title: R5020_E2_60_HiC_run2

data_processing:
Hi-C data were processed using an in-house pipeline based on TADbit. Reads were mapped according to a fragment-based strategy: each side of the sequenced read was mapped in full length to the reference genome Human Dec. 2013 (GRCh38/hg38). In the case reads were not mapped when intra-read ligation sites were found, they were split. Individual split read fragments were then mapped independently.
We used the TADbit filtering module to remove non-informative contacts and to create contact matrices.
PCR duplicates were removed and the Hi-C filters applied corresponded to potential non-digested fragments (extra-dandling ends), non-ligated fragments (dandling-ends), self-circles and random breaks.
Genome_build: hg38
Supplementary_files_format_and_content: text files contain 100kb-resolution contact matrices

source_name: endometrial adenocarcinoma

extract_protocol:
Adherent cells were directly cross-linked on the plates with 1% formaldehyde for 10min at room temperature. After addition of glycine (125mM final) to stop the reaction, cells were washed with PBS and recovered by scrapping. Cross-linked cells were incubated 30min on ice in 3C lysis Buffer (10mM Tris-HCl pH 8, 10mM NaCl, 0.2% NP40, 1X anti-protease cocktail), centrifuged 5min at 3,000 rpm and resuspended in 190uL of NEBuffer2 1X  (New England Biolabs – NEB). 10 µL of 10% SDS were added and cells were incubated for 10min at 65ºC. After addition of Triton X-100 and 15min incubation at 37ºC, nuclei were centrifuged 5min at 3,000 rpm and resuspended in 300uL of NEBuffer2 1X. Digestion was performed overnight using 400 U MboI restriction enzyme (NEB). To fill-in the generated ends with biotinylated-dATP, nuclei were pelleted and resuspended in fresh repair buffer 1x (1.5µL of 10mM dCTP; 1.5µL of 10mM dGTP; 1.5µL of 10mM dTTP; 37.5µL of 0.4mM Biotin-dATP; 50U of DNA Polymerase I Large (Klenow) fragment in 300uL NEBuffer2 1X). After 45min incubation at 37ºC, nuclei were centrifuged 5min at 3,000 rpm and ligation was performed 4h at 16ºC using 10,000 cohesive end units of T4 DNA ligase (NEB) in 1.2mL of ligation buffer (120µL of 10X T4 DNA Ligase Buffer; 100µL of 10% Triton X-100; 12µL of 10mg/mL BSA; 963µL of H2O). After reversion of the cross-link, DNA was purified by phenol extraction and EtOH precipitation. Purified DNA was sonicated to obtain fragments of an average size of 300-400 bp using a Bioruptor Pico (Diagenode; 8 cycles; 20s on and 60s off). 3µg of sonicated DNA was used for library preparation.
Biotinylated DNA was pulled down using 20uL of Dynabeads Myone T1 streptavidine beads in Binding Buffer (5mM Tris-HCl pH7.5; 0.5mM EDTA; 1M NaCl). End-repair and A-tailing were performed on beads using NEBnext library preparation end-repair and A-tailing modules (NEB). Illumina adaptors were ligated and libraries were amplified by 8 cycles of PCR. Resulting Hi-C libraries were first controlled for quality by low sequencing depth on a NextSeq500 prior to higher sequencing depth on HiSeq2000.

treatment_protocol: Adequate number of cells were seeded in culture plates using DMEM/F12 (1:1) without phenol red and supplemented with 5% dextran-coated charcoal stripped FCS and gentamycin for 48h, followed by overnight incubation in DMEM/F12 (1:1) without phenol red and without FCS. After overnight incubation, cells were treated or not with R5020 10nM and E2 10nM for 60min.

tag: disease state

value: endometrial adenocarcinoma

tag: cell line

value: Ishikawa

tag: passages

value: epithelial-like

tag: growth mode

value: adherent

value: 60min R5020+E2-treated Ishikawa cells


title: A25

status: Public on Mar 09 2022

type: SRA

city: Columbus

first: Amy

last: Hite

state: OH - Ohio

address: 1800 Cannon Drive 250 Lincoln Tower

department: Biomedical Informatics

country: USA

institute: The Ohio State University

library_source: transcriptomic

data_processing:
Reads were aligned to Rat genome Rnor6.0 with HISAT2.
counts generated for Rnor 6.0 v101 with featureCounts from the subread package.
Counts were normalized with voom and differential expression tested with limma.
Genome_build: Rnor6.0
Supplementary_files_format_and_content: Text file of voom normalized expression for each gene and each sample

molecule: polyA RNA

organism: Rattus norvegicus

source_name: Glomerular

growth_protocol: Male Wistar Rats , ~175g

extract_protocol:
On Day 11, rats were sacked, kidneys harvested and glomeruli were isolated by sieve method. Total RNA was extracted.
The mRNA libraries were generated using the following kits and conditions:   • NEBNext® Ultra™ II Directional (stranded) RNA Library Prep Kit for Illumina (NEB #E7760L)   • NEBNext Poly (A) mRNA Magnetic Isolation Module (NEB #E7490)   • NEBNext Multiplex Oligos for Illumina Unique Dual Index Primer Pairs (NEB #6442S/L)   • Library input amount: 200ng total RNA (quantified using Qubit Fluorometer) and total RNA achieved a RIN of >7  • Fragmentation: 10 minutes   • PCR: 12x   • Libraries were sequenced with Illumina NovaSeq 6000 flow cell using paired-end 150-bp format to at least 17 million passed-filter clusters/sample (equivalent to 34 million reads)

treatment_protocol: Male Wistar rats were intravenously (IV) injected with puromycin aminonucleoside (PAN) (Sigma-Aldrich, St. Louis, MO) and treatment groups were treated by oral gavage with Pioglitazone, GQ-16, or a sham vehicle daily.

tag: strain

value: Wistar

tag: Sex

value: Male

tag: tissue

value: glomeruli

tag: groups

value: PAN

tag: treatment


title: BNT_Convalescent_4_Day0

city: Bethesda

first: Hye Kyung

last: Lee

state: MD

address: 8 CENTER DR RM 107

department: National Institute of Diabetes and Digestive and Kidney (NIDDK)

institute: National Institutes of Health (NIH)

data_processing:
RNA-seq data were trimmed using trimmomatic (Bolger et al., Bioinformatics, 2014) and subsequently aligned to the reference genome hg19 applying STAR RNA-seq aligner (Dobin et al., Bioinformatics, 2013). HTSeq(Anders et al., Bioinformatics, 2015) was applied for obtain HTSeq counts.
HTSeq(Anders et al., Bioinformatics, 2015) was applied for obtain HTSeq counts.
Trimmed RNA-seq data were aligned to the human V, D and J genes and obtained immune clonotypes using MiXCR (Bolotin et al., Nat Methods, 2015; Bolotin et al., Nat Biotechnol, 2017).
Genome_build: hg19
Supplementary_files_format_and_content: HTSeq counts from RNA-seq samples
Supplementary_files_format_and_content: clonotypes from RNA-seq samples

organism: Homo sapiens

source_name: PBMCs

growth_protocol: Blood samples were collected from the convalescnet COVID-19 patients and SARS-CoV-2 naïve individuals both before and after vaccinations.

extract_protocol:
The buffy coat was extracted by centrifuge after blood sample collection and RBC was removed using RBC lysis buffer in the buffy coat. Total RNA was isolated using a Maxwell RSC simply RNA Blood purification kit.
Libraries for sequencing were prepared with TruSeq Stranded mRNA Kit following standard Illumina protocols.

tag: age

tag: gender

value: Female

tag: condition

value: COVID-19 Recovered


title: BNT_Convalescent_3_Day7


title: SDF_2A

city: Shenzhen

first: Yan

last: WANG

address: 1068 Xueyuan Ave

country: China

institute: Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences

data_processing:
Raw sequencing reads (fastq) were quality checked using SOAPnuke (v1.5.2).
Bowtie2 (v2.2.5) was applied to align the clean reads to the genomes.
The expression level of gene was calculated by RSEM (v1.2.12).
Differential expression analysis was performed using DESeq2 (v1.4.5)
Genome_build: GCF_000001405.39_GRCh38.p13
Supplementary_files_format_and_content: excel

molecule: total RNA

source_name: C28/I2 cell line

growth_protocol: C28/I2 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin–streptomycin.

extract_protocol:
RNAs were extracted from culture tissues. The samples were homogenized in Trizol (Invitrogen) and processed for RNA extraction according to the manufacturer’s instructions.
BGI in-house kit (BGI-Shenzhen, China)

treatment_protocol: C28/I2 cells were treated with or without SDF-1/natural products for 48 h and then collected for bulk RNA sequencing.

value: chondrocyte

value: SDF-1a 50 nM, 48 h


title: E2_60_HiC_run2

city: buenos aires

first: Patricia

last: Saragüeta

state: CABA

address: Vuelta de Obligado 2490

country: Argentina

institute: IByME

library_source: genomic

molecule: genomic DNA

growth_protocol: Ishikawa cells were routinely cultured in DMEM/F12 (1:1) supplemeted with 10% FCS and gentamycin

tag: cell type

value: 60min E2-treated Ishikawa cells


title: SDF_1A


title: A9

value: Ctl

value: Healthy


title: R5020_60_HiC_run2

value: 60min R5020-treated Ishikawa cells


title: BNT_Convalescent_3_Day1


title: HQJG_1A

value: SDF-1a 50 nM and Astragaloside IV 10 μM, 48 h


title: A8


title: A7


title: Untreated_T0_HiC_run2

value: endometrial adenocarcinoma

value: Ishikawa

value: untreated Ishikawa cells


title: BNT_Convalescent_2_Day7


title: C28mono3A


title: BNT_Convalescent_3_Day0


title: BNT_Convalescent_2_Day1


title: R5020_E2_60_HiC_run1

value: epithelial-like

value: adherent

value: 60min R5020+E2-treated Ishikawa cells


title: Sl13

city: Palaiseau

first: Adeline

last: SIMON

address: 22 place de l'agronomie

country: France

institute: INRAE

data_processing:
Adapters were removed with Cutadapt (Martin, 2011) .
Processed reads shorter than 16 bases were discarded.
Then, the reads were preprocessed using fastx-toolkit (http://hannonlab.cshl.edu/fastx_toolkit/), i.e. low-quality sequences were masked with fastq_quality_filter -q 30 -p 70, low-complexity sequences were masked with fastx_artifacts_filter.
Finally, identical sequences were collapsed into a single sequence (while maintaining reads counts) with fastx_collapser.
Only single sequences (called unireads) of length 20-24nt and with at least five reads per million in at least one library were kept, i.e., 146395 unireads.
Supplementary_files_format_and_content: Raw counts for the 146395 unireads in the 16 libraries (txt).

organism: Botrytis cinerea

source_name: Botrytis cinerea Sl13

growth_protocol: Botrytis cinerea strains were cultivated 48 hours on solid media made from grape juice or tomato juice supplemented with agar and covered with a sheet of cellophane.

extract_protocol:
RNAs were extracted with the TRIzol reagent (InvitroGen) and submitted to a DNAse treatment (DNA-free kit, Ambion).
Libraries were performed from at least 1µg of extracted total RNA with a RIN greater than 7. Before starting, total RNAs were purified with miRNeasy kit (Qiagen) which allows the selection of the small RNA fraction less than 100 bases. From these samples enriched in small RNAs, libraries were performed according to the protocol published by Vigneault et al. (2012) with adjustments to improve the ligation.


title: C28mono2A


title: SDF_3A


title: E2_60_HiC_run1


title: Hdac4-knockdown MC3T3_3

city: Shanghai

first: Nayoung

last: Ha

address: 639 Zhizaoju road

institute: Shanghai People's Ninth Hospital

data_processing:
The PE150 raw reads of RNA-Seq libraries were filtered by removing adaptor sequences, contamination and low-quality (phred quality < 20) reads. Reads quality was assessed using FastQC.
Sequenced reads were then mapped to the mm10 genome using STAR aligner version 2.7.3a. Reads were counted using htseq-count version 0.12.4 at the union mode.
Genome_build: mm10
Supplementary_files_format_and_content: counts

organism: Mus musculus

source_name: Pre-osteoblast

growth_protocol: MC3T3-E1 cells were purchased from Cell Bank of the Chinese Academy of Science, Shanghai, and maintained at 37 ◦C, 5% CO2. Cells were cultured in MEM-α containing 10% FBS and 1% P/S. The culture medium was changed every 2 days.

extract_protocol:
Total RNAs were extracted from each cell line using the MolPure TRIeasy Plus Total RNA kit (Yeasen, China, 19211ES60).  For each group, three independent RNA samples were prepared. RNA purity was checked using the kaiaoK5500®Spectrophotometer (Kaiao, Beijing, China). The concentration and quality of total RNA were determined by the Tecan Infinity 200Pro multi-well plate reader to measure the ratio of absorbance at 260 nm to 280 nm.
For each sample, 2 μg total RNA was used as input material for the library preparations. Sequencing libraries were then generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and RNase H. Second strand cDNA synthesis was subsequently performed using buffer, dNTPs, DNA polymerase I and RNase H. The library fragments were purified with QiaQuick PCR kits and eluted with EB buffer, followed by terminal repair, A-tailing and adapter ligation. The ligated products were retrieved and PCR amplification was performed to generate sequencing libraries. RNA concentration of library was measured using Qubit® RNA Assay Kit in Qubit® 3.0 to preliminary quantify and then dilute to 1ng/μl. Insert size was assessed using the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA), and qualified insert size was accurately quantified using a StepOnePlusTM Real-Time PCR System. The clustering of the index-coded samples was performed on a cBot cluster generation system using HiSeq PE Cluster Kit v4-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the libraries were sequenced on an Illumina HiSeq X ten platform and 150 bp paired-end reads were generated.

treatment_protocol: Three short hairpin RNA (shRNA) targeting Hdac4 sequence (NC_000067; Hdac4-shRNA1, GCAGATCCAGCGGCAGATACT; Hdac4-shRNA2, GCAGTTGTCCCGACAGCATGA; Hdac4-shRNA3, GCATGAGGCACAGTTGCATGA) and scrambled non-silencing RNA (TTCTCCGAACGTGTCACGT)) was designed and synthesized (Genomeditech). These were cloned into pGMLV-HU6-MCS-CMV-ZsGreen1-PGK-Puro lentiviral vector to form recombinant lentiviral shRNA expression vector. ShRNA-containing lentiviruses were packaged and amplified by co-transferring pGMLV-HU6-MCS-CMV-ZsGreen1-PGK-Puro vector, together with pSPAX2 and pMD2G into 293T cells (at 70%-80% cell density) with the help of Lipofectamine 2000. At 48 hours, supernatants were gathered and filtered using 0.22 μm cellulose acetate filters (Millipore, Billerica, MA). The viral titer was determined by endpoint dilution assay. MC3T3-E1 cell suspensions were formed by trypsinization. Suspensions were cultured in six-well plates at 20,000 cells per well and incubated at 37 ◦C, 5% CO2 for 24 h. Suspensions were infected with shRNA-lentiviruses with 5 μg/mL in polybrene (Beyotime, Jiangsu, China) for 12 hours and then culture medium was substituted with ordinary culture medium for 48 h. To get stable infected cells, cells were cultured with MEM-α in the presence of 5 μg/mL of puromycin (Beyotime, Jiangsu, China) for 7 days. The cells were separated into four groups: the control scramble group, and the three experimental group expressing Hdac4-shRNA1, Hdac4-shRNA2, and Hdac4-shRNA3.

tag: knockdown


title: A10

value: Wistar

value: Male

value: glomeruli


title: BNT_Convalescent_10_Day1

value: Female

value: COVID-19 Recovered


title: R5020_60_HiC_run1


title: Sl11

source_name: Botrytis cinerea Sl11


title: BNT_Convalescent_2_Day0


title: Hdac4-knockdown MC3T3_2


title: BNT_Convalescent_1_Day7


title: PAX2_E60_ChIPseq

data_processing:
Sequencing reads were trimmed to remove Illumina adaptors and low-quality ends using Trimmomatic v0.33 in single-end mode.
Trimmed reads were quality checked with FastQC and aligned to reference human genome hg38 (UCSC) using BWA v0.7.12 with default parameters, keeping alignements that mapped uniquely to the reference (Samtools v1.2).
Overlapping reads were clustered and significant signal enrichments were identified with MACS v2.1.0 using input as background signal (peak-calling). FDR value for initial peak-calling steps was set to 0.05 (q). Downstream analyses were performed with q<1e-5.
Genome_build: hg38
Supplementary_files_format_and_content: NarrowPeak files were generated with MACS software and the coverage signal files in RPM (reads per million mapped) by the bamCoverage tool from deepTools (bigwig).

extract_protocol:
Cells were incubated in 1% Formaldehyde for 10min at 37ºC. After quenching with glycine, cells were whased once in ice cold PBS and collected in PBS plus protease and phosphatase inhibitors using a scrapper. Cells were lysed in two secuential steps to release nuclear contet and inmediately sonicated in Bioruptor. Sonication was evaluated by agarose gel electrophoresis, considering it succesful when fragments were homogenously distrubuted between 200-400bp.  Enrichment of receptor-bound DNA was achieved by incubation with specific antibody against PAX2 and immunoprecipitation with protein A beads.
Libraries were prepared by the Genomics unit of the CRG Core Facility (Centre for Genomic Regulation, Barcelona, Spain) with NEBNext® ChIP-Seq Library Prep Reagent Set (ref. E6200S Illumina). Libraries were quality checked and quantified for single-end sequencing.

tag: cell modification

tag: chip antibody

value: PAX2 (BioLegend PRB-276P)

value: PAX2-immunoprecipitated DNA from 60min E2-treated cells


title: Hdac4-knockdown MC3T3_1


title: BNT_Convalescent_1_Day1


title: PAX2_R60_ChIPseq

value: PAX2-immunoprecipitated DNA from 60min R5020-treated cells


title: Sl3T

source_name: Botrytis cinerea Sl3T


title: Control MC3T3_3

value: scrambled non-silencing RNA


title: C28mono1A

value: chondrocyte


title: Sl3

source_name: Botrytis cinerea Sl3


title: BNT_Convalescent_1_Day0


title: Sl2

source_name: Botrytis cinerea Sl2


title: PAX2_T0_ChIPseq

value: PAX2-immunoprecipitated DNA from untreated cells


title: Control MC3T3_1


title: G401 MAK683 H3K4me3

first: Wei

last: Qi

state: Shanghai

address: B514, L Building

department: School of Life Science and Technology

institute: ShanghaiTech University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trim-galore (version 0.4.4_dev) and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using Bowtie2(version v1.3.0).
ChIP-seq sample depleted repeat sequences by Picard (version 2.23.6) and normalized by drosophila histone modification.
These reads were used to generate binding site with featureCounts (version v2.0.0).BW file were processed by deeptools (version 3.4.3).
Genome_build: hg19
Supplementary_files_format_and_content: counts text files were generated using featureCounts(version v2.0.0); values represent the number of reads falling in the exons.
Supplementary_files_format_and_content: bigwig files were generated using deeptools(version 3.4.3).

source_name: cancer cell

growth_protocol: G401 cell lines were cultured in DMEM with 10%FBS and 0.055 mM 2-mercaptoethanol.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
A total amount of 50 ng DNA per sample was used as input material for the ChIP sample preparations. Sequencing libraries were generated using NEBNext Ultratm DNA Library PrepKit for Illumina(NEB USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly,the Chip DNA was purified using AMPure XP system (Beckman Coulter Beverly,USA). After adenylation of 3'ends of DNA fragments, the NEB Next Adaptor with hairpin loop structure were ligated to prepare for hybridization. Then electrophoresis was used to select DNA fragments specified in length. 3 uL USER Enzyme(NEB，USA) was used with size-selected,adaptor-ligated DNA at 37C for15 min followed by5 min at 95C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index(X) Primer. At last. PCRproducts were purified(AMPure XP system) and library quality was assessed on the AgilentBioanalyzer 2100 system.

treatment_protocol: One replicate was DMSO or MAK683 treated for 3 days.


title: Control MC3T3_2


title: G401 MAK683 H3K27me3


title: prePR_R60_ChIPseq

data_processing:
Sequencing reads were trimmed to remove Illumina adaptors and low-quality ends using Trimmomatic v0.33 in single-end mode.
Trimmed reads were quality checked with FastQC and aligned to reference human genome hg19 (UCSC) using BWA v0.7.12 with default parameters, keeping alignements that mapped uniquely to the reference (Samtools v1.2).
Overlapping reads were clustered and significant signal enrichments were identified with MACS v2.1.0 using input as background signal (peak-calling). FDR value for initial peak-calling steps was set to 0.05 (q). Downstream analyses were performed with q<1e-5.
Genome_build: hg19
Supplementary_files_format_and_content: NarrowPeak files were generated with MACS software and the coverage signal files in RPM (reads per million mapped) by the bamCoverage tool from deepTools (bigwig).

extract_protocol:
Cells were incubated in 1% Formaldehyde for 10min at 37ºC. After quenching with glycine, cells were whased once in ice cold PBS and collected in PBS plus protease and phosphatase inhibitors using a scrapper. Cells were lysed in two secuential steps to release nuclear contet and inmediately sonicated in Bioruptor. Sonication was evaluated by agarose gel electrophoresis, considering it succesful when fragments were homogenously distrubuted between 200-400bp.  Enrichment of receptor-bound DNA was achieved by incubation with specific antibodies against either PR or ERalfa and immunoprecipitation with protein A beads.
Libraries were prepared by the Genomics unit of the CRG Core Facility (Centre for Genomic Regulation, Barcelona, Spain) with NEBNext® ChIP-Seq Library Prep Reagent Set (ref. E6200S Illumina). Libraries were quality checked and quantified for single-end sequencing.

treatment_protocol: Adequate number of cells were seeded in culture plates using DMEM/F12 (1:1) without phenol red and supplemented with 5% dextran-coated charcoal stripped FCS and gentamycin for 48h, followed by overnight incubation in DMEM/F12 (1:1) without phenol red and without FCS. After overnight incubation, cells were treated or not with R5020 10nM and E2 10nM for 5, 30, 60 360 min.

value: endometrial adenocarcinoma

value: PR H190 (Santa Cruz)

value: PR-immunoprecipitated DNA from 30min R5020-treated cells


title: G401 ATAC MAK683

data_processing:
Basecalls performed using CASAVA.Sequenced reads weremapped to hg19 whole genome using Bowtie2(version v2.2.9).
peaks were called using MACS2(version 2.1.0)
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated using deeptools(version 3.4.3).
Supplementary_files_format_and_content: peak text files were generated using MACS2(version 2.2.7.1)

extract_protocol:
Cells were collected and lysed to obtain purified nucleus; The Tn5 enzyme transposable reaction was carried out and the open regions of chromatin were fragmented; the fragmented DNA was purified; the purified DNA was amplified. The amplified DNA was sized to remove non-target fragments.
Librarypreparation was performed using TruePrepTM DNA Library Prep Kit V2 for Illumina kit. 1.2x agencourt Afure XP beaas(Beckman Coulter)were used to purify libraries for sequencing .150 paired-end sequencing was performed with Navoseq6000.


title: G401 ATAC DMSO

value: DMSO


title: Sl1

source_name: Botrytis cinerea Sl1


title: Sl6

source_name: Botrytis cinerea Sl6


title: Spleen, P. chabaudi-infection, Day0

city: Chongqing

first: taiping

last: Liu

address: Gaotanyan zhengjie 30, Shapingba district, Chongqing

institute: Department of Pathogenic Biology, Army Medical University (Third Military Medical University)

data_processing:
Raw sequencing data were processed using Cell Ranger (10x Genomics; v6.0.1).
The CellRanger function “count” was used to align raw reads with the STAR aligner against the mm10 reference genome.
The output “cellranger” matrices were loaded into the Seurat package (v4.0.3) in R (v4.0.3) for single-cell clustering analysis.
The Seurat package in R (v4.0.3) was used to perform differential gene expression analysis and compare the expression profiles between the two groups.
Genome_build: mm10
Supplementary_files_format_and_content: barcodes,features,matrix

source_name: Spleen

growth_protocol: For sc-RNASeq analysis, splenocytes were isolated from  P. chabaudi-infected mice (n=5) at day0, day8 and day16 post-infection.

extract_protocol:
Splenocytes were loaded on a Chromium Controller (10x Genomics, Pleasanton) at a concentration of 10^3 cells/µL per sample, to generate Gel Bead-In EMulsions (GEMs). Each GEMs is wrapped with a beads and a cell, and then cell lysis and reverse transcription reaction are carried out in GEMs to synthesize cDNA with barcode sequence. PCR amplification is carried out with cDNA. After amplification, quality inspection is carried out for the amplified products.
Barcoded sequencing libraries were constructed using the Chromium Single Cell 3’ Reagent Kits v3 (10x Genomics) according to the manufacturer’s instructions. Following library preparation, sequencing was performed with paired-end sequencing of 150 nt at each end using one lane of the NovaSeq 6000 per sample. Raw sequencing data were processed using Cell Ranger (10x Genomics; v6.0.1). The CellRanger function “count” was used to align raw reads with the STAR aligner against the mm10 reference genome. After counting nonredundant unique molecular identifiers (UMIs), single-cell digital-expression matrices were obtained.
sc-RNASeq

treatment_protocol: P. chabaudi infection

value: Spleen

tag: infection

value: P. chabaudi

value: Splenocytes

tag: time


title: Untreated_T0_HiC_run1

tag: disease state

tag: cell line

value: Ishikawa

value: epithelial-like

value: adherent

value: untreated Ishikawa cells


title: Vv9

source_name: Botrytis cinerea Vv9


title: prePR_R30_ChIPseq

tag: passages

tag: growth mode

value: PR-immunoprecipitated DNA from 5min R5020-treated cells


title: FPR_R60_ChIPseq

value: exogenous PR overexpression

value: PR-immunoprecipitated DNA from 60min R5020-treated cells


title: Vv8

source_name: Botrytis cinerea Vv8

tag: strain


title: Spleen, P. chabaudi-infection, Day8

tag: tissue


title: G401 MAK683 Input

value: Input


title: G401 DMSO H3K4me3


title: Cdc42 KO_ZnO NPs_3

city: Guangzhou

first: Ping

last: Wang

state: Guangdong

address: No. 1023-1063, Shatai South Road, Baiyun District, Guangzhou city

institute: Southern Medical University

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.

source_name: Skin

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

value: skin

value: 3 months

tag: genotype

value: zinc oxide nanoparticles (ZnO NPs)


title: FPR_R30_ChIPseq

source_name: endometrial adenocarcinoma

value: endometrial adenocarcinoma

value: PR H190 (Santa Cruz)

tag: treatment


title: Vv14

source_name: Botrytis cinerea Vv14


title: Cdc42 KO_ZnO NPs_2

tag: age


title: G401 DMSO H3K27me3

value: DMSO


title: FPR_R5_ChIPseq


title: Vv5

source_name: Botrytis cinerea Vv5


title: Cdc42 KO_ZnO NPs_1


title: Vv15

source_name: Botrytis cinerea Vv15


title: FPR_T0_ChIPseq

value: PR-immunoprecipitated DNA from untreated cells


title: Spleen, P. chabaudi-infection, Day16

value: Spleen

value: P. chabaudi


title: Cdc42 KO_3

value: control


title: Cdc42 KO_2


title: input_DNA_ChIPseq

value: Ishikawa

value: epithelial-like

value: DNA not subjected to immunoprecipitation


title: G401 in_vivo P16KO MAK683 rep2

data_processing:
Illumina PE150 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trim-galore (version 0.4.4_dev) and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using RSEM(version v1.3.0).
The number of reads falling in the exons were calculated using featureCounts (version v1.5.3) and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

growth_protocol: G401 and G402  were cultured in DMEM with 10%FBS and 0.055 mM 2-mercaptoethanol, A2780 cell line was cultured in DMEM with 10%FBS. WT or p16 KO G401 cell lines were injected subcutaneously into the right flank of female Balb/c nude mice.

extract_protocol:
RNA samples were harvested with Trizol reagent.
Total RNA was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.Ribosomal RNA (rRNA) is depleted for target transcript enrichment.Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.A total amount of 50 ng DNA per sample was used as input material for the Chip sample preparations. Sequencing libraries were generated using NEBNext Ultratm DNA Library PrepKit for Illumina(NEB USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly,the Chip DNA was purified using AMPure XP system (Beckman Coulter Beverly,USA). After adenylation of 3'ends of DNA fragments, the NEB Next Adaptor with hairpin loop structure were ligated to prepare for hybridization. Then electrophoresis was used to select DNA fragments specified in length. 3 uL USER Enzyme(NEB，USA) was used with size-selected,adaptor-ligated DNA at 37C for15 min followed by5 min at 95C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index(X) Primer. At last. PCRproducts were purified(AMPure XP system) and library quality was assessed on the AgilentBioanalyzer 2100 system.

treatment_protocol: Cell lines were treated with 3 μM MAK683 for 3 or 6 days. G401-derived xenograft carrying mice were given vehicle or 100 mg/kg MAK683 orally for 46 consecutive days before the xenograft tumor tissues were harvested.

value: G401-derived Xenogrft  tissue


title: G401 DMSO Input


title: G401 in_vivo P16KO MAK683 rep3


title: prePR_T0_ChIPseq

value: adherent


title: G401 in_vivo P16KO MAK683 rep1


title: Cdc42 KO_1


title: Vv3

source_name: Botrytis cinerea Vv3


title: B0510

source_name: Botrytis cinerea B0510


title: Vv1

source_name: Botrytis cinerea Vv1


title: G401 in_vivo P16KO DMSO rep3


title: ER_E60_ChIPseq

value: ERalfa HC-20X/H184X (Santa Cruz)

value: ER-immunoprecipitated DNA from 60min E2-treated cells


title: ER_E360_ChIPseq

value: ER-immunoprecipitated DNA from 360min E2-treated cells


title: WT_ZnO NPs_2

value: skin

value: 3 months

value: wild type


title: G401 in_vivo P16KO DMSO rep2


title: WT_ZnO NPs_1

value: zinc oxide nanoparticles (ZnO NPs)


title: PR_60_ChIPseq

value: endometrial adenocarcinoma

value: PR H190 (Santa Cruz)

value: PR-immunoprecipitated DNA from 60min R5020-treated cells


title: ER_T0_ChIPseq

value: ER-immunoprecipitated DNA from  untreated cells


title: G401 in_vivo P16KO DMSO rep1

value: DMSO


title: WT_3

value: control


title: G401 in_vivo MAK683 rep3


title: Vv3T

source_name: Botrytis cinerea Vv3T


title: PR_R30_ChIPseq

value: Ishikawa

value: epithelial-like

value: PR-immunoprecipitated DNA from 30min R5020-treated cells


title: WT_1


title: G401 in_vivo MAK683 rep2

value: G401-derived Xenogrft  tissue


title: WT_ZnO NPs_3


title: PR_R5_ChIPseq

value: adherent

value: PR-immunoprecipitated DNA from 5min R5020-treated cells


title: ER_E5_ChIPseq

value: ERalfa HC-20X/H184X (Santa Cruz)

value: ER-immunoprecipitated DNA from 5min E2-treated cells


title: WT_2

value: skin

value: 3 months


title: PR_T0_ChIPseq

value: PR-immunoprecipitated DNA from untreated cells


title: G401 in_vivo MAK683 rep1

value: wild type


title: Human retina H3K27ac HiChIP rep1 [HiChIP_LVG1OD]

city: Stanford

first: Sean

middle: K

state: CA

address: 1291 Welch Rd

institute: Stanford University

data_processing:
library strategy: HiCHIP
Demultiplexed scRNA- and scATAC-seq fastq files were inputted into the Cell Ranger ARC pipeline (version 2.0.0) from 10x Genomics to generate barcoded count matrices of gene expression and ATAC data. For each sample, count matrices were loaded in ArchR and selected for barcodes that appeared in both the scRNA-seq and scATAC-seq datasets. Samples in ArchR were quality control filtered for nuclei with 200-50,000 RNA transcripts, <1% mitochondrial reads, <5% ribosomal reads, TSS enrichment >6, and >2,500 ATAC fragments. Quality control filtered nuclei subsequently underwent automated removal of doublets using the filterDoublets function in ArchR, which identifies and removes the nearest neighbors of simulated doublets.
scRNA-seq data from nuclei remaining after quality control filtering and automated removal of doublets were analyzed using Seurat (version 3.1.5). After merging all preprocessed samples into a single Seurat object, gene expression counts were normalized using the NormalizeData function, scaled using the ScaleData function, and batch corrected using Harmony. Graph-based clustering was then performed on the Harmony-corrected data using the top 20 principal components at a resolution of 0.5. Cluster identities were manually annotated based on the expression of genes from published scRNA-seq studies of the human retina. Clusters expressing canonical marker genes from different cell types were designated as putative doublets and excluded, after which re-clustering was performed using the same parameters. Clusters with no detected marker genes were also excluded, after which the dataset was also re-clustered.
scATAC-seq data were analyzed using ArchR (version 1.0.1) based on barcoded cell type identities from scRNA-seq. For each cell type, pseudo-bulk ATAC replicates were created using the addGroupCoverages function with default parameters, which generated between two to five replicates depending on how many cells of that type were present in each sample. Chromatin accessibility peaks on chromosomes 1-22 and X and outside of blacklist regions were then called using the addReproduciblePeakSet function and MACS2, with reproducible scATAC peaks for each cell type defined as those present in at least two pseudo-bulk ATAC replicates.
HiChIP sequencing files were initially processed using the HiC-Pro pipeline (version 2.11.0) to remove duplicate reads, assign reads to MboI restriction fragments, filter for valid interactions, and generate binned interaction matrices. Filtered read pairs from HiC-Pro were subsequently converted into .hic files and inputted into HiCCUPS from the Juicer pipeline to call loops.
Genome_build: hg38
Supplementary_files_format_and_content: hic files represent all valid interaction pairs detected by HiC-Pro following H3K27ac HiChIP of retina tissue from the specified donor. bedpe files represent H3K27ac HiChIP loops detected by HiCCUPS. tsv and mtx files represent raw gene counts for each barcode in the file scRNA-seq dataset. fragments files represent aggregated scATAC-seq fragments organized by cell type.

source_name: adult human retina

extract_protocol:
HiChIP libraries were prepared according to Mumbach et al., 2016.
Nuclei were isolated from frozen retinas using the Omni-ATAC protocol (doi.org/10.17504/protocols.io.6t8herw)

value: Retina


title: G401 in_vivo DMSO rep3


title: FSK

city: Québec

first: Asma

last: Arjoune

state: Québec

address: 3326,rue de la monnerie, Appertement 1

department: Animal sciences

country: Canada

institute: Laval University

data_processing:
Ensembl was used as the source of annotated genes and transcript isoforms. Trimming of adapters was performed using Trimmomatic; sequencing adapters were removed, and base calls with a quality score below 30 were removed from the end of the reads. Trimming was performed with the minimal length set at 32nt and these reads were kept for further processing. Pseudoalignment of all transcripts described in release 91 of ENSEMBL cdna gene annotation was accomplished by the kallisto tool, Differential expression of genes was then assessed using pairwise comparisons in EdgeR. Because of the lack of replicates, dispersion within EdgeR was evaluated by grouping samples for similar comparisons (first for control, then for melatonin (MLT) and FSK samples) and dropping the factor with the lowest impact, as suggested by the EdgeR manual
Genome_build: Ensembl (release 91)
Supplementary_files_format_and_content: tab-delimited text files include log Fold change, p-value, adjsuted p-value for each Sample

source_name: KGN cells

growth_protocol: KGN cells were thawed on day 1, placed in a cell culture flask (25 cm3, Sigma-Aldrich) and sub-cultured on day 3. Confluence was never over 80%. On day 6, viable cells were placed in a 12-well dish at the density of 1.5x10^5 per well in 1.5 ml of medium and grown for 72 h.

extract_protocol:
Total RNA was isolated with AllPrep DNA/RNA Mini Kit (Qiagen, Mississauga, ON, Canada) according to the manufacturer’s instructions. Total RNA integrity and concentration were evaluated on a 2100-Bioanalyzer (Agilent Technologies, Palo Alto, CA).
The total RNA input used for sequencing was 360 ng for each treatment, a pool of 90 ng for each biological replicates. mRNA was isolated from total RNA using NEBNext Poly (A) mRNA Magnetic Isolation Module (E7490S; NEB). PolyA-selected mRNA was fragmented to a mean size of 200 nt, reverse transcribed to generate double-stranded cDNA, and converted to a paired-end library using NEBNext Ultra RNA Library Prep kit for Illumina (E7530S; NEB) according to the manufacturer’s instructions, using Agencourt AMPure XP beads and NEBNext Mutliplex Oligos for Illumina (set1, E7335S; NEB).

treatment_protocol: For all experimental conditions, the medium was replaced with charcoal-stripped (SVFA) DMEM/F12 containing antibiotics and 100 nmol L-1 of 4-androstene-3,17-dione. The 24h treatments consisted of adding either ethanol (less than 0.05% of the culture volume) as a control or additional stimulator in ethanol to obtain 1 nmol of melatonin L-1 or 1 mmol of FSK L - 1 for final concentrations. the experiment was repeated 2 times (2 different weeks) for RNA-seq analysis.

value: granulosa cells

value: 1 micromol of FSK L-1


title: Control_2

type: RNA

city: Ikoma

first: Hitomi

last: Takada

state: Nara

address: 8916-5 Takayama-cho

department: Graduate School of Science and Technology

country: Japan

institute: Nara Institute of Science and Technology

description: Gene expression in the inguinal fat derived from a healthy control patient

hyb_protocol: Cy3 labeled cDNA was resuspended in 30uL of the Hybridization Master Mix containing Gene Expression Blocking Agent and Hi-RPM Hybridization Buffer and incubated at 95°C for 3 minutes. 40uL of sample was hybridized onto the SurePrint G3 Human GE 8 × 60k Microarray Ver3.0 (G4858A, Agilent Technologies) at 65°C for 16 hours. After hybridization, the array slides were washed with Agilent Gene Expression Wash Buffer1 at room temperature for 1 minute, washed with Agilent Gene Expression Wash Buffer 2 at 37°C for 1 minite, and dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid:072363_D_F_20180928) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Inguinla fat derived from a healthy control patient

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1.8 ug cDNA using the SureTag DNA labeling kit (Agilent) according to manufacturer's instructions and purified by the purification column included in the kit. Dye incorporation and cDNA yield were checked with the NanoDrop ND-2000c Spectrophotometer.

extract_protocol: Immediately after harvest, inguinal fat was mechanically homogenized and dissolved with ISOGEN, an RNA extraction reagent (Cat# 311-02501; Nippon Gene, Tokyo, Japan). Total RNA was purified using the RNeasy Mini kit (Qiagen, Carlsbad, CA) according to the manufacturer's directions. Synthesis of cDNA was performed using the StepOnePlus real-time PCR system (Thermo Fisher Scientific, Waltham, MA) and SuperScript II reverse transcriptase (Cat# 18080093; Invitrogen, Waltham, MA). cDNA probes were labeled with Cy3 using a SureTag DNA Labeling kit (Agilent Technologies, Santa Clara, CA)

tag: hiv status

value: negatie


title: Control_1

value: negative


title: HDAC1_ChIPseq_E14_Rbbp4mut2

city: Chapel Hill

first: Weipeng

last: Mu

state: MA

address: 120 Mason Farm Road

department: Genetics

institute: UNC at Chapel Hill

data_processing:
Sequence reads were aligned to genomic sequence (mm10) with Bowtie2
MACSv2 identified ChIP-seq enrichment using the broad peaks model
Differential binding analysis were performed using CSAW

source_name: E14 mouse embryonic stem cells

growth_protocol: ES cells were cultured in Glasgow Minimum Essential Medium supplemented with 15% fetal bovine serum, 1.0 mM L-glutamine, 0.1 mM minimal essential medium-nonessential amino acids, 0.1 mM β-mercaptoethanol, and leukemia inhibitory factor.

extract_protocol:
ES cells were fixed in 0.6% formaldehyde for 10 min at room temperature. Nuclei were prepared and digested with MNase for immunoprecipitation with antibodies.
Libraries were created using Kapa hyperprep DNA library kit for Illumina sequencing

tag: antibody

value: HDAC1, Diagenode #C15410325-10

value: E14 Rbbp4mut


title: E14_Input_2_DNA

description: Input.bw

value: input


title: E2_12h_run1_RNAseq

data_processing:
Good quality 50bp reads were aligned to the reference human genome (hg19, UCSC) using Tophat software keeping those that mapped uniquely to the reference with up to two mismatches and transcript assembly, abundance quantification and differential expression analyses were performed with the Cufflinks tool.
Genes under 200bp in length or with FPKM values below 0,1 were excluded from downstream analyses. Genes were classified into induced, repressed or non-regulated depending on log2FC value relative to untreated cells (T0). Threshold value was arbitrarily set at log2FC = +/- 0.8 and q<0.05 (FDR).
Genome_build: hg19
Supplementary_files_format_and_content: text file including fpkm values for all samples of two biological replicates (run1 and run2) and fold change versus untreated sample

extract_protocol:
Cells were washed once in PBS and whole cell lysates were prepared using Trizol reagent (Invitrogen). Total RNA (>200bp) was obtain using RNeasy Plus Mini kit (Qiagen) according to manufacturer specifications.
Poly-A-enriched RNA was used to prepare libraries with TruSeq RNA Sample Preparation kit v2 y v4 (ref. RS-122-2001/2, Illumina) according to instructions from manufacturer followed by single-end (run1) and paired-end (run2) sequencing

treatment_protocol: Adequate number of cells were seeded in culture plates using DMEM/F12 (1:1) without phenol red and supplemented with 5% dextran-coated charcoal stripped FCS and gentamycin for 48h, followed by overnight incubation in DMEM/F12 (1:1) without phenol red and without FCS. After overnight incubation, cells were treated or not with R5020 10nM and E2 10nM for 12h.

value: endometrial adenocarcinoma

value: Ishikawa

tag: cell type

value: epithelial-like

value: 12h E2-treated Ishikawa cells


title: HIV_2

description: Gene expression in the inguinal fat derived from a HIV-infected patient

source_name: Inguinla fat derived from a HIV-infected patient

value: positive


title: HDAC1_ChIPseq_E14_Rbbp4mut1


title: UFM1 KO SenV Rep 2

city: Durham

first: Stacy

last: Horner

state: North Carolina

address: 213 Research Drive, CARL 0049

department: MGM

institute: Duke University

data_processing:
TrimGalore toolkit was used to process RNA-seq data
Trimmed reads were mapped to GRCh38v93
differential expression was carried out using the DESeq2
Genome_build: GRCh38v93
Supplementary_files_format_and_content: Excel spreadsheet files include log2FC

source_name: 293T cells

growth_protocol: 293T cells were grown at 37C with 5% CO2 in DMEM supplemented with 10% FBS, 1X minimum essential medium non-essential amino acids, and 25 mM HEPES

extract_protocol:
Cells were harvested in TRIzol and RNA was extracted by manufacturer protocol, after which TURBO DNase treatment was performed and RNA was phenol-chloform precipitated.
Libraries were prepared using the KAPA Stranded mRNA-Seq Kit.

treatment_protocol: after adherence, cells were infected with 200HAU SenV or mock infection

tag: crispr ko

value: UFM1 KO

value: SenV


title: G401 in_vivo DMSO rep2

source_name: cancer cell

value: DMSO

value: G401-derived Xenogrft  tissue


title: R5020_12h_run1_RNAseq

value: adherent

value: 12h R5020-treated Ishiakwa cells


title: CTRL (no treatment)

value: granulosa cells

value: no treatment


title: Untreated_T0_run1_RNAseq

value: untreated Ishikawa cells


title: HIV_1


title: UFM1 KO SenV Rep 1


title: G401 in_vivo DMSO rep1

value: wild type


title: HDAC1_ChIPseq_E14_ctrl2

value: HDAC1, Diagenode #C15410325-10

value: E14 ctrl


title: UFM1 KO SenV Rep 3


title: HCV-1

city: Seoul

first: HEE

last: CHO

address: 50 YONSEI-RO, SEODAEMUN-GU

country: South Korea

institute: Yonsei University

description: Small RNA sequencing data

data_processing:
Reads were collapsed after removal of 3' adapters using fastx-toolkit
All reads < 16 nts and > 30 nts, as well as untrimmed reads, were discarded
Reads were aligned to the hg19 genome assembly using bowtie version 1.0.1
Downloaded tRNA sequences from the Genomic tRNA database, mucroRNA sequences from miRbase database, known non-coding RNA sequences from ensemble database
Give a name according to the sequence.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include ncRNA (e.g. miRNA, tRNA) raw read counts for each sample

source_name: Liver tissue from HCV patient

growth_protocol: Huh7 cells were cultivated in Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum, 2 mM L-glutamine, 100 U/ml of penicillin, 100 μg/ml streptomycin and 0.1 mM nonessential amino acids at 37°C in 5% CO2.

extract_protocol:
Total RNA was extracted from Huh7 cells using TRIzol.
RNA was prepared for illumina sequencing using the TrueSeq Small RNA Sample preparation kit according to manufacturer's protocol.

value: liver

value: HCV patient

tag: Sex

value: Male


title: HCV-3

description: Small RNA sequencing data

value: Female


title: A2780D6 MAK683 rep3


title: UFM1 KO Mock Rep 2

value: Mock


title: A2780D6 MAK683 rep2


title: A2780D6 DMSO rep2


title: HDAC1_ChIPseq_E14_ctrl1


title: A2780D6 MAK683 rep1


title: HCV-2

description: Small RNA sequencing data


title: UFM1 KO Mock Rep 3

value: UFM1 KO


title: Rbbp4_ChIPseq_E14_Rbbp4mut1

value: RBBP4, Proteintech #20364-1-AP

value: E14 Rbbp4mut


title: NL-1

description: Small RNA sequencing data

source_name: Normal liver tissue

value: normal


title: NL-2

description: Small RNA sequencing data


title: Rbbp4_ChIPseq_E14_ctrl1


title: A2780D6 DMSO rep3

value: DMSO


title: UFM1 KO Mock Rep 1


title: H3K27ac_ChIPseq_E14_Rbbp7ko2

value: H3K27ac, Active Motif (39133)

value: E14 Rbbp7ko


title: A2780D6 DMSO rep1


title: Huh7-2

description: Small RNA sequencing data

source_name: Total small RNA from Huh7 cells

value: Hepatocellular carcinoma cell line


title: WT SenV Rep 3

value: wild-type control

value: SenV


title: H3K27ac_ChIPseq_E14_Rbbp7ko1


title: Huh7-1

description: Small RNA sequencing data


title: WT SenV Rep 2


title: A2780 MAK683 rep3

value: wild type


title: Human retina H3K27ac HiChIP rep2 [HiChIP_LGS1OD]

value: Retina

tag: chip antibody


title: A2780 MAK683 rep2


title: WT SenV Rep 1


title: H3K27ac_ChIPseq_E14_Rbbp4mut1


title: A2780 MAK683 rep1


title: WT Mock Rep 3


title: H3K27ac_ChIPseq_E14_ctrl2

value: E14 ctrl


title: WT Mock Rep 2


title: A2780 DMSO rep3


title: H3K27ac_ChIPseq_E14_ctrl1


title: 521P

city: Chicago

first: Navdeep

middle: S

last: Chandel

state: IL

address: 303 E Superior St, SQ5

department: Pulmonary and Critical Care

institute: Northwestern University

data_processing:
Raw BCL read files were demultiplexed and FASTQ files were generated using bcl2fastq and trimmed using Trimmomatic (Bolger et al., 2014)
Reads were aligned to the mouse mm10 reference genome using STAR to generate BAM files (Dobin et al., 2013)
HTSeq was used to count reads in the exons of genes (Anders et al., 2015)
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file containing matrix table with raw gene counts for every gene and every sample

source_name: Macrophages

growth_protocol: Bone marrow was isolated from mice and plated in 10cm Primaria tissue culture plates (Thermo Fisher 25382-701). To induce differentiation into macrophages, cells were cultured in RPMI containing 11mM glucose, 10% Fetal+ serum (Atlas Biologics P16E19A1), 1mM methyl-pyruvate (Sigma, 371173), 400mM uridine (Sigma, U3003), 1% antibiotic/mycotic (Thermo Fisher 15-240-062) 1% Hepes (Thermo Fisher, MT25060CI), and 4mM glutamine (Gibco; 11965-126), supplemented with 20ng/mL M-CSF (Peprotech, 315-02) at 37C with 5% CO2. Media was changed every 3 days, and BMDMs were harvested by scraping on day 6 and plated in 12-well plates (2 million cells/well), 24-well plates (940,000 cells/well), 48-well plates (300,000 cells/well), or 96-well plates (150,000 cells/well).

extract_protocol:
Samples were lysed with RLT Plus buffer (Qiagen, 74134) with β-mercaptoethanol (1%) and homogenized with QIAshredder Spin Coumns (Qiagen, 79654). RNA was extracted using the RNeasy Plus Mini Kit (Qiagen, 74134), according to the manufacturer’s protocol plus on-column DNase treatment using the RNase-Free DNase Set (Qiagen, 79254).
mRNA libraries were prepared using NEBNext Ultra Kit with polyA selection (New England BioLabs).

treatment_protocol: BMDMs were pretreated with or without 500nM piericidin A for 30 minutes before addition of 100ng/mL ultra-pure LPS for 4 hours.

value: Bone marrow derived macrophages

value: VAV-Cre NDI1

value: Piericidin


title: 521U

value: Untreated


title: 521PL

value: LPS+Piericidin


title: 521L

value: LPS


title: A2780 DMSO rep1


title: H3K27ac_ChIPseq_E14_Rbbp4mut2

value: E14 Rbbp4mut


title: K562_ZRSR2_sh1_Exp1

city: Singapore

first: Pushkar

last: Dakle

address: 14 Medical Dr

country: Singapore

institute: Cancer Science Institute of Singapore

data_processing:
MSI (mis-splicing index) values were calculated for each intron
Only those introns with a coverage of at least one read at each of their junctions and with total coverage of the two junctions being higher than 4 were considered. Also, introns which did not have a coverage of at least 1 for 95% of their length were filtered out.
To identify differentially spliced introns, differences in MSI values (ΔMSI) were calculated as ΔMSI=MSIknockout−MSIwildtype. Significance of this difference was computed using Fisher's test and the obtained p-values were corrected for multiple testing.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited output files – intronwise mis-splicing index

source_name: K562 cells

growth_protocol: K562 cells were grown in RPMI-1640 containing 10% FBS

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen) from K562 cells transduced wih either shRNAs targeting ZRSR2 or control shRNA
polyA-selected RNA was used to prepare libraries using NEBNext Ultra RNA Library Prep Kit


title: G402 MAK683 rep3


title: 520U

value: VAV-Cre WT


title: H3K27me3_ChIPseq_E14_Rbbp4mut2

value: H3K27me3, Cell Signaling # 9733


title: G402 MAK683 rep2


title: 520PL


title: E14_Input_1_DNA

description: Input.bw

value: input


title: K562_ZRSR2_sh2_Exp1


title: H3K27me3_ChIPseq_E14_Rbbp4mut1


title: 520P


title: G402 MAK683 rep1


title: K562_ZRSR2_sh2_Exp2


title: H3K27me3_ChIPseq_E14_ctrl2


title: 520L


title: H3K27me3_ChIPseq_E14_ctrl1


title: K562_Con_sh_Exp1


title: H3K27me3_ChIPseq_E14_Rbbp7ko2

value: E14 Rbbp7ko


title: 503U


title: G402 DMSO rep2

value: DMSO


title: G402 DMSO rep3


title: A2780 DMSO rep2


title: Suz12_ChIPseq_E14_Rbbp7ko2

value: SUZ12, Cell Signaling #3737


title: 503PL


title: WT Mock Rep 1

value: wild-type control

value: Mock


title: K562_Con_sh_Exp2


title: K562_ZRSR2_sh1_Exp2


title: G402 DMSO rep1

value: wild type


title: Suz12_ChIPseq_E14_Rbbp7ko1


title: G401 MAK683 rep3


title: 503P


title: H3K27me3_ChIPseq_E14_Rbbp7ko1


title: Suz12_ChIPseq_E14_Rbbp4mut2


title: G401 MAK683 rep2


title: ubp8-B

city: Montreal

first: Saima

last: Rashid

state: Quebec

address: 7141 Sherbrooke St W

department: Department of Arts and Science

institute: Concordia University

data_processing:
RNA sequencing reads were pre-processed with the sequence-grooming tool cutadapt version 0.4.1(MARTIN 2011) with the following quality trimming and filtering parameters (`--phred33 --length 36 -q 5 --stringency 1 -e 0.1`). Each set of paired-end reads was mapped against the C. albicans SC5314 haplotype A, version A22 downloaded from the Candida Genome Database (CGD) (www.candidagenome.org) using HISAT2 version 2.0.4. SAMtools was then used to sort and convert SAM files. The read alignments and C. albicans SC5314 genome annotation were provided as input into StringTie v1.3.3 (PERTEA et al. 2015) which returned gene abundances for each sample. We imported gene abundances into R and conducted differential analysis of gene count data using the DESeq2 R package (Love et al. 2014).
Genome_build: C. albicans SC5314 haplotype A, version A22
Supplementary_files_format_and_content: Tab-delimited gene abundances files

organism: Candida albicans

source_name: yeast cells

extract_protocol:
Total RNA isolation was performed as previously described (Tebbji et al, PloSGenetics 2014)
Libraries were prepared according to Illumina's mRNASeq stranded library preparation kit

treatment_protocol: growth in YPD medium at 30 degrees celcius at 220rpm

value: ubp8-delta/delta yeast cells


title: ubp8-A


title: 503L

value: Bone marrow derived macrophages


title: 496U


title: spt8-B

value: spt8-delta/delta filamentous cell


title: G401 MAK683 rep1


title: Suz12_ChIPseq_E14_Rbbp4mut1


title: spt8-A


title: Suz12_ChIPseq_E14_ctrl2

value: E14 ctrl


title: spt7-B

value: spt7-delta/delta filamentous cells


title: G401 DMSO rep3


title: 496P

value: Piericidin


title: Suz12_ChIPseq_E14_ctrl1


title: G401 DMSO rep2


title: MLT

value: granulosa cells

value: 1 nmol of melatonin L-1


title: mESC_RNAseq_Rbbp4mut2_3

data_processing:
Sequence reads were aligned to mm10 genomic sequence with STAR (v2.7.3)
Aligned reads were counted by HTSeq
differentially expressed genes between controls and mutants were analyzed using DESeq2 (v1.22.2)

extract_protocol:
Cells were lysed with the TRIzol reagent (Invitrogen) and total RNA was isolated using the Direct-zol RNA kit (Zymo).
Sequencing libraries were prepared using a Kapa mRNA HyperPrep kit as per the manufacturer's instructions

value: embryonic stem cells


title: spt7-A


title: 496L

value: VAV-Cre WT

value: LPS


title: G401 DMSO rep1


title: 461U

value: VAV-Cre NDI1

value: Untreated


title: mESC_RNAseq_Rbbp4mut2_2


title: ngg1_A

value: ngg1-delta/delta yeast cells


title: mESC_RNAseq_Rbbp4mut2_1


title: 461P


title: 461PL

value: LPS+Piericidin


title: ngg1-B


title: mESC_RNAseq_Rbbp4mut1_3


title: 460U


title: Sample 22 Arabidopsis thaliana pifq seedlings

city: riverside

first: Peter

middle: H

last: Quail

address: 7774 Kingdom Dr

department: PMB

institute: UC Berkeley

data_processing:
Reads were aligned to Arabidopsis thaliana TAIR10 genome using Bowtie2 (Langmead and Salzberg, 2012).
H3K9ac enriched regions were identified using the BayesPeak algorithm with lower-bound summarization method (Spyrou et al., 2009).
Differential enrichment analysis was performed with DiffBind (Stark, R and Brown, 2015), comparing H3K9ac enrichment in these regions among different samples. Only peaks with statistically significant different levels with an FDR ≤0.05 were used in the analysis.
Genome_build: TAIR10
Supplementary_files_format_and_content: Absolute H3K9ac peak values.xlsx

organism: Arabidopsis thaliana

source_name: Seedling

growth_protocol: Plants were germinated in true-dark conditions as described in (Leivar et al., 2008). Briefly, seeds were sterilized, plated in MS medium without sucrose, irradiated for 3h with white light to induce germination, followed by a saturating far-red light pulse during 5 min before being stratified for 4 days at 4ºC in darkness. They were grown in the dark at 21ºC for 2 days before being collected (D samples) or grown in the dark for 47 hours and treated with 10 μE⋅m−2⋅s−1 red light for 1 hour (R1 samples). White-light grown samples (WLc) were grown under continuous white-light (100 μE⋅m−2⋅s−1 PAR) after stratification for 2 days.

extract_protocol:
For each replicate, 2.5 gr of 2-day old wild-type and pifq D, R1h and WLc treated seedlings were processed as described in (Gendrel et al., 2005) using 5 µgr Diagenode Ab C15410004 H3K9ac antibody and a mix of 25/25 µl of protein-A/G dynabeads (Invitrogen).
5-10 ng of DNA per sample were used for library preparation with Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences) and 9 PCR cycles. 300-700 bp fragments were purified

value: pif1345 quadruple mutant

tag: ecotype

value: Darkness (D1)

value: Seedling

value: Total input DNA


title: SN148-B

value: wild type cells


title: 461L

value: Bone marrow derived macrophages


title: SN148-A


title: Sample 23 Arabidopsis thaliana pifq seedlings

treatment_protocol: Plants were germinated in true-dark conditions as described in (Leivar et al., 2008). Briefly, seeds were sterilized, plated in MS medium without sucrose, irradiated for 3h with white light to induce germination, followed by a saturating far-red light pulse during 5 min before being stratified for 4 days at 4ºC in darkness. They were grown in the dark at 21ºC for 2 days before being collected (D samples) or grown in the dark for 47 hours and treated with 10 μE⋅m−2⋅s−1 red light for 1 hour (R1 samples). White-light grown samples (WLc) were grown under continuous white-light (100 μE⋅m−2⋅s−1 PAR) after stratification for 2 days.

value: Darkness + 1h Red light (R1)


title: mESC_RNAseq_Rbbp4mut1_2


title: mESC_RNAseq_ctrl3


title: 496PL


title: Sample 21 Arabidopsis thaliana Col-0 seedlings

value: wild type

value: White light (W1)


title: 460P

value: Piericidin


title: mESC_RNAseq_ctrl2

value: embryonic stem cells


title: 460L


title: mESC_RNAseq_ctrl1


title: Sample 20 Arabidopsis thaliana Col-0 seedlings


title: 453U

value: VAV-Cre WT


title: swimming6 [162]

city: Fuzhou

first: Jun

last: Peng

state: Fujian

address: 1 Qiuyang Road, Minhou Shangjie

department: Academy of Integrative Medicine

institute: Fujian University of Traditional Chinese Medicine

data_processing:
Sequenced reads were trimmed for adaptor sequence, then mapped to hg38 whole genome using hisat2 v2.0.5
Raw counts and Fragments Per Kilobase Million(FPKM) were calculated by stringtie v1.3.3
Differential expression analyses were performed using the limma package.
Genome_build: GRCm38.92
Supplementary_files_format_and_content: tab_delimited text files include FPKM values for each Sample

source_name: tumor tissue

extract_protocol:
The tumor were dissected and tumor tissues were stored in liquid nitrogen until use.Total RNA was extracted with Trizol (Tiangen, Beijing, China). RNA integrity was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and RNA concentration was measured by Qubit RNA Assay Kit in a Qubit Fluorometer (Invitrogen, CA, USA).
A total amount of 1 μg RNA per sample was used. In brief, the NEBNext rRNA Depletion Kit was used to remove rRNA from the total RNA. The NEB Next Ultra RNA Library Prep Kit for Illumina (NEB, Beijing, China) was used to construct the libraries for sequencing following the manufacturer’s instructions.

value: tumor tissue

tag: group

value: swimming

value: CT-26 cells


title: 453PL


title: Sample 18 Arabidopsis thaliana pifq seedlings

value: White light (W3)


title: swimming5 [159]


title: Sample 24 Arabidopsis thaliana pifq seedlings


title: mESC_RNAseq_Rbbp4mut1_1


title: Sample 16 Arabidopsis thaliana pifq seedlings


title: 452U

value: Untreated


title: 453P


title: 460PL

value: VAV-Cre NDI1

value: LPS+Piericidin


title: Sample 14 Arabidopsis thaliana pifq seedlings

value: pif1345 quadruple mutant

value: Darkness + 1h Red light (R2)

value: Seedling


title: 453L

value: Bone marrow derived macrophages

value: LPS


title: control6 [177]

value: control


title: swimming4 [156]


title: Sample 15 Arabidopsis thaliana pifq seedlings

value: Darkness + 1h Red light (R3)


title: swimming3 [166]


title: Sample 17 Arabidopsis thaliana pifq seedlings

value: White light (W2)


title: Sample 13 Arabidopsis thaliana pifq seedlings

value: Darkness + 1h Red light (R1)


title: Sample 12 Arabidopsis thaliana pifq seedlings

value: Darkness (D3)


title: control4 [170]

value: tumor tissue


title: control5 [160]


title: swimming2 [179]

value: swimming


title: Sample 11 Arabidopsis thaliana pifq seedlings

value: Darkness (D2)


title: control3 [169]

value: CT-26 cells


title: Sample 19 Arabidopsis thaliana Col-0 seedlings

value: wild type

value: Darkness (D1)

value: Total input DNA


title: Sample 10 Arabidopsis thaliana pifq seedlings

value: pif1345 quadruple mutant


title: Sample 9 Arabidopsis thaliana Col-0 seedlings

value: White light (W3)


title: 449U

value: VAV-Cre WT

value: Untreated


title: control2 [176]


title: swimming1 [172]


title: 452PL

value: Bone marrow derived macrophages

value: LPS+Piericidin


title: 452P

value: Piericidin


title: 449PL


title: 452L

value: LPS


title: Sample 8 Arabidopsis thaliana Col-0 seedlings

value: White light (W2)

value: Seedling


title: 449L


title: 447U

value: VAV-Cre NDI1


title: control1 [167]

value: tumor tissue

value: control


title: Sample 7 Arabidopsis thaliana Col-0 seedlings

value: White light (W1)


title: 447PL


title: 447L


title: Scx-homoKO1 bulk

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

institute: Medical Institute of Bioregulation

description: bulk RNA-Seq by NEBNext Ultra II Directional RNA Library Prep Kit

data_processing:
Reads were aligned to GRCm38 using HISAT2 (version 2.0.4) and gene count was obtained by featureCount (version 1.5.0).
Genome_build: GRCm38
Supplementary_files_format_and_content: raw count matrix:(CSV) and cell barcode list(txt), gzipped

source_name: Achilles tendon tissue 2-week-old

growth_protocol: ScxGFP iPSCs were cultured on feeder cells under 2i LIF condition.

extract_protocol:
Total RNA was extracted from 2-week-old Scx KO and wild type littermates (n = 2) using TRIzol reagent (Invitrogen 15596026)
mRNA is isolated by NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, E7490) and DNA libraries were prepared using NEBNext Ultra Directional RNA Library Prep Kit (New England BioLabs, 7760)

treatment_protocol: Mesodermal cells (T0) were induced from ScxGFP iPSCs in DF (DMEM-F12) supplemented with 5% FBS, 2 mM L-glutamate, and ITS (10 ng/ml insulin, 10 ng/ml transferrin, 3 × 10^-8 M sodium selenite)  for 4 days. T0 cells were cutured in DF supplemented with 1% FBS, 2 mM L-glutamate, ITS, and 10 ng/ml recombinant human TGF-β2 for 3, 6, or, 9 days (T3, T6, T9).

tag: cell types

value: Achilles tendon


title: 449P


title: Sample 6 Arabidopsis thaliana Col-0 seedlings

value: wild type

value: Darkness + 1h Red light (R3)


title: Scx-Wt2 bulk


title: Scx-Wt1 bulk


title: T9-3 single-cells

description: R2(36bp) is insert reads and R1(15bp) is UMI(6bp) + cell barcode(9bp) reads for 384 cells. Please use 384_CellBarcode_list.txt.gz for demultiplexing.

data_processing:
Unique-molecular-identifiers and cell baecodes in the read1 were extracted using UMI-tools (version 1.0.1) with the command: umi_tools extract --bc-pattern=NNNNNNCCCCCCCCC --stdin Read1.fastq --read2-in Read2.fastq --read2-stdout --filter-cell-barcode --whitelist=384_usedCB.txt --quality-encoding phred33 --quality-filter-mask 20. Reads were aligned to GRCm38 by HISAT2 (version 2.2.1). UMI count matrix was obtained by featureCounts (version v2.0.1) and UMI-tools with the command: umi_tools count --method=unique --per-gene --per-cell --gene-tag=XT. The unique molecular identifiers duplicates were discarded.
Genome_build: GRCm38
Supplementary_files_format_and_content: raw count matrix:(CSV) and cell barcode list(txt), gzipped

source_name: Induced tenocytes

extract_protocol:
Cells were sorted and lysed in 1ul of lysis buffer containing (0.3% NP40, 0.12mM dNTPs, 1U RNase Inhibitor, 0.11 uM 384-well-unique Reverse Transcribe primer).
CEL-Seq2 protocol was used for single cell analysis with some modifications that SuperScripII enzyme to MaximaH minus (Thermo Scientific, EP0752) and 2nd strand buffers to 2nd Strand Module (NEB,E6111). 384 cells in the same plate were pooled together after reverse transcription.

value: ScxGFP iPSCs derived tenocytes

tag: stimulation

value: TGF-β2 for 9 days


title: Sample 3 Arabidopsis thaliana Col-0 seedlings

value: Darkness (D3)


title: 5_ChAT-

city: Boston

first: I-Hsiu

last: Lee

state: Massachusetts

address: 185 Cambridge Street

department: Center for Systems Biology

institute: Mass General Hospital/Harvard University

description: Chrna7+ bone marrow niche cells

data_processing:
Illumina proprietary software used for basecalling
Cell Ranger (versioin 4.0.0) was used to demultiplex raw base call files from the Illumina sequencer to produce fastq files.
Cell Ranger was used to align the reads, filter out background-associated-barcodes, count barcodes and UMIs, and generate gene-barcode matrices.
Genome_build: mm10
Supplementary_files_format_and_content: Count matrices in Market Exchange Format for sparse matrices and gzipped tsv files for genes and barcodes corresponding to row and column indices of the count matrices

source_name: Cd19-Cre Chat-fl/fl Chrna7+ bone marrow niche cells

extract_protocol:
Single cells were captured and lysed, and cDNA was synthesized and amplified in accordance to the 10X Genomics Single Cell 3’ v3 Reagent Kit user guide.
The amplified cDNA was used to construct Illumina sequencing libraries. Constructed libraries were validated and quantified with the High Sensitivity DNA chip and by real-time qPCR, and subsequently sequenced on an Illumina NextSeq 500 in high-output mode.

value: Bone marrow

value: Cd19-Cre Chat-fl/fl

tag: condition

value: steady state

value: Chrna7+ stromal cells

tag: cell selection

value: FACS-purified cells


title: Sample 4 Arabidopsis thaliana Col-0 seedlings

value: Darkness + 1h Red light (R1)


title: Sample 2 Arabidopsis thaliana Col-0 seedlings

value: Darkness (D2)

value: Seedling


title: T9-1 single-cells


title: HEK_Hneg_ILMN

city: Trento

first: Alessia

last: Del Piano

state: Trento

address: Via Sommarive 18

country: Italy

institute: IMMAGINA BioTECHNOLOGY

description: standard ribosome profiling from HEK293T cells, transiently transfected with GFP plasmid

data_processing:
Library strategy: circAID-p-seq
circAID-p-seq basecalling : Guppy 3.6.1
circAID-p-seq consensus generation: CircAidMe pipeline
Ribo-seq data from all the library construction were aligned on GRCh38.p13 for HEK293T and GRCm38.p6 for mouse tissue using Botwie 2
Alignment files were processed with Samtools version 1.9 and analyzed with the RiboWaltz R package
Genome_build: Human: GRCh38.p13 -  Mouse:GRCm38.p6
Supplementary_files_format_and_content: Excel files including a brief annotation and transcript-specific counts of ribosome protected fragments

source_name: control HEK293T cells, Riboseq/ILMN

growth_protocol: Young adult wild-type FVB mice were obtained from breeding stocks at the University of Edinburgh. HEK293 (H. Sapiens, RRID: CVCL_0045) cells were seeded at 1.5x106 cells/dish and kept in culture until reaching 80% of confluence

extract_protocol:
Libraries from RPFs isolated from HEK293T cells were prepared using the SMARTer® smRNA-Seq Kit for Illumina  and sequenced with 50 cycles single-read on an Illumina NovaSeq 6000 sequencer. Illumina libraries for RPFs from mouse liver tissue were prepared according to Ingolia et al., 2012 and were sequenced with 50 cycles single-read on an Illumina HiSeq2500 sequencer.
HEK298T cell lysates were obtained using a hypotonic lysis buffer. A total of 1.7 a.u. (A260 nm) were digested using . RPFs were generated by treating 1.7a.u. of lysate with 12.7 U of RNase I at room temperature for 45 min (as described in Clamer et al., 2018). ). Liver tissues were dissected immediately following sacrifice and pulverized under liquid nitrogen using a pestle and a mortar and the lysates obtained according to Bernabò et al.2017. Lysates were treated with RNAse I and the 80S with RPFs were isolated using sucrose gradient separation. The RPFs were purified using acidic phenol/chloroform extraction followed by PAGE extraction.
Libraries from RPFs isolated from HEK293T cells were prepared using the SMARTer® smRNA-Seq Kit for Illumina  and sequenced with 50 cycles single-read on an Illumina NovaSeq 6000 sequencer. Illumina libraries for RPFs from mouse liver tissue were prepared according to Ingolia et al., 2012 and were sequenced with 50 cycles single-read on an Illumina HiSeq2500 sequencer.
Oxford nanopore libraries for RPFs from HEK293T and mouse liver were prepared according to circAID-p-seq protocol. Briefly, upon 5′ phosphorylation of RPFs, library preparation was performed starting from 10 pmol of ADR12 used for ligation, followed by RNA self circularization and RT-RCA. The final libraries were loaded on a R9.4 flow cell and sequenced with a MinION sequencer.

treatment_protocol: HEK293T cells were  treated with or without harringtonine (2 µg/mL) for 3 min, followed by CHX (10 μg/mL) for 5 min at 37°C.

value: HEK293T, GFP transfected, cell line

tag: replicate

tag: rna fraction

value: Ribo-seq

value: smarter smRNA-seq kit Takara

tag: sequencing platform

value: Illumina

value: Treated with CHX for 5 min before cell lysis


title: T9-2 single-cells


title: 3_ChAT+

description: Chrna7+ bone marrow niche cells

source_name: Chat-fl/fl Chrna7+ bone marrow niche cells

tag: tissue

tag: genotype

value: Chat-fl/fl


title: T6-3 single-cells

value: ScxGFP iPSCs derived tenocytes

value: TGF-β2 for 6 days


title: Sample 1 Arabidopsis thaliana Col-0 seedlings

value: wild type

tag: treatment

value: Darkness (D1)


title: 4_ChAT+

description: Chrna7+ bone marrow niche cells

value: Bone marrow


title: 6_ChAT-

description: Chrna7+ bone marrow niche cells

value: Cd19-Cre Chat-fl/fl

value: steady state


title: BEAS-2B WT-2

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

description: BEAS-2B WT rep2

data_processing:
Raw reads were trimmed using cutadapt (v1.14) using the following parameters -O 5 -f  fastq --match-read-wildcards --times 2 -e 0.0 --quality-cutoff 6 -m 18 -o data.fastqTr.fq -b TCGTATGCCGTCTTCTGCTTG -b ATCTCGTATGCCGTCTTCTGCTTG -b CGACAGGTTCAGAGTTCTACAGTCCGACGATC -b GATCGGAAGAGCACACGTCTGAACTCCAGTCAC -b AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -b TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT data.fastq.gz
Trimmed reads were mapped to and filtered of repeat elements (RepBase 18.05) with STAR (2.5.2) using the following parameters: --alignEndsType  EndToEnd  --genomeDir  repbase  --genomeLoad  NoSharedMemory  --outBAMcompression  10  --outFileNamePrefix  data  --outFilterMultimapNmax  10  --outFilterMultimapScoreRange  1  --outFilterScoreMin  10  --outFilterType  BySJout  --outReadsUnmapped  Fastx  --outSAMattrRGline  ID:foo  --outSAMattributes  All  --outSAMmode  Full  --outSAMtype  BAM  Unsorted  --outSAMunmapped  Within  --outStd  Log  --readFilesIn data.fastqTr.fq  --runMode  alignReads  --runThreadN  8
Reads unmapped to repeat elements were mapped to the human genome with STAR using the same parameters as the previous step, using an hg19/ChlSab2 index in place of the repeat element index
Subread featureCounts (-a gencode.v19.annotation.gtf -s 2 -p -o counts.txt data.bam) was used to count features using human annotations (Gencode v19)
Genome_build: ChlSab2
Genome_build: hg19
Supplementary_files_format_and_content: BigWig

growth_protocol:
Vero E6 and A549-ACE2 cells were cultured in DMEM supplemented with 10% FBS.
BEAS-2B cells were cultured on Matrigel (Corning) coated plates and maintained in the PneumaCult-Ex Plus Medium (Stem Cell Technologies), supplemented with 33 µg/ml hydrocortisone (Stem Cell Technologies). Growth media was replaced every two days, and the cells were passaged every four days. Vero E6 cells were cultured in DMEM (ThermoFisher) supplemented with 10% FBS (ThermoFisher) and passaged every three days. All cell cultures were incubated at 37ºC and 5% CO2.

extract_protocol:
Trizol extraction (Fisher) and Direct-zol miniprep (Zymo Research) column purification in accordance with manufacturer protocol
Illumina Stranded mRNA Prep kit

treatment_protocol:
Vero E6 and A549-ACE2 cells were treated with 1µg/ml doxycyline and infected with SARS-CoV-2 at MOI 0.1 and MOI 3, respectively, for 48 hours before treating with Trizol.
BEAS-2B cells were treated with Trizol when 70-90% confluent.

tag: cell line


title: Scx-homoKO2 bulk

value: Achilles tendon


title: BEAS-2B WT-1

description: BEAS-2B WT rep1


title: Sample 5 Arabidopsis thaliana Col-0 seedlings

value: Darkness + 1h Red light (R2)

tag: antibody


title: PNX-7D-LECs-mm10-rep2

city: Milwaukee

first: Akiko

last: Mammoto

state: WI

address: 8701 Watertown Plank Road

institute: Medical College of Wisconsin

data_processing:
Genome alignment and expression count (STAR) were performed using Basepair.
Genome_build: mm10
Supplementary_files_format_and_content: Expression count txt files include Transcript ID, Gene Symbol, Expression Count, Fragments Per Kilobase Million (FPKM), and Transcripts Per Kilobase Million (TPM) for each sample.

source_name: Lung

extract_protocol:
Mouse lung endothelial cells were isolated from C57BL6 mouse lungs (8 week old, male) using anti-CD31 conjugated magnetic beads. RNA was extracted using QIAGEN RNeasy mini kit (Cat# 74104). 1 ug of total RNA as used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: RNA was collected from endothelial cells isolated from mouse lungs 7 days after PNX and sham-operated mouse lungs

tag: strain

value: lung

tag: cell type

value: endothelial cell

value: pneumonectomy 7days

tag: age

value: 8 week old


title: 447P

value: Bone marrow derived macrophages

value: VAV-Cre NDI1

value: Piericidin


title: A549-ACE2-APO-moi-3

description: A549-ACE2-APO cells infected with SARS-CoV-2 at MOI 3 for 48 hours

source_name: A549 cells overexpressing ACE2 and APOBEC1

tag: agent


title: T6-2 single-cells


title: HEK_Hpos_ILMN

description: standard ribosome profiling  from HEK293T cells, transiently transfected with GFP plasmid and treated with Harringtoine drug

source_name: Treated HEK293T cells, Riboseq/ILMN

value: HEK293T, GFP transfected, cell line

value: Ribo-seq

value: smarter smRNA-seq kit Takara

value: Illumina

value: Treated with harringtonine for 3 min, followed by CHX for 5 min before cell lysis


title: PNX-7D-LECs-mm10-rep1


title: HCT116_Fuso_3

city: Hangzhou

first: zhang

last: ying

address: Kaixuan Road, Jianggan District

institute: Zhejiang University

description: Gene expression after treated with Fusobacterium nucleatum

data_processing:
Clean reads were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: HCT116 cells treated with Fusobacterium nucleatum

growth_protocol: HCT116 colorectal cancer cell line was purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA), and cultured in Maccoy 5A (Genom, China) with 10 % fetal bovine serum.

extract_protocol:
Total RNAs were extracted from each cell samples using the TRIZOL reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HCT116 cells were treated with or without Fusobacterium nucleatum.

value: colorectal cancer

value: Fusobacterium nucleatum


title: T3-3 single-cells

value: ScxGFP iPSCs derived tendon progenitors

value: TGF-β2 for 3 days


title: H3

city: Bangalore

first: Purna Sudha

middle: Bindu

last: Ambaru

state: Karnataka

address: Biotech park, Electronic city, phase 1,, hosur main road, Bangalore

country: India

institute: Institute of Bioinformatics and Applied Biotechnology

description:
H3_S6_L006
Profilin knockouts (LdPfn+/-) biological replicate three is labelled as H3.

data_processing:
Bowtie2 v2.3.5.1, Tophat v2.1.1
HTSeq v0.12.4
Paired end reads were trimmed and aligned with Leishmania donovani (BPK282A1) genome using Tophat pipeline using bowtie2 aligner
alignment files were sorted using samtools view -bS and samtools view sort options
Read counts were calculated using htseq-count -f option
Genome_build: LdonovaniBPK282A1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Leishmania donovani

growth_protocol: Leishmania donovani (BPK282A1) cells were maintained in high glucose Dulbecco's modified Eagle’s medium (DMEM) (Life Technologies, Thermo Fisher Scientific) supplemented with 10% heat-inactivated fetal bovine serum (MP chemicals) and 4mg ml-1 gentamicin (MP chemicals).  Heterozygous LdPfn mutants (LdPfn+/-Hygro) were maintained in high-glucose DMEM supplemented with 10% heat-inactivated fetal bovine serum and 100µg ml-1 hygromycin B (Invitrogen) at 25oC.

extract_protocol:
Total RNA from three independent biological replicates was isolated from LdPfn+/+ (control) and LdPfn+/-Hygro (profilin knockout) promastigotes using TRIzol reagent (Ambion, Life Technologies), according to the manufacturer’s instructions. RNA samples were treated with DNase I (2μg) and the RNA concentration was determined using a spectrophotometer at A260/280 (Nanodrop ND1000, Thermo Scientific, USA). In addition, the RNA integrity was evaluated using TapeStation (Agilent) and Qubit (Invitrogen).  Using NEBNextUltraTM II RNA Library Prep Kit for Illumina, Poly (A) mRNA Magnetic isolation was performed.
Library preparations were performed using the NEBNextUltraTM II RNA Library Prep kit (Illumina), according to the manufacturer’s instructions.

tag: Stage

value: Mid-log

value: Profilin knockout (LdPfn+/-)


title: T3-2 single-cells

tag: cell types


title: HCT116_Fuso_2


title: Sham-LECs-mm10-rep2

value: lung

value: endothelial cell

value: sham operated


title: T3-1 single-cells

tag: stimulation


title: HCT116_Fuso_1


title: H2

description:
H2_S5_L006
Profilin knockouts (LdPfn+/-) biological replicate two is labelled as H2.


title: HCT116_control_3

description: Gene expression after treated with PBS control

source_name: HCT116 cells treated with PBS control


title: L3

description:
L3_S3_L006
Wild-type (LdPfn+/+) biological replicate three is labelled as L3

value: wild type (LdPfn+/+)


title: LiverC_WT_ONT

description: ribosome profiling with circAID-p-seq from mouse liver tissue

source_name: liver tissue from young adult wild-type FVB mice, circAID-p-seq/ONT

extract_protocol:
Oxford nanopore libraries for RPFs from HEK293T and mouse liver were prepared according to circAID-p-seq protocol. Briefly, upon 5′ phosphorylation of RPFs, library preparation was performed starting from 10 pmol of ADR12 used for ligation, followed by RNA self circularization and RT-RCA. The final libraries were loaded on a R9.4 flow cell and sequenced with a MinION sequencer.
HEK298T cell lysates were obtained using a hypotonic lysis buffer. A total of 1.7 a.u. (A260 nm) were digested using . RPFs were generated by treating 1.7a.u. of lysate with 12.7 U of RNase I at room temperature for 45 min (as described in Clamer et al., 2018). ). Liver tissues were dissected immediately following sacrifice and pulverized under liquid nitrogen using a pestle and a mortar and the lysates obtained according to Bernabò et al.2017. Lysates were treated with RNAse I and the 80S with RPFs were isolated using sucrose gradient separation. The RPFs were purified using acidic phenol/chloroform extraction followed by PAGE extraction.
Libraries from RPFs isolated from HEK293T cells were prepared using the SMARTer® smRNA-Seq Kit for Illumina  and sequenced with 50 cycles single-read on an Illumina NovaSeq 6000 sequencer. Illumina libraries for RPFs from mouse liver tissue were prepared according to Ingolia et al., 2012 and were sequenced with 50 cycles single-read on an Illumina HiSeq2500 sequencer.
Oxford nanopore libraries for RPFs from HEK293T and mouse liver were prepared according to circAID-p-seq protocol. Briefly, upon 5′ phosphorylation of RPFs, library preparation was performed starting from 10 pmol of ADR12 used for ligation, followed by RNA self circularization and RT-RCA. The final libraries were loaded on a R9.4 flow cell and sequenced with a MinION sequencer.

value: liver tissue

value: circAID-p-seq

value: Oxford nanopore technology

value: untreated


title: Sham-LECs-mm10-rep1

value: 8 week old


title: HCT116_control_2


title: L2

description:
L2_S2_L006
Wild-type (LdPfn+/+) biological replicate two is labelled as L2


title: LiverB_WT_ONT

value: Ribo-seq


title: T0-3 single-cells

source_name: Induced mesodermal cells

value: ScxGFP iPSCs derived mesodermal cells

value: non-treatment


title: T6-1 single-cells

value: ScxGFP iPSCs derived tenocytes

value: TGF-β2 for 6 days


title: T0-2 single-cells


title: LiverA_WT_ONT


title: HCT116_control_1

value: colorectal cancer


title: T0-1 single-cells


title: L1

description:
L1_S1_L006
Wild-type (LdPfn+/+) biological replicate one is labelled as L1

value: Mid-log


title: D24-3

status: Public on Mar 08 2022

city: Grand Forks

first: Danielle

last: Perley

state: North Dakota

address: 1301 N Columbia Rd

institute: University of North Dakota Genomics Core

data_processing:
Illumina Casava software used for basecalling.
All runs were demultiplexed using bcl2fastq to obtain raw fastq files
Adapter sequences removed using Trimmomatic with parameters ILLUMINACLIP:2:30:10 LEADING:2 TRAILING:2 SLIDINGWINDOW:4:2 MINLEN:25
Sequences aligned to B. burgdorferi reference transcriptome and counted using Salmon v1.5.2  with parameters quant -i  -1 A  --seqBias --gcBias --validateMappings
Differential expression analysis was performed using DESeq2 in R version 4.0.1
Genome_build: B. burgdorferi B31 consensus genome (NCBI RefSeq numbers AE000783 to AE000794 and AE001575 to AE001584)
Supplementary_files_format_and_content: tab-delimited text files include regularized log-transformed (rlog) gene counts for each sample as determined using DESeq2

organism: Borreliella burgdorferi

source_name: Log-phase in vitro bacterial culture

growth_protocol: All Borrelia burgdorferi clones were grown at 35°C in modified Barbour-Stoenner-Kelly medium (BSK) supplemented with 6% rabbit serum. Cell densities and growth phase were monitored by visualization under dark-field microscopy and counting using a Petroff-Hausser counting chamber. Cells were subcultured into treatment groups during mid-log phase (~3e7 cells / ml).

extract_protocol:
RNA was extracted from frozen bacterial pellets by ACGT Inc. using the Quick RNA-Microprep Kit (Zymo Research) using standard protocols.
Libraries were constructed by ACGT Inc. using the Zymo-Seq Ribofree Total RNA Library Kit (Zymo Research) using standard protocols.

treatment_protocol: Cells were subcultured for 3h or 24h in 0.2μg/mL amoxicillin, doxycycline, or media control as indicated, after which bacteria were harvested for RNA isolation.

tag: isolate

value: 24h 0.2μg/mL doxycycline


title: A24-2

value: 24h 0.2μg/mL amoxicillin


title: D24-1


title: H1

description:
H1_S4_L006
Profilin knockouts (LdPfn+/-) biological replicate one is labelled as H1.

value: Profilin knockout (LdPfn+/-)


title: A24-3


title: U24-3

value: 24h no antibiotics


title: U24-2


title: D24-2


title: D3-2

value: 3h 0.2μg/mL doxycycline


title: D3-1


title: A3-2

value: 3h 0.2μg/mL amoxicillin


title: A24-1


title: A3-3


title: U3-3

value: 3h no antibiotics


title: U3-2


title: U24-1


title: A3-1


title: U3-1


title: AGO2-CLIP: HepG2-AtRDR1(+)Dox-CLIP

city: Beijing

first: Li

last: Ding

state: Beijing

address: No.5, Yiheyuan Road

institute: Peking University

data_processing:
To analyze polyA(+) RNA-seq data, adapters of raw data were trimmed with Trimmomatic software. The quality of these data was evaluated by FastQC software. HISAT2 software with default parameters was used to align sequences to the human genome (hg38, UCSC) and the mouse genome (mm10, UCSC) based on the origin of the cell lines. Output files after sequence alignment were used to obtain gene count matrix with featureCounts software using corresponding UCSC RefSeq as gene annotations. For further analyses, gene counts in each sample were normalized to the total reads of the library to calculate reads per million (RPM).
Perl and python scripts were used to analyze small RNA-seq data. Adapters of sequences were trimmed and sequences with a length of 19-25nt were retained. To build the index of miRNA, we downloaded the mature miRNA sequences from miRBase, 3nt upstream and 3nt downstream of mature miRNA were added to the references. Each sequence was aligned to the reference using Bowtie software using the following parameters: -a -v 1 -3 3.In order to compare the miRNA expression in the line, the count of miRNAs was normalized. In RDR1 expression group, two ways were used to normalize miRNA data. Fly miRNA was added as spike-in in some samples. In non-spike-in method (including A549, HeLa, HepG2, HCT116 and NIH/3T3), the numbers of miRNAs were normalized to the numbers of total reads of the corresponding library to calculate RPM. In spike-in method (including H1299, Jurkat and RPE-1), the number of miRNAs was multiplied by a factor to make the count of fly miRNAs equal in all samples in a cell line. We used the top-10 highest expressed miRNAs as reference, which did not contain identical miRNAs in fly and human/mouse. Each of these 10 miRNAs was used to calculate a factor and the mean of these 10 factors was used as the factor for this sample for normalization. After normalization between samples within cell lines, the normalized reads of the sample with higher miRNA expression level was set at one million. In cell cycle inhibition, AGO2-CLIP and AGO2 knockdown experiments, miRNA expression was normalized with non-spike-in method. Some cell lines of RDR1 expression group were used in this analysis (A549, HeLa, HepG2). In order to be consistent with the previous analysis in RDR1 expression group, the normalized reads of the sample with higher miRNA expression level of RDR1 expression group was set at one million. In the miR-34c transfection assay, miRNA expression was normalized to the expression of endogenous miRNA, which was set at one million.
Assembly: mm10, hg38
Supplementary files format and content: Gene expression matrix

source_name: HepG2-AtRDR1 stable cell line

extract_protocol:
TRIzol reagent (Invitrogen) was used to isolate total RNA according to the manufacturer’s instructions.
RNA-seq libraries preparation using the TruSeq Stranded mRNA Sample Prep Kits (Illumina), VAHTS Stranded mRNA-seq Library Prep Kits (Vazyme) and VAHTS Ribo-off Globin & rRNA Depletion Kits(Vazyme).

tag: cell type and treatment

value: HepG2-AtRDR1 with Dox induction for 6 days followed by AGO2-CLIP

value: HepG2-AtRDR1 stable cell line


title: AGO2-CLIP: HepG2-AtRDR1(-)Dox-CLIP

value: HepG2-AtRDR1 without Dox induction followed by AGO2-CLIP


title: RNA-seq: WIBR3-EGFP

source_name: WIBR3-EGFP stable cell line

value: WIBR3 with EGFP consistent expression

value: WIBR3-EGFP stable cell line


title: RNA-seq: WPMY-1-OsRDR1(-)Dox

source_name: WPMY-1-OsRDR1 stable cell line

value: WPMY-1-OsRDR1 without Dox induction

value: WPMY-1-OsRDR1 stable cell line


title: RNA-seq: WIBR3-OsRDR1

source_name: WIBR3-OsRDR1 stable cell line

value: WIBR3 with OsRDR1 consistent expression

value: WIBR3-OsRDR1 stable cell line


title: RNA-seq: WPMY-1-OsRDR1(+)Dox

value: WPMY-1-OsRDR1 with Dox induction for 6 days


title: RNA-seq: WPMY-1-AtRDR1(-)Dox

source_name: WPMY-1-AtRDR1 stable cell line

value: WPMY-1-AtRDR1 without Dox induction

value: WPMY-1-AtRDR1 stable cell line


title: RNA-seq: RPE-1-OsRDR1(+)Dox

source_name: RPE-1-OsRDR1 stable cell line

value: RPE-1-OsRDR1 with Dox induction for 6 days

value: RPE-1-OsRDR1 stable cell line


title: RNA-seq: RPE-1-AtRDR1(+)Dox

source_name: RPE-1-AtRDR1 stable cell line

value: RPE-1-AtRDR1 with Dox induction for 6 days

value: RPE-1-AtRDR1 stable cell line


title: D3-3

value: 3h 0.2μg/mL doxycycline


title: RNA-seq: RPE-1-OsRDR1(-)Dox

value: RPE-1-OsRDR1 without Dox induction


title: RNA-seq: RPE-1-AtRDR1(-)Dox

value: RPE-1-AtRDR1 without Dox induction


title: RNA-seq: RPE-1-WT-1

value: WT


title: RNA-seq: K562-AtRDR1(+)Dox

source_name: K562-AtRDR1 stable cell line

value: K562-AtRDR1 with Dox induction for 6 days

value: K562-AtRDR1 stable cell line


title: RNA-seq: RPE-1-WT-2


title: RNA-seq: K562-OsRDR1(+)Dox

source_name: K562-OsRDR1 stable cell line

value: K562-OsRDR1 with Dox induction for 6 days

value: K562-OsRDR1 stable cell line


title: RNA-seq: K562-AtRDR1(-)Dox

value: K562-AtRDR1 without Dox induction


title: RNA-seq: K562-WT


title: RNA-seq: Jurkat-WT

description: RNA-seq-Jurkat.csv

source_name: Jurkat

value: Jurkat


title: RNA-seq: H1299-AtRDR1(+)Dox

source_name: H1299-AtRDR1 stable cell line

value: H1299-AtRDR1 with Dox induction for 6 days

value: H1299-AtRDR1 stable cell line


title: RNA-seq: H1299-OsRDR1(+)Dox

source_name: H1299-OsRDR1 stable cell line

value: H1299-OsRDR1 with Dox induction for 6 days

value: H1299-OsRDR1 stable cell line


title: RNA-seq: H1299-OsRDR1(-)Dox

value: H1299-OsRDR1 without Dox induction


title: RNA-seq: H1299-WT


title: RNA-seq: HeLa-OsRDR1(+)Dox

source_name: HeLa-OsRDR1 stable cell line

value: HeLa-OsRDR1 with Dox induction for 5 days

value: HeLa-OsRDR1 stable cell line

value: HeLa


title: RNA-seq: HeLa-AtRDR1(+)Dox

source_name: HeLa-AtRDR1 stable cell line

value: HeLa-AtRDR1 with Dox induction for 6 days

value: HeLa-AtRDR1 stable cell line


title: RNA-seq: H1299-AtRDR1(-)Dox

value: H1299-AtRDR1 without Dox induction


title: RNA-seq: HeLa-AtRDR1(-)Dox

value: HeLa-AtRDR1 without Dox induction


title: RNA-seq: HeLa-WT

source_name: HeLa

value: WT


title: RNA-seq: WPMY-1-AtRDR1(+)Dox

value: WPMY-1-AtRDR1 with Dox induction for 6 days

value: WPMY-1-AtRDR1 stable cell line


title: RNA-seq: HepG2-OsRDR1(+)Dox

source_name: HepG2-OsRDR1 stable cell line

value: HepG2-OsRDR1 with Dox induction for 6 days

value: HepG2-OsRDR1 stable cell line


title: RNA-seq: HepG2-AtRDR1(+)Dox

value: HepG2-AtRDR1 with Dox induction for 6 days

value: HepG2-AtRDR1 stable cell line


title: RNA-seq: HepG2-AtRDR1(-)Dox

value: HepG2-AtRDR1 without Dox induction


title: RNA-seq: HepG2-WT


title: RNA-seq: HepG2-OsRDR1(-)Dox

value: HepG2-OsRDR1 without Dox induction


title: RNA-seq: HCT116-OsRDR1(-)Dox

source_name: HCT116-OsRDR1 stable cell line

value: HCT116-OsRDR1 without Dox induction

value: HCT116-OsRDR1 stable cell line


title: RNA-seq: HCT116-OsRDR1(+)Dox

value: HCT116-OsRDR1 with Dox induction for 6 days


title: RNA-seq: A549-OsRDR1(-)Dox

source_name: A549-OsRDR1 stable cell line

value: A549-OsRDR1 without Dox induction

value: A549-OsRDR1 stable cell line


title: RNA-seq: K562-OsRDR1(-)Dox

value: K562-OsRDR1 without Dox induction

value: K562-OsRDR1 stable cell line


title: RNA-seq: A549-OsRDR1(+)Dox

value: A549-OsRDR1 with Dox induction for 6 days


title: RNA-seq: A549-AtRDR1(+)Dox

source_name: A549-AtRDR1 stable cell line

value: A549-AtRDR1 with Dox induction for 6 days

value: A549-AtRDR1 stable cell line


title: RNA-seq: A549-AtRDR1(-)Dox

value: A549-AtRDR1 without Dox induction


title: RNA-seq: Jurkat-AtRDR1(+)Dox

description: RNA-seq-Jurkat.csv

source_name: Jurkat-AtRDR1 stable cell line

value: Jurkat-AtRDR1 with Dox induction for 6 days

value: Jurkat-AtRDR1 stable cell line

value: Jurkat


title: RNA-seq: A549-WT

value: WT


title: RNA-seq: Jurkat-AtRDR1(-)Dox

description: RNA-seq-Jurkat.csv

value: Jurkat-AtRDR1 without Dox induction


title: RNA-seq: HeLa-OsRDR1(-)Dox

value: HeLa-OsRDR1 without Dox induction

value: HeLa-OsRDR1 stable cell line

value: HeLa


title: 3-MxA1b-flfl-2aryMA9

last: Zhu

address: 8733 W Watertown Plank Rd

institute: Versiti Blood Research Institute Milwaukee

data_processing:
Data were demultiplexed using Illumina BaseSpace
Reads were quality controlled, aligned, and expression was quantified using the BasePairTech.com "Expression Count (STAR)" pipeline.
Genome_build: mm10
Supplementary_files_format_and_content: CSV of unnormalized readcounts per gene, per sample.

source_name: mouse bone marrow

extract_protocol:
Total RNA was extracted with TRIzol reagent (Thermo Fisher Scientific, Waltham, MA ). mRNA was further extracted using NEBNext Poly(a) mRNA Magnetic Isolation Module (New England BioLabs Inc., Ipswitch, MA).
cDNA Libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England BioLabs Inc., Ipswitch, MA).

treatment_protocol: 21 days post transplantation mice receiving MxCre+ (control), Arid1b fl/fl MxCre+ (knockout), and Arid2 fl/fl MxCre+ (knockout) MLL-AF9 cells were injected with pIpC: HMW (12.5μg/gram body weight, 3 times over a one week period) (Invivogen, San Diego, CA). Bone marrow was isolated from moribund mice.

value: Arid2 fl/fl MxCre+ MLL-AF9 bone marrow leukemia cells


title: 3-MxA1b-WT-2aryMA9

value: Arid2 +/+ MxCre+ MLL-AF9 bone marrow leukemia cells


title: CD-A-ChIP

city: Indianapolis

first: Núria

last: Morral

state: IN

address: 975 West Walnut, IB130

department: Medical and Molecular Genetics

institute: Indiana University School of Medicine

data_processing:
peak
Genome_build: UCSC mm10
Supplementary_files_format_and_content: tab delimited txt files; data show differential peak and expression between the two groups

source_name: Liver tissue

extract_protocol: ChIP-seq, RNA-seq, ATAC-seq

treatment_protocol: mouse fed a high fat diet (60% kcal fat) or a control diet (18% kcal fat) for 10 weeks

value: mouse fed a control diet (18% fat)

tag: chip antibody

value: H3K9ac Millipore #17-658


title: HFD-A-ChIP

value: mouse fed a high fat diet (60% fat)


title: Input-CD-C-ChIP


title: HFD-D-ChIP


title: CD-D-ChIP


title: 1-MxA1b-flfl-2aryMA9


title: HFD-B-ChIP


title: CD-C-ChIP


title: 1-MxA1b-WT-2aryMA9


title: 3-MxA2-flfl-2aryMA9

value: Arid1b fl/fl MxCre+ MLL-AF9 bone marrow leukemia cells


title: 2-MxA1b-WT-2aryMA9


title: RNA-seq: HCT116-WT


title: 2-MxA2-flfl-2aryMA9


title: 3-MxA2-WT-2aryMA9

value: Arid1b +/+ MxCre+ MLL-AF9 bone marrow leukemia cells


title: 1-MxA2-flfl-2aryMA9


title: 1-MxA2-WT-2aryMA9


title: ARID2-flfl-VavCRE-MLL-AF9-3

value: Arid2 fl/fl VavCre+ MLL-AF9 bone marrow leukemia cells


title: ARID2-WT-VavCRE-MLL-AF9-3

value: Arid2 +/+ VavCre+ MLL-AF9 bone marrow leukemia cells


title: ARID2-flfl-VavCRE-MLL-AF9-1


title: ARID2-WT-VavCRE-MLL-AF9-1


title: ARID2-flfl-VavCRE-MLL-AF9-2


title: ARID2-WT-VavCRE-MLL-AF9-2


title: A1bVav2ary-KO1

value: Arid1b fl/fl VavCre+ MLL-AF9 bone marrow leukemia cells


title: A1bVav2ary-KO4


title: A1bVav2ary-KO3


title: 2-MxA1b-flfl-2aryMA9