title: COV021, BCR-Seq

value: female


title: Plate1-131-Liver

status: Public on Sep 15 2022

type: SRA

city: Durham

first: Scott

last: Auerbach

state: North Carolina

address: 111 TW Alexander Drive

country: USA

institute: Division of the National Toxicology Program at NIEHS

description: Plate 1_LIVER_H03

library_source: transcriptomic

data_processing: Data were processed using the Tempo-SeqR software package

molecule: total RNA

organism: Rattus norvegicus

source_name: Liver

growth_protocol: Male and female SD rats were placed on NTP-2000 diet and housed up to 5 animals per cage. After a 10-14 day quarantine, 8-10 week old animals were randomly assigned to treatment and control groups.

extract_protocol: All animals were euthanized the day after the last dose of chemical was administered and the liver and kidney were removed during necropsy. Two samples from each the left liver lobe and right kidney were collected within five minutes of termination for toxicogenomic evaluation. Tissue samples were cut into approximately 5 cubic mm pieces, aliquoted into screw-cap tubes, flash frozen in liquid nitrogen, and stored at -80 degreees C. RNA was extracted from one of the two collected samples and the extraction batch information recorded in the metadata along with the quantity and quality of each RNA sample. The RNA samples and metadata file were sent to BioSpyder for evaluation using the whole transcriptome TempOSeq platform with a minimum of 10 million reads/sample.

treatment_protocol: Each of six chemicals was given at nine doses (5 mL/kg dosing volume) to the treatment groups. A vehicle control group was also included for each treatment group. Rats received the test formulations via gavage for five consecutive days.

tag: strain

value: Sprague Dawley (SD)

tag: Sex

value: Male

tag: tissue

value: Liver

tag: chemical

value: PFHxSAm

tag: concentration

tag: unit

value: mg/kg

tag: vehicle

value: water/tween

tag: duration

value: day

tag: platfrom

value: TempO-Seq


title: 50S NaHCO3

city: El Paso

first: Eda

last: Kocui

state: TX

address: 500 W. University Avenue

department: Chemistry and Biochemistry

institute: University of Texas at El Paso

data_processing:
Library strategy: SHAPE-MaP
Base calls were performed uising Illumina RTA version 1.18. 54
The next generation sequencing reads were aligned to the rrlB and rrsB  genes of Bl21 (DE3)  E Coli and the mutations were counted using Shape-Mapper 1.2

organism: Escherichia coli

source_name: Escherichia Coli cells

growth_protocol: The cells were grown at 37ºC in 200 mL of media containing 10g/L tryptone, 1g/L yeast extract, 100μg/mL carbenicillin, and 34μg/mL chloramphenicol. When the cell reached an optical density at 600 nm of about 0.3, the cell growth was arrested by adding 200 ml of ice.

extract_protocol:
The ribosomal particles were isoalate using a  20-40% gradients were made in a buffer consisting of 20mM HEPES KOH pH 7.5, 150mM NH4Cl, 1mM MgCl2 and 4mM BME.
The NGS sequencing library was performed following the randomer workflow of the Selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) protocol(Smola et al. 2015)

treatment_protocol: the isolated ribosomal particles were treated with CMCT and NaHCO3 , NaHCO3 alone, KMnO4, or no chemical treatment

tag: genotype/variation

value: BLR (DE3) deltaDbpA, expressing wild-type  DbpA

tag: treatment

tag: molecule

value: 23S ribosomal RNA


title: COV016, BCR-Seq

city: Xian

first: chengsheng

last: zhang

state: Shaanxi

address: 277 West Yanta Road, Xi'an, Shaanxi, P.R.China

department: precision medicine center

country: China

institute: First Affiliated Hospital of Xi 'an Jiaotong University

data_processing:
Library strategy: BCR-seq
Illumina bcl2fastq software used for for basecalling.
Barcoded, full-length TCR V(D)J segments could be enriched from amplified cDNA from 5′ libraries via PCR amplification with primers specific to the TCR prior to library construction using a Chromium Single-Cell V(D)J Enrichment kit according to the manufacturer’s protocol (10X Genomics). If both T cells are expected to be present in the partitioned cell population, TCR transcripts can be enriched in separate reactions from the same amplified cDNA material. Cell Ranger for V(D)J (https://support.10xgenomics.com/single-cell-vdj) is a set of analysis pipelines that process Chromium single cell 5′ RNA-seq output to assemble, quantify, and annotate paired V(D)J transcript sequences. Cell Ranger workflow starts by demultiplexing the Illumina sequencer's base call files (BCLs) for each flowcell directory into FASTQ files. Cell calling is performed independently of V(D)J read filtering and assembly. A clonotype is a set of cells that share the same paired receptor sequences (presumably derived from the same progenitor cell) Cell barcodes are grouped together into clonotypes if they share the same set of productive CDR3 nucleotide sequences by exact match. Repertoire informations of all samples are exhibited using a set of basic features: CDR3 abundance, CDR3 bases length, Variable (V) and Joining (J) segment usage(the frequency of associated reads for each of V/J gene present in samples), the length of V/J gene in CDR3 region, and V-J gene paired frequency in CDR3 junctions. We use hierarchical cluster (https://stat.ethz.ch/R-manual/Rdevel/library/stats/html/hclust.html) and Kruskal’s Non-metric Multidimensional Scaling (isoMDS, https://cran.r-project.org/web/ packages/MASS/MASS.pdf) to estimate Immune Repertoires similarity.
Genome_build: GRCh38_v96
Supplementary_files_format_and_content: filtered_contig_annotations.zip

organism: Homo sapiens

source_name: COVID-19, Peripheral blood

extract_protocol:
Retrieving the PBMC-containing cryo-tubes from the -196℃ liquid nitrogen storage tank and placing them in a 37℃ water bath for rapid thawing. PBMCs were mixed with 10 mL washing medium (90% DMEM+10% FBS) in a 15-mL polypropylene tube and centrifuged at 500g for 20 min. The supernatant was then aspirated (repeat twice). The cell pellets were resuspended with 500 μl× PBS (0.04% BSA) in the sterile RNase-free vacutainer tubes and added with 5 ml 1× red blood cell lysis buffer (MACS 130-094-183, 10×) and incubated at room temperature for 10 min to lyse remaining red blood cells. After incubation, the suspension was centrifuged at 500g for 20 min at room temperature. The suspension was resuspended in 100 μl Dead Cell Removal MicroBeads (MACS 130-090-101) and remove dead cells using Miltenyi ® Dead Cell Removal Kit (MACS 130-090-101). Then the suspension was resuspended in 1× PBS (0.04% BSA) and centrifuged at 300 g for 3 min at 4 °C (repeat twice). The cell pellet was resuspended in 50 μl of 1× PBS (0.04% BSA). The overall cell viability was confirmed by trypan blue exclusion, which needed to be above 85%, single cell suspensions were counted using a Countess II Automated Cell Counter and concentration adjusted to 700-1200 cells/μl.
manufacturer's protocols for 5'barcoded GEX and V(D)J BCR

value: Peripheral blood

tag: cell type

value: peripheral blood mono-nuclear cells (PBMCs)

tag: age

tag: gender

value: male

tag: disease symptom

value: symptomatic

tag: disease state

value: Severe

tag: thymalfasin treatment

value: Yes

tag: disease duration

value: short term

tag: patient comorbidity

value: No


title: 19-H-3

city: Xiamen

first: Huifen

last: Cao

email: hfcao_bnu@163.com, hfcao@hqu.edu.cn

state: Fujian

address: 668 Jimei Road

department: School of Biomedical Sciences

institute: Huaqiao University

library_source: genomic

data_processing:
The genomic and mitochondrial AP site mapping was performed the same way as in the SSiNGLe-ILM protocol (https://protocolexchange.researchsquare.com/article/pex-920/v2) with the two additional filtering steps. One, PCR duplicates were removed. Two, a read-pair was used only if the first base of the read 2 aligned to the reference sequence. The coordinate of one base upstream of the first aligning base of the read 2 was assigned as the position of the AP site. In the samples used for the chrM analysis, reads were aligned separately to the chrM genome sequences and processed in the same way. Then, the coordinates of AP sites mapping to chrM were added to the BED files containing AP sites mapping to the nuclear genome.
Genome_build: HG19(GRCh37) for human reads, mm10 (GRCm38) for the mouse reads and sequences corresponding to the bacterial spike-ins listed in the file spike-ins.fa for the reads from the spike-in control experiments.
Supplementary_files_format_and_content: The *spike-ins.bed files contain coordinates of AP sites in the sequences of spike-ins. All other BED files contain coordinates of AP sites mapped to either mouse or human genomes. The 4th columns show the number of reads representing the AP site.

molecule: genomic DNA

organism: Mus musculus

source_name: Heart

growth_protocol: Human CML leukemia cell line K562 was obtained from Cell Bank of Chinese Academy of Sciences, and human cervical carcinoma HeLa cell line was obtained from National Infrastructure of Cell Line Resource. Cells were cultured in RPMI 1640 (Thermo Fisher Scientific) supplemented with 10% (v/v) heat-inactivated fetal bovine serum (FBS, ExCell Bio) and 1% (v/v) pen-strep (HyClone) at 37 °C and 5% CO2.

extract_protocol:
12 male mice of C57BL/6J strain from 4 age groups (3-, 12-, 19- and 22-month-old) were used to extract brains, hearts, livers, bone marrow, PBMCs and sperms. Red cells in bone marrow were removed by Red Blood Cell Lysis Buffer (Beyotime). PBMCs were isolated from blood using Ficoll-Paque PLUS (GE Healthcare). The motile spermatozoa were isolated from the mouse epididymal tail by collecting cells floating in the upper layer of RPMI 1640 (Thermo Fisher Scientific). The isolated tissues were immediately put into liquid nitrogen for quick freezing. The whole organs were cut into small pieces and ground into powder by tissue homogenizer in presence of liquid nitrogen to avoid heating. All ground tissue samples were stored at -80C prior to DNA isolation. Genomic DNA from human cell lines and the mouse brain, bone marrow, heart, liver and PBMCs was isolated using TIANamp Genomic DNA kit (Tiangen, DP304) with RNaseA treatment according to the manufacturer's protocols. Genomic DNA from sperm cells was extracted using Sperm DNA Purification Kit (Simgen, 4202050) following the manufacturer?s instructions. All DNA samples were eluted in UltraPure? DNase/RNase-Free Distilled Water (Invitrogen), measured the concentration using SMA6000 (Merinton) and stored at -20C.
Library construction method: SSiNGLe-AP method

treatment_protocol: Two million K562 or HeLa cells were seeded at 1 million cells per ml of culture medium without penicillin-streptomycin solution in 6-well plates. After 16 hr, cells were treated with 1.5 mM MMS (Sigma) for 1 hr or grown without MMS as control. One microgram of the K562 or HeLa genomic DNA was used directly as input into the SSiNGLe-AP protocol. For the MX treatment, after DNase fragmentation, the purified genomic DNA was incubated at 37C for 30 min in 20 µl of 50 mM K3PO4 (pH 7.0) buffer with or without 33 mM MX (Abmole). The DNA was recovered by ethanol precipitation, dissolved in 15 µl water and subjected to SSiNGLe-AP procedure starting from the blocking step preceded by denaturation. All samples were processed with SSiNGLe-AP protocol based on APE1, with exception of some samples where Endo IV was used instead as indicated.

tag: strain

tag: tissue

value: Heart

value: 19 months


title: 50S CMCT and NaHCO3 replciate 2

value: BLR (DE3) deltaDbpA, expressing wild-type DbpA

value: CMCT and NaHCO3


title: Plate1-130-Liver

description: Plate 1_LIVER_C09

value: Sprague Dawley (SD)

tag: Sex

value: Female

value: Liver

tag: chemical

value: PFHxSAm

tag: concentration

tag: unit

value: mg/kg

value: water/tween


title: 3-L-1

value: 3 months


title: 19-H-2


title: COV009, BCR-Seq

value: Peripheral blood

value: peripheral blood mono-nuclear cells (PBMCs)

value: male


title: 12-H-3

value: 12 months


title: 19-H-1


title: Plate1-128-Liver

description: Plate 1_LIVER_E09

tag: vehicle

tag: duration

value: day

tag: platfrom

value: TempO-Seq


title: 50S CMCT and NaHCO3 replciate 1

tag: genotype/variation

value: BLR (DE3) deltaDbpA, expressing wild-   type DbpA

tag: treatment

tag: molecule

value: 23S ribosomal RNA


title: Plate1-129-Liver

description: Plate 1_LIVER_H11


title: COV007, BCR-Seq

tag: cell type

tag: age

tag: gender

tag: disease symptom

value: symptomatic

value: Severe

value: No

value: short term


title: 45S NaHCO3

value: BLR (DE3) deltaDbpA, expressing R331A DbpA


title: Plate1-127-Liver

description: Plate 1_LIVER_G05

value: Sprague Dawley (SD)

value: Female

value: Liver

value: PFHxSAm


title: 45S CMCT and NaHCO3 replicate 2

value: CMCT and NaHCO3


title: Plate1-126-Liver

description: Plate 1_LIVER_E06

value: mg/kg

value: water/tween


title: Plate1-125-Liver

description: Plate 1_LIVER_B04

value: Male


title: COV012, BCR-Seq

value: Peripheral blood

value: peripheral blood mono-nuclear cells (PBMCs)

value: male

tag: disease state

tag: thymalfasin treatment

tag: disease duration

tag: patient comorbidity

value: Yes


title: COV077, BCR-Seq

tag: tissue

value: symptomatic


title: 45S CMCT and NaHCO3 replicate 1

value: 23S ribosomal RNA


title: 12-H-1

tag: strain

value: Heart

value: 12 months


title: 12-H-2


title: 35S NaHCO3

value: BLR (DE3) deltaDbpA, expressing R331A DbpA

value: 16S ribosomal RNA


title: COV013, BCR-Seq

value: Severe

value: No

value: short term


title: 3-H-3

value: 3 months


title: 35S CMCT and NaHCO3  replicated 2

value: CMCT and NaHCO3


title: COV078, BCR-Seq


title: Plate1-123-Liver

description: Plate 1_LIVER_H07

value: Sprague Dawley (SD)

tag: Sex

value: Liver

tag: chemical

value: PFHxSAm

tag: concentration

tag: unit

value: mg/kg

value: water/tween

value: day

value: TempO-Seq


title: COV011, BCR-Seq

value: Peripheral blood

value: peripheral blood mono-nuclear cells (PBMCs)

value: male

value: symptomatic

value: Yes


title: 35S CMCT  and NaHCO3 replicated 1

tag: genotype/variation

value: BLR (DE3) deltaDbpA, expressing R331A DbpA

value: 23S ribosomal RNA

value: 16S ribosomal RNA


title: 3-H-2

value: Heart

value: 3 months


title: COV157, BCR-Seq

value: Moderate

value: No

value: long term


title: Plate1-121-Liver

description: Plate 1_LIVER_H02

value: Sprague Dawley (SD)

value: Male

value: Liver

value: PFHxSAm

value: mg/kg

tag: vehicle

tag: duration

tag: platfrom


title: Plate1-122-Liver

description: Plate 1_LIVER_A10

value: water/tween

value: day

value: TempO-Seq


title: Plate1-120-Liver

description: Plate 1_LIVER_H10

value: Female


title: COV156, BCR-Seq

value: Peripheral blood

tag: cell type

value: peripheral blood mono-nuclear cells (PBMCs)

tag: age

value: female

value: symptomatic

value: Yes


title: 22-B-2

source_name: Brain

value: Brain

value: 22 months


title: Plate1-118-Liver

description: Plate 1_LIVER_C11


title: COV102, BCR-Seq

tag: gender

tag: disease symptom

value: Moderate

value: No

value: long term


title: COV101, BCR-Seq

tag: disease state

tag: thymalfasin treatment

value: short term


title: Plate1-119-Liver

description: Plate 1_LIVER_E04

value: Sprague Dawley (SD)

value: Liver

value: PFHxSAm


title: Plate1-124-Liver

description: Plate 1_LIVER_F05

value: Male

value: mg/kg

value: water/tween

value: day


title: Plate1-117-Liver

description: Plate 1_LIVER_D02

value: Female

value: TempO-Seq


title: 19-B-1

value: 19 months


title: 19-B-2


title: 3-H-1

value: Heart

value: 3 months


title: Plate1-116-Liver

description: Plate 1_LIVER_E07


title: 22-B-3

value: Brain

value: 22 months


title: 12-B-2

value: 12 months


title: COV087, BCR-Seq

value: Peripheral blood

value: peripheral blood mono-nuclear cells (PBMCs)

value: male

value: symptomatic

value: Moderate

value: Yes

tag: disease duration

tag: patient comorbidity


title: Plate1-115-Liver

description: Plate 1_LIVER_A08

tag: strain

value: Sprague Dawley (SD)

tag: tissue

value: Liver

value: PFHxSAm

value: mg/kg


title: 19-B-3


title: COV098, BCR-Seq

value: female

value: No

value: short term


title: Plate1-114-Liver

description: Plate 1_LIVER_D06

tag: Sex

value: Female

tag: chemical

value: water/tween

value: day

value: TempO-Seq


title: COV091, BCR-Seq

value: Peripheral blood


title: COV086, BCR-Seq

value: peripheral blood mono-nuclear cells (PBMCs)


title: COV076, BCR-Seq


title: Plate1-113-Liver

description: Plate 1_LIVER_F03

tag: concentration

tag: unit


title: 3-B-3

value: Brain

value: 3 months


title: 3-B-2


title: COV074, BCR-Seq

value: male

value: symptomatic

value: Moderate


title: 12-B-3

value: 12 months


title: Plate1-112-Liver

description: Plate 1_LIVER_A04

value: Sprague Dawley (SD)

value: Liver

value: PFHxSAm

tag: vehicle


title: COV089, BCR-Seq

value: female

value: No

value: long term


title: Lung mesenchymal cells in bleomycin lungs rep3

type: RNA

city: Kyoto

first: Koichi

last: Hasegawa

state: Kyoto

address: Kawahara-cho 54, Sakyo-ku

department: Respiratory medicine

country: Japan

institute: Kyoto University

description: Gene expression data from mesenchymal cells of bleomycin lungs

hyb_protocol: Following fragmentation, 3.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G

data_processing: The data were analyzed with GeneSpring software (version 13.1, Agilent Technologies, Santa Clara, USA)

label: biotin

source_name: Lung mesenchymal cells from bleomycin lungs

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

growth_protocol: C57BL/6J mice were maintained in SPF conditons.

extract_protocol: Total RNA was purified using an RNeasy mini plus kit (Qiagen, Chatsworth, CA) according to the manufacturer’s protocol.

treatment_protocol: Mice were intratracheally treated by PBS or bleomycin. Mesenchymal cells, CD45-CD31-EpCAM-cells, were isolated by flow cytometry ten days after the treatment.

value: whole lungs

tag: strains


title: 3-B-1


title: Lung mesenchymal cells in bleomycin lungs rep2


title: Lung mesenchymal cells in bleomycin lungs rep4


title: Plate1-111-Liver

description: Plate 1_LIVER_E08

value: Female

value: mg/kg

value: water/tween

tag: duration

value: day

tag: platfrom


title: Lung mesenchymal cells in bleomycin lungs rep1

tag: age


title: Lung mesenchymal cells in control lungs rep4

description: Gene expression data from mesenchymal cells of control lungs

source_name: Lung mesenchymal cells from control lungs


title: Lung mesenchymal cells in control lungs rep3


title: 12-B-1

value: Brain


title: Lung mesenchymal cells in control lungs rep1


title: CH12_HiC_C13_KI

city: Vienna

first: Tobias

last: Neumann

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

description:
CH12_HiC_C13_KI.mcool
CH12_HiC_C13_KI_5kb_domains.bed
CH12_HiC_C13_KI_20kb_w200000.PC1.bw
CH12_HiC_C13_KI_hiccups.bed

data_processing:
Hi-C
Raw paired-end reads were controlled for quality and adapters were removed with trim_galore 0.6.2 with a quality cutoff of 20
Trimmed read pairs were processed with HICUP 0.7.3 using ^GATC,MboI as restriction enzyme and mouse mm9 as reference genome
Aligned, filtered and deduplicated read pairs were converted to pairix with cooler csort 0.8.3
Resulting pairix files were then used to generate a 5kb initial contact matrix using cooler cload pairix 0.8.3 with canonical chromosome sizes of mm9 and cooler zoomify 0.8.3 was used to generate resolutions of 10kb, 20kb, 25kb, 50kb, 100kb, 200kb, 250kb, 500kb, 1Mb
Each resolution was then balanced using genome-wide KR (0.05, part of HiCExplorer) and IC (part of cooler 0.8.3) using default arguments and saved into a multicooler file
Similarly, juicer_tools 1.22.01 was used to generate hic files of the same resolutions and balanced with GW_KR for subsequent loop calling
Loops were then called with HICCUPS 1.22.01 with arguments -m 1024 -r 5000,10000,25000 -f 0.1,0.1,0.1 -k GW_KR -p 4,2,1 -i 7,5,3 -t 0.02,1.5,1.75,2 -d 20000,20000,50000
In addition, HOMER 4.10 was used to compute compartment signals and TAD annotations by first generating a ditag directory from HICUP results using makeTagDirectory. Subsequently, compartment signals were computed with runHiCpca.pl with -res 20000 -window 200000 -genome mm9 using the RefSeq gene annotation for mm9 as markers of the active compartment. TADs were called with findTADsAndLoops.pl find with -res 5000 -balance -window 50000 -genome mm9 using known duplications for mm9 (downloaded from UCSC) as bad regions.
Genome_build: UCSC mm9
Supplementary_files_format_and_content: Multicoolers contain the raw contact matrixes as well as balancing weights for KR and IC algorithms for resolutions of 5kb, 10kb, 20kb, 25kb, 50kb, 100kb, 200kb, 250kb, 500kb, 1Mb. Balancing weights for each resolution were saved in the bins table as 'weight' (KR) and 'ICE' (IC) column, respectively
Supplementary_files_format_and_content: Loop annotions were converted from the HICCUPs merged_loops.bedpe file to a 2D bed file containing columns chr1, x1, x2, chr2, y1, y2, fdrBL
Supplementary_files_format_and_content: TAD annotations were converted from  to a domains file with columns chr, start, end, name, TADscore, strand, start, end, RGB color
Supplementary_files_format_and_content: The first principal component as computed by homer was converted to bigWig with sort -k1,1 -k2,2n; bedGraphToBigWig (UCSC kent_tools/20190507-linux.x86_64) with a chromsize file containing only mm9 canonical chromosomes

growth_protocol: CH12 cells cultured in complete RPMI medium wit IL4/CD40/TGF beta stimulation.

extract_protocol:
DNA from crosslinked nuclei was digested with restriction enzyme, biotin filled ligated and streptavidin enriched
Libraries were prepared following standard Illumina protocols

tag: cell line

tag: knockdown

value: knock in


title: Plate1-110-Liver

description: Plate 1_LIVER_E03

value: Male

value: TempO-Seq


title: Lung mesenchymal cells in control lungs rep2


title: COV048, BCR-Seq

value: Peripheral blood

tag: cell type

value: peripheral blood mono-nuclear cells (PBMCs)

tag: gender

tag: disease symptom

value: symptomatic

tag: disease state

value: Moderate

value: short term

value: Yes


title: Plate1-109-Liver

description: Plate 1_LIVER_H08

tag: strain

value: Sprague Dawley (SD)

value: Liver

value: PFHxSAm


title: COV155, BCR-Seq

tag: tissue

value: female

value: asymptomatic

tag: thymalfasin treatment

value: No

tag: disease duration

tag: patient comorbidity


title: CH12_HiC_C13_deltaori_2

description:
CH12_HiC_C13_deltaori.mcool
CH12_HiC_C13_deltaori_5kb_domains.bed
CH12_HiC_C13_deltaori_20kb_w200000.PC1.bw
CH12_HiC_C13_deltaori_hiccups.bed


title: CH12_HiC_WT_2

description:
CH12_HiC_WT.mcool
CH12_HiC_WT_5kb_domains.bed
CH12_HiC_WT_20kb_w200000.PC1.bw
CH12_HiC_WT_hiccups.bed


title: Plate1-108-Liver

description: Plate 1_LIVER_A06

tag: Sex

tag: chemical

tag: concentration

tag: unit

value: mg/kg

value: water/tween

value: day


title: Vehicle-FAPs

city: Chengdu

first: Xia

last: Kang

address: Rongdu Avenue, #270

institute: General Hospital of Western Theater Command

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw reads from the RNA-seq libraries were analyzed with the free Majorbio online cloud platform (www.majorbio.com)
The expression level of each transcript was calculated using the fragments per kilobase of transcript per million mapped reads (FPKM) method
RSEM was utilized to quantify the gene abundances.
EdgeR was used for differential expression analysis.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: Matrix table with raw gene counts for differentially expressed genes

source_name: fibro/adipogenic progenitors

growth_protocol: Freshly sorted FAPs were cultured in growth medium (GM) consisting of DMEM supplemented with 20% FBS, 1% penicillin-streptomycin

extract_protocol:
Total RNA was extracted from Musclin- or vehicle-treated FAPs using TRIzol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 1 µM mouse recombinant Musclin or an equal amount of vehicle was added to the medium treating for 72 hours. The medium containing Musclin or vehicle was changed daily.

tag: treatment

value: Vehicle


title: COV147, BCR-Seq

tag: age

value: male


title: COV072, BCR-Seq

value: Peripheral blood

value: long term


title: Musclin-FAPs

value: Musclin


title: Plate1-107-Liver

description: Plate 1_LIVER_B09

value: Male

tag: vehicle

tag: duration

tag: platfrom

value: TempO-Seq


title: Plate1-106-Liver

description: Plate 1_LIVER_G04


title: COV146, BCR-Seq

tag: cell type

value: peripheral blood mono-nuclear cells (PBMCs)

tag: gender

value: short term


title: Plate1-105-Liver

description: Plate 1_LIVER_G11

value: Sprague Dawley (SD)

value: Liver


title: COV144, BCR-Seq

value: female

tag: disease symptom

tag: disease state


title: Plate1-104-Liver

description: Plate 1_LIVER_B02

tag: strain

tag: tissue

value: PFHxSAm


title: CH12_HiC_WT_1

tag: cell line

tag: knockdown


title: LiverC_Sheep [WGBS]

city: Beijing

first: Siqian

last: Chen

address: 2rd, Yuanmingyuan West Road

department: College of Animal Science and Technology

institute: China Agricultural University

data_processing:
FastQC v 0.11.2 and Trim Galore v 0.4.0 was used to assess the quality of the sequence data and filter low-quality reads (q < 30), respectively. The cleaned data were then mapped to the sscrofa11.1 genomes using bowtie2 under the Bismark software (0.14.5) with default parameters
Duplicated reads were removed using deduplicate_bismark
symmetric-cpgs was employed to obtain methyl CpG site information using methpipe software
Assembly: ARS-UCD1.2, Oar_rambouillet_v1.0, ARS1
Supplementary files format and content: CpG report files

organism: Ovis aries

source_name: liver

extract_protocol:
DNA was extracted according to the TIANamp Genomic DNA Kit protocol
DNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

tag: developmental stage

value: adult


title: CH12_HiC_shMcm_3

description:
CH12_HiC_shMcm.mcool
CH12_HiC_shMcm_5kb_domains.bed
CH12_HiC_shMcm_20kb_w200000.PC1.bw
CH12_HiC_shMcm_hiccups.bed

value: shMcm


title: LiverB_Sheep [WGBS]


title: Plate1-103-Liver

description: Plate 1_LIVER_D10

tag: Sex

tag: chemical

value: mg/kg

value: water/tween

value: day


title: COV154, BCR-Seq

value: Peripheral blood

value: male

value: asymptomatic

tag: thymalfasin treatment

value: No

tag: disease duration

tag: patient comorbidity

value: Yes


title: CH12_HiC_shMcm_2


title: TAM CCR2- RbpjiΔEC 3

city: Heidelberg

first: Elisenda

last: Alsina Sanchis

address: Im Neuenheimer Feld 280

country: Germany

institute: DKFZ

description: Gene expression data from murine peritoneal TAMs

hyb_protocol: cDNA was hybridized onto GeneChip® Mouse Genome   430 2.0 according to manufacturer's instructions.

scan_protocol: Gene Expression Microarrays were scanned using the Affymetrix GeneChip® Scanner 3000 according to GeneChip® Expression Wash, Stain and Scan Manual for Cartridge Arrays

data_processing: All intensity data were quantile normalized.

label: Biotin

source_name: peritoneal TAMs

label_protocol: Biotin

growth_protocol: Mice were housed under specific pathogen-free conditions. Administration of tamoxifen diluted in sterile peanut in 8 to 12-week-old randomized mice was performed by oral gavage once with 100 µl (1 mg tamoxifen). Three weeks after gene recombination, 5x106 ID8-luciferase (ID8-luc) ovarian cancer cells were administered i.p. in PBS and grown for four weeks.

extract_protocol: RNA was isolated using PicoPure RNA Isolation Kit (Acturus,Life Technology).

treatment_protocol: Peritoneal lavage was collected after injecting 5ml PBS cold and cell suspension was prepared for cell sorting. Samples were obteined after cell sorting of tumor-associated macrophages (TAMs) CCR2+ (CD45+, CD11b+, F4/80+, CCR2+) and TAMs CCR2- (CD45+, CD11b+, F4/80+, CCR2-) in RbpjiΔEC and control mice.

tag: sample type

value: peritoneal TAMs of C57BL/6N female, after 4 weeks ID8 i.p. tumor growth


title: LiverA_Sheep [WGBS]


title: TAM CCR2- RbpjiΔEC 1


title: Plate1-102-Liver

description: Plate 1_LIVER_A02

value: Male

tag: concentration

tag: unit

tag: vehicle

tag: duration

value: TempO-Seq


title: LiverC_Sheep

data_processing:
The adapter sequences and low-quality bases were filtered using Trimmomatic v0.39
The trimmed reads were mapped to the Ensembl 103 version of reference genomes with annotated genes using STAR aligner v 2.7.6 with the following options: “--outFilterMismatchNmax 3 –outFilterType BySJout –quantMode GeneCounts –outFilterMismatchNoverLmax 0.04 –outSAMtype SAM SortedByCoordinate”.
Gene expression levels were quantified as counts using featureCounts
Assembly: ARS-UCD1.2, Oar_rambouillet_v1.0, ARS1
Supplementary files format and content: tab-delimited text files include gene counts for each Sample

extract_protocol:
Total RNA were extracted using TRIzol method from frozen liver samples
mRNA were enriched using magnetic beads with Oligo(dT) and sheared. The cDNA was synthesized using random hexamers, end-repaired, and ligated to A base and sequencing adapters.

tag: development stage


title: CH12_HiC_shMcm_1


title: CH12_HiC_C13_deltaori_1

description:
CH12_HiC_C13_deltaori.mcool
CH12_HiC_C13_deltaori_20kb_w200000.PC1.bw
CH12_HiC_C13_deltaori_5kb_domains.bed
CH12_HiC_C13_deltaori_hiccups.bed


title: TAM CCR2- RbpjiΔEC 4


title: TAM CCR2- Control 4


title: TAM CCR2- Control 1


title: TAM CCR2- RbpjiΔEC 2


title: TAM CCR2+ RbpjiΔEC 3


title: TAM CCR2- Control 2


title: TAM CCR2- Control 3


title: TAM CCR2+ RbpjiΔEC 4


title: LiverB_Sheep


title: Plate1-101-Liver

description: Plate 1_LIVER_F12

value: Sprague Dawley (SD)

value: Liver

tag: platfrom


title: Running

description: Bone marrow from running mice

library_source: transcriptomic single cell

data_processing:
The Cell Ranger software pipeline provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

organism: Mus

source_name: murine  hindlimb

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.

value: Bone marrow

tag: group

value: running


title: TAM CCR2+ RbpjiΔEC 2


title: CH12_HiC_shLacZ_2

description:
CH12_HiC_shLacZ.mcool
CH12_HiC_shLacZ_5kb_domains.bed
CH12_HiC_shLacZ_20kb_w200000.PC1.bw
CH12_HiC_shLacZ_hiccups.bed

value: shLacZ


title: LiverA_Sheep

tag: tissue

value: liver

value: adult


title: Ground

description: Bone marrow from ground mice

value: ground


title: CH12_HiC_shLacZ_1

tag: cell line


title: R9_PFC

status: Public on Sep 14 2022

city: seoul

first: SeungHyun

last: Jung

state: seoul

address: catholic university, medical college, banpo-dong

department: Department of Biochemistry

country: South Korea

institute: Catholic University of Korea

data_processing:
Raw sequence data were first filtered and trimmed using Trimmomatic software.
The sequencing reads were then mapped onto the rattus norvegicus reference genome (Rnor_6.0, rn6) using the STAR aligner v2.5.3a
Gene-level quantification of expression was performed with HTSeq v0.9.0, according to the Ensembl transcript annotation (Rnor_6.0.91 version).
A differentially expressed gene (DEG) analysis was performed for gene sets with expression by the use of SARTools and edgeR R package.
Genome_build: rn6
Supplementary_files_format_and_content: HTSeq count matrix format: a table with counts for each feature (gene). The instructions can be found here: https://htseq.readthedocs.io/en/release_0.11.1/count.html

source_name: cells from prefrontal cortex

extract_protocol:
We performed whole-transcriptome sequencing (WTS) using total RNA from two brain areas (the medial prefrontal cortex (mPFC) and the nucleus accumbens (NAc)) of 19 rGT trained rats (risk-averse, n=9; risk-seeking, n=10). Total RNA was extracted using the miRNeasy Mini kit (Qiagen, Hilden, Germany) and quantity, and quality was measured using the Qubit (Thermo Fisher Scientific, Waltham, MA) and TapeStation (Agilent Technologies, Santa Clara, CA), respectively.
Total RNA of 36 rat brain tissues were converted into cDNA library using TruSeq RNA Library Preparation Kit v2 (Illumina, San Diego, CA). After polymerase chain reaction (PCR) amplification, the final product was assessed with a TapeStation (Agilent) and subsequently sequenced on the Illumina NovaSeq 6000 platform (Illumina) with 101-bp paired-end reads.

tag: strain

value: Sparague Dawley

value: Brain (prefrontal cortex)

tag: disease state

value: Risk-Averse


title: R9_NAC

source_name: cells from nucleus accumbens

value: Brain (nucleus accumbens)


title: R7_PFC


title: CH12_HiC_shLacZ_3

tag: knockdown


title: R7_NAC


title: TAM CCR2+ Control 4


title: TAM CCR2+ RbpjiΔEC 1


title: R4_NAC


title: R6_PFC

value: Risk-Seeking


title: TAM CCR2+ Control 2


title: R1_PFC


title: R2_PFC


title: R2_NAC


title: R1_NAC


title: TAM CCR2+ Control 1


title: N9_NAC


title: N7_NAC


title: N7_PFC


title: N6_PFC


title: N6_NAC


title: N1_NAC


title: N1_PFC


title: TAM CCR2+ Control 3


title: N3_PFC


title: N3_NAC


title: BR5_PFC


title: BR4_NAC


title: R4_PFC


title: BR9_PFC


title: BR9_NAC


title: BR5_NAC


title: BR4_PFC


title: B5_PFC


title: BR2_NAC


title: B9_NAC


title: B5_NAC


title: B9_PFC


title: B3_PFC


title: FR3

city: Guelph

first: Clarence

last: Swanton

state: Ontario

address: 50 Stone Rd. East

department: Plant Agriculture

country: Canada

institute: University of Guelph, Department of Plant Agriculture

data_processing:
RNA libraries were sequenced on an Illumina sequencer at the Genome Quebec Innovation Center (McGill University, Canada)
Differentially expressed gene (DEG) analysis was performed by Harvest Genomics Inc. (Guelph, Canada), where the quality control of raw .fastq files was performed prior to sequence alignment to the reference genome. Seuqence alignment against the refernce genome was performed using Bowtie2 v2.4.3.
Count data were retrieved using HTSeq (version 0.13.5). HTSeq counts have been filtered with counts per gene >10 among all treatments. DEGs were determined using DESeq2 (version 1.30.1). The Benjamini-Hochberg false discovery rate (FDR) correction was used within DESeq2 (version 1.30.1) to obtain adjusted p-values (padj).
Log2 fold change (lfc) tables were produced according to Zhu et al. (2018) https://doi.org/10.1093/bioinformatics/bty895. Log2 fold change tables were produced for each pairwise comparison: FR vs WF.csv; W vs FR.csv; W vs WF.csv
Assembly: reference genome (https://www.ncbi.nlm.nih.gov/assembly/GCF_000001735.4/) using Bowtie 2 v2.4.3

organism: Arabidopsis thaliana

source_name: Leaf, high red to far-red ratio (1.4), 3 weeks, artificial low red to far-red ratio (0.3), 1 week, rep 3

growth_protocol: Wild type Arabidopsis thaliana plants (ecotype Columbia) were raised in controlled environment growth chambers (Model CMP 3244 Conviron, Winnipeg, Canada) with a 12 hour photoperiod, an irradiance of 150 µmol per square meter per second, a relative humidity of 60% and a red (R) to far-red (FR) ratio R:FR ≈ 1.4. Two systems consisting of a surrogate weed and far-red LEDs were used to generate biological and artificicial low R:FR light environments with a R:FR ≈ 0.3.

extract_protocol:
Total RNA was extracted from 4-week-old Arabidopsis rosette levaves using the RNeasy PowerPlant kit (Qiagen) and the contaminating DNA was removed using the RNase-Free DNase kit (Qiagen).
RNA libraries for RNA-seq were prepared using Illumina TrueSeq RNA kit following manufacturer's protocols.

treatment_protocol:
Three red to far-red (R:FR) light treatments were applied to the wild type Arabidopsis plants. A weed-free (WF) control with a R:FR ≈ 1.4, a biological low R:FR ≈ 0.3 (weedy; W), and an artificial low R:FR ≈ 0.3 (far-red; FR). All plants were grown in the weed-free condition (R:FR ≈ 1.4) for 3 weeks. Then, one series of plants were kept in the weed-free condition as controls and parallel series of plants were transferred to the biological low R:FR ≈ 0.3 and artificial low R:FR ≈ 0.3 and sampled after 1 week.
In total, 9 samples consisting of 3 treatments (weed-free control, biological low R:FR, and artificial low R:FR light) with 3 replicates, each consisting of a pool of 4-week-old rosette leaves from 3 individual plants, were analyzed.

value: rosette leaves

tag: ecotype

value: Columbia

tag: genotype

value: WT

tag: treatment

value: WT Columbia, high red to far-red ratio (1.4), 3 weeks, artificial low red to far-red ratio (0.3), 1 week, (far-red 3; FR3)

tag: time


title: B2_PFC


title: B2_NAC


title: FR1

source_name: Leaf, high red to far-red ratio (1.4), 3 weeks, artificial low red to far-red ratio (0.3), 1 week, rep 1

value: WT Columbia, high red to far-red ratio (1.4), 3 weeks, artificial low red to far-red ratio (0.3), 1 week, (far-red 1; FR1)


title: W1

source_name: Leaf, high red to far-red ratio (1.4), 3 weeks, biological low red to far-red ratio (0.3), 1 week, rep 1

value: WT Columbia, high red to far-red ratio (1.4), 3 weeks, biological (weedy) low red to far-red ratio (0.3), 1 week, (weedy 1; W1)


title: FR2

source_name: Leaf, high red to far-red ratio (1.4), 3 weeks, artificial low red to far-red ratio (0.3), 1 week, rep 2

value: WT Columbia, high red to far-red ratio (1.4), 3 weeks, artificial low red to far-red ratio (0.3), 1 week, (far-red 2; FR2)


title: B3_NAC


title: W3

source_name: Leaf, high red to far-red ratio (1.4), 3 weeks, biological low red to far-red ratio (0.3), 1 week, rep 3

value: WT Columbia, high red to far-red ratio (1.4), 3 weeks, biological (weedy) low red to far-red ratio (0.3), 1 week, (weedy 3; W3)


title: W2

source_name: Leaf, high red to far-red ratio (1.4), 3 weeks, biological low red to far-red ratio (0.3), 1 week, rep 2

value: WT Columbia, high red to far-red ratio (1.4), 3 weeks, biological (weedy) low red to far-red ratio (0.3), 1 week, (weedy 2; W2)


title: WF2

source_name: Leaf, high red to far-red ratio (1.4), 4 weeks, rep 2

value: WT Columbia plants grown weed-free, high red to far-red ratio (1.4), 4 weeks, (weed-free 2; WF2)


title: WF1

source_name: Leaf, high red to far-red ratio (1.4), 4 weeks, rep 1

value: WT Columbia plants grown weed-free, high red to far-red ratio (1.4), 4 weeks, (weed-free 1; WF1)


title: BR2_PFC


title: Arabidopsis root cells - sc_137

first: Philip

middle: N.

last: Benfey

address: 130 Science Drive

department: Biology

institute: Duke University

data_processing:
Processed by COPILOT (https://github.com/ohlerlab/COPILOT)
Assembly: TAIR10
Supplementary files format and content: Seurat object

source_name: Arabidopsis root cells - Benfey Lab

growth_protocol: Arabidopsis accession Columbia-0 (Col-0) was used as wild type. The following lines were previously described: bri1  GABI_134E10 (Jaillais et al., 2011); bri1-116brl1brl3 triple mutant (bri1-T) (Irani et al., 2012); pGL2:BRI1-GFP/bri1-T (Vragović et al., 2015); gtl1-1 (WiscDsLox413-416C9), df1-1 (SALK_106258), and gtl1-1 df1-1 (Shibata et al., 2018); JKD-Ypet recombineering line (Moreno-Risueno et al., 2015). Seeds were sterilized using 50% (v/v) bleach with 0.05% Tween-20 for 10-15 minutes, plated on 1/2 Linsmaier and Skoog (LSP03-1LT, Caisson Labs; pH 5.7), 1% sucrose media, and stratified 2-4 days at 4°C in the dark. Plates were kept vertically in a Percival growth chamber set to 22°C, 16 hours light/8 hours dark and grown for 7 days. Chemical treatments were conducted by cooling the growth media to approximately 60°C after autoclaving and adding DMSO (a mock solvent), 1μM Brassinazole (BRZ, SML1406,  Sigma) or 100nM Brassinolide (BL, 21594, Cayman Chemical).

extract_protocol:
For each sample, ~0.5cm root tips were harvested from 1000-3000 roots and placed into a 35mm petri dish containing a 70 μm cell strainer and 4.5mL enzyme solution (1.5% [w/v] cellulase [ONOZUKA R-10, GoldBio], 0.1% Pectolyase [Sigma P3026], 0.4 M mannitol, 20 mM MES (pH 5.7), 20 mM KCl, 10 mM CaCl2, 0.1% bovine serum albumin, and 0.000194% (v/v) -mercaptoethanol). The digestion was incubated on an 85 rpm shaker at 25°C for one hour with additional stirring every 15-20 minutes. The resulting cell solution was filtered twice through 40 μm cell strainers and centrifuged for 5 minutes at 500g in a swinging bucket rotor. The pellet was washed with 2mL washing solution (0.4 M mannitol, 20 mM MES (pH 5.7), 20 mM KCl, 10 mM CaCl2, 0.1% bovine serum albumin, and 0.000194% (v/v) -mercaptoethanol), centrifuged again at 500g for 3 minutes, and the pellet resuspended in washing solution at a concentration of ~2000 cells/uL. We loaded 16,000 cells, with the aim to capture 10,000 cells per sample with the 10X Genomics Chromium 3` Gene expression v3 or v3.1 kits.
Cell barcoding and library construction were performed following the manufacturer’s instructions. cDNA and final library quality were verified using a Bioanalyzer High Sensitivity DNA Chip (Agilent) and sequenced on an Illumina NovaSeq 6000 instrument to produce 100bp paired-end reads.

treatment_protocol: For BL scRNA-seq, we first grew plants on 1 μM BRZ to deplete endogenous BRs, then transferred plants to either a fresh BRZ plate or 100nM BL. We monitored the efficacy of these treatments using a constitutively expressed 35S:BES1-GFP line. In agreement with previous reports (Gampala et al., 2007; Ryu et al., 2007; Yin et al., 2002), BES1-GFP was predominantly present in the cytoplasm under low BR conditions resulting from BRZ treatment but accumulated in the nucleus following BL treatment (Figures S1A and S1B). We performed two separate BL scRNA-seq treatment experiments. The first consisted of a BRZ and 2 hour BL treatment. The second experiment included two additional replicates of BRZ and BL 2 hours along with the other time points in our time course (BL 0.5, 1, 4, and 8 hour treatments). Each of the BL treatments was staggered so that all samples were collected simultaneously.WT, bri1-T, and pGL2:BRI1-GFP/bri1-T were similarly profiled in a side-by-side scRNA-seq experiment under control conditions with two replicates per genotype. Lastly, scRNA-seq was performed on WT, gtl1, df1, and gtl1 df1 in duplicate under control conditions.

tag: name

tag: full genotype

value: Control

tag: age

tag: timepoint

tag: time trt

tag: rep

tag: date

tag: seq run

tag: 10x chemistry

tag: number of_cells

tag: number of_genes_detected

tag: median umi_counts_per_cell


title: Arabidopsis root cells - sc_133

tag: concentration


title: Arabidopsis root cells - sc_134

value: WT Col-0


title: Arabidopsis root cells - sc_135

value: bri1-116 brl1 brl3 (bri1-T)


title: Arabidopsis root cells - sc_122


title: Arabidopsis root cells - sc_128


title: Arabidopsis root cells - sc_130


title: Arabidopsis root cells - sc_131


title: Arabidopsis root cells - sc_125


title: Arabidopsis root cells - sc_129


title: Arabidopsis root cells - sc_50

value: WT BRZ control

value: BRZ

value: Nolan_6199 (NextSeq); Nolan_6226 (NovaSeq S4)


title: Arabidopsis root cells - sc_48

value: WT BRZ then 8 hour BL

value: BL


title: Arabidopsis root cells - sc_127


title: Arabidopsis root cells - sc_126

value: WT


title: Arabidopsis root cells - sc_45

value: WT BRZ then 1 hour BL


title: Arabidopsis root cells - sc_46

value: WT BRZ then 2 hour BL


title: Arabidopsis root cells - sc_44

value: WT BRZ then 30 mins BL


title: Arabidopsis root cells - sc_123


title: Arabidopsis root cells - sc_124


title: WF3

source_name: Leaf, high red to far-red ratio (1.4), 4 weeks, rep 3

tag: tissue

value: rosette leaves

tag: ecotype

value: Columbia

value: WT Columbia plants grown weed-free, high red to far-red ratio (1.4), 4 weeks, (weed-free 3; WF3)


title: Arabidopsis root cells - sc_49

tag: genotype

tag: treatment


title: Arabidopsis root cells - sc_2

tag: name


title: Arabidopsis root cells - sc_43

tag: full genotype


title: wrky75_HN_exp2_rep3

city: Sinagpore

first: Daisuke

last: Urano

address: 1 Research Link

country: Singapore

institute: Temasek Life Science Laboratory

data_processing:
STAR for genome mapping
Genome_build: Arabidopsis thaliana (TAIR10) reference genome
Supplementary_files_format_and_content: raw counts

source_name: roots

growth_protocol: Arabidopsis thaliana var. Col-0 and knockout mutants; agb1-2, wrky40, wrky75 were growth on 1/2 MS media with 1% sucrose, 0.05% MES, 0.8% plant agar pH5.8 for seven days under long-day condition (16 hr light / 8 hr darkness, 100 µmol/m2/sec and 22°C

extract_protocol:
Roots were excised and immediately frozen in liquid nitrogen and followed by RNA extraction using Rneasy Plant Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Novoseq protocols

treatment_protocol: One-week-old of Arabidopsis seedling were treated with or without 20 mM NH4NO3 for 2hours, pH5.8 , 2-3  biological replicates. Root were excised for total RNA extraction.

value: roots

tag: age

value: high nitrogen condition


title: wrky75_HN_exp2_rep2


title: Arabidopsis root cells - sc_47

value: WT BRZ then 4 hour BL

tag: timepoint


title: wrky75_cntr_exp2_rep3

value: control condition


title: wrky75_cntr_exp2_rep2


title: wrky75_HN_exp2_rep1


title: wrky75_cntr_exp2_rep1


title: T50_3

city: tianjin

first: Defei

last: Liu

state: 天津

address: xiqidao 32

institute: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with NGSQCToolkit (v2.3).
Clear reads were mapped to Myceliophthora thermophila ATCC 42464 genome using Tophat (version 2.0.8b) with parameters -i 10 -g 1 --segment-length 24 --b2-very-sensitive --no-convert-bam --library-type fr-unstranded.
The counts of reads uniquely mapped to only one gene for each gene were calculated by HTseq-count( v0.5.4p2).
Genome_build: Myceliophthora thermophila ATCC 42464 (https://genome.jgi.doe.gov/Spoth2/Spoth2.home.html)
Supplementary_files_format_and_content: RPKM.xlsx, Readcounts.xlsx

organism: Thermothelomyces thermophilus ATCC 42464

source_name: Myceliophthora thermophila ATCC 42464

growth_protocol: The experiments were performed in 50 mL medium inoculated with 1×10^6 spores per milliliter in 250 mL Erlenmeyer flask shaken at 150 rpm. The minimal medium (per liter) contained 30 g glucose, 3 g NaNO3, 1 g K2HPO4, 0.5 g MgSO4•7H2O, 1 mL biotin (0.1 g/L), 1 mL trace elements solution (Vogel's salts) and adjusted to a pH of 6.0. The culture was incubated at 35 °C, 40°C, 45 °C and 50 °C, respectively.

extract_protocol:
Mycelia for RNA isolation were harvested at exponential growth phase (40°C, 45 °C and 50 °C at 40 h; 35 °C at 66 h). After filtration, the collected mycelia were washed twice and immediately frozen in liquid nitrogen. The samples stored at -80 °C until RNA extraction. About 100mg frozen samples were quickly ground into powder in liquid nitrogen in the mortar. Total RNA was extracted from the powder using RNeasy mini kit (Qiagen) according to the manufacturer's instruction.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: temperature

value: 50° C


title: wrky40_HN_exp2_rep2


title: Arabidopsis root cells - sc_5

value: WT Col-0

tag: time trt

tag: rep

tag: date


title: wrky40_HN_exp2_rep1


title: wrky40_cntr_exp2_rep2


title: T50_1


title: T45_2

value: 45° C


title: T50_2


title: T45_3


title: Col-0_HN_exp2_rep3

value: Col-0, WT


title: wrky40_cntr_exp2_rep1


title: Col-0_HN_exp2_rep2


title: T45_1


title: T40_4

value: 40° C


title: T40_3


title: Col-0_cntr_exp2_rep3


title: T40_2


title: wrky40_HN_exp2_rep3


title: Col-0_cntr_exp2_rep2


title: T35_2

value: 35° C


title: T35_3


title: Col-0_cntr_exp2_rep1


title: T35_1


title: agb1-2_HN_exp1_rep2

value: agb1-2, ko


title: agb1-2_HN_exp1_rep1


title: agb1-2_HN_exp1_rep3


title: ABO013

city: Saint-Hyacinthe

first: Nour

last: Abou Nader

state: Québec

address: 3200 rue sicotte

department: Biomédecine vétérinaire

institute: Université de Montréal

hyb_protocol: After fragmentation and labeling, 3.5µg DNA target was hybridized on GeneChip® Clariom™ S Mouse (Affymetrix now Thermo Fisher Scientific) and incubated at 45°C in the GeneChip® Hybridization oven 640 (Affymetrix) for 17 hours at 60 rpm. GeneChips were then washed in a GeneChips® Fluidics Station 450 (Affymetrix now ThermoFisher) using GeneChip Hybridization Wash and Stain kit according to the manufacturer’s instructions (Affymetrix now ThermoFisher).

scan_protocol: The microarrays were scanned on a GeneChip® scanner 3000 (Affymetrix now ThermoFisher).

data_processing: Results were analyzed using Transcriptome Analysis Console software (4.0). Thresholds used for p-value and fold change were 0.05 and +/-1.5 respectively.

source_name: Adrenal gland, Mst1/Mst2 mutant

label_protocol: Sense-strand cDNA was synthesized from 100 ng of total RNA, and fragmentation and labeling were performed to produce ss DNA with the GeneChip® WT Terminal Labeling Kit according to manufacturer’s instructions (Affymetrix now Thermo Fisher Scientific).

growth_protocol: Mst1(flox/flox);Mst2(flox/flox);Nr5a1-Cre mutant mice and Mst1(flox/flox);Mst2(flox/flox) control mice were tagged and genotyped by tail biopsies using PCR.

extract_protocol: Whole adrenal glands conserved at -80C were defrozen. Total RNA was extracted using the RNeasy Mini kit (Qiagen), according to the manufacturer’s instructions.

treatment_protocol: At 2 months of age, 3 control and 3 mutant mice were randomly chosen to have their adrenal glands extracted.

tag: Sex

value: Female

value: Whole adrenal gland


title: ABO010

source_name: Adrenal gland, control


title: Col-0_HN_exp1_rep1


title: Col-0_HN_exp1_rep3


title: ABO008


title: ABO007


title: ABO014


title: Col-0_HN_exp2_rep1


title: ABO012


title: agb1-2_cntr_exp1_rep3


title: agb1-2_cntr_exp1_rep1


title: agb1-2_cntr_exp1_rep2


title: Col-0_cntr_exp1_rep2


title: Combination_tumour_4 [H364]

city: Bruce

first: Kristine

last: Hardy

state: ACT

address: University of Canberra

country: Australia

institute: University of Canberra

description:
H364_S16
MDA-MB-231 cells were transplanted subcutaneously into the mammary fat pads of Balb/c nude mice and treated with intraperitoneal injections of docetaxel weekly for 3 weeks and PKC-θ peptide inhibitor daily for 5 weeks

data_processing:
Reads were cleaned with trimmomatic (v0.36)  and tagdust (v2.33)
before separately mapping to the human (Hg38) and mouse (mm10) genomes (HISAT2 v2.04, no--discordant -- nomixed).
reads that mapped to both genomes were discarded (Picard).
Gene counts were obtained using Stringtie and Ballgown
TMM and library size normalized in EdgeR.
Genome_build: hg38, mm10
Supplementary_files_format_and_content: normalised counts for Human and Mouse (gene_count_matrix_m) reads.

organism:
Homo sapiens
Mus musculus

source_name: MDA-MB-231 tumour in mouse_combination treated

growth_protocol: MDA-MB-231 Cells 2 x 10^6 in 50µl (50:50 PBS:Matrigel) were transplanted subcutaneously into the mammary fat pads of balb/c nude mice and 50 days later the tumour was excised from the sacrificed mouse.

extract_protocol:
The tumor tissues were collected in Allprotect tissue reagent kit and then processed using the Rneasy Microarray Tissue Mini Kit according to manufacturer’s protocol (tissues were lysed mechanically using the Tissue Lyser II)
Libraries were constructed with theTruSeq mRNA Paired-End kit per manufacturers instructions.

treatment_protocol: Chemotherapy (docetaxel) was administered intraperitoneally weekly for 3 weeks and PKC-θ peptide inhibitor was administered interaperitoneally daily for 5 weeks.

tag: cell line

tag: host strain

value: Balb/c nude mice

tag: drug

value: Docetaxel (4mg/kg) + PKC-θ peptide inhibitor (40mg/kg)


title: Col-0_cntr_exp1_rep3

tag: tissue


title: PKCi_tumour_3 [E349]

description:
E349_S12
MDA-MB-231 cells were transplanted subcutaneously into the mammary fat pads of Balb/c nude mice and treated with intraperitoneal injections of PKC-θ peptide inhibitor daily for 5 weeks

source_name: MDA-MB-231 tumour in mouse_inhibitior treated

value: PKC-θ peptide inhibitor (40mg/kg)


title: PDX1282a

city: indianapolis

first: nur

middle: p

last: Damayanti

state: Indiana

address: 980 w walnut st, R3/C343

institute: IUSM

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the human GRCh38/h38 reference genome available on ENSEMBL using the HISAT2.
Feature counts was used to obtain unique hits counts Biomart was used to map gene ID into Ensemble ID.
Assembly: GRCh38/h38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: PDX

growth_protocol: aXenoline was maintained in Iscove’s Modified Dulbecco's Medium (IMDM) from Gibco (12440-053) with 10% FBS. Normal human astrocyte was obtained from LONZA (CC-2565) and cultured with AGM™ Astrocyte Growth Medium BulletKit™ (CC-3186). All cultures were maintained at 37o and 5% CO2.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen) at  ~ 1.3 ug of total RNA was used for the construction of sequencing libraries.
mRNA was enriched, fragemented and paired, followed by cDNA synthesis, end repair, 5'phosphorylation and dA_Tailing.Subsequently, adaption ligation was performed, PCR enrichment and Sequncing using Illumina HISeq, PE 2x 150.

tag: cell type

value: PDX

tag: disease state

value: glioma cells

value: CDC42SE2 fusion/CDK2NA/B loss


title: PKCi_tumour_1 [E347]

description:
E347_S10
MDA-MB-231 cells were transplanted subcutaneously into the mammary fat pads of Balb/c nude mice and treated with intraperitoneal injections of PKC-θ peptide inhibitor daily for 5 weeks


title: X128b

source_name: xenoline

value: xenoline

tag: genotype


title: PKCi_tumour_2 [E348]

description:
E348_S11
MDA-MB-231 cells were transplanted subcutaneously into the mammary fat pads of Balb/c nude mice and treated with intraperitoneal injections of PKC-θ peptide inhibitor daily for 5 weeks


title: Ptutmorb

source_name: human brain tumor

value: human brain tumor


title: Chemo_tumour_3 [B335]

description:
B335_S8
MDA-MB-231 cells were transplanted subcutaneously into the mammary fat pads of Balb/c nude mice and treated with intraperitoneal injections of docetaxel weekly for 3 weeks

source_name: MDA-MB-231 tumour in mouse_chemo treated

value: Docetaxel (4 mg/kg)


title: Col-0_cntr_exp1_rep1

value: roots

tag: treatment

value: control condition


title: PDX1282b


title: Col-0_HN_exp1_rep2

value: high nitrogen condition


title: Pttumora


title: astrocytea

source_name: astrocyte

value: astrocyte

value: normal neuroglia cells

value: WT


title: TRPC6 KO Heart-2

city: Setagaya

first: Takuya

last: Kuroda

state: Tokyo

address: 1-18-1 Kamiyoga

department: Division of cell-based therapeutic products

institute: National Institute of Health and Sciences

hyb_protocol: An Affymetrix GeneChip Fluidics Station was used to perform streptavidin/phycoerythrin staining.

scan_protocol: The hybridization signals on the microarray were scanned using a GeneChip Scanner 3000.

data_processing:
The array data analysis was performed with Expression console software 1.2 (Thermo Fisher). Normalization was performed with MAS5 algorithm using a set of mouse maintenance genes (Thermo Fisher).
affymetrix-algorithm-name = ExpressionStat
affymetrix-algorithm-version = 5.0

source_name: TRPC6 KO heart

label_protocol: RNA samples were converted into biotinylated cRNA using Two-Cycle Target Labeling and Control Reagents.

extract_protocol: Total RNA was isolated from frozen mouse hearts using RNeasy Fibrous Tissue Mini Kit (Qiagen) according to the manufacturer’s instruction.

tag: strain background

value: TRPC6 KO

value: heart


title: TRPC3 KO Heart-1

source_name: TRPC3 KO heart

value: TRPC3 KO


title: Combination_tumour_3 [H363]

description:
H363_S15
MDA-MB-231 cells were transplanted subcutaneously into the mammary fat pads of Balb/c nude mice and treated with intraperitoneal injections of docetaxel weekly for 3 weeks and PKC-θ peptide inhibitor daily for 5 weeks

value: Balb/c nude mice

value: Docetaxel (4mg/kg) + PKC-θ peptide inhibitor (40mg/kg)


title: TRPC3 KO Heart-3


title: WT Heart-2

source_name: WT heart


title: TRPC6 KO Heart-3


title: TRPC3 KO Heart-2


title: WT Heart-3


title: TRPC6 KO Heart-1


title: WT Heart-1


title: Combination_tumour_2 [H362]

description:
H362_S14
MDA-MB-231 cells were transplanted subcutaneously into the mammary fat pads of Balb/c nude mice and treated with intraperitoneal injections of docetaxel weekly for 3 weeks and PKC-θ peptide inhibitor daily for 5 weeks


title: PDX1281b

value: PDX


title: PDX1281a

value: glioma cells


title: Combination_tumour_1 [H361]

description:
H361_S13
MDA-MB-231 cells were transplanted subcutaneously into the mammary fat pads of Balb/c nude mice and treated with intraperitoneal injections of docetaxel weekly for 3 weeks and PKC-θ peptide inhibitor daily for 5 weeks


title: X128a

value: CDC42SE2 fusion/CDK2NA/B loss


title: Hyg-AGX1_F383A-Nahk_Ac4GalN6yne_10uM K562_3h

city: London

first: Benjamin

last: Schumann

address: 80 Wood Lane

country: United Kingdom

institute: Imperial College London

data_processing:
Raw reads were quality and adapter trimmed using cutadapt (version 1.5) before alignment.
Reads were mapped and subsequent gene-level counted using RSEM (version 1.3.0) and STAR (version 2.5.2) against the human genome GRCh38 using annotation release 86, both from Ensembl.
Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package (version 1.24.0) within the R programming environment (version 3.6.1).
Assembly: GRCh38 release 86
Supplementary files format and content: rlog log2 normalised expression values. Rows = genes; Columns = samples.

growth_protocol: k562 cells transfected with either empty or Nahk/AGX1-F383A pleasmid were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics (100U/mL Pennicillin and 100 ug/mL Streptomycin) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was extracted from fed and unfed cells by using RNeasy Mini kit (Qiagen, Crawley, UK), DNase I (Thermo Fisher) and QIAshredder (Qiagen) according to the manufacturer’s instructions.
mRNA capture and library preparation were performed using the KAPA mRNA HyperPrep Kit according to the manufacter's instructions

treatment_protocol: Cells were incubated 16h in media only (un fed) or fed with DMSO, 10uM Ac4GalN6yne or 10uM Ac4GalNAc.

value: erythroleukemia

value: Hyg-AGX1 F383A-NahK


title: astrocyteb


title: Chemo_tumour_1 [B331]

description:
B331_S5
MDA-MB-231 cells were transplanted subcutaneously into the mammary fat pads of Balb/c nude mice and treated with intraperitoneal injections of docetaxel weekly for 3 weeks

value: Docetaxel (4 mg/kg)


title: Chemo_tumour_2 [B333]

description:
B333_S6
MDA-MB-231 cells were transplanted subcutaneously into the mammary fat pads of Balb/c nude mice and treated with intraperitoneal injections of docetaxel weekly for 3 weeks


title: Tumour_2 [A328]

description:
A328_S2
MDA-MB-231 cells were transplanted subcutaneously into the mammary fat pads of Balb/c nude mice and treated with intraperitoneal injections of vehicle control only.

source_name: MDA-MB-231 tumour in mouse

value: vehicle


title: Tumour_3 [A330]

description:
A330_S4
MDA-MB-231 cells were transplanted subcutaneously into the mammary fat pads of Balb/c nude mice and treated with intraperitoneal injections of vehicle control only.


title: Hyg-AGX1_F383A-Nahk_Ac4GalN6yne_10uM K562_2h


title: Hyg-AGX1_F383A-Nahk_Ac4GalNAc_10uM K562_2f


title: Hyg-AGX1_F383A-Nahk_Ac4GalNAc_10uM K562_1f


title: Hyg-AGX1_F383A-Nahk_Ac4GalN6yne_10uM K562_1h


title: Hyg_Ac4GalNAc_10uM K562_3e

value: Hyg


title: Hyg_Ac4GalNAc_10uM K562_1e


title: one year old Hdc+/+ stomach, biological rep1

city: Seoul

first: Kwang

middle: H

last: Kim

address: 50 Yonsei-ro

institute: Yonsei University College of Medicine

description: Gene expression data from mouse stomach tissue

hyb_protocol: Labeled DNA target was hybridized to the Affymetrix GeneChip Human or Mouse 2.0 ST Array at 45°C for 16 h.

scan_protocol: Gene Chip scanned on a GCS3000 Scanner.

data_processing: The data were summarized and normalized with the robust multiaverage(RMA) method implemented in the oligo package in Affymetrix Power Tools for DEG analysis.

source_name: stomach tissue

label_protocol: Biotinylated cDNA were perpared according to the standard Affymetrix protocol from 5.5 ug total RNA.

growth_protocol: The mice were maintained in a SPF barrier under a 12-h light cycle, and probided PicoLab Rodent Diet 20.

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

treatment_protocol: Stomach tissues were washed with PBS and cut into approximately 1-mm^3 pieces.

value: FVB


title: Hyg-AGX1_F383A-NahK_DMSO K562_3d

value: DMSO


title: one year old Hdc-/- stomach, biological rep1


title: one year old Hdc-/- stomach, biological rep2


title: vehicle treatment 1

city: Lille

first: Philippe

last: Lefebvre

address: Bâtiment J&K, Faculté de Médecine de Lille-Pôle Recherche, Boulevard du Professeur Leclerc

country: France

institute: INSERM UMR 1011, Université Lille-Nord de France

hyb_protocol: Following fragmentation, 5,5µg of ssDNA were hybridized for 16 hr at 45C on GeneChip® Mouse Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using GeneChip Scanner GCS3000

data_processing: Raw data were processed further using GIANT (Galaxy-based interactive tools for Analysis of Transcriptomic data). This user-friendly tool suite was developed in-house for microarray and RNA-seq differential data analysis. It consists of modules allowing to perform quality control (QC), Robust Multi-Average method normalization, LIMMA differential analysis, volcano plot and heatmaps.

source_name: vehicle treatment

label_protocol: Biotinylated ssDNA were prepared according to the standard Affymetrix protocol from 300ng total RNA (GeneChip® WT PLUS Reagent Kit, Affymetrix).

growth_protocol: C57BL6/J wild-type mice were purchased from Charles River Laboratories. Mice (male, 8-10 weeks) were housed in a temperature-controlled environment (25-28°C) with a 12h/12h light-dark cycle, ZT0 being lights-on. Mice had free access to water and were fed ad libitum a standard chow diet (UAR).

extract_protocol: Total RNA from mouse heart was extracted from samples previously pulverized on dry ice in liquid nitrogen using TRIzol™ Reagent according to the manufacturer’s instructions (Thermo Fisher Scientific)

treatment_protocol: Animals were injected intraperitoneally with 1mg/kg digoxin  (Nativelle  Adult)  or  vehicle (a  co-solvent  consisting  of  10%  ethanol, 40%  propylene  glycol, 0.08% citric acid, 0.3% sodium phosphate) at ZT5.

tag: treatment/time point

value: vehicle treatment  at ZT5 and sacrifice at ZT5 and sacrifice at ZT9


title: Hyg_Ac4GalN6yne_10uM K562_2g


title: Hyg-AGX1_F383A-NahK_DMSO K562_1d


title: one year old Hdc+/+ stomach, biological rep2


title: vehicle treatment 2


title: Tumor-1, NPSCC (PR)

city: Boston

first: Moshe

last: Sade-Feldmnan

state: MA

address: 255 Charles Street GRJ-910

department: Cancer Center

institute: Massachusetts General Hospital

description:
10x Genomics VDJ NextGEM v1.1
HN19-1

data_processing:
Samples were sequenced on a NextSeq 500 sequencer (Illumina), and the data was preprocessed using Cell Ranger v6.0.0 and hg19 reference genome.
Assembly: hg19
Supplementary files format and content: Compressed (.gz) raw cell count matrix after QC

source_name: NPSCC

extract_protocol:
Tumors were rapidly dissociated after the surgical procedure using the Miltenyi Biotec Human Tumor Dissociation kit (cat# 130-095-929). Each lesion was minced into 1-2mm fragments with surgical scissors in a separate 1.5ml Eppendorf tube containing 932µl DMEM, 42µl of enzyme H, 21µl od enzyme R, and 5µl of enzyme A. Next, tubes were briefly vortexed and placed in a thermomixer for 15 minutes at 37°C, 350rpm. Finally, the dissociated samples were washed through a 50µm filter and counted using a manual hemocytometer to determine cell viability and concentration.
Libraries were constructed using the VDJ NextGEM v1.1 10x Genomics Chromium kit according to the manufacturer's instructions. Assessment of libraries quality was performed after cDNA and library generation, measuring the nucleic-acid concentration (Qubit dsDNA High Sensitivity kit; Invitrogen, cat# Q32854) and size distribution (High Sensitivity BioA DNA kit; Agilent, cat# 5067-4626).

value: NPSCC

value: Single cells from tumor

value: nivolumab (anti-PD1)


title: Tumor-3, Laryngeal SCC (PD)

description:
10x Genomics VDJ NextGEM v1.1
HN19-3

source_name: Laryngeal SCC

value: Laryngeal SCC


title: vehicle treatment 3


title: TIL_NS

description: non-stimulated B cells from Tilcara mice

hyb_protocol: Samples were hybridised as per Affymetrix standard protocols

scan_protocol: Samples were scanned as per Affymetrix standard protocols

data_processing: Mogene 2.0 ST arrays were normalised using  RMA in Affy Powertools 1.16.1. Only probes annotated as ‘main’ were used. Probesets were called differential expressed if greater than Log2 0.5 different.

source_name: B lymphocyte

label_protocol: Samples were labelled as per Affymetrix standard protocols

growth_protocol: Spleens, thymi and lymph nodes were harvested from mice and single cell suspensions were prepared by sieving through a 70 µm nylon mesh filter. Cells were stained for sorting into B cell populations with antibodies APC Rat Anti-Mouse CD45R/B220 (BD Pharmingen, Cat no.: 553092.

extract_protocol: Tri-reagent was used to extract RNA as per manufacturers instructions.

treatment_protocol: Primary mouse B cells were stimulated with 10ng/mL of phorbol 12-myristate 13-acetate (PMA; Sigma-Aldrich, P8139) and 1µM calcium ionophore (I; Sigma-Aldrich, A23187) for 4 hours.

tag: genotype/variation

value: C57BL/6 Tilcara (Til), a PKCbeta mutant mice model

value: Spleens, thymi and lymph nodes

value: B lymphocyte


title: WT_ST

description: Stimulated B cells

value: wild type

value: 10ng/mL of phorbol 12-myristate 13-acetate and 1µM calcium ionophore for 4 hrs


title: TIL_ST

description: Stimulated B cells from Tilcara mice


title: WT_NS

description: non-stimulated B cells


title: Digoxin treatment 4

description: 14-MVC-251-7_Digoxin2_(MoGene-2_0-st).CEL

source_name: Digoxin treatment 1mg/kg

tag: strain

value: Digoxin treatment 1mg/kg IP dosing at ZT5 and sacrifice at ZT9


title: Tumour_1 [A327]

description:
A327_S1
MDA-MB-231 cells were transplanted subcutaneously into the mammary fat pads of Balb/c nude mice and treated with intraperitoneal injections of vehicle control only.

value: Balb/c nude mice


title: Hyg-AGX1_F383A-Nahk_Ac4GalNAc_10uM K562_3f

value: erythroleukemia

value: Hyg-AGX1 F383A-NahK


title: CRCNT049

city: Taoyuan City

first: Hsuan

address: No.259, Wenhua 1st Rd., Guishan Dist.

country: Taiwan

institute: Chang Gung University

description: CRC192-exomiR NR-gene row.txt

data_processing:
sequencing data were assessed for quality and trimmed of the primer-adaptor sequences by the Partek® Flow® Genomic Analysis Software (Partek)
Reads were alignment to the human reference genome (hg38) (by bowtie 2)
annotation of known miRNA based on miRBase
The number of reads for each miRNA was normalized to reads per million (RPM+0.0001) and quantified across all samples
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with normalized miRNA counts(RPM+0.0001) for every miRNA and every sample

source_name: CRC

extract_protocol:
Circulating small EVs were isolated from 1 mL of pre-filtered plasma using a procedure described in the exoEasy Plasma Handbook (QIAGENE). Briefly, plasma was mixed with binding buffer (XBP) and added to the exoEasy membrane affinity column for binding. After centrifugation, the flow-through was discarded and wash buffer (XWP) was added to the column to wash off nonspecifically retained materials. After EVs were bound on the exoEasy membrane affinity column as described in the isolation procedure above, the vesicles were lysed by adding QIAzol to the spin column and further collected by centrifugation (exoRNeasy, QIAGEN). Following chloroform extraction, samples were thoroughly mixed and centrifuged to separate organic and aqueous phases. The aqueous phase was recovered and mixed with ethanol. The sample-ethanol mixture was added to a RNeasy MinElute spin column and centrifuged. The column was washed once with buffer RWT and then twice with buffer RPE followed by elution of RNA in water. The RNA concentration, purity, and integrity were assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 System (Agilent Technologies, CA, USA).
Prior to sequencing experiments, RNA concentration, purity, and integrity were assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 System (Agilent Technologies, CA, USA). Illumina sequencing libraries were prepared using the NEXTflexTM small RNA-seq kit v3 Guide (Bioo Scientific, 5132-05), according to the manufacturer’s instructions. For each library, 60 ng of purified small EV RNA were ligated to 3’ and 5’ adaptors and then reverse transcribed to cDNA using adaptor-specific primers. After purification and PCR amplification using universal and specific barcode primers, the miRNA library was resolved and recovered from the 6% TBE-PAGE gel based on the corresponding size for miRNA distribution. The yield and size distribution of the small RNA libraries were assessed using the Agilent 2100 Bioanalyzer instrument with the High-Sensitivity DNA Assay (Agilent Technologies). Equal concentration of each library was sequenced on a NextSeq 500 (Illumina) platform.

value: plasma small extracellular vesicles

tag: Stage

tag: sampling time points

value: 1 (treatment naive)

tag: patient id

tag: molecule subtype

value: miRNA


title: Hyg_DMSO K562_2c

value: Hyg

value: DMSO


title: CRCNT047

description: CRC192-exomiR NR-gene row.txt

value: CRC


title: Hyg_Ac4GalN6yne_10uM K562_3g


title: Hyg_unfed K562_3a

value: unfed


title: Hyg_Ac4GalNAc_10uM K562_2e


title: Digoxin treatment 3

description: 15-MVC-251-8_Digoxin3_(MoGene-2_0-st).CEL


title: Hyg_unfed K562_1a


title: CRCNT039

description: CRC192-exomiR NR-gene row.txt


title: CRCNT038

description: CRC192-exomiR NR-gene row.txt


title: Digoxin treatment 5

description: 13-MVC-251-6_Digoxin1_(MoGene-2_0-st).CEL


title: Hyg_Ac4GalN6yne_10uM K562_1g


title: TBX20only_TBX20_CutTag

city: Birmingham

first: Changde

last: Cheng

state: Alabama

address: 1824 6th Ave S, WTI 510G

department: Department of Medicine - Hematology & Oncology

institute: The University of Alabama at Birmingham

data_processing:
Library strategy: CUT&Tag
Rawreads were subjected to adapter removal .
Sequencing reads were aligned against hg19 reference genome using bowtie2
Peaks were called by using SEACR 1.3.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

source_name: iCM fibroblasts

growth_protocol: H9Fs were cultured in DMEM medium supplement with 20% FBS and 1% Penstrep (HDF medium). HCFs were cultured with FBM2 bullet kit purchased from ATCC (HCF medium), and HFFs were cultured using IMDM with 10% FBS and 1% Pen-strep (HFF medium).

extract_protocol:
CUT&Tag DNA was prepared using CUTANA pAG-Tn5 for CUT&Tag (Epicypher), following the manufacturer’s instructions.
Library construction was performed using the NEBNext UltraII DNA Library Prep Kit from NEB (E7645S).

treatment_protocol: For reprogramming, pMXs-puro-hMGT8, pBabe-miR-133 plasmids15, pBabe-TBX20 or pBabe-EV (constructed in lab) were used for infection.

value: ESC H9 derived fibroblasts H9F

tag: primary antibody

value: Thermo Fisher, PA5-40669, R&D systems, MAB8124


title: EVonly_TBX20_CutTag


title: CRCNT031

description: CRC192-exomiR NR-gene row.txt


title: Digoxin treatment 1

description: 17-MVC-251-10_Digoxin5_(MoGene-2_0-st).CEL


title: Digoxin treatment 2

description: 16-MVC-251-9_Digoxin4_(MoGene-2_0-st).CEL


title: CRCNT030

description: CRC192-exomiR NR-gene row.txt


title: Tumor-2, NPSCC lymph node (PR)

description:
10x Genomics VDJ NextGEM v1.1
HN19-2

source_name: NPSCC lymph node

value: NPSCC lymph node

value: Single cells from tumor

value: nivolumab (anti-PD1)


title: lung tuft single cell

city: PHILADELPHIA

first: Andrew

last: Vaughan

state: United States

address: 3800 Spruce Street

institute: University of Pennsylvania

description: mouse lung 28 days post-influenza

data_processing:
Cellranger 3.1.0
Cellranger mkfastq
Genome_build: GRCm38 - mm10
Supplementary_files_format_and_content: matrix, barcodes, and features files for loading into Seurat

source_name: mouse lung 28 days post-influenza

extract_protocol:
cells sorted straight into PBS + 0.1% BSA and loaded on 10x Chromium device
Chromium Single Cell 3ʹ Feature Barcode Library Kit

value: post-influenza tuft cells sorted from  day 28 post-influenza mouse lungs

tag: tag


title: Hyg-AGX1_F383A-NahK_DMSO K562_2d

tag: cell line


title: Hyg_DMSO K562_3c


title: CRCNT027

description: CRC192-exomiR NR-gene row.txt


title: CRCNT026

description: CRC192-exomiR NR-gene row.txt


title: MGT_withTBX20_TBX5_CutTag

value: Sigma-Aldrich HPA064683


title: MGT_withTBX20_GATA4_CutTag

value: Cell Signaling  #36966


title: CRCNT048

description: CRC192-exomiR NR-gene row.txt


title: MGT_withEV_TBX5_CutTag

value: MGT+EV


title: Hyg-AGX1_F383A-NahK_unfed K562_3b

value: erythroleukemia

value: Hyg-AGX1 F383A-NahK


title: CRCNT046

description: CRC192-exomiR NR-gene row.txt

value: plasma small extracellular vesicles

value: 1 (treatment naive)


title: Hyg_DMSO K562_1c

value: Hyg


title: CRCNT020

description: CRC192-exomiR NR-gene row.txt

value: miRNA


title: Hyg-AGX1_F383A-NahK_unfed K562_1b


title: MGT_withEV_GATA4_CutTag


title: CRCNT045

description: CRC192-exomiR NR-gene row.txt

value: CRC


title: CRC350

description: CRC192-exomiR NR-gene row.txt


title: CRC349

description: CRC192-exomiR NR-gene row.txt


title: HCF TBX20 Replicate3

data_processing:
The paired-end reads were mapped to the human genome (hg19) using STAR (v2.5.1b) with default parameters.
DESeq2 was used to identify differentially identified genes between comparision groups.
The read counts for genes with average FPKM > 1 in either EV or TBX20 infected hiCMs samples were used for DESeq2 (v3.11) to define differentially expressed genes (DEGs).
Genome_build: hg19
Supplementary_files_format_and_content: raw counts

extract_protocol:
Total RNA was isolated using TRI Reagent and Direct-zol RNA Miniprep Kits (Zymo Research, R2053).
Sequencing libraries were generated using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina.

value: Primary human ventricular fibroblasts


title: Hyg-AGX1_F383A-NahK_unfed K562_2b

value: unfed


title: Hyg_unfed K562_2a


title: HCF TBX20 Replicate1


title: CRC347

description: CRC192-exomiR NR-gene row.txt


title: CRCNT033

description: CRC192-exomiR NR-gene row.txt


title: CRCNT021

description: CRC192-exomiR NR-gene row.txt


title: CRC346

description: CRC192-exomiR NR-gene row.txt


title: HCF EV Replicate3


title: CRCNT034

description: CRC192-exomiR NR-gene row.txt


title: MGT_withTBX20_IgG_CutTag

value: ESC H9 derived fibroblasts H9F

value: Thermo Fisher, PA5-40669, R&D systems, MAB8124


title: HCF EV Replicate1


title: CRC339

description: CRC192-exomiR NR-gene row.txt


title: CRCNT025

description: CRC192-exomiR NR-gene row.txt


title: MGT_withEV_IgG_CutTag


title: Day14 EV Replicate 1

tag: time point


title: CRC332

description: CRC192-exomiR NR-gene row.txt

tag: tissue


title: CRC331

description: CRC192-exomiR NR-gene row.txt


title: CRC333

description: CRC192-exomiR NR-gene row.txt


title: MGT_withTBX20_MEF2C_CutTag

tag: cell type

value: Cell Signaling  5030S


title: MGT_withEV_MEF2C_CutTag


title: HCF TBX20 Replicate2


title: Day14 TBX 20 Replicate 1


title: CRC348

description: CRC192-exomiR NR-gene row.txt

tag: disease state


title: CRC328

description: CRC192-exomiR NR-gene row.txt


title: CRC326

description: CRC192-exomiR NR-gene row.txt


title: CRC341

description: CRC192-exomiR NR-gene row.txt


title: HCF EV Replicate2


title: CRC344

description: CRC192-exomiR NR-gene row.txt


title: CRCNT019

description: CRC192-exomiR NR-gene row.txt


title: CRC324

description: CRC192-exomiR NR-gene row.txt


title: Day9 TBX20 Replicate 1


title: Day14 EV Replicate 2


title: Day14 EV Replicate 3


title: Day14 TBX 20 Replicate 3


title: CRC329

description: CRC192-exomiR NR-gene row.txt


title: CRC314

description: CRC192-exomiR NR-gene row.txt


title: Day14 TBX 20 Replicate 2


title: Day9 TBX20 Replicate 3


title: Day3 TBX20 Replicate 3


title: CRC319

description: CRC192-exomiR NR-gene row.txt


title: CRC301

description: CRC192-exomiR NR-gene row.txt


title: Day9 EV Replicate 3


title: Day3 EV Replicate 2


title: Day3 EV Replicate 3


title: CRC310

description: CRC192-exomiR NR-gene row.txt


title: CRC308

description: CRC192-exomiR NR-gene row.txt


title: Day9 EV Replicate 1


title: CRC294

description: CRC192-exomiR NR-gene row.txt


title: Day3 TBX20 Replicate 2


title: CRC298

description: CRC192-exomiR NR-gene row.txt


title: CRC293

description: CRC192-exomiR NR-gene row.txt


title: Day0 H9F Replicate 3


title: Day0 H9F Replicate 2


title: Day9 TBX20 Replicate 2


title: CRC297

description: CRC192-exomiR NR-gene row.txt


title: Day9 EV Replicate 2


title: CRC309

description: CRC192-exomiR NR-gene row.txt


title: Day0 H9F Replicate 1


title: CRC290

description: CRC192-exomiR NR-gene row.txt


title: CRC288

description: CRC192-exomiR NR-gene row.txt


title: Day3 EV Replicate 1


title: CRC300

description: CRC192-exomiR NR-gene row.txt


title: TB

data_processing:
Single-cell RNA-seq outputs were processed using the Cell Ranger (10X Genomics). Raw reads were mapped to a merged and modified genome of hg 19.
Secondary analysis was conducted using the Seurat 4.0.5 package in R version 4.1
Genome_build: hg19
Supplementary_files_format_and_content: Filtered feature-barcode matrix

extract_protocol:
HiCMs transduced with EV or TBX20 were counted to ~3X104 cells for each sample and subjected for cell sorting followed by single cell capture was performed at UAB Single Cell Sequencing core facility using 10x Genomics platform.
RNA libraries were prepared by Single Cell 3’ v3.1 kit (10xGenomics) according to the manufacturer’s manual.


title: CRC287

description: CRC192-exomiR NR-gene row.txt


title: Day3 TBX20 Replicate 1


title: EV


title: CRC283

description: CRC192-exomiR NR-gene row.txt


title: MGT+TBX20_K27m3_replicate2

data_processing:
Library strategy: CUT&RUN
Rawreads were subjected to adapter removal .
Sequencing reads were aligned against hg19 reference genome using bowtie2
Duplicates were removed with Picard.
Peaks were called by using SEACR 1.3.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

extract_protocol:
CUT&RUN DNA was prepared using CUTANA pAG-MNase for CUT&RUN (Epicypher), following the manufacturer’s instructions.
Library construction was performed using the NEBNext UltraII DNA Library Prep Kit from NEB (E7645S).

value: MGT + TBX20


title: CRC286

description: CRC192-exomiR NR-gene row.txt


title: MGT+EV_IgG

value: MGT + EV


title: CRC278

description: CRC192-exomiR NR-gene row.txt


title: CRC277

description: CRC192-exomiR NR-gene row.txt


title: CRC289

description: CRC192-exomiR NR-gene row.txt


title: MGT+TBX20_K27ac_replicate1


title: MGT+TBX20_K4m1_replicate1


title: CRC268

description: CRC192-exomiR NR-gene row.txt


title: CRC274

description: CRC192-exomiR NR-gene row.txt


title: MGT+TBX20_K4m1_replicate2


title: MGT+EV_K27m3_replicate2


title: CRC264

description: CRC192-exomiR NR-gene row.txt


title: CRC259

description: CRC192-exomiR NR-gene row.txt


title: MGT+EV_K27ac_replicate2


title: CRC271

description: CRC192-exomiR NR-gene row.txt


title: CRC265

description: CRC192-exomiR NR-gene row.txt


title: MGT+EV_K27m3_replicate1


title: MGT+EV_K27ac_replicate1


title: CRC252

description: CRC192-exomiR NR-gene row.txt


title: CRC254

description: CRC192-exomiR NR-gene row.txt


title: CRC249

description: CRC192-exomiR NR-gene row.txt


title: CRC250

description: CRC192-exomiR NR-gene row.txt


title: Day14 TBX 20 Replicate 3 [ATAC-Seq]

data_processing:
All sequencing reads were mapped to the human genome (hg19) using the Bowtie2 (v2.2.3) and reads with a mapping score > 20 were selected for data analysis, after duplicated reads removed by SAMtools (v1.9).
MACS2 were used to ATAC-seq peaks using default parameters in paired-end mode.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

extract_protocol:
50,000 cells were used for each transposition reaction. ATAC-seq was carried out utilizing the Epicentre Tn5 transposome and Illuminia kit according to standard manufacturer’s manuals.
The transposed DNA was obtained, purified using DNA purification columns and subjected to PCR amplification for library generation.


title: CRC282

description: CRC192-exomiR NR-gene row.txt


title: Day14 TBX 20 Replicate 1 [ATAC-Seq]


title: Day14 TBX 20 Replicate 2 [ATAC-Seq]


title: MGT+TBX20_K27m3_replicate1


title: CRC247

description: CRC192-exomiR NR-gene row.txt


title: MGT+TBX20_K27ac_replicate2


title: Day14 EV Replicate 2 [ATAC-Seq]


title: Day14 EV Replicate 3 [ATAC-Seq]


title: MGT+EV_K4m1_replicate2


title: CRC255

description: CRC192-exomiR NR-gene row.txt


title: CRC245

description: CRC192-exomiR NR-gene row.txt


title: CRC244

description: CRC192-exomiR NR-gene row.txt


title: Day14 EV Replicate 1 [ATAC-Seq]


title: MGT+EV_K4m1_replicate1


title: Day0 H9F Replicate 3 [ATAC-Seq]


title: CRC240

description: CRC192-exomiR NR-gene row.txt


title: CRC242

description: CRC192-exomiR NR-gene row.txt


title: CRC234

description: CRC192-exomiR NR-gene row.txt


title: Day0 H9F Replicate 1 [ATAC-Seq]


title: CRC248

description: CRC192-exomiR NR-gene row.txt


title: CRC231

description: CRC192-exomiR NR-gene row.txt


title: WT_B_1620_sRNA_rep2_sequence

city: Cambridge

first: David

last: Bartel

address: 455 Main St

institute: Whitehead Institute, MIT

description:
paired WT samples for dora[B] embryonic timecourse
mutB_timecourse_sRNA_rawreads.csv

data_processing:
Sequencing reads for sRNAseq libraries were processed and counted as previously described (Kingston and Bartel, 2021)
RNAseq reads were aligned to the genome (UCSC dm6.08 reference assembly) using STAR (V2.4, with the paramaters “--alignIntronMax 1 --runThreadN 30 --outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.04 --outFilterIntronMotifs RemoveNoncanonicalUnannotated –outSJfilterReads”) (Dobin et al., 2013), and alignments to all chromosomal genes were counted using htseq-count (with the parameters “-m union -s reverse") (Anders et al., 2015). TPM values were determined by dividing these htseq-determined counts for each gene by the median length for all isoforms of that gene, and then normalizing these values for library depth.
Genome_build: dm6
Supplementary_files_format_and_content: All processed .csv files contain non-normalized miRNA or mRNA counts for the indicated samples

organism: Drosophila melanogaster

source_name: 16-20 h embryos

growth_protocol: Drosophila S2 cells were grown at 26°C in Schneider’s Drosophila Medium (Life Technologies) supplemented with 10% heat-inactivated FBS (Life Technologies). Cells were passaged 1:5 every 3–5 days.

extract_protocol:
sRNA-seq libraries were constructed as described in the step-by-step protocol found at http://bartellab.wi.mit.edu/protocols.html, with some alterations. Briefly, between 1 and 5 ug of total RNA was mixed with size-selection markers (18- and 32-nt, 5′-radiolabeled RNAs) and 1 uL of quantitative standards (cel-lsy-6 and xtr-427) (ratios of total RNA:quantitative standards for each sample listed in Table S7). This mixture was size-selected on a denaturing gel, and then 2S rRNA was depleted by subtractive hybridization (Seitz et al., 2008). 3′ and 5′ adapters (each containing 4 random-sequence nucleotides at their ligation junctions) were then sequentially ligated using RNL2 truncated K227Q (NEB) and RNLI (NEB), respectively, in the presence of 10% polyethylene glycol (PEG 8000, NEB) and Superasin (Thermo Fischer Scientific), with gel purification following each ligation step. Purified RNA was reverse transcribed using SuperScript III (Thermo Fischer Scientific) and amplified using Kapa HiFi HotStart Ready Mix (Roche Diagnostics). Libraries were sequenced on an Illumina HiSeq platform with 50-nt single-end reads.
RNA was extracted with TRI Reagent (Life Technologies), according to the manufacturer’s protocol. Briefly, samples were homogenized in TRI reagent, and RNA was phase-separated by the addition of chloroform (J.T. Baker Analytical) at a ratio of 250 µL per 1 mL TRI Reagent. RNA was then precipitated with isopropanol, with GlycoBlue (Life Technologies) added as a co-precipitant when necessary, and pellets were washed twice with 70% ethanol prior to resuspension in water.

tag: genotype

value: WT

tag: ip target


title: CRC233

description: CRC192-exomiR NR-gene row.txt


title: WT_B_1620_sRNA_rep1_sequence


title: CRC236

description: CRC192-exomiR NR-gene row.txt


title: WT_B_1620_mRNA_rep1_sequence

description:
paired WT samples for dora[B] embryonic timecourse
mutB_timecourse_mRNA_rawreads.csv

extract_protocol:
RNA-seq libraries were prepared using the NEXTflex Rapid Directional RNA-seq Kit (Bioo Scientific) following enrichment of polyadenylated mRNAs with NEXTflex Poly(A) Beads (Bioo Scientific). Libraries were sequenced on an Illumina HiSeq platform with 50-nt single-end reads.
RNA was extracted with TRI Reagent (Life Technologies), according to the manufacturer’s protocol. Briefly, samples were homogenized in TRI reagent, and RNA was phase-separated by the addition of chloroform (J.T. Baker Analytical) at a ratio of 250 µL per 1 mL TRI Reagent. RNA was then precipitated with isopropanol, with GlycoBlue (Life Technologies) added as a co-precipitant when necessary, and pellets were washed twice with 70% ethanol prior to resuspension in water.


title: WT_B_1216_sRNA_rep2_sequence

source_name: 12-16 h embryos


title: CRC227

description: CRC192-exomiR NR-gene row.txt


title: WT_B_1216_mRNA_rep2_sequence


title: CRC221

description: CRC192-exomiR NR-gene row.txt


title: CRC223

description: CRC192-exomiR NR-gene row.txt


title: WT_B_1216_mRNA_rep1_sequence


title: CRC220

description: CRC192-exomiR NR-gene row.txt


title: WT_B_812_sRNA_rep2_sequence

source_name: 8-12 h embryos


title: CRC219

description: CRC192-exomiR NR-gene row.txt


title: Day0 H9F Replicate 2 [ATAC-Seq]

tag: treatment


title: WT_B_812_sRNA_rep1_sequence


title: CRC218

description: CRC192-exomiR NR-gene row.txt


title: WT_B_812_mRNA_rep1_sequence


title: WT_B_812_mRNA_rep2_sequence


title: CRC206

description: CRC192-exomiR NR-gene row.txt


title: WT_A_1620_sRNA_rep2_sequence

description:
paired WT samples for dora[A] embryonic timecourse
mutA_timecourse_sRNA_rawreads.csv


title: CRC212

description: CRC192-exomiR NR-gene row.txt


title: CRC228

description: CRC192-exomiR NR-gene row.txt


title: CRC202

description: CRC192-exomiR NR-gene row.txt


title: WT_B_1620_mRNA_rep2_sequence


title: CRC197

description: CRC192-exomiR NR-gene row.txt


title: WT_A_1620_mRNA_rep2_sequence

description:
paired WT samples for dora[A] embryonic timecourse
mutA_timecourse_mRNA_rawreads.csv


title: WT_A_1620_mRNA_rep1_sequence


title: CRC195

description: CRC192-exomiR NR-gene row.txt


title: WT_A_1620_sRNA_rep1_sequence


title: WT_A_1216_sRNA_rep2_sequence


title: WT_A_1216_sRNA_rep1_sequence


title: CRC203

description: CRC192-exomiR NR-gene row.txt


title: WT_A_1216_mRNA_rep2_sequence


title: WT_B_1216_sRNA_rep1_sequence


title: CRC185

description: CRC192-exomiR NR-gene row.txt


title: CRC189

description: CRC192-exomiR NR-gene row.txt


title: CRC179

description: CRC192-exomiR NR-gene row.txt


title: CRC184

description: CRC192-exomiR NR-gene row.txt


title: WT_A_1216_mRNA_rep1_sequence


title: WT_A_812_sRNA_rep2_sequence


title: CRC178

description: CRC192-exomiR NR-gene row.txt


title: WT_A_812_sRNA_rep1_sequence


title: CRC177

description: CRC192-exomiR NR-gene row.txt


title: CRC176

description: CRC192-exomiR NR-gene row.txt


title: S2_trigger_WT_3_sequence

description:
RNAseq from S2 cell trigger lines
S2_triggerline_mRNA_rawreads.csv

source_name: S2 cells


title: CRC174

description: CRC192-exomiR NR-gene row.txt


title: WT_A_812_mRNA_rep2_sequence


title: WT_A_812_mRNA_rep1_sequence


title: CRC168

description: CRC192-exomiR NR-gene row.txt


title: CRC166

description: CRC192-exomiR NR-gene row.txt


title: S2_trigger_WT_1_sequence


title: S2_trigger_zfh1_3_sequence


title: CRC165

description: CRC192-exomiR NR-gene row.txt


title: CRC162

description: CRC192-exomiR NR-gene row.txt


title: S2_trigger_zfh1_2_sequence


title: S2_trigger_wgn_4_sequence

value: wgn


title: CRC161

description: CRC192-exomiR NR-gene row.txt


title: CRC164

description: CRC192-exomiR NR-gene row.txt


title: S2_trigger_wgn_2_sequence


title: CRC157

description: CRC192-exomiR NR-gene row.txt


title: S2_trigger_kah_3_sequence

value: kah


title: S2_trigger_kah_1_sequence


title: S2_trigger_h_2_sequence

value: h


title: CRC03106

description: mCRC98_NR-gene row.txt


title: CRC03105

description: mCRC98_NR-gene row.txt


title: CRC158

description: CRC192-exomiR NR-gene row.txt


title: S2_trigger_h_1_sequence


title: S2_trigger_ago1_3_sequence


title: CRC03104

description: mCRC98_NR-gene row.txt


title: SingleCellM3

city: Perth

first: Wee Loong

last: Chin

address: Level 5, Qq Block, Qeii Medical Centre 6 Verdun St, Nedlands

institute: National Centre For Asbestos Related Diseases

data_processing:
read alignment with Kallisto
count quantification with sleuth
sleuth_to_matrix
Assembly: GRCm38.p6
Supplementary files format and content: txt files in compressed gz format

source_name: tumour

growth_protocol: Subcutaneous tumour

extract_protocol:
4 samples with gentleMACS system (Miltenyi Biotec) and other 4 with via frozen tumour dissociation with Trizol followed by chloroform extraction and purification using RNeasy MinElute
Illumina 50bp single-end sequencing

tag: age

value: 8-9 weeks

tag: gender

value: f

tag: extract protocol

value: gentleMACS

tag: tumour type

value: balb/c

tag: timepoint


title: SingleCellM4

tag: strain


title: S2_trigger_ago1_2_sequence


title: SingleCellM2


title: CRC03103

description: mCRC98_NR-gene row.txt

value: plasma small extracellular vesicles

tag: Stage

tag: sampling time points

tag: patient id

tag: molecule subtype

value: miRNA


title: CRC03102

description: mCRC98_NR-gene row.txt

value: CRC


title: S2_Ago1IP_mus308_4_sequence

description:
sRNAseq to look at siRNAs
S2_mus308_rawreads.csv


title: SingleCellM1


title: BulkM4

value: RNeasy MinElute


title: BulkM3


title: S2_Ago1IP_mus308_3_sequence


title: BulkM2


title: S2_Ago1IP_mus308_2_sequence


title: CRC03101

description: mCRC98_NR-gene row.txt

value: 1 (treatment naive)


title: BulkM1


title: CRC02606

description: mCRC98_NR-gene row.txt


title: S2_Ago1IP_mus308_1_sequence


title: CRC02602

description: mCRC98_NR-gene row.txt


title: mESCs, WT rep2

city: Beijing

first: Qiaoran

last: Xi

address: Haidian District

institute: School of Life Sciences, Tsinghua University

description:
rnaseq-TPM-nontreat-WT1-WT2-KO1-KO2.csv
CCE2

data_processing:
RNA reads were quality checked with FastQC v0.11.5 and mapped to the mouse (mm10) genome with Bowtie2 v2.3.3 using standard settings for paired reads. The .sam and .bam files were manipulate with samtools v1.9. On average, 80% of reads were uniquely mapped. Uniquely mapped reads were assigned to annotated genes with featureCounts v2.0.1 using default settings. Read counts were then normalized by library size and differential gene expression analysis based on a negative binomial distribution was conducted with DESeq2 packages in R language.
Assembly: mm10
Supplementary files format and content: Processed data provided as supplementary file (rnaseq-TPM-nontreat-WT1-WT2-KO1-KO2.csv)

source_name: mouse embryonic stem cell (mESC)

growth_protocol: ESCs were cultured on gelatin coated plates with 15% serum ESC culture medium

extract_protocol:
RNA of non-treated or activin, SB431542, BMP4, LDN193189 treated WT or HMCES-KO mESCs were purified using TIANGEN kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No treatment. Or activin A (50 ng/ml, R&D Systems), SB431542 (10 μM), BMP4 (10ng/ml), or LDN193189 (50nM) treated for 2h

value: mouse embryonic stem cell (mESC)

value: wild type

value: no treatment


title: mESCs, HMCES-KO rep2

description:
rnaseq-TPM-nontreat-WT1-WT2-KO1-KO2.csv
K82

value: HMCES-KO


title: mESCs, HMCES-KO rep1

description:
rnaseq-TPM-nontreat-WT1-WT2-KO1-KO2.csv
K81


title: S2_Ago1IP_WT_3_sequence

value: WT


title: mESCs, WT rep1

description:
rnaseq-TPM-nontreat-WT1-WT2-KO1-KO2.csv
CCE1


title: CRC02601

description: mCRC98_NR-gene row.txt


title: S2_Ago1IP_WT_2_sequence


title: CRC01809

description: mCRC98_NR-gene row.txt


title: CRC01808

description: mCRC98_NR-gene row.txt


title: E14_EpiLC_3

city: Schwerzenbach

first: Ferdinand

last: von Meyenn

state: Zurich

address: Schorenstrasse 16

department: Health Sciences and Technology

country: Switzerland

institute: ETH Zurich

data_processing:
FastQC v0.11.0 used for quality control
TrimGalore v0.6.6 used for trimming low quality bases + adapter sequences
HISAT2 v2.2.1 used for read mapping
subread v2.0.1 used for gene expression quantification
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited raw counts

source_name: Embryonic Stem Cells

growth_protocol: Mouse ESC  (mESC) were cultured on growth surface coated with 0.1% gelatin in DMEM supplemented with 15% of foetal bovine serum, 2mM L-glutamine, 0.05mM β-mercaptoethanol, 100U/mL penicillin-streptomycin, 1X non-essential amino acids and 10ng/mL mLIF (Serum LIF). Naïve mESC (2iLIF) were induced by culturing in N2B27 supplemented with 1μM MEK inhibitor PD0325901, 3μM GSK3 inhibitor CHIR99021 and 10ng/mL mLIF. mouse EpiLC was differentiated from naïve mESC by plating the cells on growth surface coated with human plasma fibronectin with N2B27 supplemented with 20ng/mL activin A, 12ng/ml bFGF and 1% KSR. The medium was changed every day for all conditions. Cells were cultured in a humidified incubator at 37°C and 5% CO2.

extract_protocol:
Total RNA for each sample was extracted using RNeasy mini kit (QIAGEN). Extracted RNA was PolyA-enriched.
RNA libraries was prepared using the TruSeq RNA Library Prep Kit v2 (Illumina) following the manufacturer’s instructions. Libraries were indexed using Illumina Indexes and 50 bp single-end sequencing was performed on Illumina HiSeq 2000 instruments (Illumina, San Diego, CA, USA).

tag: cell line

tag: cell state

value: EpiLC

tag: biological replicate


title: S2_Ago1IP_Dora_3_sequence

value: dora


title: E14_SerumLIF_1

value: Primed


title: E14_2iLIF_LT_3

value: Naive


title: E14_SerumLIF_2


title: E14_2iLIF_LT_2


title: E14_EpiLC_2


title: CRC01805

description: mCRC98_NR-gene row.txt

tag: disease state

tag: tissue


title: E14_EpiLC_1


title: CRC01802

description: mCRC98_NR-gene row.txt


title: S2_WT_3_mRNA_sequence

description:
RNAseq from WT and dora S2 cells
S2_WTDora_mRNA_rawreads.csv

tag: genotype

tag: ip target


title: WT-LDN rep2

data_processing:
RNA reads were quality checked with FastQC v0.11.5 and mapped to the mouse (mm10) genome with Bowtie2 v2.3.3 using standard settings for paired reads. The .sam and .bam files were manipulate with samtools v1.9. On average, 80% of reads were uniquely mapped. Uniquely mapped reads were assigned to annotated genes with featureCounts v2.0.1 using default settings. Read counts were then normalized by library size and differential gene expression analysis based on a negative binomial distribution was conducted with DESeq2 packages in R language.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data provided as supplementary file

treatment_protocol: No treatment. Or activin A (50 ng/ml, R&D Systems), SB431542 (10 μM), BMP4 (10ng/ml),  or LDN193189 (50nM) treated for 2h

tag: cell type

tag: treatment


title: HMCES-KO1-LDN


title: S2_Ago1IP_Dora_2_sequence


title: E14_2iLIF_LT_1


title: CRC01801

description: mCRC98_NR-gene row.txt


title: S2_WT_2_mRNA_sequence


title: S2_Ago1IP_Dora_1_sequence


title: WT-LDN rep1


title: E14_SerumLIF_3


title: HMCES-KO1-BMP4


title: CRC01605

description: mCRC98_NR-gene row.txt


title: HMCES-KO2-BMP4


title: S2_Ago1IP_WT_1_sequence


title: WT-BMP4 rep1


title: S2_Dora_3_mRNA_sequence


title: HMCES-KO2-SB


title: CRC01604

description: mCRC98_NR-gene row.txt


title: S2_Dora_2_mRNA_sequence


title: S2_WT_1_mRNA_sequence


title: WT-SB rep1


title: CRC01803

description: mCRC98_NR-gene row.txt


title: CRC01602

description: mCRC98_NR-gene row.txt


title: HMCES-KO2-LDN


title: HMCES-KO1-AC

value: activin A