title: Lane1_in_vivo_Blue1

value: Tumor tissue


title: RNA1_U251_NSFD_3DPT

status: Public on Nov 05 2024

type: SRA

city: DALLAS

first: jianjing

last: Yang

state: TX

address: 6000 Harry Hines Blvd

department: Molecular Biology

country: USA

institute: UT Southwestern Medical Center

library_source: transcriptomic

data_processing:
Reads were aligned to the human reference sequence GRCh37/hg19 with the TopHat (version 1.4.1) algorithm and transcript assembly performed with Cufflinks (version 2.1.0). Expression levels of RefSeq-annotated genes were calculated in units of fragments per kilobase of exon per million mapped fragments (FPKM) and differential expression analysis was performed with Cuffdiff (version 2.1.0). Genes were defined as significant if the following three criteria were satisfied: Student’s t-test p value ≥0.05, at least 2-fold gene expression change relative to the GFP-transduced control, and the triplicate average of ln(FPKM) ≥1 in either the experimental condition or fibroblast control. Gene ontology analysis was performed using the DAVID Functional Annotation Tool (version 6.7).
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Differential expression file (.xlsx) was generated using Cuffdiff (version 2.1.0).

molecule: total RNA

organism: Homo sapiens

source_name: U-251 Glioblastoma Cell

extract_protocol:
After cell sorting, we acquired nearly 5×10^5 U251 cells. RNA isolation was performed by TRIZOL (Life Technologies, 15596-018) followed by chloroform extraction and column-based purification kit (Zymo Research, R1016). Total RNA samples were submitted and analyzed with bioanalyzer to check RNA concentration and RNA integrity number (RIN).
1ug total RNA has been used for library preparation (Illumina, RS-122-2201)

tag: cell line

tag: cell type

value: Glioblastoma

tag: over-expression

value: NEUROG2 and SOX11

tag: media

value: Neuron induction medium supplemented with 10 microMolar forskolin and 1 microMolar dorsomorphin


title: SARC_110_PNET

city: Campinas

first: Felipe

last: Silva

address: R. Márcia Mendes, 506

country: Brazil

institute: Boldrini

data_processing:
Transcriptome raw data quality was verified with FASTQC . We used STAR-fusion to identify and annotate fusion transcripts based on discordant read alignments with default configurations. Alinment against GRCh38.primary_assembly.genome.fa and assigned mapped reads from genomic RNA sequencing to genomic features were performed using Rsubread package (v  2.18.0)
Assembly: GRCh38
Supplementary files format and content: A csv  file corresponding to gene count matrix containing assigned mapped reads from genomic RNA sequencing to genomic features

source_name: Tumour tissue

extract_protocol:
RNA was extracted with RNeasy Kit (QIAGEN, Hilden, Germany; cat. ID: 74106) and quantified with High Sensitivity Qubit™ RNA Assay Kits (Invitrogen™, Waltham, MA, USA; cat. ID: Q32855).
Transcriptome assay was performed using Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus (Illumina, San Diego, CA, USA) and sequenced on the NextSeq550 or NOVAseqX (Illumina Inc, San Diego, CA, USA). Paired-end runs were sequenced in 74 cycles per read (2 X 74), with an average of 41.5 million reads per sample.

tag: tissue

value: Tumour tissue

value: PNET


title: STSW1_S1_L002

city: Chicago

first: Christopher

last: Felicelli

state: Illinois

address: 303 East Chicago Avenue

department: Pathology

institute: Northwestern University Feinberg School of Medicine

data_processing:
Raw sequencing data, in base call format (.bcl) were demultiplexed using Space Ranger (version 2.0.0) from 10x Genomics, converting the raw data into FASTQ format.
The images were processed and manually aligned using the Loupe Browser (version 5.1.0).
pace Ranger was also used for alignment of the FASTQ files to the human probe set version 2 and to count the number of reads from each cell that aligned to each probe.
The resulting matrix files, which summarize the alignment results, were imported to Seurat (Satija Lab, NYGC) for further analysis. In Seurat, each individual sample was preprocessed, normalized, and scaled.
ll samples were then combined into a single dataset using the IntegrateData function in Seurat, adding metadata with the original sample information.
All UMAPs, Violin plots, spatial feature expression plots, and heatmaps were generated using Seurat tools. Cell types were automatically assigned using the R package scType.
Assembly: hq38
Library strategy: Spatial Transcriptomics

source_name: Uterus

growth_protocol: N/A-FFPE

extract_protocol:
1-2 curls (10um thickness each) were used for RNA extraction using Qiagen RNeasy FFPE kit (Qiagen 73504) according to manufactures’ protocol. Extracted RNA was examined by Agilent Bioanalyzer RNA pico chip to confirm the DV200 >30%.  For each FFPE sample, 1 section (5um thickness) was placed on Leica Bond plus slides. Each slide was incubated at 42°C for 3 hours followed by overnight room temperature incubation. Slides were stored in desiccated slide holders until proceeding to deparaffinization. The deparaffinization, HE stains and imaging and decrosslinking of tissue slides were performed according to 10x Genomics protocol (CG000520 Rev B) specific for Visium CytAssist spatial gene expression for FFPE kit.
he deparaffinization, HE stains and imaging and decrosslinking of tissue slides were performed according to 10x Genomics protocol (CG000520 Rev B) specific for Visium CytAssist spatial gene expression for FFPE kit. Then, the slides were proceeded to human probe (v2) hybridization and ligation using 10x Genomics Visium CytAssist spatial gene expression FFPE, human transcriptome, 6.5mm kit (10x Genomics, PN-1000520). The probes were released from tissue slide and transferred to barcoded visium slide using Visium CytAssist instrument followed by probe extension. Sequencing libraries were prepared according to manufacturer’s protocol. Multiplexed libraries were pooled and sequenced on Novaseq6000 S2 flowcell 100 cycles kit with following parameter: 28nt for Read 1 and 90nt for Read 2. The visium slide processing, library preparation and sequencing was done at Northwestern University NUseq facility core.

treatment_protocol: regions of LMBN vs LMS

value: Uterus

value: Mesenchymal

tag: genotype

value: LMBN/LMS


title: ORSAM13704-1

city: Bar Harbor

first: Gary

last: Churchill

state: Maine

address: 600 Main St

institute: The Jackson Laboratory

data_processing:
raw counts quantified by EMASE and processed by /RNAseq/Raw/GBRS/QTLViewer_setup/gathering_GBRS_total_counts.R script and gathering_GBRS_total_counts_batch2.R.
counts normalized by DESeq2 vst() function (quick version of variance stabilizing transformation).
Matrix generated by /RNAseq/Raw/GBRS/QTLViewer_setup/Processing_normalization.R and Processing_normalization_batch2.R scripts.
gene annotation file ENSEMBL version 84
Assembly: GRCm38

organism: Mus musculus

source_name: adipose-10% fat + fiber-female-CC075/UncJ x CC042/GeniUncJ)F1 -None-rep1

extract_protocol:
RNA was isolated from tissue using the MagMAX mirVana Total RNA Isolation Kit (ThermoFisher) and the KingFisher Flex purification system (ThermoFisher). Frozen tissues were pulverized using a Bessman Tissue Pulverizer (Spectrum Chemical) and homogenized in TRIzol (ThermoFisher Scientific) using a gentleMACS dissociator (Miltenyi Biotec Inc). After the addition of chloroform to the TRIzol homogenate, the RNA-containing aqueous layer was removed for RNA isolation, according to the manufacturer’s protocol, beginning with the RNA bead binding step. RNA concentration and quality were assessed using the Nanodrop 8000 spectrophotometer (Thermo Scientific) and the RNA 6000 Pico or RNA ScreenTape assay (Agilent Technologies).
2 ul of diluted (1:1000) ERCC Spike-in Control Mix 1 (Ambion by Life Technologies) was added to 100ng of each RNA sample prior to library construction.  Libraries were constructed using the KAPA mRNA HyperPrep Kit (Roche Sequencing and Life Science), according to the manufacturer’s protocol.  Briefly, the protocol entails isolation of polyA containing mRNA using oligo-dT magnetic beads, RNA fragmentation, first and second strand cDNA synthesis, ligation of Illumina-specific adapters containing a unique barcode sequence for each library, and PCR amplification.  The quality and concentration of the libraries were assessed using the D5000 ScreenTape (Agilent Technologies) and Qubit dsDNA HS Assay (ThermoFisher), respectively, according to the manufacturers’ instructions. ibraries were sequenced on an Illumina NovaSeq 6000 using the S4 Reagent Kit. Libraries were sequenced 100 bp paired-end to a targeted read depth of 30 million read pairs.

treatment_protocol: Adipose, liver, and skeletal muscle tissue from 6-month and 12-month CC-RIX cohorts underwent transcriptomic profiling. CC-RIX cohorts were exposed to sensitizer (HFHS diet) and a widely used pharmaceutical intervention (metformin). Chow (control) or high fat high sugar (HFHS) diet started at 6 weeks of age.. At six months of age, a subset of mice from each chow group and of each sex were euthanized for tissue collection.  At 7 months of age, half of the remaining mice in each diet treatment group will receive metformin treatment.  In a subset of the 12 month cohort animals, metformin (5 mg/mL) was delivered ad libitum in the drinking water (Chang, Moro et al. 2018). Terminal phenotyping and tissue collection was done at 12 months of age.  These animals also underwent metabolic phenotyping.

value: gonadal fat pad

tag: Sex

value: female

tag: strain

value: CC075/UncJ x CC042/GeniUncJ)F1

value: Outbred

tag: treatment

tag: diet

value: 10% fat + fiber

tag: sequencing id


title: SARC_111_PNET


title: Donor_3_LPS_IL1

city: Parkville

first: Boris

last: Novakovic

state: Victoria

address: Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road

country: Australia

institute: Murdoch Children's Research Institute

data_processing:
Fastq files were assessed for quality using the FastQC package and no samples were excluded from analysis. Bowtie2 was used to map reads to the human transcriptome (Ensembl, GRCh37v70), and gene expression estimates were derived using HTseq. DESeq2  was used to normalise count data and determine gene expression differences between treatments.
Assembly: hg19
Supplementary files format and content: .counts files contain unnormalized counts per gene

molecule: polyA RNA

source_name: bone marrow

growth_protocol: Human bone marrow HPCs were proliferated for 10 days in expansion medium (X-VIVO supplemented with 4% FCS, 1% p/s, 50 ng/ml SCF, 15 ng/ml TPO, 30 ng/ml IL3, 30 ng/ml Flt3L and 2 uM SR1. After that, differentiation into monocytes was done using IMDM supplemented with 10% FCS, 1% p/s, 25 ng/ml SCF and 30 ng/ml MCSF, IL3 and Fl3tL.

extract_protocol:
At the end of differentiation, monocytes were isolated using pan monocytes kit (MACS). The monocytes obtained were then stimulated for 4 hours with IMDM medium as control or LPS 10 ng/ml for 4 hours and cells were stored in RNAlater buffer. Total RNA were extracted using the QIAGEN AllPrep DNA/RNA micro-kit according to manufacturer’s instructions.
Library preparation was performed using the Illumina TruSeq stranded mRNA kit with a starting input of 300ng and libraries were sequenced on the IlluminaNovaSeq 6000 instrument generating an average of 20 million reads per sample.

value: bone marrow

tag: individual

value: Monocyte differentiated from hematopoietic progenitor cells (HPCs) from human bone marrow

value: IL1b 10 ng/mL medium control exposed HPC - differentiation into BM-mono for 7 days  - LPS HPC-derived mono (4h)


title: RNA2_U251_NSFD_1DPT


title: Donor_3_LPS_IMDM

value: IMDM medium control exposed HPC - differentiation into BM-mono for 7 days  - LPS HPC-derived mono (4h)


title: ORSAM13368-1

source_name: adipose-44% fat + fiber-male-CC002/UncJ x CC075/UncJ)F1 -None-rep1

value: male

value: CC002/UncJ x CC075/UncJ)F1

value: 44% fat + fiber


title: SARC_36_EWING

value: Tumour tissue

value: EWING


title: RNA1_U251_NSFD_1DPT

value: Glioblastoma

value: NEUROG2 and SOX11

value: Neuron induction medium supplemented with 10 microMolar forskolin and 1 microMolar dorsomorphin


title: SARC_30_EWING


title: Donor_3_uns_IL1

value: IL1b 10 ng/mL medium control exposed HPC - differentiation into BM-mono for 7 days  - unstimulated HPC-derived mono (4h)


title: ORSAM13366-1

value: gonadal fat pad


title: SARC_29_ES


title: RNA3_U251_SFD_1DPT


title: Donor_3_uns_IMDM

value: IMDM medium control exposed HPC - differentiation into BM-mono for 7 days  - unstimulated HPC-derived mono (4h)


title: RNA2_U251_NSFD_3DPT


title: ORSAM13364-1

value: Outbred


title: RNA2_U251_SFD_1DPT


title: Donor_2_LPS_IL1


title: ORSAM13363-1

source_name: adipose-44% fat + fiber-female-CC002/UncJ x CC075/UncJ)F1 -None-rep1

value: female


title: RNA1_U251_SFD_1DPT


title: ORSAM13707-1

source_name: adipose-44% fat + fiber-female-CC075/UncJ x CC042/GeniUncJ)F1 -None-rep1

value: CC075/UncJ x CC042/GeniUncJ)F1


title: Donor_2_LPS_IMDM

value: bone marrow

value: Monocyte differentiated from hematopoietic progenitor cells (HPCs) from human bone marrow


title: SARC_50_EWING


title: SARC_09_CCSK

value: Clear cell sarcoma of kidney


title: RNA3_U251_NSFD_1DPT


title: ORSAM13362-1


title: RNA3_U251_NFD_1DPT


title: ORSAM13361-1


title: Donor_2_uns_IL1


title: SARC_51_SARC_BCOR

value: BCOR-rearranged sarcoma


title: RNA2_U251_NFD_1DPT


title: Donor_2_uns_IMDM


title: RNA1_U251_NFD_1DPT


title: Donor_1_LPS_IL1

value: IL1b 10 ng/mL medium control exposed HPC - differentiation into BM-mono for 7 days  - LPS HPC-derived mono (4h)


title: CD4+_donor 2_5dpi

city: Seoul

first: Dohoon

last: Lee

address: 1, Gwanak-ro, Gwanak-gu

department: Bioinformatics Institute

country: South Korea

institute: Seoul National University

library_source: genomic

data_processing:
Quality control of HIV-1 integration site-sequencin reads was performed using FastQC v0.11.9.
To discard primers and linkers specific for integration site-sequencing from reads, we used Cutadapt v2.8 with the following option: "-u 49 -U 38 --minimum-length 36 --pair-filter any --action trim -q0,0 -a linker -A TGCTAGAGATTTTCCACACTGACTGGGTCTGAGGG -A GGGTCTGAGGG --no-indels --overlap 12"
Processed reads were aligned to the hg38 reference genome using bwa v0.7.17-r1188
Assembly: hg38
Supplementary files format and content: BED files - Genomic locations of the identified integration sites
Supplementary files format and content: csv file - Locations of the identified integration sites within the vector and their frequencies
Library strategy: Integration-site-seq

molecule: genomic DNA

extract_protocol:
gDNA was isolated using a DNA purification kit (Qiagen, 51106), according to the manufacturer’s instructions
gDNA  was digested overnight at 37°C with  each of the restriction endonucleases MseI (NEB, R0525L) and BglII (NEB, R0144L). Linker oligonucleotides, which were compatible for ligation with the MseI-generated DNA ends, were ligated with gDNA overnight at 12°C in reactions containing 1.5 μM ligated linker, 1 μg fragmented DNA, and 800 U T4 DNA ligase (NEB, M0202S). Viral LTR–host DNA junctions were amplified using semi-nested PCR with a unique linker-specific primer and LTR primers. The second round of PCR was carried out with primers binding to the LTR and the linkers for next-generation sequencing. Two PCRs were performed in parallel for the first round of PCR and five PCRs were performed in parallel for the second round of PCR to enhance library diversity.


title: Donor_1_LPS_IMDM

value: IMDM medium control exposed HPC - differentiation into BM-mono for 7 days  - LPS HPC-derived mono (4h)


title: RNA3_U251_1DPT


title: ORSAM13359-1

source_name: adipose-10% fat + fiber-male-CC024/GeniUncJ x CC002/UncJ)F1 -Metformin-rep1

value: male

value: CC024/GeniUncJ x CC002/UncJ)F1

value: Metformin

value: 10% fat + fiber


title: SARC_08_EWING

value: Tumour tissue

value: EWING


title: ORSAM13358-1

value: gonadal fat pad


title: ORSAM13357-1


title: ORSAM13354-1

source_name: adipose-10% fat + fiber-female-CC024/GeniUncJ x CC002/UncJ)F1 -Metformin-rep1


title: RNA2_U251_1DPT

value: Glioblastoma

value: Neuron induction medium supplemented with 10 microMolar forskolin and 1 microMolar dorsomorphin


title: CD4+_donor 1_5dpi


title: Donor_1_uns_IL1

value: IL1b 10 ng/mL medium control exposed HPC - differentiation into BM-mono for 7 days  - unstimulated HPC-derived mono (4h)


title: HeLa_pgR-rich_DOX pos_replicate2

source_name: HeLa

value: HeLa


title: Donor_1_uns_IMDM

value: bone marrow

value: IMDM medium control exposed HPC - differentiation into BM-mono for 7 days  - unstimulated HPC-derived mono (4h)


title: ORSAM13353-1

value: female

value: Outbred


title: RNA1_U251_1DPT


title: HeLa_pgR-rich_DOX pos_replicate1


title: ORSAM13352-1


title: IP2_NEUROG2_U251_NSFD_5DPT

data_processing:
Reads were aligned to the human reference sequence GRCh37/hg19 with the Bowtie algorithm (version 1.0.0). Peak calling, peak‑gene annotation, motif discovery (parameter: 200 nucleotide window from peak center), and generation of heatmap matrices were performed using HOMER (version 4.7). Gene ontology classification was performed using HOMER and Genomic Regions Enrichment of Annotations Tool (version 2.0.2). The UCSC Genome Browser was used to visualize tag densities and multi-experiment datasets.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Alignment files (.bam) were generated using Bowtie (version 1.0.0). UCSC.bedGraph and peak files (.txt) were generated using HOMER (version 4.7)

extract_protocol:
For chromatin immunoprecipitation experiment, U251 cell was cultured in 10 cm plate. After infected U251 cell with different prepared lentivirus, U251 cell was treated with neuron induction medium supplemented with forskolin and dorsomorphin as same as glioblastoma reprogramming process. Approximately total ~16×106 cells (4 10cm plates) were crosslinked with methanol-free formaldehyde (Thermo Scientific, 28908) at final concentration of 1% v/v for 8 minutes. Then quench the crosslinking with glycine at final concentration of 0.125 M for 5 minutes. Place plates contain U251 cells on ice, quickly twice washed with 10 ml pre-cold PBS, scraped and collected cell by centrifugation (525g, 5 minutes, 4°C). Aspirated the supernatant and resuspended cell pellet in 5 ml lysis buffer ((100 mM HEPES (pH 8.0), 85 mM KCl, 1% (v/v) IGEPAL CA-630, and 1% (v/v) cOmplete EDTA-free Protease Inhibitor Cocktail (Roche, 11873580001))) and incubated on ice for 20 minutes. Dounce homogenized U251 cells (20 repetitions) on ice and performed centrifugation (525g, 5 minutes, 4°C) to collected cell nuclei. Resuspended cell nuclei pellet in shearing buffer (50 mM HEPES (pH 8.0), 10 mM EDTA (pH 8.0), 1% (w/v) SDS, and 1% (v/v) cOmplete EDTA-free Protease Inhibitor Cocktail) and transferred to a TPX microtube (Diagenode, C-30010010-50) on ice. Shearing cell chromatin using a Bioruptor machine (Diagenode, B01010002). After Shearing, the sheared chromatin was centrifuged at 21,130 × g speed for 10 minutes at 4°C. Supernatant was collected and chromatin concentration was determined. Two samples of 10 ug chromatin has been saved, one was for input, the other was used for check chromatin shearing quality. 150 ug of chromatin with five-fold diluted by IP buffer (50 mM HEPES (pH 8.0), 20 mM NaCl, 1 mM EDTA (pH 8.0), 0.1% (v/v) Triton X-100, and 1% (v/v) cOmplete EDTA-free Protease Inhibitor Cocktail) was used for performing immunoprecipitation. HA-NGN2 or HA-SOX4/11 bound DNA fragments were immunoprecipitated with 5ug HA antibody (Abcam, AB9110). Histone H3 acetyl K27 bound DNA fragments were immunoprecipitated with histone H3 acetyl K27 antibody (Abcam, ab4729). Immunoprecipitation samples were incubated for 18 hours at 4°C with gentle rotation. Subsequently, 100 µl Magnetic Protein G Dynabeads (Life Technologies, 10003D) were resuspended in immunoprecipitation samples incubate for 2 hours at 4°C with gentle rotation to combine HA antibody. After magnetically isolation and washed, chromatin was eluted by adding 100 µl elution buffer (1% (w/v) SDS and 50 mM NaHCO3). The 10 ug chromatin input sample was eluted by 85ul elution buffer. Place those Input and IP sample to vigorous agitation (1,400 rpm, 27 °C, 30 minutes, Eppendorf Thermomixer). After subsequently treated with RNase, Proteinase K and NaCl(5M), Input and IP Chromatin was purified with a QIAquick PCR purification kit (Qiagen, 28104) according to kit manual. The chromatin concentration was determined by Qubit fluorometer and Qubit dsDNA HS assay kit (Life Technologies, Q32850) according to kit manual. 10 ng of input chromatin and 10 of HA-NGN2 or HA-SOX4/11 immunoprecipitated chromatin samples were used to build libraries by NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina kit (New England Biolabs, E6240S) for DNA sequencing. Duplicate or replicate libraries were built for each group from independent immunoprecipitations. After check library quality by bioanalyzer, DNA samples were submitted to sequencing core. Single end 50 base sequencing reads were generated and aligned to GRCh37/hg19. HOMER was used to the following analysis including Peak calling, annotation, motif discovery and GO analysis. Also, the UCSC Genome Browser was used to visualization of DNA sequencing data.
Libraries were synthesized from 10 ng purified input chromatin and 10 ng purified immunoprecipitated chromatin using a NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina (New England Biolabs, E6240S) with NEBNext Multiplex Oligos for Illumina (New England Biolabs, E7335S). Replicate libraries were prepared from independent immunoprecipitations.

value: NEUROG2 and SOX11

tag: medium

value: Supplemented with neuron induction medium containing FD

tag: chip antibody

value: anti-HA  (Abcam, ab9110)


title: INTS6 KO, mNET-seq, r2

city: Aurora

first: Ryan

last: Sheridan

state: CO

address: 12801 East 17th Avenue

institute: University of Colorado Anschutz Medical Campus

data_processing:
*library strategy: Native elongating transcript sequencing (NET-seq)
Adapters were trimmed using cutadapt version 2.3
Reads were aligned using Bowtie2 version 2.3.2
PCR duplicates were removed UMI-tools v0.5.4
Read coordinates were collapsed to a single base pair coordinate corresponding to the RNA 3’ end
Assembly: hg38
Supplementary files format and content: bigwig

growth_protocol: DMEM +10% FBS +pen/strep

extract_protocol:
Pol II-associated nascent RNA was isolated by IP
10-20ng of RNA was used with the QIAseq miRNA  kit (#331505)

value: INTS6 knockout

tag: molecule subtype

value: Nascent RNA


title: SARC_06_EWING


title: IP1_NEUROG2_U251_NSFD_5DPT


title: HeLa_pgR-rich_DOX neg_replicate2


title: ORSAM12480-1

source_name: adipose-10% fat + fiber-male-CC019/TauUncJ x CC042/GeniUncJ)F1 -None-rep1

value: male

value: CC019/TauUncJ x CC042/GeniUncJ)F1

value: 10% fat + fiber


title: control, mNET-seq, r2

value: wildtype


title: IP2_NEUROG2_U251_NSFD_3DPT


title: INTS6 KO, mNET-seq, r1


title: HeLa_pgR-rich_DOX neg_replicate1


title: IP1_NEUROG2_U251_NSFD_3DPT


title: control, mNET-seq, r1


title: HeLa_pgR-poor_DOX pos_replicate2


title: ORSAM12477-1

source_name: adipose-10% fat + fiber-female-CC019/TauUncJ x CC042/GeniUncJ)F1 -None-rep1

value: gonadal fat pad


title: HCT116 cells,OE-MST3-3

city: Beijing City

first: Shiyang Wang

middle: Shiyang

last: Wang

state: Beijing City

address: 2 West Yuanmingyuan Road, Haidian District, Beijing, China

country: China

institute: China Agricultural University

data_processing:
Library preparation for Transcriptome sequencing. Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA waspurified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation wascarried out using divalent cations under elevated temperature in First Strand SynthesisReaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer andM-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis wassubsequently performed using DNA Polymerase I and RNase H. Remaining overhangs wereconverted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’endsof DNA fragments, Adaptor with hairpin loop structure were ligated to prepare forhybridization. In order to select cDNA fragments of preferentially 370420 bp in length, thelibrary fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA).Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCRprimers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) andlibrary quality was assessed on the Agilent Bioanalyzer 2100 system.
The clustering of the index-coded samples was performed on a cBot Cluster GenerationSystem using TruSeq PE Cluster Kit v3-cBot-HS (Ilumia) according to the manufacturer'sinstructions. After cluster generation, the library preparations were sequenced on an IlluminaNovaseq platform and 150 bp paired-end reads were generated.
Assembly: Hisat2
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: HCT116 cells were maintained in IMDM supplemented with 10% fetal bovine serum (FBS) and 1% antibiotic and placed in a humidified atmosphere containing 5%CO2 at 37°C.

extract_protocol:
RNA was collected, cells were lysed with Trizol, extracted using the phenol/chloroform method, and approximately 30µg of total RNA was used for sequencing library construction.
RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).

treatment_protocol: After the cells had grown to 60% density, the overexpression plasmid was transfected into the cells with lipo2000, and fresh culture medium was replaced after 6 hours, and cellular RNA was collected after 30 hours.

value: Human colorectal cancer cell lines

value: Overexpression of MST3


title: HeLa_pgR-poor_DOX pos_replicate1

value: HeLa


title: HeLa_pgR-poor_DOX neg_replicate2


title: HCT116 cells,OE-MST3-2


title: ORSAM12474-1

source_name: adipose-44% fat + fiber-male-CC042/GeniUncJ x CC040/TauUncJ)F1 -None-rep1

value: CC042/GeniUncJ x CC040/TauUncJ)F1

value: 44% fat + fiber


title: IP1_NEUROG2_U251_NSFD_1DPT


title: IP2_NEUROG2_U251_NFD_1DPT


title: HCT116 cells,OE-MST3-1


title: ORSAM12472-1

source_name: adipose-10% fat + fiber-female-CC042/GeniUncJ x CC040/TauUncJ)F1 -None-rep1

value: female


title: HeLa_pgR-poor_DOX neg_replicate1


title: IP1_NEUROG2_U251_NFD_1DPT


title: Input_NEUROG2_U251_NSFD_5DPT


title: ORSAM12470-1

source_name: adipose-44% fat + fiber-female-CC042/GeniUncJ x CC040/TauUncJ)F1 -None-rep1

value: Outbred


title: HCT116 cells,vector-2

value: WT


title: HeLa replicate 2_5dpi


title: ORSAM12465-1

source_name: adipose-10% fat + fiber-male-CC004/TauUncJ x CC019/TauUncJ)F1 -None-rep1

value: CC004/TauUncJ x CC019/TauUncJ)F1


title: ORSAM12479-1


title: Input_NEUROG2_U251_NSFD_3DPT

source_name: U-251 Glioblastoma Cell

value: NEUROG2 and SOX11

value: Supplemented with neuron induction medium containing FD


title: CD4 12hpi RNH+IP donor 2

data_processing:
DRIPc-seq reads were quality-controlled using FastQC v0.11.9, and sequencing adapters were trimmed using Trim Galore! V0.6.6 based on Cutadapt v2.8.
Trimmed reads were aligned to the hg38 reference genome using bwa v0.7.17-r1188.
Assembly: hg38
Supplementary files format and content: BED
Library strategy: DRIPc-seq

source_name: primary CD4+

extract_protocol:
The corresponding cells were harvested and their gDNA was extracted by using standard phenol-chloroform extraction and resuspended in DNase/RNase-free water
anti-S9.6 immunoprecipitaed materials were digested with DNase I and the RNA were reverse transcribed with dUTP for library construction. cDNA were sonicated and processed to end repair and dA tailing. Adopter ligated then materials  were amplified with illumina PCR primers, 1.0 P5 and 2.0 P7. Amplicons were treated with Uracil N-Glycosylase.

value: primary CD4+


title: ORSAM12463-1

value: male


title: HeLa replicate 1_5dpi


title: IP2_NEUROG2_U251_NSFD_1DPT

value: anti-HA  (Abcam, ab9110)


title: Control Stromal cells from 7045, scRNA-seq

city: Philadelphia

first: Noor

last: Dawany

state: Pennsylvania

address: 421 Curie Blvd

institute: CHOP

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcode processing and gene counting were performed in CellRanger v6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: CellRanger filtered tab-separated barcodes, genes and matrix files

source_name: Colon

extract_protocol:
Crypts were meticulously scraped off from lamina propria layer after incubation with 2 mM EDTA in 1 mL Chelation buffer for 15 min at 4°C with rotation. The epithelial cells were obtained from the isolated crypts after digestion in 1.5 mL TrypLE along with 0.5 U/mL DNAse I (Roche) for 30 min at 37°C with 800 rpm using a ThermoMixer. The lamina propria cells were obtained from the remaining lamina propria layer after digestion in 500 μL of stroma dissociation enzyme mix (comprising with 0.13 WU/mL of Liberase-TH, 0.5U/mL DNAse I in 1x HBSS) for 30 min at 37°C with 800 rpm using a ThermoMixer and subsequent supernatant collection for three cycles in total. The Dead Cell Removal kit was employed following the manufacturer’s instructions.
Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 were used for library construction according to the manufacture’s protocol. Briefly, a total of 10,000 cells were combined with Master Mix and transferred to an assembled Chromium Next GEM Chip G, which was filled with Gel Beads or 50% Glycerol (VWR), and the setup was processed in a Chromium Controller. GEMs were incubated with Dynabeads Cleanup Mix. The resulting cDNA was then subjected to Pellet Cleanup with SPRIselect reagent. Purified cDNA sample obtained from Pellet Cleanup were subjected to Fragmentation, End Repair & A-tailing, followed by Double Sided Size Selection using SPRIselect.

value: Colon

value: Stromal

tag: disease state

value: Control


title: Input_NEUROG2_U251_NFD_1DPT


title: ORSAM12462-1

source_name: adipose-44% fat + fiber-female-CC004/TauUncJ x CC019/TauUncJ)F1 -None-rep1

value: gonadal fat pad


title: HCT116 cells,vector-1

value: Human colorectal cancer cell lines


title: CD4 3hpi RNH+IP donor 2


title: VEO-IBD Stromal cells from 0832, scRNA-seq

description: 10X Genomics

value: VEO-IBD


title: ORSAM12461-1


title: HCT116 cells,vector-3


title: ORSAM12476-1

value: CC019/TauUncJ x CC042/GeniUncJ)F1

value: 10% fat + fiber


title: ORSAM12458-1

source_name: adipose-10% fat + fiber-male-CC012/GeniUncJ x CC002/UncJ)F1 -None-rep1

value: CC012/GeniUncJ x CC002/UncJ)F1


title: INTS4_dTAG_R3

city: London

first: Richard

middle: James

last: Mitter

state: LONDON

address: 1 Midland Road

department: Bioinformatics & Biostatistics

country: United Kingdom

institute: The Francis Crick Institute

description: INTS4 dTAG, replicate 3

data_processing:
Reads were processed using the publicly available nf-core rnseq pipeline v3.3 with the STAR (Dobin et al, 2012) / RSEM (B et al 2011) option against human genome assembly GRCh38 and Ensembl release 104 transcript annotations.  Data were simultaneously aligned against Saccharomyces cerevisiae R64-1-1 cdna sequences (Ensembl 104) using the “--additional_fasta” flag in order to quantify the yeast spike-in reads
Reads Per Kilobase per Million mapped reads (RPKM) scaled BigWig files were generated by converting BAM files to bedGraph format using Deeptools’ bamCoverage function for each strand in turn using the options “--normalizeUsing RPKM --exactScaling –effectiveGenomeSize (Ramirez et al., 2014).
Assembly: GRCh38
Supplementary files format and content: Per-sample, strand-specific, RPKM normalised coverage bigwig files.

source_name: HEK293 FlpIn TREx

growth_protocol: Flp-In TREx HEK293 cells were cultured in high glucose DMEM supplemented with 10% v/v FBS, 100 U/mL penicillin, 100 μg/mL streptomycin, 2 mM L-glutamine and at 37 oC with 5% CO2 and routinely passaged 2-3 times a week.

extract_protocol:
TTchem-seq RNA preparation was performed as previously described (Gregersen et al., 2020).
TTchem-seq libraries were prepared using the KAPA RNA HyperPrep Kit (Roche, 08098093702) with the fragmentation step omitted. 75 ng of nascent RNA was denatured at 65°C for 5 min. The rest of the procedure was performed following manufacturer’s instructions, except that two SPRI bead purifications (Beckman Coulter, A63881) were carried out, with a bead-to-sample volume ratio of 0.95x and 1x respectively.

treatment_protocol: Cells were treated with either 1μM dTAG7 (final concentration) for 1hr in order to induce depletion of endogenous INTS4, or with equal volume 100% DMSO as a control.

value: HEK293 FlpIn TREx

value: 1uM dTAG7 in DMSO


title: CD4 6hpi RNH+IP donor 2


title: INTS4_dTAG_R2

description: INTS4 dTAG, replicate 2


title: VEO-IBD Epithelial cells from 0832, scRNA-seq

description: 10X Genomics

value: Epithelial


title: CD4 12hpi RNH-IP donor 2


title: Control Epithelial cells from 7045, scRNA-seq

description: 10X Genomics


title: ORSAM12455-1

source_name: adipose-44% fat + fiber-male-CC051/TauUncJ x CC060/UncJ)F1 -None-rep1

value: CC051/TauUncJ x CC060/UncJ)F1

value: Outbred

value: 44% fat + fiber


title: VEO-IBD colonoids from 0832, passage 14, HTO

description: 10X Genomics

data_processing:
Demultiplexing of base call files and gene counting using feature barcodes (for cell hashing) were performed in CellRanger v6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Demultiplexed mRNA and HTO CellRanger filtered tab-separated barcodes, genes and matrix files

source_name: Colonoid

growth_protocol: Human colonoids were seeded in 30-50 µL of Matrigel per well in 24-well plate with 500 µLhuman IntestiCult Organoid Growth Media. Colonoids were fed every other day until day 7 for collection.

extract_protocol:
Human colonoids were collected at day 10 after plating and digested with 0.05% trypsin for 10 minutes at 37°C in a bead bath (final ratio as 10% FBS was added to de-activate trypsin). Cells were further dissociated by pipetting up and down several times to get single cells. Following incubation with 1μg of TotalSeqtrade anti-human Hashtag Antibody (Hashtag 1 for untreated samples, Hashtag 2 for TNFα-treated samples,Hashtag 3 for IFNγ-treated samples,Hashtag 4 for TRAIL-treated samples) for 20min and DAPI for additional10 minutes on ice, DAPI- cells were sorted in 1xDPBS+0.04% BSA using a MoFlo Astrios sorter.
Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 with Feature Barcoding technology for Cell Surface Protein (10X Genomics) were used for library construction according to the manufacture’s protocol. The addition of Cell Hashing allowed for sample multiplexing. Briefly, a total of 10,000 cells were combined with Master Mix and transferred to an assembled Chromium Next GEM Chip G, which was filled with Gel Beads or 50% Glycerol (VWR), and the setup was processed in a Chromium Controller. GEMs were incubated with Dynabeads Cleanup Mix. The resulting cDNA was then subjected to Pellet Cleanup (for 3ʹ Gene Expression library) and Supernatant Cleanup (for Cell Surface Protein library) with SPRIselect reagent. Purified cDNA sample obtained from Pellet Cleanup were subjected to Fragmentation, End Repair & A-tailing, followed by Double Sided Size Selection using SPRIselect.

treatment_protocol: For cytokine treatments, colonoids were treated at d7-post seeding with indicated cytokines (100ng/mL TNFα, 50 ng/mL IFNγ and 100ng/mL TRAIL ) for 72 hours.

value: Colonoid

value: Colon organoid

value: VEO-IBD, variant

value: mixed sample (untreated, TNFa, IFNg, TRAIL)


title: CD4 6hpi RNH-IP donor 2

value: primary CD4+


title: VEO-IBD colonoids from 0832, passage 14, GEX

description: 10X Genomics


title: CD4 3hpi RNH-IP donor 2


title: ORSAM12453-1

source_name: adipose-10% fat + fiber-male-CC051/TauUncJ x CC060/UncJ)F1 -None-rep1

value: gonadal fat pad

value: male


title: Input_NEUROG2_U251_NSFD_1DPT

value: NEUROG2 and SOX11

value: Supplemented with neuron induction medium containing FD


title: ctrl_R3

description: control, replicate 3

value: DMSO


title: ctrl_R2

description: control, replicate 2


title: VEO-IBD colonoids from 0832, passage 12, HTO

description: 10X Genomics


title: CD4 0hpi RNH-IP donor 2


title: ORSAM12452-1

source_name: adipose-10% fat + fiber-female-CC051/TauUncJ x CC060/UncJ)F1 -None-rep1

value: female

value: 10% fat + fiber


title: VEO-IBD colonoids from 0832, passage 12, GEX

description: 10X Genomics


title: ctrl_R1

description: control, replicate 1

value: HEK293 FlpIn TREx


title: CD4 0hpi RNH+IP donor 2


title: VEO-IBD colonoids from 0832, passage 11, HTO

description: 10X Genomics

value: mixed sample (TNFa, IFNg, TRAIL)


title: ORSAM12450-1

source_name: adipose-44% fat + fiber-male-CC001/UncJ x CC042/GeniUncJ)F1 -None-rep1

value: CC001/UncJ x CC042/GeniUncJ)F1


title: CD4 6hpi Input donor 2


title: NT_R3

description: control siRNA, replicate 3

treatment_protocol: siRNAs were resuspended and stored in nuclease-free water. Transfections were carried out by mixing final concentrations of 20nM siRNA and 1:1000 Lipofectamine RNAiMAX (Thermo) in serum free media. Knock-down was achieved using two-step transfection as follows: Day 1: Cells seeded at low density (2.5x105 cells/35cm dish); Day 2: Fresh media added and cells are transfected. Day 3: Fresh media added and cells transfected again. Day 4: Cells are split into larger vessels to continue growth. Day 5: Cells are treated and harvested for experiment.

value: siRNA


title: ORSAM12451-1

value: CC051/TauUncJ x CC060/UncJ)F1

value: Outbred


title: VEO-IBD colonoids from 0832, passage 11, GEX

description: 10X Genomics

value: Colonoid

value: Colon organoid


title: NT_R2

description: control siRNA, replicate 2


title: ORSAM12400-1

source_name: adipose-10% fat + fiber-male-CC002/UncJ x CC075/UncJ)F1 -None-rep1

value: CC002/UncJ x CC075/UncJ)F1


title: INTS4_dTAG_R1

description: INTS4 dTAG, replicate 1

value: 1uM dTAG7 in DMSO


title: NT_R1

description: control siRNA, replicate 1


title: CD4 0hpi Input donor 2

value: primary CD4+


title: ORSAM12399-1

value: gonadal fat pad

value: male


title: ORSAM12454-1

value: 44% fat + fiber


title: INTS6_R3

description: INTS6 siRNA, replicate 3


title: VEO-IBD colonoids from 6697, GEX

description: 10X Genomics

value: VEO-IBD

value: mixed sample (untreated, TNFa, IFNg, TRAIL)


title: VEO-IBD colonoids from 6697, HTO

description: 10X Genomics


title: CD4 12hpi RNH+IP donor 1


title: VEO-IBD colonoids from 6612, HTO

description: 10X Genomics


title: INTS6_R1

description: INTS6 siRNA, replicate 1


title: ORSAM12394-1

source_name: adipose-44% fat + fiber-female-CC024/GeniUncJ x CC002/UncJ)F1 -None-rep1

value: female

value: CC024/GeniUncJ x CC002/UncJ)F1


title: CD4 6hpi RNH+IP donor 1


title: INTS6_R2

description: INTS6 siRNA, replicate 2

value: HEK293 FlpIn TREx


title: VEO-IBD colonoids from 6612, GEX

description: 10X Genomics


title: CD4 3hpi RNH+IP donor 1


title: CD4 12hpi Input donor 2


title: ORSAM12393-1


title: CD4 3hpi Input donor 2


title: INTS4_R3

description: INTS4 siRNA, replicate 3


title: Control colonoids from 6661, HTO

description: 10X Genomics

value: Control


title: CD4 0hpi RNH+IP donor 1


title: ORSAM12392-1


title: Control colonoids from 6661, GEX

description: 10X Genomics


title: ORSAM11818-1

source_name: adipose-44% fat + fiber-male-CC042/GeniUncJ x CC040/TauUncJ)F1 -None-rep1

value: CC042/GeniUncJ x CC040/TauUncJ)F1


title: CD4 6hpi RNH-IP donor 1


title: INTS4_R1

description: INTS4 siRNA, replicate 1

value: siRNA


title: CD4 12hpi RNH-IP donor 1


title: ORSAM11815-1

source_name: adipose-10% fat + fiber-male-CC042/GeniUncJ x CC040/TauUncJ)F1 -None-rep1

value: Outbred

value: 10% fat + fiber


title: INTS4_R2

description: INTS4 siRNA, replicate 2


title: Control colonoids from C9, GEX

description: 10X Genomics

value: Colonoid

value: Colon organoid


title: INTS12_R2

description: INTS12 siRNA, replicate 2


title: Control colonoids from C9, HTO

description: 10X Genomics


title: CD4 0hpi RNH-IP donor 1


title: scRNA-seq hPSCs shLUC

city: Shenzhen

first: Andrew

middle: P

last: Hutchins

address: 1088 Xueyuan Rd

department: Bioinformatics

institute: Southern University of Science and Technology

description: sc-RNA-seq

data_processing:
STAR --runRNGseed 42--runThreadN 16 --readFilesCommand zcat --limitSjdbInsertNsj 4000000 --limitOutSJcollapsed 5000000 --outFilterMultimapNmax 100 --winAnchorMultimapNmax 100 --outSAMmultNmax 1 --outSAMtype BAM SortedByCoordinate --twopassMode Basic --soloType Droplet --soloFeatures Gene Velocyto --soloBarcodeReadLength 0  --soloCBwhitelist version3.txt--soloUMIlen 12 --soloCBlen 16 --soloUMIstart 17 $sam_att $genome_hg38 --outFileNamePrefix ss.${out} --readFilesIn ${re} ${bc}
te_count -m genes_tes -g hg38 -i $inp -o ${out}.tsv --sc --strand --se -w version3.txt
Data was processed using scanpy
Normalised using scran
Integrated using harmonypy
Assembly: hg38
Supplementary files format and content: TSV file containing read counts for genes (columns) and barcodes (rows)

source_name: hPSCs H1

growth_protocol: The cell line used in this study was hESCs H1 cell line. hESCs were grown in mTeSR1 (Stemcell technologies: 85850) on pre-coated Matrigel plates (Corning: 354277). The medium was replaced every day. Cells were passaged by single-cell digestion with Accutase (SIGMA: A6964) every 4-5 days.

extract_protocol:
Single cell RNA-seq was performed using the 10x platform, using the manufacturers kits according to their instructions.
Library was generated using the 10x version 3 single cell RNA-seq kit according to the manufacturers instructions

treatment_protocol: The shRNA virus was packaged using PMD2G, PsPAX2 and target plasmid co-transfected into 293T cells. After 36 hours virus was collected, and purified. Two days later puromycin was used to select transfected cells.

value: hPSCs H1

value: Pluripotent Stem Cells

tag: shRNA

value: shRNA targetting LUC


title: ORSAM12395-1

source_name: adipose-10% fat + fiber-female-CC024/GeniUncJ x CC002/UncJ)F1 -None-rep1

value: gonadal fat pad


title: ORSAM11813-1

value: male


title: INTS12_R3

description: INTS12 siRNA, replicate 3

tag: cell line


title: CD4 3hpi RNH-IP donor 1

tag: cell type

value: primary CD4+


title: CD4 6hpi Input donor 1


title: ORSAM11812-1

source_name: adipose-10% fat + fiber-female-CC042/GeniUncJ x CC040/TauUncJ)F1 -None-rep1


title: INTS12_R1

description: INTS12 siRNA, replicate 1


title: ORSAM11809-1

value: CC001/UncJ x CC042/GeniUncJ)F1

value: 44% fat + fiber


title: scRNA-seq hPSCs shHNRNPU

description: sc-RNA-seq

value: shRNA targetting HNRNPU


title: CD4 12hpi Input donor 1

source_name: primary CD4+


title: ORSAM11810-1


title: Sample12

city: Milan

first: Mattia

last: Chiesa

address: Via Parea 4

department: Bioinformatics and Artificial Intelligence facility

country: Italy

institute: Centro Cardiologico Monzino IRCCS

data_processing:
Reads were aligned on human genome reference (GRCh38/hg38 version 104 ) by BWA software (v0.7.1) and mapped reads were used to quantify the gene expression, exploiting FeatureCounts (v2.0.0) .
Assembly: HG38/GRCh38.104
Supplementary files format and content: Tab-delimited text files include raw counts values for each Sample. The header of the files reports gene name and sample identifiers.

source_name: cardiac mesenchymal stromal cells

growth_protocol: The cells were cultured in Bovine Serum Albumin [BSA] Polyvinyl alcohol Essential Lipids medium

extract_protocol:
We extracted total RNA of CM and cMSC, using the total RNA purification kit (Norgen Biotek Corp.) and following the recommended protocol.
High-quality libraries were prepared using the PrepXTM RNA-Seq Library Kit for Illumina platforms.

value: cardiac mesenchymal stromal cells

tag: age

value: Female

tag: condition

value: ACM


title: Sample10


title: Sample11


title: Sample9

value: Healthy Control


title: CD4 0hpi Input donor 1


title: hPSC RNA-seq shMATR3 Repeat 1

description: hESC shMATR3#5 #1

data_processing:
STAR --readFilesCommand zcat --outFilterMultimapNmax 100 --winAnchorMultimapNmax 100 --outMultimapperOrder Random --runRNGseed 777 --outSAMmultNmax 1 --outSAMtype BAM Unsorted --twopassMode Basic --outFilterType BySJout --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --genomeDir hg38_gencode_v32_starsolo/SAindex --sjdbGTFfile gencode.v32.annotation.gtf --runThreadN 24 --readFilesIn ${p1} ${p2} --outFileNamePrefix ${out} --outTmpDir ${out}
te_count -g hg38 -i ${out}Aligned.out.bam --o ${out}tecount.tsv -m genes_tes
Tag counts were GC normalised with EDASeq
Assembly: hg38
Supplementary files format and content: genes_ntc_expression.tsv.gz: TSV file containing ensembl gene number, gene symbol, and the mean of the normalised tag count for replicate samples
Supplementary files format and content: genes_ntc_expression_nonmerged.tsv.gz:  TSV file containing ensembl gene number, gene symbol, and the merged normalised tag count for replicate samples

source_name: cell line

extract_protocol:
RNA was isolated using RNAzol RT (MRC, RN190) according to the manufacturer’s protocol and prepared for sequencing with RNA-seq NEB Next Ultra RNA Library Prep Kit (NEB, #7530). RNA quality was tested using an Agilent 2100 and a minimum RIN score of 8.0 was required for sequencing. Samples were sequenced on an Illumina Novaseq 6000.
RNA-seq NEB Next Ultra RNA Library Prep Kit   cat.7530

value: shRNA targetting MATR3


title: hPSC RNA-seq shMATR3 Repeat 3

description: hESC shMATR3#5 #3


title: ORSAM11805-1

source_name: adipose-44% fat + fiber-male-CC012/GeniUncJ x CC002/UncJ)F1 -None-rep1

tag: tissue

value: CC012/GeniUncJ x CC002/UncJ)F1

value: Outbred


title: CD4 3hpi Input donor 1


title: ORSAM11804-1

tag: genotype


title: Sample8

tag: Sex


title: hPSC RNA-seq shLUC Repeat 8

description: hESC shLuc #8


title: Jurkat 6hpi RNH+IP replicate 2

source_name: Jurkat

value: Jurkat


title: hPSC RNA-seq shMATR3 Repeat 4

description: hESC shMATR3#5 #4

value: hPSCs H1


title: ORSAM11801-1

source_name: adipose-44% fat + fiber-female-CC012/GeniUncJ x CC002/UncJ)F1 -None-rep1

value: female

tag: strain


title: Sample7


title: hPSC RNA-seq shLUC Repeat 7

description: hESC shLuc #7

value: Pluripotent Stem Cells

value: shRNA targetting LUC


title: Jurkat 3hpi RNH+IP replicate 2


title: Sample6

source_name: cardiomyocyte

value: cardiomyocyte


title: ORSAM11797-1

source_name: adipose-10% fat + fiber-male-CC075/UncJ x CC042/GeniUncJ)F1 -None-rep1

value: gonadal fat pad

value: male

value: CC075/UncJ x CC042/GeniUncJ)F1

tag: treatment

value: 10% fat + fiber


title: hPSC RNA-seq shLUC Repeat 6

description: hESC shLuc #6


title: ORSAM11807-1

tag: diet

value: 44% fat + fiber


title: Jurkat 0hpi RNH+IP replicate 2


title: hPSC RNA-seq shMATR3 Repeat 2

description: hESC shMATR3#5 #2


title: ORSAM11796-1

tag: sequencing id


title: Sample5

value: Female


title: hPSC RNA-seq shLUC Repeat 5

description: hESC shLuc #5


title: ORSAM11794-1

source_name: adipose-44% fat + fiber-female-CC075/UncJ x CC042/GeniUncJ)F1 -None-rep1


title: Jurkat 12hpi RNH-IP replicate 2


title: hPSC RNA-seq shLUC Repeat 4

description: hESC shLuc #4


title: Sample4

value: ACM


title: Jurkat 12hpi RNH+IP replicate 2


title: Jurkat 3hpi RNH-IP replicate 2


title: hPSC RNA-seq shLUC Repeat 3

description: hESC shLuc #3


title: Jurkat 6hpi RNH-IP replicate 2


title: Sample3

value: Isogenic Control


title: Sample2


title: Jurkat 0hpi RNH-IP replicate 2


title: ORSAM11792-1

source_name: adipose-10% fat + fiber-female-CC075/UncJ x CC042/GeniUncJ)F1 -None-rep1


title: ORSAM11678-1

source_name: adipose-10% fat + fiber-male-CC024/GeniUncJ x CC002/UncJ)F1 -None-rep1

value: CC024/GeniUncJ x CC002/UncJ)F1


title: ORSAM11790-1


title: hPSC RNA-seq shLUC Repeat 1

description: hESC shLuc #1


title: Sample1


title: Jurkat 6hpi Input replicate 2


title: hPSC RNA-seq shLUC Repeat 2

description: hESC shLuc #2


title: hPSC RNA-seq shHNRNPU#2 Repeat 3

description: hESC shHNRNPU#2 #3

value: shRNA targetting HNRNPU


title: Jurkat 12hpi Input replicate 2


title: ORSAM11676-1

value: Outbred


title: hPSC RNA-seq shHNRNPU#2 Repeat 2

description: hESC shHNRNPU#2 #2


title: ORSAM11675-1

source_name: adipose-44% fat + fiber-male-CC024/GeniUncJ x CC002/UncJ)F1 -None-rep1


title: Jurkat 3hpi Input replicate 2

value: Jurkat


title: Jurkat 0hpi Input replicate 2


title: ORSAM11672-1


title: Jurkat 6hpi RNH+IP replicate 1


title: Jurkat 12hpi RNH+IP replicate 1


title: hPSC RNA-seq shHNRNPU#1 Repeat 3

description: hESC shHNRNPU#1 #3

value: hPSCs H1


title: Whole_Scr_3

city: Utrecht

first: Ronald

middle: Jeroen

last: Pasterkamp

state: Utrecht

address: Universiteitsweg 100

department: Translational Neuroscience

country: Netherlands

institute: University Medical Center Utrecht

data_processing:
Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline RTA v2.7.3 and Bcl2fastq v2.17.
Quality filtered sequencing tags were stored as Raw data for further analysis. Adaptor reads were trimmed using Trimmomatic v0.30.
Reads were mapped to mouse mm10 genome using Tophat2. From the mapped reads transcripts were assembled using Cufflinks.
Differential gene expression analysis was performed using Ciffdiff (Cufflinks package).
Assembly: GRCm38 (mm10)
Supplementary files format and content: FPKM, count tables, gene annotation files and differential gene expression as .txt files

growth_protocol: Mouse N2A neuroblastoma cells (ATCC: CCL-131™). Cells were cultured in Dulbecco's modified Eagle's medium (DMEM), containing 10% FBS (Invitrogen, Carlsbad, CA) and penicillin/streptomycin (100 U/ml and 100 mg/ml, respectively) at 37oC and 5% CO2.

extract_protocol:
Cellular fractionation was performed to isolate cell nucleus and immunoprecipitation was performed as described previously (Vangoor et al., JNeu. 2019).
Three samples per group were used for RNA sequencing. The NEBNext Ultra Directional RNA Library Prep Kit for Illumina was used to process the samples. Sample preparation was performed according to NEBNext Ultra Directional Library Prep Kit for Illumina (NEB #E7420S/L) protocol. Briefly, by using the oligo-dT magnetic beads mRNA was isolated from total RNA, followed by fragmentation of the mRNA and cDNA synthesis. The resulting cDNA was ligated with the sequencing adapters and PCR amplification. The yield and quality of the samples was estimated using a Fragment analyzer, where the size of the resulting products was consistent with the size distribution showing a broad peak between 300 – 500 bp. Subsequently, clustering and DNA sequencing was performed using the Illumina cBot and HiSeq 4000, according to the manufacturer’s protocol. HiSeq control software HCS v3.3.52 was used. The sequencing experiments were performed at GenomeScan B.V., Leiden, The Netherlands.

treatment_protocol: For immunoprecipitation, 25 cm plates at ∼80–90% confluence were transfected with biotinylated mimics (25 nM final concentration) and 120 ml of TransIT-X2 Dynamic Delivery System (Mirus), to reach approximately ∼85-90% transfection efficiency.

value: Neuroblastoma

value: WT

value: Scramble overexpression


title: hPSC RNA-seq shHNRNPU#1 Repeat 2

description: hESC shHNRNPU#1 #2

value: Pluripotent Stem Cells


title: Whole_92b_3

value: miR92b overexpression


title: ORSAM11677-1

value: gonadal fat pad

value: male


title: hPSC RNA-seq shHNRNPU#1 Repeat 1

description: hESC shHNRNPU#1 #1


title: ORSAM11558-1

source_name: adipose-44% fat + fiber-male-CC011/UncJ x CC005/TauUncJ)F1 -None-rep1

value: CC011/UncJ x CC005/TauUncJ)F1


title: Jurkat 3hpi RNH+IP replicate 1


title: hPSCs Input RNA (RIP-seq) repeat 1

description: RIP-seq

data_processing:
STAR --outFilterMultimapNmax 100 --winAnchorMultimapNmax 100 --outMultimapperOrder Random --runRNGseed 777 --outSAMmultNmax 1 --outSAMtype BAM Unsorted --twopassMode Basic --outFilterType BySJout --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000
te_count -g hg38 -i ${out}Aligned.out.bam --o ${out}tecount.tsv -m genes_tes
Assembly: hg38
Supplementary files format and content: TSV file containing the Ensembl gene name, gene symbol, transcript type and normalized tag counts per million reads (CPM) for the indicated RIP-seq samples

growth_protocol: The cell line used in this study was hESCs H1 cell line. hESCs were grown in mTeSR1 (Stemcell technologies: 85850) on pre-coated Matrigel plates (Corning: 354277). The medium was replaced every day. Cells were passaged by single-cell digestion with Accutase (SIGMA: A6964) every 4-5 days. 293T cells were grown in FBS supplemented with 10% FBS.

extract_protocol:
Briefly, 5 million cells were lysis with protein lysis buffer (adding 0.2U of RiboLock RNase Inhibitor (Thermo, EO0381)). The lysate was incubator with HNRNPU antibody in 4 degrees overnight. Then add appropriate amount Protein A/G Magnetic Beads into the lysate incubate another 4 hours. Using the magnetic Beads immunoprecipitated the HNRNPU protein and interested RNA. The production was treated with DNase and proteinase K. RNA was isolated using TRIzol for next generation sequencing.
RNA-seq NEB Next Ultra RNA Library Prep Kit   cat.7530

treatment_protocol: No special treatment was performed

tag: antibody


title: Whole_Control_3

value: Control


title: Jurkat 0hpi RNH+IP replicate 1


title: ESCC_TE15_siCD63_rep1

type: RNA

city: Chiba-Shi

first: Yasunori

last: Matsumoto

state: Chiba

address: 1-8-1 Inohana, Chuo-Ku

department: Frontier Surgery

country: Japan

institute: Chiba University

hyb_protocol: A quantity of 600 ng of cRNA was aliquoted and hybridized to the microarray. Hybridization was performed using Expression Hybridization kit (Agilent) for 17 hours (65°C, 10 rpm).

scan_protocol: After hybridization, the microarrays were washed and scanned with an Agilent DNA Microarray Scanner (Agilent).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 072363_D_F_20150611) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: total RNA_TE15_siCD63_48h

label_protocol: The one-color method was performed according to Agilent's recommended one-color protocol (One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labelling), ver6.9, December 2015)). 100 ng of total RNA was mixed with spike-in controls using an Agilent One Color Spike Mix Kit (Agilent).  Quick-Amp Labelling Kit (Agilent) was used for labeling.

growth_protocol: After the following treatment, TE2 and TE15 cells were cultured for 48 hours in Dulbecco’s Modified Eagle’s Medium (DMEM) (Life Technologies, Grand Island, NY) supplemented with 10% fetal bovine serum (FBS), 100 units/ml penicillin G sodium and 100 μg/ml streptomycin in a humidified atmosphere containing 5% CO2 at 37°C.

extract_protocol: The total RNA was extracted using the RNeasy Plus Mini Kit (QIAGEN) according to the operation procedures.

treatment_protocol: TE2 and TE15 cells were seeded into a 6- well plate at a density of 2 × 10^5 cells/well and transfected with 30 pmol siRNA using the Lipofectamine™ RNAiMAX Transfection Reagent (Thermo Fisher Scientific, Cat No. 13778150) following the manufacturer’s protocol. Silencer negative control siRNA was employed concurrently. The siRNAs used were as follows: siCD63: OriGene CD63 siRNA (cat No. SR300689A), siControl: Invitrogen, Negative Control Duplex medium GCDuplex #2 (cat No. 12935-112)

value: human esophageal  squamous cell carcinoma


title: Nuc_92b_3


title: hPSCs anti-IgG (RIP-seq) repeat 2

description: RIP-seq

source_name: hPSCs H1

value: anti-IgG


title: ESCC_TE2_siCD63_rep1

source_name: total RNA_TE2_siCD63_48h


title: ORSAM11557-1

source_name: adipose-44% fat + fiber-female-CC011/UncJ x CC005/TauUncJ)F1 -None-rep1

value: female

value: 44% fat + fiber


title: Jurkat 12hpi RNH-IP replicate 1


title: hPSC RNA-seq shHNRNPU#2 Repeat 1

description: hESC shHNRNPU#2 #1

value: shRNA targetting HNRNPU


title: Nuc_Scr_3


title: ORSAM11556-1

value: Outbred


title: ORSAM11674-1

value: CC024/GeniUncJ x CC002/UncJ)F1


title: ESCC_TE2_siCont_rep1

source_name: total RNA_TE2_siCont_48h

value: siCont


title: ORSAM11559-1


title: hPSCs anti-IgG (RIP-seq) repeat 1

description: RIP-seq

value: hPSCs H1


title: Nuc_Control_3

value: Neuroblastoma

value: WT


title: ESCC_TE15_siCont_rep1

source_name: total RNA_TE15_siCont_48h


title: hPSCs anti-HNRNPU (RIP-seq) repeat 2

description: RIP-seq

value: Pluripotent Stem Cells

value: anti-HNRNPU


title: ORSAM11552-1

source_name: adipose-10% fat + fiber-male-CC011/UncJ x CC027/GeniUncJ)F1 -None-rep1

value: gonadal fat pad

value: CC011/UncJ x CC027/GeniUncJ)F1

value: 10% fat + fiber


title: Jurkat 6hpi RNH-IP replicate 1

value: Jurkat


title: hPSCs anti-HNRNPU (RIP-seq) repeat 1

description: RIP-seq


title: Whole_92b_2

value: miR92b overexpression


title: Whole_Scr_2

value: Scramble overexpression


title: ORSAM11551-1

value: male


title: 293T Input RNA (RIP-seq) repeat 1

description: RIP-seq


title: Jurkat 12hpi Input replicate 1


title: Whole_Control_2

value: Control


title: ORSAM11475-1

source_name: adipose-44% fat + fiber-male-CC002/UncJ x CC043/GeniUncJ)F1 -None-rep1

value: CC002/UncJ x CC043/GeniUncJ)F1

value: 44% fat + fiber


title: Jurkat 6hpi Input replicate 1

source_name: Jurkat


title: ORSAM11474-1

value: Outbred


title: Nuc_92b_2


title: ORSAM11554-1

value: female

value: CC011/UncJ x CC005/TauUncJ)F1


title: Nuc_Scr_2

value: Neuroblastoma


title: Jurkat 0hpi Input replicate 1


title: 293T anti-HNRNPU (RIP-seq) repeat 1

description: RIP-seq


title: ORSAM11473-1

source_name: adipose-10% fat + fiber-male-CC002/UncJ x CC043/GeniUncJ)F1 -None-rep1


title: 293T anti-HNRNPU (RIP-seq) repeat 2

description: RIP-seq


title: Jurkat 3hpi Input replicate 1


title: Nuc_Control_2

value: WT


title: ORSAM11472-1


title: hPSC MAR-seq Repeat #2

description:
MAR-seq
Hs_mar_hesc.bed.gz

data_processing:
cutadapt -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -A CTGTCTCTTATACACATCTGACGCTGCCGACGA --quality-cutoff 10 -m 50 -o ${bn}.trim.p1.fq.gz -p ${bn}.trim.p2.fq.gz ${p1} ${p2}
bowtie2 $opts -x /export/genomic/hg38/bowtie2-indeces/hg38 -1 ${p1} -2 ${p2} | grep -E -v 'chrM|chrUn|random|RANDOM|alt' | samtools view -b -q 20 -F 1804 -f 2 | samtools sort -n >${out}.bam
macs2 callpeak -q 0.05 -t ${f} -n ${bn} -g hs -f BEDPE # &>${bn}.err
redefine_peaks() from glbase3
bamCoverage -p 4 --normalizeUsing CPM --minMappingQuality 30 --ignoreDuplicates -b ${in} -o ${out}
Assembly: hg38
Supplementary files format and content: Processed files are BED format data, containing hg38 genome coordinates for the two samples after redefine_peaks was used, and bigWig binary track traces
Library strategy: MAR-seq

extract_protocol:
Briefly, 90% confluence cells were washed 3 time with DPBS on the cell culture plate. We using the cytoskeletal (CSK) extraction buffer (100 mM NaCl, 1 mM EGTA, 10 mM PIPES pH 6.8, 3 mM MgCl2, 300 mM sucrose, 0.5% v/v Triton X-100) isolate the unclears in the plate. Nuclear was crosslinked with 1% formaldehyde for 10 min at room temperature. Nuclear was digest with MspI, HaeIII, RsaI, AluI, BamHI, PvuII restriction enzymes. The nuclear was reverse crosslinked by incubate in 65 degrees overnight. DNA was extracted from the isolated nuclear matrix and the input sample. DNA was recovered by extraction with phenol: chloroform: isoamyl alcohol (25:24:1) and ethanol precipitation. The isolated input DNA was fragmented by using a Bioruptor®Plus sonication device (Diagenode) to obtain the desired DNA fragment size (enriched at 300 bp). The libraries were sequenced at Novogene via a Novaseq instrument in 150bp paired-end mode.
Libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina

value: hPSCs H1

value: Pluripotent Stem Cells


title: HeLa 12hpi RNH+IP replicate 2

source_name: HeLa

value: HeLa


title: ORSAM11471-1

data_processing:
raw counts quantified by EMASE and processed by /RNAseq/Raw/GBRS/QTLViewer_setup/gathering_GBRS_total_counts.R script and gathering_GBRS_total_counts_batch2.R.
counts normalized by DESeq2 vst() function (quick version of variance stabilizing transformation).
Matrix generated by /RNAseq/Raw/GBRS/QTLViewer_setup/Processing_normalization.R and Processing_normalization_batch2.R scripts.
gene annotation file ENSEMBL version 84
Assembly: GRCm38

source_name: adipose-44% fat + fiber-female-CC002/UncJ x CC043/GeniUncJ)F1 -None-rep1

extract_protocol:
RNA was isolated from tissue using the MagMAX mirVana Total RNA Isolation Kit (ThermoFisher) and the KingFisher Flex purification system (ThermoFisher). Frozen tissues were pulverized using a Bessman Tissue Pulverizer (Spectrum Chemical) and homogenized in TRIzol (ThermoFisher Scientific) using a gentleMACS dissociator (Miltenyi Biotec Inc). After the addition of chloroform to the TRIzol homogenate, the RNA-containing aqueous layer was removed for RNA isolation, according to the manufacturer’s protocol, beginning with the RNA bead binding step. RNA concentration and quality were assessed using the Nanodrop 8000 spectrophotometer (Thermo Scientific) and the RNA 6000 Pico or RNA ScreenTape assay (Agilent Technologies).
2 ul of diluted (1:1000) ERCC Spike-in Control Mix 1 (Ambion by Life Technologies) was added to 100ng of each RNA sample prior to library construction.  Libraries were constructed using the KAPA mRNA HyperPrep Kit (Roche Sequencing and Life Science), according to the manufacturer’s protocol.  Briefly, the protocol entails isolation of polyA containing mRNA using oligo-dT magnetic beads, RNA fragmentation, first and second strand cDNA synthesis, ligation of Illumina-specific adapters containing a unique barcode sequence for each library, and PCR amplification.  The quality and concentration of the libraries were assessed using the D5000 ScreenTape (Agilent Technologies) and Qubit dsDNA HS Assay (ThermoFisher), respectively, according to the manufacturers’ instructions. ibraries were sequenced on an Illumina NovaSeq 6000 using the S4 Reagent Kit. Libraries were sequenced 100 bp paired-end to a targeted read depth of 30 million read pairs.

value: gonadal fat pad


title: Jurkat 0hpi RNH-IP replicate 1


title: Whole_92b_1


title: hPSC MAR-seq Repeat #1

description:
MAR-seq
Hs_mar_hesc.bed.gz


title: HeLa 6hpi RNH+IP replicate 2


title: ORSAM11470-1


title: HiC hPSC shLUC Repeat 2

description: Hi-C

data_processing:
Reads were aligned using bowtie2
Hi-C matrices were generated using te_hic
Matrices were balanced usng ICE from the cooler package
TopDom (v0.3.2) was used to call TADs
Assembly: hg38
Supplementary files format and content: BED files for gaps, boundaries and domains

source_name: cell line

extract_protocol:
The cell was digested into single cell with accutase. Cell was washed three times with DPBS and crosslinked with 1% formaldehyde for 10 min at room temperature. The chromatin was digested with HindIII restriction enzyme, the biotinylated dATP was ligated in to the overhang site which generated by HindIII digestion. After reversal of crosslinks, the genome DNA was purified and sheared, the fragment was select around 300-500bp, the point ligation junctions with biotinylated dATP were pulled down with streptavidin beads and prepped for Illumina sequencing.
Libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina

value: cell line

value: shRNA targetting LUC


title: ORSAM11468-1

source_name: adipose-10% fat + fiber-female-CC002/UncJ x CC043/GeniUncJ)F1 -None-rep1

value: 10% fat + fiber


title: Whole_Control_1


title: HeLa 0hpi RNH+IP replicate 2


title: 293T anti-IgG (RIP-seq) repeat 1

description: RIP-seq

value: anti-IgG


title: ORSAM11467-1


title: HeLa 12hpi RNH-IP replicate 2


title: ORSAM11466-1

source_name: adipose-10% fat + fiber-male-CC012/GeniUncJ x CC002/UncJ)F1 -None-rep1

value: male

value: CC012/GeniUncJ x CC002/UncJ)F1


title: Nuc_92b_1

value: miR92b overexpression


title: HiC hPSC shHNRNPU Repeat 2

description: Hi-C

value: shRNA targetting HNRNPU


title: Nuc_Scr_1

value: Scramble overexpression


title: HeLa 6hpi RNH-IP replicate 2


title: HiC hPSC shHNRNPU Repeat 1

description: Hi-C


title: ORSAM11464-1

source_name: adipose-44% fat + fiber-male-CC051/TauUncJ x CC019/TauUncJ)F1 -None-rep1

value: CC051/TauUncJ x CC019/TauUncJ)F1

value: Outbred

value: 44% fat + fiber


title: HeLa 3hpi RNH-IP replicate 2


title: HNRNPU (CUT&TAG) repeat 2

data_processing:
cutadapt -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -A CTGTCTCTTATACACATCTGACGCTGCCGACGA --quality-cutoff 10 -m 50 -o ${bn}.trim.p1.fq.gz -p ${bn}.trim.p2.fq.gz ${p1} ${p2}
bowtie2 $opts -x /export/genomic/hg38/bowtie2-indeces/hg38 -1 ${p1} -2 ${p2} | grep -E -v 'chrM|chrUn|random|RANDOM|alt' | samtools view -b -q 20 -F 1804 -f 2 | samtools sort -n >${out}.bam
macs2 callpeak -q 0.05 -t ${f} -n ${bn} -g hs -f BEDPE # &>${bn}.err
bamCoverage -p 4 --normalizeUsing CPM --minMappingQuality 30 --ignoreDuplicates -b ${in} -o ${out}
Assembly: hg38
Supplementary files format and content: Processed files are BED format data, containing hg38 genome coordinates for peaks in the indicated sample, and bigWig binary track traces
Library strategy: CUT&Tag

extract_protocol:
Briefly, 1 × 105 cells were washed twice with wash buffer (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 0.5 mM spermidine and 1× protease inhibitors). Then cells were bound to concanavalin A beads (Bangs Laboratories, BP531) followed by activated with binding buffer (20 mM Tris-HCl pH 7.4, 10 mM KCl, 1 mM CaCl2 and 1mM MnCl2). The bead-bound cells were wash once with wash buffer containing 0.01% digitonin, and primary antibodies were added to bead-bound cells in antibody buffer (4 mM EDTA and 0.2% BSA in wash buffer containing 0.01% digitonin) and rotated overnight at 4 °C. The primary antibodies used: anti-HNPNPU (Abcam, ab172608), anti-MATR3 (Abcam, ab264136), anti-H3K27ac (Abcam, ab4279), anti-H3K27me3 (Millipore, 07-449,) Then, secondary antibody (Antibodies-Online, ABIN101961) was added to bead-cells-antibody in wash buffer and further incubated at RT for 1h. pG-Tn5 (Vazyme, S603-02) was add to cells in 300-wash buffer (20 mM Tris-HCl pH 7.4, 300 mM NaCl, 0.5 mM spermidine and 1× protease inhibitors, 0.01% digitonin) at RT for 1h. The Tn5 was activated with 300-wash buffer supplemented with 10 mM MgCl2 and washed five times with 500 ul 300-wash buffer. To stop the Tn5 reaction, 10 ul of 0.5 M EDTA, 3 ul of 10% SDS and 1.5 ul of proteinase K (20 mg/ml) were added 55°C for 1 h. DNA fragments were extracted and PCR amplification using NEBNext HiFi 2× PCR Master mix (NEB, M0541L) with the conditions: 72°C, 5 min, 98°C, 30s and 12-14 cycle for 98°C, 10s, 63°C, 10s and 72°C, 30s. The 300-500bp DNA fragments were purified with the VAHTS DNA Clean Beads (Vazyme, N411-02). Libraries were sequenced by an Illumina sequencer.
Libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina


title: Nuc_Control_1

value: Neuroblastoma

value: WT

value: Control


title: HeLa 0hpi RNH-IP replicate 2

value: HeLa


title: ORSAM11462-1

value: gonadal fat pad


title: Whole_Scr_1


title: HNRNPU (CUT&TAG) repeat 1

value: hPSCs H1

value: Pluripotent Stem Cells


title: Liver_ZT10_3HAKI_anti-HA_ChIP-seq-rep3

first: KUN

last: ZHU

state: PA

address: 3400 Civic Center Blvd, SCTR-12-196

institute: University of Pennsylvania

description:
3HA-REV-ERBalpha_ChIP-seq_ZT10_pooled.norm.bw
3HA-REV-ERBalpha_ChIP-seq_ZT10_pooled.narrowPeak

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq/Hiseq output.
ChIP-seq reads were trimmed by cutadapt v2.3
ChIP-seq reads were aligned to mm10 by bwa 0.7.17
Read duplicates and low MAPQ (<=30) were removed by picard 2.18.12 and samtools 1.9, respectively
MACS2 2.1.2 was used to call peaks. Peak intensity was calculated by multiBigwigSummary module from deepTools 3.3.0
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak

source_name: Liver

extract_protocol:
Isolated Liver nuclei were fixed with 1% formaldehyde for 10 minutes and followed by 45 min 1.5 mM EGS. After quenching and cell lysis, chromatin was sheared by probe sonicator.
ChIP-seq libraries were prepared by Tn5-mediated tagmentation and adapter ligation. Adapted DNA was amplified by PCR and size selected for final sequencing.

value: Liver

value: Pierce™ Anti-HA Magnetic Beads

tag: vendor

value: Thermo Fisher

tag: cat#

tag: circadian time

tag: aav virus_combinational_injection


title: Liver_ZT10_3HAKI_anti-HA_ChIP-seq-rep4


title: ORSAM11461-1

value: male


title: ORSAM11460-1

source_name: adipose-10% fat + fiber-male-CC051/TauUncJ x CC019/TauUncJ)F1 -None-rep1

value: 10% fat + fiber


title: H3K27ac (CUT&TAG) shLUC repeat 2

source_name: hPSCs H1

tag: shRNA

value: shRNA targetting LUC


title: Liver_ZT10_3HAKI_anti-HA_ChIP-seq-rep2


title: HeLa 3hpi RNH+IP replicate 2


title: HiC hPSC shLUC Repeat 1

description: Hi-C

value: cell line

tag: cell line


title: HeLa 6hpi Input replicate 2

tag: cell type


title: H3K27ac (CUT&TAG) shLUC repeat 1


title: ORSAM11458-1

value: CC051/TauUncJ x CC019/TauUncJ)F1


title: H3K4me1 (CUT&TAG) shLUC repeat 2


title: HeLa 12hpi Input replicate 2


title: HeLa 0hpi Input replicate 2


title: ORSAM11457-1

value: Outbred


title: ORSAM11455-1

source_name: adipose-44% fat + fiber-female-CC051/TauUncJ x CC019/TauUncJ)F1 -None-rep1

value: female

value: 44% fat + fiber


title: H3K4me1 (CUT&TAG) shLUC repeat 1


title: ORSAM11453-1

source_name: adipose-10% fat + fiber-male-CC019/TauUncJ x CC075/UncJ)F1 -None-rep1

value: CC019/TauUncJ x CC075/UncJ)F1


title: Liver_ZT10_3HAKI_anti-HA_ChIP-seq-rep1


title: H3K27ac (CUT&TAG) shHNRNPU#2 repeat 2

value: shRNA targetting HNRNPU


title: Liver_ZT22_3HAKI_anti-HA_ChIP-seq-rep4

description:
3HA-REV-ERBalpha_ChIP-seq_ZT22_pooled.norm.bw
3HA-REV-ERBalpha_ChIP-seq_ZT22_pooled.narrowPeak


title: Liver_ZT22_3HAKI_anti-HA_ChIP-seq-rep2


title: HeLa 6hpi RNH+IP replicate 1

value: HeLa


title: ORSAM11451-1

source_name: adipose-10% fat + fiber-female-CC019/TauUncJ x CC075/UncJ)F1 -None-rep1

value: gonadal fat pad


title: ORSAM11452-1


title: H3K27ac (CUT&TAG) shHNRNPU#2 repeat 1

value: hPSCs H1


title: H3K27ac (CUT&TAG) shHNRNPU#1 repeat 2

value: Pluripotent Stem Cells


title: HeLa 3hpi RNH+IP replicate 1


title: Liver_ZT22_3HAKI_anti-HA_ChIP-seq-rep1

value: Liver


title: Liver_ZT10_Ctrl_anti-HA_ChIP-seq

value: Pierce™ Anti-HA Magnetic Beads


title: HeLa 0hpi RNH+IP replicate 1


title: H3K27ac (CUT&TAG) shHNRNPU#1 repeat 1


title: ORSAM10477-1

source_name: adipose-10% fat + fiber-male-CC001/UncJ x CC042/GeniUncJ)F1 -None-rep1

value: CC001/UncJ x CC042/GeniUncJ)F1


title: Liver_ZT10_Ctrl_Input_ChIP-seq


title: HeLa 3hpi Input replicate 2


title: HeLa 12hpi RNH-IP replicate 1


title: ORSAM10476-1

value: male


title: Liver_ZT22_3HAKI_anti-HA_ChIP-seq-rep3

value: Thermo Fisher


title: Liver_ZT10_anti-CTCF_In-situ_ChIA-PET

data_processing:
In-situ ChIA-PET fastq reads was processed by ChIA-PIPE tool V1.0
Assembly: mm10
Supplementary files format and content: bigWig, BE3

extract_protocol:
Isolated liver nuclei were fixed with 1% formaldehyde for 10 minutes and followed by 45 min 1.5 mM EGS. After quenching and cell lysis, nuclei were permeabilized by 0.1%SDS at 62 degree for 10min, 37 degree for 20 min, 0.55% SDS at RT for 1h. The nuclei were digested by AluI enzyme and re-ligated by T4 DNA ligase sequentially. Ligated chromatin was sheared by probe sonicator.
Sheared DNA was pulldown by a specific antibody; Immunoprecipied DNA was subjected to Tn5 tagmentation, M280 Dynabeads streptavidin pull-down and PCR amplification; PCR products were subjected to size-selection and pair-end sequencing on Illumina Hiseq or Novaseq platform.

value: anti-CTCF

value: Abcam


title: H3K4me1 (CUT&TAG) shHNRNPU#2 repeat 1


title: HeLa 12hpi RNH+IP replicate 1


title: Liver_ZT22_anti-CTCF_In-situ_ChIA-PET


title: HeLa 6hpi RNH-IP replicate 1


title: ORSAM10474-1

value: 10% fat + fiber


title: H3K4me1 (CUT&TAG) shHNRNPU#1 repeat 2


title: HeLa 3hpi RNH-IP replicate 1


title: ORSAM10471-1

source_name: adipose-44% fat + fiber-female-CC001/UncJ x CC042/GeniUncJ)F1 -None-rep1

value: Outbred


title: H3K4me1 (CUT&TAG) shHNRNPU#1 repeat 1


title: Liver_ZT10_anti-HA_In-situ_ChIA-PET


title: ATAC-seq shLUC #1 repeat 2

data_processing:
cutadapt -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -A CTGTCTCTTATACACATCTGACGCTGCCGACGA --quality-cutoff 10 -m 50 -o ${bn}.trim.p1.fq.gz -p ${bn}.trim.p2.fq.gz ${p1} ${p2}
bowtie2 $opts -x /export/genomic/hg38/bowtie2-indeces/hg38 -1 ${p1} -2 ${p2} | grep -E -v 'chrM|chrUn|random|RANDOM|alt' | samtools view -b -q 20 -F 1804 -f 2 | samtools sort -n >${out}.bam
macs2 callpeak -q 0.05 -t ${f} -n ${bn} -g hs -f BEDPE # &>${bn}.err
bamCoverage -p 4 --normalizeUsing CPM --minMappingQuality 30 --ignoreDuplicates -b ${in} -o ${out}
Assembly: hg38
Supplementary files format and content: Processed files are BED format data, containing hg38 genome coordinates for peaks in the indicated sample, and bigWig binary track traces

extract_protocol:
Briefly, nuclei from 50,000 cells were extracted with lysis buffer (10 mM Tris-HCl pH 7.4 10 mM NaCl, 3 mM MgCl2, and 0.2% (v/v) IGEPAL CA-630).  Tagmentation reactions were performed by addition of 50 ul reaction mix of the TruePrep DNA Library Prep Kit (Vazyme, TD502) according to the manufacturer’s instructions. DNA fragments were cleaned up using the MinElute PCR Purification Kit (Qiagen, 28004). ATAC-seq libraries were amplified with PCR for an appropriate number of cycles 17 and the sequence index was added by TruePrep® Index Kit V2 for Illumina (Vazyme, TD202). The amplified DNA libraries were purified using the VAHTS DNA Clean Beads (Vazyme, N411-02) and sequenced on an Illumina sequencer.
ATAC-seq library was generated using the Tn5 enzyme from the TruePrep DNA Library Prep Kit V2 (Vazyme, TD501-02) as previously described (Buenrostro et al., 2013). Briefly, a total of ~50,000 cells were washed once with 50 μl of cold PBS and resuspended in 50 μl lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.2% (v/v) IGEPAL CA-630). The nuclei were centrifuged for 10 min at 500 × g at 4 °C, followed by the addition of 50 μl transposition reaction mix (25 μl TD buffer, 2.5 μl Tn5 transposase (Vazyme) and 22.5 μl nuclease-free water). Samples were PCR amplified and purified using a MinElute kit (Qiagen).

value: shRNA targetting LUC


title: ORSAM10468-1

value: female

value: CC051/TauUncJ x CC019/TauUncJ)F1

value: 44% fat + fiber


title: ORSAM10470-1


title: Liver_ZT22_anti-HA_In-situ_ChIA-PET


title: HeLa 6hpi Input replicate 1

data_processing:
DRIPc-seq reads were quality-controlled using FastQC v0.11.9, and sequencing adapters were trimmed using Trim Galore! V0.6.6 based on Cutadapt v2.8.
Trimmed reads were aligned to the hg38 reference genome using bwa v0.7.17-r1188.
Assembly: hg38
Supplementary files format and content: BED
Library strategy: DRIPc-seq

extract_protocol:
The corresponding cells were harvested and their gDNA was extracted by using standard phenol-chloroform extraction and resuspended in DNase/RNase-free water
anti-S9.6 immunoprecipitaed materials were digested with DNase I and the RNA were reverse transcribed with dUTP for library construction. cDNA were sonicated and processed to end repair and dA tailing. Adopter ligated then materials  were amplified with illumina PCR primers, 1.0 P5 and 2.0 P7. Amplicons were treated with Uracil N-Glycosylase.

value: HeLa


title: HeLa 12hpi Input replicate 1


title: ATAC-seq shLUC #1 repeat 1


title: H3K4me1 (CUT&TAG) shHNRNPU#2 repeat 2

value: shRNA targetting HNRNPU


title: WT_IP_Rep3

city: Beijing

first: Tang

last: RenkunTang

state: (optional)

address: Xiangshan, Haidian District

institute: Institute of Botany, Chinese Academy of Sciences

data_processing:
For m6A-seq data analysis, the quality of clean reads was assessed using FastQC.
Sequencing reads were mapped to the F. vesca whole genome v4.0.a2 using HISAT2.
Peak calling and differential peak analysis were carried out by a R package exomePeak with a criterion of enrichment fold change ≥ 1.5 and P value < 0.05.
ANNOVAR was applied to annotate peaks using the strawberry genome annotation file.
StringTie was employed for calculating fragments per kilobase of exon per million mapped fragments (FPKM).
Assembly: GCF_000184155.1
Supplementary files format and content: Tab-delimited tsv files include called peaks for each Sample
Supplementary files format and content: Tab-delimited tsv files include FPKM valus for each Sample

organism: Fragaria vesca

source_name: Fruit

extract_protocol:
Total RNA was extracted with the plant RNA extraction kit (Magen, R4165-02) from diploid strawberry fruit of WT and Fvalkbh10b, respectively. mRNA was isolated from the total RNA and then fragmented, followed by immunoprecipitation with specific anti-m6A antibody (Synaptic Systems, 202003).
For library construction, 50 ng of immunoprecipitated mRNAs or pre-immunoprecipitated mRNAs (input control) were used for library construction with NEBNext ultra RNA library prepare kit for illumina (NEB, E7530). High-throughput sequencing was performed on the Illumina NovaSeq 6000 sequencer with a paired-end read length of 150 bp according to the standard protocols.

value: Fruit

tag: rip antibody

value: WT


title: ORSAM10467-1

value: gonadal fat pad


title: ATAC-seq shHNRNPU #2 repeat 2

value: hPSCs H1

value: Pluripotent Stem Cells


title: ORSAM10466-1

source_name: adipose-10% fat + fiber-female-CC051/TauUncJ x CC019/TauUncJ)F1 -None-rep1


title: WT_IP_Rep2


title: WT_IP_Rep1


title: HeLa 3hpi Input replicate 1


title: ORSAM10464-1


title: HeLa 0hpi Input replicate 1


title: ATAC-seq shHNRNPU #2 repeat 1


title: WT_input_Rep2

value: none (input)


title: ORSAM10463-1


title: WT_input_Rep3


title: HeLa 0hpi RNH-IP replicate 1


title: ATAC-seq shHNRNPU #1 repeat 1


title: SAMR1, 2.5 months old, hippocampus 4

first: Letizia

last: Messa

address: Piazza Leonardo Da Vinci 32

department: Electronics, Informatics and Bioengineering

institute: Politecnico di Milano

data_processing:
Quality control of the raw data output were examined on FastQC software
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt software. UMI were detected and extracted with UMI tools
Trimmed sequence reads were mapped to GRCh38.p13 using STAR
Read count extraction was performed using FeatureCounts
Assembly: GRCm38
Supplementary files format and content: txt file for raw counts extracted with FeatureCounts

source_name: hippocampus

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA), according to the manufacturer's instructions. RNA quantity and integrity were estimated using the Qubit instrument (Invitrogen, Carlsbad, CA) and the Agilent 4200 TapeStation System (Agilent, Santa Clara, CA).

value: hippocampus


title: ATAC-seq shHNRNPU #1 repeat 2


title: ORSAM10462-1

source_name: adipose-44% fat + fiber-male-CC051/TauUncJ x CC059/TauUncJ)F1 -None-rep1

value: male

value: CC051/TauUncJ x CC059/TauUncJ)F1


title: SAMR1, 6 months old, hippocampus 4


title: SAMR1, 6 months old, hippocampus 3


title: ORSAM10461-1


title: Fvalkbh10b_IP_Rep3


title: WT_input_Rep1


title: Fvalkbh10b_IP_Rep2


title: SAMR1, 9 months old, hippocampus 2


title: ORSAM10459-1

source_name: adipose-10% fat + fiber-female-CC051/TauUncJ x CC059/TauUncJ)F1 -None-rep1

value: 10% fat + fiber


title: Fvalkbh10b_IP_Rep1


title: SAMR1, 2.5 months old, hippocampus 3


title: miTTC33, 2

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

description: TTC33 knock-down

data_processing:
Trimmomatic, version 0.39, parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:20
hisat2
Genome Analysis Toolkit, version 4.2.3.0, MarkDuplicates --REMOVE_DUPLICATES false --OPTICAL_DUPLICATE_PIXEL_DISTANCE 12000 --REMOVE_SEQUENCING_DUPLICATES true
htseq-count, version 2.0.1, parameters: --type=exon --idattr=gene_id --additional-attr=gene_name --additional-attr=gene_biotype --stranded=reverse --secondary-alignments=ignore
Assembly: Genome_build: grch38
Supplementary files format and content: htseq-count matrix, separate files for paired and unpaired reads

source_name: HEK293Flip-In T-Rex

growth_protocol: HEK293 Flip-In T-Rex cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Hot acid phenol method was used to extract total RNA. Media was discarded from culture media and the cells were washed with PBS. Cells were scrapped and resuspended in PBS. After centrifugation the supernatant was removed and cells were resuspended in 400 μl phenol solution saturated with 0.1 M citrate at pH 4.3 (Sigma; P4682) and throughly mixed. Next 400 μl of TES buffer was added (10 mM Tris pH 7.5, 5 mM EDTA, 1 % SDS). Samples were incubated with shaking at 45 min at 65 °C. After centrifugation at 4 °C for 10 min the supernatant was collected into a fresh tube and 400 μl phenol solution saturated with 0.1 M citrate at pH 4.3 was added. The samples were again incubated with shaking at 65 °C for 20 min and then centrifuged at 4 °C for 10 min. The supernatant was collected into a fresh tube and to remove remnants of phenol 400 μl of chloroform was added (C2432; Sigma). The samples were briefly vortexed at room temperature and centrifuged at 4 °C for 10 min. The supernatant was collected into a fresh tube to proceed with RNA precipitation. 45 μl of 2 M LiCl was added and 1 ml of 95 % ethanol. Samples were precipitated for 24 hours at – 80  °C, centrifuged for 25 min at 4 °C, washed with 400 μl of 80 % ethanol and after removing the supernatant dried at 37 °C. Pellets were resuspended in nuclease-free water and concentration was measured using Nanodrop apparatus.
RNA libraries for RNA-seq were prepared using NovaSeq 6000 S4 Reagent Kit following manufacturer's protocols.

treatment_protocol: Knock-down of proteins of interest was performed by addition of tetracyclin to a final concentration of 100 ng/ml for 3 days on cells seeded to obtain confluency at the end of tetracyclin treatment. Control cells not expressing microRNAs were also treated with tetracyclin.

value: HEK293Flip-In T-Rex

value: Modified human embryonic kidney 293 cells expressing microRNA against TTC33 under tetracyclin inducible promoter

value: Flp-In(TM) T-Rex(TM) 293 Cell line Thermo cat. no. R78007 miTTC33

value: Tetracyclin 100 ng/ml 3 days


title: ORSAM10460-1

value: Outbred

value: 44% fat + fiber


title: SAMR1, 6 months old, hippocampus 2


title: miCCDC97, 3

description: CCDC97 knock-down

value: Modified human embryonic kidney 293 cells expressing microRNA against CCDC97 under tetracyclin inducible promoter

value: Flp-In(TM) T-Rex(TM) 293 Cell line Thermo cat. no. R78007 miCCDC97


title: ORSAM10458-1

value: female


title: Fvalkbh10b_input_Rep3

value: Fruit


title: SAMR1, 2.5 months old, hippocampus 2


title: ORSAM10457-1

value: gonadal fat pad


title: miCCDC97, 2

description: CCDC97 knock-down


title: miTTC33, 1

description: TTC33 knock-down


title: Fvalkbh10b_input_Rep2


title: miTTC33, 3

description: TTC33 knock-down


title: ORSAM10455-1

source_name: adipose-10% fat + fiber-male-CC051/TauUncJ x CC059/TauUncJ)F1 -None-rep1


title: HEK293, 3

description: control to TTC33 and CCDC97 knock-down

value: Modified human embryonic kidney 293 cells

value: Flp-In(TM) T-Rex(TM) 293 Cell line Thermo cat. no. R78007


title: miCCDC97, 1

description: CCDC97 knock-down


title: ORSAM10454-1


title: SAMR1, 2.5 months old, hippocampus 1

value: hippocampus


title: HEK293, 2

description: control to TTC33 and CCDC97 knock-down


title: Input

data_processing:
The clean reads were mapped to the F. vesca whole genome v4.0.a2 annotation using BWA-MEM
Peak identification was performed by MACS2 using default parameters.
Binding motifs in the peak region were discovered by MEME-ChIP
depTools2 was used for calculating the distribution frequency of peaks near the transcription start site (TSS) and plotting the distribution of peaks on chromosomes.
Assembly: GCF_000184155.1
Library strategy: DAP-seq

extract_protocol:
The strawberry fruit samples were fully ground with liquid nitrogen, and then 5 g powder was weighed and dissolved in Nuclei isolation Buffer (15 mM Tris-HCl, pH 6.8, 5 mM MgCl, 60 mM KCl, 15 mM NaCl, 1 mM CaCl, 1 mM EDTA, pH 8.0, 1 mM PMSF, 0.25 M Sucrose, 0.9% Triton X-100) to isolate cell nucleus. The genome DNA from the cell nucleus was extrated using the standard CTAB method.
A genomic DNA library of Fragaria vesca was performed by a NEBNext DNA Library Prep Master Mix Set Kit for Illumina (NEB, USA, No. E7645L) following the manufacturer's protocol.


title: IP_Rep2


title: ORSAM10453-1

value: male


title: SAMR1, 9 months old, cortex 3

source_name: cortex

value: cortex


title: IP_Rep1


title: HEK293, 1

description: control to TTC33 and CCDC97 knock-down


title: SAMR1, 6 months old, hippocampus 1


title: ORSAM10449-1

source_name: adipose-44% fat + fiber-male-CC043/GeniUncJ x CC011/UncJ)F1 -None-rep1

value: CC043/GeniUncJ x CC011/UncJ)F1


title: Stage4_PDA_R3_Fg

city: East Lansing

first: Frances

last: Trail

state: Michigan

address: 612 Wilson Road

department: Plant Biology

institute: Michigan State University

data_processing:
Base calling was done by Illumina Real Time Analysis (RTA) v2.7.7 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.20.0. The low-quality reads were removed using the read filtering tool, Trimmomatic, Version 0.39. The 3’ ends of NovaSeq6000 single-end 100 bp reads were trimmed to 50 bp reads (keeping the first 50 bp) using Trimmomatic Version 0.39.
The trimmed reads were mapped to the indexed F. graminearum  reference sequences using HISAT 2.2.1.
The HISAT alignments in SAM format were then sorted and converted to BAM format using SAM tools.
Count files were then generated using HTSeq Version 0.11.1.
The DESeq2 package Version 1.30.1 in R was used to normalize the read counts and to perform differential expression analysis.
Assembly: The reference sequence used for the alignment are Fusarium graminearum PH-1 (GCA_900044135.1).
Supplementary files format and content: Tab-demilited text file includes raw counts for each sample

organism: Fusarium graminearum

source_name: Germinated conidia

growth_protocol: For total RNA extraction of each germination stage on standard medium (potato dextrose agar), a 200 µL aliquot of the conidial suspension (1 x 106 conidia/mL) of each species was inoculated onto a sterile cellophane sheet overlaid on PDA in a Petri dish (60 x 15 mm). Petri dishes containing inoculated sheets were then incubated at RT in continuous light till the conidia reached respective germination stages. Barley leaf sheaths were used to study the germination stages of Fusarium graminearum on the host.

extract_protocol:
Total RNA of F. graminearum  from cellophane membranes and infected host tissue was isolated using Trizol reagent. RNA was treated with RNase-Free DNase (Qiagen), purified further using RNA Clean and ConcentratorTM - 5 (ZymoResearch)
Libraries were prepared using the Illumina Stranded mRNA Prep - Ligation kit with IDT for Illumina RNA UD Indexes.

value: Germinated conidia

value: WT

value: 11 hours on PDA


title: Jurkat 3hpi RNH-IP replicate 1

source_name: Jurkat

value: Jurkat


title: ORSAM10448-1

value: Outbred


title: SAMR1, 6 months old, cortex 3


title: Stage4_PDA_R2_Fg


title: SAMR1, 9 months old, hippocampus 1


title: SAMR1, 2.5 months old, cortex 4


title: Fvalkbh10b_input_Rep1

value: none (input)


title: SAMR1, 6 months old, cortex 2


title: SAMR1, 6 months old, cortex 1


title: HEK293_miRNA_CTR9, 3

description: CTR9 knock-down

value: HEK293Flip-In T-Rex

value: Modified human embryonic kidney 293 cells expressing microRNA against CTR9 under tetracyclin inducible promoter

value: Flp-In(TM) T-Rex(TM) 293 Cell line Thermo cat. no. R78007 miCTR9

value: Tetracyclin 100 ng/ml 3 days


title: HEK293_miRNA_WDR61, 2

description: WDR61 knock-down

value: Modified human embryonic kidney 293 cells expressing microRNA against WDR61 under tetracyclin inducible promoter

value: Flp-In(TM) T-Rex(TM) 293 Cell line Thermo cat. no. R78007 miWDR61


title: Stage4_PDA_R1_Fg


title: IgG1, ChIP, H3K27me3, R2

city: Berlin

first: Michela

last: Di Virgilio

address: Robert-Rössle-Str. 10

country: Germany

institute: Max Delbrück Center for Molecular Medicine

data_processing:
Quality Control
Trimming
Sequence Alignment
Feature counting
bigwig file were generated by BamCoverage
Assembly: mm10
Supplementary files format and content: Tab delimited text file
Supplementary files format and content: bigwig

source_name: Splenocyte

growth_protocol: RPMI medium sup. 10%FBS, SodiumP, AA, 2-ME, L-Glu

extract_protocol:
Trizol
Based on illumina library preparation guideline
Read count extraction

treatment_protocol: LPS, IL4 (IgG1) LPS,TGFB, BAFF (IgG2b)

value: Splenocyte


title: ORSAM10443-1

first: Gary

last: Churchill

address: 600 Main St

institute: The Jackson Laboratory

source_name: adipose-44% fat + fiber-female-CC002/UncJ x CC043/GeniUncJ)F1 -None-rep1

value: gonadal fat pad

value: female

value: CC002/UncJ x CC043/GeniUncJ)F1

value: 44% fat + fiber


title: Stage3_PDA_R3_Fg

value: Germinated conidia

value: 7 hours on PDA


title: HEK293_miRNA_CTR9, 2

description: CTR9 knock-down


title: SAMR1, 2.5 months old, cortex 3

value: cortex


title: ORSAM10450-1

source_name: adipose-44% fat + fiber-female-CC051/TauUncJ x CC059/TauUncJ)F1 -None-rep1

value: CC051/TauUncJ x CC059/TauUncJ)F1


title: HEK293_miRNA_WDR61, 3

description: WDR61 knock-down


title: IgG1, ChIP, H3K27me3, R1

value: WT


title: HEK293_miRNA_CTR9, 1

description: CTR9 knock-down


title: IgG1, ChIP, H3K4me3


title: SAMR1, 9 months old, cortex 2


title: Stage3_PDA_R1_Fg


title: SAMR1, 9 months old, cortex 1


title: HEK293_control, 3

description: control to CTR9 and WDR61 knock-down

value: Modified human embryonic kidney 293 cells

value: Flp-In(TM) T-Rex(TM) 293 Cell line Thermo cat. no. R78007


title: HEK293_miRNA_WDR61, 1

description: WDR61 knock-down

value: HEK293Flip-In T-Rex


title: IgG Control, ChIP, H3K27me3


title: HEK293_control, 2

description: control to CTR9 and WDR61 knock-down


title: SAMR1, 2.5 months old, cortex 2


title: IgG Control, ChIP, H3K4me3


title: SAMR1, 2.5 months old, cortex 1


title: Stage2_PDA_R1_Fg

value: 4 hours on PDA


title: CD19 Cre/+, IgG2b, D2, R3

value: CD19 Cre/+

value: LPS+TGFB+BAFF


title: HEK293_control, 1

description: control to CTR9 and WDR61 knock-down

value: Tetracyclin 100 ng/ml 3 days


title: Stage2_PDA_R2_Fg


title: CD19 Cre/+, IgG2b, D2, R2

value: Splenocyte


title: SAMP8, 2.5 months old, hippocampus 3

value: hippocampus


title: HEK293_WT_TTseq_rep3

city: Copenhagen N

first: Jesper

last: Svejstrup

state: Denmark

address: Blegdamsvej 3, 18.6

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

description:
pFRT⁄lacZeo and pcDNA™6⁄TR (from the T-REx™ System) stably integrated
Biotinylated nascent RNA

data_processing:
fastq files were processed and aligned using the nf-core rnaseq pipeline version 3.6
reads were aligned using STAR and gene level quantification was performed with RSEM
bigwig files for fwd and reverse strand  were normalized to yeast spike ins
Assembly: Homo sapiens GRCh38 release 95
Supplementary files format and content: bigwig files normalised to yeast spike ins
Library strategy: TTchem-Seq

source_name: Human embryonic kidney

growth_protocol: RPMI1DMEM, high glucose,supplemented with 10% FBS, 100 U/mL penicillin, 100 mg/mL streptomycin

extract_protocol:
Briefly, 2 millions of WT or ARMC5 KO cells were seeded in 10cm dish, 4SU labeling was performed next day by adding 4SU directly to the tissue culture medium to a final concentration of 1 mM. Incubate the cells with 4SU for 15 min, then medium was removed, and labeling was terminated by addition of 1 mL of TRIzol (Invitrogen, 10296028) per dish. Collect the TRIzol-cell mixture into a microcentrifuge tube. Total RNA was extracted by TRIzol/chloroform extraction followed by isopropanol precipitation.
100 μg of 4SU-labeled mammalian RNA per sample and 1 μg of S. cerevisiae 4TU-labeled RNA were mixed into 100μl total volume of RNase-free water, followed by the addition of 20 μl of 1 M NaOH per sample and incubation for 20 min on ice to fragment the RNA. RNA fragmentation was terminated by addition of 80 μl of 1 M Tris, pH 6.8 per sample and proceed immediately with two rounds clean-up reaction on Micro Bio-Spin P-30 gel columns (Biorad, 7326250) to fully remove NaOH to prevent any further RNA fragmentation. Column purified RNA was biotinylated in a total volume of 250 ml, containing 10 mM Tris-HCl pH 7.4, 1mMEDTA and 5 mg MTSEA biotin-XX linker (Biotium, BT90066) for 30 min at room temperature in the dark, then was purified using phenol:chloroform extraction. Then the dissolved RNA was incubated at 65°C to denature, followed by μMACS Streptavidin Kit (Milentyl, 130-074-101) purification according to the manufacturer’s instructions to get pure biotinylated RNA. Biotinylated RNA was cleaned up using the RNeasy MinElute kit (QIAGEN, 74204), after that, the harvested RNA represents nascent RNA which could be used for making sequencing libraries

treatment_protocol: 1 mM 4SU labeling in the medium for 15 min

value: Human embryonic kidney

value: Flp-In T-REx HEK295

value: pFRT/lacZeo and pcDNATM6/TR (from the T-RExTM System) stably integrated


title: CD19 Cre/+, IgG2b, D2, R1


title: HEK293_ARMC5_KO_TTseq_rep3

description:
ARMC5 KO;pFRT⁄lacZeo and pcDNA™6⁄TR (from the T-REx™ System) stably integrated
Biotinylated nascent RNA

value: Flp-In T-REx HEK298

value: ARMC5 KO;pFRT/lacZeo and pcDNATM6/TR (from the T-RExTM System) stably integrated

value: 1 mM 4SU labeling in the medium for 15 min


title: Stage1_PDA_R3_Fg

source_name: Condia

value: Condia

value: 30 minutes on PDA


title: Stage1_PDA_R2_Fg

value: WT


title: Stage3_PDA_R2_Fg

value: Germinated conidia

value: 7 hours on PDA


title: SAMP8, 6 months old, hippocampus 3


title: HEK293_WT_TTseq_rep2

value: Flp-In T-REx HEK294


title: Stage1_PDA_R1_Fg


title: SAMP8, 6 months old, hippocampus 2


title: SAMP8, 9 months old, hippocampus 4


title: HEK293_ARMC5_KO_TTseq_rep2

value: Flp-In T-REx HEK297


title: RIF1 F/F CD19 Cre/+, IgG2b, D2, R2

value: RIF1 F/F CD19 Cre/+

value: LPS+TGFB+BAFF


title: Stage2_PDA_R3_Fg

value: 4 hours on PDA


title: NT_3

city: nanjing

first: rongjian

last: luo

state: jiangsu

address: weigang road No.1

institute: Nanjing Agricutural University

description:
processed data file: expression_measurements.txt
processed data file: LncRNA_differential_expression.xlsx

data_processing:
Illumina Casava1.7 software used for basecalling.
Cutadapt (v1.10) was used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC (v0.10.1).
Valid reads were aligned to the Oryza sativa genome assembly using Hisat (V2.0.4). Then StringTie (v1.3.0) and Ballgown were used to assemble and estimate the expression levels of all transcripts.
CPC (v0.9) and CNCI (v2.0) were used to predict coding potential and LncRNA identification.
Genome_build: Oryza sativa v7_JGI (Rice)
Supplementary_files_format_and_content: expression_measurements.txt: Tab-delimited text file includes expression measurements (FPKM values) of all transcripts for each Sample.
Supplementary_files_format_and_content: LncRNA_differential_expression.xlsx: Excel file

organism: Oryza sativa Japonica Group

source_name: Endosperm

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's protocol. The RNAs obtained were quantified and their integrity checked using a Bioanalyzer 2100 device and an RNA 6000 Nano LabChip kit (Agilent, Santa Clara, CA, USA) with RIN number >7.0. A ~10 ug of total RNA was used to deplete the ribosomal RNA fraction, using an Epicentre Ribo-Zero Gold kit (Illumina, San Diego, CA, USA). Following purification, the poly (A)- and poly(A)+ RNA fractions were fragmented by the addition of divalent cations under elevated temperature.
The RNA fragments were reverse-transcribed to create a cDNA library, following the protocol supplied with an Illumina mRNA-Seq sample preparation kit; the average insert size was 300±50bp. Paired-end sequencing was performed by LC-Bio (Hangzhou, China) using an Illumina Hiseq 4000 device.

treatment_protocol: The Japonica rice cultivar NingJing1 (cv. NJ1) raised to the booting stage in the field were removed to a growth chamber delivering a day/night temperature regime of either 36℃/33℃ (HT treatment) or 28℃/25℃ (NT treatment).

tag: cultivar

tag: development stage

value: 10 days after pollination

value: Endosperm

value: normal temperature


title: NT_2

tag: tissue


title: SAMP8, 9 months old, hippocampus 3

value: hippocampus


title: SAMP8, 9 months old, hippocampus 2


title: CD19 Cre/+, IgG1, D4, R3

value: Splenocyte

tag: genotype

value: CD19 Cre/+


title: HEK293_WT_TTseq_rep1

value: Human embryonic kidney

value: Flp-In T-REx HEK293

value: pFRT/lacZeo and pcDNATM6/TR (from the T-RExTM System) stably integrated

value: 1 mM 4SU labeling in the medium for 15 min


title: NT_1


title: RIF1 F/F CD19 Cre/+, IgG2b, D2, R3


title: SAMP8, 2.5 months old, hippocampus 2

tag: strain


title: CD19 Cre/+, IgG1, D4, R2

tag: treatment


title: RIF1 F/F CD19 Cre/+, IgG2b, D2, R1