title: miR-324_WT_4

value: rib cartilage

value: wild-type control


title: chloramphenicol-treated, biol rep2, tech rep 2

status: Public on Oct 01 2024

type: SRA

city: San Francisco

first: Brianna

middle: Lynn

last: Bibel

state: CA

department: Cellular and Molecular Pharmacology

country: USA

institute: Brianna Bibel

description: mitoribosome-protected footprints

library_source: other

data_processing:
Reads were trimmed to remove ligated 3’ linker (TAGACAGATCGGAAGAGCACACGTCTGAA) with Cutadapt
Reads without linker were discarded and the unique molecular identifier (UMI) was then extracted from remaining reads using a custom script. UMIs consisted of 5 random nucleotides at the 3’ end ligated as part of the 3’ linker
Trimmed reads were filtered after alignment using bowtie1 to human rRNA (allowing 1 internal and 1 5’ mismatch) and human tRNA (allowing 1 internal, 1 5’, and 3 3’ mismatches). Remaining reads were aligned to the GRCh38 human reference genome from GENCODE using STAR 2.7.3. For mitoRP samples with mouse spike-ins, the M17 mouse reference genome from GENCODE was merged with the human genome. STAR mismatch parameters for mitoRP and cytoRP: --outFilterMismatchNoverReadLmax 0.07 and --outFilterMismatchNmax 3. STAR parameters for RNA-seq: default
PCR duplicates were identified by their UMI and removed using a custom script
Read coverage for mitochondrial mRNA mapping mitoRP reads was transformed to A-site density using a custom script. Offsets from the 3’ end of 33:[-15], 34:[-16], 35:[-17], 36:[-17], 37:[-18], 38:[-19], 39:[-20] were used.
Coverage across each codon was calculated by summing the read counts across the three sub codon positions and counts were normalized to reads per million mitochondrial mRNA-mapped reads (rpm)
Pause scores were calculated as the fold-change over the mean of rpm-normalized values in a 21-codon sliding window
Assembly: hg38
Supplementary files format and content: *CodonCoverageEach_*.rpm.bedGraph files were made as described above, with the 4th column being codon rpm values. Plus (P) and minus (M) strand files are both given. Only read lengths given in the file name are included.
Supplementary files format and content: *CodonCoverageEach_*.rpm_pauseScorefold_win21.bedGraph files were made as described above, with the 4th column being pause scores. Plus (P) and minus (M) strand files are both given. Only read lengths given in the file name are included.

molecule: other

organism: Homo sapiens

source_name: Freestyle 293-F

growth_protocol: Cell culture and treatment FreeStyleTM 293-F cells (HEK293 cells adapted for serum-free suspension culture) were grown in suspension culture at 37°C, 5% CO2, with orbital shaking (115 rpm) in unmodified FreeStyleTM 293 Expression Medium (Gibco) in the absence of antibiotics. Cell cultures were diluted to 2 x 10^6  viable cells/mL and 50 mL portions were transferred into 125 mL flasks before use.

extract_protocol:
Mitoribosome footprint isolation: Mitoribosome footprints were prepared as described in Soto et al., 2022 with modifications. Each 10 x 10^6 cell pellet of frozen cells was resuspended in 900 μL of mito-RP lysis buffer (10mM Tris pH 7.5; 50mM NH4Cl, 20mM MgCl2, 0.25% lauryl maltoside, 10mM DTT, 1X EDTA-free protease inhibitor cocktail (Pierce) containing antibiotic or DMSO at the same concentration as in the pre-treatment) and incubated for 10 min on ice. It was then homogenized via 15 strokes of a Dounce homogenizer and centrifuged for 1 min @ 1000 x g. The supernatant was transferred to new tubes and a 25 μL portion of each was flash frozen in liquid nitrogen for total RNA sequencing. RNase If (NEB) was added to each supernatant for a final concentration of 7.25 U/μL to produce mitoribosome footprints. Samples were incubated for 30 minutes at room temperature without rotation. 80 U of SUPERaseInTM RNase Inhibitor (Invitrogen) was then added per 450 μL of digested lysate to prevent overdigestion and the digested lysate was clarified by centrifugation in a benchtop microcentrifuge @ 10,000 RPM, 5 min, 4°C. Clarified lysates were then transferred to a 10-50% linear sucrose gradient (prepared in mito-RP lysis buffer without lauryl maltoside & protease inhibitor, using a BioComp GradientMasterTM) and centrifuged for 3 h @ 4°C, SW41Ti rotor. Fractions were collected with a BioComp Piston Gradient FractionatorTM and portions corresponding to mitomonosomes (identified based on UV 260 trace and confirmed via western blot for MRPL12 and MRPS18B) were frozen @ -80°C in 3 volumes of TRIzolTM LS (Invitrogen). Footprints were then isolated using a Direct-zolTM RNA kit (Zymo) and subsequently concentrated using a RNA Clean and Concentrator-5 kit (Zymo). RNA was then size-selected by running a 15% TBE-Urea gel and extracting fragments between 28 and 40 nt in length, corresponding to mitoribosome-protected footprints.
Sequencing library preparation: Libraries were prepared from the extracted footprint RNA as described2–5 with modifications. Briefly, extracted RNA was desalted using a RNA Clean and Concentrator-5 kit (Zymo), then dephosphorylated with T4 PNK (NEB) and ligated to a preadenylated oligonucleotide linker (NI-816: 5’-/5Phos/NNNNNTAGACAGATCGGAAGAGCACACGTCTGAA/3ddC/-3’) using T4 RNA Ligase 2 truncated KQ (NEB). Unligated linker was depleted by treatment with yeast 5’-deadenylase (NEB) and RecJ exonuclease (Lucigen/Epicenter), and the linker-ligated footprints were then purified via a Oligo Clean and Concentrator kit (Zymo). The ligation products were then reverse transcribed using Protoscript II reverse transcriptase (NEB) and NI-802 primer (5’-/5Phos/ NNAGATCGGAAGAGCGTCGTGTAGGGAAAGAG/iSp18/GTGACTGGAGTTCAGACGTGTGCTC-3’). The RNA template was then hydrolyzed with NaOH. The reverse transcription products were desalted and concentrated with an Oligo Clean & Concentrator kit (Zymo), followed by gel purification via a 15% TBE-Urea PAGE gel. Extracted cDNA was then circularized using CircLigase II (Lucigen). Circular DNA was quantified via qPCR, then amplified via PCR with the forward primer NI-798 5′-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTC-3’ and a unique reverse indexing primer (containing a unique 6 nucleotide barcode) for each sample. PCR products were then purified via a DNA Clean & Concentrator 5 column (Zymo) followed by gel purification via an 8% non-denaturing TBE PAGE gel. Extracted DNA was then quantified and checked for quality with a BioAnalyzer (Agilent).
Mitoribosome profiling

treatment_protocol: To each portion of 2 x 10^6 cells, DMSO or antibiotic was added to a final concentration of 1% DMSO, 300 μM (97 μg/mL) chloramphenicol (CHL), 300 μM (101 μg/mL) linezolid (LZD), or 100 μM (155 μg/mL) retapamulin (RET). Samples were placed back into the incubator for 5 minutes before collecting cells via fast vacuum filtration through a 0.8 μM filter. The collected cells were then quickly scraped off the filter and plunged into liquid nitrogen. The frozen cells were stored at -80°C until use.

tag: cell line

value: Freestyle 293-F

tag: cell type

value: Human embryonic kidney

tag: treatment

value: 300 uM chloramphenicol


title: WT1,replicate1,sRNA-seq

city: Beijing

first: Ling

middle: Tong

last: Liu

address: No.20 Nanxincun, Xiangshan

country: China

institute: Institute of Botany, Chinese Academy of Sciences

library_source: transcriptomic

data_processing:
Adapters and low-quality reads were removed and 18-30 bp long clean reads were mapped without mismatches on the tomato reference genome (ITAG 4.0) (Tomato Genome, 2012) using bowtie.
Then all reads mapping to tRNAs, snRNAs, rRNAs, or snoRNAs were removed according to the ncRNA annotation information of the tomato.
Mapped reads from three biological replicates were pooled together and remapped to the tomato reference genome using the ShortStack software v3.8.5 (--mismatches 0 --mmap f) to annotate and quantify sRNA.
Assembly: SL4.0
Supplementary files format and content: ShortStack output

molecule: total RNA

organism: Solanum lycopersicum

source_name: 21 DAF embryo

growth_protocol: The tomato cultivar S. lycopersicum L. cv. Micro-Tom was grown in a climate-controlled chamber under a 16-h light/26°C and 8-h dark/22°C cycle with a light intensity of 100~200 μmol m-2 s-1.

extract_protocol:
Total RNAs were isolated from tomato embryos of 21 DAF using TRIzol reagent (Invitrogen, 15596026).
Libraries for sRNA-seq were generated using NEB Next® Multiplex Small RNA Library Prep Set for Illumina® (NEB E7300L).

tag: tissue

value: 21 DAF embryo

tag: cultivar

value: Micro-Tom

tag: genotype

value: WT


title: DMSO-treated, biol rep1

description: mitoribosome-protected footprints

value: 1% DMSO


title: con_rep1

city: Shijiazhuang

first: Yuchen

last: Wang

state: Hebei

address: No.12, Jiankang Road

institute: The Fourth Hospital of Hebei Medical University

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using fastp version 0.19.5；RNA-seq reads were aligned to the hg38 genome assembly using Hisat2 version 2.1.0 .
Gene abundance measurements were generationed and normalized  using Stringtie ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression were analysed  using edgeR package in R program version 3.4.3
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw fragment counts for each Sample

source_name: Human esophageal squamous cell carcinoma tissues

growth_protocol: All patients underwent thorough evaluation according to the stringent criteria established by the AJCC (American Joint Committee on Cancer) and UICC (Union for International Cancer Control).   The eighth edition of UICC's TNM staging for esophageal cancer was meticulously applied.   Specifically: 1.   R0 resection of esophageal cancer was skillfully performed.   2.   Only patients with the thoracic ESCC subtype were included.   3.   An expertly administered preoperative neoadjuvant chemotherapy regimen was utilized.   4.   Patients with abnormal heart, lung, liver, or kidney function, as well as those with unremarkable blood routine test results rendering them unsuitable for neoadjuvant chemotherapy and surgical intervention, were excluded from the study.   In total, eight esophageal cancer specimens were collected from eight patients who had undergone radical resection.   Immediately after collection, all tissue samples were gently washed with physiological saline at 4℃, rapidly snap-frozen in liquid nitrogen, and stored at -80℃ for subsequent processing.   Clinical data from the patients were meticulously collected and organized.   Subsequently, patients were stratified into two groups based on postoperative pathology: those with a CAP (College of American Pathologists) score of 0-1 were designated as the experimental group (Responder), while patients with a CAP score of 3, matched to the experimental group in terms of clinical staging (cTNM), were categorized into the control group (Non-responder).

extract_protocol:
Total RNA was extracted from tissues using the RNeasy mini kit (Qiagen, Germany).  1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The human Esophageal Carcinoma cell lines KYSE-150, TE-1 and TE-12, and human esophageal normal cells (Het-1A) were maintained in RPMI Medium 1640 (C11875500BT, Gibco) supplemented with 10% fetal bovine serum (FBS) (10270-106, Gibco) at 37°C in a humidified atmosphere containing 5% CO2 and 95% air. For maintenance, 800,000 cells were seeded into 10ml of complete media every 3–4 d in 10-cm plates. Inhibition treatment involved the LY294002, a phosphoinositide 3-kinase (PI3K) inhibitor (HY-10108, MedChemExpress, 20 μmol/L), over a 24-hour period. Following this treatment, cells were subsequently harvested for protein extraction. The backbones pcDNA3.1 vector were purchased from TsingkeBiotechnologyCo., Ltd (Beijing, China). Plasmid constructs were generated via Gibson Assembly® Master Mix – Assembly (E2611, NEB) according to Gibson Assembly® Protocol (E5510, NEB).

value: Not sensitive to chemotherapy


title: miR-324_WT_1

city: NEWCASTLE UPON TYNE

first: David

last: Young

address: Centre For Life

country: United Kingdom

institute: Newcastle University

data_processing:
Kallisto was used for pseudo-alignment and quantification, against the mouse GRCh38 (release 92) transcriptome.
Mapped transcripts were converted to a gene level using Tximport.
DESeq2 was used to calculate P-values and log2 fold-changes (logFC), using the Benjamini-Hochberg method to adjust for multiple testing.
Assembly: Mouse GRCh38 (release 92)

organism: Mus musculus

source_name: rib cartilage

extract_protocol:
RNA was extracted from the cells using trizol/mirVana miRNA Isolation Kit (Thermo Fisher Scientific), following the manufacturer’s protocol to isolate total RNA.
The sequencing library was prepared using the NEB_low_input_RNA kit following the manufacturer’s protocol. Barcoding was with the NEBNext_Multiplex Oligos for Illumina_(96 Unique Dual Index Primer Pairs)

treatment_protocol: None. Tissue was processed as decribed and RNA directly isolated.

value: chondrocyte


title: nrpd1_4,replicate4,RNA-seq

data_processing:
Reads were trimmed and filtered with Trim Galore v0.6.7 (-q 25 --length 36 --stringency 3).
Hisat2 v2.2.1 was used to align trimmed reads (four replicates of RNA-seq data) to the tomato reference genome (ITAG 4.0).
Read counts were calculated by the featureCount v2.0.1.
DESeq2 package v1.36.0 was used to detect differentially expressed genes (DEGs).
Assembly: SL4.0
Supplementary files format and content: Read counts
Supplementary files format and content: differential expression

extract_protocol:
Total RNAs were isolated from tomato embryos of 21 DAF using TRIzol reagent (Invitrogen, 15596026).
Libraries for RNA-seq were generated using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (NEB #E7775L).

value: SlNRPD1 knockout


title: test_rep4

value: Human esophageal squamous cell carcinoma tissues

value: Sensitivity to chemotherapy


title: WT3,replicate3,sRNA-seq


title: test_rep3


title: KO_5

source_name: articular cartilage

extract_protocol:
RNA was extracted from the cells using trizol/mirVana miRNA Isolation Kit (Thermo Fisher Scientific), following the manufacturer’s protocol to isolate total RNA.
The sequencing library was prepared using theNEB_low_input_RNA kit following the manufacturer’s protocol. Barcoding was with the NEBNext_Multiplex Oligos for Illumina_(96 Unique Dual Index Primer Pairs)

value: articular cartilage


title: DMSO-treated, biol rep3

description: mitoribosome-protected footprints


title: test_rep2


title: KO_4


title: Brain, Cerebellum, CB

city: Rochester

first: Roberto

last: Cattaneo

state: MN

address: 222 3rd Ave SW

department: Molecular Medicine

institute: Mayo Clinic

description: CB.FCHHWKYBBXY_L4_R1_IGAACCGCG-TGACCTTA.fastq.gz

data_processing:
fastp for trimming adapters and low quality reads
DI-tector for detection of copy-back defective viral genome (cbDVG)
bwa-mem for reads alignment, samtools and htseq-count for host transcriptome counts
Assembly: hg38
Supplementary files format and content: tab-delimited text raw counts of cbDVG for each sample
Supplementary files format and content: tab-delimited text file including raw counts of the host transcriptome for each sample
Supplementary files format and content: a text file that contains sequences of the 276 of cbDVG

source_name: Brain

extract_protocol:
RNA was extracted from frozen brain specimens using Trizol extraction protocol.
cDNA library prep was conducted using Illumina TruSeq Stranded Total RNA Sample Prep Kit (Illumina) according to the manufacturer’s protocol, which depletes ribosomal RNA.

value: Brain


title: test_rep1


title: KO_3


title: Brain, Midbrain, MB

description: MB.FCHHWKYBBXY_L4_R1_ITCATCCTT-AGCGAGCT.fastq.gz


title: Brain, Cerebellum towards the nuclei, CN

description: CN.FCHHWKYBBXY_L4_R1_ICTGCTTCC-GATAGATC.fastq.gz


title: KO_2


title: WT4,replicate4,RNA-seq


title: Brain, Brain stem, BS

description: BS.FCHHCFLBBXY_L8_R1_ICTCTCGTC-TATAACCT.fastq.gz


title: miR-324_WT_3


title: con_rep2


title: nrpd1_1,replicate1,RNA-seq


title: miR-324_WT_2


title: Hela KO + W377A 3 (batch 1)

city: Houston

first: Bin

state: TX

address: 1515 Holcombe BLVD

department: epigenetics and molecular carcinogenesis

institute: University of Texas MD Anderson Cancer Center

data_processing:
The raw data contains FASTQ files of 4 experimental conditions wild type (WT), empty vector (EV), and 2 mutation conditions W377A, Y112A. Each condition has three biological replicates. The quality of raw data is initially assessed using FastQC. Subsequently, Trim Galore is employed to eliminate any adapters from the raw data. Following this, Tophat is utilized with default settings to align and annotate sequences, utilizing the mouse reference genome obtained from Gencode version M31. Finally, splicing events are detected and analyzed using rMATS based on the Tophat alignment results. Five categories of splicing events are SE (skipped exon), RI (retained intron), MXE (mutually exclusive exons), A5SS (alternative 5’ splice site), and A3SS (alternative 3’ splice site). The FDR threshold was chosen to be 0.05.
Assembly: GRCm39
Supplementary files format and content: rMATS_result.tar.gz

source_name: Hela

growth_protocol: Hela cell line was maintained at 37 °C in Dulbecco’s modified Eagle’s medium supplemented with 10% FBS and 1% Antibiotic-Antimycotic.

extract_protocol:
Total RNA was harvested using Rneasy kit(QIAGEN, 74106)
Library was prepared by Medgenome using Illumina TruSeq stranded mRNA kit.
RNA-seq for 40M paired reads (80M total) per sample

value: Hela


title: WT3,replicate3,RNA-seq


title: Brain, Internal Capsule, IC

description: IC.FCHHWKYBBXY_L4_R1_ITCTGTTGG-TCGAATGG.fastq.gz


title: KO_1


title: Brain, Upper Brainstem, UBS

description: UBS.FCHHWKYBBXY_L4_R1_IGGTCACGA-GTATTATG.fastq.gz


title: nrpd1_3,replicate3,RNA-seq


title: Brain, Parietal lobe, PL

description: PL.FCHHWKYBBXY_L4_R1_ICTCACCAA-CTAGGCAA.fastq.gz


title: WT_5


title: WT2,replicate2,RNA-seq


title: Brain, Occipital lobe, OL

description: OL.FCHHCFLBBXY_L8_R1_ITCTCTACT-CGCGGTTC.fastq.gz


title: Hela KO + W377A 1 (batch 1)


title: nrpd1_2,replicate2,RNA-seq


title: WT1,replicate1,RNA-seq


title: WT_4


title: Brain, Temporal lobe, TL

description: TL.FCHHCFLBBXY_L8_R1_IGACCTGAA-TTGGTGAG.fastq.gz


title: WT_3


title: Hela KO + Y112A 3 (batch 1)


title: Brain, Hippocampus, HC

description: HC.FCHHWKYBBXY_L4_R1_IAGGTTATA-CAGTTCCG.fastq.gz


title: Hela KO + Y112A 2 (batch 1)


title: Brain, Frontal Cortex 3, FC3

description: FC3.FCHHWKYBBXY_L4_R1_ITATCGCAC-CTTAGTGT.fastq.gz


title: Hela KO + WT 3 (batch 1)


title: nrpd1_3,replicate3,Methyl-seq

library_source: genomic

data_processing:
Reads were trimmed and filtered with Trim Galore v0.6.7 (-q 25 --length 50 --stringency 3).
Clean reads were mapped tomato reference genome using Bismark v0.24.0 with default parameters.
Reads were deduplicated with deduplicate-bismark (--paired) and methylation calls were extracted using bismark_methylation_extractor (--paired-end --no_overlap --ignore 6 --ignore_r2 8 --comprehensive).
The R package DSS v2.44.0 was used to identify CG, CHG, and CHH DMRs with DMLtest and callDMR functions (smoothing = TRUE, delta DMR = 0.1, p.threshold DMR = 1e-3).
Assembly: SL4.0

molecule: genomic DNA

extract_protocol:
Genomic DNA was isolated from tomato embryos of 21 DAF using TIANamp Genomic DNA Kit (Cat # 4992254).
The recovered DNA was bisulfite-converted using the EZ DNA MethylationGoldTM Kit (D5006).


title: WT_1


title: Hela KO + Y112A 1 (batch 1)


title: Hela KO + W377A 2 (batch 1)


title: nrpd1_2,replicate2,Methyl-seq


title: Brain, Frontal Cortex 2, FC2

description: FC2.FCHHWKYBBXY_L4_R1_IAACTGTAG-ACGCCGCA.fastq.gz


title: WT_2


title: Brain, Frontal Cortex 1, FC1

description: FC.FCHHCFLBBXY_L8_R1_IAGTTCAGG-CCAACAGA.fastq.gz


title: WT3,replicate3,Methyl-seq


title: e11.5 whole embryo, KOAC10-2-WT

city: Ottawa

first: Balwant

last: Tuana

state: Ontario

address: 451 Smyth Road

department: Cellular and Molecular Medicine

country: Canada

institute: University of Ottawa

data_processing:
Reads were assigned to theGRCm38_GENCODE.vM19transcriptome model using Salmon and the differential expression of transcripts was analysed by DESeq2
Filter to retain only genes with 5 or more counts in two or more samples.
Trimmed sequence reads were mapped to GRCm38_GENCODE.vM19 using MultiQC
Read count extraction and normalization were performed using MulitQC report
Assembly: GRCm38_GENCODE.vM19
Supplementary files format and content: text files include FPKM values for all samples (Combined_KO_WT_191206_subset_fpkm.txt)
Supplementary files format and content: text file for breakdown of RNA-seq analysis (Rehmani_dec6_2019_RNA-seq analysis.html)
Supplementary files format and content: text file for fragment analysis and sequence counts (Rehmani_dec6_2019_Multiqc_report.html)

source_name: Whole embryo

extract_protocol:
[embryo isolation protocol] Plug-checked females underwent c-section to harvest e11.5 embryos. Tail's were taken for genotyping and remaining whole body was utilize for extracting  total RNA using Rneasy mini kit (QIAGEN) according to manufacturer protocols.
RNA was harvested using Rneasy mini kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq RNA v2 Library Preparation Kit (Illumina)

value: Whole embryo

value: Wildtype

tag: strain

tag: developmental stage

value: embryonic day 11.5


title: Hela KO + WT 2 (batch 1)


title: WT2,replicate2,Methyl-seq


title: e11.5 whole embryo, KOAC10-8-KO

value: SLMAP3 knockout


title: HGC_27_KS_3

city: Guangzhou

first: Caiqi

last: Ma

address: No.1 Xinzao Road, Panyu District

institute: Guangzhou Medical Univercity

description: HGC cell overexpession KS 3

data_processing:
To get high quality clean reads, reads were further filtered by Cutadapt1.9, then sequence quality was verified using FastQC
We aligned reads of all samples to the human reference genome using HISAT2
The mapped reads of each sample were assembled using StringTie with default parameters. Then, all transcriptomes from all samples were merged toreconstruct a comprehensive transcriptome using gffcompare software . After the final transcriptomewas generated, StringTie and ballgown  were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs bycalculating FPKM (fragment per kilobase of transcript per million mapped reads) value
Assembly: GRCh38
Supplementary files format and content: table delimited txt file includes raw counts for each sample
Supplementary files format and content: table delimited txt file includes FPKM values for each sample

molecule: polyA RNA

growth_protocol: HGC-27 cells were maitained in RPMI-1640 supplemented with 20% FBS and 1% P/S in atmosphere with 5% CO2 in 37 ℃

extract_protocol:
RNA was extracted using TRIzol reagent, 2 μg total RNA was used for the libraries construction
RNA libraries were prepared using VAHTS Universal DNA library Prep Kit for illumina

treatment_protocol: No specific treatment with two lines

value: human gastric carcinoma cell line

value: Overexpression SERPINA4

value: No treatment


title: e11.5 whole embryo, KOAC9-1-WT


title: WT1,replicate1,Methyl-seq

value: 21 DAF embryo

value: Micro-Tom

value: WT


title: Hela KO + WT 1 (batch 1)


title: A549 cells, Si-Cyclin Y#2-3

city: Wuhan

first: Zhi

middle: Wei

state: Hubei

address: No.13, Aviation Road, Baofeng Street, Qiaokou District

institute: HuaZhong University of Science and Technology

data_processing:
CLC Genomics Workbench v11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork(parameter-Quality limit:0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters-mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-limited text files include RPKM values for each Sample

source_name: lung

extract_protocol:
Cells were transfected with siRNAs, and RNA was harvested using Trizol reagent. EBNext® Ultra™ RNA Library Prep Kit for Illumina® was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacture's protocols.

value: lung

value: Human non-small cell lung cancer cells

value: Cyclin Y knockdown


title: HGC_27_KS_2

description: HGC cell overexpession KS 2


title: nrde3_HMTs, L1, rep4

city: Ann Arbor

first: Hector

last: Mendoza

state: MI

address: 1105 N University Ave

department: Molecular, Cellular and Developmental Biology

institute: University of Michigan

data_processing:
The reads were trimmed using CutAdapt v2.3.FastQC v0.11.8 was used to determine quality of data.Reads were mapped to the reference genome WBcel235 and read counts were generated using Bowtie 2 v2.4.2. Differential gene expression analysis was performed using DESeq2 v1.42.0. Downstream analyses were performed using R scripts and packages and only considered protein-coding transcripts.
Assembly: WS235
Supplementary files format and content: tab-delimited text files with normalized CPM values and DESeq2 results

organism: Caenorhabditis elegans

source_name: N2 Bristol

growth_protocol: Worms were synchronized by bleaching gravid hermaphrodites and allowing embryos to hatch overnight in M9 buffer. Newly hatched L1 animals were allowed a 3-hour recovery period on OP50 E. coli.

extract_protocol:
L1 larvae were resuspended in TRIzol and underwent repeated freeze-thaw cycles. Total RNA was extracted and purified using the Qiagen Rneasy kit with on-column DNAse digestion.
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (catalog number E7760L), and NEBNext Multiplex Oligos for Illumina Unique dual (catalog number E6448S) were used for library prep.The mRNA was fragmented and copied into first strand cDNA using reverse transcriptase and random primers. The 3' ends of the cDNA were then adenylated and adapters were ligated. The products were purified and enriched by PCR to create the final cDNA library.

treatment_protocol: Worms were grown under standard conditions.

value: N2 Bristol

value: set-32; met-2 set-25; nrde-3


title: nrde3_HMTs, L1, rep3


title: e11.5 whole embryo, KOAC8-1-WT


title: HGC_27_KS_1

description: HGC cell overexpession KS 1


title: nrpd1_1,replicate1,Methyl-seq

value: SlNRPD1 knockout


title: HGC_27_GFP_3

description: HGC cell overexpession control3

value: Overexpression GFP


title: e11.5 whole embryo, KOAC10-5-KO

value: Whole embryo


title: nrde3_HMTs, L1, rep2


title: A549 cells, Si-Cyclin Y#1-3


title: A549 cells, Si-Cyclin Y#1-2


title: HGC_27_GFP_2

description: HGC cell overexpession control2


title: A549 cells, Si-Cyclin Y#2-1


title: HGC_27_GFP_1

description: HGC cell overexpession control1


title: e11.5 whole embryo, KOAC8-6-KO


title: nrde3, L1, rep3


title: A498_shZNF395-3

city: Singapore

first: Xiaosai

last: Yao

address: 60 Biopolis Street, Genome, #02-01

country: Singapore

institute: Genome Institute of Singapore

data_processing:
RNA-seq data were mapped to hg19 (hs37d5) using STAR 25, with GENCODE annotation (gencode.v19.annotation.gtf) and recommended settings from STAR manual. Gene expression levels were quantified with STAR 26. Log fold change of differential expression genes was computed with DESeq2
Assembly: hg19
Supplementary files format and content: Deseq2 files are in tab delimited text files, including 7 standard columns "Symbol", "baseMean", "log2FoldChange", "lfcSE", "stat", "pvalue", "padj", then followed by 6 columns of raw count.

source_name: Cancer cell line

growth_protocol: Cells were grown in RPMI-1640 medium (Sigma) supplemented with 10% fetal bovine serum (Gibco). Cells were maintained in a 5% CO2-humidified incubator at 37°C.

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy Mini kit
RNAseq libraries were prepared using Illumina Tru-Seq Stranded Total RNA kit protocol

treatment_protocol: Stable knockdown of ZNF395 in ccRCC cell lines was performed using retroviral transduction with either commercially available MISSION shRNA constructs (Sigma Aldrich). MISSION shRNA glycerol stock was cultured and plasmid was extracted using NucleoBond Xtra Maxi Plus EF (MACHEREY-NAGEL). Viral particles were packaged by transfecting plasmid into HEK293T at 2 μg DNA/well of a 6-well plate using Lipofectamine 3000 (Life Technologies). A media change was performed 6 hours after transfection. The cell supernatant containing retroviral particles was harvested 48 hours post-transfection, and inoculated onto ccRCC cells, which were then selected with puromycin (2 mg/mL) for 3 days. Cells were analyzed for gene expression.  The MISSION shRNA clones used for ZNF395 knockdown are shZNF395-1(TRCN0000233231) and shZNF395-3 (TRCN0000148383).

value: ZNF395 knockdown shRNA3


title: A549 cells, Si-Cyclin Y#1-1


title: Larp7 cKO spermatocyte-rep5

city: Sendai

first: Yukiko

last: Tando

state: Miyagi

address: Seiryo-machi 4-1, Sendai, Miyagi 980-8575

country: Japan

institute: Institute of Development, Aging and Cancer, Tohoku University

data_processing:
Image analysis and base calling were performed using Real-Time Analysis Software (v1.18.64, Illumina).
Gene expression analysis involved mapping reads to the mouse genome (UCSC mm10 genome assembly and the NCBI RefSeq database) using TopHat2 (v2.1.0) and Bowtie 2 (v2.2.6.0).
FeatureCounts (packaged in Subread v1.5.0-p2) was used to calculate count data from the BAM files.
TMM normalization was performed.
Assembly: mm10
Supplementary files format and content: tab-deliminated text file include FPKM values for each sample

source_name: testis

extract_protocol:
RNA was extracted using RNeasy Micro kit (Qiagen), and used for the construction of sequencing libraries.
The libraries were constructed using an by NEBNext Ultra II RNA Library Prep Kit for Illumina 9 (BioLabs E7770S) .

value: testis


title: Larp7 cKO spermatocyte-rep4


title: nrde3, L1, rep2


title: A498_shZNF395-1

value: ZNF395 knockdown shRNA1


title: Larp7 cKO spermatocyte-rep3


title: nrde3, L1, rep1


title: A549 cells, Si-Control-3


title: A549 cells, Si-Control-2


title: e11.5 whole embryo, KOAC10-7-WT

value: Wildtype

value: embryonic day 11.5


title: A549 cells, Si-Cyclin Y#2-2


title: A549 cells, Si-Control-1


title: 786O_shZNF395-3


title: Larp7 cKO spermatocyte-rep2


title: A498_shNTC

value: non targeting control


title: nrde3_HMTs, L1, rep1


title: WT spermatocyte-rep5


title: 786O_shZNF395-1


title: hrde1_HMTs, L1, rep2

value: set-32; hrde-1 met-2 set-25


title: hrde1_HMTs, L1, rep1


title: WT spermatocyte-rep4


title: 786O_shNTC


title: WT spermatocyte-rep3


title: Rectum biopsies, week 24, no replicates P47_W24

city: New York

first: Kyungku

last: Jang

state: NY

address: 430 East 29th Street

department: Microbiology

institute: New York University

description: Rectum biopsies, week 24, no replicates

data_processing:
RNA-seq results were processed using the R package DESeq2 to obtain variance stabilized count reads, fold changes relative to specific condition, and statistical P-value.
Assembly: hg38
Supplementary files format and content: "Nornalized counts.xlsx" includes normalized read counts.

source_name: Rectum biopsies

growth_protocol: No growth protocol;the rectal pinch biospies of UC patients who received tofacitinib were collected during colonoscopy at baseline (week 0) and end of study (week 24) and stored at liquid nitrogen tank.

extract_protocol:
Total RNA was extracted from the rectum pinch biopsies using RNase Mini Kit with DNase treatment (Qiagen) according to manufacturer's supplied protocol.
The libraries for RNA-Seq analysis were generated using TruSeq Standard Total RNA Library Prep with RiboZero Gold rRNA removal kit (Illumina) according to manufacturer’s supplied protocol.

treatment_protocol: No treatment protocol; we directly isolated RNA from the biopsies that were strored with fetal bovein serum with 10% (vol/vol) dimethyl sulfoxide

value: Rectum biopsies

value: Primary tissue


title: Rectum biopsies, week 24, no replicates P46_W24

description: Rectum biopsies, week 24, no replicates


title: WT spermatocyte-rep2


title: post-perfusion_J [3_9]

city: Cambridge

first: Kasra

last: Bahadori

state: Cambridge

address: Francis Crick Avenue

department: Medicine

institute: University of Cambridge

description:
sample3_9
experiment1_rawCounts.txt
experiment2_rawCounts.txt
experiment1_normCounts.txt
experiment2_normCounts.txt

data_processing:
Libraries were sequenced on a Hiseq sequencer (Ilumina) by either Eurofins or Genewiz
Sequencing data was demultiplexed to give individual fastq files using Casava (Illumina)
FASTQC was used for quality control
Fastq files were aligned to the human genome (Hg38) using Hisat2
A table of gene counts was produced using the featureCounts function within Rsubread
Assembly: normalisation performed using DESeq2 normalisation
Supplementary files format and content: Hg38
Supplementary files format and content: tab-delimited text files include unnormalised counts for each sample

source_name: liver

extract_protocol:
RNA extracted using a pure-link RNA mini kit (Ambion)
0.3 - 0.75µg of RNA was used to produce sequencing libraries using TruSeq Stranded total RNA library prep kit (Illumina) with 14 PCR amplification cycles

value: liver

tag: person

value: J

tag: Sex

value: male

tag: 2h alt

tag: donor type

value: DCD


title: Rectum biopsies, week 0, no replicates P46_W0

description: Rectum biopsies, week 0, no replicates


title: Rectum biopsies, week 24, no replicates P45_W24

description: Rectum biopsies, week 24, no replicates


title: DN3(IK)-2day, H3K27me3, ChIP-seq, rep2

city: Hershey

first: Bing

last: He

state: PA

address: 500 University Dr

institute: Penn State University

data_processing:
Sequencing reads were mapped to the mouse genome (mm9) using Bowtie2 (v2.2.2) with default parameter setting
Samtools and PICARD were used for QC of mapped reads (MAPQ>30).
ChIP-Seq peaks were called by MACS2 using default parameter setting
Assembly: mm9
Supplementary files format and content: bigWig

source_name: JE131 cell line (DN3 cells)

growth_protocol: cells were cultured in RPMI1640 with 10% FBS at 37℃ with 5% CO2

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to instructions for Illumina ChIP-seq DNA sample prep kit or Quanta Bio sparQ DNA Library Prep Kit.

treatment_protocol: DN3 cells were transduced with retrovirus that contains HA-tagged wild-type murine Ikaros for 1 day, 2 days and 3 days.

value: JE131 cell line (DN3 cells)

value: an early T leukemia cell line that is derived from Ikaros knock-out mice

value: DN3 cells transduced with Ikaros for 2 days

tag: chip antibody


title: post-perfusion_I [3_6]

description:
sample3_6
experiment1_rawCounts.txt
experiment2_rawCounts.txt
experiment1_normCounts.txt
experiment2_normCounts.txt

value: I

value: female


title: HMTs, L1, rep3

value: N2 Bristol

value: set-32; met-2 set-25


title: HMTs, L1, rep4


title: hrde1_HMTs, L1, rep4


title: pre-perfusion_I [3_7]

description:
sample3_7
experiment1_rawCounts.txt
experiment2_rawCounts.txt
experiment3_rawCounts.txt
experiment1_normCounts.txt
experiment2_normCounts.txt
experiment3_normCounts.txt


title: HMTs, L1, rep2


title: HMTs, L1, rep1


title: hrde1_HMTs, L1, rep3


title: hrde1, L1, rep4


title: pre-perfusion_P [3_22]

description:
sample3_22
experiment1_rawCounts.txt
experiment2_rawCounts.txt
experiment3_rawCounts.txt
experiment1_normCounts.txt
experiment2_normCounts.txt
experiment3_normCounts.txt

value: P


title: DN3(IK)-1day, H3K27me3, ChIP-seq, rep2

value: DN3 cells transduced with Ikaros for 1 day


title: Rectum biopsies, week 0, no replicates P44_W0

description: Rectum biopsies, week 0, no replicates


title: Rectum biopsies, week 0, no replicates P45_W0

description: Rectum biopsies, week 0, no replicates


title: hrde1, L1, rep2


title: Rectum biopsies, week 0, no replicates P47_W0

description: Rectum biopsies, week 0, no replicates


title: DN3(IK)-2day, HDAC1, ChIP-seq, rep2


title: hrde1, L1, rep3


title: DN3(IK)-2day, H3K27me3, ChIP-seq, rep1


title: post-perfusion_P [3_21]

description:
sample3_11
experiment1_rawCounts.txt
experiment2_rawCounts.txt
experiment1_normCounts.txt
experiment2_normCounts.txt


title: DN3(IK)-1day, H3K27me3, ChIP-seq, rep1


title: Rectum biopsies, week 24, no replicates P43_W24

description: Rectum biopsies, week 24, no replicates


title: pre-perfusion_S [2_9]

description:
sample2_9
experiment3_rawCounts.txt
experiment3_normCounts.txt

value: S


title: Rectum biopsies, week 0, no replicates P42_W0

description: Rectum biopsies, week 0, no replicates


title: DN3(IK)-1day, HDAC1, ChIP-seq, rep2


title: pre-perfusion_G [2_7]

description:
sample2_7
experiment4_rawCounts.txt
experiment4_normCounts.txt

value: G

value: DBD


title: hrde1, L1, rep1


title: Rectum biopsies, week 0, no replicates P43_W0

description: Rectum biopsies, week 0, no replicates

value: Rectum biopsies

value: Primary tissue


title: DN3(IK)-3day, mRNA-seq, rep2

data_processing:
Sequencing reads were mapped to the mouse genome (mm9) using STAR (v2.6.1c) with default parameter setting
FPKM values were computed using Cufflinks (v2.2.1)
Signal file were generated using HOMER (v4.10)
Assembly: mm9
Supplementary files format and content: bigWig, FPKM

extract_protocol:
Total RNA was extracted using QIAGEN RNeasy Mini Kit.
RNA libraries were prepared using NEBNext Ultra II RNA Library Prep kit (Molt4 and W8) or NEXTflex Illumina Rapid Directional RNA-Seq Library Prep Kit (DN3)  following manufacturers' protocols.

value: transduced with retrovirus that contains HA-tagged wild-type murine Ikaros

tag: time


title: Rectum biopsies, week 0, no replicates P41_W0

description: Rectum biopsies, week 0, no replicates


title: post-perfusion_R_filter [2_6]

description:
sample2_6_filter
experiment2_rawCounts.txt
experiment2_normCounts.txt

value: liver

value: R


title: DN3(IK)-3day, mRNA-seq, rep1

value: JE131 cell line (DN3 cells)


title: Rectum biopsies, week 24, no replicates P39_W24

description: Rectum biopsies, week 24, no replicates


title: N2, L1, rep4

value: WT


title: pre-perfusion_R_filter [2_5]

description:
sample2_5_filter
experiment2_rawCounts.txt
experiment2_normCounts.txt

value: DCD


title: Rectum biopsies, week 0, no replicates P39_W0

description: Rectum biopsies, week 0, no replicates


title: N2, L1, rep3


title: DN3(IK)-2day, mRNA-seq, rep2

value: an early T leukemia cell line that is derived from Ikaros knock-out mice


title: pre-perfusion_J [3_10]

description:
sample3_10
experiment1_rawCounts.txt
experiment2_rawCounts.txt
experiment3_rawCounts.txt
experiment1_normCounts.txt
experiment2_normCounts.txt
experiment3_normCounts.txt

value: J

value: male


title: post-perfusion_Y_filter [2_37]

description:
sample2_37_filter
experiment2_rawCounts.txt
experiment2_normCounts.txt

value: Y


title: N2, L1, rep2

value: N2 Bristol


title: Rectum biopsies, week 24, no replicates P38_W24

description: Rectum biopsies, week 24, no replicates


title: DN3(IK)-2day, mRNA-seq, rep1


title: Rectum biopsies, week 0, no replicates P38_W0

description: Rectum biopsies, week 0, no replicates


title: pre-perfusion_X [2_33]

description:
sample2_33
experiment3_rawCounts.txt
experiment3_normCounts.txt

value: X


title: N2, L1, rep1


title: Rectum biopsies, week 0, no replicates P37_W0

description: Rectum biopsies, week 0, no replicates


title: mouse E-Homo.2 E12.8 embryo

city: Harbin

first: Haoran

last: Yu

address: 92 West Dazhi Street

department: School of Life Science and Technology

institute: Harbin Institute of Technology

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include FPKM for each Sample

source_name: embryo

extract_protocol:
Total RNA was extracted usingTrizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution. An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: embryo


title: pre-perfusion_Y_filter [2_36]

description:
sample2_36_filter
experiment2_rawCounts.txt
experiment2_normCounts.txt


title: DN3(wt), mRNA-seq, rep2

value: without transduction

value: control


title: Rectum biopsies, week 0, no replicates P35_W0

description: Rectum biopsies, week 0, no replicates

value: Rectum biopsies


title: mouse E-MKI.2 E12.7 embryo


title: DN3(wt),mRNA-seq, rep1


title: pre-perfusion_Z [2_31]

description:
sample2_31
experiment3_rawCounts.txt
experiment3_normCounts.txt

value: Z


title: mouse E-WT.2 E12.5 embryo


title: Rectum biopsies, week 0, no replicates P33_W0

description: Rectum biopsies, week 0, no replicates

value: Primary tissue


title: pre-perfusion_W [2_28]

description:
sample2_28
experiment4_rawCounts.txt
experiment4_normCounts.txt

value: liver

value: W

value: DBD


title: DN3(IK)-1day, mRNA-seq, rep1

value: JE131 cell line (DN3 cells)

value: transduced with retrovirus that contains HA-tagged wild-type murine Ikaros


title: DN3(IK)-1day, mRNA-seq, rep2

value: an early T leukemia cell line that is derived from Ikaros knock-out mice


title: pre-perfusion_AG [2_27]

description:
sample2_27
experiment4_rawCounts.txt
experiment4_normCounts.txt

value: AG


title: mouse E-Homo.1 E12.8 embryo


title: Rectum biopsies, week 0, no replicates P32_W0

description: Rectum biopsies, week 0, no replicates


title: post-perfusion_H [2_26]

description:
sample2_26
experiment1_rawCounts.txt
experiment2_rawCounts.txt
experiment1_normCounts.txt
experiment2_normCounts.txt

value: H

value: male

value: DCD


title: pre-perfusion_F [2_3]

description:
sample2_3
experiment4_rawCounts.txt
experiment4_normCounts.txt

value: F


title: Rectum biopsies, week 0, no replicates P34_W0

description: Rectum biopsies, week 0, no replicates


title: miR-33 HKO

city: New Haven

first: PABLO

last: FERNANDEZ-TUSSY

state: CT

address: 10 amistad street, 420C

department: Comparative Medicine

institute: Yale University

description: 10x genomics

library_source: transcriptomic single cell

data_processing:
Reads were aligned against mouse genome mm10 using the CellRanger software (10x Genomics).
Gene-barcode matrices were analyzed in R (version 3.0) using Seurat v3. Cells were filtered for more than 500 genes detected in each cell, 20,000 or less total number of molecules detected within a cell and 25% or less mitochondrial gene content.
Significant principal components of variation (PCs) were calculated using JackStraw test, and clusters were calculated with 30 PCs
Differential expression analysis was done using wilcox
Assembly: mmp10
Supplementary files format and content: Cell-gene-barcode matrices

source_name: Liver

growth_protocol: 8 week old littermates WT and miR-33HKO mice were fed a CD-HFD during 6 month.

extract_protocol:
Singlle-cell suspensions were obtained from a pull of 3 livers. Liver tissue was digested by collagenase perfusion. Single cell suspension was spin at 50g for 20min iwth no brake. Pellet containing hepatocytes was resuspended in 40% Percoll and spined twice at 50g, 5 min. Cells were then resuspended2-3ml DMEM and filtered through a 70um filter. In parallel, Supernantant containing the non-parenchymal cells was centrigfuged at 300g 4 mins with no brake. After two more spins cells were resuspened in (1:1000) L/D green in PBS and stained for 5 minutes. 70000 cells were sorted and pulled together. After counting parenchymal and non-parenchymal cells, a 1:1 hepatocytes:non-parenchymal cell suspension was prepared. Cells were counted and diluted at 1,000 cells/ ml and immediately processed for single-cell RNA sequencing.
Single cells were encapsulated into droplets and processed following standard manufacturer’s specification, using 10X Genomics GemCode technology. Cells were loaded on a 10x Genomics Chromium controller instrument to generate single-cell Gel Beads in emulsion (GEMS) at the Yale Center for Genome Analysis. Lysis and barcoded reverse transcription of polyadenylated mRNA from single cells were performed inside each GEM followed by complementary DNA (cDNA) generation using the single-Cell 3’ Regent Kits version 2 (10X Genomics). Libraries were sequenced on an Illumina HiSeq 4000 as 2x 100 paired-end reads.

value: Liver

value: liver cells

value: AlbCRE

value: 6 months CD_HFD


title: HFD_LKO, female8 ATAC-seq

city: Lincoln

first: Xinghui

last: Sun

state: NE

address: 1901 Vine Street

department: Biochemistry

institute: University of Nebraska - Lincoln

description:
LKO4
HFD_LKO_sorted.bw
hfd_bed_counts_multicov.txt

data_processing:
Raw FASTQ files were processed to remove ATAC-seq adapter sequences using trim-galore (0.6.7). Trimmed FASTQ files were aligned to the mouse reference genome mm10 using Bowtie2 (2.4.2). Mitochondrial reads and PCR duplicates were removed.
Peak calling using MACS2 (2.2.7.1) was performed as described in the PEPATAC pipeline (Grandi et al, 2022). mm10 ENCODE blacklist regions were removed.
To merge peaks from different replicates, we took the iterative overlap peak merging approach described in the PEPATAC pipeline (Grandi et al, 2022).
For differential peak analysis, we used the bedtools multicov.txt to prepare the counts of reads for each replicate within the overlap peaks. Differential peaks were identified using the DEseq2 package (4.2.0).
Peak annotation was performed with HOMER (4.11) (Heinz et al, 2010) or ChIPseeker (4.1.1) (Yu et al, 2015). Enrichr or Metascape was used for functional analysis.
Assembly: mm10
Supplementary files format and content: Bigwig
Supplementary files format and content: text files with the chromosomal coordinates and read counts over peak regions

growth_protocol: Mice were housed on a normal 12/12 light-dark cycle. Mice had ad libitum access to a normal chow diet (Envigo, cat# 2016) and water, or a HFD with 60 kcal% fat (Research Diets, D12492) and water.

extract_protocol:
Nuclei from 50 mg frozen liver were isolated following the Chang Lab protocol (Corces et al, 2017; PMID: 28846090) for ATACseq library construction.
Genomic DNA was transposed using transposase, purified using DNA Clean & concentrator-5 kit (Zymo D4014), pre-amplified with i7 and i5 indexed primers. Additional cycles were performed. Each amplified DNA library was purified using AMPure XP Reagent to remove primer dimers and large > 1,000 bp DNA fragments.
PE150

treatment_protocol: Female matrin-3 floxed mice and littermate LKO  mice were fed a chow diet (Envigo, cat# 2016) or 60% HFD (Research Diets, D12492) at 7 weeks of age for 16 weeks.

value: liver-specific knockout

value: 60% HFD for 16 weeks


title: mouse E-PKI.2 E12.6 embryo

value: embryo


title: Rectum biopsies, week 0, no replicates P30_W0

description: Rectum biopsies, week 0, no replicates

value: Rectum biopsies

value: Primary tissue


title: HFD_LKO, female7 ATAC-seq

description:
LKO3
HFD_LKO_sorted.bw
hfd_bed_counts_multicov.txt

value: liver


title: pre-perfusion_H [2_25]

description:
sample2_25
experiment1_rawCounts.txt
experiment2_rawCounts.txt
experiment3_rawCounts.txt
experiment1_normCounts.txt
experiment2_normCounts.txt
experiment3_normCounts.txt


title: mouse E-PKI.1 E12.6 embryo


title: Rectum biopsies, week 0, no replicates P31_W0

description: Rectum biopsies, week 0, no replicates


title: mouse E-WT.1 E12.5 embryo


title: pre-perfusion_AE [2_23]

description:
sample2_23
experiment4_rawCounts.txt
experiment4_normCounts.txt

value: AE

value: female

value: DBD


title: Wildtype

description: 10x genomics

value: WT


title: Rectum biopsies, week 0, no replicates P29_W0

description: Rectum biopsies, week 0, no replicates


title: HFD_LKO, female6 ATAC-seq

description:
LKO2
HFD_LKO_sorted.bw
hfd_bed_counts_multicov.txt


title: pre-perfusion_AD [2_22]

description:
sample2_22
experiment3_rawCounts.txt
experiment3_normCounts.txt

value: AD


title: DN3(IK)-3day, EZH2, ChIP-seq, rep2

value: JE131 cell line (DN3 cells)

value: an early T leukemia cell line that is derived from Ikaros knock-out mice

value: DN3 cells transduced with Ikaros for 3 days


title: HFD_LKO, female5 ATAC-seq

description:
LKO1
HFD_LKO_sorted.bw
hfd_bed_counts_multicov.txt


title: pre-perfusion_AC [2_21]

description:
sample2_21
experiment3_rawCounts.txt
experiment3_normCounts.txt

value: AC

value: DCD


title: Rectum biopsies, week 24, no replicates P28_W24

description: Rectum biopsies, week 24, no replicates


title: DN3(IK)-3day, EZH2, ChIP-seq, rep1


title: pre-perfusion_AP [2_20]

description:
sample2_20
experiment3_rawCounts.txt
experiment3_normCounts.txt

value: AP

value: male


title: HFD_flox, female4 ATAC-seq

description:
flox4
HFD_flox_sorted.bw
hfd_bed_counts_multicov.txt

value: floxed

value: 60% HFD for 16 weeks


title: DN3(IK)-2day, EZH2, ChIP-seq, rep2

value: DN3 cells transduced with Ikaros for 2 days


title: Rectum biopsies, week 24, no replicates P27_W24

description: Rectum biopsies, week 24, no replicates

value: Rectum biopsies

value: Primary tissue


title: HFD_flox, female3 ATAC-seq

description:
flox3
HFD_flox_sorted.bw
hfd_bed_counts_multicov.txt

value: liver


title: DN3(IK)-2day, EZH2, ChIP-seq, rep1


title: pre-perfusion_Q_filter [2_2]

description:
sample2_2_filter
experiment2_rawCounts.txt
experiment2_normCounts.txt

value: Q

value: female


title: HFD_flox, female2 ATAC-seq

description:
flox2
HFD_flox_sorted.bw
hfd_bed_counts_multicov.txt


title: HFD_flox, female1 ATAC-seq

description:
flox1
HFD_flox_sorted.bw
hfd_bed_counts_multicov.txt


title: DN3(IK)-1day, EZH2, ChIP-seq, rep2

value: DN3 cells transduced with Ikaros for 1 day


title: Rectum biopsies, week 0, no replicates P26_W0

description: Rectum biopsies, week 0, no replicates


title: chowLKO, female6 ATAC-seq

description:
KO_3
chowLKO_sorted.bw
chow_bed_counts_multicov.txt

value: liver-specific knockout

value: chow diet for 16 weeks


title: Rectum biopsies, week 0, no replicates P25_W0

description: Rectum biopsies, week 0, no replicates


title: DN3(wt), EZH2, ChIP-seq, rep2

value: JE131 cell line (DN3 cells)

value: an early T leukemia cell line that is derived from Ikaros knock-out mice

value: DN3 cells without transduction


title: Rectum biopsies, week 24, no replicates P25_W24

description: Rectum biopsies, week 24, no replicates


title: DN3(IK)-1day, EZH2, ChIP-seq, rep1


title: pre-perfusion_U [2_15]

description:
sample2_15
experiment4_rawCounts.txt
experiment4_normCounts.txt

value: U

value: DBD


title: Rectum biopsies, week 24, no replicates P24_W24

description: Rectum biopsies, week 24, no replicates


title: chowLKO, female5 ATAC-seq

description:
KO_2
chowLKO_sorted.bw
chow_bed_counts_multicov.txt


title: post-perfusion_Q_filter [2_13]

description:
sample2_13_filter
experiment2_rawCounts.txt
experiment2_normCounts.txt

value: DCD


title: chowLKO, female4 ATAC-seq

description:
KO_1
chowLKO_sorted.bw
chow_bed_counts_multicov.txt


title: pre-perfusion_AA [2_1]

description:
sample2_1
experiment3_rawCounts.txt
experiment3_normCounts.txt

value: AA

value: male


title: chowFlox, female3 ATAC-seq

description:
WT_3
chowFlox_sorted.bw
chow_bed_counts_multicov.txt

value: floxed


title: E155_Hdac1&2_cKO_rep3

city: Shanghai

first: Yunli

last: Xie

state: Shanghai

address: 131 Dong'an Road, Shanghai

department: Institutes of Brain Science

institute: Fudan University

data_processing:
raw data were first trimmed using Trim Galore v.0.6.7 then mapped to the mm10 genome by HISAT2 v2.2.1 with default parameters.
The number of reads mapping to each gene were counted by featureCounts v2.0.1 with parameters: -a gencode.vM20.annotation.gtf. And transcripts per million (TPM) were calculated.
Assembly: mm10

source_name: brain

extract_protocol:
Total RNA was isolated from cerebral cortices at E13.5, E14.5, E15.5 and E16.5 using TRIzol reagent (ThermoScientific) according to the manufacturer’s instructions.
Total RNA was isRNA-seq was performed at Novogene Biotech Co., Ltd in Beijing, China.

value: brain

value: mouse brain cells

value: embryonic day 15.5


title: Rectum biopsies, week 0, no replicates P23_W0

description: Rectum biopsies, week 0, no replicates

value: Rectum biopsies

value: Primary tissue


title: E155_Hdac1&2_cKO_rep2


title: pre-perfusion_T [2_16]

description:
sample2_16
experiment3_rawCounts.txt
experiment3_normCounts.txt

value: liver

value: T


title: DN3(wt), EZH2, ChIP-seq, rep1


title: pre-perfusion_V [2_17]

description:
sample2_17
experiment4_rawCounts.txt
experiment4_normCounts.txt

value: V

value: female


title: Rectum biopsies, week 0, no replicates P24_W0

description: Rectum biopsies, week 0, no replicates


title: pre-perfusion_C [1_9]

description:
sample1_9
experiment1_rawCounts.txt
experiment2_rawCounts.txt
experiment3_rawCounts.txt
experiment1_normCounts.txt
experiment2_normCounts.txt
experiment3_normCounts.txt

value: C


title: Rectum biopsies, week 24, no replicates P26_W24

description: Rectum biopsies, week 24, no replicates


title: post-perfusion_B [1_8]

description:
sample1_8
experiment1_rawCounts.txt
experiment2_rawCounts.txt
experiment1_normCounts.txt
experiment2_normCounts.txt

value: B


title: E155_Hdac1&2_cKO_rep1


title: Rectum biopsies, week 24, no replicates P22_W24

description: Rectum biopsies, week 24, no replicates


title: chowFlox, female1 ATAC-seq

description:
WT_1
chowFlox_sorted.bw
chow_bed_counts_multicov.txt

value: chow diet for 16 weeks


title: E155_Control_rep3

value: wild type


title: pre-perfusion_B [1_7]

description:
sample1_7
experiment1_rawCounts.txt
experiment2_rawCounts.txt
experiment3_rawCounts.txt
experiment1_normCounts.txt
experiment2_normCounts.txt
experiment3_normCounts.txt

value: DCD


title: Rectum biopsies, week 0, no replicates P22_W0

description: Rectum biopsies, week 0, no replicates


title: miRNA-Seq R119-H-018

description: injured knee

data_processing:
nf-core small RNA-seq pipeline (revision 1.1.0) (10.5281/zenodo.3456879) was ran with default parameters except using the flags --genome GRCm38 --protocol 'custom' --three_prime_adapter AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC --mirtrace_protocol illumina. Briefly, this pipeline performed quality control with fastQC (v0.11.9) and mirtrace (v0.11.9), trim galore (0.6.6) adaptor trimming and alignment against the mirbase mature miRNA sequence with bowtie1 (1.3.0) and counted  aligned reads with samtools (1.12)
DESeq2 was used to calculate P-values and log2 fold-changes (logFC), using the Benjamini-Hochberg method to adjust for multiple testing.
Assembly: Mouse GRCh38 (release 94)

source_name: cartilage

extract_protocol:
Femoral condyle cartilage caps were detached from underlying subchondral bone at the tidemark. RNA extraction was usingTRIzol® reagent according to manufacturer's protocol (ThermoFisher Scientific). Total RNA and miRNA were purified from the TRIzol®-cartilage mixture using a mirVana™ miR Isolation Kit.
NEBNext® Small RNA Library Prep Set for Illumina

treatment_protocol: mechanical anterior cruciate ligament (ACL) rupture

value: cartilage

value: chondrocyte


title: Rectum biopsies, week 0, no replicates P21_W0

description: Rectum biopsies, week 0, no replicates


title: miRNA-Seq R119-H-017

description: injured knee


title: pre-perfusion_AL_filter [1_5]

description:
sample1_5_filter
experiment2_rawCounts.txt
experiment2_normCounts.txt

value: AL


title: post-perfusion_AL_filter [1_6]

description:
sample1_6filter
experiment2_rawCounts.txt
experiment2_normCounts.txt


title: Rectum biopsies, week 24, no replicates P20_W24

description: Rectum biopsies, week 24, no replicates


title: post-perfusion_AO_filter [1_20]

description:
sample1_20_filter
experiment2_rawCounts.txt
experiment2_normCounts.txt

value: AO

value: male


title: post-perfusion_A [1_2]

description:
sample1_2
experiment1_rawCounts.txt
experiment2_rawCounts.txt
experiment1_normCounts.txt

value: A


title: E145_Hdac1&2_cKO_rep3

value: brain

value: mouse brain cells

value: embryonic day 14.5


title: Rectum biopsies, week 24, no replicates P18_W24

description: Rectum biopsies, week 24, no replicates

value: Rectum biopsies

value: Primary tissue


title: E155_Control_rep1

value: embryonic day 15.5


title: miRNA-Seq R119-H-013

description: Contralateral knee


title: miRNA-Seq R119-H-016

description: injured knee


title: post-perfusion_AN_filter [1_18]

description:
sample1_18_filter
experiment2_rawCounts.txt
experiment2_normCounts.txt

value: liver

value: AN


title: Rectum biopsies, week 0, no replicates P20_W0

description: Rectum biopsies, week 0, no replicates


title: E145_Hdac1&2_cKO_rep1


title: Rectum biopsies, week 24, no replicates P19_W24

description: Rectum biopsies, week 24, no replicates


title: E145_Hdac1&2_cKO_rep2


title: miRNA-Seq R119-H-015

description: Contralateral knee


title: chowFlox, female2 ATAC-seq

description:
WT_2
chowFlox_sorted.bw
chow_bed_counts_multicov.txt

value: floxed

value: chow diet for 16 weeks


title: miRNA-Seq R119-H-014

description: Contralateral knee


title: E145_Control_rep2

value: wild type


title: pre-perfusion_AN_filter [1_17]

description:
sample1_17_filter
experiment2_rawCounts.txt
experiment2_normCounts.txt

value: DCD


title: Rectum biopsies, week 0, no replicates P16_W0

description: Rectum biopsies, week 0, no replicates


title: E145_Control_rep3


title: Rectum biopsies, week 0, no replicates P18_W0

description: Rectum biopsies, week 0, no replicates


title: E145_Control_rep1


title: E155_Control_rep2


title: Rectum biopsies, week 24, no replicates P14_W24

description: Rectum biopsies, week 24, no replicates


title: miRNA-Seq R119-H-011

description: uninjured knee

value: cartilage

value: chondrocyte


title: E135_Hdac1&2_cKO_rep3

value: embryonic day 13.5


title: post-perfusion_E [1_16]

description:
sample1_16
experiment1_rawCounts.txt
experiment2_rawCounts.txt
experiment1_normCounts.txt
experiment2_normCounts.txt

value: E

value: female


title: pre-perfusion_AO_filter [1_19]

description:
sample1_19_filter
experiment2_rawCounts.txt
experiment2_normCounts.txt

value: AO

value: male


title: miRNA-Seq R119-H-010

description: uninjured knee


title: Rectum biopsies, week 24, no replicates P16_W24

description: Rectum biopsies, week 24, no replicates


title: miRNA-Seq R119-H-012

description: uninjured knee


title: pre-perfusion_AM_filter [1_13]

description:
sample1_13_filter
experiment2_rawCounts.txt
experiment2_normCounts.txt

value: AM


title: post-perfusion_AM_filter [1_14]

description:
sample1_14_filter
experiment2_rawCounts.txt
experiment2_normCounts.txt


title: E135_Hdac1&2_cKO_rep1

value: brain

value: mouse brain cells


title: pre-perfusion_E [1_15]

description:
sample1_15
experiment1_rawCounts.txt
experiment2_rawCounts.txt
experiment3_rawCounts.txt
experiment1_normCounts.txt
experiment2_normCounts.txt
experiment3_normCounts.txt


title: miRNA-Seq R119-H-008

description: uninjured knee


title: Rectum biopsies, week 24, no replicates P08_W24

description: Rectum biopsies, week 24, no replicates

value: Rectum biopsies

value: Primary tissue


title: Rectum biopsies, week 24, no replicates P13_W24

description: Rectum biopsies, week 24, no replicates


title: E135_Hdac1&2_cKO_rep2


title: Rectum biopsies, week 24, no replicates P11_W24

description: Rectum biopsies, week 24, no replicates


title: miRNA-Seq R119-H-007

description: uninjured knee


title: E135_Control_rep3


title: pre-perfusion_D [1_11]

description:
sample1_11
experiment4_rawCounts.txt
experiment4_normCounts.txt

value: liver

value: D

value: DBD


title: miRNA-Seq R119-H-006

description: injured knee


title: post-perfusion_C [1_10]

description:
sample1_10
experiment1_rawCounts.txt
experiment2_rawCounts.txt
experiment1_normCounts.txt
experiment2_normCounts.txt

value: C


title: E135_Control_rep2

value: wild type


title: miRNA-Seq R119-H-005

description: Contralateral knee

value: cartilage


title: pre-perfusion_A [1_1]

description:
sample1_1
experiment1_rawCounts.txt
experiment2_rawCounts.txt
experiment3_rawCounts.txt
experiment1_normCounts.txt
experiment2_normCounts.txt
experiment3_normCounts.txt

value: A

value: DCD


title: Rectum biopsies, week 24, no replicates P07_W24

description: Rectum biopsies, week 24, no replicates


title: miRNA-Seq R119-H-009

description: uninjured knee

value: chondrocyte


title: E135_Control_rep1

value: embryonic day 13.5


title: miRNA-Seq R119-H-004

description: Contralateral knee


title: Rectum biopsies, week 24, no replicates P03_W24

description: Rectum biopsies, week 24, no replicates


title: MUTT, 38501

type: genomic

city: Bethesda

first: Alexander

middle: Christian

last: Harris

state: Maryland

address: 50 South Drive

department: National Human Genome Research Institute

institute: National Institutes of Health

hyb_protocol: Resuspended DNA was loaded onto BeadChips arrays and hybridized overnight at at 48oC.  Single-base extension and allele-specific staining was performed by hand.

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing:
Image data was analyzed using GenomeStudio with GT module (Illumina).
genotypes AA, AB, BB, NC=no call

organism: Canis lupus familiaris

source_name: Whole Blood

label_protocol: 200ng of genomic DNA was amplified in an overnight reaction at 37oC. The amplified DNA was enzymatically fragmented, precipitated with isopropanol, and resuspended in hybridization buffer.

extract_protocol: Genomic DNA was extracted from whole blood using Proteinase K and phenol/chloroform with standard protocols.

tag: breed

value: Mixed Breed

value: Whole Blood


title: Biotinylation-DNA-seq_Coilin-si_rep2_R1

city: Yokohama

first: Hidefumi

last: Suzuki

address: Fukuura 3-9

institute: Yokohama City University

data_processing:
For biotinylation-DNA-seq, adapter sequences were trimmed using Trim Galore (v 0.64_dev), and reads were mapped to human genome GRCH38 using the Bowtie2 alignment tool (version 2.3.5.1) with the default settings. The mapped reads from each in situ biotinylation-seq dataset were subjected to count per million (CPM) normalization and then used for downstream analysis. IP/input enrichment per gene was calculated with R (v. 4.0.2) and its package rtracklayer (version 1.48.0) using the Ensembl GRCH38.92 gene annotation model.
For biotinylation-RNA-seq, adapter sequences were trimmed using Trim Galore (v 0.64_dev), and reads were mapped to Ensembl gene annotation of human genome GRCh38.p13 using hisat2 (version). Read counts were obtained using Rsubread (version 2.2.6). Differential gene expression analysis was performed using R (v. 4.0.2) package DESeq2 (v. 1.28.1). Genes with an adjusted P-value <0.01 and absolute log2 fold-change >0.5 were included in the downstream analysis.
Assembly: GRCH38 and Drosophila melanogastergenome build5.41 from NCBI
Supplementary files format and content: BigWig files include normalized count data obtained from methods shown above.

source_name: HeLa

growth_protocol: HeLa cells  were cultured in Dulbecco’s modified Eagle’s medium (08458-45; Nacalai Tesque, Kyoto, Japan) with 10% foetal bovine serum and penicillin/streptomycin under 5% CO2 at 37 ºC.

extract_protocol:
For antibody-based in situ biotinylation-seq, HeLa cells cultured in 10 cm dish were fixed with 4% PFA and permeabilized with 0.5% Triton X-100. After blocking, cells were incubated with primary antibodies, and then incubated with HRP-labeled secondary antibodies. After washing, HRP-based in situ biotinylation was performed by incubating cells with biotinylation buffer. The cells were lysed in 1% SDS RIPA buffer and were sonicated for DNA fragmentation. The biotinylated chromatin was pulled-down using SoftLinkTM Soft Release Avidin Resin (Promega), and the chromatin DNA was purified.
The sequence libraries for in situ biotinylation DNA-seq were prepared using TruSeq ChIP Library Prep Kit (Illumina, San Diego, CA). The sequence libraries for in situ biotinylation RNA-seq were prepared using SMART-Seq Stranded Kit (Takara).

value: HeLa


title: miRNA-Seq R119-H-003

city: NEWCASTLE UPON TYNE

first: David

address: Centre For Life

institute: Newcastle University

description: injured knee


title: Biotinylation-DNA-seq_Coilin-si_rep1_R1


title: MUTT, 38500


title: Rectum biopsies, week 24, no replicates P01_W24

description: Rectum biopsies, week 24, no replicates


title: miRNA-Seq R119-H-002

description: injured knee


title: Biotinylation-DNA-seq_ctrl_rep2_R1


title: Biotinylation-DNA-seq_ctrl_rep1_R1


title: MUTT, 38499


title: MUTT, 38498


title: RNA-Seq R119-H-018

description: injured knee

data_processing:
Kallisto was used for pseudo-alignment and quantification, against the mouse GRCh38 (release 92) transcriptome.
Mapped transcripts were converted to a gene level using Tximport.
DESeq2 was used to calculate P-values and log2 fold-changes (logFC), using the Benjamini-Hochberg method to adjust for multiple testing.
Assembly: Mouse GRCh38 (release 94)

extract_protocol:
Femoral condyle cartilage caps were detached from underlying subchondral bone at the tidemark. RNA extraction was usingTRIzol® reagent according to manufacturer's protocol (ThermoFisher Scientific). Total RNA and miRNA were purified from the TRIzol®-cartilage mixture using a mirVana™ miR Isolation Kit.
TruSeq Stranded Total RNA with ribo-zero GOLD RNA library prep kit


title: Rectum biopsies, week 24, no replicates P05_W24

description: Rectum biopsies, week 24, no replicates


title: miRNA-Seq R119-H-001

description: Contralateral knee


title: Biotinylation-DNA-seq_Coilin-si_input_R1


title: ARP1-KDM6A-WT-rep2

city: Gainesville

first: Alberto

last: Riva

state: FL

address: 2033 Mowry Rd

department: ICBR

institute: University of Florida

data_processing:
Reads were trimmed with trimmomatic and quality control performed with FastQC and MultiQC.
Reads were mapped to the GRCh38 transcriptome with STAR, and gene expression was quantified with RSEM.
Differential gene expression analysis was performed with DESeq2.
Additional processing and plots were performed with custom analysis scripts.
Assembly: GRCh38
Supplementary files format and content: Raw counts of

source_name: multiple myeloma

extract_protocol:
Total RNA was extracted using TRIzol reagent (ThermoFisher Scientific) and then purify on RNA Clean and Concentrator column (Zymo Research).
polyA selection

treatment_protocol: Interferon alpha 200nM for 18h

value: multiple myeloma

value: KDM6A wild type

tag: biorep


title: ARP1-KDM6A-WT-rep1


title: RNA-Seq R119-H-017

last: Young

description: injured knee


title: MUTT, 38497


title: Biotinylation-DNA-seq_ctrl_input_R1


title: RNA-Seq R119-H-016

description: injured knee


title: ARP1-KDM6A-KO-rep3

value: KDM6A knock out


title: MUTT, 38495


title: srsf2kd_r5_HK

city: Heidelberg

first: Rebecca

middle: Emma

last: Wagner

address: Inf 280 im Neuenheimer Feld

department: Cell Biology and Tumor Biology

country: Germany

institute: DKFZ

description:
final_normalized_counts_annotation_ZHC1116.txt
srsf2kd.r5

data_processing:
Reads were aligned to the hs37d5 reference genome using STAR aligner
FeatureCounts was used for gene specific quantification fo reads on the appropriate gene annotation
Raw gene count values were then used as input for a differential gene expression analysis using DESeq2 within R
Bedtools were used to generate bedGraph files and bedGraphToBigWig was used to produce BigWig files.
Assembly: hs37d5

growth_protocol: Keratinocytes were cultured with KBM-Gold (Lonza) medium  supplemented with 0.06mM CaCl and the essential growth factors supplied. FaDu cells were cultured with EMEM supplemented with 10% FBS and pen/strep. SCC25 cells were cultured in DMEM/F12 HEPES with 10% FBS and pen/strep. All cells were kept at 37 with 5% CO2

extract_protocol:
Total RNA was extracted using Trizol reagent, following manufacturer's instructions. DNA was purified using spin columns following manufacturer's instructions.
Total RNA from keratinocytes was rRNA depleted and RNA-sequencing libraries were prepped using NEB Ultra II directional kit (NEB). Total RNA from FaDu cells was used to prepare libraries using TruSeq stranded total RNA kit (Illumina). RNA from SCC25 cells and clones was used to generate RNA-sequencing libraries using stranded total RNA prep with Ribo-zero plus kit (Illumina). SLAM-sequencing libraries were prepared using Quant-seq 3' mRNA library prep kit (Lexogen). Libraries were prepared from purified DNA using the SimpleChIP, ChIP-seq DNA library prep kit for illumina (CST).

treatment_protocol: SRSF2 depletion was achieved by transfecting an siRNA pool using Lipofectamine RNAiMax

value: primary human keratinocytes

value: siRNA transfection


title: Rectum biopsies, week 0, no replicates P02_W0

description: Rectum biopsies, week 0, no replicates

value: Rectum biopsies

value: Primary tissue


title: srsf2kd_r4_HK

description:
final_normalized_counts_annotation_ZHC1116.txt
srsf2kd.r4


title: RNA-Seq R119-H-015

description: Contralateral knee


title: MUTT, 38494


title: RNA-Seq R119-H-014

description: Contralateral knee


title: srsf2kd_r3_HK

description:
final_normalized_counts_annotation_ZHC1116.txt
srsf2kd.r3


title: ARP1-KDM6A-WT-rep3


title: ARP1-KDM6A-WT-IFNa-rep3

value: Interferon alpha 200nM


title: srsf2kd_r2 _HK

description:
final_normalized_counts_annotation_ZHC1116.txt
srsf2kd.r2


title: RNA-Seq R119-H-012

description: uninjured knee


title: MUTT, 38493


title: ARP1-KDM6A-KO-rep1


title: srsf2kd_r1_HK

description:
final_normalized_counts_annotation_ZHC1116.txt
srsf2kd.r1


title: MUTT, 38491


title: RNA-Seq R119-H-013

description: Contralateral knee


title: MUTT, 38496


title: RNA-Seq R119-H-011

description: uninjured knee


title: ARP1-KDM6A-WT-Ctl-rep3

value: control


title: ctr_r4_HK

description:
final_normalized_counts_annotation_ZHC1116.txt
ctr.r4


title: ARP1-KDM6A-KO-rep2


title: ARP1-KDM6A-WT-Ctl-rep2


title: RNA-Seq R119-H-009

description: uninjured knee

value: cartilage


title: ctr_r5_HK

description:
final_normalized_counts_annotation_ZHC1116.txt
ctr.r5


title: ctr_r3_HK

description:
final_normalized_counts_annotation_ZHC1116.txt
ctr.r3


title: ARP1-KDM6A-WT-Ctl-rep1


title: BOX-, 38492

value: Boxer


title: ctr_r2_HK

description:
final_normalized_counts_annotation_ZHC1116.txt
ctr.r2


title: ARP1-KDM6A-WT-IFNa-rep2


title: ARP1-KDM6A-KO-IFNa-rep3


title: ARP1-KDM6A-WT-IFNa-rep1


title: RNA-Seq R119-H-007

description: uninjured knee


title: MUTT, 38487


title: RNA-Seq R119-H-010

description: uninjured knee


title: MUTT, 38486


title: RNA-Seq R119-H-008

description: uninjured knee


title: mouse E-MKI.1 E12.7 embryo

value: embryo


title: ctr_r1_HK

description:
final_normalized_counts_annotation_ZHC1116.txt
ctr.r1


title: MUTT, 38490


title: ARP1-KDM6A-KO-IFNa-rep1


title: ARP1-KDM6A-KO-IFNa-rep2


title: RNA-Seq R119-H-006

description: injured knee

value: chondrocyte


title: Uninjured 7mdp il11aOE hearts - 3

city: Madison

first: Kwangdeok

last: Shin

state: Wisconsin

address: 1111 Highland Ave ZN 3, 4451 WIMR II

department: Cell and Regenerative Biology

institute: University of Wisconsin Madison

description:
il11a_7mpt_gene_featureCounts
il7mpM1_S98

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCz11 using HISAT2
featurecount was used to get count of each gene
Assembly: GRCz11
Supplementary files format and content: raw gene counts for every gene and every sample

organism: Danio rerio

source_name: Hearts

extract_protocol:
Hearts were homogenized immediately after dissection and RNA was extracted using Trizol reagent. .
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 5 µM tamoxifen treatment for 24 hours

value: Hearts

value: 7 months post Tamoxifen treatment


title: MUTT, 38489

value: Mixed Breed

value: Whole Blood


title: Uninjured 7mdp il11aOE hearts - 4

description:
il11a_7mpt_gene_featureCounts
il7mpM2_S99


title: MUTT, 38488


title: ARP1-KDM6A-KO-Ctl-rep3

value: multiple myeloma


title: Uninjured 7mdp il11aOE hearts - 2

description:
il11a_7mpt_gene_featureCounts
il7mpF2_S97


title: MUTT, 38484


title: RNA-Seq R119-H-004

description: Contralateral knee


title: MUTT, 38483


title: ARP1-KDM6A-KO-Ctl-rep2


title: MUTT, 38482


title: Uninjured 7mdp il11aOE hearts - 1

description:
il11a_7mpt_gene_featureCounts
il7mpF1_S96


title: RNA-Seq R119-H-003

description: injured knee


title: Uninjured 7mpt control hearts-4

description:
il11a_7mpt_gene_featureCounts
C7mptM2_S95


title: RNA-Seq R119-H-002

description: injured knee


title: ARP1-KDM6A-KO-Ctl-rep1


title: RNA-Seq R119-H-001

description: Contralateral knee


title: MUTT, 38481


title: MUTT, 38485


title: Uninjured 7mpt control hearts-3

description:
il11a_7mpt_gene_featureCounts
C7mptM1_S94


title: EJM-KDM6A-WT-rep2

value: KDM6A wild type


title: Uninjured 7mpt control hearts-2

description:
il11a_7mpt_gene_featureCounts
C7mptF2_S93


title: MUTT, 38480


title: RNA-Seq R119-H-005

description: Contralateral knee


title: EJM-KDM6A-WT-rep3


title: MUTT, 38478


title: MUTT, 38479


title: 4375

data_processing:
Using the PartekFlow® software, version 8.0.19.0405 (Partek, Inc., St. Louis, MO) the reads were aligned with the STAR algorithm to the mouse genome mmu10.
To estimate the transcript expression abundance we used Quantify to annotation model (Partek E/M) algorithm.
Assembly: Genome_build: mmu10
Supplementary files format and content: Partek_mir33_nafl_liver_3_months_Quantify_to_annotation_model_(Partek_E_M)_Gene_counts (4)
Supplementary files format and content: raw counts

growth_protocol: 8 weeks old littermates WT and miR-33 AlbCRE mice were fed a CD-HFD during 3 months.

extract_protocol:
Mice were perfused with PBS and livers were inmediatelly frozen. Total RNA was extracted and purified using a RNA isolation Kit (Qiagen) followed by DNAse treatment to remove genomic contamination using RNA MinElute Cleanup (Qiagen). rRNA was depleted from RNA samples using Ribo-Zero rRNA Removal Kit (Illumina).
RNA libraries were with performed TrueSeq Small RNA Library preparation (Illumina).RNA libraries were sequenced for 45 cycles on Illumina HiSeq 2000 platform (1 x 75bp read length)

tag: age

value: 5 months

tag: diet

value: AlbCRE


title: 4376


title: MUTT, 38477


title: zebrafish larvae,svcv3

city: 武汉

first: zixuan

last: wang

state: 湖北省

address: 湖北省武汉市东湖南路7号

institute: 中国科学院水生生物研究所

data_processing:
Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.
Fastp (version 0.19.7) was used to perform basic statistics on the quality of the raw reads.
The clean reads were then mapped to the mouse genome using HISAT.
Assembly: GRCz11
Supplementary files format and content: FPKM values for each Sample

source_name: larvae

extract_protocol:
Whole RNA of zebrafish larvae (3 dpf) infected with or without SVCV were purified using RNeasy Mini Kit (QIAGEN NO. 74104).
Sequencing libraries were generated using the NEB Next Ultra RNA Library Prep Kit for Illumina (NEB, USA, #E7530L) accordingly to the manufacturer’s protocol, and index codes were added to assign sequences to each sample.

value: larvae

value: WT

value: svcv infection


title: EJM-KDM6A-KO-rep3

tag: cell line

value: KDM6A knock out


title: Uninjured 7mpt control hearts-1

description:
il11a_7mpt_gene_featureCounts
C7mptF1_S92

tag: treatment


title: zebrafish larvae,svcv1

address: 湖北省武汉市东湖南路7号

institute: 中国科学院水生生物研究所

tag: tissue


title: 4360


title: 4395


title: EJM-KDM6A-KO-rep2


title: AMO-KDM6A-het-rep2

value: KDM6A heterozygous


title: 4393


title: 4373


title: L917

first: Yiyangzi

last: Ma

address: No.145 Shandong Rd, Huangpu District

institute: Renji Hospital;PUMC

data_processing:
Illumina Casava software used for basecalling.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. _x000B_
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5.1b). STAR used the method of Maximal Mappable Prefix(MMP) which can generate a precise mapping result for junction reads.
HTSeq v0.6.0 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. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.10.1). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.

source_name: Intestine

extract_protocol:
Intestines were removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit v3-cBot-HS was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: intestine

value: Lactobacillus recipient mouse 4


title: AMO-KDM6A-WT-rep3


title: MUTT, 38472


title: MUTT, 38471


title: MUTT, 38470


title: KDM6A-IP-KARPAS-KDM6A-WT

data_processing:
Reads were trimmed with trimmomatic and quality control performed with FastQC and MultiQC.
Reads were mapped to the GRCh38 genome with Bowtie2.
Peak calling was performed with MACS v2.1.2
Additional processing and plots were performed with custom analysis scripts.
Assembly: GRCh38
Supplementary files format and content: Peak locations from MACS peak calling

extract_protocol:
For crosslinking, cells were pelleted and resuspended in PBS containing 1% fresh formaldehyde for 8 min at room temperature with rotation. Crosslinking was quenched by addition of 1/10 volume of 1.25M glycine and incubated for 5 minutes at room temperature with rotation. For isolation of nuclei, cell pellets were washed once in ice-cold PBS and then resuspended in lysis buffer (10% glycerol, 1% Triton TX-100, 0.1 mM EDTA, 14mM NaCl 25mM Hepes pH 7.5) and incubated for 5 minutes on ice. Cell nuclei were pelleted and incubated 5 min in wash buffer (0.1 mM EDTA, 20mM NaCl, 2mM Tris-HCl pH 7.5). Cell nuclei were pelleted and resuspended in 1 ml sonication buffer (1 mM EDTA, 10mM Tris-HCl pH 7.5) at a concentration equivalent to 10x106 cells per ml. Samples were sonicated in 1ml in AFA fiber Covaris tubes using the Covaris E220 (Woburn, MA) for 30 minutes using the following settings: 15% Duty Cycle, 200 cycles/burst, and Peak incidence 140. Prior to immunoprecipitation, sheared chromatin was diluted 1:1 in 2X ChIP dilution buffer (2% Triton X-100, 2mM EDTA, 300mM NaCl, 30mM Tris-HCl pH 8). Sheared chromatin samples were block with 20 µl Protein A/G Dyna beads (Invitrogen) for 2h at 4°C with rotation. Immunoprecipitations were performed overnight (16 hours, 4°C, with rotation) with the following antibodies: H3K27Ac (Acitve Motif #39133), H3K27me3 (Cell Signaling Technologies #9733), KDM6A (Cell Signaling Technologies #33510). Samples were washed once with ChIP dilution buffer(1% Triton X-100, 1mM EDTA, 150mM NaCl, 15mM Tris-HCl pH 8), low salt wash buffer (0.1% SDS, 1% Triton X-100, 2mM EDTA, 100mM NaCl, 20mM Tris-HCl pH 8), high salt wash buffer (0.1% SDS, 1% Triton X-100, 2mM EDTA, 500mM NaCl, 20mM Tris-HCl pH 8), LiCl wash buffer (1% deoxycholate, 1% NP-40, 2mM EDTA, 250mM LiCl, 20mM Tris-HCl pH 8), and Tris buffer (10mM Tris-HCl pH 7.5). For library construction, beads were incubated in 15 µl Tagmentase buffer with 1µl Tagment enzyme (Illumina Nextera DNA library Prep kit #15028212) and incubated at 37°C for 10 min. Immediately after, beads were washed once in 1ml ChIP dilution buffer and in 1 ml TE (10mM Tris-HCl pH 7.5, EDTA 1mM) prior to incubation in reverse crosslinking buffer (300mM NaCl, 10 mM EDTA, 0.5% SDS, 20mM Tris-HCl pH 8) for 4 hours at 65°C with shaking. Finally, proteinase K digestion was performed for 1h at 55°C with shaking prior to DNA purification using Zymogen ChIP DNA Clean and Concentrator Kit (Zymo Research, D5205, Irvine, CA).
Libraries were generated by amplification of ChIP DNA using KAPA HiFi Hotstart Library Amp kit (Roche #07959028001, Indianapolis, IN) and size selected for between 200 bp and 700 bp using Ampure beads XP (Beckman Coulter, Brea, CA). Library were quantified and QC using D1000 high-sensitivity screen tape with 4200 TapeStation Instrument (Agilent Technologies, Santa Clara, CA) and sequenced on an Ilumina Hi-Seq 3000 with 150 bp pair-end reads.

tag: ip antibody


title: MUTT, 38476


title: 4397

tag: genotype


title: 4362


title: AMO-KDM6A-WT-rep2


title: AMO-KDM6A-WT-rep1


title: KDM6A-IP-ARP1-KDM6A-WT


title: zebrafish larvae,con3

address: 湖北省武汉市东湖南路7号

institute: 中国科学院水生生物研究所

value: control


title: L907

tag: strain

value: Lactobacillus recipient mouse 1


title: MUTT, 38474


title: SHIH, 38473

value: Shih Tzu


title: zebrafish larvae,con2

address: 湖北省武汉市东湖南路7号

institute: 中国科学院水生生物研究所


title: HA-IP-ARP1-KDM6A-HAtagged

value: HA


title: zebrafish larvae,con1

address: 湖北省武汉市东湖南路7号

institute: 中国科学院水生生物研究所


title: AMO-KDM6A-het-rep3


title: AMO-KDM6A-het-rep1


title: Uninjured 7dpt control hearts-1

value: Hearts

value: 7 days post Tamoxifen treatment


title: Uninjured 7dpt il11aOE hearts - 3


title: L914

value: Lactobacillus recipient mouse 3


title: zebrafish larvae,svcv2

address: 湖北省武汉市东湖南路7号

institute: 中国科学院水生生物研究所


title: MUTT, 38465

value: Mixed Breed

value: Whole Blood


title: Uninjured 7dpt il11aOE hearts - 2


title: MUTT, 38475


title: K16

value: Klebsiella recipient mouse 1


title: Uninjured 7dpt il11aOE hearts - 1


title: MUTT, 38469


title: K4me1ARP-1E4

value: multiple myeloma


title: MUTT, 38464


title: DSRCT4.INPUT

city: Charlestown

first: Rui

last: Dong

state: MA

address: 149 13th Street

institute: Massachusetts General Hospital

data_processing:
Reads were aligned to hg19 using bwa (Li and Durbin, 2009). Aligned reads were then filtered to exclude PCR duplicates.
Assembly: hg19
Supplementary files format and content: Aligned reads were extended to 200 bp to approximate fragment sizes. Density maps were generated by counting the number of fragments overlapping each position using igvtools, and normalized to 10 million reads.

source_name: DSRCT

extract_protocol:
Chromatin from formaldehyde-fixed cells (2-5 x 10^6 cells per epitope) was fragmented to a size range of 200 - 700 bases with a Branson 250 Sonifier. Solubilized chromatin was immunoprecipitated with the indicated antibodies and Protein G-Dynabeads (Life Technologies). Immunoprecipitated DNA was extracted with AMP Pure beads(Beckman Coulter) after crosslink reversal, RNAse A and Proteinase K treatment.
ChIP DNA samples were used to generate Illumina sequencing libraries following standard protocols.

tag: cell type

value: DSRCT

value: INPUT

value: untreated


title: Uninjured 7dpt control hearts-3


title: MUTT, 38468


title: KDM6A-IP-ARP1-KDM6A-KO

value: KDM6A knock out


title: K25

value: intestine

value: Klebsiella recipient mouse 4


title: GAHD, 38463

value: Galapagos Hunting Dog


title: Uninjured 7dpt control hearts-2


title: DSRCT4.H3K9ac


title: HA-IP-ARP1-KDM6A

value: KDM6A wild type


title: L909

value: Lactobacillus recipient mouse 2


title: K23

value: Klebsiella recipient mouse 3


title: MUTT, 38466


title: K18

value: Klebsiella recipient mouse 2


title: K4me1ARP-1WT


title: GAHD, 38462


title: DSRCT4.H3K4me3


title: NC, rep3

city: Taigu

first: 弼时

last: 赵

state: --- Select One ---

address: Mingxian South Road

institute: Shanxi Agricultural University

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: ensembl_ovis_aries_oar_v3_1_gca_000298735_1
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

organism: Ovis aries

source_name: adipocyte

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: adipocyte

value: NC


title: GAHD, 38461


title: MUTT, 38467

value: Mixed Breed


title: K27me3-ARP1-KDM6A-WT


title: NC, rep2


title: NC, rep1


title: overexpressing MEOX2, rep1

value: overexpressing MEOX2


title: GAHD, 38460

value: Whole Blood


title: overexpressing MEOX2, rep3


title: K27me3-ARP1-KDM6A-KO

value: multiple myeloma


title: K27ac-ARP1-KDM6A-KO


title: overexpressing MEOX2, rep2


title: K27me3-ARP1-KDM6A-H1146E

value: KDM6A JmjD-dead


title: K27ac-ARP1-KDM6A-WT


title: K27ac-ARP1-KDM6A-H1146E


title: GAHD, 38458


title: DSRCT4.H3K27me3

value: DSRCT


title: DSRCT4.H3K4me1

value: untreated


title: GAHD, 38459


title: MH258 cells, WT, rep2

city: Chicago

first: Mark

last: Mimee

state: IL

address: Cummings Life Science Center 920 E 58th St, Room 1001

institute: University of Chicago

data_processing:
Libraries were sequenced using 2x150bp reads on NextSeq 1000
Reads were filtered for quality (FastQC), they were aligned to the MH258 reference genome (Bowtie).
Aligned reads counts were binned to reference annotations using featureCounts (Rsubread) and tested for differential expression (DESeq).
Assembly: PATRIC Genome ID 570.3961
Supplementary files format and content: csv file containing raw read counts and annotation data from PATRIC

organism: Klebsiella pneumoniae

growth_protocol: MH258 and MH258-delta-csrD cultures were grown overnight, subcultured 1:100 in LB media, and grown to mid-log phase (approximately 2 hours) as measured by OD.

extract_protocol:
Total RNA was isolated from each cell type (in biological duplicate) and purified using RNAeasy RNA extraction kit (Qiagen). RNA was then DNAse treated (TURBO) to remove all DNA
RNA was submitted to the UChicago DFI Metagenomics Core for Illumina RNAseq Library Prep. Illumina compatible libraries were generated using NEBNext® Ultra™ II Directional RNA Library Prep Kit. Ribosomal RNA depletion (NEB) was used prior to library preparation.

treatment_protocol: RNAProtect (Qiagen) was added to the cells per manufacturers protocols before RNA isolation.

value: Bacteria

value: WT

value: mid-log growth


title: input-ARP1-KDM6A-WT

value: input control


title: MH258 cells, WT, rep1


title: DSRCT4.H3K27ac


title: GAHD, 38457

value: Galapagos Hunting Dog


title: MH258 cells, deltaCsrD mutant, rep2

value: csrD deletion


title: AT0205 sRNA-Seq

city: Orbassano

first: Giulio

last: Ferrero

state: TO

address: Regione Gonzole, 10

department: Dept. Clinical and Biological Sciences

country: Italy

institute: University of Turin

data_processing:
After a quality check with FastQC tool, adapter sequences were trimmed using Cutadapt, which also removed sequences shorter than 16 nucleotides and longer than 30 nucleotides.
Reads were mapped using the STAR algorithm. Only reads that mapped unambiguously to the reference genome retrieved from miRBase 21 database (with at least 16 nucleotides aligned, and allowing a 10% mismatch) were used for the downstream analyses.
Raw counts from mapped reads were obtained using the htseq-count script from the HTSeq tools.
Assembly: hg38
Supplementary files format and content: Matrix table with the raw mature miRNA read counts for each sample

source_name: Fibroblast

growth_protocol: Fibroblasts cell lines were obtained from skin biopsies and cultured in Dulbecco’s Modified Eagle Medium (DMEM, Sigma Aldrich, Italy) with 2 mMol Glutamine, 50 U/ml penicillin, 50 µg/ml streptomycin, 1 mMol Sodium Pyruvate, and 10% FBS.

extract_protocol:
RNA extraction was performed using miRNeasy Mini Kit (Qiagen) following the manufacturer’s standard protocol including the DNAse step.
Small RNA libraries were created for 6 fibroblast samples using TruSeq Small RNA Library PrepKit v2 (Illumina, San Diego, California RS-200-0012/24/36/48). The libraries were generated following manufacturer’s instruction starting from 35 ng of purified RNA. The High Sensitivity DNA (HS-DNA) kit (Agilent Technologies, Santa Clara, California, USA5067-4626) was used to quantify the libraries using Agilent Bioanalyzer (Agilent Technologies). The 24 DNA DNA libraries were combined in equal amount to create a libraries pool. The pooled libraries underwent size selection using magnetic beads (Agencourt, Beckman Coulter, Brea, California). They were then quantified using the HS-DNA Kit (Agilent Technologies), denatured, neutralized and combined with a Phix control library (standard library normalizator). A final concentration of 1.8 pM of pooled libraries was obtained and sequenced using the NextSeq 500/550 High Output Kit v2 (75 cycles) (Illumina, FC-404-2005) on the Illumina NextSeq500 platform.

value: Fibroblast

value: Male

tag: disease

value: AT patient


title: input-ARP1-KDM6A-KO

value: KDM6A knock out


title: CS47M sRNA-Seq

tag: Sex

value: Control


title: GAHD, 38454


title: MH258 cells, deltaCsrD mutant, rep1


title: GAHD, 38456


title: C7F sRNA-Seq

value: Female


title: C6F sRNA-Seq


title: GAHD, 38455

value: Whole Blood


title: ATAC-ARP1-KDM6A-WT-rep2

extract_protocol:
Performed as described in Buenrostro et al, 2013
Libraries were size selected by SPRIselect, and library QC was performed by measuring the ratio of GAPDH promoter to a genomic desert region by qPCR prior to sequencing using a NextSeq 500 (Illumina)  (2 × 150 bp) to achieve approximately 60 million reads per sample.

value: multiple myeloma

value: KDM6A wild type


title: SF4

city: Hefe

first: sheng

last: zhang

state: Anhui Province

address: Shushan District

institute: anhui agriculture university

description: replicate=SF group biological replicate 4

data_processing:
For annotation, the genome of S. marcescens (GCF_013122155.1) and L. plantarum (GCF_032436005.1) was used as reference.
The significant differentially expressed genes were determined in different groups using the DESeq software, with the standards of P-value ≤0.05, and fold change |log2FC| ≥1.
KEGG B class database was used to classify the genes with significantly differential expression based on their functions using the tool Omicshare.
Assembly: Serratia marcescens with the Genbank accession number CP053378 and Lactobacillus plantarum with the Genbank accession number KY038178
Supplementary files format and content: txt files include gene count values for each Sample

organism: Serratia marcescens

source_name: Serratia marcescens FY

extract_protocol:
RNA was harvested using Bacteria RNA Extraction Kit (Vazyme). 1 ug of total RNA was used for the construction of sequencing libraries.
With Ribo-off rRNA Depletion Kit (Vazyme), the total bacterial RNA was subjected to rRNA removing to obtain mRNA.And then RNA libraries for RNA-seq were prepared using VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme) following manufacturer's protocols.

value: Serratia marcescens FY

value: bacteria and larvae were co-cultured


title: SF3

description: replicate=SF group biological replicate 3


title: ATAC-ARP1-KDM6A-WT-rep3


title: ATAC-ARP1-KDM6A-WT-rep1


title: S

description: 10x Genomics

data_processing:
Raw reads were aligned against the S. marcescens FY Lactobacillus plantarum FY1.Then, genome and counted by StarSolo. Sequencing data was further analyzed using the Scanpy software.
We initially reduced dimensionality of the dataset using principal components analysis (PCA), retaining 20 principal components.
Subsequent steps, like low-dimensional UMAP visualization and cell clustering via Leiden algorithm, were based on the initial PCA.
Finally, Wilcoxon rank sum was used to analyze the difference between different cluster cells.
Assembly: Serratia marcescens with the Genbank accession number CP053378 and Lactobacillus plantarum with the Genbank accession number KY038178
Supplementary files format and content: tsv files include gene counts for each Sample

source_name: WT

extract_protocol:
Up to half a million cells were collected by centrifuging at 4000 rpm for 5 min at 4℃.The supernatant was removed and cell pellets were resuspended in 2 mL ice-cold 4% formaldehyde (Sigma, 47608) and incubated with shaking overnight at 4℃. The fixative was removed by centrifuging at 4000 rpm for 5 min at 4℃ and cells were washed twice by 1 mL PBS-TRI (1x PBS supplemented with 0.1% Tween-20 and 0.1 U/mL Murine RNase inhibitor (Vazyme, R 301)). The supernatant was removed and cells were resuspended in 200 μL PBS-TRI (1x PBS supplemented with 0.1% Tween-20 and 0.2 U/mL Murine RNase inhibitor (Vazyme, R 301)).
The cell suspensions were counted with a Moxi cell counter (ORFLO Technologies, Ketchum, Idaho) and diluted according to the manufacturer’s instructions to obtain 2000-4000 single-cell per sample. Random primers were added to amplify the full length of RNA, and the resulting cDNA fragment was added with adaptor. The microbeads with cell barcode, UMI, and the cDNA fragments linked to the adaptor were combined with the mixture of enzymes and extended in the microfluidic system to obtain the labeled cDNA chain. The beads were lysed and the cDNA was used as a template for PCR amplification. All products were pooled to construct a standard sequencing library.

value: single cultivation


title: AT46 sRNA-Seq