title: 5xFAD T+ Ts PLX CTRL

city: Brussels

first: Daliya

last: Kancheva

address: Laarbeeklaan 103, Building E

country: Belgium

institute: Vrije Universiteit Brussel - VIB

description:
Heterozygous F+/T+ offspring of the cross of hemizygous 5xFAD mice overexpressing mutant human APP695 carrying EOFAD mutations K670N/M671L (Swedish), I716V (Florida), V717I (London) and mutant human PS1 harboring 2 EOFAD mutations (M146L and L286V) driven by the thymocyte differentiation antigen 1 (ThyI) promoter (F+ mice), and hemizygous Tau P301S transgenic mice (PS19), expressing human Tau-P301S (1N4R) driven by the mouse prion protein promoter (T+ mice).
metadata_Merge_5xFADTTsPLX_5xFADTTsCTRL.csv

data_processing:
Raw data bcl files were first demultiplexed using Cellranger mkfastq
Demultiplexed data was then processed using the Cellranger count pipeline
Genome_build: mm10 (mouse)
Supplementary_files_format_and_content: h5 files including raw counts (output CellRanger Count) for each sample and annotation metadata with information per cell

source_name: CD45+ cells

extract_protocol:
Processing and tissue-collection of whole brain was performed as previously described (Van Hove et al., 2019, doi: https://doi.org/10.1038/s41593-019-0393-4; Shemer et al., 2020, doi: https://doi.org/10.1016/j.immuni.2020.09.018, Kim et al., 2021, doi: https://doi.org/10.1016/j.immuni.2020.11.007). From these tissue samples, CD45+ FACS sorted immune cells were loaded on a Chromium Chip B (10x Genomics, No.1000074), or Chip G (10x Genomics, No. 2000177) on a GemCode Single Cell Instrument (10x Genomics) to generate single-cell gel beads-in-emulsion (GEM). GEMs  were prepared using the GemCode Single Cell 3’ Gel Bead according to the manufacturer’s instructions. Briefly, GEM reverse-transcription incubation was performed in a 96-deep-well reaction module at 53°C for 45 min, 85°C for 5 min and ending at 4°C. Next, GEMs were broken and complementary DNA (cDNA) was cleaned up with DynaBeads MyOne Silane Beads (10x Genomics, No. 2000048) and SPRIselect Reagent Kit (Beckman Coulter, No. B23318). Full-length, barcoded cDNA was PCR amplified with a 96-deep-well reaction module at 98°C for 3 min, eleven cycles at 98°C for 15 s, 63°C for 20 s and 72°C for 1 min, followed by one cycle at 72°C for 1 min and ending at 4°C.
Following cleaning up with the SPRIselect Reagent Kit and enzymatic fragmentation, library construction to generate Illumina-ready sequencing libraries was performed using the Library Kit (v3 and v3.1, 10xGenomics, No. 1000075) and the Chromium i7 Multiplex Kit (10x Genomics, No. 120262), according to the manufacturer's instructions. R1 (read 1 primer), P5, P7, i7 sample index and R2 (read 2 primer sequence) were added via end-repair, A-tailing, adapter ligation, post-ligation SPRIselect cleanup/size selection and sample index PCR. The cDNA content of pre-fragmentation and post-sample index PCR samples was analyzed using the 2100 BioAnalyzer (Agilent).

treatment_protocol: Seven-month-old mice, 4 mice per condition (4 WT control mice (F-/T-), 4 5xFAD mice (F+/T-) and 4 Tau-seeded 5xFAD/PS19 Tau transgenic mice (F+/T+) 3 months post injection), were sacrificed for brain isolation and single-cell processing. For single cell experiments related to PLX3397 treatment, 2 mice per condition were used (2 tau-seeded 5xFAD/PS19 tau transgenic mice (F+/T+) which received PLX3397 chow 1.5 months after tau-seeding for 1.5 months, and 2 tau-seeded 5xFAD/PS19 tau transgenic mice (F+/T+) which received control chow 1.5 months after tau-seeding for 1.5 months).

tag: strain

tag: genotype

value: 5xFADxPS19 heterozygous (F+/T+) transgenic

tag: tissue

value: whole brain CD45+ cells


title: H1944 Xenograft Dexamethason Rep 4 RNA seq

status: Public on Jun 03 2021

type: SRA

city: Utrecht

first: Stefan

last: Prekovic

address: Universiteitsweg 100

department: CMM

country: Netherlands

institute: UMC Utrecht

library_source: transcriptomic

data_processing:
Sequences were generated by the Illumina Hiseq 2500 genome analyzer (using 65bp reads) and were processed by the Illumina pipeline.
For RNA sequencing data was aligned to hg38 using TopHat and Differential expression (DE) was performed using optimized DESeq2 pipeline.
For ChIP sequencing reads were aligned to the Human Reference Genome (hg19) using BWA version 0.5.9. Reads with a BWA alignment quality score less than 20 were removed. Peaks were called MACS peak caller version 2 (Zhang Y et al. Genome Biol 2008;9(9):R137). MACS2 was run with the default parameters.
For 4C sequencing the alignment of the sequencing reads was done using bowtie2 with default parameters. We use samtools to filter for mapped reads with a minimum mapping quality score of 1. Next we extract from the reference genome all possible 4C capture sequences (in FASTA format) with the exact same length as the observed 4C captures from the sequencing run. We map and filter these reference capture sequences with the same parameters as the observed 4C reads using bowtie2 and samtools. In subsequent analysis we only include the thus mappable 4C fragment ends.
Genome_build: RNA-Seq: Hg38
Genome_build: ChIP-Seq: Hg19

molecule: total RNA

organism: Homo sapiens

source_name: Xenograft models of lung cancer cell line

growth_protocol: A549 mentained in DMEM/F12 + 10%FCS + 1%P/S. H2122/H1944/H1975/H460 mentained in RPMI + 10%FCS + 1%P/S. H1944 cells were injected to NOD-SCID mice and after engraftment treated with either Vehicle or Dexamethason (4 mg/kg).

extract_protocol:
RNA was extracted using the AllPrep DNA/RNA universal kit (Qiagen) according to the manufacturer’s instruction with Qiagen’s QIAcube robot. Samples with a RIN>8 were considered for library preparation.
Libraries were generated with the Illumina TruSeq RNA Library Preparation kit (RS-122-2001/2, Illumina Inc.) and sequenced on a HiSeq 2500 (using 65bp reads)

treatment_protocol: Cells were serum starved for 3 days, subsequently the cells either remained untreated or were treated for 2 (ChIP and 4C) or 8 (RNA seq) hours with hydrocortisone and processed for downstream analysis.

tag: crispr cell line features

tag: grna

tag: antibody

tag: viewpoints

tag: treatment

value: Dexamethasone

tag: replicate

value: Replicate 4


title: DIPG XIII Input-1105

city: CHICACO

first: Feng

last: Yue

state: ILLINOIS

address: 303 E. Superior Simpson Querrey 7-400

department: Department of Biochemistry and Molecular Genetics

country: USA

institute: Northwestern University Feinberg School of Medicine

library_source: genomic

data_processing:
RNA-seq reads were aligned to hg38 genome assembly using STAR; The TPM value of gene expression was caculated using RSEM
ChIP-seq and ATAC-seq reads were aligned to hg38 genome assembly using Bowtie2;H3K27ac, H3K27M ChIP-Seq were called using MACS2. For the H3K27ac ChIP-Seq, the peak length were fixed to 500 bp. For replicates, we used overlap optimal peaksets provided from the ENCODE ChIP-seq pipeline.
Hi-C raw FASTQ files and then mapped the trimmed files against hg38 human reference genome using runHiC pipeline. Hi-C matrix was generated using juicer Pre.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample; the narrowPeak files included the peaks for each Sample; The .hic file were the matrix of Hi-C for each Sample.

molecule: genomic DNA

source_name: DIPGXIII

growth_protocol: Cell lines were maintained in culturing media recommended by cell line providers. All cells were grown in an incubator with 5% CO2 at 37°C.

extract_protocol:
Briefly, 30-50 million cells were crosslinked using 1% formaldehyde for 10 minutes and quenched with 0.125M glycine for 5 minutes at room temperature. Cells were then rinsed, harvested, and resuspended in extraction buffer for ten minutes at 4°C, then centrifuged at 1,350xg for five minutes at 4°C. Cell pellet was resuspended and transferred to a one mL milliTUBE (520135, Covaris). After sonication (Covaris E220 ultrasonicator), samples were spun down and supernatant containing chromatin was collected. Chromatin was de-crosslinked for three hours at 65°C and DNA was extracted (28104, Qiagen). 10% sample was saved as input. Chromatin was incubated with primary antibody overnight at 4°C. The following day, protein A/G agarose beads (sc-2003, Santa Cruz Biotech) were added to the samples and incubated for 3 hours. Beads were centrifuged and washed with one mL of RIPA buffer four times. The beads and the ten mL input were eluted for 30 minutes at 65°C then spun down. Supernatant was de-crosslinked overnight 65°C. DNA was extracted and submitted for library preparation.
ChIP-Seq libraries were prepared with the KAPA Library preparation kit (KK8234, Kapa Biosystems) and NETflex DNA barcodes (514104, Bioo Scientific). A total of ten mg DNA was used as starting material for input and immunoprecipitation samples. Libraries were amplified with a thermocycler for 13 cycles. Post-amplification libraries were size-selected at 250-45bp in length using the Agencourt AMPure XP beads (A63881, Beckman Coulter).

tag: chip-antibody


title: H1944 Xenograft Dexamethason Rep 3 RNA seq

value: Replicate 3


title: prostate_cancer_primary_11

type: RNA

city: San Diego

first: Elai

last: Davicioni

state: California

address: 9725 Lusk Blvd

institute: Veracyte, Inc

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials and protocols

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data was normalized uisng SCAN (SCAN.UPC package from Bioconductor)
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg38.core.mps

label: biotin

source_name: FFPE prostate cancer

label_protocol: RNA was amplified, fragmented and biotinylated using the WT-Ovation FFPE system (NuGen, San Carlos, CA) according to the manufacturer’s recommendations with minor modifications

extract_protocol: After histopathologic review of formalin-fixed, paraffin-embedded (FFPE) tumor blocks from each case by an expert pathologists, the tumor block with the index lesion was selected for specimen processing. The index lesion was identified as the prostatectomy FFPE block with the highest pathologic Gleason grade, regardless of its volume. Two 0.6-mm diameter tissue biopsy punch tool cores were sampled to enrich for tumor cells from the highest Gleason grade in the index lesion and placed in a microfuge tube for RNA extraction.

value: FFPE prostate cancer

tag: primary gleason

tag: secondary gleason

tag: decipher risk group

value: Higher

tag: race

value: White (Non-Hispanic)


title: SF9402 Input-1105


title: H1944 Xenograft Dexamethason Rep 2 RNA seq

value: Replicate 2


title: Myh6-Cre;Vldlr f/f rep3

city: Shanghai

first: Lijuan

last: Pei

address: CHIFENG ROAD 67

country: China

institute: Tongji University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to rn6 or mm10 whole genome using hisat2 v2.1.0 with parameters -p 8 --dta -x -1 -2 -S
Raw transcripts were assembled using the StringTie (v1.3.4). Counts per million (cpm) were calculated by the edgeR (v3.20.9).
Genome_build: rn6 or mm10
Supplementary_files_format_and_content: gene count

organism: Mus musculus

source_name: day 1 mouse cardiomycytes_Myh6-Cre;Vldlr f/f

growth_protocol: Neonatal rat’s hearts were harvested from 1-day old SD rats. Next, the ventricles were separated and cut into pieces (1-3 mm2), then they were dissociated in 0.25% trypsin (Gibco, 15090046) at 4 °C overnight. Then the tissue was transferred to 0.1% collagenase type Ⅱ (Worthington, LS004176) to further digest at 37°C at 145 rpm, and the supernatant was collected into DMEM medium containing 10% FBS every 5 min. The digestion procedure was repeated 3-4 times. When the tissue was completely digested, the supernatant was centrifuged at 1500 rpm for 6 min. Then, the cells were plated in DMEM medium which containing 10% FBS, 100 unit/ml penicillin and 100 mg/ml streptomycin at 15 cm dishes at an atmosphere of 5% CO2 at 37℃ for 90 min, to remove cells that are easier attached the dishes than cardiomyocytes. Finally, the culture supernatant was collected, plated in the plates which were coated with collagen and then incubated 24 h in an atmosphere of 5% CO2 at 37 ℃ with the same medium. After 24 h, the medium was changed to cardiomyocyte medium: DMEM: F12 (1:1) medium containing 0.25% FBS, 3 mM sodium pyruvate, 0.1 mM Vitamin C and 2 mM L-Glu.

extract_protocol:
The total RNA was extracted by TRIzol extraction reagent (Invitrogen, 15596018). Furthermore, the purity and concentration of RNA were examined by measuring the absorbance value at 260 and 280 nm.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: NRVCs were add Reelin vs PBS for 48h ,transfected with 50 nM si-Vldlr or si-Thbs1 and si-control for 60h, transduced with AAV9-cTnT-Vldlr or AAV9-CMV-GFP for 72h.

tag: genotype/treatment

value: Myh6-Cre;Vldlr f/f

value: heart

tag: cell type

value: cardiomyocytes


title: Myh6-Cre;Vldlr f/f rep2


title: Myh6-Cre;Vldlr f/f rep1


title: SF9402-H3K27AC Rep 1


title: H1944 Xenograft Vehicle Rep 5 RNA seq

value: Vehicle

value: Replicate 5


title: SF8628-H3K27M Rep 1


title: SF8628-H3K27M Rep 2


title: Myh6-Cre;Vldlr f/+ rep2

source_name: day 1 mouse cardiomycytes_Myh6-Cre;Vldlr f/+

value: Myh6-Cre;Vldlr f/+


title: H1944 Xenograft Vehicle Rep 4 RNA seq


title: CD105neg LiF 4

city: MANCHESTER

first: Alexander

last: Kononov

address: Oglesby Building, 555 Wilmslow Rd,

country: United Kingdom

institute: Cancer Research UK Manchester Institute

description:
CJ31_15_sample_19_S15_L001
processed data file: Raw_data_and_in_vitro_LiF_CD105pos_vs_CD105neg_(comparison_2).txt

data_processing:
Sequencing reads (single-end) were aligned to the mouse reference genome GRCm38.mm10 using STAR aligner version 2.5.1b
Gene annotation was taken from Ensembl build 92
Read counts were determined by using the featureCounts function from Bioconductor package Rsubread version 1.28.1
Analysis of differential gene expression was performed with the DESeq2 library [3] (version 1.26.0) using raw count data for each sample and controlling for batch effects. Genes displaying an FDR-adjusted p-value ≤ 0.05 were defined as differentially expressed.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with DEseq2 normalised gene expression for every gene for every sample

source_name: Liver

growth_protocol: Fibroblasts were cultured using DMEM supplimented with 10% FBS and anti-microbials

extract_protocol:
Fibroblasts were washed with PBS and immediately lysed in RLT buffer. RNA was extracted using QIAGEN Rneasy Plus Kit according to manufacturer's recommendations
QuantSeq 3’ mRNA-Seq Library Prep Kit

tag: culture condition

value: Mono-culture

value: Liver

value: In vitro cultured liver fibroblasts (LiFs)


title: CD105neg LiF 3

description:
CJ31_20_sample_18_S20_L001
processed data file: Raw_data_and_in_vitro_LiF_CD105pos_vs_CD105neg_(comparison_2).txt

tag: strain


title: CD105neg LiF 2

description:
CJ31_16_sample_17_S16_L001
processed data file: Raw_data_and_in_vitro_LiF_CD105pos_vs_CD105neg_(comparison_2).txt


title: SF7761-H3K27M Rep 1


title: Vldlr f/f rep3

source_name: day 1 mouse cardiomycytes_Vldlr f/f

value: Vldlr f/f


title: H1944 Xenograft Vehicle Rep 2 RNA seq


title: CD105neg LiF 1

description:
CJ31_22_sample_16_S22_L001
processed data file: Raw_data_and_in_vitro_LiF_CD105pos_vs_CD105neg_(comparison_2).txt


title: DIPG007-H3K27M Rep 2


title: Vldlr f/f rep2


title: CD105pos LiF 4

description:
CJ31_09_sample_14_S9_L001
processed data file: Raw_data_and_in_vitro_LiF_CD105pos_vs_CD105neg_(comparison_2).txt


title: H1944 Xenograft Vehicle Rep 1 RNA seq

value: Replicate 1


title: DIPG XIII-H3K27AC Rep 2


title: Vldlr f/f rep1


title: H1944 Xenograft Dexamethason Rep 1 RNA seq

value: Dexamethasone


title: Myh6-Cre;Vldlr f/+ rep3


title: DIPG XIII-H3K27AC Rep 1


title: CD105pos LiF 3

description:
CJ31_21_sample_13_S21_L001
processed data file: Raw_data_and_in_vitro_LiF_CD105pos_vs_CD105neg_(comparison_2).txt


title: DIPG XIII-H3K27M Rep 2


title: CD105pos LiF 2

description:
CJ31_14_sample_12_S14_L001
processed data file: Raw_data_and_in_vitro_LiF_CD105pos_vs_CD105neg_(comparison_2).txt


title: DIPG XIII-H3K27M Rep 1


title: SF7761-H3K27M Rep 2


title: H1944 Xenograft Vehicle Rep 3 RNA seq

value: Replicate 3


title: Non-responding Patient 3_Active (S)-(+)-JQ1 [35S]

city: Philadelphia

first: John

middle: Keller

last: Everett

state: PA

address: 425 Johnson Pavilion

department: Microbio

institute: University of Pennsylvania

description:
Infusion Product
RNA-seq_S5_35S_178512334_S5

data_processing:
Transcriptomic data was analyzed using our comprehensive pipeline of computational, bioinformatics and statistical tools.
GSEA analysis (https://www.gsea-msigdb.org/gsea/index.jsp) was carried out using default parameter settings.
Hallmark gene sets (MSigDB H), published gene sets (MSigDB C5) and curated gene sets of gene ontology from the biomedical literature (e.g., MSigDB C2, C7) were used for analysis.
Genome_build: hg38
Supplementary_files_format_and_content: csv formatted table of raw counts
Supplementary_files_format_and_content: csv formatted table of standardized counts

source_name: T-cells

extract_protocol:
CLL patient CD8+ CAR T cells were purified
Illumina TruSeq RNA v2 prep

tag: subject status/id

value: Non-responding Patient 3

tag: timepoint

value: Day 0

value: T-cells

tag: cell subtype

value: Active (S)-(+)-JQ1


title: Non-responding Patient 3_Inactive (R)-(-)-JQ1 [35R]

description:
Infusion Product
RNA-seq_S6_35R_178512334_S6

value: Inactive (R)-(-)-JQ1


title: Myh6-Cre;Vldlr f/+ rep1

tag: tissue

value: heart


title: CD105neg PaF 4

description:
CJ31_18_sample_9_S18_L001
processed data file: Raw_data_and_in_vitro_PaF_CD105pos_vs_CD105neg_(comparison_1).txt

source_name: Pancreas

value: Pancreas

value: In vitro cultured pancreatic fibroblasts (PaFs)


title: DIPG IV-H3K27M Rep 2

source_name: DIPGIV


title: Non-responding Patient 2 _Inactive (R)-(-)-JQ1 [22R]

description:
Infusion Product
RNA-seq_S4_22R_178512334_S4

value: Non-responding Patient 2


title: CD105pos LiF 1

description:
CJ31_06_sample_11_S6_L001
processed data file: Raw_data_and_in_vitro_LiF_CD105pos_vs_CD105neg_(comparison_2).txt


title: Non-responding Patient 4_Active (S)-(+)-JQ1 [45S]

description:
Infusion Product
RNA-seq_S7_45S_178512334_S7

value: Non-responding Patient 4


title: CD105neg PaF 3

description:
CJ31_10_sample_8_S10_L001
processed data file: Raw_data_and_in_vitro_PaF_CD105pos_vs_CD105neg_(comparison_1).txt

value: Mono-culture


title: Non-responding Patient 2 _Active (S)-(+)-JQ1 [22S]

description:
Infusion Product
RNA-seq_S3_22S_178512334_S3


title: DIPG IV-H3K27M Rep 1


title: CD105neg PaF 2

description:
CJ31_04_sample_7_S4_L001
processed data file: Raw_data_and_in_vitro_PaF_CD105pos_vs_CD105neg_(comparison_1).txt


title: Non-responding Patient 1 _Inactive (R)-(-)-JQ1 [16R]

description:
Infusion Product
RNA-seq_S2_16R_178512334_S2

value: Non-responding Patient 1


title: Non-responding Patient 4_Inactive (R)-(-)-JQ1 [45R]

description:
Infusion Product
RNA-seq_S8_45R_178512334_S8


title: CD105neg PaF 1

description:
CJ31_01_sample_6_S1_L001
processed data file: Raw_data_and_in_vitro_PaF_CD105pos_vs_CD105neg_(comparison_1).txt


title: Non-responding Patient 1 _Active (S)-(+)-JQ1 [16S]

description:
Infusion Product
RNA-seq_S1_16S_178512334_S1


title: CD105pos PaF 4

description:
CJ31_23_sample_4_S23_L001
processed data file: Raw_data_and_in_vitro_PaF_CD105pos_vs_CD105neg_(comparison_1).txt


title: D3_HMGB1_DMOG 3

city: Manhasset

first: Myoungsun

last: Son

state: NY

address: 350 Community Drive

department: Center for Autoimmune Musculoskeletal and Hematopoietic Diseases

institute: Feinstein Institute for Medical Research

data_processing:
The quality of paired reads were checked using FASTQC (v0.11.7)
Reads were aligned against human GRCh38 (hg38) genome using HISAT2 (v2.0.5)
Each gene-level raw counts were calculated using featureCounts (v1.5.2)
Genome_build: GRCh38
Supplementary_files_format_and_content: raw count table

source_name: CD14+ monocytes

growth_protocol: Purified monocytes (1x106 cells/ml) were incubated in X-Vivo 15 serum free medium (Lonza, 04-418Q).

extract_protocol:
Cell pellets were snap frozen on dry ice, mRNA was purified using Illumina TruSeq RNA Sample Prep Kit  with 1 ug of total RNA for the construction of sequencing libraries.
Standard RNA-seq (unstranded library prep with polyA selection) using the NEBNext Ultra RNA Library Preparation Kit
Unstranded RNA-seq

treatment_protocol: Monocytes were pre-incubated with 25 μM DMOG (Cayman, 71210) for 1 hour, then HMGB1 (1 μg/ml) was added in X-Vivo 15 media.

value: PBMCs from Healthy Donor


title: Female_LPS_3

city: New York

first: Philip

last: Hasel

address: 435 E 30th St

institute: NYU Langone Medical Centre

data_processing:
NovaSeq 6000 followed by RTA v3.4.4 for basecalling
Cell Ranger (v3.0.2) was used to align reads to mm10
Genome_build: mm10

extract_protocol:
Single cells were run on the 10xChromium system
Single cell libraries were generated using the 10xGenomic library kit

treatment_protocol: Female and male Aldh1l1egfp mice were either injected with 5 mg/kg LPS or saline for 24h and astrocytes FACS-purified

tag: stimulation

value: LPS

value: Cortical astrocytes

tag: Sex

value: Female

tag: time point

tag: age

tag: genotype


title: DIPG 1114-H3K27M Rep 1

tag: chip-antibody


title: DIPG 1114-H3K27AC Rep 1


title: Male_LPS_2

value: Male


title: CD105pos PaF 3

description:
CJ31_13_sample_3_S13_L001
processed data file: Raw_data_and_in_vitro_PaF_CD105pos_vs_CD105neg_(comparison_1).txt


title: Male_LPS_3


title: prostate_cancer_primary_7

value: FFPE prostate cancer

tag: primary gleason

tag: secondary gleason

value: Lower

value: African American


title: D3_HMGB1 3

tag: treatment


title: D3_HMGB1_DMOG 1


title: CD105pos PaF 2

description:
CJ31_07_sample_2_S7_L001
processed data file: Raw_data_and_in_vitro_PaF_CD105pos_vs_CD105neg_(comparison_1).txt


title: CD105pos PaF 1

description:
CJ31_12_sample_1_S12_L001
processed data file: Raw_data_and_in_vitro_PaF_CD105pos_vs_CD105neg_(comparison_1).txt


title: DIPG 1114-H3K27M Rep 2


title: Mia_shGOT1_plsdox_3

city: Ann Arbor

first: Brian

last: Magnuson

state: MI

address: 1500 East Medical Center Drive

institute: University of Michigan

data_processing:
Sequencing was performed on a NovaSeq-6000 (Illumina, San Diego, CA) with 300 total cycles of paired-end sequencing (150 cycles per read) according to the manufacturer's protocol. Bcl2fastq2 Conversion Software (Illumina, San Diego, CA) was used to generate demultiplexed Fastq files.
Reads were trimmed using Trimmomatic v0.39 (Bolger et al. Bioinformatics. 2014) with parameters ILLUMINACLIP: TruSeq3-PE.fa:2:30:10:2:true LEADING:3 TRAILING:3 MINLEN:35 SLIDINGWINDOW:4:15. Paired-end alignments and gene level counts were obtained using RSEM v1.3.1 (Li and Dewey. BMC Bioinformatics. 2011). STAR v2.5.2a was the aligner called by RSEM and the default parameters were used (Dobin et al. Bioinformatics. 2013.)
The human reference sequence hg38/GRCh38 and annotations, including gene IDs, were obtained from Gencode v29 (Frankish et al. Nucleic Acids Res. 2018).
Supplementary files: sample matrices (tab-delimited text with headers) for counts, FPKM, and TPM are provided. For the genes matrices (e.g. genes.counts.txt) the first 8 columns contain gene annotations, some of which (transcript_name, ensembl_transcript, and transcript_type) contain comma-separated lists. For isoforms matrices (e.g. isoforms.counts.txt) the first 7 columns contain transcript annotations.
Genome_build: hg38
Supplementary_files_format_and_content: Sample genes and isoforms files are standard RSEM output (tab-delimited text files with headers).  See documentation for descriptions at http://deweylab.biostat.wisc.edu/rsem/rsem-calculate-expression.html.

molecule: polyA RNA

growth_protocol: MiaPaCa2 and Tu8902 cell lines were validated by STR profiling and tested negative for mycoplasma infection (Lonza, LT07-701). Cells were maintained at 37ºC and under 5% CO2 in DMEM (GIBCO, #11965) supplemented with 10% FBS.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, 74104) and reverse transcription was performed from 2 µg of total RNA using the iScript cDNA synthesis kit (BioRad,1708890) according to the manufacturer’s instructions.
Samples (RIN > 7) were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (cat. E7760L) with Poly(A) mRNA Magnetic Isolation Module (cat. E7490L) and NEBNext Multiplex Oligos for Illumina (unique dual-index primers; cat. E6440L). PolyA+ mRNA was fragmented (10 min) and reverse-transcribed into first-strand cDNA, followed by end repair, dA tailing, and ligation of NEBNext adapters. Libraries were amplified using 11 PCR cycles and assessed by TapeStation (Agilent) and qPCR using Kapa’s library quantification kit for Illumina Sequencing platforms (cat. KK4835).

treatment_protocol: For shRNA-induced samples ("plsdox"), media was supplemented with doxycycline-hyclate (Dox) at 1µM/mL (Sigma, D9891) for 5 days prior to RNA extraction.

value: pancreatic cancer

tag: cell line

tag: genotype/variation

value: GOT1 knockdown


title: D3_HMGB1 2


title: Mia_shGOT1_plsdox_1

tag: cell type


title: Mia_shGOT1_mnsdox_3

value: control


title: D3_HMGB1_DMOG 2


title: Female_LPS_2


title: Male_LPS_1


title: Co-transplant with KPC PDA tumours cells and CD105neg PaFs 3

description:
CD105neg 3
CJ28_16_9-2_S16_L002

source_name: PDA tumour cells = KPC GEMM mouse Pdx1-Cre; KrasLSL-G12D/+; Trp53LSL-R172H/+ (KPC). PaFs = C57BL/6J

extract_protocol:
Tumors were collected, lysed in 500ul trizol utilizing a TissueLyser and RNA collected using DirectZol (Zymo) according to manufacturers recommendations
QuantSeq 3’ mRNA-Seq Library Prep Kit

tag: strain

tag: culture condition/tissue

value: Subcutaneous tumour after 10 days of growth


title: DIPG 1114-H3K27AC Rep 2


title: Male_Saline_3

value: Saline


title: D3_HMGB1 1


title: D3_DMOG 3

value: DMOG


title: Mia_shGOT1_mnsdox_2


title: Mia_shGOT1_plsdox_2


title: Female_LPS_1


title: Mia_shGOT1_mnsdox_1


title: Co-transplant with KPC PDA tumours cells and CD105neg PaFs 1

description:
CD105neg 1
CJ28_08_9-4_S8_L002


title: D3_DMOG 2


title: Tu8902_shGOT1_plsdox_3


title: Male_Saline_2


title: Co-transplant with KPC PDA tumours cells and CD105neg PaFs 4

description:
CD105neg 4
CJ28_25_9-5_S25_L002


title: Co-transplant with KPC PDA tumours cells and CD105pos PaFs 2

description:
CD105pos 2
CJ28_03_6-3_S3_L002


title: Co-transplant with KPC PDA tumours cells and CD105pos PaFs 3

description:
CD105pos 3
CJ28_14_6-4_S14_L002


title: D3_control 2

value: DMSO


title: Tu8902_shGOT1_plsdox_2


title: D3_control 3


title: Female_Saline_1


title: Tu8902_shGOT1_mnsdox_2


title: D3_DMOG 1


title: Tu8902_shGOT1_mnsdox_1


title: L-DOPA+R lesioned side_rep 2

city: Budapest

first: Ábel

last: Fóthi

state: Please Select

address: Magyar Tudosok korutja 2.

country: Hungary

institute: Institute of Enzymology, RCNS

data_processing:
Basecalling was performed with Illumina Casava
The reads were adapter trimmed by TrimGalore v0.4.0 using RRBS option
Trimmed reads were mapped to rn6 genome with Bismark v014.3 with -n1 option
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited txt files include methylation values for each sample

organism: Rattus norvegicus

source_name: striatum

growth_protocol: rats were maintained under standard housing conditions

extract_protocol:
Column extraction with Qiagen kit
Diagenode Premium RRBS kit

treatment_protocol: Rats received unilateral injectiontion of 6-OHDA at PND 21 in the medial forebrain bundle at PND 21. This was followed by a 2-weeks sub-chronic treatment (from PND 35 to PND 49)  according to their respective group (L-DOPA, UNT, L-DOPA+Riluzole). The rats received one final  treatment at PND 53, striata were collected and analyzed for changes in methylation levels.

tag: side

value: lesioned side

tag: lesion

tag: systemic treatment

value: L-DOPA + Riluzole


title: Tu8902_shGOT1_plsdox_1


title: L-DOPA+R lesioned side_rep 3


title: C42_shYY1_replicate_1

city: DURHAM

first: Chenxi

last: Xu

state: North Carolina

address: 3 Genome Court

department: Department of Pharmacology and Cancer Biology

institute: Duke university

data_processing:
RNA-seq reads were mapped using MapSplice and quantified using RSEM. Read counts were upper-quantile normalized and log2 transformed.
Raw read counts were used for differential gene expression analysis by DESeq.
Genome_build: hg19
Supplementary_files_format_and_content: matrix of RNA-seq read counts

source_name: C42 cells

growth_protocol: 22Rv1 and C42 prostate cancer cells were grown in RPMI1640 base medium plus 10% of FBS and 1% of antibiotics.

extract_protocol:
RNA was extracted by using Qiagen RNeasy Mini Kit. 1 ug of total RNA for the construction of the pooled sequencing libraries.
NEBNext Ultra II RNA library Prep kit (NEB, #E7770) was used

tag: lentivirus


title: Male_Saline_1

tag: stimulation

tag: tissue

tag: Sex


title: C42_shYY1_replicate_2


title: Female_Saline_2

tag: time point

tag: age

tag: genotype


title: Male_LPS_5_24h

data_processing:
Sequenced reads were trimmed for adaptor sequences, aligned to the mm10 reference genome using HISAT2 followed by transcript assembly and quantification using StringTie
Differential gene expression was assessed using DESeq2. Expression values are given as FPKM.
Genome_build: mm10
Supplementary_files_format_and_content: xlxs file with FPKM values for each sample and adjusted p-values for differential gene expression calculated using DESeq2

extract_protocol:
Astrocyte were FACS-purified and RNA extracted using the Agilent Absolutely Total RNA Purification Kit
cDNA was generated using the SMART-seq HT kit and libraries were generated using the Nextera XT kit (Takara Bio).

treatment_protocol: Female or male Aldh1l1egfp mice were either injected with 5 mg/kg LPS or saline for 3h, 24h or 72h


title: L-DOPA+R lesioned side_rep 1


title: L-DOPA+R control side_rep 3

value: unlesioned side


title: Female_LPS_3_72h

value: LPS


title: C42_shEV_replicate_2

value: shEV


title: Co-transplant with KPC PDA tumours cells and CD105pos PaFs 4

description:
CD105pos 4
CJ28_15_6-5_S15_L002


title: Co-transplant with KPC PDA tumours cells and CD105neg PaFs 2

description:
CD105neg 2
CJ28_09_9-1_S9_L002


title: Male_LPS_4_24h

value: Cortical astrocytes


title: Co-transplant with KPC PDA tumours cells and CD105pos PaFs 1

description:
CD105pos 1
CJ28_02_6-2_S2_L002


title: D3_control 1

value: PBMCs from Healthy Donor


title: L-DOPA+R control side_rep 1


title: L-DOPA+R control side_rep 2


title: Female_LPS_2_72h

value: Female


title: Tu8902_shGOT1_mnsdox_3


title: Female_LPS_1_72h


title: C42_shEV_replicate_1


title: Male_LPS_2_24h

value: Male


title: 22Rv1_shYY1_replicate_1

source_name: 22Rv1 cells


title: 22Rv1_shYY1_replicate_2


title: L-DOPA lesioned side_rep 3

value: L-DOPA


title: Male_LPS_1_24h


title: 22Rv1_shEV_replicate_1


title: Female_LPS_4_24h


title: 22Rv1_shEV_replicate_2


title: L-DOPA lesioned side_rep 2


title: Female_LPS_3_24h


title: L-DOPA lesioned side_rep 1


title: L-DOPA control side_rep 3


title: L-DOPA control side_rep 2


title: L-DOPA control side_rep 1


title: Male_LPS_3_24h


title: Nalm6 treated CART+imatinib5uM rep2

city: Hangzhou

first: Jiang

last: Penglei

address: Yuhangtang Road 866

department: School of basic medicine science

institute: Zhejiang University

description: sample 2 Nalm6 treated CART+imatinib5uM

data_processing:
Illumina Casava1.8 software used for basecalling.
Clean RNA-Seq reads for each sample were aligned to the human reference genome GRCh38 (ENSEMBL release 94) by HISAT2 v2.0.5 with default setting.
FeatureCounts v1.5.0-p3 was used to quantify genes expression level with parameter “-Q 10 -B -C”.
The normalized counts were calculated in edgeR v3.22.3 and were used to calculate Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) according to total length of all exons of each gene.
Genome_build: GRCh38
Supplementary_files_format_and_content: all_samples_FPKM.csv:  Comma separated text files with FPKM values for each sample
Supplementary_files_format_and_content: all_samples_FPKM.csv:  Comma separated text files with raw gene counts for every gene and every sample

source_name: CART

extract_protocol:
Total RNA was extracted from CART cells in control and treatment groups according to the manufacturer’s protocol.
cDNA libraries were constructed using the NEBNext® UltraTM RNA Library Prep Kit (Illumina) and sequenced on an Illumina Hiseq platform and 150 bp paired-end reads were generated.

value: CD19-targeted Chimeric antigen receptor T cells (CART) cells

tag: treatmemt

value: Nalm6 treated CART+imatinib5uM


title: Female_LPS_5_3h


title: Nalm6 treated CART+imatinib5uM rep1

description: sample 1 Nalm6 treated CART+imatinib5uM


title: Nalm6 treated CART+dasatinib30nM rep2

description: sample 2 Nalm6 treated CART+dasatinib30nM

value: Nalm6 treated CART+dasatinib30nM


title: Untreated lesioned side_rep 3

value: saline


title: Female_LPS_3_3h


title: Female_LPS_4_3h


title: Untreated lesioned side_rep 2


title: Nalm6 treated CART+dasatinib30nM rep1

description: sample 1 Nalm6 treated CART+dasatinib30nM


title: Female_LPS_2_3h


title: Nalm6 treated CART rep2

description: sample 2 Nalm6 treated CART

value: Nalm6 treated CART


title: Female_LPS_2_24h


title: Female_LPS_1_3h


title: Untreated control side_rep 3


title: control-rep2

description: sample 2 control

value: control


title: LNCaP_DHT_YY1_ChIP

data_processing:
All reads were mapped to the human genome (hg19) using the BWA alignment software. Unique reads mapped to a single best-matching location with no more than two mismatches were kept, which were then subject to removal of reads generated by PCR- caused duplicates using the Picard and Samtools.
The MACS2 software was used for peak identification with data from input as controls and default parameters.
Alignment files in the bam format were transformed into read coverage files (bigwig format) using DeepTools.
Profiles of ChIP-Seq read densities were displayed in the Integrative Genomics Viewer (IGV, Broad Institute).
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

source_name: LNCaP cells

growth_protocol: LNCaP cells were grown in RPMI1640 plus 10% of FBS and 1% of antibiotics. For compound treatment, cells were under ligand-starved conditions using the phenol red-free RPMI-1640 base medium supplemented with charcoal-stripped serum, followed by treatment with DMSO or Dihydrotestosterone (DHT) for 6hrs.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with specific antibodies against YY1 (Santa Cruz cat#sc7341)
Libraries were prepared by NEBNext Ultra II kit (NEB, #E7645L)

treatment_protocol: For ChIP-seq experiments, cells were grown in medium and collected, followed by cell fixation with 1% of formaldehyde, sonication, antibody enrichment, ChIP DNA recovery, library generation and parallel sequencing.

value: LNCaP

tag: treatment

value: DHT-treated

tag: chip antibody

value: Mouse anti-YY1 (Santa Cruz sc7341)


title: Female_Saline_4_72h

value: Saline


title: control-rep1

description: sample 1 control


title: Untreated control side_rep 2

value: unlesioned side


title: Untreated lesioned side_rep 1

value: lesioned side


title: Female_LPS_1_24h

value: LPS

value: Cortical astrocytes


title: LNCaP_DHT_YY1_ChIP_INPUT

tag: cell line

value: none; input


title: Female_Saline_3_72h

value: Female


title: Untreated control side_rep 1


title: Pt5_D7

city: Turku

first: Maija

last: Hollmén

address: Tykistökatu 6A 4th floor

country: Finland

institute: University of Turku

description:
processed data file: Raw_read_counts.txt
processed data file: Gene_expression_FPKM.txt
processed data file: Pt5_D7_DEGs.txt

data_processing:
Base calling with Illumina CASAVA software.
Raw reads were filtered to remove reads with adaptor contamination, uncertain nucleotides (N >10%) or low-quality nucleotides (>50% bases with Q-score <20).
High-quality reads were mapped to GRCh38 human reference genome using HISAT2 v2.05 and gene expression levels (FPKM) quantified using HTSeq v0.6.1.
Differently expressed genes in comparison to pre-dose (D0) samples were identified in each patient from TMM-normalized counts with DEGseq as genes with Benjamini-Hochberg adjusted p-value <0.005 and |log2(FoldChange)| >1.
Genome_build: GRCh38
Supplementary_files_format_and_content: Gene_expression_FPKM.txt: Matrix table with FPKM values for every gene and every sample.
Supplementary_files_format_and_content: Raw_read_counts.txt: Matrix table with raw read counts for every gene and every sample.
Supplementary_files_format_and_content: *_DEGs.txt: Tab-limited text files include differently expressed genes on day 1 and day 7 (post-dose) in comparison to day 0 (pre-dose) for each patient.

source_name: Blood (PBMCs)

extract_protocol:
Peripheral blood mononuclear cells were isolated using Ficoll-Paque PLUS (GE healthcare), enriched for CD14+ monocytes with magnetic separation beads (Miltenyi Biotech) and monocyte total RNA extracted using TRIsure (BioLine).
RNA libraries were prepared using NEBNext ultra RNA library prep kit for Illumina (NEB) following manufacturer's recommendations.

tag: patient id

value: anti-Clever-1 therapy

tag: timepoint

value: Post-dose D7

tag: cell type

value: CD14+ monocyte


title: Female_Saline_2_72h


title: Female_Saline_1_72h


title: Bu_rep2

city: Guangzhou

first: Fagui

last: Zou

address: No. 74, Zhongshan Er Road, Guangzhou

institute: Sun Yat-sen University

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2)  by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using STAR (v1.5.1)
The read counts were extracted using HTSeq-count （v0.11.3）
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: splenic CD19+ B cells

extract_protocol:
RNA was extracted using Trizol reagent. mRNA was enriched with oligo(dT)-attach magnetic beads and fragmented into small pieces, cDNA library was generated using random hexamer-primed reverse transcription followed by second-strand cDNA synthesis and sequenced on an MGI 2000 platform (BGI, Shenzhen, China).
RNA libraries were prepared for sequencing using standard BGI 2000 protocols

tag: strain

value: 6-8 week

value: treated with LPS+sodium butyrate


title: LNCaP_MOCK_YY1_ChIP_INPUT

value: EtOH-treated


title: Pt5_D1

description:
processed data file: Raw_read_counts.txt
processed data file: Gene_expression_FPKM.txt
processed data file: Pt5_D1_DEGs.txt

value: Post-dose D1


title: Bu_rep3


title: Pt5_D0

description:
processed data file: Raw_read_counts.txt
processed data file: Gene_expression_FPKM.txt
processed data file: Pt5_D1_DEGs.txt
processed data file: Pt5_D7_DEGs.txt

value: Pre-dose D0


title: 22Rv1_DHT_YY1_ChIP

data_processing:
All reads were mapped to the human genome (hg19) using the BWA alignment software. Unique reads mapped to a single best-matching location with no more than two mismatches were kept, which were then subject to removal of reads generated by PCR- caused duplicates using the Picard and Samtools.
The matched input data of 22Rv1 cells (both mock and DHT-treated) were previously published by us (available from NCBI GEO #GSE94013) and used herein for normalization of 22Rv1 YY1 ChIP-seq datasets.
The MACS2 software was used for peak identification with data from input as controls and default parameters.
Alignment files in the bam format were transformed into read coverage files (bigwig format) using DeepTools.
Profiles of ChIP-Seq read densities were displayed in the Integrative Genomics Viewer (IGV, Broad Institute).
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

growth_protocol: 22Rv1 cells were grown in RPMI1640 plus 10% of FBS and 1% of antibiotics. For compound treatment, cells were under ligand-starved conditions using the phenol red-free RPMI-1640 base medium supplemented with charcoal-stripped serum, followed by treatment with DMSO or Dihydrotestosterone (DHT) for 6hrs.

tag: antibody used

tag: treatment condition

value: DHT-treated


title: Pt3_D7

description:
processed data file: Raw_read_counts.txt
processed data file: Gene_expression_FPKM.txt
processed data file: Pt3_D7_DEGs.txt


title: LNCaP_MOCK_YY1_ChIP

value: LNCaP

value: Mouse anti-YY1 (Santa Cruz sc7341)


title: Male_Saline_4_24h

value: Saline

value: Male


title: Male_Saline_5_24h


title: Bu_rep1


title: CK_rep3

value: treated with LPS


title: Nalm6 treated CART rep1

description: sample 1 Nalm6 treated CART

value: CD19-targeted Chimeric antigen receptor T cells (CART) cells

value: Nalm6 treated CART


title: Pt3_D1

description:
processed data file: Raw_read_counts.txt
processed data file: Gene_expression_FPKM.txt
processed data file: Pt3_D1_DEGs.txt


title: Pt3_D0

description:
processed data file: Raw_read_counts.txt
processed data file: Gene_expression_FPKM.txt
processed data file: Pt3_D1_DEGs.txt
processed data file: Pt3_D7_DEGs.txt


title: CK_rep2


title: aspf3_XO_3

city: Jena

first: Sascha

last: Schäuble

address: Beutenbergstraße 11a

country: Germany

institute: Leibniz Institute for Natural Product Research and Infection Biology

description:
counts.tsv
mrn.tsv

data_processing:
quality control with FastQC (v0.11.5)
quality trimming of raw data with trimmomatic (v0.36)
mapping with HiSat2 (v2.1.0)
read counting with featureCounts (v1.20.6)
Genome_build: AspGD, s03-m05-r11_2018-08-19
Supplementary_files_format_and_content: counts.tsv  (tab delimited text file with unnormalized read counts)
Supplementary_files_format_and_content: mrn.tsv  (tab delimited text file with MRN normalised read counts)

organism: Aspergillus fumigatus

source_name: Δasp f3

extract_protocol:
Qiagen RNeasy Mini Kit
adapter ligation; single end; poly-A filter; unspecific

value: {delta}asp f3

value: hyphae

value: 150 µM xanthine, 100 µg/mL (0.2 units/mL) xanthine oxidase (Sigma-Aldrich, Taufkirchen, Germany)

tag: medium

value: Czapec Dox (BD, Franklin Lakes, NJ, USA)


title: aspf3_XO_2

description:
counts.tsv
mrn.tsv


title: 22Rv1_MOCK_YY1_ChIP


title: Male_Saline_2_24h

tag: stimulation

value: Cortical astrocytes


title: CK_rep1

value: 6-8 week


title: Pt2_D7

description:
processed data file: Raw_read_counts.txt
processed data file: Gene_expression_FPKM.txt
processed data file: Pt2_D7_DEGs.txt

value: anti-Clever-1 therapy

value: Post-dose D7

value: CD14+ monocyte


title: aspf3_XO_1

description:
counts.tsv
mrn.tsv

tag: tissue


title: datf1dpcr1 cells transformed with pREP41 rep2

city: Kolkata

first: Geetanjali

last: Sundaram

address: 35 Ballugunje circular road

department: Biochemistry

country: India

institute: University of Calcutta

data_processing:
Raw sequence data generation was done using Fastq file followed by data quality check.
Mapping is done to the reference genome using Hisat2 to evaluate sample quality
Differential expression analysis using Cuffdiff.
Gene Ontology Annotations were assigned using Uniprot and pombase
genome build: ASM294v2
Supplementary_files_format_and_content: counts, FPKM

organism: Schizosaccharomyces pombe

source_name: whole organism

growth_protocol: All cells were grown at 30°C. For overexpression experiments, cells were grown overnight in Edinburgh minimal medium (EMM)-Leu supplemented with 20uM thiamine, harvested, washed, resuspended in EMM-Leu-thiamine, and incubated for another 24 h at 30°C.

extract_protocol:
RNA was extracted using Trizol Reagent
TruSeqstranded mRNA sample preparation protocol was used for library preparation

value: unicellular eukaryote

value: h+ leu1 ura4pcr1::ura4+atf1::kanMX6


title: Pt2_D1

description:
processed data file: Raw_read_counts.txt
processed data file: Gene_expression_FPKM.txt
processed data file: Pt2_D1_DEGs.txt

value: Post-dose D1


title: aspf3_no_3

description:
counts.tsv
mrn.tsv


title: Female_Saline_5_24h

value: Saline

tag: Sex

value: Female


title: datf1dpcr1 cells transformed with pREP41 rep1


title: Pt2_D0

description:
processed data file: Raw_read_counts.txt
processed data file: Gene_expression_FPKM.txt
processed data file: Pt2_D1_DEGs.txt
processed data file: Pt2_D7_DEGs.txt

value: Pre-dose D0


title: Female_Saline_4_24h

tag: time point


title: datf1 cells transformed with Pcr1 rep2

value: h- atf1::ura4 +


title: aspf3_no_1

description:
counts.tsv
mrn.tsv


title: Pt21_D7

description:
processed data file: Raw_read_counts.txt
processed data file: Gene_expression_FPKM.txt
processed data file: Pt21_D7_DEGs.txt


title: aspf3_no_2

description:
counts.tsv
mrn.tsv


title: Male_Saline_3_24h

value: Male

tag: age


title: Female_Saline_3_24h

tag: genotype


title: datf1 cells transformed with Pcr1 rep1


title: WT_XO_3

description:
counts.tsv
mrn.tsv

source_name: wild type D141

value: wild type D141


title: datf1 cells transformed with pREP41 rep2


title: Pt21_D0

description:
processed data file: Raw_read_counts.txt
processed data file: Gene_expression_FPKM.txt
processed data file: Pt21_D1_DEGs.txt
processed data file: Pt21_D7_DEGs.txt


title: Pt21_D1

description:
processed data file: Raw_read_counts.txt
processed data file: Gene_expression_FPKM.txt
processed data file: Pt21_D1_DEGs.txt


title: Female_Saline_1_24h


title: WT_XO_2

description:
counts.tsv
mrn.tsv

value: hyphae


title: Male_Saline_1_24h


title: Female_Saline_4_3h


title: Intestine-scATAC-Sample1

city: Boston

first: Ramesh

last: Shivdasani

state: MA

address: 450 Brookline Ave. Dana 720D

department: Medical Oncology

institute: Dana Farber Cancer Institute

data_processing:
Alignment: ChIP-seq, ATAC-seq:bowtie2; RNA-seq: STAR; scATAC: CellRanger
CHIP-seq peak calling, ATAC-seq peak calling: MACS, version 2.0
Genome_build: hg19, mm10
Supplementary_files_format_and_content: ATAC-seq, ChIP-seq, CUT&RUN: bigwig file for visualizing aligned sequence tags; RNA-seq: unprocessed gene counts; scATAC-seq: unfiltered peak-cell counts

source_name: Primary human duodenal biopsy sample

extract_protocol:
Nuclei were isolated from fresh frozen clinical biopsy specimens by douncing in nuclear lysis buffer. Nuclei were purified by sorting using DAPI as a nuclear stain.
Once nuclei were purified bulk transposition was carried out using Tn5 (10x Genomics) followed by formation of gel emulsion beads to encapsulate individual nuclei separately and initial library amplification was carried out.
Libraries were prepared using the 10x Genomics scATAC library preparation reagents and 50bp paired end sequencing was performed on the Novaseq SP flowcell (Illumina)

value: Fresh frozen endoscopic biopsy

tag: antibody


title: WT_XO_1

description:
counts.tsv
mrn.tsv

tag: treatment

value: 150 µM xanthine, 100 µg/mL (0.2 units/mL) xanthine oxidase (Sigma-Aldrich, Taufkirchen, Germany)

value: Czapec Dox (BD, Franklin Lakes, NJ, USA)


title: Female_Saline_2_24h

value: Cortical astrocytes


title: WT_no_3

description:
counts.tsv
mrn.tsv


title: Stomach-scATAC-Sample2

source_name: Primary human stomach body biopsy sample

extract_protocol:
Nuclei were isolated from fresh frozen clinical biopsy specimens by douncing in nuclear lysis buffer. Nuclei were purified using Iodixanol density gradient centrifugation.
Once nuclei were purified bulk transposition was carried out using Tn5 (10x Genomics) followed by formation of gel emulsion beads to encapsulate individual nuclei separately and initial library amplification was carried out.
Libraries were prepared using the 10x Genomics scATAC library preparation reagents and 50bp paired end sequencing was performed on the Novaseq SP flowcell (Illumina)


title: wt cells transformed with Pcr1 rep2


title: Female_Saline_3_3h


title: WT_no_2

description:
counts.tsv
mrn.tsv


title: wt cells transformed with Pcr1 rep1


title: Stomach-scATAC-Sample1


title: wt cells transformed with pREP41 rep2


title: Female_Saline_1_3h


title: WT_no_1

description:
counts.tsv
mrn.tsv


title: wt cells transformed with pREP41 rep1


title: Barretts-scATAC-Sample2

source_name: Primary human Barretts metaplasia biopsy sample

extract_protocol:
Nuclei were isolated from fresh frozen clinical biopsy specimens by douncing in nuclear lysis buffer.
Once nuclei were purified bulk transposition was carried out using Tn5 (10x Genomics) followed by formation of gel emulsion beads to encapsulate individual nuclei separately and initial library amplification was carried out.
Libraries were prepared using the 10x Genomics scATAC library preparation reagents and 50bp paired end sequencing was performed on the Novaseq SP flowcell (Illumina)


title: Barretts-scATAC-Sample1


title: datf1 cells transformed with pREP41 rep1


title: H3K9me3_Lmb_C

status: Public on Jun 02 2021

city: Thiverval-Grignon

first: Jessica

middle: Louise

last: SOYER

address: Avenue Lucien Brétignières

department: SPE

country: France

institute: INRAE

data_processing:
Mapping against the reference genome of Lmb (Dutreux et al., 2018) or Lml (Grandaubert et al., 2014) using Bowtie2 (Langmead and Salzberg, 2012) with default parameters
Peak calling using RSEG (Song & Smith, 2011)
Genome_build: Lmb (Dutreux et al., 2018); Lml (Grandaubert et al., 2014)
Supplementary_files_format_and_content: Peak calling analysis was performed on each ChIP sequencing dataset, to identify significantly enriched domains for either H3K4me2, H3K9me3 or H3K27me3, using RSEG (Song and Smith, 2011).   The processed files provide, for each individual sample, location of the significantly enriched domains, in a .bed file.

organism: Plenodomus lingam/Leptosphaeria maculans 'brassicae' group

source_name: mycelium

growth_protocol: mycelium of Lmb and Lml were grown on V8 agar medium at 25°C for seven days. Then 10 plugs of mycelium were inoculated into 100 ml of Fries liquid medium in Roux bottle. Mycelia were harvested after growing for 7 days at 25°C

extract_protocol:
ChIP was performed from freshly-harvested mycelium grown in Fries liquid culture, as described in Soyer et al. (2015b), with minor modifications. ChIP was performed on native material (without crosslinking) using antibodies targeting histone modifications H3K4me2 (Merck ref. 07-030), H3K9me3 (Active Motif, Carlsbad, CA, USA; ref. 39161), or H3K27me3 (Active Motif, Carlsbad, CA, USA; ref. 39155).
Libraries were prepared from all biological replicates, individually, according to the Illumina TruSeq protocol “Ultra Low Input DNA library”. Libraries were sequenced with an Illumina HiSeq 2000 genome analyzer at the Max Planck Genome centre Cologne, Germany (https://mpgc.mpipz.mpg.de/home/).

treatment_protocol: mycelium was filtered and washed thoroughly with distilled water

value: mycelium

tag: growth condition

value: axenic

tag: chip antibody


title: H3K27me3_Lmb_C

value: H3K27me3 (Active Motif, Carlsbad, CA, USA; ref. 39155)


title: H3K9me3_Lmb_A

value: H3K9me3 (Active Motif, Carlsbad, CA, USA; ref. 39161)


title: H3K4me2_Lmb_C

value: H3K4me2 (Merck ref. 07-030)


title: Female_Saline_3


title: H3K27me3_Lmb_B


title: H3K4me2_Lmb_A


title: H3K9me3_Lmb_B


title: H3K27me3_Lmb_A


title: MCF

city: Qingdao

first: Kaoshan

last: Chen

address: No. 72 Binhai Road

department: School of Life Science

institute: Shandong University

description: Sample cells were collected after being cultured by the fresh cell-free filtrates of co-culture fermentation broth of B. amyloliquefaciens and T. longibrachiatum

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) for the construction of libraries, and samples were then sequenced with the Illumina HiSeq 2500 platform, to generate paired-end reads.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Reference genome and gene model annotation files were downloaded from genome website directly. Both building index of reference genome and aligning clean reads to reference genome were used Bowtie2-2.2.3. (Langmead, B. and S. L. Salzberg, 2012)
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene.
Genome_build: NCBI reference sequence: NC_014551.1
Supplementary_files_format_and_content: FPKM of each gene

organism: Bacillus amyloliquefaciens

source_name: bacterial cell

extract_protocol:
The cultures were incubated at 30 ± 2 ℃ and shaken at 150 rpm for 24 h. Sample cells were harvested by centrifugation (10,000 g, 4 ℃), washed with sterile water, and then centrifuged and stored in liquid nitrogen immediately.
A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

tag: broth treatment

value: MCF


title: BCF

description: Sample cells were collected after being cultured by the fresh cell-free filtrates of B. amyloliquefaciens fermentation broth

value: BCF


title: Female_Saline_2_3h

value: Saline

value: Female


title: aSAH-LVE_PLM22

city: Lexington

first: Wang-Xia

last: Wang

state: Kentucky

address: 800 S Limestone

institute: University of Kentucky

description:
DCV+/PBD3
SAMPLE 133

data_processing:
Web-based software (ThermoFisher Cloud Software - Relative Quantification) provided by ThermoFisher was used to determine the relative threshold cycle (Crt)
Raw Crt values and the geometric mean of a given sample was used to obtain ΔCrt values calculated as ΔCrt = Crt-target - Crt-geomean for each miRNA.

label: FAM

source_name: plasma

extract_protocol: CSF and plasma total RNA were isolated using miRNeasy Serum/Plasma Advanced Kit (Cat #: 217204, Qiagen, Hilden, Germany) following manufacturer’s protocol.

tag: analysis group

value: GroupC

tag: dcv diagnosis

value: Yes

tag: technical replicates


title: aSAH-LVE_PLM13

description:
DCV-/PBD3
SAMPLE 132

value: No


title: aSAH-LVE_PLM30

description:
DCV-/PBD3
SAMPLE 135


title: aSAH-LVE_PLM34

description:
DCV-/PBD3
SAMPLE 136


title: aSAH-LVE_PLM26

description:
DCV+/PBD3
SAMPLE 134


title: aSAH-LVE_CSF13

description:
DCV-/PBD3
SAMPLE 126

source_name: cerebral spinal fluid


title: aSAH-LVE_CSF26

description:
DCV+/PBD3
SAMPLE 128


title: aSAH-LVE_CSF22

description:
DCV+/PBD3
SAMPLE 127


title: aSAH-LVE_CSF30

description:
DCV-/PBD3
SAMPLE 129


title: aSAH-LVE_CSF34

description:
DCV-/PBD3
SAMPLE 130


title: aSAH-LVE_PLM4

description:
DCV-/PBD3
SAMPLE 131


title: H3K4me2_Lmb_B

tag: strain


title: aSAH-LVE_CSF4

description:
DCV-/PBD3
SAMPLE 125


title: aSAH-092019-WX#31

description:
DCV-/PBD7
SAMPLE 123

value: GroupB


title: aSAH-092019-WX#28

description:
DCV+/PBD7
SAMPLE 120


title: aSAH-092019-WX#30

description:
DCV+/PBD7
SAMPLE 122


title: aSAH-092019-WX#29

description:
DCV-/PBD7
SAMPLE 121


title: aSAH-092019-WX#26

description:
DCV-/PBD3
SAMPLE 118


title: aSAH-092019-WX#32

description:
DCV+/PBD7
SAMPLE 124


title: aSAH-092019-WX#25

description:
DCV+/PBD3
SAMPLE 117


title: aSAH-092019-WX#24

description:
DCV-/PBD3
SAMPLE 116


title: aSAH-092019-WX#27

description:
DCV+/PBD3
SAMPLE 119


title: aSAH-092019-WX#23

description:
DCV+/PBD3
SAMPLE 115


title: aSAH-092019-WX#7

description:
DCV-/PBD3
SAMPLE 113


title: aSAH-092019-WX#8

description:
DCV-/PBD7
SAMPLE 114


title: aSAH-092019-WX#5

description:
DCV+/PBD3
SAMPLE 111


title: aSAH-092019-WX#6

description:
DCV+/PBD7
SAMPLE 112


title: aSAH-092019-WX#3

description:
DCV-/PBD3
SAMPLE 109


title: aSAH-092019-WX#4

description:
DCV-/PBD7
SAMPLE 110


title: aSAH-092019-WX#2

description:
DCV+/PBD7
SAMPLE 108


title: aSAH-092019-WX#39

description:
DCV-/PBD7
SAMPLE 103


title: aSAH-092019-WX#40

description:
DCV+/PBD7
SAMPLE 104


title: aSAH-092019-WX#42

description:
DCV+/PBD7
SAMPLE 106


title: aSAH-092019-WX#41

description:
DCV-/PBD7
SAMPLE 105


title: aSAH-092019-WX#1

description:
DCV+/PBD3
SAMPLE 107


title: aSAH-092019-WX#38

description:
DCV+/PBD7
SAMPLE 102


title: aSAH-092019-WX#36

description:
DCV-/PBD3
SAMPLE 100


title: aSAH-092019-WX#37

description:
DCV+/PBD3
SAMPLE 101


title: aSAH-092019-WX#35

description:
DCV+/PBD3
SAMPLE 99


title: aSAH-092019-WX#33

description:
DCV+/PBD3
SAMPLE 97


title: aSAH-092019-WX#16

description:
DCV-/PBD7
SAMPLE 96


title: aSAH-092019-WX#15

description:
DCV-/PBD3
SAMPLE 95


title: aSAH-092019-WX#14

description:
DCV+/PBD7
SAMPLE 94


title: aSAH-092019-WX#13

description:
DCV+/PBD3
SAMPLE 93


title: aSAH-092019-WX#9

description:
DCV+/PBD3
SAMPLE 89


title: aSAH-092019-WX#10

description:
DCV+/PBD7
SAMPLE 90


title: aSAH-092019-WX#12

description:
DCV-/PBD7
SAMPLE 92


title: aSAH-PLM52

description:
HC
SAMPLE 88

value: GroupA

value: HC


title: aSAH-PLM47

description:
HC
SAMPLE 83


title: aSAH-PLM50

description:
HC
SAMPLE 86


title: aSAH-PLM51

description:
HC
SAMPLE 87


title: aSAH-PLM45

description:
HC
SAMPLE 81


title: aSAH-PLM49

description:
HC
SAMPLE 85


title: aSAH-PLM46

description:
HC
SAMPLE 82


title: aSAH-PLM39

description:
DCV-/PBD3
SAMPLE 79


title: aSAH-PLM40

description:
DCV-/PBD7
SAMPLE 80


title: aSAH-092019-WX#34

description:
DCV-/PBD3
SAMPLE 98


title: aSAH-PLM37

description:
DCV+/PBD3
SAMPLE 77


title: aSAH-PLM35

description:
DCV+/PBD3
SAMPLE 75


title: aSAH-PLM36

description:
DCV+/PBD7
SAMPLE 76


title: aSAH-PLM34

description:
DCV+/PBD7
SAMPLE 74


title: aSAH-PLM38

description:
DCV+/PBD7
SAMPLE 78


title: aSAH-PLM33

description:
DCV+/PBD3
SAMPLE 73


title: aSAH-092019-WX#11

description:
DCV-/PBD3
SAMPLE 91


title: aSAH-PLM32

description:
DCV+/PBD7
SAMPLE 72


title: aSAH-PLM29

description:
DCV+/PBD3
SAMPLE 69


title: aSAH-PLM31

description:
DCV+/PBD3
SAMPLE 71


title: aSAH-PLM30

description:
DCV+/PBD7
SAMPLE 70


title: aSAH-PLM48

description:
HC
SAMPLE 84


title: aSAH-PLM27

description:
DCV+/PBD3
SAMPLE 67


title: aSAH-PLM26

description:
DCV-/PBD7
SAMPLE 66


title: aSAH-PLM25

description:
DCV-/PBD3
SAMPLE 65


title: aSAH-PLM24

description:
DCV-/PBD7
SAMPLE 64


title: aSAH-PLM22

description:
DCV-/PBD7
SAMPLE 62


title: aSAH-PLM21

description:
DCV-/PBD3
SAMPLE 61


title: aSAH-PLM23

description:
DCV-/PBD3
SAMPLE 63


title: aSAH-PLM20

description:
DCV-/PBD7
SAMPLE 60


title: aSAH-PLM18

description:
DCV+/PBD7
SAMPLE 58


title: aSAH-PLM15

description:
DCV-/PBD3
SAMPLE 55


title: aSAH-PLM17

description:
DCV+/PBD3
SAMPLE 57


title: aSAH-PLM16

description:
DCV-/PBD7
SAMPLE 56


title: aSAH-PLM19

description:
DCV-/PBD3
SAMPLE 59


title: aSAH-PLM14

description:
DCV-/PBD7
SAMPLE 54


title: aSAH-PLM13

description:
DCV-/PBD3
SAMPLE 53


title: aSAH-PLM12

description:
DCV-/PBD7
SAMPLE 52


title: aSAH-PLM11

description:
DCV-/PBD3
SAMPLE 51


title: aSAH-PLM28

description:
DCV+/PBD7
SAMPLE 68


title: aSAH-PLM8

description:
DCV-/PBD7
SAMPLE 50


title: aSAH-PLM3

description:
DCV-/PBD3
SAMPLE 47


title: aSAH-PLM7

description:
DCV-/PBD3
SAMPLE 49


title: aSAH-PLM2

description:
DCV+/PBD7
SAMPLE 46


title: aSAH-PLM4

description:
DCV-/PBD7
SAMPLE 48


title: aSAH-PLM1

description:
DCV+/PBD3
SAMPLE 45


title: aSAH-CSF52

description:
HC
SAMPLE 44


title: aSAH-CSF47

description:
HC
SAMPLE 39


title: aSAH-CSF46

description:
HC
SAMPLE 38


title: aSAH-CSF51

description:
HC
SAMPLE 43


title: aSAH-CSF49

description:
HC
SAMPLE 41


title: aSAH-CSF45

description:
HC
SAMPLE 37


title: aSAH-CSF39

description:
DCV-/PBD3
SAMPLE 35


title: aSAH-CSF38

description:
DCV+/PBD7
SAMPLE 34


title: aSAH-CSF37

description:
DCV+/PBD3
SAMPLE 33


title: aSAH-CSF36

description:
DCV+/PBD7
SAMPLE 32


title: aSAH-CSF50

description:
HC
SAMPLE 42


title: aSAH-CSF35

description:
DCV+/PBD3
SAMPLE 31


title: aSAH-CSF34

description:
DCV+/PBD7
SAMPLE 30


title: aSAH-CSF33

description:
DCV+/PBD3
SAMPLE 29


title: aSAH-CSF31

description:
DCV+/PBD3
SAMPLE 27


title: aSAH-CSF29

description:
DCV+/PBD3
SAMPLE 25


title: aSAH-CSF28

description:
DCV+/PBD7
SAMPLE 24


title: aSAH-CSF30

description:
DCV+/PBD7
SAMPLE 26


title: aSAH-CSF32

description:
DCV+/PBD7
SAMPLE 28


title: aSAH-CSF26

description:
DCV-/PBD7
SAMPLE 22


title: aSAH-CSF22

description:
DCV-/PBD7
SAMPLE 18


title: aSAH-CSF25

description:
DCV-/PBD3
SAMPLE 21


title: aSAH-CSF23

description:
DCV-/PBD3
SAMPLE 19


title: aSAH-CSF48

description:
HC
SAMPLE 40


title: aSAH-CSF40

description:
DCV-/PBD7
SAMPLE 36


title: aSAH-CSF24

description:
DCV-/PBD7
SAMPLE 20


title: aSAH-CSF21

description:
DCV-/PBD3
SAMPLE 17


title: aSAH-CSF18

description:
DCV+/PBD7
SAMPLE 14


title: aSAH-CSF17

description:
DCV+/PBD3
SAMPLE 13


title: aSAH-CSF12

description:
DCV-/PBD7
SAMPLE 8


title: aSAH-CSF15

description:
DCV-/PBD3
SAMPLE 11


title: aSAH-CSF16

description:
DCV-/PBD7
SAMPLE 12


title: aSAH-CSF8

description:
DCV-/PBD7
SAMPLE 6


title: aSAH-CSF14

description:
DCV-/PBD7
SAMPLE 10


title: aSAH-CSF7

description:
DCV-/PBD3
SAMPLE 5


title: aSAH-CSF11

description:
DCV-/PBD3
SAMPLE 7


title: aSAH-CSF27

description:
DCV+/PBD3
SAMPLE 23


title: aSAH-CSF4

description:
DCV-/PBD7
SAMPLE 4


title: aSAH-CSF1

description:
DCV+/PBD3
SAMPLE 1


title: aSAH-CSF2

description:
DCV+/PBD7
SAMPLE 2


title: aSAH-CSF20

description:
DCV-/PBD7
SAMPLE 16


title: CUTTag_CX3CR1_5

city: Chicago

first: Weiguo

last: Cui

state: IL

address: 303 E Chicago Ave

department: Pathology

institute: Northwestern University

data_processing:
Library strategy: CUT&TAG ChIPseq
Reads were aligned to mouse reference genome mm10 using Bowtie2.
Reads were then filtered using SAMtools
Peaks were called using SEACR (version1.1) (Meers et al., 2019) with options: 0.01 non stringent.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using the bamCoverage function of deepTools.

source_name: GP33-41 tetramer+ or GP276-286 tetramer+ CD8 T cells

extract_protocol:
50000 to 100000 cells each CD8 subset were used for library construction using CUT&Tag ChIP-Seq approach (version 2) (Kaya-Okur, Wu et al. 2019) (step wise protocol can be found in https://www.protocols.io/view/bench-top-cut-amp-tag-z6hf9b6).
(Kaya-Okur et al., 2019) (step wise protocol can be found at https://www.protocols.io/view/bench-top-cut-amp-tag-z6hf9b6).

treatment_protocol: Three LCMV-specific (GP33-41 tetramer+ or GP276-286 tetramer+) CD8 subsets were sort-purified from spleen and lymph nodes of C57BL/6 mice 3-5 weeks’ post LCMV-Cl13 infection.

tag: infection

value: 3-5 weeks post LCMV-Cl13 infection

value: spleen and lymph nodes

tag: sample type

tag: transcription factor

value: BATF


title: aSAH-CSF19

description:
DCV-/PBD3
SAMPLE 15


title: CUTTag_CX3CR1_3

tag: tissue


title: CUTTag_CX3CR1_1


title: CUTTag_DN_1


title: CUTTag_DN_5


title: CUTTag_DN_2


title: CUTTag_LY108_4


title: aSAH-CSF13

description:
DCV-/PBD3
SAMPLE 9


title: CUTTag_LY108_2


title: CUTTag_LY108_1


title: aSAH-CSF3

description:
DCV-/PBD3
SAMPLE 3


title: CUTTag_igg

value: IGG


title: lncRNA Knee Osteoarthritis patients replicate2

first: Jun

last: Jing

state: Guangdong

address: 107 Riverside Road, Guangzhou, Guangdong Province 510120, China

department: Department of Rheumatology

institute: Sun Yat-sen Memorial Hospital, Sun Yat-sen University

description:
Knee Osteoarthritis patients replicate2
lncRNA and mRNA expression in Osteoarthritis Knee

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies).

source_name: Osteoarthritis Knee

label_protocol: LncRNA and mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen).

extract_protocol: Total RNA was isolated from cartilage of KOA patients and healthy volunteers using TRIzol reagent. RNA integrity was assessed by standard denaturing agarose gel electrophoresis. The RNA samples were labeled, purified and amplified. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner

treatment_protocol: The cartilage of KOA patients and healthy volunteers were collected from tibia plateau. All samples were immediately frozen in liquid nitrogen before RNA isolation.

value: cartilage


title: Allergen-treated mutant rep 2

city: Baltimore

first: Danh

middle: Cong

last: Do

state: MD

address: 5501 Hopkins Bayview Circle, 3A.4

department: Medicine

institute: Johns Hopkins University

data_processing:
RNAseq reads were aligned to the mouse reference genome GRCm 38 using STAR aligner version 2.7.2b
BAM file outputs from STAR were annotated using Partek Genomic Suite (v6.6) and the RefSeq database (RefSeq 21)
Differential analysis was performed with Cufflink 2.21
Fold induction of gene expression (average (AV) ± s.d) was calculated from RNA expression in CRE-treated WT group when compared with CRE-treated RhoA knockout group
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files including the average FPKM values of the four biological replicates

source_name: lung tissue

growth_protocol: AT2 cells were cultured in medium containing a 1:1 mixture of DMEM/F-12 supplemented with 10% FBS, 100 U/ml sodium penicillin G, and 100 µg/ml streptomycin.

extract_protocol:
total RNA was extracted using TRIzol Reagent
mRNA was enriched using oligo dT beads and then fragmented chemically by incubating at 94℃ for 8 min. cDNA was synthesized with SuperScript II. After purification using AMPure XP beads, the double-stranded cDNA was ligated to TruSeq RNA adapters followed by 15 cycles of amplification and library purification

treatment_protocol: Treated with cockroach (CRE, Greer Laboratory) allergen at 50 ug/mL for 16 h at 37'C

tag: cell type

value: alveolar type 2 cells

tag: passage

value: single passage primary cell

tag: agent

value: cockroach allergen


title: Allergen-treated mutant rep 1

tag: genotype


title: Allergen-treated wildtype rep 4

value: wildtype


title: Allergen-treated mutant rep 3


title: Allergen-treated wildtype rep 3


title: Allergen-treated mutant rep 4


title: Allergen-treated wildtype rep 2


title: lncRNA Knee Osteoarthritis patients replicate1

description:
Knee Osteoarthritis patients replicate1
lncRNA and mRNA expression in Osteoarthritis Knee


title: lncRNA healthy controls replicate1

description:
healthy controls replicate1
lncRNA and mRNA expression in healthy knee

source_name: healthy Knee


title: lncRNA Knee Osteoarthritis patients replicate3

description:
Knee Osteoarthritis patients replicate3
lncRNA and mRNA expression in Osteoarthritis Knee


title: lncRNA healthy controls replicate3

description:
healthy controls replicate3
lncRNA and mRNA expression in healthy knee


title: lncRNA healthy controls replicate2

description:
healthy controls replicate2
lncRNA and mRNA expression in healthy knee


title: tumor_2_rest_2

city: Cambridge

first: Alex

middle: S

last: Genshaft

state: Massachusetts

address: 77 Massachusetts Ave

institute: MIT

data_processing:
Illumina bcl2fastq v2.17.1.14 was used to generate .fastq files from .bcl files
Reads aligned and pre-processed according to the DropSeq Computational Protocol v2.0 (https://github.com/broadinstitute/Drop-seq)
to summarize:  1) Read 1 split into the first 12 base pairs, describing the cell barcode and 13-20th base pairs, encoding the unique molecular identifier (UMI)  2) cell barcodes, UMIs, and read 2 sequences with low base quality discarded, trimming for primer sequences or poly-T tails  3) read 2 alignd to mouse genome mm10 using STAR v2.5.2b with default parameters  4) Aligned sequences merged by cell barcode and UMI, sequences corresponding to barcodes wtih hamming edit distance 1 merged
Genome_build: mm10
Supplementary_files_format_and_content: Processed data is a tab delimited text file containing a digital gene expression matrix with the number of UMIs for each gene (rows) and cell barcode (columns)

source_name: KP tumor

growth_protocol: All studies were performed under animal protocols approved by the Harvard Medical School and Massachusetts Institute of  Technology (MIT)  Institutional Animal Care and Use Committees (IACUC).

extract_protocol: Single-cell RNA capture, barcoding, and multiplexing according to the Seq-Well method (Gierahn et al Nature Methods 2017)

tag: region

value: whole tumor

tag: tumor


title: tumor_2_rest_3


title: tumor_2_rest_1


title: tumor_1_rest_3


title: tumor_2_outer

value: healthy/tumor border


title: Botulinum toxin A-treated uterus-day8-2

city: SEONGNAM-SI

first: YOUN JUNG

last: KANG

address: 335 PANGYO-RO

department: MEDICINE

country: South Korea

institute: CHA University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: uterus

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

value: uterus

tag: treatment

value: Botulinum toxin A-treated - day8


title: Botulinum toxin A-treated uterus-day8-3


title: Botulinum toxin A-treated uterus-day8-1


title: tumor_1_outer


title: tumor_1_rest_2


title: tumor_1_rest_1


title: Botulinum toxin A-treated uterus-day3-1

value: Botulinum toxin A-treated - day3


title: Botulinum toxin A-treated uterus-day3-2


title: Allergen-treated wildtype rep 1


title: Saline-treated uterus-1

value: saline


title: Saline-treated uterus-2


title: 206_72h

city: Davis

first: Payam

last: Vahmani

address: One Shields Avenue

department: Department of Animal Science

institute: University of California Davis

data_processing:
Reads were trimmed using Trimmomatic v0.39 using default parameters and a minimum length of 36 bp.
Quality control was performed using FastQC v0.11.8. Reads were mapped to the ARS-UCD1.2 bovine genome assembly using STAR v2.7.0f with the following parameters: quantMode GeneCounts.
Read counts were obtained using featureCounts v1.6.4 with the following parameters: -s 0 -p -t exon -g gene_id -a Bos_taurus.ARS-UCD1.2.95.gtf.
Genome_build: ARS-UCD1.2
Supplementary_files_format_and_content: The file read_counts_reverse_strand.txt is a tab seperated file that contains the read counts from the reverse strand for all 35 samples.

organism: Bos taurus

source_name: Longissimus thoracis et lumborum muscle

extract_protocol:
Core muscle tissue samples from the longissimus thoracis et lumborum were collected at 5 different time points [0 h (45 min post-mortem), 6 h, 24 h, 48 h, and 72 h (drip cooler)] post-mortem from the left-side carcasses above the grading site , and immediately frozen in liquid nitrogen, and then stored at -80 °C temperature until RNA extraction. The RNA was extracted using Qiagen RNAeasy mini kit (Qiagen N.V., Valenca, CA, United States) according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using Illumina Stranded mRNA Prep protocol.

tag: sampling time point

tag: weight (kg)

value: Longissimus thoracis et lumborum muscle


title: 202_48h


title: 202_72h


title: 206_24h


title: 206_48h


title: 202_06h


title: 202_00h


title: 201_72h


title: 201_24h


title: 201_48h


title: 107_72h


title: 107_48h


title: 107_24h


title: 201_06h


title: 104_06h


title: 107_00h


title: 104_72h


title: 107_06h


title: 104_24h


title: 104_00h


title: 206_00h


title: 202_24h


title: 201_00h


title: 103_72h


title: 206_06h


title: UbxIVa-Hth-Exd.30mer1.R3

city: Merced

first: Hans

middle: Tomas

last: Rube

state: CA

address: 5200 North Lake Rd.

department: Bioengineering

institute: UC Merced

description:
synthetic DNA
SELEX-seq for Hth/Exd/Ubx
UbxIVa-Hth-Exd.30mer1.100000.tsv.gz

data_processing:
Library strategy: SELEX-seq
SELEX-seq/EpiSELEX-seq/K_D-seq: Low-quality reads were filtered out using fasts_quality_filter -Q 33 -q 20 -p 10 (FASTX toolkit 0.0.12; Hannon lab). Reads with the correct flanking identified, retained, trimmed, and the remaining variable sequence was, if needed, reverse reverse-complemented. Kinase sequencing: The deep sequencing data was processed as described previously (Shah, eLife, 2018). The paired-end reads were merged using FLASH and the adapter sequences were trimmed using the software Cutadapt. The remaining sequences were translated into amino acid codes, and sequences containing stop codons were removed.
Next count tables were generated. These enumerate the probes in each SELEX round (for SELEX-seq and EpiSELEX-seq), in the input/bound/free libraries (for K_D-seq), and in the input/modified libraries (for Kinase sequencing). Because ProBound only needs a limited number of reads, the data was randomly down-sampled to 100k reads for SELEX-seq and EpiSELEX-seq and 1M reads for K_D-seq, and binding models were learned by ProBound using the resulting tables.
Supplementary_files_format_and_content: Tab-separated files enumerating the occurrence of each probe sequence (first column) in each sequencing library (following columns). Because ProBound only needs limited data, each library was randomly downsampled to 100k reads for the SELEX-seq and EpiSELEX-seq and 1M reads for the K_D-seq.

organism: Drosophila melanogaster

source_name: in-vitro purification

extract_protocol: SELEX-seq: The Hth-Exd-Ubx SELEX experiment was carried out following previously published methods (Slattery, Cell, 2011). Briefly, after expressing and purifying the wild-type homeodomain proteins, a final concentration of ~50 nM was assembled, incubated with excess DNA (10-20 fold) for 30 minutes, and loaded onto an EMSA gel. A DNA library with 30 randomized bases was used. The TF-bound fraction was isolated from the gel, amplified, and either subjected to another round of enrichment or prepared for sequencing. An all, three rounds of enrichment were performed. After each selection round, the DNA was extracted from the gel and amplified by using Ilumina’s small RNA primer sets. Sequencing barcodes were added in a five cycle PCR step and the final library was gel-purified using a native TBE-gel before sequencing. Libraries were sequenced at the New York Genome Center using separate lanes on an Illumina HiSeq 2000 sequencing machine. EpiSELEX-seq:  ATF4 protein purification and EpiSELEX-seq experiments were performed as described previously (Kribelbauer, Cell reports, 2017). Purified CEBPg protein was kindly donated by the Lomvardas lab at the Zuckerman Institute at Columbia University. To generate randomized 5hmC or 6mA libraries, single-stranded oligos with a 16-bp randomized region were ordered from TriLink Biotechnologies, substituting i) deoxycytidine triphosphate (dCTP) with deoxy-(5hm)-cytidine triphosphate (d5hmCTP), or ii) deoxyadenosine triphosphate (dATP) with deoxy-(6m)-adenosine triphosphate (d6ATP) during the synthesis step. For double-stranding, a standard mix of deoxy-nucleotides was used, resulting in hemi-modified libraries. 5mCpG libraries were generated by enzymatic treatment with M.SssI (NEB). The library sequences consisted of constant  left (GGTAGTGGAGG-) and right (-CCAGGGAGGTGGAGTAGG) adapters flanking a library specific barcode and a 16bp randomized sequence: -TGGG-CCTGG-N16- (no modification), -GCAC-CCTGG-N16- (5mCpG), -CAGT-CCTGG-N16- (5hmC), and -AGTG-CCTGG-N16- (6mA). K_D-seq: 6xHis tagged Drosophila Distalless (Dll) protein lacking amino acids N terminal to its homeodomain was purified by standard procedures. The 10mer R0 library was generated by annealing the library oligo GTTCAGAGTTCTACAGTCCGACCTGG-10N-CCAGGACTCGGACCTGGACTAGG and the SELEX-R primer CCTAGTCCAGGTCCGAGT, followed by a Klenow mediated primer extension reaction. The SELEX procedure was largely the same as previously described (Slattery, Cell, 2011), except that a Cy5 labeled DNA probe, instead of a P32 labeled probe, was used as the marker to indicate where the bound and unbound fractions were. For each SELEX condition, 15ul of protein solution (at 2x final concentration) in dialysis buffer (20mM HEPES pH8.0, 200mM NaCl, 10% glycerol, 2mM MgCl2, 0.05% Tween-20) was made. The library mixture was made by adding desired amount of the R0 library to 6ul of 5x binding buffer (50mM Tris-HCl pH7.5, 250mM NaCl, 5mM MgCl2, 20% glycerol, 2.5mM DTT, 2.5mM EDTA, ~125ng/ul polydIdC, 100ng/ul BSA, 0.125% Tween-20), and filling to 15ul with H2O. The protein and DNA parts were mixed and incubated at room temperature for 30 to 40 minutes before loading the gel. After running the gel, gel slices corresponding to the bound and unbound fractions were cut from the gel and purified. Each purified SELEX DNA was properly diluted such that the PCR program gave good library yield for all samples. The libraries were pooled and sequenced using Illumina Nextseq 550, following standard procedures. Kinase sequencing: The degenerate peptide library contained 11-residue sequences with five randomized amino acids flanking either side of a fixed central tyrosine residue: GCTGGCCAGTCTGGCCAG-NNSNNSNNSNNSNNStatNNSNNSNNSNNSNNS-GGAGGGCAGTCTGGGCAGTCTG. These sequences were fused to the eCPX bacterial surface display scaffold (Rice, Protein Engineering, Design & Selection, 2008). This construct was inserted into the SfiI-digested pBAD33-eCPX plasmid, as described previously (Shah, eLife, 2018). Transformed DH5a cells were grown overnight in liquid culture and the plasmid DNA library was extracted and purified using a commercial midiprep kit. A phosphotyrosine monoclonal antibody, pY20, conjugated to the fluorophore, perCP-eFluor 710 (Invitrogen), was biotinylated before use in the specificity screen. The catalytic domain of the human tyrosine kinase c-Src was screened against the degenerate peptide library as described previously (Shah, eLife, 2018), with one main difference being the use of magnetic beads to isolate phosphorylated cells, rather than fluorescence-activated cell sorting. Time points were taken at 5, 20, and 60 minutes. The phosphorylated cells were isolated with Dynabeads FlowComp Flexi (Invitrogen) following the manufacturer’s protocol. In total, two populations were collected for each time point: cells that did not bind to the magnetic beads and eluted after each wash (unbound) and cells that bound to the magnetic beads and eluted after the addition of the release buffer (bound). After isolation of these two populations, the cell pellet was collected, lysed, and used as a template in a PCR reaction (Shah, eLife, 2018). The product of this PCR reaction was then used as a template for a second PCR reaction to append a unique 5’ and 3’ indices. Each sample was pooled to equal molarity and sequenced by paired-end Illumina sequencing on a MiSeq instrument.

tag: variable region length

tag: left flank

value: GTTCAGAGTTCTACAGTCCGACGATC

tag: right flank

value: CCCGGGTCGTATGCCGTCTTCTGCTTG

tag: round / concentrations


title: 103_06h


title: 103_24h


title: 103_00h


title: UbxIVa-Hth-Exd.30mer1.R1


title: UbxIVa-Hth-Exd.30mer1.R2


title: 101_72h


title: HK2 IL1beta&Empagliflozin 02

city: Innsbruck

first: Johannes

last: Leierer

address: Anichstr. 35

department: Internal Medicine IV - Nephrology

country: Austria

institute: Medical University Innsbruck

description: gene expression

hyb_protocol: Hybridization to oligonucleotide microarrays (Human GE 4x44K v2, G4845A) according to manufacturers protocol

scan_protocol: Arrays were scanned at 5 µm using an Axon Gene Pix 4000B scanner (Molecular Devices, Sunnyvale, CA) and signal intensity data extracted using Agilent Feature Extraction software (v.9.5.3.1).

data_processing: Data preprocessing consisted of (i) excluding low abundance features (intensity values < 1.5 above background signals), (ii) quantil-quantil data normalization, and (iii) summarization of identical sequence spots.

source_name: proximal tubule cell line

label_protocol: Cyanine 3 (Cy3) labelled cRNA was generated with the LowInput QuickAmp Labeling Kit (5190-2305) for hybridization to oligonucleotide microarrays (Human GE 4x44K v2, G4845A).

growth_protocol: Human kidney 2 (HK-2) cells obtained from American Type Culture Collection (Rockville, MD) were cultured in Keratinocyte–Serum-Free Medium (KSFM) containing 5,8 mmol/l glucose (i.e. normo-glycemic condition), 10% FBS, 5 ng/mL recombinant epidermal growth factor (rEGF), 0.05 mg/mL bovine pituitary extract (BPE), 100 units/mL penicillin, and 100 μg/mL streptomycin.  RPTEC/TERT1 cells obtained from Evercyte GmBH (Vienna, Austria) were propagated in DMEM-Ham's F-12 5 mmol/L glucose (1:1) medium supplemented with 5 μg/mL insulin, 5 μg/mL transferrin, 5 ng/mL sodium selenite, 10 ng/mL recombinant human EGF, 36 ng/mL hydrocortisone, 1X GlutaMAXTM, 100 units/mL penicillin and 100 μg/mL streptomycin. Cells were grown at 37°C in a humidified 5% CO2 atmosphere, and split at a 1:10 (HK2) or 1:6 (RPTEC/TERT1) ratio once a week or cultured to confluence, serum- and supplement-starved for 24 h, and then – after an additional medium change - used for experiments.

extract_protocol: After 24 hours total RNA was isolated with RNeasy Mini Kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s protocol

treatment_protocol: Stimulations with empagliflocin (500nM) and IL‑1β (10ng/ml)

value: kidney

tag: cell line

value: proximal tubule


title: RPTEC IL1beta&Empagliflozin 02

description: gene expression


title: 101_24h


title: 104_48h


title: 101_00h


title: F2 Embry.63 T CM mi 384 Mu

city: Dummerstorf

first: Siriluck

last: Ponsuksili

address: Wilhelm-stahl-allee 2

institute: FBN

description:
microRNA expression data from skeletal muscle of 63 dpc of F2 population based breed Pi and DL.
Muscle samples of foetuses (F2) derived from the F1 sows were collected and evaluated at gestational day 63. Muscle (longissimus dorsi) samples were immediately frozen in liquid nitrogen and stored at -80°C until RNA extraction.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 42C on Affymetrix GeneChip miRNA arrays. GeneChips were washed and processed to detect biotin-containing transcripts by Streptavidin-PE (Phycoerythrin) conjugate.

scan_protocol: Scanning using the GeneChip scanner 3000 were performed according to Affymetrix protocols

data_processing: Data were analysed with Expression Console and quantify by med polish

organism: Sus scrofa

source_name: Musculus longissimus dorsi tissue from 63 dpc pig

label_protocol: Biotinylated cRNA were prepared from miRNA according to FlashTag Biotin RNA Labeling Kit for Affymetrix GeneChip miRNA arrays (Genisphere, Hatfield, PA, USA) according to the manufacturer’s recommendations Affymetrix GeneChip miRNA Array protocols (Affymetrix, Santa Clara, CA, USA)

extract_protocol: Total RNA was isolated using Qiagen miReasy Mini kit TRI Reagent (Qiagen, Hilden, Germany) according to the manufacturer’s protocol for small-RNA. Then small RNA was cleaned up using the Rneasy MinElute Clean up kit  (Qiagen, Hilden, Germany).

tag: breed

value: F2 based German Landrace (DL) x Pietrain (Pi)

value: Musculus longissimus dorsi

tag: age

value: 63 days post conception (dpc)


title: F2 Embry.63 T CM mi 355 Mu

tag: tissue


title: 103_48h


title: SAM24363101 3d Ecc15 StatGFP negative-4

city: South San Francisco

first: Jason

middle: A

last: Hackney

address: 1 DNA Way

department: Department of Bioinformatics and Computational Biology

institute: Genentech, Inc.

data_processing:
Reads were aligned to the reference Drosophila genome (BDGP6), using GSNAP (version 2013-11-10) with gene models were based on the Flybase Drosophila Melanogaster Annotation Set (v6.02), and the following parameters: -M 2 -n 10 -B 2 -i 1 -N 1 -w 200000 -E 1 --pairmax-rna=200000 --clip-overlap.
Reads falling within coding sequences were counted to determine an estimate of gene expression.
Genome_build: BDGP6
Supplementary_files_format_and_content: Tab-delimited text files with count values for each sample
Supplementary_files_format_and_content: Tab-delimited text files with count values for all samples

source_name: Brain

extract_protocol:
Standard total RNA extraction using Trizol
Total RNA was quantified with Qubit RNA HS Assay Kit (Thermo Fisher Scientific) and quality was assessed using RNA ScreenTape on 4200 TapeStation (Agilent Technologies). cDNA library was generated from 2 nanograms of total RNA using Smart-Seq V4 Ultra Low Input RNA Kit (Takara cat#: 634894). 150 picograms of cDNA was used to make sequencing libraries by Nextera XT DNA Sample Preparation Kit (Illumina cat#: FC-131-1024). Libraries were quantified with Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and the average library size was determined using D1000 ScreenTape on 4200 TapeStation (Agilent Technologies).

tag: infection

value: Ecc15 4h infection

tag: statgfp

value: StatGFP negative


title: F2 Embry.63 T CM mi 376 Mu


title: F2 Embry.63 T CM mi 360 Mu


title: F2 Embry.63 T CM mi 363 Mu


title: F2 Embry.63 T CM mi 352 Mu


title: initialPool.30mer1.R0

description:
synthetic DNA
SELEX-seq for Hth/Exd/Ubx (input)


title: SAM24363100 3d Ecc15 StatGFP negative-3


title: F2 Embry.63 T CM mi 370 Mu


title: SAM24363099 3d Ecc15 StatGFP negative-2


title: F2 Embry.63 T CM mi 377 Mu


title: HK2 IL1beta&Empagliflozin 01

description: gene expression

tag: cell type


title: SAM24363097 3d Ecc15 StatGFP positive-4

value: StatGFP positive


title: SAM24363098 3d Ecc15 StatGFP negative-1


title: RPTEC IL1beta&Empagliflozin 01

description: gene expression


title: 101_48h


title: F2 Embry.63 T CM mi 338 Mu


title: F2 Embry.63 T CM mi 340 Mu


title: F2 Embry.63 T CM mi 327 Mu


title: F2 Embry.63 T CM mi 329 Mu


title: 101_06h


title: SAM24363096 3d Ecc15 StatGFP positive-3


title: SAM24363094 3d Ecc15 StatGFP positive-1


title: SAM24363093 3d Mock StatGFP negative-4

value: Mock


title: F2 Embry.63 T CM mi 324 Mu


title: F2 Embry.63 T CM mi 320 Mu


title: F2 Embry.63 T CM mi 313 Mu


title: F2 Embry.63 T CM mi 312 Mu


title: SAM24363092 3d Mock StatGFP negative-3


title: SAM24363090 3d Mock StatGFP negative-1


title: SAM24363089 3d Mock StatGFP positive-4


title: SAM24363095 3d Ecc15 StatGFP positive-2


title: SAM24363088 3d Mock StatGFP positive-3


title: F2 Embry.63 T CM mi 311 Mu


title: SAM24363086 3d Mock StatGFP positive-1


title: SAM24363087 3d Mock StatGFP positive-2


title: F2 Embry.63 T CM mi 303 Mu


title: F2 Embry.63 T CM mi 297 Mu


title: F2 Embry.63 T CM mi 307 Mu


title: F2 Embry.63 T CM mi 274 Mu


title: F2 Embry.63 T CM mi 281 Mu


title: VirE2 Non-induced + Agro 12 hours replicate 3

city: WEST LAFAYETTE

first: Shaojun

last: Xie

state: Indiana

address: 3135 Decatur Street

institute: Purdue University

description:
12 hours in control solution (B5 liquid media plus DMSO) plus A. tumefaciens strain A136 at 10^8 cfu/mL
Mock12hRep3

data_processing:
RNA was submitted to the Purdue Genomics Core Facility for sequencing after treatment with DNase I to remove any contaminating genomic DNA (Pilot Study-Replicate 1). Ribosomal RNA was depleted and cDNA libraries (stranded) were prepared from each of the samples before sequencing. Between 15 to 23 million reads were obtained for each sample (100 nucleotides per read) which were quality trimmed and mapped to the A. thaliana genome using TopHat (Trapnell et al., 2010). Differentially expressed genes were determined from the mapped (bam) files using Cuffdiff from the Cufflinks suite of programs (Trapnell et al., 2010). Custom perl scripts were used to extract genes for which fold-changes of 3 or greater occurred between the induced and non-induced control samples at their respective time points. The resulting genes were annotated by hand and separated into categories based on their Gene Ontology (GO) functions.
Second study (replicates 2 and 3): Sequence quality was assessed using FastQC (v 0.11.7) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) for all samples and quality and adapter trimming was done using TrimGalore (0.4.4) (Krueger, 2017) to remove the sequencing adapter sequences and bases with Phred33 scores less than 30. The resulting reads of length >25 bases were retained (original read length = 50 and lib type = unstranded) respectively. The quality trimmed reads were mapped against the reference genome using STAR (Dobin et al., 2013) (v 2.5.4b). STAR derived mapping results and annotation (GTF/GFF) file for reference genome were used as input for HTSeq (Anders et al., 2015) package (v 0.7.0) to obtain the read counts for each gene feature for each replicate. Counts from all replicates were merged using custom Perl scripts to generate a read count matrix for all samples.
The merged counts matrix was used for downstream differential gene expression analysis. Genes that did not have counts in all samples were removed from the count matrix and genes that had counts in some samples but not in others were changed from 0 to 1 in order to avoid having infinite values calculated for the fold change. Differential gene expression (DEG) analysis between treatment and control was carried out using ‘R’ (v 3.5.1; http://www.r-project.org/) with two different methods (DESeq2 and edgeR). Basic exploration of the read count data file such as accessing data range, library sizes, etc. was performed to ensure data quality. An edgeR object was created by combining the count's matrix, library sizes, and experimental design using the edgeR (Robinson et al., 2010) (v 3.24.3) package. Normalization factors were calculated for the count's matrix, followed by estimation of common dispersion of counts. An exact test for differences between the negative binomial distribution of counts for the two experimental conditions resulted in finding differential expression, which was then adjusted for multiple hypothesis testing. DESeq2 (Love et al., 2014) (v 1.22.2) was also used to find differentially expressed genes. Both use an estimate variance-mean test based on a model using the negative binomial distribution. The significant genes were identified by examining the adjusted p-value.
Additionally, STAR mapping (bam) files were used for analysis by the Cuffdiff from Cufflinks (v 2.2.1) (Trapnell et al., 2010) suite of programs which perform DE analysis based on FPKM values. Cuffdiff uses bam files to calculate Fragments per Kilobase of exon per Million fragments mapped (FPKM) values, from which differential gene expression between the pairwise comparisons can be ascertained. Differentially expressed gene lists detected by at least two or more methods (DESeq2, edgeR, and Cufflinks) were generated using custom Perl scripts.
Gene annotations were retrieved from BioMart databases using biomartr package in ‘R’. The "transcript_biotype", "description" attributes were extracted using mart = "plants_mart" and dataset = "athaliana_eg_gene". GO enrichment analysis was also performed using DEGs from two or more methods while using two replicates. Singular Enrichment Analysis (SEA) from agriGO (Du et al, 2010) was used to perform GO enrichment analysis (count = 5 with Fisher exact t-test with multiple testing). A GO enrichment analysis was performed using the PANTHER Classification system and online tools (http://geneontology.org/docs/go-enrichment-analysis/).
Supplementary_files_format_and_content: Count_matrix.txt

organism: Arabidopsis thaliana

source_name: Root tissue

growth_protocol: Inducible VirE2 seedlings (T3 generation) were germinated on B5 medium containing 100 mg/mL Timentin and 20 mg/mL hygromycin. The seedlings were transferred after two weeks to plates containing B5 medium lacking antibiotics. These plates were placed vertically in racks to promote root growth on the surface of the medium.

extract_protocol:
RNA was isolated from non-induced and induced roots in the presence of Agrobacterium after 0, 3, and 12 h of treatment using TriZol reagent (http://www.thermofischer.com). A total of 2 µg of total RNA was treated with Ambion DNase I (Thermo Fisher Scientific) before submitting the RNA for sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After 10 days of growth (see above), the plates were placed horizontally and B5 liquid medium containing 1 mM β-estradiol dissolved in DMSO (b-estradiol solution) or B5 plus DMSO only (control solution) with A. tumefaciens strain A136 at a concentration of 10^8 cfu/mL was pipetted onto the surface until a thin layer covered the root tissue (4-5 mL). Roots from 30 plants were cut after 0, 3, or 12 hours treatment, rinsed with sterile water, dried on a paper towel, and frozen in liquid nitrogen before RNA extraction.

tag: parental ecotype

tag: transgenic line

value: Inducible VirE2 Line 10-9 T3 generation

tag: agent

tag: time point

value: 12 hours


title: SAM24363091 3d Mock StatGFP negative-2


title: F2 Embry.63 T CM mi 283 Mu


title: VirE2 Induced + Agro 12 hours replicate 2

description:
12 hours in induction solution (B5 liquid media plus 1 µM β-estradiol) plus A. tumefaciens strain A136 at 10^8 cfu/mL
Treated12hRep2

value: induction solution (B5 liquid media plus 1 microM Beta-estradiol) plus A. tumefaciens strain A136 at 10^8 cfu/mL


title: F2 Embry.63 T CM mi 272 Mu


title: VirE2 Non-induced + Agro 12 hours replicate 2

description:
12 hours in control solution (B5 liquid media plus DMSO) plus A. tumefaciens strain A136 at 10^8 cfu/mL
Mock12hRep2


title: VirE2 Induced + Agro 12 hours replicate 3

description:
12 hours in induction solution (B5 liquid media plus 1 µM β-estradiol) plus A. tumefaciens strain A136 at 10^8 cfu/mL
Treated12hRep3


title: VirE2 Induced + Agro 12 hours replicate 1

description:
12 hours in induction solution (B5 liquid media plus 1 µM β-estradiol) plus A. tumefaciens strain A136 at 10^8 cfu/mL
Treated12hRep1


title: miRNA Knee Osteoarthritis patients replicate3

city: Guangzhou

description:
Knee Osteoarthritis patients replicate3
miRNA expression in Osteoarthritis Knee

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v14.9 software package (Agilent Technologies).

label_protocol: total miRNA from each sample was labeled with Cyanine 3-pCp under the action of T4 RNA ligase.

extract_protocol: The cartilage of KOA patients and healthy volunteers were collected from tibia plateau. All samples were immediately frozen in liquid nitrogen before RNA isolation.

value: cartilage


title: miRNA Knee Osteoarthritis patients replicate2

description:
Knee Osteoarthritis patients replicate2
miRNA expression in Osteoarthritis Knee


title: miRNA Knee Osteoarthritis patients replicate1

description:
Knee Osteoarthritis patients replicate1
miRNA expression in Osteoarthritis Knee


title: WCJLS_Input

city: shanghai

first: jiaxiang

last: zhang

state: shanghai

address: 650 Xinsongjiang Rd

department: Department of Critical Care Medicine

institute: Shanghai Jiaotong University

data_processing:
Illumina Bcl2FastQ  software used for basecalling
Adaptor and low-quality bases were trimmed with Trimmomatictools(version:0.36), and the clean reads undergone rRNA deleting through RNAcentral to get effective reads.Genomic alignment (hg19 from UCSC genome browser) was using Tophat(version:2.0.13)to get uniquely mapping reads.
MACS2(version 2.1.0.20151222) was employed to perform m6A peak calling.Then using Hommer(version:4.8)  to annotate the m6A Peaks.The nucleotides in m6A Peaks region were used for detection of the consensus  m6A motif by DREME (version:4.11.1) and MEME(version:4.11.1). Motif central enrichment was performed by  CentriMo (version:4.11.1).Differential methylation was determined by Pyicoenrich(version:2.0.7)
Genome_build: hg19
Supplementary_files_format_and_content: peak.txt：a tabular file which contains information about called peaks
Supplementary_files_format_and_content: CentriMo (version:4.11.1).Differential methylation was determined by Pyicoenrich(version:2.0.7)

source_name: fibrotic lung

extract_protocol:
50 μg RNA was isolated from human lung tissues using Trizol reagent followed by purification using RiboMinusTM Eukaryote Kit v2 (A15020, Invitrogen). Purified RNA was chemically fragmented into approximately 100 nt using Ambion RNA fragmentation regents and subjected to immunoprecipitation using m6A antibody.
library strategy: MeRIP-seq

value: lung

tag: source

value: IPF lung tissue

tag: merip antibody


title: miRNA healthy controls replicate2

description:
healthy controls replicate2
miRNA expression in healthy knee