title: Sample 52_ChIPseq SOX17 INPUT day5 sgLNCSOX17 rep3

city: Berlin

first: Helene

last: Kretzmer

address: Ihnestraße 63

department: Genome Regulation

institute: Max Planck Institute for Molecular Genetics

description: processed data file: AM-Other-235_241_peaks.narrowPeak

data_processing:
cHi-C (Sample 1 - Sample 4):
Raw sequence reads of capture Hi-C (cHi-C) were mapped to the hg19 version of the human genome using BWA (v0.7.17-r1188) with parameters (mem -A 1 -B 4 -E 50 -L 0).
Mapped reads were further processed by HiCExplorer (v3.6) to remove duplicated reads and reads from dangling ends, self-circle, self-ligation and same fragments
4Cseq (Sample 5 - Sample 16):
The raw sequencing reads were trimmed by using cutadapt (--discard-untrimmed -e 0.05 -m 25) to remove primer sequences and restriction enzyme sequences. The reads without matching those sequences were removed from further analysis. The remaining reads were then mapped to the reference sequences GRCh37/hg19 by bowtie2 (default parameters). An iterative mapping procedure was performed. Specifically, the full-length reads were first mapped to genome. The unmapped reads were then cut by 5-nt from 3-prime each time until they were successfully mapped to genome. The final mapped reads were assigned to valid fragments. The fragment counts were then normalized by RPM (Reads Per Million) and smoothed by averaging the counts of the closest 5 fragments.
RNAseq (Sample 17 - Sample 40):
All RNAseq samples were pre-processed using cutadapt to remove adapter and trim low quality bases.
Reads were subsequently aligned against the human reference genome hg19 using STAR (parameter: outSAMtype BAM SortedByCoordinate --outSAMattributes Standard --outSAMstrandField intronMotif --outSAMunmapped Within --quantMode GeneCounts).
Stringtie was used for calculation of strand-specific TPMs.
ChIPseq SOX17 (Sample 41 - Sample 52):
The ChIP-seq sequencing data as well as the control input sequencing were aligned to the human reference genome (hg19) using BWA mem using the default parameter.
GATK was used to obtain alignment metrics and remove duplicates.
Peaks were called using the MACS2 (2.1.2_dev) peakcall function using default parameters.
Oxford Nanopore cDNA seq (Sample 53):
Oxford Nanopore Technologies derived runs were processed using the Nanopype pipeline (v1.1.0) .
The basecaller Guppy (v4.0.11) was used with the r9.4.1 high-accuracy configuration. Quality filtering was disabled for any basecalling.
Base-called reads were aligned against the human reference genome hg19 using minimap2 (v2.10) with the Oxford Nanopore Technologies parameter preset for spliced alignments (-ax splice -uf -k14). Only unique alignments (-F 2304) are reported.
Genome_build: hg19
Supplementary_files_format_and_content: h5 of contact counts
Supplementary_files_format_and_content: bedGraph of contact RPM
Supplementary_files_format_and_content: tsv of TPM values
Supplementary_files_format_and_content: bigWig and BED of signal and peaks
Supplementary_files_format_and_content: BAM of read alignment

source_name: Chromatin Immunoprecipitation seq for SOX17 of day5 CRISPRi cells expressing sgLNCSOX17 gRNA

growth_protocol:
hiPSCs/ESCs culture:
ZIP13K2 hiPSCs were maintained in mTeSR1 (Stemcell Technologies, 85850) on pre-coated culture ware (1:100 diluted Matrigel (Corning, 354234) in KnockOut DMEM (Thermo Fisher Scientific, 10829-018)). Clump-based cell splitting was performed by incubating the cells in final 5 mM EDTA pH 8,0 (Thermo Fisher Scientific, 15575-038) in DPBS (Thermo Fisher Scientific, 14190250) 5 min at 37°C, 5% CO2. Single cell splitting was performed by incubating the cells with Accutase (Sigma-Aldrich, A6964) supplemented with 10 µM Y-27632 (Tocris, 1254) for 15 min at 37°C, 5% CO2. Cell counting was performed using a 1:1 diluted single-cell suspensions in 0,4% Trypan Blue staining-solution (Thermo Fisher Scientific, 15250061) on the Countess II automated cell-counter (Thermo Fisher Scientific). Wash-steps were performed by spinning cell-suspensions at 300 x g 5 min at room temperature (RT).
Endoderm derivation:
To guarantee high reproducibility, constant media-quality, and mTeSR1 compatibility, definitive endoderm differentiations were exclusively performed utilizing the STEMdiff Trilineage Endoderm Differentiation media (Stemcell Technologies, 05230). Single cell suspensions of mTeSR1 maintained ZIP13K2 hiPSCs were seeded into the respective culture formats according to the required cell-number as recommended by the manufacturer’s instructions. Media change using the STEMdiff Trilineage Endoderm Differentiation media was performed on a daily bases according to the manufacturer’s instructions. Cells were then collected at required timepoints by washing the plate with DPBS before single-cell dissociation was performed with Accutase for 15 min at 37°C, 5% CO2. Single cell suspensions of definitive endoderm (EN) differentiated cells were utilized for further downstream analysis (qPCR, Western Blot, FACS etc.).
Generation of pancreatic progenitors:
Pancreatic progenitor (PP) differentiation was performed as previously described 4 with minor changes. Briefly, single cell suspensions of ZIP13K2 hiPSCs (s. hiPS cell culture) were seeded at a density of 5 x 105 cells /cm2 in mTeSR1 supplemented with 10 µM Y-27632. After 24 h, culture medium was replaced with S1-media (Final 11,6 g/L MCDB131, Sigma Aldrich, M8537-1L; 2 mM D-+-Glucose, Sigma Aldrich, G7528-250G; 2,46 g/L NaHCO3, Sigma Aldrich, S5761-500G; 2% FAF-BSA, Proliant Biologicals, 68700-1; 1:50000 of 100 x ITS-X, Thermo Fisher Scientific, 51500056; 1 x GlutaMAX, Thermo Fisher Scientific, 35050-038; 0,25 mM ViatminC, Sigma-Aldrich, A4544-100G; 1% Pen-Strep, Thermo Fisher Scientific, 15140122) supplemented with final 100 ng/ml Activin-A (R&D Systems, 338-AC-01M) and 1,4 µg/ml CHIR99021 (Stemgent, 04-0004-10). The following 2 days, cells were cultured in S1-media supplemented with final 100 ng/ml Activin-A. Next, cells were cultured in S2-media (Final 11,6 g/L MCDB131; 2 mM D-+-Glucose; 1,23 g/L NaHCO3; 2% FAF-BSA; 1:50000 of 100 x ITS-X; 1 x GlutaMAX; 0,25 mM ViatminC; 1% Pen-Strep) supplemented with final 50 ng/ml KGF (Peprotech, 100-19-1MG) for 48 h. After these 48 h, cells were cultured in S3-media (Final 11,6 g/L MCDB131; 2 mM D-+-Glucose; 1,23 g/L NaHCO3; 2% FAF-BSA; 1:200 of 100 x ITS-X; 1 x GlutaMAX; 0,25 mM ViatminC; 1% Pen-Strep) supplemented with final 50 ng/ml KGF (Peprotech, 100-19-1MG), 200 nM LDN193189 (Sigma Aldrich, SML0559-5MG), 0,25 µM Sant-1 (Sigma Aldrich, S4572-5MG), 2 µM Retinoic Acid (Sigma Aldrich, R2625-50MG), 500 nM PDBU (Merck Millipore, 524390-5MG) and 10 µM Y-27632 for 24 h. Finally, cells were cultured in the previous S3-media composition w/o supplementation of LDN193189 for 24 h. Between daily media changes, cells were washed once with 1 x DPBS. Throughout the entire differentiation process, cells were cultured at 37°C, 5% CO2 in 100 µl media /cm2.

extract_protocol: ZIP13K2-derived EN cells (5 x 106 /IP) were harvested and cross-linked in 1% formaldehyde (Thermo Fisher Scientific, 28908) in DPBS for 10 min at RT, followed by quenching with final 125 mM Glycine (Sigma-Aldrich, 50046) for 5 min at RT. Cross-linked cells were then centrifuged at 500 x g at 4°C and washed twice with ice cold DPBS. Cell lysis was performed by resuspending the pellet in 500 μl Cell Lysis Buffer (Final 10mM Tris-HCl, pH 8,0 (Sigma Aldrich, T2694); 85mM KCl (Sigma Aldrich, P9541); 0,5% NP40 (Sigma Aldrich, 56741); 1 x cOmplete, EDTA-free Protease Inhibitor Cocktail (Sigma Aldrich, 11873580001)) followed by 10 min incubation on ice. After the incubation, lysed cells were centrifuged at 2500 x g for 5 min at 4°C. Supernatant was carefully removed and the extracted nuclei were then resuspended in 230 μl Nuclei Lysis Buffer (Final 10mM Tris-HCl, pH 7,5 (Sigma Aldrich, T2319)); 1% NP40; 0,5% sodium deoxycholate (Sigma Aldrich, D6750); 0,1% SDS (Thermo Fisher Scientific, AM9820); 1 x cOmplete, EDTA-free Protease Inhibitor Cocktail). Following 10 min incubation on ice, each 260 μl sample was split into two microTUBEs (Covaris, 520045) and chromatin was sonicated using a Covaris E220 Evolution with the following settings: Temperature à 4°C; Peak power à 140; Duty factor à 5,0; Cycles/Burst à 200; Duration à 750 sec. After sonication, sheared chromatin (ranging from 200-600bp) was transferred in a new 1,5 ml tube and centrifuged at max speed for 10 min at 4°C. Supernatant was then transferred into a new tube and volume was increased to 1 ml /sample with ChIP Dilution Buffer (Final 16,7mM Tris-HCl, pH 8,0; 1,2mM EDTA (Sigma Aldrich, 03690)); 167mM NaCl (Sigma Aldrich); 1,1% Triton-X (Sigma Aldrich); 0,01% SDS; 1 x Protease Inhibitor). 50μl (5%) was then transferred into a new tube and frozen at -20°C as INPUT. 1μg of SOX17 antibody /106 initial cells was added to the 950 μl left, and immunoprecipitation was carried out at 4°C o/n on a rotator (s. Suppl. Table 3). The next day, 50μl of Dynabeads Protein G (Thermo Fisher Scientific, 10004D) /IP were washed twice with ice cold ChIP Dilution Buffer and then added to each IPs. IP/bead mixes were incubated for 4 hours at 4°C on a rotor. Next, bead/chromatin complexes were washed twice with Low Salt Wash Buffer at 4°C (Final 20 mM Tris-HCl, pH 8,0; 2 mM EDTA; 150 mM NaCl (Sigma-Aldrich, S6546); 1% Triton-X; 0,1% SDS), twice with High Salt Wash Buffer at 4°C (Final 20 mM Tris-HCl, pH 8,0; 2 mM EDTA; 500 mM NaCl; 1% Triton-X; 0,1% SDS), twice with LiCl Wash Buffer at 4°C (Final 10 mM Tris-HCl, pH 8,0; 1mM EDTA; 250mM LiCl (Sigma Aldrich, L9650); 1% sodium deoxycholate (Sigma Aldrich); 1% NP40), twice with TE pH 8,0 (Sigma Aldrich, 8890) at room temperature and finally eluted twice in 50 μl freshly prepared ChIP Elution Buffer (Final 0,5% SDS; 100 mM NaHCO3 (Sigma Aldrich, S5761)) at 65°C for 15 min (total 100 μl final eluent). Thawed INPUTS and eluted IPs were next reverse cross-linked at 65°C o/n after the addition of 16 ul freshly prepared Reverse Crosslinking Salt Mixture (Final 250 mM Tris-HCl, pH 6,5 (Sigma Aldrich, 20-160); 62,5 mM EDTA; 1,25M NaCl; 5 mg/ml Proteinase K (Thermo Fisher Scientific, AM2548)). The following day phenol:chloroform (Thermo Fisher Scientific, 15593031) extraction followed by precipitation was performed to isolate DNA. IPs and INPUTS were then quantified and NGS libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs, #E7645) following the manufacturer’s instructions. Library quality and size distribution was verified using a TapeStation D5000 HS kit (Agilent Technologies, 5067-5592). Samples were sequenced with a coverage of 50 M paired end reads (2 x 100 bp) /sample on a NovaSeq (Illumina).

tag: cell line/type

value: ZIP13K2 - hiPSCs

value: Fragmented gDNA


title: sample_92_dm

status: Public on Feb 08 2023

type: SRA

city: Bethesda

first: Iago

last: Pinal-Fernandez

state: MARYLAND

address: 50 South Drive, Room 1142, Building 50, MSC 8024

department: NIAMS

country: USA

institute: NIH

library_source: transcriptomic

data_processing:
Demultiplexing with bcl2fastq/2.20.0.
Raw sequencing data was cleaned using fastp/0.21.0.
The abundance of each gene was generated using Salmon/1.5.2.
Quality control output was summarized using multiqc/1.11.
Assembly: hg38
Supplementary files format and content: anonym_counts_hg38.tsv: Tab-delimited text file includes the counts for each sample.

molecule: total RNA

organism: Homo sapiens

source_name: muscle

extract_protocol:
Trizol
NeoPrep system according to the TruSeqM Stranded mRNA Library Prep protocol (Illumina, San Diego, CA), or with the NEBNext Poly(A) mRNA Magnetic Isolation Module and UltraTM II Directional RNA Library Prep Kit for Illumina (New England BioLabs, ref. #E7490 and #E7760).

tag: tissue

value: muscle

tag: diagnosis

value: myositis (DM)


title: sample_88_dm


title: sample_89_dm


title: sample_91_dm


title: sample_90_dm


title: 1S neuron, seqment A1, animal 4, cell d225020

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

data_processing:
NextSeq 500 sequencing using v3 chemistry. Software: Control v2.2.58, RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
Gene expression was quantified using RSEM version 1.3.0 and STAR version 2.5.3a alignment to a transcriptome derived from the human BDGP6 primary assembly and a version 92 annotation.
Assembly: BDGP6 Drosophila melanogaster assembly with version 92 annotation
Supplementary files format and content: 1b1sm_isoform_intCt.txt.gz is a tab delimited text file of isoform counts
Supplementary files format and content: 1b1sm_isoform_l2tpm.txt.gz is a tab delimited text file of isoform l2tpm vaules
Supplementary files format and content: 1b1sm_l2tpm.txt.gz is a tab delimited text file of gene l2tpm vaules
Supplementary files format and content: 1b1sm_intCt.txt.gz is a tab delimited text file of gene counts

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: neuron

growth_protocol: Fly stocks were raised at 25°C on standard molasses food in an incubator with 12 hrs day/night cycle. Actively crawling 3rd instar larvae that are size and age matched were used for all experiments.

extract_protocol:
Cellular material was aspirated in whole-cell patch electrodes and transferred to 384 well plates followed by extraction with XXX
RNAseq libraries from single cells were prepared using a modified version of the SMART-seq2 single-cell protocol (Picelli et al., 2013, Trombetta et al., 2014). RNA from single cells was placed in Hard-Shell 384-well plates (Catalog #HSP3801) in minimal volume (<2uL). cDNA was prepared following the standard protocol using 1/3 of the recommended volumes for all reagents utilizing a Mosquito HV automated liquid handler (SPT Labtech). Amplified cDNA was purified using 0.75X SPRI beads, quantified using picogreen and spot-checked on the Fragment Analyzer (Agilent). Dual indexed Illumina libraries were prepared from cDNA using a reduced volume NexteraXT reaction (1:12) on the Mosquito HV (Hendricks et al., in preparation). Final libraries were quantified using picogreen and spot-checked on the Fragment Analyzer before pooling and final quantification using qPCR on a Roche LC480II.

value: neuron

tag: segment

tag: cell type

tag: animal

tag: gender

value: M

tag: strain

tag: genotype


title: sample_86_dm


title: 1S neuron, seqment A2, animal 4, cell d225017


title: 1S neuron, seqment A4, animal 4, cell d225019


title: 1S neuron, seqment A6, animal 4, cell d225016


title: sample_84_dm


title: sample_93_dm


title: sample_87_dm


title: Sample 51_ChIPseq SOX17 INPUT day5 sgLNCSOX17 rep2

country: Germany

description: processed data file: AM-Other-234_240_peaks.narrowPeak

library_source: genomic

molecule: genomic DNA

tag: molecule subtype


title: Sample 47_ChIPseq SOX17 INPUT day5 sgCtrl rep1

description: processed data file: AM-Other-230_236_peaks.narrowPeak

source_name: Chromatin Immunoprecipitation seq for SOX17 of day5 CRISPRi cells expressing sgCtrl gRNA


title: Sample 49_ChIPseq SOX17 INPUT day5 sgCtrl rep3

description: processed data file: AM-Other-232_238_peaks.narrowPeak


title: Sample 48_ChIPseq SOX17 INPUT day5 sgCtrl rep2

description: processed data file: AM-Other-231_237_peaks.narrowPeak


title: Sample 50_ChIPseq SOX17 INPUT day5 sgLNCSOX17 rep1

description: processed data file: AM-Other-233_239_peaks.narrowPeak


title: Sample 46_ChIPseq SOX17 IP day5 sgLNCSOX17 rep3


title: sample_83_dm


title: sample_96_dm


title: sample_94_dm


title: sample_81_dm


title: sample_82_dm


title: Sample 45_ChIPseq SOX17 IP day5 sgLNCSOX17 rep2


title: 1S neuron, seqment A2, animal 4, cell d225015


title: 1S neuron, seqment A3, animal 4, cell d225014


title: sample_80_dm


title: 1S neuron, seqment A3, animal 4, cell d225013


title: sample_85_dm


title: Sample 44_ChIPseq SOX17 IP day5 sgLNCSOX17 rep1


title: sample_79_dm


title: sample_78_as

value: myositis (AS)


title: sample_77_as


title: 1S neuron, seqment A6, animal 4, cell d225018


title: 1S neuron, seqment A2, animal 4, cell d225012


title: sample_76_as


title: sample_73_as


title: sample_74_as


title: 1B neuron, seqment A8, animal 4, cell d225011


title: sample_72_as


title: Sample 42_ChIPseq SOX17 IP day5 sgCtrl rep2


title: Sample 40_RNAseq day9 PP sgLNCSOX17 rep3

description: processed data file: TPMs_D9.bed

source_name: Bulk RNA-sequencing of day9 CRISPRi cells expressing sgLNCSOX17 gRNA

extract_protocol: ZIP13K2 hiPSCs and their derived EN cultures were treated with Accutase for 15 min at 37°C, 5% CO2 to obtain a single cell suspension. Cells were then collected, washed with ice cold DPBS and centrifuged at 4°C, 300 x g for 5 min. Subsequently, 350 µl of RLT Plus buffer containing 1% β-mercaptoethanol (Thermo) was added to the cell pellets for cell lysis. After dissociation by trituration and vortexing, RNA was extracted using RNeasy Plus Micro Kit (Qiagen) and RNA concentration and quality was measured using the Agilent RNA 6000 Pico Kit (Agilent Technologies, 5067-1513) on an Agilent 2100 Bioanalyzer. All samples analyzed had a RINe value higher than 8,0, and were subsequently used for library preparation. mRNA libraries were prepared using KAPA Stranded RNA-Seq Kit (KapaBiosystem) according to the manufacturer’s instructions. 500 ng of total RNA was used for each sample to enter the library preparation protocol. For adapter ligation dual indexes were used (NEXTFLEX® Unique Dual Index Barcodes NOVA-514150) at a working concentration of 71nM (5 µl of 1 uM stock in each 70 µl ligation reaction). Quality and concentration of the obtained libraries were measured using Agilent High Sensitivity D5000 ScreenTape (Agilent-Technologies, 5067- 5592) on an Agilent 4150 TapeStation. All libraries were sequenced using 100 bp paired-end sequencing (200 cycles kit) on a NovaSeq platform at a minimum of 25 million fragments /sample.


title: Sample 41_ChIPseq SOX17 IP day5 sgCtrl rep1


title: sample_70_as


title: Sample 39_RNAseq day9 PP sgLNCSOX17 rep2

description: processed data file: TPMs_D9.bed


title: sample_71_as


title: 1B neuron, seqment A8, animal 3, cell d225010


title: 1B neuron, seqment A7, animal 3, cell d225009


title: sample_68_as


title: sample_69_as


title: 1B neuron, seqment A6, animal 3, cell d225008


title: 1B neuron, seqment A5, animal 3, cell d225007


title: Sample 38_RNAseq day9 PP sgLNCSOX17 rep1

description: processed data file: TPMs_D9.bed


title: sample_67_as


title: sample_66_as


title: sample_65_as


title: 1B neuron, seqment A3, animal 3, cell d225006


title: sample_75_as


title: sample_64_as


title: 1B neuron, seqment A5, animal 2, cell d225005

value: F


title: sample_62_as


title: sample_63_as


title: Sample 35_RNAseq day9 PP sgCtrl rep1

description: processed data file: TPMs_D9.bed

source_name: Bulk RNA-sequencing of day9 CRISPRi cells expressing sgCtrl gRNA


title: Sample 36_RNAseq day9 PP sgCtrl rep2

description: processed data file: TPMs_D9.bed


title: Sample 37_RNAseq day9 PP sgCtrl rep3

description: processed data file: TPMs_D9.bed


title: Sample 34_RNAseq day5 sgLNCSOX17 rep3

description: processed data file: TPMs_D5.bed

source_name: Bulk RNA-sequencing of day5 CRISPRi cells expressing sgLNCSOX17 gRNA


title: 1B neuron, seqment A2, animal 2, cell d225003


title: sample_60_ibm

value: myositis (IBM)


title: 1S neuron, seqment A2, animal 1, cell d225002


title: sample_61_as


title: sample_58_ibm


title: scRNA-seq_IR_56h_Ki67-RFPcells_rep2

city: Nanjing

first: Lei

last: Chen

address: No.2 Sipailou

country: China

institute: Southeast University

library_source: transcriptomic single cell

data_processing:
For RNA-seq, raw sequencing reads (fastq) were first quality checked using fastQC (v0.11.3) and were further aligned to mouse (mm9) genomes using Tophat2 (v2.1.0) to generate bam files. Cuffquant (v2.2.1) was used to generate cxb files from bam files. Cuffnorm (v2.2.1) was performed to calculate FPKM values using quartile normalization. Cuffdiff (v2.2.1) was applied to identify differentially expressed genes between groups using quartile normalization and per-condition dispersion.
For scRNA-seq of organoid samples, prior to processing, a mouse STAR reference was generated using a mouse genome FASTA build from the Ensembl 102 release and GTF annotations from GENCODE (GRCm39 vM29 2022.04) using STAR’s genomeGenerate function. BCLs derived from Illumina sequencing of PIPseq samples were demultiplexed and output in FASTQ format using BCL-convert v4.0.3. Barcode whitelisting and error correction were performed using PIPseeker v0.55. Reads passing this stage were then aligned to the mouse reference genome using STARsolo (STAR v2.7.10a). An aligned, sorted BAM file was generated by STAR, which included required information for RNA velocity analysis. Cell calling was performed using PIPseeker’s transcript-count thresholding approach and sensitivity 3 was chosen for all samples, which most closely targeted the first inflection point after the knee point on the barcode-rank plot. For sorted Ki67-RFP+ DAPI- cells, samples were processed in the same way, but using salmon v1.4 instead of STAR. A reference genome was first built from the same sources as above using the salmon index command with a 19-bp k-mer size.
For ATAC-seq, paired-end ATAC-seq fastq file was quality checked using fastQC. ATAC-seq adapter sequences were removed from each read file using CutAdapt (v1.9.1). Each read file was then aligned to the mouse mm9 genome using bowtie2. Picard (v2.18.27) was used to determine the median alignment size of each alignment bam file. Peak region bed files were called from each alignment bam file using MACS2 (v2.1.0). MACS2 was run with a “shift” distance of -0.5 times the median alignment size and an “extsize” distance equal to the median alignment size for each alignment bed file. The peak files were filtered against ENCODE blacklist, which is known to yield false ChIP-seq signals due to the inaccuracies of a particular genome assembly. BEDtools was used to subtract the sites on the ENCODE blacklist.
Assembly: RNA-seq and ATAC-seq: mm9; scRNA-seq: mm39
Supplementary files format and content: RNA-seq: fpkm_table.txt files.
Supplementary files format and content: scRNA-seq: barcodes.tsv, genes.tsv, and matrix.mtx files.
Supplementary files format and content: ATAC-seq: bigwig, Peaks BED files.

organism: Mus musculus

source_name: Sorted Ki67-RFP positive crypt cells

extract_protocol:
Crypts were isolated from proximal half of small intestine of Mki67tm1.1Cle/J mice after 56 hours post-irradiation and their non-IR littermate control. Briefly, freshly harvested intestine was flushed with cold PBS, opened longitudinally, cut into 1 cm pieces, and then rotated in 3 mM EDTA in PBS at 4 °C for 5 minutes, 10 minutes and 40 minutes (refreshing EDTA/PBS every time). The tissue was then vigorously shaken to release the epithelium, and non-IR crypts passed through a 70-μm cell strainer. 100-μm cell strainer was used in IR samples, as crypts were expanded during regeneration after IR. Crypts were pelleted by centrifugation at 300 g for 3 minutes at 4 °C and then washed with cold PBS. To dissociate single cells for FACS, isolated crypts were further rotated with 5U/ml dispase (Stem Cell 07913) and 200 U/ml of DNase I (Sigma D4513) at 37 °C for 30 minutes, and were then washed twice with 1% BSA/PBS, and filtered with a 40-μm cell strainer. Cells were prepared in 1% BSA/PBS with 200 U/ml of DNase I for sorting. Ki67-RFP+ DAPI- cells from mice 56 hours post-IR and non-IR condition were detected and sorted with Beckman Coulter Astrios EQ High Speed Cell Sorter, respectively. Dead cells were eliminated using 0.5 μg/ml DAPI. Kaluza analysis 2.1.3 software was used for FACS data analysis. Total 5500 cells were sorted and concentrated into 5 μL for initiating the PIPseq pipeline (PIPseq™ T2 3' Single Cell Capture and Lysis Kit v2.1, Fluent BioSciences). Cells were captured and lysed according to the manufacturer’s instructions.
PIPseq™ T2 Single Cell Sequencing Kit (v2.1, Fluent BioSciences).

value: Sorted Ki67-RFP positive crypt cells

tag: treatment

value: 12 Gy whole-body IR


title: sample_57_ibm


title: Sample 33_RNAseq day5 sgLNCSOX17 rep2

description: processed data file: TPMs_D5.bed


title: sample_59_ibm


title: Sample 32_RNAseq day5 sgLNCSOX17 rep1

description: processed data file: TPMs_D5.bed


title: 1S neuron, seqment A3, animal 1, cell d225001


title: Sample 31_RNAseq day3 sgLNCSOX17 rep3

description: processed data file: TPMs_D3.bed

source_name: Bulk RNA-sequencing of day3 CRISPRi cells expressing sgLNCSOX17 gRNA


title: Sample 43_ChIPseq SOX17 IP day5 sgCtrl rep3


title: sample_56_ibm


title: scRNA-seq_Non-IR_Ki67-RFPcells

value: Non-IR control


title: scRNA-seq_D8_IROrganoids_TGFB1_24h

source_name: Primary intestinal organoids

extract_protocol:
Primary cultured organoids were collected by removing Matrigel using cold PBS. Matrigel droplets containing organoids were disrupted. Organoids were pelleted by centrifugation at 300 g for 3 minutes at 4 °C and washed with cold PBS. After removing the PBS and Matrigel, organoids were resuspended in 1 mL pre-warmed (37 °C) TrypLE, and rotated at 37 °C for 15 to 30 minutes until organoids were dissociated into single cells (confirmed via microscope). Cells were pelleted at 300 g for 3 minutes at 4 °C, and washed with cold PBS. Cells were passed through SP Bel-Art Flowmi 40 μm cell strainer and collected into a new protein LoBind tube.
30,000 cells were prepared as mentioned above and used for ATAC-seq as described previously (Buenrostro et al., 2013; Buenrostro et al., 2015) with slight modifications. Briefly, cells were centrifuged at 500 g for 5 minutes at 4°C and resuspended in ice-cold lysis buffer (10 mM Tris, pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.1% NP-40). Cells were then centrifuged at 500 g for 10 minutes at 4°C. The isolated nuclear pellets were incubated with a 50 μl reaction of Tn5 Transposase (Illumina Tagment DNA Enzyme and Buffer Large Kit 20034198) for 30 minutes at 37°C. The transposed chromatin was purified with MinElute PCR purification kit (QIAGEN REF 28004), and PCR was amplified with high-fidelity 2X PCR Master Mix (New England Biolabs M0541). One-third of the maximum fluorescent intensity during a qPCR trial run was used to determine the additional cycles for library prep.
PIPseq™ T2 Single Cell Sequencing Kit (v2.1, Fluent BioSciences).

value: Primary intestinal organoids

value: WT

value: 4 Gy IR on Day 4, 1 ng/mL TGFB1 for 24h before Day 8 collection


title: sample_55_ibm


title: scRNA-seq_D8_IROrganoids_TGFB1_15h

value: 4 Gy IR on Day 4, 1 ng/mL TGFB1 for 15h before Day 8 collection


title: scRNA-seq_IR_56h_Ki67-RFPcells_rep1


title: Sample 30_RNAseq day3 sgLNCSOX17 rep2

description: processed data file: TPMs_D3.bed


title: Sample 29_RNAseq day3 sgLNCSOX17 rep1

description: processed data file: TPMs_D3.bed


title: Sample 28_RNAseq day0 sgLNCSOX17 rep3

description: processed data file: TPMs_D0.bed

source_name: Bulk RNA-sequencing of day0 CRISPRi cells expressing sgLNCSOX17 gRNA


title: scRNA-seq_D8_IROrganoids_TGFB1_0h

value: 4 Gy IR on Day 4, Vehicle for 24h before Day 8 collection


title: sample_52_ibm


title: sample_51_ibm


title: Back skin 2

city: Lancaster

first: Barbara

middle: Bo-Ju

last: Shih

address: Bailrigg

department: Biomedical and Life Sciences

country: United Kingdom

institute: Lancaster University

data_processing:
Basecall data generated by the NextSeq 1000/2000 Control Software (Version 1.4.1.39716)
cellranger mkfastq was used go generated fastq
cellranger count (--include-introns --expect-cells=10,000) was used for generating the processed data files
Genome_build: GRCh38 (version 2020-A; pre-built index provided by 10x Genomics)
Supplementary_files_format_and_content: barcodes.tsv, genes.tsv, and matrix.mtx

source_name: Back

extract_protocol:
Collected tissue was flash frozen and stored at -80C. Nuclei were isolated by homogenization in EZ Nuclei Lysis Buffer, washed, and prepared for cDNA library generation.
NextSeq 1000/2000 P3 Reagents (100 cycles) v3 Kit (#20040559)
Libraries were pooled  in equimolar quantities and PhiX Control v3 (#FC-110-3001) library was spiked in to the run  at a concentration of ~1% to help with cluster resolution and facilitate troubleshooting in case  of any problems with the run. Sequencing was run on NextSeq 2000 platform (Illumina Inc, #SY-415-1002)

tag: tissue type

value: skin

tag: tissue location

value: Back


title: Back skin 3

data_processing:
Basecall data generated by the NextSeq 1000/2000 Control Software (Version 1.4.1.39716)
cellranger mkfastq was used go generated fastq
cellranger count (--include-introns --expect-cells=10,000) was used for generating the processed data files
Assembly: GRCh38 (version 2020-A; pre-built index provided by 10x Genomics)
Supplementary files format and content: barcodes.tsv, genes.tsv, and matrix.mtx


title: Sample 26_RNAseq day0 sgLNCSOX17 rep1

description: processed data file: TPMs_D0.bed

value: ZIP13K2 - hiPSCs


title: Sample 27_RNAseq day0 sgLNCSOX17 rep2

description: processed data file: TPMs_D0.bed


title: sample_49_ibm

value: muscle


title: sample_48_ibm


title: Dorsal skin 2

source_name: Finger

value: Finger

value: Dorsal


title: sample_54_ibm


title: Back skin 1


title: sample_53_ibm


title: scRNA-seq_D8_IROrganoids_TGFB1_6h

value: 4 Gy IR on Day 4, 1 ng/mL TGFB1 for 6h before Day 8 collection


title: Sample 22_RNAseq day3 sgCtrl rep3

description: processed data file: TPMs_D3.bed

source_name: Bulk RNA-sequencing of day3 CRISPRi cells expressing sgCtrl gRNA


title: Sample 25_RNAseq day5 sgCtrl rep3

description: processed data file: TPMs_D5.bed

source_name: Bulk RNA-sequencing of day5 CRISPRi cells expressing sgCtrl gRNA


title: sample_50_ibm


title: sample_46_ibm


title: Sample 23_RNAseq day5 sgCtrl rep1

description: processed data file: TPMs_D5.bed


title: Dorsal skin 1


title: sample_45_ibm


title: Sample 24_RNAseq day5 sgCtrl rep2

description: processed data file: TPMs_D5.bed


title: sample_44_imnm

value: myositis (IMNM)


title: Sample 19_RNAseq day0 sgCtrl rep3

description: processed data file: TPMs_D0.bed

source_name: Bulk RNA-sequencing of day0 CRISPRi cells expressing sgCtrl gRNA


title: Sample 20_RNAseq day3 sgCtrl rep1

description: processed data file: TPMs_D3.bed


title: TT_CSS_4

type: RNA

city: Brisbane

first: Colleen

last: Nelson

state: Queensland

address: 199 Ipswich Road

department: Institute of Health and Biomedical Innovation; Vancouver Prostate Centre

country: Australia

institute: Queensland University of Technology; University of British Columbia

description:
total cellular RNA
Total cellular RNA extracted from cells in androgen deprived culture (charcoal-stripped-serum), RNA input sample for the immunoprecipitation.

hyb_protocol: Cy3 labeled cRNA was hybridised onto a custom Agilent oligo micrarray at 65⁰C for 17 hours.

scan_protocol: Arrays were scanned on an Agilent scanner (G2565CA) using the Agilent Scan Control Software (A.8.4.1) and feature extraction was performed using the Agilent Feature Extraction Software (10.7).

data_processing: Differential expression was determined using the Baysian adjusted t-statistic linear model of the ‘Linear Models for Microarray Data’ (LIMMA) package in R. Data was annotated using Gencode v21 / Ensembl 77 (GRCh38).

source_name: LNCaP prostate cancer cell line

label_protocol: RNA was amplified and labelled using the Agilent Low Input Quick Amp Labeling Kit according to the manufacturer's protocol.

growth_protocol: LNCaP cells were cultured in phenol-red free RPMI-1640 medium + 5% FBS for 72 hrs at 37°C in a humidified atmosphere containing 5% CO2. For androgen deprivation, media was then replaced by RPMI+5% CSS (charcoal stripped serum) and cultured for another 48 hrs. For androgen stimulation, media was then changed to RPMI+5% CSS + 10 nM Dihydrotestosterone (or vehicle control) and cultured for 48 hrs before harvest.

extract_protocol: RNA was extracted using the RNeasy Micro Kit (Qiagen #74004) according to the manufacturer’s protocol, including DNase-I treatment.

tag: cell line

value: LNCaP

value: Prostate cancer cell line

tag: condition

value: CSS

tag: antibody


title: YBX1-IP_DHT_2

description:
RNA co-immunoprecipitated with YB-1 antibody
RNA bound in YB-1 containing RNP granules was co-immunoprecipitated from cells grown in androgen stimulated culture (dehydrotestosterone) using an N-terminal antibody against YB-1

value: DHT


title: tφ, control

city: Leuven

first: Rob

last: Lavigne

address: Kasteelpark Arenberg 21

department: Biosystems

country: Belgium

institute: KU Leuven

data_processing:
Live basecalling and demultiplexing by the MinIT device with build-in Guppy software (v3.2.10) in high accuracy mode.
Identification and orientation of full-length reads using Pychopper (v2.5.0)
Read trimming using Cutadapt (v2.7)
Mapping reads against reference genomes of P. aeruginosa PaLo41 and LUZ100 using minimap2
Peak calling using termseq-peaks scripts
Assembly: SAMN30382022 (LUZ100), SAMN18631029 (PaLo41).
Supplementary files format and content: Narrowpeak files generated by peak calling (The references used in the narrowpeaks file do not have a GenBank accession number yet. The genome submissions are still under review. They are submitted under the biosamples above.)

organism: Pseudomonas aeruginosa

source_name: bacterial cell

growth_protocol: P. aeruginosa cells were grown to exponential phase in LB medium and infected with phage LUZ100 at an MOI of 10. Culture samples were taken at 0 minutes and 4, 8, 12, 16, 20, 24, 28, 32, 36 and 40 minutes post-infection.

extract_protocol:
All samples, aside from 0 min, were pooled together and homogenized (sample tφ). The resulting samples t0 (uninfected) and tφ (phage infected) were subjected to hot phenol treatment and ethanol precipitation to extract and purify  the RNATotal RNA was extracted using hot-phenol extraction, followed by DNAse treatment.
Total RNA was enriched for primary transcripts using the ONT-cappable-seq enrichment protocol. In parallel, control samples were subjected to similar environmental conditions. The RNA was reverse transcribed, PCR amplified and barcoded accoriding to Oxford Nanopore Technology cDNA-PCR protocol (SQK-PCS109 combined with SQK-PBK004). The amplified cDNA samples were pooled together in a final library.

treatment_protocol: Total RNA was extracted using hot-phenol extraction, followed by DNAse treatment. The enriched samples were subjected to an enrichment procedure based on streptavidin beads to enrich for primary transcripts. For the control samples the enrichment steps were omitted.

value: bacterial cell

value: no enrichment

tag: infection

value: Pseudomonas virus LUZ100

tag: time

value: pooled samples from different timepoints during infection


title: Sample 18_RNAseq day0 sgCtrl rep2

description: processed data file: TPMs_D0.bed

tag: cell line/type


title: TT_DHT_3

description:
total cellular RNA
Total cellular RNA extracted from cells in androgen stimulated culture (dehydrotestosterone treated), RNA input sample for the immunoprecipitation.


title: YBX1-IP_DHT_1


title: Sample 21_RNAseq day3 sgCtrl rep2

description: processed data file: TPMs_D3.bed


title: TT_DHT_1


title: YBX1-IP_DHT_3


title: tφ, enriched

value: enriched for primary RNAs


title: sample_42_imnm

source_name: muscle

tag: tissue

tag: diagnosis


title: sample_47_ibm

value: myositis (IBM)


title: YBX1-IP_CSS_4

description:
RNA co-immunoprecipitated with YB-1 antibody
RNA bound in YB-1 containing RNP granules was co-immunoprecipitated from cells grown in androgen deprived culture (charcoal-stripped-serum) using an N-terminal antibody against YB-1

tag: cell type


title: TT_CSS_1


title: t0, control

value: pre-infection


title: TT_CSS_2


title: Sample 4_cHi-C day5 sgLNCSOX17 rep2

data_processing:
library strategy: Capture Hi-C
cHi-C (Sample 1 - Sample 4):
Raw sequence reads of capture Hi-C (cHi-C) were mapped to the hg19 version of the human genome using BWA (v0.7.17-r1188) with parameters (mem -A 1 -B 4 -E 50 -L 0).
Mapped reads were further processed by HiCExplorer (v3.6) to remove duplicated reads and reads from dangling ends, self-circle, self-ligation and same fragments
4Cseq (Sample 5 - Sample 16):
The raw sequencing reads were trimmed by using cutadapt (--discard-untrimmed -e 0.05 -m 25) to remove primer sequences and restriction enzyme sequences. The reads without matching those sequences were removed from further analysis. The remaining reads were then mapped to the reference sequences GRCh37/hg19 by bowtie2 (default parameters). An iterative mapping procedure was performed. Specifically, the full-length reads were first mapped to genome. The unmapped reads were then cut by 5-nt from 3-prime each time until they were successfully mapped to genome. The final mapped reads were assigned to valid fragments. The fragment counts were then normalized by RPM (Reads Per Million) and smoothed by averaging the counts of the closest 5 fragments.
RNAseq (Sample 17 - Sample 40):
All RNAseq samples were pre-processed using cutadapt to remove adapter and trim low quality bases.
Reads were subsequently aligned against the human reference genome hg19 using STAR (parameter: outSAMtype BAM SortedByCoordinate --outSAMattributes Standard --outSAMstrandField intronMotif --outSAMunmapped Within --quantMode GeneCounts).
Stringtie was used for calculation of strand-specific TPMs.
ChIPseq SOX17 (Sample 41 - Sample 52):
The ChIP-seq sequencing data as well as the control input sequencing were aligned to the human reference genome (hg19) using BWA mem using the default parameter.
GATK was used to obtain alignment metrics and remove duplicates.
Peaks were called using the MACS2 (2.1.2_dev) peakcall function using default parameters.
Oxford Nanopore cDNA seq (Sample 53):
Oxford Nanopore Technologies derived runs were processed using the Nanopype pipeline (v1.1.0) .
The basecaller Guppy (v4.0.11) was used with the r9.4.1 high-accuracy configuration. Quality filtering was disabled for any basecalling.
Base-called reads were aligned against the human reference genome hg19 using minimap2 (v2.10) with the Oxford Nanopore Technologies parameter preset for spliced alignments (-ax splice -uf -k14). Only unique alignments (-F 2304) are reported.
Genome_build: hg19
Supplementary_files_format_and_content: h5 of contact counts
Supplementary_files_format_and_content: bedGraph of contact RPM
Supplementary_files_format_and_content: tsv of TPM values
Supplementary_files_format_and_content: bigWig and BED of signal and peaks
Supplementary_files_format_and_content: BAM of read alignment

source_name: Capture Hi-C seq of day5 endoderm derived CRISPRi cells expressing sgLNCSOX17 gRNA

extract_protocol: cHi-C libraries were prepared from CRISPRi sgCtrl or sgLNCSOX17 EN cells. 5 x 106 ZIP13K2-derived EN cells were harvested and washed with ice cold DPBS. Cell lysis, NlaIII (NEB, R0125) digestion and proximity-ligation was performed according to the Franke et al. protocol8 with minor changes. Adaptors were added to DNA fragments and amplified according to Agilent Technologies instructions for Illumina sequencing. The library was hybridized to the custom-designed SureSelect probes (Agilent Technologies, 5190-4806 / 3253271) (s. probe list in Suppl. Table 3) and indexed for sequencing of 200 M fragments /sample (100 bp paired-end) following the Agilent instructions. Capture Hi-C experiments were performed as biological duplicates.

value: ZIP13K2 - hiPSCs

value: Enriched fragmented gDNA


title: sample_41_imnm

value: muscle


title: Sample 53_Oxford Nanopore cDNA seq day5

data_processing:
library strategy: cDNA library sequencing
cHi-C (Sample 1 - Sample 4):
Raw sequence reads of capture Hi-C (cHi-C) were mapped to the hg19 version of the human genome using BWA (v0.7.17-r1188) with parameters (mem -A 1 -B 4 -E 50 -L 0).
Mapped reads were further processed by HiCExplorer (v3.6) to remove duplicated reads and reads from dangling ends, self-circle, self-ligation and same fragments
4Cseq (Sample 5 - Sample 16):
The raw sequencing reads were trimmed by using cutadapt (--discard-untrimmed -e 0.05 -m 25) to remove primer sequences and restriction enzyme sequences. The reads without matching those sequences were removed from further analysis. The remaining reads were then mapped to the reference sequences GRCh37/hg19 by bowtie2 (default parameters). An iterative mapping procedure was performed. Specifically, the full-length reads were first mapped to genome. The unmapped reads were then cut by 5-nt from 3-prime each time until they were successfully mapped to genome. The final mapped reads were assigned to valid fragments. The fragment counts were then normalized by RPM (Reads Per Million) and smoothed by averaging the counts of the closest 5 fragments.
RNAseq (Sample 17 - Sample 40):
All RNAseq samples were pre-processed using cutadapt to remove adapter and trim low quality bases.
Reads were subsequently aligned against the human reference genome hg19 using STAR (parameter: outSAMtype BAM SortedByCoordinate --outSAMattributes Standard --outSAMstrandField intronMotif --outSAMunmapped Within --quantMode GeneCounts).
Stringtie was used for calculation of strand-specific TPMs.
ChIPseq SOX17 (Sample 41 - Sample 52):
The ChIP-seq sequencing data as well as the control input sequencing were aligned to the human reference genome (hg19) using BWA mem using the default parameter.
GATK was used to obtain alignment metrics and remove duplicates.
Peaks were called using the MACS2 (2.1.2_dev) peakcall function using default parameters.
Oxford Nanopore cDNA seq (Sample 53):
Oxford Nanopore Technologies derived runs were processed using the Nanopype pipeline (v1.1.0) .
The basecaller Guppy (v4.0.11) was used with the r9.4.1 high-accuracy configuration. Quality filtering was disabled for any basecalling.
Base-called reads were aligned against the human reference genome hg19 using minimap2 (v2.10) with the Oxford Nanopore Technologies parameter preset for spliced alignments (-ax splice -uf -k14). Only unique alignments (-F 2304) are reported.
Genome_build: hg19
Supplementary_files_format_and_content: h5 of contact counts
Supplementary_files_format_and_content: bedGraph of contact RPM
Supplementary_files_format_and_content: tsv of TPM values
Supplementary_files_format_and_content: bigWig and BED of signal and peaks
Supplementary_files_format_and_content: BAM of read alignment

source_name: Oxford Nanopore cDNA long reads sequencing of day5 endoderm cells

extract_protocol: Isolation of poly(A)-enriched mRNA was performed using the Dynabeads mRNA DIRECT purification kit (Thermo Fisher Scientific, 61011) according to the manufacturer’s instruction with minor modifications. ZIP13K2-derived EN cells were washed once with DPBS and dissociated with Accutase for 15 min at 37°C, 5% CO2. Enzymatic reaction was quenched by adding mTeSR1 and cells were counted using the Countess II automated cell-counter. A total of 4 x 106 viable cells were centrifuged for 5 min at 4°C, 300 x g. The supernatant was discarded and cells were washed with 1 ml of ice-cold DPBS and centrifuged as described above. The supernatant was completely removed and the cell pellet was carefully resuspended in 1,25 ml Lysis/Binding buffer. In order to reduce viscosity resulting from released genomic DNA, the samples were passed through a 21 gauge needle (Becton Dickinson, 304432) for five times and subsequently added to the pre-washed Oligo(dT)25 beads. Hybridization of the beads/mRNA complex was carried out for 10 min on a Mini Rotator (Grant-bio) and vials were placed on a DynaMag2 magnet (Thermo Fisher Scientific, 12321D) until the beads were fully immobilized. The DNA containing supernatant was removed and the beads were resuspended twice with 2 ml of Buffer A following a second wash step with two times 1 ml of Buffer B. Purified RNA was eluted with 10 µl of pre-heated Elution Buffer (10 mM Tris-HCl pH 7,5) for 5 min at 80°C and quantified with a Qubit Fluorometer (Thermo Fisher Scientific) using the RNA HS Assay Kit (Thermo Fisher Scientific, Q32852). Eluted RNA samples were immediately used for preparation of Nanopore sequencing libraries or kept at -80°C. Preparation of RNA sequencing libraries was performed following the manufacturer’s instructions (ONT, SQK-PCS109) with minor modifications. Briefly, 50 ng of freshly prepared poly(A)-enriched mRNA was subjected to reverse transcription and strand-switching reaction. A total of four PCR reactions, each containing 5 µl of reverse transcribed cDNA, was used for the attachment of rapid primers (cPRM). Sufficient amplification of long cDNA molecules was enabled by setting the PCR extension time to 19 min and a total of 12 x cycles were used for amplification. Samples were treated with 1 µl of Exonuclease I (New England Biolabs, M0293S) and subsequently pooled for SPRI bead cleanup. Wash steps were performed using 80% ethanol solution and beads were eluted in 60 µl of 50°C pre-heated nuclease-free water. Samples were then incubated for additional 20 min at 50°C. Eluted DNA was combined with 5 µl adapter mix (AMX), 25 µl ligation buffer (LNB) from ONTs ligation sequencing kit (ONT, SQK-LSK109) and 10 µl of NEBNext Quick T4 DNA Ligase (New England Biolabs, E6056S). Ligation mix was incubated at RT for 30 min. Removal of short DNA fragments was achieved by adding 40 µl of Agencourt AMPure XP beads (Beckmann Coulter, A63881) combined with 2 wash steps with 250 µl of long fragment buffer (LFB) included in ONTs ligation sequencing kit. The final library was eluted with 13 µl elution buffer (EB) for 20 min at 48°C and DNA concentration was quantified using the Qubit dsDNA BR assay kit (Thermo Fisher Scientific, Q32850). A total of 400 ng was carefully mixed with 37,5 µl sequencing buffer (SQB), 25,5 µl of loading beads (LB) and loaded onto a primed MinION flow cell (ONT, R9.4.1 FLO-MIN106).


title: TT_DHT_2


title: TT_CSS_3


title: t0, enriched


title: Sample 3_cHi-C day5 sgLNCSOX17 rep1


title: sample_40_imnm


title: sample_39_imnm


title: Sample 2_cHi-C day5 sgCtrl rep2

source_name: Capture Hi-C seq of day5 endoderm derived CRISPRi cells expressing sgCtrl gRNA


title: menF/ubiC KO adapted 4, rep 1

city: La Jolla

first: Cameron

last: Lamoureux

state: CA

address: 9500 Gilman Drive

department: Bioengineering

institute: University of California San Diego

description:
quinone__menFubiC_ale4__1
quinone_log_tpm.csv
quinone_counts.csv

data_processing:
Raw read trimming was performed with Trim Galore using the default options, followed by FastQC on the trimmed reads.
Reads were aligned to the E. coli K-12 MG1655 reference genome (NC_000913.3) using bowtie with the following optional arguments: -X 1000, -3 3, -n 2
Read direction was inferred with RSEQC.
Read counts were generated with featureCounts with the following optional arguments: -p -B -C -P --fracOverlap 0.5
Quality control metrics were assembled with MultiQC and the final expression was reported in units of log2-transformed transcripts per million for each gene.
Assembly: NC_000913.3
Supplementary files format and content: quinone_log_tpm.csv contains log2[TPM] values for all samples and genes.
Supplementary files format and content: quinone_counts.csv contains raw read counts as computed by featureCounts for all samples and genes.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: GMOS menF/ubiC KO adapted

extract_protocol:
3 ml of cell broth (at an A600 ≈ 0.6) was immediately added to two volumes of Qiagen RNA-protect Bacteria Reagent (6 ml), vortexed for 5 s, incubated at room temperature for 5 min and immediately centrifuged for 10 min at 17,500 r.p.m. The supernatant was decanted, and the cell pellet was stored at −80 °C. Cell pellets were thawed and incubated with Ready-Lyse Lysozyme, SuperaseIn, protease K and 20% SDS for 20 min at 37 °C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase treatment was performed for 30 min at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA nano chip on a bioanalyser. The ribosomal RNA was removed using an Illumina Ribo-Zero rRNA removal kit for Gram-negative bacteria.
A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around 300 bp

value: GMOS menF/ubiC KO adapted

tag: culture type

value: batch


title: Sample 1_cHi-C day5 sgCtrl rep1


title: sample_38_imnm

value: myositis (IMNM)


title: menF/ubiC KO adapted 3, rep 2

description:
quinone__menFubiC_ale3__2
quinone_log_tpm.csv
quinone_counts.csv


title: sample_37_imnm


title: menF/ubiC KO adapted 3, rep 1

description:
quinone__menFubiC_ale3__1
quinone_log_tpm.csv
quinone_counts.csv


title: menF/ubiC KO adapted 4, rep 2

description:
quinone__menFubiC_ale4__2
quinone_log_tpm.csv
quinone_counts.csv


title: YBX1-IP_CSS_2

value: LNCaP


title: sample_36_imnm


title: YBX1-IP_CSS_1

value: Prostate cancer cell line


title: YBX1-IP_CSS_3

value: CSS


title: menF/ubiC KO adapted 2, rep 2

description:
quinone__menFubiC_ale2__2
quinone_log_tpm.csv
quinone_counts.csv


title: sample_43_imnm


title: sample_34_imnm


title: sample_35_imnm


title: menF/ubiC KO adapted 2, rep 1

description:
quinone__menFubiC_ale2__1
quinone_log_tpm.csv
quinone_counts.csv


title: menF/ubiC KO adapted 1, rep 2

description:
quinone__menFubiC_ale1__2
quinone_log_tpm.csv
quinone_counts.csv


title: MITF_mutant_IgG_CnR_rep2

city: Iowa City

first: Colin

last: Kenny

state: Iowa

address: 51 Newton Road 100 Bowen Science Building Iowa

department: Anatomy and Cell Biology

institute: University of Iowa

description: Paired 2x150bp fastq

data_processing:
Library strategy: CUT&RUN
Paired-end FastQ files were downloaded from the sequencing facility’s website and processed through FastQC  (Galaxy Version 0.72+galaxy1) for quality control
Reads were trimmed to remove adaptor sequences using Trim Galore (Galaxy Version 0.6.3)
Bowtie2 (Galaxy Version 2.3.4.3+ galaxy 0) was used to map the reads against the hg19 genome assembly. The --very-sensitive-local parameter was applied. Any reads not considered the primary alignment or without mapped mate were excluded by using samtools (version 1.3.1).
For generation of BigWig files the deepTools package (version 3.3.0) was used. With the help of the ‘bamCompare’ command the controls IgG and were subtracted from the CUT&RUN tracks. The resulting BigWig files were normalised using the RPKM option. Other options applied were ‘--binSize 50’  and ‘--centerReads’ for highest possible resolution and sharper signals.
Genome_build: Hg19
Supplementary_files_format_and_content: BigWig files representing CUT&RUN-seq for anti-MITF and anti-TFAP2a in SkMel28 WT and mutant cells lines

growth_protocol: SkMel28 cell lines were cultured in RPMI media containing 10% FBS and 1% PS. Cells were maintained in log-phase growth (approximately 80% confluent) and media changed every 24 hrs

extract_protocol: CUT&RUN libraries were prepared using the KAPA Hyper Prep Kit (Roche). Quality control post-library amplification was conducted using the 2100 Bioanalyzer for fragment analysis. Libraries were pooled to equimolar concentrations and sequenced with paired-end 150 bp reads on an Illumina NovaSeq 6000 instrument.

value: Melanoma cell

value: MITF mutant


title: sample_33_imnm


title: TFAP2a;TFAP2c mutant_clone2_IgG_CnR_rep2

description: Paired 2x150bp fastq

value: TFAP2a;TFAP2c mutant


title: MITF_mutant_IgG_CnR_rep1

description: Paired 2x150bp fastq


title: TFAP2a;TFAP2c mutant_clone1_IgG_CnR_rep2

description: Paired 2x150bp fastq


title: Sample 17_RNAseq day0 sgCtrl rep1

description: processed data file: TPMs_D0.bed


title: menF/ubiC KO adapted 1, rep 1

description:
quinone__menFubiC_ale1__1
quinone_log_tpm.csv
quinone_counts.csv


title: DHT_4

description: Cells were seeded at a density of 6,000 cells/cm2 into RPMI+5% FBS and cultured for 72 hrs, followed by 48 hrs in RPMI+5% CSS (charcoal stripped serum) before treatment with 10 nM Dihydrotestosterone (DHT, dissolved in EtOH) in fresh RPMI+5% CSS for 48 hrs.

value: DHT


title: TFAP2a;TFAP2c mutant_clone2_IgG_CnR_rep1

description: Paired 2x150bp fastq


title: DHT_1


title: TFAP2a;TFAP2c mutant_clone1_IgG_CnR_rep1

description: Paired 2x150bp fastq


title: sample_32_imnm


title: CSS_4

description: Cells were seeded at a density of 6,000 cells/cm2 into RPMI+5% FBS and cultured for 72 hrs, followed by 48 hrs in RPMI+5% CSS (charcoal stripped serum) before control vehicle treatment with 0.02% EtOH for 48 hrs.


title: DHT_2


title: DHT_3


title: menF/ubiC KO, rep 2

description:
quinone__delmenFubiC__2
quinone_log_tpm.csv
quinone_counts.csv

source_name: GMOS menF/ubiC KO

value: GMOS menF/ubiC KO


title: CSS_3


title: menF/ubiC KO, rep 1

description:
quinone__delmenFubiC__1
quinone_log_tpm.csv
quinone_counts.csv


title: sample_31_imnm


title: scRNA KO-LEENE-1

city: Duarte

first: Zhen

address: 1500 E Duarte Rd

department: DMRI

institute: City of Hope

description: Single-cell RNA sequencing assay

data_processing:
10X Genomics cellranger (v3.1) was used to process sequencing data produced from Chromium Single Cell Gene Expression assay
Assembly: hg38
Supplementary files format and content: Three processed data files per each sample: a matrix file (.mtx format) with UMI counts per each gene (rows) and single cell (columns); genes list (.tsv format) with the list of genes (features) detected; cell barcodes list (.tsv format) with the list of barcodes of the single cells in the sample.

source_name: KO mice subjected to Hindlimb ischemia (HLI) as day 0. On Day 1 and Day 4, Ad-LEENE intra-muscle injection was performed. Muscle was harvested after one week and EC was enriched by using CD144 beads.

growth_protocol: Mice fed with chow diet

extract_protocol:
Single-cell suspension was prepared by using the 10XGenomics Chromium Controller
10X Genomics Single Cell 3' v3.1 gene expression

treatment_protocol: Mice with HLI for one week were subjected to Ad-GFP or Ad-LEENE intra-muscle injection twice a week.

value: CD144-enriched cells

tag: assay

value: scRNA-seq


title: scRNA KO-GFP-2

description: Single-cell RNA sequencing assay

source_name: KO mice subjected to Hindlimb ischemia (HLI) as day 0. On Day 1 and Day 4, Ad-GFP intra-muscle injection was performed. Muscle was harvested after one week and EC was enriched by using CD144 beads.


title: sample_30_imnm


title: menF KO adapted 4, rep 2

description:
quinone__menF_ale8__2
quinone_log_tpm.csv
quinone_counts.csv

source_name: GMOS menF KO, adapted

tag: strain

value: GMOS menF KO, adapted


title: sample_29_imnm


title: scRNA KO-GFP-1

description: Single-cell RNA sequencing assay


title: AC_null_clone2_MITF_CnR_rep2

description: Paired 2x150bp fastq

tag: genotype


title: AC_null_clone1_MITF_CnR_rep1

description: Paired 2x150bp fastq


title: sample_28_imnm


title: CSS_2


title: CSS_1


title: AC_null_clone2_MITF_CnR_rep1

description: Paired 2x150bp fastq


title: FBS_2

description: Cells were seeded at a density of 6,000 cells/cm2 into RPMI+5% FBS and cultured for 72 hrs.

value: FBS


title: AC_null_clone1_MITF_CnR_rep2

description: Paired 2x150bp fastq


title: FBS_1


title: KO-LEENE-2

description: polyA RNA enriched

data_processing:
Illumina bcl2fastq version 2.18 used for base calling
Reads were aligned to the mm10 genome assembly using STAR (2.5.4b) with parameter '--sjdbGTFfile'
featureCounts from Subread package (2.0.0) was used to count the number of uniquely mapped reads over exons (-t) per each gene. Strand specific parameter (-s) set to 0
Assembly: mm10
Supplementary files format and content: The processed counts.txt file is a tab-delimited table which includes annotation columns (‘Geneid’, ‘Chr’, ‘Start’, ‘End’, ‘Strand’ and ‘Length’) and data columns (eg. read counts for genes for each library).

growth_protocol: Mice fed with high-fat high-sucrose diet

extract_protocol:
CD144-enriched cells were subjected to reverse transcription from the 10XGenomics 3' gene expression assay without the Gel bead-in-emulsion step
The libraries were constructed using the 10XGenomics 3' gene expression kit (v3.1) following the user manual

treatment_protocol: Mice subjected to HLI for one week and Adenovirus Ad-GFP or Ad-LEENE intra muscle injection twice a week.

value: RNA-seq


title: menF KO adapted 3, rep 2

description:
quinone__menF_ale7__2
quinone_log_tpm.csv
quinone_counts.csv


title: menF KO adapted 4, rep 1

description:
quinone__menF_ale8__1
quinone_log_tpm.csv
quinone_counts.csv


title: FBS_3


title: KO-LEENE-1

description: polyA RNA enriched


title: menF KO adapted 3, rep 1

description:
quinone__menF_ale7__1
quinone_log_tpm.csv
quinone_counts.csv


title: sample_26_imnm

value: muscle


title: MITF_mutant_TFAP2a_CnR_rep2

description: Paired 2x150bp fastq


title: sample_27_imnm


title: KO-GFP-2

description: polyA RNA enriched


title: menF KO adapted 2, rep 2

description:
quinone__menF_ale6__2
quinone_log_tpm.csv
quinone_counts.csv


title: MITF_mutant_TFAP2a_CnR_rep1

description: Paired 2x150bp fastq


title: sample_25_imnm


title: KO-GFP-1

description: polyA RNA enriched


title: menF KO adapted 2, rep 1

description:
quinone__menF_ale6__1
quinone_log_tpm.csv
quinone_counts.csv


title: sample_24_imnm


title: scRNA KO-LEENE-2

description: Single-cell RNA sequencing assay


title: AC_null_clone2_TFAP2a_CnR_rep2

description: Paired 2x150bp fastq


title: AC_null_clone2_TFAP2a_CnR_rep1

description: Paired 2x150bp fastq


title: AC_null_clone1_TFAP2a_CnR_rep2

description: Paired 2x150bp fastq


title: menF KO adapted 1, rep 2

description:
quinone__menF_ale5__2
quinone_log_tpm.csv
quinone_counts.csv


title: menF KO adapted 1, rep 1

description:
quinone__menF_ale5__1
quinone_log_tpm.csv
quinone_counts.csv


title: AC_null_clone1_TFAP2a_CnR_rep1

description: Paired 2x150bp fastq


title: menF KO, rep 2

description:
quinone__delmenF__2
quinone_log_tpm.csv
quinone_counts.csv

source_name: GMOS menF KO

value: GMOS menF KO


title: sample_22_imnm


title: LPS_UDCA_4

first: Yu

last: Pi

state: Jiangsu

address: NO. 1 Weigang, Nanjing Agricultural University

institute: Nanjing Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Transcripts Per Million reads (TPM) were calculated. In short, firstly, divide the read counts by the length of each gene in kilobases and get the reads per kilobase (RPK). Secondly, count up all the RPK values in a sample and divide this number by 1,000,000 and get the “per million” scaling factor. Finally, divide the RPK values by the “per million” scaling factor.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Processed_data.txt Tab-delimited text file includes TMP values for each Sample of every gene with gene ID, gene name, and gene description.

source_name: macrophage cells

extract_protocol:
After 24 hr treatments and collected the J774A.1 cells. The total RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: LPS + UDCA

tag: treatment time

value: 24 hr


title: Batteriota of aortic valve from patient I9

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

country: Italy

institute: University of Florence

data_processing:
demultiplexing: from raw to demultiplexed fastq files please contact IGA Technology Services (Udine, Italy)
primer check and trimming: qiime cutadapt trim-paired  --i-demultiplexed-sequences demux-paired-end.qza --p-adapter-f  ' CCTACGGGNGGCWGCAG... GGATTAGAWACCCBNGTAGTC '   --p-adapter-r  ' GACTACNVGGGTWTCTAATCC... CTGCWGCCNCCCGTAGG ' –o-trimmed-sequences trimmed-seqs.qza --p-discard-untrimmed --verbose
quality check: qiime demux summarize  --i-data trimmed-seqs.qza --o-visualization demux.qzv
quality trimming, pair merging and ASV table creation: qiime dada2 denoise-paired --i-demultiplexed-seqs trimmed-seqs.qza --p-trim-left-f 0    --p-trim-left-r 0    –p-trunc-len-f 241 --p-trunc-len-r 201 --o-table table.qza --o-representative-sequences rep-seqs.qza --o-denoising-stats denoising-stats.qza
taxonomic assignment (RDP): qiime feature-classifier classify-consensus-vsearch --i-query rep-seqs.qza --i-reference-reads silva-138-99-seqs.qza --i-reference-taxonomy silva-138-99-tax.qza --p-perc-identity 0.99 --o-classification taxonomy_vsearch.qza --verbose
further analyses: R phyloseq package (see https://github.com/matteoramazzotti/papers)
Supplementary files format and content: otu_taxa.txt

source_name: 16S rRNA V3-V4 sequencing of a human aortic valve

growth_protocol: Sample were stored at -80°C

extract_protocol:
Genomic DNA was extracted using the DNeasy PowerSoil Pro Kit (Qiagen, Hilden, Germany)
Illumina 16S Metagenomic Sequencing Library Preparation protocol ( see https://emea.support.illumina.com)

tag: nationality

value: Italy

tag: gender

value: F

value: No

tag: age

tag: atrial fibrillation(af)

value: no

tag: smoke

tag: calcification degree

value: Severe

value: Yes


title: LPS_UDCA_3

tag: cell line

tag: treatment


title: sample_21_imnm

value: myositis (IMNM)


title: WT-GFP-2

description: polyA RNA enriched

source_name: WT mice subjected to Hindlimb ischemia (HLI) as day 0. On Day 1 and Day 4, Ad-GFP intra-muscle injection was performed. Muscle was harvested after one week and EC was enriched by using CD144 beads.


title: menF KO, rep 1

description:
quinone__delmenF__1
quinone_log_tpm.csv
quinone_counts.csv

value: batch


title: sample_20_imnm


title: LPS_UDCA_2


title: sample_19_imnm


title: Batteriota of aortic valve from patient I8

value: M

value: Mild


title: Glucose Adapted Strain, rep 2

description:
quinone__glu_ale4__2
quinone_log_tpm.csv
quinone_counts.csv

source_name: Glucose media optimized strain

value: Glucose media optimized strain


title: Batteriota of aortic valve from patient I7


title: LPS_UDCA_1


title: Glucose Adapted Strain, rep 1

description:
quinone__glu_ale4__1
quinone_log_tpm.csv
quinone_counts.csv


title: Batteriota of aortic valve from patient I6


title: sample_18_imnm


title: sample_17_imnm


title: WT-GFP-1

description: polyA RNA enriched

value: CD144-enriched cells


title: LPS_4

value: LPS


title: Batteriota of aortic valve from patient I5

value: yes


title: sample_23_imnm

value: muscle


title: LPS_3


title: LPS_2


title: sample_15_imnm


title: sample_16_imnm


title: Batteriota of aortic valve from patient I3


title: LPS_1


title: Batteriota of aortic valve from patient I4


title: sample_14_imnm


title: Bp wildtype rep 3

city: Honolulu

first: Tung

last: Hoang

state: Hi

address: 1800 East-west Road

department: School of life sciences

institute: University of Hawaii at Manoa

data_processing:
Rockhopper tool designed specifically for analysis of bacterial RNA-Seq was used for the analysis
Supplementary files format and content: .xlsx files include RPKM and normalized expression from triplicates of each strain

organism: Burkholderia pseudomallei

source_name: gram negative bacterium

growth_protocol: Bp wildtype strain1026b and sapR::T24 insertion mutant, were grown overnight in 3 ml LB broth in a 37 oC shaking incubator, subcultured to grow to mid exponential phase for RNA extraction.

extract_protocol:
Total RNA from 12 ml culture of each strain was isolated using TRIzol® reagent and purify through QIAGEN RNeasy plus mini kit according to the manufacturer’s instructions.
Sequencing was performed by the Tufts University Core Facility Genomics on the Illumina HiSeq 2500 platform after rRNA depletion and library generation.

value: gram negative bacterium

value: WT

value: overnight growth, and subculture to expoenential phase


title: SapR mutant rep 1

value: SapR mutant


title: Bp wildtype rep 2


title: Batteriota of aortic valve from patient I1

value: Italy

value: No


title: SapR mutant rep 3


title: Batteriota of aortic valve from patient I2

value: F

value: no

value: Severe


title: SapR mutant rep 2


title: Bp wildtype rep 1


title: sample_12_imnm

extract_protocol:
Trizol
NeoPrep system according to the TruSeqM Stranded mRNA Library Prep protocol (Illumina, San Diego, CA), or with the NEBNext Poly(A) mRNA Magnetic Isolation Module and UltraTM II Directional RNA Library Prep Kit for Illumina (New England BioLabs, ref. #E7490 and #E7760).

value: myositis (IMNM)


title: Batteriota of aortic valve from patient G20

value: Germany

value: M

value: Yes


title: sample_13_imnm


title: sample_10_imnm


title: Batteriota of aortic valve from patient G18


title: sample_11_imnm


title: Batteriota of aortic valve from patient G17


title: Batteriota of aortic valve from patient G19


title: sample_9_imnm


title: Batteriota of aortic valve from patient G16


title: sample_8_imnm


title: sample_7_imnm


title: Batteriota of aortic valve from patient G15

value: Mild


title: sample_6_imnm


title: Batteriota of aortic valve from patient G14


title: Batteriota of aortic valve from patient G13


title: sample_5_imnm


title: Batteriota of aortic valve from patient G12


title: sample_4_imnm


title: GMLP iCLIP iLIN28 rep 3

city: Lund

first: Phuong

last: Cao Thi Ngoc

address: BMC, B1222b, Klinikgatan 26

country: Sweden

institute: Lund University

data_processing:
The reads were classified into samples according to sample-specific barcodes. The barcodes and UMIs, 5 nucleotide unique sequence identifiers introduced during RT step, were removed and appended to the read name using UMI-tools
The sequences were trimmed the 3’ adaptor sequence (AGATCGGAAGAGCGGTTCAG) by cutadapt v2.9 (Martin M 2011) with parameter -m set to 18  and mapped to mouse genome mm10 using STAR v2.5.2b (Dobin A et al. 2013) with the following parameters: --outFilterMismatchNoverReadLmax 0.04 --outFilterMismatchNmax 999 --outFilterMultimapNmax 1 (unique mapping) or --outFilterMultimapNmax 100 (multiple mapping).
PCR duplicates were removed based on UMIs using UMI-tools.
Peak identification was performed using Piranha v1.2.1 (Uren et al., 2012) and motif analysis was performed using the MEME (Bailey TL et al. 2015). Peaks were annotated using Gencode vM25, miRBase and GtRNAdb2.
Assembly: mm10
Supplementary files format and content: bigwig files

source_name: Bone marrow cells

extract_protocol:
Cells were harvested and lysed in iCLIP lysis buffer, sonicated, then extracts were treated with RNase I and TURBO Dnase. Supernatants were incubated with pre-washed anti-FLAG magnetic beads. Lysis buffer was applied to the samples. RNA digestion was performed.
Membranes containing protein-RNA complexes were excised and incubated in PK buffer. RNA was extracted using Phase Lock Gel Heavy tube (VWR) and ethanol-precipitated. cDNA synthesis was performed using using Superscript III. cDNA was circularized using CircLigase II in the presence of 1M Betaine (Epicenter), annealed with 0.25 μM Cut oligo and digested with BamHI . Digested cDNA was ethanol-precipitated and resuspended in 21 μL of water. 1 μL of cDNA was used for PCR amplification using HF Phusion with 18-21 PCR cycles. Libraries were sequenced on an Illumina MiSeq machine, with single-end for 50 cycles using MiSeq Reagent Kit v2 (50-cycles)

value: Bone marrow cells

value: GMLP

value: LIN28B x MLL-ENL


title: sample_2_imnm

data_processing:
Demultiplexing with bcl2fastq/2.20.0.
Raw sequencing data was cleaned using fastp/0.21.0.
The abundance of each gene was generated using Salmon/1.5.2.
Quality control output was summarized using multiqc/1.11.
Assembly: hg38
Supplementary files format and content: anonym_counts_hg38.tsv: Tab-delimited text file includes the counts for each sample.

value: muscle


title: Batteriota of aortic valve from patient G11


title: Batteriota of aortic valve from patient G10

value: yes


title: sample_3_imnm


title: GMLP iCLIP iLIN28 rep 1


title: sample_1_imnm


title: GMLP WT

value: MLL-ENL


title: HREC siAPEX1 knockdown P6

city: Indianapolis

first: Kelley

last: Mark

state: Indiana

institute: Herman B Wells Center for Pediatric Research

data_processing:
Base calling and quality scoreing were performed by Real-Time Analysis (RTA) v2 in Illumina NovaSeq 6000
The bcl2fastq2 Conversion software were used to convert base call (bcl) files to FASTQ files, and trim adapter sequence at the same time.
The reads were mapped to the mouse genome using STAR (v2.7.2a) RNA-seq aligner with the following parameter: “--outSAMmapqUnique 60”.
Uniquely mapped sequencing reads were assigned to GENCODE 31 genes using featureCounts (from subread v2.0.1) with the following parameters: “-s2 –p –Q 10”.
The data was filtered using read count per million (CPM) > 0.5 in more than 3 of the samples, normalized using TMM (trimmed mean of M values) method and subjected to differential expression analysis using likelihood ratio test method in edgeR (v3.38.4).
Assembly: hg38
Supplementary files format and content: raw counts

source_name: Human retinal microvascular endothelial cell

growth_protocol: HREC were grown with EGM-2 media in a humidified 37°C incubator with 5% CO2

extract_protocol:
Total RNA was extracted from cells using the Qiagen RNeasy Mini kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using KAPA mRNA Hyperprep Kit (KK8581), Dual Index, following manufacturer's protocols.

treatment_protocol: HREC were transfected with siRNA (APEX1) along with siRNA SCR (scrambled control) for 48h. Lipofectamine RNAiMAX was the transfection reagent.

value: endothelial cell

value: primary cells, WT

value: siRNA, 48h post transfection


title: Hi-C_adipocytes

city: Wuhan

first: LI

last: LI

state: Hubei

address: 185 Donghu Road

institute: wuhan university school of basic medical sciences

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version: 0.36), low-quality reads were discarded and adaptor sequences were trimmed
The BWA package was used to map the  sequences against the human reference genome with the parameter -n 0. Mapped  reads with MAPQ quality scores ≥20 were chosen for further analysis.
We applied the ICE  method to normalize the interaction matrix for different resolutions
If a region between two adjacent boundaries was less than 400 kb, the region was  marked as a TAD boundary
The Juicer pipeline’s HiCCUPS was applied for discovery of locally enriched  peaks
Genome_build: hg19
Supplementary_files_format_and_content: A/B compartment

source_name: adipocytes

extract_protocol:
The cross-linked cells were lysed in lysis buffer,fragmentation of the genome using restriction enzymes
Hi-C libraries were prepared for sequencing using standard Illumina protocols

value: bone

value: adipocytes


title: KO CD19+CD103-, biological rep2

city: Cardiff

first: James

middle: Alexander

last: Pearson

address: Tenovus Building, School of Medicine

institute: Cardiff University

description: NLRP6-deficient Non-obese diabetic mice

hyb_protocol: GeneChip® WT Plus Reagent Kit was used for sample preparation and ss-cDNA generation (Thermo Fisher Scientific, Waltham, MA, USA).  Affymetrix GeneChip Mouse Gene 2.0 ST arrays were washed using the GeneChip® Fludics Station 450. All the reactions and hybridizations were carried out according to the manufacturer's protocol.

scan_protocol: Gene chips were scanned with the GeneChip Scanner 3000

data_processing: Data were normalized to control probes and adjusted p values were calculated.  Microarray analysis was conducted using Ingenuity Pathway Analysis (IPA) software (QIAGEN).

label: biotin

source_name: Spleen

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 150 ng total RNA

growth_protocol: cells were isolated directly ex vivo from spleen of 12-16-week old WT and NLRP6 KO mice

extract_protocol: RNA was extracted by Trizol and then cleaned up using a RNeady Mini Kit (QIAGEN)

treatment_protocol: cd103+ and cd103- b cells were FACS-sorted (gated on live, single TCRbeta-CD11b-CD11c-CD19+ cells prior to gating on CD103+ or CD103-)

value: 12-16 weeks


title: WT CD19+CD103+, biological rep2

description: NLRP6-deficient Non-obese diabetic mice


title: KO CD19+CD103+, biological rep2

description: NLRP6-deficient Non-obese diabetic mice


title: KO CD19+CD103-, biological rep1

description: Non-obese diabetic mice


title: KO CD19+CD103+, biological rep1

description: Non-obese diabetic mice


title: WT CD19+CD103-, biological rep2

description: NLRP6-deficient Non-obese diabetic mice


title: 205624640073_R08C01

type: genomic

city: Heidelberg

first: Daniel

last: Schrimpf

address: Im Neuenheimer Feld 224

department: Neuropathology

institute: University Hospital Heidelberg, Intitute of Pathology

description:
Methylation data from tumor sample
Sample 250

hyb_protocol: Illumina protocol

scan_protocol: Illumina iScan System according to the manufacturer's protocol

data_processing:
Bioconductor (Version 3.3) package minifi (Version 1.18) using function 'preprocessIllumina'  Average beta
processed data file includes: Average Beta

source_name: SLCT

label_protocol: Illumina protocol

extract_protocol: Illumina protocol

treatment_protocol: An automated extraction was done with a Maxwell system (Promega, Fitchburg, WI, USA) and the Maxwell 16 FFPE Plus LEV DNA Purification Kit according to the manufacturer’s instructions.

value: tumor

tag: tissue preparation

value: FFPE


title: 205624640073_R03C01

description:
Methylation data from tumor sample
Sample 251

tag: tissue


title: WT CD19+CD103-, biological rep1

description: Non-obese diabetic mice


title: WT CD19+CD103+, biological rep1

description: Non-obese diabetic mice


title: 205624640073_R07C01

description:
Methylation data from tumor sample
Sample 249


title: HREC siAPEX1 knockdown P5

value: Human retinal microvascular endothelial cell


title: Hi-C_osteoblasts

source_name: osteoblasts

value: osteoblasts


title: HREC siAPEX1 knockdown P4


title: 205624640073_R05C01

description:
Methylation data from tumor sample
Sample 248


title: GMLP iCLIP iLIN28 rep 2


title: HREC siAPEX1 knockdown P3


title: Hi-C_BMMSCs

source_name: BMMSCs

value: BMMSCs


title: 205624640073_R04C01

description:
Methylation data from tumor sample
Sample 247


title: HREC SCR P6


title: ATAC-Seq_BMMSCs

data_processing:
Raw data were stored in FASTQ format, including the base sequence and  corresponding quality information. Adaptor-polluted or low-quality reads were then  filtered out to get the clean data
Clean data were mapped to reference genome by Bowtie2, and visualized by IGV
The enrichment analysis of  GO term (http://geneontology.org/) or KEGG pathway (http://www.kegg.jp/) was  based on hypergeometric test with the threshold q value < 0.05, to find the significant  enrichment of detected genes.
Genome_build: hg19
Supplementary_files_format_and_content: Peaks corresponding  to the open region in genome were detected by MACS2

extract_protocol:
Around 50,000 living cells were taken for each library preparation. The cells were  lysed in 1 × Lysis Buffer to get the nuclei
TruePrep DNA Library Prep Kit for Illumina was used to construct the transposase-treated libraries


title: 205624640073_R02C01

description:
Methylation data from tumor sample
Sample 246


title: 205624640018_R08C01

description:
Methylation data from tumor sample
Sample 244


title: ATAC-Seq_adipocytes


title: HREC SCR P5


title: HREC SCR P4


title: ost-3

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version: 0.36), low-quality reads were discarded and adaptor sequences were trimmed
Reads mapped to the exon regions of each gene were counted by featurecouts (Subread-1.5.1; Bioconductor) and FPKMs were calculated. Genes differential expressed between groups were identified using DESeq2
A corrected P-value cutoff of 0.05 and Fold-change cutoff of 2 were used to judge the statistical significance of gene expression differences.
Genome_build: hg19
Supplementary_files_format_and_content: gene transfer format,used to annotate genes

extract_protocol:
mRNAs were extracted from samples using TRIzol (Invitrogen) following the methods by Chomczynski
RNA libraries were prepared for sequencing using standard Illumina protocols


title: ATAC-Seq_osteoblasts


title: 205624640073_R01C01

description:
Methylation data from tumor sample
Sample 245


title: 205624640018_R06C01

description:
Methylation data from tumor sample
Sample 243


title: HREC MOCK P6

value: lipfectamine reagents, 48h post


title: HREC MOCK P5


title: 205605880173_R01C01

description:
Methylation data from tumor sample
Sample 242


title: ost-1


title: ost-2


title: FAT-3


title: 205605880167_R03C01

description:
Methylation data from tumor sample
Sample 241


title: HREC MOCK P4


title: FAT-2


title: 3999100019_R05C02

description:
Methylation data from tumor sample
Sample 162

source_name: PINB


title: 9444375114_R04C01

description:
Methylation data from tumor sample
Sample 163


title: HREC SCR P3


title: 205624640075_R04C01

description:
Methylation data from tumor sample
Sample 240


title: 3999078080_R06C01

description:
Methylation data from tumor sample
Sample 161


title: HREC MOCK P3


title: 205624640075_R03C01

description:
Methylation data from tumor sample
Sample 239


title: FAT-1


title: 200397860068_R04C02

description:
Methylation data from tumor sample
Sample 156

value: Frozen


title: BMMSC-3


title: 9878820127_R01C01

description:
Methylation data from tumor sample
Sample 164


title: 200394970024_R04C01

description:
Methylation data from tumor sample
Sample 155


title: 205624640075_R02C01

description:
Methylation data from tumor sample
Sample 238


title: 205624640075_R01C01

description:
Methylation data from tumor sample
Sample 237


title: BMMSC-2


title: 9376538153_R02C01

description:
Methylation data from tumor sample
Sample 154


title: BMMSC-1


title: 3999100040_R01C01

description:
Methylation data from tumor sample
Sample 152


title: 8942351007_R01C01

description:
Methylation data from tumor sample
Sample 153


title: 205624640074_R05C01

description:
Methylation data from tumor sample
Sample 235


title: 3999100019_R06C02

description:
Methylation data from tumor sample
Sample 151


title: 205624630054_R07C01

description:
Methylation data from tumor sample
Sample 234


title: 3999078080_R01C02

description:
Methylation data from tumor sample
Sample 150


title: 205624630054_R04C01

description:
Methylation data from tumor sample
Sample 233


title: GG63dd Total RNA human primary ery Rep 1 (RNASeq)

city: Philadelphia

first: Gerd

last: Blobel

state: Pennsylvania

address: 3615 Civic Center Blvd., Abramson Research Center 316H

department: Hematology

institute: Children's Hospital of Philadelphia

data_processing:
The sequence reads were processed using the ENCODE3 long RNA-seq pipeline (https://www.encodeproject.org/pipelines/ENCPL002LPE/).
Gene set Gencode v29 was used for mapping the reads to the human genome (hg38 assembly) using STAR, followed by RSEM for gene quantifications.
Assembly: hg38 assembly
Supplementary files format and content: TSV Files represent expected_count, TPM, FPKM values.

source_name: Primary CD34+ cell culture

growth_protocol: Peripheral blood mononuclear cells were obtained from the University of Pennsylvania Human Immunology Core (Philadelphia, PA). CD34+ cells were purified by using a MACS MicroBead kit (Miltenyi) and cultured in a 3-phase in vitro culture. For Phase I medium, IMDM was supplemented with 100 ng/mL human SCF, 1 ng/mL IL-3, 3 units/mL erythropoietin, 2% penicillin/streptomycin, 200 μg/mL holo-transferrin, 10 μg/ml insulin, 5% human A/B plasma and 10 μg/mL heparin. For Phase II medium, the IL-3 was withdrawn after 9 days of culture. For Phase III medium, the cells were cultured with IMDM supplemented with 3 units/mL erythropoietin, 2% penicillin/streptomycin, 1 mg/mL holo-transferrin, 10 μg/ml insulin, 5% human A/B plasma and 10 μg/mL heparin. Cells were maintained in Phase I from the day of collection until day 8, at which time cells were spin-infected and transitioned to Phase II media. On day 13 of culture, cells were transitioned to Phase III media

extract_protocol:
RNA samples were harvested in TRIzol (ThermoFisher Scientific) and purified with the RNeasy Mini kit (Qiagen). For RNA-Seq, approximately 200 ng of RNA was then depleted for rRNA using the Ribo-Zero removal reagents and protocol from the ScriptSeq Complete kit (Illumina Cat # BHMR1224), followed by purification using the RNeasy MinElute Clean Up kit (Qiagen Cat # 74202).
Sequencing libraries were then constructed from depleted RNA using the TruSeq Stranded Total RNA kit (Illumina Cat # 20020598) and PCR-amplified for 13 cycles. The size and quality of each library were then evaluated by Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA), and quantified using qPCR. Libraries were sequenced in paired-end mode on the NextSeq 500 to generate 2 x 76 bp reads using Illumina-supplied kits as appropriate.

treatment_protocol: Lentiviral stocks were generated by co-transfection of the previously described gene transfer plasmids (pcl20-ANK-GFP, pcl20-ANK-GG23DD-IRES-GFP, pcl20-ANK-GG38DD-IRES-GFP, pcl20-ANK-GG63DD-IRES-GFP, pcl20-ANK-GG52DD-IRES-GFP, or the previously described pcl20-ANK-GG1DD-IRES-GFP), together with the envelope plasmid (VSV-G), the packaging plasmid (pMDLg/p RRE), and the pRSV-REV plasmid into 293T cells, and viral supernatant harvested and concentrated by ultracentrifugation. The ZF proteins tested in the present study bind to sequences located at -443 bp (GG23), -182 bp (GG38), -114 bp (GG63 and GG1) and -45 bp (GG52) with respect to the HBG1/2 transcription start sites, following previously established design principles, including target sites located in accessible chromatin as well as at sites at which there are no known transcription factor binding sites. Specifically, the tested ZF constructs target the following sequences located in the gamma-globin promoter region: GG23, TTAGGCATAGGTCCAGGATT; GG38, TTGAGATAGTGTGGGGAAGG; GG63 and GG1, GGTCAAGGCAAGGCTGGCCA; GG52, AGCCGCCGGCCCCTGGCCTC.

value: Three-phase in vitro culture of CD34+ primay human cells

tag: day of isolation

value: Day 13 of culture

tag: zf vector


title: GG52dd Total RNA human primary ery Rep 2 (RNASeq)

tag: cell type


title: GG52dd Total RNA human primary ery Rep 1 (RNASeq)


title: GG38dd Total RNA human primary ery Rep 2 (RNASeq)


title: 205624630054_R01C01

description:
Methylation data from tumor sample
Sample 232


title: GG38dd Total RNA human primary ery Rep 1 (RNASeq)


title: 205624630010_R05C01

description:
Methylation data from tumor sample
Sample 230


title: GG1dd Total RNA human primary ery Rep 2 (RNASeq)


title: 200394970115_R03C01

description:
Methylation data from tumor sample
Sample 139


title: 200394970046_R01C02

description:
Methylation data from tumor sample
Sample 138


title: 205624630010_R01C01

description:
Methylation data from tumor sample
Sample 229


title: 200397860056_R06C01

description:
Methylation data from tumor sample
Sample 140


title: 200394970034_R05C01

description:
Methylation data from tumor sample
Sample 137


title: GG1dd Total RNA human primary ery Rep 1 (RNASeq)


title: 205605880173_R03C01

description:
Methylation data from tumor sample
Sample 228


title: 205605880168_R08C01

description:
Methylation data from tumor sample
Sample 227


title: GFP only Total RNA human primary ery Rep 2 (RNASeq)

value: GFP only


title: GG63dd Total RNA human primary ery Rep 2 (RNASeq)


title: 205624640074_R08C01

description:
Methylation data from tumor sample
Sample 236


title: GFP only Total RNA human primary ery Rep 1 (RNASeq)


title: 200394970025_R05C01

description:
Methylation data from tumor sample
Sample 135


title: 200394970026_R06C01

description:
Methylation data from tumor sample
Sample 136


title: 205605880168_R07C01

description:
Methylation data from tumor sample
Sample 226


title: 200394970024_R05C01

description:
Methylation data from tumor sample
Sample 134


title: 205605880168_R05C01

description:
Methylation data from tumor sample
Sample 225


title: duxa_2

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

institute: Max Planck Institute for Heart and Lung Research

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q20 in a window of 20 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl human genome version hg38 (Ensembl release 104) with STAR 2.7.10a (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Aligned reads were filtered to remove: duplicates with Picard 2.27.1 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), spliced, multi-mapping, ribosomal, or mitochondrial reads.
Peak calling was performed with Macs version 3.0.0a6 with FDR < 0.1 (Zhang et al., Model-based Analysis of ChIP-Seq). Peaks overlapping ENCODE blacklisted regions (known misassemblies, satellite repeats) were excluded.
Peaks were unified to represent a common set of regions for all samples and counts were produced with bigWigAverageOverBed (UCSC Toolkit).
The raw count matrix was normalized with DESeq2 version 1.30.1 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
Peaks were annotated with the gene + promoter (TSS +- 5000 nt) with the largest overlap based on Ensembl release 104.
Assembly: hg38

extract_protocol:
DNA was purified using the NucleoSpin Gel and PCR Clean-up kit (Macherey-Nagel, 740609)
2-3ng of DNA was used as input for TruSeq ChIP Library Preparation Kit (Illumina) with following modifications. Instead of gel-based size selection before final PCR step, libraries were size selected by SPRI-bead based approach after final PCR with 18 cycles. In detail, samples were 1st cleaned up by 1x bead:DNA ratio to eliminate residuals from PCR reaction, followed by 2-sided-bead cleanup step with initially 0.6x bead:DNA ratio to exclude larger fragments. Supernatant was transferred to new tube and incubated with additional beads in 0.2x bead:DNA ratio for eliminating smaller fragments, like adapter and primer dimers. Bound DNA samples were washed with 80% ethanol, dried and resupended in TE buffer. Library integrity was verified with LabChip Gx Touch 24 (Perkin Elmer). Sequencing was performed on the NextSeq500 instrument (Illumina) using v2 chemistry with 1x75bp single end setup.

tag: transfected with

value: plasmid encoding for a V5-epitope tagged DUXA

value: WT

tag: chip antibody

value: V5 (Abcam ab9116)


title: 200397860069_R01C01

description:
Methylation data from tumor sample
Sample 141


title: 205624630011_R01C01

description:
Methylation data from tumor sample
Sample 231


title: 205605880168_R01C01

description:
Methylation data from tumor sample
Sample 224


title: 101178130116_R04C02

description:
Methylation data from tumor sample
Sample 133


title: 205605880167_R05C01

description:
Methylation data from tumor sample
Sample 223


title: 9878820122_R02C01

description:
Methylation data from tumor sample
Sample 117

source_name: MEPL


title: duxa_1_input

tag: genotype

value: none (input)


title: duxa_1


title: 205624640074_R07C01

description:
Methylation data from tumor sample
Sample 222


title: dux4_2

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q20 in a window of 20 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl human genome version hg38 (Ensembl release 104) with STAR 2.7.10a (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Aligned reads were filtered to remove: duplicates with Picard 2.27.1 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), spliced, multi-mapping, ribosomal, or mitochondrial reads.
Peak calling was performed with Macs version 3.0.0a6 with FDR < 0.1 including input samples (Zhang et al., Model-based Analysis of ChIP-Seq).
Peaks overlapping ENCODE blacklisted regions (known misassemblies, satellite repeats) were excluded.
Peaks were unified to represent a common set of regions for all samples and counts were produced with bigWigAverageOverBed (UCSC Toolkit).
The raw count matrix was normalized with DESeq2 version 1.30.1 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
Peaks were annotated with the gene + promoter (TSS +- 5000 nt) with the largest overlap based on Ensembl release 104.
Assembly: hg38

value: plasmid encoding for a V5-epitope tagged DUX4


title: dux4_1


title: 205624640074_R06C01

description:
Methylation data from tumor sample
Sample 221


title: 205624640074_R01C01

description:
Methylation data from tumor sample
Sample 220


title: 9878820122_R04C01

description:
Methylation data from tumor sample
Sample 114


title: 205624640073_R06C01

description:
Methylation data from tumor sample
Sample 219


title: 9980102032_R06C01

description:
Methylation data from tumor sample
Sample 113


title: 9878820122_R06C01

description:
Methylation data from tumor sample
Sample 115


title: 9878820122_R03C01

description:
Methylation data from tumor sample
Sample 110


title: 205605880168_R03C01

description:
Methylation data from tumor sample
Sample 217


title: 205624640074_R04C01

description:
Methylation data from tumor sample
Sample 216


title: 205624630054_R06C01

description:
Methylation data from tumor sample
Sample 214


title: 205624630011_R03C01

description:
Methylation data from tumor sample
Sample 213


title: 9878820122_R05C01

description:
Methylation data from tumor sample
Sample 108


title: 205605880168_R04C01

description:
Methylation data from tumor sample
Sample 215


title: 9878820121_R01C02

description:
Methylation data from tumor sample
Sample 109


title: 205624630010_R08C01

description:
Methylation data from tumor sample
Sample 212


title: 9878820121_R03C02

description:
Methylation data from tumor sample
Sample 106


title: 205624630010_R07C01

description:
Methylation data from tumor sample
Sample 211


title: 9878820121_R04C01

description:
Methylation data from tumor sample
Sample 116


title: 205624630010_R02C01

description:
Methylation data from tumor sample
Sample 209


title: 205624640018_R07C01

description:
Methylation data from tumor sample
Sample 218


title: 9980102032_R02C02

description:
Methylation data from tumor sample
Sample 112


title: Mouse liver, metastatic, conventionnal scRNA-seq, replicate 1, WTA

city: Zürich

first: Kristina

last: Handler

address: Winterthurerstrasse

department: Institute of Experimental Immunology

country: Switzerland

institute: University of Zürich

data_processing:
zUMIs (v. 2.9.4)
Assembly: GRCm38 vM25 genecode
Supplementary files format and content: 3 UMI and 3 read count tables; gene-wise counts for exon, intron and exon+intron (.rds format)

source_name: Liver

extract_protocol:
in-vitro digestion
BD Rhapsody: WTA kit

value: Liver cells

value: Liver

tag: strain

value: intrasplenic injection with mouse colon cancer organoids

tag: disease state

value: metastatic liver

tag: termination

value: 2 weeks after injection

value: 8-10 weeks old


title: 9980102032_R01C02

description:
Methylation data from tumor sample
Sample 111

value: tumor

value: FFPE


title: dux4_1_input


title: APOE_H1

city: Nanjing

first: Dijun

last: Chen

address: Xianlin

department: Life Sciences

institute: Nanjing University

data_processing:
Illumina Casava1.7 software used for basecalling.
sequenced reads were trimmed to remove adapter and low quality reads with Tim Galore v 0.6.6 program
clean reads were mapped to the human genome using STAR
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Brain

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

value: Brain

value: KA-induced TLE model

value: Treated with KA and APOE


title: 205624630010_R03C01

description:
Methylation data from tumor sample
Sample 210


title: dux4_2_input


title: APOE_H2


title: 205605880173_R04C01

description:
Methylation data from tumor sample
Sample 205


title: 205605880173_R06C01

description:
Methylation data from tumor sample
Sample 207


title: 205605880173_R02C01

description:
Methylation data from tumor sample
Sample 204


title: APOE_H3


title: APOE_L2


title: APOE_L3


title: 205605880168_R06C01

description:
Methylation data from tumor sample
Sample 203


title: KA_H3

value: Treated with KA


title: 205605880168_R02C01

description:
Methylation data from tumor sample
Sample 202


title: 205605880167_R08C01

description:
Methylation data from tumor sample
Sample 201


title: 9878820121_R05C02

description:
Methylation data from tumor sample
Sample 107


title: Mouse liver, metastatic, conventionnal scRNA-seq, replicate 2, WTA

tag: age


title: 205605880167_R07C01

description:
Methylation data from tumor sample
Sample 200


title: KA_H1


title: KA_L3


title: 205605880167_R06C01

description:
Methylation data from tumor sample
Sample 199


title: 205605880173_R08C01

description:
Methylation data from tumor sample
Sample 208


title: 205605880173_R05C01

description:
Methylation data from tumor sample
Sample 206


title: KA_L2


title: 205624630054_R03C01

description:
Methylation data from tumor sample
Sample 198


title: KA_L1


title: 205624630054_R02C01

description:
Methylation data from tumor sample
Sample 197


title: CTRL_L3

value: Untreated


title: 205624630033_R08C01

description:
Methylation data from tumor sample
Sample 196


title: CTRL_L2


title: KA_H2


title: APOE_L1


title: 205624630033_R07C01

description:
Methylation data from tumor sample
Sample 195


title: WT rep3

first: Dominik

last: Schaack

address: Im Neuenheimer Feld 420

institute: Heidelberg University Hospital

data_processing:
Sequenced reads were depleted from ribosomal reads using SortMeRNA v2.1b and trimmed for adaptor sequences and low-quality reads by Trimmomatic v0.36. Remaining reads were then mapped to Gencode Release M17 primary assembly reference genome utilizing STAR v2.6.0c considering read strand specificity.
After conversion to sorted binary alignment format (BAM) by SAMtools v1.8.3, sample-wise count tables were generated by htseq-count v0.9.1 with the “-s yes” option set. In case technical replicates were present, count tables were summarized per sample.
Assembly: Gencode Release M17 (GRCm38.p6)
Supplementary files format and content: Tab-delimited text files include raw count values for each gene

source_name: Whole lung tissue

extract_protocol:
RNA was extracted from whole lung tissue by RNeasy mini kit (Qiagen, Venlo, Netherlands)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Whole lung tissue

value: wild type


title: CTRL_L1


title: 203293640063_R06C01

description:
Methylation data from tumor sample
Sample 192

source_name: PPB III


title: WT rep4


title: WT rep2


title: 202905570063_R07C01

description:
Methylation data from tumor sample
Sample 190

source_name: PIS DICER1


title: 202915470040_R02C01

description:
Methylation data from tumor sample
Sample 191


title: 202905570063_R04C01

description:
Methylation data from tumor sample
Sample 188