title: 4C H7 rep1

city: NEW YORK

first: Alex

last: Penev

address: 540 First Ave

institute: NYU Langone Medical Center

data_processing:
Library strategy: 4C-seq
Sequencing of libraries was performed by NYU Genome Technology on Illumina HiSeq 2500 sequencer.
Alignment was performed as in (Buenrostro et al. 2013) to the hg19 human reference genome.
Peak calling was done using macs2 using parameters described in (Corces et al. 2017).
IGV was used to visualize sequencing data tracks and bedtools was used for find regions of overlap between ATAC-seq and 4C data.
4C sequencing data was analyzed using the 4Cker software package described in (Raviram et al. 2016) using the recommended parameters.
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak ATAC-seq files, .bed 4C files

source_name: Embryonic stem cell line

growth_protocol: ARPE-19 cells were growth in culture-coated 10cm plates in Dulbecco’s Modified Eagle Medium (DMEM, Corning) supplemented with 10% fetal bovine serum (FBS, Gibco), 2 mM L-glutamine (Gibco), 100 U/ml Penicillin-Streptomycin (Gibco), and 0.1 mM MEM non-essential amino acids (Gibco). H7 cells were cultured in mTeSR Plus (STEMCELL) media supplemented with 100 U/ml Penicillin-Streptomycin (Gibco) and passaged with EDTA every 2-3 days.

extract_protocol:
Library preparation for Circular Chromosome Conformation Capture (4C) was performed as described in (van de Werken et al. 2012) with the exception of initial fixation and lysis procedure, which was adapted from (Miele et al. 2009). 1x107 ARPE or H7 ESCs were dissociated and resuspended in 5ml PBS containing 10% BCS. Cells were crosslinked by adding 5ml of 4% formaldehyde in PBS and incubating at room temperature (RT) for 10 minutes with gentle rocking. Reaction was quenched by adding 2.5ml 2.5M glycine, mixing well and incubating at RT for 5 minutes, then on ice for 15 minutes. Cells were pelleted at 800xg for 10 minutes, resuspended in 1ml of cold Lysis Buffer 1 (10mM Tris pH 8.0, 10mM NaCl, 0.2% IGE-PAL, Protease inhibitor (Roche)) and incubated on ice for 15 minutes. Cells were then dounce-homogenized on ice with a B-type pestle twice for 15 minutes with a minute rest on ice in between. Sample was pelleted at 2500xg for 5 minutes and the pellet was washed with 1x Cutsmart buffer (NEB) and pelleted again. Samples were further processed as described in (van de Werken 2012) using DpnII primary digestion and Csp6I secondary digestion.  ATAC-seq was performed on 5x10^5 ARPE and H7 cells in triplicate as described in (Buenrostro et al. 2015).
Sequencing library was prepared as described using Expand Long Template polymerase (Roche) and Illumina adaptor sequence-containing primers unique to the hTERT fragend. ATAC-seq was performed on 5x10^5 ARPE and H7 cells in triplicate as described in (Buenrostro et al. 2015).

value: embryonic stem cell


title: SI07

status: Public on Mar 04 2021

type: SRA

city: Chapel Hill

first: Jesse

last: Niehaus

state: NC

address: 116 Manning Drive, 7008B Mary Ellen Jones Building

department: Neuroscience Center

country: USA

institute: University of North Carolina at Chapel Hill

library_source: transcriptomic

data_processing:
Cells and UMIs demultiplexed, quality filtered, and poly-A trimmed using FASTQ files were converted to BAM format, tagged with cell and molecular barcodes, quality-filtered, trimmed, polyA-trimmed, and converted back to FASTQ as previously described (Macosko et al., 2015; Shekhar et al., 2016). Reads were aligned to a mouse-human hybrid genome (mm10-hg19) using STAR (Dobin et al., 2013), then sorted, merged, and exon-tagged as described (Macosko et al., 2015; Shekhar et al., 2016). Bead synthesis errors were corrected as described (Shekhar et al., 2016), and BAM files were separated into those containing mouse or human reads. UMIs were determined to be species-specific if >90% of the transcripts came from that species or considered a doublet if neither species achieved 90% specificity. UMIs were not considered if the transcript count sum (mouse+human) was less than 500. Gene expression matrices were then created using only the mouse-specific UMIs, as described (Macosko et al., 2015; Shekhar et al., 2016). Gene expression matrices were combined from multiple biological replicates; data values for one or more replicates that did not detect a given gene were assigned to zero. Processing steps utilized the Drop-seq Toolkit v1.12 where possible. Drop-seq_tools-2.3
Cells expressing fewer than 400 unique genes or whose mitochondrial transcripts exceeded 10% of total transcripts were removed. Genes were removed if they were not represented in at least 30 cells with at least 3 transcripts. We then performed two rounds of batch correction (by animal cohort and Drop-seq day) using ComBat (Johnson et al., 2007). The resulting gene expression matrix was median centered and log-transformed to generate our finalized dataset.
Clusters were established and optimized using “significant” principal components (PCs) as described previously (Loo et al., 2019; Shekhar et al., 2016). Briefly, eigenvalues were calculated from randomly permutating out dataset (n=1000). PCs with eigenvalues greater than those generated from random permutations were used for clustering (n = 60). Louvain-Jaccard clustering was performed with a silhouette score-optimized (Pearson correlation distance) nearest neighbor parameter as described previously (Loo et al., 2019; Shekhar et al., 2016). This resulted in 20 cell clusters.
To resolve cell types with more specificity, the above pipeline was performed a second time on each of the initial 20 clusters. The second clustering iteration was identical to the first with two key cluster refinement exceptions. First, a set of oligodendrocyte-related genes were removed for the second round of clustering (with the exception of the two initial clusters that were classified as oligodendrocytes) in order to remove unwanted signal caused by myelin debris. Second, clusters lacking at least one marker gene (enriched by > 1.0 log10 fold-change compared to other clusters) were merged with the next most similar cluster (Pearson correlation). This resulted in 69 clusters transcriptionally distinct clusters. After annotating each of the 69 clusters, three low-quality clusters were removed based on signs of doublets (expressing genes from two cell types), resulting in 66 final clusters.
Genome_build: mm10hg19 hybrid
Supplementary_files_format_and_content: tab-delineated .txt; gene expression matrix

molecule: total RNA

organism: Mus musculus

source_name: L1-6 mouse spinal cord

extract_protocol:
Animals were perfused with aCSF supplemented with ion channel inhibitors. Lumbar spinal cord segments were dissected and dissociated in aCSF supplemented with 2mg/mL Collagenase + 2mg/mL Protease from streptomyces griseus. A percoll gradient was used to isolate cells from debris. Cells were then methanol fixed and stored in -80 before being rehydrated for Drop-seq.
Drop-seq was carried out as described (Loo et al 2019). RNAs were captured with Chemgenes oligodT barcoded beads (Macosko2015). Reverse transcription was performed using Maxima H Minus Reverse Transcriptase (ThermoFisher; EP0751). Libraries were amplified with KAPA Hi-Fi master mix and tagged using a Nextera XT DNA sample preparation kit (N701-N707, N711, N712, N714-N726)
Single-cell RNA seq (Drop-seq); Pooled libraries

tag: spike-ins

value: Human embryonic kidney cell

tag: dropseq day

tag: cohort


title: 4C ARPE19 rep3

state: NY

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

source_name: Retinal pigment epithelial cell line

tag: cell type

value: retinal pigment epithelial cell

tag: cell line


title: 4C ARPE19 rep1


title: CRISPRi_screen_Plasmid_Lib

city: Berlin

first: Till

last: Schwämmle

state: Berlin

address: Ihnestrasse 63

department: Otto-Warburg-Laboratory

country: Germany

institute: Max Planck Institute for Molecular Genetics

data_processing:
Library strategy: CRISPR screen
Alignment and read counting was performed using MAGeCK (0.5.9.3) with options [count --norm-method control] for all samples together (Li et al. 2014, Li et al. 2015).
Statistical analysis was performed using MAGeCK (0.5.9.3) with options [mle --norm-method control --max-sgrnapergene-permutation 350] (Li et al. 2014, Li et al. 2015)
Genome_build: -
Supplementary_files_format_and_content: Char_candidate_RE.txt: Characterization of the candidatate regulatory elements including genomic location, origin, length and number of guides
Supplementary_files_format_and_content: Char_guides.txt: Characterization of the gRNA library including location, orientation and sequence
Supplementary_files_format_and_content: raw_counts.txt: Raw counts of the individual samples assessed using MAGeCK count
Supplementary_files_format_and_content: mageck_mle.txt: Statistical analysis of the REs calculated using MAGeCK mle (normalized using the NT controls)

organism: synthetic construct

source_name: Plasmid DNA

growth_protocol: TX1072 XX SP107 cells were grown on gelatin-coated flasks in serum-containing ES cell medium (DMEM (Sigma), 15% ESC-grade FBS (Gibco), 0.1mM β-mercaptoethanol, 1000 U/ml leukemia inhibitory factor (LIF, Millipore)) at a density of 3.13*10^4 cells/cm2.

extract_protocol:
The PrimeFlow RNA assay (Thermofisher) was used according to the manufacturer’s recommendations. Specifically, the assay was performed in conical 96-well plates for a total of 200 million cells per replicate with 5 million cells per well  using Xist specific probes, labelled with Alexa-Fluor647 (VB1-14258). 20 million cells were snap-frozen after the two fixation steps to be used as the Unsorted fraction.  Samples were resuspended in PrimeFlow™ RNA Storage Buffer before flow cytometry. Here, four different populations were sorted according to Xist expression. In more detail, a Xist-negative population was taken from the bottom-15% of Xist-expressing cells. Three Xist-positive populations were taken in 15%-intervals from the top Xist-expressing cells (0-15% = High, 15-30% = Medium, 30-45% = Low). Around 11-15 million cells were recovered per fraction. After sorting, the cell pellets were snap-frozen and stored at -80°C.  DNA from frozen cell pellets was isolated through phenol/chloroform extraction. Cell pellets were thawed and resuspended in 250 µl of lysis buffer (1% SDS (Thermo Fisher Scientific), 0.2 M NaCl and 5 mM DTT (Roth) in TE Buffer) and incubated overnight at 65°C. The next day 200 µg of RNAse A (Thermo Fisher Scientific) were added and the samples were incubated at 37°C for 1 h. 100 µg of Proteinase K (Sigma) were subsequently added, followed by a 1 h incubation at 50°C. Phenol/chloroform/isoamyl alcohol (Roth) was added to each sample in a 1:1 ratio, the mixture was vortexed for 1 min and subsequently centrifuged at 16,000 x g for 10 min at room temperature. The aqueous phase was transferred to a new tube, 1 ml 100% EtOH, 90 µl 5 M NaCl and 1µl Pellet Paint (Merck) was added to each sample, mixed, and incubated at -80°C for 1 h. DNA was pelleted by centrifugation for 16,000 x g for 15 min at 4°C, pellets were washed twice with 70% EtOH, air-dried and resuspended in 50 µl water.
The genomically integrated sgRNA cassette was amplified in two successive PCR reactions as described previously with minor modifications (Shalem et al. 2014). In order to ensure proper library coverage (>300x), 14.5 µg of each sample were amplified using the ReadyMix Kapa polymerase (Roche) with a total of 20 cycles and an annealing temperature of 55°C. Between 0.1-2 µg genomic DNA was amplified per 50 µl PCR reaction. In particular, in samples stained with Flow-FISH the PCR was inhibited at higher DNA concentrations such that up to 145 PCR reactions had to be performed per sample. Successful amplification was verified on a 1% agarose gel and the reactions were pooled. The PCR product was isolated and concentrated using the Zymo DNA Clean and Concentrator Kit. A second nested PCR was performed to attach sequencing adaptors and sample barcodes using 2.5-50µl of the product from the first PCR as template, with a total of 11 cycles and an annealing temperature of 55°C. Resulting amplicons were loaded on a 1% agarose gel and purified using the Nucleospin Gel and PCR clean-up kit (Macherey-Nagel). Libraries were sequenced paired-end 75bp on the NextSeq 500 platform yielding approximately 4*105 fragments per sample.

treatment_protocol: The TX SP107 mESC line, carrying an ABA-inducible dCas9-KRAB system, were passaged for two passages in Serum+LIF-containing medium before a total of 6.000.000 cells were transduced with viral supernatant of the sgRNA library (MOI = 0.3). Puromycin selection (1 ng/µl, Sigma) was started two days after transduction and kept for the rest of the experiment. At the next passage, the cells were transferred into a LIF-medium supplemented with 2i (3 μM Gsk3 inhibitor CT-99021, 1 μM MEK inhibitor PD0325901, Axon). After two more passages,d ifferentiation was induced for 2 days by 2i/LIF withdrawal in DMEM supplemented with 10% FBS and 0.1mM β-mercaptoethanol in fibronectin-coated (10 μg/ml) tissue culture plates.

tag: condition

value: Library

tag: replicate

tag: strain background

tag: assay

value: CRISPRi-Screen

value: Plasmid DNA


title: CD42 positive megakaryocytes replicate 2

city: Amsterdam

first: Monika

middle: C

last: Wolkers

address: Plesmanlaan 125

department: Hematopoiesis

country: Netherlands

institute: Sanquin Blood foundation

description:
TPM_MK42pos_2
C2MK42pos

data_processing:
The quality of raw ribo-seq reads was assessed using FastQC. Reads were trimmed for sequencing adapters using Trimmomatic version 0.39, excluding reads <25 and >35nt long. Trimmed reads were then mapped with Salmon on the human transcriptome (GRCh38 release 92) to get TPM normalized counts. Using a k-mer of 11 performed best for ribo-seq mapping to build the Salmon index. The BAM files resulting from genome (GRCh37 release 75) mapping with STAR were further processed in Ribo-seQC to assess the data quality.
Genome_build: GRCh38 realease 92 counts / GRC37 release 75 for QC
Supplementary_files_format_and_content: TPM counts of ribo-seq data

source_name: CD42 positive megakaryocytes

growth_protocol: In-vitro megakaryocyte differentiation: Megakaryocytes were cultured from human cord blood-derived CD34+ cells. Cord blood was diluted in PBS, loaded on ficoll-pague (GE Healthcare) and centrifuged 15 minutes at 400g. The white blood cell layer was collected from the ficoll gradient, washed twice in PBS+ 1mM EDTA + 0.2% HSA. CD34+ cells were purified with anti-CD34 Microbeads (Miltenyi biotec 130-046-702) and MACS LS column (Miltenyi, 130-042-401) according to manufacturer’s guidelines. Purity for CD34+ cells was >90%, as determined by flow-cytometry with anti-CD34 antibody (#581-PE; Beckman Coulter, measured on Beckman Coulter FC500). CD34+ cells were seeded at a density of 50.000 cells/well in a 12 well plate in CellgroSGM (CellGenix) supplemented with 100ng/mL human recombinant TPO and 10ng/mL IL1b.  At day 3, 1:1 Fresh media was added with an additional 10ng/mL TPO and 1ng/mL IL1b. On day 5, cells were split at a density of 100.000 cells in 6 wells plates, and fresh media with 10ng/mL TPO and 1ng/mL IL1b was added. On day 10, cells were harvested and supplemented with 100ug/mL Cycloheximide in culture medium prior to cell sorting.    Megakaryocyte selection  Cultures cells were harvested when >85% of cells were CD41a+ (CD41a-APC; clone HIP8), as determined by flow-cytometry. Cells were pelleted at 120g for 1 minute at 4ºC and washed once in ice cold buffer (PBS, 1mM EDTA, 0.2% HSA + 100ug/mL cycloheximide). Two-step selection was performed on ice with EasySep® Human PE-Positive Selection Kit (18551), using anti-human CD42b-PE (clone HIP1, BD Pharmingen, 555473) according to manufacturer’s guidelines. CD41a+ CD42b- and CD41a+ CD42b+ cell fractions were selected, washed using PBS + 100ug/mL cycloheximide, and kept on ice until further processing. Viability of the cells was >90% (7-AAD, Biolegend), and purity for CD41a+ CD42b- was >85% and CD41a+ CD42b+ was >50%, as determined by flow-cytometry. Cells were immediately used for processing.

extract_protocol:
Cell lysis and RNA isolation for ribosomal footprinting was performed according to Ignolia et al. with some adaptations. Briefly, CD42- and CD42+ selected megakaryocytes were pelleted. Cell pellets were dissolved in 150uL ice cold lysis buffer (20mM Tris pH 7.4, 250mM NaCl2, 5mM MgCl2, 0.5% Triton X-100, 1mM Dithiotreitol (DTT), 0.024U/uL Turbo DNAse (Ambion), 0.01U/uL RNAseOUT (Invitrogen) and 100g/mL Cycloheximide). The lysate was immediately used for ribosomal footprint preparation.
Samples were kept on ice for 10 minutes and regularly vortexed to fully lyse the outer membranes and release the ribosomes. Lysates were spun at 20.000g for 10min at 4ºC and supernatant was harvested to remove the remaining pelleted cell debris and nuclei. Lysates were treated with 2uL of RNAse 1 (Ambion) and incubated at 37ºC for 45 minutes. The reaction was stopped by the addition of 5uL SUPERAseIN RNAse inhibitor. Lysates were loaded on a 1M 0.150mL Sucrose cushion in 8x34 mm polycarbonate thick wall tubes and centrifuged at 120.000g for 30 minutes in a TLA-120.1 rotor in a pre-cooled 4ºC table top ultracentrifuge. The pellet was resuspended using 100uL resuspension buffer (10mM Tris pH 7.0, 1% SDS and 0.01U/uL proteinase K (NEB)) for 30 minutes at 37ºC. Footprints were subsequently extracted with miRNAeasy kit according to manufacturer’s guidelines for small RNA. rRNA contamination was removed using the Ribo-Zero gold rRNA removal kit (epicenter/Illumina; 20020596). Footprint RNA quality was assessed using the Agilent Bioanalyzer using the RNA chip. Footprints were selected for 26-34nt with custom markers on Elchrom Scientific ORIGINS system and short fragment gels, using gel electro-elution into Spectra/Por 3 3.5KD MWCO dialysis membranes. Libraries were produced using the Art-Seq kit (Epicentre/Illumina) according to the manufacturer’s protocol. The quality of libraries was assessed on Agilent Bioanalyzer with high sensitivity DNA chip and quantified using qPCR with the KAPA library quantification kit (KK4824). Libraries were pooled to a 2nM concentration and 50bp single-end reads were sequenced on HiSeq 2000 (Illumina).
50bp single-end reads were sequenced on HiSeq 2000 (Illumina).

value: Cultured human cord blood-derived CD34+ cells

tag: cell subtype

value: CD42 positive megakaryocytes


title: CD42 negative megakaryocytes replicate 2

description:
TPM_MK42neg_2
C2MK42neg

source_name: CD42 negative megakaryocytes

value: CD42 negative megakaryocytes


title: CD42 positive megakaryocytes replicate 1

description:
TPM_MK42pos_1
C1MK42pos


title: CD42 negative megakaryocytes replicate 3

description:
TPM_MK42neg_3
C3MK42neg


title: CD42 negative megakaryocytes replicate 1

description:
TPM_MK42neg_1
C1MK42neg


title: CD42 negative megakaryocytes RNA-seq replicate 1

description:
C1MK42neg
MK1_42neg_RNA

data_processing:
FastQC
Quasi-mapping and counting with Salmon version 0.13.1 onto the human transcriptome ENSEMBL, GRCh38 release 92 and summed-up per gene using Ensembl BioMart annotations.
The quality of RNA-seq reads was assessed using FastQC version 0.11.8 (Simon Andrews, Babraham institute). Data were aligned to the human genome (GRCh37 / hg19-release75) using STAR version 2.5.2b allowing for chimeric detection, with an overhang ‘anchor’ of 15 nt on either side of the read. The chimeric output file of STAR was analyzed with DCC 0.4.6 and CircExplorer2 (CE2) 2.3.2 to detect, filter, and annotate circRNA. CircRNA expression was considered low confidence when at least 2 junction reads were found in at least 1 sample by both DCC and CE, and high confidence detection when at least 2 junction reads were found in all biological replicates of one specific cell type, by both tools.
Genome_build: circRNA: hg19/ mRNA: hg38 (coding transcriptome only)
Supplementary_files_format_and_content: Xlsx file containing the mRNA TPM counts (summed-up per gene)
Supplementary_files_format_and_content: csv file containing the raw counts of low-confidence circRNA detected by both DCC and CE2

growth_protocol: In-vitro megakaryocyte differentiation  Megakaryocytes were cultured from human cord blood-derived CD34+ cells. Cord blood was diluted in PBS, loaded on ficoll-pague (GE Healthcare) and centrifuged 15 minutes at 400g. The white blood cell layer was collected from the ficoll gradient, washed twice in PBS+ 1mM EDTA + 0.2% HSA. CD34+ cells were purified with anti-CD34 Microbeads (Miltenyi biotec 130-046-702) and MACS LS column (Miltenyi, 130-042-401) according to manufacturer’s guidelines. Purity for CD34+ cells was >90%, as determined by flow-cytometry with anti-CD34 antibody (#581-PE; Beckman Coulter, measured on Beckman Coulter FC500). CD34+ cells were seeded at a density of 50.000 cells/well in a 12 well plate in CellgroSGM (CellGenix) supplemented with 100ng/mL human recombinant TPO and 10ng/mL IL1b.  At day 3, 1:1 Fresh media was added with an additional 10ng/mL TPO and 1ng/mL IL1b. On day 5, cells were split at a density of 100.000 cells in 6 wells plates, and fresh media with 10ng/mL TPO and 1ng/mL IL1b was added. On day 10, cells were harvested and supplemented with 100ug/mL Cycloheximide in culture medium prior to cell sorting.    Megakaryocyte selection  Cultures cells were harvested when >85% of cells were CD41a+ (CD41a-APC; clone HIP8), as determined by flow-cytometry. Cells were pelleted at 120g for 1 minute at 4ºC and washed once in ice cold buffer (PBS, 1mM EDTA, 0.2% HSA + 100ug/mL cycloheximide). Two-step selection was performed on ice with EasySep® Human PE-Positive Selection Kit (18551), using anti-human CD42b-PE (clone HIP1, BD Pharmingen, 555473) according to manufacturer’s guidelines. CD41a+ CD42b- and CD41a+ CD42b+ cell fractions were selected, washed using PBS + 100ug/mL cycloheximide, and kept on ice until further processing. Viability of the cells was >90% (7-AAD, Biolegend), and purity for CD41a+ CD42b- was >85% and CD41a+ CD42b+ was >50%, as determined by flow-cytometry. Cells were immediately used for processing.

extract_protocol:
Cell lysis and RNA isolation for RNA sequencing was performed according to Ignolia et al. with some adaptations. Briefly, CD42- and CD42+ selected megakaryocytes were pelleted. Cell pellets were dissolved in 150uL ice cold lysis buffer (20mM Tris pH 7.4, 250mM NaCl2, 5mM MgCl2, 0.5% Triton X-100, 1mM Dithiotreitol (DTT), 0.024U/uL Turbo DNAse (Ambion), 0.01U/uL RNAseOUT (Invitrogen) and 100ug/mL Cycloheximide). The lysate was immediately split in two aliquots of 50uL for total RNA-sequencing. 2.5uL SuperaseIN RNAse inhibitor (Invitrogen) was immediately added to the total RNA sample, and total RNA was extracted using the miRNAeasy kit (Qiagen) according to manufacturer’s protocol.
RNA quality was assessed on Agilent bioanalyzer RNA chip (all samples with RIN >9.0), and quantified using Qubit 2.0 (Thermofisher). Ribosomal RNA was removed using Ribo Zero Gold (Epicentre/Illumina; 20020596) using the manufacturer’s protocol, and the cDNA library was constructed with the KAPA stranded RNA-seq kit (KAPA biosystems KK8400) according to manufacturer’s protocol with Illumina Truseq forked adapters. Library quality was assessed on Agilent Bioanalyzer High sensitivity DNA chip and quantified using qPCR with the KAPA library quantification kit (KK4824). Libraries were pooled to a 2nM concentration and 125bp paired-end reads were sequenced on HiSeq 2000 (Illumina).


title: CD42 positive megakaryocytes RNA-seq replicate 1

description:
C1MK42pos
MK1_42pos_RNA


title: WT MTJ scRNAseq

city: Sakhnin

first: Wesal

middle: Yaseen

last: Badarne

address: P.O box 2016

department: Department of Genetics and Developmental Biology.

country: Israel

institute: Technion

data_processing:
The RNAseq data was generated on Illumina NextSeq500, high-output mode (Illumina, FC-404-2005)
75 bp paired-end reads (Read1- 26 bp, Read2- 58 bp, Index- 8 bp)
Mouse datasets (fasta and gtf files, version mm10) were downloaded from the 10x genomics site.
Primary analysis was performed using 10X Genomics software - Cell Ranger-V3.0.2.
Data was analyzed using Seurat R package (Seurat_3.0.0.9100)
Genome_build: mm10

source_name: single cells from the MTJ region

extract_protocol:
Cells of the myotendinous region were isolated mechanically and enzymaticaly using trypsin centrifuged and resuspended with BioAmf. Using a wide-bore pipette tip cells were  thoroughly mixed to get single cells, centrifuged and resuspended with 1X PBS with 0.04% BSA.
1 RNA single cell library was prepared according to 10X manufacture protocol (Chromium Single Cell 3’ Library & Gel Bead Kit v2, PN-120237) using 18000 input cells.
Illumina NextSeq500, high-output mode (Illumina, FC-404-2005)

tag: strain

tag: tissue

value: limb myotendinous junction

value: fibroblasts and myoblast


title: CD42 negative megakaryocytes RNA-seq replicate 3

description:
C3MK42neg
MK3_42neg_RNA


title: 4C H7 rep2


title: CD42 positive megakaryocytes replicate 3

description:
TPM_MK42pos_3
C3MK42pos


title: 4C ARPE19 rep2


title: BL6_hippocampus_18mon_male_643

city: Irvine

first: Narges

last: Rezaie

state: California

address: 2218 Biological Sciences III

institute: University of California, Irvine

data_processing:
alignment STAR (2.5.1b-static)
quantification RSEM (1.2.22)
Genome_build: mm10
Supplementary_files_format_and_content: quantification per count, Transcripts Per Million(TPM)

growth_protocol: After weaning, they were housed together with littermates and aged until the harvest dates.

extract_protocol:
QIAGEN RNAeasy
Modified SMART-seq2

value: hippocampus

tag: Sex

value: male

tag: time (month)


title: BL6_hippocampus_18mon_male_785


title: BL6_hippocampus_18mon_female_790

value: female


title: BL6_hippocampus_18mon_female_788


title: BL6_hippocampus_18mon_male_641


title: BL6_hippocampus_18mon_male_566


title: BL6_hippocampus_18mon_male_301


title: BL6_hippocampus_18mon_female_777


title: BL6_hippocampus_18mon_female_762


title: BL6_hippocampus_18mon_female_767


title: BL6_hippocampus_18mon_female_793


title: BL6_hippocampus_18mon_female_642


title: CD42 positive megakaryocytes RNA-seq replicate 2

description:
C2MK42pos
MK2_42pos_RNA


title: CD42 negative megakaryocytes RNA-seq replicate 2

description:
C2MK42neg
MK2_42neg_RNA


title: BL6_hippocampus_18mon_female_630


title: BL6_hippocampus_18mon_female_536


title: BL6_hippocampus_18mon_female_537


title: BL6_hippocampus_18mon_female_795


title: BL6_hippocampus_18mon_female_639


title: BL6_hippocampus_18mon_female_534


title: BL6_hippocampus_18mon_female_304


title: BL6_hippocampus_18mon_female_302


title: 5xFAD_hippocampus_18mon_male_627


title: 5xFAD_hippocampus_18mon_male_617


title: 5xFAD_hippocampus_18mon_male_786


title: 5xFAD_hippocampus_18mon_male_640


title: 5xFAD_hippocampus_18mon_male_567


title: 5xFAD_hippocampus_18mon_male_565


title: 5xFAD_hippocampus_18mon_male_513


title: 5xFAD_hippocampus_18mon_male_317


title: 5xFAD_hippocampus_18mon_male_561


title: 5xFAD_hippocampus_18mon_female_787


title: 5xFAD_hippocampus_18mon_female_794


title: 5xFAD_hippocampus_18mon_male_298


title: 5xFAD_hippocampus_18mon_female_776


title: 5xFAD_hippocampus_18mon_female_535


title: BL6_cortex_18mon_male_785

value: cortex


title: 5xFAD_hippocampus_18mon_female_768


title: 4C H7 rep3


title: BL6_cortex_18mon_male_643


title: BL6_cortex_18mon_male_641


title: BL6_cortex_18mon_male_566


title: BL6_cortex_18mon_male_301


title: BL6_cortex_18mon_female_788


title: BL6_cortex_18mon_female_790


title: BL6_cortex_18mon_female_762


title: BL6_cortex_18mon_female_777


title: BL6_cortex_18mon_female_642


title: BL6_cortex_18mon_female_639


title: 5xFAD_hippocampus_18mon_female_791


title: BL6_cortex_18mon_female_630


title: BL6_cortex_18mon_female_767


title: BL6_cortex_18mon_female_793


title: BL6_cortex_18mon_female_795


title: BL6_cortex_18mon_female_537


title: 5xFAD_cortex_18mon_male_640


title: BL6_cortex_18mon_female_534


title: BL6_cortex_18mon_female_302


title: BL6_cortex_18mon_female_536


title: BL6_cortex_18mon_female_304


title: 5xFAD_cortex_18mon_male_627


title: 5xFAD_cortex_18mon_male_561


title: 5xFAD_cortex_18mon_male_565


title: 5xFAD_cortex_18mon_male_513


title: 5xFAD_cortex_18mon_male_567


title: 5xFAD_cortex_18mon_male_617


title: 5xFAD_cortex_18mon_male_298


title: 5xFAD_cortex_18mon_male_786


title: 5xFAD_cortex_18mon_male_317


title: 5xFAD_cortex_18mon_female_787


title: 5xFAD_cortex_18mon_female_776


title: 5xFAD_cortex_18mon_female_791


title: 5xFAD_cortex_18mon_female_768


title: 5xFAD_cortex_18mon_female_535


title: BL6_hippocampus_12mon_male_792


title: BL6_hippocampus_12mon_male_452


title: BL6_hippocampus_12mon_male_315


title: BL6_hippocampus_12mon_male_305


title: BL6_hippocampus_12mon_female_624


title: BL6_hippocampus_12mon_female_551


title: BL6_hippocampus_12mon_female_542


title: 5xFAD_hippocampus_12mon_male_380


title: 5xFAD_hippocampus_12mon_male_379


title: BL6_hippocampus_12mon_female_500


title: BL6_hippocampus_12mon_female_497


title: 5xFAD_hippocampus_12mon_male_634


title: 5xFAD_hippocampus_12mon_male_378


title: 5xFAD_hippocampus_12mon_male_377


title: 5xFAD_cortex_18mon_female_794


title: BL6_cortex_12mon_male_456


title: 5xFAD_hippocampus_12mon_female_498


title: 5xFAD_hippocampus_12mon_female_543


title: BL6_cortex_12mon_male_792


title: 5xFAD_hippocampus_12mon_female_541


title: BL6_cortex_12mon_male_315


title: 5xFAD_hippocampus_12mon_female_499


title: BL6_cortex_12mon_male_305


title: BL6_hippocampus_12mon_male_456


title: BL6_cortex_12mon_male_452


title: BL6_cortex_12mon_female_624


title: BL6_cortex_12mon_female_551


title: BL6_cortex_12mon_female_500


title: 5xFAD_cortex_12mon_male_380


title: coculture.shEphB6.35.1

city: Padova

first: Marco

last: Montagner

state: PD

address: viale G. Colombo, 3

country: Italy

institute: University of Padua

description:
shEphB6 sequence: CCGGCCACAGCCTGAGCAAACAAATCTCGAGATTTGTTTGCTCAGGCTGTGGTTTTTG
HOO649A28

data_processing:
Biological replicate libraries were prepared using the polyA KAPA mRNA HyperPrep Kit and sequenced on Illumina HiSeq 4000 platform, generating ~24 million 100bp single-end reads per sample. Read quality trimming and adaptor removal was carried out using Trimmomatic (version 0.36).
The RSEM package (version 1.3.30)  in conjunction with the STAR alignment algorithm (version 2.5.2a)  was used for the mapping and subsequent gene-level counting of the sequenced reads with respect to Ensembl human GRCh38.89 version transcriptome. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package (version 1.18.1)
Genome_build: Ensembl mouse GRCm38.89
Supplementary_files_format_and_content: Tab delimited text files containing normalised data. Rows represent Ensembl mouse genes and columns represent individual samples.

source_name: Culture on plastic

growth_protocol: MLNL medium (low-glucose DMEM/1% FCS)

extract_protocol:
Total RNA was extracted using RNeasy Plus Micro Kit (Qiagen) following manifacturer's protocol
RNA samples were assessed for quantity and integrity using the NanoDrop 8000 spectrophotometer v.2.0 (Thermo Fisher Scientific) and Agilent 2100 Bioanalyser (Agilent Technologies), respectively. Biological replicate libraries were prepared using the polyA KAPA mRNA HyperPrep Kit and sequenced on Illumina HiSeq 4000 platform, generating ~24 million 100bp single-end reads per sample.

treatment_protocol: D2.0R-EGFP-shControl or D2.0R-EGFP-shEphB6 (1,8x105 cells/well) were plated on top of AT1-like cells (1,36x106 cells/sample) in MLNL medium (in 60 mm dish) for three days before separation by Fluorescence-Activated Cell Sorter (FACS) based on EGFP signal. EGFP-+cells (D2.0R cells) were subjected to analysis.

tag: treatment

value: D2.0R-EGFP-shEphB6 cells cocultured with AT1-like cells


title: 5xFAD_cortex_12mon_male_634


title: BL6_cortex_12mon_female_497


title: 5xFAD_cortex_12mon_male_379


title: 5xFAD_cortex_12mon_male_378


title: 5xFAD_cortex_12mon_male_377


title: 5xFAD_cortex_12mon_female_544


title: 5xFAD_hippocampus_12mon_female_544


title: 5xFAD_cortex_12mon_female_499


title: 5xFAD_cortex_12mon_female_541


title: 5xFAD_cortex_12mon_female_498


title: 5xFAD_cortex_12mon_female_543


title: BL6_hippocampus_8mon_female_348


title: BL6_hippocampus_8mon_female_340


title: BL6_hippocampus_8mon_male_389


title: BL6_hippocampus_8mon_female_338


title: BL6_hippocampus_8mon_male_396


title: BL6_hippocampus_8mon_female_351


title: BL6_hippocampus_8mon_male_399


title: 5xFAD_hippocampus_8mon_male_387


title: 5xFAD_hippocampus_8mon_male_390


title: BL6_cortex_12mon_female_542


title: 5xFAD_hippocampus_8mon_male_300


title: BL6_hippocampus_8mon_male_410


title: 5xFAD_hippocampus_8mon_male_307


title: 5xFAD_hippocampus_8mon_male_299


title: 5xFAD_hippocampus_8mon_female_341


title: 5xFAD_hippocampus_8mon_female_339


title: 5xFAD_hippocampus_8mon_female_342


title: 5xFAD_hippocampus_8mon_female_312


title: 5xFAD_hippocampus_8mon_female_295


title: BL6_hippocampus_8mon_male_412


title: BL6_cortex_8mon_male_412


title: BL6_cortex_8mon_male_396


title: BL6_cortex_8mon_male_410


title: BL6_cortex_8mon_male_399


title: BL6_cortex_8mon_female_351


title: BL6_cortex_8mon_male_389


title: BL6_hippocampus_8mon_female_322


title: BL6_cortex_8mon_female_348


title: BL6_cortex_8mon_female_340


title: BL6_cortex_8mon_female_322


title: 5xFAD_cortex_8mon_male_387


title: 5xFAD_cortex_8mon_male_307


title: BL6_cortex_8mon_female_338


title: 5xFAD_cortex_8mon_male_299


title: 5xFAD_cortex_8mon_male_300


title: 5xFAD_cortex_8mon_female_341


title: 5xFAD_cortex_8mon_female_342


title: 5xFAD_cortex_8mon_female_339


title: 5xFAD_cortex_8mon_female_295


title: BL6_hippocampus_4mon_male_465


title: 5xFAD_cortex_8mon_female_312


title: BL6_hippocampus_4mon_male_525


title: BL6_hippocampus_4mon_male_526


title: BL6_hippocampus_4mon_male_466


title: BL6_hippocampus_4mon_male_445


title: BL6_hippocampus_4mon_female_518


title: BL6_hippocampus_4mon_female_507


title: CD42 positive megakaryocytes RNA-seq replicate 3

description:
C3MK42pos
MK3_42pos_RNA


title: BL6_hippocampus_4mon_female_432


title: BL6_hippocampus_4mon_female_330


title: 5xFAD_hippocampus_4mon_male_464


title: 5xFAD_hippocampus_4mon_male_451


title: 5xFAD_cortex_8mon_male_390


title: 5xFAD_hippocampus_4mon_male_446


title: 5xFAD_hippocampus_4mon_female_511


title: 5xFAD_hippocampus_4mon_female_434


title: coculture.9.2

description:
shEphB6 sequence: CCGGCCACAGCCTGAGCAAACAAATCTCGAGATTTGTTTGCTCAGGCTGTGGTTTTTG
HOO649A26

data_processing:
Biological replicate libraries were prepared using the polyA KAPA mRNA HyperPrep Kit and sequenced on Illumina HiSeq 4000 platform, generating ~24 million 100bp single-end reads per sample. Read quality trimming and adaptor removal was carried out using Trimmomatic (version 0.36).
The RSEM package (version 1.3.30)  in conjunction with the STAR alignment algorithm (version 2.5.2a)  was used for the mapping and subsequent gene-level counting of the sequenced reads with respect to Ensembl human GRCh38.89 version transcriptome. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package (version 1.18.1)
Genome_build: Ensembl human GRCh38.89
Supplementary_files_format_and_content: Tab delimited text files containing normalised data. Rows represent Ensembl human genes and columns represent individual samples.

treatment_protocol: D2.0R-EGFP-shControl or D2.0R-EGFP-shEphB6 (1,8x105 cells/well) were plated on top of AT1-like cells (1,36x106 cells/sample) in MLNL medium (in 60 mm dish) for three days before separation by Fluorescence-Activated Cell Sorter (FACS) based on EGFP signal. EGFP- cells (AT1-like cells) were subjected to analysis.

value: AT1-like cells cultivated on plastic together with D2.0R-EGFP-shEphB6 cells


title: BL6_cortex_4mon_male_466


title: 5xFAD_hippocampus_4mon_female_430


title: coculture.9.1

description:
shEphB6 sequence: CCGGCCACAGCCTGAGCAAACAAATCTCGAGATTTGTTTGCTCAGGCTGTGGTTTTTG
HOO649A25


title: coculture.5.3

description:
shControl sequence: CCGGGCGCGATAGCGCTAATAATTTCTCGAGAAATTATTAGCGCTATCGCGCTTTTT
HOO649A31

value: AT1-like cells cultivated on plastic together with D2.0R-EGFP-shControl cells


title: coculture.9.3

description:
shEphB6 sequence: CCGGCCACAGCCTGAGCAAACAAATCTCGAGATTTGTTTGCTCAGGCTGTGGTTTTTG
HOO649A27


title: coculture.7.2

description:
shEphB6 sequence: CCGGCGAGAGGTTGACCCTACATATCTCGAGATATGTAGGGTCAACCTCTCGTTTTT
HOO649A20


title: 5xFAD_hippocampus_4mon_female_431


title: coculture.5.2

description:
shControl sequence: CCGGGCGCGATAGCGCTAATAATTTCTCGAGAAATTATTAGCGCTATCGCGCTTTTT
HOO649A14


title: BL6_cortex_4mon_male_445


title: BL6_cortex_4mon_female_518


title: coculture.7.1

description:
shEphB6 sequence: CCGGCGAGAGGTTGACCCTACATATCTCGAGATATGTAGGGTCAACCTCTCGTTTTT
HOO649A19


title: BL6_hippocampus_4mon_female_331


title: coculture.7.3

description:
shEphB6 sequence: CCGGCGAGAGGTTGACCCTACATATCTCGAGATATGTAGGGTCAACCTCTCGTTTTT
HOO649A21


title: BL6_cortex_4mon_male_525


title: coculture.5.1

description:
shControl sequence: CCGGGCGCGATAGCGCTAATAATTTCTCGAGAAATTATTAGCGCTATCGCGCTTTTT
HOO649A13


title: 5xFAD_hippocampus_4mon_male_463


title: monoculture3

value: AT1-like cells cultivated on plastic


title: 5xFAD_hippocampus_4mon_male_450


title: monoculture2


title: BL6_cortex_4mon_female_507


title: BL6_cortex_4mon_female_432


title: BL6_cortex_4mon_female_331


title: monoculture1


title: 5xFAD_hippocampus_4mon_female_433


title: RYB_sample2_3118

city: London

first: Silvia

last: Marino

address: 4, Newark St

country: United Kingdom

institute: Queen Mary University of London

description:
r2yb3118
BulkData_rawcounts_Unfiltered.csv
dxr.ryb.csv

data_processing:
Quality control and trimming were performed via FastQC and TrimGalore, respectively. Read mapping was performed using STAR v. 2.7.0 with default parameters. R v. 3.5.1. was used to perform the rest of the RNA-Sequencing analysis. Bioconductor packages NOISeq, biomaRt were used to filter the data and annotate the genes, respectively. Specifically, lowly expressed genes (TPM < 1) and genes associated with Mt-RNA and rRNA were filtered out.
Genome_build: Ensembl GRCh38
Supplementary_files_format_and_content: tables of read counts and spliced counts (.csv)

source_name: Tumour Sample

growth_protocol: U3118 and U3082 GIC cells were obtained from The Human Glioblastoma cell culture resource 6 and cultured on Primaria 60 mm dish (Corning 353802) coated with laminin (Sigma) at a final concentration of 10μg/ml. Media is prepared as follows: Neurobasal (Gibco 21103-049)  and DMEM/F12 glutamax (Gibco 31331-093) in 1:1 proportion, 5 ml of Pen-Strep (Gibco 15140-122), B27 50 X (12587-010,) and N2 100 X (17502-048). Before adding to the cells, media is supplemented with human EGF (Preprotech AF100-15) to final concentration 10ng/ml and human FGF-basic (Preprotech 100-18B) to final.

extract_protocol:
Total RNA was isolated from cell pellets using RNeasy Micro purification kit (Qiagen). RNA was digested with DNaseI (Applied Biosystem) in column following manufacturer’s instructions.
Total RNA was sequenced using HiSeq platform with paired-end 150 bp (PE-150), 20 M reads at Novogene, Cambridge, UK

tag: cell types

value: patient-derived GIC

tag: sample type

value: RYB


title: 5xFAD_cortex_4mon_male_464


title: BL6_cortex_4mon_female_330


title: RYB_sample2_3082

description:
r2yb3082
BulkData_rawcounts_Unfiltered.csv
dxr.ryb.csv


title: RYB_sample1_3118

description:
r1yb3118
BulkData_rawcounts_Unfiltered.csv
dxr.ryb.csv


title: 5xFAD_cortex_4mon_male_463


title: 5xFAD_cortex_4mon_male_451


title: RYB_sample1_3082

description:
r1yb3082
BulkData_rawcounts_Unfiltered.csv
dxr.ryb.csv


title: BL6_cortex_4mon_male_526


title: PRP_sampe2_3118

description:
p2rp3118
BulkData_rawcounts_Unfiltered.csv
dxr.prp.csv

value: PRP


title: 5xFAD_cortex_4mon_male_450


title: 5xFAD_cortex_4mon_male_446


title: BL6_cortex_4mon_male_465


title: PRP_sample2_3082

description:
p2rp3082
BulkData_rawcounts_Unfiltered.csv
dxr.prp.csv


title: 5xFAD_cortex_4mon_female_511


title: PRP_sample1_3118

description:
p1rp3118
BulkData_rawcounts_Unfiltered.csv
dxr.prp.csv


title: 5xFAD_cortex_4mon_female_434


title: 5xFAD_cortex_4mon_female_431


title: PRP_sample1_3082

description:
p1rp3082
BulkData_rawcounts_Unfiltered.csv
dxr.prp.csv


title: Sl_TK24-DG2-P41_Talc_production_start_A

city: Bielefeld

first: Christian

last: Ruckert-Reed

address: Sequenz 1

department: Medical School OWL

institute: Bielefeld University

data_processing:
Basecalls were performed using RTA v 1.18.66.3
Sequenced reads were mapped to the CP071123.1 whole genome using bowtie2 v2.3.2 with parameters -X 600
Raw read counts per gene were calculated using featureCounts v2.0.0 with parameters -O -M -t gene -g locus_tag -s 1
Read cound normalization and data analysis were performed using DESeq2
Genome_build: CP071123
Supplementary_files_format_and_content: tab-delimited text files contain normalized read counts derived via DESeq2 for each gene
Supplementary_files_format_and_content: tab-delimited matrix table with raw read counts for every gene and every sample

organism: Streptomyces lividans

source_name: cell culture grown in SGG with added talc microparticles

growth_protocol: Liquid SGG medium was used for pre- and main cultures for bottromycin production and contained per liter: 10 g soluble starch (Sigma-Aldrich), 10 g glycerol, 2.5 g corn steep powder (Sigma-Aldrich), 5 g bacto peptone (Becton & Dickinson), 2 g yeast extract (Becton & Dickinson), 1 g sodium chloride, and 21 g MOPS. The pH of the medium was adjusted to 7.2, using 6 M NaOH. One loop of spores was scratched from a five-day old plate culture and used to inoculate a liquid pre-culture, which was grown overnight in a 500 mL baffled shake flask with 50 mL medium and 30 g soda-lime glass beads (5 mm, Sigma-Aldrich). When the pre-culture reached the late exponential phase, an appropriate amount of cells was collected (8500 x g, room temperature, 5 min), resuspended in 10 mL fresh medium, and used to inoculate the main-culture (50 mL medium in 500 mL baffled shake flasks). All cultivation experiments were conducted in triplicate on a rotary shaker (28 °C, 230 rpm, 75% relative humidity, 5 cm shaking diameter, Multitron, Infors AG, Bottmingen, Switzerland).

extract_protocol:
Total RNA was isolated using the Quick-RNA Miniprep Plus kit (Zymo Research, Freiburg, Germany). After DNase treatment, the obtained RNA was purified (RNA Clean & Concentrator-5 kit, Zymo Research) and quantified (DropSense 16, Trinean NV, Gent, Belgium).
To construct whole transcriptome cDNA libraries, 2.5 μg of total RNA each was depleted of rRNA (Ribo-Zero rRNA Removal Kit (Bacteria), Illumina, San Diego, CA, USA). Successful rRNA removal was validated (Agilent RNA Pico 6000 kit, Agilent 2100 Bioanalyzer, Agilent Technologies). The obtained mRNA was converted into a cDNA library according to the TruSeq Stranded mRNA Sample Preparation guide (Illumina). Appropriate cDNA quality and quantity was validated (Agilent High Sensitivity DNA kit, Agilent 2100 Bioanalyzer, Agilent Technologies). Sequencing was performed on an Illumina HiSeq 1500 instrument using 70 bases read length (Illumina).

treatment_protocol: The control culture was grown in pure SGG medium. For the experiment culture, talc microparticles (hydrous magnesium silicate, 3MgO∙4SiO2∙H2O, 10 µm, Sigma-Aldrich) were resuspended in 50 mM Na-acetate buffer (pH 6.5), autoclaved at 121°C for 20 min, and added to the sterile medium prior to inoculation. Samples were taken during growth phase (12h after inoculation) early production phase (24h after inoculation), and main production phase (48h after inoculation).

value: talc; grown in liquid medium with added talc microparticles

tag: time point


title: Sl_TK24-DG2-P41_Talc_growth_phase_C

value: growth phase (12h after inoculation)


title: Sl_TK24-DG2-P41_Talc_production_main_B

value: late production phase (48h after inoculation)


title: Sl_TK24-DG2-P41_Talc_production_main_A


title: Sl_TK24-DG2-P41_Talc_production_start_C

value: early production phase (24h after inoculation)


title: Sl_TK24-DG2-P41_Talc_growth_phase_B


title: Control_sample2_3118

description:
c2tr3118
BulkData_rawcounts_Unfiltered.csv

value: Control


title: Sl_TK24-DG2-P41_Talc_production_main_C


title: Sl_TK24-DG2-P41_Control_production_main_C

source_name: cell culture grown in pure SGG

value: control; untreated


title: Sl_TK24-DG2-P41_Talc_production_start_B


title: Sl_TK24-DG2-P41_Talc_growth_phase_A


title: Sl_TK24-DG2-P41_Control_production_main_B


title: 5xFAD_cortex_4mon_female_430


title: Sl_TK24-DG2-P41_Control_production_main_A


title: CBX_sample2_3118

description:
c2bx3118
BulkData_rawcounts_Unfiltered.csv
dxr.cbx.csv

value: CBX


title: CUT&Tag_TX1072_XO_IgG_d4_r2

data_processing:
Library strategy: CUT&Tag
Read sequences were trimmed using Trim Galore (0.6.4) with options [--paired --nextera] (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)
An “N-Masked” genome of the mouse reference genome mm10 was generated using SNPsplit (0.3.2). For this, all the polymorphic sites of the hybrid strain Mus musculus CAST/EiJ and Mus musculus C57BL/6 were masked by ambiguity nucleobase ‘N’ as described previously (Pacini et al. 2020, Barros de Andrade E Sousa et al. 2019).
The trimmed FASTQ files were aligned to the masked mm10 genome using bowtie2 (2.3.5) with the options [--local --very-sensitive-local -X 2000] (Langmead and Salzberg 2012)
SAM files were translated into BAM files, filtered for paired and mapped reads and sorted using samtools (1.10) with options [view -b -h -f 2 -q 20] and [sort] (Li et al., 2009).
Blacklisted regions for mm10 (ENCODE Project Consortium 2012) were removed using bedtools (2.29.2) with options [intersect -v] (Quinlan and Hall 2010).
BigWig tracks were created using deepTools2 (3.4.1) with options [bamCoverage -e -bs 10 --normalizeUsing CPM -ignore chrX chrY] (Ramírez et al. 2016) and visualized using the UCSC Genome Browser (Kent et al. 2002).
Peaks were called using MACS2 (2.1.2) with options [callpeak -f BAMPE -g mm -q 0.05] (Zhang et al. 2008).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig: Coverage tracks
Supplementary_files_format_and_content: narrowPeak: Peak files

source_name: Mouse embryonic stem cells

growth_protocol: TX1072 XXΔXic and TX1072 XO Cells were grown on gelatin-coated flasks in serum-containing ES cell medium (DMEM (Sigma), 15% ESC-grade FBS (Gibco), 0.1mM β-mercaptoethanol, 1000 U/ml leukemia inhibitory factor (LIF, Millipore)), supplemented with 2i (3 μM Gsk3 inhibitor CT-99021, 1 μM MEK inhibitor PD0325901, Axon).

extract_protocol:
For each CUT&Tag reaction 100.000 cells were collected and washed once with Wash buffer (20 mM HEPES-KOH, pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 10 mM Sodium butyrate, 1 mM PMSF). 10ul Concanavalin A (Bangs Laboratories) beads were equilibrated with 100ul Binding buffer (20 mM HEPES-KOH, pH 7.5, 10 mM KCl, 1 mM CaCl2, 1mM MnCl2) and afterwards concentrated in 10ul binding buffer. The cells were bound to the Concanavalin A beads  by incubating for 10 minutes at room temperature with rotation. Following this, the beads were separated on a magnet and resuspended in 100ul chilled Antibody buffer (Wash buffer with 0.05% Digitonin and 2mM EDTA) with subsequently 1ul of primary antibody and incubated on a rotator for 3h at 4°C. After magnetic separation the beads were resuspended in 100ul chilled Dig-wash buffer (Wash buffer with 0.05% Digitonin) containing 1ul of matching secondary antibodies and were incubated for 1h at 4°C with rotation. The beads were washed three times with ice cold Dig-wash buffer and resuspended in chilled Dig-300 buffer (20 mM HEPES-KOH, pH 7.5, 300 mM NaCl, 0.5 mM Spermidine, 0.01% Digitonin, 10 mM Sodium butyrate, 1 mM PMSF) with 1:250 diluted 3xFLAG-pA-Tn5 preloaded with Mosaic-end adapters. After incubation for 1h at 4°C with rotation, the beads were washed four times with chilled Dig-300 buffer and resuspended in 50ul Tagmentation buffer (Dig-300 buffer 10 Mm MgCl2). Tagmentation was performed for 1h at 37°C and subsequently stopped by adding 2.25 µL 0.5M EDTA, 2.75 µL 10% SDS and 0.5 µL 20 mg/mL Proteinase K and vortexing for 5 seconds. DNA fragments were solubilized overnight at 55°C followed by 30 minutes at 70°C to inactivate residual Proteinase K. DNA fragments were purified with the ChIP DNA Clean & Concentrator kit (Zymo Research) and eluted with 25 ul elution buffer according to the manufacturer's guidelines.
NGS libraries were generated by amplifying the CUT&Tag DNA fragments with i5 and i7 Nextera barcoded HPLC grade primers using NEBNext® HiFi 2x PCR Master Mix (New England BioLabs) on a thermocycler with the following program: 72 °C for 5 min, 98 °C for 30 sec, 98 °C for 10 sec, 63 °C for 10 sec (14-15 Cycles for step 3-4)  and 72°C for 1 min. Post PCR cleanup was performed with Ampure XP beads (Beckman Coulter). For this 0.95x volume of Ampure XP beads were mixed with the NGS libraries and incubated at room temperature for 10 minutes. After magnetic separation, the beads were washed three times on the magnet with 80% ethanol and the libraries eluted with Tris-HCl, pH 8.0. The quality of the purified NGS libraries was assessed with the BioAnalyzer High Sensitivity DNA system (Agilent Technologies). Sequencing libraries were pooled in equimolar ratios cleaned for another round with  1.2x volume of Ampure XP beads as before and eluted in 20ul Tris-HCl, pH 8.0. The sequencing library pool quality was assessed with the BioAnalyzer High Sensitivity DNA system (Agilent Technologies) and subjected to Illumina PE75 next generation sequencing on the NextSeq500 platform to approximately 5 million fragments per library.

treatment_protocol: Differentiation was induced for 0, 2 or 4 days by 2i/LIF withdrawal in DMEM supplemented with 10% FBS and 0.1mM β-mercaptoethanol at a density of 1.56*10^4 cells/cm2 in fibronectin-coated (10 μg/ml) tissue culture plates.

value: TX1072 XO

tag: target

value: IgG

value: Day 4

value: CAST / C57BL/6

value: CUT&Tag

value: Mouse embryonic stem cells


title: Sl_TK24-DG2-P41_Control_production_start_B


title: CBX_sample2_3082

description:
c2bx3082
BulkData_rawcounts_Unfiltered.csv
dxr.cbx.csv


title: Sl_TK24-DG2-P41_Control_production_start_A


title: Control_sample1_3118

description:
c1tr3118
BulkData_rawcounts_Unfiltered.csv


title: CUT&Tag_TX1072_XO_IgG_d4_r1


title: 5xFAD_cortex_4mon_female_433

value: cortex

value: female


title: Sl_TK24-DG2-P41_Control_growth_phase_B


title: Sl_TK24-DG2-P41_Control_growth_phase_C


title: Sl_TK24-DG2-P41_Control_growth_phase_A


title: Control_sample2_3082

description:
c2tr3082
BulkData_rawcounts_Unfiltered.csv

value: patient-derived GIC


title: Control_sample1_3082

description:
c1tr3082
BulkData_rawcounts_Unfiltered.csv


title: CBX_sample1_3082

description:
c1bx3082
BulkData_rawcounts_Unfiltered.csv
dxr.cbx.csv


title: BMI1_sample2_3082

description:
b2mi3082
BulkData_rawcounts_Unfiltered.csv
dxr.bm1.csv


title: High PAC 3

city: Frederiksberg C

first: Andrew

last: Williams

state: --- Select One ---

address: Dyrlægevej 100

country: Denmark

institute: University of Copenhagen

data_processing:
BGI internal software used to remove adpators and low quality reads.
Mapped to Mus Musculus (mm10) using HISAT
DEG assessed using DeSeq2 and NOIseq
Genome_build: mm10
Supplementary_files_format_and_content: count data and FPKM for each sample.

source_name: high PAC_Intestinal tissue

growth_protocol: Female mice were 8 weeks of age, and were gavaged with water of PAC (200mg/kg, derived from grape extract) every 2nd day over a period of ten days.

extract_protocol:
Tissue was collected at euthanasia. Total RNA was extracted using miRNAeasy kits (Qiagen).
Standard BGI protocol.

tag: age

value: 8 weeks

value: gavaged with high molecular weight PAC

value: Intestinal tissue


title: CBX_sample1_3118

description:
c1bx3118
BulkData_rawcounts_Unfiltered.csv
dxr.cbx.csv


title: Low PAC 4

source_name: low PAC_Intestinal tissue

value: gavaged with low molecular weight PAC


title: Sl_TK24-DG2-P41_Control_production_start_C

value: early production phase (24h after inoculation)


title: High PAC 2


title: High PAC 1


title: High PAC 5


title: High PAC 4


title: CUT&Tag_TX1072_XO_H3K36me3_d4_r2

tag: cell type


title: Low PAC 3


title: Low PAC 5


title: CUT&Tag_TX1072_XO_H2AK119ub_d4_r1

tag: cell line


title: BMI1_sample2_3118

description:
b2mi3118
BulkData_rawcounts_Unfiltered.csv
dxr.bm1.csv


title: CUT&Tag_TX1072_XO_H2AK119ub_d4_r2

tag: condition


title: CUT&Tag_TX1072_XO_H3K27me3_d4_r1

tag: replicate


title: BMI1_sample1_3118

description:
b1mi3118
BulkData_rawcounts_Unfiltered.csv
dxr.bm1.csv


title: BMI1_sample1_3082

description:
b1mi3082
BulkData_rawcounts_Unfiltered.csv
dxr.bm1.csv


title: Control_water 3

source_name: control_Intestinal tissue

value: gavaged with water


title: CUT&Tag_TX1072_XO_H3K9me3_d4_r1

tag: strain background


title: Control_water 4


title: CUT&Tag_TX1072_XO_H3K36me3_d4_r1

tag: assay


title: Control_water 2


title: CUT&Tag_TX1072_XO_H3K27me3_d4_r2


title: shCHD7, anti-H3K27me3, line 3021, replica 2

description:
Processed file obtained by merging replicas
K27_shC_3021_peaks.broadPeak

data_processing:
RNA-Seq
Quality control was performed with FastQC and adapter sequences were removed using Trimgalore 0.6.5. Reads were then aligned to human reference genome using STAR v2.6.1, with gene count quantification mode, retaining only uniquely mapped reads. Lowly expressed genes (CPM < 1) were filtered out via a custom-made script in R v.3.5.3 and further biotype filtering was performed in R with the Bioconductor packages NOISeq (Tarazona et al., 2015) and biomaRt (Durinck et al., 2009), removing residual highly expressed mitochondrial and ribosomal RNA.
CHIP-Seq
The quality of ChIP-Seq samples was assessed via FastQC and TrimGalore v0.6.5, removing low quality and adapter sequences. The average Phred score of the surviving reads across all samples was 30. The alignment to the reference genome was performed via Bowtie v2.3.4 with default parameters, in concomitance with the usage of samtools for the post-processing and sorting of the Binary Alignment Map (bam) files. After performing post-alignment quality checks, peaks were called via the MACS2 algorithm (subroutine callpeak) against the corresponding input background and merging the corresponding replicas (n=2) for each antibody/condition. The shifting model was disabled to make different datasets comparable and the “--broad” option was enabled for the analysis of the histone mark H3K27me3.  A minimum fold enrichment of 2 was selected with an FDR of 0.05, in both narrow peak and broad peak (--broad-cutoff) statistical analyses.
Genome_build: Ensembl GRCh38
Supplementary_files_format_and_content: ChIP-Seq: list of peaks called via MACS2 (.bed); RNA-Seq: raw read counts called via STAR

growth_protocol: ICb1299 were cultured in DMEM (high glucose, GlutaMAX™, ThermoFisher) supplemented with 10% foetal bovine serum (FBS, Gibco) and 1% Penicillin-Streptomycin (Gibco). CHLA-01-Med G4 MB cells were purchased from ATCC (CRL3021) and cultured as described previously (Badodi et al., 2019). Briefly, cells were grown in DMEM-F12 (Gibco) supplemented with B27 (Gibco), 20 ng/mL human epidermal growth factor (EGF, Peprotech) and 10 ng/mL human basic fibroblast growth factor (FGF, Peprotech). MB subtype identity for the two cell lines has been previously shown (Badodi et al., 2017; Shu et al., 2008).

extract_protocol:
RNA-Seq:Total RNA was extracted with RNA/DNA/Protein Purification Plus kit (Norgen) following manufacturer's instruction. ChIP-Seq: BMI1, CHD7, H3K4me3 and H3K27me3 ChIPs were performed using ChIP-IT High Sensitivity kit (Active Motif) following manufacturer’s instructions. Briefly, 1x106 cells were fixed with formaldehyde-based fixing solution for 15 minutes at room temperature and lysed with provided lysis solution supplemented with protease inhibitors. Next, nuclei pellets were lysed and chromatin sonicated with Bioruptor Plus sonication device (Diagenode) to obtain DNA fragments within the recommended 200-1200bp range. 25µg or 10µg of sheared chromatin was then incubated with 4µg of antibody against BMI1 (BMI1, clone AF27, Active Motif), CHD7 (ab117522, abcam), H3K27me3 (Diagenode) or H3K4me3 (Diagenode) overnight at 4°C with rotation. Following incubation with Protein G agarose beads, bound chromatin was washed, eluted and purified following manufacturer’s protocols. Validation by qPCR-ChIP on target genes was done before proceeding to sequencing.
RNA-Seq: Total RNA was extracted with RNA/DNA/Protein Purification Plus kit (Norgen), polyA mRNA was selected and library prepared using the NEBNext Ultra II Directional RNA Library Prep kit. Libraries were size selected, multiplexed and 75bp paired-end sequences were obtained with HiSeq4000 (Illumina). ChIP-Seq: ChIPed DNA was end-repaired, A-tailed and adapter-ligated before size selection and amplification. The obtained libraries were QC’ed and multiplexed before 75 bp paired end sequencing on HiSeq4000 (Illumina).

treatment_protocol: GIPZ lentiviral shRNA vectors containing a hairpin sequence targeting BMI1 or CHD7 and the coding sequences for GFP and puromycin resistance gene were purchased from Dharmacon, UK. Packaging, virus production and determination of titre were carried out as previously reported (Badodi et al., 2017). Cells were infected overnight at a multiplicity of infection (MOI) of 1. After 96h from the infection, puromycin selection at a concentration of 2.5 µg/ml was applied to enrich for the transduced population. The efficacy of gene silencing was assessed by qRT-PCR or Western blot analysis.

tag: shRNA

value: shCHD7, line 3021

tag: antibody


title: CUT&Tag_TX1072_XO_H3K4me1_d4_r2


title: Low PAC 2

tag: strain

tag: tissue


title: dietD14071610_hypo_1

city: BEIJING

first: Yingga

last: Wu

state: BEIJING

address: No.1 West Beichen Road,Chaoyang District

country: China

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

data_processing:
Sub-pixel Registration used for basecalling
FASTQ raw data files were measured by using fastQC (www.bioinformatics.bbsrc.ac.uk/projects/fastqc/) quality control tool
Raw reads were aligned to the Mus musculus reference genome (GRCm38) using HISAT2-2.1.0 (Kim et al., 2015; Pertea et al., 2016) and Samtools-1.2 modules (Li et al., 2009).
FeatureCounts (Liao et al., 2014) tool in Subread-5.0 (Liao et al., 2013) was used to get counts for each sample from BAM files which was obtained from alignment step.
Counts were normalized by the trimmed means of M values (TMM normalization) (Robinson and Oshlack, 2010) method in the edgeR (Anders et al., 2013; Lund et al., 2012; McCarthy et al., 2012; Robinson et al., 2010; Robinson and Oshlack, 2010; Robinson and Smyth, 2007) package.
Supplementary_files_format_and_content: Excel file with gene counts for every gene and every sample

source_name: Hypothalamus

extract_protocol:
Hypothalamus was cut from total brain and total RNA was extratced using Trizol reagent.
RNA libraries were prepared for sequencing using standard Beijing Genomic Institute (BGI) protocols.

value: Hypothalamus

value: 20%fat 20%protein diet


title: dietD14071610_hypo_2


title: CUT&Tag_TX1072_XO_H3K4me1_d4_r1

value: TX1072 XO


title: dietD14071607_hypo_2

value: 20%fat 5%protein diet


title: dietD14121906_hypo_2

value: 20%fat 2.5%protein diet


title: Low PAC 1

tag: Sex


title: dietD14071607_hypo_1

tag: treatment


title: dietD14121905_hypo_2

value: 20%fat 1%protein diet


title: Scramble, anti-H3K27me3, line 3021, replica 2

description:
Processed file obtained by merging replicas
K27_Scr_3021_peaks.broadPeak

value: Scarmble, line 3021


title: Scramble, anti-BMI1, line 3021, replica 2

description:
Processed file obtained by merging replicas
BMI1_Scr_3021_peaks.narrowPeak


title: Control_water 5


title: dietD14121905_hypo_1


title: CUT&Tag_TX1072_XO_H3K27ac_d4_r1

value: Day 4

value: CAST / C57BL/6

value: CUT&Tag

value: Mouse embryonic stem cells


title: CUT&Tag_TX1072_XO_H3K9me3_d4_r2


title: shCHD7, Input, line 3021, replica 2

description: Input file only used as background

value: shCHD7,line 3021


title: dietD14071604_hypo_2

value: 60%fat 20%protein diet


title: Scramble, Input, line 3021, replica 2

description: Input file only used as background

value: Scramble,line 3021


title: dietD14071604_hypo_1


title: CUT&Tag_TX1072_XO_H3K4me3_d4_r1


title: shCHD7, anti-H3K4me3, line 3021, replica 2

description:
Processed file obtained by merging replicas
K4_shC_3021_peaks.narrowPeak


title: dietD14071601_hypo_2

value: 60%fat 5%protein diet


title: dietD14071601_hypo_1


title: Control_water 1

value: female

value: 8 weeks

value: gavaged with water

value: Intestinal tissue


title: shCHD7, anti-BMI1, line 3021, replica 2

description:
Processed file obtained by merging replicas
BMI1_shC_3021_peaks.narrowPeak

value: shCHD7, line 3021


title: CUT&Tag_TX1072_XO_H3K27ac_d4_r2

value: TX1072 XO


title: dietD14121904_hypo_2

value: Hypothalamus

value: 60%fat 2.5%protein diet


title: CUT&Tag_TX1072_XO_IgG_d2_r2

value: IgG

value: Day 2


title: dietD14121904_hypo_1


title: dietD14121906_hypo_1

value: 20%fat 2.5%protein diet


title: dietD14121903_hypo_1

value: 60%fat 1%protein diet


title: DTaP_stim_20

city: Marcy L'Etoile

first: Emilie

last: Chautard

address: 1541 Avenue Marcel Mérieux

country: France

institute: Sanofi

description: 16h in vitro incubation with RPMI medium and pertussis antigens pool

data_processing:
Cellranger mkfastq v3.0.2 to generate FASTQ
Cell Ranger count v3.0.2 to generate 10X filtered output files
Genome_build: Sscrofa11.1, Ensembl release 98
Supplementary_files_format_and_content: [Cellranger files]

organism: Sus scrofa domesticus

source_name: PBMC

extract_protocol:
Cell suspension was mixed with master mix and loaded with Single Cell 3′ Gel Beads and Partitioning Oil into a Single Cell 3′ Chip. RNA transcripts from single cells were uniquely barcoded and reverse-transcribed within droplets. cDNA molecules were pooled and the cDNA pool then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library.
10x Genomics Chromium 3' v3 Single Cell Gene Expression Kit

treatment_protocol: PBMC extraction using ficoll gradient followed by 16h in vitro incubation with RPMI medium

value: Gottingen

value: blood

value: post natal month 12

value: 2 DTaP immunization followed by 1 Tdap injection


title: dietD14121903_hypo_2


title: shCHD7, anti-H3K27me3, line 3021, replica 1


title: shCHD7, anti-H3K4me3, line 3021, replica 1


title: CUT&Tag_TX1072_XO_IgG_d2_r1

value: CAST / C57BL/6

value: CUT&Tag

value: Mouse embryonic stem cells


title: DTaP_ctrl_6

description: 16h in vitro incubation with RPMI medium


title: DTaP_stim_1


title: CUT&Tag_TX1072_XO_H3K4me3_d4_r2

value: Day 4


title: Scramble, anti-H3K4me3, line 3021, replica 2

description:
Processed file obtained by merging replicas
K4_Scr_3021_peaks.narrowPeak

value: Scarmble, line 3021


title: CUT&Tag_TX1072_XO_H3K36me3_d2_r2


title: CUT&Tag_TX1072_XO_H2AK119ub_d2_r2


title: Scramble, anti-H3K27me3, line 3021, replica 1


title: shCHD7, anti-BMI1, line 3021, replica 1

value: shCHD7, line 3021


title: TBS_ctrl_24

value: 3 TBS injections


title: CUT&Tag_TX1072_XO_H3K36me3_d2_r1

value: TX1072 XO


title: TBS_ctrl_5


title: DTaP_ctrl_1


title: Scramble, anti-H3K4me3, line 3021, replica 1


title: Scramble, anti-BMI1, line 3021, replica 1


title: CUT&Tag_TX1072_XO_H3K27me3_d2_r2


title: Control-1

city: Beijing

first: Liangquan

last: Zhu

email: 1367391894@qq.com, sunshijing@dbn.cn

address: No. 8, Zhongguancun South Street, Haidian District

institute: China Institute of Veterinary Drug Control

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to reference genome
count counting
Genome_build: MacFas_5.0
Supplementary_files_format_and_content: TXT file contain counts for each sample

organism: Macaca fascicularis

source_name: blood

growth_protocol: On day 4 p.i., blood was collected from nonpregnant experimental monkeys. Total RNA was extracted and purified. The purity, molar concentration and integrity of RNA were determined by Nanodrop, Qubit 2.0, and Aglient 2100, respectively, to ensure that the samples used for transcriptomic sequencing were qualified.

extract_protocol:
Total RNA was extracted from cell  by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 4200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: injected with PBS

value: female

value: 3 years old

tag: weight

value: about 2.5kg


title: S2-4

value: immunized with Brucella live vaccine S2 strain


title: Control-2

value: male


title: CUT&Tag_TX1072_XO_H3K27me3_d2_r1

value: Day 2


title: S2-3

value: blood


title: CUT&Tag_TX1072_XO_H2AK119ub_d2_r1


title: shCHD7, Input, line 3021, replica 1

description: Input file only used as background


title: S2-2


title: CUT&Tag_TX1072_XO_H3K9me3_d2_r2


title: S2-1


title: Vector -2

city: West Lafayette

first: Qing

last: Deng

state: Indiana

address: 915 W. State Street

department: Department of Biological Sciences

institute: Purdue University

data_processing:
Base calling and quality scoreing were performed by Real-Time Analysis (RTA) v2
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 zebrafish genome using STAR (v2.5) RNA-seq aligner with the following parameter “--outSAMmapqUnique 60”.
Uniquely mapped sequencing reads were assigned to genes using featureCounts (from subread v1.5.1) with the following parameters: “-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 edgeR (v3.20.8).
Genome_build: GRCz11
Supplementary_files_format_and_content: Raw counts

organism: Danio rerio

source_name: neutrophils

growth_protocol: zebrafish embryos were grow to 3 day post fertilization in embryonic media

extract_protocol:
tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing.
mRNA sequencing library were constructed withSMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Clontech Laboratories, Inc.).

treatment_protocol: transgenic zebrafish lines were used to produce embryos. For miR-99 target discovery, transgenic lines expressing miR-99 or a vector control together with a GFP reporter were used.

value: neutrophils

tag: genotype/variation

value: overexpressing vector


title: shCHD7, anti-H3K27me3, line 1299, replica 2

description:
Processed file obtained by merging replicas
K27_shC_1299_peaks.broadPeak

value: shCHD7,line 1299


title: 27_high proviral copies

city: Kraków

first: Tomasz

last: Szmatola

address: Redzina 1c

department: OMEI

country: Poland

institute: University of Agriculture in Krakow

data_processing:
The raw sequences were quality controlled using FastQC.
Flexbar software was used to remove Illumina adapters, reads of low quality (<20 phred quality) and shorter than 35.
The raw reads were aligned to the Capra hircus ARS1 (GCA_001704415.1)  with Tophat software on default settings
The obtained reads were counted with the use of htseq-count which were the input for DESeq2 analysis
The differential expression estimation was proceed with utilization of DESeq2 Bioconductor R-project package.
Genome_build: Capra hircus ARS1 (GCA_001704415.1)
Supplementary_files_format_and_content: Text files (.txt) containing raw gene counts used for DESeq2 analysis

organism: Capra hircus

source_name: whole blood

extract_protocol:
The total RNA was isolated from whole blood of  goats selected based on of provirus copy number,  and which were the most homogeneous within the groups. Isolation was performed using MagMAX™ for Stabilized Blood Tubes RNA Isolation Kit (Thermo Fisher Scientific), according to the protocol. The possible RNA contamination with DNA was removed using TURBO DNase™ (Thermo Fisher Scientific). The quality and quantity of obtained RNA were check using Nanodrop 2000 Spectrophotometer (Thermo Scientific) and TapeStation 2200 System (Agilent) using Agilent RNA ScreenTape (Agilent). The samples with RIN (RNA integrity number) value above 8 were used to further analysis.
The cDNA libraries were prepared from 300ng of total RNA by using TruSeq RNA Kit v2 kit (Cat#FC-122-1001) according to protocol.

tag: viral load

value: high

tag: breed

value: Carpathian goat

tag: gender


title: 8_high proviral copies


title: CUT&Tag_TX1072_XO_H3K9me3_d2_r1

tag: target

value: CAST / C57BL/6

value: CUT&Tag

tag: cell type

value: Mouse embryonic stem cells


title: Scramble, Input, line 3021, replica 1

description: Input file only used as background

value: Scarmble, line 3021


title: shCHD7, anti-H3K4me3, line 1299, replica 2

description:
Processed file obtained by merging replicas
K4_shC_1299_peaks.narrowPeak


title: CUT&Tag_TX1072_XO_H3K4me1_d2_r2

tag: cell line

value: TX1072 XO

tag: condition


title: CUT&Tag_TX1072_XO_H3K4me1_d2_r1

tag: replicate

tag: strain background


title: shCHD7, anti-BMI1, line 1299, replica 2

description:
Processed file obtained by merging replicas
BMI1_shC_1299_peaks.narrowPeak

tag: shRNA


title: CUT&Tag_TX1072_XO_H3K27ac_d2_r2

tag: assay


title: 31_high proviral copies

value: female


title: 32_high proviral copies


title: 33_high proviral copies


title: 30_low proviral copies

value: low


title: 15_low proviral copies


title: Scramble, anti-H3K27me3, line 1299, replica 2

description:
Processed file obtained by merging replicas
K27_Scr_1299_peaks.broadPeak

value: Scarmble, line 1299

tag: antibody


title: 26_low proviral copies

tag: tissue


title: CUT&Tag_TX1072_XO_H3K27ac_d2_r1


title: Scramble, anti-BMI1, line 1299, replica 2

description:
Processed file obtained by merging replicas
BMI1_Scr_1299_peaks.narrowPeak


title: CUT&Tag_TX1072_XO_H3K4me3_d2_r2


title: Scramble, anti-H3K4me3, line 1299, replica 2

description:
Processed file obtained by merging replicas
K4_Scr_1299_peaks.narrowPeak


title: 12_low proviral copies


title: 25_low proviral copies


title: CUT&Tag_TX1072_XO_H3K4me3_d2_r1


title: 4_low proviral copies


title: 6_high proviral copies


title: shCHD7, Input, line 1299, replica 2

description: Input file only used as background


title: atypical medullary, biol rep not relevant

type: RNA

city: Olomouc

first: Jan

last: Bouchal

address: Hnevotinska 3

department: Department of Clinical and Molecular Pathology

country: Czech Republic

institute: Palacky University

description: miRNA expression data from the microdissected tissue

hyb_protocol: Total RNA was polyadenylated, labeled, ligated by FlashTag and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The arrays were then washed using Affymetrix Fluidic station 450, and scanned using the Gene Chip Scanner 3000 7G.

data_processing: For the microarray analysis, the resulting CEL files were read andprocessed by R, ver. 3.5.0 (2018-04-23) (R Core Team, 2018). RMA procedure was applied for pre-processing. The linear models for microarrays (limma) were applied for comparison of resulting miRNA expression in tumor and non-tumor morphologies. Expression feature set in R (Eset.RData) is provided along with CEL files.

label: biotin

source_name: atypical medullary TNBC

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: not relevant

extract_protocol: Total RNA including small RNA was purified from microdissected FFPE samples using the AllPrep DNA/RNA FFPE kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.

treatment_protocol: not relevant

value: FFPE (formalin-fixed paraffin-embedded) tissue

tag: genotype

value: female Caucasian

tag: age

value: 28  years

tag: ptnm

value: pT1c   pN0   pMx


title: CUT&Tag_TX1072_XO_IgG_d0_r2

value: IgG

value: Day 0


title: mucinous-hyalinized, biol rep not relevant

source_name: hyalinized structures of mucinous TNBC

value: 61  years

value: pT1b   pN0   pMx


title: secretory, biol rep not relevant

source_name: secretory TNBC

value: 54  years


title: pure medullary, biol rep not relevant

source_name: pure medullary TNBC

value: 38  years


title: shCHD7, anti-H3K27me3, line 1299, replica 1

value: shCHD7,line 1299


title: Scramble, Input, line 1299, replica 2

description: Input file only used as background

value: Scramble,line 1299


title: micropapillary-periphery, biol rep not relevant

source_name: periphery of micropapillary morphology of TNBC

value: 67  years


title: micropapillary-centre, biol rep not relevant

source_name: centre of micropapillary morphology of TNBC


title: mucinous-cell cluster, biol rep not relevant

source_name: cell cluster within mucinous TNBC


title: Scramble, anti-H3K27me3, line 1299, replica 1

source_name: Tumour Sample


title: cribriform, biol rep not relevant 1

source_name: cribriform structures of TNBC

value: 78  years

value: pT1c   pN1   pMx


title: tumor with rich ECM, biol rep not relevant

source_name: tumor with rich extracellular matrix (ECM)


title: shCHD7, anti-BMI1, line 1299, replica 1

value: shCHD7, line 1299


title: cribriform, biol rep not relevant 2

value: 63  years

value: pT1a   pN0   pMx


title: CUT&Tag_TX1072_XO_H2AK119A_d0_r2

source_name: Mouse embryonic stem cells

value: TX1072 XO

value: CAST / C57BL/6

value: CUT&Tag

value: Mouse embryonic stem cells


title: CUT&Tag_TX1072_XO_IgG_d0_r1

value: IgG

value: Day 0


title: CUT&Tag_TX1072_XO_H2AK119ub_d0_r1


title: tubular, biological rep 4

source_name: tubular structures of TNBC

value: FFPE (formalin-fixed paraffin-embedded) tissue

value: female Caucasian

value: 69  years

value: pT1c   pN0   pMx


title: CUT&Tag_TX1072_XO_H3K36me3_d0_r2


title: tubular, biological rep 3


title: tubular, biological rep 2

value: 47  years


title: CUT&Tag_TX1072_XO_H3K36me3_d0_r1


title: tubular, biological rep 1


title: shCHD7, Input, line 1299, replica 1

description: Input file only used as background

value: shCHD7,line 1299


title: giant-cell, biol rep not relevant

source_name: presence of giant-cells

value: 54  years

value: pT1b   pN0   pMx


title: CUT&Tag_TX1072_XO_H3K27me3_d0_r2


title: Scramble, anti-BMI1, line 1299, replica 1

value: Scarmble, line 1299


title: CIS lymphocytic infiltration, biological rep 2

source_name: CIS lymphocytic infiltration

value: 76  years


title: CIS lymphocytic infiltration, biological rep 3

value: 70  years


title: Scramble, Input, line 1299, replica 1

description: Input file only used as background

value: Scramble,line 1299


title: CUT&Tag_TX1072_XO_H3K27me3_d0_r1

value: TX1072 XO

value: CAST / C57BL/6


title: CIS lymphocytic infiltration, biological rep 1

value: pT1c   pN1   pMx


title: tumor lymphocytic infiltration, biological rep 3

source_name: tumor lymphocytic infiltration

value: 28  years


title: tumor lymphocytic infiltration, biological rep 4

value: 66  years


title: CUT&Tag_TX1072_XO_H3K9me3_d0_r2

value: Day 0

value: CUT&Tag

value: Mouse embryonic stem cells


title: spindle, biological rep 8

source_name: spindle cell morphology of TNBC

value: FFPE (formalin-fixed paraffin-embedded) tissue

value: female Caucasian

value: pT1c   pN0   pMx


title: Scramble, anti-H3K4me3, line 1299, replica 1


title: spindle, biological rep 7


title: shCHD7, line 3021, replica 2

value: shCHD7, line 3021


title: tumor lymphocytic infiltration, biological rep 2

value: 63  years


title: shCHD7, line 3021, replica 1


title: CUT&Tag_TX1072_XO_H3K9me3_d0_r1


title: CUT&Tag_TX1072_XO_H3K4me1_d0_r2


title: tumor lymphocytic infiltration, biological rep 1

value: 47  years


title: spindle, biological rep 5

value: 50  years


title: spindle, biological rep 6


title: spindle, biological rep 4


title: CUT&Tag_TX1072_XO_H3K4me1_d0_r1


title: Scarmble, line 3021, replica 2

value: Scarmble, line 3021


title: spindle, biological rep 3

value: 38  years


title: CUT&Tag_TX1072_XO_H3K27ac_d0_r2

value: TX1072 XO


title: spindle, biological rep 2

value: 74  years


title: spindle, biological rep 1

value: pT1c   pN1   pMx


title: Scarmble, line 3021, replica 1


title: shCHD7, line 1299, replica 2

value: shCHD7, line 1299


title: CUT&Tag_TX1072_XO_H3K27ac_d0_r1

value: CAST / C57BL/6


title: apocrine, biological rep 10

source_name: apocrine cell morphology of TNBC

value: 66  years


title: CUT&Tag_TX1072_XO_H3K4me3_d0_r2

value: Day 0

value: CUT&Tag


title: apocrine, biological rep 9

value: FFPE (formalin-fixed paraffin-embedded) tissue

value: pT1b   pN0   pMx


title: shCHD7, anti-H3K4me3, line 1299, replica 1


title: apocrine, biological rep 8

value: female Caucasian

value: pT1c   pN0   pMx


title: apocrine, biological rep 5


title: shCHD7, line 1299, replica 1


title: Scarmble, line 1299, replica 1

value: Scarmble, line 1299


title: apocrine, biological rep 6

value: 70  years


title: apocrine, biological rep 4

value: 61  years


title: CUT&Tag_TX1072_XXdXic_IgG_d4_r2

value: TX1072 XXdXic

value: IgG

value: Day 4

value: Mouse embryonic stem cells


title: Scarmble, line 1299, replica 2


title: A549_JUND_FLAG cells treated with DEX for 12h - input control - rep3

city: Durham

first: Charles

middle: A

last: Gersbach

state: North Carolina

address: 101 science drive rm 2323

institute: Duke University

description: ChIP-seq

data_processing:
Sequences for TruSeq Illumina adapters were removed from the raw reads using Trimmomatic v0.32 (Bolger et al., 2014).
Single-end reads were mapped using Bowtie (v1.0.0 PMID: 19261174) against hg38 genome with flags -v 2 -X 2000 --best --strata -m 1.
Aligned reads were assigned to genes in the GENCODE v22 comprehensive gene annotation using the featureCounts command in the subread package with default settings (v1.4.6-p4)
Duplicates were removed using Picard MarkDuplicates v1.130
Low mappability or blacklisted regions identified by the ENCODE project (Consortium, 2012) were filtered out from the final BAM files
Using the sequenced input controls, binding regions were identified using the callpeak function in MACS2 v2.1.0.20151222 (Zhang et al., 2008).
Signal files were generated with deeptools bamCoverage (v3.0.1 PMID:24799436) ignoring duplicates, extending reads 200bp and converting the read counts to RPKMs.
Genome_build: hg38
Supplementary_files_format_and_content: bigWig signal in RPMs

extract_protocol:
Harvested plates at timepoints (0, 1, 4, 8, 12)
ChIP-seq libraries were prepared using a Kapa Hyper Prep kit.

treatment_protocol: Treated with 100 uM Dexamethasone

tag: time point

value: adenocarcinomic human alveolar basal epithelial


title: CUT&Tag_TX1072_XXdXic_H2AK119ub_d4_r2


title: apocrine, biological rep 2

value: 55  years


title: apocrine, biological rep 3

value: 54  years

value: pT1c   pN1   pMx


title: apocrine, biological rep 1

value: 36  years


title: invasive, biological rep 10

source_name: invasive front of TNBC

value: 63  years

value: pT1a   pN0   pMx


title: A549_JUND_FLAG cells treated with DEX for 12h - input control - rep1

description: ChIP-seq


title: invasive, biological rep 11

value: FFPE (formalin-fixed paraffin-embedded) tissue


title: invasive, biological rep 9

value: female Caucasian

value: 66  years


title: CUT&Tag_TX1072_XXdXic_H2AK119ub_d4_r1

value: CAST / C57BL/6

value: CUT&Tag


title: CUT&Tag_TX1072_XXdXic_H3K36me3_d4_r2


title: invasive, biological rep 7


title: A549_JUND_FLAG cells treated with DEX for 08h - input control - rep3

description: ChIP-seq


title: invasive, biological rep 8

value: pT1b   pN0   pMx


title: invasive, biological rep 6

value: pT1c   pN0   pMx


title: apocrine, biological rep 7

value: 70  years


title: A549_JUND_FLAG cells treated with DEX for 08h - input control - rep2

description: ChIP-seq


title: A549_JUND_FLAG cells treated with DEX for 08h - input control - rep1

description: ChIP-seq


title: CUT&Tag_TX1072_XO_H3K4me3_d0_r1

value: TX1072 XO

value: Day 0


title: invasive, biological rep 5


title: CUT&Tag_TX1072_XXdXic_IgG_d4_r1

value: TX1072 XXdXic

value: IgG

value: Day 4

value: Mouse embryonic stem cells


title: invasive, biological rep 3


title: CUT&Tag_TX1072_XXdXic_H3K27me3_d4_r2


title: CUT&Tag_TX1072_XXdXic_H3K27me3_d4_r1


title: invasive, biological rep 2

value: 55  years


title: A549_JUND_FLAG cells treated with DEX for 04h - input control - rep1

description: ChIP-seq

value: adenocarcinomic human alveolar basal epithelial


title: invasive, biological rep 1

value: 36  years


title: CIS, biological rep 9

source_name: ductal carcinoma in situ

value: FFPE (formalin-fixed paraffin-embedded) tissue


title: A549_JUND_FLAG cells treated with DEX for 01h - input control - rep2

description: ChIP-seq


title: CUT&Tag_TX1072_XXdXic_H3K9me3_d4_r2


title: CUT&Tag_TX1072_XXdXic_H3K9me3_d4_r1


title: CIS, biological rep 8

value: female Caucasian

value: 61  years


title: CIS, biological rep 7

value: 63  years

value: pT1a   pN0   pMx


title: CIS, biological rep 6

value: 66  years

value: pT1b   pN0   pMx


title: CIS, biological rep 5

value: pT1c   pN0   pMx


title: CUT&Tag_TX1072_XXdXic_H3K4me1_d4_r2

value: CAST / C57BL/6

value: CUT&Tag


title: A549_JUND_FLAG cells untreated - input control - rep3

description: ChIP-seq


title: CIS, biological rep 3

value: 78  years

value: pT1c   pN1   pMx


title: CUT&Tag_TX1072_XXdXic_H3K36me3_d4_r1

value: TX1072 XXdXic

value: Day 4


title: CIS, biological rep 4

value: 54  years


title: A549_JUND_FLAG cells untreated - input control - rep2

description: ChIP-seq

value: adenocarcinomic human alveolar basal epithelial


title: CUT&Tag_TX1072_XXdXic_H3K4me1_d4_r1

value: Mouse embryonic stem cells


title: CIS, biological rep 2

value: FFPE (formalin-fixed paraffin-embedded) tissue

value: 74  years


title: CIS, biological rep 1

value: female Caucasian

value: 70  years


title: CUT&Tag_TX1072_XXdXic_H3K27ac_d4_r2


title: normal, biological rep 14

source_name: normal ducts and lobules, tumor adjacent

value: 63  years

value: pT1a   pN0   pMx


title: A549_JUND_FLAG cells untreated - input control - rep1

description: ChIP-seq


title: invasive, biological rep 4

value: 76  years


title: CUT&Tag_TX1072_XXdXic_H3K27ac_d4_r1


title: A549_JUND_FLAG cells treated with DEX for 01h - input control - rep3

description: ChIP-seq


title: A549_JunB_FLAG cells treated with DEX for 12h - input control - rep3

description: ChIP-seq


title: normal, biological rep 13

value: 66  years

value: pT1c   pN0   pMx


title: normal, biological rep 11

value: 28  years


title: CUT&Tag_TX1072_XXdXic_H3K4me3_d4_r2

value: CAST / C57BL/6

value: CUT&Tag


title: normal, biological rep 10

value: pT1b   pN0   pMx


title: A549_JunB_FLAG cells treated with DEX for 12h - input control - rep2

description: ChIP-seq


title: normal, biological rep 12

value: 50  years


title: A549_JUND_FLAG cells treated with DEX for 01h - input control - rep1

description: ChIP-seq


title: A549_JunB_FLAG cells treated with DEX for 12h - input control - rep1

description: ChIP-seq


title: normal, biological rep 7

value: 47  years


title: CUT&Tag_TX1072_XXdXic_H3K4me3_d4_r1

value: TX1072 XXdXic

value: Day 4


title: CUT&Tag_TX1072_XXdXic_IgG_d2_r2

value: IgG

value: Day 2

value: Mouse embryonic stem cells


title: normal, biological rep 6

value: FFPE (formalin-fixed paraffin-embedded) tissue

value: female Caucasian

value: 61  years


title: normal, biological rep 4

value: 74  years


title: CUT&Tag_TX1072_XXdXic_IgG_d2_r1


title: normal, biological rep 3

value: 67  years


title: A549_JunB_FLAG cells treated with DEX for 08h - input control - rep2

description: ChIP-seq

value: adenocarcinomic human alveolar basal epithelial


title: A549_JunB_FLAG cells treated with DEX for 08h - input control - rep3

description: ChIP-seq


title: normal, biological rep 2

value: pT1c   pN1   pMx


title: CUT&Tag_TX1072_XXdXic_H2AK119ub_d2_r2

value: CAST / C57BL/6


title: A549_JunB_FLAG cells treated with DEX for 08h - input control - rep1

description: ChIP-seq


title: normal, biological rep 1

value: 36  years

value: pT1c   pN0   pMx


title: CUT&Tag_TX1072_XXdXic_H2AK119ub_d2_r1

value: CUT&Tag


title: A549_JunB_FLAG cells treated with DEX for 04h - input control - rep3

description: ChIP-seq


title: Pat17_Ctrl_4

city: Freiburg

first: Roman

last: Sankowski

address: Breisacher Str. 64

department: Institute of Neuropathology

institute: University of Freiburg Medical Center

description: library of 192

data_processing:
For image aquisition, intensity extraction and basecalling HiSeq Control Software 2.0.2, RTA 2.4.11 / Recipe Fragment 2.0.0.2
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all gene models based on the mouse ENCODE VM9 release downloaded from the UCSC genome browser comprising 57,207 isoforms derived from 57,207 gene loci with 57,114 isoforms mapping to fully annotated chromosomes (1 to 19, X, Y, M). All isoforms of the same gene were merged to a single gene locus. Furthermore, gene loci overlapping by >75% were merged to larger gene groups. This procedure resulted in 34,111 gene groups.
The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier (UMI). The remainder of the left read contains a poly(T) stretch. The left read was not used for quantification. For each cell barcode, the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus.
The number of observed UMIs was converted into transcript counts using Seurat v3 (Stuart*, Butler*, et al. Cell 2019, doi: https://doi.org/10.1016/j.cell.2019.05.031).
Genome_build: human ENCODE V24 release
Supplementary_files_format_and_content: CSV files, columns represent each cell barcode (total barcodes used = 192), rows represent the geneid and the values in the file are the quantified number of transcripts.

molecule: polyA RNA

source_name: Temporal Lobe

growth_protocol: Patients must have provided informed consent for inclusion into the study

extract_protocol:
Dapi-CD45+Lin- cells were FACS sorted into 384-well plates
As described in mCEL-Seq2 protocol (Hashimshony et al. 2016 and Herman et al. 2018)
Adapted from TruSeq Small RNA Library Preparation Protocol

treatment_protocol: Control samples were surgically removed from radiologically healthy brain regions. GBM samples were from viable tumor regions. All samples were confirmed histologically

tag: group

value: Ctrl

value: CD45+Lin- FACS-sorted cells


title: CUT&Tag_TX1072_XXdXic_H3K36me3_d2_r2

value: TX1072 XXdXic


title: Pat17_Ctrl_3

description: library of 192


title: normal, biological rep 9

value: 38  years


title: normal, biological rep 8

value: 63  years


title: Pat17_Ctrl_2

description: library of 192


title: CUT&Tag_TX1072_XXdXic_H3K36me3_d2_r1

value: Day 2

value: Mouse embryonic stem cells


title: Pat17_Ctrl_1

description: library of 192


title: A549_JunB_FLAG cells treated with DEX for 04h - input control - rep2

description: ChIP-seq


title: A549_JunB_FLAG cells treated with DEX for 04h - input control - rep1

description: ChIP-seq


title: Pat16_IDHmut_GBM_2

description: library of 192


title: Pat16_IDHmut_GBM_1

description: library of 192


title: normal, biological rep 5

value: FFPE (formalin-fixed paraffin-embedded) tissue

value: female Caucasian

value: 78  years


title: A549_JunB_FLAG cells treated with DEX for 01h - input control - rep3

description: ChIP-seq


title: Pat15_IDHmut_GBM_2

description: library of 192


title: Pat15_IDHmut_GBM_1

description: library of 192


title: Pat14_IDHwt_GBM_2

description: library of 192


title: A549_JunB_FLAG cells treated with DEX for 01h - input control - rep2

description: ChIP-seq


title: CUT&Tag_TX1072_XXdXic_H3K9me3_d2_r2


title: Pat14_IDHwt_GBM_1

description: library of 192


title: A549_JunB_FLAG cells treated with DEX for 01h - input control - rep1

description: ChIP-seq


title: CUT&Tag_TX1072_XXdXic_H3K9me3_d2_r1


title: Pat13_IDHwt_GBM_1

description: library of 192


title: A549_JunB_FLAG cells untreated - input control - rep3

description: ChIP-seq


title: Pat12_Ctrl_3

description: library of 192


title: CUT&Tag_TX1072_XXdXic_H3K4me1_d2_r2


title: Pat13_IDHwt_GBM_2

description: library of 192


title: A549_JunB_FLAG cells untreated - input control - rep2

description: ChIP-seq


title: CUT&Tag_TX1072_XXdXic_H3K4me1_d2_r1


title: Pat11_Ctrl_4

description: library of 192


title: CUT&Tag_TX1072_XXdXic_H3K27me3_d2_r2


title: Pat12_Ctrl_1

description: library of 192


title: A549_JunB_FLAG cells untreated - input control - rep1

description: ChIP-seq


title: Pat12_Ctrl_2

description: library of 192


title: Pat11_Ctrl_2

description: library of 192


title: A549_FOSL2_FLAG cells treated with DEX for 12h - input control - rep3

description: ChIP-seq


title: CUT&Tag_TX1072_XXdXic_H3K27ac_d2_r2


title: Pat11_Ctrl_1

description: library of 192


title: CUT&Tag_TX1072_XXdXic_H3K27ac_d2_r1


title: Pat10_IDHmut_GBM_2

description: library of 192


title: CUT&Tag_TX1072_XXdXic_H3K27me3_d2_r1


title: Pat10_IDHmut_GBM_1

description: library of 192


title: A549_FOSL2_FLAG cells treated with DEX for 12h - input control - rep2

description: ChIP-seq


title: Pat9_IDHwt_GBM_4

description: library of 192


title: A549_FOSL2_FLAG cells treated with DEX for 12h - input control - rep1

description: ChIP-seq


title: CUT&Tag_TX1072_XXdXic_H3K4me3_d2_r2


title: Pat9_IDHwt_GBM_3

description: library of 192


title: CUT&Tag_TX1072_XXdXic_H3K4me3_d2_r1


title: A549_FOSL2_FLAG cells treated with DEX for 08h - input control - rep3

description: ChIP-seq


title: Pat9_IDHwt_GBM_1

description: library of 192


title: CUT&Tag_TX1072_XXdXic_IgG_d0_r2

value: IgG

value: Day 0


title: Pat8_IDHmut_GBM_1

description: library of 192


title: Pat8_IDHmut_GBM_2

description: library of 192


title: A549_FOSL2_FLAG cells treated with DEX for 08h - input control - rep2

description: ChIP-seq

value: adenocarcinomic human alveolar basal epithelial


title: CUT&Tag_TX1072_XXdXic_IgG_d0_r1

value: CAST / C57BL/6


title: Pat11_Ctrl_3

description: library of 192


title: A549_FOSL2_FLAG cells treated with DEX for 08h - input control - rep1

description: ChIP-seq


title: Pat7_Ctrl_4

description: library of 192


title: CUT&Tag_TX1072_XXdXic_H2AK119ub_d0_r2


title: Pat7_Ctrl_2

description: library of 192


title: Pat7_Ctrl_3

description: library of 192


title: A549_FOSL2_FLAG cells treated with DEX for 04h - input control - rep3

description: ChIP-seq


title: CUT&Tag_TX1072_XXdXic_H2AK119ub_d0_r1


title: Pat6_Ctrl_4

description: library of 192


title: Pat6_Ctrl_2

description: library of 192


title: Pat7_Ctrl_1

description: library of 192


title: A549_FOSL2_FLAG cells treated with DEX for 04h - input control - rep2

description: ChIP-seq


title: CUT&Tag_TX1072_XXdXic_H3K36me3_d0_r2


title: Pat9_IDHwt_GBM_2

description: library of 192


title: CUT&Tag_TX1072_XXdXic_H3K36me3_d0_r1


title: Pat5_IDHmut_GBM_3

description: library of 192


title: A549_FOSL2_FLAG cells treated with DEX for 04h - input control - rep1

description: ChIP-seq


title: Pat5_IDHmut_GBM_4

description: library of 192


title: Pat5_IDHmut_GBM_2

description: library of 192


title: A549_FOSL2_FLAG cells treated with DEX for 01h - input control - rep3

description: ChIP-seq


title: A549_FOSL2_FLAG cells treated with DEX for 01h - input control - rep2

description: ChIP-seq


title: Pat5_IDHmut_GBM_1

description: library of 192


title: CUT&Tag_TX1072_XXdXic_H3K27me3_d0_r1


title: Pat4_Ctrl_4

description: library of 192


title: Pat4_Ctrl_3

description: library of 192


title: A549_FOSL2_FLAG cells treated with DEX for 01h - input control - rep1

description: ChIP-seq


title: CUT&Tag_TX1072_XXdXic_H3K9me3_d0_r2


title: Pat6_Ctrl_3

description: library of 192


title: Pat4_Ctrl_2

description: library of 192


title: A549_FOSL2_FLAG cells untreated - input control - rep3

description: ChIP-seq


title: CUT&Tag_TX1072_XXdXic_H3K9me3_d0_r1


title: Pat4_Ctrl_1

description: library of 192


title: Pat3_IDHwt_GBM_1

description: library of 192


title: A549_FOSL2_FLAG cells untreated - input control - rep2

description: ChIP-seq


title: Pat6_Ctrl_1

description: library of 192


title: A549_FOSL2_FLAG cells untreated - input control - rep1

description: ChIP-seq


title: Pat2_IDHwt_GBM_1

description: library of 192


title: CUT&Tag_TX1072_XXdXic_H3K27me3_d0_r2


title: Pat1_Ctrl_5

description: library of 192


title: Pat1_Ctrl_4

description: library of 192


title: Pat1_Ctrl_3

description: library of 192


title: A549_FOSL1_FLAG cells treated with DEX for 12h - input control - rep3

description: ChIP-seq


title: CUT&Tag_TX1072_XXdXic_H3K27ac_d0_r1


title: Pat1_Ctrl_1

description: library of 192


title: CUT&Tag_TX1072_XXdXic_H3K4me3_d0_r2


title: A549_FOSL1_FLAG cells treated with DEX for 08h - input control - rep3

description: ChIP-seq


title: Pat2_IDHwt_GBM_2

description: library of 192


title: CUT&Tag_TX1072_XXdXic_H3K4me3_d0_r1


title: A549_FOSL1_FLAG cells treated with DEX for 08h - input control - rep1

description: ChIP-seq


title: Pat3_IDHwt_GBM_2

description: library of 192


title: CUT&Tag_TX1072_XXdXic_H3K4me1_d0_r2


title: CUT&Tag_TX1072_XXdXic_H3K4me1_d0_r1


title: A549_FOSL1_FLAG cells treated with DEX for 04h - input control - rep3

description: ChIP-seq


title: CUT&Tag_TX1072_XXdXic_H3K27ac_d0_r2


title: A549_FOSL1_FLAG cells treated with DEX for 12h - input control - rep2

description: ChIP-seq


title: A549_FOSL1_FLAG cells treated with DEX for 04h - input control - rep2

description: ChIP-seq


title: Pat1_Ctrl_2

description: library of 192


title: A549_FOSL1_FLAG cells treated with DEX for 04h - input control - rep1

description: ChIP-seq