title: 20150603_MatterCancerRun5_E5_05


title: 20150528_MatterCancerRun4_D8_08

status: Public on Jun 20 2021

type: RNA

city: Basel

first: Matthias

middle: Sebastian

last: Matter

state: BS

address: Schönbeinstrasse 40

department: Institute of Pathology

country: Switzerland

institute: University of Basel

hyb_protocol: The samples were hybridized with a panel of mRNA:tag-specific nCounter capture and barcoded reporter probes identifying mRNA associated with cancer development.  Sample preparation was done according to the nCounter® mRNA Expression Assay User Manual. After the hybridization protocol, the samples were processed on the Prep Station from NanoString.

scan_protocol: Scan protocol was performed according to the nCounter® mRNA Expression Assay User Manual for the nCounter® PanCancer Pathways Panel. 12 samples per plate/cartridge were processed and scanned. From each patient the 1st and 2nd biopsy was always run on the same plate. Scanning was done using the Digital Analyzer.

data_processing: The raw data was normalized as described in the manual using Nsolver Software 3.0 by using the following genes as housekeeping genes: C10orf76, PIAS1, DNAJC14, TTC31, SFSA3, and ERCC3. Because additional samples of a related project were run at the same time on the some arrays,  these additional samples were included in the normalization process, however not analyzed for the present study. These samples are labelled as "Used for normalization" in the raw data section. Samples, which did not fulfill quality criteria as described in the user manual, were excluded from further analysis. No background subtraction was performed with the NSolver Software 3.0. Data analysis was performed using the Qlucore software (Lund, Sweden). All values were log transformed. Data was always analyzed paired between 1st and 2nd biopsy of the same patient (which were always run on the same plate/cartridge) using patient identification as an eliminating factor to remove batch effects between runs. Statistically significant difference between 1st and 2nd biopsy was calculated using a paired t-test.

label: nCounter

molecule: total RNA

organism: Homo sapiens

source_name: HCC 2nd Biopsy

label_protocol: 100 ng total RNA was prepared for mRNA expression analysis according to the nCounter® mRNA Expression Assay User Manual

extract_protocol: On average 5 sections at 10um thickness were cut from a paraffin block. Afterwards, total RNA extraction was performed using Qiagen FFPE total RNA/DNA extraction kit (Cat No./ID: 80234).

tag: tissue

value: Liver tissue

tag: fibrosis stage

tag: age

tag: liver disease


title: 20140918MMh_87 H MC 72 03_03

hyb_protocol: The samples were hybridized with a panel of miRNA:tag-specific nCounter capture and barcoded reporter probes. Sample preparation was done according to the nCounter® miRNA Expression Assay User Manual. After the hybridization protocol the samples were processed on the Prep Station from NanoString.

scan_protocol: Scan protocol was performed according to the nCounter® miRNA Expression Assay User Manual. 12 samples per plate/cartridge were processed and scanned. From each patient the 1st and 2nd biopsy was always run on the same plate. Scanning was done using the Digital Analyzer.

data_processing: The raw data was normalized as described in the manual using Nsolver Software 3.0 by using the geometric mean of the top 50 most expressed miRNAs as described in the user manual and described before (e.g. Valeri N Cancer Cell 2016). Because additional samples of a related project were run at the same time on the some arrays,  these additional samples were included in the normalization process, however not analyzed for the present study. These samples are labelled as "Used for normalization" in the raw data section. Samples, which did not fulfill quality criteria as described in the user manual, were excluded from further analysis. No background subtraction was performed with the NSolver Software 3.0. Data analysis was performed using the Qlucore software (Lund, Sweden). For analysis a threshold of 64 was set and all values were log transformed. Data was always analyzed paired between 1st and 2nd biopsy of the same patient (which were always run on the same plate/cartridge) using patient identification as an eliminating factor to remove batch effects between runs. Statistically significant difference between 1st and 2nd biopsy was calculated using a paired t-test.

source_name: Tumor-free 1st Biopsy

label_protocol: 100 ng total RNA was prepared for miRNA expression analysis according to the nCounter® miRNA Expression Assay User Manual


title: UPN_203_BM

type: genomic

city: Perugia

first: Cristina

last: Mecucci

address: Piazzale Menghini n.9

department: Department of Medicine, Hematology and Bone Marrow Transplantation Unit

country: Italy

institute: University of Perugia

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to the array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations 450 and scanned using the Gene Chip Scanner 3000 7G.

data_processing:
Protocol was supported by Affymetrix GeneChip Command Console (AGCC) software. Analysis was performed through Affymetrix Chromosome Analysis 3.2 (ChAS) software with filters set at 400 Kb dimension for Copy Number Alterations (CNAs) and 10 Mb dimensions for copy neutral loss of heterozygosity (cnLOH). Our data refer to NetAffx Build 33.2 (hg19) database.
affymetrix-array-type = CytoScanHD_Array
affymetrix-algorithm-param-ArraySet = CytoScanHD_Array
program-name = C:\Program Files\Affymetrix\ChAS\apt-copynumber-cyto-ssa.exe
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

label: Biotin

molecule: genomic DNA

source_name: Diffuse Large B-cell Lymphoma case with a TERT promoter variant, who later developed Chronic Myelomonocytic Leukemia

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: DNA were extracted from bone marrow cells of patient through phenol/chloroform extraction. DNA quality and quantity was assessed using Denovix Spectrophotometer and agarose gel electrophoresis.

tag: cytogenetics

value: not available

tag: mutations

value: TET2 p.N1888Kfs*22 homozygous

tag: cell type

value: Unsorted Bone Marrow Cells


title: 20140918MMg_82 G MC 69 10_10


title: 20140918MMg_77 G MC 67 05_05


title: 20150528_MatterCancerRun4_D10_10

source_name: HCC 1st Biopsy


title: 20140918MMh_85 H MC 71 01_01


title: 20140918MMg_84 G MC 68 12_12


title: 20150528_MatterCancerRun4_D7_07


title: 20150528_MatterCancerRun4_D4_04


title: 20150528_MatterCancerRun3_C4_04


title: 20150528_MatterCancerRun4_D5_05


title: 20140919MMl_L MC 100 11_11


title: 20140918MMg_75 G MC 66 03_03


title: RPE-1_siTP53_Nutlin_1_RNAseq

type: SRA

city: Jena

first: Martin

last: Fischer

state: Thuringia

address: Beutenbergstraße 11

department: Computational Biology

country: Germany

institute: Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)

library_source: transcriptomic

data_processing:
Quantification and quality check of libraries were performed using the Agilent Bioanalyzer 2100 in combination with the DNA 7500 Kit. Sequence information was extracted in FastQ format using Illumina's bcl2FastQ v2.20.0.422.
We utilized Trimmomatic v0.39 (5nt sliding window approach, mean quality cutoff 22) for read quality trimming according to inspections made from FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) v0.11.9 reports. Illumina universal adapter as well as mono- and di-nucleotide content was clipped using Cutadapt v2.10. Potential sequencing errors were detected and corrected using Rcorrector v1.0.3.1. Ribosomal RNA (rRNA) transcripts were artificially depleted by read alignment against rRNA databases through SortMeRNA v2.1. The preprocessed data was aligned to the reference genome hg38, retrieved along with its gene annotation from Ensembl v.92, using the mapping software segemehl v0.3.4 with adjusted accuracy (95%) and split-read option enabled (RNA-seq) or disabled (ChIP-seq). Mappings were filtered by Samtools v1.10 for uniqueness and properly aligned mate pairs. We removed duplicated reads with Picard MarkDuplicates v2.23.4.
Read quantification was performed on exon level using featureCounts v1.6.5, parametrized according to the strand specificity inferred through RSeQC v3.0.0. Differential gene expression and its statistical significance was identified using DeSeq2 v1.20.0.
Genome_build: hg38
Supplementary_files_format_and_content: .tsv DESeq2 output

molecule: polyA RNA

extract_protocol:
Total cellular RNA was extracted using the RNeasy Plus Mini Kit (Qiagen, Hilden, Germany) following the manufacturer protocol.
Libraries were constructed from 500 ng of total RNA using NEBNext Ultra II RNA - polyA+ (mRNA) Kit following the manufacturer's description.

treatment_protocol: Treated for 24h with 10 µM Nutlin-3a or DMSO solvent control

tag: treatment

tag: cell line


title: RPE-1_siTP53_Nutlin_2_RNAseq


title: 20150528_MatterCancerRun3_C3_03


title: BB2

city: Nanjing

first: Mingliang

last: Ji

state: Jiangsu

address: Dingjiaqiao Road 87

country: China

institute: Zhongda Hospital,school of medicine, southeast university

data_processing:
Basecalls performed using  Solexa pipeline v1.8
The trimmed reads (trimmed 5’,3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.0.5)software
The transcript abundances for each sample was estimated with StringTie（1.3.1c）
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.6.0)
Genome_build: hg19
Supplementary_files_format_and_content: FPKM

organism: Mus musculus

source_name: chondrocytes

extract_protocol:
fresh 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.
The total RNA was processed by NEBNext® Poly(A) mRNA Magnetic Isolation Module (or rRNA removal by RiboZero Magnetic Gold Kit) to enrich mRNA, and the product RNA was used for construction Library, via KAPA Stranded RNA-Seq Library Prep Kit (Illumina). Sequencing libraries, denatured by 0.1 M NaOH to generate single-stranded DNA, as amplified in situ Illumina cBot (TruSeq SR Cluster Kit v3-cBot-HS (# GD-401-3001, Illumina)). The ends of the generated fragments was used to run 150 Cycles by the Illumina HiSeq 4000 Sequencer.
RNA libraries were prepared for sequencing using standard Illumina Hiseq protocols.

tag: genotype

value: Eldr cKI


title: BB1


title: BB3


title: 20150123JWMM_18 MAC6_06


title: RPE-1_siTP53_Nutlin_3_RNAseq


title: RPE-1_siTP53_DMSO_3_RNAseq

value: DMSO


title: 20140808_Matterrescan_MAMA09_09


title: AA3

value: control


title: RPE-1_siANKRA2_Nutlin_3_RNAseq


title: RPE-1_siANKRA2_Nutlin_2_RNAseq


title: RPE-1_siTP53_DMSO_1_RNAseq


title: RPE-1_siTP53_DMSO_2_RNAseq


title: RPE-1_siANKRA2_Nutlin_1_RNAseq


title: AA2


title: AA1


title: RPE-1_siANKRA2_DMSO_3_RNAseq


title: KneeCartilage_Healthy_rep1

description: Gene expression in normal cartilage tissue

hyb_protocol: Agilent protocol

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

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

extract_protocol: Total cellular RNA from cultured chondrocytes was extracted and purified using the Total RNA kit according to the manufacturer’s instructions (Omega).RNA was quantified using a NanoDrop-1000. spectrophotometer

treatment_protocol: Normal cartilage samples were obtained from trauma patients without the joint disease. Samples of OA cartilage were obtained from patients undergoing knee replacement surgery. Every sample was divided into some pieces and was immediately stored in liquid nitrogen.

value: KneeCartilage

tag: disease

value: Healthy


title: KneeCartilage_Healthy_rep3


title: KneeCartilage_Osteoarthritis_rep2

description: Gene expression in osteoarthritis cartilage tissue

value: Osteoarthritis


title: PKP2 reverted hiPSC-epicardial cells [KOH2275-25]

city: Utrecht

first: Eva

last: van Rooij

state: Utrecht

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

data_processing:
strand-specific single-end 75bp reads were generated on an Illumina NextSeq 500
Reads were mapped to human reference genome GRCh37 and quantified against the corresponding ensemble gene annotation list using STAR v 2.4.2a.
Differential expression was calculated using DESeq2 v1.2 with pooled dispersion estimates
Genome_build: GRCh37
Supplementary_files_format_and_content: reads count

source_name: PKP2 reverted hiPSC-epicardial cells

growth_protocol: Epicardal cells were genarated from hiPSCs according to the protocol described in Bao et al., 2017

extract_protocol:
Total RNA was isolated from day 30 PKP2 c.2013delC and reverted hiPSC-epicardial cells and subjected to RNA sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: hiPSC-derived epicardial cells

value: PKP2 wild type

value: day 30 of differentiation


title: PKP2 reverted hiPSC-epicardial cells [KOH2275-26]


title: PKP2 reverted hiPSC-epicardial cells [KOH2275-24]


title: PKP2 reverted hiPSC-epicardial cells [KOH2275-23]


title: KneeCartilage_Osteoarthritis_rep3


title: KneeCartilage_Osteoarthritis_rep1


title: RPE-1_siANKRA2_DMSO_2_RNAseq


title: KneeCartilage_Healthy_rep2


title: PKP2 mutant hiPSC-epicardial cells [KOH2275-22]

source_name: PKP2 mutant hiPSC-epicardial cells

value: PKP2 c.2013delC


title: RPE-1_siANKRA2_DMSO_1_RNAseq


title: RPE-1_siRFX7_Nutlin_2_RNAseq


title: PKP2 mutant hiPSC-epicardial cells [KOH2275-21]


title: RPE-1_siRFX7_Nutlin_1_RNAseq


title: B1

value: Eldr cKO


title: B3


title: PKP2 mutant hiPSC-epicardial cells [KOH2275-20]


title: RPE-1_siRFX7_DMSO_2_RNAseq


title: B2


title: PKP2 mutant hiPSC-epicardial cells [KOH2275-19]


title: A3


title: A2


title: RPE-1_siControl_Nutlin_3_RNAseq


title: RPE-1_siControl_Nutlin_2_RNAseq


title: RPE-1_siControl_Nutlin_1_RNAseq


title: RPE-1_siRFX7_Nutlin_3_RNAseq


title: PKP2 mutant hiPSC-epicardial cells rep2

data_processing:
During sequencing, Read 1 was assigned 26 base pairs and was used for identification of the Illumina library barcode, cell barcode and UMI. R2 was assigned 60 base pairs and used to map to the reference transcriptome of Hg19 with BWA
Data was demultiplexed.
Raw read counts (included as count tables "ReadCounts") were converted to umi counts (referred to as "barcode counts"); an additional correction was performed based on binominal statistics, resulting in "transcript counts".
Post-processing of count tables: after loading count tables mitochondrial transcript counts were removed, as were genes expressed in less than 10 cells. Consecutively, cells with a remaining transcript count < 5000 were removed. The count tables in the data attached here do contain those cells and genes.
Genome_build: Hg19
Supplementary_files_format_and_content: Count tables of raw reads ("readcounts"), umi counts ("barcode counts"), and corrected umi counts ("transcript counts"). Columns are single cells (and each file corresponds to one sample), rows indicate genes and chromosomal origin using HGNC symbols and "chrX" where X indicates chromosome of origin. Files are labeled by identifiers described above, R1 and R2 indicate to read 1 and read 2. S1-4 enumerates the samples. (HUB = Hubrecht, AK = Arwa Kohela)

source_name: epicardial cells

extract_protocol:
Day 70 PKP2 c.2013delC and reverted hiPSC-epicardial cells were dissociated and single-cell sorted using the FACSJazz™ Cell Sorter (BD Biosciences) into 384-well plates containing 384 primers and Mineral oil (Sigma-Aldrich). After sorting, plates were snap-frozen on dry ice and stored at -80°C.
Libraries were constructed by Single Cell Discoveries according to an adapted version of the SORT-seq protocol (Muraro et al. (2016), A Single-Cell Transcriptome Atlas of the Human Pancreas. Cell Syst).
scRNA-seq

value: day 70 of differentiation


title: 20150603_MatterCancerRun5_E2_02


title: A1


title: PKP2 reverted hiPSC-epicardial cells rep2


title: RPE-1_siControl_DMSO_2_RNAseq


title: PKP2 reverted hiPSC-epicardial cells rep1


title: 20150624_MatterCancerRun11_M4_04


title: RPE-1_siControl_DMSO_3_RNAseq


title: RPE-1_siControl_DMSO_1_RNAseq


title: 28 day old lettuce leaves, replicate 3 [L101]

city: Merritt Island

first: Jamie

middle: J

last: Foster

state: FL

address: 505 Odyssey Way

country: USA

institute: University of Florida

description: Nanopore MinION Flowcell FAL1190

data_processing:
RNA sequencing data were based called in real time using the MinKNOW software von the MinIT device. All FASTQ files (with a threshold of Q5) for each sample were concatenated and used in the downstream bioinformatics pipeline. Briefly, MinION sequencing statistics were analyzed using Nanoplot v1.0.0 and filtered for reads with  read length 100 bp ≥ 30000 bp and minimum Q score of 5 using filtlong v0.2.0. Adapters were trimmed using Porechop v0.2.4.38 Host transcripts that mapped to the Lactuca sativa (Lettuce) (GCF_002870075.1_Lsat_Salinas_v7_genomic.fna.gz ) and Helianthus annuus (common sunflower)(GCA_002127325.1_HanXRQr1.0_genomic.fna.gz) genomes were removed using bowtie2 and rRNA was removed using SortMeRNA v2.1.40. Taxonomic classification of the removed 16S and 18S rRNA reads was performed with Kraken2 v2.0.8b using the curated RefSeq NCBI microbial genome database containing archaea, bacteria, fungi, protozoa and viruses reference genome sequences.   The remaining metatranscriptome sequences were annotated through BLAST+ v2.9.0 and Trinotate v3.0 (http://trinotate.github.io) Uniprot database. No assembly was performed on the reads before the annotation. Coding sequences (CDS) assigned to viruses and eukaryotes apart from fungi were excluded in the analysis (https://www.uniprot.org/uploadlists/). In addition, taxa assigned to Cyanobacteria which represents a substantial number of reads were excluded  as well as transcripts associated with photosynthesis genes. These steps were performed to prevent the inclusion of possible mis-assigned chloroplast transcripts. Abundance of transcripts that had Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations were normalized using the transcripts per million method (TMM). KEGG annotated association with their respective pathways were performed using the R package KEGGREST.  The gene networking analysis was completed using the R package Phyloseq v1.19.1.
Genome_build: GCF_002870075.1_Lsat_Salinas_v7_genomic.fna.gz
Genome_build: GCA_002127325.1_HanXRQr1.0_genomic.fna.gz
Supplementary_files_format_and_content: *kraken2.report.txt =  Taxonomy diversity report, raw counts
Supplementary_files_format_and_content: *.bacterial.all.merge.data.csv, raw counts and gene descriptions for bacterial genes in each sample
Supplementary_files_format_and_content: *.fungal.all.merge.data.csv, raw counts and gene descriptions for fungal genes in each sample
Supplementary_files_format_and_content: bacteria.combined.KEGGmap.evalue0.05.csv; Bacterial metatranscriptome combined normalized counts and gene descriptions
Supplementary_files_format_and_content: fungi.combined.KEGGmap.evalue0.05.csv; Fungal metatranscriptome normalized counts and gene descriptions

organism: Lactuca sativa

source_name: 28 day old lettuce leaves

growth_protocol: Red romaine lettuce, Lactuca sativa cv ‘Outredgeous’ were grown in environmentally controlled growth chambers at Kennedy Space Center (KSC), FL. Seeds were batch sanitized with a bleach-hydrochloric acid solution for 1 h and allowed to off-gas for 24 h prior to planting. Sanitization was verified by placing seeds on trypticase soy agar (TSA) and inhibitory mold agar (IMA) plates and allowed to incubate for 48-72 h at 30°C. Four sanitized seeds were place in each 4-inch pots containing greens grade arcillite, a calcined clay, and time release fertilizer. Plants were then grown in Environmental Controlled Growth Chambers under conditions simulating those aboard the ISS (RH-50%, CO2-3000 ppm, and temperature 23 ºC). The growth cycle was established at 16h/8h light dark cycles with 200-300 µmol fluorescent lights and all were on automatic watering with DI water with daily monitoring. Pots were thinned to one plant each at day 7 and samples were harvested at day 28 for leafy greens.  Leaf tissue from each pf the three pots (L93, L96, and L101) were placed immediately into RNAlater™ (Ambion, Grand Island, NY, USA) and stored at -80 ºC until ready for RNA extraction.

extract_protocol:
Total RNA was extracted from each of the three lettuce leave replicates (denoted as L93, L96 and L101) with the RNeasy Plant Mini Kit following the manufacturer’s protocol (Qiagen, Valencia, CA, USA). RNA was DNase-treated with the optional on column digestion following the manufacturer’s protocol (Qiagen, Valencia, CA, USA).  A modified enrichment method was developed to process the RNA samples for compatibility with Nanopore library preparation protocols.35 Using an average of 14µg total RNA, the Invitrogen Dynabeads polyA enrichment protocol (Thermo Fisher, Carlsbad, CA, USA) was performed keeping the polyA depleted material and discarding the polyA enriched material. The polyA depleted material was then purified with the Zymo RNA clean and concentration kit according to the manufacturer’s protocol (Zymo Research, Irvine, CA, USA). Purified RNA was processed using the Invitrogen RiboMinusTM plant kit for removal of plant ribosomal RNA per the manufacturer’s protocol (Thermo Fisher, Carlsbad, CA, USA). 1-10ug of host depleted RNA form each sample was then A-tailed using Poly(A) polymerase (New England Biolabs, Ipswich, MA, USA) for 25 mins at 37ºC.  RNA quantity and quality were assessed with QubitTM fluorometer (Version 4.0, InvitrogenTM, Thermo Fisher Scientific) and Agilent 2100 Bioanalyzer (Agilent Technologies, Inc.) respectively. Bioanalyzer 6000 Nano RNA Eukaryotic program was used to assess the quality of the RNA. The samples were stored at -80°C until ready for library preparation.
Library preparation for cDNA-PCR sequencing was performed using the SQK-PCS109 sequencing kit following the manufacturer’s instructions (Oxford Nanopore Technologies, Oxford, UK). Briefly, 50ng of processed RNA sample from L93, L96 and L101were reverse transcribed using Maxima H Minus Reverse Transcriptase (Thermo Fisher), and left to incubate in the thermal cycler at 42°C for 90 min and 85°C for 5 min. To amplify the products without introducing biasness, full length transcripts were selected by PCR using LongAmp Taq 2x Master Mix (New England Biolabs, Ipswich, MA, USA) with the following cycling conditions, an initial denaturing step at 95°C for 5 min, then 14 cycles of 15 s at 95°C, 15 s at 62°C, and 1 min at 65°C, followed by a final extension step at 65°C for 6 mins and a hold at 4°C. The products were then using Agencourt AMPure XP beads (Beckman Coulter, Indianapolis, IN) with 1.8 (v/v) ratio of beads to reaction mixture.
cDNA library using 100 fmol of amplified cDNA with adapters was loaded onto a FLO-MIN106 flowcell and the RNA library was sequenced on a MinION device for 48 h. Basecalling was perform in real-time using the MinIT device. L93, L96 and L101 replicates were sequenced on individual flowcells FAL87564, FAL08147, and FAL1190 respectively to provide information about the process reproducibility and variability.

treatment_protocol: Baseline lettuce leaf metatranscriptomics was performed with 3 replicates. No other treatment was compared to the baseline samples.

tag: cultivar

value: Outredgeous

value: Wild Type

tag: developemental stage

value: 28 days old plant, 16h/8h light dark cycles

value: Leaves

tag: biosource type

value: RNAlater fixed_sample


title: 28 day old lettuce leaves, replicate 2 [L96]

description: Nanopore MinION Flowcell FAL08147


title: 28 day old lettuce leaves, replicate 1 [L93]

description: Nanopore MinION Flowcell FAL87564


title: RPE-1_siRFX7_DMSO_1_RNAseq


title: FLP_TET_1

status: Public on Jun 19 2021

city: BIRMINGHAM

first: Hurmuz

last: CEYLAN

address: School of Biosciences, University of Birmingham,, Edgbaston B15 2TT

country: United Kingdom

institute: University of Birmingham

data_processing:
Quality control was performed on fastq files using fastqc. Raw files were aligned with STAR using default parameters. LibiNorm count was used in HTseq compatible mode, unstranded and feature type = exon to obtain counts. DESeq2 was used for differential expressed genes analysis
Genome_build: GRCh38
Supplementary_files_format_and_content: COUNTS

source_name: Human Embryonic Kidney

growth_protocol: Cells were grown in DMEM medium  supplemented with 10% heat-inactivated FBS  and 1% Penicillin/Streptomycin at 37°C under 5% CO2

extract_protocol:
The total RNA extractions were performed with TRIzol  according to the manufacturers’ instructions.
RNA libraries were prepared for sequencing using QuantSeq 3′ mRNA-Seq Library Prep Kit REV for Illumina (LECOGEN) kit protocols

treatment_protocol: Cells were transfected siRNAs or induced with tetracycline for 48 hours .

tag: condition

value: Tetracycline induced

value: Flp-In T-REx 293


title: RPRD1B_FL_TET_2


title: RPRD1B_FL_TET_1


title: FLP_TET_2


title: RPRD1B_FL_2

value: untreated


title: FLP-1


title: RPRD1A_RPRD1B_RPRD2_KD_1

value: siRNA transfected

tag: knockdown


title: RPRD1B_FL_1


title: FLP-2


title: RPRD1B_RPRD2_KD_2


title: RPRD1B_RPRD2_KD_1


title: RPRD1A_RPRD2_KD_2


title: PKP2 mutant hiPSC-epicardial cells rep1


title: RPRD1A_RPRD1A_KD_2


title: RPRD1A_RPRD1A_KD_1


title: RPE-1_siRFX7_DMSO_3_RNAseq

value: DMSO


title: RPRD2_KD_2


title: RPRD2_KD_1


title: RPRD1A_KD_2


title: RPRD1B_KD_2


title: RPRD1B_KD_1


title: CTRL-2

value: control


title: CTRL-1


title: RPRD1A_RPRD1B_RPRD2_KD_2


title: RPRD1A_RPRD2_KD_1


title: day3 n1

city: Frankfurt am Main

first: Lukas

last: Jost

address: Altenhöferallee 3

institute: GenXPro GmbH

data_processing:
Library strategy: MACE-seq
Illumina bcl2fastq software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and bad quality as well as MACE specific polyA stretches; PCR artifacts were deduplicated based on Unique Molecular Identifier sequences
Cleaned reads were mapped onto GRCh38 genome using bowtie2 and raw counts were obtained using HTSeq
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include count values for each group
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: HEK293T cells with constitutive MLL-AF4 plus inducible AF4-MLL (48h)

growth_protocol: stably transfected HEK293T cells were expanded in DMEM/FCS

extract_protocol:
Qiagen RNA Purification with DNAse I treatment
Three prime End sequencing using GenXPro-MACE-Seq technique (GenXPro GmbH, Frankfurt Germany) including UMIs for PCR-dupliacate removal.
Massive Analysis of cDNA ends (MACE-Seq)

treatment_protocol: transgene induction was carried out with 1µg/ml doxyxcycline for 48h

value: HEK293T kidney cells

tag: transfection

value: transgene was induced for 48h by 1 ug/ml Doxycycline


title: day28 n2

source_name: HEK293T cells with constitutive MLL-AF4

value: constitutive MLL-AF4


title: day0 n3


title: day3 n2

value: constitutive MLL-AF4 plus inducible AF4-MLL (48h)


title: day3 n3


title: MockControl wDOX3

source_name: HEK293T cells with empty vector (pSBTet-GP)

value: empty vector (pSBTet-GP)


title: day28 n3


title: day12 n3


title: MockControl wDOX1


title: day0 n1


title: day0 n2


title: Patient_after_5_sessions_of_acupuncture

city: Daejeon

first: Sang-Min

last: Park

address: Youseong-Daero

department: College of Pharmacy

country: South Korea

institute: Chungnam National University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Bowtie2.
Read count extraction and nomalization were performed using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: Whole blood

extract_protocol:
The PAXgene Blood miRNA Kit (Qiagen, Hilden, Germany) was used for total RNA isolation from whole blood samples of a representative patient before acupuncture, and after 5 sessions and 8 sessions of acupuncture treatment.
Library construction for control and test RNAs was performed using the QuantSeq 3’mRNA-Seq Library Prep Kit (Lexogen Inc., Austria).

treatment_protocol: Acupuncture treatment was given to the participants on the dorsal side for 2 days per week for 4 weeks.

value: treated with 5 sessions of acpuncture


title: MockControl wDOX2


title: Patient_before_acupuncture


title: day12 n1


title: Patient_after_8_sessions_of_acupuncture

value: treated with 8 sessions of acpuncture


title: RPRD1A_KD_1


title: 6291 RNA_seq

city: Saint Louis

first: Takeshi

last: Egawa

state: MO

address: 660 South Euclid

department: Pathology and Immunology

institute: Washington University School of Medicine

data_processing:
RNA-Seq: Sequencing reads were mapped to the mouse genome mm10 using STAR with default options.
ChIP-Seq: Sequenced reads were mapped to the mouse genome mm9 using bowtie-2 with default parameters and the Homer program was used for peak calling, motif analysis and visualization on the UCSC genome browser.
Genome_build: RNA-Seq mm10; ChIP-Seq mm9
Supplementary_files_format_and_content: RNA-Seq: Excel table containint RPKM values for all sequenced samples  ChIP-Seq: BedGraph files obtained through Homer

source_name: B220+ B cells

extract_protocol:
RNA-Seq: Cells were sorted using Aria-II and RNA was extracted with Trizol according to manufacturer's instructions, followed by treatment with rDNase from Nucleospin RNA XS extraction kit (Macherey-Nagel)  ChIP-Seq: Cells were enriched using MACS CD19 microbeads and LS columns, fixed with 1% pfa at RT for 10 min. Chromatin was precipitated using 5 μg of anti-AP4, 1 μg of anti-H3K27ac (ab4729, Abcam), and 5 μg of anti-rabbit IgG (Thermofisher) and Dynabeads protein-G magnetic beads (Life Technologies).  After reverse crosslinking, precipitated DNA was purified using a GenElute PCR Clean Up Kit (Sigma) and quantitated using a Qubit DNA quantitation kit (Life Technologies).
RNA-Seq: Library preparation was performed with 0.1-1ug of total RNA, integrity was determined using an Agilent bioanalyzer or tapestation. Ribosomal RNA was removed by a hybridization method using Ribo-ZERO kits (Illumina). mRNA was then fragmented in buffer containing 40mM Tris Acetate pH 8.2, 100mM Potassium Acetate and 30mM Magnesium Acetate and heating to 94 degrees for 150 seconds. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer’s instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3’ ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 15 cycles using primers incorporating the p5 and p7 sequences and unique index tags. Fragments were sequenced on an Illumina HiSeq2500 or HiSeq3000 using single reads extending 50 bases.  ChIP_Seq Library preparation was performed with 10ng of chIP DNA, size range was assayed on Agilent Bioanalyzer High Sensitivity DNA chips. ChIP DNA was blunt ended, had addition of “A” base to 3’ end, and had sequencing adapters ligated to the ends. The fragments were size selected to 200-600 base pairs, and underwent amplification for 15 cycles with primers incorporating p5 and p7 sequences and a unique index tag for multiplexing. The resulting libraries were sequenced using the Illumina HiSeq3000 as single reads extending 50 bases.

value: EuMyc Tfap4-Het (LOH)

value: pro/pre-B tumor cells


title: 6292 RNA_seq

value: EuMyc Tfap4-Het


title: 8 RNA_seq


title: 6297 RNA_seq


title: 3 RNA_seq

value: EuMyc Tfap4-WT


title: 7078 RNA_seq

source_name: B220+IgM- B cells

value: pre-transformed pro/pre-B BM cells


title: 7077 RNA_seq


title: day12 n2


title: 6739 RNA_seq


title: 6867 RNA_seq


title: 7097 RNA_seq


title: 6870 RNA_seq


title: 7076 RNA_seq

value: WT

value: normal pro/pre-B BM cells


title: 7074 RNA_seq


title: 7099 RNA_seq


title: 6741 RNA_seq


title: 6735 RNA_seq


title: 7072 RNA_seq


title: Human organoid D56 FXS3_1

city: Houston

first: Ziyi

last: Li

state: TX

address: 1400 Pressler Street

institute: MD Anderson Cancer Center

data_processing:
For bulk RNA-seq data, data were aligned by STAR using reference genome hg19 or mm9. The raw counts were obtained by counting the overlaps between reads and gene regions.
For single-cell data: Two of each human D56 forebrain organoids generated from wild type and FXS patients were dissociated with Accutase solution (Sigma-Aldrich) and the single cell suspension was subjected to Chromium 10x Genomics 10X Genomics Chromium Controller (Emory Integrated Genomics Core) with 5000 target cell number and HiSeq4000 sequencing (Novogene Inc.).  Briefly, the captured cells were processed for barcoding and generation of a single cell library with Chromium Next GEM Single Cell 3′ Library kit, and the resulting single cell libraries were sequenced with HiSeq 4000. Using Cell Ranger 3.0.2 from 10X Genomics, raw Chromium scRNA-seq output was processed to align reads, generate feature-barcode matrices and perform clustering and gene expression analysis. The HG19 assembly was used to map the sequence reads.
Genome_build: hg19 for human samples and mm9 for mouse samples
Supplementary_files_format_and_content: Processed data file format and content: Raw counts by gene for bulk RNA-seq (human organoids, human fetal brain and mouse fetal brain) are provided in csv files. Raw counts by FMRP targets for eCLIP (human organoids and mouse fetal brain) are provided in csv files. Raw counts by gene for single cell RNA-seq (human organoids) are provided in csv files.

source_name: Human organoid

growth_protocol: Organoid cultures with iPS cells reprogrammed from control and FXS individuals were grown routinely with spinning bioreactor (SpinΩ).

extract_protocol:
Samples for RNA-seq were extracted with Trizol and single cells for single cell RNA-seq were obtained with Accutase from organoids. The UV crosslinked samples fro eCLIP were lysed in lysis buffer (50 mM Tris-HCl pH7.5, 100 mM NaCl, 1% NP-40, 0.1% SDS, 0.5% sodium deoxycholate and protease inhibitor) on ice for 10-30 min followed by digestion with RNase I and DNase (Invitrogen) at 37C for 5 min.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: date

value: Day 56

tag: phenotype

value: FXS

tag: tissue type

value: Organoids


title: Human organoid D56 FXS3_2


title: Human organoid D56 Control3_2

value: Control


title: Human organoid D56 Control3_1


title: A549dox

city: Kraków

first: Joanna

last: Bereta

address: Gronostajowa 7

department: Cell Biochemistry

country: Poland

institute: Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University

data_processing:
Basecalling, quality control, mapping and read counts on Ion Torrent Suite v. 5.12.1
Genome_build: hg38
Supplementary_files_format_and_content: RawCount Excel file containing numbers of reads for all genes

growth_protocol: The cells were grown in DMEM + 10% tet-free FBS at standard conditions (37°C, 5% CO2, 95% humidity).

extract_protocol:
The cells were lysed in RNA Extracol; total RNA was isolated using Direct-Zol RNA Mini Kit. poly(A)+ RNA was isolated using Dynabead mRNA DIRECT Micro Purification Kit
libraries were prepared according to the manufacturer's protocol with the Ion Total RNA-Seq Kit v2 (ThermoFisher)

treatment_protocol: doxycycline 100 ng/ml; 24 h or left untreated

value: lung carcinoma

value: doxycycline 100 ng/ml, 24 h


title: A549

value: non treated


title: U251

value: glioblastoma astrocytoma


title: U251dox


title: Human iPSC FXS2_2

source_name: induced pluripotent stem cells

value: iPSC


title: 7075 RNA_seq


title: Human iPSC FXS2_1


title: eCLIP mouse embryonic cortex IgG [Mouse_IgG]

description:
J-1_S1
processed data file: eCLIP_Mouse_RawCounts.csv

source_name: Mouse organoid

tag: strain background

value: Embryonic cortex

tag: ip anitbody

value: IgG


title: eCLIP mouse embryonic cortex Input [Mouse_Input]

description:
Mouse_Input
processed data file: eCLIP_Mouse_RawCounts.csv

value: Input


title: eCLIP mouse embryonic cortex IP [Mouse_Fmrp eCLIP3]

description:
L10_L4_IP
processed data file: eCLIP_Mouse_RawCounts.csv


title: Human iPSC Control2_2


title: eCLIP mouse embryonic cortex IP [Mouse_Fmrp eCLIP2]

description:
J-2_S2
processed data file: eCLIP_Mouse_RawCounts.csv


title: Human iPSC FXS1_1


title: Human iPSC FXS1_2


title: Human iPSC Control2_1


title: Human iPSC Control1_2


title: eCLIP mouse embryonic cortex IP [Mouse_Fmrp eCLIP1]

description:
J-4_S4
processed data file: eCLIP_Mouse_RawCounts.csv


title: CD5lo rep1

city: Hwasun-eup, Hwasun-gun

first: Jae-Ho

last: Cho

state: Jeollanam-do

address: 264, Seoyang-ro

institute: CHONNAM NATIONAL UNIVERSITY

hyb_protocol: Following fragmentation, 0.75 ug of cRNA were hybridized to the Illumina Expression Beadchip according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Illumina Bead Array Reader Confocal Scanner

data_processing: Array data export processing and analysis was performed using Illumina GenomeStudio v2011.1 (Gene Expression Module v1.9.0)

label: biotin

source_name: Lymph nodes

label_protocol: Biotinylated cRNA were prepared from 0.55 ug total RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin,TX)

extract_protocol: Lymph nodes were harvested from 8~12 week old C57BL/6 mice. Single cells from the lymph nodes were stained with fluorochrome conjugated antibodies, followed by FACS-purification of naive CD8+ T cell subsets (CD5lo, CD5hi Ly6C-, and CD5hi Ly6C+). The purified cells were used to prepare RNA using TriZOL.

treatment_protocol: ex vivo

tag: strain

tag: state

value: ex vivo

tag: tissue

value: Lymph nodes

value: Naive CD8 T cells

tag: cell subset


title: CD5hi Ly6C- rep2

tag: cell type

value: CD5hi Ly6C-


title: Mouse E13.5 Cortex_WT [Mouse E13.5 Cortex_WT2]

description:
BrainFmr1WT2_USR16088447L_HHHKKBBXX_L7
processed data file: Mouse_FetalBrain_RawCounts.csv

source_name: Mouse fetal brain

tag: phenotype/genotype

value: WT


title: Mouse E13.5 Cortex_WT [Mouse E13.5 Cortex_WT3]

description:
BrainFmr1WT3_USR16088448L
processed data file: Mouse_FetalBrain_RawCounts.csv


title: CD5lo rep2


title: CD5hi Ly6C+ rep2

value: CD5hi Ly6C+


title: CD5hi Ly6C- rep1


title: CD5hi Ly6C+ rep1


title: Human iPSC Control1_1


title: Mouse E13.5 Cortex_WT [Mouse E13.5 Cortex_WT1]

description:
BrainFmr1WT1_USR16088446L
processed data file: Mouse_FetalBrain_RawCounts.csv


title: Mouse E13.5 Cortex_KO [Mouse E13.5 Cortex_KO3]

description:
BrainFmr1KO3_USR16088451L
processed data file: Mouse_FetalBrain_RawCounts.csv

value: KO


title: eCLIP human organoids IP [Human_FMRP eCLIP3]

description:
J-10_S10
processed data file: eCLIP_Human_RawCounts.csv

value: Organoids


title: Mouse E13.5 Cortex_KO [Mouse E13.5 Cortex_KO2]

description:
BrainFmr1KO2_USR16088450L
processed data file: Mouse_FetalBrain_RawCounts.csv


title: eCLIP human organoids input [Human_Input]

description:
Human_Input
processed data file: eCLIP_Human_RawCounts.csv


title: Mouse E13.5 Cortex_KO [Mouse E13.5 Cortex_KO1]

description:
BrainFmr1KO1_USR16088449L_HHHKKBBXX_L7
processed data file: Mouse_FetalBrain_RawCounts.csv


title: eCLIP human organoids IgG [Human_IgG]

description:
J-11_S11
processed data file: eCLIP_Human_RawCounts.csv


title: JC004

city: New York

first: Anqi

last: Shao

state: NY

address: 1150 St. Nicholas Ave.

institute: Columbia University

data_processing:
Illumina RTA for base calling
bcl2fastq2 2.17 for converting BCL to fastq coupled with adpator trimming
STAR 2.5.2b and featureCounts v1.5.0-p3 for mapping reads to reference genome
DESeq2 for differential analysis
Genome_build: mm10
Supplementary_files_format_and_content: excel sheet includes normalized counts for each samples from DESeq2 analysis

source_name: CD200R+ cSCC-infiltrating myeloid cells

extract_protocol:
Total RNA was extracted from 1-2x10e6 FACS-sorted CD11b+CD200R1+ cells from orthotopic cSCCs. Poly-A pull-down method was used to to enrich mRNAs from total RNA samples (200ng-1ug per sample, RIN>8 required) and proceed on library preparation by using Illumina TruSeq RNA prep kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: FACS-sorted cSCC-infiltrating myeloid cells

value: FVB/N

tag: genotype


title: 13 input

library_source: genomic

source_name: CD19+ B cells

value: EuMyc Tfap4-Het

value: pre-transformed pro/pre-B BM cells


title: eCLIP human organoids IP [Human_FMRP eCLIP2]

description:
J-8_S8
processed data file: eCLIP_Human_RawCounts.csv


title: 50 input

value: EuMyc Tfap4-WT


title: eCLIP human organoids IP [Human_FMRP eCLIP1]

description:
J-7_S7
processed data file: eCLIP_Human_RawCounts.csv


title: 63 input


title: 68 AP4


title: Human fetal cortex_control [CTRL_Fetal Cortex_Male_PCW 23 weeks_2]

description:
A2
processed data file: Human_FetalBrain_RawCounts.csv

source_name: Human fetal brain

value: PCW 23 weeks

value: CTRL

value: Fetal cortex


title: 18 input


title: JC002

value: WT(Wild type)


title: JC001


title: 66 input


title: 63 AP4


title: 13 AP4


title: JC003


title: 68 input


title: Human fetal cortex_control [CTRL_Fetal Cortex_Male_PCW 23 weeks_1]

description:
A1
processed data file: Human_FetalBrain_RawCounts.csv


title: MIA-PaCa2 AMG510re rep2

city: Taipei

first: Yung-Ming

last: Jeng

address: No.7, Zhongshan S. Rd., Zhongzheng Dist.

country: Taiwan

institute: National Taiwan University Hospital

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh37 whole genome using STAR v2.7.2b
Reads number were calculated using RSEM v1.3.1.
Genome_build: GRCh37
Supplementary_files_format_and_content: Matrix table with counts for every gene and every sample

growth_protocol: The cells are grown in DMEM supplemented with 10% fetal calf serum

extract_protocol:
Total RNA was isolated from cells using Trizol reagent (Life Technologies, Invitrogen, Carlsbad, CA), according to the manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For the resistant group, the cells were growing in medium with increasing dose of AMG510 for two month reaching a final dose of 5 uM

tag: cell line

value: pancreatic cancer

tag: treatment

value: AMG511 resistant


title: Human fetal cortex_FXS [FXS Fetal Cortex_Male_PCW 23 weeks]

description:
CS6
processed data file: Human_FetalBrain_RawCounts.csv

value: FXS


title: 66 AP4


title: 50 AP4


title: 18 AP4


title: 68 H3K27Ac


title: Human organoid D84 FXS-KO2

data_processing:
For bulk RNA-seq data, data were aligned by STAR using reference genome hg19 or mm9. The raw counts were obtained by counting the overlaps between reads and gene regions.
Genome_build: hg19 for human samples and mm9 for mouse samples
Supplementary_files_format_and_content: raw counts

extract_protocol: none provided by the submitter

value: Day 84


title: 63 H3K27Ac


title: MIA-PaCa2 untreated rep2

value: untreated


title: 13 H3K27Ac


title: 50 H3K27Ac


title: 66 H3K27Ac


title: MIA-PaCa2 untreated rep1


title: Human organoid D84 FXS-KO1


title: Human organoid D84 control2

value: WT


title: Human Organoid Single Cell FXS 2 [SC_FXS2]


title: 18 H3K27Ac


title: MIA-PaCa2 AMG510re rep1

value: AMG510 resistant


title: Human Organoid Single Cell FXS 1 [SC_FXS1]

value: Organoids


title: Human organoid D84 control1


title: 7681 RNA_seq

value: EuMyc Tfap4-KO

value: pro/pre-B tumor cells


title: Set2_Y236F_rep3

city: wuhan

first: yuchao

last: Mei

address: Bayi Road

department: Colleage of Life Science

institute: Wuhan University

data_processing:
Low quality reads and adaptor contamination were removed by Trimmomatic v0.38. The reads obtained from each sample were mapped to the yeast genome SacCer3 (https://www.yeastgenome.org/) with Tophat (version 2.1.1).
In SET2 deletion mutants, the BAM file was divided into forward and reverse strand by BEDtools (version 2.29.2). Samtools (version 1.10) was used to filter antisense reads of both forward and reverse strands by SAM flags. BEDtools software was used to get the reads of intergenic region. Finally, the antisense reads from the forward strand, the reverse strand, and the intergenic region are merged together to obtain an integrated BAM file.
Antisense reads were assembled without reference genome annotation in Cufflinks (version 2.2.1). The expression levels of antisense transcripts with P value < 0.05 were analyzed using the gene annotation file of antisense transcripts by Cuffdiff.
Genome_build: SacCer3
Supplementary_files_format_and_content: Antisense_expression_matrix.xlsx: Gene expression are quantified using HTSeq (Version 0.13.5).

organism: Saccharomyces cerevisiae BY4741

source_name: yeast cells

growth_protocol: Yeast cells were grown overnight in YPD or SD medium at 30 °C, diluted to an OD600 of 0.2 and collected when the OD600 reached 0.8.

extract_protocol:
Cells were harvested by spinning down with 3000 rpm for 5 min, then cell pellets were washed with 10 ml sterile water twice. Total RNA was extracted with HiPure Yeast RNA Kit (Magen R4182-02). For preparation of mRNA, 20 μg of total RNA was diluted into 50 μL DEPC water and incubated with 50 μL mRNA capture beads as followed as the protocol described in the product manual (Vazyme N401-01).
The enriched mRNA was used for strand-specific library construction by the KAPA Stranded RNA-Seq Library Preparation Kit (KAPA KK8401) through a dUTP-method.

value: set2_Y236F mutant


title: Human Organoid Single Cell control 1 [SC_CTRL1]


title: Human Organoid Single Cell control 2 [SC_CTRL2]


title: 7686 RNA_seq


title: Human fetal cortex_FXS [FXS Fetal Cortex_Female_PCW 24 weeks]

description:
CS3
processed data file: Human_FetalBrain_RawCounts.csv

value: PCW 24 weeks


title: 7358 RNA_seq

value: EuMyc Tfap4-Het (LOH)


title: Set2_Y236F_rep1


title: Human organoid D56 FXS-KO2

value: Day 56

value: KO


title: Human organoid D56 FXS-KO1


title: 7388 RNA_seq


title: Human organoid D56 control2


title: Set2_Y149F_rep2

value: set2_Y149F mutant


title: ACHN_50nM PA_Rep3

city: Guangzhou

first: Lan

last: Tang

state: Guangdong

address: 1838  Guangzhou North Ave,

department: School of Pharmaceutical Science

institute: Southern Medical University

data_processing:
Illumina Casava1.8 software used for base-calling.
Reads containing adapter, reads containing ploy-N and low quality reads were trimmed.
STAR2.5.1b was used for alignment.
The counts and Fragments Per Kilobase of exon per Megabase of library size (FPKM) of genes were calculated and normalized by RESM1.2.28.
Genome_build: hg38
Supplementary_files_format_and_content: Gene count
Supplementary_files_format_and_content: Gene FPKM

source_name: human renal cell carcinoma cells

extract_protocol:
ACHN cells upon treatment of PA (25nM, 50nM) or DMSO (0.1%) were grown on the 6-well cell culture plates,which were devided into three groups with 3 duplicate samples. Centrifugal column were used to extract total cellular RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: human renal cell carcinoma cells

value: ACHN

tag: agent

value: 50nM Piericidin A

tag: culture medium

value: MEM

tag: growth characteristic

value: adherent


title: 7277 RNA_seq


title: ACHN_50nM PA_Rep2


title: Human organoid D56 control1

tag: date


title: Set2_Y149F_rep3


title: 7503 RNA_seq

value: EuMyc Tfap4-Het


title: Set2_Y236F_rep2


title: ACHN_50nM PA_Rep1


title: Set2_Y149F_rep1


title: Human organoid D28 FXS-KO2

value: Day 28

tag: phenotype


title: ACHN_25nM PA_Rep3

value: 25nM Piericidin A


title: Set2_del_rep3

value: set2 deletion


title: Set2_del_rep2


title: Human organoid D28 FXS-KO1

tag: tissue type

value: Organoids


title: Human organoid D28 control2

value: WT


title: Set2_del_rep1


title: 7283 RNA_seq

value: EuMyc Tfap4-WT

value: pro/pre-B tumor cells


title: ACHN_25nM PA_Rep1


title: 7169 RNA_seq


title: Human organoid D28 control1


title: 7291 RNA_seq


title: ACHN_0.1% DMSO_Rep3

value: DMSO


title: ACHN_0.1% DMSO_Rep2


title: 6988 RNA_seq


title: WT_rep2

value: wild type


title: WT_rep3


title: StSS1-UDP rep2

city: shanghai

first: Ming

last: Zhao

address: 130 Meilong Road, Xuhui District

institute: East China University of Science and Technology

data_processing:
FastqStat.jar V1.0 software was used for basecalling.
HiSat2 was used for read alignment.
FastQC v0.11.4 software was used for quality assessment of sequencing data.
Diamond v0.9.19.120 software was used fo KEGG analysis.
Genome_build: https://www.ncbi.nlm.nih.gov/genome/1888?genome_assembly_id=204998
Genome_build: FASTA with predicted RNA sequence is available on the series record.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample.

organism: Streptomyces lividans

growth_protocol: Strains were grown in TBS medium until 84 h

extract_protocol:
rRNA was removed with Ribo-Zero Magnetic kit. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: age

value: SM regulatory strain


title: ACHN_25nM PA_Rep2


title: ACHN_0.1% DMSO_Rep1


title: WT_rep1


title: StSS1-UDP rep3


title: 7293 RNA_seq


title: sh4-2

city: Changsha

first: yuan

middle: yu

last: zi

address: Changsha Xiangya Road

institute: Xiangya hospital

data_processing:
using Illumina Novaseq platform
Index of the reference genome was built using Hisat2 v2.0.5
Genome_build: hg18
Supplementary_files_format_and_content: FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.

source_name: cell line

extract_protocol:
RNA was harvested using Trizol reagent. Sequencing was completed by Novogene.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Lung cancer


title: sh1-1


title: NC-2


title: PMP12-16-UDP rep3

value: PM regulatory strain


title: Human Organoid Single Cell FXS 3

value: Day 56

value: FXS


title: Human Organoid Single Cell control 3

value: CTRL


title: sh1-2


title: 3 days post-injury

city: Livermore

first: Stephen

middle: Patrick

last: Wilson

state: CA

address: 7000 East Ave

department: BBTD

institute: LLNL

data_processing:
Cellranger mkfastq to generate FASTQ.
Cellranger count to generate count matrix.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.tar: Tar archives of Cell Ranger files. Gene list (features.tsv), cell barcodes (barcodes.tsv), and gene/barcode matrices (matrix.mtx) are provided for each experimental group.

source_name: Connective tissue-forming cells from the knee joints

extract_protocol:
Mice were euthanized and injured and uninjured hindlimbs were collected by removing the legs at the hip joint and storing on ice in Dulbecco’s Modified Eagle Medium Nutrient Mixture F-12 (DMEM/F-12) (Thermo Fisher Scientific, Waltham, MA, USA). Articular cartilage from tibia and femora was isolated by cutting ~1 mm of tissue from the end of both long bones at the knee joint. For each experimental group, cartilage tissue from 5 mice was pooled, and digested to a single cell suspension in 5 mL of 0.2% Collagenase 2 solution (2mg/mL Thermo Fisher Scientific, Waltham, MA, USA) while shaking at 37 °C for a total of 2 hours in 30-minute intervals. Interval fractions were filtered through a 70 μm Nylon cell strainer into DMEM/F12 with 10% fetal bovine serum (FBS) and kept on ice. Remaining undigested cartilage tissue was further digested in 5 mL of fresh Collagenase 2 digestion media. After the final digestion interval, cells were pelleted via centrifugation for 10 min at 500 G at 4oC, incubated on ice with ACK lysis buffer (Thermo Fisher Scientific, Waltham, MA, USA), for red blood cell removal. Cells were stained with the following antibodies for flow cytometry and FACS analysis: CD45 APC-Cy7 (BioLegend, San Diego, CA, USA, 103116 (1:100)), Ter119 APC (Miltenyi Biotec, Bergisch Gladbach, Germany, 130-102-290, (1:10)), and DAPI (Thermo Fisher Scientific, Waltham, MA, USA). Immune and Erythroid contamination was depleted via double negative selection (CD45-; Ter119-) using the BD FACSMelody (San Jose, CA, USA).
Library preparation was performed using Chromium Single Cell 3′ GEM, Library & Gel Bead Kit v3 (10x Genomics, Pleasanton, CA, USA; Catalog no. 1000075) following the manufacturer’s protocol and sequenced using Illumina NextSeq 500 targeting approximately 50,000 reads per cells.

treatment_protocol: 10-week-old C57Bl/6J (BL6) mice (purchased from Jackson Laboratory Bar Harbor, ME, USA; Stock No: 000664) were subjected to anterior cruciate ligament injury using a non-invasive single dynamic tibial compressive overload model.

value: 10 weeks

value: Injured knee joints

tag: time point

value: 3 DPI

value: Articular cartilage at knee joint

value: CD45-;Ter119- cells


title: 7 days post-injury

tag: strain

value: 7 DPI


title: Uninjured

value: Uninjured


title: StSS1-UDP rep1


title: PMP12-16-UDP rep2


title: sh4-1


title: NC-1


title: PBMCs, TCDD 2

status: Public on Jun 18 2021

city: Kansas City

first: Khursheed

last: Iqbal

state: Kansas

address: 3901 Rainbow Blvd

department: Pathology

institute: University of Kansas Medical Center

data_processing:
The Cell Ranger Single-Cell Software Suite (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) was used to perform sample demultiplexing, barcode processing, and single-cell 3' gene counting. The reads were aligned to the rn6 reference genome. BAM files produced by the 10x Genomics/Cell Ranger pipeline
Genome_build: rn6
Supplementary_files_format_and_content:  Genes.tsv, Barcodes.tsv, Matrix.mtx

organism: Rattus norvegicus

source_name: PBMC

extract_protocol: Single cells were captured into droplets using 10x chromium device followed by preparation of single-cell cDNA libraries with the 10x protocol.

value: gestational day 13.5

value: TCDD

value: PBMC


title: PMP12-16-UDP rep1


title: PBMCs, TCDD 1


title: PBMCs, OIL 1

value: control


title: PBMCs, OIL 2


title: iPS cell replicate 3

city: Tokyo

first: Shin

last: Hatou

address: #305, 1-13-7 Nihombashi-Muromachi, Chuo

country: Japan

institute: Cellusion Inc

hyb_protocol: 600 ng of Cy3-labelled cRNA  was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan  (Scan resolution 3 um, TIFF file dynamic range；20bit).

data_processing: The scanned images were analyzed with Feature Extraction 12.0.3.1 (Agilent) using default parameters

source_name: Ff-I01s04 iPS cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA using Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy mini spin columns (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: HCE cells were harvested from donor cornea. Three lots of CECSi cells and two lots of NCCs were derived from three lots of Ff-I01s04 iPS cells

extract_protocol: RNA was prepared using the RNeasy kit (Qiagen, Valencia, CA). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: not applicable

value: blood


title: iPS cell replicate 2


title: LBTV_418

city: Fukuoka

first: Kohta

last: Miyawaki

address: 3-1-1, Maidashi, Higashi-ku

institute: Kyushu University

hyb_protocol: 300 ng total RNA was hybridized to gene-specific probes at 65˚C for 18 hours and then purified and deposited onto glass cartridges using the “high sensitivity” setting on the nCounter™ Prep Station (NanoString Technologies, Seattle, WA, USA).

scan_protocol: The number of barcodes hybridized to specific RNA targets on cartridges were directly counted by the nCounter™ Digital Analyzer with 555 fields of view setting.

data_processing: Normalization of RNA loading was performed using the geometric mean of 15 housekeeping genes (ABCF1, ALAS1, EEF1G, G6PD, GAPDH, GUSB, HPRT1, OAZ1, POLR1B, POLR2A, PPIA, SDHA, TBP, TUBB, and RPL19).

source_name: Diffuse Large B-cell Lymphoma

extract_protocol: Total RNA was extracted from DLBCL FFPE samples using a RNeasy FFPE extraction kit (QIAGEN, Hilden, Germany) after deparaffinization with Deparaffinization Solution (QIAGEN), based on the manufacturer’s instruction.

tag: disease state

value: Diffuse Large B-cell Lymphoma

tag: Sex

value: F

tag: cell of origin by lymph2cx

value: ABC

tag: status disease-free survival_0 relapse_dead_1

tag: survival time (day)

value: DLBCL FFPE tissue


title: LBTV_463

value: M

tag: tissue


title: CECSi cell replicate 2


title: NCC replicate 2


title: NCC replicate 1


title: CECSi cell replicate 3


title: CECSi cell replicate 1


title: iPS cell replicate 1


title: shNR4A2_THP1 Control_rep3

city: Dublin

first: Eoin

middle: P

last: Cummins

state: Dublin

address: UCD Conway Institute of Biomolecular and Biomedical Research, UCD Belfield

department: Conway Institute/School of Medicine

country: Ireland

institute: University College Dublin

data_processing:
Raw data quality was evaluated with Fast QC, and per base quality score distribution plotted
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted. Since a strand-specific library preparation was performed, the reads were strand-specifically counted.
Genome_build: Homo sapiens GRCh38 reference genome

growth_protocol: The appropriate number of shNT, shNR4A2 and shNR4A3 THP-1 cells were counted, centrifuged at 1,200rpm (290xg) and the supernatant was removed. Cells were transferred to an environmental gas chamber (37℃, 5% CO2) and resuspended in buffered DMEM media supplemented with 10% FBS, 1% P/S. at a concentration of 750,000 cells/ml (3 million cells/ 4 mls media on 60mm plastic petri dishes). Cells were incubated for 2 hours. LPS-stimulated cells were treated with 2.5ug/ml LPS  for a further 2 hours before lysis.

extract_protocol:
Cells were collected and total mRNA was extracted using the Omega EZNA Total RNA Kit I, as per the manufacturer’s instructions.
cDNA library preparation was performed with polyA selection using Illumina HiSeq, 2x150bp configuration, single index, per lane. ~350M raw paired-end reads per lane. Library preparation and sequencing were performed by Genewiz (Germany).

treatment_protocol: Cells were treated +/- LPS for 2hrs

tag: cell line

value: Human monocytic leukaemia_ THP1

tag: lentiviral particle transduction

value: NR4A2 targeting shRNA


title: shNR4A2_THP1 + LPS (2.5ug/ml) (2hrs)_rep3


title: shNR4A3_THP1 Control_rep3

value: NR4A3 targeting shRNA


title: shNR4A3_THP1 + LPS (2.5ug/ml) (2hrs)_rep1


title: shNR4A2_THP1 + LPS (2.5ug/ml) (2hrs)_rep2


title: shNR4A3_THP1 Control_rep2


title: shNR4A3_THP1 + LPS (2.5ug/ml) (2hrs)_rep3


title: shNR4A2_THP1 + LPS (2.5ug/ml) (2hrs)_rep1


title: shNR4A3_THP1 Control_rep1


title: shNR4A3_THP1 + LPS (2.5ug/ml) (2hrs)_rep2


title: HCE cell replicate 2

source_name: corneal endothelial cells

value: mean donor age 62.8

value: cornea


title: HCE cell replicate 1


title: HCE cell replicate 3


title: shNT_THP1 + LPS (2.5ug/ml) (2hrs)_rep3

value: non-target shRNA


title: shNR4A2_THP1 Control_rep2


title: LBTV_417

value: GCB


title: LBTV_416


title: day28 n1

city: Frankfurt am Main

first: Lukas

last: Jost

address: Altenhöferallee 3

institute: GenXPro GmbH

data_processing:
Library strategy: MACE-seq
Illumina bcl2fastq software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and bad quality as well as MACE specific polyA stretches; PCR artifacts were deduplicated based on Unique Molecular Identifier sequences
Cleaned reads were mapped onto GRCh38 genome using bowtie2 and raw counts were obtained using HTSeq
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include count values for each group
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: HEK293T cells with constitutive MLL-AF4

extract_protocol:
Qiagen RNA Purification with DNAse I treatment
Three prime End sequencing using GenXPro-MACE-Seq technique (GenXPro GmbH, Frankfurt Germany) including UMIs for PCR-dupliacate removal.
Massive Analysis of cDNA ends (MACE-Seq)

tag: cell type

value: HEK293T kidney cells

tag: transfection

value: constitutive MLL-AF4


title: LBTV_499


title: shNR4A2_THP1 Control_rep1


title: LBTV_415


title: shNT_THP1 Control_rep1


title: shNT_THP1 Control_rep3


title: shNT_THP1 Control_rep2


title: LBTV_413


title: shNT_THP1 + LPS (2.5ug/ml) (2hrs)_rep1


title: LBTV_414


title: LBTV_412


title: LBTV_409


title: RNA_F1_C57xSPRET_BMDM_basal_rep2

city: La Jolla

first: Christopher

middle: K

last: Glass

address: 9500 Gilman Drive

department: CMM

institute: University of California, San Diego

description: processed data file: RNA_TPM_F1_C57xSPRET.tsv

data_processing:
FASTQ files from sequencing experiments were mapped to the custom genome of the corresponding mouse strain using STAR with default parameters (Dobin et al., 2013). Mapped data for strains other than C57 were later shifted to the mm10 genome using MMARGE (Link et al., 2018). F1 data were mapped to both C57 and NOD or SPRET genomes, which were represented in separate columns in the processed TPM file. Human data were mapped to hg38. HOMER was used to convert aligned reads into “tag directories” for downstream quantitative analysis (Heinz et al., 2010).
Transcripts were quantified by TPM values generated by the “analyzeRepeats” script of HOMER with the parameters -condenseGenes -count exons -tpm. Differentially expressed genes were identified by feeding raw read counts into DESeq2 (Love et al., 2014) through the “getDiffExpression” script of HOMER.
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited text file: table of TPM values and differential gene expression analysis results from DESeq2

growth_protocol: Bone marrow was isolated from mice and differentiated for 7 days using media containing M-CSF to bone marrow-derived macrophages (BMDMs) as described previously (Link et al., 2018).

extract_protocol:
Total RNA was isolated from in vitro culture cells and purified using a Direct-zol RNA MicroPrep Kit (Zymo Research) according to the manufacturer’s instructions (Zymo Research).
Poly A enriched mRNA was fragmented, in 2x Superscript III first-strand buffer with 10mM DTT (Thermo Fisher Scientific), by incubation at 94°C for 9 minutes, then immediately chilled on ice before the next step. The 10 µL of fragmented mRNA, 0.5 µL of Random primers (3 µg/µL) (Thermo Fisher Scientific), 0.5 µL of Oligo dT primer (50 µM) (Thermo Fisher Scientific), 0.5 µL of SUPERase-In (Ambion), 1 µL of dNTPs (10 mM) and 1 µL of DTT (10 mM) were heated at 50°C for one minute. At the end of incubation, 5.8 µL of water, 1 µL of DTT (100 mM), 0.1 µL Actinomycin D (2 µg/µL), 0.2 µL of 1% Tween-20 (Sigma) and 0.5 µL of Superscript III (Thermo Fisher Scientific) were added and incubated in a PCR machine using the following conditions: 25°C for 10 minutes, 50°C for 50 minutes, and a 4°C hold. The product was then purified with RNAClean XP beads (Beckman Coulter) according to manufacturer's instruction and eluted with 10 µL nuclease-free water. The RNA/cDNA double-stranded hybrid was then added to 1.5 µL of Blue Buffer (Enzymatics), 1.1 µL of dUTP mix (10 mM dATP, dCTP, dGTP and 20 mM dUTP), 0.2 µL of RNAse H (5 U/µL), 1.05 µL of water, 1 µL of DNA polymerase I (Enzymatics) and 0.15 µL of 1% Tween-20. The mixture was incubated at 16°C for 2.5 hours. The resulting dUTP-marked dsDNA was purified using 28 µL of SpeedBeads (GE Healthcare), diluted with 20% PEG8000, 2.5M NaCl to final of 13% PEG, eluted with 40 µL EB buffer (10 mM Tris-Cl, pH 8.5) and frozen at -80°C. The purified dsDNA (40 µL) underwent end repair by blunting, A-tailing and adapter ligation using barcoded adapters (NextFlex, Bioo Scientific). Libraries were PCR-amplified for 16 cycles, size selected by gel extraction.

treatment_protocol: Macrophages were left untreated or treated with 20 ng/mL mouse recombinant IL-4 (Peprotech) for 1, 6 or 24 hours

value: FSC

value: BMDMs (bone marow-derived macrophages)


title: RNA_F1_C57xSPRET_BMDM_24hIL4_rep2

tag: treatment


title: LBTV_410


title: RNA_F1_C57xSPRET_BMDM_24hIL4_rep1


title: LBTV_411


title: LBTV_407


title: LBTV_513


title: LBTV_408


title: Synchronous_DLD1_control_rep1

city: Goettingen

first: Argyris

last: Papantonis

address: Robert-Koch-Str 40

department: Department of Pathology

institute: University Medical Center Goettingen

description:
G2 phase arrest by 21h treatment with a RO-3306 inhibitor, washout, cells continue in the cell cycle for 6 h and Re-enter G1 phase
Sync_control_poolrepmean_scaled_RPKM.bw

data_processing:
mapped with Bowtie2 to hg38 and dm6
filtered to remove non-primary, unmapped, duplicate and mitochondrial reads
spike-in scaling factors calculated from dm6 mapped reads with ChIPseqSpike
scaled with spike-in scaling factors and RPKM normalized with Deeptools to produce bigwig files
Genome_build: hg38

source_name: colorectal adenocarcinoma cell lines

growth_protocol: POLR2A-mAID-mClover DLD-1  were passaged in RPMI-1640 medium supplemented with 10% FBS under 5% CO2.

extract_protocol:
Transposase-accessible chromatin was obtained from frozen human DLD1 and D. Melanogaster S2 cells according to ATAC-seq protocol (Buenrostro et al. 2013; 2015), with modifications. Briefly, 100 000 DLD1 cells per replicate were spiked-in with 200 S2 cells, washed in PBS and lysed in cell lysis buffer (10 mM Tris-Hcl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.1% Tween-20 and 0.01% digitonin) for 3 minutes (Corces et al. 2017). Lysates were washed with washing buffer (10 mM Tris-Hcl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20) and pelleted. Isolated nuclei were resuspended in transposase reaction mix (25 ul 2X TD buffer, 16.5 ul 1X PBS, 0.5 ul 10% Tween-20, 0.5 ul 1% digitonin, 2.5 ul of Tn5 Transposase and 5 ul of nuclease-free H2O) and incubated at 37°C for 30 minutes on thermomixer at 1000 rpm. Transposase reaction was terminated by addition of stop buffer (50 mM Tris-Hcl pH 8, 10 mM EDTA, 1% SDS) (Stewart-Morgan, Reverón-Gómez, and Groth 2019). Reaction components were removed with DNA Clean&Concentrator kit (Zymo) and extracted chromatin was used for library construction and subsequent sequencing.
Standard DNA library prep (Buenrostro et al 2015)

treatment_protocol: Inducible depletion of RPB1 initiated via treatment with doxycycline for 24 h to induce TIR1 expression, before addition of 500 µM indole-3-acetic acid solution (“auxin”). For cell synchronization, G2/M arrest was achieved by addition of 10 µM RO-3306 inhibitor for 21 h. Following this incubation time, cells were washed with PBS, and auxin-supplemented medium was added for up to 6 h to allow cells to quantitatively enter G1. At this point, cells were harvested, where applicable resuspended in 1 µg/ml propidium iodide to counterstain DNA, and sorted using a FACS Canto II flow cytometer.

tag: genotype

tag: cell cycle

value: synchronous G1 reenter sorted

tag: agent

value: untreated


title: Synchronous_DLD1_control_rep2


title: Synchronous_DLD1_auxin_rep1

description:
G2 phase arrest by 21h treatment with a RO-3306 inhibitor, washout, cells continue in the cell cycle for 6 h and Re-enter G1 phase
Sync_auxin_poolrepmean_scaled_RPKM.bw

value: 14h treatment with Auxin


title: shNT_THP1 + LPS (2.5ug/ml) (2hrs)_rep2


title: Synchronous_DLD1_auxin_rep2


title: LBTV_509

value: Diffuse Large B-cell Lymphoma

tag: age

value: ABC


title: RNA_F1_C57xNOD_BMDM_24hIL4_rep2

description: processed data file: RNA_TPM_F1_C57xNOD.tsv

value: FCN


title: LBTV_512

value: F

value: DLBCL FFPE tissue


title: LBTV_511


title: RNA_F1_C57xSPRET_BMDM_basal_rep1


title: RNA_F1_C57xNOD_BMDM_24hIL4_rep1


title: LBTV_508


title: RNA_F1_C57xNOD_BMDM_basal_rep1


title: RNA_F1_C57xNOD_BMDM_basal_rep2


title: LBTV_510

value: M

value: Unclassified


title: iSLAMseq_Rhox10_8h_2

first: Kun

last: Tan

address: 2880 Torrey Pines Scenic Dr. Room 4812

department: Department of Obstetrics, Gynecology, and Reproductive Sciences

institute: UCSD

data_processing:
iSLAMseq: Reads were filtered for quality and aligned with SLAM-DUNK (v0.4.3) against the full reference genome (mm10), reporting up to 100 alignments for multi-mappers and activating the multi-mapper retention strategy, filtering for variants with a variant fraction of 0.2. Gene and 3' UTR annotations were obtained from the UCSC table browser (https://genome.ucsc.edu/cgi-bin/hgTables). T > C conversion rate was determined for each position along the custom defined counting windows by normalizing to genomic T content and coverage of each position and averaged per UTR. Differential gene expression calling was performed on raw read counts with ≥2 T>C conversions using limma (v3.42.2)
genome build: Mus musculus (mm10) genome.
Matrix table with raw gene counts

source_name: testis

growth_protocol: For both CUT&Tag and iSLAMseq, mouse germline stem (GS) cells were dissociated from neonatal (P0-P1) testes and cultured in IMDM/SFM medium.

extract_protocol:
iSLAMseq was performed as previously described (Herzog et al., 2017).
iSLAMseq: libraries were prepared using Quant-seq mRNA 3′ end library preparation kit (Lexogen) according to the instructions of the manufacturer.

treatment_protocol: iSLAMseq: Endogenous Rhox10 in mouse GS was knocked-down using an shRNA lentivirus and purified on the basis of GFP fluorescence by FACS. A lentivirus expression vector carrying the Rhox10-ERT2-mCherry fusion gene was used to make a conditional inducible Rhox10 expression in response to 4-Hydroxytamoxifen. 2 millions GS cells were prepared for each sample, six time points with two biological replicates were performed. Samples from Rhox10-kd; ERT2-mCherry empty vector served as the control.

tag: group

value: germline stem cells

value: testis


title: iSLAMseq_Rhox10_8h_1

tag: strain


title: LBTV_504

tag: disease state


title: LBTV_505

tag: Sex


title: iSLAMseq_Rhox10_4h_2


title: iSLAMseq_Rhox10_4h_1


title: iSLAMseq_Rhox10_2h_1


title: iSLAMseq_Rhox10_2h_2


title: LBTV_501

tag: cell of origin by lymph2cx


title: iSLAMseq_Rhox10_0.5h_1


title: iSLAMseq_Rhox10_0.5h_2


title: LBTV_507

tag: status disease-free survival_0 relapse_dead_1


title: iSLAMseq_Rhox10_1h_2


title: LBTV_502

value: GCB

tag: survival time (day)


title: LBTV_506

tag: tissue


title: iSLAMseq_Rhox10_1h_1


title: LBTV_493


title: LBTV_498


title: LBTV_496


title: LBTV_492


title: LBTV_497


title: LBTV_503


title: LBTV_494


title: LBTV_495


title: iSLAMseq_Rhox10_0h_1


title: iSLAMseq_Ctrl_8h_2


title: iSLAMseq_Ctrl_4h_2


title: LBTV_491


title: LBTV_488


title: LBTV_487


title: iSLAMseq_Ctrl_8h_1


title: LBTV_490


title: iSLAMseq_Rhox10_0h_2


title: iSLAMseq_Ctrl_1h_2


title: iSLAMseq_Ctrl_2h_1


title: iSLAMseq_Ctrl_2h_2


title: LBTV_489


title: iSLAMseq_Ctrl_1h_1


title: LBTV_486


title: iSLAMseq_Ctrl_0.5h_2


title: iSLAMseq_Ctrl_0h_2


title: iSLAMseq_Ctrl_0.5h_1


title: LBTV_484


title: RNAseq KO2

data_processing:
RNAseq: Reads were filtered for quality and aligned with STAR (2.5.2b) against Mus musculus, release-96, Ensembl genome (GRCm38). The exon counts were aggregated for each gene to build a read count table using SubRead function featureCounts. DEGs were defined using DESeq2.
genome build: Mus musculus, release-96, Ensembl genome (GRCm38).
Matrix table with raw gene counts

extract_protocol:
RNAseq: Total RNA was extracted using the RNeasy Plus Micro Kit (Qiagen), following the manufacturer’s protocol.
RNAseq: 30 ng of total RNA was used to make the library using the NEBNext Ultra II Directional RNA Library Prep kit (New England Biolabs), as per manufacturer's instructions.

treatment_protocol: RNAseq: Mice were crossed with OCT4-eGFP mice. eGFP+ cells were sorted by fluorescence-activated cell sorting (FACS). For each sample analyzed, testes from 3 individuals were pooled.

value: purified germ cells


title: LBTV_483


title: RNAseq KO3


title: LBTV_481


title: iSLAMseq_Ctrl_4h_1


title: iSLAMseq_Ctrl_0h_1


title: LBTV_480


title: LBTV_482


title: LBTV_479


title: RNAseq WT4

value: wild-type


title: RNAseq WT3


title: LBTV_476


title: RNAseq KO1


title: LBTV_473


title: LBTV_474


title: LBTV_485


title: LBTV_470


title: RNAseq WT2


title: LBTV_469


title: liver, 517 ko  - TA-10 (ATAC-seq)

city: Chicago

first: Tatiana

middle: L.

last: Fonseca

state: IL

address: 5841 S. Maryland Ave. MC1027, room N246B

department: Medicine

institute: University of Chicago

data_processing:
The remaining adapter sequences were removed using NGmerge v 0.3. Sequencing -reads were aligned to the Mouse mm10 genome build using BWA v.0.7.17 and annotated using the gencode.vM24.
Sequence quality was assessed using FastQC and tools from the Picard suite including CollectInsertSizeMetrics.
Aligned reads were further filtered to remove chimeric, duplicate, supplementary, and low-quality (MAPQ < 30) alignments.
We determined open-chromatin regions (peaks) using Genrich v0.6 (q-value threshold = 0.05). Run by individual sample, genrich would find only a handful of peaks which very obviously were not due to ATAC enrichment.
These regions were merged across samples into a blacklist of regions and excluded from consideration. Ultimately genrich was run using all samples grouped together while ignoring the blacklisted regions. Differential peaks were identified by overlap subtraction to find open chromatin regions unique to each condition.
Genome_build: mm10
Supplementary_files_format_and_content: peak text files from diff. Cre vs KO and KO vs Cre

source_name: liver nuclei

extract_protocol:
Frozen livers were processed for nuclei isolation using a detergent-free kit (Invent; cat # NI-024). 50,000 nuclei were used for the transposase reaction. The final libraries were purified using Agencourt AMPure XP beads (Beckman Coulter), and quality checked using a Bioanalyzer High Sensitivity DNA Analysis kit (Agilent); concentration was measured through a qPCR-based method (KAPA Library Quantification Kit for Illumina Sequencing Platforms). Samples were pair-end sequenced with the Illumina HiSeq 4000 platform at the University of Chicago Genomics Facility.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

tag: developmental stage

value: adult


title: RNAseq WT1


title: LBTV_467


title: LBTV_468


title: RNAseq KO4


title: liver, 293 ko - TA-9 (ATAC-seq)


title: LBTV_431


title: liver, 490 cre - TA-5 (ATAC-seq)

value: control


title: LBTV_478


title: LBTV_421


title: liver, 207 cre - TA-3 (ATAC-seq)


title: liver, 245 ko - TA-7 (ATAC-seq)


title: liver, 176 ko - TA-6 (ATAC-seq)


title: liver, 178 cre - TA-2 (ATAC-seq)


title: LBTV_466


title: LBTV_429


title: LBTV_427


title: LBTV_454


title: LBTV_455


title: LBTV_457


title: RNA_SPRET_BMDM_timecourse_6hIL4_rep2

description: processed data file: RNA_TPM_DESeq2_timecourse.tsv

data_processing:
FASTQ files from sequencing experiments were mapped to the custom genome of the corresponding mouse strain using STAR with default parameters (Dobin et al., 2013). Mapped data for strains other than C57 were later shifted to the mm10 genome using MMARGE (Link et al., 2018). F1 data were mapped to both C57 and SPRET genomes, which were represented in separate columns in the processed TPM file. Human data were mapped to hg38. HOMER was used to convert aligned reads into “tag directories” for downstream quantitative analysis (Heinz et al., 2010).
Transcripts were quantified by TPM values generated by the “analyzeRepeats” script of HOMER with the parameters -condenseGenes -count exons -tpm. Differentially expressed genes were identified by feeding raw read counts into DESeq2 (Love et al., 2014) through the “getDiffExpression” script of HOMER.
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited text file: table of TPM values and differential gene expression analysis results from DESeq2

value: SPRET/EiJ

value: IL-4 6h

value: BMDMs (bone marow-derived macrophages)


title: RNA_SPRET_BMDM_timecourse_24hIL4_rep2


title: LBTV_459

value: Diffuse Large B-cell Lymphoma

value: ABC


title: RNA_SPRET_BMDM_timecourse_24hIL4_rep1


title: RNA_SPRET_BMDM_timecourse_1hIL4_rep2

value: IL-4 1h


title: RNA_SPRET_BMDM_timecourse_6hIL4_rep1


title: RNA_SPRET_BMDM_timecourse_1hIL4_rep1


title: RNA_SPRET_BMDM_timecourse_basal_rep2


title: RNA_C57_BMDM_timecourse_24hIL4_rep2


title: LBTV_465

value: F

value: DLBCL FFPE tissue


title: LBTV_461

value: M

value: Unclassified


title: LBTV_464


title: RNA_SPRET_BMDM_timecourse_basal_rep1


title: liver, 164 cre - TA-1 (ATAC-seq)


title: RNA_C57_BMDM_timecourse_6hIL4_rep1


title: RNA_C57_BMDM_timecourse_6hIL4_rep2


title: RNA_C57_BMDM_timecourse_1hIL4_rep2


title: RNA_C57_BMDM_timecourse_24hIL4_rep1


title: LBTV_458


title: LBTV_451


title: LBTV_445


title: LBTV_449


title: LBTV_447


title: LBTV_446


title: RNA_C57_BMDM_timecourse_basal_rep2


title: RNA_SPRET_BMDM_24hIL4_rep2

description: processed data file: RNA_TPM_DESeq2_5strains.tsv


title: RNA_C57_BMDM_timecourse_basal_rep1


title: RNA_SPRET_BMDM_24hIL4_rep3


title: LBTV_452


title: LBTV_450


title: RNA_SPRET_BMDM_24hIL4_rep1


title: RNA_SPRET_BMDM_basal_rep3


title: RNA_SPRET_BMDM_basal_rep1


title: RNA_PWK_BMDM_24hIL4_rep3

value: PWK/PhJ


title: RNA_SPRET_BMDM_basal_rep2


title: RNA_PWK_BMDM_24hIL4_rep1


title: RNA_PWK_BMDM_basal_rep2


title: RNA_PWK_BMDM_24hIL4_rep2


title: RNA_NOD_BMDM_24hIL4_rep3

value: NOD/ShiLtJ


title: RNA_NOD_BMDM_24hIL4_rep2


title: RNA_PWK_BMDM_basal_rep1


title: RNA_C57_BMDM_timecourse_1hIL4_rep1


title: LBTV_444


title: RNA_NOD_BMDM_basal_rep2


title: RNA_NOD_BMDM_24hIL4_rep1


title: RNA_NOD_BMDM_basal_rep1


title: LBTV_395


title: LBTV_433

value: GCB


title: LBTV_443


title: RNA_BALB_BMDM_24hIL4_rep1

value: BALB/cJ


title: LBTV_438


title: LBTV_437


title: RNA_NOD_BMDM_basal_rep3


title: LBTV_442


title: LBTV_441


title: LBTV_436


title: LBTV_419


title: LBTV_391


title: LBTV_396


title: LBTV_389


title: LBTV_426


title: LBTV_386


title: LBTV_424


title: LBTV_390


title: LBTV_393


title: LBTV_435


title: LBTV_420


title: LBTV_392


title: LBTV_422


title: RNA_BALB_BMDM_basal_rep3


title: RNA_BALB_BMDM_24hIL4_rep3


title: RNA_BALB_BMDM_basal_rep2


title: RNA_BALB_BMDM_basal_rep1


title: LBTV_388


title: LBTV_385


title: LBTV_384


title: RNA_BALB_BMDM_24hIL4_rep2


title: RNA_C57_BMDM_24hIL4_rep3


title: RNA_C57_BMDM_24hIL4_rep1


title: RNA_C57_BMDM_24hIL4_rep2


title: LBTV_382


title: RNA_C57_BMDM_basal_rep3


title: RNA_C57_BMDM_basal_rep2


title: LBTV_380


title: RNA_C57_BMDM_basal_rep1


title: ChIP_CEBPb_LyzMCreEgr2flfl_BMDM_24hIL4_rep2

description:
processed data file:
TF_tagCounts_around_24hIL4inducedEGR2Peaks_EGR2KO.txt

data_processing:
FASTQ files from sequencing experiments were mapped to the custom genome of the corresponding mouse strain using Bowtie2 with default parameters (Langmead and Salzberg, 2012). Mapped data for strains other than C57 were later shifted to the mm10 genome using MMARGE (Link et al., 2018). Human data were mapped to hg38. HOMER was used to convert aligned reads into “tag directories” for downstream quantitative analysis (Heinz et al., 2010).
The reproducible enriched regions (i.e. peaks) were identified by first using HOMER (Heinz et al., 2010) to call unfiltered 200-bp peaks (command “findPeaks -style factor -L 0 -C 0 -fdr 0.9 -size 200”) and then running IDR (Li et al., 2011) on replicates with default parameters.
Normalized tag counts were computated using HOMER annotatePeaks.pl script with parameter "-norm 1e7". Histone markers were counted within +/- 500 bp around peaks, while transcription factor binding tags were counted within +/- 300 bp.
Genome_build: mm10, hg38
Supplementary_files_format_and_content: Tab delimited text file containing called peaks in the HOMER peak file format

extract_protocol:
For histone marks, PU.1, CEBPb and RNA Pol2 ChIP-seqs, culture media was removed and plates were washed once with PBS and then fixed for 10 minutes with 1% formaldehyde (Thermo Fisher Scientific) in PBS at room temperature and reaction was then quenched by adding glycine (Thermo Fisher Scientific) to 0.125M. For STAT6, PPARg, and Egr2 ChIP-seq, cells were cross-linked for 30 minutes with 2mM DSG (Pierce) in PBS at room temperature. Subsequently cells were fixed for 10 minutes with 1% formaldehyde at room temperature and the reaction was quenched with 0.125M glycine. After fixation, cells were washed once with cold PBS and then scraped into supernatant using a rubber policeman, pelleted for 5 minutes at 400xG at 4°C. Cells were transferred to Eppendorf DNA Lobind tubes and pelleted at 700xG for 5 minutes at 4°C, snap-frozen in liquid nitrogen and stored at -80°C until ready for ChIP-seq protocol preparation.Chromatin immunoprecipitation (ChIP) was performed in biological replicates as described previously (Seidman et al., 2020). Samples were sonicated using a probe sonicator in 500 µl lysis buffer (10 mM Tris/HCl pH 7.5, 100 mM NaCl, 1 mM EDTA, 0.5mM EGTA, 0.1% deoxycholate, 0.5% sarkozyl, 1 × protease inhibitor cocktail). After sonication, 10% Triton X-100 was added to 1% final concentration and lysates were spun at full speed for 10 minutes. 1% was taken as input DNA, and immunoprecipitation was carried out overnight with 20 µl Protein A Dynabeads (Invitrogen) and 2 µg specific antibodies for PU.1 (Santa Cruz, sc-352X), H3K4me2 (Millipore, 07-030), H3K4me3 (Millipore, 04-745), H3K27ac (Active Motif, 39135), RNA Pol2 (Genetex, GTX102535), STAT6 (Santa Cruz, sc-374021), Egr2 (abcam, ab43020) and CEBP- (Santa Cruz, sc-150). Beads were washed three times each with wash buffer I (20mM Tris/HCl, 150mM NaCl, 0.1% SDS, 1% Triton X-100, 2mM EDTA), wash buffer II (10mM Tris/HCl, 250mM LiCl, 1% IGEPAL CA-630, 0.7% Na-deoxycholate, 1mM EDTA), TE 0.2% Triton X-100 and TE 50mM NaCl and subsequently resuspended 25 µl 10 mM Tris/HCl pH 8.0 and 0.05% Tween-20 and sequencing libraries were prepared on the Dynabeads as described below.
ChIP libraries were prepared while bound to Dynabeads using NEBNext Ultra II Library preparation kit (NEB) as previously described (Heinz et al., 2018). DNA was polished, polyA-tailed and ligated after which dual UDI (IDT) or single (Bioo Scientific) barcodes were ligated to it. Libraries were eluted and crosslinks reversed by adding to the 46.5 µl NEB reaction 16 µl water, 4 µl 10% SDS, 4.5 µl 5M NaCl, 3 µl 0.5 M EDTA, 4 µl 0.2M EGTA, 1 µl RNAse (10 mg/ml) and 1 µl 20 mg/ml proteinase K, followed by incubation at 55C for 1 hour and 75C for 30 minutes in a thermal cycler. Dynabeads were removed from the library using a magnet and libraries were cleaned up by adding 2 µl SpeedBeads 3 EDAC (Thermo) in 124 µl 20% PEG 8000/1.5 M NaCl, mixing well, then incubating at room temperature for 10 minutes. SpeedBeads were collected on a magnet and washed two times with 150 µl 80% ethanol for 30 seconds. Beads were collected and ethanol removed following each wash. After the second ethanol wash, beads were air dried and DNA eluted in 12.25 µl 10 mM Tris/HCl pH 8.0 and 0.05% Tween-20. DNA was amplified by PCR for 14 cycles in a 25 µl reaction volume using NEBNext Ultra II PCR master mix and 0.5 µM each Solexa 1GA and Solexa 1GB primers. Libraries were size selected using TBE gels for 200 – 500 bp and DNA eluted using gel diffusion buffer (500 mM ammonium acetate, pH 8.0, 0.1% SDS, 1 mM EDTA, 10 mM magnesium acetate) and purified using ChIP DNA Clean & Concentrator (Zymo Research).

value: LyzM-Cre Egr2 fl/fl

tag: chip antibody

value: CEBPb (Santa Cruz, sc-150, lot D0915)


title: LBTV_379


title: ChIP_CEBPb_Egr2flfl_BMDM_24hIL4_rep2

value: Egr2 fl/fl

tag: cell type


title: LBTV_378


title: ChIP_CEBPb_LyzMCreEgr2flfl_BMDM_basal_rep2


title: ChIP_PU1_LyzMCreEgr2flfl_BMDM_24hIL4_rep2

value: PU1 (Santa Cruz, sc-352X, lot L2012)


title: LBTV_374


title: LBTV_369


title: LBTV_370


title: LBTV_377


title: LBTV_373


title: LBTV_376


title: LBTV_368


title: ChIP_CEBPb_Egr2flfl_BMDM_basal_rep2


title: ChIP_PU1_LyzMCreEgr2flfl_BMDM_basal_rep2


title: ChIP_PU1_LyzMCreEgr2flfl_BMDM_24hIL4_rep1


title: LBTV_367


title: ChIP_PU1_LyzMCreEgr2flfl_BMDM_basal_rep1


title: LBTV_366


title: LBTV_365


title: LBTV_383


title: ChIP_PU1_Egr2flfl_BMDM_24hIL4_rep2


title: LBTV_375


title: LBTV_362


title: LBTV_364


title: ChIP_PU1_Egr2flfl_BMDM_24hIL4_rep1


title: ChIP_PU1_Egr2flfl_BMDM_basal_rep1


title: ChIP_PU1_Egr2flfl_BMDM_basal_rep2


title: ChIP_PPARg_LyzMCreEgr2flfl_BMDM_24hIL4_rep1

value: PPARg (Santa Cruz, sc-271392 and sc-7273, lots G0210 and J1415)


title: ChIP_PPARg_LyzMCreEgr2flfl_BMDM_basal_rep1

value: BMDMs (bone marow-derived macrophages)


title: ChIP_STAT6_LyzMCreEgr2flfl_BMDM_24hIL4_rep2

value: STAT6 (Santa Cruz, sc-374021, lot L0916)


title: ChIP_PPARg_Egr2flfl_BMDM_basal_rep1


title: ChIP_PPARg_Egr2flfl_BMDM_24hIL4_rep1


title: ChIP_STAT6_LyzMCreEgr2flfl_BMDM_24hIL4_rep1


title: LBTV_359

value: Diffuse Large B-cell Lymphoma


title: LBTV_356


title: LBTV_360


title: LBTV_358


title: LBTV_355

value: ABC


title: LBTV_352


title: LBTV_353

value: F


title: LBTV_351

value: DLBCL FFPE tissue


title: ChIP_STAT6_LyzMCreEgr2flfl_BMDM_basal_rep1


title: ChIP_STAT6_Egr2flfl_BMDM_24hIL4_rep2


title: ChIP_STAT6_Egr2flfl_BMDM_24hIL4_rep1


title: ChIP_STAT6_Egr2flfl_BMDM_basal_rep2


title: LBTV_349

value: M


title: LBTV_350


title: ChIP_STAT6_Egr2flfl_BMDM_basal_rep1


title: LBTV_347


title: LBTV_348

value: Unclassified


title: ChIP_STAT6_LyzMCreEgr2flfl_BMDM_basal_rep2


title: LBTV_345


title: ChIP_H3K4me2_LyzMCreEgr2flfl_BMDM_24hIL4_rep1

description:
processed data file:
histone_tagCounts_around_24hIL4inducedEGR2Peaks_EGR2KO.txt


title: LBTV_354


title: LBTV_343


title: LBTV_339


title: ChIP_H3K4me2_LyzMCreEgr2flfl_BMDM_basal_rep1


title: LBTV_342


title: LBTV_340


title: ChIP_H3K4me2_Egr2flfl_BMDM_24hIL4_rep2


title: ChIP_H3K4me2_Egr2flfl_BMDM_24hIL4_rep1


title: ChIP_H3K4me2_Egr2flfl_BMDM_basal_rep1


title: ChIP_H3K4me2_Egr2flfl_BMDM_basal_rep2


title: LBTV_338


title: ChIP_PolII_LyzMCreEgr2flfl_BMDM_basal_rep1

value: PolII (Genetex, GTX102535, lot 39918)


title: LBTV_341


title: ChIP_H3K4me2_LyzMCreEgr2flfl_BMDM_basal_rep2


title: ChIP_H3K4me2_LyzMCreEgr2flfl_BMDM_24hIL4_rep2


title: ChIP_PolII_LyzMCreEgr2flfl_BMDM_24hIL4_rep1


title: ChIP_PolII_Egr2flfl_BMDM_24hIL4_rep1


title: ChIP_PolII_Egr2flfl_BMDM_basal_rep1


title: LBTV_346


title: LBTV_337


title: ChIP_H3K27ac_LyzMCreEgr2flfl_BMDM_24hIL4_rep2


title: LBTV_335


title: LBTV_334


title: LBTV_336


title: ChIP_H3K27ac_LyzMCreEgr2flfl_BMDM_24hIL4_rep1


title: LBTV_333


title: LBTV_332


title: ChIP_H3K27ac_LyzMCreEgr2flfl_BMDM_basal_rep1


title: LBTV_331


title: ChIP_H3K27ac_Egr2flfl_BMDM_24hIL4_rep2


title: LBTV_330


title: LBTV_329


title: ChIP_H3K27ac_Egr2flfl_BMDM_24hIL4_rep1


title: LBTV_328


title: ChIP_H3K27ac_Egr2flfl_BMDM_basal_rep2


title: ChIP_CEBPb_SPRET_BMDM_24hIL4_rep2

description:
processed data file:
ChIP_CEBPb_SPRET_BMDM_24hIL4.idr.txt

value: SPRET/EiJ


title: ChIP_CEBPb_SPRET_BMDM_24hIL4_rep1


title: LBTV_325


title: LBTV_326


title: LBTV_324


title: LBTV_322

value: GCB


title: ChIP_CEBPb_SPRET_BMDM_basal_rep2

description:
processed data file:
ChIP_CEBPb_SPRET_BMDM_basal.idr.txt


title: ChIP_CEBPb_PWK_BMDM_24hIL4_rep2

description:
processed data file:
ChIP_CEBPb_PWK_BMDM_24hIL4.idr.txt

value: PWK/PhJ


title: LBTV_320


title: ChIP_CEBPb_PWK_BMDM_24hIL4_rep1


title: ChIP_H3K27ac_LyzMCreEgr2flfl_BMDM_basal_rep2

value: LyzM-Cre Egr2 fl/fl


title: LBTV_318


title: LBTV_317


title: ChIP_CEBPb_PWK_BMDM_basal_rep2

description:
processed data file:
ChIP_CEBPb_PWK_BMDM_basal.idr.txt

value: CEBPb (Santa Cruz, sc-150, lot D0915)


title: ChIP_CEBPb_NOD_BMDM_24hIL4_rep2

description:
processed data file:
ChIP_CEBPb_NOD_BMDM_24hIL4.idr.txt

value: NOD/ShiLtJ


title: LBTV_316


title: LBTV_314


title: ChIP_H3K27ac_Egr2flfl_BMDM_basal_rep1

value: Egr2 fl/fl


title: ChIP_CEBPb_NOD_BMDM_24hIL4_rep1


title: LBTV_327


title: ChIP_CEBPb_NOD_BMDM_basal_rep2

description:
processed data file:
ChIP_CEBPb_NOD_BMDM_basal.idr.txt


title: LBTV_311


title: LBTV_313


title: ChIP_CEBPb_BALB_BMDM_24hIL4_rep2

description:
processed data file:
ChIP_CEBPb_BALB_BMDM_24hIL4.idr.txt

value: BALB/cJ


title: ChIP_CEBPb_SPRET_BMDM_basal_rep1

value: BMDMs (bone marow-derived macrophages)


title: ChIP_CEBPb_BALB_BMDM_basal_rep2

description:
processed data file:
ChIP_CEBPb_BALB_BMDM_basal.idr.txt


title: ChIP_CEBPb_BALB_BMDM_basal_rep1


title: LBTV_309


title: LBTV_307


title: LBTV_306


title: ChIP_CEBPb_PWK_BMDM_basal_rep1


title: ChIP_CEBPb_C57_BMDM_24hIL4_rep2

description:
processed data file:
ChIP_CEBPb_C57_BMDM_24hIL4.idr.txt


title: LBTV_304


title: ChIP_CEBPb_C57_BMDM_24hIL4_rep1


title: LBTV_315


title: ChIP_CEBPb_C57_BMDM_basal_rep2

description:
processed data file:
ChIP_CEBPb_C57_BMDM_basal.idr.txt


title: ChIP_CEBPb_C57_BMDM_basal_rep1


title: LBTV_303


title: ChIP_PU1_SPRET_BMDM_24hIL4_rep2

description:
processed data file:
ChIP_PU1_SPRET_BMDM_24hIL4.idr.txt

value: PU1 (Santa Cruz, sc-352X, lot L2012)


title: LBTV_302

value: Diffuse Large B-cell Lymphoma


title: LW_rep2_INPUT

city: Nanchang

first: Zhimin

last: Zhou

address: 888 Lushan Middle Avenue

institute: 江西农业大学

data_processing:
Trimmed clean reads were mapped to the pig reference genome Sscrofa 11.1  using Burrows- Wheeler Aligner (BWA) (Abuin et al., 2015), allowing two mismatches
Removing duplicated ChIP-seq reads using samtools
Calculating the Spearman correlation coefficients of bam files of various ChIP-seq samples using deepTools bamCorrelate module
MACS (Model-based Analysis for ChIP-Seq) version 2.1.0 peak caller was applied to infer the histone modification regions, i.e., peaks
Peak regions identified in individual samples were integrated by intersecting all peaks across data sets, with less than 1 kb distance between summits using bedtools version 2.27.0
Genome_build: Sscrofa 11.1

organism: Sus scrofa

source_name: Large White

extract_protocol:
C arefully dissected pituitary glands,Chromatin immunoprecipitation was performed using the SimpleChIP® Plus Enzymatic Chromatin IP Kit (Magnetic Beads, 9005)
ChIP libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: Large White

value: pituitary

value: post natal day 150


title: LW_rep2_H3K4me3


title: ChIP_PU1_SPRET_BMDM_24hIL4_rep1

tag: treatment


title: ChIP_CEBPb_NOD_BMDM_basal_rep1


title: LW_rep1_H3K4me3


title: LW_rep1_INPUT


title: ChIP_CEBPb_BALB_BMDM_24hIL4_rep1


title: LW_rep1_H3K27ac


title: ChIP_PU1_SPRET_BMDM_basal_rep2

description:
processed data file:
ChIP_PU1_SPRET_BMDM_basal.idr.txt


title: LBTV_310

value: M

value: ABC

value: DLBCL FFPE tissue


title: ChIP_PU1_SPRET_BMDM_basal_rep1

value: SPRET/EiJ


title: BMX_rep2_H3K4me3

source_name: Bama Xiang

value: Bama Xiang

value: post natal day 132


title: LBTV_305

value: F

value: GCB


title: ChIP_PU1_PWK_BMDM_24hIL4_rep1

description:
processed data file:
ChIP_PU1_PWK_BMDM_24hIL4.idr.txt

value: PWK/PhJ


title: BMX_rep2_H3K27ac


title: LW_rep2_H3K27ac


title: BMX_rep2_INPUT


title: ChIP_PU1_PWK_BMDM_basal_rep2

description:
processed data file:
ChIP_PU1_PWK_BMDM_basal.idr.txt


title: ChIP_PU1_PWK_BMDM_basal_rep1


title: BMX_rep1_H3K4me3


title: BMX_rep1_INPUT


title: ChIP_PU1_NOD_BMDM_24hIL4_rep1

description:
processed data file:
ChIP_PU1_NOD_BMDM_24hIL4.idr.txt

value: NOD/ShiLtJ


title: BMX_rep1_H3K27ac


title: ChIP_PU1_NOD_BMDM_24hIL4_rep2


title: ChIP_PU1_NOD_BMDM_basal_rep2

description:
processed data file:
ChIP_PU1_NOD_BMDM_basal.idr.txt


title: Hb9::GFP e10.5 MN rep2

city: Cambrdige

first: Jennifer

last: Hammelman

state: MA

address: 32 Vassar Street

institute: MIT

description: FACS purified GFP+

data_processing:
Reads trimmed for adaptors and low quality bases using Trimgalore (Cutadapt v0.6.2)
Reads were aligned with bwa mem (v0.7.1.7) with default parameters.
Duplicate reads were marked and removed with samtools (v1.7.2) markdup
Peaks were called using MACS2 (v2.2.7.1) with the parameters -f BAMPE -g mm -p 0.01 --shift -36 --extsize 73 --nomodel --keep-dup all --call-summits.
ENCODE blacklist regions ENCSR535HHO were excluded from downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: MACS2 narrowPeak calls from pooled replicates

source_name: Hb9::GFP e10.5 MN

extract_protocol:
phenol chloroform extraction and ethanol precipitation
ATAC libraries were amplified by following the published protocol (Buenrostro et al., 2015). All ATAC-seq libraries required 8-9 total amplification cycles. ATAC-seq libraries were sequenced at the MIT BioMicroCenter. Paired end sequencing was performed using the 75nt Nextseq kit.

value: mouse embryonic day 10.5

value: spinal motor neurons


title: Hb9::GFP e10.5 MN rep1

description: FACS purified GFP+


title: ChIP_PU1_NOD_BMDM_basal_rep1

value: BMDMs (bone marow-derived macrophages)

value: PU1 (Santa Cruz, sc-352X, lot L2012)


title: ChIP_PU1_BALB_BMDM_24hIL4_rep2

description:
processed data file:
ChIP_PU1_BALB_BMDM_24hIL4.idr.txt

value: BALB/cJ


title: ChIP_PU1_BALB_BMDM_24hIL4_rep1


title: DIO NCT-1 intestine

city: San Diego

first: Brian

last: James

address: 10901 North Torrey Pines Road

department: Genomics

institute: Sanford Burnham Prebys Medical Discovery Institute

data_processing:
Read data was processed in BaseSpace (basespace.illumina.com).
Reads were aligned to to Mus musculus genome (mm10) using STAR aligner (https://code.google.com/p/rna-star/) with default settings.
Differential transcript expression was determined using the Cufflinks Cuffdiff package (https://github.com/cole-trapnell-lab/cufflinks).
Genome_build: Mus musculus genome mm10
Supplementary_files_format_and_content: Read FPKM and Log2 fold differential expression, and FDR corrected Q-values

source_name: intestine

growth_protocol: 16 weeks old C57BL/6J DIO male mice (cat#380050)

extract_protocol:
Intestine from DMSO or NCT treated mice was removed, flash frozen in liquid nitrogen, and RNA harvested using Trizol reagent.
PolyA RNA was isolated using the NEBNext® Poly(A) mRNA Magnetic Isolation Module and barcoded libraries were made using the NEBNext® Ultra II™ Directional RNA Library Prep Kit for Illumina®(NEB, Ipswich MA).  Libraries were pooled and single end sequenced (1X75) on the Illumina NextSeq 500 using the High output V2 kit (Illumina Inc., San Diego CA).

treatment_protocol: High fat diet mice treated with DMSO or NCT for 2 weeks with intraperitoneal injection.

value: 16weeks old

value: NCT treated 200 mg/kg bid 14 days


title: ChIP_PU1_BALB_BMDM_basal_rep2

description:
processed data file:
ChIP_PU1_BALB_BMDM_basal.idr.txt


title: DIO DMSO-2 intestine

value: DMSO control


title: ChIP_PU1_BALB_BMDM_basal_rep1


title: ChIP_PU1_PWK_BMDM_24hIL4_rep2


title: ChIP_PU1_C57_BMDM_24hIL4_rep2

description:
processed data file:
ChIP_PU1_C57_BMDM_24hIL4.idr.txt