and then liver tissues were isolated. Liver tissues were soaked in RNAlater Stabilizaion Reagent (QIAGEN) overnight at 4°C and stored in a deep freezer at -80°C until extraction.

value: Liver

tag: treated with

value: nfkbiz-expressing AAV8 vector

tag: disease state

value: NAFLD model


title: HRSS345D-HD5

type: protein

city: Philadelphia

first: lei

last: guan

address: 433 S University Ave.

institute: university of pennsylvania

description: healthy donor 5 cd8 T cell treated HRSS345D WM9 sEVS

hyb_protocol: Cells were washed by PBS for 3 times before lysis, Samples were probed with antibodies by CSA amplification approach and visualized by DAB colorimetric reaction.

scan_protocol: the array were performed by the protocol from RPPA Core Facility, MD Anderson Cancer Center, Slides were scanned on a flatbed scanner to produce 16-bit tiff image. Spots from tiff images were identified and the density was quantified by Array-Pro Analyzer.

data_processing: Relative protein levels for each sample were determined by interpolation of each dilution curves from the standard curve (supercurve) of the slide (antibody).  Supercurve is constructed by a script in R written by Bioinformatics.  These values (given as Log2 values) are defined as Supercurve Log2 (Raw) value

label: antibody

molecule: protein

source_name: cd8 T cells

label_protocol: antibody

growth_protocol: Human CD8 T cells growth T cell culture medium(Thermo) with 10% FBS(Gibco)

extract_protocol: Cells were lysised by Cell Lysis Buffer: 1% Triton X-100, 50mM HEPES, pH 7.4, 150mM NaCl, 1.5mM MgCl2, 1mM EGTA, 100mM NaF, 10mM Na pyrophosphate, 1mM Na3VO4, 10% glycerol, containing freshly added protease and phosphatase inhibitors from Roche Applied Science Cat. # 05056489001 and 04906837001, respectively

treatment_protocol: Human  CD8 T cells were treated with small extracellular vesicles derived from WM9 cells. Human CD8 T cells were stimulated with anti-CD3 and anti-CD28 antibodies for 24 h befor treatment

value: human blood

tag: donor

value: healthy donor 5

tag: cell type

value: cd8 T cell

tag: agent

value: HRSS345D WM9 sEVS


title: Liver_Nfkbiz_4w_rep2


title: Usp16KO-2cell-1

data_processing:
Raw reads were trimmed to 50 bp and were mapped to the mouse genome (mm9) using Tophat v2.1.1 with default parameters. Only uniquely mapped reads could be subsequently assembled into tran- scripts guided by the reference annotation (UCSC gene models) using Cufflinks v2.2.1. The expression level of each gene was quantified with normalized FPKM (fragments per kilobase of exon per million mapped fragments).
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values of all Polysome-seq samples

source_name: mouse 2-cell embryo

growth_protocol: The embyos are clutured in KSOM in vitro

extract_protocol:
Embryos were collected from indicated genotypes (10 embryos per sample). Each sample was directly lysed with 4 ul lysis buffer (0.2% Triton X-100, RNase inhibitor, dNTPs, oligo-dT primers) and immediately used for cDNA synthesis using the Smart-seq2 method as described previously (Picelli et al, 2014).
Sequencing libraries were constructed from 500 pg of amplified cDNA using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD503) according to manufacturer’s instructions. Barcoded libraries were pooled and sequenced on the Illumina HiSeq X Ten platform with 150 bp paired-end reads

treatment_protocol: After zona pellucida removed by acid M2 medium (1% HCl), oocytes were collected within less than 0.5 μl 0.2% BSA/DPBS.

value: Usp16 maternal -/ paternal +

tag: Stage

value: 2-cell embryo


title: ZZM-Tumor

source_name: Kidney Malignancy  with HIV tissue3

value: Kidney Malignancy  with HIV tissue3

tag: gender

tag: age


title: Usp16KO-2cell-2

tag: genotype/variation


title: HRSWT-HD5

description: healthy donor 5 cd8 T cell treated HRSWT WM9 sEVS

value: HRSWT WM9 sEVS


title: HRSS345A-HD5

description: healthy donor 5 cd8 T cell treated HRSS345A WM9 sEVS

value: HRSS345A WM9 sEVS


title: Usp16KO-1cell-2

source_name: mouse 1-cell embryo

value: 1-cell embryo


title: Usp16KO-1cell-1


title: WKD-Paracancerous

source_name: Paracancerous tissue2

value: Paracancerous tissue2


title: ZZM-Paracancerous

source_name: Paracancerous tissue3

value: Paracancerous tissue3


title: JF-Tumor

source_name: Kidney Malignancy  with HIV tissue1

value: Kidney Malignancy  with HIV tissue1

value: male


title: HRSS345D-HD4

description: healthy donor 4 cd8 T cell treated HRSS345D WM9 sEVS

value: healthy donor 4


title: WT-2cell-2

value: wild type


title: HRSS345A-HD4

description: healthy donor 4 cd8 T cell treated HRSS345A WM9 sEVS


title: Liver_Nfkbiz_4w_rep1

value: Liver

tag: strain

value: nfkbiz-expressing AAV8 vector

value: NAFLD model


title: Liver_Luciferase_4w_rep3

description: Gene expression data from the liver of luciferase-expressing AAV8 vector-treated mice fed a high-fat diet (CDAHFD) for 4 weeks.

source_name: Liver of luciferase-expressing AAV8 vector-treated mice fed a high-fat diet (CDAHFD) for 4 weeks

value: luciferase-expressing AAV8 vector


title: WT-1cell-2


title: Liver_Luciferase_4w_rep1


title: HRSWT-HD4

description: healthy donor 4 cd8 T cell treated HRSWT WM9 sEVS

value: human blood

value: cd8 T cell


title: WKD-Tumor

source_name: Kidney Malignancy  with HIV tissue2

value: Kidney Malignancy  with HIV tissue2


title: Vehicle-HD5

description: healthy donor 5 cd8 T cell treated Vehicle

value: healthy donor 5

value: Vehicle


title: Vehicle-HD4

description: healthy donor 4 cd8 T cell treated Vehicle


title: WT-2cell-1

value: 2-cell embryo


title: HRSS345D-HD3

description: healthy donor 3 cd8 T cell treated HRSS345D WM9 sEVS

value: healthy donor 3

value: HRSS345D WM9 sEVS


title: Kidney carcinoma cells - A-498, PDL1-IFNg, rep1

city: Rockville

first: Alexis

middle: L

last: Norris

state: MD

address: 7500 Standish Place

institute: US FDA

description: Sample 10

data_processing:
Base calling with bcl2fastq2 version 2.19.0
Sequencing reads were trimmed using trimmomatic (version 0.36.6; parameters: SLIDINGWINDOW:4:20 MINLEN:50)
Aligned to GRCh38/hg38 using HISAT2 (version 2.1.0; parameters: --n-ceil L,0.0,0.15 --mp 6,2 --no-softclip --np 1 --rdg 5,3 --rfg 5,3 --sp 2,1 --score-min L,0.0, -0.2 --pen-cansplice 0 --pen-noncansplice 12 --pen-canintronlen G,-8.0,1.0 --pen-noncanintronlen G,-8.0,1.0 --min-intronlen 20 --max-intronlen 500000)
Gene counts were estimated using featureCounts (version 1.6.3; parameters: -s 1 -t 'exon' -g 'gene_id' -J -Q 12 --minOverlap 1 --fracOverlap 0 --fracOverlapFeature 0) with GENCODE gene annotation (version 33; Ensembl version 99)
Assembly: hg38
Supplementary files format and content: FASTQ files have adapters trimmed but were not trimmed for quality using trimmomatic.
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: The ccRCC cell lines 786-O and A498 were purchased from ATCC. They were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) growth media containing 25mM glucose and glutamine supplemented with 10% heat-inactivated fetal bovine serum and 1% penicillin-streptomycin at 37⁰C in a humidified atmosphere of 5% CO2. Stable 786-O and A498 cell lines expressing Renilla luciferase were generated by transducing cells with LP462-025 lentiviral particles (Genecopia). Briefly, 786-O and A498 cells were transduced with lentiviral particles at a MOI (multiplicity of infection) of 5 in complete media with polybrene at a concentration of 5 μg/mL. Transduced cells were selected with media containing puromycin at a concentration of 4 μg/mL. Renilla Luciferase activity in cells was measured according to the manufacturer protocol.

extract_protocol:
Total RNA from three groups (Cnsi, Cnsi-IFNγ, and PD-L1si IFNγ) for both A498 and 786-O cell lines, was extracted using RNeasy Mini Kit (Qiagen, Germany) according to the manufacturer’s protocol. Quality of the RNA samples was checked using the Agilent Bioanalyzer RNA Nano Chip (Santa Clara, CA) to determine RNA Integrity Number (RIN) ≥ 8.
RNA samples were processed following the Illumina (San Diego, CA) TruSeq Stranded messenger RNA Sample Preparation Kit performed at FDA Core Facility (36). Briefly, poly (A) tailed RNA was purified from 100-200 ng of total RNA, fragmented, and reverse-transcribed into cDNAs. Double strand cDNAs were adenylated at the 3’ ends and individually indexed, followed by limited-cycle (15) amplification.

treatment_protocol: On-Target plus SMARTpool small interfering RNAs (siRNAs) against PD-L1 was purchased from Dharmacon. All siRNA transfections were conducted at a final concentration of 20 nM using Lipofectamine RNAiMAX (Invitrogen) following the manufacturer instructions. Non-targeting pool siRNA was used as a control (Cnsi). Transient silencing experiments had four groups, Cnsi (control scrambled siRNA, untreated), Cnsi IFNγ (IFNγ treated), PD-L1si (PD-L1 siRNA) and PD-L1si IFNγ (PD-L1 siRNA and IFNγ treatment). A498 and 786-O cells were transfected with control (scrambled siRNA) or PD-L1 siRNA, at the end of 24 hours of transfection, select groups were treated with IFNγ (50 ng/mL) for another 24 hours.

value: clear cell renal cell carcinoma (ccRCC)

value: Kidney carcinoma cells

tag: sirna

value: PD-L1 siRNA

tag: genotype

value: PD-L1 knockout

tag: treatment

value: Interferon gamma


title: Kidney carcinoma cells - A-498, PDL1-IFNg, rep2

description: Sample 11


title: KO, rep2

city: shanghai

first: Qianwen

last: Hu

address: 重庆南路280号

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Using HISAT2 RNA-sequencing alignment software, the raw reads were aligned to the mouse reference genome (version mm10). The mapping rate was 96%, on average, across all the samples in the dataset.
The alignment files (bam files) were processed to generate read counts for every gene using HISAT and HTSeq.
The read counts were normalized using the R package DESeq2 and then were centered and scaled for each gene, generating z-scores. P values obtained from multiple tests were adjusted using the Benjamini-Hochberg correction.
Assembly: mm10 (GRCm38)
Supplementary files format and content: genes.readcount.csv: Comma-separated text file containing read count for each gene.

source_name: GC B cell

extract_protocol:
IgD- CD19+CD95+CD38- GC B cells were FACS-sorted and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Bach2+/+ Aicdacre or Bach2fl/fl Aicdacre mice were immunized with SRBC and sacrificed for analysis at day10.

value: spleen

value: CD19+ IgD- CD95+ CD38- GC B cells

value: Bach2f/f Aicdacre

value: SRBC immunization


title: KO, rep3


title: Kidney carcinoma cells - A-498, PDL1, rep3

description: Sample 9

source_name: Kidney carcinoma cells - A-498, PDL1


title: Kidney carcinoma cells - A-498, PDL1-IFNg, rep3

description: Sample 12


title: Kidney carcinoma cells - A-498, PDL1, rep2

description: Sample 8


title: JF-Paracancerous

source_name: Paracancerous tissue1

value: Paracancerous tissue1

value: male


title: HRSS345A-HD3

description: healthy donor 3 cd8 T cell treated HRSS345A WM9 sEVS

value: human blood

value: cd8 T cell

value: HRSS345A WM9 sEVS


title: KO, rep1


title: WT, rep3

value: Bach2+/+ Aicdacre


title: WT-1cell-1

value: wild type

value: 1-cell embryo


title: Kidney carcinoma cells - A-498, PDL1, rep1

description: Sample 7

value: clear cell renal cell carcinoma (ccRCC)


title: HRSS345D-HD2

description: healthy donor 2 cd8 T cell treated HRSS345D WM9 sEVS

value: healthy donor 2

value: HRSS345D WM9 sEVS


title: Vehicle-HD3

description: healthy donor 3 cd8 T cell treated Vehicle

value: healthy donor 3

value: Vehicle


title: Kidney carcinoma cells - A-498, Control-IFNg, rep3

description: Sample 6

value: Kidney carcinoma cells

value: Control scrambled siRNA

value: control

value: Interferon gamma


title: Liver_Luciferase_4w_rep2

value: Liver

value: luciferase-expressing AAV8 vector

value: NAFLD model


title: HRSS345A-HD2

description: healthy donor 2 cd8 T cell treated HRSS345A WM9 sEVS

value: human blood

value: cd8 T cell


title: WT, rep1

value: spleen

value: CD19+ IgD- CD95+ CD38- GC B cells

value: Bach2+/+ Aicdacre

value: SRBC immunization


title: Kidney carcinoma cells - A-498, Control, rep3

description: Sample 3

source_name: Kidney carcinoma cells - A-498, Control

value: clear cell renal cell carcinoma (ccRCC)


title: Kidney carcinoma cells - A-498, Control-IFNg, rep2

description: Sample 5


title: Vehicle-HD2

description: healthy donor 2 cd8 T cell treated Vehicle

value: healthy donor 2