title: mr_013_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

value: Asian

tag: age

tag: gender

tag: smoking status (prev)

tag: smoking status (curr)

tag: diagnosis

tag: duration of disease (yrs)

tag: steroids (medication)

value: Grade 3


title: H1299 cells, Si-FIBP#2 rep3

status: Public on Jun 06 2022

type: SRA

city: wuhan

first: Xu

last: YunHong

state: hubei

address: xinhua road

department: Union Hospital

country: China

institute: Huazhong University of Science and Technology

description:
H1299 cells were transfected indicated Scramble or Si-FIBP
Si2_3

library_source: transcriptomic

data_processing:
The raw paired end reads were trimmed and quality controlled by SeqPrep (https://github.com/jstjohn/SeqPrep) and Sickle (https://github.com/najoshi/sickle) with default parameters
clean reads were separately aligned to reference genome with orientation mode using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml) softwar
The mapped reads of each sample were assembled by StringTie(https://ccb.jhu.edu/software/stringtie/index.shtml? t=example) in a reference-based approach
Genome_build: NCBI genom build 36
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Homo sapiens

source_name: Human Lung cancer cell line

growth_protocol: cells were cultured at 37C in DMEM or RPMI1640 containing 10% fetal calf serum in 5% CO2/95% humidified air

extract_protocol:
Total RNA was extracted from the tissue using TRIzol Reagent (Plant RNA Purification Reagent
for plant tissue) according the manufacturer's instructions (Invitrogen) and genomic DNA was
removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser
(Agilent) and quantified using the ND-2000 (NanoDrop Technologies). high-quality RNA
was used to
Construct sequencing library:
RNA-seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit
from Illumina (San Diego, CA) using 1u of total RNA. Shortly, messenger RNA was isolated
according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation
buffer firstly. Secondly double-stranded cDNA was synthesized using a SuperScript
double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers (Illumina).
Then the synthesized cDNA was subjected to end-repair, phosphorylation and ¡®A¡¯ base addition
according to Illumina's library construction protocol. Libraries were size selected for cDNA target
fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion
DNA polymerase (NEB) for 15 PCR cycles. After quantified by TBS380, paired-end RNA-seq
sequencing library was sequenced with the Illumina HiSeq xten/NovaSeq 6000 sequencer (2 x 150bp read length).

tag: cell line

tag: cell type

value: Human Lung cancer cell line

tag: treatment

value: transfected with Si-FIBP#2

tag: genotype

value: FIBP depleted


title: Liver, 48 hr after 1Gy Dose, Sample 22

type: RNA

city: Northbrook

first: Michael

last: Falduto

state: IL

address: 1808 Janke, Unit M

country: USA

institute: GenUs BioSystems, Inc.

description: Liver 1Gy_22

hyb_protocol: 1 µg of purified cRNA was fragmented to uniform size and applied to Agilent Porcine (v2) Gene Expression Microarrays 4x44K Design ID 026440 (Agilent Technologies, Santa Clara, CA) in hybridization buffer. Arrays were hybridized at 65° C for 17 hrs. in a rotating incubator, washed at 37° C for 1 min, and stained with Streptavidin-Alexa555.

scan_protocol: Rinsed and dried arrays were scanned with an Agilent G2505C Microarray Scanner (Agilent Technologies, Santa Clara, CA) at 5 µm resolution.

data_processing: Agilent Feature Extraction software was used to process the scanned images from arrays (gridding and feature intensity extraction) and the data generated for each probe on the array was analyzed with GeneSpring GX v7.3.1 software (Agilent Technologies, Santa Clara, CA).

label: Alexa 555

organism: Mus musculus

source_name: Liver, 48 hr after 1Gy Dose

label_protocol: Labeled cRNA was prepared from total RNA samples. Briefly, the Poly(A)+ RNA population within total RNA was amplified using MessageAMP II (Applied Biosystems, Foster City, CA).  After a second round of reverse transcription, second-strand cDNA synthesis, and purification of double-stranded cDNA, in vitro transcription was performed using T7 RNA polymerase in the presence of Biotin-11-UTP.  The quantity and quality of the cRNA was assayed by spectrophotometry and on the Agilent Bioanalyzer.

extract_protocol: Approximately 100 µg of powdered sample was lysed with 700 µl of QIAzol lysis buffer (Cat # 79306, QIAGEN) and homogenized by passing the solution through QIAshredder spin columns (Cat # 79654, QIAGEN). RNA isolation was performed using standard miRNeasy mini kit (Cat # 217004, QIAGEN) according to the manufacturer’s protocol. Quality and quantity of the RNA samples were assessed using a DeNovix DS-11 nanodrop spectrophotometer (DeNovix, DE, US) and Agilent Bioanalyzer with the RNA6000 Nano Lab Chip (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Six- to 8-week old female C57BL/6 J mice were given total-body irradiation (TBI) with X-rays using the Small Animal Radiation Research Platform (SARRP Xstrahl Ltd.). Mice were placed in plastic containers and exposed to a single surface dose of 1, 2, 4, 8, or 12 Gy at a dose rate of 1.05 Gy/min. Control mice (0 Gy) were placed in the same type of plastic container and sham irradiated.

tag: strain

value: C57BL/6 J

tag: Sex

value: female

tag: tissue

value: Liver

tag: treatment/time point

value: 48 hr after 1Gy Dose


title: H1299 cells, Si-FIBP#2 rep1

description:
H1299 cells were transfected indicated Scramble or Si-FIBP
Si2_1


title: SNU1_TP53KO_MMC3UM_36hours

city: Shanghai

first: Jingyu

last: Lang

address: 320 Yueyang Road

institute: Shanghai Institutes for Biological Sciences

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to transcriptome gtf file version GRCh38_ensembl_v80 using Salmon v0.8.1 with parameters --gcBias
Transcript Per Kilobase of exon per Megabase of library size (TPM) were quantified using Salmon v0.8.1. from Patro, R. et al, 2017, Nature Methods
The top20 upregulated and top20 downregulated genes by MMC treatment in SNU1_TP53_WT cells were caculated by MMV vs DMSO.(The  TPM lower than 15 in DMSO were excluded)
Genome_build: GRCh38_ensembl_v80
Supplementary_files_format_and_content: xlsx files include TPM values for each Sample.

extract_protocol:
After cells were treated with MMC or vehicle for 36 hours, the cells were harvesed and lysed  in Trizol reagent and total RNA was eztracted.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: gastric cancer cell line

value: mitomycin C (3µM 36hours)


title: mr_012_pre

city: Worcester

first: Jing

last: Wang

state: MA

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

tag: pathotype

value: Lymphoid

tag: biologic

value: Etanercept

tag: status

value: Mod-Responder

tag: bx rna conc. (ng/ul)

tag: bx rna volume (ul)

tag: bx rna yield (ng)

tag: rin

value: Caucasian

value: F

value: No

value: RA

value: Yes

tag: location of joint biopsy

value: Wrist

tag: aggregational histological score

value: Grade 2

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

tag: rf

tag: acpa (ccp)

tag: radiographic erosion


title: mr_013_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: Asian

tag: age

tag: gender

tag: smoking status (prev)

tag: smoking status (curr)

tag: diagnosis

tag: duration of disease (yrs)

tag: steroids (medication)

value: Diffuse


title: H1299 cells, Si-FIBP#1 rep3

description:
H1299 cells were transfected indicated Scramble or Si-FIBP
Si1_3

tag: cell line

tag: cell type

value: Human Lung cancer cell line

tag: treatment

value: transfected with Si-FIBP#1

tag: genotype

value: FIBP depleted


title: Liver, 48 hr after 2Gy Dose, Sample 3

description: Liver 2Gy_3

source_name: Liver, 48 hr after 2Gy Dose

tag: strain

value: C57BL/6 J

tag: Sex

value: female

tag: tissue

value: Liver

tag: treatment/time point

value: 48 hr after 2Gy Dose


title: mr_011_post

tag: timepoint

tag: pathotype

value: Lymphoid

tag: biologic

value: Certolizumab

tag: status

value: Mod-Responder

tag: bx rna conc. (ng/ul)

tag: bx rna volume (ul)

tag: bx rna yield (ng)

tag: rin

value: African

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

tag: rf

tag: acpa (ccp)

tag: radiographic erosion


title: Liver, 48 hr after 0Gy Dose, Sample 21

description: Liver 0Gy_21

source_name: Liver, 48 hr after 0Gy Dose

tag: strain

tag: Sex

tag: tissue

tag: treatment/time point

value: 48 hr after 0Gy Dose


title: Cigarette smoke exposure_4w

city: Osaka

first: Shugo

last: Suzuki

state: Osaka

address: 1-4-3 Asahi-machi, Abeno-ku

department: Molecular Pathology

country: Japan

institute: Osaka Metropolitan University Graduate School of Medicine

description: Gene expression data from lung of cigarette smoke exposure male mice for 4 weeks

hyb_protocol: cRNA was hybridized to Affymetrix  Clariom D Assay Mouse array, washed and stained according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Affymetrix scanner.

data_processing: The raw data were normalized with SST-RMA algorithm (gene level) using Affymetrix Expression Console 1.4.1 software.

label: biotin

source_name: lung, cigarette smoke exposure male mice for 4 weeks

label_protocol: The cRNA was amplified, labeled using GeneChip WT PLUS Reagent Kit according to the manufacturer's instructions.

extract_protocol: RNeasy Mini Kit was performed according to the manufacturer's instructions.

treatment_protocol: Male 10-week-old C57BL mice were exposed to clean air (control) or mainstream cigarette smoke for 1 h/day (10 to 11 AM), 5 days/ week, for 2 or 4 weeks.

value: Male

tag: age

value: 14 weeks

tag: gender

value: male


title: SNU1_WT_MMC3UM_36hours

tag: cell type

value: gastric cancer cell line

tag: genotype

tag: treatment

value: mitomycin C (3µM 36hours)


title: H1299 cells, Si-FIBP#2 rep2

description:
H1299 cells were transfected indicated Scramble or Si-FIBP
Si2_2

tag: cell line

value: Human Lung cancer cell line

value: transfected with Si-FIBP#2

value: FIBP depleted


title: Control_4w

description: Gene expression data from lung of Control male mice

source_name: lung, control male mice


title: SNU1_TP53KO_vehicle_36hours

value: Vehicle (0.1% DMSO)


title: Liver, 48 hr after 0Gy Dose, Sample 1

description: Liver 0Gy_1

value: C57BL/6 J

value: female

value: Liver


title: Liver, 48 hr after 1Gy Dose, Sample 2

description: Liver 1Gy_2

value: 48 hr after 1Gy Dose


title: mr_010_post

tag: timepoint

value: Post

tag: pathotype

value: Lymphoid

tag: biologic

value: Certolizumab

tag: status

value: Mod-Responder

tag: bx rna conc. (ng/ul)

tag: bx rna volume (ul)

tag: bx rna yield (ng)

tag: rin

tag: ethnicity

value: Asian

value: M

tag: smoking status (prev)

value: Yes

tag: smoking status (curr)

tag: diagnosis

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 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)


title: SNU1_WT_vehicle_36hours

tag: cell type

value: gastric cancer cell line

tag: genotype

tag: treatment


title: Cigarette smoke exposure_2w

description: Gene expression data from lung of cigarette smoke exposure male mice for 2 weeks

source_name: lung, cigarette smoke exposure male mice for 2 weeks

tag: strain

tag: Sex

value: Male

tag: age

value: 12 weeks

tag: gender

value: male


title: Control_2w


title: Liver, 48 hr after 1Gy Dose, Sample 12

description: Liver 1Gy_12

value: C57BL/6 J

value: female

tag: tissue

value: Liver

tag: treatment/time point


title: Liver, 48 hr after 0Gy Dose, Sample 11

description: Liver 0Gy_11

value: 48 hr after 0Gy Dose


title: H1299 cells, Si-FIBP#1 rep1

description:
H1299 cells were transfected indicated Scramble or Si-FIBP
Si1_1

tag: cell line

value: Human Lung cancer cell line

value: transfected with Si-FIBP#1

value: FIBP depleted


title: mr_010_pre

tag: timepoint

value: Pre

tag: pathotype

value: Lymphoid

tag: biologic

value: Certolizumab

tag: status

value: Mod-Responder

tag: bx rna conc. (ng/ul)

tag: bx rna volume (ul)

tag: bx rna yield (ng)

tag: rin

tag: ethnicity

value: Asian

value: M

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

value: Grade 3

tag: inflammatory score

tag: swollen joint count (28)

tag: haq-di score

tag: crp

tag: esr

tag: rf

tag: acpa (ccp)

tag: radiographic erosion


title: NX210d-3

city: changsha

first: LI

last: Biao

address: Nongda South Road

department: College of Animal Science and Technology

institute: Hunan Agricultural University

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Genome_build: excel,expression profiles
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Sus scrofa

source_name: Sus scrofa (pig)

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

tag: tissue

value: Ningxiang pig-derived spleen

tag: developmental stage

value: post natal day 210


title: H1299 cells, Scramble rep2

description:
H1299 cells were transfected indicated Scramble or Si-FIBP
NC2

tag: cell line

tag: cell type

tag: treatment

value: transfected with Scramble

tag: genotype

value: control


title: H1299 cells, Scramble rep3

description:
H1299 cells were transfected indicated Scramble or Si-FIBP
NC3


title: NX210d-2


title: H1299 cells, Si-FIBP#1 rep2

description:
H1299 cells were transfected indicated Scramble or Si-FIBP
Si1_2


title: H1299 cells, Scramble rep1

description:
H1299 cells were transfected indicated Scramble or Si-FIBP
NC1


title: NX210d-1


title: mr_008_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

tag: smoking status (prev)

value: No

tag: smoking status (curr)

tag: diagnosis

value: RA

tag: duration of disease (yrs)

tag: steroids (medication)

value: Elbow

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)


title: mr_009_post

tag: timepoint

tag: pathotype

tag: biologic

tag: status

tag: bx rna conc. (ng/ul)

tag: bx rna volume (ul)

value: Asian or Asian British - Indian

value: F

tag: location of joint biopsy

value: Wrist

tag: aggregational histological score

value: Diffuse

tag: inflammatory score

tag: swollen joint count (28)

tag: haq-di score

tag: crp

tag: esr

tag: rf

tag: acpa (ccp)

tag: radiographic erosion


title: K562_Input.rep2

city: Chicago

first: Ruitu

last: Lyu

address: 929 E 57th Street

department: Chemistry

institute: The University of Chicago

library_source: genomic

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.

molecule: genomic DNA

source_name: Human myelogenous leukemia 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.

tag: cell type

value: Human myelogenous leukemia cells

tag: treatment

value: untreated

tag: genotype

value: wild type

tag: tag

value: Input


title: CspE crosslinked replicate 1

city: Würzburg

first: Lars

last: Barquist

state: Bayern

address: Josef-Schneider-Straße 2 / Bau D15

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research

description:
CLIP-seq
789_CspE_R1_XL

data_processing:
Reads were trimmed for adaptors and a minimum read quality of 20 using cutadapt 1.15
Reads were mapped to O78-9 genome and plasmids p789-1, p789-2 and p789-3 (CP010315.1, CP010316 (p789-1), CP010317, and CP010318, respectively) obtained from NCBI using READemption version 0.3.7
Only uniquely mapping reads were retained, and used as input for PEAKachu in adaptive peak calling mode using the default DESeq normalization between conditions.
Assembly: CP010315.1, CP010316, CP010317, CP010318
Supplementary files format and content: csv, called peaks for CspC
Supplementary files format and content: csv, called peaks for CspE

organism: Escherichia coli

source_name: bacteria

growth_protocol: Bacteria were grown up to OD600 of 1.2-1.4 and processed.

extract_protocol:
phenol chloroform isoamyl alcohol (PCI) RNA extraction on the eluted samples
NEBNext Multiplex Small RNA Library Prep Set for Illumina

treatment_protocol: For each biological replicate, 200 mL bacterial culture were grown to OD600 of 2.0. Half of the culture was treated directly and half was irradiated with UV-C light at 800 mJ/cm2.

tag: strain

value: bacteria

value: CspE-FLAG

value: UV cross-linked


title: mr_007_post

tag: timepoint

tag: pathotype

value: Myeloid

tag: biologic

value: Certolizumab

tag: status

value: Mod-Responder

tag: bx rna conc. (ng/ul)

tag: bx rna yield (ng)

tag: rin

tag: ethnicity

value: Asian

tag: age

tag: gender

value: M

tag: smoking status (prev)

value: Yes

tag: smoking status (curr)

tag: diagnosis

tag: duration of disease (yrs)

tag: steroids (medication)

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)


title: NX90d-3

tag: tissue

value: Ningxiang pig-derived spleen

tag: developmental stage

value: post natal day 90


title: mr_009_pre

tag: timepoint

value: Pre

tag: pathotype

value: Lymphoid

tag: biologic

tag: status

tag: bx rna conc. (ng/ul)

tag: bx rna volume (ul)

tag: bx rna yield (ng)

tag: rin

value: Asian or Asian British - Indian

value: F

value: No

value: RA

tag: location of joint biopsy

value: Wrist

tag: aggregational histological score

value: Grade 3

tag: inflammatory score

tag: swollen joint count (28)

tag: haq-di score

tag: crp

tag: esr

tag: rf

tag: acpa (ccp)

tag: radiographic erosion


title: NX90d-2

tag: tissue

tag: developmental stage


title: mr_008_pre

tag: timepoint

tag: pathotype

tag: biologic

tag: status

tag: ethnicity

tag: age

tag: gender

tag: smoking status (prev)

tag: smoking status (curr)

tag: diagnosis

tag: duration of disease (yrs)

tag: steroids (medication)

value: Elbow

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)


title: K562_spKAS-seq.rep2

tag: cell type

value: Human myelogenous leukemia cells

tag: treatment

value: untreated

tag: genotype

value: wild type

tag: tag

value: strand specific KAS-seq


title: NX90d-1

tag: tissue

tag: developmental stage


title: K562_Input.rep1

value: Input


title: mr_007_pre

tag: timepoint

tag: pathotype

value: Myeloid

tag: biologic

value: Certolizumab

tag: status

value: Mod-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: Yes

tag: location of joint biopsy

value: Knee

tag: aggregational histological score

value: Diffuse

tag: inflammatory score

tag: swollen joint count (28)

tag: haq-di score

tag: crp

tag: esr

tag: rf

tag: acpa (ccp)

tag: radiographic erosion


title: NX30d-3

tag: tissue

value: Ningxiang pig-derived spleen

tag: developmental stage

value: post natal day 30


title: NX30d-2


title: K562_spKAS-seq.rep1

tag: cell type

tag: treatment

tag: genotype

tag: tag


title: HEK293_Triptolide_spKAS-seq.rep2

source_name: Human embryonic kidney cells

value: Human embryonic kidney cells

value: treat with triptolide for 2h


title: mr_006_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)

tag: smoking status (curr)

value: No

tag: diagnosis

value: RA

tag: duration of disease (yrs)

tag: steroids (medication)

value: MCP

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)


title: NX30d-1

tag: tissue

tag: developmental stage


title: mr_006_pre

tag: timepoint

value: Pre

tag: pathotype

value: Myeloid

tag: biologic

value: Certolizumab

tag: status

value: Mod-Responder

tag: bx rna conc. (ng/ul)

tag: bx rna volume (ul)

tag: bx rna yield (ng)

tag: rin

tag: location of joint biopsy

tag: aggregational histological score

tag: inflammatory score

tag: swollen joint count (28)

tag: haq-di score

tag: crp

tag: esr

tag: rf

tag: acpa (ccp)

tag: radiographic erosion


title: HepG2_spKAS-seq.rep1

source_name: Human liver cancer cells

tag: cell type

value: Human liver cancer cells

tag: treatment

value: untreated

tag: genotype

value: wild type

tag: tag

value: strand specific KAS-seq


title: HepG2_spKAS-seq.rep2


title: mr_005_pre

tag: timepoint

tag: pathotype

tag: biologic

tag: status

tag: bx rna conc. (ng/ul)

tag: bx rna volume (ul)

tag: ethnicity

value: Asian

tag: age

tag: gender

tag: smoking status (prev)

tag: smoking status (curr)

tag: diagnosis

tag: duration of disease (yrs)

tag: steroids (medication)

value: Yes

value: Wrist

value: Diffuse

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)


title: HEK293_Triptolide_spKAS-seq.rep1

tag: cell type

value: Human embryonic kidney cells

tag: treatment

value: treat with triptolide for 2h

tag: genotype

tag: tag


title: mr_005_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

value: F

value: No

value: RA

tag: location of joint biopsy

tag: aggregational histological score

tag: inflammatory score

tag: swollen joint count (28)

tag: haq-di score

tag: crp

tag: esr

tag: rf

tag: acpa (ccp)

tag: radiographic erosion


title: Female Blimp1 KO mice 1

city: manhasset

first: kyungwoo

last: lee

state: NY

address: 350 community drive

institute: Feinstein Institute

data_processing:
sample’s sequences are aligned utilizing STAR v2.4.2a
GENCODE GFF3 annotation for feature counting
DESeq2 differential gene expression analysis
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: spleen

extract_protocol:
RNA was harvested using Rneasy micro kit (Qiagen). 50 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-seq2 mRNA-Seq Library Prep Kit following manufacturer's protocols.

tag: tissue

value: spleen

tag: cell type

value: Tfh

tag: genotype

value: Blimp1 KD


title: Female Blimp1 KO mice 3


title: Female Blimp1 KO mice 2


title: D4-500-3_Rep1

city: London

first: M Joaquina

last: Delas

address: 1 Midland Road

department: Briscoe Lab

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
Data was processed using the nf-core rnaseq pipeline with the following options: --star_index 'star_ercc_mm10_genome' --gtf 'mm10.refGene_wERCC.gtf' --fc_group_features_type gene_id --fc_extra_attributes gene_id -r 1.4.2
Gene counts were obtained from featureCounts with the option ignoreDup=TRUE to try and remove PCR duplicates.
Samples were excluded from downstream analysis based on a number of QC criteria particularly applicable to this type of low input samples from PFA-fixed cells including: too small proportion of the library being of mouse origin (excess spike-in representation), large number of overepresented sequences, and loss of dynamic range in spike-in quantification.
Assembly: mm10

molecule: polyA RNA

growth_protocol: Mouse ES cell lines were maintained in ES cell medium with 1000 U/ml LIF (Chemicon, Int ESG1107) on mitotically inactive primary mouse embryo fibroblasts (feeders) in ES cell medium (Dulbecco’s Modified Eagle Medium (DMEM) Knock Out (Gibco, Cat No. 10829-018) complemented with 10% Foetal Bovine Serum, Penicillin/Streptomycin (Gibco, Cat No. 15140122), 2mM L-Glutamine (Gibco, Cat No. 25030024), 2mM Non-essential amino acids (Gibco, Cat No. 11140-035), and 0.1 mM 2-mercaptoethanol (Gibco, Cat. No. 21985-023)). For spinal cord neural differentiation, ES cells were dissociated using 0.05% trypsin-EDTA (Gibco, Cat No. 25300054) and then plated onto 0.1% gelatinised (Gibco) tissue culture plates for three successive periods of 15 mins to remove feeders. Differentiations were carried out in N2B27 media (Advanced DMEM - F12 (Gibco, Cat No. 21331-020) and Neurobasal medium (Gibco, Cat No. A35829-01) (1:1), supplemented with 1xN2 (Gibco), 1xB27 (Gibco), 2 mM L-glutamine (Gibco, Cat No. 25030024), 40 μg/ml BSA (Sigma), and 0.1 mM 2-mercaptoethanol (Gibco, Cat. No. 21985-023)) with the indicated additives. Cells were plated onto 6-well plates (Corning, Cat. No. 353046) precoated in Matrigel (Corning, Cat. No. 356231) diluted 1/50 and 1/100 in Advanced DMEM - F12 (Gibco, Cat No. 21331-020) at a density of 20,000 cells per 35mm well in 1.5 ml. The media was supplemented on the different days as follows: Day 0 to Day 2, 10ng/ml bFGF (R&D, Cat No. 100-18B) and 5 μM LGK (Cayman Chemical Company, Cat. No. 1.800.364.9897); Day2 to Day 3 for 20 h, 10ng/ml bFGF (R&D, Cat No. 100-18B), 5 μM CHIR99021 (Axon Medchem, Cat. No. 1386), 10 μM SB-431542 (Tocris, Cat. No. S0400), and 2μM  DMH1 (Adooq Bioscience, Cat. No. A12820); from Day 3 onwards, 100 nM RA (Sigma, Cat No. R2625) and either 0 nM, 10 nM, 100 nM or 500 nM SAG (Merck, Cat. No. 566660-5mg).

extract_protocol:
Crosslinked and TF-Sorted RNA-seq was performed as described in the associated manuscript. In brief, cells were PFA fixed, stained with intracellular antibodies and flow sorted. After reverse crosslinking, RNA was extracted using the RecoverAll RNA/DNA Isolation Kit (Thermo Fisher Scientific AM1975)
Libraries were built using SMART-Seq HT kit (Takara Cat no 634437) followed by Nextera XT DNA Library Preparation Kit (Illumina FC-131-1096). Prior to library preparation 1 ul of ERCC spike-ins was added for QC later assessments

treatment_protocol: 0 nM, 10 nM, 100 nM or 500 nM SAG

tag: cell line

tag: treatment


title: mr_003_post

tag: timepoint

tag: pathotype

value: Fibroid

tag: biologic

value: Etanercept

tag: status

value: Mod-Responder

tag: bx rna conc. (ng/ul)

tag: bx rna volume (ul)

tag: bx rna yield (ng)

tag: rin

tag: ethnicity

value: Caucasian

tag: gender

tag: smoking status (prev)

tag: smoking status (curr)

tag: diagnosis

tag: duration of disease (yrs)

tag: steroids (medication)

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)


title: Female control mice 3

tag: tissue

tag: cell type

tag: genotype

value: control


title: Female control mice 2


title: Amphimedon queenslandica, poly(A) captured mRNA-Seq, E

city: Brisbane

first: Xue Yan

last: Xiang

address: St Lucia

department: Biological Sciences

country: Australia

institute: The University of Queensland

data_processing:
Raw paired-end reads were processed with Trimmomatic (v0.36) with first 10bp cropped and a 4bp sliding window of trimming.Average quality threshold was set at 20 and reads smaller than 60bp was discarded.
Filtered, paired-end reads were aligned to the updated genomes using HISAT2 (v 2.0.5) with default parameters.
Number of aligned reads were counted with htseq-count (v 0.11.2) from HTSea framework with default parameters and stranded was set to reverse.
Assembly: Amphimedon queenslandica version 3 (Aqu3.1), AqS1v2, AqS2v2 and AqS3v2
Supplementary files format and content: count matrix, reads counts of genes

organism: Amphimedon queenslandica

source_name: marine demosponge A. queenslandica holobiont tissue

extract_protocol:
Total RNA was extracted separately from the six replicated biopsies using TRIzol (Sigma-Aldrich) and DNA was removed with Deoxyribonuclease I (Invitrogen)
Three of the samples (D,E, and F) were subjected to the standard TruSeq Stranded mRNA-seq workflow, using the poly-A pulldown and standard protocol with 1 µg total RNA as input. The other three samples (A,B,and C; 2.5 µg total RNA each) were first rRNA-depleted using the Ribo-Zero Gold ribosomal RNA Removal Kit. 100 ng of the depleted RNA was then used as input to the mRNA-seq protocol, but omitting the poly-A pulldown and instead of starting at the RNA fragmentation step.

treatment_protocol: To increase the proportional representation of the low abundance bacterial symbionts in the biopsies, bacteria were enriched by a series of centrifugation and filtration steps.

tag: strategy

value: poly(A) captured mRNA-Seq


title: Amphimedon queenslandica, poly(A) captured mRNA-Seq, F

value: marine demosponge A. queenslandica holobiont tissue


title: HEK293_DRB_2h_release_1h_spKAS-seq.rep2

tag: treatment

value: treat with DRB for 2h, then release 1h

value: wild type

tag: tag

value: strand specific KAS-seq


title: HEK293_DRB_2h_release_2h_spKAS-seq.rep1

value: Human embryonic kidney cells

value: treat with DRB for 2h, then release 2h


title: HEK293_DRB_2h_release_1h_spKAS-seq.rep1


title: Female control mice 1


title: Amphimedon queenslandica, poly(A) captured mRNA-Seq, D


title: mr_003_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

value: F

tag: smoking status (prev)

value: No

value: Yes

tag: location of joint biopsy

value: Wrist

tag: aggregational histological score

value: Diffuse

tag: inflammatory score

tag: swollen joint count (28)

tag: haq-di score

tag: crp

tag: esr

tag: rf

tag: acpa (ccp)

tag: radiographic erosion


title: mr_002_post

tag: timepoint

value: Post

tag: pathotype

value: Fibroid

tag: biologic

value: Etanercept

tag: status

tag: bx rna conc. (ng/ul)

tag: bx rna volume (ul)

value: Jamaican

tag: smoking status (curr)

tag: diagnosis

value: RA

tag: duration of disease (yrs)

tag: steroids (medication)

value: Pauci-immune

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)


title: mr_004_post

value: Myeloid

value: Certolizumab

value: Mod-Responder

tag: bx rna yield (ng)

tag: rin

tag: ethnicity

value: Asian

tag: age

tag: gender

tag: smoking status (prev)

tag: location of joint biopsy

tag: aggregational histological score

tag: inflammatory score

tag: swollen joint count (28)

tag: haq-di score

tag: crp

tag: esr

tag: rf

tag: acpa (ccp)

tag: radiographic erosion


title: HEK293_DRB_2h_release_30min_spKAS-seq.rep2

tag: cell type

value: Human embryonic kidney cells

tag: treatment

value: treat with DRB for 2h, then release 30min

tag: genotype

value: wild type

tag: tag

value: strand specific KAS-seq


title: Amphimedon queenslandica, ribosomal RNA depleted RNA-Seq, C

tag: tissue

value: marine demosponge A. queenslandica holobiont tissue

tag: strategy

value: ribosomal RNA depleted RNA-Seq


title: HEK293_DRB_2h_release_2h_spKAS-seq.rep2

value: treat with DRB for 2h, then release 2h


title: Amphimedon queenslandica, ribosomal RNA depleted RNA-Seq, B


title: mr_002_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

value: F

tag: smoking status (prev)

value: No

tag: smoking status (curr)

tag: diagnosis

tag: duration of disease (yrs)

tag: steroids (medication)

value: Yes

value: Wrist

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)


title: HEK293_DRB_2h_release_30min_spKAS-seq.rep1

tag: cell type

tag: treatment

tag: genotype

tag: tag


title: WT+shScr+vehicle inguinal white adipoctyes mRNA rep. 3

city: Boston

first: NORC

last: Boston

address: 3 Blackfan Circle, CLS0733

institute: Beth Israel Deaconess Medical Center

description:
translating inguinal white adipocytes mRNA
biological replicate

data_processing:
RNA-Seq data were mapped and quantified using Salmon (Patro et al., 2017)
Gene abundances were summarized from transcript abundances using the tximport package for R (Soneson et al., 2015)
Low expressed genes (log2 CPM≥1) were filtered out, and differentially expressed genes were defined at log2 fold-change (FC) ≥0.6 and log2 false discovery rate (FDR)≤0.05 using EdgeR (Robinson et al., 2010).
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-separated-values files containing, per-sample, transcript-level quantifications given by Salmon. each file contains (in order): a mapping from the transcript ID to the transcript’s legnth, effective length, the transcripts-per-million mappings observed, and the number of reads mapped to the transcript

source_name: inguinal white adipocytes

extract_protocol:
Total RNA was isolated using Zymo direct-zol RNA prep. Extracted RNA was treated with NEBNext rRNA Depletion Kit v2.
RNA was converted into double stranded cDNA using NEBNext iWAT mRNA Second Strand Synthesis Module. cDNA was tagmented and amplified for 12 cycles by using Nextera XT DNA Library Preparation Kit.

tag: strain

tag: perturbation

value: scramble shRNA

value: vehicle


title: mr_004_pre

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

tag: age

tag: gender

tag: smoking status (prev)

value: RA

tag: location of joint biopsy

tag: aggregational histological score

value: Diffuse

tag: inflammatory score

tag: swollen joint count (28)

tag: haq-di score

tag: crp

tag: esr

tag: rf

tag: acpa (ccp)

tag: radiographic erosion


title: Amphimedon queenslandica, ribosomal RNA depleted RNA-Seq, A

tag: tissue

tag: strategy


title: WT+shScr+vehicle inguinal white adipoctyes mRNA rep. 2

tag: strain

tag: genotype

tag: perturbation

tag: treatment


title: mr_001_post

tag: timepoint

value: Post

tag: pathotype

value: Fibroid

tag: biologic

tag: status

value: Mod-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)

tag: diagnosis

tag: duration of disease (yrs)

tag: steroids (medication)

value: Pauci-immune

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)


title: HEK293_DRB_2h_release_15min_spKAS-seq.rep2

tag: cell type

value: Human embryonic kidney cells

tag: treatment

value: treat with DRB for 2h, then release 15min

tag: genotype

value: wild type

tag: tag

value: strand specific KAS-seq


title: WT+shScr+vehicle inguinal white adipoctyes mRNA rep. 1

tag: strain

tag: perturbation


title: mr_001_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

value: F

tag: smoking status (prev)

value: No

tag: location of joint biopsy

tag: aggregational histological score

tag: inflammatory score

tag: swollen joint count (28)

tag: haq-di score

tag: crp

tag: esr

tag: rf

tag: acpa (ccp)

tag: radiographic erosion

value: Yes


title: nr_015_post

tag: timepoint

tag: pathotype

value: Lymphoid

tag: biologic

value: Etanercept

tag: status

value: Non-Responder

tag: bx rna conc. (ng/ul)

tag: bx rna volume (ul)

value: M

tag: smoking status (curr)

tag: diagnosis

tag: duration of disease (yrs)

tag: steroids (medication)

value: MCP

value: Grade 3

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)


title: HEK293_DRB_2h_release_15min_spKAS-seq.rep1

tag: cell type

tag: treatment

tag: genotype

tag: tag


title: WT+shScr+cAMP inguinal white adipoctyes mRNA rep. 3

tag: strain

tag: perturbation

value: scramble shRNA

value: 3',5'-cyclic AMP


title: Hippocampus stress 1

city: St Petersburg

first: Konstantin

middle: Andreevich

last: Demin

address: University Embankment, 7/9

country: Russia

institute: Saint Petersburg State University

data_processing:
STAR spliced aligner
featureCounts
Assembly: Rnor_6.0
Supplementary files format and content: xlsx raw counts for each sample

organism: Rattus norvegicus

source_name: Hippocampus

growth_protocol: Rats (male: 1.5-2.5 months) were kept under standard conditions (20–22°C, 55% humidity, food and water ad libitum, 12:12 h light/dark cycle; lights on 08:00). All rats were from the same population and were randomly allocated into experimental groups using a random

extract_protocol:
Rats were quickly euthanized in small animal inhalation anesthesia chamber (SomnoSuite, Kent Scientific, Connecticut, USA) using 5 % isoflurane, and their brains dissected on ice and stored in liquid nitrogen for analyses. RNA isolation was performed using TRI-reagent (MRC, Catalog number 118), according to manufacturer instructions. RNA quality was verified with Quantus, electrophoresis, and QIAxel. PolyA RNA was purified with Dynabeads mRNA Purification Kit (Ambion).
Illumina library was made from polyA RNA with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB) according to manual

tag: tissue

value: Hippocampus

value: Wistar

value: 12-weeks chronic stress


title: HEK293_DRB_2h_spKAS-seq.rep1

value: Human embryonic kidney cells

value: treat with DRB for 2h

value: wild type


title: HEK293_DRB_2h_spKAS-seq.rep2

value: strand specific KAS-seq


title: Hippocampus stress 3


title: Hippocampus stress 2


title: WT+shScr+cAMP inguinal white adipoctyes mRNA rep. 2


title: nr_015_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

value: Caucasian

tag: age

tag: gender

tag: smoking status (prev)

value: No

tag: smoking status (curr)

value: RA

tag: location of joint biopsy

tag: aggregational histological score

tag: inflammatory score

tag: swollen joint count (28)

tag: haq-di score

tag: crp

tag: esr

tag: rf

tag: acpa (ccp)

tag: radiographic erosion


title: WT+shScr+cAMP inguinal white adipoctyes mRNA rep. 1

tag: strain

tag: genotype

tag: perturbation

tag: treatment


title: nr_014_post

tag: timepoint

value: Post

tag: pathotype

value: Lymphoid

tag: biologic

value: Etanercept

tag: status

value: Non-Responder

tag: bx rna conc. (ng/ul)

tag: bx rna volume (ul)

tag: bx rna yield (ng)

tag: rin

tag: ethnicity

value: Chinese

tag: age

tag: gender

value: F

tag: diagnosis

tag: duration of disease (yrs)

tag: steroids (medication)

value: Yes

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)


title: Hippocampus stress, lipopolysacharide 2

tag: tissue

value: Hippocampus

tag: genotype

value: Wistar

tag: treatment

value: 12-weeks chronic stress, 4-weeks lipopolysacharide 0.1 mg/kg injection each week


title: WT+shAppbp2+vehicle inguinal white adipoctyes mRNA rep. 3

tag: strain

value: wild type

tag: perturbation

value: Appbp2 shRNA

value: vehicle


title: Hippocampus stress, lipopolysacharide 3


title: HEK293_DRB_1h_spKAS-seq.rep2

tag: cell type

value: Human embryonic kidney cells

value: treat with DRB for 1h

tag: tag

value: strand specific KAS-seq


title: WT+shAppbp2+vehicle inguinal white adipoctyes mRNA rep. 2


title: Hippocampus stress, lipopolysacharide 1


title: HEK293_DRB_1h_spKAS-seq.rep1


title: HEK293_DRB_30min_spKAS-seq.rep2

value: treat with DRB for 30min


title: WT+shAppbp2+vehicle inguinal white adipoctyes mRNA rep. 1


title: Hippocampus stress, fluoxetine and lipopolysacharide 3

value: 12-weeks chronic stress, 4-weeks fluoxetine 5 mg/kg orally each day and lipopolysacharide 0.1 mg/kg injection each week


title: HEK293_DRB_30min_spKAS-seq.rep1


title: nr_013_pre

tag: timepoint

value: Pre

tag: pathotype

value: Lymphoid

tag: biologic

value: Etanercept

tag: status

value: Non-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

tag: smoking status (prev)

value: No

tag: smoking status (curr)

value: RA

tag: location of joint biopsy

value: MTP

tag: aggregational histological score

value: Grade 2

tag: inflammatory score

tag: swollen joint count (28)

tag: haq-di score

tag: crp

tag: esr

tag: rf

tag: acpa (ccp)

tag: radiographic erosion


title: Hippocampus stress, fluoxetine and lipopolysacharide 2

tag: tissue

value: Hippocampus

tag: genotype

value: Wistar

tag: treatment


title: WT+shAppbp2+cAMP inguinal white adipoctyes mRNA rep. 2

tag: strain

value: wild type

tag: perturbation

value: Appbp2 shRNA

value: 3',5'-cyclic AMP


title: nr_012_post

tag: timepoint

value: Post

tag: pathotype

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: F

tag: smoking status (prev)

value: Yes

tag: diagnosis

tag: duration of disease (yrs)

tag: steroids (medication)

value: MCP

value: Grade 3

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)


title: HEK293_DRB_15min_spKAS-seq.rep2

tag: cell type

value: Human embryonic kidney cells

tag: treatment

value: treat with DRB for 15min

tag: genotype

tag: tag

value: strand specific KAS-seq


title: nr_012_pre

tag: timepoint

value: Pre

tag: pathotype

value: Lymphoid

tag: biologic

tag: status

value: Non-Responder

tag: bx rna conc. (ng/ul)

tag: bx rna volume (ul)

tag: bx rna yield (ng)

tag: rin

tag: ethnicity

tag: smoking status (curr)

value: RA

value: No

tag: location of joint biopsy

value: Wrist

tag: aggregational histological score

tag: inflammatory score

tag: swollen joint count (28)

tag: haq-di score

tag: crp

tag: esr

tag: rf

tag: acpa (ccp)

tag: radiographic erosion


title: Hippocampus stress, fluoxetine and lipopolysacharide 1

tag: tissue

value: Hippocampus

tag: genotype

value: Wistar

tag: treatment

value: 12-weeks chronic stress, 4-weeks fluoxetine 5 mg/kg orally each day and lipopolysacharide 0.1 mg/kg injection each week


title: nr_013_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)

value: Asian

tag: age

tag: gender

tag: smoking status (prev)

tag: diagnosis

tag: duration of disease (yrs)

tag: steroids (medication)

value: MTP

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)


title: nr_011_post

tag: timepoint

tag: pathotype

value: Myeloid

tag: biologic

tag: rin

tag: ethnicity

value: Caucasian

value: F

value: Yes

tag: smoking status (curr)

tag: location of joint biopsy

tag: aggregational histological score

value: Diffuse

tag: inflammatory score

tag: swollen joint count (28)

tag: haq-di score

tag: crp

tag: esr

tag: rf

tag: acpa (ccp)

tag: radiographic erosion


title: WT+shAppbp2+cAMP inguinal white adipoctyes mRNA rep. 1

tag: strain

tag: genotype

value: wild type

tag: perturbation

value: Appbp2 shRNA

tag: treatment

value: 3',5'-cyclic AMP


title: HEK293_DRB_15min_spKAS-seq.rep1

tag: cell type

value: Human embryonic kidney cells

value: treat with DRB for 15min

tag: tag

value: strand specific KAS-seq


title: Hippocampus stress, fluoxetine and eicosapentaenoic acid 2

tag: tissue

value: Hippocampus

value: Wistar

value: 12-weeks chronic stress, 4-weeks fluoxetine 5 mg/kg and eicosapentaenoic acid 275 mg/kg orally each day


title: nr_014_pre

tag: timepoint

value: Pre

tag: pathotype

value: Lymphoid

tag: biologic

value: Etanercept

tag: status

value: Non-Responder

tag: bx rna conc. (ng/ul)

tag: bx rna volume (ul)

tag: bx rna yield (ng)

tag: rin

tag: ethnicity

value: Chinese

tag: age

tag: gender

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

value: Wrist

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)


title: WT+shAppbp2+cAMP inguinal white adipoctyes mRNA rep. 3

tag: strain

tag: genotype

value: wild type

tag: perturbation

tag: treatment


title: Prdm16-KO+shScr+vehicle inguinal white adipoctyes mRNA rep. 2

value: Prdm16 knockout

value: scramble shRNA

value: vehicle


title: HEK293_50k_cells_Input.rep2

tag: cell type

value: Human embryonic kidney cells

value: untreated

tag: tag

value: Input


title: HEK293_50k_cells_spKAS-seq.rep2

value: strand specific KAS-seq


title: nr_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

value: F

tag: smoking status (prev)

value: Yes

tag: smoking status (curr)

tag: aggregational histological score

value: Pauci immune

tag: inflammatory score

tag: swollen joint count (28)

tag: haq-di score

tag: crp

tag: esr

tag: rf

tag: acpa (ccp)

tag: radiographic erosion


title: Hippocampus stress, fluoxetine and eicosapentaenoic acid 1

tag: tissue

value: Hippocampus

tag: genotype

value: Wistar

tag: treatment

value: 12-weeks chronic stress, 4-weeks fluoxetine 5 mg/kg and eicosapentaenoic acid 275 mg/kg orally each day


title: Prdm16-KO+shScr+vehicle inguinal white adipoctyes mRNA rep. 1

tag: strain

tag: perturbation


title: Prdm16-KO+shScr+cAMP inguinal white adipoctyes mRNA rep. 3

value: 3',5'-cyclic AMP


title: nr_011_pre

tag: timepoint

value: Pre

tag: pathotype

tag: biologic

value: Etanercept

tag: status

value: Non-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: No

tag: diagnosis

value: RA

tag: duration of disease (yrs)

tag: steroids (medication)

tag: location of joint biopsy

value: Wrist

value: Diffuse

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)


title: HEK293_50k_cells_spKAS-seq.rep1

tag: cell type

value: Human embryonic kidney cells

tag: treatment

value: untreated

tag: genotype

value: wild type

tag: tag

value: strand specific KAS-seq


title: nr_009_post

tag: timepoint

value: Post

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

value: F

tag: smoking status (prev)

tag: smoking status (curr)

tag: aggregational histological score

tag: inflammatory score

tag: swollen joint count (28)

tag: haq-di score

tag: crp

tag: esr

tag: rf

tag: acpa (ccp)

tag: radiographic erosion

value: Yes


title: Hippocampus stress, fluoxetine 3

tag: tissue

value: Hippocampus

tag: genotype

value: Wistar

tag: treatment

value: 12-weeks chronic stress, 4-weeks fluoxetine 5 mg/kg orally each day


title: Hippocampus stress, fluoxetine and eicosapentaenoic acid 3

value: 12-weeks chronic stress, 4-weeks fluoxetine 5 mg/kg and eicosapentaenoic acid 275 mg/kg orally each day


title: Prdm16-KO+shScr+vehicle inguinal white adipoctyes mRNA rep. 3

tag: strain

value: Prdm16 knockout

tag: perturbation

value: scramble shRNA

value: vehicle


title: Prdm16-KO+shScr+cAMP inguinal white adipoctyes mRNA rep. 2

value: 3',5'-cyclic AMP


title: Hippocampus stress, fluoxetine 1


title: HEK293_no_RNaseH_Input.rep2

tag: cell type

value: Human embryonic kidney cells

value: no RNaseH

tag: tag

value: Input


title: nr_009_pre

tag: timepoint

value: Pre

tag: pathotype

tag: biologic

tag: status

value: Non-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

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

value: Wrist

value: Diffuse

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)


title: HEK293_no_RNaseH_Input.rep1

tag: cell type

tag: treatment

tag: genotype

value: wild type

tag: tag


title: Prdm16-KO+shScr+cAMP inguinal white adipoctyes mRNA rep. 1

tag: strain

tag: perturbation


title: Prdm16-KO+shAppbp2+vehicle inguinal white adipoctyes mRNA rep. 3

value: Appbp2 shRNA


title: HEK293_spKAS-seq.rep2

value: untreated

value: strand specific KAS-seq


title: nr_010_post

tag: timepoint

value: Post

tag: pathotype

value: Myeloid

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: Caucasian

tag: age

tag: gender

value: F

tag: smoking status (prev)

value: Yes

tag: smoking status (curr)

tag: aggregational histological score

value: Pauci immune

tag: inflammatory score

tag: swollen joint count (28)

tag: haq-di score

tag: crp

tag: esr

tag: rf

tag: acpa (ccp)

tag: radiographic erosion


title: Hippocampus stress, eicosapentaenoic acid 3

tag: tissue

value: Hippocampus

tag: genotype

value: Wistar

tag: treatment

value: 12-weeks chronic stress, 4-weeks eicosapentaenoic acid 275 mg/kg orally each day


title: nr_007_post

tag: timepoint

tag: pathotype

tag: biologic

value: Certolizumab

tag: status

value: Non-Responder

tag: bx rna conc. (ng/ul)

tag: bx rna volume (ul)

tag: bx rna yield (ng)

tag: rin

tag: ethnicity

value: Asian

value: No

tag: diagnosis

value: RA

tag: duration of disease (yrs)

tag: steroids (medication)

tag: location of joint biopsy

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)


title: Hippocampus stress, eicosapentaenoic acid 2

tag: tissue

tag: genotype

tag: treatment


title: Prdm16-KO+shAppbp2+vehicle inguinal white adipoctyes mRNA rep. 2

tag: strain

value: Prdm16 knockout

tag: perturbation

value: Appbp2 shRNA

value: vehicle


title: nr_007_pre

tag: timepoint

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: age

tag: gender

tag: smoking status (prev)

tag: smoking status (curr)

value: Wrist

tag: aggregational histological score

value: Diffuse

tag: inflammatory score

tag: swollen joint count (28)

tag: haq-di score

tag: crp

tag: esr

tag: rf

tag: acpa (ccp)

tag: radiographic erosion


title: Hippocampus stress, eicosapentaenoic acid 1

tag: tissue

tag: genotype

tag: treatment


title: nr_006_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: M

value: Yes

tag: diagnosis

tag: duration of disease (yrs)

tag: steroids (medication)

tag: location of joint biopsy

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)


title: HEK293_spKAS-seq.rep1

tag: cell type

value: Human embryonic kidney cells

tag: treatment

value: untreated

tag: genotype

value: wild type

tag: tag

value: strand specific KAS-seq


title: Hippocampus control 3

tag: tissue

value: Hippocampus

value: Wistar

value: Experimentally naïve


title: nr_006_pre

tag: timepoint

tag: pathotype

tag: biologic

value: Certolizumab

tag: status

value: Non-Responder

tag: bx rna conc. (ng/ul)

tag: bx rna volume (ul)

tag: bx rna yield (ng)

tag: rin

value: Asian

tag: age

tag: gender

tag: smoking status (prev)

tag: smoking status (curr)

value: RA

value: No

tag: aggregational histological score

value: Under QC Assessment

tag: inflammatory score

tag: swollen joint count (28)

tag: haq-di score

tag: crp

tag: esr

tag: rf

tag: acpa (ccp)

tag: radiographic erosion


title: Prdm16-KO+shAppbp2+vehicle inguinal white adipoctyes mRNA rep. 1

tag: strain

tag: genotype

value: Prdm16 knockout

tag: perturbation

value: Appbp2 shRNA

tag: treatment

value: vehicle


title: C16_D75_Conjunctival_Culture

city: NEWCASTLE

first: Megan

middle: Saphana Rose

last: Hasoon

address: Newcastle University

institute: Newcastle University

data_processing:
The sequencing data was aligned to human reference genome (GRCh38) and the Sars_CoV_2 reference (Ensembl ASM985889v3) using CellRanger Version 3.0.1. The Seurat R library was used for the downstream analysis.  The filtered_feature_bc_matrix were imported into R and QC filtering applied. The thresholds were applied to the data were a minimum counts per cell of  2000, minimum genes per cell of 500 and maximum percentage mitochondria of 20%. The DoubletFinder package  (McGinnis et al., 2019) was used to find and remove doublets. We performed two integrated analyses of the data. Firstly the mock samples were combined to study the clustering profiles without infection and secondly the mock and exposed cells were integrated together. Seurat (Butler et al., 2018) was used to normalise the data and the first 2000 highly variable genes, identified through vst selection were chosen for the clustering analysis. The gene expression values were then scaled and the number of counts, number of genes and percentage of mitochondria reads per cell were regressed. A PCA dimension reduction was applied using the selected highly variable genes. This was followed by Harmony (Korsunsky et al., 2019) batch correction where batch was set to sample ID. We then constructed a shared nearest-neighbour graph using the first 10 components of the harmony embeddings. Clusters within the graph using a range of resolutions from 0.2 – 2.2. We chose a resolution of 2.2 which over-clustered the data then applied the FindAllMarkers function and annotated the clusters based on the expression of marker genes as either superficial conjunctival epithelium, conjunctival epithelial progenitors, basal conjunctival epithelium or fibroblasts. The exposed cells were then classified into infected and bystander and differential expression was performed with the following contrasts: infected vs mock; bystander vs mock; and infected vs bystander. ISG and NFKβ target gene scores were generated using the AddModuleScore, which calculates the average expression for each group. The ISG gene list was taken from a published IFN-treated nasal cell dataset (Ziegler et al., 2020), while the NF-ΚB target gene list was obtained from an online resource (BostonUniversity, 2021). UMAP dimension reduction was performed and the DimPlot and FeaturePlot functions were used to visualise the clusters and expression of genes in individual cells and the DotPlot function was used to visualise the expression of genes within cell types and conditions.
The following filtering thresholds were applied to the data: minimum counts per cell of  2000, minimum genes per cell of 500 and maximum percentage mitochondria of 20%
The DoubletFinder R package was used to find and remove doublets.
Seurat was used to normalise the data and the first 2000 highly variable genes, identified through vst selection were chosen for the clustering analysis.
The gene expression values were then scaled and the number of counts, number of genes and percentage of mitochondria reads per cell were regressed.
A PCA dimension reduction was applied using the selected highly variable genes.
This was followed by Harmony batch correction where batch was set to sample ID. We then constructed a shared nearest-neighbour graph using the first 10 components of the harmony embeddings
Clusters within the graph using a range of resolutions from 0.2 – 2.2. We chose a resolution of 2.2
Genome_build: GRCh38
Supplementary_files_format_and_content: text file of meta data, text file of umap embeddings and matrix of raw gene counts for each cell

source_name: Human Tissue Donation, Conjunctival cells

growth_protocol: ALI differentiation of conjunctival epithelial cells was performed using a method developed for differentiation of lung epithelial basal cells described by Dvijodrski et al. (2021). 250,000 conjunctival epithelial cells were detached from feeders as described above and seeded onto matrigel coated 24 well inserts (ThinCertsTM, Greiner Bio-one) and fed apically and basally with BEGM Bronchial Epithelial Cell Growth Medium Bullet Kit (Lonza) supplemented with 10µM Y26732 (Sigma Aldrich) and incubated for 48-72 hours until confluent. Once confluent, the apical medium was removed, and the cells were basally with PneumaCult media (StemCell Technologies) for up to 75 days.

extract_protocol: Single cell RNA-Seq was performed on cells harvested 24 hours after infection. ALI cultures were washed apically and basally in 1xPBS and dissociated in 100µl 0.025% Trypsin-EDTA (ThermoFisher Scientific) for 15 minutes at 37°C. Trypsin-EDTA was neutralised, and cells were counted on a haemocytometer to get an optimum concentration of 1000 cells per microliter. Suspensions were centrifuged at 400g for 3 minutes and resuspended in 0.04%BSA/PBS solution.  For scRNA-Seq cells were captured and libraries generated using the Chromium Single Cell 3′ Library & Gel Bead Kit, version 3.1 (10x Genomics). scRNA-Seq libraries were sequenced to 50,000 reads per cell on an Illumina NovaSeq 6000.

treatment_protocol: A clinical isolate from Public Health England of SARS-CoV-2 (BetaCoV/England/2/2020) virus was propagated once in Vero E6 cells. The same viral stock was used for all experiments. Infections of ALI cultures were performed at day 30 of differentiation as previously described (Hatton et al., 2021). In brief the virus was diluted in DMEM (ThermoFisher Scientific) to achieve  MOIs of 0.5 and added to the apical side. After 2 hours of incubation, the virus containing medium was removed and the cells were fed basally with PneumaCult media. DMEM was used as inoculum for mock infections. The apical washes in 1xphosphate-buffer solution (1xPBS) were collected at 2, 6, 24, 48 and 72 hours and used for plaque assays.

tag: cell type

value: Conjunctival cells

tag: cell line

tag: condition

value: mock

tag: day


title: mr_011_pre

tag: timepoint

value: Pre

tag: pathotype

value: Lymphoid

tag: biologic

tag: status

value: Mod-Responder

tag: bx rna conc. (ng/ul)

tag: bx rna volume (ul)

tag: bx rna yield (ng)

tag: rin

tag: ethnicity

value: African

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 3

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)

value: Yes


title: Hippocampus control 2

tag: tissue

value: Hippocampus

tag: genotype

value: Wistar

tag: treatment

value: Experimentally naïve


title: Prdm16-KO+shAppbp2+cAMP inguinal white adipoctyes mRNA rep. 3

tag: strain

tag: perturbation

value: 3',5'-cyclic AMP


title: Prdm16-KO+shAppbp2+cAMP inguinal white adipoctyes mRNA rep. 2

value: Prdm16 knockout


title: C10_neg_D30_Conjunctival_Culture

source_name: Human ALI organotypic conjunctival culture model

tag: cell type

value: conjunctival culture model

tag: cell line

tag: condition

tag: day


title: Hippocampus control 1


title: nr_005_pre

source_name: Synovial Tissue

tag: timepoint

tag: pathotype

value: Myeloid

tag: biologic

value: Certolizumab

tag: status

value: Non-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

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

value: Diffuse

tag: inflammatory score

tag: swollen joint count (28)

tag: haq-di score

tag: crp

tag: esr

tag: rf

tag: acpa (ccp)

tag: radiographic erosion


title: Lim_Conj_SARS-CoV-2_6_D30

tag: cell type

tag: cell line

tag: condition

value: mock

tag: day


title: nr_004_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)

tag: smoking status (curr)

value: Wrist

tag: aggregational histological score

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)


title: Prdm16-KO+shAppbp2+cAMP inguinal white adipoctyes mRNA rep. 1

tag: strain

tag: genotype

tag: perturbation

value: Appbp2 shRNA

tag: treatment


title: Lim_Conj_SARS-CoV-2_5_D30

tag: cell type

tag: cell line

tag: condition

value: sars-cov-2 infected

tag: day


title: nr_004_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)

tag: diagnosis

tag: duration of disease (yrs)

tag: steroids (medication)

tag: location of joint biopsy

tag: inflammatory score

tag: swollen joint count (28)

tag: haq-di score

tag: crp

tag: esr

tag: rf

tag: acpa (ccp)

tag: radiographic erosion


title: Lim_Conj_SARS-CoV-2_4_D30

tag: cell type

tag: cell line

tag: condition

tag: day


title: Lane4

city: La Jolla

first: Seoyeon

last: Lee

state: California

address: 9500 Gilman Dr.

institute: University of California, San Diego

data_processing:
Libraries were preprocessed as previously described [PMID: 29434377]. Fastq files from two sequencing runs were merged and demultiplexed by adding the cell barcode to each read. Demultiplexed pair-end reads were aligned to mm10 using Bowtie2 with the parameters: bowtie2 -p 16 -t -X 2000-no-mixed-no-discordant [PMID: 22388286]. After alignment, reads were sorted by read name using samtools [PMID: 19505943]. Pair-end reads with low mapping quality fragments < MAPQ 30 and improperly paired fragments (SAM flag = 1804) were removed. Reads were separated based on the cell barcode and reads belonging to the same cell barcode were deduplicated. PCR duplicate reads and mitochondrial reads were removed.
We first filtered out cells which have less than 1,000 reads. Then we generated a cell-by-10kb-window sparse matrix using snapATAC [PMID: 33637727]. We normalized the cell-by-windows matrix by a TF-IDF transformation using Signac [PMID: 29608179]. After clustering, peak calling was performed using MACS2 callpeak command with the parameters: -nomodel -shift -100 extsize 200 -keep-dup-all -q0.05 [PMID: 30078704]. The summits were extended ±250bp. The peak sites identified from each cluster were merged and used to create a cell-by-peak matrix. Cells with less than 0.15 reads in peak ratio were removed. Then, the cells with >0.2 doublet scores identified by scrublet [PMID: 30954476] were further removed.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts, barcods, peaks and sample information

source_name: Inguinal adipose tissue

extract_protocol:
Inguinal adipose tissues were collected from mice before any intervention and after 1, 3 or 7. Whole adipose tissues were minced on dry ice. 80-100 mg of chopped adipose tissue were transferred to a chilled 40 mL Dounce Homogenize containing 25 mL homogenize buffer (320 mM sucrose, 0.1 mM EDTA, 0.1 % NP40, 5 mM CaCl2, 3 mM Mg(Ac)2, 10 mM Tris pH 7.8, protease inhibitors (Pierce #88666), 0.016 mM PMSF, 0.33 mM β-mercaptoethanol) [PMID: 28846090]. Tissue was homogenized immediately via 10 gentle strokes of the loose pestle and then 10 gentle strokes of the tight pestle on ice using a Dounce Tissue Grinder (Wheaton #357546). The homogenate was filtered through a 40 μm nylon mesh (VWR #10199-658) and centrifuged for 10 min at 500 g. The top fat layer was discarded, and the supernatant was transferred into a new tube without disrupting the pellet. The samples were then resuspended in 5 vol. of ice-cold ATAC-Resuspension Buffer Wash (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% Tween 20 in water) and centrifuged for 5 min at 500 g in a swinging bucket rotor centrifuge (Eppendorf #5920R) at 4°C. Nuclei pellets were resuspended in 1X Tagmentation Buffer (10 mM Tris pH 7.4, 5 mM MgCl2, 10 % DMF, 33 % 1X PBS (without Ca++ and Mg++), 0.1 % Tween-20, 0.01 % Digitonin (ThermoFisher #BN2006)).
snATAC-seq was performed as described previously [PMID: 29434377], with minor modifications. Nuclei concentration was adjusted to 160,000 nuclei/mL in 1X Tagmentation Buffer. 8 μL of nuclei were distributed into each well of a 96-well plate (1,280 nuclei/well) containing 1 μL of each ME-A or ME-B carrying barcoded transposome per well at ~1.5 μM. Tagmentation was performed at 50°C for 30 min. Following tagmentation, 10 μL of 40 μM EDTA was added each well and the plate was incubated at 37°C for 15 min to terminate the Tn5 reaction. Next, 20 μL of sort buffer (2 % BSA and 2 mM EDTA in PBS) was added to each well. All wells were pooled and centrifuged for 5 min at 500 g. Nuclei were resuspended in sort buffer with 10% DMSO and frozen at -80°C until ready for fluorescence activated nuclei sorting (FANS).   After thawing at 37°C for 1 min, nuclei were centrifuged for 5 min at 500 g and resuspended in 1 mL of sort buffer. Nuclei were filtered through a 35 μm mesh (Corning #352235) and stained with 3 μM Draq7 (Abcam #ab109202) before FANS. 25 Draq7+ nuclei were sorted into each well of second 96-well plates containing 16.5 μL of elution buffer (2 % BSA and 10 mM Tris pH 8.0) using a BD FASC Melody. Gating was selected to isolate single Draq7+ nuclei. After sorting, plates were frozen at -80°C until PCR amplification.   For PCR amplification, 2 μL of 0.2% SDS were added to each well and the plate was incubated for 7 min at 55°C to denature transposase. 2.5 μL of 10% Triton X-100 were added to each well to quench SDS. 1.5 μL of 25 μM Primer i5 and 1.5 μL of 25 μM Primer i7 (Supplementary Table 1) were added to each well and the plate was gently vortexed and spun down briefly. 25 μL of PCR mix (Q5 DNA polymerase (NEB #M0491), 2 mM dNTP, Q5 buffer and 1X GC Enhancer) were added to each well. PCR was performed using the following protocol: 72°C 5 min, 98°C 30 sec, 13 cycles of: [98°C 10 sec, 63°C 30 sec, 72°C 30 sec], 72°C 5 min, held at 4°C. All wells were pooled. Amplified DNA libraries were purified using MinElute columns (Qiagen #28004) using a vacuum apparatus (Qiagen #19413), washed twice with 750 μL Buffer PE (Qiagen #19065) and spun down at maximum speed for 1 min. Samples were eluted twice with warm buffer EB (10 mM Tris pH 8). The size selection was performed using Ampure XP Bead (Beckman Coulter #A63880). The concentration of each pooled PCR plate library was measured using a Qubit fluorimeter (Invitrogen, Qubit dsDNA HS Assay Kit, #Q32851) and library fragment distribution was quantified on Agilent Bioanalyzer. Libraries were subjected to digital PCR on a Bio-Rad QX200 droplet digital PCR system with the following oligos: forward, AGCAGAAGACGGCATACGAGAT; reverse ATACGGCGACCACCGAGATC; internal /56-FAM/TCTTATACACATCTGAGGCGG/3BHQ_1/. Libraries were loaded at 8 pM on a mid-lane output PE 150bp. Libraries were sequenced on a Nextseq500 sequencer (Illumina) using custom read primers.

treatment_protocol: Six-weeks old C57BL/6J mice were purchased from Jackson Laboratories. Mice were acclimated to the facility for two-weeks and maintained at room temperature (RT, 22°C) for 14 days before intervention. Mice were randomly assigned to cold (6.5°C) or CL-316,243 (CL, 1 mg/kg), a β3-adrenergic receptor (Adrb3) selective agonist treatment group. Mice were exposed to cold and Adrb3 agonist for 0, 1, 3, or 7 days respectively.

tag: strain

tag: age

value: 8 weeks

value: male

tag: treatment

value: cold exposure or CL treatment for 0, 1, 3, and 7 days

tag: tissue

value: Inguinal adipose tissue


title: pilB::Tn5 Mutant (Btn5) Biofilm Fraction in Fresh BG-11 Media on Day 4, Replicate #3

first: Ryan

last: Simkovsky

address: 9500 Gilman Drive

institute: University of California San Diego

description: Btn5_BG_BF_D4 Replicate 3

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.

value: Cyanobacterial cell

tag: genotype

value: Fresh BG-11

tag: time

value: Day 4

tag: fraction

value: Biofilm


title: pilB::Tn5 Mutant (Btn5) Biofilm Fraction in Fresh BG-11 Media on Day 4, Replicate #1

description: Btn5_BG_BF_D4 Replicate 1


title: pilB::Tn5 Mutant (Btn5) Biofilm Fraction in Fresh BG-11 Media on Day 4, Replicate #2

description: Btn5_BG_BF_D4 Replicate 2


title: C10_pos_D30_Conjunctival_Culture

value: conjunctival culture model


title: nr_003_post

tag: timepoint

tag: pathotype

value: Myeloid

tag: biologic

value: Certolizumab

tag: status

value: Non-Responder

tag: bx rna conc. (ng/ul)

tag: bx rna volume (ul)

tag: bx rna yield (ng)

tag: rin

tag: ethnicity

tag: gender

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

value: MCP

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


title: Lane2

tag: strain

tag: age

value: 8 weeks

tag: treatment

tag: tissue


title: Lane3

value: male


title: Lim_Conj_SARS-CoV-2_3_D30

tag: cell type

tag: cell line

tag: condition

value: sars-cov-2 infected

tag: day


title: nr_003_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

value: Caucasian

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

value: Grade 1

tag: inflammatory score

tag: crp

tag: esr

tag: rf

tag: acpa (ccp)

tag: radiographic erosion


title: nr_005_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)

value: Asian

tag: age

value: Knee

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


title: Hippocampus stress, fluoxetine 2

tag: tissue

value: Hippocampus

tag: genotype

value: Wistar

tag: treatment

value: 12-weeks chronic stress, 4-weeks fluoxetine 5 mg/kg orally each day


title: pilB::Tn5 Mutant (Btn5) Planktonic Fraction in Fresh BG-11 Media on Day 4, Replicate #3

description: Btn5_BG_Su_D4 Replicate 3

tag: cell type

value: Cyanobacterial cell

tag: strain

value: Fresh BG-11

tag: time

value: Day 4

tag: fraction

value: Supernatant


title: nr_002_post

tag: timepoint

tag: pathotype

value: Fibroid

tag: biologic

value: Etanercept

tag: status

value: Non-Responder

tag: bx rna conc. (ng/ul)

tag: bx rna volume (ul)

tag: bx rna yield (ng)

tag: rin

tag: ethnicity

tag: gender

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

value: Wrist

tag: aggregational histological score

value: Diffuse

tag: inflammatory score

tag: crp

tag: esr

tag: rf

tag: acpa (ccp)

tag: radiographic erosion


title: NP_1K rep2 for ATAC-seq

city: Guangzhou,

first: Jinna

last: Wu

state: Guangdong,

address: 58 Zhongshan Road 2

institute: The First Affiliated Hospital of Sun Yat-sen University

data_processing:
Cutadapt (v2.5) was used to trim adapters and filter for sequences.
For RNA-seq: The 150 bp paired-end reads were mapped to the reference genome by using hisat2 (v2.1.0. For ATAC-seq: The 150 bp paired-end reads were mapped to the reference genome by using bowtie2 (v2.11.1).
For RNA-seq: The reads mapped the genome were calculated using featureCounts (v1.6.3). For ATAC-seq: Significant peak regions of each samples were identified using MACS2 (v2.1.2) with parameters "-q 0.05 --nomodel --shift -100 --extsize 200".
Genome_build: hg38
Supplementary_files_format_and_content: 20210107_ZhouTaiFeng_mRNA-seq_hisat.counts.txt for RNA-seq samples, narrowPeak fo r ATAC-seq samples

source_name: nucleus pulposus cells

extract_protocol:
Total RNA was isolated from samples using TRIzol reagent.
For RNA-seq: VAHTSTM Stranded mRNA-seq Library Prep Kit for Illumina v2 was used for library construction. For ATAC-seq,briefly, nuclei were isolated from 50,000 cells for transposition reaction with EpiTM ATAC-seq kit (Epibiotek). DNA were purified with PCR purification kit (Qiagen) and amplified with NEBNext high-fidelity 2X PCR Master Mix (New England Biolabs) to generate libraries.

tag: cell type

value: nucleus pulposus cells

tag: treatment

value: 1kPa hydrogel


title: F_02032017

first: Ionita

middle: Calin

last: Ghiran

address: 3 Blackfan Circle

department: Medicine

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.

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.

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: Sex

value: female


title: pilB::Tn5 Mutant (Btn5) Planktonic Fraction in Fresh BG-11 Media on Day 4, Replicate #2

description: Btn5_BG_Su_D4 Replicate 2

value: Cyanobacterial cell

tag: strain

tag: genotype

value: Fresh BG-11

tag: time

value: Day 4

tag: fraction


title: Lane1

tag: age

value: 8 weeks

value: male

value: cold exposure or CL treatment for 0, 1, 3, and 7 days

value: Inguinal adipose tissue


title: NP_40K rep2 for ATAC-seq

value: 40kPa hydrogel


title: M_02032017

tag: diagnosis


title: pilB::Tn5 Mutant (Btn5) Planktonic Fraction in Fresh BG-11 Media on Day 4, Replicate #1

description: Btn5_BG_Su_D4 Replicate 1

value: Supernatant


title: nr_001_post

tag: timepoint

value: Post

tag: pathotype

value: Fibroid

tag: biologic

value: Certolizumab

tag: status

value: Non-Responder

tag: bx rna conc. (ng/ul)

tag: bx rna volume (ul)

tag: bx rna yield (ng)

tag: rin

tag: ethnicity

value: Asian

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: Wrist

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: nr_002_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

tag: smoking status (prev)

tag: diagnosis

value: Under QC Assessment

tag: rf

tag: acpa (ccp)

tag: radiographic erosion


title: 1C 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: Citrate


title: Wild Type in Fresh BG-11 Media on Day 4, Replicate #3

description: WT_BG_D4 Replicate 3

tag: cell type

value: Cyanobacterial cell

tag: strain

tag: genotype

value: Wild Type

tag: treatment

value: Fresh BG-11

tag: time

value: Day 4

tag: fraction

value: Supernatant


title: nr_001_pre

tag: timepoint

tag: pathotype

value: Fibroid

tag: biologic

value: Certolizumab

tag: status

value: Non-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: F

value: No

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: esr


title: Wild Type in Fresh BG-11 Media on Day 4, Replicate #2

description: WT_BG_D4 Replicate 2

tag: cell type

tag: strain

tag: genotype

tag: treatment

tag: time

tag: fraction


title: NP_1K rep2 for RNA-seq

description:
20210107_ZhouTaiFeng_mRNA-seq_hisat.counts.txt
1KNP2m

value: nucleus pulposus cells

value: 1kPa hydrogel


title: 6S 02032017

source_name: Serum

tag: diagnosis

value: Healthy Subject

tag: anatomical location

value: Entire cardiovascular system

tag: tissue

value: Serum

tag: rna source

value: total cell-free biofluid RNA

tag: rna isolation kit


title: r_019_pre

tag: timepoint

value: Pre

tag: pathotype

value: Lymphoid

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)

tag: duration of disease (yrs)

tag: steroids (medication)

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: rf

tag: acpa (ccp)

tag: radiographic erosion

value: Yes


title: r_019_post

tag: timepoint

value: Post

tag: pathotype

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

tag: age

tag: diagnosis

value: Under QC Assessment

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: NP_1K rep1 for RNA-seq

description:
20210107_ZhouTaiFeng_mRNA-seq_hisat.counts.txt
1KNP1m

tag: cell type

tag: treatment


title: Wild Type in Fresh BG-11 Media on Day 4, Replicate #1

description: WT_BG_D4 Replicate 1

value: Cyanobacterial cell

tag: strain

tag: genotype

value: Wild Type

value: Fresh BG-11

tag: time

value: Day 4

tag: fraction

value: Supernatant


title: 4H 02032017

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

value: Heparin


title: pilB::Tn5 Mutant (Btn5) in Conditioned Media on Day 1, Replicate #3

description: Btn5_CM_D1 Replicate 3

value: Conditioned Media (CM)

value: Day 1


title: 1E 02032017

tag: diagnosis

value: total cell-free biofluid RNA

value: EDTA


title: NP_1K rep1 for ATAC-seq

value: nucleus pulposus cells

value: 1kPa hydrogel


title: NP_40K rep2 for RNA-seq

description:
20210107_ZhouTaiFeng_mRNA-seq_hisat.counts.txt
40kNP2m

value: 40kPa hydrogel


title: r_018_post

tag: timepoint

value: Post

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: F

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

value: Wrist

tag: aggregational histological score

value: Grade 2

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: rf

tag: acpa (ccp)

tag: radiographic erosion


title: pilB::Tn5 Mutant (Btn5) in Conditioned Media on Day 1, Replicate #2

description: Btn5_CM_D1 Replicate 2

tag: cell type

value: Cyanobacterial cell

tag: strain

tag: genotype

tag: treatment

value: Conditioned Media (CM)

tag: time

value: Day 1

tag: fraction

value: Supernatant


title: 5H 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: Heparin


title: NP_40K rep1 for RNA-seq

description:
20210107_ZhouTaiFeng_mRNA-seq_hisat.counts.txt
40kNP1m

value: nucleus pulposus cells

value: 40kPa hydrogel


title: NP_40K rep1 for ATAC-seq


title: r_017_post

tag: timepoint

value: Post

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)

tag: duration of disease (yrs)

tag: steroids (medication)

tag: location of joint biopsy

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: physician global assessment of disease activity (vas)

tag: haq-di score

tag: crp

tag: esr


title: 2E 02032017

tag: diagnosis

tag: anatomical location

tag: tissue

tag: rna source

tag: rna isolation kit

tag: anticoagulant

value: EDTA


title: GS612_BMP4

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.

tag: cell type

value: Glioblastoma

tag: passage

tag: treatment

tag: bmp4 sensitivity

value: Resistant


title: pilB::Tn5 Mutant (Btn5) in Conditioned Media on Day 1, Replicate #1

description: Btn5_CM_D1 Replicate 1

value: Cyanobacterial cell

tag: strain

tag: genotype

value: Conditioned Media (CM)

tag: time

value: Day 1

tag: fraction

value: Supernatant


title: GS612_NT

description: PolyA RNA

value: No treatment


title: 5C 02032017

value: Healthy Subject

value: Entire cardiovascular system

value: Plasma

value: total cell-free biofluid RNA

value: miRcury biofluids (Exiqon)

value: Citrate


title: GS832_BMP4

description: PolyA RNA

value: Sensitive


title: pilB::Tn5 Mutant (Btn5) in Fresh BG-11 Media on Day 1, Replicate #3

description: Btn5_BG_D1 Replicate 3

value: Fresh BG-11