title: H520.Cntrl1

description: RNA-Seq data, H520 Cell Line, Control Treatment, replicate 1


title: Antral epithelial cells, freshly extracted, replica 3

status: Public on Aug 21 2023

type: SRA

city: Lausanne

first: Matthias

last: Lutolf

address: Route Cantonale

country: Switzerland

institute: EPFL

library_source: transcriptomic

data_processing:
Alignment with STAR version 2.7.0e
Default parameters except peOverlapNbasesMin=12, peOverlapMMp=0.1, quantMode=geneCounts
Assembly: mm10
Supplementary files format and content: tab-delimited raw counts

molecule: total RNA

organism: Mus musculus

source_name: Antral epithelium

extract_protocol:
Rneasy Micro Kit (Qiagen)
QuantSeq 3' mRNA-Seq Library Prep Kit FWD

tag: tissue

value: Antral epithelium


title: aHepGHRkd _replicate2_D4

city: Boston

first: David

middle: J.

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

country: USA

institute: Boston University

data_processing:
RNA-seq data was processed using a custom pipeline, as described in Connerney et al., 2017 (PMID: 28323953)
Sequence reads were mapped to the mouse genome (mm9) using STAR aligner.
FeatureCounts (Liao, 2014, Bioinformatics) was used to obtain read counts for a total of 75,798 genes, including RefSeq genes and lncRNA genes defined in: Goldfarb CN et al, Endocrinology (2022) PMID: 35512247. Mature (spliced) RNAs were quantified by counting sequence reads that map to a concatenated sequence comprised of the union of the exonic regions for all isoforms of a given gene.
Differential expression analysis was performed with edgeR as described in Robinson et al., 2010 (PMID: 19910308)
Assembly: mm9
Supplementary files format and content: Microsoft Excel file containing normalized read counts and differential expression results for a set of 75,798 mouse mm9 genes comprised of the following: n = 20,884 RefSeq protein coding genes, n=48,360 mouse liver-expressed lncRNAs genes, n=2,061 RefSeq non-coding genes (NR accession numbers) that do not overlap with the set of 48,360 lncRNAs, n =4,490 Ensembl non-coding lncRNAs that do not overlap either the RefSeq NR gene set or the 48,360 lncRNA gene set, and n=3 other lncRNAs with interesting liver functions (lnc-LFAR1, LeXis, Lnclgr). Further details about these genes are provided in the annotation fields of the processed data file and in Goldfarb CN et al, Endocrinology (2022) PMID: 35512247.

source_name: liver

growth_protocol: All Ghrfl/fl mice were housed in a specific pathogen-free barrier facility maintained at 22-24C with a 12h light/12h dark cycle and were fed standard chow diet.

extract_protocol:
Livers were weighed and snap-frozen in liquid nitrogen and stored at -80C.  Total RNA from livers (6 mice/group), from GHR-intact controls, aHepGHRkd, aHepGHRkd+rIGF1 and aHepGHRkd+STAT5bCA mice were extracted using Rneasy Plus Mini Kit (Cat# 74134; Qiagen). Total RNA was quality checked (RIN>7) using the Agilent Bioanalyser 2100 system.
polyA-seelcted RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: aHepGHRkd were generated by treating 10-12 week-old male and female Ghrfl/fl littermates with a single lateral tail vein injection of 1.5*E11 genome copies (GC) of an adeno-associated virus serotype 8 (AAV8) vector bearing a hepatocyte-specific thyroxine-binding globulin promoter (TBGp) driving a Cre recombinase transgene [AAV8-TBGp-Cre; AAV.TBG.PI.Cre.rBG (AAV8), Addgene, Watertown, MA, diluted in 100ul sterile PBS)]. To maintain hepatocyte IGF1 expression in aHepGHRkd, a subset of mice were co-injected with AAV8-TBGp-Cre (1.5*E11 GC) + AAV8-TBGp-rIGF1 (2.0*E11 GC; AAV8.TBG.PI.ratIGF1.WPRE.bGH). In a subset of mice, a constitutively active STAT5b (STAT5bCA) was used to sustain STAT5b activity in aHepGHRkd, by co-injecting with AAV8-TBGp-Cre (1.5*E11 GC) + AAV8-TBGp-STAT5bCA (0.75*E11 GC; AV8.TBG.PI.N-FLAG-mSTAT5bCA.WPRE.bGH). Injection of an AAV8-TBGp-Null (pAAV8.TBG.PI.Null.bGH, Addgene) was used to generate control mice and to equalize the total amount of AAV8 injected in each mouse across groups (3.5*E11 GC).

tag: group

value: aHepGHRkd

tag: replicate

value: liver

tag: strain

tag: cell type

value: Hepatocyte

tag: Sex

value: Male

tag: genotype

value: GHRfl/fl

tag: age

value: 10-12 weeks-old

tag: time point

value: 7 days after AAV-injection

tag: diet

value: Chow diet


title: NMR, Liver, CEBPA, NMR35, vl0427

city: London

first: Diego

last: Villar

address: 4 Newark Street, Blizard Institute

country: United Kingdom

institute: Queen Mary University of London

description: ChIP-seq

library_source: genomic

data_processing:
ChIP-seq peak files were generated my MACS2 callPeak function (default parameters).
4C data was processed with pipe4C (Krijger et al. 2020)
Supplementary files format and content: MACS2 peak files for each ChIP and input combination (.narrowPeak extension)
Supplementary files format and content: 4C wig files for each 4C experiment

molecule: genomic DNA

organism: Heterocephalus glaber

source_name: Liver

extract_protocol:
Tissues were prepared by direct perfusion of the liver with PBS, followed by dicing the whole organs (liver and heart) in small pieces around 1cm3. Blood clots within the heart ventricles were removed. Cross-linking of the diced tissue was performed in 1% formaldehyde solution for 20 min, addition of 250 mM glycine and incubation for a further 10 min to neutralize the formaldehyde. After homogenization of cross-linked tissues in a dounce tissue grinder, samples were washed twice with PBS and lysed according to published protocols (SCHMIDT et al. 2009 for ChIP and Krijger et al. 2020 for 4C) to solubilize DNA-protein complexes. For ChIP, chromatin was fragmented to 300 bp average size by sonication on a Misonix sonicator 3000 with a 418 tip (1/16 inch diameter). Chromatin from 50-200 mg of dounced tissue was used for each ChIP experiment using antibodies against H3K4me3 (millipore 05-1339), H3K27ac (abcam ab4729), H3K4me1 (abcam ab8895), TBX5 (Insight bio sc-515536), RXRA (sc-553), FOXA1 (ab70382), HNF4A (ARP31946), CEBPA (sc-9314) and HNF6 (sc-13050). For 4C, locus-specific 4C templates were made using two rounds of enzyme digestion (primary and secondary) and ligation. Purified 4C templates were amplified by inverse PCR with bait-specific primers.
Illumina sequencing libraries were prepared from ChIP-enriched or 4C-enriched DNA using ThruPLEX DNA-seq library preparation kit (Takara Bio) or NEBNext Ultra II DNA Library Prep Kit for Illumina with up to 10ng of input DNA and 8-15 PCR cycles. After PCR, libraries were pooled in equimolar concentrations and sequenced on Illumina HiSeq 4000, NextSeq 500 or NovaSeq 6000 instruments.
ChIP-Seq, 4C-Seq

treatment_protocol: We performed chromatin immunoprecipitation experiments followed by high throughput sequencing (ChIP-seq) or 4C-seq using liver and heart tissue samples isolated from naked mole-rat, Damaraland mole-rat, guinea pig and mouse. At least two independent biological replicates from different animals were performed for each species and antibody. Wherever possible, tissues from young adult males were used. Tissues were prepared immediately post-mortem (typically within an hour) to maximize experimental quality. Post-mortem tissues were kept on ice until processed to minimize potential loss of protein-DNA interactions during post-mortem time. Sample allocations to experimental batches were randomised to ensure unbiased distributions of species, tissue, individual and sex, using the R/Bioconductor package OSAT (YAN et al. 2012).

value: Liver

value: wild-type

tag: developmental stage

value: adult

tag: age (months)

value: male

tag: individual

tag: antibody

value: CEBPA

tag: treatment


title: miR-34abc-KO_5FU_1

city: Munich

first: Markus

last: Kaller

address: Thalkirchner Str. 36

country: Germany

institute: LMU Munich

data_processing:
alignment : RNA-Seq FASTQ files were processed using the RNA-Seq module implemented in the CLC Genomics Workbench v20.0.2 software (Qiagen Bioinformatics) and mapped to the GRCh38/hg38 human reference genome and its associated gene and transcript annotation (ENSEMBL) using the settings mismatch cost = 2, insertion cost = 2, deletion cost = 3, length fraction = 0.8, similarity fraction = 0.8
expression : RNA-Seq FASTQ files were processed using the RNA-Seq module implemented in the CLC Genomics Workbench v20.0.2 software (Qiagen Bioinformatics) and mapped to the GRCh38/hg38 human reference genome and its associated gene and transcript annotation (ENSEMBL) using the settings mismatch cost = 2, insertion cost = 2, deletion cost = 3, length fraction = 0.8, similarity fraction = 0.8
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text files include raw gene counts for each sample

organism: Homo sapiens

growth_protocol: The human colorectal cancer cell line HCT116 and its derivatives generated here were grown in McCoy’ 5A medium (Invitrogen, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (FBS) (Invitrogen), 100 units/ml penicillin and 0.1 mg/ml streptomycin

extract_protocol:
Total RNA from HCT116 cells was isolated using the High Pure RNA Isolation Kit (Roche) with an on-column DNase digestion.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: colon

tag: cell line


title: wildtype_5FU_3


title: NMR, Liver, HNF4A, NMR35, vl0424

description: ChIP-seq


title: NMR, Liver, CEBPA, NMR30, vl0426

description: ChIP-seq


title: Control _replicate6_D24

value: Control


title: aHepGHRkd _replicate6_D19


title: Antral epithelial cells, freshly extracted, replica 1


title: Antral epithelial cells, freshly extracted, replica 2


title: aHepGHRkd _replicate1_D2


title: NMR, Liver, HNF4A, NMR30, vl0423

description: ChIP-seq


title: wildtype_5FU_2


title: NMR, Liver, FOXA1, NMR35, vl0421

description: ChIP-seq


title: Control _replicate5_D21


title: Control _replicate4_D18


title: NMR, Liver, FOXA1, NMR30, vl0420

description: ChIP-seq


title: BJIKT treated  AD mice fed a Low Ahr ligand diet_4

city: Daejeon

first: You Mee

last: Ahn

address: Yuseong-daero, Yuseong-gu

country: South Korea

institute: KOREA INSTITUTE OF ORIENTAL MEDICINE

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

source_name: Skin

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

value: Skin

value: WT

value: Low AhR + AD +BJ


title: BJIKT treated  AD mice fed a Low Ahr ligand diet_3


title: BJIKT treated  AD mice fed a Low Ahr ligand diet_2


title: miR-34abc-KO_3

value: control


title: NMR, Liver, RXRA, NMR35, vl0418

description: ChIP-seq

value: RXRA


title: miR-34abc-KO_2


title: Control _replicate3_D10

value: liver

value: Hepatocyte

value: Male


title: Control _replicate2_D9

value: GHRfl/fl

value: 10-12 weeks-old

value: 7 days after AAV-injection


title: NMR, Liver, RXRA, NMR30, vl0417

description: ChIP-seq

value: Liver

value: wild-type


title: AD mice fed a Low Ahr ligand diet group_4

value: Low AhR + AD


title: Control _replicate1_D1

value: Chow diet


title: BJIKT treated  AD mice fed a Low Ahr ligand diet_1


title: miR-34abc-KO_1

value: colon


title: DMR, Liver, input, DMR3,  vl0071

organism: Fukomys damarensis

value: adult

value: 36 (estimated)

value: male

value: input


title: wildtype_3

value: control


title: murine liver, BV

city: Beijing

first: Pan

last: Shen

address: Courtyard 27, Taiping Road

country: China

institute: BIRM

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software (verison 7.0.0).
Assembly: mm10
Supplementary files format and content: Scaled expression matrix files

extract_protocol:
Mice were anesthetized using pentobarbital sodium and the livers were perfused with a two-step perfusion method through portal vein. Pre-warmed first perfusion solution (ionized water containing 8 mg/mL NaCl, 0.402 mg/mL KCl, 0.094 mg/mL NaH2PO4·2H2O, 0.2865 mg/mL Na2HPO4·12H2O, 2.383 mg/mL HEPES, 0.19 mg/mL EGTA, 0.3528 mg/mL NaHCO3 and 0.901 mg/mL glucose, pH = 7.4) was perfused at a rate of 6 mL/min for about 8 minutes, followed by the perfusion of pre-warmed second perfusion solution (DMEM medium containing 0.6 mg/mL type VI collagenase, 0.1 mg/mL trypsin inhibitor, 1 mg/mL DNase I, 5 mg/mL BSA, 5 mM CaCl2, pH = 7.4) at a rate of 5 mL/min for 6 minutes. The perfused liver was subsequently dissected using forceps and dissociated with the digestion solution (DMEM medium containing 5 mg/mL BSA and 5 Mm EDTA) for 10 minutes to obtain single-cell suspension. Hepatocytes and non-parenchymal cells (NPCs) were then separated through a centrifugation at 50 g for 3 minutes. For each group, equal amount of the same type of cells from distinct mouse were mixed. Dead cells in hepatocytes and non-parenchymal cells were removed separately using Dead Cell Removal Kit (Miltenyi Biotec, 130-090-101) for higher sequencing quality.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Kunming mice

value: 6-8 weeks old

value: 200 mg/kg bavachin

tag: time

value: 7 days


title: wildtype_5FU_1

tag: tissue


title: DMR, Liver, input, DMR6,  vl0069

value: 48 (estimated)

value: female


title: AD mice fed a Low Ahr ligand diet group_2

value: Skin

value: WT


title: wildtype_2

value: wild-type


title: DMR, Heart, input, DMR1,  vl0067

source_name: Heart

value: Heart


title: wildtype_1


title: LC_M22_4

city: Sacramento

first: Ying

last: Hu

email: yinghu0821@gmail.com, yighu@ucdavis.edu

state: CA

address: 4645 2nd Ave, Research III building, 3400 Suite

department: Department of Pathology and Laboratory Medicine

institute: UC Davis

data_processing:
Libraries were sequenced on Novaseq6000 using PE150 sequencing. Reads quality was checked using the fastqc (v0.11.7, https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
RNA-Seq data was analyzed using a Salmon-tximport-DESeq2 pipeline. The pair-ended reads (FASTQ format) were mapped to the reference mouse genome assembly (GRCm39, GENCODE release 25) and quantified with Salmon.
Gene-level counts were imported with tximport and differential expression analysis was performed with DESeq2 (version 1.18) with the corrected p value < 0.05 and fold change > 1.5.
Assembly: mm39
Supplementary files format and content: tab-delimited text files include normalized read count values for each Sample

growth_protocol: Female 6-week-old FVB/N mice were obtained from the Jackson Laboratory (Sacramento, CA, USA). Liver tumors were produced via sleeping beauty transposon (SB)-mediated hydrodynamic injection using the plasmids pT3-EF1α-HA-myr-AKT, pT3-EF1α-N90-β-catenin, pT/Caggs-Nras-v12, and pCMV-SB11. Briefly, the oncogene plasmids along with SB were diluted in 2 mL phosphate-buffered saline (PBS) and injected into mouse tail vein within 5~7 seconds.

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Total RNA was extracted using TRIzol Reagent ) . 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using using NEBNext Ultra II non-directional RNA Library Prep kit (New England Biolabs, Inc., Ipswich, MA, USA). Library quality and concentration were assessed with Labchip and qPCR.

treatment_protocol: miR-22 was delivered by adeno-associated virus vector, serotype 8 (AAV8, Applied Biological Materials Inc., Richmond, BC, USA). One dose (1x1012 GC/kg) of AAV8-miR-22 or AAV8 blank control was injected intravenously at one-week post oncogene injection. Livers were harvested at 5-week post oncogene injection.

value: Liver

value: WT with HCC

value: AAV overexpressed miR-22

value: 4 weeks


title: Low Ahr ligand diet group_4

value: Low AhR


title: AD mice fed a Low Ahr ligand diet group_1

value: Low AhR + AD


title: DMR, Liver, H3K4me1, DMR6,  vl0061

value: adult


title: LC_M22_3


title: DMR, Liver, H3K27ac, DMR6,  vl0060


title: normal3, RNA-seq

city: Weifang

first: Dongyuan

last: Sun

state: Shandong

address: 7166,BaoTong West Street

institute: Weifang Medical University

description:
N3.Input
LncRNA Expression Profiling.xlsx
Gene Expression Profiling.xlsx
CircRNA Expression Profiling.xlsx

data_processing:
Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30.
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3).
circRNA: The high quality reads were aligned to the reference genome/transcriptome with STAR software (v2.5.1b) and circRNAs were detected and identified with DCC software (v0.4.4). edgeR software (v3.16.5) was used to normalized the data and perform differentially expressed circRNA analysis. GO and KEGG analysis were performed for the differentially expressed circRNA-associated genes.
LncRNA & mRNA: The high quality reads were aligned to the reference genome with hisat2 software (v2.0.4). Then, HTSeq software (v0.9.1) was used to get the gene level (mRNA) and transcript level (lncRNA) raw count as the expression profiling, and edgeR (v3.16.5) was used to perform normalization and differentially expressed mRNAs were identified by p-value and fold change. GO and Pathway enrichment analysis were also performed based on the differentially expressed mRNAs. LncRNA target genes were predicted by the locations to nearby genes. And GO and Pathway analysis were performed on these target genes.
Assembly: HG19
Supplementary files format and content: excel files:Expression Profiling for each sample

source_name: normal tissues

growth_protocol: Tissue with a diameter of 0.5~1 cm was taken from the centre of the patient's OSCC tissue. Normal tissue of similar size was taken from the patient at a distance of more than 3 cm from the OSCC tissue edge.

extract_protocol:
Total RNA extraction was provided by Cloud-seq Biotech Inc. (Shanghai, China). RNA was extracted using TRIzol Reagent (Invitrogen, Carlsbad,CA, USA) according to the manufacturer's instructions.A NanoDrop ND-1000 instrument (Thermo Fisher Scientific, Waltham, MA, USA) was used to measure the RNA concentration of each sample, controlling OD 260/280 values of 1.8-2.1 to ensure good RNA purity.
RNA high throughput sequencing was performed by Cloud-Seq Biotech (Shanghai, China). Briefly, total RNA was used for removing the rRNAs with GenSeq® rRNA Removal Kit (GenSeq, Inc.). Then, the rRNA-depleted samples were subjected to library construction with GenSeq® Low Input RNA Library Prep Kit (GenSeq, Inc.) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an Illumina Novaseq instrument with 150bp paired end reads.

treatment_protocol: The samples were collected, rinsed with saline, and rapidly cryopreserved in liquid nitrogen.

value: normal tissues

tag: merip antibody


title: normal2, RNA-seq

description:
N2.Input
LncRNA Expression Profiling.xlsx
Gene Expression Profiling.xlsx
CircRNA Expression Profiling.xlsx


title: LC_M22_2


title: Low Ahr ligand diet group_3


title: normal1, RNA-seq

description:
N1.Input
LncRNA Expression Profiling.xlsx
Gene Expression Profiling.xlsx
CircRNA Expression Profiling.xlsx


title: DMR, Liver, H3K4me1, DMR3,  vl0059

value: 36 (estimated)

value: male


title: cancer3, RNA-seq

description:
C3.Input
LncRNA Expression Profiling.xlsx
Gene Expression Profiling.xlsx
CircRNA Expression Profiling.xlsx

source_name: OSCC tissues

value: OSCC tissues


title: LC_AC_3

value: AAV blank control


title: DMR, Liver, H3K27ac, DMR3,  vl0058


title: AD mice fed a Low Ahr ligand diet group_3


title: Low Ahr ligand diet group_1


title: LC_AC_4

value: female


title: cancer2, RNA-seq

description:
C2.Input
LncRNA Expression Profiling.xlsx
Gene Expression Profiling.xlsx
CircRNA Expression Profiling.xlsx


title: DMR, Heart, H3K27ac, DMR11,  vl0056

value: 48 (estimated)


title: DMR, Heart, H3K27ac, DMR3,  vl0055


title: Control_4

value: Skin

value: WT

value: Control


title: Control_3


title: murine liver, control

description: 10x Genomics

value: Liver

value: Kunming mice

value: 6-8 weeks old

value: normal saline

value: 7 days


title: HL_3

value: No treatment as a baseline control

value: No treatment


title: HL_2


title: Control_2


title: DMR, Heart, input, DMR3,  vl0052

value: Heart

value: wild-type

value: adult

value: input


title: HL_1


title: normal3, MeRIP-seq

description:
N3.IP
Methylated_RNA_sites.circRNA.xlsx
Methylated_RNA_sites.LncRNA.xlsx
Methylated_RNA_sites.mRNA.xlsx

data_processing:
Briefly, Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30.
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). First, clean reads of input libraries were aligned to reference genome by STAR software.
Then circRNAs were identified by DCC software using the STAR alignment results. After that, clean reads of all libraries were aligned to the reference genome by Hisat2 software (v2.0.4).was used to normalized the data and perform differentially expressed circRNA analysis. GO and KEGG analysis were performed for the differentially expressed circRNA-associated genes.
Methylated sites on RNAs (peaks) were identified by MACS software. Differentially methylated sites were identified by diffReps. These peaks identified by both softwares overlapping with exons of mRNA, LncRNA and circRNA were figured out and chosen by home-made scripts.
Assembly: HG19
Supplementary files format and content:  excel files:Methylated sites for each Sample

extract_protocol:
Total RNA extraction was provided by Cloud-seq Biotech Inc. (Shanghai, China). RNA was extracted using TRIzol Reagent (Invitrogen, Carlsbad,CA, USA) according to the manufacturer's instructions.A NanoDrop ND-1000 instrument (Thermo Fisher Scientific, Waltham, MA, USA) was used to measure the RNA concentration of each sample, controlling OD 260/280 values of 1.8-2.1 to ensure good RNA purity.
The m7G-IP-Seq service was provided by CloudSeq Inc. (Shanghai, China). Total RNA was decapping with mRNA decapping enzyme (New England Biolabs), and then subjected to immunoprecipitation with the GenSeq® m7G-IP Kit (GenSeq Inc.) by following the manufacturer’s instructions. Briefly, RNA was randomly fragmented to ~200 nt with RNA fragmentation reagents supplied in the kit. Protein A/G beads were coupled to the m7G antibody by rotating at room temperature for 1 h. The RNA fragments were incubated with the bead-linked antibodies and rotated at 4°C for 4 h. After incubation, the RNA/antibody complexes were washed for several times, and then, captured RNA was eluted from the complexes and purified. RNA libraries for IP and input samples were then constructed with GenSeq® Low Input Whole RNA Library Prep Kit (GenSeq, Inc.) by following the manufacturer’s instructions. Libraries were qualified using Agilent 2100 bioanalyzer and then sequenced in a NovaSeq platform (Illumina).
MeRIP-seq

value: normal tissues

value: m7G antibody


title: normal2, MeRIP-seq

description:
N2.IP
Methylated_RNA_sites.circRNA.xlsx
Methylated_RNA_sites.LncRNA.xlsx
Methylated_RNA_sites.mRNA.xlsx


title: WGBS_USC_S2

city: SAINT LOUIS

first: Daofeng

last: Li

state: MO

address: 4515 McKinley Avenue

department: Genetics

institute: Washington University in St. Louis

description: WGBS of primary bladder epithelial stem cells: S2

data_processing:
For WGBS, reads were sequenced using NovaSeq platform and aligned to mm10 using Bismark. For Cutandrun and ATAC, reads were sequenced using Nextseq platform and aligned to mm10 using bowtie2. ATAC and Cutandrun peaks were called using MACS2. For Cutandrun, peaks were called with parameters for narrow (H3K4me3 and H3K27ac) and broad (H3K27me3) peaks. For Cutandrun and ATAC, reads were normalized for read coverage and for fraction of reads in consensus peaks.
Assembly: mm10
Supplementary files format and content: reads are aligned to mm10

source_name: Sensitized C3H/HeN USCs

growth_protocol: Primary bladder epithelial stem cells were grown in matirgel with 50% L-WRN conditioned media (Miyoshi et al. 2013).

extract_protocol:
For WGBS, genomic DNA (gDNA) was prepared from the cells using DNeasy Blood & Tissue kit (Qiagen, ID 69504). For CUT&RUN, 0.2 × 10^6 USCs were slightly cross linked in 0.1% formaldehyde, fixed cell pellets may be stored at -80°C before using. H3K4Me3, H3K27ac and H3K27Me3 CUT&RUN was performed using CUT&RUN Assay Kit (Cell Signaling, 86652)
For WGBS, using 200 ng of gDNA and 0.4ng lambda DNA was bisulfite treated using EZ DNA Methylation-Direct kit (Zymo, D5020) and processed with xGen™ Methyl-Seq Library Prep (IDT, 10009824) to generate Illumina-compatible WGBS libraries. For CUT&RUN, sequencing library was prepared with Ultra II DNA library Prep Kit (NEB, E7645)

treatment_protocol: No treatment was applied to the cell lines before profile.

value: urothelial stem cells (USCs)

tag: infection history

value: Sensitized


title: Low Ahr ligand diet group_2

value: Skin

value: WT

value: Low AhR


title: cancer3, MeRIP-seq

description:
C3.IP
Methylated_RNA_sites.circRNA.xlsx
Methylated_RNA_sites.LncRNA.xlsx
Methylated_RNA_sites.mRNA.xlsx

value: OSCC tissues


title: DMR, Heart, H3K4me3, DMR11,  vl0049

value: 48 (estimated)

value: male


title: ATAC of primary bladder epithelial stem cells: Naïve 1

description: Adult Naïve C3H/HeN primary blader epithelial stem cells

source_name: Adult Naive C3H/HeN USCs

tag: strain

value: Adult Naive


title: WGBS_USC_S1

description: WGBS of primary bladder epithelial stem cells: S1

tag: cell type


title: cancer2, MeRIP-seq

description:
C2.IP
Methylated_RNA_sites.circRNA.xlsx
Methylated_RNA_sites.LncRNA.xlsx
Methylated_RNA_sites.mRNA.xlsx


title: WGBS_USC_R4

description: WGBS of primary bladder epithelial stem cells: R4

source_name: Resolved C3H/HeN USCs

value: Resolved


title: normal1, MeRIP-seq

description:
N1.IP
Methylated_RNA_sites.circRNA.xlsx
Methylated_RNA_sites.LncRNA.xlsx
Methylated_RNA_sites.mRNA.xlsx


title: ATAC of primary bladder epithelial stem cells: Resolved 1

description: Resolved C3H/HeN primary blader epithelial stem cells


title: DMR, Heart, H3K4me3, DMR3,  vl0047

value: 36 (estimated)

tag: Sex


title: cancer1, RNA-seq

description:
C1.Input
LncRNA Expression Profiling.xlsx
Gene Expression Profiling.xlsx
CircRNA Expression Profiling.xlsx


title: cancer1, MeRIP-seq

description:
C1.IP
Methylated_RNA_sites.circRNA.xlsx
Methylated_RNA_sites.LncRNA.xlsx
Methylated_RNA_sites.mRNA.xlsx


title: LC_AC_2

value: Liver

tag: genotype

value: WT with HCC

value: female

value: AAV blank control

value: 4 weeks


title: ATAC of primary bladder epithelial stem cells: Resolved 4


title: DMR, Heart, input, DMR11,  vl0053

value: Heart

value: wild-type

value: adult

value: input


title: WGBS_USC_R1

description: WGBS of primary bladder epithelial stem cells: R1

value: urothelial stem cells (USCs)


title: Control_1

value: Skin

value: WT

value: Control


title: DMR, Heart, H3K4me1, DMR1,  vl0003

value: 48 (estimated)

value: male


title: DMR, Heart, H3K4me1, DMR11,  vl0050


title: WGBS_USC_N3

description: WGBS of primary bladder epithelial stem cells: N3

value: Adult Naive


title: ATAC of primary bladder epithelial stem cells: Sensitized 1

description: Sensitized C3H/HeN primary blader epithelial stem cells

value: Sensitized


title: 8_T216_p637_LV_GEN9_RNA170521

city: Milan

first: Anna Sofia

last: Tascini

address: Via Olgettina, 60

department: Center for Omics Science

country: Italy

institute: IRCCS, Ospedale San Raffaele

description: MATR3 overexpression,  RNA preparared on 17/05/2021

data_processing:
Low quality reads and Illumina adapters were trimmed using Trimmomatic (version 0.39).
The remaining reads were mapped to the reference human genome GRCh38, using STAR aligner (version 2.5.3a)
Uniquely mapped reads were assigned to the corresponding genes using the featureCounts (version1.6.4). Only reads mapped to exons were considered in the counting procedure. Genomic features were annotated according to Gencode basic annotations (Gencode realise 31).
Assembly: GRCh38
Supplementary files format and content: Matrix tables with raw gene counts for every gene and every sample

source_name: muscle cells from FSHD patients

growth_protocol: Primary muscle cells were grown in F10 medium (Sigma-Aldrich), supplemented with 20% FBS, 1% Pen-Strep, 10 ng/ml bFGF (Tebu-bio), and 1 μM dexamethasone (Sigma-Aldrich). To induce differentiation, myoblasts were plated at a confluence of 45,000 cells/cm2 and 24h after seeding, growth medium was replaced by DMEM:F12 (1:1, Sigma-Aldrich) supplemented with 20% knockout serum replacer (KOSR, Thermo Fisher Scientific), 3.151 g/L glucose, 10 mM MEM non-essential amino acids (Thermo Fisher Scientific), 100 mM sodium pyruvate (Thermo Fisher Scientific). Differentiation was carried out for 96h.

extract_protocol:
RNA extraction using PureLink RNA Mini Kit (catalog # 12183025, Life Technologies), following manifacturer's protocol. cDNA synthesis using SuperScript® III First-Strand Syntesis SuperMix for qRT-PCR (cat. #11752-250, Life Technologies)
NGS libraries were generated with the mRNA Stranded TruSeq protocol. Libraries were barcoded, pooled and sequenced on Illumina Nova-Seq 6000 sequencing system in paired-end reads mode, with reads 100nt long.

treatment_protocol: 24h after induction of differentiation, cells were transduced with a control lentivirus carrying GFP-only (GFP, p459) or a GFP-MATR3 N-term lentivirus carrying a fragment of MATR3 from aa 1 to aa 287 fused to GFP(GFP-MATR3 Nterm, p637), and harvested for RNA extraction 96h after induction of differentiation

tag: condition

tag: batch

tag: disease

value: FSHD


title: DMR, Heart, H3K27ac, DMR1,  vl0002

tag: developmental stage


title: 7_T216_p637_LV_PG_RNA050721

description: MATR3 overexpression, RNA preparared on 05/07/2021


title: ATAC of primary bladder epithelial stem cells: Naïve 3


title: ATAC of primary bladder epithelial stem cells: Sensitized 2


title: WGBS_USC_N1

description: WGBS of primary bladder epithelial stem cells: N1


title: DMR, Heart, H3K4me1, DMR3,  vl0048

tag: age (months)

value: 36 (estimated)


title: Cutrun_H3K27me3_USC_S2

description: H3K27me3 CUT&RUN of primary bladder epithelial stem cells: S2

data_processing:
For WGBS, reads were sequenced using NovaSeq platform and aligned to mm10 using Bismark. For Cutandrun and ATAC, reads were sequenced using Nextseq platform and aligned to mm10 using bowtie2. ATAC and Cutandrun peaks were called using MACS2. For Cutandrun, peaks were called with parameters for narrow (H3K4me3 and H3K27ac) and broad (H3K27me3) peaks. For Cutandrun and ATAC, reads were normalized for read coverage and for fraction of reads in consensus peaks.
Assembly: mm10
Supplementary files format and content: reads are aligned to mm10
Library strategy: CUT&RUN


title: DMR, Heart, H3K4me3, DMR1,  vl0001

tag: individual


title: E1_part4

first: Cheng

last: Jin

state: State...

address: dongdansantiao num5

institute: Chinese Academy of Medical Sciences

data_processing:
Raw sequencing reads were processed using the Cell Ranger v.3.0.1 pipeline from 10X Genomics. In brief, reads from each sample were demultiplexed, aligned to the mouse mm10 genome and unique molecular identifier (UMI) counts were quantified per gene per cell to generate a gene-barcode matrix. Default parameters were used.
Genome_build: mm10
Supplementary_files_format_and_content: gene-barcode matrix generated using the Cell Ranger v.3.0.1 pipeline from 10X Genomics

source_name: 2-month-old THY1+ MACS-sorted

extract_protocol:
The testis were minced and digested in collagenase type IV (1 mg/ml) at 37C for 15 min. During the process of digestion, the tissues were pipetted up and down once every five minutes. The digestion process was stopped with DMEM (containing 10% FBS). The MACS-sorted THY1+ cell suspension was filtered through 40-μm nylon mesh. After centrifugation, the cells were suspended in 0.04% BSA in PBS for loading on the 10x Chromium chip.
Cell capturing and library preparation were carried as kit instructions (Chromium Single Cell Kit [v2 chemistry]). In brief, 8000 cells were targeted for capture per sample, after cDNA synthesis,10-12 cycles were used for library amplification. The resultant libraries were size selected, pooled, and sequenced on an Illumina Novaseq 6000 instrument.

tag: age


title: 6_T216_p637_LV_PG_RNA050721


title: 5_T216_p637_LV_PG_RNA050721


title: 4_T216_p459_LV_GEN9_RNA170521

description: empty vector control, RNA preparared on 17/05/2021

value: EV


title: E1_part3


title: Cutrun_H3K27me3_USC_S1

description: H3K27me3 CUT&RUN of primary bladder epithelial stem cells: S1


title: E1_part2


title: Cutrun_H3K27me3_USC_R4

description: H3K27me3 CUT&RUN of primary bladder epithelial stem cells: R4

value: Resolved


title: 3_T216_p459_LV_PG_RNA050721

description: empty vector control, RNA preparared on 05/07/2021


title: Cutrun_H3K27me3_USC_R1

description: H3K27me3 CUT&RUN of primary bladder epithelial stem cells: R1


title: E1_part1


title: 2_T216_p459_LV_PG_RNA050721


title: Cutrun_H3K27me3_USC_N3

description: H3K27me3 CUT&RUN of primary bladder epithelial stem cells: N3


title: IgG-rep3

data_processing:
Library strategy: CUT&TAG
Raw reads were analyzed by removing low-quality or adaptor sequences using Trim_galore (v0.5.0) and cleaned reads were mapped to the reference genome mm10 using Bowtie2 (v2.2.5).
We used MACS2 (v2.1.2) to call peaks found in different groups.
Genome_build: mm10
Supplementary_files_format_and_content: peak files

extract_protocol:
FACS-sorted GFP+ SSCs from the Foxc2CRE/+;R26T/Gf/f mice 3 days after tamoxifen induction were used to perform the CUT&Tag assay.
CUT&Tag assay was performed using CUT&Tag 2.0 High-Sensitivity Kit (Novoprotein scientific Inc., Cat# N259-YH01). In brief, cells were harvest by trypsin and enriched by ConA-magnetic beads. 10,000 cells were re-suspended in 100 mL Dig-wash Buffer (20 mM HEPES pH 7.5; 150 mM NaCl; 0.5 mM Spermidine; 13 Protease inhibitor cocktail; 0.05% Digitonin) containing 2 mM EDTA and a 1:100 dilution of primary SC35 antibody. The primary antibody was incubated overnight at 4°C. Beads were washed in Dig-wash Buffer 3 times and incubated with porcine anti-mouse secondary antibody for 1 hour at a dilution of 1:200. After incubation, the beads were washed 3 times in Dig-Hisalt Buffer (0.05% Digitonin, 20 mM HEPES, pH 7.5, 300 mM NaCl, 0.5 mM Spermidine, 13 Protease inhibitor cocktail). Cells were incubated with proteinA-Tn5 transposome at 25°C for 1 h and washed 3 times in Dig-Hisalt buffer to remove unbound proteinA-Tn5. Next, cells were re-suspended in 100mL Tagmentation buffer (10 mM MgCl2 in Dig-Hisalt Buffer) and incubated at 37°C for 1 h. The tagmentation was terminated by adding 2.25 mL of 0.5 M EDTA, 2.75 mL of 10% SDS and 0.5 mL of 20 mg/mL Proteinase K at 55°C for 1 hour. The DNA fragments were extracted by phenol chloroform and used for sequencing on an Illumina HiSeq instrument (Illumina NovaSeq 6000) to generate 2 × 150-bp paired-end reads following the manufacturer’s instructions.

treatment_protocol: We performed CUT&Tag (cleavage under targets and tagmentation) on the GFP+ SSCs from the Foxc2CRE/+;R26T/Gf/f mice 3 days after tamoxifen induction.

tag: chip antibody

value: anti-IgG

value: GFP+ SSCs


title: 1_T216_p459_LV_PG_RNA050721


title: FOXC2-rep3


title: MP46_R1_p24_CTCF

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

country: France

institute: Institut Curie

data_processing:
The quality control of the fastq files was performed using FastQC.
The sequences were aligned on hg19 assembly using bowtie2. Duplicates were marked and filtered out using Picard tools MarkDuplicates and samtools.
The peak calling was performed using macs2 callpeak function. The parameter --broad was used for the Histone samples, not for the transcription factor samples.
Assembly: hg19
Supplementary files format and content: bigWig ChIP-seq profiles

source_name: PDX of uveal melanoma

growth_protocol: Normal uveal melanocytes from an healthy donors, obtained after enucleations were dissociated and maintained in culture from choroidal membranes from Pr Simon Saule’s lab and Dr Geraldine Liot. After enzymatic (with collagenase) and mechanical dissociation, primary cells were cultured in HAM/F12 supplemented with 10% FBS, Penicillin 100 U/mL, Streptomycin 100 U/mL, 2mM L-glutamine, 2.5µg/mL Amphotericin B. Extemporaneously completed media was supplemented with 0.1mM IBMX, 10ng/µL of Cholera toxin (10 ng/ml final), and 10mg/mL FGF and filter with a 0.22µm filter. Cell were maintained in a humidified atmosphere with 5% CO2 at 37°C , and culture medium was exchanged twice a week.   MP41 and MP46 xenograft tumors were harvested before they reached a volume of 1 cm3 following ethical rules, and processed immediately for dissociation, immunolabelling and sorting based on Crépin R, Gentien D et al. et al protocol (2017).

extract_protocol:
ChIP of H2AUb, H3K4me and H3K27me3 were performed from 6 millions of cells originating from Patient Derived Tumour grafts; magnetic Dynabeads coupled to Protein A were used for the IP (Invitrogen). Sonication was performed to obtain fragment size of 150-300 bp. Chip of H3K27Ac and CTCF were performed according the Diagneode protocols. The chromatin was prepared using the iDeal ChIP-seq Kit for Transcription Factors (Diagenode Cat# C01010170). Chromatin was sheared using Bioruptor® Pico sonication device (Diagenode Cat# B01060001) combined with the Bioruptor® Water cooler for 10 cycles using a 30’’ [ON] 30’’ [OFF] settings to obtain fragment size of 150-300 bp. Per H3K27Ac and CTCF ChIP,  2 millions of cells were prepared in 100μl. The library preparation has been conducted by Diagenode ChIP-seq/ChIP-qPCR Profiling service (Diagenode Cat# G02010000). Libraries were prepared using IP-Star® Compact Automated System (Diagenode Cat# B03000002) from input and ChIP’d DNA using MicroPlex Library Preparation Kit v3 (96 indexes) (Diagenode Cat# C05010004). Optimal library amplification was assessed by qPCR using KAPA SYBR® FAST (Sigma-Aldrich) on LightCycler® 96 System (Roche) and by using High Sensitivity NGS Fragment Analysis Kit (DNF-474) on a Fragment Analyzer™ (Agilent). Libraries were then purified using Agencourt® AMPure® XP (Beckman Coulter) and quantified using Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific, Q32854). Finally their fragment size was analised by High Sensitivity NGS Fragment Analysis Kit (DNF-474) on a Fragment Analyzer™ (Agilent).
Libraries were prepared accordingly to manufactures (TruSeq ChIP sample Prep Kit, Illumina). Sequencing was performed on a Illumina Hi-Seq 2500 (H2Aub, H3K4me3, H3k27me3) and on a Illumina NovaSeq (ChIPseq H3K27Ac, CTCF)

treatment_protocol: Cells obtained from subcultre or cell sorting were counted and 6 million cells were resuspended in 1xPBS with 1%, v/v freshly opened formaldehyde at a concentration of  1x106 cells per 1ml PBS. Cells were icubated at room temperature for 15 minutes with gentle rocking. A glycine solution was added to a final concentration of 0.125M to quench the reaction. The mixture was incubated at room temperature for 5 minutes on rocker. Cells were centrifuged for 5 minutes at 300xG (1000rpm) at 4°C. The supernatant was discarded  into an appropriate collection container, and cells were resuspended in 1ml of cold 1X PBS and spin for 5 minutes at 00xG (1000rpm) at 4°C. The supernatant was discarded. This washing step was repeated one more time, the supernatant was removed and cell pellets were flash-freezon in a dry ice/ethanol bath and stored at -80°C before ChIPseq experiments

tag: type of sample

value: UM sorted cells

tag: origin

value: MP46 PDX

tag: biological and technical replicate

value: Biological replicate 2 - technical replicate 1

tag: antibody


title: Cutrun_H3K4me3_USC_S2

description: H3K4me3 CUT&RUN of primary bladder epithelial stem cells: S2

value: urothelial stem cells (USCs)

tag: infection history


title: Cutrun_H3K27me3_USC_N1

description: H3K27me3 CUT&RUN of primary bladder epithelial stem cells: N1

tag: strain


title: IgG-rep2

tag: cell type


title: MP46_R2_p24_CTCF

value: Biological replicate 1 - technical replicate 1


title: Cutrun_H3K4me3_USC_S1

description: H3K4me3 CUT&RUN of primary bladder epithelial stem cells: S1


title: FOXC2-rep2


title: MP46_R2_p24_H3K27Ac

value: CTCF


title: MP46_R1_p24_H3K27Ac


title: Cutrun_H3K4me3_USC_R4

description: H3K4me3 CUT&RUN of primary bladder epithelial stem cells: R4


title: Cutrun_H3K4me3_USC_R1

description: H3K4me3 CUT&RUN of primary bladder epithelial stem cells: R1


title: FOXC2-rep1


title: Cutrun_H3K4me3_USC_N3

description: H3K4me3 CUT&RUN of primary bladder epithelial stem cells: N3


title: MP46_R1_p24_Input

value: DNA Input


title: R21039009-F2-F2-4

data_processing:
Raw sequencing reads were processed using the Cell Ranger v.3.0.1 pipeline from 10X Genomics. In brief, reads from each sample were demultiplexed, aligned to the mouse mm10 genome and unique molecular identifier (UMI) counts were quantified per gene per cell to generate a gene-barcode matrix.
Then data from multiple samples were aggregated and normalized to the same sequencing depth, resulting in a combined gene-barcode matrix of all samples. Default parameters were used.
Genome_build: mm10
Supplementary_files_format_and_content: gene-barcode matrix generated using the Cell Ranger v.3.0.1 pipeline from 10X Genomics

source_name: cKO

value: Thy1+ spermatogonia


title: R21039009-F2-F2-3


title: MP41_R2_p11_H3K27Ac

value: MP41 PDX


title: Cutrun_H3K4me3_USC_N1

description: H3K4me3 CUT&RUN of primary bladder epithelial stem cells: N1

value: Adult Naive


title: Cutrun_H3K27ac_USC_S2

description: H3K27ac CUT&RUN of primary bladder epithelial stem cells: S2

value: Sensitized


title: R21039009-F2-F2-2


title: RNASeq of planctonic culture of Pseudomonas aeruginosa PAO1 ΔPA0290 mutant at OD 2 replicate 2

city: Braunschweig

last: Preusse

address: Inhoffenstr. 7

department: Molecular Bacteriology

institute: Helmholtz Center for Infection Research

description: 250122_mgu19_RNAseq_PAO1-TTN_d03790_PL_2

data_processing:
cutadapt ( --nextseq-trim=20 -g TTTTT;min_overlap=1 -G GGGGGGG;min_overlap=3 -m 36)
bowtie2 ( --very-sensitive-local -I 100 -X 1200 --fr )
featurecounts (-p -Q 20 10 -t CDS,tRNA,rRNA -g locus --extraAttributes name)
Assembly: NC_008463.1
Supplementary files format and content: reads_per_gene.csv - reads per gene with samples in separate columns

organism: Pseudomonas aeruginosa PAO1

growth_protocol: Bacterial subcultures were grown in liquid LB, at 37 °C and 180 rpm shaking until OD 2.0

extract_protocol:
RNA extraction was done as previously described (Schinner et al., 2020)
Illumina TruSeq kit

treatment_protocol: Bacterial cell pellets were resuspended in RNAprotect.

tag: cell line

value: bacteria

tag: treatment

value: RNAprotect


title: MP41_R1_p10_H3K27Ac


title: Cutrun_H3K27ac_USC_S1

description: H3K27ac CUT&RUN of primary bladder epithelial stem cells: S1


title: R21039009-F2-F2-1

tag: genotype


title: RNASeq of planctonic culture of Pseudomonas aeruginosa PAO1 ΔPA0290 mutant at OD 2 replicate 1

description: 250122_mgu19_RNAseq_PAO1-TTN_d03790_PL_1


title: MP41_R2_p11_CTCF


title: Cutrun_H3K27ac_USC_R4

description: H3K27ac CUT&RUN of primary bladder epithelial stem cells: R4


title: R21039008-F1-F1-4

source_name: control


title: RNASeq of planctonic culture of Pseudomonas aeruginosa PAO1 ΔPA3177 mutant at OD 2 replicate 2

description: 250122_mgu19_RNAseq_PAO1-TTN_d23130_PL_2


title: MP41_R1_p10_CTCF


title: IgG-rep1


title: MP41_R2_p11_Input


title: Cutrun_H3K27ac_USC_R1

description: H3K27ac CUT&RUN of primary bladder epithelial stem cells: R1


title: RNASeq of planctonic culture of Pseudomonas aeruginosa PAO1 ΔPA3177 mutant at OD 2 replicate 1

description: 250122_mgu19_RNAseq_PAO1-TTN_d23130_PL_1


title: R21039008-F1-F1-3


title: MP46_R2_p24_Input


title: Cutrun_H3K27ac_USC_N3

description: H3K27ac CUT&RUN of primary bladder epithelial stem cells: N3


title: MP41_R1_p10_Input


title: R21039008-F1-F1-2


title: RNASeq of planctonic culture of Pseudomonas aeruginosa PAO1 at OD 2 replicate 2

source_name: PAO1 WT

value: PAO1 WT

value: WT


title: Cutrun_H3K27ac_USC_N1

description: H3K27ac CUT&RUN of primary bladder epithelial stem cells: N1


title: R21039008-F1-F1-1


title: Thermoneutral temp2

status: Public on Aug 20 2023

city: Shanghai

first: Yu

address: Minhang Dongchuan Road No.500

institute: East China Normal University

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 mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
RNA Methylated sites (peaks) were identified by MACS2. HOMER (Hypergeometric Optimization of Motif EnRichment) was used to find motif sequence. Differentially methylated sites on RNAs were identified by diffReps.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include methylation levels for each gene
Library strategy: MeRIP-Seq

source_name: Adipocytes

extract_protocol:
Methylated RNA Immunoprecipitation Sequencing was performed by Cloudseq Biotech Inc. (Shanghai, China) according to the published procedure with slight modifications.
Library generation with NEBNext UltraTM RNA Library Prep Kit (NEB).

tag: tissue

value: Inguinal white adipose tissues

tag: protocol

value: 30degreeC for 7 days


title: RNASeq of planctonic culture of Pseudomonas aeruginosa PAO1 at OD 2 replicate 1


title: Cold temp1

value: 4degreeC for 7 days


title: Cold temp2


title: Thermoneutral temp3_RIP

value: anti-m6A polyclonal antibody (Synaptic Systems, 202003)


title: Thermoneutral temp1_RIP


title: Thermoneutral temp3


title: Cold temp3_RIP


title: Thermoneutral temp1


title: Cold temp3


title: Cold temp2_RIP


title: Thermoneutral 3

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 mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Fat tissues frozen on dry ice, and 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 constructed by TruSeq® RNA LT Sample Prep Kit v2 (illumina, USA) following the manufacturer’s protocol and quantified by Qubit (invitrogen, USA) for cluster generation.


title: Cold temp1_RIP


title: Thermoneutral 2


title: Thermoneutral 1


title: Cold temp 3


title: EMP popn 3 bio rep 1 technical rep 2

city: Palo Alto

first: Reema

last: Baskar

address: 3373 Hillview Ave

institute: Stanford University

data_processing:
Raw fastq data was put through pepATAC pipeline to obtain bam and bed files outputs, along with detailed QC on library such as TSS score and fragment length distribution.
Consensus bed file was created for each experiment across technical and biological replicates using Chraccr package. Exact code in github and zenodo as referred to in paper.
Count matrix contains raw insertion counts across samples for all peaks in consensus peakset and can be used for any relevant downstream analysis.
Assembly: hg19
Supplementary files format and content: Bigwig file output from pepATAC processing pipeline.

source_name: bone marrow

growth_protocol: Frozen CD34-enriched cells from bone marrow or mobilized peripheral blood were used.

extract_protocol:
Fast-ATAC seq protocol was used to lysis and transpose cells before extracting DNA.
Library was constructed after 8-12 rounds of PCR with appropriate ATAC primers and size selected using AMPure XP beads.
Fast-ATAC seq

treatment_protocol: Cells were thawed and suspended in in cell staining media (CSM: PBS with 0.5% BSA and 0.02% sodium azide and benzonase 25x108U/mL (Sigma)) with TruStain FC blocker for 10min at RT prior to staining. Next, the cocktail of surface antibodies was added (as described in paper) and cells were stained in the dark for 30 min on ice and then washed in CSM. Prior to data acquisition, cell suspensions were spiked with 7-AAD (BioLegend) to label non-viable cells.

value: bone marrow

value: bone marrow progenitors

tag: cell population

value: EMP popn


title: Cold temp 2


title: EMP popn 3 bio rep 3 technical rep 2


title: Cold temp 1


title: Thermoneutral temp2_RIP


title: EMP popn 3 bio rep 2 technical rep 2


title: EMP popn 3 bio rep 1 technical rep 1


title: EMP popn 2 bio rep 3 technical rep 1


title: EMP popn 2 bio rep 2 technical rep 1


title: EMP popn 2 bio rep 3 technical rep 2


title: EMP popn 2 bio rep 1 technical rep 2


title: EMP popn 2 bio rep 2 technical rep 2


title: EMP popn 1 bio rep 3 technical rep 1


title: EMP popn 1 bio rep 2 technical rep 2


title: CMP (MDP popn) bio rep 3 technical rep 1

value: CMP (MDP popn)


title: CMP (MDP popn) bio rep 3 technical rep 2


title: EMP popn 3 bio rep 3 technical rep 1


title: CMP (MDP popn) bio rep 2 technical rep 2


title: EMP popn 1 bio rep 1 technical rep 2


title: CMP (MDP popn) bio rep 2 technical rep 1


title: CMP (MDP popn) bio rep 1 technical rep 2


title: CMP (MDP popn) bio rep 1 technical rep 1


title: EMP popn 2 bio rep 1 technical rep 1


title: Sample-6, HAstV1_24h, scRNAseq

city: Memphis

first: Stacey

last: Schultz-Cherry

state: TN

address: 262 Danny Thomas Place

institute: St. Jude Children's Research Hospital

description: 10x Genomics

data_processing:
The gene counting and aggregation were made using the Cell Ranger software v6.1.1
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Human colorectal adenocarcinoma cell line

growth_protocol: Caco-2 cells were grown in MEM containing penicillin-streptomycin, Sodium pyruvate, Glutamax, and FBS

extract_protocol:
Caco-2 cells were washed with PBS and treated with trypsin to make a single cell suspension, then filtered through a 70uM filter. Cells were spun down and resuspended in the appropriate volume for 10x scRNA-seq.
Libraries were made according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Caco-2 cells were resuspended in the master mix and loaded with a target cell recovery of 6,000 cells together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). RNA was reverse transcribed into cDNA, which was cleaned using Silane DynaBeads and amplified. Fragments were cleaned using SPRIselect reagent.

treatment_protocol: Caco-2 cells were infected in serum-free media with HAstV-1 or mock control at an MOI of 10

tag: donor age

value: 72 years

value: infected with HAstV-1

tag: timepoint


title: Sample-4, HAstV1_4h, scRNAseq

description: 10x Genomics

value: Human colorectal adenocarcinoma cell line


title: C90107_M0_3

city: Oxford

first: Kevin

last: Talbot

address: John Radcliffe Hospital, Headley Way

department: Nuffield Department of Clinical Neurosciences

institute: University of Oxford

data_processing:
Paired end sequencing was performed using a NovaSeq6000 platform (Illumina, NovaSeq 6000 S2/S4 reagent kit, v1.5, 300 cycles), generating a raw read count of a minimum of 30M reads per sample
Paired-end reads were mapped to the human GRCh38.p13 reference genome (https://www.gencodegenes.org) using HISAT2 v2.2.1 (Kim et al., 2019).
The counts table was obtained using FeatureCounts v2.0.1 (Liao et al., 2014)
Normalization of counts and differential expression analysis was performed using DESeq2 v1.28.1 (Love et al., 2014)
Assembly: GRCh38.p13
Supplementary files format and content: csv file includes normalized DESeq2 counts for all samples

growth_protocol: differentiation in monoculture for ~14 days

extract_protocol:
RNA was extracted using an RNAeasy Mini Plus kit (Qiagen) according to the manufacturer’s instructions
Material was quantified using RiboGreen (Invitrogen) on the FLUOstar OPTIMA plate reader (BMG Labtech) and the size profile and integrity analysed on the 2200 or 4200 TapeStation (Agilent, RNA ScreenTape). RIN estimates for all samples were between 9.2 and 9.9. Input material was normalised to 100 ng prior to library preparation. Polyadenylated transcript enrichment and strand specific library preparation was completed using NEBNext Ultra II mRNA kit (NEB) following manufacturer’s instructions. Libraries were amplified (14 cycles) on a Tetrad (Bio-Rad) using in-house unique dual indexing primers (based on (Lamble et al., 2013)). Individual libraries were normalised using Qubit, and the size profile was analysed on the 2200 or 4200 TapeStation. Individual libraries were normalised and pooled together accordingly. The pooled library was diluted to ~10 nM for storage. The 10 nM library was denatured and further diluted prior to loading on the sequencer

treatment_protocol: ±48 hours stimulation with LPS 100 ng/mL (unstimulated ='M0'; stimulated='M1')

value: iPSC microglia in monoculture

value: C9ORF72 HRE

tag: Sex

value: male

value: differentiation in monoculture for 14 days, no stimulation ('M0')


title: EMP popn 1 bio rep 3 technical rep 2


title: Sample-5, HAstV1_8h, scRNAseq

description: 10x Genomics


title: Sample-1, Mock_4h, scRNAseq

description: 10x Genomics

value: mock infected


title: Sample-2, Mock_8h, scRNAseq

description: 10x Genomics


title: C90107_M1_3

value: differentiation in monoculture for 14 days, 48 hours stimulation with LPS 100 ng/mL ('M1')


title: EMP popn 1 bio rep 2 technical rep 1


title: Sample-3, Mock_24h, scRNAseq

description: 10x Genomics


title: C90202_M0_3

value: female


title: C90412_M0_3


title: 841_M1_3

value: WT


title: EMP popn 1 bio rep 1 technical rep 1


title: C90412_M1_3


title: 841_M0_3


title: C90107_M1_2


title: 856_M1_3


title: C90107_M0_2


title: OX3_M1_2


title: OX3_M0_2


title: 856_M1_2


title: OX3_M0_3


title: C90202_M1_3


title: OX3_M1_3


title: 856_M0_2


title: 841_M1_2


title: 841_M0_2


title: C90412_M0_2


title: 856_M0_3


title: C90202_M0_2


title: EMP popn 3 bio rep 2 technical rep 1


title: C90412_M1_2


title: C90202_M1_2


title: C90107_M1_1


title: C90107_M0_1


title: OX3_M1_1


title: 5XFAD.Cpa3+/+ (MC WT), bio rep 4, scRNA-Seq

first: Kashish

last: Chetal

address: 55 Fruit St

department: Molecular biology

institute: MGH

description: 10x Genomics

data_processing:
CellRanger (v4.0.0) was used for sequences alignment and generate read counts per gene in each cell.
Downstream analysis was performed using the Seurat 3.2.3 package (Butler et al, 2018)
Exclude cells with <200 expressed genes, genes expressed in <3 cells and cells with mitochondrial transcripts > 10%
Assembly: mm10
Supplementary files format and content: Cellranger output files -Tab separated values files and Matrix files

source_name: Cortex

extract_protocol:
The cortical brain tissue from both hemispheres was dissected and placed in 0.66 mg/ml pre-warmed papain/RPMI medium in C-tubes. The tissues were dissociated using a Gentle MACS dissociator for 37 seconds, followed by incubation at 37°C for 15 minutes under rotation. Next, 0.66 mg/ml pre-warmed collagenase D/RPMI medium was added, and the tissues were dissociated again for 31 seconds using the Gentle MACS dissociator. Next, DNase I (Worthington) was added to the final concentration of 125 U/ml, and the mixture was incubated for another 10 minutes at 37°C under rotation. The tissues were then dissociated for 61 seconds using the Gentle MACS dissociator. The cell suspensions were incubated for 15 min at 37°C under rotation. After the final incubation, we mixed the suspension with neutralization buffer (2% FCS and 1 mM EDTA in PBS) and broke down the tissues by pipetting. The cells were filtered and centrifuged at 400 x g for 8 minutes at 4°C. The supernatant was aspirated, and the cells were resuspended in 27% percoll. The cells were centrifuged again at 850 x g for 40 minutes at 4°C with a deceleration of 4, and then washed and lysed for red blood cells. The cell suspension was resuspended in cold FACS buffer without azide and the viable cells were counted before library preparation.
Library was performed according to the manufacturer's instructions.

value: Cortex

value: brain cells


title: 5XFAD.Cpa3Cre/+ (MC KO), bio rep 3, scRNA-Seq

description: 10x Genomics


title: 5XFAD.Cpa3+/+ (MC WT), bio rep 3, scRNA-Seq

description: 10x Genomics


title: patient 4

type: RNA

city: Fuzhou

first: Hailong

last: Huang

state: Fujian

address: No.18 Daoshan Road, Gulou District

institute: Fujian Maternity and Child Health Hospital

description: circRNA expression in human plasma

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays V2 (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

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

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the R software limma package. Differentially expressed circRNAs with statistical significance between two groups were identified through Volcano Plot filtering. Differentially expressed circRNAs between two samples were identified through Fold Change filtering. Hierarchical Clustering was performed to show the distinguishable circRNAs expression pattern among samples.

source_name: β-thalassemia patient

label_protocol: Total RNA from each sample was treated with Rnase R to enrich circular RNA. The enriched circular RNA was then amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.).

extract_protocol: Total RNA from the peripheral blood samples was isolated using a PAXgene Blood RNA Kit (Qiagen) according to the manufacturer’s protocol.

value: blood

tag: gender


title: patient 3

description: circRNA expression in human plasma


title: patient 6

description: circRNA expression in human plasma


title: patient 5

description: circRNA expression in human plasma


title: normal control 4

description: circRNA expression in human plasma

source_name: healthy people


title: normal control 5

description: circRNA expression in human plasma


title: OX3_M0_1


title: 5XFAD.Cpa3Cre/+ (MC KO), bio rep 2, scRNA-Seq

description: 10x Genomics


title: normal control 6

description: circRNA expression in human plasma


title: patient 2

description: circRNA expression in human plasma


title: patient 1

description: circRNA expression in human plasma


title: normal control 2

description: circRNA expression in human plasma


title: normal control 3

description: circRNA expression in human plasma


title: C90412_M1_1


title: 5XFAD.Cpa3Cre/+ (MC KO), bio rep 1, scRNA-Seq

description: 10x Genomics


title: 5XFAD.Cpa3Cre/+ (MC KO), bio rep 4, scRNA-Seq

description: 10x Genomics


title: 5XFAD.Cpa3+/+ (MC WT), bio rep 1, scRNA-Seq

description: 10x Genomics


title: 5XFAD.Cpa3+/+ (MC WT), bio rep 2, scRNA-Seq

description: 10x Genomics


title: normal control 1

description: circRNA expression in human plasma


title: C90412_M0_1


title: Treat   Mouse liver cells 2

city: 郑州

first: yucheng

last: li

state: 河南省

address: 河南省郑州市金水区博学路街道金水东路156号

institute: Henan University of Chinese Medicine

description: Treat2 Treat

data_processing:
Cytoscape 3.8.2 software for basic calls
Splice the sequencing readings to obtain the linker sequence, and use magnetic beads to screen and purify its fragment size., Then, PCR was used to form a library with a fragment size of 300bp ± 50bp
After obtaining sequencing offline data, the offline data is first filtered to obtain high-quality sequencing data (Clean Data). Then, the high-quality sequencing data is compared to the reference genome of the species in this project, and gene expression quantification, GSEA, gene difference analysis, enrichment analysis, and other analyses are performed
The raw data generated by sequencing needs to be preprocessed and filtered (filter standard reference analysis method described in English) to obtain valid data (Clean Data), then compared with the reference genome, and finally subjected to gene quantitative analysis. The following table lists the data quality during the data analysis process.
Comparing high reliability data (Clean Data) to the reference genome of the species in this project will obtain comprehensive alignment information. At the same time, based on the gene location information specified in the genome annotation file gtf, statistics will be conducted separately: 1) Comparing sequencing data with reference genome reads statistics; 2) Regional distribution statistics of sequencing data compared to reference genomes.
Assembly: Hisat2
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

molecule: polyA RNA

source_name: liver

extract_protocol:
Using TRIzol (Thermofisher, 15596018), separate and purify the RNA of the total sample according to the operating plan provided by the manufacturer
Preparation of RNA library using standard Illumina protocol for sequencing

value: liver

value: treated


title: Model  Mouse liver cells 3

address: 河南省郑州市金水区博学路街道金水东路156号

description: Model3 Model

value: model


title: Treat   Mouse liver cells 1

address: 河南省郑州市金水区博学路街道金水东路156号

description: Treat1 Treat


title: Treat   Mouse liver cells 3

address: 河南省郑州市金水区博学路街道金水东路156号

description: Treat3 Treat


title: 856_M0_1


title: C90202_M1_1


title: Model  Mouse liver cells 2

address: 河南省郑州市金水区博学路街道金水东路156号

description: Model2 Model


title: CR_6_KO_CH3

city: San Antonio

first: Hui

last: Yang

state: Texas

address: 5114 medical dr.

institute: UTHSCSA

data_processing:
Raw data of each sample was quality controlled by fastqc and trimmed by TrimGalore
clean reads were aligned to mouse reference genome using bowtie2
The raw sam files generated by bowtie2 were sorted and reads on mitochondrion or with low Mapping quality (<30) were filtered using samtools
Sambamba was used to remove PCR duplications
Peak calling was performed with homer with options: findPeaks
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files were generated using deeptools(bamCoverage --normalizeUsing CPM)
Supplementary_files_format_and_content: Peak files were generated using homer

source_name: Bone marrow

extract_protocol:
The gemonic DNA covered by indicated antibodies were digested by pAG-Mnase and purified using DNA purification kit(NEB).
The CUT&RUN libraries were prepared using the NEBNext Ultra II DNA library prep kit and sequenced with pared-end 75 bp on an Illumina NextSeq 500 system
CUT&RUN

treatment_protocol: BM c-Kit+ and LSK cells from Mx1Cre+ Brd4 flox/fox and WT littermates were purified by sorting 14 days after poly(I:C) injection.

value: Lin-cKit+ bone marrow cells

tag: c&r antibody

value: Clipping H3(Cell signaling, 1257)


title: Model  Mouse liver cells 1

address: 河南省郑州市金水区博学路街道金水东路156号

description: Model1 Model


title: Gp120_A

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: Gene Expression after 24hour of recombinant HIV-1 gp120 protein treatment

hyb_protocol: Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327)

scan_protocol: Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift gene based analysis.

organism: Bos taurus

source_name: Bovine Eye Ball

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). The total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: Primary Bovine muller glia were cultured in DMEM media for 18- 21 days in vitro.

extract_protocol: Treated astrocyte cells were harvested by using TRIzol™ Reagent (Cat. No: 15596018) InvitrogenTM. By using 200 μl of chloroform reagent, phase separation was obtained after centrifugation at 12000 rpm for 15 minutes at 4 degree C. The clear upper aqueous phase was collected and the RNA was precipitated by using 500 μl ice cold isopropanol. Isopropanol is removed then by using 70% ethanol at 12000 rpm for 10 minutes. Then the precipitate was air dried and dissolved in RNase free water.

treatment_protocol: Primary Bovine muller glia were cultured and treated with 100ng/ml HIV-1 TAT and 60ng/ml HIV-1 gp120 for 24hours. Cells were collected in TRIZOL for RNA isolation.

value: muller glia


title: C90202_M0_1

value: iPSC microglia in monoculture


title: Control Mouse liver cells 3

address: 河南省郑州市金水区博学路街道金水东路156号

description: Control3 Control

value: control


title: CR_19_WT_CH3


title: Control Mouse liver cells 2

address: 河南省郑州市金水区博学路街道金水东路156号

description: Control2 Control


title: CR_1_KO_CH3


title: TAT_C

description: Gene Expression after 24hour of recombinant HIV-1 TAT protein treatment


title: CR_11_WT_CH3


title: 841_M1_1

value: male


title: CR_81_KO_H3K4me3

value: H3K4me3(Epicypher, 13-0041)


title: 841_M0_1

value: differentiation in monoculture for 14 days, no stimulation ('M0')


title: Gp120_B


title: TAT_B


title: Control Mouse liver cells 1

address: 河南省郑州市金水区博学路街道金水东路156号

description: Control1 Control


title: 856_M1_1

value: differentiation in monoculture for 14 days, 48 hours stimulation with LPS 100 ng/mL ('M1')


title: Gp120_C


title: Control A

description: Gene Expression after 24hour


title: Control_B

description: Gene Expression after 24hour


title: CR_11_WT_H3K4me3


title: CR_61_KO_H3K122AC


title: S-N, S, rep3

city: Changchun

first: Yinghua

last: Zhao

address: Dongminzhu street 519

institute: 1st hosptal of Jinli University

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw paired end reads were trimmed and quality controlled by Fastp (https://github.com/OpenGene/fastp )with parameters -q 20 --length_required 30 -5 20 -3 20 -W 4 -M 20 -n 0.
Then clean reads were separately aligned to reference genome with orientation mode using hisat software.
The expression level of each transcript was calculated according to the fragments per Transcripts Per Million reads (TPM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file includes TPM values for each Sample

source_name: Human embryonic kidney 293T cells

growth_protocol: HEK293T cell lines were grown and maintained in DMEM, high glucose (Hyclone) containing 10% heat-inactivated FBS (BBI), 100 U/ml of ampicillin, and 100 μg/ml of streptomycin (Sangon).

extract_protocol:
Total RNA was extracted from the sample using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >10μg) was used to construct sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: transfected with or without poly (I:C) , and treated for 24 hours

value: human embryonic kidney cells

value: stably-expressing SARS-CoV N protein

value: treated with poly(I:C) for 24 hours


title: CR_19_KO_H3K4me3


title: CR_3_WT_H3K4me3


title: S-N, S, rep2


title: S-N, S, rep1


title: CR_45_WT_H3K122AC


title: CR_37_WT_H3K122AC


title: Tmem119-creERT2-cGaswt/wt microglia whole brain mouse 2, scRNAseq

city: Lausanne

first: Andrea

last: Ablasser

address: route Cantonale

institute: EPFL

data_processing:
Illumina BCL convert was used to demultiplex reads
10X Genomics Cell Ranger Single Cell Software Suite v7.0.0 was used to perform barcode processing and 3’ gene counting using 10X Genomics custom annotation of murine genome assembly mm10
Analysis was performed using Seurat in R
Assembly: mm10
Supplementary files format and content: tab-seperated filtered values and matrix files

source_name: hippocampus

extract_protocol:
Nuclei from mouse brain were extracted by homogenizing mouse brain tissues in Nuclei EZ Lysis Buffer using a douncer. Nuclei were then loaded into a Chromium Single Cell Controller.
ChromiumSingle Cell 3’ Library & Gel Bead Kit v3.1

treatment_protocol: Aged mice were injected intraperitoneally with 750 nmol H151 or DMSO per mouse five days a week for 8 weeks. The mice were rested for 8 weeks, and 8 weeks of treatment were repeated one more time.

value: hippocampus

value: microglia

value: WT


title: Tmem119-creERT2-cGaswt/wt microglia whole brain mouse 3, scRNAseq


title: S-N, rep3

value: untreated


title: S-N, rep2


title: CR_17_KO_H3K27AC

value: H3K27Ac(Diagenode, C15410174)


title: CR_14_WT_H3K27AC

value: Lin-cKit+ bone marrow cells


title: CR_25_KO_H3K27AC


title: Tmem119-creERT2-cGaswt/R241E microglia whole brain mouse 4, scRNAseq


title: Tmem119-creERT2-cGaswt/wt microglia whole brain mouse 1, scRNAseq


title: CR_21_WT_H3K27AC


title: Tmem119-creERT2-cGaswt/R241E microglia whole brain mouse 3, scRNAseq


title: Tmem119-creERT2-cGaswt/wt microglia whole brain mouse 4, scRNAseq


title: S-2-N, S, rep3

value: stably-expressing SARS-CoV-2 N protein


title: CR_110_WT_BRD4

value: Brd4(active motif 39909)


title: S-N, rep1


title: CR_7_WT_BRD4


title: CR_90_KO_BRD4


title: Tmem119-creERT2-cGaswt/R241E microglia whole brain mouse 2, scRNAseq


title: CR_53_KO_H3K122AC


title: KO_156_ATAC

data_processing:
Raw data of each sample was quality controlled by fastqc and trimmed by TrimGalore
clean reads were aligned to mouse reference genome using bowtie2
The raw sam files generated by bowtie2 were sorted and reads on mitochondrion or with low Mapping quality (<30) were filtered using samtools
Sambamba was used to remove PCR duplications
Peak calling was performed with MACS2 with options: -g mm -n test -B -q 0.05
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files were generated using deeptools(bamCoverage --normalizeUsing CPM)
Supplementary_files_format_and_content: NarrowPeak files were generated using MACS2

extract_protocol:
ATAC-seq DNA were treated and extracted following the Omni-ATAC protocol.
TheATACseq libraries were prepared using the NEBNext high-fidelity 2x PCR master mix and sequenced with a paired-end 150 bp on an Illumina NextSeq 500 system.

treatment_protocol: BM Lin-c-Kit+ cells from Mx1Cre+ Brd4 flox/fox and WT littermates were purified by sorting 14 days after poly(I:C) injection.


title: KO_155_ATAC


title: Tmem119-creERT2-cGaswt/R241E microglia whole brain mouse 1, scRNAseq


title: S-2-N, S, rep1


title: WT_142_ATAC


title: Young mouse brain 3

data_processing:
Aligned to GRCm39 using STAR aligner
Counts generated using featureCounts
read count analysis and normalization was performed using DESeq2
Assembly: GRCm39
Supplementary files format and content: tab delimited text file with RAW counts of all samples
Supplementary files format and content: tab delimited text file with Normalized counts of all samples

extract_protocol:
RNA was extracted by Trizol/chloroform and purified with Qiagen Rneasy kit, 800ng of RNA was used for library generation
TruSeq mRNA stranded


title: CR_31_KO_BRD4


title: H1944_Unsorted_CTRL_C_S30

city: Berlin

first: Gaetano

last: Gargiulo

address: Robert-Rössle-Straße 10

institute: Max-Delbrück-Centrum für Molekulare Medizin

data_processing:
Data demultiplexing was performed with bcl2fastq (v2.20.0)
Demultiplexed data was aligned to MGT#1-containing GRCh38 custom reference genome with STAR (v2.6.0c).
Count matrices were generated using HTSeq (v0.12.3).
Assembly: Custom MGT#1-containing GRCh38
Supplementary files format and content: Tab-delimited text file containing raw counts for each sample

source_name: Lung Adenocarcinoma

growth_protocol: A549 and H1944 human lung cancer cell lines were cultured in RPMI medium (Gibco) supplemented with 10% fetal bovine serum (FBS, from Gibco) and penicillin and streptomycin (100 U/ml; Gibco) at 37°C in a 5% CO2 and 95% air incubator.

extract_protocol:
RNA was isolated from the cells using the TRIzol Reagent (Invitrogen, #15596026), followed by isopropanol precipitation and AMPure XP beads (A63881) purification. The extracted RNA was then quantified and its quality profiled using the Qubit RNA HS Assay Kit (Invitrogen, Q32855) and the High Sensitivity RNA ScreenTape System (Agilent, #5067-5581), respectively.
The SMARTer Stranded Total RNA-Seq Kit v2-Pico Input Mammalian (Takara Bio, #634413) was used for to generate the RNA-seq libraries from 10 ng of total RNA according to the manufacturer’s protocol.

treatment_protocol: A549 and H1944 cells were treated with either GSK126 (5μM) or TGF-β1 (5 ng/ml) for 11 days.

value: Lung Adenocarcinoma

value: Cell line

value: Naive


title: Young mouse brain 2


title: S-2-N, rep3


title: S-2-N, rep2


title: H1944_Unsorted_CTRL_A_S28


title: TAT_ A

value: muller glia


title: H1944_High_TGFB_C_S27

value: TGF-beta1 (5 ng/ml, 11 days)


title: Young mouse brain 1


title: H1944_High_TGFB_B_S25


title: H1944_Low_TGFB_B_S24


title: H1944_Low_TGFB_C_S26


title: GFP, S, rep3

value: stably-expressing GFP


title: S-2-N, rep1

value: human embryonic kidney cells


title: H1944_High_TGFB_A_S23


title: Aged mouse brain 3, 24w H151 treatment


title: S-2-N, S, rep2


title: H1944_High_GSK_C_S21

value: GSK126 (5 uM, 11 days)


title: WT_157_ATAC


title: GFP, S, rep2

value: treated with poly(I:C) for 24 hours


title: GFP, S, rep1


title: H1944_Low_TGFB_A_S22


title: Aged mouse brain 1, 24w H151 treatment

value: hippocampus


title: H1944_High_GSK_B_S19


title: H1944_Low_GSK_B_S18


title: Aged mouse brain 2, 24w H151 treatment


title: H1944_Unsorted_CTRL_B_S29


title: GFP, rep3


title: Aged mouse brain 3, 24w DMSO treatment

value: DMSO


title: H1944_Low_GSK_C_S20


title: H1944_High_GSK_A_S17


title: H1944_Low_GSK_A_S16


title: Aged mouse brain 2, 24w DMSO treatment

value: WT


title: Aged mouse brain 1, 24w DMSO treatment


title: A549_Unsorted_CTRL_B_S14


title: GFP, rep1

value: untreated


title: GFP, rep2


title: A549_Unsorted_CTRL_C_S15


title: A549_Unsorted_CTRL_A_S13


title: A549_High_TGFB_C_S12


title: A549_Low_TGFB_A_S7

value: TGF-beta1 (5 ng/m, 11 days)


title: A549_High_TGFB_A_S8


title: A549_High_TGFB_B_S10


title: A549_Low_GSK_C_S5


title: Tmem119-creERT2-cGaswt/wt microglia mouse 1, scRNAseq

data_processing:
Illumina BCL convert was used to demultiplex reads
10X Genomics Cell Ranger Single Cell Software Suite v7.0.0 was used to perform barcode processing and 3’ gene counting using 10X Genomics custom annotation of murine genome assembly mm10
Analysis was performed using Seurat in R
Assembly: mm10
Supplementary files format and content: tab-seperated values and matrix files

extract_protocol:
Nuclei from mouse brain were extracted by homogenizing mouse brain tissues in Nuclei EZ Lysis Buffer using a douncer. Nuclei were labelled with DAPI and sorted for sequencing. To enrich microglial cells, in addition to DAPI staining, nuclei were stained with anti-RBFOX3/NeuN-647. Sorted nuclei were then loaded into a Chromium Single Cell Controller.
ChromiumSingle Cell 3’ Library & Gel Bead Kit v3.1

value: microglia


title: A549_Low_TGFB_C_S11


title: Tmem119-creERT2-cGaswt/R241E microglia mouse 2, scRNAseq


title: A549_High_GSK_B_S4


title: A549_Low_GSK_A_S1


title: Tmem119-creERT2-cGaswt/wt microglia mouse 2, scRNAseq


title: A549_High_GSK_A_S2


title: Tmem119-creERT2-cGaswt/R241E microglia mouse 1, scRNAseq


title: HCC1143-2

city: Honolulu

first: Ken

middle: M.

last: Nakatsu

state: Hawaii

address: Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine, Biosciences Building 325B, 651 IIalo Street

department: Quantitative Health Sciences

institute: John A. Burns School of Medicine

data_processing:
UMIs and adapters were removed with UMI-tools and AdapterRemoval
Raw reads were processed through out new pipeline, sRNAfrag.
Assembly: hg38
Supplementary files format and content: Raw count data from our pipeline for snoRNA fragments.

extract_protocol:
Total RNA was isolated from cells using miRNeasy Mini Kit (QIAGEN). Briefly, cells grown at 80\% confluence in a 100 mm cell culture dish were washed with PBS and collected in a 1.5 ml centrifuge tube. Cells suspended in approximately 200ul of PBS were sonicated under RNase-free conditions. Then, the lysate was treated with 700 ul of QIAzol (QIAGEN) and 140 ul of chloroform to isolate nucleic acids in the aqueous phase. RNA was extracted following the manufacturer’s instruction and eluted with 30 uL of nucleic acid-free water. Finally, one ul of RNase inhibitor was added to the solution. The RNA quality and concentration were measured by nanodrop (Thermo Fisher Scientific) and Agilent 2100 Bioanalyzer (Agilent).
QIAseq miRNA Library Kits (QIAGEN) and QIAseq miRNA NGS 12 Index IL (QIAGEN) were used for library construction.


title: T47D-1


title: HCC1143-1


title: T47D-2


title: HMEC-1

source_name: HMEC

value: HMEC


title: IMR32-1


title: SK-N-SH-2

source_name: SK-N-SH

value: SK-N-SH


title: Tmem119-creERT2-cGaswt/wt microglia mouse 3, scRNAseq


title: Irradiated, H151, replicate 4

data_processing:
reads were aligned with STAR aligner
counts were generated with HTSeq Count
Analysis was performed using voom-Limma
Assembly: hg38
Supplementary files format and content: tab-delimited text file containing normalized counts of all samples

source_name: WI-38 cells

growth_protocol: Cells were cultured under 5% CO2 and 5% O2at 37°C in Dulbecco’s modified Eagle medium containing 10% (v/v) fetal calf serum, 1% (v/v) penicillin (100 IU ml-1)/streptomycin (100 μg ml-1).

extract_protocol:
Rneasy mini kit
TruSeq mRNA stranded LT

value: WI-38 cells


title: Irradiated, H151, replicate 2


title: Irradiated, H151, replicate 1


title: Irradiated, H151, replicate 3


title: Hui-KO2

data_processing:
Sequencing results from 10x Genomics were demultiplexed and converted to FASTQ format by cellranger  with a parameter of mkfastq
The FASTQ data was aligned to mouse reference genome and quantified using cellranger with default parameters
Genome_build: mm10
Supplementary_files_format_and_content: h5 files of filtered counts for all genes in each cell

extract_protocol:
Cells were pooled from two different mice for each genotype
The libraries for each single cell sample were prepared using the Chromium Single Cell Gene Expression 3’ Version 3 Kit (10X Genomics) with the Chromium Controller.
single-cell RNA-seq

value: cKit+ bone marrow cells


title: ZH11-KO1 panicle, biol rep 3

city: Yangzhou

first: Rujia

last: Chen

address: Wenhui

institute: Yangzhou unversity

data_processing:
The generated reads were firstly filtered and then mapped onto the reference genome of Oryza sative using HISAT2
The featureCounts software was used to count the read numbers mapped to each gene.
DESeq2 was used to detect differentially expressed genes of knockout and overexpression lines compared to WT plants
Assembly: Os-Nipponbare-Reference-IRGSP-1.0
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Oryza sativa

source_name: panicle

extract_protocol:
RNA was harvested using the RNA extraction kit (Tiangen Biotech). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEB mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: panicle

value: OsGSE9 knockout

tag: time

value: before heading date


title: Hui-KO1


title: A549_Low_GSK_B_S3

value: Lung Adenocarcinoma

value: Cell line


title: ZH11-KO1 panicle, biol rep 2


title: Irradiated, DMSO, replicate 3

value: IR + DMSO


title: Hui-WT2


title: Irradiated, DMSO, replicate 2


title: Irradiated, DMSO, replicate 4


title: ZH11-OE1 panicle, biol rep 3

value: OsGSE9 overexpression


title: ZH11-KO1 panicle, biol rep 1


title: Hui-WT1


title: Irradiated, DMSO, replicate 1


title: IMR32-2


title: Yang-10X-KO

value: LSK bone marrow cells


title: Yang-10X-WT


title: SK-N-SH-1


title: ZH11-OE1 panicle, biol rep 2


title: Control, H151, replicate 4


title: Control, H151, replicate 3


title: KO-156

data_processing:
The fastq files were quality controlled by fastqc and trimmed by Trimmomatic
Clean reads were aligned to the reference genome using STAR
The raw read counts of each gene were calculated using HTSeq
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Total RNA from individual mice was isolated with TRIzol reagent (Invitrogen)
The RNA libraries were prepared with the NEB Ultra RNA kit and followed by sequencing with a read length of 2 × 150 bp using the NovaSeq 6000.

value: Lin-cKit+ bone marrow cells


title: ZH11 panicle, biol rep 3

value: WT


title: Control, H151, replicate 2


title: KO-138


title: ZH11 panicle, biol rep 2


title: KO-115


title: KO-98


title: ZH11 panicle, biol rep 1


title: Control, DMSO, replicate 4

value: DMSO


title: WT-124


title: ZH11-OE1 panicle, biol rep 1


title: Control, DMSO, replicate 3


title: HeLa, NSUN6, KO, Noc48h

city: Guangzhou

first: Rui

last: Zhang

address: No. 135, Xingang Xi Road

institute: Sun Yat-sen University

data_processing:
Adapters were trimmed with cutadapt-1.13 (-e 0.25 -q 25 –trim-n -a NNNNNNAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A NNNNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAG). Adapter-trimmed reads were quality trimmed with Trimmomatic-0.36 (PE mode, HEADCROP:10 SLIDINGWINDOW:4:22 AVGQUAL:25 MINLEN:40).
Clean reads were mapped to Ensembl GRCh37.75 genome and transcriptome with hisat2-2.10 (-k 10, --fr, --rna-strandness FR --no-mixed), uniquely alignment only0. Unmapped reads were further mapped to transcriptome with bowtie2-2.2.9 (-end-to-end, --fr --gbar 5, --mp 5, -k 10, -R 2, -D 5). Unique alignments mapped to the same gene location were used. Transcriptome alignments were liftOver to genomic coordinates with a custom script. Hisat2 alignmets and bowtie2 alignmets were merged.
Pileup was performed using samtools API pysam to get base counts.
Custom scripts were used to call m5C sites from samples:  (i) C+T coverage >= 20; (ii) C count >= 3; (iii) m5C level >= 0.1; (iv) signal ratio >= 0.9 at certain C-cutoff (mostly at 2-5) and (v) one-side binomial P value < 0.001
Genome_build: hg19
Supplementary_files_format_and_content: CSV files recording the coverage, m5C level, P-value for m5C sites

source_name: HeLa

growth_protocol: Cell lines were maintained in DMEM (Gibco) supplemented with 10% FBS (HyClone).

extract_protocol:
Total RNA was isolated with TRIzol reagent and Direct-zol RNA MiniPrep kit; for cytoplasm/nuclear fractions, cells were fractionated using the PARIS kit (Ambion) according to the manufacturer’s instructions. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads (Vazyme).
100ng-1μg of polyadenylated RNA was converted using the EZ RNA methylation kit (Zymo Research) with 3 cycles of [70 C 10 min, 64 C 45 min] and 37 C 30 min for desulfonation. The converted RNA was fragmented into 150~200 nt fragments by incubation at 94 °C for 8 minutes in fragmentation buffer (NEBNext Ultra II Directional RNA Library Prep Kit, NEB). The fragmented RNA was then used for library construction, following the manufacturer’s protocol (NEBNext Ultra II Directional RNA Library Prep Kit, NEB).

treatment_protocol: Cells were treated by 100 ng/ml Nocodazole for 48 hours before harvest. For knock down experiment, we treated the cells with 100 ng/ml Nocodazole after transfected by siRNA for 72 hours.

value: HeLa

value: NSUN6 KO

value: Noc 48h


title: HeLa, NSUN5, KO, Noc48h

value: NSUN5 KO


title: WT-119


title: HeLa, NSUN2, KO, Noc48h

value: NSUN2 KO


title: Control, DMSO, replicate 1

value: WI-38 cells


title: WT-100


title: ssccp1Δ-1

status: Public on Aug 19 2023

first: Enping

last: Cai

address: Wushan Road, Tianhe District

department: College of Plant Protection

institute: South China Agricultural University

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GCA_001010845.1 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
We used clusterProfiler R package to test the statistical enrichment of differential expression genes in KEGG pathways. We use the local version of the GSEA analysis tool http://www.broadinstitute.org/gsea/index.jsp, GO, KEGG data set were used for GSEA independently.
Assembly: GCA_001010845.1

organism: Sporisorium scitamineum

source_name: sporidia

growth_protocol: The fresh haploid sporidia of MAT-1 and ssccp1Δ-1 strains allowed to grow in YePSA medium at 28 ℃ for 24 h

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit following manufactuer’s protocols

value: sporidia

value: ssccp1 mutant


title: MAT-1


title: Control, H151, replicate 1


title: HeLa, Nop2, KD, Noc48h

value: Nop2 (NSUN1) KD


title: Control, DMSO, replicate 2


title: MYMG_4d_rep1

city: Hamilton

first: Evan

last: Shepherdson

state: Ontario

address: 1280 Main St W

country: Canada

institute: McMaster University

data_processing:
RNA-seq reads were aligned to the Streptomyces venezuelae genome GCA_001886595.1 using Bowtie2
Aligned reads were sorted using Samtools sort and a counts file was generated using HTseq-count
Counts files were processed using DESeq2 to generate a table of normalized transcript abundance measurements and to analyze statistical changes in expression between sample conditions
Assembly: GCA_001886595.1
Supplementary files format and content: Matrix table with normalized transcript abundance for every gene in samples isolated from MYMG at 2, 4, and 7 days of growth in .csv file format
Supplementary files format and content: Matrix table with normalized transcript abundance for every gene in samples isolated from MYM and MYMG at 4 days of growth in .csv file format
Supplementary files format and content: Matrix table with normalized transcript abundance for every gene in all samples in .csv file format

organism: Streptomyces venezuelae

source_name: Bacterial cells

growth_protocol: 10 uL of a Streptomyces venezuelae overnight culture were spotted to solid growth medium and incubated at 30 degrees Celsius. After specified incubation times, total RNA was extracted from cell lysates.

extract_protocol:
Lysates were generated by vortexing bacterial cells with glass beads in a guanidinium thiocyanate saturated lysis buffer. Total RNA was extracted with acidified phenol:chloroform
rRNA was depleted from total RNA samples using a Ribo-Zero rRNA Removal Kit (Bacteria) from Illumina. Libraries were constructed using an NEBNext Ultra II Direcitonal RNA Library Prep Kit for Illumina.

value: Bacterial cells

tag: growth medium

value: Malt extract - yeast extract - maltose - glycerol (MYMG)

tag: incubation time

value: 4 days


title: MYM_4d_rep2

value: Malt extract - yeast extract - maltose (MYM)


title: MYMG_7d_rep2

value: 7 days


title: MYM_4d_rep1


title: MYMG_2d_rep1

value: 2 days


title: MYMG_4d_rep2


title: MYMG_2d_rep2


title: WT-122

value: Lin-cKit+ bone marrow cells


title: MYMG_7d_rep1


title: U87_sh107_rep2

city: Kanazawa

first: Shin-ichi

last: Horike

state: Ishikawa

address: 13-1 Takaramachi

department: Research Center for Experimental Modeling of Human Disease

country: Japan

institute: Kanazawa University

description: Gene expression seven days after shRNA lentivirus infection

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >25.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Fragmentation Buffer (Agilent) and 2x Blocking Agent (Agilent) following the manufacturer's instructions. On completion of the fragmentation reaction, 55 ul of 2x GE Hybridization Buffer HI-RPM(Agilent) was added to the fragmentation mixture and hybridized to  Whole Human Genome microarry 4x44K Ver. 2.0 (G4845A, Agilent Technologies)  for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2539A) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol AgilentHD_GX_1Color and Grid: 026652_D_F_20120130) to obtain background subtracted and spatially detrended Processed Signal intensities.
Data were normalized and filtered wtih three filters with GeneSpring software 13 (Agilent Technologies). In brief, raw data were normalized with their 75 percentile values. In the first filter, when the value of a probe was lower than  20 percentile value in any samples, the probe was excluded. In the second filter, when the flag of a probe was compromised in any samples, the probe was exluded. In the last filter, when the value (log scale) of CV was over 50 percent in both conditions, the probe was exluded. After flitering, control probes were excluded, and log scale values were transformed into normal scale.

source_name: U87, NUP107 knocked down cell, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: 10% FBS DMEM + 1%penicillin/streptomycin

extract_protocol: Total RNA was extracted with NucleoSpin RNA (Macherey-Nagel) according to the manufacturer's instructions.

value: Cancer cell line

value: NUP107 knocked down


title: U87_sh107_rep1

source_name: U87, NUP107 knocked down cell, replicate 1


title: MYM_2d_rep2


title: U87_shNT_rep1

source_name: U87, negative control cell, replicate 1

value: negative control


title: MYM_2d_rep1


title: stomach blood sinus_2

city: Cincinnati

first: Joshua

last: Waxman

state: OH

address: 240 Albert Sabin Way

department: Molecular Cardiovascular Biology Division

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Ciona paired-end RNA-seq reads were aligned to the UCSC Ciona genome, ci3, using STAR aligner after trimming the Illumina adapter using cutadapt
Gene expression levels were quantified as raw read counts using FeatureCounts in the subread package with an option, “-O --fracOverlap 0.8”, and with a proper strand option (-s).
Given the mixed sequencing batches and library types, we incorporated RUVseq batch correction (RUVs, k=1) in DESeq2 differential analysis.
Differentially expressed genes were identified by FDR < 0.05. Hierarchical clustering was performed using the Pearson correlation coefficient as a similarity measure under Ward’s criterion, and a heatmap was visualized in z-score.
Assembly: Ciona robusta (Ciona intestinalis A) version KH (ci3)
Supplementary files format and content: text of DESeq2 data with LogFC, P-value, FDR, normalized expression, and raw counts

organism: Ciona robusta

source_name: isolated stomach blood sinus

extract_protocol:
Hearts from adult Ciona robusta were dissected and placed into RNAlater. The different sections of the heart – pharyngeal blood sinus, stomach blood sinus, and cardiac region were then dissected in RNAlater and in RNeasy lysis buffer. The pooled sections of the heart were sonicated and the RNA was collected using the RNeasy kit.
RNA libraries were prepared for sequencing using standard protocols

value: isolated stomach blood sinus

value: wild caught

value: adult


title: stomach blood sinus_1


title: U87_shNT_rep2

source_name: U87, negative control cell, replicate 2


title: A549 cells, SEMA5A_Empty, rep2

city: Taipei

first: Liang-Chuan

last: Lai

state: Taiwan

address: 1 Jen-Ai Road, Sec 1

department: Physiology

country: Taiwan

institute: National Taiwan University

description:
SAMPLE 11
replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with IlluminaGUI in R

label: Biotin

source_name: A549 cells

label_protocol: Biotinylated cRNA were prepared with the Invitrogen Illumina™ TotalPrep™ RNA Amplification Kit

growth_protocol: A549 cells were cultured in Roswell Park Memorial Institute (RPMI) 1640 medium (GIBCO; Thermo Fisher, Waltham, MA, USA) with 10% fetal bovine serum (FBS) (Millipore, US Origin, Korea Eligible) and 1% penicillin-streptomycin (GIBCO)

extract_protocol: Total RNA was extracted from cultured cells using NucleoZOL reagent (Machery-Nagel, Düren, Germany) according to the manufacturer’s protocol

treatment_protocol: Cells were transfected with different domains of SEMA5A expressing plasmids and control plasmid by jetPRIME transfection reagent (Polyplus-transfection, Illkirch, France) according to the manufacturer’s protocol.

value: A549 non-small cell lung cancer cell line

tag: transfection


title: pharungeal blood sinus_2

source_name: isolated pharyngeal blood sinus

value: isolated pharyngeal blood sinus


title: A549 cells, SEMA5A_Empty, rep3

description:
SAMPLE 12
replicate 3


title: A549 cells, SEMA5A_Full, rep3

description:
SAMPLE 9
replicate 3


title: pharyngeal blood sinus_1