title: UM1 [scRNA-seq]

city: Paris

first: Paul

last: Gueguen

address: 26 rue D'Ulm

department: Inserm U932

country: France

institute: Institut Curie

description: single cell RNA-seq

data_processing:
sample de-multiplexing and alignment was performed using Cell Ranger Single Cell Software Suite (v3.0.2)
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed files are raw count UMI matrices which are given by Cellranger pipeline and Seurat objects with the RNA matrix in the RNA assay, and the TotalSeq information in the ADT assay.

source_name: Uveal Melanoma

extract_protocol: RNA from was extracted according to the Single Cell VDJ 5' Reagent kits.

value: Uveal Melanoma


title: inflorescence meristems, myb3r4_rep3

status: Public on Mar 26 2021

type: SRA

city: Cambridge

first: Weibing

last: Yang

state: Select...

address: 47 Bateman Street, Cambridge

country: United Kingdom

institute: Sainsbury Laboratory  University of Cambridge

library_source: transcriptomic

data_processing:
The raw reads obtained from the sequencing facilities were analyzed in house. We first assessed the quality of reads using FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc/).Read were aligned to the TAIR10 transcriptome using Salmon (Patro et al., 2017). For each gene, read abundance were computed.
Genome_build: TAIR10
Supplementary_files_format_and_content: rna-seq_combined_read.txt

molecule: total RNA

organism: Arabidopsis thaliana

source_name: myb3r4 inflorescence meristems

growth_protocol: Arabidopsis plants were grown in a growth chamber under the following conditions: long-day photoperiod (16-h light/8-h dark), light intensity 170 μmoles m-2 s-1, day/night temperature 21°C/17 °C. Shortly after bolting (with stem length ~1 cm), the shoot apices were cut and the SAMs were dissected by removing fully open flowers.

extract_protocol:
Total RNA was isolated from 36 dissected inflorescence meristems using RNeasy Mini Kit (QIAGEN Cat No./ID: 74104), following the manufacturer’s instructions. RNA quality and integrity was assessed on the Agilent 2200 TapeStation.
After the QC procedures, mRNA from eukaryotic organisms is enriched using oligo(dT) beads. For prokaryotic organisms or eukaryotic organisms' long-non-coding libraries,  rRNA is removed using the Ribo-Zero kit that leaves the mRNA. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using  mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the  second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and  PCR enrichment.The qualified libraries are fed into Illumina sequencers after pooling according to its effective concentration and expected data volume.

tag: genotype

tag: tissue

value: inflorescence meristems

tag: shift experiment


title: UM2_3 [scADT-seq]

description: Antibody Derived Tag

library_source: genomic

data_processing:
Library strategy: single cell ADT-seq
sample de-multiplexing and alignment was performed using Cell Ranger Single Cell Software Suite (v3.0.2)
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed files are filtered contigs annotations files which are given by Cellranger pipeline.

molecule: genomic DNA

organism: Homo sapiens

extract_protocol: Feature Barcoding with Biolegend TotalSeq-A antibodies


title: inflorescence meristems, myb3r4_rep2


title: mouse_kidney_control_NEBNext_kit_rep2

city: Boston

first: Saumya

last: Gupta

state: MA

address: 450 Brookline Ave

department: Cancer Biology

country: USA

institute: Dana-Farber Cancer Institute

description:
mouse left kidney, control sample, RNA input 100ng, library sequenced using NEBNext kit, library preparation replicate 2
kidney_RNAseq_allelic_counts.csv
kidney_RNAseq_allelic_imbalance.csv

data_processing:
Reference preparation: we created two custom parental genomes (“pseudogenomes” (Crowley et al., 2015; Zou et al., 2014); or “pseudocontigs” when we have phasing by contigs) for each organism, we used a custom script (all custom software tools mentioned are available on Github https://github.com/gimelbrantlab/QCumber). We also created a vcf-file with one allele considered as a reference (maternal 129S1 or first phased allele) and the other as an alternative allele. Only heterozygous sites were used.
Alignment: RNA-seq reads were aligned with STAR aligner v.2.5.4a (Dobin et al., 2013) on each of two pseudogenomes, with default threshold on quality of alignment. Only uniquely alligned reads were used.
Allele assigment. Given vcf file with heterozygous positions, coverage over each SNP was calculated using custom script based on samtools mpileup and parsed to obtain the table with allelic counts. Data processing steps from read alignment to allelic counts were based on the GATK pipeline (Castel et al., 2015).
Allele counting per gene. All exons belonging to the same gene were merged into a single gene model based on GTF file (RefSeq GTF files, GRCm38.68 and GRCh37.63, were downloaded from Ensemble ftp://ftp.ensembl.org/pub/release-68/gtf/ (Zerbino et al., 2018)), excluding overlapping regions that belong to multiple genes. This step was based on the GATK pipeline (Castel et al., 2015).
AI point estimate per gene obtained as a proportion of maternal gene counts to total allelic gene counts
Genome_build: mm10
Supplementary_files_format_and_content: allelic counts, allelic imbalance with confidence intervals

organism: Mus musculus

source_name: mouse left kidney tissue

extract_protocol:
Total RNA was isolated using Trizol from a freshly collected kidney tissue of an adult female mouse of 129S1 x Cast/Ei F1 background. Isolated RNA was DNase-treated with RQ1 DNase (Promega).
Library preparation was done using NEBNext Ultra RNA Poly-A kit (mentioned as NEBNext in the sample name) or Clonetech SMARTseqv4 kit (mentioned as SMARTseq in the sample name), according to manufacturers’ instructions. Input RNA amount varied depending on the sample

tag: strain

value: 129S1/SvImJ x CAST/EiJ F1

tag: drug treatment

value: control

tag: library replicates

tag: Sex

value: female


title: UM2_3 [scTCR-seq]

description: TCR enrichment from amplified cDNA

data_processing:
Library strategy: single cell TCR-seq
sample de-multiplexing and alignment was performed using Cell Ranger Single Cell Software Suite (v3.0.2)
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed files are filtered contigs annotations files which are given by Cellranger pipeline.

extract_protocol: TCR libraries was extracted according to the Single Cell VDJ 5' Reagent Kits


title: UM1 [scTCR-seq]

description: TCR enrichment from amplified cDNA


title: UM2_3 [scRNA-seq]

description: single cell RNA-seq


title: 600µm microtumor Day 6, biological rep3

type: RNA

city: Pittsburgh

first: Shilpa

last: Sant

state: PA

address: 700 Technology Drive

department: Pharmaceutical Sciences

institute: University of Pittsburgh

description: Gene expression data from large 600μm microtumors cultured for 6 days and harvested on day 6

hyb_protocol: Following fragmentation and labeling, 2.4 ug of cDNA were hybridized for 16hr at 45oC with 60 RPM rotation on Genechip Clariom S Human arrays. GeneChips were washed and stained on an Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using  a GeneChip 3000 scanner with 7G upgrade and autoloader.

data_processing: Data were analyzed with Expression Console 1.2.0.20

label: biotin

source_name: Large 600μm microtumors cultured for 6 days and harvested on day 6

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix Pico protocol from 5ng total RNA (GeneChip Pico Reagent Kit User Guide, Rev.4).

growth_protocol: T47D cells were grown in DMEM media (10-013-CV). Microtumors of diameters <150 µm ‘small’ microtumors and >500 µm ‘large’ microtumors were obtained by seeding T47D cells in non-adhesive 1x1 cm2 polyethylene glycol (PEG) hydrogel microwell devices  fabricated using polydimethyl siloxane (PDMS) stamps containing posts of either 150 µm or 600 µm in diameter with equal height.

extract_protocol: Total RNA was extracted using GeneJET RNA purification kit (K0732) acoording to the manufacturer's instructions.

treatment_protocol: 3D microtumors were generated from the same breast cancer cell line model, T47D, without any external stimulus. The small (<150 µm) T47D microtumors, large (>500µm) T47D microtumors and CM induced 150 µm microtumors were harvested at specific timepoints on day 1 and day 6, and placed on ice in the Trizol solution.

tag: cell line


title: CM150µm microtumor Day 6, biological rep1

description: Gene expression data from small 150μm microtumors treated with secretome of large 600μm microtumors from day 3 and harvested on day 6

source_name: Small 150μm microtumors treated with secretome of large 600μm microtumors from day 3 and harvested on day 6


title: CM150µm microtumor Day 6, biological rep3


title: inflorescence meristems, myb3r1_rep3

source_name: myb3r1 inflorescence meristems


title: inflorescence meristems, myb3r1_rep2


title: CM150µm microtumor Day 6, biological rep2


title: MDA231_shPYK2_b [60_Y]

city: Rehovot

first: Sima

last: Lev

address: 234 Herzl St.

department: Molecular Cell Biology

country: Israel

institute: Weizmann Institute of Science

data_processing:
Libraries were sequenced by the Illumina Novaseq 6000 using SP mode 100 cycles kit (Illumina)
Mapping of sequences to the genome was performed by the UTAP pipeline (UTAP: User-friendly Transcriptome Analysis Pipeline, Kohen et al. BMC Bioinformatics 2019, 20(1):154))
Reads were trimmed using cutadapt (DOI: 10.14806/ej.17.1.200) (parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a “A{10}” –times 2 -u 3 -u -3 -q 20 -m 25).
The remaining reads were mapped to the genome (hg38) using STAR (DOI: 10.1093/bioinformatics/bts635) v2.4.2a (parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic, –alignSoftClipAtReferenceEnds No).
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with gene counts for every gene and every sample

source_name: Breast cancer cell line

growth_protocol: MDA-MB-231 cells were transduced with PLKO (control) or shPYK2 KD lentivirus and grown in selection medium (RPMI supplemented with 10% FBS, 1% Penicillin-Streptomycin solution and 1.5µg/ ml Puromycine) for 2 passages before RNA extraction.

extract_protocol:
RNA was extracted from 4 - 6 million cells per samples using TRI reagent (Sigma), following standard extraction protocol.
RNAseq libraries were constructed by applying a bulk adaptation of the MARS‐seq protocol (Jaitin et al. 2014 Science.343:776-9).

tag: shRNA


title: 600µm microtumor Day 6, biological rep1


title: Liver_E2F2_HFD_rep3

city: Leioa

first: Patricia

last: Aspichueta

address: Barrio Sarriena s/n

department: Physiology

country: Spain

institute: University of the Basque Country UPV/EHU

description: Hepatic gene expression after E2F2 knockout mice were exposed to diethylnitrosamine and high fat diet

hyb_protocol: Samples were analysed using Agilent SurePrint G3 Mouse GE 8x60K microarrays (Design ID 028005) (Agilent Technologies), with 55,681 mouse features represented.  600 ng of labeled cRNA samples were hybridized at 65 ºC for 17 h in a SureHyb hybridization chamber (Agilent Technologies).

scan_protocol: The arrays were scanned immediately after washing on a G2565CA DNA microarray scanner, with ozone-barrier slide covers (Agilent Technologies) using one-color AgilentG3_GX_1color scanner protocol for HD microarray formats (scanner settings Dye channel: Green, Scan Region: Agilent HD (61x21.6 mm), Scan resolution 3 um, Tiff file dynamic range 20 bit, Green PMT gain 100 %)

data_processing:
The scanned images were analyzed with Feature Extraction Software v 10.7.3.1.  (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028005_D_F_20140728) to obtain background subtracted and spatially detrended Processed Signal intensities. Raw data from Feature Extraction software was subsequently processed on GeneSpring GX 12.5 (Agilent Technologies). GeneSprings transforms all FE Flags to a single Detection Flag and calculates the geometric mean of replicated probes.
Data were normalized by quantile normalization and centered by mean.

source_name: Liver, E2F2 knockout mice, diethylnitrosamine treatment, high fat diet, replicate 3

label_protocol: RNA samples were labeled and hybridized following standard Agilent Protocol One-Color Microarray-Based Gene Expression analysis (Low Input Quick Amp Labeling) v 6.5. Briefly, 50 ng of total RNA were retrotranscribed and labeled using Low imput Quick Amp Labeling kit one color (Agilent Technologies) following manufacturer instructions. First, total RNA was retrotranscribed with AffinityScript Reverse Transcriptase (Agilent Technologies), using Oligo dT primers coupled to T7 promoter. Double stranded cDNA synthesized by AffinityScript RT was in vitro transcribed by T7 RNA pol in the presence of Cy3-CTP to generate amplified and labeled cRNA. Labeled samples are purified with silica-based RNeasy spin columns (Qiagen, Hilden, Germany). After labeling and purification, cRNA was quantified with NanoDrop 1000 spectrophotometer in order to determine the yield and specific activity of each reaction.

growth_protocol: 5-6 mice were placed in each cage and were housed at 22 °C with an artificial 12 hours light (8:00 to 20:00)/12 hours dark cycle. Food and water were provided ad libitum.

extract_protocol: Total RNA was extracted from liver homogenates using Trizol Reagent (Invitrogen, USA) and according to the manufacturer instructions.

treatment_protocol: WT (129/Sv x C57BL/6),  E2f1-/- and E2f2-/- mice were administered a single injection of DEN (25 mg/kg of mice, Sigma-Aldrich, USA) intraperitoneally on postnatal day 14. After weaning at 1 month old, mice were fed a HFD (60 % fat calories mouse diet, F3282, Bio-Serv, USA) for 32 weeks and sacrificed at 9 months old. Mice were fasted for 4 hours and were euthanized with sodium pentobarbital (Abbott Laboratorios, Spain) injected intraperitoneally (60 mg/kg of mice in PS). Liver was collected and washed in cold PBS. Then, it was frozen in liquid nitrogen and stored at -80 °C until analysis were performed.

value: Liver

value: E2F2 Knockout

tag: treatment

value: Dietylnitrosamine

tag: diet

value: High fat diet


title: MDA231_PLKO_b [59_Y]

value: PLKO


title: 600µm microtumor Day 1, biological rep3

description: Gene expression data from large 600μm microtumors cultured on day 0 and harvested on day 1

source_name: Large 600μm microtumors cultured on day 0 and harvested on day 1


title: inflorescence meristems, myb3r1_rep1


title: 600µm microtumor Day 1, biological rep2


title: inflorescence meristems, myb3r4_rep1


title: 150µm microtumor Day 6, biological rep3

description: Gene expression data from small 150μm microtumors cultured for 6 days and harvested on day 6

source_name: Small 150μm microtumors cultured for 6 days and harvested on day 6


title: h2a.w-2 bisulfite-seq rep 2

city: Los Angeles

first: Colette

middle: L

last: Picard

state: California

address: 610 Charles E Young Dr East, Room 4045

department: Molecular, Cell and Developmental Biology

institute: University of California - Los Angeles

data_processing:
For all libraries except BS-seq: reads were trimmed and quality-filtered using trim-galore v.0.5.0 with parameters -q 25 -a AGATCGGAAGAG, and all other params default.
ChIP-seq datasets: reads were mapped to TAIR10 using bowtie2 v.2.3.4.3 (parameters: -N 0 -L 22, all others default). Only reads with a single best alignment to the genome were kept for further analysis. Probable PCR duplicates were removed using MarkDuplicates from the Picard Tools suite. Pileup tracks of each ChIP-seq sample over its matched H3 sample (log2) were generated using the deeptools v.3.3.0 function bamCompare, while coverage tracks of input samples were generated using deeptools function bamCoverage; both functions used parameters --normalizeUsing CPM, --binSize 10.
ATAC-seq datasets: reads were mapped to TAIR10 using bowtie2 v.2.3.4.3 (parameters: -N 0 -L 22, all others default). Only properly paired reads with a single best alignment to the genome were kept for further analysis. Probable PCR duplicates were removed using MarkDuplicates from the Picard Tools suite. Sample tracks were obtained using Genrich (https://github.com/jsh58/Genrich) with parameters -p 0.01, -a 200, -l 100, -g 100. ChrM, ChrC, and several high-copy number rRNA regions were excluded from the analysis (provided as a supplementary file in the paper).
RNA-seq datasets: reads were mapped to TAIR10 using STAR v.2.7.0c (parameters: --alignIntronMin 70 --alignIntronMax 5000 --alignMatesGapMax 100000 -outFilterMismatchNoverReadLmax 0.05, all others default). Only pairs with a single best alignment to the genome were kept for further analysis. Probable PCR duplicates were removed using MarkDuplicates from the Picard Tools suite.  Read counts for each gene and TE were obtained using htseq-count (parameters: --nonunique none -m intersection-strict) using the araport11 annotations (PMID: 27862469). Differential expression analysis was performed using DESeq2 (PMID: 25516281), and genes were considered differentially expressed with an adjusted p-value < 0.05 and abs[log2(fold change)] > 1.
BS-seq datasets: analysis was performed as previously reported (Bourguet et al. 2018, PMID: 30574575). Briefly, different reads with identical sequences were presumed to be PCR duplicates and removed prior to mapping. Reads were mapped to TAIR10 using BS-Seeker2 v.2.1.5, allowing 4% mismatches, resulting in a 'CGmap file'. Methylation values were only called from uniquely-mapped reads. bigWig tracks were created from the CGmap files by retaining all cytosine positions with 8 or more read coverage, computing %methylation, and converting the resulting bedGraph files to bigWig using the UCSC bedGraphToBigWig function.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig tracks for all ChIP-seq samples (except for input samples) are provided, containing normalized sequencing depth of the IP sample vs. its matched input control. For input DNA samples, bigWig tracks contain coverage normalized by total library depth (CPM) instead. For ATAC-seq, normalized coverage tracks created by Genrich are provided. For RNA-seq, the output of DESeq2 analysis is provided, including overall per-gene/TE expression estimates (baseMean), log2(WT / mutant) (mutant = h2a.w-1 or h2a.w-2), and the adjusted p-value. Note that positive log2(FC) numbers indicate that mutant > WT, negative numbers indicate mutant < WT. For BS-seq, 'CGmap' text files containing all methylation data are provided, along with separate bigWig tracks of methylation levels for CG, CHG and CHH methylation. Only positions with 8+ coverage were used to generate the bigWig files.

source_name: h2a.w-2 bisulfite-seq_seedlings

growth_protocol: Plants were grown in long-day conditions (16h light, 8h dark) at 23°C with 50% relative humidity.

extract_protocol:
DNA was extracted from 10-day-old seedlings using the Wizard Genomic DNA Purification kit (Promega).
Bisulfite conversion, library preparation and sequencing were performed at the Beijing Genomics Institute (Hong Kong). Methylated adapters were ligated prior to bisulfite treatment using the ZYMO EZ DNA methylation Gold kit. Libraries were sequenced PE 150 bp on HiSeq X Ten.

treatment_protocol: no treatment

tag: ecotype background

tag: developmental stage

value: 10-day-old seedlings


title: MDA231_shPYK2_a [58_Y]


title: Liver_E2F2_HFD_rep1

source_name: Liver, E2F2 knockout mice, diethylnitrosamine treatment, high fat diet, replicate 1


title: Liver_E2F2_HFD_rep4

source_name: Liver, E2F2 knockout mice, diethylnitrosamine treatment, high fat diet, replicate 4


title: 600µm microtumor Day 1, biological rep1


title: 600µm microtumor Day 6, biological rep2


title: Liver_E2F1_HFD_rep4

description: Hepatic gene expression after E2F1 knockout mice were exposed to diethylnitrosamine and high fat diet

source_name: Liver, E2F1 knockout mice, vehicle treatment, chow diet, replicate 4

value: E2F1 Knockout


title: 150µm microtumor Day 6, biological rep1


title: Liver_E2F2_HFD_rep2

source_name: Liver, E2F2 knockout mice, diethylnitrosamine treatment, high fat diet, replicate 2


title: inflorescence meristems, Col-0_rep3

source_name: Col0 WT inflorescence meristems

value: Col0 WT


title: Liver_E2F1_HFD_rep3

source_name: Liver, E2F1 knockout mice, vehicle treatment, chow diet, replicate 3


title: WT bisulfite-seq rep 2

source_name: WT bisulfite-seq_seedlings

value: wild-type


title: inflorescence meristems, Col-0_rep2


title: MDA231_PLKO_a [57_Y]


title: 150µm microtumor Day 6, biological rep2


title: inflorescence meristems, Col-0_rep1


title: JNHJ04_B

city: Delft

first: Raúl

middle: Antonio

last: Ortiz-Merino

address: van der Maasweg 9

department: Biotechnology

country: Netherlands

institute: Delft University of Technology

data_processing:
RNAseq reads were mapped to the genome using bowtie v1.2.1.1 with parameters  -v 0 -k 10 --best -M 1
Alignments were filtered and sorted using samtools (v1.3.1)
Read counts were obtained with featureCounts (v1.6.0) using parameters -B -C t
Differential gene expression analysis was performed using edgeR (v3.28.1). Genes with 0 read counts in all conditions were filtered out from the analysis, same as genes with less than 10 counts per million
Counts were normalized using the TMM method, and dispersion was estimated using generalized linear models
Differentially expressed genes were then calculated using a log ratio test adjusted with the Benjamini-Hochberg method. Absolute log2 fold-change values > 2, false discovery rate < 0.5, and P value < 0.05 were used as significance cutoffs.
Genome_build: Not available yet
Supplementary_files_format_and_content: counts_opar.txt: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: DE_21_opar.txt: TSV file with differentially expressed genes from micro-aerobic to aerobic
Supplementary_files_format_and_content: DE_31_opar.txt: TSV file with differentially expressed genes from strain IMX2167 chemostat vs aerobic batch
Supplementary_files_format_and_content: DE_43_opar.txt: TSV file with differentially expressed genes from IMX2167 chemostat vs CBS11895wt chemostat
Supplementary_files_format_and_content: DE_46_opar.txt: TSV file with differentially expressed genes from strain CBS11895wt chemostat vs aerobic batch
Supplementary_files_format_and_content: DE_61_opar.txt: TSV file with differentially expressed genes from strain IMX2167 aerobic batch vs CBS11895wt aerobic batch

molecule: polyA RNA

organism: Ogataea parapolymorpha

source_name: Bioreactor cell culture sample

extract_protocol:
Cells were flash frozen on liquid nitrogen, and RNA was harvested using acidic phenol chloroform extraction. Illumina TruSeq stranded mRNA LT protocol (#15031047) with polyA enrichment was used with approximately 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: gut2{delta} ndi/nde{delta}

value: Batch Aerobic, 7.5 g/L glucose, SM medium, pH=6


title: JNHJ04_C

value: Chemostat Aerobic, 7.5 g/L glucose, SM medium, D = 0.1 h-1, pH=5


title: Liver_E2F1_HFD_rep2

source_name: Liver, E2F1 knockout mice, vehicle treatment, chow diet, replicate 2


title: Liver_E2F1_HFD_rep1

source_name: Liver, E2F1 knockout mice, vehicle treatment, chow diet, replicate 1


title: JNHJ03_C


title: S3E

city: Birmingham

first: Andrzej

middle: T

last: Slominski

state: AL

address: 1720 2nd Avenue South

department: Dermatology

institute: UAB

data_processing:
Illumina bcl2fastq version 2.2.0 was used for basecalling
Trim Galore! version 0.6.2 was used to trim the raw sequence FASTQ files wih parameters --paired; --trim1
STAR version 2.7.0 was used to align the trimmed FASTQ files with parameters --outReadsUnmapped Fastx; --outSAMtype BAM SortedByCoordinate; --outSAMattributes All; --readFilesCommand gunzip -c
HTSeq-Count version 0.11.2 was used to estimate transcript abundances from STAR alignment BAM files with parameters -m union; -r pos; -t exon; -i gene_id; -a 10; -s no; -f bam
DESeq2 was used to normalize and calculate differential expression following their vignette and default settings
Genome_build: Gencode GRCh38 p7 Release 25
Supplementary_files_format_and_content: Tab delimited text file containing raw count values for each gene in each sample

source_name: Keratinocytes

growth_protocol: Foreskins  from human patients (Caucasian)  were collected. To isolate keratinocytes from the epidermis  was separated from the dermis using dispase and a suspension of single keratinocytes was prepared for culturing in vitro. Cells were grown in complete keratinocytes media with supplements. Cells in their early passages (2nd) were used for experiments. The cells were treated with the compounds dissolved in ethanol. The final concentration of ethanol in the media was 0.1%, while of the compounds was 10^-5 M

extract_protocol:
After 24 h of incubation, cells were harvested for RNA isolation (RNAeasy Micro kit, Qiagen) following the manufacturers’ protocol. At least 500 ng of RNA for each sample was used for RNASeq processing and analysis  done by Novogen Corporation Inc (Sacramento, CA). Sample quality and concentration were determined using Agilent 2100.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Epidermal human primary keratinocytes were treated with melatonin, 6-hydroxymelatonin or AFMK, diluted in ethanol in keratinocyte media containing 0.5% BSA. Final concentration of the melatonin derivatives was 10 uM, with the final ethanol concentration being 0.1% which was also used as a vehicle control.

tag: cell type

value: Keratinocytes

value: Skin

value: Ethanol


title: S3M

value: Melatonin


title: S3A

value: AFMK


title: Liver_WT_HFD_rep4

description: Hepatic gene expression after wild type mice were exposed to diethylnitrosamine and high fat diet

source_name: Liver, Wild type mice, diethylnitrosamine treatment, high fat diet, replicate 4

value: Liver

value: Wild type


title: ELOX52-10R

value: Chemostat aerobic, 7.5 g/L glucose, SM urea medium, D = 0.1 h-1, pH=6, antifoam pluronic acid, 84 mg/L Tween 80, 10 mg/L ergosterol


title: Liver_WT_HFD_rep3

source_name: Liver, Wild type mice, diethylnitrosamine treatment, high fat diet, replicate 3

value: Dietylnitrosamine

value: High fat diet


title: HEK Rot treated Bio 2

first: Yanqiang

last: Li

address: 300 Longwood Ave.

department: Cardiology Department

institute: Boston Children's Hospital

data_processing:
High-throughput sequencing generated sequences for each  sample and the raw reads passed quality filtering (Q > 17 and length >= 25 bp). Raw reads were first subject to 3’ adapter removal. Clean reads of fastq file were transferred into fasta file.
Sequencing reads were aligned to the human genome (hg19) with TopHat2 (v2.0.9) (Kim et al. 2013). For mRNA analyses, the RefSeq database (Build 37.3) was chosen as the annotation references.
Read counts of annotated genes were obtained by the Python software HTSeq-count (Anders et al. 2015). The read counts of each transcript were normalized to the length of the individual transcript and to the total mapped fragment counts in each sample and expressed as fragments per kilobase of exon per million fragments mapped (FPKM) of mRNAs in each sample.
Differentially expressed genes were defined as those with a 1.5 fold change in expression using a FDR<0.05 from the edgeR package (Robinson et al. 2010).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file include raw counts for 4 Samples.

source_name: human embryonic kidney cells

growth_protocol: HEK293 cells were cultured in high glucose Dulbecco's Modified Eagle Medium (DMEM) with 10% (v/v) fetal bovine serum (FBS) in an incubator at 37 °C with 5% CO2.

extract_protocol:
Total RNAs from exposed and control groups  were isolated and quality controlled with protocols from Illumina. A total amount of 2μg RNA per sample was used as input material for library construction.
A total of 2ug per sample was used for library construction using the TruSeq Sample Preparation kit from Ilumina (San Diego, CA). Poly-A containing mRNA molecules were isolated from total RNA using oligo-dT attached magnetic beads. Isolated mRNA was then fragmented and synthesized into double stranded cDNA according to kit instructions. Ligation of unique Ilumina adapter indices was completed for each sample before bead purification.

treatment_protocol: At approximately 60% confluent, cells were treated with fresh medium containing DMSO (<0.002%) or Rotenone (200 nM) for 24h.

value: human embryonic kidney cell (HEK)

value: wild type

value: rotenone


title: S1M


title: ELOX52-09R

value: wild-type


title: mouse 6 RT 6-1

city: Dalian

first: Bo

last: Liu

address: 9 Western Section, Lvshun South Street

country: China

institute: Dalian Medical University

hyb_protocol: Hybridization was performed overnight on a μParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies) (1). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://www.mirbase.org/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 L 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics)

data_processing: Data were analyzed by first subtracting the background, then the signals were normalized using a Lowess (locally weighted regression) filter. The raw microarray data set was filtered according to a standard procedure to exclude spots with minimum intensity. It was arbitrarily set to an intensity parameter of P100 for the miRNA microarray data. Spots with diameters less than 10 μm and flagged spots were also excluded from the analyses.

source_name: RA-treated

label_protocol: Labeling of total RNA was performed according to the protocol from LC Science for a single-color experiment with no modification.

extract_protocol: Total RNA was isolated with the Total RNA Purification Kit (Norgen Biotek Corporation, Thorold, Canada) according to the manufacture's instructions

value: RA-treated


title: HEK Rot treated Bio 1


title: mouse 4 RT 4-1


title: mouse 5 RT 5-1


title: HEK Vehicle

value: Vehicle


title: ELOX37-10R

value: Chemostat micro-aerobic, 20 g/L glucose, SM urea medium, D = 0.1 h-1, micro-aerobic, pH=6, antifoam pluronic acid, 420 mg/L Tween 80, 10 mg/L ergosterol


title: S1E

value: Keratinocytes


title: HEK Control

value: Control


title: Liver_WT_HFD_rep2

source_name: Liver, Wild type mice, diethylnitrosamine treatment, high fat diet, replicate 2


title: Liver_WT_HFD_rep1

source_name: Liver, Wild type mice, diethylnitrosamine treatment, high fat diet, replicate 1


title: JNHJ03_B

value: gut2{delta} ndi/nde{delta}

value: Batch Aerobic, 7.5 g/L glucose, SM medium, pH=6


title: mouse 3 NT 3-1

source_name: control

value: nomal


title: NC_NgCtrl3_cycle4_Rep1

city: Hong Kong

first: Jian

last: Yan

state: Hong Kong Special Administrative Region

address: 83 Tat Chee Avenue, Kowloon

department: Department of Biomedical Sciences

institute: City University of Hong Kong

description:
processed data file: 0_PA_all_PWM_results.txt
processed data file: 1_PA_all_PWM_FIMO_genome_scan_results_reshaped_bed6_plus.sorted.txt

data_processing:
Library strategy: HT-SELEX
Illumina Casava v1.7 software used for basecalling.
Quality control of the raw sequencing data using FastQC version v0.11.7 with default parameters.
Sequences from the 40-nt random region without bases annotated as N were extracted using a custom script and used for further analyses.
Autoseed software was used for motif analysis.
Use R ggseqlogog package to build motif logos.
Genome_build: Pseudomonas aeruginosa PAO1 (GCF_000006765.1, ASM676v1)
Supplementary_files_format_and_content: 0_PA_all_PWM_results.txt: Tab-delimited text file includes position weight matrix (PWM) results for each transcription factor (TF).
Supplementary_files_format_and_content: 1_PA_all_PWM_FIMO_genome_scan_results_reshaped_bed6_plus.sorted.txt: Tab-delimited text file includes all TFs' genome wide target scan results based on the output of FIMO software.

organism: Pseudomonas aeruginosa PAO1

source_name: Negative Control 3

growth_protocol: The E. coli strains for protein purification were grown at 37 ℃ in LB (Luria-Bertani) broth with shaking at 220 rpm or on LB agar plates until OD600=0.6.

extract_protocol:
The pellet was suspended in 12 ml buffer A and lysed by sonication at ten seconds interval for 20 minutes and then centrifuged at 4 °C (12000 rpm, 30 min) to collect protein supernatant. The supernatant was filtered with a 0.45 μm filter and the filtrate was added into a Ni-NTA column (Bio-Rad) which had been equilibrated with buffer A before using. The Ni-NTA column was eluted with 30 ml gradient from 60 to 500 mM imidazole prepared in buffer A gradually.
HT-SELEX was performed by using selection ligands containing an 8 bp barcode before and after the 40 bp randomized region for Illumina system or a 10 bp barcode after the 40 bp randomized region for BGI system, respectively. The ligand libraries were produced by PCR amplification using the primers in Supplementary Table3 and 40 bp randomized oligo as template. The libraries were sequenced using Illumina HiSeq X Ten or BGI MGISEQ-2000 sequencer to analyze the uniformity of each base (A, T, C, G). Then, 100-200 ng protein and 5 ul selection ligands were added into Promega binding buffer (10mM Tris pH7.5, 50mM NaCl, 1 mM DTT, 1mM MgCl2, 4% glycerol, 0.5mM EDTA, 5µg/ml poly-dIdC (Sigma P4929)) until the total volume reached 25 ul. After incubating for 30 min at room temperature, the 150 ul Promega buffer (without poly-dIdC) containing 10 ul Ni Sepharose 6 Fast Flow resin (GE Healthcare 17-5318-01) equilibrated in binding buffer was added into the mixture and incubated for 60 min with a gentle shaking at room temperature. After binding, the resin beads were consecutively washed with a gentle shaking for 12 times with 200 μl of Promega binding buffer (without poly-dIdC). It took 5 min for each washing. Subsequently, the residual moisture on beads was carefully cleared by a soft centrifuging at 500 g for 30 s, and then the bound DNA was re-suspended by using 200 uL double-distilled water. Finally, about 20 uL bound DNA was performed for PCR amplification using Phusion DNA polymerase (NEB M0530L) with the primers in Supplementary Table3, and the resulting PCR products were used as selection ligands for the next cycle of HT-SELEX. This process was repeated four times. After each cycle, the purified PCR products from each HT-SELEX cycle were pooled and sequenced using Illumina HiSeq X Ten or BGI MGISEQ-2000 sequencer.

treatment_protocol: 0.5 mM IPTG (Isopropyl β-D-1-Thiogalactopyranoside) was added into the bacterial culture to induce each TF expression at 16 °C for 16 h.

value: no protein

tag: growth phase

tag: transcription factor


title: ELOX37-10L


title: mouse 2 NT 2-1


title: PMN from blood of tumor burden patient, 2

status: Public on Mar 25 2021

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

data_processing:
cellranger v3.1.0 was executed with refdata-cellranger-hg19 transcriptome
Genome_build: hg19
Supplementary_files_format_and_content: standard cellranger output

source_name: polymorphonuclear neutrophils

extract_protocol:
FACS sorted PMNs were processed according to 10x genomics protocol
Single cell libraries were prepared with isolated PBMCs using Chromium Single Cell 3’ v2 Reagent Kits
10x genomics single cell RNA-seq

tag: disease state

value: tumor burden

value: polymorphonuclear neutrophils

tag: replicate


title: PMN from blood of healthy donors, 2

value: healthy


title: PMN from blood of healthy donors, 1


title: PMN from blood of tumor burden patient, 1


title: mouse 1 NT 1-1

tag: tissue


title: S36

value: Skin


title: S1A

value: AFMK


title: rs4854158KO SK-N-SH cells before RA treatment_rep2

city: Guangzhou

first: Qiyang

state: Guangdong

address: 1838 Guangzhou Ave North

institute: Southern Medical University

data_processing:
The raw reads were subjected to quality control with FastQC.
The clean reads generated from the raw reads with Trimmomatic.
The clean reads were mapped to the h19 assembly in the Ensembl database using TopHat2.
We used stringtie to quantify the expression levels as FPKM values and then used Cuffdiff with FDR correction and an FC method to identify DEGs
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: SKN-SH cells

growth_protocol: SK-N-SH cells were cultured in high-glucose Dulbecco's Modified Eagle's medium (DMEM, Gibco) supplemented with 10% fetal bovine serum (FBS; FSP500, ExCell Bio) and maintained at 37°C with 5% CO2.

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

treatment_protocol: Differentiation of SK-N-SH cells into neuron-like cells was induced with 10 µM all-trans retinoic acid (ATRA, Sigma). Briefly, the cells were cultured in differentiation medium for 3 days 24 h after the cells had been seeded into a 100-mm dish in normal DMEM with 2.5% fetal bovine serum and 10 µM ATRA (dissolved in ethanol), and the differentiation medium was changed every 24 h.

value: brain

value: neuroblastoma

tag: genotype

value: untreated


title: rs4854158KO SK-N-SH cells before RA treatment_rep1


title: WT SK-N-SH cells before RA treatment_rep2

value: wild type


title: rs4854158KO SK-N-SH cells after RA treatment_rep2

value: treated with RA for 72 hours


title: WT SK-N-SH cells after RA treatment_rep1


title: WT SK-N-SH cells after RA treatment_rep2


title: WT SK-N-SH cells before RA treatment_rep1


title: rs4854158KO SK-N-SH cells after RA treatment_rep1


title: CUL4B

city: Beijing

first: Yan

last: Wang

address: No. 10, Xitoutiao, You An Men, Fengtai District

department: Department of Biochemistry and Molecular Biology

institute: Capital Medical University

data_processing:
Base-Calling was performed by CASAVA version 1.4
The high quality reads were mapped to the Human genome 19 of Ensembl by using Bowtie(version 0.12.8) with the default parameter.
Data were filtered using the following specification: A Perl program was used to filter of low quality sequences from raw sequencing data. The quality of each base was checked from the first base of each read. Once a low-quality base (quality<10) was  found,  it was removed together with following sequences. For paired-end reads, if one read was less than 30 bases after the trimming of low quality bases, the whole paired-end reads were  removed.
The expression peaks were detected by MACS (Model-based Analysis for ChIP-Seq) using the parameter
Genome_build: hg19
Supplementary_files_format_and_content: Supplementary_files_format_and_content: wig files were generated using MACS.

growth_protocol: MDA-MB-231 cells were cultured in L-15 medium supplemented with 10% fetal bovine serum (FBS). Cells were maintained in a humidified incubator equilibrated without CO2 at 37 ℃.

extract_protocol:
10 ng of ChIP DNA was end polished with T4 DNA polymerase and kinase. An 'A' base was added to the polished DNA fragments, followed by the Qiaquick column clean up. Solexa adaptors were ligated to the ChIP DNA fragments and enriched by 15 cycles of PCR amplification. 200-300 bp size fractions were selectively isolated from the 1% agarose gel and eluted by the Qiagen gel extraction kit. The extracted DNA was quantified by picogreen assay and subjected to HiSeq2000 sequencing according to the manufacturer‘s instructions.
DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For a ChIP assay, approximately 5 x 10^7 cells were used.The chromatin DNA precipitated by antibodies against CUL4B. The DNA was purified with the Qiagen PCR purification kit.

tag: chip antibody

value: CUL4B (Sigma C9995)


title: Mix.1

city: Lyon

first: Yanis

last: ZEKRI

address: 32-34 Avenue Tony Garnier

institute: IGFL-ENS

data_processing:
Reads were mapped on mouse mm10 genome using Bowtie Galaxy version 2.3.2.2 with default parameters
Read were counted using htseqcount Galaxy version 0.6.1galaxy3 using these parameters // Mode : Union / Stranded : Reverse / Minimul alignement quality : 10 / Feature type : exon / ID Attribute : gene name
Differential gene expression analysis was performed for all groups comparison (treatments vs control or treatment vs treatment) with Deseq2 (Galaxy Version 2.1.8.3, one-factor, parametric fit type, automatic outlier replacement and filtering, p-adjusted values <0.05; minimum read number > 10)
Heatmap were made using Clustvis web tool (https://biit.cs.ut.ee/clustvis/)
Genome_build: mm10
Supplementary_files_format_and_content: raw count files

source_name: Pups striatum

extract_protocol:
Striatum RNA was extracted using the Macherey-Nagel NucleoSpin RNA II kit
cDNA libraries were prepared using the total RNA SENSE kit (Lexogen, Vienna Austria) and deep sequencing was performed on a NextSeq500 (Illumina) sequencer

value: Striatum

value: Mix of paraquat and titanium dioxide

tag: strain

tag: age

value: post-natal day 14


title: Mix.2


title: S16

value: Keratinocytes


title: Ti.3

value: Titanium dioxide


title: Mix.3


title: Mix.4


title: input DNA


title: Ti.4


title: Ti.2


title: Ti.1


title: PQT.3

value: Paraquat


title: PQT.2


title: CTRL.4

value: Untreated


title: PQT.1


title: CTRL.2


title: CTRL.3


title: CTRL.1


title: tklf2-2

first: dongwei

state: Guangdong province

address: 190 Kai Yuan Avenue, Science Park

department: South China Institute for Stem Cell Biology and Regenerative Medicine

institute: Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
ATAC-seq reads were aligned to the mm10 genome assembly using bowtie2 with options --very-sensitive
Data were filterd using samtools -q  35 and awk '!x[$0]++'
peaks were called using run_dfilter15 with options -non-zero -bs=100 -ks=20 -lpval=3 -refine -std=5
Genome_build: mm10
Supplementary_files_format_and_content: wig file were generated with genomeCoverageBed and bedGraphToBigWig. Scores represent the number of fragments overlapping each genomic position.

source_name: Day 3 sample of overexpression Klf2 during primed to naïve transition

growth_protocol: ESCs cells cells were cultured in N2B27+2i+LIF medium, EpiSCs were maintained in FN medium which comprised F12 / Neurobasal (1:1) with N2, B27, NEAA, GlutaMAX, BSA, 100 mM 2-mercaptoethanol, 20 ng/ml ActivinA and 20 ng/ml bFGF

extract_protocol:
A total of 50,000 cells were washed once with cold PBS and resuspended in 50ul lysis buffer. The suspension of nuclei was then centrifuged for 10 min at 500g at 4°C, followed by the addition of 50 μl transposition reaction mix (25 μl TD buffer, 2.5 μl Tn5 transposase and 22.5 μl nuclease-free H2O) of Nextera DNA library Preparation Kit (96 samples) (FC-121-1031, Illumina), and incubated at 37°C for 30min. DNA was isolated using a MinElute Kit (Qiagen).
ATAC-seq libraries were first subjected to 5 cycles of pre-amplification. To determine the suitable number of cycles required for the second round of PCR the library was assessed by quantitative PCR as described5, and the library was then PCR amplified for the appropriate number of cycles. Libraries were purified with a Qiaquick PCR (Qiagen) column. Library concentration was measured using a KAPA Library Quantification kits (KK4824) according to the manufacturers instructions. Library integrity was checked by gel electrophoresis. Finally, the ATAC library was sequenced on a NextSeq 500 using a NextSeq 500 High Output Kit v2 (150 cycles) (FC-404-2002, Illumina) according to the manufacturers instructions.

treatment_protocol: ESCs were digested to single cells and replanted in serum coated 6-well plate at a density of 1×104 per well. After 8 hours, the ESCs culture medium was removed, and cells were washed with DPBS twice carefully. FN medium plus XAV939 (2 μM) and IWR-1 (2.5 μM) was used to converse ESCs to iEpiSCs. FN+X/I medium were changed everyday, and EpiSC-like colonies were emerged at 4-5 days. iEpiSCs were cultured as EpiSCs

value: Day 3 sample of overexpression Klf2 during primed to naive transition


title: tNr5a1-2

source_name: Day 3 sample of overexpression Nr5a1 during primed to naïve transition

value: Day 3 sample of overexpression Nr5a1 during primed to naive transition


title: tSox2-2

source_name: Day 3 sample of overexpression Sox2 during primed to naïve transition

value: Day 3 sample of overexpression Sox2 during primed to naive transition


title: tEsrrb-2

source_name: Day 3 sample of overexpression Esrrb during primed to naïve transition

value: Day 3 sample of overexpression Esrrb during primed to naive transition


title: dox 0 ponA 0 MEF

city: Gainesville

first: Joseph

middle: Anthony

last: Ellis

state: FL

address: 1200 Newell Drive, ARB R3-234

department: Biochemistry and Molecular Biology

institute: University of Florida

description: rRNA depleted total RNA

data_processing:
STAR (v2.7.5c) genome indexes were generated using FASTA and gtf files downloaded from Ensembl FTP
raw FASTQ files were aligned to STAR (v2.7.5c) using the above generated genomes (additional paramters: --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --alignEndsType EndToEnd)
Skipped Exon event Percent Spliced In (Ψ) values were calculated by rMATS (v4.1.0; additional paramters: --cstat 0.01) using STAR output sortedByCoord.out.bam files
Genome_build: hg38, mm10
Supplementary_files_format_and_content: "SE.MATS.JCEC.txt" contains skipped exon junction counts and PSI values

source_name: Embryonic Kidney

growth_protocol: ddHEKs were routinely cultured as a monolayer in DMEM (Corning) supplemented with 10 % FBS (Corning), 10 μg/mL blasticidin (Gibco), 150 μg/mL hygromycin (Gibco), and 2 μg/mL puromycin (Gibco) at 37 °C under 5 % CO2. ddMEFs were also cultured as a monolayer in DMEM (Corning) supplemented with 10% FBS (Corning), 1% penicillin-streptomycin (Gibco), and 2 μg/mL puromycin (Gibco).

extract_protocol:
RNA to be utilized for RNAseq experiments was harvested 24 hours post-drug treatment utilizing the Aurum Total RNA Mini kit (Bio-Rad) and DNase treated on column.
RNAseq libraries (500 ng, RQN > 9) were prepared using the NEBNext Ultra II Directional RNA Library Kit for Illumina with NEBNext rRNA depletion (Bio-Rad). Protocols were followed as per the manufacturer’s guidelines except that 40X adaptor dilutions were utilized, 4X lower concentrations of index primers were used, all bead incubations were performed at room temperature, and 10 cycles of library amplification were performed.
Libraries were pooled, and 2 x 76 paired-end sequencing performed using the Illumina NextSeq 500 (Illumina, San Diego, CA, USA).

treatment_protocol: cells were plated in twelve-well plates at a density of 6 x 104 cells/well or 3 x 105 cells/well for ddMEFs and ddHEKs, respectively. After 24 hours, fresh doxycycline was prepared and added to the cells at the appropriate concentrations to induce a range of HA-MBNL1 or GFP-MBNL1 protein expression (0 or 10 ng/mL for ddHEKs, 0 or 1000 ng/mL for ddMEFs). To induce mOrange-RBFOX1, fresh ponasterone-A (Thermo Fisher Scientific) was dissolved in 100% ethanol and then added to the media (final concentration = 10 μM). Cells were then harvested 24 hours post-drug treatment for experimental analysis.

tag: treatment doxycycline

tag: treatment ponasterone a


title: dox 1000 ponA 1 MEF

description: rRNA depleted total RNA

value: 10 uM


title: dox 1000 ponA 0 MEF

description: rRNA depleted total RNA


title: tEsrrb-1


title: dox 0 ponA 1 MEF

description: rRNA depleted total RNA


title: PEA Exposure P0-P5 replicate 4 [P0P5_PEA4]

city: Kansas City

first: Congrong

middle: Ron

last: Yu

state: Missouri

institute: Stowers Insitute for Medical Research

description:
n_*_1_TGACCA
processed data file: PEA_norm_counts.txt

data_processing:
Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18
PEA Data: Raw FASTQ files were concatenated across all flow-cell lanes
Selective alignment was performed w/ Salmon v1.3.0 on each sample FASTQ to mm10 transcriptome (ENSEMBL Release 100) with 'salmon quant --index salmon_index -libType SR --unmatedReads sample.fq --seqBias --gcBias'
Count normalization was performed with the DESeq function using DESeq2 v1.30.0
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited matrix tables with DESeq2 normalized gene counts for every gene and every sample

source_name: PEA Exposure P0-P5_olfactory epithelium

extract_protocol:
Olfactory epithelial tissue was removed directly into Trizol reagent for RNA harvesting.
Kir Data: Illumina mRNA-Seq Sample Prep Kit (Cat#RS-930-1001) was used with 2 ug of total RNA for construction of sequencing libraries.
PEA Data: Illumina TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold Set A (Cat#RS-122-2301) and Ribo-Zero Gold Set B (Cat#RS-122-2302) was used with 7.5 ug of total RNA for construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: PEA-treated mice were exposed to PEA continuously from P0 until P5

tag: strain background

tag: genotype/variation

value: postnatal day 5

value: PEA exposure from P0 to P5

value: Olfactory Epithelium


title: tTfcp2l1-2

source_name: Day 3 sample of overexpression Tfcp2l1 during primed to naïve transition

value: Day 3 sample of overexpression Tfcp2l1 during primed to naive transition


title: PEA Control - No PEA Exposure replicate 3 [P0P5_Ctrl3]

description:
n_*_1_CAGATC
processed data file: PEA_norm_counts.txt

source_name: PEA Control - No PEA Exposure_olfactory epithelium

value: wild type

tag: treatment

value: Control


title: tTfcp2l1-1


title: tSox2-1


title: PEA Exposure P0-P5 replicate 1 [P0P5_PEA1]

description:
n_*_1_ATCACG
processed data file: PEA_norm_counts.txt


title: PEA Control - No PEA Exposure replicate 4 [P0P5_Ctrl5]

description:
n_*_1_ACTTGA
processed data file: PEA_norm_counts.txt


title: PEA Control - No PEA Exposure replicate 2 [P0P5_Ctrl2]

description:
n_*_1_GCCAAT
processed data file: PEA_norm_counts.txt


title: PEA Control - No PEA Exposure replicate 1 [P0P5_Ctrl1]

description:
n_*_1_ACAGTG
processed data file: PEA_norm_counts.txt


title: PEA Exposure P0-P5 replicate 3 [P0P5_PEA3]

description:
n_*_1_TTAGGC
processed data file: PEA_norm_counts.txt


title: AG3095_DN2a_LSK_DNase

city: SEATTLE

first: John

middle: A

last: Stamatoyannopoulos

state: WA

address: 2211 Elliott Avenue, 6th Floor

department: Genome Sciences

institute: Altius Institute / University of Washington

data_processing:
Basecalling, RTA v1.13
Alignments to GRCh38, BWA v0.7.12
Read processing, Samtools v1.2
Read density, Bedops v2.4.15
Peak calling, Hotspot2 v2.1.1
Genome_build: mm10
Supplementary_files_format_and_content: 5% FDR hotspot peak calls as a .bed file, normalized density bigWig file

source_name: LSK

extract_protocol:
PEG precipitation and size fractionation of DNA
Low-input single-stranded library construction protocol as per PMIDs 23493070 & 26771485
DNase-Seq

tag: differentiation


title: AG3096_DN2b_LSK_DNase


title: tNr5a1-1


title: O9_S345: Single HEK293T cell

city: Stanford

first: Alina

last: Isakova

state: CA

address: 318 Campus drive

department: Bioengineering

institute: Stanford University

data_processing:
The analysis of Smart-seq-total v1 and Smart-seq-total v2 data were carried out as described in GitHub Smart-seq-total page (https://github.com/aisakova/smart-seq-total/blob/master/README.md).
SST-UMI-raw-tn5+noTn5.tsv is a total count from "noTn5" and "tn5" samples (15 cells).
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files of count tables

source_name: Cultured cells

growth_protocol: HEK293T cells were cultured in complete DMEM high glucose medium (Gibco, ThermoFisher 11965092) supplemented with 5% Fetal Bovine Serum (ThermoFisher 16000044), 1mM Sodium Pyruvate (ThermoFisher 11360070) and 100 μg/mL Pencillin/Streptomycin (ThermoFisher 15070063). They were collected 2h after passaging and sorted in 384-well paltes with 0.3 uL of lysis buffer in each well.

extract_protocol:
Lysis plates were prepared by dispensing 0.3μL lysis buffer (4 U Recombinant RNase Inhibitor (RRI) (Takara Bio, 2313B), 0.12% TritonTM X-100 (Sigma, 93443-100ML), 1μM Smart-seq-total oligo-dT primer (see Supplementary Table 3 for a full list of oligos used in the present study) into 384-well hard-shell PCR plates (Bio-Rad HSP3901) using Mantis liquid handler (Formulatrix). All plates were sealed with AlumaSeal CS Films (Sigma-Aldrich Z722634), spun down and snap-frozen on dry ice.   Cells were stained with calcein-AM and ethidium homodimer-1 (LIVE/DEAD® Viability/Cytotoxicity Kit, ThermoFisher L3224) and individual live cells were sorted in 384 well lysis plates using SONY sorter (SH800S) with 100um nozzle chip. Plates were spun down and stored at -80 degrees immediately after sorting.
Smart-seq-total v2

tag: cell line


title: O8_S344: Single HEK293T cell


title: O7_S343: Single HEK293T cell


title: O5_S341: Single HEK293T cell


title: O6_S342: Single HEK293T cell


title: tklf2-1

tag: cell type


title: O2_S338: Single HEK293T cell


title: PEA Exposure P0-P5 replicate 2 [P0P5_PEA2]

description:
n_*_1_CGATGT
processed data file: PEA_norm_counts.txt


title: O21_S357: Single HEK293T cell


title: O15_S351: Single HEK293T cell


title: O23_S359: Single HEK293T cell


title: O19_S355: Single HEK293T cell


title: O20_S356: Single HEK293T cell


title: O24_S360: Single HEK293T cell


title: O17_S353: Single HEK293T cell


title: O1_S337: Single HEK293T cell


title: O11_S347: Single HEK293T cell


title: O12_S348: Single HEK293T cell


title: O13_S349: Single HEK293T cell


title: N7_S319: Single HEK293T cell


title: O16_S352: Single HEK293T cell


title: O3_S339: Single HEK293T cell


title: N8_S320: Single HEK293T cell


title: O14_S350: Single HEK293T cell


title: O18_S354: Single HEK293T cell


title: N9_S321: Single HEK293T cell


title: O4_S340: Single HEK293T cell


title: O10_S346: Single HEK293T cell


title: N23_S335: Single HEK293T cell


title: O22_S358: Single HEK293T cell


title: N6_S318: Single HEK293T cell


title: N4_S316: Single HEK293T cell


title: N24_S336: Single HEK293T cell


title: N3_S315: Single HEK293T cell


title: N22_S334: Single HEK293T cell


title: N19_S331: Single HEK293T cell


title: N16_S328: Single HEK293T cell


title: N17_S329: Single HEK293T cell


title: N18_S330: Single HEK293T cell


title: N12_S324: Single HEK293T cell


title: N15_S327: Single HEK293T cell


title: N11_S323: Single HEK293T cell


title: N10_S322: Single HEK293T cell


title: N2_S314: Single HEK293T cell


title: N14_S326: Single HEK293T cell


title: N1_S313: Single HEK293T cell


title: M9_S297: Single HEK293T cell


title: M8_S296: Single HEK293T cell


title: N5_S317: Single HEK293T cell


title: N13_S325: Single HEK293T cell


title: M7_S295: Single HEK293T cell


title: M4_S292: Single HEK293T cell


title: M3_S291: Single HEK293T cell


title: M6_S294: Single HEK293T cell


title: M24_S312: Single HEK293T cell


title: M23_S311: Single HEK293T cell


title: M5_S293: Single HEK293T cell


title: M22_S310: Single HEK293T cell


title: M21_S309: Single HEK293T cell


title: M20_S308: Single HEK293T cell


title: M18_S306: Single HEK293T cell


title: N21_S333: Single HEK293T cell


title: M19_S307: Single HEK293T cell


title: M2_S290: Single HEK293T cell


title: M14_S302: Single HEK293T cell


title: M13_S301: Single HEK293T cell


title: M15_S303: Single HEK293T cell


title: M17_S305: Single HEK293T cell


title: M10_S298: Single HEK293T cell


title: L8_S272: Single HEK293T cell


title: L9_S273: Single HEK293T cell


title: L7_S271: Single HEK293T cell


title: L4_S268: Single HEK293T cell


title: L5_S269: Single HEK293T cell


title: M11_S299: Single HEK293T cell


title: L22_S286: Single HEK293T cell


title: L2_S266: Single HEK293T cell


title: M16_S304: Single HEK293T cell


title: L15_S279: Single HEK293T cell


title: M1_S289: Single HEK293T cell


title: L14_S278: Single HEK293T cell


title: L24_S288: Single HEK293T cell


title: N20_S332: Single HEK293T cell


title: L3_S267: Single HEK293T cell


title: L6_S270: Single HEK293T cell


title: L23_S287: Single HEK293T cell


title: M12_S300: Single HEK293T cell


title: L19_S283: Single HEK293T cell


title: L12_S276: Single HEK293T cell


title: L18_S282: Single HEK293T cell


title: L17_S281: Single HEK293T cell


title: K8_S248: Single HEK293T cell


title: L16_S280: Single HEK293T cell


title: L21_S285: Single HEK293T cell


title: L13_S277: Single HEK293T cell


title: K9_S249: Single HEK293T cell


title: L11_S275: Single HEK293T cell


title: K6_S246: Single HEK293T cell


title: L1_S265: Single HEK293T cell


title: K4_S244: Single HEK293T cell


title: K5_S245: Single HEK293T cell


title: L10_S274: Single HEK293T cell


title: L20_S284: Single HEK293T cell


title: K23_S263: Single HEK293T cell


title: K3_S243: Single HEK293T cell


title: K22_S262: Single HEK293T cell


title: K24_S264: Single HEK293T cell


title: K20_S260: Single HEK293T cell


title: K21_S261: Single HEK293T cell


title: K18_S258: Single HEK293T cell


title: K19_S259: Single HEK293T cell


title: K2_S242: Single HEK293T cell


title: K17_S257: Single HEK293T cell


title: K15_S255: Single HEK293T cell


title: K16_S256: Single HEK293T cell


title: K14_S254: Single HEK293T cell


title: K13_S253: Single HEK293T cell


title: K12_S252: Single HEK293T cell


title: K7_S247: Single HEK293T cell


title: K1_S241: Single HEK293T cell


title: J7_S223: Single HEK293T cell


title: J6_S222: Single HEK293T cell


title: J9_S225: Single HEK293T cell


title: J8_S224: Single HEK293T cell


title: J5_S221: Single HEK293T cell


title: J4_S220: Single HEK293T cell


title: J24_S240: Single HEK293T cell


title: J3_S219: Single HEK293T cell


title: J22_S238: Single HEK293T cell


title: J21_S237: Single HEK293T cell


title: K11_S251: Single HEK293T cell


title: J17_S233: Single HEK293T cell


title: J18_S234: Single HEK293T cell


title: J15_S231: Single HEK293T cell


title: J13_S229: Single HEK293T cell


title: J11_S227: Single HEK293T cell


title: J14_S230: Single HEK293T cell


title: J16_S232: Single HEK293T cell


title: J1_S217: Single HEK293T cell


title: K10_S250: Single HEK293T cell


title: I9_S201: Single HEK293T cell


title: J12_S228: Single HEK293T cell


title: I6_S198: Single HEK293T cell


title: I7_S199: Single HEK293T cell


title: I5_S197: Single HEK293T cell


title: I8_S200: Single HEK293T cell


title: J23_S239: Single HEK293T cell


title: J20_S236: Single HEK293T cell


title: I4_S196: Single HEK293T cell


title: I3_S195: Single HEK293T cell


title: I22_S214: Single HEK293T cell


title: I24_S216: Single HEK293T cell


title: I21_S213: Single HEK293T cell


title: I23_S215: Single HEK293T cell


title: J2_S218: Single HEK293T cell


title: I19_S211: Single HEK293T cell


title: J19_S235: Single HEK293T cell


title: I18_S210: Single HEK293T cell


title: I17_S209: Single HEK293T cell


title: J10_S226: Single HEK293T cell


title: I15_S207: Single HEK293T cell


title: I12_S204: Single HEK293T cell


title: I13_S205: Single HEK293T cell


title: I11_S203: Single HEK293T cell


title: I10_S202: Single HEK293T cell


title: I1_S193: Single HEK293T cell


title: H9_S177: Single HEK293T cell


title: H8_S176: Single HEK293T cell


title: H7_S175: Single HEK293T cell


title: H6_S174: Single HEK293T cell


title: I20_S212: Single HEK293T cell


title: I2_S194: Single HEK293T cell


title: H22_S190: Single HEK293T cell


title: H24_S192: Single HEK293T cell


title: H23_S191: Single HEK293T cell


title: H3_S171: Single HEK293T cell


title: H20_S188: Single HEK293T cell


title: H2_S170: Single HEK293T cell


title: H17_S185: Single HEK293T cell


title: H18_S186: Single HEK293T cell


title: I14_S206: Single HEK293T cell


title: H16_S184: Single HEK293T cell


title: I16_S208: Single HEK293T cell


title: H15_S183: Single HEK293T cell


title: H14_S182: Single HEK293T cell


title: H12_S180: Single HEK293T cell


title: H11_S179: Single HEK293T cell


title: H10_S178: Single HEK293T cell


title: H1_S169: Single HEK293T cell


title: H13_S181: Single HEK293T cell


title: H5_S173: Single HEK293T cell


title: G8_S152: Single HEK293T cell


title: G5_S149: Single HEK293T cell


title: G7_S151: Single HEK293T cell


title: G9_S153: Single HEK293T cell


title: G6_S150: Single HEK293T cell


title: G4_S148: Single HEK293T cell


title: H4_S172: Single HEK293T cell


title: H21_S189: Single HEK293T cell


title: G24_S168: Single HEK293T cell


title: G3_S147: Single HEK293T cell


title: H19_S187: Single HEK293T cell


title: G2_S146: Single HEK293T cell


title: G20_S164: Single HEK293T cell


title: G19_S163: Single HEK293T cell


title: G22_S166: Single HEK293T cell


title: G23_S167: Single HEK293T cell


title: G18_S162: Single HEK293T cell


title: G17_S161: Single HEK293T cell


title: G15_S159: Single HEK293T cell


title: G16_S160: Single HEK293T cell


title: G14_S158: Single HEK293T cell


title: G13_S157: Single HEK293T cell


title: G12_S156: Single HEK293T cell


title: F8_S128: Single HEK293T cell


title: G10_S154: Single HEK293T cell


title: F9_S129: Single HEK293T cell


title: G1_S145: Single HEK293T cell


title: F6_S126: Single HEK293T cell


title: F7_S127: Single HEK293T cell


title: F4_S124: Single HEK293T cell


title: F3_S123: Single HEK293T cell


title: G21_S165: Single HEK293T cell


title: F20_S140: Single HEK293T cell


title: F23_S143: Single HEK293T cell


title: F2_S122: Single HEK293T cell


title: F18_S138: Single HEK293T cell


title: F21_S141: Single HEK293T cell


title: F19_S139: Single HEK293T cell


title: F17_S137: Single HEK293T cell


title: F16_S136: Single HEK293T cell


title: F11_S131: Single HEK293T cell


title: F13_S133: Single HEK293T cell


title: F10_S130: Single HEK293T cell


title: F14_S134: Single HEK293T cell


title: F12_S132: Single HEK293T cell


title: G11_S155: Single HEK293T cell


title: F1_S121: Single HEK293T cell


title: E8_S104: Single HEK293T cell


title: E9_S105: Single HEK293T cell


title: F24_S144: Single HEK293T cell


title: E7_S103: Single HEK293T cell


title: E6_S102: Single HEK293T cell


title: F5_S125: Single HEK293T cell


title: E4_S100: Single HEK293T cell


title: F22_S142: Single HEK293T cell


title: E5_S101: Single HEK293T cell


title: E23_S119: Single HEK293T cell


title: E24_S120: Single HEK293T cell


title: E3_S99: Single HEK293T cell


title: E22_S118: Single HEK293T cell


title: E21_S117: Single HEK293T cell


title: E2_S98: Single HEK293T cell


title: E20_S116: Single HEK293T cell


title: E18_S114: Single HEK293T cell


title: E19_S115: Single HEK293T cell


title: E17_S113: Single HEK293T cell


title: E16_S112: Single HEK293T cell


title: E15_S111: Single HEK293T cell


title: E14_S110: Single HEK293T cell


title: E1_S97: Single HEK293T cell


title: E12_S108: Single HEK293T cell


title: E11_S107: Single HEK293T cell


title: E10_S106: Single HEK293T cell


title: D8_S80: Single HEK293T cell


title: E13_S109: Single HEK293T cell


title: D9_S81: Single HEK293T cell


title: D6_S78: Single HEK293T cell


title: D4_S76: Single HEK293T cell


title: D24_S96: Single HEK293T cell


title: D20_S92: Single HEK293T cell


title: D23_S95: Single HEK293T cell


title: D5_S77: Single HEK293T cell


title: D22_S94: Single HEK293T cell


title: D19_S91: Single HEK293T cell


title: D2_S74: Single HEK293T cell


title: D16_S88: Single HEK293T cell


title: D18_S90: Single HEK293T cell


title: D17_S89: Single HEK293T cell


title: D15_S87: Single HEK293T cell


title: D14_S86: Single HEK293T cell


title: D13_S85: Single HEK293T cell


title: D10_S82: Single HEK293T cell


title: D12_S84: Single HEK293T cell


title: D11_S83: Single HEK293T cell


title: D1_S73: Single HEK293T cell


title: C8_S56: Single HEK293T cell


title: C9_S57: Single HEK293T cell


title: C5_S53: Single HEK293T cell


title: C7_S55: Single HEK293T cell


title: D3_S75: Single HEK293T cell


title: C6_S54: Single HEK293T cell


title: D7_S79: Single HEK293T cell


title: C4_S52: Single HEK293T cell


title: C20_S68: Single HEK293T cell


title: C3_S51: Single HEK293T cell


title: C19_S67: Single HEK293T cell


title: C22_S70: Single HEK293T cell


title: C21_S69: Single HEK293T cell


title: C24_S72: Single HEK293T cell


title: C23_S71: Single HEK293T cell


title: C2_S50: Single HEK293T cell


title: C18_S66: Single HEK293T cell


title: C17_S65: Single HEK293T cell


title: C14_S62: Single HEK293T cell


title: C16_S64: Single HEK293T cell


title: C15_S63: Single HEK293T cell


title: C12_S60: Single HEK293T cell


title: C13_S61: Single HEK293T cell


title: C10_S58: Single HEK293T cell


title: C1_S49: Single HEK293T cell


title: C11_S59: Single HEK293T cell


title: B8_S32: Single HEK293T cell


title: B9_S33: Single HEK293T cell


title: B5_S29: Single HEK293T cell


title: B6_S30: Single HEK293T cell


title: B3_S27: Single HEK293T cell


title: B23_S47: Single HEK293T cell


title: B7_S31: Single HEK293T cell


title: B22_S46: Single HEK293T cell


title: B24_S48: Single HEK293T cell


title: B21_S45: Single HEK293T cell


title: F15_S135: Single HEK293T cell


title: B20_S44: Single HEK293T cell


title: B19_S43: Single HEK293T cell


title: B2_S26: Single HEK293T cell


title: B16_S40: Single HEK293T cell


title: B17_S41: Single HEK293T cell


title: B13_S37: Single HEK293T cell


title: B18_S42: Single HEK293T cell


title: B12_S36: Single HEK293T cell


title: B15_S39: Single HEK293T cell


title: B11_S35: Single HEK293T cell


title: A8_S8: Single HEK293T cell


title: A6_S6: Single HEK293T cell


title: B1_S25: Single HEK293T cell


title: A5_S5: Single HEK293T cell


title: A4_S4: Single HEK293T cell


title: A9_S9: Single HEK293T cell


title: A7_S7: Single HEK293T cell


title: A23_S23: Single HEK293T cell


title: A22_S22: Single HEK293T cell


title: A20_S20: Single HEK293T cell


title: A21_S21: Single HEK293T cell


title: B4_S28: Single HEK293T cell


title: A3_S3: Single HEK293T cell


title: A19_S19: Single HEK293T cell


title: A2_S2: Single HEK293T cell


title: A17_S17: Single HEK293T cell


title: A18_S18: Single HEK293T cell


title: A15_S15: Single HEK293T cell


title: B14_S38: Single HEK293T cell


title: A14_S14: Single HEK293T cell


title: B10_S34: Single HEK293T cell


title: A12_S12: Single HEK293T cell


title: A1_S1: Single HEK293T cell


title: A10_S10: Single HEK293T cell


title: A11_S11: Single HEK293T cell


title: A13_S13: Single HEK293T cell


title: C8_S32_Tn5: Single HEK293T cell


title: C4_S28_Tn5: Single HEK293T cell


title: B7_S7_Tn5: Single HEK293T cell


title: B4_S4_Tn5: Single HEK293T cell


title: C1_S25_Tn5: Single HEK293T cell


title: B23_S23_Tn5: Single HEK293T cell


title: C5_S29_Tn5: Single HEK293T cell


title: A24_S24: Single HEK293T cell


title: B22_S22_Tn5: Single HEK293T cell


title: B14_S14_Tn5: Single HEK293T cell


title: B19_S19_Tn5: Single HEK293T cell


title: B2_S2_Tn5: Single HEK293T cell


title: B18_S18_Tn5: Single HEK293T cell


title: B11_S11_Tn5: Single HEK293T cell


title: B10_S10_Tn5: Single HEK293T cell


title: C5_S29_noTn5: Single HEK293T cell


title: C8_S32_noTn5: Single HEK293T cell


title: C4_S28_noTn5: Single HEK293T cell


title: B1_S1_Tn5: Single HEK293T cell


title: A16_S16: Single HEK293T cell


title: C1_S25_noTn5: Single HEK293T cell


title: B4_S4_noTn5: Single HEK293T cell


title: B23_S23_noTn5: Single HEK293T cell


title: B22_S22_noTn5: Single HEK293T cell


title: B18_S18_noTn5: Single HEK293T cell


title: B11_S11_noTn5: Single HEK293T cell


title: B2_S2_noTn5: Single HEK293T cell


title: B10_S10_noTn5: Single HEK293T cell


title: B7_S7_noTn5: Single HEK293T cell


title: SEM_UBE2T-sgRNA2_S13_R1_001

city: Cold Spring Harbor

first: Xiaoli

middle: Sky

last: Wu

state: New York

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

data_processing:
alignment to hg38 with hisat2
count gene abundance with htseq-count
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited text file with counts aligned to custom protein coding gtf

source_name: AML

extract_protocol: TRIZOL

treatment_protocol: CRISPR KO or cDNA overexpression

value: AML

tag: pertubation

value: UBE2T KO


title: MOLM13_OE_2

value: empty vector Overexpression


title: SEM_FANCD2-sgRNA2_S15_R1_001

value: FANCD2 KO


title: MOLM13_OE_1


title: MOLM13_ALDH2_OE_1

value: ALDH2 Overexpression


title: SEM_sgNEG-2_S12_R1_001

value: control KO


title: MOLM13_sgNEG


title: SEM_sgNEG-1_S11_R1_001


title: MOLM13_UBE2T_sgRNA2


title: B19_S19_noTn5: Single HEK293T cell


title: MOLM13_ALDH2_OE_2


title: SEM_UBE2T-sgRNA3_S14_R1_001


title: MOLM13_FANCD2_sgRNA2


title: B14_S14_noTn5: Single HEK293T cell


title: dox 1000 ponA 1 HEK

description: rRNA depleted total RNA

value: 10 ng/mL


title: MOLM13_sgNEG2


title: dox 0 ponA 1 HEK

description: rRNA depleted total RNA


title: MOLM13_UBE2T_sgRNA3


title: MOLM13_FANCD2_sgRNA3


title: dox 0 ponA 0 HEK

description: rRNA depleted total RNA


title: dox 1000 ponA 0 HEK

description: rRNA depleted total RNA


title: B1_S1_noTn5: Single HEK293T cell


title: MOLM13_ALDH1_OE_1

value: ALDH1 Overexpression


title: MOLM13_ALDH1_OE_2


first: Noa

last: Novershtern

address: Weizmann Institute

department: Molecular Genetics

institute: Weizmann Institute of Science

description:
Poly-A RNA-seq
WIBR3_primed_2
processed data: counts_batch5.txt
WIBR3 hPSCs in mTeSR medium replication 2

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files.
reads were aligned to hg38 Genome using STAR aligner
counts were generated with HTSeq
Dataset was filtered to include genes that have at least one call > 10
All samples were normalized using DESeq 2 (default parameters)
Batch effect correction was done by substructing the minimal normzlied count of each gene in each batch.
Genome_build: hg38
Supplementary_files_format_and_content: matrix with counts of all genes and samples in the batch. Pre-normalization

source_name: human embryonic stem cells

growth_protocol: Maintenance of human naïve pluripotent cells were conducted using "Enhanced NHSM" (ENHSM) as detailed in bayerl et.al in feeder free conditions on plates coated with 1% Matrigel (BD- FAL356231). Maintenance of human primed pluripotent cells were conducted using mTESR (Ludwing and Thomson: Curr. Protoc. Stem Cell Biol. 2:1C.2.1-1C.2.16) in feeder free conditions on plates coated with 1% Matrigel

extract_protocol:
Total RNA was isolated from indicated cell lines and extracted from Trizol pellets by chloroform-phenol extraction protocol.
Total RNA was then utilized for RNA-Seq by ScriptSeq Preparation Kit v2 (Illumina) according to manufacturer’s instruction.

tag: culture conditions

value: mTeSR (primed)

tag: batch


description:
Poly-A RNA-seq
WIBR2_HENSM_ACT_8
processed data: counts_batch5.txt
WIBR2 hPSCs in HENSM + Activin medium, replication 8

value: HENSM + Activin


description:
Poly-A RNA-seq
WIBR2_primed_3
processed data: counts_batch5.txt
WIBR2 hPSCs in mTeSR medium replication 3


description:
Poly-A RNA-seq
WIBR3_HENSM_ACT_1
processed data: counts_batch5.txt
WIBR3 hPSCs in HENSM + Activin medium, replication 1


description:
Poly-A RNA-seq
WIBR2_HENSM_ACT_9
processed data: counts_batch5.txt
WIBR2 hPSCs in HENSM + Activin medium, replication 9


description:
Poly-A RNA-seq
WIBR2_primed_4
processed data: counts_batch5.txt
WIBR2 hPSCs in mTeSR medium replication 4


description:
Poly-A RNA-seq
WIBR3_primed_1
processed data: counts_batch5.txt
WIBR3 hPSCs in mTeSR medium replication 1


description:
Poly-A RNA-seq
WIBR3_HENSM_ACT_2
processed data: counts_batch5.txt
WIBR3 hPSCs in HENSM + Activin medium, replication 2


title: CaptureC_SNV_Ery_iPSC_C-SNV_LA06_rep1

city: Oxford

first: Yavor

last: Bozhilov

state: Oxfordshire

address: John Radcliffe Hospital, Headington, Weatherall Institiute of Molecular Medicine

institute: WIMM, Oxford University

description: DpnII digested 3C library, enriched for fragments of interest by oligonucleotide pulldown

data_processing:
Library strategy: NG_Capture-C
Adaptor Removal: Trim Galore
Fragment reconstruction into a single read: Flash
In silico restriction enzyme digestion of FASTQ file (nlaIIIPE.pl)
Alignment: Bowtie 2
Processing: Removal of PCR duplicates; Parsing of informative reads and mapping to restriction enzyme fragments (CCanalyser2.pl)
Processing: Combining data from multiple replicates (custom scripts)
Processing: Removal of ploidy regions and off target capture (custom scripts)
Genome_build: hg18
Supplementary_files_format_and_content: custom format (chr start stop interactions viewpoint)

source_name: iPSC diffrentiation to Erythroid cells

growth_protocol: Prior to the initiation of differentiation protocol, human iPSCs were cultured for at least 15 days on Vitronectin (Invitrogen) coated plates (Corning; TC treated) in STEMPRO hESC media (Invitrogen) supplemented with 20ng/ml bFGF (RnD). Cultures were maintained in this way for 5-6 passages at high confluency and split 1 in 4 when over 85% confluent. Human iPSCs were differentiated as published by Olivier et al., 2016 and harvested on day 21 of the differentiation protocol. Flow cytometry analysis was performed on 2x105 cells resuspended in 200μl of 2% bovine serum albumin (SIGMA) in phosphate buffered saline and labelled for 20 minutes at 4oC with fluorescein isothiocyanate (FITC) conjugated anti-CD71 (BD Biosciences; 555536) and phycoerythrin (PE) conjugated anti-CD235a (BD Biosciences; 340947). After staining cells were harvested and resuspended in PBS containing 0.02% Hoechst 33258 pentahydrate nucleic acid stain (Invitrogen). Analysis was performed on an Attune NxT Flow Cytometer (Invitrogen) and subsequently using FlowJo software for gating on viable single cell events and representing the data as a dot plot. Morphological analysis was preformed using a modified Wright stain on a Hemateck 03564647 slide strainer (BAYER). The slides were then imaged on a Nikon inverted microscope.

extract_protocol:
3C Libraries were generated according to the NG Capture-C protocol (Downes, D.J. et al 2020). Briefly, cells were crosslinked with 2% formaldehyde (10 minutes, room temperature); quenched with cold glycine; washed in phosphate buffered saline; resuspended in cold lysis buffer (tris 10mM, NaCl 10mM, NP40 0.2%, complete proteinase inhibitor (Roche)) and snap frozen to -80. Cells were thawed on ice, washed in milliq dH2O and Dounce homogenised on ice (x 40 strokes). Cells were then resuspended with 0.25% SDS and restriction enzyme buffer and incubated at 37C for 1h at 1400rpm on a Comfort Thermomixer (Eppendorf) followed by a further incubation of 1h following the addition of triton X100 (final concentration 1.67%). An overnight digestion was performed using Dpn II (500U /ml (NEB) at 37C / 1400 rpm). The digested chromatin was ligated overnight (Fermentas HC Ligase final concentration 10U/ml) at 16 degrees at 1400 rpm on the Thermomixer. The samples were then decrosslinked overnight at 65C with Proteinase K (Roche) followed by a 30 min incubation at 37C with RNAse (Roche). Phenol/Chloroform extraction was then performed followed by an Ethanol precipitation and a wash with 70% Ethanol. Digestion efficiencys were assessed by gel electrophoresis (1% agarose) and RT-PCR (Taqman), which showed digestion efficiencies in excess of 70%. DNA content of the Dpn II 3C libraries were quantitated using a Qubit fluorometer (Life technologies)
5-10ug of each library was sheared using a Covaris S2 in milliq dH2O. Covaris settings used were: duty cycle 10%, Intensity 5, Cycles/burst 200, Time 6 cycles of 60seconds, Set Mode Frequency sweeping Temperature 4 to 7 degrees. Following shearing DNA was purified using AMPureXP beads (Agencourt) and DNA quality assessed on a Bioanalyser 2100 using a DNA High Sensitivity Chip (Agilent). DNA end repair and adapter ligation was performed using the NEB Next or NEB Ultra DNA sample preparation reagent kits, depending on the amount of DNA available, using the standard protocol. Biotinylated capture oligonucleotides were designed to the ends of the viewpoint fragments. Where possible 1-2ug of each adapter ligated library were hybridized with the biotinylated capture oligonucleotides, using the Nimblegen SeqCap reagents and an adapted protocol. The quality of the resultant captured library was assessed by Agilent tapestation or bioanalyser (D1000). The resulting libraries were sequenced using Illumina Nextseq 500 (150 bp paired-end reads)

value: Erythroid

tag: day of differentiation

value: Day 21

value: C-SNV allele homozygous

tag: Sex

value: Female


title: CaptureC_SNV_Ery_iPSC_C-SNV_LA13_rep1

tag: genotype


title: CaptureC_Prom_Ery_iPSC_WT_AH017_rep3

value: Wild type


title: CaptureC_Prom_Ery_iPSC_WT_AH017_rep1


title: CaptureC_Prom_Ery_iPSC_WT_SBAD02_rep3

value: Male


title: CaptureC_SNV_Ery_iPSC_C-SNV_LA01_rep1


title: CaptureC_Prom_Ery_iPSC_WT_AH017_rep2


title: CaptureC_SNV_Ery_iPSC_WT_AH017_rep3


title: CaptureC_SNV_Ery_iPSC_WT_AH017_rep1


title: CaptureC_Prom_Ery_iPSC_WT_SBAD02_rep1


title: CaptureC_Prom_Ery_iPSC_C-SNV_LA06_rep1


title: CaptureC_Prom_Ery_iPSC_WT_SBAD02_rep2


title: CaptureC_Prom_Ery_iPSC_Vas_Clone2_rep1

value: Promoter insertion anti-sense


title: CaptureC_Prom_Ery_iPSC_Vas_Clone3_rep1


title: CaptureC_Prom_Ery_iPSC_Vas_Clone1_rep1


title: CaptureC_Prom_Ery_iPSC_C-SNV_LA13_rep1


title: CaptureC_Prom_Ery_iPSC_INV_Clone3_rep1

value: Inversion of C-SNV promoter


title: CaptureC_Prom_Ery_iPSC_INV_Clone2_rep1


title: CaptureC_Prom_Ery_iPSC_INV_Clone1_rep1


title: CaptureC_Prom_Ery_iPSC_C-SNV_LA01_rep1


title: CaptureC_Enh_Ery_iPSC_WT_SBAD02_rep3


title: CaptureC_SNV_Ery_iPSC_WT_AH017_rep2


title: CaptureC_Enh_Ery_iPSC_Vas_Clone2_rep1


title: CaptureC_Enh_Ery_iPSC_WT_SBAD02_rep2


title: CaptureC_Enh_Ery_iPSC_Vas_Clone3_rep1


title: CaptureC_Enh_Ery_iPSC_WT_AH017_rep2


title: CaptureC_Enh_Ery_iPSC_INV_Clone3_rep1


title: CaptureC_Enh_Ery_iPSC_INV_Clone2_rep1


title: CaptureC_Enh_Ery_iPSC_Vas_Clone1_rep1


title: CaptureC_Enh_Ery_iPSC_C-SNV_LA13_rep1


title: CaptureC_Enh_Ery_iPSC_C-SNV_LA06_rep1


title: RNAseq_pA+_Ery_iPSC_WT_AH017_rep3

data_processing:
Mapping: STAR --runThreadN 4 --outFilterMultimapNmax 1
Duplicate removal: samtools rmdup
Genome_build: hg19; custom chr16 sequence fasta files on GSE159871: chr16_hg19_INV.fa.gz, chr16_hg19_Vas.fa.gz, chr16_hg19_Vs.fa.gz
Supplementary_files_format_and_content: bigwig: forward reads (deeptools) - bamCoverage -p4 --binSize 1 --normalizeUsingRPKM --filterRNAstrand forward
Supplementary_files_format_and_content: bigwig: reverse reads (deeptools) - bamCoverage -p4 --binSize 1 --normalizeUsingRPKM --filterRNAstrand reverse

extract_protocol:
isolation protocol: 1-5x10e6 cells were fixed in 1 ml TRI-reagent (Sigma), snap frozen and stored at -80ºC.
RNA was isolated from 5×106 day 21 erythroid cells using the Direct-zol RNA kit (Zymo) as per manufacturer’s instructions. DNase I digestion was performed on column. RNA purity was assessed using Nanodrop ND-1000 spectrophotometer (ThermoFisher Scientific). RNA integrity was analysed using RNA ScreenTape Assay (Agilent)
For RNA-seq total RNA was treated with Turbo DNAse (Invitrogen) at 25 ºC for 60 min, then RNA was separated using phenol-chloroform isoamylalcohol and a PhaseLock Light-gel tube (5Prime).  Treated RNA was precipitated at -80 ºC overnight with sodium acetate, glycoblue, and 75 % ethanol, before centrifugation (12,000 rcf, 4 ºC), 75 % ethanol wash and resuspension in DEPC-treated water. Globin and rRNA sequences were depleted from up to 5 µg of treated RNA using Globin-Zero Gold (Illumina), before PolyA selection with NEBNext Poly(A) mRNA Magnetic Isolation module (New England Biolabs), and indexing with NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs) following the manufacturers’ instructions.

tag: rna population

value: polyA RNA


title: RNAseq_pA-_Ery_iPSC_WT_SBAD02_rep1

value: non-polyA RNA


title: RNAseq_pA+_Ery_iPSC_WT_SBAD02_rep1


title: RNAseq_pA-_Ery_iPSC_WT_AH017_rep3


title: CaptureC_Enh_Ery_iPSC_C-SNV_LA01_rep1


title: RNAseq_pA+_Ery_iPSC_WT_AH017_rep2


title: RNAseq_pA+_Ery_iPSC_WT_AH017_rep1


title: RNAseq_pA-_Ery_iPSC_WT_AH017_rep2


title: RNAseq_pA+_Ery_iPSC_WT_SBAD02_rep3


title: CaptureC_Enh_Ery_iPSC_WT_AH017_rep3


title: RNAseq_pA-_Ery_iPSC_WT_AH017_rep1


title: CaptureC_Enh_Ery_iPSC_INV_Clone1_rep1


title: RNAseq_pA-_Ery_iPSC_Vs_Clone3_rep1

value: Promoter insertion sense


title: RNAseq_pA+_Ery_iPSC_WT_SBAD02_rep2


title: RNAseq_pA+_Ery_iPSC_Vs_Clone2_rep1


title: RNAseq_pA-_Ery_iPSC_WT_SBAD02_rep3


title: RNAseq_pA-_Ery_iPSC_WT_SBAD02_rep2


title: CaptureC_Enh_Ery_iPSC_WT_AH017_rep1


title: RNAseq_pA+_Ery_iPSC_Vas_Clone3_rep1


title: RNAseq_pA-_Ery_iPSC_Vas_Clone3_rep1


title: RNAseq_pA-_Ery_iPSC_Vs_Clone2_rep1


title: RNAseq_pA-_Ery_iPSC_Vs_Clone1_rep1


title: RNAseq_pA+_Ery_iPSC_Vas_Clone2_rep1


title: RNAseq_pA-_Ery_iPSC_Vas_Clone2_rep1


title: RNAseq_pA+_Ery_iPSC_Vas_Clone1_rep1


title: RNAseq_pA+_Ery_iPSC_INV_Clone1_rep1


title: RNAseq_pA-_Ery_iPSC_Vas_Clone1_rep1


title: RNAseq_pA-_Ery_iPSC_INV_Clone2_rep1


title: RNAseq_pA+_Ery_iPSC_C-SNV_LA13_rep1


title: RNAseq_pA+_Ery_iPSC_Vs_Clone3_rep1


title: RNAseq_pA-_Ery_iPSC_INV_Clone1_rep1


title: RNAseq_pA+_Ery_iPSC_INV_Clone2_rep1


title: RNAseq_pA+_Ery_iPSC_Vs_Clone1_rep1


title: RNAseq_pA-_Ery_iPSC_C-SNV_LA13_rep1


title: RNAseq_pA+_Ery_iPSC_C-SNV_LA01_rep1


title: RNAseq_pA-_Ery_iPSC_C-SNV_LA06_rep1


title: ChIP_RNAPII_Ery_iPSC_WT_SBAD02_rep3

description: Genome-wide library of Immunoprecipitated fragments

data_processing:
Mapping : bowtie -m 2 --maxIns 350, genome
For un-mapping reads : trimming adaptors trim_galore -- length 10, combining overlapping R1-R2 reads : flash -m 9 -x 0.125
Combining trimmed+flashed and originally mapped reads, mapping again with  bowtie -m 2 --maxIns 350
Removing read pairs overlapping Blacklisted regions
Removing duplicates : samtools rmdup
Reconstructing sequenced fragments from R1+R2 read pairs ( bedtools bedpe | cut -f 1,2,6) - for visualisation
Pileup of fragments (bedtools genomecov -counts)
Generating bigwig tracks
Genome_build: hg19; custom chr16 sequence fasta files on GSE159871: chr16_hg19_INV.fa.gz, chr16_hg19_Vas.fa.gz, chr16_hg19_Vs.fa.gz
Supplementary_files_format_and_content: bigWig : (DEEPtools) bamCoverage converison of filtered fragments (reconstructed, duplicate-filtered fragments : see above) from bam to bigwig,  (--binSize 10 --normalizeUsingRPKM --minMappingQuality 30)

extract_protocol:
isolation protocol: Cells were fixed at 2.5x10^6 cells/ml of 10% FCS RPMI media (Gibco) with 1% formaldehyde (SIGMA) for 10min at RT. Fixed cells were lysed at 5x10^7 cells/ml of cell lysis buffer (5mM PIPES (Gibco), 85mM KCl, 0.5% NP-40 (SIGMA)) + proteinase inhibitor (PI) (ROCHE) on ice for 20min. The lysed fixed nuclei were lysed in nuclear lysis buffer (50mM Tris-HCl, 10mM EDTA (both from Life Technologies) 1% SDS (SIGMA)) +PI at a concentration of 1x10^8 cells/ml. The nuclear lysis was sonicated using the Covaris S220 Focused-ultrasonicator in 130μl microTUBEs (Covaris). The sonicated lysate was spun at max speed at 10°C to remove insoluble material. The clear fixed chromatin was diluted 1 in 10 with RIPA buffer w/o SDS +PI (10mM Tris-HCl, 1mM EDTA, 0.5mM EGTA (SIGMA), 1% Triton X-100 (SIGMA), 0.1% Na Deoxycholate (SIGMA), 140mM NaCl). The diluted chromatin was precleared twice with 10µl of a 1:1 mix of Protein A and Protein G Dynabeads (Invitrogen) by incubating at 4°C for 30mins and discarding the beads. The pre-cleared chromatin was incubated with the appropriate amount of antibody coupled to a 100µl 1:1 mix of Protein A and Protein G Dynabeads at 4°C overnight. The antibodies used are: RNA Polymerase II N-20 antibody SC-899 (Santa Cruz Biotechnology) 6μg per 1ml of chromatin from 1x10^7 cells; Monoclonal anti-acetyl-Histone H3 (Lys27) antibody 17-683 (Merck Millipore) 2μg per 1ml of chromatin from 1x10^7 cells; Polyclonal anti-trimethyl-Histone H3 (Lys4) antibody 07-473 (Merck Millipore) 1μg per 1ml of chromatin from 1x10^7 cells; Polyclonal anti-monomethyl-Histone H3 (Lys4) antibody ab195391 (Abcam) 4μg per 1ml of chromatin from 1x10^7 cells; Polyclonal anti-GATA1 antibody ab11852 (Abcam) 8μg per 1ml of chromatin from 1x10^7 cells; Policlonal anti-CTCF antibody 07-729 (Merck Millipore) 10μl serum per 1ml of chromatin from 1x10^7 cells. Polyclonal anti-KLF1 antibody was kindly provided by the Perkins Laboratory, Translational Research Institute, Brisbane, Australia (used 30μl serum per 1ml of chromatin from 1x10^7 cells). Chromatin bound beads were washed twice with RIPA (10mM Tris-HCl, 1mM EDTA, 0.5mM EGTA, 1% Triton X-100, 0.1% SDS, 0.1% Na Deoxycholate, 140mM NaCl) +PI, then twice with high salt RIPA (same as RIPA but with 500mM NaCl) +PI, once with LiCl RIPA (same as RIPA but with 250mM LiCl instead of NaCl) +PI and twice with TE buffer. Chromatin was eluted off beads using 20mM Tris-HCl, 5mM EDTA, 50mM NaCl, 1% SDS, 130µg/ml RNase A, 65µg/ml Proteinase K. Eluted chromatin and Input samples were incubated at 65°C overnight to de-crosslink DNA from protein.
DNA was purified by phenol-chloroform extraction and ethanol precipitation with NaOAc, and 1 µl GlycoBlue (Invitrogen). ChIP enrichment was determined by RT-qPCR
NEBNext Ultra II DNA Library Prep kit for Illumina (NEB).

tag: antibody

tag: differentiation day


title: ChIP_RNAPII_Ery_iPSC_C-SNV_LA13_rep1

value: RNA Polymerase II N-20 antibody SC-899 (Santa Cruz Biotechnology)


title: ChIP_RNAPII_Ery_iPSC_WT_SBAD02_rep2


title: ChIP_RNAPII_Ery_iPSC_INV_Clone2_rep1


title: ChIP_RNAPII_Ery_iPSC_WT_AH017_rep2


title: ChIP_RNAPII_Ery_iPSC_WT_SBAD02_rep1


title: ChIP_RNAPII_Ery_iPSC_WT_AH017_rep3


title: ChIP_RNAPII_Ery_iPSC_WT_AH017_rep1


title: ChIP_H3K4me3_Ery_iPSC_WT_AH017_rep3

value: anti-trimethyl-Histone H3 (Lys4) antibody 07-473 (Merck Millipore)


title: ChIP_H3K4me3_Ery_iPSC_WT_AH017_rep1


title: ChIP_RNAPII_Ery_iPSC_Vs_Clone2_rep1


title: ChIP_H3K4me3_Ery_iPSC_Vs_Clone3_rep1


title: ChIP_RNAPII_Ery_iPSC_INV_Clone1_rep1


title: ChIP_RNAPII_Ery_iPSC_Vs_Clone3_rep1


title: ChIP_H3K4me3_Ery_iPSC_Vs_Clone1_rep1


title: ChIP_RNAPII_Ery_iPSC_C-SNV_LA06_rep1


title: RNAseq_pA+_Ery_iPSC_C-SNV_LA06_rep1


title: CaptureC_Enh_Ery_iPSC_WT_SBAD02_rep1


title: ChIP_H3K4me3_Ery_iPSC_WT_SBAD02_rep2


title: RNAseq_pA-_Ery_iPSC_C-SNV_LA01_rep1


title: ChIP_H3K4me3_Ery_iPSC_Vs_Clone2_rep1


title: ChIP_RNAPII_Ery_iPSC_C-SNV_LA01_rep1


title: ChIP_H3K4me3_Ery_iPSC_WT_AH017_rep2


title: ChIP_H3K4me3_Ery_iPSC_WT_SBAD02_rep1


title: ChIP_H3K4me3_Ery_iPSC_INV_Clone2_rep1


title: ChIP_H3K4me3_Ery_iPSC_C-SNV_LA13_rep1


title: ChIP_RNAPII_Ery_iPSC_Vs_Clone1_rep1


title: ChIP_H3K4me3_Ery_iPSC_C-SNV_LA06_rep1


title: ChIP_H3K4me3_Ery_iPSC_INV_Clone1_rep1


title: ChIP_H3K4me1_Ery_iPSC_WT_SBAD02_rep2

value: anti-monomethyl-Histone H3 (Lys4) antibody ab195391 (Abcam)


title: ChIP_H3K4me1_Ery_iPSC_WT_SBAD02_rep3


title: ChIP_H3K4me3_Ery_iPSC_C-SNV_LA01_rep1


title: ChIP_H3K4me1_Ery_iPSC_WT_SBAD02_rep1


title: ChIP_H3K4me1_Ery_iPSC_WT_AH017_rep3


title: ChIP_H3K4me3_Ery_iPSC_WT_SBAD02_rep3


title: ChIP_H3K4me3_Ery_iPSC_Vas_Clone3_rep1


title: ChIP_H3K4me3_Ery_iPSC_Vas_Clone1_rep1


title: ChIP_H3K4me3_Ery_iPSC_Vas_Clone2_rep1


title: ChIP_H3K4me1_Ery_iPSC_Vs_Clone3_rep1


title: ChIP_H3K4me1_Ery_iPSC_WT_AH017_rep1


title: ChIP_H3K4me1_Ery_iPSC_Vs_Clone2_rep1


title: ChIP_H3K4me1_Ery_iPSC_Vs_Clone1_rep1


title: ChIP_H3K4me1_Ery_iPSC_Vas_Clone3_rep1


title: ChIP_H3K4me1_Ery_iPSC_Vas_Clone2_rep1


title: ChIP_H3K27ac_Ery_iPSC_WT_SBAD02_rep3

value: anti-acetyl-Histone H3 (Lys27) antibody 17-683 (Merck Millipore)


title: ChIP_H3K4me1_Ery_iPSC_C-SNV_LA06_rep1


title: ChIP_H3K4me1_Ery_iPSC_C-SNV_LA13_rep1


title: ChIP_H3K27ac_Ery_iPSC_WT_SBAD02_rep2


title: ChIP_H3K4me1_Ery_iPSC_C-SNV_LA01_rep1


title: ChIP_H3K27ac_Ery_iPSC_WT_SBAD02_rep1


title: ChIP_H3K4me1_Ery_iPSC_WT_AH017_rep2


title: ChIP_H3K27ac_Ery_iPSC_WT_AH017_rep2


title: ChIP_H3K27ac_Ery_iPSC_WT_AH017_rep3


title: ChIP_H3K27ac_Ery_iPSC_WT_AH017_rep1


title: ChIP_H3K4me1_Ery_iPSC_Vas_Clone1_rep1


title: ChIP_H3K27ac_Ery_iPSC_Vas_Clone3_rep1


title: ChIP_H3K27ac_Ery_iPSC_Vas_Clone1_rep1


title: ChIP_H3K27ac_Ery_iPSC_Vs_Clone2_rep1


title: ChIP_H3K27ac_Ery_iPSC_Vs_Clone3_rep1


title: ChIP_H3K27ac_Ery_iPSC_C-SNV_LA06_rep1


title: ChIP_CTCF_Ery_iPSC_WT_AH017_rep3

value: CTCF antibody 07-729 (Merck Millipore)


title: ChIP_H3K27ac_Ery_iPSC_C-SNV_LA01_rep1


title: ChIP_CTCF_Ery_iPSC_C-SNV_LA13_rep1


title: ChIP_CTCF_Ery_iPSC_WT_AH017_rep1


title: ChIP_CTCF_Ery_iPSC_C-SNV_LA01_rep1


title: ChIP_CTCF_Ery_iPSC_WT_AH017_rep2


title: ChIP_CTCF_Ery_iPSC_C-SNV_LA06_rep1


title: ATAC_Ery_iPSC_WT_SBAD02_rep2

description: Genome-wide library of tagmented fragments

data_processing:
Mapping : bowtie -m 2 --maxIns 350, genome
For un-mapping reads : trimming adaptors trim_galore -- length 10, combining overlapping R1-R2 reads : flash -m 9 -x 0.125
Combining trimmed+flashed and originally mapped reads, mapping again with  bowtie -m 2 --maxIns 350
Removing read pairs overlapping Blacklisted regions
Removing duplicates : samtools rmdup
Reconstructing sequenced fragments from R1+R2 read pairs ( bedtools bedpe | cut -f 1,2,6) - for visualisation
Pileup of fragments (bedtools genomecov -counts)
Generating bigwig tracks
Genome_build: hg19; custom chr16 sequence fasta files: chr16_hg19_INV.fa.gz, chr16_hg19_Vas.fa.gz, chr16_hg19_Vs.fa.gz
Supplementary_files_format_and_content: bigWig : (DEEPtools) bamCoverage converison of filtered fragments (reconstructed, duplicate-filtered fragments : see above) from bam to bigwig,  (--binSize 10 --normalizeUsingRPKM --minMappingQuality 30)

extract_protocol:
Assay for transposition of active chromatin sequencing (ATAC-Seq) was performed as previously published (Buenrostro, 2013) on single cell suspensions. 60000-80000 cells were used per biological replicate. Cells were lysed and nuclei were isolated prior to transposition with Tn5 transposase (Nextera, Illumina) for 30 minutes at 37°C. DNA was purified using a MinElute kit (Qiagen).
Libraries were amplified and barcoded using the NEBNext 2xMastermix (NEB) and the custom primers as published in Buenrostro et al., 2013. ATAC-Seq libraries profiles were visualized using D1000 tape on the Tapestation (Agilent). The libraries were quantified using the universal library quantification kit (KAPA Biosystems).


title: ATAC_Ery_iPSC_WT_SBAD03_rep1


title: ATAC_Ery_iPSC_WT_SBAD02_rep1


title: ChIP_H3K27ac_Ery_iPSC_C-SNV_LA13_rep1


title: ATAC_Ery_iPSC_Vs_Clone1_rep1


title: ATAC_Ery_iPSC_Vs_Clone2_rep1


title: ATAC_Ery_iPSC_Vs_Clone3_rep1


title: ATAC_Ery_iPSC_WT_AH017_rep1


title: ChIP_H3K27ac_Ery_iPSC_Vas_Clone2_rep1


title: ChIP_H3K27ac_Ery_iPSC_Vs_Clone1_rep1


title: ATAC_Ery_iPSC_Vas_Clone1_rep1


title: ATAC_Ery_iPSC_TtoC_Clone2_rep1

value: T to C allele  homozygous edit


title: ATAC_Ery_iPSC_TtoC_Clone4_rep1

value: Erythroid


title: ATAC_Ery_iPSC_TtoC_Clone3_rep1

value: Day 21


title: ATAC_Ery_iPSC_INV_Clone3_rep1


title: ATAC_Ery_iPSC_nonINV_Clone2_rep1

value: Lox site insertion non-inverted


title: ATAC_Ery_iPSC_WT_SBAD02_rep3


title: ATAC_Ery_iPSC_Vas_Clone2_rep1


title: ATAC_Ery_iPSC_nonINV_Clone3_rep1

value: Female


title: ATAC_Ery_iPSC_TtoC_Clone1_rep1


title: ATAC_Ery_iPSC_INV_Clone2_rep1


title: ATAC_Ery_iPSC_INV_Clone1_rep1


title: ATAC_Ery_iPSC_CtoT_Clone2_rep1

value: C to T allele  homozygous edit


title: ATAC_Ery_iPSC_CtoT_Clone3_rep1


title: ATAC_Ery_iPSC_CtoT_Clone4_rep1


title: ATAC_Ery_iPSC_C-SNV_LA01_rep1

value: C-SNV allele homozygous


title: ATAC_Ery_iPSC_CtoT_Clone1_rep1


title: ATAC_Ery_iPSC_Vas_Clone3_rep1

value: Male

value: Promoter insertion anti-sense


title: Rheumatoid Arthritis 10 - input

city: Glasgow

middle: Joseph

last: Cole

address: University Avenue

institute: University of Glasgow

data_processing:
The read quality of ChIP-seq dataset was verified using fastQC (v0.11.7) with each sample showing a mean per base quality > 30 at all read positions.
The data aligned to the human genome (GRCh38 version 94) using bowtie 2 (v2.3.5) with default parameters for indexing and alignment.
A mean alignment of 28 million uniquely mapping reads per sample (74%) was observed.
Per sample wig files were generated using the PeakRanger (1.18) wig command with --format bam. Bigwigs were generated from the wig files using UCSC tools wigToBigWig (v4), with chromosome sizes as determined by UCSC tools faSize.
The per sample H3K4me3 peaks were called with macs2 (v2.1.1.20160309) callpeak using the input BAM file for each sample as the control, a genome size of 2,945,849,067bp and specifying --format BAM.
Genome_build: Hg38
Supplementary_files_format_and_content: Peak text files

source_name: Rheumatoid Arthritis_input

growth_protocol: Freshly isolated PBMCs were suspended in DPBS supplemented with 1% FBS, 0.1% NaN3 and 5mM EDTA and stained for flow cytometry.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were prepared using the NEB NEXT UltraII DNA-library prep kit (E7645S for ChiP and E7600S for input) and samples were sequenced on an Illumina Next-Seq to a mean depth of 38 million reads. The read length was 75pb SE.

tag: subject status

value: Rheumatoid Arthritis

value: blood-derived monocytes


title: Rheumatoid Arthritis 9 - input


title: Rheumatoid Arthritis 7 - input


title: Rheumatoid Arthritis 5 - input


title: Rheumatoid Arthritis 8 - input


title: Rheumatoid Arthritis 6 - input


title: ATAC_Ery_iPSC_nonINV_Clone1_rep1


title: Rheumatoid Arthritis 2 - input


title: Rheumatoid Arthritis 3 - input


title: Rheumatoid Arthritis 4 - input


title: Rheumatoid Arthritis 1 - input


title: Healthy Control 2 - input

source_name: Healthy control_input

value: Healthy control


title: Healthy Control 5 - input


title: Rheumatoid Arthritis 10 - H3K4me3

source_name: Rheumatoid Arthritis_H3K4me3

tag: chip antibody

value: H3K4me3 (Anti-trimethyl-Histone H3 (Lys4), Merck Millipore,07-473)


title: Healthy Control 1 - input


title: Rheumatoid Arthritis 9 - H3K4me3


title: Rheumatoid Arthritis 8 - H3K4me3


title: Healthy Control 3 - input


title: Rheumatoid Arthritis 7 - H3K4me3


title: Rheumatoid Arthritis 6 - H3K4me3


title: Rheumatoid Arthritis 4 - H3K4me3


title: Rheumatoid Arthritis 5 - H3K4me3


title: Rheumatoid Arthritis 2 - H3K4me3


title: Rheumatoid Arthritis 3 - H3K4me3


title: Healthy Control 5 - H3K4me3

source_name: Healthy control_H3K4me3


title: Rheumatoid Arthritis 1 - H3K4me3


title: Healthy Control 4 - H3K4me3


title: Healthy Control 4 - input


title: Healthy Control 3 - H3K4me3


title: Healthy Control 1 - H3K4me3


title: BT549 DSL3 RNA-seq #3

city: Lund

first: Phuong

last: Cao Thi Ngoc

address: BMC, B1222b, Klinikgatan 26

country: Sweden

institute: Lund University

data_processing:
RNA-seq datasets were aligned to the hg38 human genome using STAR v2.5.2b with the parameter outFilterMultimapNmax set to 1.
Bioconductor package DESeq2 was used to analyze differential gene expression.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files

source_name: BT549 cells

growth_protocol: BT549 human breast cancer cell line (ATCC) were cultured in RPMI+10%FBS+0.023U/ml Insulin+1%Penicilin/Streptomycin under standard conditions (5% CO2 humified chamber).

extract_protocol:
Total RNA from the cells was prepared using the Direct-zol™ RNA MicroPrep (Zymo Research Corporation) according to manufacturer's protocol. DNAse in column treatment was performed according to guidelines of the producer. Integrity and quantity of the resulting RNA was confirmed by RNA Nano LabChip Bioanalyzer run (Agilent).
Libraries were constructed from 300 ng of total RNA using the TruSeq Stranded Total RNA LT Sample Prep (with  Ribo-Zero treatment and single indexing). Quality of libraries was ensured with Bioanalyzer High Sensitivity DNA kit (Agilent). Sequencing was performed using the NextSeq 500 High Output v2 kit (75 cycles) Illumina platform.

treatment_protocol: Parental BT549 cell line was subjected to targeted editing of SF3A3 5'UTR locus with gRNAs against SL3 translational element. After single-cell sorting and expansion, clones were checked for type of editing by Sanger sequencing. For experiment, cells were seeded and  harvested at ~80% confluency 24 hours afterwards into Trizol reagent.

value: BT549 cells


title: BT549 DSL3 RNA-seq #2


title: Rheumatoid Arthritis 11 - H3K4me3


title: BT549 DSL3 RNA-seq #1


title: BT549 WT RNA-seq #1

value: WT


title: BT549 WT RNA-seq #2


title: WIBR2 hPSCs in tHENSM medium (titrated Erki 0.33mM), replication 2

city: Rehovot

description:
Poly-A RNA-seq
WIBR2 hPSCs in tHENSM medium (titrated Erki 0.33mM), batch 4, replication 2
counts_batch4.txt
WIBR2_tHENSM_2

growth_protocol: Maintenance of human naïve pluripotent cells were conducted using "Enhanced NHSM" (HENSM) as detailed in bayerl et.al in feeder free conditions on plates coated with 1% Matrigel (BD- FAL356231). Maintenance of human primed pluripotent cells were conducted using mTESR (Ludwing and Thomson: Curr. Protoc. Stem Cell Biol. 2:1C.2.1-1C.2.16) in feeder free conditions on plates coated with 1% Matrigel

value: tHENSM