title: HRasV12_GBM_DropSeq

extract_protocol:
Primary mouse tumors were dissected out of the mouse brain and minced finely with a pair of safety blades. The cell suspension was then added to a solution of 2 mL collagenase IV and incubated at 37 C for 20 min with mild agitation. Collagenase was neutralized following the addition of serum free media, and cell suspension was passed through a 40 uM filter. Cells were pelleted and resuspended in RBC Lysis Buffer (Sigma, 11814389001). After one minute of incubation, buffer was neutralized using PBS and cells were pelleted again using centrifugation. Cells were resuspended in 0.01% BSA and were submitted to the CCHMC Gene Expression Core for either Drop-Seq or 10x Chromium 3v3 Profiling.
Library Constructed by CCHMC Gene Expression Core using Drop-Seq protocol from Teich Lab

value: Brain Tumor

value: Boy/J

value: untreated


title: HBO treatment2

status: Public on Oct 08 2021

type: SRA

city: Beijing

first: Xuehua

last: Liu

address: 8 Gongti South Road, Chaoyang District Beijing

department: Department of Hyperbaric Oxygen

country: China

institute: Beijing Chaoyang Hospital, Capital Medical University

library_source: transcriptomic

data_processing:
illumina Hiseq 2500 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 whole genome using Hisat2（version:2.0.4）
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi A et al., Nat Methods, 2008. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Mus musculus

source_name: spinal cord

extract_protocol:
Spinal cord tissues were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. TransZol Up Plus RNA Kit（Cat#ER501-01，Trans）was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: tissue

value: spinal cord

tag: age

value: 7-9 weeks

tag: genotype

value: wild type

tag: treatment

value: HBO treatment


title: SF3B1 H698D-mut strain2 rep1

city: Shanghai

first: Zhan

last: Ding

address: FengLin 300

institute: CAS Center for Excellence in Molecular Plant Science

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality
Reads mapped to dm6 whole genome using hisat2(v2.1.0) with defeault parameters. Reference genome and gene model annotation files were downloaded from FlyBase r6.16.
FeatureCounts(v1.6.3) was used to count the reads numbers mapped to each gene.
The abundance of each gene was calculated by stringtie(v2.0).
Genome_build: dm6
Supplementary_files_format_and_content: tab-delimited text files include gene abundance values for each Sample .

molecule: polyA RNA

organism: Drosophila melanogaster

extract_protocol:
Total RNAs from larvae were isolated by TRIzol (Ambion) and treated with RNase-free DNase I (Invitrogen). For RT-PCR, cDNAs were reverse transcribed using RevertAid Reverse Transcriptase (Thermo) and amplified by Ex-Taq (TaKaRa).A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

tag: developmental stage

value: Whole Body


title: LbCR4-RNA.LbNOX.Reg.5

city: San Francisco

first: Louis

last: Ptacek

state: CA

country: USA

institute: University of California San Francisco

data_processing:
Using standard parameters, sequences were aligned to the mm10 genome with STAR (v2.5.2) and assigned to Ensembl features (GRCm38.vM12) with subread:featureCounts (v1.5.1). Analysis of differential expression was performed with standard parameters in DESeq2 (v1.24.0) after removal of genes with 0 read counts. FDR-adjusted p-value cutoff for significance was set to 0.05.
genome_build: mm10
supplementary_files_format_and_content:tab delimited text files contain non-normalized counts per gene. Generated with subread:featurecounts

source_name: Liver

extract_protocol:
RNA was isolated from 10-20mg of liver tissue using trizol reagent and purified on the Zymo Direct-Zol RNA miniprep kit. RNA quality was assessed by Bioanalyzer (Agilent). RNAs with a RNA Integrity Number (RIN) greater than 8 were used for library prep.
Libraries were constructed from 250 ng of RNA using the NEBNext RNA Ultra Directional library prep kit from NEB. Average library size and concentration were determined by Bioanalyzer and qPCR (NEBNext Library Quant kit), respectively, prior to pooling.

value: 6 months

value: Reg 1 month

tag: collection timepoint


title: HRasV12_GBM_10X_scRNAseq

city: Cincinnati

first: Qing

middle: Richard

last: Lu

email: raorr@mail.uc.edu, richard.lu@cchmc.org

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

data_processing:
RNA-seq reads in FASTQ format were first subjected to quality control to assess the need for trimming of adapter sequences or bad quality segments. The programs used in these steps were FastQC v0.11.7, Trim Galore! v0.4.2  and cutadapt v1.9.1.
The trimmed reads were aligned to the reference human genome version GRCm38/mm10 with the program STAR v2.6.1e
Aligned reads were stripped of duplicate reads with the program sambamba v0.6.8
Gene-level expression was assessed by counting features for each gene, as defined in the NCBI's RefSeq database
Read counting was done with the program featureCounts v1.6.2 from the Rsubread package
For single cell RNA-seq datasets, gene barcode matrix files were generated from fastq files using the cellranger count method.
Genome_build: mm10
Supplementary_files_format_and_content: Single cell RNA-seq datasets have counts from CellRanger
Supplementary_files_format_and_content: RNA-seq datasets have count matrices combining samples from the same experiments

source_name: Mouse Brain Tumor

extract_protocol:
Primary mouse tumors were dissected out of the mouse brain and minced finely with a pair of safety blades. The cell suspension was then added to a solution of 2 mL collagenase IV and incubated at 37 C for 20 min with mild agitation. Collagenase was neutralized following the addition of serum free media, and cell suspension was passed through a 40 uM filter. Cells were pelleted and resuspended in RBC Lysis Buffer (Sigma, 11814389001). After one minute of incubation, buffer was neutralized using PBS and cells were pelleted again using centrifugation. Cells were resuspended in 0.01% BSA and were submitted to the CCHMC Gene Expression Core for either Drop-Seq or 10x Chromium 3v3 Profiling.
Library was constructed by CCHMC Gene Expression Core using Chromium 3v3 kit

tag: cell type


title: HUVEC_siDDX24_rep1

city: Zhuhai

first: Fangbin

last: Chen

state: Guangdong

address: Meihua East Road No.52

institute: Sun Yat-sen University

data_processing:
Basecalls performed using CASAVA version 1.9.
Raw data  sequenced reads were trimmed for adaptor sequence by Trimmomatic-0.39.
Clean data RNA-seq reads were aligned to the GRCh38.p13 genome assembly by STRA version= 2.7.7a.
Counts of reads aligning to known genes were generated by featureCounts by RSEM.
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Homo sapiens

source_name: human umbilical vein endothelial cells

growth_protocol: Cells cultured in Endothelial Cell Medium (ScienCell) supplemented with 10% fetal bovine serum (FBS, ScienCell), 1% endothelial cell growth supplement (ECGS, ScienCell), and grown at 37 °C in a 5% CO2 humid atmosphere.

extract_protocol:
RNA was extracted using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: siNRA transfection with Lipofectamine 3000 following the manufacturer's instructions

value: non-brain endothelial cell

tag: transfection

value: DDX24 siRNA


title: LbCR4-RNA.LbNOX.Reg.2


title: LbCR4-RNA.LbNOX.Reg.1


title: HBO treatment1


title: SF3B1 H698D-mut strain1 rep2


title: SF3B1 H698D-mut strain1 rep3


title: HUVEC_siNC_rep1

value: control siRNA


title: cytokine&ponesimod_48h [6-HPA]

city: La Jolla

first: Yasuyuki

last: Kihara

state: California

address: 10901 N Torrey Pines Rd

institute: Sanford Burnham Prebys Medical Discovery Institute

data_processing:
Raw FASTQ files were input into the cellranger count pipeline (Cell Ranger V4.0.0, 10x Genomics) for barcode correction, alignment to the GRCh38 genome, and UMI collapsing.
gene-UMI count matrices from individual samples were normalized, clustered, and integrated in Seurat V3.1.
Genome_build: GRCh38
Supplementary_files_format_and_content: We provide the error-corrected gene-UMI count matrices that were directly ouput by Cellranger. We also provide a cell-level metadata file that contains only quality-filtered cells as well as the corresponding cell type annotations that are included in our final analysis.

source_name: human primary astrocytes (Lonza Cat# CC-2565)

growth_protocol: Cells were plated on 6 cm dishes at 500,000 cells, and stimulated with or without cytokine mixture (25 ng/mL each; TNF-a, IFN-g, IL-17, IL-1b, and IL-6) in the presence or absence of ponesimod for 24 h or 48 hrs. Cells were detached and resuspended with PBSE + BSA to obtain around 1,000 cells/µL, and the counts were confirmed by CountessTM II (Thermo Fisher Scientific).

extract_protocol:
Single-cell capture (target capture of 10,000 cells per sample) and library preparation was conducted using Chromium Single Cell 3' GEM, Library & Gel Bead Kit v3 (10x Genomics, Cat # PN-1000075) and Chromium Chip B Single Cell Kit (10X Genomics, Cat # PN-1000074) and according to manufacturer's instruction.
Single-nucleus libraries were prepared using standard Illumina protocols and were sequenced on the Illumina NovaSeq 6000 machine at GENEWIZ, Inc.

treatment_protocol: Ponesimod was delivered to cells by mixing into the culture media at 1 μM.

value: human primary astrocytes


title: SF3B1 H698R-mut strain1 rep1


title: cytokine&ponesimod_24h [5-HPA]


title: SF3B1 H698D-mut strain1 rep1


title: ponesimod_48h [4-HPA]


title: Control3

value: no injury


title: Spinal cord injury2

value: injury


title: Control2


title: cytokines_24h [2-HPA]


title: no_treatment [1-HPA]


title: LbCR4-RNA.NULL.Reg.2


title: LbCR4-RNA.LbNOX.Reg.3


title: Spinal cord injury3


title: LbCR4-RNA.NULL.Reg.4


title: cytokines_48h [3-HPA]


title: LbCR4-RNA.NULL.Reg.5


title: ChIPseq Dnmt3a LPS KO input

status: Public on Oct 07 2021

city: Boston

first: Peter

middle: Geon

last: Kim

state: MA

address: 360 Longwood Ave, Lc8202

department: Hematology/Oncology

institute: Dana Farber Cancer Institute

description: ChIP

library_source: genomic

data_processing:
For RRBS, quality control was obtained using Trim Galore v0.4.5 (Krueger, Babraham Bioinformatics). Trimmed reads were aligned to the mm10 genome database via Bismark v0.22.3 using paired-end settings, and reads from the same biological sample were merged at the time of methylation calling. Differential methylation analysis was performed using MethylKit.
For ATAC-seq, quality control was obtained using Trim Galore v0.4.5 (Krueger, Babraham Bioinformatics). Trimmed reads were aligned to the mm10 genome via bowtie2.2.9 using–very-sensitive –X2000 –no-mixed –no-discordant. Duplicates were removed using MarkDuplicates in Picard/2.8.0. ATAC shifts were performed using alignmentSieve in deepTools/3.5.0. Peaks were called using Macs2/2.1.1 using –f BAMPE –keep-dup all –B –SPMR –nomodel –p 1e-2. For biological duplicates, peaks were filtered using an Irreproducible Discovery Rate (IDR) < 0.05.
For ChIP-seq, trimmed reads were aligned to the mm10 genome via bowtie2.2.9 using– very-sensitive –X2000 –no-mixed –no-discordant. Duplicates were marked using MarkDuplicates in Picard/2.8.0. Peaks were called using Macs2/2.1.1 using –f BAMPE –B –SPMR –nomodel –p 1e-5. For each biological triplicate, peaks were filtered using ChIP-R at the default alpha of 0.05. Peaks were annotated using HOMER/4.9.
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph, bigwig

molecule: genomic DNA

source_name: macrophages

growth_protocol: BMDMs were derived from whole bone marrow cells and were cultured in DMEM with heat-inactivated 10% fetal calf serum with pen/strep/glutamine and 30ng/ml of M-CSF, changed every 3-4 days.

extract_protocol:
RRBS libraries were made from 300 ng of purified DNA using Zymo-Seq RRBS Kit according to manufacturer instructions. ATAC sequencing libraries were made according to manufacturer instructions (Active Motif). ChIP-sequencing libraries were made according to manufacturer instructions (SimpleChIP, Cell Signaling) but cells were also sheared to 100-300 bp using Covaris sonicator.
Libraries were constructed per protocol for Nextseq 550 or Novaseq SP.

treatment_protocol: On day of collection, for ATAC-seq or CHIP-seq, samples were treated with LPS 10ng/ml for 6 hours.

tag: Stage


title: ChIPseq WT LPS input

description: ChIP


title: ChIPseq Dnmt3a KO input

description: ChIP


title: Control1


title: Spinal cord injury1


title: LbCR4-RNA.NULL.Reg.3


title: ChIPseq Dnmt3a KO rep2 LPS-nfkb

description:
ChIP
chipr_D_LPS_Nfkb_optimal.bed


title: Whole blood, healthy individual, no treatment 1

type: RNA

city: Brussels

first: Frédéric

middle: A

last: HOUSSIAU

address: Avenue Hippocrate 10

department: Institut de recherche expérimentale et clinique (IREC)

country: Belgium

institute: Université catholique de Louvain

description:
Baseline sample 1
A2786_11

hyb_protocol: Following fragmentation and biotin labeling, 4.4 µg of cDNA were hybridized for 16 hours at 45C on GeneChip Human Genome U133 Plus 2.0 array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 3000.

data_processing: The data were analyzed and RMA normalized using the Affymetrix Expression Console software v.1.4.1.

label: biotin

source_name: Whole blood, no treatment

label_protocol: 100 ng total RNA was labeled using the NuGen WB Solution kit according to the manufacturer's instructions.

extract_protocol: Total RNA was extracted from PAXgene blood RNA tubes using the QIASymphony SP extraction robot from QIAGEN. The QIASymphony PAXgene blood RNA Extraction kit and PAXgene_RNA protocol were used.

treatment_protocol: Patients with SLE (185) with moderate to severe disease activity and positive interferon (IFN) gene signature were randomised to receive IFN-K or PBO intramuscular injections (on W0, W1, W4 and W12 and W24). At randomisation (D0) and W12, W24 and W36, the IFN gene signature, including the 21 IFN-regulated genes, was evaluated by Affymetrix.

tag: diagnosis

value: Healthy

value: Blood


title: ChIPseq Dnmt3a KO rep3-nfkb

description:
ChIP
chipr_D_NT_Nfkb_optimal.bed


title: LbCR4-RNA.NULL.Reg.1


title: 2m_P2_ATF3_BioRep2

first: liping

last: liu

state: Beijing

address: Yiheyuanlu 5#

institute: Peking University

data_processing:
Library strategy: CUT&TAG
Sequencing adapters and low quality reads were removed from the raw data with Trimmomatic (V0.39).
Reads aligned to mm10 with bowtie2 (V2.3.5.1).
MACS2 was used to call peaks, and DiffBind (V2.12.0) was used for filtration and feature count of peaks.
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph

growth_protocol: Fresh isolated fibroblast from 2-month-old mice cultured with high-glucose DMEM supplemented with 10% fetal serum, 1% penicillin-streptomycin and 0.01% plasmocin. When cell attained 80-90% confluence, they were passaged at 1:3 ratio in 10cm dishes.

extract_protocol:
Libraries were prepared in situ
CUT&Tag was performed with Hyperactive In-Site ChIP Library Prep Kit (Vazyme Biotech, TD902). In brief, 60,000 cells were incubated with 10 μl pre-washed ConA beads for 10 min. Primary antibody (E2F4, Proteintech, 10923-1-AP, 1:50; ATF3, abcam, ab207434, 1:50) was added and cultured for 2 hours at room temperature.As a negative control, we just simply omitted the primary antibody according to the Nature protocols (Kaya-Okur, Wu et al. 2020). After washing twice with dig-wash buffer, Secondary antibody was added and incubated at room temperature for 45 min. After washing twice with dig-wash buffer, 0.58 μl pG-Tn5 was added with 100μl dig-300 buffer. Samples were incubated at room temperature for 1 hour and then washed twice with dig-wash buffer. 300μl tagmentation buffer was added and incubated at 37 °C for 1h. The reaction was stopped with 10μl 0.5M EDTA, 3μl 10% SDS and 2.5μl 20mg/ml Proteinase K. After extraction with phenol-chloroform and ethanol precipitation, PCR was performed to amplify the libraries using 16 cycles. All libraries were sequenced by Illumina Hiseq PE150.As a negative control, we just simply omitting the primary antibody according to the Nature protocol (Kaya-Okur, Wu et al. 2020).

treatment_protocol: serial passage

value: skin

value: fibroblast

tag: passage

tag: chip antibody


title: ChIPseq Dnmt3a KO rep1 LPS-nfkb

description:
ChIP
chipr_D_LPS_Nfkb_optimal.bed


title: Wild Type rep1


title: ChIPseq WT rep3 LPS-nfkb

description:
ChIP
chipr_WT_LPS_Nfkb_optimal.bed


title: ChIPseq WT rep2 LPS-nfkb

description:
ChIP
chipr_WT_LPS_Nfkb_optimal.bed


title: ChIPseq Dnmt3a KO rep1-nfkb

description:
ChIP
chipr_D_NT_Nfkb_optimal.bed


title: ChIPseq WT rep1 LPS-nfkb

description:
ChIP
chipr_WT_LPS_Nfkb_optimal.bed


title: ChIPseq WT input

description: ChIP


title: Wild Type rep2


title: ChIPseq Dnmt3a KO rep3 LPS-Irf3

description:
ChIP
chipr_D_LPS_Irf_optimal.bed


title: ChIPseq WT rep2-nfkb

description:
ChIP
chipr_WT_NT_Nfkb_optimal.bed


title: ChIPseq Dnmt3a KO rep3 LPS-nfkb

description:
ChIP
chipr_D_LPS_Nfkb_optimal.bed


title: ChIPseq WT rep1-nfkb

description:
ChIP
chipr_WT_NT_Nfkb_optimal.bed


title: ChIPseq Dnmt3a KO rep2-nfkb

description:
ChIP
chipr_D_NT_Nfkb_optimal.bed


title: Wild Type rep3


title: ChIPseq Dnmt3a KO rep1-Irf3

description:
ChIP
chipr_D_NT_Irf_optimal.bed


title: ChIPseq Dnmt3a KO rep2-Irf3

description:
ChIP
chipr_D_NT_Irf_optimal.bed


title: ChIPseq WT rep1 LPS-Irf3

description:
ChIP
chipr_WT_LPS_Irf_optimal.bed


title: ChIPseq Dnmt3a KO rep2 LPS-Irf3

description:
ChIP
chipr_D_LPS_Irf_optimal.bed


title: ChIPseq Dnmt3a KO rep1 LPS-Irf3

description:
ChIP
chipr_D_LPS_Irf_optimal.bed


title: ChIPseq WT rep1-Irf3

description:
ChIP
chipr_WT_NT_Irf_optimal.bed


title: ATAC Dnmt3a KO rep1 LPS


title: ChIPseq WT rep3-Irf3

description:
ChIP
chipr_WT_NT_Irf_optimal.bed


title: ATAC WT rep2 LPS


title: ChIPseq WT rep2-Irf3

description:
ChIP
chipr_WT_NT_Irf_optimal.bed


title: ATAC WT rep2


title: ATAC WT rep1


title: RRBS Dnmt3a KO rep3

description: RRBS


title: RRBS Dnmt3a KO rep5

description: RRBS


title: ATAC WT rep1 LPS


title: RRBS WT rep5

description: RRBS


title: ATAC Dnmt3a KO rep1


title: RRBS WT rep1

description: RRBS


title: RRBS Dnmt3a KO rep4

description: RRBS


title: ChIPseq WT rep3-nfkb

description:
ChIP
chipr_WT_NT_Nfkb_optimal.bed


title: RNA-seq Dnmt3a KO rep1 [D_KO_BMDM_9]

data_processing:
Raw sequencing fastq files were trimmed with Trimmomatic (v0.39) with a minimum trimmed length of 36bp.
Sequencing data was mapped to mm10 database using STAR v2.7.0a.
Counts were called using featureCounts excluding multimapped reads.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: macrophages_Dnmt3a KO

extract_protocol:
Total RNA from BMDMs were isolated using the RNeasy protocol (Qiagen).
10ng of RNA was used to generate libraries using the NEBNext Ultra RNA Library Prep Kit (E7530) with Poly(A) mRNA Magnetic Isolation Module (E7490).

tag: genotype/variation

value: Dnmt3a KO

value: BMDMs (bone marrow derived macrophages)


title: RRBS Dnmt3a KO rep1

description: RRBS


title: ATAC Dnmt3a KO rep2


title: ChIPseq WT rep2 LPS-Irf3

description:
ChIP
chipr_WT_LPS_Irf_optimal.bed


title: RRBS Dnmt3a KO rep2

description: RRBS


title: RRBS WT rep4

description: RRBS


title: RRBS WT rep3

description: RRBS


title: RNA-seq WT rep2 [WT_BMDM_2]

value: WT


title: RNA-seq WT rep4 [WT_BMDM_4]


title: RNA-seq Dnmt3a KO rep4 [D_KO_BMDM_12]


title: RRBS WT rep2

description: RRBS


title: ATAC Dnmt3a KO rep2 LPS


title: WT_replicate3

city: Montpellier

first: Alexandre

last: Djiane

address: 208 rue des apothicaires

department: IRCM

country: France

institute: Inserm

data_processing:
Illumina RTA software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to dm6 whole genome using TopHat v2.0.9 (with Bowtie v2.1.0)
Raw counts per gene (union of its different exons) was performed by HTSeq-count using the union mode and stranded=reverse. We used the factors obtained by TMM (edgeR) to normalize read counts.
Differential expression was estimated using DESeq.
Genome_build: dm6
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: 3rd intar larva wing disc

extract_protocol:
60 wing imaginal discs were dissected in cold PBS and pooled. Total RNA was extracted using Trizol and genomic DNA was removed using Ambion's DNA-free kit (#AM 1906).  Illumina TruSeq Stranded mRNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: y-, w-, abxUbx-Flp / w-; Act>y+>Gal4, UAS eGFP / UAS Nicd; FRT82B tubGal80 / FRT82B

value: wing disc

value: 6 days after egg laying

tag: condition

value: Wild-type control


title: RNA-seq Dnmt3a KO rep2 [D_KO_BMDM_10]


title: LbCR4-RNA.NULL.CR.5

value: 6 months

value: CR 1 month


title: WT_replicate2


title: S_replicate3

value: w- / w-; + ; FRT82B scrib1 / Df(3R)BSC752

value: Wing discs fully mutant for scrib


title: WT_replicate1

value: y-, w-, abxUbx-Flp / w-; Act>y+>Gal4, UAS eGFP / +; FRT82B tubGal80 / FRT82B


title: S_replicate2


title: RNA-seq WT rep3 [WT_BMDM_3]


title: NS_replicate1

value: y-, w-, abxUbx-Flp / w-; Act>y+>Gal4, UAS eGFP / UAS Nicd; FRT82B tubGal80 / FRT82B scrib1

value: Overexpression of activated Notch (Nicd) and mutant for scribble (scrib1)


title: N_replicate3

value: Overexpression of activated Notch (Nicd)


title: RNA-seq WT rep1 [WT_BMDM_1]


title: N_replicate2


title: FL LMPP 4 Vec-Cre+ (control)

city: Edinburgh

first: Katrin

last: Ottersbach

address: 5 Little France Drive

department: Centre for Regenerative Medicine

country: United Kingdom

institute: University of Edinburgh

data_processing:
Raw reads were trimmed using Trimmomatic
Raw ends were aligned with Kallisto (v0.43.1) (GRCh38 for human and GRCm38 for mouse)
The Bioconductor package Tximport was used to import transcript-level abundance, estimated counts and transcript lengths (v.3.5 )
Batch correction was performed using limma
were filtered for genes with low counts across samples
Genome_build: GRCh38 for human and GRCm38 for mouse
Supplementary_files_format_and_content: raw counts and log normalised counts

source_name: Lin- Sca1+ ckit+ CD45+ B220- CD19- Flt3+ cells

extract_protocol:
cells were sorted from freshly isolated mouse tissues or previously frozen human tissues; single cell preparations were stained with cell surface markers and directly sorted into lysis buffer
SMARTer® 125 Stranded Total RNA-Seq Kit v1 and 2-Pico Input Mammalian

value: Vec-Cre+ (control)

value: foetal liver


title: FL LMPP 2 Mll-AF4+


title: FL LMPP 4 wild-type

value: wild-type


title: BM LMPP 1 wild-type

value: bone marrow

value: 8-10 weeks


title: FL LMPP 1 Vec-Cre+ (control)


title: S_replicate1


title: FL LMPP 3 wild-type


title: RNA-seq Dnmt3a KO rep3 [D_KO_BMDM_11]

value: Dnmt3a KO

value: BMDMs (bone marrow derived macrophages)


title: FL LMPP 3 Vec-Cre+ (control)


title: FL LMPP 1 Mll-AF4+


title: BM LMPP 3 wild-type


title: NS_replicate2

value: wing disc

value: 6 days after egg laying


title: NS_replicate3


title: FL LMPP 2 Vec-Cre+ (control)


title: BM LMPP 4 wild-type


title: N_replicate1

value: y-, w-, abxUbx-Flp / w-; Act>y+>Gal4, UAS eGFP / UAS Nicd; FRT82B tubGal80 / FRT82B


title: FL LMPP 3 Mll-AF4+


title: SC2

city: Houston

first: Arjun

last: Bhattacharya

state: TX

address: 1155 Pressler Street

department: Epidemiology

institute: University of Texas MD Anderson Cancer Center

data_processing:
mRNA were quantified through pseudo-alignment with salmon 1.5.2 mapped to the GENCODE Release 31 (GRCh37) reference transcriptome.
RNA-seq quantified counts (transcripts per kilobase million) were imported using tximeta and summarized to the gene-level.
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text file for normalized expression for each sample

growth_protocol: The JEG-3 choriocarcinoma cells were purchased from the American Type Culture Collection (Manassas, VA). Cells were grown in Gibco RMPI 1640, supplemented with 10% fetal bovine serum (FBS), and 1% penicillin/streptomycin at 37°C in 5% CO2. Cells were plated at 2.1 x 106 cells per 75 cm3 flask and incubated under standard conditions until achieving roughly 90% confluence.

extract_protocol:
Treated and untreated JEG-3 cells were harvested in 350µL of buffer RLT plus. Successive RNA extraction was performed using the AllPrep DNA/RNA/miRNA Universal Kit according to the manufacturer’s protocol. RNA was quantified using a NanoDrop 1000 spectrophotometer (Thermo Scientific, Waltham, MA). RNA was then converted to cDNA, the next step toward analyzing gene expression. Treated and untreated samples of JEG-3 RNA previously extracted using the AllPrep DNA/RNA/miRNA Universal Kit were submitted to the High Throughput Sequencing Facility at UNC Chapel Hill for RNA sequencing.
Total RNA samples were submitted for sequencing using the HS4000 HO platform. Samples were sequenced in duplicate, and libraries were prepped with the Kapa Stranded mRNA-Seq kit from Illumina Platforms. Sequencing was performed after all samples passed QAQC, with a paired-end read type, with a read length of 2x75.

treatment_protocol: To investigate the effects of gene silencing, we used AUMsilence FANA oligonucleotides for mRNA knockdown of EPS15 (AUM Bio Tech, Philadelphia, PA) and subsequent analysis of predicted downstream target genes SPATA13 and FAM214A. On the day of treatment, cells were seeded in a 24-well culture plate at 0.05 x 106 cells per well. Cells were plated in biological duplicate. FANA oligos were dissolved in nuclease-free water to a concentration of 500µM, added to cell culture medium to reach a final concentration of 20µM and incubated for 24 hours at 37°C in 5% CO2.

value: placenta choriocarcinoma

tag: cell line


title: FL LMPP 1 wild-type


title: A549_NC1

city: Chuo-ku

first: Yusuke

last: Yamamoto

state: Tokyo

address: 5-1-1, Tsukiji, Chuo-ku

country: Japan

institute: National cancer center research institute

description: Total RNA extracted form A549 cancer cells, and 100 ng of RNA for analysis

hyb_protocol: Gene Expression Hybridization Kit and Gene Expression Wash Pack (Agilent)

scan_protocol: Agilent SureScan G4900DA

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: NC1 transfected A549 cancer cells (negative control)

label_protocol: Low Input Quick Amp Labeling Kit (Agilent Technologies)

growth_protocol: HCT116 and A549 cell lines were cultured in  McCoy's 5A (Gibco) and DMEM medium (Nacalai tesque) supplemented with 10% heat-inactivated FBS and 1% AA at 37 °C in 5% CO2. Fibroblast lines were cultured in Dulbecco’s modified Eagle medium (DMEM; Invitrogen, CA, USA) with 10% fetal bovine serum and 100 μg/ml penicillin/streptomycin and 0.5 mM sodium pyruvate (Sigma-Aldrich, MO, USA).

extract_protocol: Total RNA was extracted using QIAzol and the miRNeasy Mini Kit (Qiagen, Hilden, Germany) according to manufacturer’s protocols. RNA was quantified using a NanoDrop-1000 spectrophotometer and a Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, Calif.).

treatment_protocol: Cancer cells (HCT116 and A549) were transfected with miR-891b or NC1 by using Dharmafect1

value: lung cancer cells

tag: state

value: Netative control


title: SC1

tag: tissue


title: HCT116_NC1

description: Total RNA extracted form HCT116 cancer cells, and 100 ng of RNA for analysis

source_name: NC1 transfected HCT116 cancer cells (negative control)

value: colorectal cancer cells


title: FL LMPP 2 wild-type

tag: age


title: KD2


title: KD1


title: A549_miR-891b

source_name: miR-891b transfected A549 cancer cells


title: CB HSC/MPP 3

source_name: CD34+ CD38- CD45RA- cells

tag: genotype

value: cord blood

value: 13-19 weeks


title: SGC7901_NC_rep 1

city: Shiyan

first: Qin

last: Shanshan

address: Renmin Road 30, Maojian District

institute: Institute of Basic Medical Sciences, School of Basic Medical Sciences, Hubei University of Medicine

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads were mapped to human genome assembly GRCh38 (ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz) using HISAT2 with default parameters.
HTSeq v0.11.2 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_26/gencode.v26.annotation.gtf.gz.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file include count and FPKM values for each Sample

growth_protocol: The human gastric cancer cell line SGC7901 was purchased from the Shanghai Cell Bank of Chinese Academy of Sciences (Shanghai, China). The cells were cultured in DMEM medium containing 10% fetal bovine serum (FBS), 100 U/mL penicillin, 100 U/mL streptomycin and 0.03% glutamine at 37 oC in 5% CO2.

extract_protocol:
Gastric cancer cells were grown in 6-well plates and transfected with NC siRNAs and the NR2F1-AS1-targeted siRNAs. After 48 hours, remove the medium and directly add 800μL Trizol into the 6-well plate to harvest samples. Total RNA was extracted using Trizol reagent (Invitrogen, USA) according to the manufacturer’s instructions. The RNA purity and concentration was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA).
A total amount of 1.5 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: The GC cells were seeded into 6-well plates and grown overnight. The next day, when the cell plating density reached 20%-30%, GC cells were transfected with NC siRNAs and the NR2F1-AS1-targeted siRNAs (final concentration, 50 nM) by Lipofectamine 2000 (Invitrogen) according to the manufacturer’s instructions. At 48 h post-transfection, cells were harvested for RNA sequencing.

value: gastric cancer cell line

value: negative control siRNA


title: FL HSC/MPP 3

value: foetal liver


title: SGC7901_NC_rep 2


title: HCT116_miR-891b

source_name: miR-891b transfected HCT116 cancer cells


title: SGC7901_NR2F1-AS1_siRNA1#1


title: CB HSC/MPP 1

value: wild-type


title: FL HSC/MPP 4


title: CB HSC/MPP 2


title: FL LMPP 3

source_name: CD34+ CD38- CD45RA+ cells


title: SGC7901_NR2F1-AS1_siRNA1#2


title: FL LMPP 2


title: Calu3 Negative Control [siNC] rep3

city: Cleveland

first: Ann

last: Harris

state: Ohio

address: 2109 Adelbert Rd Building

department: Genetics and Genome Sciences

institute: Case Western Reserve University

data_processing:
Sequences were mapped to the hg19 human genome with STAR 2.6 (https://github.com/alexdobin/STAR)
Aligned reads were assigned to genomic features with featureCounts version 1.6.3 in the Subread package (http://subread.sourceforge.net/) to estimate expression levels for each transcript.
Differential gene expression was analyzed using DEseq2 version 1.22.1 (https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html). Samples were normalized and expressed as DESEQ2 normalized counts and both a test statistic (P-value) and an adjusted P-value (q-value) were calculated.
Normalized counts were subjected to principal component analysis
Gene ontology analysis was performed using gProfiler.
Genome_build: hg19
Supplementary_files_format_and_content: Excel files include normalized count values for each Sample

source_name: Calu3 Negative Control

growth_protocol: Cells were grown in indicated medias using standard methods

extract_protocol:
Confluent Calu-3 cells were harvested for RNA extraction using TRIzol. RNA quality was confirmed by Nanodrop measurement of OD 260/280 and 260/230 ratios and stored at -80oC under ethanol. 1ug RNA was used for RNA-seq library preparation.
RNA-seq libraries were prepared using the TruSeq RNA Sample Preparation Kit v2 (Low-Throughput protocol, Illumina).

treatment_protocol: Samples were treated with negative control siRNA (D-001206-14-05, Dharmacon) or siRNA targeting KLF5 (M-006377-00-0005) each at 20 nmol using RNAiMax transfection reagent (Life Technologies)

value: Human lung adenocarcinoma cell line


title: Calu3 KLF5 KD [siKLF5] rep1

source_name: Calu3 KLF5 KD


title: Calu3 KLF5 KD [siKLF5] rep2


title: FL HSC/MPP 1


title: FL LMPP 4


title: DU16.02S0003378

city: Münster

first: Klaus

last: Schughart

address: Von-Esmarch-Str 56

department: Virology

country: Germany

institute: University Münster

data_processing:
Reads were quality checked with package FastQC (version 0.11.4,), then trimmed using Trimgalore (version 0.4.4) with default settings.
Trimmed reads were mapped to human genome annotation hg38 (ENSMBL hg38 release 91) using STAR (version 2.5.2b, (Dobin and Gingeras, 2015)) with default settings.
Mapped reads were counted using RsubRead (version 1.32.4, (Liao et al., 2019)). Reads for beta-globin were set to 1000. Raw counts were then normalized using DESeq2 (version 1.16.1, (Love et al., 2014)).
Sex was validated by gene expression for Y-specific genes and corrected if different from recorded sex. Outliers based on PCA plot (one sample) was removed.
Genome_build: ENSMBL hg38 release 91
Supplementary_files_format_and_content: txt matrix with log2 normalized values per sample.

source_name: blood

extract_protocol:
Whole blood RNA was extracted from PAX gene tubes as described in the manufacturer’s protocol (QIAGEN PreAnalytiX)
Quality and integrity of total RNA was controlled on Agilent Technologies 2100 Bioanalyzer (Agilent Technologies; Waldbronn, Germany). Library construction: Globin mRNA was depleted from total RNA using GLOBINclear Kit, human (ThermoFisher, Invitrogen). Subsequently, a strand-specific RNA sequencing library was generated using NEBNext® Ultra  II Directional RNA Library Prep Kit (New England Biolabs) according to manufacturer’s protocols.
The library was sequenced on Illumina HiSeq 4000 using HiSeq 3000/4000 SBS Kit (300 cycles) with an average of 40 million reads per RNA sample

treatment_protocol: Blood samples from patients and controls were collected and stored in PAX tubes.

tag: status

value: Dengue virus infected patient

tag: Sex

value: MALE


title: DU16.02S0003381


title: DU16.02S0003382

value: Influenza virus infected patient

value: FEMALE


title: DU16.02S0003373


title: DU16.02S0003375


title: DU16.02S0004272

value: Entero/Rhinovirus infected patient


title: DU16.02S0003377


title: FL LMPP 1


title: DU16.02S0003376


title: DU16.02S0003371


title: DU16.02S0003372


title: DU16.02S0003368


title: DU16.02S0003367


title: DU16.02S0003374


title: DU16.02S0003366

value: other respiratory RNA virus infected patient (Parainfluenza virus and Respiratory Syncytial virus)


title: DU16.02S0003369


title: DU16.02S0003358


title: DU16.02S0003360


title: DU16.02S0003362


title: DU16.02S0003364


title: DU16.02S0002967


title: DU14.03S25711


title: DU16.02S0003363


title: DU14.03S30819


title: DU14.03S31088


title: DU16.02S0003359


title: DU14.03S22993


title: DU14.03S25849

value: Metapneumovirus infected patient


title: DU16.02S0003354


title: DU14.03S19621


title: FL HSC/MPP 2


title: DU16.02S0003352


title: DU16.02S0003361


title: DU14.03S19068


title: DU14.03S24608


title: DU14.03S15598


title: DU14.03S11164

value: DNA virus infected patient (Adenovirus, Cytomegalovirus, Ebstein-Barr virus, Herpes Simplex virus)


title: DU14.03S08151


title: DU16.02S0003357


title: DU14.03S18614


title: DU14.03S10013


title: DU14.03S17495


title: DU14.03S08801


title: DU14.03S17131


title: DU14.03S08903


title: DU14.03S07907


title: Calu3 Negative Control [siNC] rep1


title: DU14.03S07495


title: DU14.03S15202


title: DU14.03S07556


title: DU14.03S04255


title: DU16.02S0003380


title: DU14.03S07771


title: BM LMPP 2 wild-type

value: bone marrow

value: 8-10 weeks


title: DU14.03S07593


title: DU14.03S08128


title: Calu3 KLF5 KD [siKLF5] rep3


title: DU14.03S07351


title: DU14.03S03418


title: DU14.03S04175


title: DU14.03S07780


title: DU14.03S03561


title: DU14.03S04104


title: DU14.03S02910


title: DU14.03S03316


title: DU14.03S04196


title: DU14.03S02866


title: DU14.03S00813


title: DU14.03S03945


title: DU14.03S03735


title: DU14.03S03009


title: DU14.03S02748


title: DU14.03S00358


title: DU16.02S0003353


title: DU14.03S00172


title: DU10.01S14247


title: DU10.01S14804


title: DU10.01S13779


title: DU14.03S03397


title: DU10.01S14343


title: DU10.01S13231


title: DU10.01S14284


title: DU10.01S12321


title: DU14.03S00506


title: DU10.01S12203


title: DU10.01S12041


title: DU10.01S11324


title: DU10.01S10657


title: DU10.01S11165


title: DU10.01S10363


title: DU10.01S10275


title: DU10.01S10106


title: DU10.01S10224


title: DU10.01S09779


title: DU10.01S10183


title: DU10.01S09709


title: DU10.01S09697


title: DU10.01S09450


title: DU10.01S09643


title: DU16.02S0003383


title: DU10.01S12479


title: DU10.01S09552


title: DU10.01S09356


title: DU10.01S09264


title: DU10.01S09096


title: DU10.01S09322


title: DU10.01S07991


title: DU10.01S07115


title: DU10.01S06791


title: DU10.01S04464


title: DU10.01S04189


title: DU10.01S05584


title: DU10.01S04155


title: DU10.01S04039


title: DU10.01S03941


title: DU10.01S03580


title: DU10.01S03944


title: DU10.01S03235


title: DU10.01S03395


title: DU10.01S03255


title: DU10.01S03084


title: DU16.02S0003370


title: DU10.01S01431


title: DU10.01S02652


title: DU10.01S02595


title: DU10.01S02888


title: DU10.01S02271


title: DU10.01S02558


title: DU10.01S01994


title: DU10.01S01044


title: DU10.01S01098


title: DU10.01S01100


title: DU09.03S94461


title: DU10.01S01353


title: DU10.01S03344


title: DU09.03S82841


title: DU09.03S93809


title: DU09.03S93650


title: DU09.03S92607


title: DU09.03S82808


title: DU09.03S82801


title: DU09.03S82766


title: DU09.03S82797


title: M cell

city: Nanjing

first: tao

middle: shen

last: tong

address: Weigang street 1st

institute: Nanjing Agricultural University

description: Single cell RNA sequencing

data_processing:
Single-cell raw fastq files were processed by 10X Chromium cell ranger pipeline v3.0.2
Genome_build: B73v4
Supplementary_files_format_and_content: H5 files for expression matrix in single cell resolution
Supplementary_files_format_and_content: Csv files for 2 componet of tsne dimension.

organism: Zea mays

source_name: Mesophyll cells

extract_protocol:
The cut pieces were immediately put into a new petri dish containing an enzymatic digestive medium (0.6 M D-Mannitol, 1.5% (w/v) cellulose (Onozuka RS), 0.75% (w/v) macerozyme (Onozuka R-10), 10 mM MES (pH 5.8), 0.1% BSA, 20 mM KCl, 10 mM CaCl2), then shaken and vacuumed for 30-60 min followed by incubation for 4 h under the dark condition on the shaker with the speed of 55 rpm at 26 ℃.10 ml W5 buffer (154 mM NaCl ,125 mM CaCl2, 5 mM KCl, 5 mM glucose, 0.03% MES (pH 5.8)) was added to dilute the digestive medium for releasing the M cells as many as possible. After filtering through the 35 µm nylon net, filtrate was pelleted by centrifuge at 80 g for 5 min, and the pellet was re-suspended in 10 ml W5 buffer. The procedures with centrifuge and resuspension in W5 buffer were repeated for 3-4 times for purification of M cells. After checking the purity of M cells under a light microscope, the purified M cell pellet was quick frozen in liquid nitrogen and stored in -80 ℃ for later use.
M cell isolation procedures were the same as those mentioned above for RNA-seq and ChIP-seq assay. Single M cells were quality controlled and collected for 10X Single-Cell RNA-seq (scRNA-seq) library preparation using 10X Genomics Single Cell system following manufacture’s instruction (10X Genomics, CA, USA). The barcoded scRNA-seq library was sequenced with the 150-bp paired-end mode using the Illumina NovaSeq platform

tag: strain

value: Mesophyll cells

value: 14 days


title: DU09.03S82762


title: Bovine IVD scRNAseq - Animal ID 8  - Disc 2

city: New York

first: Robert

last: Sebra

state: NY

address: One Gustave L. Levy Place

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
[Data Processing and Standardization]  Counts matrix was generated through 10X Genomics Cell Ranger software v5.0.0. The raw base call files were demultiplexed using Cell Ranger mkfastq pipeline to generate FASTQ files. Cellranger count pipeline was applied to the FASTQs to perform alignment against BosTaurus ARS-UCD 1.2.102 reference build, filtering, barcode counting and Unique Molecular Identifier counting. The feature-barcode matrices were analyzed through a series of open-source R platforms.
[Data Processing and Standardization]  Cells with high mitochondrial gene percentage, few unique molecular identifiers, and high total gene counts, were filtered. Data was merged, normalized, and scaled through functions on Searat.
Counts matrix generated through Cell Ranger v5.0.0
Raw base call files demultiiplexed with Cell Ranger mfastq pipeline
Cell Range count pipeline used for alignment ot BosTaurus ARC-UCD 1.2.102 reference
Feature filtering using Seurat for genes detected in less than 0.5% of the individual sample cells.
Filter cell barcodes with low Unique Molecular Identifier, sample dependent filtering
Filter cell barcodes with high total feature count, sample dependent filtering
Filter cell barcodes with high percentage mitochondrial genes, sample dependent filteirng
Supplementary_files_format_and_content: tsv.gz files are generated by Cellranger. Each contain either detected cellular barcodes or features for expression matrices.
Supplementary_files_format_and_content: mtx.gz files are the expression matrices generated by Cellranger.
Supplementary_files_format_and_content: rds files contain Seurat R objects

organism: Bos taurus

source_name: Intervertebral Disc

extract_protocol:
[Dissociation Protocol]  IVDs were surgically dissected from bovine tails to remove all fat, muscle and ligamentous tissue. Bovine tails were processed within 4 hrs of slaughter. We isolated two IVDs from two animals and one IVD from the third animal. Isolated IVDs were serially washed aseptically with 1X phosphate buffered saline (PBS, Fisher Scientific, Waltham, MA), 70% ethanol (Fisher Scientific), a wash solution of 1.5% Fungizone (Fisher Scientific) and 3% penicillin-streptomycin (PS, Fisher Scientific), then 1X PBS. Cleaned IVDs were cut into quarters and stored overnight at 4°C in MACS Tissue Storage Solution (Miltenyi Biotec, Bergish Gladbach, Germany).
[Dissociation Protocol] Quartered IVDs were minced into small pieces (~3 mm2), digested using 0.2% pronase (Fisher Scientific) for 1 hr, then digested overnight using 400 U/mL collagenase I (Fisher Scientific). Both digestion solutions were prepared using high-glucose Dulebbco’s Modified Eagle’s Medium (DMEM, Fisher Scientific) supplemented with 2% PS, and tissues were digested in a humidified incubator at 37°C and 20% O2. Resulting single-cell suspensions were concentrated to a density of 1x10^6 cells/mL in Dulbecco's PBS (Sigma Aldrich).
[Single Cell RNA Sequencing]  Cells were processed according to Chromium 3’ Gene Expression V3 Kit (10X Genomics, Pleasanton, CA) using manufacturer’s guidelines. An estimated 5,000 cells were loaded onto each channel with a targeted cell recovery of 3,000 cells/sample. This was followed by sequencing on a S1 NovaSeq chip (Illumina Inc., San Diego, CA). Qubit 3 (Fisher Scientific) and 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) were used for quality check of cDNA. The output BAM file, a binary text file containing the sequence alignment data from sequencing, was processed through 10X Genomics Cell Ranger software v3.1.0. Sequencing generated scRNA-seq data with ~20,000 2x150bp reads per cell and 14,555 total cells sequenced

tag: animal id

value: Intervertebral Disc

tag: disc id from surigcal site

tag: dead cell cleanup

value: No


title: Bovine IVD scRNAseq - Animal ID 8  - Disc 1

value: Yes


title: DU09.03S82720


title: Bovine IVD scRNAseq - Animal ID 6  - Disc 4


title: DU09.03S82691


title: DU09.03S82647


title: DU09.03S82688


title: DU09.03S82654


title: Bovine IVD scRNAseq - Animal ID 6  - Disc 3


title: DU09.03S73307


title: DU09.03S82638


title: DU09.03S82789


title: DU16.02S0003351


title: DU09.03S18143


title: DU09.03S18123


title: DU09.03S82705


title: Bovine IVD scRNAseq - Animal ID 7  - Disc 3


title: DU09.03S17784


title: DU09.03S16165


title: DU09.03S16310


title: DZP2-HGC5-HG-whole genome analysis

type: genomic

city: Hangzhou

first: Daoqiong

last: Zheng

state: Zhejiang

address: 866 Yuhangtang Road

department: Institute of Microbiology

institute: College of Life Sciences, Zhejiang University

hyb_protocol: The hybridization reactions were prepared using an Agilent Oligo aCGH/ChIP-on-Chip Hybridization kit (5188-5220) following kit instructions. Arrays were incubated for 24 hours at 62°. Following hybridization, the arrays were washed for 5 minutes in Oligo aCGH/ChIP-on-Chip Wash Buffer 1 (Agilent 5188-5221) and 1 minute in Oligo aCGH/ChIP-on-Chip Wash Buffer 2 (Agilent 5188-5222) that was pre-warmed to 37°. The arrays were then scanned at wavelengths of 635 and 532 nm using the GenePix scanner and the GenePix Pro software using settings recommended by the manufacturer.Microarrays could be re-used approximately 4-6 times by removing the hybridized labeled DNA sequences from the oligonucleotides. Microarrays and gasket slides were stripped separately in 1x stripping buffer (10 mM potassium phosphate, pH6.6). The slides were slowly heated to the boiling point in the stripping buffer for 30-45 minutes. After stripping, they were transferred to deionized water, and then slowly removed and stored in a nitrogen cabinet. The gasket slides were centrifuged at 500 rpm to remove excess liquid. Labels on microarrays were removed prior to stripping.

scan_protocol: The data generated by GenePix Pro were exported as .gpr files and analyzed with a homemade software pipeline. Probes that were flagged by the software were deleted from the analysis.

data_processing: The data generated by GenePix Pro were exported to text files and analyzed with Microsoft Excel. The 635 nm/532 nm ratio was analyzed for each oligonucleotide. The average value of the median ratios of the control probes was calculated and used to normalize the ratios of the experimental probes to a value of 1 by dividing each probe ratio by the average control probe ratio. The Whole genome arrays were completed with Agilent platform with Design ID Agilent-027438 was used. Sectored colonies were mapped using Agilent platforsm with Design IDs Agilent-031671, which contains probes specific only to chromosome IV, and Agilent-047217, which contains many probes on chromsome IV, but few probes near the telomere and centromere of all chromosomes.

organism: Saccharomyces cerevisiae

source_name: cell culture of strain DZP2-HGC5

label_protocol: DNA from these colonies was labeled with Cy5, and mixed with control DNA (DNA from the strain JSC24) labeled with Cy3. The two samples were mixed and competitively hybridized to the SNP microarrays.

growth_protocol: Yeast cells were grown at 30 degree.

extract_protocol: Genomic DNA were prepared by standard procedures (St. Charles et al., 2012)

treatment_protocol: DZP2-derived isolates were grown on both HG (3% raffinose, 0.05% galactose) and LG (3% raffinose and 0.005% galactose) plates from a single cell to a colony (roughly 25 cell divisions) for two cycles, these independent colonies were purified on HG plates. Genomic DNA from independent DZP2-derived colonies was extracted and analyzed by the whole-genome microarrays.

tag: ploidy

value: diploid strain

tag: strain background

source_name: cell culture of JSC24

value: control strain JSC24


title: DZP2-HGC6-LG-whole genome analysis

source_name: cell culture of strain DZP2-HGC6


title: DZP2-HGC4-HG-whole genome analysis

source_name: cell culture of strain DZP2-HGC4


title: DZP2-HGC3-HG-whole genome analysis

source_name: cell culture of strain DZP2-HGC3


title: DU09.03S16143


title: DU09.03S18159


title: DZP2-HGC2-HG-whole genome analysis

source_name: cell culture of strain DZP2-HGC2


title: DU09.03S15421


title: DZP2-HGC1-HG-whole genome analysis

source_name: cell culture of strain DZP2-HGC1


title: DZP2-9-LG-whole genome analysis

source_name: cell culture of strain DZP2-9


title: DU09.03S14677


title: DZP2-7-LG-whole genome analysis

source_name: cell culture of strain DZP2-7


title: DU09.03S12067


title: DU09.03S12234


title: DZP2-6-LG-whole genome analysis

source_name: cell culture of strain DZP2-6


title: DZP2-8-LG-whole genome analysis

source_name: cell culture of strain DZP2-8


title: DZP2-4-LG-whole genome analysis

source_name: cell culture of strain DZP2-4


title: DZP2-33-LG-whole genome analysis

source_name: cell culture of strain DZP2-33


title: DU09.03S11725


title: DU09.03S11356


title: DZP2-32-LG-whole genome analysis

source_name: cell culture of strain DZP2-32


title: DU09.03S14714

source_name: blood


title: DU09.02S35110


title: DZP2-30-LG-whole genome analysis

source_name: cell culture of strain DZP2-30


title: DU14.03S06868


title: DZP2-5-LG-whole genome analysis

source_name: cell culture of strain DZP2-5


title: DZP2-31-LG-whole genome analysis

source_name: cell culture of strain DZP2-31


title: DU09.03S09325


title: DZP2-25-LG-whole genome analysis

source_name: cell culture of strain DZP2-25

source_name: cell culture of JSC24


title: DZP2-3-LG-whole genome analysis

source_name: cell culture of strain DZP2-3


title: DU09.02S34056


title: Calu3 Negative Control [siNC] rep2

source_name: Calu3 Negative Control

value: Human lung adenocarcinoma cell line


title: DU09.02S31149

value: MALE


title: DU09.02S29092


title: DU09.02S29076


title: DU09.02S35120


title: DU09.03S03208


title: DU09.02S27307


title: miRNA-seq exp_1

city: Guangzhou

first: Yiyang

last: Xu

address: 74 ZHONGSHAN SECOND ROAD

institute: Sun Yat-Sen University

description: All.miRNA.mature.Counts.exp.txt.gz

data_processing:
RNA-seq: Reads filtering under criteria removing reads with 20% of the base quality lower than 13
RNA-seq: HISAT2.1.0 mapping to reference genome
RNA-seq: count counting
miRNA-seq: We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)base quality >15 b) 17bp < read length < 26bp.
miRNA-seq: Utilizing the BWA software, we mapped the clean data to miRBase 22.0 human miRNA database and GRCh38 genome.
miRNA-seq: count counting
Genome_build: GRCh38

source_name: hBMSCs

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

treatment_protocol: For osteogenic differentiation induction, hBMSCs were seeded in six-well plates at a density of 2 × 104/cm2. Each well contained 2 mL complete osteogenic-induced medium manufactured by Cyagen Biosciences. Total RNA was extracted from the BMSCs with TRIzol reagent

tag: treatment

value: day 21 of osteogenic induction

tag: tissues

value: Bone marrow


title: miRNA-seq exp_3

description: All.miRNA.mature.Counts.exp.txt.gz


title: DZP2-2-LG-whole genome analysis

source_name: cell culture of strain DZP2-2


title: DU09.02S27188


title: DZP2-19-LG-whole genome analysis

source_name: cell culture of strain DZP2-19


title: miRNA-seq exp_2

description: All.miRNA.mature.Counts.exp.txt.gz


title: DZP2-21-LG-whole genome analysis

source_name: cell culture of strain DZP2-21


title: DU09.02S25803


title: DZP2-11-LG-whole genome analysis

source_name: cell culture of strain DZP2-11


title: DZP2-23-LG-whole genome analysis

source_name: cell culture of strain DZP2-23


title: DZP2-14-LG-whole genome analysis

source_name: cell culture of strain DZP2-14


title: DZP2-12-LG-whole genome analysis

source_name: cell culture of strain DZP2-12


title: DZP2-1-LG-whole genome analysis

source_name: cell culture of strain DZP2-1


title: DZP2-10-LG-whole genome analysis

source_name: cell culture of strain DZP2-10


title: DU09.02S20393

source_name: blood


title: miRNA-seq control_2

description: All.miRNA.mature.Counts.exp.txt.gz

value: day 0 of osteogenic induction


title: miRNA-seq control_1

description: All.miRNA.mature.Counts.exp.txt.gz


title: RNA-seq exp_2

description: All.counts.exp.txt.gz


title: DU09.02S24035


title: DU09.02S25735

value: FEMALE


title: RNA-seq control_3

description: All.counts.exp.txt.gz


title: DU09.02S16995


title: DU09.02S16973


title: DU09.02S18570


title: RNA-seq exp_3

description: All.counts.exp.txt.gz


title: DU09.02S16981


title: miRNA-seq control_3

description: All.miRNA.mature.Counts.exp.txt.gz


title: RNA-seq exp_1

description: All.counts.exp.txt.gz


title: DU09.02S16961


title: DU10.01S10249

value: Influenza virus infected patient


title: RNA-seq control_2

description: All.counts.exp.txt.gz


title: DU09.02S14204


title: RNA-seq control_1

description: All.counts.exp.txt.gz


title: DU09.02S12199


title: DU09.02S12209


title: Calu-3 CEBPB ChIP-seq rep2

data_processing:
Libraries were sequenced on Illumina HiSeq2500 machines.
Data was analyzed using ENCODE (phase-3) transcription factor and histone ChIP-seq pipeline https://github.com/ENCODE-DCC/chip-seq-pipeline2
Genome_build: hg19
Supplementary_files_format_and_content: bigWig; regionPeak

source_name: Calu-3 CEBPB ChIP-seq

extract_protocol:
Cells were lysed in lysis buffer (5mM PIPES pH 8.0, 85mM KCL, 0.5% NP-40, 1x Protease Inhibitor Cocktail (Roche)). Nuclei were isolated by centrifugation, lysed in RIPA buffer (1x PBS, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, Protease Inhibitor Cocktail), and sonicated. Protein-DNA complexes were isolated with rabbit anti-KLF5 (Yang Y, et al. Cancer Biol Ther. 2005) [Calu-3 KLF5 Rep1], Santa Cruz sc-398470 [Calu-3 KLF5 Rep2, 16HBE14o- KLF5], Santa Cruz sc-7962 [Calu-3 CEBPB]
DNA ends were blunted using T4 DNA polymerase, Klenow DNA polymerase, and T4 polynucleotide kinase. Next, DNA was incubated with Klenow exo- to add 5’ adenine overhangs. Multiplex adaptors were then ligated to the ends and converted to dsDNA using 5 cycles of PCR. DNA was size-selected to contain fragments between 200 and 300bp and PCR amplified for 5 cycles. DNA was purified with 1.2x AMPure XP beads. Sequencing was performed on an Illumina Hi-Seq.

tag: cell type

value: Human bronchial epithelial cells

tag: chip antibody

value: Santa Cruz sc-7962

tag: growth media

value: DMEM + 10% FBS


title: L. interrogans mutant Man1474 with an inactivated LIMLP_10155 (perRA) gene replicate #1

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

institute: Institut Pasteur

description:
mutant perRAperRB_1 (R1)
R1_TGACCA_L002
processed data file: RvsWT.complete.txt

data_processing:
Genome_build: interrogans serovar Manilae strain UP-MMC-NIID LP, from MicroScope Platform
Supplementary_files_format_and_content: Matrix from DESeq2
Reads were cleaned of adapter sequences and low-quality sequences using cutadapt version 1.11
Bowtie version 1.2 with default parameters, was used for alignment on the reference genome (L. interrogans serovar Manilae strain UP-MMC-NIID LP, from MicroScope Platform).
Genes were counted using featureCounts version 1.4.6-p3 from Subreads package (parameters: -t CDS -g locus_tag -s 1)
Count data were analyzed using R version 3.5.1 and the Bioconductor packageDE Seq2 version 1.20.0f. The normalization and dispersion estimation were performed with DESeq2 using the default parameters and statistical tests for differential expression were performed applying the independent filtering algorithm. A generalized linear model was set in order to test for the differential expression between all conditions. For each pairwise comparison, raw p-values were adjusted for multiple testing according to the Benjamini and Hochberg (BH) procedure and genes with an adjusted p-value lower than 0.05 were considered differentially expressed.

organism: Leptospira interrogans serovar Manilae

growth_protocol: strains were kept as a -150°C frozen stock in 2.5% DMSO. WT and perRB mutant strains were propagated in hamster to recover fully virulent strains. The double perRAperRB mutant which is avirulent was kept as a -150°C frozen stock in 2.5% DMSO.

extract_protocol:
From 0.5 μg of total RNA, we depleted ribosomal RNAs using the Ribo-Zero rRNA Removal Kit (Bacteria) from Illumina. On these rRNA-depleted RNAs, the sequencing libraries were constructed using the TruSeq Stranded mRNA Sample preparation kit following the manufacturer’s instructions (Illumina). The directional libraries were controlled on Bioanalyzer DNA1000 Chips (Agilent Technologies) and concentrations measured with the Qubit® dsDNA HS Assay Kit (ThermoFisher). Sequences of 65 bases were generated on the Illumina Hiseq 2500 sequencer.
Harvested cells were resuspended in 1 ml TRIzol (ThermoFisher Scientific) and stored at -80°C. Nucleic Acids were extracted with chloroform and precipitated with isopropanol as described earlier (zavala-Alvarado et al., 2020). Contaminating genomic DNA was removed by DNAse treatment using the RNAse-free Turbo DNA-freeTM turbo kit (ThermoFisher Scientific) as described by the manufacturer. The integrity of RNAs (RIN > 8.0) was verified by the Agilent Bioanalyzer RNA NanoChips (Agilent technologies, Wilmington, DE).

treatment_protocol: All strains were grown exponentially in EMJH medium at 30°C

tag: mutation

value: Transposon insertion in the LIMLP_05620 ORF at position +265 bp and inactivation of LIMLP_10155 by allelic exchange

value: {delta}perRA perRB::KmR


title: 16HBE14o- KLF5 ChIP-seq rep1

source_name: 16HBE14o- KLF5 ChIP-seq

tag: cell line

value: Santa Cruz sc-398470


title: 16HBE14o- KLF5 ChIP-seq rep2


title: Calu-3 CEBPB ChIP-seq rep1


title: L. interrogans mutant Man1474 replicate #3

description:
mutant perRB_3 (11158-3)
11158-3_L008
processed data file: 11158vswt.complete.txt

source_name: L. interrogans mutant Man1474

tag: strain origin

value: Mutant strain propagated in hamster to ensure full virulence

value: Transposon insertion in the LIMLP_05620 ORF at position +265 bp


title: WT L. interrogans replicate #2.2

description:
WT2
WT2_ACAGTG_L002
processed data file: RvsWT.complete.txt

source_name: WT L. interrogans

value: Isolated originally from a leptospirosis patient from Filipinas. Propagated in Hamster to ensure full virulence

tag: genotype

value: WT


title: WT L. interrogans replicate #2.3

description:
WT3
WT3_CAGATC_L002
processed data file: RvsWT.complete.txt


title: L. interrogans mutant Man1474 replicate #2

description:
mutant perRB_2 (11158-2)
11158-2_L008
processed data file: 11158vswt.complete.txt


title: WT L. interrogans replicate #1.1

description:
wt1
wt1_L008
processed data file: 11158vswt.complete.txt


title: WT L. interrogans replicate #1.2

description:
wt2
wt2_L008
processed data file: 11158vswt.complete.txt


title: Calu-3 KLF5 ChIP-seq rep2

source_name: Calu-3 KLF5 ChIP-seq


title: Calu-3 KLF5 ChIP-seq rep1

value: rabbit anti-KLF5 (Yang Y, et al. Cancer Biol Ther. 2005)


title: L. interrogans mutant Man1474 replicate #1

description:
mutant perRB_1 (11158-1)
11158-1_L008
processed data file: 11158vswt.complete.txt


title: iCLIP sample using OAS1 specific antibody, mock treated, replicate 3 [OAS3-]

city: Glasgow

first: Marko

last: Noerenberg

address: Sir Michael Stoker Building

department: MRC-University of Glasgow Centre for Virus Research

institute: University of Glasgow

data_processing:
library strategy: iCLIP2
Basecalling was done on the Illumina NextSeq sequencer with the Illumina Real Time Analysis software version 2.11.3
Sequenced reads were demultiplexed and adapter trimmed.
Reads were aligned to GRCh38 and SARS-CoV-2 reference sequence using STAR with end-to-end mode.
5'-most read positions were extracted and peak-calling was performed with R/bioconductor package DEWSeq.
Genome_build: GRCh38, NC_045512.2
Supplementary_files_format_and_content: Bed file of iCLIP binding sites
Supplementary_files_format_and_content: Tab delimited file of DEWSeq enrichment analysis output

growth_protocol: AAT-OAS1p46-RNase L CRISPR Guide 5 cells were seeded in 10cm tissue culture plates with 3.5x106 cells/plate the day before infection. The following day, cells were either infected with SARS-CoV-2-CVR-GLA1 at MOI 2 in a 6 ml volume of DMEM supplemented with 2% FCS or mock treated with medium only. After 1 hour virus/mock adsorption the medium was changed to 12 ml fresh DMEM supplemented with 2% FCS. After 24 hours incubation, cells were washed with ice cold PBS and UV irradiated using 150 mJ/cm2 at 254 nm.

extract_protocol:
Cells were lysed in 1 mL lysis buffer (NaCl 100 mM, MgCl2 5 mM, Tris pH 7.5 10 mM, IGEPAL 0.5%, SDS 0.1%, Na deoxycholate 0.5%, DTT 1 mM, 0.1 mM AEBSF) and processed through an modified iCLIP2 protocol. Details can be found in "A Prenylated dsRNA Sensor Protects Against Severe COVID-19", Wickenhagen et al.
iCLIP2 (Buchbender 2020) and eCLIP (Van Nostrand 2016)

value: AAT-OAS1p46-RNase L CRISPR Guide 5

tag: infection

value: Uninfected

tag: antibody

value: OAS1 Rabbit monoclonal antibody (Clone D1W3A, Cell Signaling Technology, 14498S )


title: iCLIP sample using rabbit isotype control antibody, SARS-CoV2 infected, replicate 3 [IgG3+]

treatment_protocol: The following day, cells were either infected with SARS-CoV-2-CVR-GLA1 at MOI 2 in a 6 ml volume of DMEM supplemented with 2% FCS or mock treated with medium only. After 1 hour virus/mock adsorption the medium was changed to 12 ml fresh DMEM supplemented with 2% FCS. After 24 hours incubation, cells were washed with ice cold PBS and UV irradiated using 150 mJ/cm2 at 254 nm.

value: Infected with SARS-CoV-2-CVR-GLA1

value: rabbit isotype control antibody


title: iCLIP sample using rabbit isotype control antibody, mock treated, replicate 1 [IgG1-]


title: iCLIP sample using rabbit isotype control antibody, SARS-CoV2 infected, replicate 2 [IgG2+]


title: iCLIP sample using rabbit isotype control antibody, mock treated, replicate 2 [IgG2-]


title: WT L. interrogans replicate #1.3

description:
wt3
wt3_L008
processed data file: 11158vswt.complete.txt


title: L. interrogans mutant Man1474 with an inactivated LIMLP_10155 (perRA) gene replicate #2

description:
mutant perRAperRB_2 (R2)
R2_GCCAAT_L002
processed data file: RvsWT.complete.txt


title: L. interrogans mutant Man1474 with an inactivated LIMLP_10155 (perRA) gene replicate #3

description:
mutant perRAperRB_3 (R3)
R3_CTTGTA_L002
processed data file: RvsWT.complete.txt


title: iCLIP sample using OAS1 specific antibody, mock treated, replicate 1 [OAS1-]


title: iCLIP sample using OAS1 specific antibody, SARS-CoV2 infected, replicate 3 [OAS3+]


title: iCLIP sample using OAS1 specific antibody, SARS-CoV2 infected, replicate 2 [OAS2+]


title: iCLIP sample using OAS1 specific antibody, mock treated, replicate 2 [OAS2-]


title: WT L. interrogans replicate #2.1

description:
WT1
WT1_CGATGT_L002
processed data file: RvsWT.complete.txt


title: iCLIP sample using OAS1 specific antibody, SARS-CoV2 infected, replicate 1 [OAS1+]


title: iCLIP sample using rabbit isotype control antibody, SARS-CoV2 infected, replicate 1 [IgG1+]


title: Size matched input SARS-CoV2 infected, replicate 3 [SMI3+]

source_name: Size matched input SARS-CoV2 infected


title: Size matched input mock treated, replicate 2 [SMI2-]

source_name: Size matched input mock treated


title: Size matched input mock treated, replicate 1 [SMI1-]


title: Size matched input mock treated, replicate 3 [SMI3-]


title: Size matched input SARS-CoV2 infected, replicate 2 [SMI2+]


title: Size matched input SARS-CoV2 infected, replicate 1 [SMI1+]


title: DZP2 BIR sector-P2BIR8

source_name: cell culture of strain P2BIR8

treatment_protocol: DZP2 cells were incubated in the absence of galactose (YPD medium) for 12 hours, and then the cells were plated on HGMAB6 plates to allow sectored colony formation. After incubation at 30°C for 3 days, genomic DNA from the red/white (crossover outcomes) and white/pink (BIR outcomes) sides of independent DZP2-derived sectored colonies was separately extracted and analyzed by the SNP-specific microarrays.

value: diploid strain

tag: strain

source_name: cell culture of JSC24

value: control strain JSC24


title: Abl_RTF1_rep2

city: Durham

first: Zhong

last: Chen

state: NC

address: 905 S. LaSalle Street

department: Pathology

institute: Duke University

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie-1.0.0 with the following parameters -v 3 -k 3 -m 2. And only those reads with unique or two mapped locations are remained for further analysis.
Each mapped reads has been extended into a 300 bp fragment (presumably coinciding with library size) in a direction from 5'-3' along with chromosome axis. And the bigwig files would be made on these processed alignments.
Genome_build: hg19

source_name: prostate

growth_protocol: LNCaP-abl cells were cultured in RPMI 1640 (Invitrogen) supplemented with 10% charcoal-stripped FBS (Omega Scientific) and 1mM L-glutamine.

extract_protocol:
cells were grown to 70%-80% confluence, and crosslinked with 1% formaldehyde for 10 min at room temperature. After washing twice with cold PBS, cells were collected and resuspended in lysis buffer (1% SDS, 5 mM EDTA, 50 mM Tris (pH 8.0), 1x protease and phosphatase inhibitors). After sonication, the soluble chromatin was diluted in 1% Triton X-100, 2 mM EDTA, 150 mM NaCl, 20 mM Tris (pH 8.0), 1x protease and phosphatase inhibitors). Then samples were precleared and immunoprecipitated with the appropriate antibodies overnight at 4°C. The next day, protein A or G beads blocked with BSA were added for 2 h at 4°C, and then washed sequentially for 10 min with TSE I (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris (pH 8.0), 150 mM NaCl), TSE II (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris (pH 8.0), 500 mM NaCl), buffer III (0.25 M LiCl, 1% NP-40, 1% deoxycholate, 1 mM EDTA, 10 mM Tris (pH 8.0), and TE buffer (10 mM Tris (pH 8.0), 1mM EDTA (pH 8.0)). DNA was eluted in Elution buffer (1% SDS, 0.1M NaHCO3) at room temperatue for 30 min. The crosslinking was reversed by incubation for 16 h at 65°C. During the purification, ChIP DNA was treated with DNase-free RNase for 30 min at 37°C.
Libraries were prepared according to NEBNext ChIP-Seq Library Prep Master Mix Set (E6240L). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 10 or 14 cycles and library fragments of ~300 bp (insert plus adaptor and PCR primer sequences) were band isolated from an E-gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq2000 following the manufacturer's protocols.

treatment_protocol: Cells were treated with 300 nM FP for indicated time.

value: prostate cancer cells

tag: passages

value: LNCaP-abl

value: no treatment

tag: sirna

value: Rtf1 (Abcam, ab99362)


title: Abl_RTF1_rep4


title: Abl_RTF1_rep3


title: DZP2 BIR sector-P2BIR9

source_name: cell culture of strain P2BIR9


title: DZP2 BIR sector-P2BIR6

source_name: cell culture of strain P2BIR6


title: DZP2 BIR sector-P2BIR7

source_name: cell culture of strain P2BIR7


title: Abl_RTF1_rep1


title: DZP2 BIR sector-P2BIR5

source_name: cell culture of strain P2BIR5


title: DZP2 BIR sector-P2BIR28

source_name: cell culture of strain P2BIR28


title: DZP2 BIR sector-P2BIR27

source_name: cell culture of strain P2BIR27


title: DZP2 BIR sector-P2BIR26

source_name: cell culture of strain P2BIR26


title: DZP2 BIR sector-P2BIR30

source_name: cell culture of strain P2BIR30


title: DZP2 BIR sector-P2BIR29

source_name: cell culture of strain P2BIR29


title: DZP2 BIR sector-P2BIR25

source_name: cell culture of strain P2BIR25


title: DZP2 BIR sector-P2BIR31

source_name: cell culture of strain P2BIR31


title: DZP2 BIR sector-P2BIR22

source_name: cell culture of strain P2BIR22


title: DZP2 BIR sector-P2BIR3

source_name: cell culture of strain P2BIR3


title: DZP2 BIR sector-P2BIR32

source_name: cell culture of strain P2BIR32


title: Abl_LEO1_rep4

value: leo1 (Bethyl Laboratories, A300-175A)


title: Abl_LEO1_rep2


title: Abl_LEO1_rep3


title: DZP2 BIR sector-P2BIR23

source_name: cell culture of strain P2BIR23


title: DZP2 BIR sector-P2BIR21

source_name: cell culture of strain P2BIR21

source_name: cell culture of JSC24


title: DZP2 BIR sector-P2BIR24

source_name: cell culture of strain P2BIR24


title: DZP2 BIR sector-P2BIR4

source_name: cell culture of strain P2BIR4


title: siCon-FP-40-5095_rep4

source_name: prostate

value: flavopiridol, 300 nM, 40min

value: phosphorylated RNA pol II (Abcam, phospho S2)


title: DZP2 BIR sector-P2BIR2

source_name: cell culture of strain P2BIR2


title: Abl_LEO1_rep1


title: DZP2 BIR sector-P2BIR20

source_name: cell culture of strain P2BIR20


title: siCon-FP-30-5095_rep4

value: flavopiridol, 300 nM, 30min


title: DZP2 BIR sector-P2BIR18

source_name: cell culture of strain P2BIR18


title: DZP2 BIR sector-P2BIR16

source_name: cell culture of strain P2BIR16


title: DZP2 BIR sector-P2BIR19

source_name: cell culture of strain P2BIR19


title: siCon-FP-40-5095_rep5


title: siCon-FP-30-5095_rep3


title: siCon-FP-40-5095_rep3


title: siCon-FP-40-5095_rep2


title: siCon-FP-30-5095_rep5


title: DZP2 BIR sector-P2BIR12

source_name: cell culture of strain P2BIR12


title: siCon-FP-30-5095_rep2


title: siCon-FP-20-5095_rep5

value: flavopiridol, 300 nM, 20min


title: DZP2 BIR sector-P2BIR15

source_name: cell culture of strain P2BIR15


title: DZP2 BIR sector-P2BIR10

source_name: cell culture of strain P2BIR10


title: siCon-FP-20-5095_rep4


title: siCon-FP-20-5095_rep3


title: siCon-FP-20-5095_rep2


title: DZP2 CO sector-P2S61W

source_name: cell culture of strain P2S61W


title: siCon-FP-10-5095_rep5

value: flavopiridol, 300 nM, 10min


title: DZP2 BIR sector-P2BIR13

source_name: cell culture of strain P2BIR13


title: DZP2 CO sector-P2S6R

source_name: cell culture of strain P2S6R


title: DZP2 BIR sector-P2BIR14

source_name: cell culture of strain P2BIR14


title: DZP2 CO sector-P2S9R

source_name: cell culture of strain P2S9R


title: DZP2 CO sector-P2S58R

source_name: cell culture of strain P2S58R

source_name: cell culture of JSC24


title: DZP2 CO sector-P2S6W

source_name: cell culture of strain P2S6W


title: DZP2 BIR sector-P2BIR17

source_name: cell culture of strain P2BIR17


title: DZP2 CO sector-P2S5R

source_name: cell culture of strain P2S5R


title: DZP2 BIR sector-P2BIR11

source_name: cell culture of strain P2BIR11


title: DZP2 CO sector-P2S8R

source_name: cell culture of strain P2S8R


title: DZP2 CO sector-P2S8W

source_name: cell culture of strain P2S8W


title: DZP2 CO sector-P2S61R

source_name: cell culture of strain P2S61R


title: DZP2 CO sector-P2S60R

source_name: cell culture of strain P2S60R


title: DZP2 CO sector-P2S57R

source_name: cell culture of strain P2S57R


title: DZP2 CO sector-P2S58W

source_name: cell culture of strain P2S58W


title: siCon-FP-10-5095_rep4

source_name: prostate


title: DZP2 CO sector-P2S59R

source_name: cell culture of strain P2S59R


title: siCon-FP-10-5095_rep3


title: DZP2 CO sector-P2S60W

source_name: cell culture of strain P2S60W


title: DZP2 CO sector-P2S5W

source_name: cell culture of strain P2S5W


title: DZP2 CO sector-P2S59W

source_name: cell culture of strain P2S59W


title: DZP2 BIR sector-P2BIR1

source_name: cell culture of strain P2BIR1


title: DZP2 CO sector-P2S9W

source_name: cell culture of strain P2S9W

source_name: cell culture of JSC24


title: DZP2 CO sector-P2S55W

source_name: cell culture of strain P2S55W


title: siCon-FP-10-5095_rep2


title: DZP2 CO sector-P2S56R

source_name: cell culture of strain P2S56R


title: DZP2 CO sector-P2S57W

source_name: cell culture of strain P2S57W


title: siCon-FP-0-5095_rep3

value: flavopiridol, 300 nM, 0min


title: DZP2 CO sector-P2S56W

source_name: cell culture of strain P2S56W


title: siCon-FP-0-5095_rep5


title: siCon-FP1h-40-5095_rep5

value: flavopiridol, 300 nM, 1hr; release 40min


title: siCon-FP1h-40-5095_rep4


title: siCon-FP-0-5095_rep2


title: siCon-FP1h-40-5095_rep3


title: siCon-FP1h-40-5095_rep2


title: siCon-FP-0-5095_rep4


title: siCon-FP1h-30-5095_rep5

value: flavopiridol, 300 nM, 1hr; release 30min


title: DZP2 CO sector-P2S55R

source_name: cell culture of strain P2S55R


title: DZP2 CO sector-P2S52R

source_name: cell culture of strain P2S52R


title: DZP2 CO sector-P2S54W

source_name: cell culture of strain P2S54W


title: DZP2 CO sector-P2S51W

source_name: cell culture of strain P2S51W


title: siCon-FP1h-30-5095_rep4


title: DZP2 CO sector-P2S53W

source_name: cell culture of strain P2S53W


title: DZP2 CO sector-P2S53R

source_name: cell culture of strain P2S53R


title: DZP2 CO sector-P2S47R

source_name: cell culture of strain P2S47R


title: DZP2 CO sector-P2S52W

source_name: cell culture of strain P2S52W


title: DZP2 CO sector-P2S48R

source_name: cell culture of strain P2S48R


title: DZP2 CO sector-P2S54R

source_name: cell culture of strain P2S54R


title: DZP2 CO sector-P2S48W

source_name: cell culture of strain P2S48W


title: siCon-FP1h-30-5095_rep3

source_name: prostate


title: siCon-FP1h-30-5095_rep2


title: DZP2 CO sector-P2S49R

source_name: cell culture of strain P2S49R

source_name: cell culture of JSC24


title: DZP2 CO sector-P2S47W

source_name: cell culture of strain P2S47W


title: siCon-FP1h-20-5095_rep4

value: flavopiridol, 300 nM, 1hr; release 20min


title: siCon-FP1h-20-5095_rep3


title: DZP2 CO sector-P2S45R

source_name: cell culture of strain P2S45R


title: DZP2 CO sector-P2S50W

source_name: cell culture of strain P2S50W


title: DZP2 CO sector-P2S45W

source_name: cell culture of strain P2S45W


title: DZP2 CO sector-P2S43W

source_name: cell culture of strain P2S43W


title: DZP2 CO sector-P2S43R

source_name: cell culture of strain P2S43R


title: DZP2 CO sector-P2S49W

source_name: cell culture of strain P2S49W


title: DZP2 CO sector-P2S51R

source_name: cell culture of strain P2S51R


title: DZP2 CO sector-P2S44R

source_name: cell culture of strain P2S44R


title: DZP2 CO sector-P2S44W

source_name: cell culture of strain P2S44W


title: siCon-FP1h-10-5095_rep5

value: flavopiridol, 300 nM, 1hr; release 10min


title: DZP2 CO sector-P2S42R

source_name: cell culture of strain P2S42R

value: diploid strain


title: DZP2 CO sector-P2S50R

source_name: cell culture of strain P2S50R

value: control strain JSC24


title: DZP2 CO sector-P2S42W

source_name: cell culture of strain P2S42W


title: DZP2 CO sector-P2S46W

source_name: cell culture of strain P2S46W


title: DZP2 CO sector-P2S46R

source_name: cell culture of strain P2S46R


title: DZP2 CO sector-P2S41R

source_name: cell culture of strain P2S41R


title: siCon-FP1h-20-5095_rep2

source_name: prostate

value: prostate cancer cells


title: siCon-FP1h-20-5095_rep5

value: LNCaP-abl


title: DZP2 CO sector-P2S41W

source_name: cell culture of strain P2S41W

source_name: cell culture of JSC24


title: DZP2 CO sector-P2S39R

source_name: cell culture of strain P2S39R


title: DZP2 CO sector-P2S39W

source_name: cell culture of strain P2S39W


title: DZP2 CO sector-P2S3R

source_name: cell culture of strain P2S3R


title: DZP2 CO sector-P2S37W

source_name: cell culture of strain P2S37W


title: DZP2 CO sector-P2S3W

source_name: cell culture of strain P2S3W


title: DZP2 CO sector-P2S37R

source_name: cell culture of strain P2S37R


title: DZP2 CO sector-P2S38R

source_name: cell culture of strain P2S38R


title: DZP2 CO sector-P2S40W

source_name: cell culture of strain P2S40W


title: DZP2 CO sector-P2S40R

source_name: cell culture of strain P2S40R


title: DZP2 CO sector-P2S36R

source_name: cell culture of strain P2S36R


title: DZP2 CO sector-P2S35W

source_name: cell culture of strain P2S35W


title: siCon-FP1h-10-5095_rep4


title: DZP2 CO sector-P2S34W

source_name: cell culture of strain P2S34W


title: DZP2 CO sector-P2S38W

source_name: cell culture of strain P2S38W


title: siCon-FP1h-0-5095_rep5

value: flavopiridol, 300 nM, 1hr; release 0min


title: siCon-FP1h-0-5095_rep3


title: siCon-FP1h-10-5095_rep3


title: DZP2 CO sector-P2S36W

source_name: cell culture of strain P2S36W


title: DZP2 CO sector-P2S34R

source_name: cell culture of strain P2S34R


title: DZP2 CO sector-P2S30W

source_name: cell culture of strain P2S30W


title: DZP2 CO sector-P2S2W

source_name: cell culture of strain P2S2W

source_name: cell culture of JSC24


title: siPAF-FP1h-40-5095_rep5

source_name: prostate


title: DZP2 CO sector-P2S30R

source_name: cell culture of strain P2S30R


title: DZP2 CO sector-P2S29W

source_name: cell culture of strain P2S29W


title: DZP2 CO sector-P2S33R

source_name: cell culture of strain P2S33R


title: siCon-FP1h-0-5095_rep2


title: siPAF-FP1h-40-5095_rep3


title: DZP2 CO sector-P2S32W

source_name: cell culture of strain P2S32W


title: DZP2 CO sector-P2S33W

source_name: cell culture of strain P2S33W


title: DZP2 CO sector-P2S31W

source_name: cell culture of strain P2S31W


title: DZP2 CO sector-P2S27W

source_name: cell culture of strain P2S27W


title: DZP2 CO sector-P2S35R

source_name: cell culture of strain P2S35R


title: siCon-FP1h-10-5095_rep2


title: DZP2 CO sector-P2S26W

source_name: cell culture of strain P2S26W


title: siPAF-FP1h-30-5095_rep5


title: DZP2 CO sector-P2S32R

source_name: cell culture of strain P2S32R


title: siCon-FP1h-0-5095_rep4


title: siPAF-FP1h-30-5095_rep4


title: siPAF-FP1h-40-5095_rep4


title: DZP2 CO sector-P2S31R

source_name: cell culture of strain P2S31R


title: siPAF-FP1h-40-5095_rep2


title: siPAF-FP1h-30-5095_rep2


title: siPAF-FP1h-20-5095_rep5


title: siPAF-FP1h-30-5095_rep3


title: DZP2 CO sector-P2S2R

source_name: cell culture of strain P2S2R


title: DZP2 CO sector-P2S25W

source_name: cell culture of strain P2S25W


title: siPAF-FP1h-20-5095_rep4


title: siPAF-FP1h-20-5095_rep3


title: siPAF-FP1h-20-5095_rep2


title: DZP2 CO sector-P2S29R

source_name: cell culture of strain P2S29R


title: siPAF-FP1h-10-5095_rep4


title: siPAF-FP1h-10-5095_rep5


title: DZP2 CO sector-P2S27R

source_name: cell culture of strain P2S27R


title: DZP2 CO sector-P2S26R

source_name: cell culture of strain P2S26R

source_name: cell culture of JSC24


title: DZP2 CO sector-P2S25R

source_name: cell culture of strain P2S25R


title: DZP2 CO sector-P2S24W

source_name: cell culture of strain P2S24W


title: DZP2 CO sector-P2S20R

source_name: cell culture of strain P2S20R


title: siPAF-FP1h-10-5095_rep3

source_name: prostate


title: DZP2 CO sector-P2S23R

source_name: cell culture of strain P2S23R


title: DZP2 CO sector-P2S21R

source_name: cell culture of strain P2S21R


title: DZP2 CO sector-P2S1R

source_name: cell culture of strain P2S1R


title: DZP2 CO sector-P2S24R

source_name: cell culture of strain P2S24R


title: DZP2 CO sector-P2S20W

source_name: cell culture of strain P2S20W


title: DZP2 CO sector-P2S22R

source_name: cell culture of strain P2S22R


title: DZP2 CO sector-P2S22W

source_name: cell culture of strain P2S22W


title: DZP2 CO sector-P2S18R

source_name: cell culture of strain P2S18R


title: DZP2 CO sector-P2S21W

source_name: cell culture of strain P2S21W


title: DZP2 CO sector-P2S1W

source_name: cell culture of strain P2S1W


title: siPAF-FP1h-10-5095_rep2


title: DZP2 CO sector-P2S23W

source_name: cell culture of strain P2S23W


title: DZP2 CO sector-P2S18W

source_name: cell culture of strain P2S18W


title: DZP2 CO sector-P2S19R

source_name: cell culture of strain P2S19R

source_name: cell culture of JSC24


title: DZP2 CO sector-P2S19W

source_name: cell culture of strain P2S19W


title: DZP2 CO sector-P2S17W

source_name: cell culture of strain P2S17W


title: siPAF-FP1h-0-5095_rep5

source_name: prostate


title: DZP2 CO sector-P2S17R

source_name: cell culture of strain P2S17R


title: DZP2 CO sector-P2S16W

source_name: cell culture of strain P2S16W


title: DZP2 CO sector-P2S16R

source_name: cell culture of strain P2S16R


title: siPAF-FP1h-0-5095_rep4


title: DZP2 CO sector-P2S14W

source_name: cell culture of strain P2S14W


title: DZP2 CO sector-P2S15R

source_name: cell culture of strain P2S15R


title: siPAF-FP1h-0-5095_rep3


title: 13_Th0_r2

city: Bethesda

first: Hong-wei

last: Sun

state: MD

address: 9000 Rockville Pile

department: Office of Science & Technology

institute: NIAMS

description:
s13_Th0_r2
processed data file: RNA-seq_IL27_TGF_beta-treatment_s8-s14_fpkm_for_GEO.xls

data_processing:
The libraries were sequenced for 100 cycles (single read) using the HiSeq 2000 (Illumina). Sequence reads from each cDNA library were mapped onto the mouse genome (build mm9) using tophat 2.0.3. The obtained data were used to calculate gene expression values (fpkm) using Cufflinks 1.3.0.
Genome_build: mm9
Supplementary_files_format_and_content: Excel file with fpkm values

source_name: CD4+ T cells

extract_protocol:
total RNA was prepared from 1 million cells using the mirVana miRNA Isolation Kit (Thermo Fisher Scientific).
1 µg of total RNA was used to prepare the RNA-seq library using the TruSeq SRRNA Sample Prep Kit (Illumina, San Diego, CA, USA), according to the manufacturer’s instructions.

value: Naive CD4+ T cells (CD4+CD62LhiCD44loCD25- cells)

value: cultured in plate-bound anti-CD3 and anti-CD28 (10 μg/ml each) in combination with anti-IFN-γ, anti-IL-4 and anti-IL-2 antibody.


title: siPAF-FP1h-0-5095_rep2


title: DZP2 CO sector-P2S15W

source_name: cell culture of strain P2S15W


title: siPAF-FP-40-5095_rep5

value: flavopiridol, 300 nM, 40min


title: 11_Th17_b_r2

description:
s11_Th17_b_r2
processed data file: RNA-seq_IL27_TGF_beta-treatment_s8-s14_fpkm_for_GEO.xls

value: cultured in plate-bound anti-CD3 and anti-CD28 (10 μg/ml each) in combination with 2 ng/ml TGF-β, 20 ng/ml IL-6, anti-IFN-γ, and 10 μg/ml anti-IL-2 antibody (S4B6).


title: 10_iTreg_r2

description:
s10_iTreg_r2
processed data file: RNA-seq_IL27_TGF_beta-treatment_s8-s14_fpkm_for_GEO.xls

value: cultured in plate-bound anti-CD3 and anti-CD28 (10 μg/ml each) in combination with 20 ng/ml TGF-β, 50 U/ml IL-2, and anti-IFN-γ antibody.


title: 14_IL27_plus_TGF_beta_r2

description:
s14_IL27_plus_TGF_beta_r2
processed data file: RNA-seq_IL27_TGF_beta-treatment_s8-s14_fpkm_for_GEO.xls

value: cultured in plate-bound anti-CD3 and anti-CD28 (10 μg/ml each) in combination with 20 ng/ml IL-27, 2 ng/ml TGF-β, anti-IFN-γ, anti-IL-2, and anti-IL-4 20 ng/ml IL-27, 2 ng/ml TGF-β, anti-IFN-γ, anti-IL-2, and anti-IL-4 antibody.


title: 12_Th17_23_r2

description:
s12_Th17_23_r2
processed data file: RNA-seq_IL27_TGF_beta-treatment_s8-s14_fpkm_for_GEO.xls

value: cultured in plate-bound anti-CD3 and anti-CD28 (10 μg/ml each) in combination with 20 ng/ml IL-1β, 20 ng/ml IL-6, 50 ng/ml IL-23, anti-IFN-γ, anti-IL-2, 5 μg/ml anti-TGF-β1 (R&D Systems), and 5 μg/ml anti-TGF-β2/1.2 antibody (R&D Systems).


title: T_C_T5

city: Athens

first: Ronan

middle: Kevin

last: Carroll

state: OHIO

address: 107 Irvine Hall

department: Biological Sciences

institute: Ohio University

data_processing:
Raw data files (.fastq) were imported into the CLC Genomics Workbench software platform for analysis
Reads corresponding to ribosomal RNA were filtered out and removed
Expression values were caculated using the "RNA-Seq Analysis" function in CLC Genomics Workbench
Replicate data sets were grouped
For differential expression analysis of samples at T=0 replicate data sets were grouped and normalized using "quantile normalization"
Genome_build: The reference genome used for the analysis was based on NC_007793 and included annotations for sRNA genes (https://dx.doi.org/10.6084/m9.figshare.2061132.v1)
Supplementary_files_format_and_content: Expression values for each sample are calculated as RPKM values. For differential expression analysis of samples at T=0 the RPKM values were  normalized and the "Normalized expression values" are presented in the excel files

organism: Staphylococcus aureus

source_name: Bacterial cells, pelleted

growth_protocol: Strains were grown in TSB medium at 37°C with shaking

extract_protocol:
Total bacterial RNA was isolated utilizing the Qiagen RNeasy mini kit and contaminating DNA was removed by treatment with Ambion DNA-free; total RNA, rRNA-depleted
Library construction was performed using the Illumina TruSeq Stranded mRNA Sample Prep Kit

treatment_protocol: Samples were snap frozen in liquid nitrogen and stored at -80°C prior to RNA extraction

tag: growth medium

value: TSB

tag: temperature

tag: exposed to

value: rifampicin

tag: time

value: 10 min


title: siPAF-FP-30-5095_rep5

tag: treatment

value: flavopiridol, 300 nM, 30min

value: phosphorylated RNA pol II (Abcam, phospho S2)


title: siPAF-FP-40-5095_rep2

tag: cell type


title: DZP2 CO sector-P2S12W

source_name: cell culture of strain P2S12W

tag: ploidy

value: diploid strain

tag: strain background


title: siPAF-FP-40-5095_rep3

tag: chip antibody


title: 9_Th2_r2

description:
s9_Th2_r2
processed data file: RNA-seq_IL27_TGF_beta-treatment_s8-s14_fpkm_for_GEO.xls

value: cultured in plate-bound anti-CD3 and anti-CD28 (10 μg/ml each) in combination with 20 ng/ml IL-4 and 10 μg/ml anti-IFN-γ antibody (XMG1.2).


title: T_C_T2_5


title: T_C_T10


title: DZP2 CO sector-P2S10W

source_name: cell culture of strain P2S10W

value: control strain JSC24


title: DZP2 CO sector-P2S12R

source_name: cell culture of strain P2S12R


title: DZP2 CO sector-P2S13W

source_name: cell culture of strain P2S13W


title: siPAF-FP-30-5095_rep4

value: prostate cancer cells

tag: cell line

value: LNCaP-abl


title: 8_Th1_r2

description:
s8_Th1_r2
processed data file: RNA-seq_IL27_TGF_beta-treatment_s8-s14_fpkm_for_GEO.xls

value: Naive CD4+ T cells (CD4+CD62LhiCD44loCD25- cells)

value: cultured in plate-bound anti-CD3 and anti-CD28 (10 μg/ml each) in combination with 20 ng/ml IL-12 and 10 μg/ml anti-IL-4 antibody (11B.11).


title: T_C_T0

value: wild-type


title: T_B_T10


title: siPAF-FP-40-5095_rep4

value: flavopiridol, 300 nM, 40min


title: DZP2 CO sector-P2S14R

source_name: cell culture of strain P2S14R


title: 7_IL27_plus_TGF_beta_r1

description:
s7_IL27_plus_TGF_beta_r1
processed data file: RNA-seq_IL27_TGF_beta-treatment_s1-s7_fpkm_for_GEO.xls


title: T_B_T5


title: siPAF-FP-30-5095_rep2


title: siPAF-FP-30-5095_rep3


title: DZP2 CO sector-P2S13R

source_name: cell culture of strain P2S13R

source_name: cell culture of JSC24


title: DZP2 CO sector-P2S10R

source_name: cell culture of strain P2S10R


title: siPAF-FP-20-5095_rep5

source_name: prostate

value: flavopiridol, 300 nM, 20min


title: T_A_T10

value: 5 min


title: T_A_T2_5


title: siPAF-FP-20-5095_rep2


title: 5_Th17_23_r1

description:
s5_Th17_23_r1
processed data file: RNA-seq_IL27_TGF_beta-treatment_s1-s7_fpkm_for_GEO.xls

value: cultured in plate-bound anti-CD3 and anti-CD28 (10 μg/ml each) in combination with 20 ng/ml IL-1β, 20 ng/ml IL-6, 50 ng/ml IL-23, anti-IFN-γ, anti-IL-2, 5 μg/ml anti-TGF-β1 (R&D Systems), and 5 μg/ml anti-TGF-β2/1.2 antibody (R&D Systems).


title: T_B_T0

value: TSB


title: 6_Th0_r1

description:
s6_Th0_r1
processed data file: RNA-seq_IL27_TGF_beta-treatment_s1-s7_fpkm_for_GEO.xls

value: cultured in plate-bound anti-CD3 and anti-CD28 (10 μg/ml each) in combination with anti-IFN-γ, anti-IL-4 and anti-IL-2 antibody.


title: siPAF-FP-20-5095_rep3


title: T_A_T0

value: rifampicin


title: WT_C_T10

value: 2.5 min


title: siPAF-FP-20-5095_rep4

value: phosphorylated RNA pol II (Abcam, phospho S2)


title: siPAF-FP-10-5095_rep3

value: flavopiridol, 300 nM, 10min


title: 3_iTreg_r1

description:
s3_iTreg_r1
processed data file: RNA-seq_IL27_TGF_beta-treatment_s1-s7_fpkm_for_GEO.xls

value: cultured in plate-bound anti-CD3 and anti-CD28 (10 μg/ml each) in combination with 20 ng/ml TGF-β, 50 U/ml IL-2, and anti-IFN-γ antibody.


title: WT_C_T5


title: siPAF-FP-10-5095_rep2


title: 1_Th1_r1

description:
s1_Th1_r1
processed data file: RNA-seq_IL27_TGF_beta-treatment_s1-s7_fpkm_for_GEO.xls


title: T_A_T5


title: 4_Th17_b_r1

description:
s4_Th17_b_r1
processed data file: RNA-seq_IL27_TGF_beta-treatment_s1-s7_fpkm_for_GEO.xls

value: cultured in plate-bound anti-CD3 and anti-CD28 (10 μg/ml each) in combination with 2 ng/ml TGF-β, 20 ng/ml IL-6, anti-IFN-γ, and 10 μg/ml anti-IL-2 antibody (S4B6).


title: siPAF-FP-0-5095_rep5

value: prostate cancer cells

value: flavopiridol, 300 nM, 0min


title: T_B_T2_5


title: WT_C_T2_5


title: siPAF-FP-10-5095_rep5

value: LNCaP-abl


title: siPAF-FP-10-5095_rep4


title: siPAF-FP-0-5095_rep4


title: 2_Th2_r1

description:
s2_Th2_r1
processed data file: RNA-seq_IL27_TGF_beta-treatment_s1-s7_fpkm_for_GEO.xls

value: Naive CD4+ T cells (CD4+CD62LhiCD44loCD25- cells)

value: cultured in plate-bound anti-CD3 and anti-CD28 (10 μg/ml each) in combination with 20 ng/ml IL-4 and 10 μg/ml anti-IFN-γ antibody (XMG1.2).


title: WT_C_T0

value: wild-type


title: NIH 3T3, RSL-1, biological rep1

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description: Cells harvested after RSL1 treatment

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 4, from SAS. Gene expression profiling was performed using arrays of Mouse430_2-type from Affymetrix. A Custom CDF Version 10 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

source_name: NIH 3T3 cells treated with 200 nM RSL-1 and harvested 24 and harvested after 24hrs

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: 7500/cm2 of NIH 3T3 cells were seeded on 14.5 cm petri dish and cultivated overnight in DMEM containing 4.5 g/l glucose (Gibco, Carlsbad, CA, USA) supplemented with 10% foetal bovine serum (Sigma Aldrich, St. Louis, MO, USA), 5% penicillin/streptomycin sulfate (Gibco, Carlsbad, CA, USA), G418 (500 mg/ml; Roche Applied Science, Penzberg, Germany) and hygromycin (500 mg/ml; Merck, Darmstadt, Germany). Cells were kept at 37°C under 5% CO2 atmosphere and 95% humidity.

extract_protocol: Trizol extraction (Thermo Fisher Scientific, Waltham, MA, USA) of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: NIH 3T3 cells were treated with 200 nM RheoSwitch Ligand (RSL-1) purchased from New England Biolabs (Ipswich, MA, USA). Cells were harvested 24 hours after the RSL-1 treatment.


title: siPAF-FP-0-5095_rep3


title: NIH 3T3, RSL-1, biological rep3

description: Cells harvested after RSL1 treatment


title: WT_B_T5


title: WT_B_T2_5

value: 0 min


title: WT_B_T10


title: siPAF-FP-0-5095_rep2


title: siCon-FP1h-40-PAF_rep4

value: flavopiridol, 300 nM, 1hr; release 40min

value: PAF1 (Abcam, ab20662)


title: siCon-FP1h-40-PAF_rep5


title: NIH 3T3-RheoSwitch-Ier2, RSL-1, biological rep3

description: Cells harvested after RSL1 treatment

source_name: NIH 3T3-RheoSwitch-Ier2 cells treated with 200 nM RSL-1, and harvested after 24hrs


title: siCon-FP1h-40-PAF_rep3


title: NIH 3T3, DMSO, biological rep2

description: Cells harvested after DMSO treatment

source_name: NIH 3T3 cells treated with corresponding volume of DMSO and harvested after 24hrs

value: DSMO


title: siCon-FP1h-30-PAF_rep5

value: flavopiridol, 300 nM, 1hr; release 30min


title: WT_A_T10

value: TSB

value: rifampicin


title: siCon-FP1h-40-PAF_rep2


title: WT_A_T0


title: NIH 3T3, DMSO, biological rep3

description: Cells harvested after DMSO treatment


title: Fibroblast_F1_PladB2

city: Shenzhen

first: Lei

last: Li

state: --- Select a state ---

address: China

department: Institute of Systems and Physical Biology

institute: Shenzhen Bay Laboratory

description:
PladB_vs_DMSO.total.RI.MATS.JC.txt
DMSO.allelic.SE.MATS.JC.txt

data_processing:
Sequenced reads from cortex, heart, and kidney were trimmed from 3' end into 76 bp, and all reads are aligned to reference genome mm10 and reference genome of SPRET/EiJ (http://www.sanger.ac.uk/) separately by HISAT2 (version 2.0.1) with parameters -p 12 -k 2 --reorder –no-softclip
Reads were assigned to the genome with less mapping edit distance. The reads with equal mapping distance to both genomes were designated as common reads.
Genomic alignment coordinates of the reads that were assigned to SPRET/EiJ were then converted to the corresponding locations in the C57BL/6J reference genome using the g2gtools software (version 0.1.29)
Alternative splicing detection and differential analysis between alleles were performed by rMATS with unambiguously assigned reads only
Alternative splicing detection and differential analysis between union reads (unambiguously assigned allelic reads plus common reads) and unambigously assigned reads were performed by rMATS
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files generated by rMATS include PSI value of each event for the two alleles in each sample
Supplementary_files_format_and_content: tab-delimited text files generated by rMATS include PSI value of each event for the total in each sample

organism:
Mus musculus
Mus spretus

source_name: Fibroblast

growth_protocol: The embryonic stem cells (ES cells) were cultured in Neuralbasal-DMEM/F12 (Gibco) with N2B27 (Invitrogen), 2i (Selleck), LIF (Millipore). The mouse fibroblast cells were cultured in DMEM containing 10% FBS and 1% P/S.

extract_protocol:
Mice were sacrificed at the age of eight weeks, and tissues were dissected and stored in -80°C before RNA extraction. Total RNA was extracted from all tissues and cells using TRIzol reagent according to the manufacturer’s protocol (Life Technologies).
mRNA libraries were prepared using standard Illumina protocols for strand-specific sequencing

treatment_protocol: For perturbing splicing machinery in fibroblast, Pladienolide B (#16538, Cayman) was prepared in DMSO at 0.1 mM, and used to treat fibroblast cells at 0.1 µM for 4 hours. Control fibroblast cells were treated with same amount of DMSO for 4 hours.

value: C57BL/6J x SPRET/EiJ

tag: tissue

value: Fibroblast

value: treated with Pladienolide B at 0.1 microM for four hours


title: siCon-FP1h-30-PAF_rep4


title: WT_B_T0

tag: genotype


title: NIH 3T3, RSL-1, biological rep2

description: Cells harvested after RSL1 treatment


title: NIH 3T3, DMSO, biological rep1

description: Cells harvested after DMSO treatment


title: WT_A_T2_5


title: siCon-FP1h-30-PAF_rep3