title: L428_H2A.B_rep2 (CUT&RUN)

description:
L428_H2A.B_rep2 (CUT&RUN)
L428_H2AB_q20_nodup_spikeins_norm.bw

data_processing:
Library strategy: CUT&RUN
The CUT&RUN samples were mapped to the Homo sapiens (hg38) genome assembly using Bowtie2 with the default parameters, after the adaptor trimming by Trimmomatic. The high quality and uniquely mapped reads with a mapping quality MAPQ > 20 were used for further analysis. We obtained the spike-in reads by mapping the reads to the Drosophila melanogaster (dm6) genome assembly. We generated coverage tracks for CUT&RUN samples, which were normalized to spike-ins.
The ATAC-seq samples in two biological replicates in two cell lines were mapped to the Homo sapiens (hg38) genome assembly using Bowtie2 with default parameters after adaptor trimming by Trimmomatic. The high quality and uniquely mapped reads (MAPQ > 20) and the reads filtered for PCR-duplicates by Picard were used for further analysis.
After trimming the adaptor sequences using Trimmomatic, the RNA-seq samples in three replicates from the wild type and H2A.B mutant in two cell lines, L1236 and L428, were mapped to the Homo sapiens (hg38) genome assembly using HISAT2. Gene annotation was obtained from the UCSC hg38 gene annotation in iGenomes. The sequencing reads were assigned to genes by featureCounts in Rsubread package in Bioconductor.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig for coverage and RNA-seq counts for all genes

source_name: L428 cell line

growth_protocol: The L1236 and L428 cell lines were routinely cultured in RPMI-1640 growth medium supplemented with 10% heat-inactivated foetal bovine serum (HI-FBS), 1% L-glutamine (200 mM stock), and 1% Penicillin-Streptomycin (10,000 units penicillin and 10 mg streptomycin/mL stock). Cells were cultured in T75 flasks and maintained in a humidified cell culture incubator at 37 ˚C and 5% CO2.

extract_protocol:
The targeted DNA fragments were isolated and purified following the CUT&RUN protocol developed in Henikoff lab (Skene et al. 2018). Drosophila spike-in DNA was added to each sample for normaliztion.
The sequencing libraries were prepared using NEBNext Ultra II DNA library prep kit for Illumina following the kit manual with modification. During the PCR amplification step, 12 PCR cycles were performed, with a combined annealing and extension step for 10 s, to minimize the large DNA fragments

value: pan- H2A.B (Home-made)

tag: spike-in organism

value: Drosophila melanogaster


title: SCCOHT, UGS649

status: Public on Jun 02 2021

type: genomic

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

country: France

institute: Institut Curie

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human EPIC Beadchip using Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
RnBeads Bioconductor R package (version 1.6.1)
matrix processed value definition: beta-value

label: cy3, cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Fresh frozen sample

label_protocol: Illumina Protocol

extract_protocol: Illumina Protocol

tag: gender

value: Female

tag: sample type

value: SCCOHT

tag: disease state

value: tumour


title: L1236-shNTC-day5_rep2 (RNA-seq)

type: SRA

city: CANBERRA

first: Jiayu

last: Wen

state: ACT

address: 133 Garran Rd

department: Department of Genome Science

country: Australia

institute: John Curtin School of Medical Research, The Australian National University

description:
L1236-shNTC-day5_rep2 (RNA-seq)
L1236_RNAseq_counts.xlsx

library_source: transcriptomic

data_processing:
The CUT&RUN samples were mapped to the Homo sapiens (hg38) genome assembly using Bowtie2 with the default parameters, after the adaptor trimming by Trimmomatic. The high quality and uniquely mapped reads with a mapping quality MAPQ > 20 were used for further analysis. We obtained the spike-in reads by mapping the reads to the Drosophila melanogaster (dm6) genome assembly. We generated coverage tracks for CUT&RUN samples, which were normalized to spike-ins.
The ATAC-seq samples in two biological replicates in two cell lines were mapped to the Homo sapiens (hg38) genome assembly using Bowtie2 with default parameters after adaptor trimming by Trimmomatic. The high quality and uniquely mapped reads (MAPQ > 20) and the reads filtered for PCR-duplicates by Picard were used for further analysis.
After trimming the adaptor sequences using Trimmomatic, the RNA-seq samples in three replicates from the wild type and H2A.B mutant in two cell lines, L1236 and L428, were mapped to the Homo sapiens (hg38) genome assembly using HISAT2. Gene annotation was obtained from the UCSC hg38 gene annotation in iGenomes. The sequencing reads were assigned to genes by featureCounts in Rsubread package in Bioconductor.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig for coverage and RNA-seq counts for all genes

molecule: total RNA

source_name: L1236 cell line

growth_protocol: The L1236 and L428 cell lines with doxycycline-inducible shNTC or shH2A.B expression were routinely cultured in RPMI-1640 growth medium supplemented with 10% heat-inactivated foetal bovine serum (HI-FBS), 1% L-glutamine (200 mM stock), and 1% Penicillin-Streptomycin (10,000 units penicillin and 10 mg streptomycin/mL stock), and 0.2 μg/mL puromycin. Cells were cultured in T75 flasks and maintained in a humidified cell culture incubator at 37 ˚C and 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent (Thermo Fisher Scientific) .The genomic DNA was removed using the  TURBO DNA-free kit (Thermo Fisher Scientific)  following the kit manual.
The sequencing libraries  for L1236 were prepared using the Illumina TruSeq Stranded mRNA library prep kit coupled with poly-A selection, using standard Illumina protocols. The sequencing libraries for L428  were prepared using the Illumina TruSeq RNA Sample Prep Kit coupled with poly-A selection, using standard Illumina protocols.

treatment_protocol: 0.5 x106 cells were seeded per well in 4 mL RPMI-1640 grwoth medium in 6-well plates. Eeach well was supplemented with 0.1 μg/mL doxycycline for induction of shRNA expression.  Three replicates of each L1236- shNTC and L1236-shH2A.B cells were collected for RNA extraction on day 2 and day 5 post doxycyline induction.

tag: cut&run antibody

value: shNTC (Non-targeting control)

tag: cell line

value: Day 5


title: Lml_axenic_B

city: Thiverval-Grignon

first: Jessica

middle: Louise

last: SOYER

address: Avenue Lucien Brétignières

department: SPE

institute: INRAE

data_processing:
Mapping against the reference genome of Lmb (Dutreux et al., 2018) or Lml (Grandaubert et al., 2014) using STAR (Langmead and Salzberg, 2012) with default parameters
Genome_build: Lmb (Dutreux et al., 2018); Lml (Grandaubert et al., 2014)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample, rpkm values estimated with function rpkm_count of EdgeR (Robinson et al., 2010)

organism: Plenodomus lingam/Leptosphaeria maculans 'lepidii' group

source_name: mycelium

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

extract_protocol:
Total RNA was extracted following protocol by Fudal et al. (2007)
The NEBNext Ultra Directional RNA Library Prep Kit for Illumina (cat. # E7420L New England BioLabs) was used to prepare all RNA-seq libraries, following the manufacturer’s instructions. Sequencing was performed by the GenomEast platform, a member of the ‘France Génomique’ consortium (ANR-10-INBS-0009). Samples were run in 9-plex on an Illumina HiSeq 4000 in paired mode, 2x50 bp.

treatment_protocol: mycelium was filtered and washed thoroughly with distilled water, placed in liquid nitrogen until RNA extraction

tag: strain

value: IBCN84 (Grandaubert et al., 2014)

tag: tissue

value: mycelium

tag: growth condition

value: axenic


title: FRAS190074378

city: Wenzhou

first: Xiaofang

last: Zhu

state: Zhejiang Province

address: Nan Bai Xiang Street

department: Rheumatology

country: China

institute: First Affiliated Hospital of Wenzhou Medical University

data_processing:
Illumina bcl2fastq software used for basecalling.
Using Cutadapt adapters and TrimGalore, raw reads were trimmed and low-quality reads were filtered. Quality-control reports of sequence reads were obtained using FastQC software.
The sequencing data were aligned to the human reference genome "hg38" using STAR software.
The read count files were filtered with low expression and normalized using the DESeq2 package.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample

source_name: salivary glands

extract_protocol:
Total RNA was isolated from frozen salivary gland samples using TRIzol Reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions. RNA purity was checked using a Nano Photometer spectrophotometer (IMPLEN, Westlake Village, CA, USA).
The quality of the RNA used to construct the cDNA library was verified (RNA integrity numbers >9) using an RNA 6000 Nano kit with the Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA, USA). With input material of 3 mg RNA per sample, we constructed sequencing libraries using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) and subsequently performed the sequence on an Illumina HiSeq platform.

value: salivary glands

value: non-ILD-pSS


title: L1236_IgG_rep2 (CUT&RUN)

description:
L1236_IgG_rep2 (CUT&RUN)
L1236_IgG_q20_nodup_spikeins_norm.bw

library_source: genomic

value: IgG


title: DNA methylation from liver sample 75

city: New York

first: Gabriela

last: Hernandez-Meza

state: New York

address: 1 Gustave L. Levy Place

country: USA

institute: Mount Sinai

description:
9247377204_R06C02
Cirrhosis liver sample

hyb_protocol: Bisulphite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450k BeadChip using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting.

data_processing:
BeadStudio software v3.2
Unmethylated_methylated_signal_intensities.txt: Unmethylated and methylated signal intensities, p-values.

label: not provided

source_name: Liver sample 75

label_protocol: Standard Illumina Protocol.

extract_protocol: For DNA extraction, we used the Qiagen RNeasy Mini and Invitrogen ChargeSwitch genomic DNA Mini Tissue according to standard instructions.

value: Liver

tag: diagnosis

value: Cirrhosis


title: Lml_axenic_A


title: FRAS190074392


title: DNA methylation from liver sample 70

description:
9247377204_R01C02
Cirrhosis liver sample

source_name: Liver sample 70


title: FRAS190074375


title: FRAS190074322


title: H3K27me3_Lml_C

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

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

treatment_protocol: mycelium was filtered and washed thoroughly with distilled water

tag: chip antibody


title: DNA methylation from liver sample 73

description:
9247377204_R04C02
Cirrhosis liver sample

source_name: Liver sample 73


title: DNA methylation from liver sample 72

description:
9247377204_R03C02
Cirrhosis liver sample

source_name: Liver sample 72


title: L1236_IgG_rep1 (CUT&RUN)

description:
L1236_IgG_rep1 (CUT&RUN)
L1236_IgG_q20_nodup_spikeins_norm.bw


title: L1236_H2A.B_rep2 (CUT&RUN)

description:
L1236_H2A.B_rep2 (CUT&RUN)
L1236_H2AB_q20_nodup_spikeins_norm.bw


title: FRAS190074394


title: L428-shNTC-day5_rep2 (RNA-seq)

description:
L428-shNTC-day5_rep2 (RNA-seq)
L428_RNAseq_counts.xlsx


title: H3K9me3_Lml_C

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


title: DNA methylation from liver sample 77

description:
9257625022_R02C01
Cirrhosis liver sample

source_name: Liver sample 77


title: DNA methylation from liver sample 80

description:
9257625022_R05C01
Cirrhosis liver sample

source_name: Liver sample 80


title: DNA methylation from liver sample 74

description:
9247377204_R05C02
Cirrhosis liver sample

source_name: Liver sample 74


title: H3K4me2_Lml_C

value: H3K4me2 (Merck ref. 07-030)


title: FRAS190074402


title: H3K27me3_Lml_B

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


title: DNA methylation from liver sample 82

description:
9257625022_R02C02
Cirrhosis liver sample

source_name: Liver sample 82


title: FRAS190074408


title: L428_H2A.B_rep1 (CUT&RUN)

description:
L428_H2A.B_rep1 (CUT&RUN)
L428_H2AB_q20_nodup_spikeins_norm.bw

value: pan- H2A.B (Home-made)

value: Drosophila melanogaster


title: H3K9me3_Lml_B


title: L428_IgG_rep1 (CUT&RUN)

description:
L428_IgG_rep1 (CUT&RUN)
L428_IgG_q20_nodup_spikeins_norm.bw


title: FRAS190074410


title: DNA methylation from liver sample 64

description:
9257625025_R06C02
Cirrhosis liver sample

source_name: Liver sample 64


title: OCILY1_DMSOV_14D

city: Bellinzona

first: Luciano

last: Cascione

state: Ticino

address: Via Chiesa 5

department: Lymphoma & Genomics Research Program

country: Switzerland

institute: IOR

description: Sample 37

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using STAR
For each gene, the counts per millions have been normalized (TMM normalization, edgeR) and logged (base 2)
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with log2 counts per million (CPM) for every gene and every sample

growth_protocol: All cell lines were cultured according to the recommended conditions. All media were supplemented with foetal bovine serum, penicillin-streptomycin-neomycin (5,000 units penicillin, 5 mg streptomycin and 10 mg neomycin/mL, Sigma) and L-glutamine (1%). Cell line identity was authenticated by short tandem repeat (STR) DNA profiling.

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: cells treated for 6 hours and 14 days with DMSO, vorinostat or pracinostat

tag: treatment

value: DMSO

tag: time point

value: 14 Days


title: FRAS190074373


title: L428-shNTC-day5_rep1 (RNA-seq)

description:
L428-shNTC-day5_rep1 (RNA-seq)
L428_RNAseq_counts.xlsx

value: shNTC (Non-targeting control)


title: L428_IgG_rep2 (CUT&RUN)

description:
L428_IgG_rep2 (CUT&RUN)
L428_IgG_q20_nodup_spikeins_norm.bw


title: DNA methylation from liver sample 65

description:
9247377204_R01C01
Cirrhosis liver sample

source_name: Liver sample 65


title: FRAS190074416


title: DNA methylation from liver sample 69

description:
9247377204_R05C01
Cirrhosis liver sample

source_name: Liver sample 69


title: H3K4me2_Lml_B


title: PFEIFFER_VORINO_14D

description: Sample 36

source_name: PFEIFFER

value: PFEIFFER

value: VORINOSTAT


title: H3K27me3_Lml_A

value: IBCN84 (Grandaubert et al., 2014)

value: mycelium


title: FRAS190074417

value: salivary glands


title: DNA methylation from liver sample 71

description:
9247377204_R02C02
Cirrhosis liver sample

source_name: Liver sample 71


title: DNA methylation from liver sample 67

description:
9247377204_R03C01
Cirrhosis liver sample

source_name: Liver sample 67


title: PFEIFFER_DMSOV_14D

description: Sample 35


title: H3K9me3_Lml_A

value: axenic


title: FRAS190074420

value: non-ILD-pSS


title: WSUDLCL2_VORINO_14D

description: Sample 34


title: H3K4me2_Lml_A


title: FRAS190074426


title: L1236_H2A.B_rep1 (CUT&RUN)

description:
L1236_H2A.B_rep1 (CUT&RUN)
L1236_H2AB_q20_nodup_spikeins_norm.bw

source_name: L1236 cell line


title: FRAS190074430


title: TOLEDO_VORINO_14D

description: Sample 32

source_name: TOLEDO

value: TOLEDO


title: log_riboseq_1

city: New Delhi

first: G Aneeshkumar

last: Arimbasseri

state: Delhi

address: Aruna Asaf Ali Marg

department: Molecular Genetics Laboratory

country: India

institute: National Institute of Immunology

description: Ribosome profiling data

data_processing:
Casava 1.7 for base calling
Reads were mapped to M. tb genome using Bowtie2.
P site phasing was done using custom scripts written in python 3.
Read counts per gene was calculated using HTseq-count
Genome_build: ASM19595v2
Supplementary_files_format_and_content: Read counts per gene

organism: Mycobacterium tuberculosis

source_name: In vitro cultured bacterial cells

growth_protocol: Mycobacterium tuberculosis H37Rv cells were grown to log hase (OD600 0.4-0.6) in 7H9 broth at 37ºC with shaking.

extract_protocol:
Cells after treatment was harvested by rapid centrifugation followed by mechanical lysis in presence of a lysis buffer containing chloramphenicol. Lysate was cleared and digested with a combination of RNAse T1 (4U) and Mnase (4U) for 45 minutes at room temperature. Monosome fractions were isolated using sucrose gradient ultracentrifugation.
Library preparation was done exactly as described in Ingolia, N., Brar, G., Rouskin, S. et al. The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nat Protoc 7, 1534–1550 (2012). https://doi.org/10.1038/nprot.2012.086.
Others (Ribo-seq)

treatment_protocol: For oxidative stress, cells grown to log phase was harvested and transferred to fresh 7H9 media containing 50µM cumene hydroperoxide and incubated at 37ºC for 1 hour. For pH stress log phase cells were harvested and transferred to fresh 7H9 media whose pH was adjusted to 4.5 and incubated for 1 hour at 37ºC.

tag: condition

value: Log phase


title: WSUDLCL2_DMSOV_14D

description: Sample 33


title: log_riboseq_2

description: Ribosome profiling data


title: FRAS190074405

source_name: salivary glands


title: FRAS190074434


title: TOLEDO_DMSOV_14D

description: Sample 31


title: FRAS190074436


title: DNA methylation from liver sample 62

description:
9257625025_R04C02
Cirrhosis liver sample

source_name: Liver sample 62

value: Liver

value: Cirrhosis


title: DNA methylation from liver sample 60

description:
9257625025_R02C02
Cirrhosis liver sample

source_name: Liver sample 60


title: pH_riboseq

description: Ribosome profiling data

value: pH stress


title: SUDHL4-VORINO-14D


title: FRAS190074437


title: DNA methylation from liver sample 61

description:
9257625025_R03C02
Cirrhosis liver sample

source_name: Liver sample 61


title: OCILY1_PRACINO_6HRS

description: Sample 30

value: PRACINOSTAT

value: 6 Hours


title: DNA methylation from liver sample 68

description:
9247377204_R04C01
Cirrhosis liver sample

source_name: Liver sample 68


title: DNA methylation from liver sample 63

description:
9257625025_R05C02
Cirrhosis liver sample

source_name: Liver sample 63


title: FRAS190074438


title: SUDHL6_PRACINO_6HRS

description: Sample 29


title: FRAS190074440


title: ox_stress_riboseq_1

description: Ribosome profiling data

value: Oxidative stress


title: ox_stress_riboseq_2

description: Ribosome profiling data


title: PFEIFFER_PRACINO_6HRS

description: Sample 28


title: DNA methylation from liver sample 59

description:
9257625025_R05C01
Cirrhosis liver sample

source_name: Liver sample 59


title: FRAS190074441


title: PFEIFFER_DMSO_6HRS

description: Sample 27

value: DMSO


title: FRAS190074442


title: FRAS190074443


title: DNA methylation from liver sample 57

description:
9257625025_R03C01
Cirrhosis liver sample

source_name: Liver sample 57


title: TOLEDO_PRACINO_6HRS

description: Sample 25


title: FRAS190074452


title: DNA methylation from liver sample 58

description:
9257625025_R04C01
Cirrhosis liver sample

source_name: Liver sample 58


title: WSUDLCL2_PRACINO_6HRS

description: Sample 26


title: FRAS190074454


title: OCILY1_VORINO_6HRS

description: Sample 23


title: FRAS190075084


title: OCILY1_DMSO_6HRS

description: Sample 22


title: log_tRNA

description: tRNAseq data


title: FRAS190074448


title: DNA methylation from liver sample 56

description:
9257625025_R02C01
Cirrhosis liver sample

source_name: Liver sample 56


title: FRAS190074457


title: FRAS190074428

value: ILD-pSS


title: SUDHL6_DMSO_6HRS

description: Sample 20


title: DNA methylation from liver sample 55

description:
9257625025_R01C01
Cirrhosis liver sample

source_name: Liver sample 55


title: FRAS190074381


title: DNA methylation from liver sample 50

description:
9247377175_R02C02
Cirrhosis liver sample

source_name: Liver sample 50


title: FaDu/DDP4

type: RNA

city: Changsha

first: Wei

last: LI

state: Hunan

address: Tongzipo Road

department: Department of Otorhinolaryngology-head and neck surgery

institute: Third Xiangya hospital of Central South University

description:
ceRNA
induced cisplatin-resistant FaDu cell strain

hyb_protocol: Each slide was hybridized with 600 ng Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

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

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

source_name: cells, induced cisplatin-resistance

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

growth_protocol: Cultured in MEM medium containing 10% FBS with 5% CO2 at 37℃

extract_protocol: Total RNA was checked for a RIN number to inspect RNA integrity by an Agilent  Bioanalyzer  2100  (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified byRNeasy  micro  kit  (Cat#74004, QIAGEN,  GmBH,  Germany)  and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany)

treatment_protocol: FaDu/DDP4 was induced chemoresistance by 0.5-1 μg/ml cisplatin for four times.

tag: chemoresistance

value: cisplatin-resistance


title: DNA methylation from liver sample 54

description:
9247377175_R06C02
Cirrhosis liver sample

source_name: Liver sample 54


title: PFEIFFER_VORINO_6HRS

description: Sample 19

source_name: PFEIFFER

value: PFEIFFER

value: VORINOSTAT


title: FaDu

description:
ceRNA
hypopharyngeal cancer cell line

source_name: cells, in vitro

value: FaDu


title: DNA methylation from liver sample 66

description:
9247377204_R02C01
Cirrhosis liver sample

source_name: Liver sample 66


title: WSUDLCL2_VORINO_6HRS

description: Sample 18


title: SUDHL4_PRACINO_6HRS

description: Sample 24


title: FRAS190074301

source_name: salivary glands

value: salivary glands


title: WSUDLCL2_DMSO_6HRS

description: Sample 17


title: DNA methylation from liver sample 51

description:
9247377175_R03C02
Cirrhosis liver sample

source_name: Liver sample 51


title: TOLEDO_VORINO_6HRS

description: Sample 16

source_name: TOLEDO


title: FRAS190074240


title: SUDHL4_VORINO_6HRS

description: Sample 14


title: FRAS190053279


title: FRAS190074386


title: SUDHL4_DMSO_6HRS

description: Sample 13


title: FRAS190074365


title: DNA methylation from liver sample 48

description:
9247377175_R04C01
Cirrhosis liver sample

source_name: Liver sample 48


title: DNA methylation from liver sample 53

description:
9247377175_R05C02
Cirrhosis liver sample

source_name: Liver sample 53


title: OCILY1_PRACINO_14D

description: Sample 12

value: 14 Days


title: TOLEDO_DMSO_6HRS

description: Sample 15


title: FRAS190074251


title: DNA methylation from liver sample 47

description:
9247377175_R03C01
Cirrhosis liver sample

source_name: Liver sample 47


title: DNA methylation from liver sample 52

description:
9247377175_R04C02
Cirrhosis liver sample

source_name: Liver sample 52


title: DNA methylation from liver sample 49

description:
9247377175_R05C01
Cirrhosis liver sample

source_name: Liver sample 49


title: FRAS190053198


title: SUDHL4_DMSOV_14D

description: Sample 11


title: DNA methylation from liver sample 45

description:
9247377175_R01C01
Cirrhosis liver sample

source_name: Liver sample 45


title: DNA methylation from liver sample 46

description:
9247377175_R02C01
Cirrhosis liver sample

source_name: Liver sample 46


title: FRAS190074338


title: PFEIFFER_PRACINO_14D

description: Sample 9


title: OCILY1_DMSOP_14D

description: Sample 10


title: FRAS190053293


title: FRAS190053298


title: WSUDLCL2_PRACINO_14D

description: Sample 7


title: FRAL190074243


title: WSUDLCL2_DMSOP_14D

description: Sample 6


title: DNA methylation from liver sample 43

description:
9247377017_R04C02
Cirrhosis liver sample

source_name: Liver sample 43


title: TOLEDO_PRACINO_14D

description: Sample 5


title: DNA methylation from liver sample 42

description:
9247377017_R03C02
Cirrhosis liver sample

source_name: Liver sample 42


title: FRAS190036208


title: DNA methylation from liver sample 37

description:
9247377017_R04C01
Cirrhosis liver sample

source_name: Liver sample 37


title: DNA methylation from liver sample 44

description:
9247377017_R05C02
Cirrhosis liver sample

source_name: Liver sample 44


title: DNA methylation from liver sample 39

description:
9247377017_R06C01
Cirrhosis liver sample

source_name: Liver sample 39


title: FRAS190036227


title: DNA methylation from liver sample 38

description:
9247377017_R05C01
Cirrhosis liver sample

source_name: Liver sample 38


title: FRAS190053179


title: FRAS190036277


title: SUDHL4_PRACINO_14D

description: Sample 3


title: DNA methylation from liver sample 40

description:
9247377017_R01C02
Cirrhosis liver sample

source_name: Liver sample 40


title: DNA methylation from liver sample 35

description:
9247377017_R02C01
Cirrhosis liver sample

source_name: Liver sample 35


title: SUDHL4_DMSOP_14D

description: Sample 2


title: FRAS190053171

source_name: salivary glands


title: DNA methylation from liver sample 32

description:
9247377011_R04C02
Cirrhosis liver sample

source_name: Liver sample 32


title: DNA methylation from liver sample 41

description:
9247377017_R02C02
Cirrhosis liver sample

source_name: Liver sample 41


title: DNA methylation from liver sample 31

description:
9247377011_R03C02
Cirrhosis liver sample

source_name: Liver sample 31


title: OCILY1_VORINO_14D

description: Sample 1


title: FRAS190053173


title: DNA methylation from liver sample 33

description:
9247377011_R05C02
Cirrhosis liver sample

source_name: Liver sample 33


title: DNA methylation from liver sample 36

description:
9247377017_R03C01
Cirrhosis liver sample

source_name: Liver sample 36


title: TOLEDO_DMSOP_14D

description: Sample 4

source_name: TOLEDO


title: DNA methylation from liver sample 34

description:
9247377017_R01C01
Cirrhosis liver sample

source_name: Liver sample 34


title: PFEIFFER_DMSOP_14D

description: Sample 8

source_name: PFEIFFER


title: FRAS190036206


title: Line15#33

city: London

first: Michael

middle: A

last: Skinner

address: St Mary's Campus, Norfolk Place

department: Faculty of Medicine, Section of Virology

country: United Kingdom

institute: Imperial College London

description: tissue harvested at 72 hours post infection

data_processing:
Illumina data were processed using RTA with default filter and quality settings then the reads were demultiplexed (allowing no mismatches in the index sequence) with CASAVA
Paired Fastq files were imported into CLC bio’s Genomics Workbench (CLC bio, Qiagen Bioinformatics, Aarhus, Denmark), quality-controlled and thereafter processed using that package (versions 12.0.3)
After quality control, the reads were subjected to quality trimming then mapped and aligned against ENSEMBL galGal5-annotated genes (GRCg6a; 03-07-2019) for quantitative analysis of expression using CLC's  RNA-Seq Analysis tool.
RPKM expression levels, Fold change and False Discovery Rates (FDR) were calculated using CLC's Test Differential Expression tool
Genome_build: 86
Supplementary_files_format_and_content: TAB-delimited text files, prepared with CLC bio GWB, showing gene expression analysis for each sample  (not filtered for NaN, INF, -INF); TAB-delimited text files, prepared with CLC bio GWB using the Test Differential Expression tool to compare Hi versus Lo pathogenicity samples and Line 15 versus Line W

organism: Gallus gallus

source_name: bursa of Fabricius (BF)

growth_protocol: chickens of different White Leghorn inbred lines were infected with IBDV strain UK661 intra-nasally and the bursa of Fabricius (BF) was harvested at 72 hours post-infection

extract_protocol:
total RNA was extracted using an RNeasy kit (Qiagen) according to the manufacturer's instructions. Each sample is from one individual bird.
RNA libraries were prepared and sequenced using the Illumina HiSeq2000 system at the Beijing Genomics Institute (BGI, Hong Kong) using standard Illumina protocols.Poly (A) mRNA was purified from total RNA using magnetic beads with oligo (dT) (New England BioLabs, UK). The mRNA was then broken into short fragments using divalent cations at an elevated temperature. Using these cleaved RNA fragments as templates, random hexamer primers (Ivitrogen, Carlsbad, CA) was used for first-strand cDNA synthesis, followed by second-strand cDNA synthesis using DNA polymerase I (New England BioLabs, UK) and RNase H (Invitrogen).

treatment_protocol: The harvested tissue was frozen at -80C in RNALater prior to RNA extraction

tag: line of chicken

tag: sex of chicken

value: F

value: IBDV UK661 72h

tag: clinical score

tag: clinical grade

value: LO

tag: virus vp2 gene copy number per g tissue


title: FRAS190053282

tag: disease state


title: FRAS190053211


title: FRAS190053283


title: Line15#32


title: DNA methylation from liver sample 30

description:
9247377011_R02C02
Cirrhosis liver sample

source_name: Liver sample 30

value: Liver


title: FRAS190053322


title: DNA methylation from liver sample 26

description:
9247377011_R04C01
Cirrhosis liver sample

source_name: Liver sample 26

value: Cirrhosis


title: FRAS190053331


title: LineWmock#15

value: W

value: Mock 72h

value: MOCK


title: LineWmock#14


title: DNA methylation from liver sample 27

description:
9247377011_R05C01
Cirrhosis liver sample

source_name: Liver sample 27


title: Line15#31

value: M


title: FRAS190074379


title: L428-shNTC_rep2 (ATAC-seq)

description:
L428-shNTC_rep2 (ATAC-seq)
L428_NTC_q20_nodup_norm.bw

source_name: L428 cell line

growth_protocol: The L1236 and L428 cell lines with doxycycline-inducible shNTC or shH2A.B expression were routinely cultured in RPMI-1640 growth medium supplemented with 10% heat-inactivated foetal bovine serum (HI-FBS), 1% L-glutamine (200 mM stock), and 1% Penicillin-Streptomycin (10,000 units penicillin and 10 mg streptomycin/mL stock). Cells were cultured in T75 flasks and maintained in a humidified cell culture incubator at 37 ˚C and 5% CO2.

extract_protocol: ATAC-seq was performed as previously described (Corces et al., 2017), where 50,000 cells were applied for each reaction.

treatment_protocol: 1x106 cells were seeded in 10 mL RPMI-1640 grwoth medium in a T25 flask. For L1236 cells, 0.1 μg/mL doxycycline was added to induce the shRNA expression. For L428 cells, 1 μg/mL doxycycline was added to induce the shRNA expression. Growth medium was refrehsed every two days. The cells were collected for assay on day 5 post doxycyline induction of shRNA expression.

tag: cut&run antibody

value: shNTC (Non-targeting control)


title: LineW#36

value: MED


title: FRAS190053156

value: ILD-pSS


title: DNA methylation from liver sample 29

description:
9247377011_R01C02
Cirrhosis liver sample

source_name: Liver sample 29


title: LineW#33

value: HI


title: L428-shNTC_rep1 (ATAC-seq)

description:
L428-shNTC_rep1 (ATAC-seq)
L428_NTC_q20_nodup_norm.bw

tag: cell line


title: FRAS190053302


title: LineW#32


title: L428-shH2A.B-rep2 (ATAC-seq)

description:
L428-shH2A.B-rep2 (ATAC-seq)
L428_KD_q20_nodup_norm.bw


title: DNA methylation from liver sample 21

description:
9247377003_R04C02
Cirrhosis liver sample

source_name: Liver sample 21


title: FRAS190074247


title: L428-shH2A.B-rep1 (ATAC-seq)

description:
L428-shH2A.B-rep1 (ATAC-seq)
L428_KD_q20_nodup_norm.bw


title: L1236-shNTC_rep2 (ATAC-seq)

description:
L1236-shNTC_rep2 (ATAC-seq)
L1236_NTC_q20_nodup_norm.bw

source_name: L1236 cell line


title: LineOmock#12

value: O


title: LineOmock#16


title: DNA methylation from liver sample 25

description:
9247377011_R03C01
Cirrhosis liver sample

source_name: Liver sample 25


title: FRAS190074279

source_name: salivary glands


title: LineO#23


title: DNA methylation from liver sample 24

description:
9247377011_R02C01
Cirrhosis liver sample

source_name: Liver sample 24


title: Line15#35


title: FRAS190053313


title: L1236-shNTC_rep1 (ATAC-seq)

description:
L1236-shNTC_rep1 (ATAC-seq)
L1236_NTC_q20_nodup_norm.bw


title: DNA methylation from liver sample 22

description:
9247377003_R05C02
Cirrhosis liver sample

source_name: Liver sample 22


title: FRAS190074342


title: DNA methylation from liver sample 28

description:
9247377011_R06C01
Cirrhosis liver sample

source_name: Liver sample 28


title: LineO#22


title: L1236-shH2A.B_rep1 (ATAC-seq)

description:
L1236-shH2A.B_rep1 (ATAC-seq)
L1236_KD_q20_nodup_norm.bw


title: LineO#21

description: tissue harvested at 72 hours post infection


title: DNA methylation from liver sample 20

description:
9247377003_R03C02
Cirrhosis liver sample

source_name: Liver sample 20


title: FRAS190074299


title: LineO#20


title: WTUnt  rep 3

city: Gainesville

first: Alberto

last: Riva

state: FL

address: 2033 Mowry Rd

department: ICBR

institute: University of Florida

description:
Replicate 3
WTUT3_1

data_processing:
Base calling performed with Illumina CASAVA
Alignment to hg38 genome with STAR v. 2.6.1d
Normalization of raw counts with TMM
Unsupervised hierarchical clustering of 2000 genes with highest variance.

source_name: Osteosarcoma cell line

growth_protocol: U2OS overexpression cell lines were plated in biological triplicates at 0.6 ´ 106 cells/well in 60 cm dish

extract_protocol:
Total RNA was extracted with the Direct-zol RNA MiniPrep kit (Zymo Research) following the manufacturer’s instructions
NEBNext® UltraTM RNA Library Prep Kit

treatment_protocol: Cells were treated with 10 uM Ara-C for the indicated time points

tag: strain name

tag: drug treatment

value: Untreated

tag: genotype

value: Wild type Dnmt3a


title: LineO#19


title: DNA methylation from liver sample 18

description:
9247377003_R01C02
Cirrhosis liver sample

source_name: Liver sample 18

tag: tissue

tag: diagnosis


title: DNA methylation from liver sample 15

description:
9247377003_R04C01
Cirrhosis liver sample

source_name: Liver sample 15


title: LineCmock#6

source_name: bursa of Fabricius (BF)

value: C

tag: treatment


title: DNA methylation from liver sample 19

description:
9247377003_R02C02
Cirrhosis liver sample

source_name: Liver sample 19


title: WTUnt  rep 1

description:
Replicate 1
WTUT1_1


title: FRAS190074447

value: salivary glands


title: LineCmock#1


title: DNA methylation from liver sample 16

description:
9247377003_R05C01
Cirrhosis liver sample

source_name: Liver sample 16


title: WT24HR Tr rep3

description:
Replicate 3
WT24H3_1

value: 24hr post treatment


title: DNA methylation from liver sample 17

description:
9247377003_R06C01
Cirrhosis liver sample

source_name: Liver sample 17


title: DNA methylation from liver sample 14

description:
9247377003_R03C01
Cirrhosis liver sample

source_name: Liver sample 14


title: Neonatal Rat Cardiac Fibroblast - Treatment rep 3

city: Chicago

first: Brenda

last: Russell

state: IL

address: 835 S Wolcott Ave

department: Physiology

institute: University Illinois at Chicago

data_processing:
Raw reads were aligned to the rat reference genome (rn6) in a splice-aware manner using the STAR aligner. We quantified the expression level of ENSEMBL genes using FeatureCounts. Differential expression statistics were computed using edgeR , and p-values were adjusted for multiple testing using the false discovery rate (FDR) correction of Benjamini and Hochberg . Pathway analysis of differentially expressed genes was performed in Ingenuity Pathway Analysis.
Genome_build: rn6
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Rattus norvegicus

source_name: Neonatal rat ventricular cardiac fibroblast

growth_protocol: Cardiac fibroblasts were grown on glass substrates treated with only fibronectin (UT) or fibronectin plus TTR fibrils (TTR).

extract_protocol:
Maxwell® RSC simplyRNA Cells (Promega) with inclusion of DNAse treatment step. RNA samples were quantified using NanoDrop™ One Spectrophotometer (Thermo Scientific) and analyzed for integrity using Agilent 4200 TapeStation. Levels of remaining DNA were checked using Qubit fluorometer (Invitrogen). DNA amounts did not exceed 10% of the total amount of Nucleic Acid.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were grown on their indicated substrate for 48 hours prior to RNA extraction.

value: ventricles

tag: cell type

value: Cardiac fibroblast

tag: age

value: neonatal


title: L1236-shH2A.B_rep2 (ATAC-seq)

description:
L1236-shH2A.B_rep2 (ATAC-seq)
L1236_KD_q20_nodup_norm.bw


title: DNA methylation from liver sample 12

description:
9247377003_R01C01
Cirrhosis liver sample

source_name: Liver sample 12

value: Liver

value: Cirrhosis


title: Neonatal Rat Cardiac Fibroblast - Treatment rep 2


title: LineC#8

value: IBDV UK661 72h


title: DNA methylation from liver sample 23

description:
9247377011_R01C01
Cirrhosis liver sample

source_name: Liver sample 23


title: LineC#12

value: M

value: LO


title: WT24HR Tr rep1

description:
Replicate 1
WT24H1_1


title: Neonatal Rat Cardiac Fibroblast - Treatment rep 1


title: DNA methylation from liver sample 11

description:
9247377010_R05C02
Cirrhosis liver sample

source_name: Liver sample 11


title: WT24HR Tr rep2

description:
Replicate 2
WT24H2_1


title: Neonatal Rat Cardiac Fibroblast - control rep 3


title: LineC#11

value: F


title: DNA methylation from liver sample 8

description:
9247377010_R02C02
Cirrhosis liver sample

source_name: Liver sample 8


title: MUTUnt  rep 3

description:
Replicate 3
MUTUT3_1

value: Dnmt3a R882H mutation


title: Neonatal Rat Cardiac Fibroblast - control rep 2


title: DNA methylation from liver sample 9

description:
9247377010_R03C02
Cirrhosis liver sample

source_name: Liver sample 9


title: MUTUnt  rep 2

description:
Replicate 2
MUTUT2_1


title: Neonatal Rat Cardiac Fibroblast - control rep 1


title: DNA methylation from liver sample 5

description:
9247377010_R05C01
Cirrhosis liver sample

source_name: Liver sample 5


title: DNA methylation from liver sample 13

description:
9247377003_R02C01
Cirrhosis liver sample

source_name: Liver sample 13


title: DNA methylation from liver sample 10

description:
9247377010_R04C02
Cirrhosis liver sample

source_name: Liver sample 10


title: DNA methylation from liver sample 7

description:
9247377010_R01C02
Cirrhosis liver sample

source_name: Liver sample 7


title: Nic-3

city: Huainan

first: Li

last: Zhou

state: AnHui

address: 168 Taifeng Road

department: School of Medicine

country: Zimbabwe

institute: Anhui University of Science and Technology

description: Hippocampal gene expression in nicotine offspring-3

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions.

scan_protocol: After RNA labeling and hybridization, slides were scanned by Agilent DNA Microarray Scanner.

data_processing: Raw data were normalized and analyzed using GeneSpring GX v12.1 software (Agilent Technologies, Santa Clara, CA).

organism: Mus musculus

source_name: hippocampus-3, 20day,200 μg/ml nicotine

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNeasy mini column (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated from the hippocampus using Trizol extraction method according to manufacturer’s instructions (Invitrogen). The hippocampal RNA was analyzed using Arraystar RNA Flash Labeling Kit. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: vehicle offspring:1% saccharin；nicotine offspring：200 μg/ml nicotine

tag: strain

value: Hippocampus

value: postnatal day 20

value: 200 μg/ml nicotine


title: FRAS190074363

source_name: salivary glands

value: ILD-pSS


title: Line15mock#14

description: tissue harvested at 72 hours post infection

source_name: bursa of Fabricius (BF)

tag: line of chicken

value: Mock 72h

value: MOCK


title: MUTUnt  rep 1

description:
Replicate 1
MUTUT1_1

source_name: Osteosarcoma cell line

value: Untreated


title: LineC#10

value: C

tag: sex of chicken


title: IL12_6_2

city: Jinhua

first: Weiqiang

last: Lin

state: Zhejiang

address: Shangcheng street N1

institute: The Fourth Affiliated Hospital, Institute of Translational Medicine, Zhejiang University School of Medicine

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were build index by hisat2, and masked for low-complexity or low-quality sequence.
Mapped to mm9 whole genome using hisat2 and exported StringTie readable format files.
Expression values for all genes in each sample (FPKM) were calculated by StringTie.
Differentially expressed mRNAs between the paired groups were analyzed by using DEGseq.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Gene_counts_matrix.txt: Matrix table with raw gene counts for every gene and every sample.
Supplementary_files_format_and_content: Gene_Expression_Summary.txt: Tab-delimited text file includes FPKM values for each Sample.

source_name: mouse podocyte cell line

extract_protocol:
Total RNA was extracted from each tissue sample using Trizol method.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: IL-12 for 6hr


title: IL12_6_1


title: Mut24HR Tr rep 3

description:
Replicate 3
MUT24H3_1

value: 24hr post treatment


title: Line15mock#13

tag: clinical score


title: Line15#36

tag: clinical grade


title: Mut24HR Tr rep 2

description:
Replicate 2
MUT24H2_1


title: Control_2

value: Control


title: Nic-2

description: Hippocampal gene expression in nicotine offspring-2

source_name: hippocampus-2, 20day,200 μg/ml nicotine


title: FRAS190074422

value: salivary glands


title: WTUnt  rep 2

description:
Replicate 2
WTUT2_1

value: Wild type Dnmt3a


title: Line15#34

value: IBDV UK661 72h

tag: virus vp2 gene copy number per g tissue


title: Mut24HR Tr rep 1

description:
Replicate 1
MUT24H1_1


title: Control_1


title: DNA methylation from liver sample 3

description:
9247377010_R03C01
Cirrhosis liver sample

source_name: Liver sample 3

value: Liver

value: Cirrhosis


title: DNA methylation from liver sample 4

description:
9247377010_R04C01
Cirrhosis liver sample

source_name: Liver sample 4


title: EVUnt rep 3

description:
Replicate 3
EVUT3_1

value: Empty Vector


title: EVUnt rep 2

description:
Replicate 2
EVUT2_1


title: Plate3_18_E0771shRNA4

city: Rehovot

first: Ester

last: Feldmesser

state: Rehovot

address: POB 25

department: Life Science Core Facilities

country: Israel

institute: Weizmann Institute

description: shLmna rep3

data_processing:
Library strategy: MARS-seq
Samples were demultiplexed using the barcode present in R2 read and the barcode was transferred to the title of R1
Cutadapt was used to trim low quality, poly A and adapter sequences (parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a “A{10}” –times 2 -u 3 -u -3 -q 20 -m 25).
Sequences were mapped to the UCSC mm10 mouse genome using STAR v2.4.2a
Quantification was performed using the 3’ of RefSeq annotated genes (1,000 bases upstream of the 3’ end and 100 bases downstream)and HTSeq count (DOI: 10.1093/bioinformatics/btu638)
UMI information was integrated into the BAM files as tags, using a python script. UMI counting was done after marking duplicates.
DESeq2 (doi: 10.1186/s13059-014-0550-8) was used for normalization and detection of differentially expressed genes. Raw p-values were adjusted for multiple testing using the procedure of Benjamini and Hochberg.
Batch effects were removed from the read counts using the ComBat function from the sva R package (Johnson et al. 2007 Biostatistics. 2007; 8(1):118-27). The normalized, batch corrected and log2 transformed read counts outputted by ComBat were used to draw plots.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files include gene raw reads (matrix_genes); normalized batch corrected counts using the Combat package (combat_corrected_counts) and DESeq2 statistical analysis file.

source_name: breast cancer cells

growth_protocol: E0771 breast adenocarcinoma cells were grown in DMEM supplemented with 10% FBS, 1 mM sodium pyruvate and 10 mM HEPES. At 37°C and 5% of CO2

extract_protocol:
RNA was isolated using Dynabeads mRNA Direct Kit (Thermo Fisher Scientific) following manufacturer's instructions.
We used a derivation of the MARS-seq as described (Jaitin et al. Science 2014), developed for single cell MARS-seq to produce 3' expression libraries. 3' RNA-seq for digital gene expression quantitation (single end protocol R2 used for 7N barcode + 8N UMI in fastq header)

treatment_protocol: Lentiviruses were produced by co-transfecting HEK293T cells with the shControl or shLmna vectors and three helper plasmids (Gag-Pol, Rev and VSV-G,) using Lipofectamine® 2000. The virus-containing medium was harvested 48 or 72 hours after transfection and subsequently precleaned by a brief centrifugation at 600 x g and a 0.45 µm filtration. Viruses were collected and concentrated with a precipitation solution (40% PEG8000 and 2.5N NaCl) as described (Guo et al. 2012) and stored at -20°C overnight. A day later, the medium was thawed and centrifuged at 2,400 x g for 30 min at RT. The viral pseudoparticles were resuspended in 200 µl culture medium and mixed with 2.5x104 E0771 cells for 12 hr. 36 hours after viral transduction, puromycin was added to the culture medium at a concentration of 3 µg/ml and tumor cells were selected and expanded, with growth medium replaced every 48 hours. The mean knockdown levels were subsequently assessed by Western blotting.

value: breast cancer

tag: genotype/variation

value: shLmna


title: mouse epididymis caput scRNA-seq

city: Nantong

first: Gangcai

last: Xie

state: Jiangsu

address: Number 9, Se Yuan Road

department: Medical school

institute: Nantong University

description: epididymis caput segment scRNASeq

data_processing:
reads filtering and adapter trimming by Fastp 0.19.5
reads mapping done by STAR-2.7.3a
umi_tools was used for integrated scRNA-seq analyzing, including cell barcode extraction, cell id assignment, UMI counting
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: gene expression matrix file, containing UMI counts values for all the detected genes of each single cell in all the three epididymal regions

source_name: Caput epididymis

extract_protocol:
The tissue pieces were digested in 2 ml GEXSCOPETM Tissue Dissociation Solution (Singleron Biotechnologies) at 37 ℃ for 15 min in a 15 ml centrifuge tube with continuous agitation. Following digestion, a 40-micron sterile strainer (Corning) was used to separate cells from cell debris and other impurities. To remove red blood cells, 2 mL GEXSCOPETM Red Blood Cell Lysis Buﬀer (Singleron) was added to the cell suspension and incubated at 25°C for 10 minutes. The mixture was then centrifuged at 1000 rpm for 5 min and cell pellet was re-suspended in PBS. Cells were counted with TC20 automated cell counter (Bio-Rad).
Single cell suspension was loaded onto a microfluidic chip (part of Singleron GEXSCOPETM Single Cell RNAseq Kit, Singleron Biotechnologies) and single cell RNA-seq libraries were constructed according to manufacturer’s instructions (Singleron Biotechnologies). The resulting single cell RNAseq libraries were sequenced on Illumina HiSeq X10 instrument with 150bp paired end reads.

value: epididymis caput

value: No treatment


title: mouse epididymis corpus scRNA-seq

description: epididymis corpus segment scRNASeq

source_name: Corpus epididymis

value: epididymis corpus


title: Plate3_17_E0771shRNA4

description: shLmna rep2


title: Nic-1

description: Hippocampal gene expression in nicotine offspring-1

source_name: hippocampus-1, 20day,200 μg/ml nicotine

value: Hippocampus

value: postnatal day 20

value: 200 μg/ml nicotine


title: EVUnt rep 1

description:
Replicate 1
EVUT1_1

value: Untreated


title: Sac-3

description: Hippocampal gene expression in vehicle offspring-3

source_name: hippocampus-3, 20day, 1% saccharin

value: 1% saccharin


title: Plate3_16_E0771shRNA4

description: shLmna rep1


title: mouse epididymis cauda scRNA-seq

description: epididymis cauda segment scRNASeq

source_name: Cauda epididymis

value: epididymis cauda


title: EV24HR Tr rep 3

description:
Replicate 3
EV24H3_1

value: 24hr post treatment


title: Sac-2

description: Hippocampal gene expression in vehicle offspring-2

source_name: hippocampus-2, 20day, 1% saccharin


title: Sac-1

description: Hippocampal gene expression in vehicle offspring-1

source_name: hippocampus-1, 20day, 1% saccharin


title: EV24HR Tr rep 2

description:
Replicate 2
EV24H2_1


title: DNA methylation from liver sample 2

description:
9247377010_R02C01
Cirrhosis liver sample

source_name: Liver sample 2


title: F2 Embry.63 T CM WT 384Mu

city: Dummerstorf

first: Siriluck

last: Ponsuksili

address: Wilhelm-stahl-allee 2

country: Germany

institute: FBN

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

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 42 C on Affymetrix Porcine Snowball Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Data were analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500.

label: biotin

organism: Sus scrofa

source_name: Musculus longissimus dorsi tissue from 63 dpc pig

label_protocol: biotin-labeled cRNAs were prepared according to the standard Affymetrix protocol from 500 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was isolated using TRI Reagent (Sigma, Taufkirchen, Germany) according to the manufacturer’s protocol. After DNaseI treatment the RNA was cleaned up using the RNeasy Kit (Qiagen, Hilden, Germany).

tag: breed

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

value: Musculus longissimus dorsi

value: 63 days post conception (dpc)


title: Plate3_14_E0771shControl

description: shControl rep2

tag: cell line

value: shControl


title: FaDu

description:
miRNA
hypopharyngeal cancer cell line

source_name: cells, in vitro

tag: chemoresistance

value: FaDu


title: RNA-seq of strain VB019 (dnaN-E202K) rep 3

city: Buffalo

first: Mark

middle: D

last: Sutton

address: 955 Main Street

department: Biochemistry

institute: University at Buffalo, SUNY

description: RNA (depleted of rRNA)

data_processing:
Base-calling – illumina RTA 1.17.21.3
Demultiplexing – Illumina bcl2fastq
Alignments – Tophat 2.1.0 (For alignments, we used tophat against the E. coli MG1655 genome annotation set and reference)
Quan.fica.on – Cufflinks 2.2.1
Supplementary_files_format_and_content: FPKMs in excel file

organism: Escherichia coli

source_name: E. coli RNA

growth_protocol: Strains were grown at 37ºC with aeration to exponential phase in Luria-Bertani medium (LB: 10 g/l tryptone, 5 g/l yeast extract, 10 g/l NaCl).

extract_protocol:
RNA was extracted using phenol-chloroform and was sbsequently depleted of ribosomal RNA using the Bacterial Ribo-Zero rRNA Removal Kit (Illumina) as per the manufacturer’s recommendations.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: genetic background

value: E. coli K12


title: F2 Embry.63 T CM WT 377Mu


title: Plate3_13_E0771shControl

description: shControl rep1

value: breast cancer


title: RNA-seq of strain VB019 (dnaN-E202K) rep 2

description: RNA (depleted of rRNA)


title: shLmna rep2

description:
Plate3_11_B16F10shLmna
B16F10 melanoma cells stably expressing Lmna shRNA

data_processing:
Samples were demultiplexed using the barcode present in R2 read and the barcode was transferred to the title of R1
Cutadapt was used to trim low quality, poly A and adapter sequences (parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a ?A{10}? ?times 2 -u 3 -u -3 -q 20 -m 25).
Sequences were mapped to the UCSC mm10 mouse genome using STAR v2.4.2a
Quantification was performed using the 3? of RefSeq annotated genes (1,000 bases upstream of the 3? end and 100 bases downstream)and HTSeq count (DOI: 10.1093/bioinformatics/btu638)
UMI information was integrated into the BAM files as tags, using a python script. UMI counting was done after marking duplicates.
DESeq2 (doi: 10.1186/s13059-014-0550-8) was used for normalization and detection of differentially expressed genes. Raw p-values were adjusted for multiple testing using the procedure of Benjamini and Hochberg.
Batch effects were removed from the read counts using the ComBat function from the sva R package (Johnson et al. 2007 Biostatistics. 2007; 8(1):118-27). The normalized, batch corrected and log2 transformed read counts outputted by ComBat were used to draw plots.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files include gene raw reads (matrix_genes); normalized batch corrected counts using the Combat package (combat_corrected_counts) and DESeq2 statistical analysis file.

source_name: melanoma cells

growth_protocol: B16F10 melanoma cells were grown in DMEM supplemented with 10% FBS

treatment_protocol: Lentiviruses were produced by co-transfecting HEK293T cells with the shControl or shLmna vectors and three helper plasmids (Gag-Pol, Rev and VSV-G,) using Lipofectamine® 2000. The virus-containing medium was harvested 48 or 72 hours after transfection and subsequently precleaned by a brief centrifugation at 600 x g and a 0.45 µm filtration. Viruses were collected and concentrated with a precipitation solution (40% PEG8000 and 2.5N NaCl) as described (Guo et al. 2012) and stored at -20°C overnight. A day later, the medium was thawed and centrifuged at 2,400 x g for 30 min at RT. The viral pseudoparticles were resuspended in 200 µl culture medium and mixed with 2.5x104 B16F10 cells for 12 hr. 36 hours after viral infection, puromycin was added to the culture medium at a concentration of 2.5 µg/ml and tumor cells were selected and expanded, with growth medium replaced every 48 hours. The mean knockdown levels were subsequently assessed by Western blotting.

tag: kd

value: shLmna


title: EV24HR Tr rep 1

description:
Replicate 1
EV24H1_1

source_name: Osteosarcoma cell line

tag: strain name

tag: drug treatment

tag: genotype

value: Empty Vector


title: RNA-seq of strain VB001 (dnaN+) rep 3

description: RNA (depleted of rRNA)


title: RNA-seq of strain VB019 (dnaN-E202K) rep 1

description: RNA (depleted of rRNA)


title: RNA-seq of strain VB001 (dnaN+) rep 2

description: RNA (depleted of rRNA)


title: shLmna rep1

description:
Plate3_10_B16F10shLmna
B16F10 melanoma cells stably expressing Lmna shRNA


title: shControl rep2

description:
Plate3_8_B16F10shControl
B16F10 melanoma cells stably expressing Control shRNA


title: shControl rep1

description:
Plate3_7_B16F10shControl
B16F10 melanoma cells stably expressing Control shRNA


title: F2 Embry.63 T CM WT 376Mu

tag: tissue


title: RNA-seq of strain VB001 (dnaN+) rep 1

description: RNA (depleted of rRNA)


title: DNA methylation from liver sample 1

description:
9247377010_R01C01
Cirrhosis liver sample

source_name: Liver sample 1

value: Liver

tag: diagnosis

value: Cirrhosis


title: FaDu/DDP4

description:
miRNA
induced cisplatin-resistant FaDu cell strain

source_name: cells, induced cisplatin-resistance

value: cisplatin-resistance


title: S10_SLX-8111.DNAA014_merged

city: Cambridge

first: Adriana

last: Ordonez

address: Cambridge Biomedical Campus Keith Peters Building, Hills Rd

department: Clinical Biochemistry

institute: University of Cambridge

description: Hi Seq 400, Single Read, 50bp

data_processing:
Library strategy: CRISPR screen
A comprehensive quality control was performd by  using the Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) computational software. This involved quantification of Total HiSeq read counts, percentage of mapped reads to the CHO library, the number of sgRNA in the library, the number of sgRNA with zero read counts,  the GiniIndex of the read count distribution and the frequency distribution of sgRNA in each sample.
Generation of a total read counts table and normalized read count table using MAGECK software (Li et al., 2014)
Identification of positively and negatively selected sgRNA and generation of the corresponding gene list by comparing single samples using MAGeCK tool.
Genome_build: Chinese Hamster Ovary (CHO) CRISPR library.  File used sgRNA sequence is available on the series record.
Supplementary_files_format_and_content: CHO_SLX_8111_190218_counts.txt: raw HiSeq read counts
Supplementary_files_format_and_content: CHO_SLX_8111_190218_counts_normalized.txt: normalized HiSeq read counts
Supplementary_files_format_and_content: S8_S9vsS1_S2.gene_summary.txt: Rank of genes enriched in cells infected with the “derivative enriched Lib2” doxycycline-treated and sorted, relative to cells infected with the “unenriched Lib0” untreated and unsorted

organism: Cricetulus griseus

source_name: Cell line (CHO-K1)_ DNA

growth_protocol: 2.1×10^8 CHO-K1 cells expressing the polymerogenic α1ATH334D mutant under a tetracycline inducible promoter Tet-on were initially  infected with the Library 1 (L1) at a multiplicity of infection (MOI) of 0.3  and selected with 8 µg/ml puromycin for 7 days. Expression of α1AT was induced with 10 ng/ml doxycycline for 24 hrs. Afterwards, the cells were fixed and permeabilised for intracellular staining of α1AT polymers using the polymer-specific monoclonal antibody 2C1 (Mab2C1). Approximately 6.6×10^7 Mab2C1-stained fixed cells were subjected to FACS and collected in 3 bins according to their fluorescence intensity (Mab2C1): ‘brightest' (B), ‘medium' (M) , and ‘dull' (D). Rounds of enrichment were carried on by extracting the genomic DNA of the ‘brightest’-binned fixed cells and recovering by PCR a 220bp fragment containing the sgRNA-bearing region. The amplicon was ligated into the parental lentiviral backbone  to generate derivative enriched libraries (called Lib1 [L1] and Lib2 [L2]) that were used to perform two successive cycles of infection of ~2×10^7 parental CHO-K1 Tet-on_α1ATH334D_Cas9 cells. In each round an equal number of infected, untreated (UT) cells (no doxycycline) or uninfected, doxycycline-treated (T) cells were passed without sorting as a control group.

extract_protocol:
Genomic DNA from fixed, enriched, and sorted populations as well as fixed, unsorted libraries was extracted from ~1-3×106 and ~3.6×107 cells respectively, by incubation in proteinase K solution [100 mM Tris-HCl pH 8.5, 5 mM EDTA, 200 mM NaCl, 0.25% SDS, 0.2 mg/ml Proteinase K] overnight at 50°C. To reverse formaldehyde crosslinks, samples were supplemented with 500 mM NaCl and incubated at 65°C for 16 hrs.
Integrated sgRNA sequences were amplified by nested PCR and the adaptors for Illumina sequencing (HiSeq4000) were introduced at the final amplification round. After quantification the products were subjected to NGS sequencing using custom primer and the illumina indexing primer with single-end reads of 50 bp on a hiseq 4000. The sequences were processed and guide counts, gene rankings and statistics were generated using MAGECK software (Li et al., 2014).

tag: reagent label

tag: treatment

value: Infected with Lib2 (L2)_Treated (T) and Sorted (S)_Medium (M) population


title: S11_SLX-8111.DNAA010_merged

description: Hi Seq 400, Single Read, 50bp

value: Infected with Lib2 (L2)_Treated (T) and Sorted (S)_Dull (D) population


title: 20201205_DlldN-12UB

city: Merced

first: Hans

middle: Tomas

last: Rube

state: CA

address: 5200 North Lake Rd.

department: Bioengineering

institute: UC Merced

description:
synthetic DNA
K_D-seq for Dll
20201205_DlldN-12.1000000.tsv.gz

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

organism: Drosophila melanogaster

source_name: in-vitro purification

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

tag: variable region length

tag: left flank

value: GAGTTCTACAGTCCGACCTGG

tag: right flank

value: CCAGGACTCGGACCTGGA

tag: round / concentrations

value: R1, unbound, [DNA]=20nM, [TF]=100nM


title: 20201205_DlldN-12B

value: R1, bound, [DNA]=20nM, [TF]=100nM


title: 20201205_DlldN-11UB

description:
synthetic DNA
K_D-seq for Dll
20201205_DlldN-11.1000000.tsv.gz

value: R1, unbound, [DNA]=20nM, [TF]=330nM


title: 20201205_DlldN-11B

value: R1, bound, [DNA]=20nM, [TF]=330nM


title: S8_SLX-8111.DNAA003_merged

description: Hi Seq 400, Single Read, 50bp

value: Infected with Lib2 (L2)_Treated (T) and Sorted (S)_Brightest (B) population


title: S9_SLX-8111.DNAA004_merged

description: Hi Seq 400, Single Read, 50bp

value: Infected with Lib2 (L2)_Treated (T) and Sorted (S)_Brightest (B) population (duplicate)


title: S7_SLX-8111.DNAA001_merged

description: Hi Seq 400, Single Read, 50bp

value: Infected with Lib2 (L2)_Untreated (UT) and Unsorted (US) (duplicate)


title: 20201205_DlldN-10UB

description:
synthetic DNA
K_D-seq for Dll
20201205_DlldN-10.1000000.tsv.gz

value: R1, unbound, [DNA]=20nM, [TF]=1000nM


title: 20201205_DlldN-10B


title: S5_SLX-8111.DNAA019_merged

description: Hi Seq 400, Single Read, 50bp

value: Infected with Lib1 (L1)_Treated (T) and Sorted (S)_Medium (M) population


title: S6_SLX-8111.DNAA002_merged

description: Hi Seq 400, Single Read, 50bp

value: Infected with Lib2 (L2)_Untreated (UT) and Unsorted (US)


title: 20201205_DlldN-9UB

description:
synthetic DNA
K_D-seq for Dll
20201205_DlldN-9.1000000.tsv.gz

value: R1, unbound, [DNA]=20nM, [TF]=3300nM


title: F2 Embry.63 T CM WT 363Mu

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

value: Musculus longissimus dorsi

tag: age

value: 63 days post conception (dpc)


title: F2 Embry.63 T CM WT 355Mu

tag: breed


title: F2 Embry.63 T CM WT 340Mu


title: F2 Embry.63 T CM WT 360Mu


title: F2 Embry.63 T CM WT 352Mu


title: F2 Embry.63 T CM WT 338Mu


title: F2 Embry.63 T CM WT 324Mu


title: S4_SLX-8111.DNAA012_merged

description: Hi Seq 400, Single Read, 50bp

value: Infected with Lib1 (L1)_Treated (T) and Sorted (S)_Brightest (B) population

tag: cell line


title: F2 Embry.63 T CM WT 327Mu


title: F2 Embry.63 T CM WT 320Mu


title: F2 Embry.63 T CM WT 329Mu


title: 20201205_DlldN-9B

value: GAGTTCTACAGTCCGACCTGG


title: S3_SLX-8111.DNAA006_merged

description: Hi Seq 400, Single Read, 50bp

value: Infected with Lib1 (L1)_Untreated (UT) and Unsorted (US)


title: F2 Embry.63 T CM WT 370Mu


title: F2 Embry.63 T CM WT 313Mu


title: 20201205_DlldN-8UB

description:
synthetic DNA
K_D-seq for Dll
20201205_DlldN-8.1000000.tsv.gz

value: CCAGGACTCGGACCTGGA

value: R1, unbound, [DNA]=100nM, [TF]=100nM


title: 20201205_DlldN-8B


title: S1_SLX-8111.DNAA005_merged

description: Hi Seq 400, Single Read, 50bp

value: Infected with Lib0 (L0) _Untreated (UT) and Unsorted (US)


title: 20201205_DlldN-7UB

description:
synthetic DNA
K_D-seq for Dll
20201205_DlldN-7.1000000.tsv.gz

value: R1, unbound, [DNA]=100nM, [TF]=330nM


title: Lmb_axenic_C

city: Thiverval-Grignon

first: Jessica

last: SOYER

address: Avenue Lucien Brétignières

institute: INRAE

data_processing:
Mapping against the reference genome of Lmb (Dutreux et al., 2018) or Lml (Grandaubert et al., 2014) using STAR (Langmead and Salzberg, 2012) with default parameters
Genome_build: Lmb (Dutreux et al., 2018); Lml (Grandaubert et al., 2014)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample, rpkm values estimated with function rpkm_count of EdgeR (Robinson et al., 2010)

organism: Plenodomus lingam/Leptosphaeria maculans 'brassicae' group

source_name: mycelium

extract_protocol:
Total RNA was extracted following protocol by Fudal et al. (2007)
The NEBNext Ultra Directional RNA Library Prep Kit for Illumina (cat. # E7420L New England BioLabs) was used to prepare all RNA-seq libraries, following the manufacturer’s instructions. Sequencing was performed by the GenomEast platform, a member of the ‘France Génomique’ consortium (ANR-10-INBS-0009). Samples were run in 9-plex on an Illumina HiSeq 4000 in paired mode, 2x50 bp.

tag: strain

value: mycelium

tag: growth condition

value: axenic


title: DNA methylation from liver sample 6

description:
9247377010_R06C01
Cirrhosis liver sample

data_processing:
BeadStudio software v3.2
Unmethylated_methylated_signal_intensities.txt: Unmethylated and methylated signal intensities, p-values.

source_name: Liver sample 6

extract_protocol: For DNA extraction, we used the Qiagen RNeasy Mini and Invitrogen ChargeSwitch genomic DNA Mini Tissue according to standard instructions.

value: Liver

value: Cirrhosis


title: 20201205_DlldN-7B


title: S2_SLX-8111.DNAA016_merged

description: Hi Seq 400, Single Read, 50bp

value: Infected with Lib0 (L0) _Untreated (UT) and Unsorted (US) (duplicate)


title: Lmb_axenic_A


title: F2 Embry.63 T CM WT 311Mu


title: F2 Embry.63 T CM WT 307Mu


title: F2 Embry.63 T CM WT 312Mu


title: 20201205_DlldN-6UB

description:
synthetic DNA
K_D-seq for Dll
20201205_DlldN-6.1000000.tsv.gz

value: R1, unbound, [DNA]=100nM, [TF]=1000nM


title: F2 Embry.63 T CM WT 303Mu


title: F2 Embry.63 T CM WT 297Mu


title: 20201205_DlldN-6B


title: 20201205_DlldN-5UB

description:
synthetic DNA
K_D-seq for Dll
20201205_DlldN-5.1000000.tsv.gz

value: R1, unbound, [DNA]=100nM, [TF]=3300nM


title: R16_t1h_50mM

city: Jouy-en-Josas

first: Cyprien

last: Guérin

address: INRAE - Domaine de Vilvert

description:
R16_1C_S21
R16_1C_S21

data_processing:
Low quality triming with sickle (version 1.33, options: -t sanger -x -n -q 20 -l 20)
Read mapping using bowtie2 (version 2.2.6, options: -N 1 -L 16 -R 4)
Read counts on each allelic variant were obtained using HTSeq-count (version 0.10.0)
Genome_build: Bc407 reference genome assembly (NC_018877.1)

organism: Bacillus cereus

source_name: Bacteria

growth_protocol: Bc407 was grown in LB medium at 37°C with agitation (200rpm) until the end of the exponential growth phase (OD600= 2). Then bacteria were diluted 1/100 in RPMI 1640 Medium GlutaMAXTM (SKU 61870-010, Thermofisher), and exposed to diverse stresses for 15min or 60min at 37°C without agitation. NOC5 (146724-82-5, Calbiochem) was used as NO donor at a final concentration of 10 and 50µM. Sodium nitrite (7632-00-0 Sigma-Aldrich) was used at 2.5 mM, Potassium nitrate (7757-79-1, Merck) at 20 mM and hydrogen peroxide solution (7722-84-1, Sigma-Aldrich) at 0.03% (V/V)

extract_protocol:
Bacterial pellets were frozen in liquid nitrogen. The pellet introduce in Lysing Matrix B tubes (MP Biomedicals) and high-speed homogenized in FastPrep-24™ 5G Instrument in presence of phenol. Then impurities were extracted from the aqueous phase in three stages: one step with trizol and two with chloroform. The RNAs in the aqueous phase are then precipitated with isopropanol and dissolved in purified water.
Transcriptome library preparation and sequencing was performed by I2BC Paris-Saclay platform on the Illumina NextSeq sequencer to generate paired-end 40 bp reads bearing strand specificity

tag: time

tag: concentration no (um)

tag: biological replicate


title: R16_t1h_10mM

description:
R16_1B_S20
R16_1B_S20


title: R16_t1h_0mM

description:
R16_1A_S19
R16_1A_S19


title: Lmb_axenic_B


title: 20201205_DlldN-4UB

description:
synthetic DNA
K_D-seq for Dll
20201205_DlldN-4.1000000.tsv.gz

value: R1, unbound, [DNA]=500nM, [TF]=100nM


title: 20201205_DlldN-4B


title: R16_t15min_50mM

description:
R16_15C_S18
R16_15C_S18


title: F2 Embry.63 T CM WT 283Mu

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

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

value: Musculus longissimus dorsi


title: R16_t15min_10mM

description:
R16_15B_S17
R16_15B_S17


title: F2 Embry.63 T CM WT 281Mu

value: 63 days post conception (dpc)


title: 20201205_DlldN-3UB

description:
synthetic DNA
K_D-seq for Dll
20201205_DlldN-3.1000000.tsv.gz

value: GAGTTCTACAGTCCGACCTGG

value: R1, unbound, [DNA]=500nM, [TF]=330nM


title: F2 Embry.63 T CM WT 274Mu


title: F2 Embry.63 T CM WT 272Mu


title: MPLE_Intestine_3

city: Santiago

first: Felipe

middle: E.

last: Reyes-López

state: Santiago

address: Av. Libertador Bernado O'Higgins 3363

country: Chile

institute: Universidad de Santiago de Chile

description: A total of 300 gilthead seabream (body weight, BW = 5.0 ± 0.2 g; mean ± standard deviation) were obtained from a commercial fish farm, Piscicultura Marina Mediterránea SL (Andromeda Group, Burriana, Spain) and transported to the experimental facilities of IRTA in Sant Carles de la Ràpita (Tarragona, Spain).

hyb_protocol: The hybridization protocol was carried out according to Agilent's instructions. Briefly, 1.65 μg of Cy3-labeled cRNA (specific activity >6.0 pmol Cy3/mg cRNA) was fragmented at 60°C for 30 min in a total reaction volume of 55 µl containing 25X Agilent fragmentation buffer and 10X Agilent blocking agent. On completion of the fragmentation reaction, 55 µl of 2X GEx hybridization buffer was added to the fragmentation mixture and hybridized to S. aurata array (ID 024502, Agilent) at 65°C and 10 rpm for 17 hours in a rotating hybridization oven.

scan_protocol: After hybridization, microarrays were washed 1 min at room temperature (RT) with GEWash Buffer 1 (Agilent), 1 min with GE Wash buffer 2 (Agilent) pre-incubated at 37°C, 45 s at RT with Acetonitrile (Sigma, St Louis, MO, USA), and 30 s at RT with stabilization and drying solution (Agilent). Slides were scanned immediately afterwashing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area: 61 x21.6 mm; Scan resolution: 5 µm; Dye channel set to green; Green PMT: 100%). Spot intensities and other quality control features were extracted with Feature Extraction software version 10.4.0.0 (Agilent).

data_processing: For microarray analysis, a percentile shift normalization was carried out and then data were filtered by expression (standard deviation) among groups. Then, gene-level analysis was conducted in order to obtain the median of signal intensities from spots within a probe set. Statistical test (t-test unpaired) was done with GeneSpring software GX 14.3 to obtain the differentially expressed genes (p-value < 0.05) between control and treatments.

organism: Sparus aurata

source_name: intestine of gilthead sea bream fed 0.1% MPLE diet pool 3

label_protocol: One-color microarray was carried out according to manufacturer’s protocols. Briefly, 200 ng of total RNA was reversed transcribed along with spike-in (Agilent One-Color RNA Spike-In kit, Agilent Technologies, USA). Then, the solution was used as template for Cyanine-3 (Cy3) labeled cRNA synthesis and amplification with the Low Input Quick Amp Labelling kit (Agilent).  Samples of cRNA were purified using the RNeasy micro kit (Qiagen). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: Total RNA was extracted from GALT using  the RNeasy® Mini Kit (Qiagen, Germany). Total RNA was eluted in a final volume of 35 μL nuclease-free water and treated with DNAse using the DNA-freeᵀᴹ DNA Removal Kit according to manufacturer’s instructions (Invitrogen, Thermo Fisher Scientific, Lithuania). Total RNA concentration and purity were quantified using a Nanodrop-2000® spectrophotometer (Thermo Scientific, USA) and stored at -80 °C until analysis. Prior to hybridization with microarrays, samples were diluted to 133.33 ng/µL concentration and checked for integrity using an Agilent 2100 Bioanalyzer (Agilent Technologies, Spain). All the RNA analysed in this study were selected by the criteria of a RIN value > 8.5.

treatment_protocol: All animal experimental procedures were conducted in compliance with the experimental research protocol approved by the Committee of Ethics and Animal Experimentation of the Institut de Recerca i Tecnologia Agroalimentàries (IRTA) and in accordance with the Guidelines of the European Union Council (86/609/EU) for the use of laboratory animals. After transport, fish received three treatments with hydrogen peroxide and two treatments with formaldehyde (150 ppm, during one hour each) to treat injuries and avoid the presence of any parasite. After the on-growing period of 92 days, 300 fish (BW = 26.0 ± 0.2 g) were randomly distributed in eight aerated 450 L square-shaped tanks with smoothed corners, using an IRTAmar® recirculation system (5-10 % water replacement per day) under natural photoperiod. Water temperature (22-27 °C), oxygen (6.1 ± 0.2 mg/L) and pH (7.2 ± 0.01) were daily controlled, whereas salinity (35‰) as well as ammonia (0.13 ± 0.1 mg NH4+ L−1) and nitrite (0.18 ± 0.1 mg NO2- L−1) levels were weekly monitored. The nutritional assay was carried out in four replicate tanks with an initial density of 2 kg/m3 (35 fish per tank). Fish were fed both diets two times per day at the daily rate of 3.0% of the stocked biomass, which approached apparent satiation.  At day 92 of feeding, three fish were randomly selected from each tank (n total= 12 fish per dietary treatment), euthanized with anaesthetic (MS-222, Sigma-Aldrich) and a section from the mid-anterior intestine was sampled and stored in RNAlater™, incubated overnight at 4 °C, and stored at -80 °C until analysed.

value: Intestine

value: juveniles, 190 g


title: 20201205_DlldN-3B

value: CCAGGACTCGGACCTGGA


title: 20201205_DlldN-5B


title: R16_t15min_0mM

description:
R16_15A_S16
R16_15A_S16


title: R16_t0min_0mM

description:
R16_T0_S15
R16_T0_S15


title: MPLE_Intestine_1

source_name: intestine of gilthead sea bream fed 0.1% MPLE diet pool 1


title: Control_Intestine_3

source_name: control group pool 3

value: juveniles, 174 g


title: MPLE_Intestine_2

source_name: intestine of gilthead sea bream fed 0.1% MPLE diet pool 2


title: 20201205_DlldN-2UB

description:
synthetic DNA
K_D-seq for Dll
20201205_DlldN-2.1000000.tsv.gz

value: R1, unbound, [DNA]=500nM, [TF]=1000nM


title: 20201205_DlldN-2B


title: Control_Intestine_1

source_name: control group pool 1


title: Control_Intestine_2

source_name: control group pool 2


title: HUVECs cells stimulated with Mannitol+nLDL rep2

city: Nanjing

first: Zhiguang

last: Shi

address: 101Longmian Avenue, Jiangning District

institute: Nanjing Medical University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using HISAT2 v2.1.0 with parameters -x --no-unal --un-conc
Fragments Per Kilobase of exon model per Million mapped fragments(FPKM) were calculated using RSEM v1.3.0 with default parameters.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with FPKM for every gene and every sample

source_name: umbilical cord

growth_protocol: HUVECs were  isolated from human umbilical cords, cultured in Endothelial Cell Medium (ECM, ScienCell, CA, USA) supplemented with 5% FBS and endothelial cell growth supplement (ECGS) at 37 ℃ in an incubator with 5% CO2. Cells at fourth passages were used for isolation of total RNA

extract_protocol:
HUVECs were washed with PBS,  RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HUVECS were treated with HG (25mM) and oxLDL (50 μg/ml) for 24 hours, the negative control cells were treated with Mannitiol  (25mM) and nLDL  (50 μg/ml) for 24 hours

value: Mannitol (25mM) + nLDL (50 ug/ml) for 24 hours


title: HUVECs cells stimulated with HG+oxLDL rep2

value: HG (25mM) + oxLDL (50 ug/ml) for 24 hours


title: HUVECs cells stimulated with HG+oxLDL rep1


title: R14_t1h_0mM

description:
R14_1A_S12
R14_1A_S12


title: R14_t15min_50mM

description:
R14_15C_S11
R14_15C_S11


title: sh-FGD5-AS1-rep3

city: Shanghai

first: Xingyu

last: Zhang

address: No.1678, Dong Fang Road

institute: Shanghai Jiaotong University School of Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequence quality was analyzed by FastQC v 0.11.9. Read pairs with low quality were removed using Trim_Galore! v 0.6.5 and  rRNA Sequences  were removed with SortMeRNA v 2.1.
The clean data were aligned to human reference genome  using STAR v2.7.
Gene counts were summarized using  featureCounts v 2.0.0.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample.

source_name: human embronic heart tissue

growth_protocol: The CCC-HEH-2 human cardiac myocytes were were cultured in Dulbecco's modified Eagle's medium  containing 10% fetal bovine serum at 37°C with 5% CO2.

extract_protocol:
The complete cellular RNA was extracted with TRIzol reagent, and  1 ug of total RNA was reverse transcripted into cDNA by  Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001)  for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard IIIumina protocols.

value: human embronic heart tissue

tag: gender

value: male

value: 11 weeks

tag: genotype


title: R14_t1h_10mM

description:
R14_1B_S13
R14_1B_S13


title: 20201205_DlldN-1B

description:
synthetic DNA
K_D-seq for Dll
20201205_DlldN-1.1000000.tsv.gz


title: sh-FGD5-AS1-rep2

tag: tissue


title: 20201205_R0

description:
synthetic DNA
K_D-seq input


title: sh-FGD5-AS1-rep1


title: R14_t15min_10mM

description:
R14_15B_S10
R14_15B_S10


title: R14_t1h_50mM

description:
R14_1C_S14
R14_1C_S14


title: R14_t15min_0mM

description:
R14_15A_S9
R14_15A_S9


title: HUVECs cells stimulated with Mannitol+nLDL rep1


title: R14_t0min_0mM

description:
R14_T0_S8
R14_T0_S8


title: sh-NC-rep3

value: sh-NC


title: R12_t1h_50mM

description:
R12_1C_S7
R12_1C_S7


title: sh-NC-rep2


title: 20201205_DlldN-1UB

value: R1, unbound, [DNA]=500nM, [TF]=3300nM


title: R12_t1h_0mM

description:
R12_1A_S5
R12_1A_S5


title: R12_t15min_50mM

description:
R12_15C_S4
R12_15C_S4


title: sh-NC-rep1


title: R12_t15min_10mM

description:
R12_15B_S3
R12_15B_S3


title: R12_t0min_0mM

description:
R12_T0_S1
R12_T0_S1


title: R12_t1h_10mM

description:
R12_1B_S6
R12_1B_S6


title: wildtype_control_rep9

status: Public on Jun 01 2021

city: Cologne

first: Tak

last: Lee

address: Carl-von-Linne weg 10

institute: Max Planck Institute for Plant Breeding Research

data_processing:
RNAseq reads of FASTQ format were processed to remove low quality reads and reads containing adapter and poly-N sequences. Q20, Q30 and GC content of the clean data were calculated
The quality of the FASTQ files were validated with FastQC (v0.11.8)
The resulting reads from the raw fastq data were quality controlled and and mapped to the O. sativa reference genome Os-Nipponbare-Reference-IRGSP-1.0 using STAR (2.7.3a)
The raw counts and FPKM (Fragments per kilobase per million mapped reads) values were calculated with featureCounts in R package Rsubread (2.0.0)
The TPM (Transcripts per million) values were calculated by custom python script using the raw counts file
Genome_build: Os-Nipponbare-Reference-IRGSP-1.0
Supplementary_files_format_and_content: tab separated files with the corresponding expression values

organism: Oryza sativa Japonica Group

source_name: whole root

growth_protocol: Plants were watered every second day, the first two weeks with reverse osmosis water (R-O H2O) followed by low Pi fertilization every other watering day with half-strength Hoagland solution containing 25 μM KH2PO4.

extract_protocol:
RNA was extracted using the TRIzol method
1 μg RNA per sample was used for library preparation generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, Hitchin, United Kingdom) following manufacturer’s instructions. Library quality was monitored on the Agilent Bioanalyzer 2100 system

treatment_protocol: The AM fungal model species R. irregularis (DAOM197198) was employed for all inoculation assays. Spores extracted from Agrobacterium rhizogenes transformed carrot hairy root cultures (Bécard and Fortin, 1988) were used. Aliquoted inoculum was applied onto the substrate of half-filled cones (12 cm depth, 2.5 cm diameter), after which sand substrate was replenished and germinated seedlings transferred to the containers.

tag: cultivar

value: Nipponbare

tag: inoculum

value: R. irregularis (DAOM197198)

value: wild type

value: whole root


title: wildtype_control_rep10


title: wildtype_control_rep6


title: wildtype_control_rep7


title: Plate3_15_E0771shControl

description: shControl rep3

source_name: breast cancer cells

value: breast cancer

tag: genotype/variation

value: shControl


title: wildtype_control_rep5


title: S27336_MB: Medulloblastoma, #4

city: Chiba

first: Kazuhiro

last: DAINO

address: 4-9-1 Anagawa, Inage-ku

country: Japan

institute: National Institutes for Quantum and Radiological Science and Technology

description: Medulloblastoma, #4

hyb_protocol: Slides were hybridised in 1X Agilent Blocking Agent/Hi-RPM Buffer for 24 hours at 67°C in a rotating hybridization oven, then washed with the Agilent Oligo aCGH Buffer 1 and Buffer 2 in an ozone-depleted hood.

scan_protocol: Scanned on an Agilent microarray scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

source_name: Medulloblastoma of neutron-irradiated mouse

label_protocol: Labeling reactions with cyanine 5-UTP and cyanine 3-UTP were performed according to the Agilent SureTag DNA labeling kit (Agilent Technologies, Santa Clara, CA, USA).

growth_protocol: Mice were housed in autoclaved cages and maintained in a room with a controlled temperature (23 ± 1°C) and humidity (50 ± 5%) under a regular 12-hours light, 12-hours dark cycle. They were fed a standard laboratory animal diet (MBR-1; Funabashi Farm, Tokyo, Japan) and sterilized water ad libitum.

extract_protocol: Genomic DNA was extarcted by QIAmp DNA Micro kit (Qiagen).

treatment_protocol: Mice were left untreated or were subjected to whole-body irradiated with neutrons at postnatal day 4 or 10.

value: Medulloblastoma

value: Female

value: Ptch1+/- mice with a hybrid C3H × C57BL/6 F1

source_name: Normal ear

value: Ear skin


title: wildtype_control_rep4


title: DCN_non-tinnitus_rep1

city: Seoul

first: Munyoung

last: Chang

address: 102 Heukseok-ro, Dongjak-gu

department: Otorhinolaryngology-Head and Neck Surgery

country: South Korea

institute: Chung-Ang University College of Medicine

description: miRNA expression at 3 weeks post noise exposure in rat dorsal cochlear nucleus without tinnitus

hyb_protocol: Labeled samples were hybridized to GeneChip miRNA 4.0 microarrays (Affymetrix Inc., Santa Clara, CA). A hybridization mixture including control oligo B2, 20× hybridization controls (bioB, bioC, bioD, cre), 27.5% formamide, DMSO, 2× hybridization buffer, and water was applied to all samples. Hybridization was performed in an Affymetrix GeneChip Hybridization Oven 640 at 48°C and 60 rpm for 16 h overnight. Arrays were stained with stain cocktails (stain cocktails 1 and 2) and washed in an Affymetrix GeneChip Fluidics Station 450 using the FS450_0002 fluidics protocol.

scan_protocol: Processed microarray slides were scanned with an Affymetrix GeneChip Scanner 3000 (Affymetrix Inc., Santa Clara, CA).

data_processing:
All arrays were analyzed using Transcriptome Analysis ConsoleTM (TAC) software. CEL files were generated and imported into the Gene Expression Workflow in GeneSpring GX version 14.9.1 (Agilent Technologies Inc., Santa Clara, CA). Background correction, log2 transformation, and probe set summarization were conducted using default settings in GeneSpring software. Subsequent principal component analysis was conducted using a covariance dispersion matrix, as part of the quality control of data. Unpaired t-tests were performed to compare the individual gene expression data.
rawdata_all probe.xlsx contains all the information.

source_name: Dorsal cochlear nucleus, 3w, noise exposure, non-tinnitus, replicate 1

label_protocol: RNA was labeled using the FlashTag Biotin RNA Labeling Kit (Affymetrix Inc., Santa Clara, CA).

extract_protocol: RNA was extracted from the sample using the TRI REAGENT (MRC, Cincinnati, OH, USA) according to the manufacturer’s instructions. Following homogenization, 1 ml of solution was transferred to a 1.5 ml Eppendorf tube and centrifuged at 12,000 g for 10 min at 4°C to remove insoluble material. The supernatant containing RNA was collected, mixed with 0.2 ml of chloroform, and centrifuged at 12,000 g for 15 min at 4°C. After RNA in the aqueous phase was transferred into a new tube, the RNA was precipitated by mixing 0.5 ml of isopropyl alcohol and recovered by centrifuging the tube at 12,000 g for 10 min at 4°C. The RNA pellet was washed briefly in 1 ml of 75% ethanol and centrifuged at 7,500 g for 5 min at 4°C. Finally, the total RNA pellet was dissolved in Nuclease-water, and its quality and quantity was assessed by Agilent bioanalyzer 2100 analysis.

treatment_protocol: Twelve week-old-male Sprague-Dawley rats were used. All rats were exposed to 6-8 kHz narrow-band noise at 110 dB SPL for 2 h, with the left ear plugged and sutured.

value: Sprague-Dawley

tag: group

value: non-tinnitus

value: dorsal cochlear nucleus of brain tissue


title: S26391_MB: Medulloblastoma, #2

description: Medulloblastoma, #2

value: Male


title: wildtype_control_rep2


title: S26447_MB: Medulloblastoma, #3

description: Medulloblastoma, #3


title: DCN_non-tinnitus_rep2

source_name: Dorsal cochlear nucleus, 3w, noise exposure, non-tinnitus, replicate 2

value: male


title: R12_t15min_0mM

description:
R12_15A_S2
R12_15A_S2


title: DCN_non-tinnitus_rep3

source_name: Dorsal cochlear nucleus, 3w, noise exposure, non-tinnitus, replicate 3


title: CD73+ AD-MSCs of mice rep3

city: Xinxiang

first: Huifang

last: Hou

address: 601 Jinsui Avenue

institute: Xinxiang Medical University

description: CD73+AD-MSCs were isolated using flow cytometry and then cultured.

hyb_protocol: Following fragmentation, 10ug of cRNA were hybridized for 16 hr at 45C on PrimeView Human Gene Expression Array. GeneChips were washed and stained in the GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 .

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method.

source_name: CD73 positive adipose derived mesenchymal stem cells of the C57BL/6 mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 12ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells were cultured with low sugar DMEM(Dulbecco’s modified Eagle’s medium) containing 10% FBS (Fetal bovine serum; Hyclone, USA).

extract_protocol: Total RNA were extracted using Trizol. The RNA quantity and quality were measured by NanoDrop 2000.

treatment_protocol: The same number of cells were digested and centrifuged, and then the cells were collected in RNA enzyme free Ep tubes.

tag: cell type

value: AD-MSCs were isolated from adipose tissues surrounding the groin of mice.


title: S26303_MB: Medulloblastoma, #1

description: Medulloblastoma, #1


title: DCN_tinnitus_rep3

description: miRNA expression at 3 weeks post noise exposure in rat dorsal cochlear nucleus with tinnitus

source_name: Dorsal cochlear nucleus, 3w, noise exposure, tinnitus, replicate 3

value: tinnitus


title: CD73+ AD-MSCs of mice rep1


title: CD73- AD-MSCs of mice rep1

description: CD73- AD-MSCs were isolated using flow cytometry and then cultured.

source_name: CD73 negative adipose derived mesenchymal stem cells of the C57BL/6 mice


title: CD73- AD-MSCs of mice rep3


title: CD73+ AD-MSCs of mice rep2


title: DCN_tinnitus_rep2

source_name: Dorsal cochlear nucleus, 3w, noise exposure, tinnitus, replicate 2


title: wildtype_control_rep1

value: Nipponbare


title: DCN_tinnitus_rep1

source_name: Dorsal cochlear nucleus, 3w, noise exposure, tinnitus, replicate 1


title: ark1ark2_doublemutant_rep10

value: R. irregularis (DAOM197198)

value: ark1ark2 double mutant


title: wildtype_control_rep8

value: wild type

value: whole root