title: MAb-ID bulk GATC NPC_d6 control

city: Utrecht

first: Robin H.

last: van der Weide

state: Utrecht

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

data_processing:
Reads of the raw sequencing output conform to a MAb-ID specific layout of 5'-[3 nt UMI][4 nt SBC part 1][3 nt UMI][4 nt SBC part 2]AGGGCCGC[8 nt ABBC][genomic sequence]-3'. Raw R1-reads were demultiplexed on the expected barcode-sequences using CutAdapt 3.047, with the following custom settings. First, we only allow matches with at least a 29 nt overlap and only keep reads directly starting with the adapter (i.e., an anchored 5’ adapter). The maximum error rate setting of 2 makes it possible to retain reads with 1) two mismatches in the specified adapter-sequence (ignoring the UMI) and 2) a one nucleotide insertion or deletion (indel) at the start of the read due to digestion-ligation or sequencing(-library) errors. Demultiplexed reads are parsed through a custom script to classify reads on correct adapter-structures on a 7-tiered range. Reads in class-1 adhere perfectly to the barcode-expectations, while class-7 reads only contain the AGGGCCGC-sequence at the expected location. Reads typically fall into class 1 (average for figure 1: 95%). This classification allows fine control on which reads should be retained. For this manuscript, we only allow classes 1 and 2 (1 nucleotide indel in the first UMI) to ensure the highest possible quality. Finally, the script creates a fastq.gz-file, adding the UMI-sequences to the read-ID for downstream processing and removing the adapter sequence. Custom pipelines and scripts are available on https://github.com/KindLab.
Demultiplexed and filtered reads were processed in a similar fashion to Rooijers et al.13, with the additional flexibility to set the selected restriction site motif. Briefly, reads are aligned using Bowtie version 2.4.148 in unpaired mode, using default end-to-end parameters. We used the UCSC hg19 reference genome for K562 samples and the NCBI mm10 reference genome for mESC/mEN-samples (both references were downloaded from https://benlangmead.github.io/aws-indexes). Alignments with a mapping quality lower than 10 or not at the expected ligation-site (5’ for the MboI-motif or 5’+ 1 for the MseI-motif) were discarded. For reads originating from mixed sorting single-cell samples (e.g., K562 and mESC), a new hybrid reference genome was built by concatenating hg19 and mm10. Aligned reads to this reference were subsequently mapped to the individual references for further downstream processing by Bowtie using the --very-sensitive -N 1 parameters. Mouse allele-specific reads were assigned by mapping mm10-reads to 129/Sv and Cast/Eij reference genomes. We designated reads to one of the genotypes if it mapped better (i.e., lower edit-distance or higher alignment-score) to one of the references.
Aligned reads are UMI-flattened and counted per restriction site, like in the scDamID-protocol. We allowed up to 1000 UMI’s per site in the bulk analyses and up to 2 UMI’s per site in the single-cell analyses. UMI-counts per sample were binned (5kb, 20kb, and 100kb), loaded into R and stored into singleCellExperiment-containers. Counts in bins overlapping regions of known problematic nature (i.e., blacklist-regions55) or low mappability are set to zero. Normalization of the data was performed by calculating RPKM-values for both samples and control (see eq. 1) and calculating the fold-change over control with a pseudocount of 1.
Assembly: UCSC hg19 and NCBI mm10
Supplementary files format and content: bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of UMI's at a given genomic coordinate.
Supplementary files format and content: MM files are sparse matrices and generated using the Matrix R package. Columns denote single cells, rows denote 100kb genomic bins, and values denote the number of UMI-flattened counts.
Library strategy: MAb-ID

growth_protocol: All cell lines were grown in a humidified chamber at 37 °C in 5% CO2, and were routinely tested for mycoplasma. K562 cells were cultured in suspension on 10-cm dishes in Roswell Park Memorial Institute 1640 (RPMI 1640, Gibco, 61870010) supplemented with 10% FBS (Sigma, F7524, lot BCBW6329) and 1% Pen/Strep (Gibco, 15140122). Cells were passaged every 2-3 days. Mouse F1 hybrid Cast/EiJ x 129SvJae embryonic stem cells (mESCs; a gift from the Joost Gribnau laboratory) were cultured on 6-well plates with irradiated primary mouse embryonic fibroblasts (MEFs) in mESC culture media (CM) defined as follows: Glasgow's MEM (G-MEM, Gibco, 11710035) supplemented with 10% FBS, 1% Pen/Strep, 1x GlutaMAX (Gibco, 35050061), 1x MEM non-essential amino acids (Gibco, 11140050), 1 mM sodium pyruvate (Gibco, 11360070), 0.1 mM β-mercaptoethanol (Sigma, M3148) and 1000 U/mL ESGROmLIF (EMD Millipore, ESG1107). mESCs were alternatively cultured in feeder-free conditions on gelatin coated plates (0.1% gelatin, in house) in 60%-BRL medium, defined as a mix of 40% CM medium (as defined) and 60% conditioned CM medium (incubated 1 week on Buffalo Rat Liver cells), supplemented with 10% FBS, 1% Pen/Strep, 1x GlutaMAX, 1x MEM non-essential amino acids, 0.1 mM β-mercaptoethanol and 1000 U/mL ESGROmLIF. Cells were split every 2-3 days and medium was changed every 1-2 days. This mESC cell line does not contain a Y chromosome. To harvest, cells were washed once with Phosphate Buffered Saline (PBS, in house) and incubated with TrypLE Express Enzyme (Gibco, 12605010) for 3 minutes at 37 °C. Cells were dissociated by pipetting and TrypLE was inactivated by diluting cells five-fold in CM medium, before proceeding with fixation and permeabilization as described.

extract_protocol:
Cells were harvested (~10 x 106 cells) and washed once with PBS. All centrifugation steps were at 200 g for 4 minutes at 4 °C. Cells were fixated in 1% formaldehyde (Sigma, F8875) in PBS for 5 minutes, before quenching the reaction with 125 mM final concentration of glycine (Sigma, 50046) and placing the cells on ice. All subsequent steps were performed on ice or at 4⁰C. Cells were washed three times with PBS before resuspension in Wash buffer 1 (20mM HEPES pH 7.5 (Gibco, 15630-056), 150 mM NaCl, 66.6 µg/mL Spermidine (Sigma, S2626), 1X cOmplete™ protease inhibitor cocktail (Roche, 11697498001), 0.05% Saponin (Sigma, 47036), 2mM EDTA) and transferred to a 1.5 mL protein LoBind Eppendorf tube (Eppendorf, EP0030108116-100EA). Cells were permeabilized for 30 minutes at 4 ⁰C on a tube roller. Bovine Serum Albumin (BSA, Sigma, A2153) was added to 5 mg/mL final concentration and incubated for another 60 minutes at 4 ⁰C on a tube roller. Permeabilized nuclei were used for antibody incubation.
Samples ligated with unique SBC adapters were pooled, either 2-4 1000 nuclei samples or a full 384-well plate were pooled for combined in vitro transcription (IVT). To reduce batch effects, controls (secondary antibody-conjugates without primary antibody incubation) were pooled with their corresponding samples whenever possible. For 384-well plates, mineral oil was removed by spinning the sample for 2 minutes at 2000 g and transferring the liquid phase to a clean tube, which was repeated three times. After pooling, samples were incubated for 10 minutes with 1.0 volume CleanNGS magnetic beads (CleanNA, CPCR-0050), diluted 1:4 to 1:10 in bead binding buffer (20% PEG 8000, 2.5 M NaCl, 10 mM Tris–HCl, 1 mM EDTA, 0.05% Tween 20, pH 8.0 at 25 °C). The bead dilution ratio depended on the total volume, 1:4 for 1000 nuclei samples and 1:10 for a full 384-well plate. Samples were placed on a magnetic rack (DynaMag™-2, ThermoFisher, 12321D) to collect beads on the side of the tube. Beads were washed two times with 80% ethanol and briefly allowed to dry before resuspending in 8 µL water. In vitro transcription was performed by adding 12 µL IVT mix from the MEGAScript T7 kit (Invitrogen, AM1334) for 14 hours at 37 ⁰C before holding at 4 ⁰C. Library preparation was subsequently performed as described previously 13,46, using 5 µL of aRNA and 8 to 11 PCR cycles, depending on the aRNA yield. Purified aRNA from different IVT reactions (with unique SBC adapters) can be pooled before proceeding with cDNA synthesis to reduce batch effects. Libraries were run on the Illumina NextSeq500 platform with high output 1x75 bp, the Illumina NextSeq2000 platform with high output 1x100 bp or the Illumina NextSeq2000 platform with high output 2x100 bp.

treatment_protocol: For differentiation towards the neural lineage, mESCs were taken in culture on MEFs and subsequently passaged 3 times in feeder-free conditions in 60%-BRL medium. On day 0 of the differentiation, mESCs were plated on gelatin-coated 6-well plates (0.15% gelatin, Sigma, G1890) at a density of 2.5 x 104 cells per cm2 in N2B27 medium defined as follows: 0.5x Dulbecco's Modified Eagle Medium/Nutrient Mixture F-12 (DMEM-F12, Gibco, 11320033), 0.5x Neurobasal medium (Gibco, 21103049), 15mM HEPES (Gibco, 15630080), 0.5x N-2 supplement (Gibco, 17502048), 0.5x B-27 serum-free supplement (Gibo, 17504044) and 0.1 mM β-mercaptoethanol. From day 3 of differentiation, cells were washed daily with DMEM-F12 medium and refreshed with N2B27 medium. To harvest on day 5 of differentiation, cells were washed once with DMEM-F12 and incubated for 1 minute at room temperature with Accutase Enzyme Detachment Medium (Invitrogen, 00-4555-56). Cells were dissociated by pipetting and Accutase was inactivated by diluting cells ten-fold in DMEM-F12 or N2B27 medium, before proceeding with fixation and permeabilization as described.

tag: cell count


title: MAb-ID bulk TTAA NPC_d6 control

status: Public on Sep 20 2023

type: SRA

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: cell line


title: RP58N

city: Kalyani

first: Partha

middle: P.

last: Majumder

state: West Bengal

country: India

institute: National Institute of Biomedical Genomics

library_source: transcriptomic

data_processing:
Raw sequencing reads were converted to FASTQ files; data quality was assessed using FASTQC (https://qubeshub.org/resources/fastqc). Low quality reads and adapter sequences were removed. RNA-sequence data were processed in accord with the TCGA mRNA Analysis pipeline (https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline/).
Assembly: hg19 (NCBI 37)
Supplementary files format and content: TXT

molecule: total RNA

organism: Homo sapiens

source_name: biopsy of normal

extract_protocol:
total RNA was extracted using RNeasy kit (QIAGEN)
RNA sequencing libraries were generated using TruSeq RNA Library Prep Kit v2 (Illumina), following the manufacturer’s protocol

tag: tissue

value: biopsy of normal

tag: patient id

tag: recurrence

value: NR

tag: survival

value: ALIVE

tag: age

tag: Sex

value: Male

tag: tobacco

value: YES

tag: grade

value: ModeratelyDifferentiated


title: A rep 8

city: Muenster

first: Marcos

middle: J.

last: Araúzo-Bravo

address: Rogentstrasse

department: Cell and Developmental Biology

country: Germany

institute: Max Planck Institute for Molecular Biomedicine

description: replicate 8

data_processing:
Isolated eccDNAs were mapped with Circle_Finder integrating the mm10 built of the mouse genome. The minNonOverlap between two split reads equaled to 10.  eccDNA sizes were assessed from mt-free DNAs, indicating that 100Kb is a cutoff for all short circles.
eccDNAs with a length greater than Lmax = 100Kb were filtered out. Clusters of circles within a distance smaller than Dmin = 10b were merged and summed up as split reads of the merged circles.  Split reads with less than two junction tags (JTmin = 2) were excluded.
Circle annotations were accomplished using bedtools intersect of the resulting eccDNA bed files, implementing a Genecodemm10.bed file with the gene coordinates.
To quantificy the produced per gene eccDNAs (PpGCs) we unified the circles based on genes, i.e., all the eccDNAs that carried the same gene or fragment of this gene were grouped together.  Unified eccDNAs were scaled by gene length, multiplying each Produced per Gene eccDNA i (PpGCi) by a scale factor LMax/Li,  where LMax is the length of the longest gene found in the dataset, and Li is the length of the gene i.
Data equalization was performed by the log2(PpGC+1) transform on of the quantified PpGCs. In-house software was used to merge the PpGCsresults into a single text file used in the downstream analysis in Matlab (MathWorks).  We performed quantile normalization to equalize the data and stabilized them through the log2 transform of the data plus one.  The heatmap of the most highly variable PpGCs, the hierarchical clustering dendrograms  (calculated using the unweighted pair group method with arithmetic mean and Euclidean distance measure),  and the PCAs were performed using in?home functions developed in Matlab (MathWorks).
Assembly: mm10
Supplementary files format and content: tab-delimited text file include log2 produced per gene eccDNAs (PpGCs) values for each sample

source_name: spinal cord

growth_protocol: The B6.Cg-Tg(SOD1*G93A)1Gur/J strain (stock # 004435, Jackson Laboratory, Bar Harbor, ME, USA) served to induce an ALS-like phenotype in Mus musculus. The ALS pathology is provoked by the constitutive overexpression of a human mutant superoxide dismutase1 gene (hSOD1G93A)  compromising the SOD1 capacity to neutralize superoxide anion radicals.  Motor symptoms in male mutants developed at ages between 18-21 weeks and were assessed according to a standardized,  investigator-neutral clinical score protocol.  Inclusion of males only required the manifestation of a severity score of 1 or 2 within the target age indicated.  Sex- and age-matched C57BL/6J mice served as controls.  Animals that did not timely develop a motor phenotype were excluded from the study.  Tissue extraction:  After score approval, animals were euthanized by an overdose of volatile isoflurane CP (CP Pharma, Burgdorf, Germany).  The spine was microscopically dissected from surrounding tissue, the vertebral column was opened and the myelon was exposed.  The spinal cord was excavated in toto, detached from meninges and transferred to ice-cold PBS.  The cervical segment was dissected from thoracic and lumbar parts, collected into Eppendorf tubes and immediately frozen at -80°C for further analysis.

extract_protocol:
Total DNA extracted from mouse cervical spinal cord was digested with exonuclease V (New England Biolabs) to remove linear DNA. 50,000 copies of the plasmid p4339, 20,000 copies of YGPM25009 and 10,000 copies of pBR322  were added as internal controls to 400ng of DNA per sample.  These DNA mixtures were incubated at 37C with 30IU exonuclease V (RecBCD), 1X NEBuffer 4, and 1mM ATP.  Every 24 hours, 30IU fresh exonuclease V and 1mM ATP was added to the reactions, which were incubated for 7 days in total.  After 7 days, exonuclease reactions were inactivated for 30 min at 70C and subjected to DNA clean-up  with Agencourt AMPure XP beads (BD) according to the manufacturer?s instructions.  Briefly, reactions were mixed with 1.8x beads solution and incubated at RT for 5 min to bind.  Supernatants were discarded, beads were washed twice with 80% ethanol and briefly evaporated.  DNA was eluted in 60microl of 10mM Tris-HCl, pH 8.  Removal of linear DNA was confirmed by PCR analysis of the presence of the Cox5b sequence in DNA before and after treatment.  15microl of exonuclease-digested DNA were subjected to rolling circle amplification using TruePrime RCA (4BaseBio) according to manufacturer's instructions.  Briefly, DNA was denatured for 3 min with buffer D and neutralized with buffer N.  Denatured DNA was mixed with enzyme 1, enzyme 2, dNTPs and reaction buffer and incubated at 30C for 48 hours.  Afterwards, reactions were inactivated for 10 min at 65C.
After DNA extraction from control and ALS samples, the phi29-polymerase amplified DNA strands were sheared into fragments of 200 bp and approx. 400(350bp) bp in size using a Covaris LE220 ultrasonicator (Covaris, Brighton, UK)  with operating parameters set as the following: 20s ultrasound, acoustic duty factor 25%, peak incident power 500W,  cycles per burst 500, 24 cycles.  Appropriate fragment size (200-500bp) was captured with the aid of AMPure XP beads (Agencourt, Beverly, USA).  Fragmented DNA was then incubated with Bacteriophage T4 DNA polymerase (ENZYMATICS, Beverly, USA)  for 30 min at 20C for trimming to obtain blunt ends devoid of 3'-overhangs or 5'-gaps, which were further 3?-adenlyated to create sticky ends.  These DNA fragments were ligated at both ends to T-tailed adapters and amplified via PCR according to the following step-wise procedures:  3 min at 95C followed by 8 cycles of 20 sec at 98C, 15 sec at 60C, 30 sec at 72C, 10 min at 72C for further elongation.  The obtained PCR products were purified via AMPure XP beads (Agencourt, Beverly).  The DNA library was sequenced on BGISEQ-500 by paired-end sequencing of 150bp intervals both from the forward and reverse strand,  with an average sequencing data of 138M reads per library, to provide high-quality alignment across all genomic regions.

treatment_protocol: After score approval, animals were euthanized by an overdose of volatile isoflurane CP (CP Pharma, Burgdorf, Germany). The spine was microscopically dissected from surrounding tissue, the vertebral column was opened and the myelon was exposed.  The spinal cord was excavated in toto, detached from meninges and transferred to ice-cold PBS.  The cervical segment was dissected from thoracic and lumbar parts, collected into Eppendorf tubes and immediately frozen at -80°C for further analysis.  DNA isolation : DNA extraction from individual cervical spinal cord samples of control and mutant animals was performed according  to kit-facilitated standard procedures (Nucleospin tissue DNA/RNA and Protein kit, Macherhey Nagel GmbH & Co KG, Germany).  Briefly, each tissue specimen was thawed and homogenized with a motorized pestle applying 25microl of proteinase k to the initial buffer system.  Each suspension was vortexed vigorously and the homogenate was kept at 56C overnight.  The next day, the samples were vortexed, supplemented by the indicated buffer solution and incubated at 70C for 10 min.  For DNA extraction, 210microl of ethanol were added to each sample suspension.  Solutions were poured on the nucleospin columns placed into the collection tubes and centrifuged at 11,000 x g for 1 min.  The flow-through was discarded and the columns were again centrifuged as aforementioned.  The extracted DNA was washed in 500 microl of appropriate buffer solution and centrifuged.  The flow-through was discarded and the column was centrifuged as before.  The washing step was repeated with an adequate buffer solution.  The flow-through was discarded and the empty column was centrifuged as before to dry the silica membrane,  then transferred to a sterile 1.5 ml Eppendorf tube.  The collected genomic DNA was eluted in 30 microl of appropriate pre-warmed buffer and incubated at RT for 2 min,  then centrifuged at 11,000 x g for 2 min.  The genomic DNA concentration of each sample was measured spectrophotometrically by NanoDrop systems.

value: spinal cord

tag: condition

value: ALS

tag: strain


title: MAb-ID bulk TTAA mESC control

source_name: mESC

value: mESC


title: LPL7_Pre GEX

city: Duarte

first: Szymon

last: Szymura

state: CA

address: 1500 E Duarte Rd

department: Toni Stephenson Lymphoma Center

country: USA

institute: City of Hope

description: scRNA-seq

library_source: transcriptomic single cell

data_processing:
The alignments, demultiplexing, barcode processing and gene counting was performed using CellRanger software version 3.1.0
Assembly: hg19
Supplementary files format and content: Matrix files of gene counts

source_name: bone marrow

extract_protocol:
Snap frozen bone marrow samples were thawed in culture media, washed with wash buffer and loaded onto 10x Genomics Chromium Chip
Library preparation for gene expression was performed using 5' 10x Genomics Kit according to manufacturer's protocol

value: bone marrow

value: primary cells

tag: cell type

value: bone marrow cells

tag: individual

value: Patient LPL7

tag: treatment

value: Pre


title: MAb-ID bulk GATC mESC control


title: RP57T

source_name: biopsy of tumor

value: biopsy of tumor


title: RP57N


title: LPL7_Post GEX

description: scRNA-seq

value: Post


title: A rep 3

description: replicate 3


title: A rep 4

description: replicate 4


title: RP57M

source_name: biopsy of margin

value: biopsy of margin


title: Control_tumorTreg_1

city: Bethesda

first: Thomas

middle: Joshua

last: Meyer

state: Maryland

address: 41 Center Drive, Building 41, Room B620

department: National Cancer Institute

institute: National Institutes of Health

data_processing:
Six mRNA-Seq samples were pooled and sequenced on NextSeq 2000 P2 using SMARTer ultra-low input RNA v4 -Nextera XT DNAand paired-end sequencing.
Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt before alignment with the reference genome (mm10) and the annotated transcripts (GENCODE_M21) using STAR.
The gene expression quantification analysis was performed for all samples using STAR/RSEM tools.
Low count genes were filtered prior to CPM and quantile normalization using Limma voom followed by differential expression of genes analysis.
Assembly: mm10; GENCODE_M21
Supplementary files format and content: Comma-separated values (.csv) file containing a matrix of normalized expression produced in this study.

source_name: tumor

growth_protocol: Not applicable.

extract_protocol:
Solid tumors were mechanically isolated, digested with Liberase TL and DNase I, tumor cells depleted on a Percoll gradient, and infiltrating cells washed and stained with Blue Live/Dead dye and antibodies against CD45, CD4, CD25, and sorted on a BD FACSAria Fusion. Total RNA was extracted using Qiagen RNeasy mini kits.
The SMARTer Ultra Low Input RNA Kit was used to generate cDNA, which was then made into a sequencing ready library using the Nextera® XT DNA Sample Preparation Kit from Illumina. The final purified sequencing ready library was quantitated by qPCR before cluster generation and sequencing on Illumina NextSeq 2000 P2 run.

treatment_protocol: Not applicable.

value: tumor

value: B16.F10 melanoma

tag: genotype

value: LiberaseTL+DNaseI digestion, FACS sorting

tag: time

value: day 15 after tumor inoculation


title: LPL6_Pre GEX

description: scRNA-seq

value: Patient LPL6


title: LPL8_Pre_Post HTO

description:
scRNA-seq
LPL8_barcodes.tsv.gz
LPL8_features.tsv.gz
LPL8_matrix.mtx.gz
HTO_details_README.txt

library_source: other

molecule: protein

value: Patient LPL8

value: Pre, Post


title: A rep 2

description: replicate 2

value: spinal cord

value: ALS


title: MAb-ID bulk mESC primary conjugate: H3K9me3

value: mESC

tag: cell count

tag: antibody


title: A rep 1

description: replicate 1

tag: tissue


title: MAb-ID bulk mESC primary conjugate: Lamin B1

tag: cell line

value: Lamin B1


title: LPL5_Pre GEX

description: scRNA-seq

value: bone marrow

value: primary cells

value: bone marrow cells

value: Patient LPL5


title: C rep 10

description: replicate 10

value: Control


title: RP56T

value: biopsy of tumor

tag: patient id

tag: recurrence

value: NR

value: ALIVE

value: Female

value: ModeratelyDifferentiated


title: A rep 5

description: replicate 5


title: C rep 9

description: replicate 9


title: LPL5_Post GEX

description: scRNA-seq

value: Post


title: MAb-ID bulk mESC primary conjugate: H3K4me1


title: RP56N

value: biopsy of normal

tag: survival

tag: age


title: MAb-ID bulk mESC primary conjugate: H3K36me3


title: RP58M

value: biopsy of margin

tag: Sex

value: Male

tag: tobacco

value: YES


title: C rep 8

description: replicate 8

value: spinal cord

tag: condition


title: MAb-ID bulk mESC primary conjugate: H3K27me3

value: mESC


title: LPL4_Pre GEX

description: scRNA-seq

value: bone marrow

value: Patient LPL4

value: Pre


title: RP56M

tag: grade


title: LPL4_Post GEX

description: scRNA-seq

value: primary cells

tag: cell type

value: bone marrow cells


title: C rep 7

description: replicate 7

value: Control

tag: strain


title: RP55T

value: biopsy of tumor

value: NR


title: LPL3_Pre GEX

description: scRNA-seq

tag: individual

value: Patient LPL3

tag: treatment


title: LPL2_Pre GEX

description: scRNA-seq

value: Patient LPL2


title: RP55M

value: ALIVE


title: scMAb-ID library (index 31)

description:
scMAbID_countMatrix_100kb_hg19.MM
scMAbID_countMatrix_100kb_mm10.MM

source_name: mESC, NPC_d6

value: mESC, NPC_d6

value: H3K9me3, H3K36me3, Lamin B1, H3K27me3, H3K27ac, H3K4me1


title: MAb-ID bulk mESC primary conjugate: H3K27ac


title: LPL3_Post GEX

description: scRNA-seq

value: Post


title: RP54N

value: biopsy of normal

value: R

value: DIED

value: Male

value: NO

value: PoorlyDifferentiated


title: C rep 5

description: replicate 5

value: spinal cord


title: RP54T


title: scMAb-ID library (index 12)


title: LPL2_Post GEX

description: scRNA-seq

value: bone marrow

value: primary cells

value: bone marrow cells


title: C rep 3

description: replicate 3

value: Control


title: C rep 4

description: replicate 4


title: C rep 6

description: replicate 6


title: scMAb-ID library (index 14)


title: C rep 2

description: replicate 2


title: RP54M

value: biopsy of margin


title: C rep 1

description: replicate 1


title: Mixed scRNA-seq Trichoplax sp. H2  and  Cladtertia collaboinventa 2 clicktags

city: Barcelona

first: Arnau

last: Sebe-Pedros

address: Dr. Aiguader 88

department: Systems Biology

country: Spain

institute: Centre for Genomic Regulation

description:
Cladtertia collaboinventa
Clicktags to demultiplex single-cells from H2 and H23. See Readme_ClickTag_demultiplexing.xlsx for details.
TrH2.umimatrix.cell_annotations.tsv
TrH2.umimatrix.genes.tsv
TrH2.umimatrix.mtx.gz
HoiH23.umimatrix.cell_annotations.tsv
HoiH23.umimatrix.genes.tsv
HoiH23.umimatrix.mtx.gz

data_processing:
scRNA-seq: We used CellRanger 6.1.1 (10X Genomics) to map reads and count unique molecular identifiers (UMIs) per gene per cell. We used the --force-cells flat to set a constant number of 20,000 per experiment (well in excess of the expected number cells for each case, as we intended to remove non-cells from the dataset using our own procedure; see below). We used whole gene bodies to guide the mapping of reads to the genome (--transcriptome flag). We also extended gene ranges to include proximal scRNA-seq peaks located downstream of each gene (in the region 5 kbp downstream of each gene, or less if another gene was closer to that peak). For details on clicktag barcode demultiplexing see Readme_ClickTag_demultiplexing.xlsx file.
ATAC-seq: Reads were mapped using bwa 0.7.17, using the mem algorithm. The resulting BAM files were filtered using the alignmentSieve utility from the deeptools 3.5.1 package, in order to filter out weak alignments (with minimum mapping quality or MAPQ = 30) and shifting the left and right ends of reads according to usual ATAC specifications (+4/−5 bp in the positive and negative strands, activated with the --ATACshift flag in deeptools). Duplicated reads were removed using biobambam2 2.0.87, and the resulting alignments were coordinate-sorted with the same tool. Then, we concatenated all the ATAC-seq libraries for each species. bigWig files were generated with deepTools v3.5.2 bamCoverage function.
ChIP-seq: The ChIP-seq libraries corresponding to H3K4me2 and H3K4me3 were mapped to their corresponding species with bwa mem, using the same procedure as described for ATAC-seq (except for the adjustment of read end coordinates specific to ATAC libraries).
Assembly: Trichoplax adhaerens: GCA_000150275.1
Assembly: Trichoplax sp. H2: GCA_003344405.1
Assembly: Hoilungia honkgongensis: https://bitbucket.org/molpalmuc/hoilungia-genome/src/master/
Assembly: Cladtertia collaboinventa: https://www.frontiersin.org/articles/10.3389/fevo.2022.1016357/full
Supplementary files format and content: For ATAC-seq and ChIP-seq: bigWig coverage files (bw extension)
Supplementary files format and content: For scRNA_seq: TSV file with CellIDs and associated metadata (in the same order as in the UMI matrix)
Supplementary files format and content: For scRNA_seq: TSV file with gene names associated to the UMI matrix
Supplementary files format and content: For scRNA_seq: MTX file containin gene x cell UMI counts

molecule: polyA RNA

organism:
Trichoplax sp. H2
Hoilungia sp. H23

source_name: Whole adult specimens

extract_protocol:
Cells were fixed using the ACME protocol (10.1186/s13059-021-02302-5), FACS sorted, and processed with the 10X Genomics Chromium Single Cell 3' scRNAseq v3.1 kit.
Adult specimens were fixed, dissociated and pooled before sorting single-cells for scRNAseq. The same procedure was followed for chromatin profiling experiments, except that cells were used fresh for ATAC-seq and fixed with 1% formaldehyde (10 min) for ChIP-seq

value: Whole adult specimens

tag: genotype

value: Wild type


title: RP53T

value: biopsy of tumor

value: NR

value: ALIVE

value: YES


title: Mixed scRNA-seq Trichoplax sp. H2  and  Cladtertia collaboinventa 2

description:
Cladtertia collaboinventa
TrH2.umimatrix.cell_annotations.tsv
TrH2.umimatrix.genes.tsv
TrH2.umimatrix.mtx.gz
HoiH23.umimatrix.cell_annotations.tsv
HoiH23.umimatrix.genes.tsv
HoiH23.umimatrix.mtx.gz


title: Hoilungia hongkongensis H3K4me2 ChIP-seq

organism: Hoilungia hongkongensis

extract_protocol:
ChIP-seq was performed as described in 10.1038/s41559-018-0575-6.
Adult specimens were fixed, dissociated and pooled before sorting single-cells for scRNAseq. The same procedure was followed for chromatin profiling experiments, except that cells were used fresh for ATAC-seq and fixed with 1% formaldehyde (10 min) for ChIP-seq

tag: chip antibody

value: ChIP-seq ab32356, Abcam


title: ATRT, CAL-SHH, scRNAseq, ATRT61

city: Paris

first: Mamy

middle: Jean de Dieu

last: ANDRIANTERANAGNA

state: Ile de France

address: 26 rue d'Ulm

department: Centre de Recherche

country: France

institute: Institut Curie

description: 10x Genomics

data_processing:
The demultiplexing, mapping, gene counting and aggregation were made using the Cell Ranger software v3.1.0
Assembly: hg19
Supplementary files format and content: Tab-separated values files and matrix files

source_name: tumor sample

extract_protocol:
Tumor samples cut in small pieces then dissociated 30 min at 37°C in CO2-independent medium (Gibco) + 0,4 g/l of human albumin (Vialebex) with Liberase TL (Roche) 150 mg/ml and DNase 1 (Sigma) 150 mcg/ml. Dissociated cells were then filtered with a 40 mm cell strainer, then washed and resuspended with C02-independent medium + 0,4 g/l of human albumin. Cells were then continuously maintained on ice or at 4°C. In case of lot of blood cells, the Debris removal kit (Miltenyi Biotec) was used according to the manufacturer’s protocol. To enrich in tumoral cells (human samples) the Tumor Cell Isolation Kit (Miltenyi Biotec) was used according to the manufactu  rer’s protocol. Cells were then resuspended in PBS + BSA 0.04%. Samples were prepared for concentration of 800 cell/mcl.
Sample preparations were loaded on a 10x Chromium instrument (10x Genomics) and libraries were prepared using a Single Cell 3’ Reagent Kit (V2 chemistry, 10X Genomics) according to the manufacturer’s protocol, targeting 1000 recovered cells per sample. Single cells were included and barcoded into droplets together with gel beads coated with unique barcodes, unique molecular identifiers (UMI), and poly(dT) sequences, followed by in droplet reverse transcription to generate barcoded full-length cDNA. cDNA was subsequently recovered from droplets, then cleaned up with Dynabead MyOne Silane Beads (Thermo Fisher Scientific), then amplified with the following protocol: 98°C- 3min; 12x (98°C-15s, 67°C-20s, 72°C-1 min); held at 4°C. Amplified cDNA product was cleaned up using the SPRI select Reagent Kit (Beckman Coulter). Indexed libraries were constructed following these steps: 1. Fragmentation, end repair and A-tailing; 2. Size selection with SPRI select beads; 3. Adaptor ligation; 4. Post-ligation cleanup with SPRI select beads; 5. Sample index PCR and final cleanup with SPRI selects beads. Library and quality assessment were achieved using dsDNA High Sensitivity Assay Kit and Bioanalyzer Agilent System. Indexed libraries were tested for quality, equimolarly pooled and sequenced on an Illumina HiSeq2500 using paired-end 26x98 bp as sequencing mode, targeting at least 50 000 reads par cell.

value: tumor cells

value: tumor sample

tag: age at_diagnosis_(year)


title: RP55N

tag: tissue

value: biopsy of normal

value: Male


title: RP53N

value: PoorlyDifferentiated


title: Mixed scRNA-seq Trichoplax sp. H2  and  Cladtertia collaboinventa 1 clicktags


title: Hoilungia hongkongensis H3K4me3 ChIP-seq

value: ChIP-seq antibody 07-473, Millipore


title: scMAb-ID library (index 16)

tag: cell line

value: mESC, NPC_d6

tag: cell count

tag: antibody

value: H3K9me3, H3K36me3, Lamin B1, H3K27me3, H3K27ac, H3K4me1


title: RP53M

tag: patient id

tag: recurrence

tag: survival


title: Mixed scRNA-seq Trichoplax sp. H2  and  Cladtertia collaboinventa 1


title: RP51T

tag: age

tag: Sex

tag: tobacco

value: NO


title: Hoilungia hongkongensis ATAC

extract_protocol:
ATAC-seq was performed using the Omni-ATAC protocol (10.1038/nmeth.4396) and using custom Tn5 enzyme
Adult specimens were fixed, dissociated and pooled before sorting single-cells for scRNAseq. The same procedure was followed for chromatin profiling experiments, except that cells were used fresh for ATAC-seq and fixed with 1% formaldehyde (10 min) for ChIP-seq


title: ATRT, CAL-SHH, scRNAseq, ATRT41

description: 10x Genomics

tag: cell type


title: Trichoplax adhaerens H3K4me3 ChIP-seq

organism: Trichoplax adhaerens


title: ATRT, CAL-SHH, scRNAseq, ATRT40

description: 10x Genomics


title: Hoilungia hongkongensis scRNA-seq 3

description:
Hhon.umimatrix.cell_annotations.tsv
Hhon.umimatrix.genes.tsv
Hhon.umimatrix.mtx.gz


title: CD8 Top 15 B

city: Amsterdam

first: Kaspar

last: Bresser

address: Plesmanlaan 125

department: Hematopoeisis

institute: Sanquin

data_processing:
Sequencing adapters were trimmed using cutadapt using the settings -n 2, -e 0.2 and -M 62.
aligned to the UTR library using bowtie2 in local mode
PCR hybrids that were generated during library amplification were removed from the alignment file using a custom script
Read counts were obtained using htseq-count
sequence motifs detected with less than 10 reads across all samples were excluded from the analysis, and individual libraries were normalized to 10,000 reads
Assembly: Not applicable
Library strategy: Amplicon sequencing

source_name: Primary CD8+ T cells

extract_protocol:
Retroviral library was produced by transfecting 4.5 ug of the library plasmid DNA into FLYRD18 retroviral packaging cells, as described above. HEK and HeLa cells were cultured to a density of 60% prior to addition of virus-containing supernatants, and subsequently expanded for 10 days. PBMCs were activated with αCD3/ αCD28 and spinfected with virus-containing supernatants, as described above, and expanded for 10 days in RPMI supplemented with 10% fetal bovine serum (FBS; Bodinco), 2 mM L-glutamine, 20 IU/mL penicillin G sodium salts, 20 μg/mL streptomycin sulfate (all Sigma Aldrich), Non-Essential Amino Acids (Gibco), Sodium pyruvate (Gibco), 50 IU/mL recombinant human (rh) IL-2 (Proleukin, Novartis), 5 ng/mL rhIL-15 (Peprotech), and 10 ng/mL rhIL7 (Miltenyi). Transduction efficiencies were kept between 5-10% in order to minimize multiple transgene integrations. After expansion cells were harvested and stained with Near-IR live/dead marker (Life Technologies) for dead cell exclusion, in addition to anti-CD8-AF700 (Biolegend) and anti-CD4-BV510 (Biolegend) in the case of the T cell assay. The top and bottom 15% GFP expressing cells, in addition to the full GFP-positive fraction, were sorted on a FACS Aria II (BD Biosciences). The sorted cells were subsequently pelleted and resuspended in 1 µl DirectPCR Lysis Reagent (Viagen) per 2,500 cells, supplemented with 0.5 mg/ml proteinase K (Viagen). The obtained lysate was incubated at 55 C for 3 hours, followed by 85 C for 45 minutes, and 95 C for 5 minutes.
An initial pre-amplification of the synthetic 3’UTRs was performed on 20 µl lysate (±50,000 cells) in a 100 µl reaction volume using the NEBnext kit (NEB) and 10 µM forward (5’-AAAGACCCCAACGAGAAGC-3’) and reverse (5’-AGTCTATAGCTACTAGGCG-3’) primers. An initial touchdown stage was performed dropping the annealing temperature 1 C per cycle from 58 C to 50 C (8 cycles), followed by 12 cycles at 50 C. Extension time was kept at 20 seconds. This initial PCR was performed in duplicate for each sample, as a technical control. Excess primers were removed from each reaction by incubating 20 µl of the initial PCR volume with 40 U Exonuclease I (NEB) at 37 C for 15 minutes, followed by a heat-inactivation at 80 C for 15 minutes. Each of these samples were subsequently used as template for a second PCR, with primers (Forward: 5’-ACACTCTTTCCCTACACGACGCTCTTCCGATCTAGACCCCAACGAGAAGCGCGATCAC-3’, Reverse: 5’-GACTGGAGTTCAGACGTGTGCTCTTCCGATCTAGTCTATAGCTACTAGGCGATA-3’) designed to amplify the product and attach partial Illumina adapters. This second PCR was performed using the NEBnext kit (NEB), and consisted of 16 cycles with a constant annealing temperature of 65 C and extension time of 30 seconds. Correct products (±275 base pairs) were purified from a 2% agarose gel using the Monarch® DNA Gel Extraction Kit (NEB). Purified products were sequenced using the Amplicon-EZ service from Genewiz (Azenta Life Sciences).

value: Primary CD8+ T cells


title: CD8 Top 15 A


title: RP51N

tag: grade


title: Trichoplax adhaerens H3K4me2 ChIP-seq

value: Whole adult specimens


title: Trichoplax adhaerens ATAC

value: Wild type


title: RP51M

value: biopsy of margin


title: RP50T

value: biopsy of tumor

value: NR


title: Hoilungia hongkongensis scRNA-seq 1


title: LPL1_Pre GEX

description: scRNA-seq

value: bone marrow

value: primary cells

value: bone marrow cells

tag: individual

value: Patient LPL1

value: Pre


title: Trichoplax adhaerens scRNA-seq 1

description:
Tadh.umimatrix.cell_annotations.tsv
Tadh.umimatrix.genes.tsv
Tadh.umimatrix.mtx.gz


title: LPL1_Post GEX

description: scRNA-seq

tag: treatment

value: Post


title: RP50N

value: biopsy of normal

value: ALIVE

value: Male

value: PoorlyDifferentiated


title: Vgat-Cre_vDNA_rep_3

city: St. Louis

first: Joseph

last: Dougherty

state: MO

address: Couch Biomedical Research Bldg 06316

department: Genetics

institute: Washington University of St. Louis

data_processing:
Barcodes were counted a custom python script. https://bitbucket.org/jdlabteam/mpra_lib_1.0_methods_paper/src/master/
Supplementary files format and content: hg19 derived sequences (120 bp context of 3' UTR)
Supplementary files format and content: tab-delimited text; barcode counts for each RNA and DNA sample.

growth_protocol: Cells were grown in basal medium (2% FBS in DMEM) with 1% penicillin-streptomycin at 37°C, 5% CO2.

extract_protocol:
N2a cells lifted in 250uL PBS and 750µL Trizol, followed by addition of 200uL chloroform and cleanup of the aqueous phase using the Zymo Clean and Concentrator 5 kit per manufacturer instructions. Vglut-cre and Vgat-cre brains were harvested at P21 and homogenized. Lysates were clarified and mixed 3:1 with Trizol, followed by addition of 200uL chloroform and cleanup of the aqueous phase using the Zymo Clean and Concentrator 5 kit per manufacturer instructions.
Reporter-specific cDNA synthesis using a reverse-complementary primer, followed by PCR, digestion, adapter ligation, and index PCR. DNA from viral prep/cells was prepared simultaneously, starting with the first PCR step.

treatment_protocol: Cells were transfected (lipofectamine) with MPRA plasmid library in basal medium without antibiotic for ~12 hours and collected 48 hours post-transfection

value: GABAergic interneurons

tag: strain

value: post natal day 21


title: CD8 Lib GFP B

value: Primary CD8+ T cells


title: ATRT, CAL-SHH, scRNAseq, ATRT50

description: 10x Genomics

value: tumor cells

value: tumor sample


title: Vgat-Cre_410_Rep_2


title: RP50M

value: biopsy of margin

value: NO


title: CD8 Bottom 15 B


title: CD8 Lib GFP A


title: Vgat-Cre_410_Rep_1


title: MRL_ActiveDisease_1

city: Charlottesville

first: Loren

last: Erickson

state: Virginia

address: 345 Crispell Drive

department: Department of Microbiology, Immunology, and Cancer Biology

institute: University of Virginia

description: 10x Genomics

data_processing:
Sequencing reads were processed with 10x Genomics Cell Ranger software (v 7.0.1) using the standard pipeline.
Assembly: mm10
Supplementary files format and content: Tab-separated value files and matrix files

source_name: Spleen

extract_protocol:
IL-10 producing B cells were isolated from total splenocytes using the Mouse Regulatory B Cell Isolation Kit (Miltenyi Biotech).
Libraries were prepared using 10x Genomics Chromium Single Cell 3' V3.1 chemistry (Dual Index) according to the manufacturer's protocol.

value: Spleen

tag: Stage

value: active-disease (10-12 weeks)

value: IL10+ B Cell

tag: genotype

value: MRL/Mp-Faslpr


title: MRL_ActiveDisease_2

description: 10x Genomics

tag: tissue


title: MRL_PreDisease_2

description: 10x Genomics

value: pre-disease (6-8 weeks)


title: RP49T

value: biopsy of tumor

value: R

value: DIED


title: Hoilungia hongkongensis scRNA-seq 2

value: Whole adult specimens

value: Wild type


title: CD8 Bottom 15 A


title: Vgat-Cre_vDNA_rep_1_L2

tag: cell line

value: GABAergic interneurons


title: RP49N

value: biopsy of normal

value: Male

value: PoorlyDifferentiated


title: MRL_PreDisease_1

description: 10x Genomics


title: CD4 Top 15 B

source_name: Primary CD4+ T cells

value: Primary CD4+ T cells


title: RP49M

value: biopsy of margin


title: Vgat-Cre_410_Rep_4

value: post natal day 21


title: Vgat-Cre_vDNA_rep_1


title: RP48T

value: NR

value: YES

value: WellDifferentiated


title: CD4 Top 15 A


title: Vgat-Cre_410_Rep_3


title: CD4 Bottom 15 A


title: CD4 Bottom 15 B


title: RP48N


title: ATGB24

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

institute: CIBEREHD

description:
CD31' endothelial cells of control naive mice
G3

data_processing:
Mapping of the reads were obtained using the STAR program against human genome (GRCm38) and the quantification of genes and transcripts were done with the RSEM program using  GENCODE.vM15 database .
We use TMM method and limma-voom transformation from rounded expected counts to normalize the non biological variability
Mus musculus (GRCm38)
Assembly: RSEM expected counts

source_name: RNAseq of CD31' endothelial cells of control naive mice

growth_protocol: Mice were anesthetized with isoflurane and euthanized by cervical dislocation. The brain was carefully collected and immersed in Hanks’ Balanced Salt solution w/o ions (HBSS w/o Ca2+ and Mg2+; #14175-053, Thermo Fisher Scientific) on ice. The forebrain was dissected with a scalpel, discarding the cerebellum and the olfactory bulbs, and the ipsilateral brain hemisphere was minced in small pieces. The Neural Tissue Dissociation Kit - P (NTDK, #130-092-628, Miltenyi Biotec) based on the enzymatic dissociation with papain was used to homogenize the tissue. Mechanical dissociation was performed with the gentleMACS™ Octo Dissociator (#130-096-427, Miltenyi Biotec: 1x m_Brain_1 program and 1x ABDK_37C program by Miltenyi) with the tissue immersed in the buffers and enzymes from the NTDK kit, according to manufacturer instructions. The tissue was then filtered through a 70 m cell strainer (#352350, Falcon) previously humidified with HBSS with Ca2+ and Mg2+ (#14025-092, Thermo Fisher Scientific). Then, cells were separated from myelin by an immunomagnetic separation method. Brain cells were incubated with Myelin Removal Beads II (#130-096-733, Miltenyi Biotec) and then passed through LS Columns (#130-042-401, Miltenyi Biotec) held onto the OctoMACS Separator (#130-091-051, Miltenyi Biotec) and to the MACS® MultiStand (#130-042-303, Miltenyi Biotec). Unspecific binding was blocked by incubation for 10 min with anti CD16/CD32 in FACS buffer at 4°C. Live/dead Aqua cell stain was used to determine the viability of cells. Cells were incubated with the following primary antibodies during 30 minutes at 4°C: CD11b (clone M1/70, APC-Cy7, #557657, BD Pharmingen), CD45 (clone 30-F11, FITC, #553080, BD Pharmingen), CD31 (clone 390, PE-Cyanine7, #25-0311-82, eBioscience). After washing with FACS Stain Buffer (#554656, BD Biosciences), the cells were sorted in a BD FACS Aria II or a FACS Aria SORP sorter (BD Biosciences). Endothelial cells were collected in sterile DPBS (#14190-094, Thermo Fisher Scientific), centrifuged, and resuspended in lysis buffer (from PureLink™ RNA Micro Kit #12183016, Invitrogen) supplemented with 10% β-mercaptoethanol and finally snap-frozen in dry ice.

extract_protocol:
RNA was extracted from samples of FACS-sorted endothelial cells with PicoPure™ RNA Isolation Kit (#KIT0204, Thermo Fisher Scientific) following manufacturer instructions with minor modifications. RNA was precipitated with 70% ethanol. To avoid genomic DNA contamination a DNAse step was performed using Invitrogen™ PureLink™ DNase Set (#12185010, Invitrogen). RNA quantity and purity were assessed with the Pico Kit Assay on the Agilent 2100 Bioanalyzer System.
SMARTseq2 NEBNext

treatment_protocol: no treatments

tag: group

value: control

value: brain


title: Vgat-Cre_410_Rep_6_L2


title: RP48M


title: C3

city: Guangzhou

first: Yao

last: Kong

address: Zhongshan Second Road

country: China

institute: Guangdong Provincial People's Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome (version:hg38) using HISAT2 (version:2.0.4).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: KRASG12D PADC NAT

extract_protocol:
The indicated KRASG12D PDAC tissues and NATs were harvested and subjected into extracting the total RNA by TRIZOL (Invitrogen, Carlsbad, CA, USA). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: KRASG12D PADC NAT


title: ATGB23


title: Vgat-Cre_410_Rep_5


title: ATGB19

description:
CD31' endothelial cells 1 day after ischemia (ipsilateral hemisphere)
G1

source_name: RNAseq of CD31' endothelial cells 1 day after ischemia (ipsilateral hemisphere)

value: ischemia


title: C2


title: RP47T

value: biopsy of tumor

value: R

value: ALIVE

value: NO

value: ModeratelyDifferentiated


title: RP47N

value: biopsy of normal

value: Male


title: ATGB18


title: C1


title: Vgat-Cre_410_Rep_6

value: GABAergic interneurons


title: ATGB26


title: Vgat-Cre_vDNA_rep_2_L2


title: RP47M

value: biopsy of margin


title: ATGB25


title: ATGB14


title: Vgat-Cre_410_Rep_1_L2

value: post natal day 21


title: ATGB12


title: RP46T

value: NR


title: N3

source_name: KRASG12D PDAC

value: KRASG12D PDAC


title: N2


title: RP46N

source_name: biopsy of normal


title: N1


title: RNAseq contralateral 9

description: RNAseq contralateral

growth_protocol: This method is used to precipitate endothelial cells from transgenic Ribotag-Pdgf-β1 Cre mice. Mice were anesthetized with isoflurane and euthanized by cervical dislocation. Brain tissue samples (cortex)  from  the ipsilateral (ischemic) and contralateral hemispheres were homogenized in 3% (weight-volume) buffer containing 1.5M TRIS pH 7.4, 1M KCl, 1M MgCl2 and 10% Igepal (#CA-630, Alfa Aesar) supplemented with 1M 1,4-Dithiothreitol (#3483-12-3, DTT Sigma Aldrich), protease inhibitors (#P8340, Sigma), 200 UI/ml RNAsin (#N2115, Promega), 5mg/ml cycloheximide (#C1988, Sigma) and heparin (ROVI, 5,000Ul/ml). Homogenization was performed in a 7 ml-glass Douncer homogenizer (#9063, Sigma) passing the pestle-A 15 times and 15 times more with the pestle-B. Then the lysate was incubated in rotation at 4°C with 2 mg/ml mouse monoclonal (IgG1, k) anti-hemagglutinin (HA.11 Epitope Tag) antibody (clone 16B12, #901513, Biolegend) for 3 hours. Then 300 ml Dynabeads Protein G (#10004D, Thermo Fisher Scientific) were added and the mix was incubated 2 more hours in the same conditions. Finally, a magnetic stand (#10723874, Invitrogen - DynaMag™-2) was used to remove all the non-bound sample. Several washes with a high-salt buffer were performed to ensure specific binding of the beads to our target sample. Lysis buffer (#74034, Qiagen) supplemented with 10% b-mercaptoethanol was added to elute the sample. Finally, the sample was separated from eluted magnetic beads by strong vortex.

extract_protocol: RNA from the Ribotag precipitated samples was purified with the RNeasy Plus Micro Kit (#74034, Qiagen) for elimination of genomic DNA. RNA was precipitated with 80% ethanol and the RNA was eluted with H2O RNase-free.

value: CC


title: RP46M


title: RNAseq ipsilateral 8

description: RNAseq ipsilateral

value: CI


title: Lut_2

city: tianjin

first: shijiao

last: cai

address: Qixiangtai road

institute: Tianjin Medical University

data_processing:
lllumina bcl2fastq 2.0 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence,and masked for low-complexity or low-quality sequen then mapped to rn6 whole genome using HISAT2.
Transcript abundance values were obtained from gene-level count matrices were generated by StringTie.
Gene counts were normalized using geometric mean in DESeq2 package.
Differential gene expression by DEseq2 was performed on normalized gene counts.
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: H22 was cultured using RPMI-1640 containing 10% fetal bovine serum and 1% penicillin–streptomycin at 5% CO2 and 37 °C.

extract_protocol:
RNA was harvested using Rneasy mini plus kit(Qiagen).1.3ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTERmRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: 200mg/kg luteolin or 0.5% carboxymethyl cellulose sodium were administered strictly once daily for 21 days in a volume of 0.2 ml when the tumor volume reached ∼50 mm3.

value: tumor

value: Hepatocellular carcinoma

value: WT

value: 200mg/kg luteolin


title: Lut_3


title: N3 rep3

source_name: PADC NAT

extract_protocol:
The indicated PDAC tissues and NATs were harvested and subjected into extracting the total RNA by TRIZOL (Invitrogen, Carlsbad, CA, USA). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: normal adjacent tissue


title: RP43T

value: biopsy of tumor

value: ALIVE

value: Female

value: YES

value: PoorlyDifferentiated


title: N2 rep2


title: RP43N

value: biopsy of normal


title: N1 rep1


title: Con_3

value: 0.5% carboxymethyl cellulose sodium


title: Lut_1


title: RNAseq contralateral 7

description: RNAseq contralateral

value: brain


title: RP43M

value: biopsy of margin

value: NR


title: RNAseq contralateral 3

description: RNAseq contralateral

value: CC


title: RNAseq ipsilateral 3

description: RNAseq ipsilateral

value: CI


title: Con_2

value: tumor


title: Vgat-Cre_vDNA_rep_2

value: GABAergic interneurons

value: post natal day 21


title: Con_1

value: Hepatocellular carcinoma

value: WT


title: RP42N

value: R

value: Male

value: ModeratelyDifferentiated


title: C2 rep2

source_name: PDAC

value: PDAC


title: RP42T

value: biopsy of tumor

value: ALIVE

value: YES


title: C3 rep3


title: C1 rep1


title: RP42M


title: RNAseq contralateral 1

description: RNAseq contralateral

value: brain


title: RNAseq ipsilateral 7

description: RNAseq ipsilateral


title: Nilotinib plus CQ

city: hangzhou

first: huang

last: xiangliang

address: hanzghou, China

institute: zhejiang university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm8
Supplementary files format and content: tab-delimited xls files include RPKM values for each sample.

source_name: HUVEC Cells

extract_protocol:
Cell culture supernatant was removed and RNA was harvested using TRIzol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA-seq libraries were prepared using Illumina RNA-Seq Preparation Kit.

value: Nilotinib plus CQ-treated

tag: time point

value: 12 hours after treatment


title: N4_8c4_1324 (18 months, male)

city: Saarbruecken

first: Gilles

last: Gasparoni

state: Saarland

address: Campus

department: Genetics Department

institute: Saarland University

description: RRBS with HaeIII restriction enzyme

data_processing:
after a quality control with FastQC (www.bioinformatics.bbsrc.ac.uk/projects/fastqc/), reads were adapter-trimmed (Q < 20) with Trim Galore! version 0.4.2 (www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
reads were aligned to mm10 assembly with the BWA (v0.6.2) wrapper methylCtools (v 0.9.2).
Samtools (v1.3) and Picard tools (v1.115) (http://broadinstitute.github.io/picard) were used for converting, merging, and indexing of the alignment files.
SNP aware realignment to identify single nucleotide polymorphisms (SNPs) for accurate identification of methylated cytosines and methylation calls were performed with the bisulfite SNP calling software Bis-SNP.
Assembly: mm10
Supplementary files format and content: bed file with CpG methylation values (chr, start, end, methylation, coverage, strand, start, end, qualityMetrics).

source_name: brain

extract_protocol:
100,000 cerebral endothelial cells were sort-ed in FACS buffer (1X PBS, 2%FCS and 2mM EDTA) at 4°C and centrifuged (500g, 5 minutes at, 4°C). The supernatant was discarded, the cells were snap frozen in liquid nitrogen and stored at –80°C till further processing. For lysing the cells, 200 µL solution A (25mM EDTA, 75mM NaCl), 200 µL solution B (10 mM EDTA, 10 mM Tris-HCl, 1% SDS) and 10 µL Proteinase K (20 µg/µL) were added to the frozen cell pellet, followed by a brief vortex and incubation at 55°C. Phenol-chloroform-isoamyl (25:24:1) and chloroform-isoamyl (24:1) were used for liquid phase separation of the genomic DNA. Glycogen (20 µg/ µL), 0.1x volume (20 µL) of 3M Sodium Ace-tate and 2.5x volume (500 µL) of ice-cold 100% ethanol were added and incubated overnight at –20°C for precipitation of genomic DNA. The pellet of genomic DNA obtained was washed with 70% ethanol and dissolved in 40 µL pre-warmed 1x Tris-EDTA (TE buffer) at 45°C for 2 hours. DNA concentration was measured using a Qubit double stranded high sensitivity DNA assay kit (Life Technologies) according to the manufacturer’s instructions. Restriction was performed on 26 µL DNA template using 1 µL HaeIII restriction enzyme (New England Biolabs) and 3 µL 10x Cutsmart buffer (New England Biolabs) at 37°C for 18 hours. A-Tailing was performed with 1 µl Klenow Fragment (3′ → 5′exo−, 5 U/µl, NEB) and 1 µl dATP (10 mM, NEB) at 37 °C for 30 min followed by enzyme inactivation at 75 °C for 20 min. Unique molecular identifier adapters (TruSeq Single Index Set B, Illumina) were ligated using 1 µl adapters (10 µM), 0.5 µl T4 Ligase (2,000 U/µl, NEB), 2 µl ATP (10 mM, NEB) and 1 µl Cutsmart buffer (10X, NEB)  at 16 °C for 18 hours, followed by enzyme inactivation 65°C for 20 minutes. Bisulfite conversion and subse-quent cleanup was performed using EZ-DNA Methylation Gold Kit (Zymo Research) according to the manufacturer’s instructions and the bisulfite-converted genomic library was eluted in 24 µL nuclease-free water. The library was amplified by polymerase chain reaction using 0.6 µl each of primers (10 µM, Primer i5: AATGATACGGCGACCACCGAGATCTACAC, Primer i7: CAA-GCAGAAGACGGCATACGAGAT), 0.6 µl Hot Start Taq (5 U/µl, Qiagen), 3 µl Hotstar PCR Buffer (10X, Qiagen), 1.2 µl MgCl2 (25 mM) and 2 µl dNTPs (10 mM) in a 30 µl reaction with 95°C for 15 min, 20 cycles of 95°C for 40 s, 58°C for 1 minute, 72°C for 1 min, 72°C for 12 min and hold at 4°C. The amplified RRBS library was cleaned using 0.8x volume (40 µL) of Ampure beads XP (Beckman Coulter) according to the manufacturer’s instruction and eluted in 20 µL of 0.1X TE buffer. Six animals (3 males and 3 females) belonging to each of the age-groups of 2, 6, 12, and 18 months (total n = 24) were used for RRBS. The RRBS library was analyzed with Bioanalyzer High-Sensitivity DNA Analysis kit (Agilent), and the concentration was determined using the Qubit HS DNA kit (Life Technologies). The sequencing was performed on Illumina HiSeq2500 sequencing system at the University of Saarland, Saarbrücken, and generated ap-prox. 50 Million 100 bp single-end reads per sample.ATAC-seq data processing. The adapter sequence and 3’ ends with base quality (PHRED score) of less than 20 in the FASTQ files obtained from the sequencing were trimmed with Trim Galore (v0.4.2) software. Following adapter trimming and removing low quality nucleotides, the FASTQ files were mapped to the mouse reference genome (GRCm38/mm10)  using the GEM62 mapper. Duplicated reads found after alignment with GEM mapper were annotated with Picard tools (v1.115) (http://broadinstitute.github.io/picard). MACS263 (v2.1.0) was used to call Nucleosome Depleted Regions (NDRs) after downsampling the reads into similar number to avoid any bias in the downstream analyses due to sequencing depth. The parameters used in the MACS2 were: –shift -100, –extsize 200, –nomodel and –keep-dup all. Differentially accessible regions were calculated using a linear model accounting for gender. Peaks which overlap with the black list regions defined by ENCODE (https://doi.org/10.1038/s41598-019-45839-z) were excluded from the analysis. RRBS data processing. Sequencing reads were trimmed using the Trim Galore (v0.4.2) soft-ware (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to remove the adapter contamination and the 3’ ends with base quality (PHRED score) of less than 20. The trimmed reads were then aligned to the mouse reference genome (GRCm38/mm10) using the BWA64 (v0.6.2) wrapper methylCtools65 (v0.9.2). Samtools66 (v1.3) and Picard tools (v1.115) (http://broadinstitute.github.io/picard) were used for converting, merging, and indexing of the alignment files. SNP aware realignment to identify single nucleotide polymorphisms (SNPs) for accurate identification of methylated cytosines and methylation calls were performed with the bisulfite SNP calling software Bis-SNP67. MethylKit68 (v1.3.1) was used for tiling (1kb tiles, min 3 CpGs per tile, each CpG with minimum coverage of 5) . Association of DNA methylation and ageing was calculated using a linear regression model with gender and coverage as covariates. Obtained p-values were corrected for multiple testing using Benjamini Hochberg correction.
endothelial cells from brain were FACS enriched.
RRBS protocol using restriction enzyme HaeIII
DNA was fragmented with HaeII restriction enzyme. Fragments were end-repaired and A-tailed, followed by NGS adaptor (methylated) ligation using T4 ligase. Fragments were then bisulfite converted and amplified by PCR.

treatment_protocol: all animals were wildtype, several subgroups of female and males with four different ages.

value: male

value: 18 months

value: FACS enriched brain endothelial cells


title: WT_iso1

first: Claudia

last: van Tiel

address: Meibergdreef 15

department: Medical Biochemistry

institute: Amsterdam UMC

data_processing:
Bases were called using Illumina CASAVA 1.8.2
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Skewer 0.2.2
Reads were aligned to the mouse genome mm10 by HISAT2 2.1.0
BAM files were indexed and filitered on MAPQ > 15 with SAM Tools 1.16.1
Raw tag counts per gene were counted using HOMER2's analyzeRepeats.pl script
Assembly: mm10
Supplementary files format and content: matrix of raw reads

source_name: spleen

extract_protocol:
Cells were lysed in RLT buffer and total RNA was isolated using the RNeasy mini kit with on-column DNase treatment (Qiagen)
RNA seq libraries were generated using the KAPA mRNA Hyperprep kit protocol

treatment_protocol: Single cell suspensions were prepared from spleens by meshing the organs through a 70-µm filter and red blood cells were lyzed by 5 minutes incubation  on ice in hypotonic lysis buffer followed by a PBS washing step and cells were resuspended in Flow Cytometry Buffer. Naïve CD4+ T cells were sorted using FACSAria II SORP cell sorter, spun down and  cultured in plates coated with with 1µg/ml αCD3e and either 19µg/ml αCD40L or 19µg/ml Isotype control.

value: spleen

value: CD4+ T cells

value: wt

value: isotype antibody


title: WT_iso3


title: N5_8c10_1325 (18 months, female)

description: RRBS with HaeIII restriction enzyme

value: female

value: WT


title: Nilotinib

value: Nilotinib-treated


title: RP40M

source_name: biopsy of margin

extract_protocol:
total RNA was extracted using RNeasy kit (QIAGEN)
RNA sequencing libraries were generated using TruSeq RNA Library Prep Kit v2 (Illumina), following the manufacturer’s protocol

value: biopsy of margin

tag: patient id

value: NR

value: Male

value: NO

value: ModeratelyDifferentiated


title: Control

value: Control


title: WT_CD40L3

value: αCD40L antibody


title: N7_8b1_1327 (18 months, male)

description: RRBS with HaeIII restriction enzyme

value: brain

value: male


title: RNAseq ipsilateral 1

description: RNAseq ipsilateral

value: CI


title: Blood_S7_MO

city: Madrid

first: Enrique

last: Vazquez de Luis

state: Madrid

address: Melchor Fernandez Almagro, 3

institute: CNIC

description: matched control: GSM4751527

data_processing:
Illumina Casava software used for basecalling and bcl2fastq for demultiplexing.
Sequenced reads quality was evaluated from FastQC.
Reads were trimmed for Illumina adaptors with cutadapt.
Reference Genome was indexed from RSem (Li B et al. 2011) and sequence reads were aligned using RSem.
RNA-Seq data were normalized using Transcripts Per Million (TPM) Trimmed Mean of M values (Robinson MD and A Oshlack 2010).
Genome_build: Human sequenced genome GRCh38 v91
Supplementary_files_format_and_content: Tab-delimited text files include raw, TPM and RPKM (Reads Per Kilobase Million) values for each sample.

source_name: Blood

extract_protocol:
Total RNA was isolated using RNeasy Micro Kit (Qiagen) and was quantified and purity checked using a NanoDrop ND-1000 (Thermo Scientific, Waltham, MA, USA). RNA integrity was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA)
Stranded: 200 ng of total RNA were used with NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs) to construct index-tagged cDNA libraries. Libraries were quantified using a Qubit™ dsDNA HS assay with the Qubit fluorometer (Life Technologies, Carlsbad, California). Average library size and the size distribution were determined using a DNA 1000 assay in an Agilent 2100 Bioanalyzer. Libraries were normalized to 10nM using Tris-Cl 10mM, pH8.5 with 0.1% Tween 20.
Low Input: Low Input RNAs were used to amplify the cDNA using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech-Takara). 1 ng of amplified cDNA was used to generate barcoded libraries using the Nextera XT DNA library preparation kit (Illumina). Libraries were quantified using a Qubit™ dsDNA HS assay with the Qubit fluorometer (Life Technologies, Carlsbad, California). Average library size and the size distribution were determined using a DNA 1000 assay in an Agilent 2100 Bioanalyzer. Libraries were normalized to 10nM using Tris-Cl 10mM, pH8.5 with 0.1% Tween 20.
Libraries were applied to an Illumina flow cell for cluster generation (SR Cluster Kit cBot) and sequence-by-synthesis single reads of 60 base length using the SBS Kit (Illumina) were generated on the HiSeq 2500 following the standard sequencing protocol. Reads were further processed using the bcl2fastq package (Illumina) to split reads according to adapter indexes and produce fastq files. RNA-Seq was performed at the Genomics Unit of the Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid.

value: Blood

tag: disease state

value: Sjogren's Syndrome

tag: library type

value: Stranded

value: Monocytes


title: N3_7b9_1323 (18 months, female)

description: RRBS with HaeIII restriction enzyme

value: female

tag: age

value: 18 months

value: FACS enriched brain endothelial cells


title: RP38N

value: biopsy of normal

tag: recurrence

tag: survival

value: ALIVE

tag: Sex


title: WT_CD40L1

value: spleen

tag: cell type

value: CD4+ T cells

value: wt


title: RP38T

source_name: biopsy of tumor

value: biopsy of tumor

value: NR

value: Male

tag: tobacco

value: NO

tag: grade

value: ModeratelyDifferentiated


title: WT_CD40L2

tag: strain

tag: treatment

value: αCD40L antibody


title: N2_7b7_1322 (18 months, female)

description: RRBS with HaeIII restriction enzyme

value: brain

tag: genotype

value: WT


title: Blood_S2_MO

description: matched control: GSM4751521

tag: tissue

value: Blood

value: Sjogren's Syndrome

value: Stranded

value: Monocytes


title: RP38M

value: biopsy of margin


title: KO_iso3

value: cre

value: isotype antibody


title: WT_iso2

value: spleen

value: CD4+ T cells


title: N6_3f2_1326 (18 months, male)

description: RRBS with HaeIII restriction enzyme

value: male

value: 18 months

value: FACS enriched brain endothelial cells


title: RP40N

value: biopsy of normal

value: NR

value: ALIVE

value: Male

value: NO


title: KO_iso2


title: RP37T

value: biopsy of tumor

value: ModeratelyDifferentiated


title: CQ

value: CQ-treated

value: 12 hours after treatment


title: RP40T


title: RP37N


title: KO_iso1


title: Blood_S1rep_MO

description: matched control: GSM4751518

value: Blood

value: Sjogren's Syndrome

value: Stranded

value: Monocytes


title: Blood_S7_CD1c

description: matched control: GSM4751525

value: Low Input

value: Dendritic Cells Cd1c+


title: RP37M

value: biopsy of margin


title: Adipoq overexpressed kidney rep3

city: Dallas

first: Toshiharu

last: Onodera

state: TX

address: 5323 Harry Hines Boulevard

department: Touchstone diabetes center

institute: UT Southwestern medical center

data_processing:
Indexes of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5).
Alignments were parsed using Tophat program
differential expressions were determined through DESeq2/edgeR
HTSeq v0.6.1 was used to count the read numbers mapped of each gene.

source_name: Kidney

extract_protocol:
Liver tissue was harvested and frozen in liquid nitrogen. RNA was exteracted by trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Treat doxicycline 600mg/kg for 4 days and harvested kidney.

value: Kidney

value: kidney Adiponectin overexpression


title: Blood_S6_CD1c

description: matched control: GSM4751523


title: Adipoq overexpressed kidney rep2


title: Blood_S6_MO

description: matched control: GSM4751526


title: N1_3f6_1321 (18 months, female)

description: RRBS with HaeIII restriction enzyme

value: brain

value: female

value: 18 months

value: WT

value: FACS enriched brain endothelial cells


title: RP36T

first: Partha

last: Majumder

institute: National Institute of Biomedical Genomics

data_processing:
Raw sequencing reads were converted to FASTQ files; data quality was assessed using FASTQC (https://qubeshub.org/resources/fastqc). Low quality reads and adapter sequences were removed. RNA-sequence data were processed in accord with the TCGA mRNA Analysis pipeline (https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline/).
Assembly: hg19 (NCBI 37)
Supplementary files format and content: TXT

value: biopsy of tumor

value: NR

value: ALIVE

value: Male

value: NO

value: WellDifferentiated


title: Blood_S2_CD1c

description: matched control: GSM4751520

value: Blood

value: Sjogren's Syndrome


title: Adipoq overexpressed kidney rep1


title: RP36N

value: biopsy of normal


title: 19e_5_1625 (2 months, female)

description: RRBS with HaeIII restriction enzyme

value: 2 months


title: 19e_4_1622 (2 months, female)

description: RRBS with HaeIII restriction enzyme


title: Control kidney rep3

value: Kidney


title: Blood_S1rep_CD1c

description: matched control: GSM4751517

value: Low Input

value: Dendritic Cells Cd1c+


title: Blood_S7_CD141

description: matched control: GSM4751524

value: Dendritic Cells Cd141+


title: Control kidney rep1


title: Blood_S2_CD141

description: matched control: GSM4751519


title: Control kidney rep2


title: mouse RT, R26-SHH, R26P87

description: 10x Genomics

data_processing:
The demultiplexing, mapping, gene counting and aggregation were made using the Cell Ranger software v3.1.0
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: tumor sample

value: tumor cells

value: tumor sample

value: Rosa 26-CreERT2::Smarcb1flox/flox


title: 17b9_1629 (2 months, female)

description: RRBS with HaeIII restriction enzyme

value: brain

value: female

value: WT

value: FACS enriched brain endothelial cells


title: 18b5_1630 (6 months, female)

description: RRBS with HaeIII restriction enzyme

value: 6 months


title: 20b2_1632 (6 months, male)

description: RRBS with HaeIII restriction enzyme

value: male


title: RP35T

value: biopsy of tumor

value: NR

value: ALIVE

value: Male

value: NO

value: ModeratelyDifferentiated


title: RP35N

value: biopsy of normal


title: Blood_S1rep_CD141

description: matched control: GSM4751516

value: Blood

value: Sjogren's Syndrome

value: Low Input

value: Dendritic Cells Cd141+


title: mouse RT, R26-SHH, R26P27

description: 10x Genomics

value: tumor cells

value: tumor sample

value: Rosa 26-CreERT2::Smarcb1flox/flox


title: Blood_S6_CD141

description: matched control: GSM4751522


title: 17b5_1627 (2 months, female)

description: RRBS with HaeIII restriction enzyme

value: brain

value: female

value: 2 months

value: WT

value: FACS enriched brain endothelial cells


title: 19e_6_1631 (2 months, female)

description: RRBS with HaeIII restriction enzyme


title: RP34N

value: NR

value: ALIVE

value: YES

value: WellDifferentiated


title: RP34T

value: biopsy of tumor

value: Male


title: 19b11_1616 (6 months, female)

description: RRBS with HaeIII restriction enzyme

value: 6 months


title: with_boric_acid_rep1

city: Hirosawa Wako city, Saitama prefecture, Japan

first: Shintaro

last: Iwasaki

department: Cluster for Pioneering Research

country: Japan

institute: RIKEN

description: The reporter contains a part of the uORF of Arabidopsis thaliana's NIP5;1 and firefly luciferase ORF

data_processing:
Library strategy: Ribosome profiling
Basecalling with RTA(Real-Time Analysis): ver2.7.7
3' adapter trimming with FastX-toolkit
Library sorting based on sample barcode sequence with custom script
Random barcode triming with custom script
rRNA and other non-coding RNA alignment with STAR(2.7.0a)
Alignment with STAR(2.7.0a)
Read quantitation using fp-transcript
Genome_build: Custom reporter sequence
Supplementary_files_format_and_content: Text files contain seven columns: 1. Consecutive number;2. Distance from start codon (nt);3. Distance from start codon (codon);4. Frame;5. Nucleotide;6. Amino acid;7. Read count

molecule: other

organism: Arabidopsis thaliana

source_name: in vitro translated mRNA in WGL (Promega)

extract_protocol:
In vitro translation reactions were buffer-exchanged to lysis buffer
MNase footprinting, ribosome pelletting, 17-34 nt gel excision, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, PCR amplification

treatment_protocol: Wheat germ extract (Promega) was used for in vitro transaltion with or without boric acid

tag: extracted molecule

value: other


title: mouse, primary RT, R26P115

data_processing:
Raw data were processed using an in-house pipeline developed at the Institut Curie Bioinformatics Core Facility, following standard analysis in the field and available at https://github.com/bioinfo-pf-curie/RNA-seq.
Sequencing adaptors were trimmed using TrimGalore!
read QC were performed using fastqc
read mapping on mm10 reference genonme were performed using STAR (version 2.5.3a) and the refFlat gene annotation downloaded from UCSC
duplicated reads were marked with picard and removed
Assembly: mm10
Supplementary files format and content: a single tab-delimited text file includes matrix raw count values of all samples (sample name in column and gene name in row).
Supplementary files format and content: a single tab-delimited text file includes matrix TPM values of all samples (sample name in column and gene name in row).

source_name: primary RT

growth_protocol: Mice were monitored for tumour formation at least 3 times per week. The observation period encompassed at least 18 months. The animals who showed clinical behaviour (neurologic symptoms or distress) were euthanized, tumours and all organs were taken and fixed in AFA for histology or were frozen in -80°C until RNA extraction.

extract_protocol:
The tumour RNAs were extracted using a miRNeasy mini kit (Qiagen ref: 217004) according to manufacturer procedure.
Barcoded Illumina compatible libraries were generated from 750 ng of total RNA for each sample using TruSeq Stranded mRNA Library Preparation Kit (Illumina, San Diego, California, U.S.,). Libraries were sequenced using the illumina NovaSeq platform in the 100 bp paired-end mode.

tag: tumor location

value: intra-cranial, extra-CNS

value: Female

tag: age (days)

value: primary RT


title: mouse RT, R26-SHH, R26P26

description: 10x Genomics

extract_protocol:
Tumor samples cut in small pieces then dissociated 30 min at 37°C in CO2-independent medium (Gibco) + 0,4 g/l of human albumin (Vialebex) with Liberase TL (Roche) 150 mg/ml and DNase 1 (Sigma) 150 mcg/ml. Dissociated cells were then filtered with a 40 mm cell strainer, then washed and resuspended with C02-independent medium + 0,4 g/l of human albumin. Cells were then continuously maintained on ice or at 4°C. In case of lot of blood cells, the Debris removal kit (Miltenyi Biotec) was used according to the manufacturer’s protocol. To enrich in tumoral cells (human samples) the Tumor Cell Isolation Kit (Miltenyi Biotec) was used according to the manufactu  rer’s protocol. Cells were then resuspended in PBS + BSA 0.04%. Samples were prepared for concentration of 800 cell/mcl.
Sample preparations were loaded on a 10x Chromium instrument (10x Genomics) and libraries were prepared using a Single Cell 3’ Reagent Kit (V2 chemistry, 10X Genomics) according to the manufacturer’s protocol, targeting 1000 recovered cells per sample. Single cells were included and barcoded into droplets together with gel beads coated with unique barcodes, unique molecular identifiers (UMI), and poly(dT) sequences, followed by in droplet reverse transcription to generate barcoded full-length cDNA. cDNA was subsequently recovered from droplets, then cleaned up with Dynabead MyOne Silane Beads (Thermo Fisher Scientific), then amplified with the following protocol: 98°C- 3min; 12x (98°C-15s, 67°C-20s, 72°C-1 min); held at 4°C. Amplified cDNA product was cleaned up using the SPRI select Reagent Kit (Beckman Coulter). Indexed libraries were constructed following these steps: 1. Fragmentation, end repair and A-tailing; 2. Size selection with SPRI select beads; 3. Adaptor ligation; 4. Post-ligation cleanup with SPRI select beads; 5. Sample index PCR and final cleanup with SPRI selects beads. Library and quality assessment were achieved using dsDNA High Sensitivity Assay Kit and Bioanalyzer Agilent System. Indexed libraries were tested for quality, equimolarly pooled and sequenced on an Illumina HiSeq2500 using paired-end 26x98 bp as sequencing mode, targeting at least 50 000 reads par cell.

value: tumor cells

value: tumor sample

value: Rosa 26-CreERT2::Smarcb1flox/flox


title: RP35M

value: biopsy of margin

tag: patient id

value: NO

value: ModeratelyDifferentiated


title: 17b6_1628 (2 months, female)

description: RRBS with HaeIII restriction enzyme

value: brain

value: female

value: 2 months

value: WT

value: FACS enriched brain endothelial cells


title: with_boric_acid_rep2


title: 16e_3_1621 (2 months, male)

description: RRBS with HaeIII restriction enzyme

value: male


title: mouse, primary RT, R26P87

value: intra-cranial, intra-CNS

value: not available

tag: time point


title: no_boric_acid_rep2

value: other


title: RP34M

value: NR

value: ALIVE

value: Male

value: YES

value: WellDifferentiated


title: RP36M

value: biopsy of margin


title: RP33T

value: biopsy of tumor


title: no_boric_acid_rep1


title: RP33N

value: biopsy of normal


title: 15b3_1623 (2 months, male)

description: RRBS with HaeIII restriction enzyme

value: brain


title: 15b4_1624 (2 months, male)

description: RRBS with HaeIII restriction enzyme


title: 16a3_1626 (6 months, male)

description: RRBS with HaeIII restriction enzyme

value: 6 months


title: mouse, primary RT, R26P123

value: extra-cranial, jaw

value: Female

value: primary RT


title: mouse, primary RT, R26P170

value: intra-cranial, extra-CNS


title: 15b2_1615 (2 months, male)

description: RRBS with HaeIII restriction enzyme

value: male

value: 2 months

value: WT

value: FACS enriched brain endothelial cells


title: RP33M

value: NR

value: ALIVE


title: 14c8_1620 (12 months, female)

description: RRBS with HaeIII restriction enzyme

value: female

value: 12 months


title: mouse, primary RT, 29225D

value: Male


title: RP32N

value: DIED

value: NO

value: ModeratelyDifferentiated


title: 13a3_1613 (12 months, male)

description: RRBS with HaeIII restriction enzyme

value: brain


title: RP32M

value: biopsy of margin


title: scMAb-ID library (index 47), bone marrow and K562

city: Utrecht

first: Robin H.

last: van der Weide

address: Uppsalalaan 8

institute: Hubrecht Institute

description:
H3K9me3, H3K36me3, Lamin B1, H3K27me3, H3K27ac, H3K4me12
scMAbID_boneMarrow.MM.txt

data_processing:
Reads of the raw sequencing output conform to a MAb-ID specific layout of 5'-[3 nt UMI][4 nt SBC part 1][3 nt UMI][4 nt SBC part 2]AGGGCCGC[8 nt ABBC][genomic sequence]-3'. Raw R1-reads were demultiplexed on the expected barcode-sequences using CutAdapt 3.047, with the following custom settings. First, we only allow matches with at least a 29 nt overlap and only keep reads directly starting with the adapter (i.e., an anchored 5’ adapter). The maximum error rate setting of 2 makes it possible to retain reads with 1) two mismatches in the specified adapter-sequence (ignoring the UMI) and 2) a one nucleotide insertion or deletion (indel) at the start of the read due to digestion-ligation or sequencing(-library) errors. Demultiplexed reads are parsed through a custom script to classify reads on correct adapter-structures on a 7-tiered range. Reads in class-1 adhere perfectly to the barcode-expectations, while class-7 reads only contain the AGGGCCGC-sequence at the expected location. Reads typically fall into class 1 (average for figure 1: 95%). This classification allows fine control on which reads should be retained. For this manuscript, we only allow classes 1 and 2 (1 nucleotide indel in the first UMI) to ensure the highest possible quality. Finally, the script creates a fastq.gz-file, adding the UMI-sequences to the read-ID for downstream processing and removing the adapter sequence. Custom pipelines and scripts are available on https://github.com/KindLab.
Demultiplexed and filtered reads were processed in a similar fashion to Rooijers et al.13, with the additional flexibility to set the selected restriction site motif. Briefly, reads are aligned using Bowtie version 2.4.148 in unpaired mode, using default end-to-end parameters. We used the UCSC hg19 reference genome for K562 samples and the NCBI mm10 reference genome for mESC/mEN-samples (both references were downloaded from https://benlangmead.github.io/aws-indexes). Alignments with a mapping quality lower than 10 or not at the expected ligation-site (5’ for the MboI-motif or 5’+ 1 for the MseI-motif) were discarded. For reads originating from mixed sorting single-cell samples (e.g., K562 and mESC), a new hybrid reference genome was built by concatenating hg19 and mm10. Aligned reads to this reference were subsequently mapped to the individual references for further downstream processing by Bowtie using the --very-sensitive -N 1 parameters. Mouse allele-specific reads were assigned by mapping mm10-reads to 129/Sv and Cast/Eij reference genomes. We designated reads to one of the genotypes if it mapped better (i.e., lower edit-distance or higher alignment-score) to one of the references.
Aligned reads are UMI-flattened and counted per restriction site, like in the scDamID-protocol. We allowed up to 1000 UMI’s per site in the bulk analyses and up to 2 UMI’s per site in the single-cell analyses. UMI-counts per sample were binned (5kb, 20kb, and 100kb), loaded into R and stored into singleCellExperiment-containers. Counts in bins overlapping regions of known problematic nature (i.e., blacklist-regions55) or low mappability are set to zero. Normalization of the data was performed by calculating RPKM-values for both samples and control (see eq. 1) and calculating the fold-change over control with a pseudocount of 1.
Assembly: UCSC hg19 and NCBI mm10
Supplementary files format and content: bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of UMI's at a given genomic coordinate.
Supplementary files format and content: MM files are sparse matrices and generated using the Matrix R package. Columns denote single cells, rows denote 100kb genomic bins, and values denote the number of UMI-flattened counts.
Library strategy: MAb-ID

organism:
Homo sapiens
Mus musculus

source_name: bone marrow

extract_protocol:
Cells were harvested (~10 x 106 cells) and washed once with PBS. All centrifugation steps were at 200 g for 4 minutes at 4 °C. Cells were fixated in 1% formaldehyde (Sigma, F8875) in PBS for 5 minutes, before quenching the reaction with 125 mM final concentration of glycine (Sigma, 50046) and placing the cells on ice. All subsequent steps were performed on ice or at 4⁰C. Cells were washed three times with PBS before resuspension in Wash buffer 1 (20mM HEPES pH 7.5 (Gibco, 15630-056), 150 mM NaCl, 66.6 µg/mL Spermidine (Sigma, S2626), 1X cOmplete™ protease inhibitor cocktail (Roche, 11697498001), 0.05% Saponin (Sigma, 47036), 2mM EDTA) and transferred to a 1.5 mL protein LoBind Eppendorf tube (Eppendorf, EP0030108116-100EA). Cells were permeabilized for 30 minutes at 4 ⁰C on a tube roller. Bovine Serum Albumin (BSA, Sigma, A2153) was added to 5 mg/mL final concentration and incubated for another 60 minutes at 4 ⁰C on a tube roller. Permeabilized nuclei were used for antibody incubation.
Samples ligated with unique SBC adapters were pooled, either 2-4 1000 nuclei samples or a full 384-well plate were pooled for combined in vitro transcription (IVT). To reduce batch effects, controls (secondary antibody-conjugates without primary antibody incubation) were pooled with their corresponding samples whenever possible. For 384-well plates, mineral oil was removed by spinning the sample for 2 minutes at 2000 g and transferring the liquid phase to a clean tube, which was repeated three times. After pooling, samples were incubated for 10 minutes with 1.0 volume CleanNGS magnetic beads (CleanNA, CPCR-0050), diluted 1:4 to 1:10 in bead binding buffer (20% PEG 8000, 2.5 M NaCl, 10 mM Tris–HCl, 1 mM EDTA, 0.05% Tween 20, pH 8.0 at 25 °C). The bead dilution ratio depended on the total volume, 1:4 for 1000 nuclei samples and 1:10 for a full 384-well plate. Samples were placed on a magnetic rack (DynaMag™-2, ThermoFisher, 12321D) to collect beads on the side of the tube. Beads were washed two times with 80% ethanol and briefly allowed to dry before resuspending in 8 µL water. In vitro transcription was performed by adding 12 µL IVT mix from the MEGAScript T7 kit (Invitrogen, AM1334) for 14 hours at 37 ⁰C before holding at 4 ⁰C. Library preparation was subsequently performed as described previously 13,46, using 5 µL of aRNA and 8 to 11 PCR cycles, depending on the aRNA yield. Purified aRNA from different IVT reactions (with unique SBC adapters) can be pooled before proceeding with cDNA synthesis to reduce batch effects. Libraries were run on the Illumina NextSeq500 platform with high output 1x75 bp, the Illumina NextSeq2000 platform with high output 1x100 bp or the Illumina NextSeq2000 platform with high output 2x100 bp.

treatment_protocol: For differentiation towards the neural lineage, mESCs were taken in culture on MEFs and subsequently passaged 3 times in feeder-free conditions in 60%-BRL medium. On day 0 of the differentiation, mESCs were plated on gelatin-coated 6-well plates (0.15% gelatin, Sigma, G1890) at a density of 2.5 x 104 cells per cm2 in N2B27 medium defined as follows: 0.5x Dulbecco's Modified Eagle Medium/Nutrient Mixture F-12 (DMEM-F12, Gibco, 11320033), 0.5x Neurobasal medium (Gibco, 21103049), 15mM HEPES (Gibco, 15630080), 0.5x N-2 supplement (Gibco, 17502048), 0.5x B-27 serum-free supplement (Gibo, 17504044) and 0.1 mM β-mercaptoethanol. From day 3 of differentiation, cells were washed daily with DMEM-F12 medium and refreshed with N2B27 medium. To harvest on day 5 of differentiation, cells were washed once with DMEM-F12 and incubated for 1 minute at room temperature with Accutase Enzyme Detachment Medium (Invitrogen, 00-4555-56). Cells were dissociated by pipetting and Accutase was inactivated by diluting cells ten-fold in DMEM-F12 or N2B27 medium, before proceeding with fixation and permeabilization as described.   Mice with the C57BL/6NCrl genotype were used for bone marrow isolations, 4 female littermates of 9 weeks old were sacrificed. To isolate bone marrow cells, the tibia and femur bones from the hindlegs were removed. The top of the bone was removed and the marrow was flushed out using a syringe with HBSS buffer (Gibco, 14025092). Cells were isolated from the marrow by pipetting up and down several times and poured through a 70 μm cell strainer (Greiner, 542070) before diluting in 25 mL HBSS buffer. Cells were centrifuged for 10 minutes at 300 g at 4 °C. Supernatant was removed, cells were resuspended in 10 mL PBS and centrifuged at 500g for 5 min.  After removing the supernatant, cells were counted using a TC20™ Automated Cell Counter (BioRad, 1450102) and diluted in 300 μL PBS per 1 x 106 cells. Per 300 μL PBS, 700 μL ice-cold Ethanol (100%, Boom, 84028185) was added dropwise while vortexing the suspension, to reach a 70% Ethanol final concentration. Cells were fixed for 1 hour at -20 °C. After fixation completed, cells were washed with Wash buffer 1 (20mM HEPES pH 7.5 (Gibco, 15630-056), 150 mM NaCl, 66.6 μg/mL Spermidine (Sigma, S2626), 1X cOmplete™ protease inhibitor cocktail (Roche, 11697498001), 0.05% Tween20 (Sigma, P9416), 2mM EDTA).  Finally, cells were stored in Wash buffer 1 containing 10% DMSO (Calbiochem, 317275) and frozen at -80 °C.

value: bone marrow

tag: cell line

tag: cell count


title: scMAb-ID library (index 46), bone marrow and K562

description:
H3K9me3, H3K36me3, Lamin B1, H3K27me3, H3K27ac, H3K4me11
scMAbID_boneMarrow.MM.txt


title: 13a2_1619 (12 months, male)

description: RRBS with HaeIII restriction enzyme

tag: age


title: mouse, primary RT, 29941C

value: primary RT


title: mouse, primary RT, 29050A

value: intra-cranial, intra-CNS

value: Female


title: scMAb-ID library (index 45), bone marrow and K562

description:
H3K9me3, H3K36me3, Lamin B1, H3K27me3, H3K27ac, H3K4me10
scMAbID_boneMarrow.MM.txt


title: 13a1_1612 (12 months, male)

description: RRBS with HaeIII restriction enzyme

value: male


title: scMAb-ID library (index 44), bone marrow and K562

description:
H3K9me3, H3K36me3, Lamin B1, H3K27me3, H3K27ac, H3K4me9
scMAbID_boneMarrow.MM.txt


title: RP31T

city: Kalyani

value: biopsy of tumor

tag: recurrence

tag: survival

value: WellDifferentiated


title: RP31N

value: biopsy of normal

value: NR

tag: Sex


title: mouse, primary RT, 43998A

value: extra-cranial, mouth


title: scMAb-ID library (index 48), bone marrow and K562

description:
H3K9me3, H3K36me3, Lamin B1, H3K27me3, H3K27ac, H3K4me13
scMAbID_boneMarrow.MM.txt


title: 12d1_1618 (12 months, male)

description: RRBS with HaeIII restriction enzyme

value: 12 months

value: WT

tag: cell type

value: FACS enriched brain endothelial cells


title: scMAb-ID library (index 43), bone marrow and K562

description:
H3K9me3, H3K36me3, Lamin B1, H3K27me3, H3K27ac, H3K4me8
scMAbID_boneMarrow.MM.txt


title: 12d4_1611 (12 months, female)

description: RRBS with HaeIII restriction enzyme

value: female


title: RP30T

value: ALIVE

value: Male

tag: tobacco

value: YES

tag: grade

value: ModeratelyDifferentiated


title: RP31M

value: biopsy of margin


title: scMAb-ID library (index 42), bone marrow and K562

description:
H3K9me3, H3K36me3, Lamin B1, H3K27me3, H3K27ac, H3K4me7
scMAbID_boneMarrow.MM.txt

value: bone marrow


title: mouse, primary RT, 43992A

value: intra-cranial, extra-CNS

value: Female

value: primary RT


title: mouse, primary RT, 43989C


title: scMAb-ID library (index 22), bone marrow and K562

description:
H3K9me3, H3K36me3, Lamin B1, H3K27me3, H3K27ac, H3K4me5
scMAbID_boneMarrow.MM.txt


title: RP30N


title: 12a9_1614 (12 months, female)

description: RRBS with HaeIII restriction enzyme

value: brain

tag: strain


title: mouse, primary RT, 43987A

value: extra-cranial, jaw

tag: genotype


title: scMAb-ID library (index 23), bone marrow and K562

description:
H3K9me3, H3K36me3, Lamin B1, H3K27me3, H3K27ac, H3K4me6
scMAbID_boneMarrow.MM.txt

tag: tissue


title: mouse, primary RT, 43990A

value: extra-cranial, nose


title: mouse, primary RT, 38594A

value: intra-cranial, intra-CNS

value: not available


title: mouse, primary RT, R26P98


title: 12c2_1617 (12 months, male)

description: RRBS with HaeIII restriction enzyme

value: male

value: 12 months

value: WT


title: scMAb-ID library (index 20), bone marrow and K562

description:
H3K9me3, H3K36me3, Lamin B1, H3K27me3, H3K27ac, H3K4me3
scMAbID_boneMarrow.MM.txt


title: RP32T

value: biopsy of tumor

value: NR

value: DIED

value: NO


title: RP29M

value: biopsy of margin

value: ALIVE

value: Male

value: YES

value: PoorlyDifferentiated


title: scMAb-ID library (index 18), bone marrow and K562

description:
H3K9me3, H3K36me3, Lamin B1, H3K27me3, H3K27ac, H3K4me1
scMAbID_boneMarrow.MM.txt

value: bone marrow


title: mouse, primary RT, 29048

value: Female

value: primary RT


title: 8b3 (18 months, male)

description: ATAC-seq

data_processing:
after a quality control with FastQC (www.bioinformatics.bbsrc.ac.uk/projects/fastqc/), reads were adapter-trimmed (Q < 20) with Trim Galore! version 0.4.2 (www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
reads were aligned to mm10 assembly with the GEM mapper.
duplicated reads were identified using Picard tools (v1.115).
reads were downscaled to avoid any bias in the downstream analysis due to variations in sequencing depth.
nucleosome depleted regions (NDRs) were called using MACS2 (v2.1.0) using the following settings: -shift -100, -extsize 200, -nomodel, -keep-dup all.
peaks which overlap with the black regions as defined by ENCODE (https://doi.org/10.1038/s41598-019-45839-z) were excluded.
Assembly: mm10
Supplementary files format and content: bed file with ATAC peak call positions.

extract_protocol:
Cerebral endothelial cells were sorted into FACS buffer (1X PBS, 2%FCS and 2mM EDTA) at 4°C and the assay for transposa-se-accessible chromatin sequencing (ATAC-seq) was performed according to a protocol adapted from Buenrostro et al57. 50,000 endothelial cells were spun down (500g, 5 minutes, 4°C), supernatant was removed and the cell pellet was resuspended in cold DNase inhibiting buffer (1 M KCl, 5 M NaCl, 1 M Tris-HCl, 0.5 M EGTA and 0.5 M Spermidine) containing prote-ase inhibitor cocktail (Roche). 0.1% IGEPAL® CA-630 (Sigma) was added to the suspension followed by gently inverting the tube 3-4 times and incubation on ice for 5 minutes. The nuclei were spun down (500g, 5 minutes, 4°C), supernatant was removed and resuspended in the DNase inhibiting buffer. The nuclei were again centrifuged (500g, 9 minutes, 4°C), the superna-tant was removed, and the pellet was resuspended in 50 µL reaction mixture, containing 25 µL 2X TD buffer, 22.5 µL nuclease-free water, and 2.5 µL Tn5 transposase enzyme (Nextera DNA Library Preparation Kit, Illumina, FC-121-1030). The tagmentation reaction was performed at 37 °C for 30 min followed by purification of library using MinElute PCR Purification Kit (Qiagen). The library was eluted in 26 µL elution buffer (Qiagen) and stored at –80°C until amplification. For amplification, 20 µL library was added to 30 µL PCR mix containing 25 µL NEB Next High Fidelity 2X Master Mix (New England Biolabs), 1 µL each Nextera i5 and i7 indexed primers as forward and reverse primers, and 3 µL nuclease-free water. The amplification was carried out in following steps – one cycle of 72°C for 5 minutes and 98°C for 30 seconds, 12 cycles of 98°C for 10 seconds, 63°C for 30 seconds and 72°C for 1 minute and one cycle of 72°C for 5 minutes. The amplified library was cleaned using 0.8x volume (40 µL) of Ampure beads XP (Beckman Coulter) according to the manufacturer’s instruction and eluted in 20 µL of 0.1X TE buffer. Six animals (3 males and 3 females) belonging to each of the age-groups of 2, 6, 12 and 18 months (total n = 24) were used for the ATAC-seq study. The quality of the ATAC library was analyzed with Bioanalyzer High-Sensitivity DNA Analysis kit (Agilent) and the concentration of the library was determined using the Qubit HS DNA kit (Life Technologies). The ATAC libraries were sequenced on an Illumina HiSeq2500 sequencing system at the University of Saarland, Saarbrücken and generated approx. 50 million 100 bp paired end reads for each sample.
endothelial cells from brain were FACS enriched.
native nuclei were tagmented with Tn5 transposase which was preloaded with Nextera NGS adaptors. After column-based purification, fragmented were amplified by PCR.

value: brain

value: 18 months

value: FACS enriched brain endothelial cells


title: scMAb-ID library (index 23)

description:
scMAbID_countMatrix_100kb_hg19.MM
scMAbID_countMatrix_100kb_mm10.MM

source_name: mESC, NPC_d6, K562

value: mESC, NPC_d6, K562

tag: antibody

value: H3K9me3, H3K36me3, Lamin B1, H3K27me3, H3K27ac, H3K4me1


title: scMAb-ID library (index 19), bone marrow and K562

description:
H3K9me3, H3K36me3, Lamin B1, H3K27me3, H3K27ac, H3K4me2
scMAbID_boneMarrow.MM.txt


title: RP29T

value: biopsy of tumor


title: RP28N

value: biopsy of normal

value: NR

value: ModeratelyDifferentiated


title: 4g2a (18 months, male)

description: ATAC-seq

value: male

value: WT


title: RP28T

value: ALIVE

value: Male


title: scMAb-ID library (index 22)


title: mouse, primary RT, 43825B

tag: tumor location

value: extra-cranial, back


title: 7b9 (18 months, female)

description: ATAC-seq

value: female


title: 7b7 (18 months, female)

description: ATAC-seq


title: 8d9a (18 months, female)

description: ATAC-seq


title: RP29N

value: YES

value: PoorlyDifferentiated


title: RP27T

value: R

value: DIED

value: NO


title: scMAb-ID library (index 21), bone marrow and K562

description:
H3K9me3, H3K36me3, Lamin B1, H3K27me3, H3K27ac, H3K4me4
scMAbID_boneMarrow.MM.txt

value: bone marrow


title: RP28M

value: biopsy of margin


title: mRNA LgDel +/- 3

city: Basel

first: Antonio

middle: Jose

last: Santinha

address: Mattenstrasse 26

department: D-BSSE

country: Switzerland

institute: ETH Zurich

description:
P1875_NGS_229
10x Genomics
lgdel_model.rds

data_processing:
The demultiplexing, barcodes processing, gene counting, and aggregation were made using Cell Ranger software v5.0.1 (10xGenomics.). gRNA counting, gRNA-nucleus association, and downstream analyses were done with custom-made scripts in R.
Assembly: GRCm38
Supplementary files format and content: rds

source_name: Prefrontal cortex of adult mice

extract_protocol:
Nuclei isolation was performed with mechanical and chemical tissue dissociation procedures using a tissue grinder (Sigma-Aldrich, D8938) and ice-cold nuclei isolation buffer (Sigma-Aldrich, NUC101-1KT). Isolated nuclei solutions were spiked with 2 mL/mL of Vybrant DyeCycle Ruby Stain (ThermoFisher, V10273) and sorted in a MA900 apparatus (Sony).
Nuclei were sequenced with a Chromium Single Cell 5ʹ Reagent Kit v1 (10x Genomics). To capture gRNA molecules, we altered the reverse transcription (RT) reaction to additionally include a gRNA-constant-region-targeting RT primer. After cDNA amplification, gene expression and gRNA expression cDNA fractions were separated. The gene expression library was constructed accordingly with the manufacturer’s instructions. The gRNA expression library was subjected to a sample indexing PCR and sequenced alongside the gene expression library with an Illumina NovaSeq 100 cycle kit.
Chromium Single Cell 5ʹ Reagent Kit v1 with altered reverse transcription reaction to additionally include a gRNA-constant-region-targeting RT primer.

value: Prefrontal cortex of adult mice

value: Mouse brain cells

value: LgDel +/-


title: mRNA LgDel +/- 2

description:
P1875_NGS_228
10x Genomics
lgdel_model.rds