title: V5-ZBTB14_CnR

data_processing:
RNA-seq data: Trimmomatic (Bolger et al., 2014) (v0.39) and parameters: ILLUMINACLIP:adapters.fa:2:30:10 SLIDINGWINDOW:4:20 MINLEN:36.
Read pairs that survived trimming were aligned to the mouse reference genome (build mm10) using STAR (Dobin et al., 2013) (v2.7.5c) and default single-pass parameters.
PCR duplicate read alignments were flagged using Picard-tools (2019) MarkDuplicates (v2.23.4).
Uniquely aligned, non-PCR-duplicate reads were kept for downstream analysis using Samtools (Li et al., 2009) view (v1.10) and parameters: -q 255 -F 1540.
Bigwig files were generated using deeptools (Ramírez et al., 2016) bamCoverage (v3.3.0) and visualized in IGV (Thorvaldsdottir et al., 2013) (v2.8.9).
CRISPR Screen : The sgRNA distribution and enrichment at different time points were analyzed with the MAGeCK workflow (Doench et al, 2016)
ChIP-seq data : FASTQ reads were trimmed using Trimmomatic (v0.39) and parameters:ILLUMINACLIP:illumina_adapters.fa:2:30:10 SLIDINGWINDOW:4:20 MINLEN:36. Trimmed reads were aligned using Bowtie2 (v2.4.1) in --local mode. Following alignment, Picard (v2.23.4) CleanSam, SamFormatConverter, SortSam and Markduplicates were used to generate a duplicate-marked bam file. The resulting bam files were converted to bigwig using deeptools (v3.3.0) Bamcoverage and options –ignoreDuplicates –normalizeUsing CPM –minMappingQuality 10 –ignoreForNormalization chrX chrY chrM.
WGBS data : As described in Miura et al 2019 NAR, the sequenced reads were mapped with BMap and summarized with an in-house pipeline, with custom scripts archived using GitHub (https://github.com/FumihitoMiura/Project-2).
Assembly: mm10
Supplementary files format and content: All processed files are in bigWig format. RNA-seq: genomic coverage counts, WGBS: percent methylation over CpGs covered by at least 5 reads, ChIP-seq/CUT&RUN-seq: signal coverage
Library strategy: CUT&RUN-seq

extract_protocol:
Genomic DNA was extracted after CUT&RUN with QIAmp DNA Mini kit (Qiagen), according to the manufacturer’s instructions.
Libraries were prepared with KAPA HyperPrep kit (Roche), following the manufacturer’s instructions.

tag: ip antibody

value: V5 (Invitrogen #R960-25)


title: Kdm5c_RNA_clone2

status: Public on Mar 10 2023

type: SRA

city: Paris

first: Pierre-Antoine

last: Defossez

address: 35 rue Hélène Brion

country: France

institute: Epigenetics and Cell Fate Unit

library_source: transcriptomic

data_processing:
RNA-seq data: Trimmomatic (Bolger et al., 2014) (v0.39) and parameters: ILLUMINACLIP:adapters.fa:2:30:10 SLIDINGWINDOW:4:20 MINLEN:36.
Read pairs that survived trimming were aligned to the mouse reference genome (build mm10) using STAR (Dobin et al., 2013) (v2.7.5c) and default single-pass parameters.
PCR duplicate read alignments were flagged using Picard-tools (2019) MarkDuplicates (v2.23.4).
Uniquely aligned, non-PCR-duplicate reads were kept for downstream analysis using Samtools (Li et al., 2009) view (v1.10) and parameters: -q 255 -F 1540.
Bigwig files were generated using deeptools (Ramírez et al., 2016) bamCoverage (v3.3.0) and visualized in IGV (Thorvaldsdottir et al., 2013) (v2.8.9).
CRISPR Screen : The sgRNA distribution and enrichment at different time points were analyzed with the MAGeCK workflow (Doench et al, 2016)
ChIP-seq data : FASTQ reads were trimmed using Trimmomatic (v0.39) and parameters:ILLUMINACLIP:illumina_adapters.fa:2:30:10 SLIDINGWINDOW:4:20 MINLEN:36. Trimmed reads were aligned using Bowtie2 (v2.4.1) in --local mode. Following alignment, Picard (v2.23.4) CleanSam, SamFormatConverter, SortSam and Markduplicates were used to generate a duplicate-marked bam file. The resulting bam files were converted to bigwig using deeptools (v3.3.0) Bamcoverage and options –ignoreDuplicates –normalizeUsing CPM –minMappingQuality 10 –ignoreForNormalization chrX chrY chrM.
WGBS data : As described in Miura et al 2019 NAR, the sequenced reads were mapped with BMap and summarized with an in-house pipeline, with custom scripts archived using GitHub (https://github.com/FumihitoMiura/Project-2).
Assembly: mm10
Supplementary files format and content: All processed files are in bigWig format. RNA-seq: genomic coverage counts, WGBS: percent methylation over CpGs covered by at least 5 reads, ChIP-seq/CUT&RUN-seq: signal coverage

molecule: polyA RNA

organism: Mus musculus

extract_protocol:
Total RNA was extracted from the cells with RNEasy Plus Mini kit (Qiagen), according to the manufacturer’s instructions.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNALibrary Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

tag: cell line

tag: cell type

value: mouse embryonic stem cells

tag: genotype

value: Kdm5c KO


title: KDM5C_WT_ChIP_rep2

library_source: genomic

molecule: genomic DNA

extract_protocol:
Reverse cross-linked DNA was purified by ChIP DNA Clean&Concentrator kit (Zymo Research).
Libraries were prepared with KAPA HyperPrep kit (Roche), following the manufacturer’s instructions.

value: KDM5C (Invitrogen #A301-034A)

value: WT


title: KDM5C_WT_ChIP_rep1


title: Zbtb14_RNA_clone1

value: Zbtb14 KO


title: input_CnR

extract_protocol:
Genomic DNA was extracted from the cells with QIAmp DNA Mini kit (Qiagen), according to the manufacturer’s instructions.
Libraries were prepared with KAPA HyperPrep kit (Roche), following the manufacturer’s instructions.


title: input_WT_ChIP_rep1


title: Emx1-cre(+/-)::MDMD::Axin2(-/-) cell et E11.5_rep7

city: Beijing

first: Zhenhua

last: Chen

state: China

address: West Beichen Road, Olympic Village, Beijing

department: State Key Laboratory of Molecular Development Biology

country: China

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

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR(2.7.0a) with with default parameter settings.
Fastq reads were filtered using Trimmomatic to discard low-quality reads and trim poor-quality bases.The remaining clean reads were aligned to GRCm38 (mm10) genome. STAR with default parameter settings was used for alignment to generate  BAM files. Gene-counting tools, featureCounts were used to generate TPM(transcripts per million) gene counts per cell/sample.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with  gene TPM for every gene and every sample

molecule: total RNA

source_name: Neural progenitor cells

extract_protocol:
Emx1-CreERT2::MADM-11::Axin2LacZ/+ mice were breed and medial cortex were dissociated at E11.5.Axin2+/+ and Axin2-/- cells were separated for single cell rna-seq.Dosal diencephalon and ventral diencephalon were collected for Bulk RNA-seq at E10.5 wild type mice.
RNA libraries were prepared for sequencing using standard Illumina protocols and smart-seq2 protocals


title: Serum_RNA_rep3


title: Kdm5c_RNA_clone1


title: Serum_RNA_rep2


title: input_WT_ChIP_rep2


title: 2i_RNA_rep2


title: 2i_RNA_rep1


title: 2i_RNA_rep3


title: WT_pool_mutations

data_processing:
RNA-seq data: Trimmomatic (Bolger et al., 2014) (v0.39) and parameters: ILLUMINACLIP:adapters.fa:2:30:10 SLIDINGWINDOW:4:20 MINLEN:36.
Read pairs that survived trimming were aligned to the mouse reference genome (build mm10) using STAR (Dobin et al., 2013) (v2.7.5c) and default single-pass parameters.
PCR duplicate read alignments were flagged using Picard-tools (2019) MarkDuplicates (v2.23.4).
Uniquely aligned, non-PCR-duplicate reads were kept for downstream analysis using Samtools (Li et al., 2009) view (v1.10) and parameters: -q 255 -F 1540.
Bigwig files were generated using deeptools (Ramírez et al., 2016) bamCoverage (v3.3.0) and visualized in IGV (Thorvaldsdottir et al., 2013) (v2.8.9).
CRISPR Screen : The sgRNA distribution and enrichment at different time points were analyzed with the MAGeCK workflow (Doench et al, 2016)
ChIP-seq data : FASTQ reads were trimmed using Trimmomatic (v0.39) and parameters:ILLUMINACLIP:illumina_adapters.fa:2:30:10 SLIDINGWINDOW:4:20 MINLEN:36. Trimmed reads were aligned using Bowtie2 (v2.4.1) in --local mode. Following alignment, Picard (v2.23.4) CleanSam, SamFormatConverter, SortSam and Markduplicates were used to generate a duplicate-marked bam file. The resulting bam files were converted to bigwig using deeptools (v3.3.0) Bamcoverage and options –ignoreDuplicates –normalizeUsing CPM –minMappingQuality 10 –ignoreForNormalization chrX chrY chrM.
WGBS data : As described in Miura et al 2019 NAR, the sequenced reads were mapped with BMap and summarized with an in-house pipeline, with custom scripts archived using GitHub (https://github.com/FumihitoMiura/Project-2).
Assembly: mm10
Supplementary files format and content: All processed files are in bigWig format. RNA-seq: genomic coverage counts, WGBS: percent methylation over CpGs covered by at least 5 reads, ChIP-seq/CUT&RUN-seq: signal coverage
Library strategy: Amplicon-sequencing

extract_protocol:
Genomic DNA was extracted from the cells with QIAmp DNA Mini kit (Qiagen), according to the manufacturer’s instructions. Genomic regions of interest were amplified by PCR.
Sequencing library is generated using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs, England) and following manufactures’ recommendations. The genomic DNA is randomly fragmented to a size of 350bp by Bioruptor, then DNA fragments are narrowly size selected with sample purification beads. The selected fragments are then end polished, A-tailed, and ligated with the full-length adapter. After these treatments, these fragments are filtered with beads again. At last, the library is analyzed for size distribution by Agilent2100 Bioanalyzer and quantified using real-time PCR.


title: Clone3_pool_mutations

value: Pool KO


title: Clone2_pool_mutations


title: Myeloid cells from naïve mice, rep 2, HTO-derived cDNA

city: South San Francisco

first: Daniel

middle: R

last: Lu

state: CA

address: 750 Gateway Blvd, Suite 100

country: USA

institute: Amgen

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)
barcodes10.tsv.gz
features10.tsv.gz
matrix10.mtx.gz

library_source: other

data_processing:
FASTQ files were processed using the 10x Genomics cellranger pipeline (v4.0.0) to generate count matrices containing gene expression and HTO counts per cell barcode. Gene expression reads were aligned to the mm10 genome build with Ensembl 93 annotations, and HTO reads were aligned to a custom reference.
Filtering of poor-quality transcriptomes was performed by removing cell barcodes more than 3 MAD below the median read count, <250 mRNA features, <500 UMI, sequence saturation < 50%, and % mtRNA reads > 20%.
HTO assignments were matched back to animal/tissue classifications using Seurat (v3.9.9). HTO classification enabled cell multiplet removal. Remaining multiplets were removed using the R package DoubletFinder.
Dimension reduction, clustering, and differential expression analyses were performed using Seurat. Batch/technical variation was corrected for using Harmony.
Assembly: mm10-3.0.0
Supplementary files format and content: 10x Genomics cellranger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

molecule: protein

source_name: Lung

extract_protocol:
Lung tissue was dissected and dissociated from tumor-bearing mice and tumor-naïve mice using Collagenase A with DNaseI. After cells were strained and treated with ACK RBC lysis solution, cells were stained with FACS antibody and sample hashing antibodies. Cells from different animals and tissue types were then pooled together and sorted for encapsulation using a 10x Chromium Controller for 10x Chromium 3' scRNAseq preparation.
Libraries were prepared using the Chromium Single Cell 3ʹ v3 protocol (10x Genomics) and a custom hashtag oligo (HTO) library preparation protocol for TotalSeq-A antibodies (provided by BioLegend). Endogenous mRNA and HTO barcodes were reverse-transcribed and labeled with a shared cellular barcode. Labeled cDNAs were then pooled and amplified by PCR using primers for amplifying cellular mRNA and primers for amplifying HTOs. PCR Products derived from mRNA (>300bp) and products from HTOs (180bp) were separated using SPRI bead size selection was performed to separate both the mRNA-derived cDNA (>300bp) and the antibody-derived tagged cDNAs (180bp).
For mRNA-derived cDNA library preparation, we followed the Chromium Single Cell 3' v3 protocol provided by 10x Genomics. Single-index (i7) library barcodes were appended during SI-PCR.
For the HTO-derived cDNA library preparation, we performed amplification using the KAPA HiFi HotStart ReadyMix using the conditions: 98°C for 2' followed by 13 cycles of 98°C for 20"; 64°C for 30"; 72°C for 20" and final elongation at 72°C for 5' with D70x_LONG primers (containing Illumina i7 sequencing adapters).
Following the final bead purification, all libraries were pooled as 80% mRNA library and 20% HTO library before sequencing.

value: KPT-SPC-CreER

tag: tissue

value: Lung

tag: disease state

value: Tumor-naïve

value: Myeloid cells

tag: library type

value: HTO

tag: antibodies/tags

value: Anti CD45 + Anti MHC classI :Naive-Mouse4/TotalSeq-A0301 ; Naive-Mouse5/TotalSeq-A0302 ; Naive-Mouse6/TotalSeq-A0303


title: Clone1_pool_mutations


title: Myeloid cells from naïve mice, rep 1, mRNA-derived cDNA

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA
barcodes9.tsv.gz
features9.tsv.gz
matrix9.mtx.gz

value: mRNA


title: Non-immune cells from naïve mice, rep 2, mRNA-derived cDNA

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA
barcodes8.tsv.gz
features8.tsv.gz
matrix8.mtx.gz

value: Non-immune cells, enriched for epithelial cells


title: Spop_RNA_clone2

value: Spop KO


title: Mcm3ap_RNA_clone1

value: Mcm3ap KO


title: Kdm5c_RNA_clone3


title: tdTom-pos myeloid cells from tumor-bearing mice, rep 2, mRNA-derived cDNA

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA
barcodes4.tsv.gz
features4.tsv.gz
matrix4.mtx.gz

value: Tumor-bearing


title: Serum_RNA_rep1

value: mouse embryonic stem cells


title: tdTom-pos myeloid cells from tumor-bearing mice, rep 1, mRNA-derived cDNA

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA
barcodes3.tsv.gz
features3.tsv.gz
matrix3.mtx.gz


title: Myeloid cells from naïve mice, rep 2, mRNA-derived cDNA

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA
barcodes10.tsv.gz
features10.tsv.gz
matrix10.mtx.gz


title: tdTom-neg myeloid cells from tumor-bearing mice, rep 1, HTO-derived cDNA

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)
barcodes1.tsv.gz
features1.tsv.gz
matrix1.mtx.gz

value: Anti CD45 + Anti MHC classI :Uninvolved-Mouse1/TotalSeq-A0301 ; Tumor-Mouse1/TotalSeq-A0302 ; Uninvolved-Mouse2/TotalSeq-A0303 ; Tumor-Mouse2/TotalSeq-A0304 ; Uninvolved-Mouse3/TotalSeq-A0305 ; Tumor-Mouse3/TotalSeq-A0306


title: Myeloid cells from naïve mice, rep 1, HTO-derived cDNA

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)
barcodes9.tsv.gz
features9.tsv.gz
matrix9.mtx.gz


title: Young S2 H10

city: Saint Louis

first: Jonathan

last: Kipnis

state: MO

address: 4515 McKinley Ave

department: Pathology and Immunology

institute: Washington University in Saint Louis

description: RNA was isolated from 5 mice

data_processing:
Demultiplexing with custom Python and perl script
Aligned to the Ensembl release 76 top-level assembly with STAR version 2.5.1a
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5
Assembly: mm10
Supplementary files format and content: gzipped csv file with raw gene counts for all cells in each sample

source_name: Brain meninges

extract_protocol: Mice were given a lethal dose of anesthetics via i.p. Euthasol (10% v/v) and transcardial perfusion performed with 0.025% heparin in PBS. Mice were decapitated immediately posterior to the occipital bone, and overlying skin and muscle was removed from the skull. Meninges were peeled from the skull cap using fine forceps, and placed in ice-cold DMEM for the entirety of collection. Meninges were then digested for 15 minutes at 37 °C with constant agitation using 1 mL of pre-warmed digestion buffer (DMEM, with 2% FBS, 1 mg/mL collagenase VIII (Sigma Aldrich), and 0.5 mg/mL DNase I (Sigma Aldrich)), filtered through a 70 μm cell strainer, and neutralized with 1 mL of complete medium (DMEM with 10% FBS). An additional 2 mL of FACS buffer was added, samples were centrifuged at 400 × g for five minutes, and resuspended in FACS buffer and kept on ice. Cells were resuspended in FACS buffer with 1:100 CD16/32 Fc block. They were stained with CD31, CD45, Podoplanin and Lyve1, washed, and resuspended in DAPI-containing FACS buffer. Single meningeal lymphatic endothelial cells were sorted as Live (DAPI-) CD45- CD31+ PDPN+ Lyve1+ cells using a FACS Aria II. Individual cells were sorted into 96-well plates containing 2 µL of 10X RNA lysis buffer (Takara) and 5% RNAse out (Takara) and rapidly frozen over dry ice. Library preparation was performed with 2 μL of single cell lysates arrayed in 96-well PCR  plates.  ds-cDNA was prepared using a protocol adapted from the Takara-Clontech SMARTer methods and scaled to a 5μL reaction volume. This method introduces a unique barcode upstream of the polyA tail using a modified oligo-dT primer. Briefly, 0.5μLof the Takara dilution buffer with 5% RNase inhibitor and 0.25μL of 25μM FACSseq barcode primer was added to the lysate and heated to 72 °C for 3 minutes. Then, 2.25 μL of the reverse transcription master mix was added to each well with 1 μL 5X first strand buffer, 0.125μL 100 mM DTT, 0.25 μL 20mM dNTPs, 0.25 μL, 50μM FACSseq TSO primer, 0.125 μLRNase inhibitor, and 0.5 μL SMARTscribe reverse transcriptase (Takara). The reaction was incubated at 42 °C for 90 minutes, 70 °C for 10minutes, then a 4 °C hold. All wells from the plate were then pooled and purified with Ampure XP beads (Beckman Coulter) with a 1X ratio. cDNA was eluted in 39μLwater. cDNA was amplified using 5 μL10X PCR buffer, 2 μL10mM dNTPs, 2 μL 12μM FACSseq206TSO PCR primer, 2 μL 50X Advantage 2 Polymerase (Takara). PCR conditions were 95 °C for 1 minute, 16 cycles of 95 °C for 15 seconds, 65 °C for 30 seconds, 68 °C for 6 minutes, 1 cycle of 72 °C for 10 minutes, followed by a 4 °C hold. cDNA was purified with 1.2XAmpure bead cleanup, measured with 209 Qubit  dsDNA  assay, and visualized on bioanalyzer. cDNA was fragmented using a Covaris E220 210 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt ended, had an A base added to the 3’ ends, and had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 16 cycles using a standard Illumina i7 primer to introduce an index sequence and FACSseq Lib PCR 1.0 specific to fragments containing the cell barcode added during cDNA synthesis. Fragments were sequenced on an Illumina NextSeq using paired end reads with 25 cycles for read 1, 7 cycles for the i7 index, and 100 cycles for the paired read. The sequencing run was performed with a custom sequencing primer for read 1 to read the 10bp barcode unique to each cell. The i7 index allows for multiple plates to be sequenced together. Read 2 contains the mRNA sequences. Two plates (S1 and S2) for each age time point were sequenced in separate sequencing runs.

value: Brain meninges

tag: age

value: 2-3 months

value: Lymphatic endothelial cells

tag: gender

value: male


title: Young S2 H9

description: RNA was isolated from 5 mice


title: Young S2 H11

description: RNA was isolated from 5 mice


title: Non-immune cells from naïve mice, rep 1, mRNA-derived cDNA

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA
barcodes7.tsv.gz
features7.tsv.gz
matrix7.mtx.gz

value: KPT-SPC-CreER


title: Young S2 H5

description: RNA was isolated from 5 mice


title: Young S2 H6

description: RNA was isolated from 5 mice


title: Non-immune cells from naïve mice, rep 1, HTO-derived cDNA

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)
barcodes7.tsv.gz
features7.tsv.gz
matrix7.mtx.gz

value: Lung


title: Young S2 H4

description: RNA was isolated from 5 mice


title: Young S2 H2

description: RNA was isolated from 5 mice


title: tdTom-neg non-immune cells from tumor-bearing mice, HTO-derived cDNA

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)
barcodes6.tsv.gz
features6.tsv.gz
matrix6.mtx.gz


title: Young S2 H1

description: RNA was isolated from 5 mice


title: tdTom-neg non-immune cells from tumor-bearing mice, mRNA-derived cDNA

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA
barcodes6.tsv.gz
features6.tsv.gz
matrix6.mtx.gz


title: tdTom-pos neoplastic cells from tumor-bearing mice, mRNA-derived cDNA

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA
barcodes5.tsv.gz
features5.tsv.gz
matrix5.mtx.gz


title: Young S2 G11

description: RNA was isolated from 5 mice


title: Young S2 G9

description: RNA was isolated from 5 mice


title: tdTom-pos myeloid cells from tumor-bearing mice, rep 2, HTO-derived cDNA

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)
barcodes4.tsv.gz
features4.tsv.gz
matrix4.mtx.gz


title: tdTom-pos myeloid cells from tumor-bearing mice, rep 1, HTO-derived cDNA

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)
barcodes3.tsv.gz
features3.tsv.gz
matrix3.mtx.gz


title: Young S2 G4

description: RNA was isolated from 5 mice


title: tdTom-neg myeloid cells from tumor-bearing mice, rep 2, HTO-derived cDNA

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)
barcodes2.tsv.gz
features2.tsv.gz
matrix2.mtx.gz


title: Young S2 G2

description: RNA was isolated from 5 mice


title: tdTom-neg myeloid cells from tumor-bearing mice, rep 2, mRNA-derived cDNA

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA
barcodes2.tsv.gz
features2.tsv.gz
matrix2.mtx.gz


title: Young S2 F12

description: RNA was isolated from 5 mice


title: Young S2 F11

description: RNA was isolated from 5 mice


title: Young S2 F10

description: RNA was isolated from 5 mice


title: Non-immune cells from naïve mice, rep 2, HTO-derived cDNA

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)
barcodes8.tsv.gz
features8.tsv.gz
matrix8.mtx.gz

value: Tumor-naïve


title: Young S2 F8

description: RNA was isolated from 5 mice


title: Young S2 H12

description: RNA was isolated from 5 mice


title: Young S2 G12

description: RNA was isolated from 5 mice


title: tdTom-neg myeloid cells from tumor-bearing mice, rep 1, mRNA-derived cDNA

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA
barcodes1.tsv.gz
features1.tsv.gz
matrix1.mtx.gz

value: Myeloid cells

value: RNA


title: Young S2 F7

description: RNA was isolated from 5 mice


title: Young S2 F5

description: RNA was isolated from 5 mice


title: Young S2 F4

description: RNA was isolated from 5 mice


title: Young S2 F6

description: RNA was isolated from 5 mice


title: Young S2 H8

description: RNA was isolated from 5 mice


title: Young S2 G5

description: RNA was isolated from 5 mice


title: Young S2 F3

description: RNA was isolated from 5 mice


title: Young S2 H7

description: RNA was isolated from 5 mice


title: tdTom-pos neoplastic cells from tumor-bearing mice, HTO-derived cDNA

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)
barcodes5.tsv.gz
features5.tsv.gz
matrix5.mtx.gz

value: HTO


title: Young S2 F2

description: RNA was isolated from 5 mice


title: Young S2 G10

description: RNA was isolated from 5 mice


title: Young S2 G7

description: RNA was isolated from 5 mice


title: Young S2 G6

description: RNA was isolated from 5 mice


title: Young S2 G8

description: RNA was isolated from 5 mice


title: Young S2 E5

description: RNA was isolated from 5 mice


title: Young S2 E4

description: RNA was isolated from 5 mice


title: Young S2 E3

description: RNA was isolated from 5 mice


title: Young S2 H3

description: RNA was isolated from 5 mice


title: Young S2 G3

description: RNA was isolated from 5 mice


title: Young S2 E10

description: RNA was isolated from 5 mice


title: Young S2 F9

description: RNA was isolated from 5 mice


title: Young S2 D12

description: RNA was isolated from 5 mice


title: Young S2 E11

description: RNA was isolated from 5 mice


title: Young S2 G1

description: RNA was isolated from 5 mice


title: Young S2 F1

description: RNA was isolated from 5 mice


title: Young S2 D7

description: RNA was isolated from 5 mice


title: Young S2 D10

description: RNA was isolated from 5 mice


title: Young S2 E12

description: RNA was isolated from 5 mice


title: Young S2 D6

description: RNA was isolated from 5 mice


title: Young S2 D4

description: RNA was isolated from 5 mice


title: Young S2 E2

description: RNA was isolated from 5 mice


title: Young S2 E9

description: RNA was isolated from 5 mice


title: Young S2 D3

description: RNA was isolated from 5 mice


title: Young S2 E7

description: RNA was isolated from 5 mice


title: Young S2 D1

description: RNA was isolated from 5 mice


title: Young S2 C12

description: RNA was isolated from 5 mice


title: Young S2 E6

description: RNA was isolated from 5 mice


title: Young S2 C11

description: RNA was isolated from 5 mice


title: Young S2 C6

description: RNA was isolated from 5 mice


title: Young S2 C7

description: RNA was isolated from 5 mice


title: Young S2 C3

description: RNA was isolated from 5 mice


title: Young S2 C1

description: RNA was isolated from 5 mice


title: Young S2 D9

description: RNA was isolated from 5 mice


title: Young S2 D5

description: RNA was isolated from 5 mice


title: Young S2 B12

description: RNA was isolated from 5 mice


title: Young S2 D8

description: RNA was isolated from 5 mice


title: Young S2 C2

description: RNA was isolated from 5 mice


title: Young S2 B9

description: RNA was isolated from 5 mice


title: Young S2 B10

description: RNA was isolated from 5 mice


title: Young S2 D2

description: RNA was isolated from 5 mice


title: Young S2 E8

description: RNA was isolated from 5 mice


title: Young S2 B3

description: RNA was isolated from 5 mice


title: Young S2 B1

description: RNA was isolated from 5 mice


title: Young S2 C10

description: RNA was isolated from 5 mice


title: Young S2 E1

description: RNA was isolated from 5 mice


title: Young S2 A11

description: RNA was isolated from 5 mice


title: Young S2 B7

description: RNA was isolated from 5 mice


title: Young S2 A8

description: RNA was isolated from 5 mice


title: Young S2 D11

description: RNA was isolated from 5 mice


title: Young S2 A4

description: RNA was isolated from 5 mice


title: Young S2 A6

description: RNA was isolated from 5 mice


title: Young S2 C5

description: RNA was isolated from 5 mice


title: Young S2 C9

description: RNA was isolated from 5 mice


title: Young S2 C8

description: RNA was isolated from 5 mice


title: Young S2 C4

description: RNA was isolated from 5 mice


title: Young S2 A1

description: RNA was isolated from 5 mice


title: Young S2 B5

description: RNA was isolated from 5 mice


title: Young S2 B8

description: RNA was isolated from 5 mice


title: Young S2 B6

description: RNA was isolated from 5 mice


title: Young S2 B11

description: RNA was isolated from 5 mice


title: Young S2 A10

description: RNA was isolated from 5 mice


title: Young S2 A12

description: RNA was isolated from 5 mice


title: Young S2 B2

description: RNA was isolated from 5 mice


title: Young S2 B4

description: RNA was isolated from 5 mice


title: Young S2 A9

description: RNA was isolated from 5 mice


title: Aged S2 H5

description: RNA was isolated from 5 mice

value: 20-24 months


title: Aged S2 H2

description: RNA was isolated from 5 mice


title: Aged S2 H1

description: RNA was isolated from 5 mice


title: Aged S2 G11

description: RNA was isolated from 5 mice


title: Young S2 A7

description: RNA was isolated from 5 mice


title: Young S2 A5

description: RNA was isolated from 5 mice


title: Aged S2 G9

description: RNA was isolated from 5 mice


title: Young S2 A3

description: RNA was isolated from 5 mice


title: Young S2 A2

description: RNA was isolated from 5 mice


title: Aged S2 H10

description: RNA was isolated from 5 mice


title: Aged S2 G2

description: RNA was isolated from 5 mice


title: Aged S2 H11

description: RNA was isolated from 5 mice


title: Aged S2 H12

description: RNA was isolated from 5 mice


title: Aged S2 F12

description: RNA was isolated from 5 mice


title: Aged S2 H9

description: RNA was isolated from 5 mice


title: Aged S2 H7

description: RNA was isolated from 5 mice


title: Aged S2 F10

description: RNA was isolated from 5 mice


title: Aged S2 H6

description: RNA was isolated from 5 mice


title: Aged S2 H4

description: RNA was isolated from 5 mice


title: Aged S2 G10

description: RNA was isolated from 5 mice


title: Aged S2 G12

description: RNA was isolated from 5 mice


title: Aged S2 F8

description: RNA was isolated from 5 mice


title: Aged S2 H3

description: RNA was isolated from 5 mice


title: Aged S2 G7

description: RNA was isolated from 5 mice


title: Aged S2 G5

description: RNA was isolated from 5 mice


title: Aged S2 G6

description: RNA was isolated from 5 mice


title: Aged S2 H8

description: RNA was isolated from 5 mice


title: Aged S2 G4

description: RNA was isolated from 5 mice


title: Aged S2 G3

description: RNA was isolated from 5 mice


title: Aged S2 G1

description: RNA was isolated from 5 mice


title: Aged S2 F6

description: RNA was isolated from 5 mice


title: Aged S2 F5

description: RNA was isolated from 5 mice


title: Aged S2 G8

description: RNA was isolated from 5 mice


title: Aged S2 F11

description: RNA was isolated from 5 mice


title: Aged S2 F4

description: RNA was isolated from 5 mice


title: Aged S2 F2

description: RNA was isolated from 5 mice


title: Aged S2 F7

description: RNA was isolated from 5 mice


title: Aged S2 E12

description: RNA was isolated from 5 mice


title: Aged S2 F1

description: RNA was isolated from 5 mice


title: Diluted control_rep3

type: RNA

city: Taipei

first: Sue

last: Lin-Chao

address: 128 Academia Road, Section 2, Nankang,

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

hyb_protocol: Following labelling, 5 μg of Cy3-cDNA were hybridized for 18 h at 42ºC in MAUIHybridizer with Nimblegen 385K E. coli tilling array by using Nimblegen hybridization kit. Afterwards the array was washed using Nimblegen washing buffers followed by drying on a microarray dryer.

scan_protocol: The microarray slides were scanned using the Axon GenePix 4200A Microarray Scanner at 5 µm resolution and PMT of 480. The scanned images were processed using the NimbleScan software.

data_processing: The array images were further processed using Nimblegen's standard protocol for Nimblescan ChIP data extraction. All raw data were then normalized by using ANAIS (http://anais.versailles.inra.fr/) to obtain gene expression levels.

organism: Escherichia coli

source_name: total RNA from E coli of Diluted control_rep3

label_protocol: RNA was further converted to labelled cDNA, which was then hybridized with a whole genome tiling arrays (NimbleGen) using standard NimbleGen operating protocols. Briefly, double-stranded cDNA was synthesized using Nimblegen cDNA synthesis kit using 10 μg total RNA and up to 1 μg cDNA was labelled with Cy3-9 mer primers by using Nimblegen labeling kit.

growth_protocol: Anaerobic, 37°C in M9+0.4% glucose

extract_protocol: Total RNA was extracted using hot acidic phenol method (Lin-Chao S and Cohen SN. Cell, 1991. 65(7): 1233-42). Briefly, aliquots (43 mL) of cell cultures grown anaerobically in M9/glucose medium as previously described (Murashko ON and Lin-Chao S. Proc Natl Acad Sci U S A. 2017 Sep 19;114(38): E8025-E8034) were mixed with cold stop solution (5% phenol in ethanol) at an 8:1 ratio. The cells were collected by centrifugation (4000 g, 4°C, 15 min), suspended in 2 mL KJ medium (50 mM glucose, 25 mM Tris-HCl pH 8.0, 10 mM EDTA pH 8.0, 100 mM NaCl), then added into boiling 2 mL lysis buffer (0.2 M NaCl, 20 mM Tris-HCl pH 7.5, 40 mM EDTA, 0.5% SDS), and incubated in boiling water for 30 sec followed by addition of 2 mL acidic phenol (pH 4.5). Then, the content of each tube was gently mixed by inverting the tube ~20 times. Total RNA was extracted into aqueous phase by centrifugation (4000 g, 4ºC for 1 h). Then, RNA was precipitated by adding 1 volume of isopropanol and 1/10 volume of 3 M sodium acetate (pH 7.8), and RNA suspensions were stored at -20ºC. Prior use, RNA was precipitated by centrifugation (30,000 g, 4ºC for 15 min), washed with 70% ethanol, centrifugated again (30,000 g, 4ºC for 15 min) and suspended in 20 μL water.  The purified RNA was first analyzed by Bioanalyzer (Agilent 2100). The ratio of rRNAs [23S / 16S] greater than 1.4 was considered to correspond to RNA of high quality and therefore it was further used for tiling array.

treatment_protocol: control without NaF, followed by 5x dilution

tag: strain

tag: replicate


title: Aged S2 E7

description: RNA was isolated from 5 mice


title: Aged S2 F9

description: RNA was isolated from 5 mice


title: Aged S2 E6

description: RNA was isolated from 5 mice


title: SAS-Nrf2E79Q, RT+CB-839, rep2

city: Stanford

first: Li

last: Guan

state: California

address: 269 Campus dr, CCSR, Room 1230

institute: Stanford University, Radiation Oncology

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
We performed STAR(15) (v2.5) mapping reads to the reference human genome GRCh38.
The method of Maximal Mappable Prefix (MMP) was used to generate a precise mapping result for junction reads.
HTSeq(16) v0.6.1 was used to count the read numbers mapped of each gene.
Assembly: human genome GRCh38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Homo sapiens

source_name: SAS

growth_protocol: SAS cells were maintained in DMEM supplemented with 10% fetal calf serum (FCS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was isolated using Trizol (Catalog# 15596026, Invitrogen)
Library preparation and RNA sequencing were performed by Novogene via Illumina platforms based on mechanism of SBS (Sequencing by synthesis).

treatment_protocol: Nrf2WT or Nrf2E79Q SAS cells were pretreated with 0.1μM CB-839 or vehicle for 24 hours, then irradiated (4 Gy). RT was performed as previously described(14) using a 225kVp cabinet x-ray irradiator filtered with 0.5 mm Cu (IC-250, Kimtron Inc.).

value: SAS

value: Oral Squamous Cell Carcinoma Cell Line

tag: treatment


title: Aged S2 F3

description: RNA was isolated from 5 mice


title: Diluted 70 mM NaF_rep2

source_name: total RNA from E coli of Diluted 70 mM NaF_rep2

treatment_protocol: treatment with 70 mM NaF at OD460=~0.4 for 8 min, followed by 5x dilution


title: Aged S2 E11

description: RNA was isolated from 5 mice


title: 20 mM NaF_rep3

source_name: total RNA from E coli of 20 mM NaF_rep3

treatment_protocol: treatment with 20 mM NaF at OD460=~0.4 for 8 min


title: Aged S2 E10

description: RNA was isolated from 5 mice


title: Diluted 20 mM NaF_rep1

source_name: total RNA from E coli of Diluted 20 mM NaF_rep1

treatment_protocol: treatment with 20 mM NaF at OD460=~0.4 for 8 min, followed by 5x dilution


title: 70 mM NaF_rep3

source_name: total RNA from E coli of 70 mM NaF_rep3

treatment_protocol: treatment with 70 mM NaF at OD460=~0.4 for 8 min


title: Diluted 70 mM NaF_rep3

source_name: total RNA from E coli of Diluted 70 mM NaF_rep3


title: Aged S2 E9

description: RNA was isolated from 5 mice


title: Diluted 20 mM NaF_rep3

source_name: total RNA from E coli of Diluted 20 mM NaF_rep3


title: Diluted control_rep1

source_name: total RNA from E coli of Diluted control_rep1


title: Diluted 20 mM NaF_rep2

source_name: total RNA from E coli of Diluted 20 mM NaF_rep2


title: 70 mM NaF_rep1

source_name: total RNA from E coli of 70 mM NaF_rep1


title: SAS WT cells, RT+CB-839, rep2


title: SAS-Nrf2E79Q, RT+CB-839, rep3


title: Diluted control_rep2

source_name: total RNA from E coli of Diluted control_rep2


title: Diluted 70 mM NaF_rep1

source_name: total RNA from E coli of Diluted 70 mM NaF_rep1


title: SAS-Nrf2E79Q, RT+CB-839, rep1


title: SAS WT cells, RT+CB-839, rep1


title: Aged S2 E5

description: RNA was isolated from 5 mice


title: SAS-Nrf2E79Q, RT, rep3

value: Radiation


title: control_rep2

source_name: total RNA from E coli of control_rep2

treatment_protocol: control without NaF


title: Aged S2 E1

description: RNA was isolated from 5 mice


title: SAS-Nrf2E79Q, RT, rep1


title: 20 mM NaF_rep1

source_name: total RNA from E coli of 20 mM NaF_rep1


title: 20 mM NaF_rep2

source_name: total RNA from E coli of 20 mM NaF_rep2

treatment_protocol: treatment by 20 mM NaF at OD460=~0.4 for 8 min


title: Aged S2 E2

description: RNA was isolated from 5 mice

source_name: Brain meninges


title: SAS-Nrf2E79Q, RT, rep2


title: SAS WT cells, RT, rep2


title: Aged S2 E4

description: RNA was isolated from 5 mice


title: SAS WT cells, RT+CB-839, rep3


title: 70 mM NaF_rep2

source_name: total RNA from E coli of 70 mM NaF_rep2

treatment_protocol: treatment by 70 mM NaF at OD460=~0.4 for 8 min


title: Aged S2 E3

description: RNA was isolated from 5 mice


title: Aged S2 D9

description: RNA was isolated from 5 mice


title: Aged S2 D7

description: RNA was isolated from 5 mice


title: Aged S2 E8

description: RNA was isolated from 5 mice


title: Aged S2 D12

description: RNA was isolated from 5 mice


title: Aged S2 D6

description: RNA was isolated from 5 mice


title: SAS WT cells, RT, rep3

source_name: SAS


title: control_rep3

source_name: total RNA from E coli of control_rep3


title: Aged S2 D11

description: RNA was isolated from 5 mice


title: SAS WT cells, CB-839, rep3


title: Aged S2 D4

description: RNA was isolated from 5 mice


title: SAS WT cells, CB-839, rep2


title: control_rep1

source_name: total RNA from E coli of control_rep1


title: Aged S2 D3

description: RNA was isolated from 5 mice


title: Aged S2 D10

description: RNA was isolated from 5 mice


title: Aged S2 D8

description: RNA was isolated from 5 mice


title: SAS WT cells, RT, rep1


title: Aged S2 C12

description: RNA was isolated from 5 mice


title: SAS-Nrf2E79Q, CB-839, rep3


title: Aged S2 D5

description: RNA was isolated from 5 mice


title: SAS WT cells, Control, rep3

value: Control


title: SAS-Nrf2E79Q, CB-839, rep1


title: SAS-Nrf2E79Q, Control, rep3


title: Aged S2 C10

description: RNA was isolated from 5 mice


title: SAS WT cells, Control, rep1


title: Aged S2 D1

description: RNA was isolated from 5 mice


title: Aged S2 C8

description: RNA was isolated from 5 mice


title: Aged S2 C11

description: RNA was isolated from 5 mice


title: SAS-Nrf2E79Q, Control, rep2


title: SAS WT cells, Control, rep2


title: Aged S2 C5

description: RNA was isolated from 5 mice


title: Aged S2 C9

description: RNA was isolated from 5 mice


title: SD_MV28

city: Ithaca

first: Nancy

last: Ruiz-Uribe

state: NY

address: 526 Campus Rd B35 Weill Hall

department: Biomedical Engineering

institute: Cornell University

data_processing:
Cutadapt was used to trim low quality bases and adapters.
STAR was used to align raw sequencing reads to the human GRCh37 reference genome.
Raw read counts were calculated using HTseq-count
Differential expression analysis was performed using DEseq2 package - details_counts.txt contains the raw counts file
GSEA and iDEP were used for gene set enrichment analysis
Assembly: mm10
Supplementary files format and content: details_count.txt is a tab-delimited text file that includes the raw counts for each sample

source_name: WT SC

extract_protocol:
RNA was isolated from microvessels after surgery  as previously described [Lee, Uchida et. al., 2019]. In brief, procedures were conducted in a cold room to minimize cell activation. Ipsilateral cortices were homogenized with MCDB131 medium (Thermo Fisher Scientific, 10372019) with 0.5% fatty acid free BSA (Millipore Sigma, 126609). The homogenate was centrifuged at 2000 g for 5 minutes at 4°C. The pellet was suspended in 15% dextran (molecular weight ∼70 kDa, Millipore Sigma, 31390) in PBS and centrifuged at 10000 g for 15 minutes at 4°C. The pellet was resuspended in MCDB131 with 0.5% fatty acid free BSA and centrifuged at 2000 g for 10 min at 4°C. The pellet contained the microvessels.Isolated cerebral microvessels were homogenized in appropriate amount of RLT lysis buffer to lyse the multicellular structures. Lysed samples were then loaded onto a column-based shredder (QIAshredder, Qiagen, Germany) and centrifuged (8000g for 2min at room temperature) to eluate the homogenized lysate. Thereafter, the lysate was processed using total RNeasy mini kit (Qiagen, Germany). In brief, the lysate was resuspended in 1:1 volume 70% ethanol and loaded onto extraction column and centrifuged (8000g for 2min) at room temperature. DNase-I digestion was performed on-column for samples with 1U of TURBO-DNase (Invitrogen, ThermoFisher Scientific) and incubated for 15min at room temperature. Then columns were washed with appropriate amount of wash buffer and finally total RNA was eluted using 20-25 µl of nuclease free water.
RNA integrity and other quality control measures were performed along with ribosomal RNA depletion before cDNA library preparation (Genomics core facility, Weill Cornell Medicine). cDNA libraries were made using the Illumina TruSeq Stranded mRNA Library Prep kit

treatment_protocol: 10 mg/kg i.p. dose of gp91-ds-tat (NOX2 inhibitor) or sgp91-ds-tat (control) every two days for two weeks

value: Brain cortex

value: Endothelial/pericyte/astrocytic endfeet

value: WT

value: SC


title: SD_MV23


title: Aged S2 C2

description: RNA was isolated from 5 mice

value: Brain meninges

value: Lymphatic endothelial cells


title: SD_MV29

source_name: WT NOX2


title: SAS WT cells, CB-839, rep1


title: SAS-Nrf2E79Q, CB-839, rep2


title: Aged S2 D2

description: RNA was isolated from 5 mice

value: male


title: Aged S2 C7

description: RNA was isolated from 5 mice


title: SD_MV22


title: SD_MV27


title: Aged S2 C6

description: RNA was isolated from 5 mice


title: Aged S2 C4

description: RNA was isolated from 5 mice


title: Aged S2 C3

description: RNA was isolated from 5 mice


title: Aged S2 B11

description: RNA was isolated from 5 mice


title: Aged S2 B8

description: RNA was isolated from 5 mice


title: SAS-Nrf2E79Q, Control, rep1


title: SD_MV9


title: SD_MV16

source_name: APP SC

value: APP


title: Aged S2 C1

description: RNA was isolated from 5 mice


title: Aged S2 B12

description: RNA was isolated from 5 mice


title: SD_MV17

source_name: APP NOX2


title: SD_MV14


title: Aged S2 B5

description: RNA was isolated from 5 mice


title: SD_MV5


title: SD_MV1


title: Aged S2 B2

description: RNA was isolated from 5 mice


title: Aged S2 B3

description: RNA was isolated from 5 mice


title: SD_MV10


title: Aged S2 B4

description: RNA was isolated from 5 mice


title: Aged S2 B7

description: RNA was isolated from 5 mice


title: NSC,BEP,scRNAseq

city: Evanston

first: Prithvijit

last: Mukherjee

state: IL

address: 2145 Sheridan Road

institute: Northwestern University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Cell Ranger (version 6) was used for demultiplexing, barcoded processing, gene counting and aggregation. The FASTQ files for each sample were aligned to the mouse reference genome (GRCm38) to generate the matrix files for subsequent analyses
Further processing was done with Seurat v4.0.4 (cell and gene filtering, clustering, differential gene expression analysis), TopGO (gene ontology analysis) and fgsea (gene set enrichment analysis).
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: brain

growth_protocol: Neural progenitors were isolated and cultured as neurospheres from postnatal day 1 mice in DMEM/F12 (Gibco) supplemented with 1% N2 and 2% B27 supplements (Gibco), 1% Penicillin-Streptomycin-Glutamine (PSG, Gibco) and 20 ng/mL Human Recombinant Epidermal Growth Factor (EGF).

extract_protocol:
Plated neural progenitors were dissociated using 0.05% Trypsin-EDTA 4hrs after electroporation (BEP and LEP). The cells were then washed are resuspended in PBS for viability analysis (Trypan Blue) prior to library preparation and sequencing.
Single cell gel bead generation and barcoding was performed with 10,000 cells from each experimental condition using the NextGEM single cell 3’ v3 expression chip on the Chromium platform (10x Genomics) using maufacturer's protocols.

treatment_protocol: 50,000 postnatal neural progenitors plated on poly-D-lysine (PDL)-coated polystyrene dishes (NUNC) or PDL-coated Localized Electroporation Devices (LEPD) were cultured for 16 hours prior to BEP treatment using Lonza 4D Nucleofector Y unit (Program DS137) or LEP treatment on LEPDs (20V, 400 pulses).

value: brain

value: Neural Stem Cells (NSCs)

tag: time

value: 4 hrs post treatment

tag: developmental stage

value: NSCs from Postnatal Day 1 Mice

value: Bulk Electroporation


title: SD_MV8


title: Aged S2 B1

description: RNA was isolated from 5 mice

value: 20-24 months


title: SD_MV11


title: NSC,Control,scRNAseq

description: 10x Genomics


title: Aged S2 B9

description: RNA was isolated from 5 mice


title: Aged S2 A12

description: RNA was isolated from 5 mice


title: SD_MV6


title: NSC,LEP,scRNAseq

description: 10x Genomics

value: Localized Electroporation


title: Aged S2 A11

description: RNA was isolated from 5 mice


title: Aged S2 A10

description: RNA was isolated from 5 mice


title: Aged S2 A9

description: RNA was isolated from 5 mice


title: SD_MV4


title: ce_ABX_LD240_4

city: Yangzhou

first: Yongkang

last: Zhen

state: — Please Select —

address: Yangzhou University

institute: Yangzhou University

description:
16S_feature_table
16S_ASVs_taxonomy
16S_fasta_file

data_processing:
Paired-end reads generated from Illumina platforms were processed and merged using FLASH software (v1.2.7)
Quality filtering on the raw reads were then performed under specific filtering conditions to obtain the high-quality clean tags according to the Fqtrim software (v0.9.4). Chimeric sequences were filtered using VSEARCH software (v2.3.4)
Finally, the feature table and feature sequence were obtained after dereplication using DADA2 software (v1.10.1)
Assembly: The V3-V4 region of the prokaryotic small-subunit (16S) rRNA gene was amplified with primers 341 F (5′-CCTACGGGNGGCWGCAG-3′) and 805 R (5′-GACTACHVGGGTATCTAATCC-3′)
Supplementary files format and content: excel files named "16S_feature _table", "16S_ASVs_taxonomy", and "16S_fasta_file"of ASVs profiles  for each sample
Library strategy: 16S

extract_protocol:
Microbial DNA from different rumen digesta samples was extracted using TIANamp Stool DNA Kit
SMRTbell libraries were prepared using the Pacific Biosciences SMRTbellTM Template Prep kit

tag: sample

value: cecal content

tag: diet

value: antibiotics infusion


title: ce_ABX_LD240_5


title: ce_ABX_LD240_3


title: Aged S2 A8

description: RNA was isolated from 5 mice


title: SD_MV2

value: Brain cortex


title: ce_ABX_LD240_1


title: Aged S2 A5

description: RNA was isolated from 5 mice


title: Aged S2 A4

description: RNA was isolated from 5 mice


title: Aged S2 A6

description: RNA was isolated from 5 mice


title: ce_ABX_LD168_5


title: ce_ABX_LD168_2


title: Aged S2 A1

description: RNA was isolated from 5 mice


title: ce_ABX_LD168_4


title: ce_ABX_LD168_3


title: ce_ABX_LD240_6


title: Aged S2 A2

description: RNA was isolated from 5 mice


title: ce_ABX_LD168_1


title: Aged S2 A7

description: RNA was isolated from 5 mice


title: ce_ABX_LD168_6


title: ce_ABX_LD1212_5


title: ce_ABX_LD240_2


title: ce_ABX_LD1212_4


title: ce_ABX_LD1212_3


title: ce_ABX_LD1212_2


title: Young S1 H8

description: RNA was isolated from 5 mice

value: 2-3 months


title: Young S1 H9

description: RNA was isolated from 5 mice


title: Young S1 H7

description: RNA was isolated from 5 mice


title: Young S1 H10

description: RNA was isolated from 5 mice


title: ce_ABX_LD1212_1


title: Young S1 H6

description: RNA was isolated from 5 mice


title: ce_ABX_LD816_6


title: Young S1 H5

description: RNA was isolated from 5 mice


title: ce_ABX_LD816_5


title: Young S1 H12

description: RNA was isolated from 5 mice


title: ce_ABX_LD816_3


title: Young S1 H3

description: RNA was isolated from 5 mice


title: Young S1 H2

description: RNA was isolated from 5 mice


title: Young S1 H11

description: RNA was isolated from 5 mice


title: Young S1 H1

description: RNA was isolated from 5 mice


title: Young S1 H4

description: RNA was isolated from 5 mice


title: Young S1 G12

description: RNA was isolated from 5 mice


title: ce_ABX_LD024_6


title: ce_ABX_LD816_1


title: ce_ABX_LD024_5


title: Young S1 G11

description: RNA was isolated from 5 mice


title: ce_ABX_LD024_4


title: ce_ABX_LD816_2


title: Young S1 G8

description: RNA was isolated from 5 mice


title: Young S1 G10

description: RNA was isolated from 5 mice


title: Young S1 G9

description: RNA was isolated from 5 mice


title: ce_ABX_LD024_3


title: Young S1 G7

description: RNA was isolated from 5 mice


title: ce_ABX_LD024_1


title: ce_ABX_LD816_4


title: ce_CD_LD240_6

value: chow diet


title: ce_CD_LD240_5


title: Young S1 G5

description: RNA was isolated from 5 mice


title: Young S1 G4

description: RNA was isolated from 5 mice


title: ce_CD_LD240_3


title: Young S1 G3

description: RNA was isolated from 5 mice


title: Young S1 G2

description: RNA was isolated from 5 mice


title: ce_CD_LD240_2


title: ce_CD_LD240_4


title: ce_CD_LD240_1


title: Young S1 G1

description: RNA was isolated from 5 mice


title: ce_CD_LD168_6


title: Young S1 F11

description: RNA was isolated from 5 mice


title: Young S1 F12

description: RNA was isolated from 5 mice


title: ce_CD_LD168_5


title: ce_CD_LD168_4


title: Young S1 F10

description: RNA was isolated from 5 mice


title: ce_ABX_LD024_2


title: Young S1 F9

description: RNA was isolated from 5 mice


title: ce_CD_LD168_3


title: Young S1 F8

description: RNA was isolated from 5 mice


title: Young S1 G6

description: RNA was isolated from 5 mice


title: ce_CD_LD168_2


title: ce_CD_LD168_1


title: Young S1 F7

description: RNA was isolated from 5 mice


title: Young S1 F6

description: RNA was isolated from 5 mice


title: ce_CD_LD1212_6


title: ce_CD_LD1212_5


title: Young S1 F4

description: RNA was isolated from 5 mice


title: Young S1 F5

description: RNA was isolated from 5 mice


title: ce_CD_LD1212_2


title: Aged S2 B6

description: RNA was isolated from 5 mice


title: Young S1 F1

description: RNA was isolated from 5 mice


title: ce_CD_LD1212_3


title: ce_CD_LD1212_1


title: Young S1 E11

description: RNA was isolated from 5 mice


title: ce_CD_LD816_7


title: Young S1 E12

description: RNA was isolated from 5 mice


title: ce_CD_LD816_6


title: Young S1 E10

description: RNA was isolated from 5 mice


title: ce_CD_LD816_5


title: ce_CD_LD816_4


title: Young S1 E9

description: RNA was isolated from 5 mice


title: ce_CD_LD816_3


title: Young S1 E7

description: RNA was isolated from 5 mice


title: Young S1 E8

description: RNA was isolated from 5 mice


title: ce_CD_LD816_2


title: Young S1 E6

description: RNA was isolated from 5 mice


title: ce_CD_LD1212_4


title: ce_CD_LD816_1


title: Young S1 F3

description: RNA was isolated from 5 mice


title: ce_CD_LD024_6


title: Young S1 E4

description: RNA was isolated from 5 mice


title: Young S1 F2

description: RNA was isolated from 5 mice


title: Young S1 E5

description: RNA was isolated from 5 mice


title: ce_CD_LD024_5


title: Young S1 E3

description: RNA was isolated from 5 mice


title: ce_CD_LD024_3


title: Young S1 E1

description: RNA was isolated from 5 mice


title: Young S1 E2

description: RNA was isolated from 5 mice


title: ce_CD_LD024_2


title: ce_CD_LD024_4


title: Young S1 D12

description: RNA was isolated from 5 mice


title: co_ABX_LD240_6

value: colonic centent


title: Young S1 D11

description: RNA was isolated from 5 mice

value: Brain meninges


title: Young S1 D10

description: RNA was isolated from 5 mice

value: Lymphatic endothelial cells


title: co_ABX_LD240_4


title: co_ABX_LD240_5


title: Young S1 D8

description: RNA was isolated from 5 mice

value: male


title: Young S1 D9

description: RNA was isolated from 5 mice


title: co_ABX_LD240_3


title: co_ABX_LD240_2


title: Young S1 D7

description: RNA was isolated from 5 mice


title: co_ABX_LD240_1


title: Young S1 D6

description: RNA was isolated from 5 mice


title: co_ABX_LD168_6


title: co_ABX_LD168_5


title: Young S1 D3

description: RNA was isolated from 5 mice


title: co_ABX_LD168_4


title: Young S1 D2

description: RNA was isolated from 5 mice


title: Aged S2 A3

description: RNA was isolated from 5 mice


title: co_ABX_LD168_2


title: Young S1 D5

description: RNA was isolated from 5 mice


title: co_ABX_LD168_1


title: Young S1 C12

description: RNA was isolated from 5 mice


title: Young S1 C10

description: RNA was isolated from 5 mice


title: Young S1 C9

description: RNA was isolated from 5 mice


title: Young S1 C8

description: RNA was isolated from 5 mice


title: co_ABX_LD1212_4


title: Young S1 C7

description: RNA was isolated from 5 mice


title: co_ABX_LD1212_2


title: co_ABX_LD1212_1


title: Aged S2 B10

description: RNA was isolated from 5 mice


title: Young S1 C6

description: RNA was isolated from 5 mice


title: Young S1 D4

description: RNA was isolated from 5 mice


title: Young S1 D1

description: RNA was isolated from 5 mice


title: co_ABX_LD024_6


title: Young S1 C4

description: RNA was isolated from 5 mice


title: Young S1 C3

description: RNA was isolated from 5 mice


title: co_ABX_LD816_3


title: Young S1 C5

description: RNA was isolated from 5 mice


title: co_ABX_LD816_2


title: ce_CD_LD024_1


title: Young S1 C1

description: RNA was isolated from 5 mice


title: Young S1 C11

description: RNA was isolated from 5 mice


title: co_ABX_LD816_1


title: Young S1 C2

description: RNA was isolated from 5 mice


title: co_ABX_LD168_3


title: co_ABX_LD816_5


title: co_ABX_LD024_5


title: co_ABX_LD816_4


title: co_ABX_LD024_4


title: co_ABX_LD024_3


title: Young S1 B11

description: RNA was isolated from 5 mice


title: co_ABX_LD1212_6


title: Young S1 B9

description: RNA was isolated from 5 mice


title: Young S1 B10

description: RNA was isolated from 5 mice


title: co_ABX_LD1212_3


title: co_ABX_LD1212_5


title: co_CD_LD240_4


title: co_ABX_LD024_2


title: co_CD_LD240_3


title: Young S1 B7

description: RNA was isolated from 5 mice


title: Young S1 B8

description: RNA was isolated from 5 mice


title: co_CD_LD168_6


title: co_ABX_LD024_1


title: Young S1 B2

description: RNA was isolated from 5 mice


title: Young S1 A10

description: RNA was isolated from 5 mice


title: co_CD_LD168_4


title: Young S1 B5

description: RNA was isolated from 5 mice


title: Young S1 B4

description: RNA was isolated from 5 mice


title: Young S1 B1

description: RNA was isolated from 5 mice


title: Young S1 A11

description: RNA was isolated from 5 mice


title: Young S1 A12

description: RNA was isolated from 5 mice


title: Young S1 B12

description: RNA was isolated from 5 mice


title: Young S1 B6

description: RNA was isolated from 5 mice


title: co_CD_LD240_5


title: co_CD_LD240_1


title: co_CD_LD240_2


title: Young S1 B3

description: RNA was isolated from 5 mice


title: co_CD_LD168_5


title: Young S1 A8

description: RNA was isolated from 5 mice


title: co_CD_LD168_2


title: co_CD_LD168_1


title: Young S1 A7

description: RNA was isolated from 5 mice


title: Young S1 A5

description: RNA was isolated from 5 mice


title: co_CD_LD1212_6


title: Young S1 A6

description: RNA was isolated from 5 mice


title: Young S1 A9

description: RNA was isolated from 5 mice


title: Young S1 A4

description: RNA was isolated from 5 mice


title: co_CD_LD1212_5


title: co_CD_LD1212_4


title: Young S1 A2

description: RNA was isolated from 5 mice


title: Young S1 A1

description: RNA was isolated from 5 mice


title: co_CD_LD1212_1


title: co_CD_LD1212_2


title: co_CD_LD816_6


title: Young S1 A3

description: RNA was isolated from 5 mice


title: co_CD_LD1212_3


title: co_CD_LD816_4


title: co_CD_LD240_6


title: Aged S1 H8

description: RNA was isolated from 5 mice


title: Aged S1 H11

description: RNA was isolated from 5 mice


title: Aged S1 H7

description: RNA was isolated from 5 mice


title: co_CD_LD816_5


title: Aged S1 H10

description: RNA was isolated from 5 mice


title: Aged S1 H9

description: RNA was isolated from 5 mice


title: co_CD_LD816_3


title: co_CD_LD024_6


title: co_CD_LD816_2


title: Aged S1 H6

description: RNA was isolated from 5 mice


title: co_CD_LD816_1


title: co_CD_LD168_3


title: co_CD_LD024_5


title: Aged S1 H5

description: RNA was isolated from 5 mice


title: OTD treated, NOG-TKm30 mice liver, transplanted with human hepatocytes

city: Osaka

first: Shugo

last: Suzuki

state: Osaka

address: 1-4-3 Asahi-machi, Abeno-ku

department: Molecular Pathology

country: Japan

institute: Osaka Metropolitan University Graduate School of Medicine

data_processing:
Quality trimming and adapter clipping of the read data were performed using Trimmomatic version 0.38.
Trimmed reads were mapped to the transcript in the human  reference sequence hg38 using Bowtie2 aligner within RSEM.
Read count extraction and normalization were performed using edgeR program.
Assembly: hg38
Supplementary files format and content: tab-delimited text file. normalized CPM count matrix with GeneSymbol index.

source_name: Liver

growth_protocol: Female 6- or 7-week-old NOG mice expressing HSVtk mutant clone 30 cDNA under the control of mouse transthyretin gene enhancer/promoter (NOG-TKm30 mice) were transplanted with commercially available human hepatocytes (humanized-liver mice).

extract_protocol:
RNeasy Mini Kit was performed according to the manufacturer's instructions.
The sequencing libraries were prepared from 200 ng of total RNA with MGIEasy rRNA Depletion Kit and MGIEasy RNA Directional Library Prep Set (MGI Tech Co., Ltd.) according to the manufacturer's instructions.

treatment_protocol: Female 16-week-old humanized-liver mice were treated with 0 or 0.6% ortho-toluidine (OTD) for 1 week and 0 or 0.3% OTD for 3 weeks (totally 4 weeks treatment).

value: Liver

value: primary cultuer cell

tag: Sex

value: female

value: OTD

value: 4 weeks


title: co_CD_LD024_4


title: co_CD_LD024_3


title: control, NOG-TKm30 mice liver, transplanted with human hepatocytes

value: Control


title: Aged S1 H12

description: RNA was isolated from 5 mice

value: 20-24 months


title: Aged S1 H4

description: RNA was isolated from 5 mice


title: co_CD_LD024_1


title: co_CD_LD024_2


title: Aged S1 H3

description: RNA was isolated from 5 mice


title: HGNET CIC fusion-positive case 12

type: genomic

city: Heidelberg

last: Schrimpf

address: Im Neuenheimer Feld 224

department: Neuropathology

country: Germany

institute: University Hospital Heidelberg, Intitute of Pathology

description:
HGNET CIC fusion-positive
SAMPLE_12

hyb_protocol: Illumina protocol

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

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

label: Cy3, Cy5

source_name: HGNET CIC fusion-positive

label_protocol: Illumina protocol

extract_protocol: Illumina protocol

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

value: pediatric CNS tumor

tag: tissue preparation

value: Frozen


title: HGNET CIC fusion-positive case 13

description:
HGNET CIC fusion-positive
SAMPLE_13


title: Control sample 28 (white matter)

city: Campinas

first: Fabio

last: Rogerio

state: Sao Paulo

address: Rua Tessália Vieira de Camargo, 126

department: Department of Pathology,

country: Brazil

institute: University of Campinas – UNICAMP

data_processing:
Sequence alignment was performed with STAR (https://github.com/alexdobin/STAR); transcriptome  analysis was performed with DESeq2 package (http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html)
Assembly: Homo sapiens GRCh37/hg19 assembly
Supplementary files format and content: comma-separated-values files  containing FeatureCounts for each sample

source_name: Frontal Lobe

extract_protocol:
Frozen samples were serially cut in cryostat, mounted in PEN membrane covered slides, stained with Cresyl Violet and dehydrated with an ethanol series. The gray (cortical layer) and white matters were mechanically dissected from 3 – 4 sections per sample. Total RNA from each dissected sample was extracted and purified with Trizol.
cDNA libraries were produced from 200ng of total RNA using the TruSeq Stranded total RNA kit according to the manufacturer protocol. Sequencing was performed in a HiSeq 2500 platform, in High-Output mode, producing 100-bp paired-end sequences.

value: Frontal Lobe

value: Control (autopsy)


title: Control sample 29 (white matter)


title: HGNET CIC fusion-positive case 9

description:
HGNET CIC fusion-positive
SAMPLE_9

value: FFPE


title: FCD IIb sample 19 (white matter)

value: FCD IIb


title: Control sample 27 (white matter)


title: Control sample 26 (white matter)


title: Aged S1 G12

description: RNA was isolated from 5 mice

tag: cell type


title: Aged S1 H2

description: RNA was isolated from 5 mice

tag: genotype


title: FCD IIb sample 17 (white matter)

tag: tissue


title: Aged S1 H1

description: RNA was isolated from 5 mice


title: HGNET CIC fusion-positive case 6

description:
HGNET CIC fusion-positive
SAMPLE_6


title: FCD IIb sample 16 (white matter)

tag: disease state


title: FCD IIb sample 14 (white matter)


title: FCD IIb sample 15 (white matter)


title: FCD IIa sample 8 (white matter)

value: FCD IIa


title: FCD IIb sample 12 (white matter)


title: FCD IIb sample 13 (white matter)


title: HGNET CIC fusion-positive case 4

description:
HGNET CIC fusion-positive
SAMPLE_4


title: Aged S1 G10

description: RNA was isolated from 5 mice

value: Brain meninges


title: HGNET CIC fusion-positive case 10

description:
HGNET CIC fusion-positive
SAMPLE_10


title: Aged S1 G9

description: RNA was isolated from 5 mice

value: Lymphatic endothelial cells


title: HGNET CIC fusion-positive case 3

description:
HGNET CIC fusion-positive
SAMPLE_3


title: FCD IIa sample 5 (white matter)


title: FCD IIa sample 6 (white matter)


title: Aged S1 G7

description: RNA was isolated from 5 mice

value: male


title: HGNET CIC fusion-positive case 2

description:
HGNET CIC fusion-positive
SAMPLE_2


title: FCD IIa sample 2(white matter)


title: FCD IIa sample 3 (white matter)


title: HGNET CIC fusion-positive case 8

description:
HGNET CIC fusion-positive
SAMPLE_8


title: Aged S1 G8

description: RNA was isolated from 5 mice


title: Aged S1 G11

description: RNA was isolated from 5 mice


title: Control sample 29 (gray matter)


title: FCD IIa sample 1 (white matter)


title: HGNET CIC fusion-positive case 5

description:
HGNET CIC fusion-positive
SAMPLE_5


title: Control sample 28 (gray matter)


title: Aged S1 G6

description: RNA was isolated from 5 mice


title: Control sample 27 (gray matter)


title: sciPlexGxE_2

city: New York

first: José

middle: L

last: McFaline-Figueroa

email: jm5200@columbia.edu, joselmc@uw.edu

institute: Columbia University

description: sci-Plex-GxE combined chemical and genetic profiling of A172, T98G and U87MG dCas9-KRAB cellsgenetically perturbed for the human protein kinome exposed to small molecules targeting the receptor tyrosine kinase pathway. Specifically, Lapatinib, Nintedanib, Trametinib, ZSTK474 or dmso vehicle control.

data_processing:
Expression matrices, cell annotations and gene annotations were generated according to the protocol described in our manuscript as well as in Cao et al. 2019 Nature 566(7745) p. 496-502 (three level sci-RNA-seq).
Nuclear barcodes "hash" sequences were extracted from fastq files if the first 10 bp of read 2 match a hash from the appropriate hashSampleSheet.txt (2nd column) within a hamming distance of 2, the last column of the hashSampleSheet.txt file pertains to whether 1 or 2 hashes were used to identify a condition (only single hashes were used, associated metadata to deconvolve hash combinations can be found in the appropriate hashTable_metadata.txt file). Reads were then deduplicated by cell barcode and UMI to create a file of hash UMI counts (hashTable.out files) for each nuclear transcriptome in the  experiment. Tab-delimited columns of hashTable.out files correspond to a sample id, the cell barcode identified for that hash, a "_" delimited string with treatment metadata, an axis id for each hash (not used in these experiments), and umi counts for each hash. The first tab-delimited column of the appropriate hashSampleSheet.txt files contains metadata for the experiment divided by underscores. For sciPlexGxE_1, the first "_" delimited string corresponds to the hash plate used, and the second to the well within the hash plate, the third denotes the cell line, the fourth the CRISPR system (CRISPRi for gene knockdown and CRISPRa for overexpression), the fifth to the experiment (MMR or HPRT1 perturbation), the sixth to the dose of the drug and the seventh to the specific drug, and the last "_" string corresponds to the well format of multiwell plates. For sciPlexGxE_2, only the hash oligo was specified. Please refer to the separate hash metadata file (sciPlexGxE_2_hash_metadata.txt). For sciPlex_3, the first "_" delimited string corresponds to the hash plate used, the second to the well within the hash plate, the third denotes the cell line, the fourth to the specific drug, the fifth to the dose of the drug and the six and seventh to biological replicate. For sciPlex_4, the first "_" delimited string corresponds to the hash plate used, the second to the dose of drug, the third denotes the specific drug, the fourth the concentration of trametinib used for combinatorial exposure, and the fifth to the biological replicate. Note that the cell line was assigned based on the RT barcode during the first indexing step of combinatorial indexing RNA-seq.
Single-guide RNA (sgRNA) sequences were extracted from fastq files if a sequence contained a TGTGG at position 3-7 of read 2 and the 18 base pairs spanning position 24-42 of read 2 match a sgRNA from the appropriate gRNASampleSheet.txt (2nd column) within a hamming distance of 2, the last column of the gRNASampleSheet.txt file pertains to whether 1 or 2 sgRNAs were expected K562_hashTable_metadata.txt). Reads were then deduplicated by cell barcode and UMI to create a file of sgRNA read counts (gRNATable.out files). The first tab-delimited column of the appropriate gRNASampleSheet.txt file contains sgRNA metadata where the first “_” delimited string denotes the targeted gene, non-targeting control (NTC) or random control (radnom), and the second the sgRNA rank from Horlbeck et al. 2016 eLife 5:e19760. The second column refers to the 19 bp protospacer sequence in positions 24-42 of read 2. The full protospacer sequences can be found in the appropriate gRNA_whitelist.txt file.
Assembly: GRCh38
Supplementary files format and content: Expression matrices are output by our pipeline in matrix market exchange format and the cell and gene annotation files that accompany these files are in tsv file format.

source_name: A172, T98G and U87MG cells

growth_protocol: All cell lines were cultured in DMEM supplemented with 10% FBS and 1% penn-strep. For genetically pertrubed experiments, glioblastoma cells expressing either dCas9-KRAN or dCAS9-SunTag were transduced with a CROPseq lentiviral library targeting genes of interest or non-targeting control single-guide RNAs as described in our Methods section and McFaline-Figueroa et. al. 2019 Nature Genetics, 51, p. 1389-1398.

extract_protocol:
72 (sciPlexGxE_2,sciPlex_3,sciPlex_4) or 96 (sciPlexGxE_1) hours after drug exposure, cells were harvested following the sciPlexGxE or sci-Plex protocols as described in the methods section of our manuscript. Nuclei were isolated in-well and nuclei barcoded by fixation of well-specific barcode containing oligonucleotides. After fixation wells were pooled and nuclei pellets flash frozen until sci-RNA-seq library preparation.
Nucle were subjected tothree-level sci-RNA-seq following the protocols described in  Cao et al. 2019 Nature 566(7745) p. 496-502. For sciPlexGxE experiments, changes to protocol include the addition of a CROP-seq targeting RT primer and an enrichment PCR for the capture of sgRNA contaitnign puromycin mRNA transcripts delivered by lentiviral transdution of the CROP-seq system.

treatment_protocol: Cells were seeded at 10,000 (sciPlexGxE_1) or 25,000 (sciPlexGxE_2,sciPlex_3,sciPlex_4) cells per well in 96 well plates. 24 hours after seeding cells were exposed to increasing doeses of small molecules or dmso vehicle control.

tag: cell line

value: A172, T98G and U87MG cells

value: Human glioblastoma brain cancer cells expressing dCas9-KRAB and further transduced to express single-guide RNAs against 522 protein kinases or non-targeting control single-guide RNAs.

value: Cells were treated with increasing doses of the small molecules Lapatinib, Nintedanib, Trametinib, ZSTK474 or dmso vehicle control.


title: FCD IIb sample 19 (gray matter)


title: FCD IIb sample 18 (gray matter)


title: TRAF7, KLF4, rep 5

city: Oklahoma City

first: Alla

last: Tsytsykova

state: OK

address: 1122 NE 13th Street

department: Neurosurgery

institute: OUHSC

data_processing:
Sequencing was done from both ends.
Post-sequence reads were quality-filtered for length and contaminants and were trimmed for Illumina adapters.
Resulting reads were pseudo-aligned to coding regions of the human reference genome using STAR.
Assembly: Homo Sapiens(GRCh38/hg38)
Supplementary files format and content: BAM files for all samples and an Excel file with raw counts (FPKM) of sequencing reads (the rows are features/genes and the columns are samples)

source_name: primary tumor

growth_protocol: Twenty tumor samples from 20 female patients (one sample/patient) diagnosed with meningioma at University of Oklahoma Medical Center were included in the study. All procedures were approved by the institutional review board (IRB) of the University of Oklahoma Health Sciences Center (OUHSC) (IRB protocol number 10195).

extract_protocol:
Total RNA was extracted using the RNeasy Plus Micro Kit (QIAGEN, 74034) and QIAshredder (QIAGEN, 79656) according to the manufacturer’s instructions.
Preparation of cDNA libraries and sequencing (Illumina platform) was conducted by Novogene Co., LTD.

treatment_protocol: For RNA extraction, resected tissues were immediately submerged in RNAlater® Solution, kept at room temperature for 24 hours, and stored frozen long term (Fisher Scientific, AM7023).

value: primary tumor

value: Human meningioma

value: TRAF7/KLF4 mut

value: adult brain tumor


title: Control sample 26 (gray matter)


title: TRAF7, KLF4, rep 4


title: FCD Iia sample 4 (white matter)


title: FCD IIb sample 14 (gray matter)


title: FCD IIb sample 15 (gray matter)


title: Aged S1 G2

description: RNA was isolated from 5 mice

value: 20-24 months


title: Aged S1 G3

description: RNA was isolated from 5 mice


title: TRAF7, KLF4, rep 3


title: FCD IIb sample 17 (gray matter)


title: FCD IIa sample 9 (gray matter)


title: Aged S1 G1

description: RNA was isolated from 5 mice


title: FCD IIa sample 7 (gray matter)


title: Aged S1 F12

description: RNA was isolated from 5 mice


title: TRAF7, AKT1, rep 5

value: TRAF7/AKT1 mut


title: FCD IIa sample 8 (gray matter)

value: Frontal Lobe


title: TRAF7, KLF4, rep 1


title: Aged S1 F11

description: RNA was isolated from 5 mice


title: Aged S1 G5

description: RNA was isolated from 5 mice


title: FCD IIa sample 4 (gray matter)


title: FCD IIa sample 6 (gray matter)


title: FCD IIa sample 3 (gray matter)


title: Aged S1 F10

description: RNA was isolated from 5 mice


title: FCD IIa sample 1 (gray matter)


title: TRAF7, AKT1, rep 3


title: TRAF7, AKT1, rep 4


title: D283_SMARCA4_shRNA2

city: Navi Mumbai

first: Neelam

middle: V

last: Shirsat

state: Maharashtra

address: Kharghar, Sector 21

department: Shirsat Lab

country: India

institute: Advanced Centre for Treatment, Research and Education in Cancer. Tata Memorial Centre

data_processing:
Illumina bcl2fastq2 was used for base calling
The fastq data was aligned to the Human genome GRCh37-hg19 assembly using HISAT2 aligner
HTseq algorithm was used to derive the raw count of the number of reads per transcript from the aligned sequence file in the BAM format
DESeq2 algorithm was used for normalization of the HTSeq count data using the variance stabilized transformation as well as for identifying genes differentially expressed upon miR-592 expression.
Assembly: GRCh37-hg19
Supplementary files format and content: tab-delimited text files containing counts per gene normalized using the variance stabilized transformation

source_name: Medulloblastoma cell line

growth_protocol: HD-MB03, D425 and D283 medulloblastoma cell lines and their polyclonal populations expressing empty vector or shRNA targeting SMARCA4 in a doxycycline-inducible manner were grown in Dulbecco's Modified Eagle's Medium/F12  medium at 37 °C in a CO2 incubator.

extract_protocol:
Total RNA was extracted using Qiagen RNAeasy mini kit as per manufacturer's protocol.
Librarieswere prepared from Poly-A enriched fraction of total RNA using the Illumina TruSeq RNA library preparation kit version 2.0
The libraries were sequenced in a 100 nucleotide single-end read run on the Illumina Hiseq 2500 platform

treatment_protocol: The cells were treated with 1 µg/ml doxycycline for 72 h for the induction of shRNA expression

value: Medulloblastoma

tag: condition

value: shSMARCA4 expressing


title: Aged S1 F9

description: RNA was isolated from 5 mice

tag: age


title: TRAF7, AKT1, rep 2


title: FCD IIb sample 13 (gray matter)

value: FCD IIb


title: D283_SMARCA4_shRNA1


title: Neuro133_D283_WT2

value: vector control expressing


title: TRAF7, KLF4, rep 2


title: D425_SMARCA4_shRNA2


title: D425_WT2

value: wild-type


title: Aged S1 F7

description: RNA was isolated from 5 mice

value: Brain meninges

value: Lymphatic endothelial cells

tag: gender


title: Aged S1 F5

description: RNA was isolated from 5 mice

value: male


title: HD-MB03_SMARCA4_shRNA2

value: shARID1B expressing


title: Aged S1 F6

description: RNA was isolated from 5 mice


title: Aged S1 G4

description: RNA was isolated from 5 mice


title: Aged S1 F8

description: RNA was isolated from 5 mice


title: Neuro28_D283_WT1


title: NF2, rep 6

value: NF2 loss/mut


title: D425_SMARCA4_shRNA1


title: NF2, rep 9

value: primary tumor


title: HD-MB03_SMARCA4_shRNA1


title: TRAF7, AKT1, rep 1

value: Human meningioma


title: ce_ABX_LD1212_6

tag: strain

value: cecal content

value: antibiotics infusion


title: D425_WT3


title: NF2, rep 10

value: adult brain tumor


title: HD-MB03_WT1


title: NF2, rep 7


title: HD-MB03_WT2


title: Aged S1 F3

description: RNA was isolated from 5 mice

value: 20-24 months


title: NF2, rep 8


title: Acanthaomeba castellanii, E3

city: Tainan City

first: Wei-Chen

last: Lin

address: No.1, University Road

institute: National Cheng Kung University

data_processing:
To determine gene expression profiles of amoeba, we also downloaded mRNA data (including 28,949 genes) from NCBI, followed by analysis with CLC Genomics Workbench (version 9.5.4).
The RNAseq data were first loaded into CLC, followed by trimming low quality sequence with the parameter specified: limit=0.05.
Mapping the reads after trimming to mRNA data set to determine gene expression profile with the default parameters.

organism: Acanthamoeba castellanii

extract_protocol:
The total RNA of A. castellanii was extracted with Direct-zolTM RNA MiniPrep (AYMO RESEAECH) according to the manufacturer’s protocol. The samples were treated with DNase I at 37°C for 30 minutes. DNase I was removed by phenol-chloroform extraction and total RNA was reprecipitated using sodium acetate and ethanol. The total RNA was eluted in nucleic acid-free water.
The protocol for strand-specific sample preparation was ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre, USA).

value: protist

value: heat-killed E. coli feed


title: Aged S1 F1

description: RNA was isolated from 5 mice


title: Aged S1 F4

description: RNA was isolated from 5 mice


title: Aged S1 E12

description: RNA was isolated from 5 mice


title: Acanthaomeba castellanii, Mock

value: regular cuture


title: D425_WT1

value: Medulloblastoma


title: Aged S1 F2

description: RNA was isolated from 5 mice


title: NF2, rep 3


title: WT, 3dpi, Rep3

city: Seville

first: Blanca

last: Navarrete

state: Seville

address: Ctra. de Utrera, Km 1

department: Genetic

country: Spain

institute: Pablo de Olavide University (UPO)

data_processing:
Sequence reads were trimmed removing adaptor sequences, contamination (reads in which unknown bases are more than 10%), and low-quality reads (the percentage of low quality bases is over 50%) from raw reads
Trimmed sequence reads were mapped to U. maydis genome using HISAT2 and reads from infected plant tissues were previously filtered against the annotated maize genome
Reads were counted for U. maydis using the HTseq tool in the Galaxy platform.
For expression analysis, only uniquely mapping exon read counts were considered. Pairwise comparisons were performed using the R package DESeq2 (Love et al., 2014)
Assembly: Ustilago maydis (p3_t237631_Ust_maydi_v2GB)
Supplementary files format and content: Raw Count data table contains the read counts from Htseq

organism: Mycosarcoma maydis

growth_protocol: For axenic growth, cells from exponential culture in YEPSL medium were collected. For filament-formation conditions, cells incubated in PD-Charcoal plates for 18 hours were harvested. Cells from infected leave were harvested by excising 2–3 cm segments from below the injection hole.

extract_protocol:
All the samples were ground into a powder using a mortar/pestle under liquid nitrogen. Total RNA was purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) and the Direct-zol RNA Miniprep Plus Kit (Zymo Research, Irvine, CA, USA).
RNA libraries for RNA-seq were performed by BGI TECH SOLUTIONS (HONGKONG) CO., LIMITED

value: WT

value: Inside Z. maize at 3 days post infecion


title: Ppit2:sir2, 3dpi, Rep1

value: Ppit2:sir2 >1c


title: Ppit2:sir2, 3dpi, Rep2


title: Liver, control female NOG-TKm30 mice

data_processing:
Quality trimming and adapter clipping of the read data were performed using Trimmomatic version 0.38.
Trimmed reads were mapped to the transcript in the human  reference sequence mm10 using Bowtie2 aligner within RSEM.
Read count extraction and normalization were performed using edgeR program.
Assembly: mm10
Supplementary files format and content: tab-delimited text file. normalized CPM count matrix with GeneSymbol index.

treatment_protocol: Female 16-week-old C57BL mice were treated with 0 or 0.6% ortho-toluidine (OTD) for 1 week and 0 or 0.3% OTD for 3 weeks (totally 4 weeks treatment).

value: Liver

value: female

value: Control

value: 16 weeks


title: WT, 3dpi, Rep1


title: Aged S1 E11

description: RNA was isolated from 5 mice

value: Brain meninges

value: Lymphatic endothelial cells

value: male


title: Liver, OTD treated female NOG-TKm30 mice

value: OTD


title: R366 E11.5 Medial cortex

data_processing:
The sequencing data were processed using an open-source pipeline (https://github.com/MGI-tech-bioinformatics/DNBelab_C_Series_HT_scRNA-analysis-software)
Fastq reads were filtered using Trimmomatic to discard low-quality reads and trim poor-quality bases.The remaining clean reads were aligned to GRCm38 (mm10) genome. STAR with default parameter settings was used for alignment to generate  BAM files. Gene-counting tools, featureCounts were used to generate TPM(transcripts per million) gene counts per cell/sample.
Seurat R package (v4) was used for standard Single-cell RNA sequencing data analysis.
Assembly: mm10
Supplementary files format and content: Matrix table with  gene TPM for every gene and every sample; WT_all_cell_20220427.rds. rds are serialized R objects of the Bioconductor class ExpressionSet that contains the final data used to generate the results. It can be imported into R with readRDS(“WT_all_cell_20220427.rds”). It contains the gene counts, sample metadata, and feature metadata for single cells that passed quality control.

source_name: E11.5 Medial cortex

extract_protocol:
The medial cortex was dissociated at E11.5 for Single-cell RNA sequencing. And we using AnnexinV and PI co-staining protocol to sort AnnexinV positive, PI negative and AnnexinV, PI double negative cells for bulk RNA sequencing.
The Single-cell RNA sequencing libraries were prepared for sequencing following the manufacturer’s recommendations for the DNBelab C Series High-throughput Single-cell System (BGI-research). The bulk RNA sequencing libraries were applied to modify smart-seq2 protocols.

tag: development stage


title: R367 E11.5 Medial cortex


title: NF2, rep 2

value: primary tumor

value: Human meningioma

value: NF2 loss/mut

tag: treatment

value: adult brain tumor


title: Aged S1 E9

description: RNA was isolated from 5 mice

source_name: Brain meninges

value: 20-24 months


title: NF2, rep 5

tag: time


title: Aged S1 E8

description: RNA was isolated from 5 mice


title: WT, 3dpi, Rep2


title: NF2, rep 4


title: RNA-seq-22Rv1-CK1α-OE-rep1

city: lexington

first: Jinghui

last: Liu

state: KY

address: Room 352, HEALTHY KENTUCKY RESEARCH BUILDING, 760 Press Avenue

institute: University of Kentucky

data_processing:
CRISPR screen sequenced reads were mapped to sgRNA kinome library
sgRNA counts and gene beta score and FDR were calculated by MAGeCK v0.5.8
RNA-seq reads were mapped to human reference genome (GRCh38p12) via HISAT2 v2.1.0
The raw read counts on genes were derived by featureCounts from the subread package v1.5.1 in unstranded mode, based on Ensembl gene annotation release 92.
Assembly: GRCh38p12
Supplementary files format and content: Matrix table with sgRNA raw counts, normalized counts for each sample; gene beta score, p value, FDR for each sample.
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: prostate cancer cell line

growth_protocol: 22Rv1 cells were cultured in RPMI-1640 medium (Sigma-Aldrich) contained 10% fetal bovine serum (Atlanta Biologicals, GA, USA), 100 U/ml of penicillin and 100 μg/ml streptomycin.

extract_protocol:
The genomic DNA was extracted with a DNeasy Blood & Tissue Kit (Qiagene).Total RNA was purified using an RNeasy Mini kit (Qiagene)
libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 22Rv1 cells were treated with 20 µM Enzalutamide or DMSO for one week.

value: prostate cancer cell line


title: Aged S1 E6

description: RNA was isolated from 5 mice

data_processing:
Demultiplexing with custom Python and perl script
Aligned to the Ensembl release 76 top-level assembly with STAR version 2.5.1a
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5
Assembly: mm10
Supplementary files format and content: gzipped csv file with raw gene counts for all cells in each sample


title: Ppit2:sir2, 3dpi, Rep3


title: THY_CD_LD168_3

data_processing:
Briefly, the Fastp software (v0.23.1) was firstly used to perform quality control on the raw data and obtain clean data. Then, the HISAT2 software (v2.1.0) was used to align the obtained clean data referred to the latest reference genome in mouse (GRCm39). After that, the Samtools software (v.1.10) was used to sort and convert the SAM files to BAM format, and finally, the Stringtie software (v2.2.1) was used to assemble and quantify the transcripts and genes based on read counts.
Assembly: GRCm39
Supplementary files format and content: a excel file named "RNA_Seq_processed_data" of raw counts  for each sample

source_name: Thymus gland

extract_protocol:
Total RNA  was extracted and purified using a TRIzol reagent (Invitrogen, Carlsbad, CA, USA) for transcriptomic sequencing
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Thymus gland

tag: diets

value: chow diet


title: THY_CD_LD168_2


title: THY_CD_LD240_1


title: THY_CD_LD240_3


title: THY_CD_LD240_2


title: R368 E11.5 Medial cortex

city: Beijing

last: Chen

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


title: Aged S1 E10

description: RNA was isolated from 5 mice

extract_protocol: Mice were given a lethal dose of anesthetics via i.p. Euthasol (10% v/v) and transcardial perfusion performed with 0.025% heparin in PBS. Mice were decapitated immediately posterior to the occipital bone, and overlying skin and muscle was removed from the skull. Meninges were peeled from the skull cap using fine forceps, and placed in ice-cold DMEM for the entirety of collection. Meninges were then digested for 15 minutes at 37 °C with constant agitation using 1 mL of pre-warmed digestion buffer (DMEM, with 2% FBS, 1 mg/mL collagenase VIII (Sigma Aldrich), and 0.5 mg/mL DNase I (Sigma Aldrich)), filtered through a 70 μm cell strainer, and neutralized with 1 mL of complete medium (DMEM with 10% FBS). An additional 2 mL of FACS buffer was added, samples were centrifuged at 400 × g for five minutes, and resuspended in FACS buffer and kept on ice. Cells were resuspended in FACS buffer with 1:100 CD16/32 Fc block. They were stained with CD31, CD45, Podoplanin and Lyve1, washed, and resuspended in DAPI-containing FACS buffer. Single meningeal lymphatic endothelial cells were sorted as Live (DAPI-) CD45- CD31+ PDPN+ Lyve1+ cells using a FACS Aria II. Individual cells were sorted into 96-well plates containing 2 µL of 10X RNA lysis buffer (Takara) and 5% RNAse out (Takara) and rapidly frozen over dry ice. Library preparation was performed with 2 μL of single cell lysates arrayed in 96-well PCR  plates.  ds-cDNA was prepared using a protocol adapted from the Takara-Clontech SMARTer methods and scaled to a 5μL reaction volume. This method introduces a unique barcode upstream of the polyA tail using a modified oligo-dT primer. Briefly, 0.5μLof the Takara dilution buffer with 5% RNase inhibitor and 0.25μL of 25μM FACSseq barcode primer was added to the lysate and heated to 72 °C for 3 minutes. Then, 2.25 μL of the reverse transcription master mix was added to each well with 1 μL 5X first strand buffer, 0.125μL 100 mM DTT, 0.25 μL 20mM dNTPs, 0.25 μL, 50μM FACSseq TSO primer, 0.125 μLRNase inhibitor, and 0.5 μL SMARTscribe reverse transcriptase (Takara). The reaction was incubated at 42 °C for 90 minutes, 70 °C for 10minutes, then a 4 °C hold. All wells from the plate were then pooled and purified with Ampure XP beads (Beckman Coulter) with a 1X ratio. cDNA was eluted in 39μLwater. cDNA was amplified using 5 μL10X PCR buffer, 2 μL10mM dNTPs, 2 μL 12μM FACSseq206TSO PCR primer, 2 μL 50X Advantage 2 Polymerase (Takara). PCR conditions were 95 °C for 1 minute, 16 cycles of 95 °C for 15 seconds, 65 °C for 30 seconds, 68 °C for 6 minutes, 1 cycle of 72 °C for 10 minutes, followed by a 4 °C hold. cDNA was purified with 1.2XAmpure bead cleanup, measured with 209 Qubit  dsDNA  assay, and visualized on bioanalyzer. cDNA was fragmented using a Covaris E220 210 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt ended, had an A base added to the 3’ ends, and had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 16 cycles using a standard Illumina i7 primer to introduce an index sequence and FACSseq Lib PCR 1.0 specific to fragments containing the cell barcode added during cDNA synthesis. Fragments were sequenced on an Illumina NextSeq using paired end reads with 25 cycles for read 1, 7 cycles for the i7 index, and 100 cycles for the paired read. The sequencing run was performed with a custom sequencing primer for read 1 to read the 10bp barcode unique to each cell. The i7 index allows for multiple plates to be sequenced together. Read 2 contains the mRNA sequences. Two plates (S1 and S2) for each age time point were sequenced in separate sequencing runs.


title: NF2, rep 1


title: THY_CD_LD168_1


title: RNA-seq-22Rv1-CK1α-KO-rep3


title: THY_CD_LD1212_2


title: THY_CD_LD1212_3


title: Aged S1 E5

description: RNA was isolated from 5 mice


title: RNA-seq-22Rv1-CK1α-KO-rep2


title: Aged S1 E4

description: RNA was isolated from 5 mice


title: THY_CD_LD1212_1


title: THY_CD_LD816_2


title: RNA-seq-22Rv1-CK1α-KO-rep1


title: RNA-seq-22Rv1-CK1α-OE-rep3


title: Aged S1 E7

description: RNA was isolated from 5 mice


title: THY_CD_LD816_1


title: RNA-seq-22Rv1-Ctrl-rep3


title: RNA-seq-22Rv1-CK1α-OE-rep2


title: Aged S1 E3

description: RNA was isolated from 5 mice


title: THY_CD_LD024_3


title: THY_CD_LD024_2


title: Aged S1 E2

description: RNA was isolated from 5 mice


title: THY_CD_LD024_1


title: Aged S1 E1

description: RNA was isolated from 5 mice


title: RNA-seq-22Rv1-Ctrl-rep2


title: Aged S1 D12

description: RNA was isolated from 5 mice


title: MAG_CD_LD240_3

source_name: Mammary gland

value: Mammary gland


title: MAG_CD_LD240_1


title: CRISPR-22Rv1-ENZA-rep2

description:
CRISPR-22Rv1-ENZA-rep2
paired-end but just used R1

value: Enzalutamide


title: RNA-seq-22Rv1-Ctrl-rep1


title: MAG_CD_LD240_2


title: THY_CD_LD816_3


title: MAG_CD_LD168_3


title: MAG_CD_LD168_2


title: Aged S1 D11

description: RNA was isolated from 5 mice


title: MAG_CD_LD1212_3


title: CRISPR-22Rv1-Ctrl-rep1

description:
CRISPR-22Rv1-Ctrl-rep1
paired-end but just used R1

value: DMSO


title: CRISPR-22Rv1-Ctrl-rep2

description:
CRISPR-22Rv1-Ctrl-rep2
paired-end but just used R1


title: MAG_CD_LD1212_1


title: CRISPR-22Rv1-ENZA-rep1

description:
CRISPR-22Rv1-ENZA-rep1
paired-end but just used R1


title: MAG_CD_LD168_1


title: Aged S1 D10

description: RNA was isolated from 5 mice


title: Aged S1 D9

description: RNA was isolated from 5 mice


title: Aged S1 D8

description: RNA was isolated from 5 mice


title: MAG_CD_LD816_2


title: CRISPR-22Rv1-bsl

description:
CRISPR-22Rv1-bsl
paired-end but just used R1


title: MAG_CD_LD816_1


title: Aged S1 D7

description: RNA was isolated from 5 mice


title: MAG_CD_LD024_3


title: MAG_CD_LD816_3


title: MAG_CD_LD024_2


title: Aged S1 D6

description: RNA was isolated from 5 mice


title: MAG_CD_LD1212_2


title: SPL_CD_LD240_3

source_name: Spleen

value: Spleen


title: SPL_CD_LD240_2


title: MAG_CD_LD024_1


title: Aged S1 D4

description: RNA was isolated from 5 mice


title: Aged S1 D5

description: RNA was isolated from 5 mice


title: SPL_CD_LD168_2


title: SPL_CD_LD168_3


title: Aged S1 D2

description: RNA was isolated from 5 mice


title: HL-60_WT_replicate3

city: Plovdiv

first: Yordan

last: Sbirkov

address: 15 A Vassil Aprilov Blvd

department: Medical Biology

country: Bulgaria

institute: Medical University of Plovdiv

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials. Staining, washing and scanning on the final day of this protocol was performed and the images were processed by the affymetrix software to produce .CEL files, which were then used for the bioinformatics analysis of the arrays.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were processed using Partek software. Batch effect remove function in Partek was applied after GC-RMA quantile normalisation

label: biotin

label_protocol: ss-cDNA was digested and labelled according to manufacturers protocol (WT plus kit by Affymetrix).

growth_protocol: HL-60 cells were obtained from the German Collection of Microorganisms and Cell Cultures (DSMZ) and maintained in them RPMI 1640 (Sigma) supplemented with 10% FBS (Gibco), 100 μml−1 penicillin and 100 μg ml−1 streptomycin. For EZH2 KD experiments, HL-60 cells were grown in puromycin (1.5 µM) for at least 3 days, then allowed to recover and expand for another few days before experiments were set up.

extract_protocol: Total RNA was isolated using the ZR RNA MiniPrep Kit (Zymo Research). The concentration and quality of the total RNA was assessed on an Agilent 2100 BioAnalyzer (Agilent Technologies). cDNA, cRNA and then single-stranded cDNA were made with a number of amplification and purification steps in between following standard Affymetrix protocol and using WT plus kit by Affymetrix

treatment_protocol: Cells were treated with 10µM GSK343 or 2.5µM HKMTI-1-005 (+/- 0.1µM AtRA) for 3 days.

value: Acute myeloid leukaemia

value: WT


title: Aged S1 D3

city: Saint Louis

last: Kipnis

institute: Washington University in Saint Louis

description: RNA was isolated from 5 mice

value: Brain meninges

value: Lymphatic endothelial cells


title: SPL_CD_LD1212_2


title: SPL_CD_LD1212_3


title: SPL_CD_LD168_1


title: HL-60_WT_replicate2


title: SPL_CD_LD1212_1


title: SPL_CD_LD816_3


title: Aged S1 D1

description: RNA was isolated from 5 mice

value: male


title: Aged S1 C12

description: RNA was isolated from 5 mice


title: SPL_CD_LD816_2


title: SPL_CD_LD816_1


title: SPL_CD_LD240_1


title: SPL_CD_LD024_3


title: HL-60_WT+ATRA_replicate3

value: WT+ATRA


title: SPL_CD_LD024_2


title: HL-60_WT_replicate1


title: Aged S1 C11

description: RNA was isolated from 5 mice


title: Aged S1 C10

description: RNA was isolated from 5 mice


title: SPL_CD_LD024_1


title: HL-60_WT+ATRA_replicate2


title: CEC_CD_LD240_3

source_name: Cecum epithelium

value: Cecum epithelium


title: HL-60_EZH2_KD_shEZH2#2_replicate3


title: CEC_CD_LD240_2


title: Aged S1 C9

description: RNA was isolated from 5 mice


title: HL-60_WT+ATRA_replicate1


title: CEC_CD_LD168_3


title: CEC_CD_LD240_1


title: CEC_CD_LD168_4


title: CEC_CD_LD168_2


title: HL-60_EZH2_KD_shEZH2#2_replicate1


title: HL-60_EZH2_KD_shEZH2#2+ATRA_replicate1


title: Aged S1 C6

description: RNA was isolated from 5 mice


title: CEC_CD_LD1212_3


title: CEC_CD_LD1212_2


title: HL-60_EZH2_KD_shEZH2#2+ATRA_replicate3


title: CEC_CD_LD1212_1


title: CEC_CD_LD816_3


title: CEC_CD_LD816_4


title: HL-60_EZH2_KD_shEZH2#1_replicate1


title: HL-60_EZH2_KD_shEZH2#1_replicate3


title: Aged S1 C4

description: RNA was isolated from 5 mice


title: CEC_CD_LD816_1


title: CEC_CD_LD816_2


title: Aged S1 C3

description: RNA was isolated from 5 mice


title: Aged S1 C8

description: RNA was isolated from 5 mice


title: CEC_CD_LD024_3


title: HL-60_EZH2_KD_shEZH2#1+ATRA_replicate3


title: Aged S1 C5

description: RNA was isolated from 5 mice


title: HL-60_non-targeting_control_Scr_replicate3


title: CEC_CD_LD168_1


title: CEC_CD_LD024_2


title: Aged S1 C2

description: RNA was isolated from 5 mice


title: CEC_CD_LD024_4


title: Aged S1 C7

description: RNA was isolated from 5 mice


title: HL-60_EZH2_KD_shEZH2#1+ATRA_replicate1


title: JEJ_CD_LD240_3

source_name: Jejunum epithelium

value: Jejunum epithelium


title: Aged S1 C1

description: RNA was isolated from 5 mice


title: CEC_CD_LD024_1


title: HL-60_non-targeting_control_Scr_replicate2


title: Aged S1 B12

description: RNA was isolated from 5 mice


title: JEJ_CD_LD240_2


title: HL-60_non-targeting_control_Scr+ATRA_replicate3


title: JEJ_CD_LD240_1


title: Aged S1 B11

description: RNA was isolated from 5 mice


title: HL-60_non-targeting_control_Scr_replicate1


title: JEJ_CD_LD168_3


title: JEJ_CD_LD168_1


title: Aged S1 B10

description: RNA was isolated from 5 mice


title: JEJ_CD_LD1212_2


title: Aged S1 B9

description: RNA was isolated from 5 mice


title: JEJ_CD_LD1212_3


title: JEJ_CD_LD1212_1


title: JEJ_CD_LD816_3


title: JEJ_CD_LD816_2


title: Aged S1 B8

description: RNA was isolated from 5 mice


title: JEJ_CD_LD024_3


title: HL-60_non-targeting_control_Scr+ATRA_replicate1


title: JEJ_CD_LD024_2


title: Aged S1 B7

description: RNA was isolated from 5 mice


title: Aged S1 B6

description: RNA was isolated from 5 mice


title: JEJ_CD_LD168_2


title: COL_ABX_LD240_3

source_name: Colon epithelium

value: Colon epithelium

value: antibiotics infusion


title: COL_ABX_LD240_2


title: Aged S1 B4

description: RNA was isolated from 5 mice

value: 20-24 months


title: Aged S1 B5

description: RNA was isolated from 5 mice


title: COL_ABX_LD240_1


title: HL-60_EZH2_KD_shEZH2#1+ATRA_replicate2