title: F1_Plate 8A

description:
Library name: BSSE-QGF-131167
Smart-seq2


title: H1_Plate 8A

status: Public on Oct 09 2025

type: SRA

city: London

first: Francesca

middle: M.

last: Spagnoli

address: Great Maze Pond

department: CGTRM

country: United Kingdom

institute: King's College London

description:
Library name: BSSE-QGF-131169
Smart-seq2

library_source: transcriptomic single cell

data_processing:
Libraries were sequenced SR75 on an Illumina NextSeq 500 system (75 cycles High Output v2.5 kit).
Sequence reads were trimmed for quality control with trim_galore (v.0.6.5) and uniquely aligned to mouse reference genome (GRCm38) using kallisto pseudo-mode(v.0.46.1).
Transcript-level counts were converted into gene-level counts using tximport (v1.18.0) with mm10 Refseq
Assembly: UCSC, mm 10 (GRCm38)
Supplementary files format and content: TSV text file including a table of genes (rows) x cells (columns) showing counts  per single cell. Processed data file includes only samples that passed QC check.

molecule: total RNA

organism: Mus musculus

source_name: Dorsal Pancreas

extract_protocol:
Dorsal pancreatic tissue (E12.5) was dissected from Tg(Prox1-EGFP), Tg(Nkx2.5-Cre;mTmG) and Tg(Nkx3.2-Cre;mTmG) transgenic mice and dissociated into single-cell suspensions. GFP+ cells were FACS-sorted at 4°C using an Aria II or Aria III flow cytometer (BD) into 96-well plates containing cell lysis buffer. Plates containing FACS-sorted cells were then frozen and kept at -80°C until shipment to the Genomic Facility for library preparation and sequencing.
Libraries were prepared for sequencing using Nextera XT DNA library preparation kit (Illumina) protocols.

tag: tissue

value: Dorsal Pancreas

tag: developmental stage

tag: genotype


title: Panel II_E14.5_19

type: RNA

description: HybISS, Cartana

hyb_protocol: not applicable

scan_protocol: not applicable

data_processing: After quality control samples were processed by CARTANA Sweden (a subsidiary of 10X Genomics), for in situ barcode sequencing, imaging, and data processing. CSV files contain reads coordinates and gene information of segmented spots. The coordinates are in pixel unit. Scaling factor is 0.32 um/pixel. (0,0) is at northwest (top-left corner). Downstream processing  was performed using either SSAM pipeline (https://github.com/pnucolab/ssam) or a pipeline involving nuclear segmentation using Cellpose 2.0 (https://github.com/MouseLand/cellpose), reads to cell assignment using pciSeq (https://github.com/acycliq/pciSeq) and single-cell mapping into the spatial data using Tangram (https://github.com/broadinstitute/Tangram).

label: not applicable

source_name: E14.5_Pancreas, spleen, duodenum

label_protocol: not applicable

growth_protocol: Standard mouse housing conditions

extract_protocol: E12.5, E14.5 and E17.5 embryonic pancreas were dissected and fixed overnight in 4% PFA. Samples were equilibrated in 20% sucrose solution and embedded in OCT compound (Sakura). 10 mm-thick cryosections were stored at -80°C. The starting day of the experiment, sections were kept at 60°C for an hour before post-fixation with 4% PFA for 5 minutes. After washes, sections were serially dehydrated in 50%, 70% and 100% Ethanol and then subjected to antigen retrieval in Citrate buffer. Gene panels were then hybridized overnight at 37°C. Ligation and following steps were performed using the High Sensitivity Library Preparation Kit from CARTANA AB (10x Genomics). Incubations were performed in SecureSealTM chambers (Grace Biolabs, Bend, OR, USA). Slow Fade Antifade Mountant (Thermo Fisher Scientific, Waltham, MA, USA, ref S36936) was used for optimal handling and imaging of tissue sections.

treatment_protocol: not applicable

value: Pancreas, spleen, duodenum

tag: age

tag: strain


title: Panel II_E14.5_11

description: HybISS, Cartana


title: Panel II_E14.5_13

description: HybISS, Cartana


title: A2_Plate 8A

description:
Library name: BSSE-QGF-131170
Smart-seq2


title: Panel II_E14.5_16

description: HybISS, Cartana


title: C2_Plate 8A

description:
Library name: BSSE-QGF-131172
Smart-seq2


title: D2_Plate 8A

description:
Library name: BSSE-QGF-131173
Smart-seq2


title: Panel II_E14.5_10

description: HybISS, Cartana


title: Panel II_E14.5_5

description: HybISS, Cartana


title: F2_Plate 8A

description:
Library name: BSSE-QGF-131175
Smart-seq2


title: Panel II_E14.5_8

description: HybISS, Cartana


title: Panel II_E14.5_4

description: HybISS, Cartana


title: G2_Plate 8A

description:
Library name: BSSE-QGF-131176
Smart-seq2


title: Panel II_E14.5_2

description: HybISS, Cartana


title: E2_Plate 8A

description:
Library name: BSSE-QGF-131174
Smart-seq2


title: H2_Plate 8A

description:
Library name: BSSE-QGF-131177
Smart-seq2


title: Panel II_E12.5_20

description: HybISS, Cartana

source_name: E12.5_Pancreas, spleen, duodenum


title: B3_Plate 8A

description:
Library name: BSSE-QGF-131179
Smart-seq2


title: D4_plate 7A

description:
Library name: BSSE-QGF-121186
Smart-seq2


title: Panel II_E12.5_19

description: HybISS, Cartana


title: G1_Plate 8A

description:
Library name: BSSE-QGF-131168
Smart-seq2


title: C3_Plate 8A

description:
Library name: BSSE-QGF-131180
Smart-seq2


title: A3_Plate 8A

description:
Library name: BSSE-QGF-131178
Smart-seq2


title: D3_Plate 8A

description:
Library name: BSSE-QGF-131181
Smart-seq2


title: Panel II_E12.5_18

description: HybISS, Cartana


title: E3_Plate 8A

description:
Library name: BSSE-QGF-131182
Smart-seq2


title: B2_Plate 8A

description:
Library name: BSSE-QGF-131171
Smart-seq2


title: Panel II_E12.5_17

description: HybISS, Cartana


title: F3_Plate 8A

description:
Library name: BSSE-QGF-131183
Smart-seq2


title: Panel II_E12.5_15

description: HybISS, Cartana


title: G3_Plate 8A

description:
Library name: BSSE-QGF-131184
Smart-seq2


title: Panel II_E12.5_13

description: HybISS, Cartana


title: H3_Plate 8A

description:
Library name: BSSE-QGF-131185
Smart-seq2


title: Panel II_E12.5_11

description: HybISS, Cartana


title: B4_Plate 8A

description:
Library name: BSSE-QGF-131187
Smart-seq2


title: Panel II_E12.5_12

description: HybISS, Cartana


title: A4_Plate 8A

description:
Library name: BSSE-QGF-131186
Smart-seq2


title: Panel II_E12.5_8

description: HybISS, Cartana


title: Panel II_E12.5_9

description: HybISS, Cartana


title: D4_Plate 8A

description:
Library name: BSSE-QGF-131189
Smart-seq2


title: Panel II_E12.5_3

description: HybISS, Cartana


title: F4_Plate 8A

description:
Library name: BSSE-QGF-131191
Smart-seq2


title: C4_Plate 8A

description:
Library name: BSSE-QGF-131188
Smart-seq2


title: Panel II_E12.5_28

description: HybISS, Cartana


title: Panel II_E12.5_27

description: HybISS, Cartana


title: Panel I_E17.5_4

description: HybISS, Cartana

source_name: E17.5_Pancreas, spleen, duodenum


title: Panel II_E12.5_4

description: HybISS, Cartana


title: E4_Plate 8A

description:
Library name: BSSE-QGF-131190
Smart-seq2


title: H4_Plate 8A

description:
Library name: BSSE-QGF-131193
Smart-seq2


title: Panel I_E17.5_5

description: HybISS, Cartana


title: Panel I_E17.5_2

description: HybISS, Cartana


title: Panel I_E17.5_3

description: HybISS, Cartana


title: A5_Plate 8A

description:
Library name: BSSE-QGF-131194
Smart-seq2


title: B5_Plate 8A

description:
Library name: BSSE-QGF-131195
Smart-seq2


title: C5_Plate 8A

description:
Library name: BSSE-QGF-131196
Smart-seq2


title: G4_Plate 8A

description:
Library name: BSSE-QGF-131192
Smart-seq2


title: D5_Plate 8A

description:
Library name: BSSE-QGF-131197
Smart-seq2


title: E5_Plate 8A

description:
Library name: BSSE-QGF-131198
Smart-seq2


title: Panel I_E14.5_8

description: HybISS, Cartana


title: F5_Plate 8A

description:
Library name: BSSE-QGF-131199
Smart-seq2


title: Panel I_E14.5_10

description: HybISS, Cartana


title: Panel I_E14.5_7

description: HybISS, Cartana


title: G5_Plate 8A

description:
Library name: BSSE-QGF-131200
Smart-seq2


title: H5_Plate 8A

description:
Library name: BSSE-QGF-131201
Smart-seq2


title: Panel I_E14.5_6

description: HybISS, Cartana


title: Panel I_E14.5_5

description: HybISS, Cartana


title: A6_Plate 8A

description:
Library name: BSSE-QGF-131202
Smart-seq2


title: Panel I_E14.5_4

description: HybISS, Cartana


title: B6_Plate 8A

description:
Library name: BSSE-QGF-131203
Smart-seq2


title: C6_Plate 8A

description:
Library name: BSSE-QGF-131204
Smart-seq2


title: Panel I_E14.5_1

description: HybISS, Cartana


title: D6_Plate 8A

description:
Library name: BSSE-QGF-131205
Smart-seq2


title: Panel I_E14.5_2

description: HybISS, Cartana


title: E6_Plate 8A

description:
Library name: BSSE-QGF-131206
Smart-seq2


title: Panel I_E12.5_5

description: HybISS, Cartana


title: Panel I_E17.5_1

description: HybISS, Cartana


title: Panel I_E14.5_3

description: HybISS, Cartana


title: Panel I_E12.5_6

description: HybISS, Cartana


title: Panel I_E12.5_4

description: HybISS, Cartana


title: Panel I_E14.5_9

description: HybISS, Cartana


title: H6_Plate 8A

description:
Library name: BSSE-QGF-131209
Smart-seq2


title: Panel I_E12.5_2

description: HybISS, Cartana


title: G6_Plate 8A

description:
Library name: BSSE-QGF-131208
Smart-seq2


title: Panel I_E12.5_3

description: HybISS, Cartana


title: A7_Plate 8A

description:
Library name: BSSE-QGF-131210
Smart-seq2


title: B7_Plate 8A

description:
Library name: BSSE-QGF-131211
Smart-seq2


title: F6_Plate 8A

description:
Library name: BSSE-QGF-131207
Smart-seq2


title: Panel I_E12.5_1

description: HybISS, Cartana


title: D7_Plate 8A

description:
Library name: BSSE-QGF-131213
Smart-seq2


title: C7_Plate 8A

description:
Library name: BSSE-QGF-131212
Smart-seq2


title: Tumor1, adult, multiome, snRNA

city: Los Angeles

first: Claire

last: Arata

email: carata@usc.edu, clairearata@gmail.com

state: CA

address: 1425 San Pablo St

department: Stem Cell

country: USA

institute: University of Southern California

description: Library name: Sample 11

data_processing:
The count matrices of both multiome and snATACseq data were analyzed by R (v4.1.3) package Seurat (v4.3.0) and Signac (v1.6.0). For snRNAseq, Cellranger matrices for 7 dpf EWSR1::FLI1+ and 7 dpf control trunk were merged (merge, Seurat-methods) and then filterered based on nFeature_RNA >200, nFeature_RNA < 2500, and  nCount_RNA <2000. Matricies were then normalized (NormalizeData) and scaled for the top 2000 variable genes (FindVariableFeatures, method = “vst” and ScaleData). The scaled matrices were dimensionally reduced to 20 principal components (RunPCA) using variable features. The data were then subjected to neighbor finding (FindNeighbors) and clustering (FindClusters, resolution = 0.4) with input from the first through twentieth LSIs. For snATACseq datasets, Cellranger (10x Genomics) 7 dpf EWSR::FLI11+ and 7 dpf control trunk aggregated matrices were filtered for peak_region_fragments < 8000, pct_reads_in_peaks > 45, blacklist_ratio < 0.7, blacklist_ratio > 0.3, nucleosome_signal <1, nucleosome_signal > 0.2, and TSS.enrichment > 0.2. They were then normalized using RunTFIDF and RunSVD functions. The neighbor finding, clustering, and visualization were performed (RunUMAP, FindNeighbors, FindClusters, algorithm = 3 for FindClusters with resolution = 0.8) with input of the second to thirtieth LSIs. For snRNAseq (Fig. 3), tumor and control datasets were merged (merge, Seurat-methods), matrices were normalized (NormalizeData) and scaled for the top 500 variable genes (FindVariableFeatures, method = “vst” and ScaleData). The scaled matrices were dimensionally reduced to 15 principal components (RunPCA) based on JackStrawPlot and ElbowPlot.
Assembly: GRCz11
Supplementary files format and content: Count matricies in H5 file format; fragments files (cellranger output); bigWig files correspond to the snATAC samples.

molecule: polyA RNA

organism: Danio rerio

source_name: head tumor

growth_protocol: The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments (10885). Zebrafish embryos (Danio rerio) were raised in embryo media at 28.5°C. For adults, in the institute vivarium according to Protocol 10885.

extract_protocol:
Trunks from converted -28.5Sox10:Cre; actab2:loxP-BFP-STOP-loxP-DsRed (Sox10>DsRed) or -28.5Sox10:Cre;actab2:loxP-BFP-STOP-loxP-DsRed; Ubi:loxP-DsRed-STOP-loxP-GFP-2A-EF1 (Sox10>GFP-2A-EF1) fish at 7 dpf were cut posterior to ear and excluding swim bladder at all stages, cut into multiple pieces,  and placed in cold 1x PBS. Tumors from Sox10>GFP-2A-EF1 or normal tissue from control fish were dissected from young adult fish, cut into multiple pieces, and placed in cold 1x PBS. 1x PBS was then removed and replaced with pre-warmed Accumax. Samples were placed on a nutator at 30-32 °F, followed by mechanical dissociation by pipetting every 10 min (Innovative Cell Technologies Inc, AM105) for 1.5-2 hours. Cells were pelleted (200 × g, 10 min, 4 °C), supernatant was removed (leaving roughly 200 µL) and replaced with 1 mL of cold Hank’s Buffer solution (0.25% BSA, 10mM HEPES, 1x HBBS). Cells were vortexed to resuspend and pelleted again (376 × g, 5 min, 4 °C), supernatant removed (leaving roughly 100 µL) and replaced with 100 µL of cold 1x PBS per 24 trunk reaction. Pellets were resuspended by vortexing and filtered through 40 µm strainers (Corning, 431750). Cells derived from fish at  7 dpf were resuspended, placed on ice and fluorescence-activated cell sorted (FACS) for DsRed (control) or GFP (EWSR1::FLI1+). All samples were subjected to nuclei isolation according to manufacturer’s instructions (10x Genomics, protocol CG000169, “Low Cell Input Nuclei Isolation”).
Multiome and snATACseq libraries were prepared using 10x Genomics Chromium Next GEM  Single Cell Multiome ATAC + Gene Expression or Chromium Next GEM Single Cell ATAC v2 according to the manufacturer’s instructions and sequenced using Illumina NextSeq or HiSeq. Sequenced data was aligned using Cellranger-arc v2.0.2, Cellranger-atac v2.0.0, Cellranger v6.0.2  or Cellranger-arc v8.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.

value: head tumor

tag: cell type

value: various

value: WIK


title: Tumor1, adult, multiome, snATAC

description: Library name: Sample 10

library_source: genomic single cell

molecule: genomic DNA


title: F7_Plate 8A

description:
Library name: BSSE-QGF-131215
Smart-seq2


title: Control adult, multiome, snATAC

description: 10x Genomics, Multiome

data_processing:
The count matrices of both multiome and snATACseq data were analyzed by R (v4.1.3) package Seurat (v4.3.0) and Signac (v1.6.0). For snRNAseq, Cellranger matrices for 7 dpf EWSR1::FLI1+ and 7 dpf control trunk were merged (merge, Seurat-methods) and then filterered based on nFeature_RNA >200, nFeature_RNA < 2500, and  nCount_RNA <2000. Matricies were then normalized (NormalizeData) and scaled for the top 2000 variable genes (FindVariableFeatures, method = “vst” and ScaleData). The scaled matrices were dimensionally reduced to 20 principal components (RunPCA) using variable features. The data were then subjected to neighbor finding (FindNeighbors) and clustering (FindClusters, resolution = 0.4) with input from the first through twentieth LSIs. For snATACseq datasets, Cellranger (10x Genomics) 7 dpf EWSR::FLI11+ and 7 dpf control trunk aggregated matrices were filtered for peak_region_fragments < 8000, pct_reads_in_peaks > 45, blacklist_ratio < 0.7, blacklist_ratio > 0.3, nucleosome_signal <1, nucleosome_signal > 0.2, and TSS.enrichment > 0.2. They were then normalized using RunTFIDF and RunSVD functions. The neighbor finding, clustering, and visualization were performed (RunUMAP, FindNeighbors, FindClusters, algorithm = 3 for FindClusters with resolution = 0.8) with input of the second to thirtieth LSIs. For snRNAseq (Fig. 7), tumor and control datasets were merged (merge, Seurat-methods), matrices were normalized (NormalizeData) and scaled for the top 500 variable genes (FindVariableFeatures, method = “vst” and ScaleData). The scaled matrices were dimensionally reduced to 15 principal components (RunPCA) based on JackStrawPlot and ElbowPlot.
Assembly: GRCz11
Supplementary files format and content: Count matricies in H5 file format; fragments files (cellranger output); bigWig files correspond to the snATAC samples.

source_name: trunk

value: trunk

value: adult

value: tubingen/WIK


title: E7_Plate 8A

description:
Library name: BSSE-QGF-131214
Smart-seq2


title: Control adult, multiome, snRNA

description: 10x Genomics, Multiome


title: G7_Plate 8A

description:
Library name: BSSE-QGF-131216
Smart-seq2


title: Tumor adult, multiome, snATAC

description: 10x Genomics, Multiome

source_name: trink tumor

value: trink tumor


title: H7_Plate 8A

description:
Library name: BSSE-QGF-131217
Smart-seq2


title: A8_Plate 8A

description:
Library name: BSSE-QGF-131218
Smart-seq2


title: B8_Plate 8A

description:
Library name: BSSE-QGF-131219
Smart-seq2


title: D8_Plate 8A

description:
Library name: BSSE-QGF-131221
Smart-seq2


title: 7dpf -28.5_Sox10:dsRed>GFP-2a-EWSFLI, GFP+, trunk, multiome, snATAC

description: 10x Genomics, Multiome

value: 7 dpf


title: 7dpf -28.5_Sox10:dsRed>GFP-2a-EWSFLI, GFP+, trunk, snATAC

description: 10x Genomics, snATACseq

value: tubingen


title: C8_Plate 8A

description:
Library name: BSSE-QGF-131220
Smart-seq2


title: 7dpf -28.5_Sox10:dsRed>GFP-2a-EWSFLI, GFP+, trunk, multiome, snRNA

description: 10x Genomics, Multiome


title: Algae NAME-seq

city: Houston

first: Tao

middle: P.

last: Wu

state: TX

address: One Baylor Plaza, MS BCM225

department: Molecular and Human Genetics

institute: Baylor College of Medicine

library_source: genomic

data_processing:
sequencing reads were trimmed using cutadapt (v1.18) to remove adaptors. Duplicated reads were removed using BBMAP (v38.84)34 clumpify package.
Fastq reads and fasta reference were converted to AT-only format (convert all purine to A and all thymine to T). Converted fastq reads were aligned to reference using bowtie2 (v2.3.5.1)
AT only sam files were converted back to sam files with original reads using custom python scripts. NM and MD tags were recalculated using samtools (1.9) calmd. The alignments in sam files were filtered by recreated MD tag to keep allowed base mutation (A to G and C to T)
Base count at each genomic location was generated by igvtools (v2.5.3) and customed python scripts
SNPs information at AT positions are generated by GATK (4.1.7.0)
Assembly: NC_000913.3; CP023448.1; Creinhardtii_281_v5.0; hg38
Supplementary files format and content: Comma-separated values, base content after nitrite treatment
Supplementary files format and content: BED, SNP information to filter 6mA

organism: Chlamydomonas reinhardtii

extract_protocol:
Genomic DNA was extrated using DNeasy Blood and Tissue Kit according to the manufacturer's instructions (Qiagen, 69506)
Genomic DNA was fragmentized to 500-800 bp using Covaris S220 Focused-ultrasonicator. Fragmented gDNA was subjected to nitrite treatment. The treated DNA was used to construct sequencing library by customed protocol.
Methyl-seq

tag: cell line

value: Unicellular eukarytoes

value: Wild-type

tag: treatment


title: MmKidAt_20221026E_ATAC

city: Saint Louis

first: Madhurima

last: Kaushal

address: 1 Brookings Dr

institute: Washington University in St Louis

description: Library name: MmKidAt_20221026E_ATAC

data_processing:
Raw fastq data were processed with the cellranger-arc (v2.0.2) software with the GRCm39 mouse genome reference.
Assembly: GRCm39
Supplementary files format and content: Genes expression files in the Market EXchange format (MEX) that is comprised of the tab seperated files for the columns which are cell ids (*barcodes.tsv.gz), the rows which are Ensembl gene ids (*features.tsv.gz) and gene expression counts (*matrix.mtx.gz).
Supplementary files format and content: Chromatin accessibility (ATAC-seq) processed files are the Hierarchical Data Format (H5), *feature_bc_matrix.h5 file containing the count of reads within individual called peaks and the tab separated file *fragments.tsv file containing the positions of mapped reads, cell ids which each reads are assigned and value representing the number of reads aligned to the same positions.

source_name: old,Female,wt

extract_protocol:
10x Chromium Nuclei Isolation Kit (Sample User Guide, CG000505 Rev A)
Single nuclei suspensions were generated from OCT embedded tissue sections following manufacturer's protocols using the 10X Genomics Chromium Nuclei Isolation Kit (PN-1000494). Single nuclei ATAC and Genes Expression libraries were generated from nuclei suspensions following manufacturer's protocols using the 10X Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit (PN-1000283).

value: kidney

tag: Sex

value: Female

value: old

value: wildtype


title: E8_Plate 8A

description:
Library name: BSSE-QGF-131222
Smart-seq2

value: Dorsal Pancreas


title: MmKidAt_20221026D_ATAC

description: Library name: MmKidAt_20221026D_ATAC


title: MmKidAt_20221026D_RNA

description: Library name: MmKidAt_20221026D_RNA


title: Adult 1

city: Marseille

first: Stéphane

last: ZAFFRAN

address: 27 Bd JEan Moulin

country: France

institute: Aix Marseille Université

library_source: transcriptomic

data_processing:
Image analysis and base calling were performed using RTA 1.18.61
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw count for each sample

organism: Homo sapiens

source_name: Aortic Valve

extract_protocol:
RNA was harvest using NucleoSpin RNA, Mini kit (Machery-Nagel). 1ug of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using

value: Aortic Valve


title: Adult 2


title: MmKidAt_20221026E_RNA

description: Library name: MmKidAt_20221026E_RNA


title: MmKidAt_20221026C_ATAC

description: Library name: MmKidAt_20221026C_ATAC


title: F8_Plate 8A

description:
Library name: BSSE-QGF-131223
Smart-seq2


title: MmKidAt_20221026C_RNA

description: Library name: MmKidAt_20221026C_RNA


title: G8_Plate 8A

description:
Library name: BSSE-QGF-131224
Smart-seq2


title: MmKidAt_20221026B_ATAC

description: Library name: MmKidAt_20221026B_ATAC

source_name: middle-aged,Female,wt

value: middle-aged


title: H8_Plate 8A

description:
Library name: BSSE-QGF-131225
Smart-seq2


title: MmKidAt_20221026B_RNA

description: Library name: MmKidAt_20221026B_RNA


title: MmKidAt_20221026A_ATAC

description: Library name: MmKidAt_20221026A_ATAC


title: A9_Plate 8A

description:
Library name: BSSE-QGF-131226
Smart-seq2


title: 20PCW 2


title: 20PCW 1


title: MmKidAt_20221026A_RNA

description: Library name: MmKidAt_20221026A_RNA


title: Tumor adult, multiome, snRNA

description: 10x Genomics, Multiome

value: various


title: B9_Plate 8A

description:
Library name: BSSE-QGF-131227
Smart-seq2


title: MmKidAt_20221005E_ATAC

description: Library name: MmKidAt_20221005E_ATAC


title: Adult 3


title: MmKidAt_20221005D_RNA

description: Library name: MmKidAt_20221005D_RNA

source_name: mature,Female,wt

value: mature


title: MmKidAt_20221005D_ATAC

description: Library name: MmKidAt_20221005D_ATAC


title: 13PCW 1


title: C9_Plate 8A

description:
Library name: BSSE-QGF-131228
Smart-seq2


title: 13PCW 2


title: D9_Plate 8A

description:
Library name: BSSE-QGF-131229
Smart-seq2


title: MmKidAt_20221005C_ATAC

description: Library name: MmKidAt_20221005C_ATAC


title: 9PCW 3


title: E9_Plate 8A

description:
Library name: BSSE-QGF-131230
Smart-seq2


title: MmKidAt_20221005B_RNA

description: Library name: MmKidAt_20221005B_RNA


title: F9_Plate 8A

description:
Library name: BSSE-QGF-131231
Smart-seq2


title: MmKidAt_20221005A_ATAC

description: Library name: MmKidAt_20221005A_ATAC

source_name: old,Male,wt

value: Male


title: G9_Plate 8A

description:
Library name: BSSE-QGF-131232
Smart-seq2


title: MmKidAt_20221005A_RNA

description: Library name: MmKidAt_20221005A_RNA


title: 9PCW 1


title: MmKidAt_20220921G_ATAC

description: Library name: MmKidAt_20220921G_ATAC


title: MmKidAt_20220921F_ATAC

description: Library name: MmKidAt_20220921F_ATAC


title: 13PCW 3


title: MmKidAt_20220921F_RNA

description: Library name: MmKidAt_20220921F_RNA


title: H9_Plate 8A

description:
Library name: BSSE-QGF-131233
Smart-seq2


title: SCLC P4

city: Erlangen

first: Lydia

last: Meder

state: Bavaria

address: Glückstr. 6

department: Experimentelle Medizin 1

country: Germany

description: Library name: Sample 3

data_processing:
Transfering gene counts to CPM using GENAVi
GSEA using VolcaNoiseR
Assembly: mm10
Supplementary files format and content: counts per million; .xlsx-file
Supplementary files format and content: .fastq.gz

source_name: lung origin

growth_protocol: The cell lines were cultured under conditions of 5% CO2 and 37°C. The cell culture media RPMI medium 1640 (Thermo Fisher Scientific Inc., USA) was supplemented with 10% FBS (PAN-Biotech, Aidenbach, Germany), 50U/ml Penicillin, 50μg/ml Streptomycin.

extract_protocol:
RNA was harvested using the RNeasy Mini Kit (Qiagen N.v., Netherlands) according to manufacturer’s instruction.
RNA libraries for RNASeq are generated using TruSeq total RNA. 1µg of total RNAwas used for library preparation.

treatment_protocol: Cells were seeded and cultured under standard conditions without any treatment prior to RNA extraction.

value: lung origin

value: small cell lung cancer

value: epithelial

value: SCLC WT 3


title: SCLC M1

description: Library name: Sample 4

value: SCLC WT 4


title: MmKidAt_20220921G_RNA

description: Library name: MmKidAt_20220921G_RNA


title: MmKidAt_20221005E_RNA

description: Library name: MmKidAt_20221005E_RNA


title: MmKidAt_20220921E_ATAC

description: Library name: MmKidAt_20220921E_ATAC

source_name: middle-aged,Male,wt


title: MmKidAt_20220921D_ATAC

description: Library name: MmKidAt_20220921D_ATAC


title: B10_Plate 8A

description:
Library name: BSSE-QGF-131235
Smart-seq2


title: MmKidAt_20220921E_RNA

description: Library name: MmKidAt_20220921E_RNA


title: SCLC P5

description: Library name: Sample 2

value: SCLC WT 2


title: MmKidAt_20221005C_RNA

description: Library name: MmKidAt_20221005C_RNA


title: MmKidAt_20220921D_RNA

description: Library name: MmKidAt_20220921D_RNA


title: MmKidAt_20220921C_ATAC

description: Library name: MmKidAt_20220921C_ATAC


title: SCLC P1

description: Library name: Sample 1

value: SCLC WT 1


title: C10_Plate 8A

description:
Library name: BSSE-QGF-131236
Smart-seq2


title: 9PCW 2


title: MmKidAt_20221005B_ATAC

description: Library name: MmKidAt_20221005B_ATAC

value: kidney


title: Ly35

description: Library name: Sample 5

data_processing:
CellRanger analysis pipeline from 10x Genomics was used to perform the processing of raw FASTQ files for standard bioinformatic analysis.
For cell clustering and visualization in 2 dimensions (UMAP), annotation of cell types, cell type differential gene expression analysis and visualization, we utilized the Scanpy Python package.
Clusters were identified using the Phenograph-louvain 33 clustering algorithm integrated in Scanpy. The analyses were performed in Python using Scanpy and anndata.
Assembly: mm10
Supplementary files format and content: comma seperated value (.csv); comma as seperator

source_name: SCLC lung tumor

growth_protocol: Tumors were induced upon adenoviral Cre inhalation mediating the functional depletion of Rb1 and Trp53 in the murine lung, tumor growth to create a target lesions measurable by µCT took app. 6 month, upon target lesion detection therapy regimen has been been started

extract_protocol:
Murine SCLC tumor samples were harvested from lungs of treated mice, washed in PBS, covered by Tissue Preservation Buffer (Singleron Biotechnologies) and shipped on ice. Samples were processed within 72 hours after tumor isolation using sCelLiVETM Tissue Dissociation Buffer (Singleron Biotechnologies) and microfluidic SCOPE-chipTM
scRNA-seq

treatment_protocol: Treatments were administered every three days as follows: Vehicle (phosphate-buffered saline; PBS); Combination therapy of a-PD-1 with 10 mg/kg BW, ERBB2i with 10 mg/kg BW at a concentration of BW via oral application.

value: SCLC lung tumor

value: neuroendocrine origin

value: Rb1 fl/fl x Trp53 fl/fl

value: Mubritinib + aPD-1 in response


title: MmKidAt_20220921B_ATAC

description: Library name: MmKidAt_20220921B_ATAC

source_name: mature,Male,wt

value: wildtype


title: MmKidAt_20220921B_RNA

description: Library name: MmKidAt_20220921B_RNA


title: Ly29

description: Library name: Sample 4

value: Vehicle


title: MmKidAt_20220921A_ATAC

description: Library name: MmKidAt_20220921A_ATAC


title: E10_Plate 8A

description:
Library name: BSSE-QGF-131238
Smart-seq2

value: Dorsal Pancreas


title: Ly16

description: Library name: Sample 3


title: MmKidAt_20220921A_RNA

description: Library name: MmKidAt_20220921A_RNA

value: mature


title: F10_Plate 8A

description:
Library name: BSSE-QGF-131239
Smart-seq2


title: C57BL/6J, Olfactory epithelium, pS6-IP, O&C 3

city: Dalseong-gun

first: Minseok

last: Kim

state: Daegu

address: 333, Techno jungang-daero, Hyeonpung-eup

department: Department of Brain Sciences

country: South Korea

institute: Daegu Gyeongbuk Institute of Science & Technology

description: Library name: O&C 3

library_source: other

data_processing:
RNA-seq data analysis was performed using a combination of Python (v3.12.3) and R (v4.4.2) environments. The sequencing reads were aligned to the Mus musculus reference genome GRCm39 using STAR aligner (v2.7.10b). Transcript quantification was performed with Salmon (v1.10.1) to generate gene-level count tables.
Assembly: Mus musculus GRCm39
Supplementary files format and content: Tab-delimited text file containing raw gene counts across all samples and gene identifiers for all genes.

molecule: other

source_name: Olfactory epithelium

extract_protocol:
Olfactory epithelium tissues were rapidly collected from mice immediately after odorant exposure and perfused with chilled buffer (PBS, 5mM NaF, 2.5mM Na3VO4, 2.5mM Na4P2O7, 5mM β-glycerophosphate, 100μg/mL cycloheximide, protease inhibitor). The tissues were homogenized in a buffer containing 10mM HEPES (pH 7.4), 150mM KCl, 10mM MgCl2, 100mM calyculin A, 0.5mM DTT, 100U/mL RNasin, 250μg/mL cycloheximide, and protease inhibitors using a TissueLyser II (Qiagen) for 2 minutes at 20Hz. Homogenates were centrifuged at 2,000×g for 10 minutes at 4°C. The supernatant was supplemented with 0.7% NP-40, incubated on ice, and centrifuged at 20,000×g for 10 minutes at 4°C. For pS6-immunoprecipitation, the supernatant was incubated with Protein A Dynabeads pre-coupled to anti-phospho-S6 antibody (Invitrogen 44-923G) for 1 hour at room temperature. After four washes with high-salt buffer (10 mM HEPES (pH 7.4), 350 mM KCl, 5 mM MgCl2, 2 mM DTT, 1% NP-40, 100 U/mL RNasin, and 100 μg/mL cycloheximide), RNA was eluted with Buffer RLT and purified using the RNeasy Mini Kit (Qiagen) with on-column DNase digestion.
Libraries were prepared using the TruSeq Stranded mRNA Sample Prep kit (Illumina), and sequencing was carried out on an Illumina NovaSeq 6000 platform according to the manufacturer's protocols.

treatment_protocol: Mice were individually housed in odor-free chambers and habituated for four hours prior to odorant exposure. For binary mixture conditions (acetophenone–decanal or octanal–cis-3-hexenol at a 1:1 ratio), two delivery paradigms were used. In the “+” mixture condition, 10 μL of each odorant (20 μL total) was applied together on the same piece of filter paper, allowing physical mixing prior to evaporation. In the “&” mixture condition, 10 μL of each odorant was applied separately to two distinct filter papers, which were positioned approximately 1 mm apart within the culture dish, permitting mixing to occur only in the air phase. Control animals were exposed to empty filter papers (No-odor). Mice were exposed to their assigned condition for 90 minutes, and three biological replicates were prepared for each experimental group.

value: Olfactory epithelium

value: Wildtype

value: male

value: Octanal & Cis-3-hexenol

tag: batch

value: ADOC


title: C57BL/6J, Olfactory epithelium, pS6-IP, O&C 2

description: Library name: O&C 2


title: A10_Plate 8A

description:
Library name: BSSE-QGF-131234
Smart-seq2

source_name: Dorsal Pancreas


title: Ly10

description: Library name: Sample 2

value: epithelial

value: Mubritinib


title: C57BL/6J, Olfactory epithelium, pS6-IP, O&C 1

description: Library name: O&C 1


title: G10_Plate 8A

description:
Library name: BSSE-QGF-131240
Smart-seq2


title: C57BL/6J, Olfactory epithelium, pS6-IP, O+C 3

description: Library name: O+C 3

value: Octanal + Cis-3-hexenol


title: C57BL/6J, Olfactory epithelium, pS6-IP, O+C 2

description: Library name: O+C 2


title: C57BL/6J, Olfactory epithelium, pS6-IP, O+C 1

description: Library name: O+C 1


title: Ly8

description: Library name: Sample 1

value: Mubritinib + aPD-1


title: C57BL/6J, Olfactory epithelium, pS6-IP, A&D 3

description: Library name: A&D 3

value: Acetophenone & Decanal


title: H10_Plate 8A

description:
Library name: BSSE-QGF-131241
Smart-seq2


title: SCLC ERBB2 KO 3

description: Library name: 183139_A10_CO_SCLC_8

data_processing:
Transfering gene counts to CPM using GENAVi
GSEA using VolcaNoiseR
Assembly: mm10
Supplementary files format and content: comma seperated value (.csv); comma as seperator.xlsx-file

treatment_protocol: In murine derived SCLC cells a RNA-guided Cas9 ERBB2 KO Knock-out (KO) was achieved applying the Santa Cruz CRISPR construct transfection according to manufacturer’s advices. 24 h prior to transfection cells were seeded in 6 well plates and transfected with Lipofectamine® LTX Plus reagent. After 48 h of puromycin selection, single clones were plate-sorted. The efficiency of the knock-out was validated with western blot and flow cytometry. follwoed by puromycin selection and GFP based cell sorting.

value: lung origin

value: small cell lung cancer

value: SCLC ERBB2 KO


title: MmKidAt_20220921C_RNA

description: Library name: MmKidAt_20220921C_RNA

value: kidney

value: Male

value: middle-aged

value: wildtype


title: A11_Plate 8A

description:
Library name: BSSE-QGF-131242
Smart-seq2

value: Dorsal Pancreas


title: C57BL/6J, Olfactory epithelium, pS6-IP, A&D 2

description: Library name: A&D 2

value: Olfactory epithelium

value: Wildtype


title: C57BL/6J, Olfactory epithelium, pS6-IP, A&D 1

description: Library name: A&D 1

value: male


title: B11_Plate 8A

description:
Library name: BSSE-QGF-131243
Smart-seq2


title: D10_Plate 8A

description:
Library name: BSSE-QGF-131237
Smart-seq2


title: C57BL/6J, Olfactory epithelium, pS6-IP, A+D 3

description: Library name: A+D 3

value: Acetophenone + Decanal

value: ADOC


title: C57BL/6J, Olfactory epithelium, pS6-IP, A+D 2

description: Library name: A+D 2


title: C11_Plate 8A

description:
Library name: BSSE-QGF-131244
Smart-seq2


title: SCLC ERBB2 KO 2

description: Library name: 183131_A10_CO_SCLC_3

value: epithelial


title: C57BL/6J, Olfactory epithelium, pS6-IP, Control 1

description: Library name: Control 1

value: No odor (Control)


title: E11_Plate 8A

description:
Library name: BSSE-QGF-131246
Smart-seq2


title: SIRT3 cohoused KO BNST 3

city: Daejeon

first: Min Joung

last: Lee

address: Munhwa-ro 266

department: Department of Biochemistry

institute: Chungnam National University School of Medicine

description: Library name: 3B_coKO

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to GRCm39(NCBI) whole genome using Tophat
FPKM calculation using Cufflink
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include Read count values for each Sample

source_name: brain, BNST

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using the NEBNext Ultra II Directional RNA-Seq Kit standard protocols.

value: brain, BNST

value: SIRT3 KO

value: cohoused


title: SIRT3 cohoused KO BNST 2

description: Library name: 2B_coKO


title: SCLC WT 1

description: Library name: 183126_A10_CO_SCLC_1

value: lung origin

value: small cell lung cancer

value: SCLC WT


title: SIRT3 cohoused KO BNST 1

description: Library name: 1B_coKO


title: TX229

description: Library name: Sample 2

data_processing:
standard cellranger for single cell RNA version 7.0.0.
To maximize sensitivity for whole transcriptome 3’/5’ Single Cell Gene Expression and 3’ Cell Multiplexing experiments, introns will be included in the analysis by default for cellranger count and multi.
No quality filtering or adapter trimming was applied to the FastQ files.
Assembly: GRCm38
Supplementary files format and content: comma seperated value (.csv); comma as seperator

source_name: PBMC

extract_protocol:
150 µl blood was drawn from treated mice in heparin coated tubes. Red blood cells were lysed by treating the sample with 850 µl ACK lysis buffer for 10 min at RT followed by washing with PBS. Cells were then resuspended in MACS buffer and negatively selected for CD3 using the Pan T Cell Isolation Kit II, mouse (Miltenyi Biotec, Germany).
10X Genomics kits were used according to manufacturer protcol, libraries were generated and sequenced on an Illumina instrument using 2 × 150-bp paired end sequencing.

value: PBMC

value: T lymphocytes

value: vehicle


title: SIRT3 cohoused WT BNST 3

description: Library name: 3B_coWT

value: WT


title: G11_Plate 8A

description:
Library name: BSSE-QGF-131248
Smart-seq2

value: Dorsal Pancreas


title: SCLC WT 3

description: Library name: 183137_A10_CO_SCLC_7


title: SIRT3 KO BNST 5

description: Library name: 5B_KO


title: SIRT3 cohoused WT BNST 1

description: Library name: 1B_coWT


title: SCLC WT 2

description: Library name: 183133_A10_CO_SCLC_5


title: TX202

description: Library name: Sample 1


title: H11_Plate 8A

description:
Library name: BSSE-QGF-131249
Smart-seq2


title: SIRT3 cohoused WT BNST 2

description: Library name: 2B_coWT


title: snmCT_sep2022_mbd56_P7

first: Colette

middle: L

last: Picard

state: California

address: 610 Charles E Young Dr East, Room 4045

department: Molecular, Cell and Developmental Biology

institute: University of California - Los Angeles

description:
mbd56_2_RNAseq_count_matrix.txt.gz
pseudobulk_mbd56_GN_CHGme.bed.gz
pseudobulk_mbd56_GN_CHHme.bed.gz
pseudobulk_mbd56_GN_CpGme.bed.gz
pseudobulk_mbd56_MN_CHGme.bed.gz
pseudobulk_mbd56_MN_CHHme.bed.gz
pseudobulk_mbd56_MN_CpGme.bed.gz
pseudobulk_mbd56_MNtoVN_CHGme.bed.gz
pseudobulk_mbd56_MNtoVN_CHHme.bed.gz
pseudobulk_mbd56_MNtoVN_CpGme.bed.gz
pseudobulk_mbd56_SN_CHGme.bed.gz
pseudobulk_mbd56_SN_CHHme.bed.gz
pseudobulk_mbd56_SN_CpGme.bed.gz
pseudobulk_mbd56_VN1_CHGme.bed.gz
pseudobulk_mbd56_VN1_CHHme.bed.gz
pseudobulk_mbd56_VN1_CpGme.bed.gz
pseudobulk_mbd56_VN1to2_CHGme.bed.gz
pseudobulk_mbd56_VN1to2_CHHme.bed.gz
pseudobulk_mbd56_VN1to2_CpGme.bed.gz
pseudobulk_mbd56_VN2_CHGme.bed.gz
pseudobulk_mbd56_VN2_CHHme.bed.gz
pseudobulk_mbd56_VN2_CpGme.bed.gz
pseudobulk_mbd56_VN3_CHGme.bed.gz
pseudobulk_mbd56_VN3_CHHme.bed.gz
pseudobulk_mbd56_VN3_CpGme.bed.gz
pseudobulk_mbd56_VN4_CHGme.bed.gz
pseudobulk_mbd56_VN4_CHHme.bed.gz
pseudobulk_mbd56_VN4_CpGme.bed.gz
pseudobulk_mbd56_VN5_CHGme.bed.gz
pseudobulk_mbd56_VN5_CHHme.bed.gz
pseudobulk_mbd56_VN5_CpGme.bed.gz

data_processing:
Libraries were sequenced using a paired-end 100x100bp protocol on Novaseq 6000. Each 384 well plate was sequenced separately, and the sequencing data were  processed using a custom pipeline (available here: TODO: TBD), which handled demultiplexing, quality filtering, alignment, and initial processing (obtaining gene counts etc.). These are briefly described below.
Read pairs were initially demultiplexed to assign each to a well according to its well barcode, with the same list of barcodes used for each plate. See supplementary file feature_README.txt.
As recommended in Luo et al. 2017 Science, to remove bias due to random priming and adaptase behavior, paired-end reads were  hard trimmed by 10bp at both 5’ and 3’ ends, and the 5’ end of read 1 (containing the well barcode) was trimmed by an additional 8 bp to remove the barcodes. Demux reads were trimmed for adapter sequences and filtered to remove low quality sequences using trim_galore with options -a AGATCGGAAGAG -q 25 --stringency 3 (Babraham Institute).
High quality reads were aligned to the transcriptome using STAR with options --alignEndsType EndToEnd --outFilterType BySJout --outFilterMultimapNmax 1 --winAnchorMultimapNmax 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.05 --alignIntronMin 70 --alignIntronMax 5000 --outFilterIntronMotifs RemoveNoncanonical, and only unique alignments were kept.
Reads that did not align to the (unconverted) transcriptome  were then aligned to the bisulfite-converted genome using Bismark with options -N 0 -L 20 --non_directional, again retaining only unique alignments. All alignments were then filtered to remove PCR duplicates using picard tools’ MarkDuplicates function (Broad Institute).
RNA-seq read counts per gene were obtained using htseq-count, while per-site  bisulfite-seq data was extracted from the bismark BAM file using the bismark_methylation_extractor function.
Assembly: TAIR10
Supplementary files format and content: RNA-seq count matrices contain one row per gene, and one column per nucleus. Column labels are P[plate #]_[well ID], so P8_J18 is plate 8, well J18. Note that only wells that passed basic QC were included.
Supplementary files format and content: WGBS processed data files are BED-like files containing data pseudobulked across all nuclei of indicated genotype in indicated cluster and sequence context (CG, CHG and CHH). Columns indicate (1) chromosome, (2) cytosine location (0-based), (3) location + 1, (4) # reads unmethylated at this position, (5) # reads methylated at this position, (6) % methylation (methylated / (meth + unmeth)), (7) number of nuclei that had 1+ reads overlapping this position, (8) number of samples that had 1+ reads overlapping this position (either 1 or 2, since we have 2 replicates/samples)
Library strategy: snmCT-seq

organism: Arabidopsis thaliana

source_name: pollen

growth_protocol: Plants were grown on soil in greenhouse under long-day conditions (16h light / 8h dark)

extract_protocol:
Nuclei extraction from pollen was performed as in Ichino et al. 2022 Cell Rep. We harvested ~ 5 mL unopened flower buds + 1 open flower per inflorescence, and ground buds in 0.1M mannitol in a mortar on ice by gently tapping. The suspension was transferred to a 50mL conical tube and vortexed intermittently for 30 sec to release spores, then filtered through a 100 um nylon membrane, then two 60 um membranes. Samples were spun 10 min 900 g at 4C with slow acceleration and braking. Pellets were resuspended in ice-cold 0.1 M mannitol, and layered above 3 mL 20% Percoll diluted in 0.1M mannitol, then centrifuged 450 g 10 min 4C. This was repeated twice. Spores were pelleted 5 min 500 g 4C, and resuspended in 800 uL Glbraith buffer + bMe. This mixture was transferred to 1.5 mL tubes containing 100 uL acid-washed 0.5 mm glass beads (Sigma), and vortexed max speed 2 min total in cold, alternating 7 sec vortex, 3 sec invert for 1st min, then 7s vortex, 2s invert for second min. Nuclei were filtered through a 10um nylon filter. Nuclei were spun 5 min 500 g 4C, and pellets were gently resuspended in Sysmex nuclei extraction buffer and DAPI buffer (1:8 ratio). Nuclei were filtered through a 35 um nylon mesh into a FACS tube and immediately sorted, using DAPI to detect nuclei. Individual nuclei were sorted into a 384 well plate pre-filled with the buffer for reverse transcription (see library construction protocol below).
Each 384 well plate was processed separately, with 8 plates prepared per sample (note plate 8 of Col rep 2 and 1 of mbd56 rep 2 failed and were not sequenced). Library preparation was performed as described in Luo et al. 2022 Cell Genomics, omitting the accessibility portion of the assay (the GpC methyltransferase treatment). Briefly, RNA was first reverse-transcribed using a template-switching reaction (see SMART-seq protocols) with an oligo-dT primer in the presence of 5'-methyl-dCTP, so that all cytosines in cDNA are methylated. cDNA amplification was performed using KAPA2G DNA polymerase for TODO: TBD cycles. DNA was digested into smaller fragments using Uracil DNA gycosylase + Endonuclease VIII. then bisulfite converted using the Zymo EZ-96 DNA methylation-direct kit with reduced volume.
single cell multiomics

value: pollen

tag: time

tag: ecotype

value: mbd5 mbd6


title: SIRT3 KO BNST 3

description: Library name: 3B_KO


title: D11_Plate 8A

description:
Library name: BSSE-QGF-131245
Smart-seq2


title: SIRT3 KO BNST 1

description: Library name: 1B_KO


title: C57BL/6J, Olfactory epithelium, pS6-IP, A+D 1

description: Library name: A+D 1

value: Olfactory epithelium

value: Wildtype

value: male

value: Acetophenone + Decanal


title: SIRT3 KO BNST 4

description: Library name: 4B_KO

value: brain, BNST


title: C57BL/6J, Olfactory epithelium, pS6-IP, Control 2

description: Library name: Control 2

value: No odor (Control)

value: ADOC


title: A12_Plate 8A

description:
Library name: BSSE-QGF-131250
Smart-seq2


title: SIRT3 WT BNST 3

description: Library name: 3B_WT


title: C57BL/6J, Olfactory epithelium, pS6-IP, Control 3

description: Library name: Control 3


title: SIRT3 WT BNST 2

description: Library name: 2B_WT


title: snmCT_sep2022_mbd56_P6


title: SCLC ERBB2 KO 1

description: Library name: 183129_A10_CO_SCLC_2

value: lung origin

value: epithelial

value: SCLC ERBB2 KO


title: B12_Plate 8A

description:
Library name: BSSE-QGF-131251
Smart-seq2


title: F11_Plate 8A

description:
Library name: BSSE-QGF-131247
Smart-seq2


title: C12_Plate 8A

description:
Library name: BSSE-QGF-131252
Smart-seq2


title: SIRT3 WT BNST 1

description: Library name: 1B_WT


title: snmCT_sep2022_mbd56_P5


title: D12_Plate 8A

description:
Library name: BSSE-QGF-131253
Smart-seq2


title: snmCT_sep2022_mbd56_P4


title: SIRT3 cohoused KO amygdala 3

description: Library name: 3A_coKO

source_name: brain, amygdala

value: brain, amygdala

value: SIRT3 KO

value: cohoused


title: SIRT3 cohoused KO amygdala 2

description: Library name: 2A_coKO


title: SIRT3 cohoused KO amygdala 1

description: Library name: 1A_coKO


title: snmCT_sep2022_mbd56_P8


title: SIRT3 cohoused WT amygdala 3

description: Library name: 3A_coWT

value: WT


title: E12_Plate 8A

description:
Library name: BSSE-QGF-131254
Smart-seq2

value: Dorsal Pancreas


title: F12_Plate 8A

description:
Library name: BSSE-QGF-131255
Smart-seq2


title: snmCT_sep2022_mbd56_P3

value: pollen


title: SIRT3 cohoused WT amygdala 1

description: Library name: 1A_coWT


title: SIRT3 KO amygdala 5

description: Library name: 5A_KO


title: H12_Plate 8A

description:
Library name: BSSE-QGF-131257
Smart-seq2


title: snmCT_sep2022_mbd56_P2

value: mbd5 mbd6


title: SIRT3 KO amygdala 1

description: Library name: 1A_KO


title: snmCT_sep2022_Col0_P7

description:
Col_2_RNAseq_count_matrix.txt.gz
pseudobulk_Col_GN_CHGme.bed.gz
pseudobulk_Col_GN_CHHme.bed.gz
pseudobulk_Col_GN_CpGme.bed.gz
pseudobulk_Col_MN_CHGme.bed.gz
pseudobulk_Col_MN_CHHme.bed.gz
pseudobulk_Col_MN_CpGme.bed.gz
pseudobulk_Col_MNtoVN_CHGme.bed.gz
pseudobulk_Col_MNtoVN_CHHme.bed.gz
pseudobulk_Col_MNtoVN_CpGme.bed.gz
pseudobulk_Col_SN_CHGme.bed.gz
pseudobulk_Col_SN_CHHme.bed.gz
pseudobulk_Col_SN_CpGme.bed.gz
pseudobulk_Col_VN1_CHGme.bed.gz
pseudobulk_Col_VN1_CHHme.bed.gz
pseudobulk_Col_VN1_CpGme.bed.gz
pseudobulk_Col_VN1to2_CHGme.bed.gz
pseudobulk_Col_VN1to2_CHHme.bed.gz
pseudobulk_Col_VN1to2_CpGme.bed.gz
pseudobulk_Col_VN2_CHGme.bed.gz
pseudobulk_Col_VN2_CHHme.bed.gz
pseudobulk_Col_VN2_CpGme.bed.gz
pseudobulk_Col_VN3_CHGme.bed.gz
pseudobulk_Col_VN3_CHHme.bed.gz
pseudobulk_Col_VN3_CpGme.bed.gz
pseudobulk_Col_VN4_CHGme.bed.gz
pseudobulk_Col_VN4_CHHme.bed.gz
pseudobulk_Col_VN4_CpGme.bed.gz
pseudobulk_Col_VN5_CHGme.bed.gz
pseudobulk_Col_VN5_CHHme.bed.gz
pseudobulk_Col_VN5_CpGme.bed.gz

value: wild-type


title: G12_Plate 8A

description:
Library name: BSSE-QGF-131256
Smart-seq2


title: snmCT_sep2022_Col0_P6


title: SIRT3 KO amygdala 3

description: Library name: 3A_KO


title: SIRT3 WT amygdala 3

description: Library name: 3A_WT


title: snmCT_sep2022_Col0_P5


title: SIRT3 WT amygdala 2

description: Library name: 2A_WT


title: SIRT3 WT amygdala 1

description: Library name: 1A_WT


title: B1_Plate 8B

description:
Library name: BSSE-QGF-131260
Smart-seq2


title: C57BL/6J, Olfactory epithelium, pS6-IP, FM condition, FM Mixture 3

description: Library name: FM Mixture 3

data_processing:
RNA-seq data analysis was performed using a combination of Python (v3.12.3) and R (v4.4.2) environments. The sequencing reads were aligned to the Mus musculus reference genome GRCm39 using STAR aligner (v2.7.10b). Transcript quantification was performed with Salmon (v1.10.1) to generate gene-level count tables.
Assembly: Mus musculus GRCm39
Supplementary files format and content: Tab-delimited text files containing raw gene counts across all samples. Each file includes gene identifiers and expression values (raw counts) for entire genes.

treatment_protocol: Mice were individually housed in odor-free chambers and habituated for four hours prior to odorant exposure. For each experimental condition, 10 μL of odorant solution was deposited onto a 1 cm × 1 cm filter paper, which was then placed in a 35 mm culture dish inside the chamber. The odorant conditions included single odorants (acetophenone, decanal, octanal, cis-3-hexenol; all 100%, Merck), binary mixtures (acetophenone-decanal, octanal–cis-3-hexenol; 1:1 ratio), or complex fragrances (Floral, Mint and Floral-Mint Mixture; blended by ScentOn, Inc.). Control animals were exposed to empty filter paper (No-odor). Mice were exposed to their assigned condition for 90 minutes. Each experimental group consisted of three biological replicates.

value: Olfactory epithelium

value: Wildtype

value: Floral + Mint Fragrance

value: FM condition


title: A1_Plate 8B

description:
Library name: BSSE-QGF-131259
Smart-seq2


title: C57BL/6J, Olfactory epithelium, pS6-IP, FM condition, FM Mixture 2

description: Library name: FM Mixture 2

value: male


title: snmCT_sep2022_Col0_P4


title: C1_Plate 8B

description:
Library name: BSSE-QGF-131261
Smart-seq2


title: C57BL/6J, Olfactory epithelium, pS6-IP, FM condition, Mint 2

description: Library name: Mint 2

value: Mint Fragrance


title: D1_Plate 8B

description:
Library name: BSSE-QGF-131262
Smart-seq2


title: C57BL/6J, Olfactory epithelium, pS6-IP, FM condition, Mint 3

description: Library name: Mint 3


title: snmCT_sep2022_Col0_P2


title: E1_Plate 8B

description:
Library name: BSSE-QGF-131263
Smart-seq2


title: C57BL/6J, Olfactory epithelium, pS6-IP, FM condition, FM Mixture 1

description: Library name: FM Mixture 1


title: snmCT_sep2022_Col0_P3


title: C57BL/6J, Olfactory epithelium, pS6-IP, FM condition, Floral 3

description: Library name: Floral 3

value: Floral fragrance


title: C57BL/6J, Olfactory epithelium, pS6-IP, FM condition, Mint 1

description: Library name: Mint 1


title: SIRT3 KO amygdala 4

description: Library name: 4A_KO


title: SIRT3 cohoused WT amygdala 2

description: Library name: 2A_coWT


title: F1_Plate 8B

description:
Library name: BSSE-QGF-131264
Smart-seq2


title: snmCT_jun2022_mbd56_P8

description:
mbd56_1_RNAseq_count_matrix.txt.gz
pseudobulk_mbd56_GN_CHGme.bed.gz
pseudobulk_mbd56_GN_CHHme.bed.gz
pseudobulk_mbd56_GN_CpGme.bed.gz
pseudobulk_mbd56_MN_CHGme.bed.gz
pseudobulk_mbd56_MN_CHHme.bed.gz
pseudobulk_mbd56_MN_CpGme.bed.gz
pseudobulk_mbd56_MNtoVN_CHGme.bed.gz
pseudobulk_mbd56_MNtoVN_CHHme.bed.gz
pseudobulk_mbd56_MNtoVN_CpGme.bed.gz
pseudobulk_mbd56_SN_CHGme.bed.gz
pseudobulk_mbd56_SN_CHHme.bed.gz
pseudobulk_mbd56_SN_CpGme.bed.gz
pseudobulk_mbd56_VN1_CHGme.bed.gz
pseudobulk_mbd56_VN1_CHHme.bed.gz
pseudobulk_mbd56_VN1_CpGme.bed.gz
pseudobulk_mbd56_VN1to2_CHGme.bed.gz
pseudobulk_mbd56_VN1to2_CHHme.bed.gz
pseudobulk_mbd56_VN1to2_CpGme.bed.gz
pseudobulk_mbd56_VN2_CHGme.bed.gz
pseudobulk_mbd56_VN2_CHHme.bed.gz
pseudobulk_mbd56_VN2_CpGme.bed.gz
pseudobulk_mbd56_VN3_CHGme.bed.gz
pseudobulk_mbd56_VN3_CHHme.bed.gz
pseudobulk_mbd56_VN3_CpGme.bed.gz
pseudobulk_mbd56_VN4_CHGme.bed.gz
pseudobulk_mbd56_VN4_CHHme.bed.gz
pseudobulk_mbd56_VN4_CpGme.bed.gz
pseudobulk_mbd56_VN5_CHGme.bed.gz
pseudobulk_mbd56_VN5_CHHme.bed.gz
pseudobulk_mbd56_VN5_CpGme.bed.gz


title: C57BL/6J, Olfactory epithelium, pS6-IP, FM condition, Floral 1

description: Library name: Floral 1


title: C57BL/6J, Olfactory epithelium, pS6-IP, FM condition, Floral 2

description: Library name: Floral 2


title: G1_Plate 8B

description:
Library name: BSSE-QGF-131265
Smart-seq2


title: snmCT_sep2022_Col0_P1


title: C57BL/6J, Olfactory epithelium, pS6-IP, FM condition, control 3

description: Library name: Control 3 (FM condition)

value: No odor (Control)


title: C57BL/6J, Olfactory epithelium, pS6-IP, OC condition, OC Mixture 2

description: Library name: OC Mixture 2

value: Octanal + Cis-3-hexenol

value: OC condition


title: snmCT_jun2022_mbd56_P6


title: H1_Plate 8B

description:
Library name: BSSE-QGF-131266
Smart-seq2


title: C57BL/6J, Olfactory epithelium, pS6-IP, FM condition, control 1

description: Library name: Control 1 (FM condition)


title: A2_Plate 8B

description:
Library name: BSSE-QGF-131267
Smart-seq2


title: snmCT_jun2022_mbd56_P7


title: C57BL/6J, Olfactory epithelium, pS6-IP, OC condition, OC Mixture 3

description: Library name: OC Mixture 3


title: snmCT_jun2022_mbd56_P5


title: snmCT_jun2022_mbd56_P4


title: C57BL/6J, Olfactory epithelium, pS6-IP, OC condition, Cis-3-hexenol 2

description: Library name: Cis-3-hexenol 2


title: C57BL/6J, Olfactory epithelium, pS6-IP, OC condition, Cis-3-hexenol 1

description: Library name: Cis-3-hexenol 1


title: snmCT_jun2022_mbd56_P3


title: C2_Plate 8B

description:
Library name: BSSE-QGF-131269
Smart-seq2


title: C57BL/6J, Olfactory epithelium, pS6-IP, OC condition, Octanal 3

description: Library name: Octanal 3

value: Octanal


title: B2_Plate 8B

description:
Library name: BSSE-QGF-131268
Smart-seq2


title: C57BL/6J, Olfactory epithelium, pS6-IP, OC condition, Octanal 2

description: Library name: Octanal 2


title: snmCT_jun2022_mbd56_P2


title: C57BL/6J, Olfactory epithelium, pS6-IP, OC condition, control 3

description: Library name: Control 3 (OC condition)


title: C57BL/6J, Olfactory epithelium, pS6-IP, FM condition, control 2

description: Library name: Control 2 (FM condition)


title: C57BL/6J, Olfactory epithelium, pS6-IP, AD condition, AD Mixture 3

description: Library name: AD Mixture 3

value: Acetophenone + Decanal

value: AD condition


title: D2_Plate 8B

description:
Library name: BSSE-QGF-131270
Smart-seq2

value: Dorsal Pancreas


title: snmCT_jun2022_mbd56_P1

value: pollen


title: F2_Plate 8B

description:
Library name: BSSE-QGF-131272
Smart-seq2


title: C57BL/6J, Olfactory epithelium, pS6-IP, OC condition, OC Mixture 1

description: Library name: OC Mixture 1


title: E2_Plate 8B

description:
Library name: BSSE-QGF-131271
Smart-seq2


title: snmCT_jun2022_Col0_P8

description:
Col_1_RNAseq_count_matrix.txt.gz
pseudobulk_Col_GN_CHGme.bed.gz
pseudobulk_Col_GN_CHHme.bed.gz
pseudobulk_Col_GN_CpGme.bed.gz
pseudobulk_Col_MN_CHGme.bed.gz
pseudobulk_Col_MN_CHHme.bed.gz
pseudobulk_Col_MN_CpGme.bed.gz
pseudobulk_Col_MNtoVN_CHGme.bed.gz
pseudobulk_Col_MNtoVN_CHHme.bed.gz
pseudobulk_Col_MNtoVN_CpGme.bed.gz
pseudobulk_Col_SN_CHGme.bed.gz
pseudobulk_Col_SN_CHHme.bed.gz
pseudobulk_Col_SN_CpGme.bed.gz
pseudobulk_Col_VN1_CHGme.bed.gz
pseudobulk_Col_VN1_CHHme.bed.gz
pseudobulk_Col_VN1_CpGme.bed.gz
pseudobulk_Col_VN1to2_CHGme.bed.gz
pseudobulk_Col_VN1to2_CHHme.bed.gz
pseudobulk_Col_VN1to2_CpGme.bed.gz
pseudobulk_Col_VN2_CHGme.bed.gz
pseudobulk_Col_VN2_CHHme.bed.gz
pseudobulk_Col_VN2_CpGme.bed.gz
pseudobulk_Col_VN3_CHGme.bed.gz
pseudobulk_Col_VN3_CHHme.bed.gz
pseudobulk_Col_VN3_CpGme.bed.gz
pseudobulk_Col_VN4_CHGme.bed.gz
pseudobulk_Col_VN4_CHHme.bed.gz
pseudobulk_Col_VN4_CpGme.bed.gz
pseudobulk_Col_VN5_CHGme.bed.gz
pseudobulk_Col_VN5_CHHme.bed.gz
pseudobulk_Col_VN5_CpGme.bed.gz


title: C57BL/6J, Olfactory epithelium, pS6-IP, OC condition, control 2

description: Library name: Control 2 (OC condition)


title: C57BL/6J, Olfactory epithelium, pS6-IP, OC condition, control 1

description: Library name: Control 1 (OC condition)


title: G2_Plate 8B

description:
Library name: BSSE-QGF-131273
Smart-seq2


title: C57BL/6J, Olfactory epithelium, pS6-IP, AD condition, AD Mixture 2

description: Library name: AD Mixture 2


title: C57BL/6J, Olfactory epithelium, pS6-IP, AD condition, AD Mixture 1

description: Library name: AD Mixture 1


title: C57BL/6J, Olfactory epithelium, pS6-IP, OC condition, Cis-3-hexenol 3

description: Library name: Cis-3-hexenol 3


title: H2_Plate 8B

description:
Library name: BSSE-QGF-131274
Smart-seq2


title: C57BL/6J, Olfactory epithelium, pS6-IP, AD condition, Decanal 2

description: Library name: Decanal 2

value: Decanal


title: C57BL/6J, Olfactory epithelium, pS6-IP, AD condition, Decanal 3

description: Library name: Decanal 3


title: snmCT_jun2022_Col0_P7

value: wild-type


title: snmCT_jun2022_Col0_P6


title: A3_Plate 8B

description:
Library name: BSSE-QGF-131275
Smart-seq2


title: C57BL/6J, Olfactory epithelium, pS6-IP, AD condition, Acetophenone 3

description: Library name: Acetophenone 3

value: Olfactory epithelium

value: Acetophenone


title: C57BL/6J, Olfactory epithelium, pS6-IP, AD condition, Decanal 1

description: Library name: Decanal 1

value: Wildtype


title: snmCT_jun2022_Col0_P5


title: C57BL/6J, Olfactory epithelium, pS6-IP, AD condition, Acetophenone 2

description: Library name: Acetophenone 2


title: C57BL/6J, Olfactory epithelium, pS6-IP, OC condition, Octanal 1

description: Library name: Octanal 1


title: C57BL/6J, Olfactory epithelium, pS6-IP, AD condition, Acetophenone 1

description: Library name: Acetophenone 1


title: B3_Plate 8B

description:
Library name: BSSE-QGF-131276
Smart-seq2


title: snmCT_jun2022_Col0_P4


title: C57BL/6J, Olfactory epithelium, pS6-IP, AD condition, control 3

description: Library name: Control 3 (AD condition)


title: C57BL/6J, Olfactory epithelium, pS6-IP, AD condition, control 2

description: Library name: Control 2 (AD condition)


title: C3_Plate 8B

description:
Library name: BSSE-QGF-131277
Smart-seq2


title: C57BL/6J, Olfactory epithelium, pS6-IP, AD condition, control 1

description: Library name: Control 1 (AD condition)


title: C57BL/6J, Olfactory epithelium, total RNA, OC condition, OC Mixture 2

description: Library name: OC Mixture 2

extract_protocol:
Olfactory epithelium tissues were rapidly collected from mice immediately after odorant exposure and perfused with chilled buffer (PBS, 5mM NaF, 2.5mM Na3VO4, 2.5mM Na4P2O7, 5mM β-glycerophosphate, 100μg/mL cycloheximide, protease inhibitor). The tissues were homogenized in a buffer containing 10mM HEPES (pH 7.4), 150mM KCl, 10mM MgCl2, 100mM calyculin A, 0.5mM DTT, 100U/mL RNasin, 250μg/mL cycloheximide, and protease inhibitors using a TissueLyser II (Qiagen) for 2 minutes at 20Hz. Homogenates were centrifuged at 2,000×g for 10 minutes at 4°C. The supernatant was supplemented with 0.7% NP-40, incubated on ice, and centrifuged at 20,000×g for 10 minutes at 4°C. A 50μL aliquot of the olfactory epithelium homogenate was mixed with 350μL of Buffer RLT (Qiagen) and incubated on ice for 5 minutes. Total RNA was purified using the RNeasy Mini Kit (Qiagen) according to the manufacturer's protocol, including on-column DNase digestion.
Libraries were prepared using the TruSeq Stranded mRNA Sample Prep kit (Illumina), and sequencing was carried out on an Illumina NovaSeq 6000 platform according to the manufacturer's protocols.

treatment_protocol: Mice were individually housed in odor-free chambers and habituated for four hours prior to odorant exposure. For each experimental condition, 10 μL of odorant solution was deposited onto a 1 cm × 1 cm filter paper, which was then placed in a 35 mm culture dish inside the chamber. The odorant conditions included single odorants (acetophenone, decanal, octanal, cis-3-hexenol; all 100%, Merck), or binary mixtures (acetophenone-decanal, octanal–cis-3-hexenol; 1:1 ratio). Control animals were exposed to empty filter paper (No-odor). Mice were exposed to their assigned condition for 90 minutes. Each experimental group consisted of three biological replicates.


title: C57BL/6J, Olfactory epithelium, total RNA, OC condition, OC Mixture 3

description: Library name: OC Mixture 3


title: snmCT_jun2022_Col0_P3


title: snmCT_jun2022_Col0_P2


title: C57BL/6J, Olfactory epithelium, total RNA, OC condition, OC Mixture 1

description: Library name: OC Mixture 1


title: E3_Plate 8B

description:
Library name: BSSE-QGF-131279
Smart-seq2


title: RNA_lib3_mbd56_SWAP_line3_rep2

data_processing:
Reads were filtered based on quality score and trimmed to remove Illumina adapters using Trim Galore (Babraham Institute). The filtered reads were mapped to the Arabidopsis reference genome (TAIR10) using STAR, allowing 5% of mismatches (-outFilterMismatchNoverReadLmax 0.05) and unique mapping (--outFilterMultimapNmax 1). PCR duplicates were removed using MarkDuplicates from the Picard Tools suite.
Coverage tracks for visualization in the genome browser were generated using Deeptools 3.0.2 bamCoverage with the options --normalizeUsing CPM and --binSize 10
The numbers of reads mapping to genes or transposable elements were determined using HTseq with the option --mode=intersection-strict. We used as reference the “Pollen transcriptome reannotation” file previously generated and available on github (https://github.com/clp90/mbd56_pollen/, file mikado_refine_version2_final_noAS_wCM.gtf). All transcript types were analyzed together in the DEG analysis (genes, TEs, and other undefined non-coding transcripts).
Assembly: TAIR10
Supplementary files format and content: Counts matrices contain one row per gene, and one column per sample. Column names match sample names.
Supplementary files format and content: Coverage .bw tracks are files in bigWig format containing normalized sequencing read depth for each sample, obtained from deeptools bamCoverage with the "CPM" normalization option and binsize 10.

source_name: mature pollen

extract_protocol:
Pollen and RNA extraction was performed following protocol in Ichino et al. 2022. Briefly, ~500 uL of open flowers were harvested into 1.7 mL epp tubes, then 700 uL of Galbraith buffer (45 mM MgCl2, 30 mM C6H5Na3O7.2H2O [Trisodium citrate dihydrate], 20 mM MOPS, 0.1% [v/v] Triton X-100, pH 7, 5 l per ml of 14.3M Beta-mercaptoethanol [CAS-60-24-2, Fisher Scientific]) was added and samples were vortexed at max strength 2 min at 4C to release pollen from anthers. The suspension was filtered with an 80 um nylon mesh into a new 1.5 ml tube. The procedure was repeated one more time with the same flowers to increase the yield of pollen. The two aliquots of filtered pollen suspension were combined and centrifuged for 5 min at 500 g, 4°C. The pollen pellet was frozen in liquid nitrogen and stored at -80C. This procedure was repeated on consecutive days to obtain replicates. Frozen flower bud or pollen samples were disrupted with a tissue grinder and RNA extraction was performed with the Zymo Direct-zol RNA MiniPrep kit (Zymo Research) with on-column DNase I digestion.
RNA-seq libraries were generated using the TruSeq Stranded mRNA Library Prep Kit (Illumina), following the manufacturer’s instructions and starting with 500-1000 ng of RNA as input and sequenced on a Novaseq 6000 machine.

value: mature pollen


title: snmCT_jun2022_Col0_P1


title: C57BL/6J, Olfactory epithelium, total RNA, OC condition, Cis-3-hexenol 2

description: Library name: Cis-3-hexenol 2

value: male


title: C57BL/6J, Olfactory epithelium, total RNA, OC condition, Cis-3-hexenol 1

description: Library name: Cis-3-hexenol 1


title: F3_Plate 8B

description:
Library name: BSSE-QGF-131280
Smart-seq2


title: C57BL/6J, Olfactory epithelium, total RNA, OC condition, Octanal 3

description: Library name: Octanal 3


title: G3_Plate 8B

description:
Library name: BSSE-QGF-131281
Smart-seq2


title: MMR131

type: genomic

city: Toronto

first: Uri

last: Tabori

state: Ontario

address: 170 Elizabeth St

department: Haematology/Oncology

country: Canada

institute: Sick Kids

description:
Methylation data from brain tumor sample.
206601460194_R05C01

hyb_protocol: Illumina protocol.

scan_protocol: Signal was read with the iScan or NextSeq 550 systems (Illumina).

data_processing:
Methylation data from Illumina Infinium HumanMethylation450 and MethylationEPIC BeadChips were combined and preprocessed with normal-exponential out-of-band background (Noob) correction using the minfi (v.1.50.0) package in R.
Beta values normalized with minfi using the preprocessNoob method and a beta offset of 0.

label: cy3, cy5

source_name: Primary MMRD Glioma

label_protocol: Illumina protocol.

extract_protocol: DNA was extracted from tumour and blood samples using different kits as appropriate for the sample type and format: Qiagen DNeasy Blood & Tissue Kit (Cat No./ID96504) for frozen tissue, and MasterPure Complete DNA and RNA Purification Kit (Epicentre #MC85200) for formalin fixed paraffin embedded tissue.

value: Primary MMRD Glioma

tag: subgroup


title: C57BL/6J, Olfactory epithelium, total RNA, OC condition, Octanal 2

description: Library name: Octanal 2


title: RNA_lib3_mbd56_SWAP_line3_rep1


title: A4_Plate 8B

description:
Library name: BSSE-QGF-131283
Smart-seq2

data_processing:
Libraries were sequenced SR75 on an Illumina NextSeq 500 system (75 cycles High Output v2.5 kit).
Sequence reads were trimmed for quality control with trim_galore (v.0.6.5) and uniquely aligned to mouse reference genome (GRCm38) using kallisto pseudo-mode(v.0.46.1).
Transcript-level counts were converted into gene-level counts using tximport (v1.18.0) with mm10 Refseq
Assembly: UCSC, mm 10 (GRCm38)
Supplementary files format and content: TSV text file including a table of genes (rows) x cells (columns) showing counts  per single cell. Processed data file includes only samples that passed QC check.


title: RNA_lib3_mbd56_SWAP_line2_rep2


title: C57BL/6J, Olfactory epithelium, total RNA, OC condition, Octanal 1

description: Library name: Octanal 1


title: H3_Plate 8B

description:
Library name: BSSE-QGF-131282
Smart-seq2


title: MMR127

description:
Methylation data from brain tumor sample.
206601460194_R08C01


title: C57BL/6J, Olfactory epithelium, total RNA, OC condition, control 3

description: Library name: Control 3 (OC condition)


title: B4_Plate 8B

description:
Library name: BSSE-QGF-131284
Smart-seq2


title: MMR122

description:
Methylation data from brain tumor sample.
206522880071_R08C01


title: RNA_lib3_mbd56_SWAP_line1_rep1


title: C4_Plate 8B

description:
Library name: BSSE-QGF-131285
Smart-seq2


title: C57BL/6J, Olfactory epithelium, total RNA, OC condition, control 2

description: Library name: Control 2 (OC condition)


title: C57BL/6J, Olfactory epithelium, total RNA, OC condition, Cis-3-hexenol 3

description: Library name: Cis-3-hexenol 3


title: MMR118

description:
Methylation data from brain tumor sample.
206687200027_R05C01


title: E4_Plate 8B

description:
Library name: BSSE-QGF-131287
Smart-seq2


title: MMR116

description:
Methylation data from brain tumor sample.
206359150101_R01C01


title: D4_Plate 8B

description:
Library name: BSSE-QGF-131286
Smart-seq2


title: RNA_lib3_mbd56_rep2


title: RNA_lib3_mbd56_rep1


title: C57BL/6J, Olfactory epithelium, total RNA, OC condition, control 1

description: Library name: Control 1 (OC condition)


title: RNA_lib3_mbd56_rep3


title: MMR115

description:
Methylation data from brain tumor sample.
205715830011_R07C01


title: C57BL/6J, Olfactory epithelium, total RNA, AD condition, AD Mixture 3

description: Library name: AD Mixture 3


title: C57BL/6J, Olfactory epithelium, total RNA, AD condition, AD Mixture 2

description: Library name: AD Mixture 2


title: MMR129

description:
Methylation data from brain tumor sample.
206601460194_R06C01


title: RNA_lib3_Col_SWAP_line3_rep2


title: RNA_lib3_mbd56_SWAP_line1_rep2


title: MMR114

description:
Methylation data from brain tumor sample.
206359150101_R02C01


title: MMR113

description:
Methylation data from brain tumor sample.
205841310088_R07C01


title: D3_Plate 8B

description:
Library name: BSSE-QGF-131278
Smart-seq2


title: F4_Plate 8B

description:
Library name: BSSE-QGF-131288
Smart-seq2


title: G4_Plate 8B

description:
Library name: BSSE-QGF-131289
Smart-seq2


title: C57BL/6J, Olfactory epithelium, total RNA, AD condition, Decanal 3

description: Library name: Decanal 3


title: MMR112

description:
Methylation data from brain tumor sample.
206359150101_R03C01


title: RNA_lib3_Col_SWAP_line2_rep2


title: A5_Plate 8B

description:
Library name: BSSE-QGF-131291
Smart-seq2


title: RNA_lib3_Col_SWAP_line3_rep1


title: C57BL/6J, Olfactory epithelium, total RNA, AD condition, Decanal 2

description: Library name: Decanal 2


title: H4_Plate 8B

description:
Library name: BSSE-QGF-131290
Smart-seq2


title: RNA_lib3_Col_SWAP_line1_rep2


title: MMR108

description:
Methylation data from brain tumor sample.
206359150101_R06C01


title: B5_Plate 8B

description:
Library name: BSSE-QGF-131292
Smart-seq2


title: MMR106

description:
Methylation data from brain tumor sample.
206359150101_R07C01


title: C57BL/6J, Olfactory epithelium, total RNA, AD condition, Acetophenone 3

description: Library name: Acetophenone 3


title: C5_Plate 8B

description:
Library name: BSSE-QGF-131293
Smart-seq2


title: RNA_lib3_Col_SWAP_line1_rep1


title: MMR105

description:
Methylation data from brain tumor sample.
205841310088_R01C01


title: C57BL/6J, Olfactory epithelium, total RNA, AD condition, Acetophenone 2

description: Library name: Acetophenone 2


title: C57BL/6J, Olfactory epithelium, total RNA, AD condition, Decanal 1

description: Library name: Decanal 1


title: D5_Plate 8B

description:
Library name: BSSE-QGF-131294
Smart-seq2


title: C57BL/6J, Olfactory epithelium, total RNA, AD condition, AD Mixture 1

description: Library name: AD Mixture 1


title: MMR99

description:
Methylation data from brain tumor sample.
206687200027_R03C01


title: C57BL/6J, Olfactory epithelium, total RNA, AD condition, Acetophenone 1

description: Library name: Acetophenone 1


title: E5_Plate 8B

description:
Library name: BSSE-QGF-131295
Smart-seq2


title: MMR100

description:
Methylation data from brain tumor sample.
206687200027_R04C01


title: RNA_lib2_mbd567_rep3


title: F5_Plate 8B

description:
Library name: BSSE-QGF-131296
Smart-seq2


title: RNA_lib3_Col_rep2

value: Col


title: MMR98

description:
Methylation data from brain tumor sample.
205567990086_R05C01


title: RNA_lib3_Col_rep1


title: MMR97

description:
Methylation data from brain tumor sample.
206687200027_R02C01


title: G5_Plate 8B

description:
Library name: BSSE-QGF-131297
Smart-seq2


title: C57BL/6J, Olfactory epithelium, total RNA, AD condition, control 2

description: Library name: Control 2 (AD condition)

value: No odor (Control)


title: H5_Plate 8B

description:
Library name: BSSE-QGF-131298
Smart-seq2


title: RNA_lib2_mbd567_rep2


title: MMR96

description:
Methylation data from brain tumor sample.
206687200027_R01C01


title: C57BL/6J, Olfactory epithelium, total RNA, AD condition, control 1

description: Library name: Control 1 (AD condition)


title: A6_Plate 8B

description:
Library name: BSSE-QGF-131299
Smart-seq2


title: RNA_lib2_mbd567_rep1


title: RNA_lib2_mbd56_rep3


title: MMR92

description:
Methylation data from brain tumor sample.
206848800070_R02C01


title: RNA_lib3_Col_rep3


title: MMR86

description:
Methylation data from brain tumor sample.
206522890082_R01C01


title: B6_Plate 8B

description:
Library name: BSSE-QGF-131300
Smart-seq2


title: Aged3_10X

city: San Francisco

first: Diana

middle: Matthew

last: Laird

address: 35 Medical Center Way RM913D

institute: University of California

description:
Library name: Sample 11
10X Genomics

data_processing:
Sequencing and Demultiplexing: 10X libraries were pooled and sequenced on NovaSeq S2 flow cells. Smart-seq2 libraries were pooled equimolar in sets of 4 to 16 384-well plates and sequenced on NextSeq 2000 P3 and NovaSeq S4 flow cells using the following cycling parameters:  Read 1: 100 cycles, Index 1: 12 cycles, Index 2: 12 cycles, Read 2: 100 cycles. The target read depth was 1–2 million paired-end reads per sample for Smart-seq2 libraries and 20,000 reads per cell for 10X 3’ GEX libraries. Raw BCL files were converted to FASTQ format and demultiplexed using Illumina’s bcl2fastq software (v2.20.0.422). For 10X Genomics libraries, FASTQ files were further processed and demultiplexed using CellRanger (v7.0.1).
Alignment and Gene Quantification: 10X Genomics data were aligned using CellRanger (v7.0.1) with the mm10 (mouse) reference genome. Smart-seq2 mouse reads were aligned to Gencode M31 (GRCm39) using STAR (v2.7.10a) with the following parameters:    ```   --outFilterMultimapNmax 20    --outSAMstrandField intronMotif    --outSAMtype BAM Unsorted    --outSAMattributes NH;HI;NM;MD    --outReadsUnmapped fastx    --alignIntronMin 20    --alignIntronMax 1000000    --alignMatesGapMax 1000000    --alignSJoverhangMin 8    --alignSJDBoverhangMin 1    ``` Gene counts were generated using HTSeq-count (v2.0.5) with stranded="no" and mode="intersection-nonempty". Gene counts were produced using HTSeq (v2.0.5) with stranded="false" and mode="intersection-nonempty".
Analysis: Samples were integrated usinf harmony and analysed using Seurat's standard workflow.
Non-Project Cell Removal: Within two of our samples (Young2, Aged2), naked mole rat iPSCs were added to the mouse cell suspension before sequencing for a separate experiment. All Oct4-positive naked mole rat cells that were successfully aligned to the mouse genome were removed.
Assembly: Mouse 10X: mm10 Mouse SS2:  GRCm39
Supplementary files format and content: Processed data is provided as (.csv) files and contain a gene count matrix of cell IDs post SoupX ambient RNA removal but pre Seurat filtration.

source_name: Ovary

extract_protocol:
To minimize batch effects, young and aged murine ovaries were collected on the same day for sequencing. Following removal of murine ovaries and receipt of human ovaries, surrounding tissue was removed by fine dissection. Ovaries were gently chopped using a razor blade and then transferred to a Conical tube with 2 mg/mL collagenase type IV (Gibco, 17104019) in DMEM (Gibco, 11960044). Tubes were incubated at +37oC shaking at 250rpm for 20 min then centrifuged at 250 x g for 5min. The supernatant was aspirated and 0.25 % trypsin-EDTA (Gibco, 25200056) was added. Tubes were incubated at +37oC shaking at 250rpm for 20 min then centrifuged at 250 x g for 5 min. The supernatant was aspirated, and the tissue was quenched with 10% FBS (Gibco, 10438026) in DMEM. Using a P1000, tissue was gently triturated to generate a single cell suspension. The cell suspension was filtered using a reversible 37µm sieve (STEMCELL Technologies, 27215). The sieve was rinsed with quench buffer (<37µm filtered flow through) and then flipped and placed in a new tube for rinsing with quench buffer (>37µm unfiltered mature oocyte pool hand-picked for SmartSeq2).
Smart-seq2 Library Preparation: Single oocytes were handpicked using an EZ-Grip pipette with a 125 μm EZ-Tip, briefly washed in 0.04% BSA-PBS, and transferred into individual wells containing lysis buffer master mix. Lysed oocytes were snap-frozen on dry ice and stored at −80°C for further processing by the Genomics Platform at the Chan Zuckerberg Biohub SF.   Reverse transcription (RT) and complementary DNA (cDNA) synthesis were performed in 96-well plates using the Smart-seq2 protocol. To preserve RNA integrity, 2–4 lysis plates were thawed on ice and processed in a pre-PCR laboratory. RT master mix (6 μL per well in 96-well plates; 0.6 μL per well in 384-well plates) was prepared using the following components: 0.06 μL 1M MgCl₂, 2 μL 5× First-Strand Buffer (Takara Bio, 639538), 2 μL 5M Betaine, 0.5 μL 100 mM DTT, 0.1 μL 100 μM TSO (Exiqon, 5′-AAGCAGTGGTATCAACGCAGAGTGAATrGrGrG-3′), 0.25 μL RRI, 1 μL SmartScribe Reverse Transcriptase (Takara Bio, 639538), and 0.09 μL water. The RT master mix was dispensed into each well using an SPT Labtech Dragonfly Discovery liquid handler. Plates were sealed with a clear microseal, centrifuged at 1,000 rcf for 1 min, and incubated in a thermal cycler (Applied Biosystems ProFlex or Bio-Rad C1000 Touch Thermal Cycler**) under the following conditions: 42°C for 90 min, followed by 70°C for 5 min.  SmartSeq2 library construction: Second-strand synthesis and cDNA amplification were performed by adding 15 μL of cDNA master mix per 96-well plate (1.5 μL per 384-well plate), containing 12.5 μL KAPA HiFi HotStart ReadyMix 2X (Kapa Biosystems, KK2602), 0.25 μL 10 μM IS PCR primer (IDT, 5′-AAGCAGTGGTATCAACGCAGAGT-3′), 0.113 μL Lambda Exonuclease (NEB, M0262L), and 2.14 μL water. The cDNA master mix was dispensed using an SPT Labtech Dragonfly Discovery, and the plates were sealed, centrifuged at 1,000 rcf for 1 min, and subjected to the following cycling conditions: 37°C for 30 min; 95°C for 3 min; 21 cycles of 98°C for 20 s, 67°C for 15 s, 72°C for 4 min; followed by a final extension at 72°C for 5 min.   cDNA quantity was spot-checked using a Quant-iT dsDNA High Sensitivity Kit (Thermo Fisher, Q33120) and fluorescence was measured using a SpectraMax M5 microplate reader (Molecular Devices). cDNA quality was assessed on an Agilent 5300 Fragment Analyzer. High-concentration cDNA samples were diluted 1:10 with nuclease-free water for optimal enzymatic fragmentation.   Library preparation was performed using Illumina’s Nextera XT DNA Library Prep Kit (FC-131-1096), miniaturized for 384-well plates using an SPT Labtech Firefly liquid handler. Briefly, 0.4 μL cDNA (<1 ng) was stamped into each well of a 384-well plate, followed by 1.4 μL of tagmentation master mix (0.2 μL Tagment DNA buffer (TD) and 1.2 μL Amplicon Tagment Mix (ATM)). The plates were sealed, centrifuged at 2,000 rcf for 1 min, and incubated at 55°C for 5 min. Tagmentation was stopped by adding 0.4 μL of Neutralize Tagment Buffer (NT), followed by centrifugation at 2,000 rcf for 5 min.   Index PCR was performed by adding 1.2 μL of Nextera PCR Master Mix (NPM) and 0.8 μL of Nextera index adapters (0.4 μL of 5 μM i5 indexing primer, 0.4 μL of 5 μM i7 indexing primer, IDT). The thermal cycling program consisted of: 72°C for 3 min; 95°C for 30 s; 12 cycles of 95°C for 10 s, 55°C for 30 s, 72°C for 30 s; followed by a final extension at 72°C for 5 min.   Barcoded libraries were pooled using an SPT Labtech Mosquito LV, purified with two consecutive 0.7× AMPure XP bead clean-ups (Beckman Coulter, A63881), and eluted in 30 μL of nuclease-free water. Library fragment size was analyzed on an Agilent 4150 Tapestation System with D5000 ScreenTape (5067-5588) and quantified via qPCR (Bio-Rad CFX96 RT System) using the KAPA Library Quantification Kit (Kapa Biosystems, KK4923).  10X Genomics Library Preparation: Filtered cell suspensions were counted and adjusted to 1,000 cells/μL in 0.04% BSA (Research Products International, A30075) in 1X PBS. Library preparation was performed by the UCSF Genomics CoLabs using the 10X Genomics Chromium Next GEM Single Cell 3’ Kit with dual indexing, following the manufacturer’s protocol.

value: Ovary

value: Whole Organ


title: MMR84

description:
Methylation data from brain tumor sample.
206848800070_R05C01


title: RNA_lib2_mbd56_rep2


title: RNA_lib2_mbd56_rep1


title: C6_Plate 8B

description:
Library name: BSSE-QGF-131301
Smart-seq2


title: D6_Plate 8B

description:
Library name: BSSE-QGF-131302
Smart-seq2


title: C57BL/6J, Olfactory epithelium, total RNA, AD condition, control 3

description: Library name: Control 3 (AD condition)


title: MMR82

description:
Methylation data from brain tumor sample.
206848800070_R07C01


title: MMR83

description:
Methylation data from brain tumor sample.
206848800070_R06C01


title: RNA_lib2_mbd7_rep2


title: E6_Plate 8B

description:
Library name: BSSE-QGF-131303
Smart-seq2


title: F6_Plate 8B

description:
Library name: BSSE-QGF-131304
Smart-seq2


title: Aged1_10X

description:
Library name: Sample 7
10X Genomics


title: RNA_lib2_mbd7_rep1


title: MMR81_T1

description:
Methylation data from brain tumor sample.
205041750156_R01C01


title: G6_Plate 8B

description:
Library name: BSSE-QGF-131305
Smart-seq2


title: RNA_lib2_Col_rep3


title: MMR80

description:
Methylation data from brain tumor sample.
206842050081_R07C01


title: H6_Plate 8B

description:
Library name: BSSE-QGF-131306
Smart-seq2


title: RNA_lib2_Col_rep2


title: MMR79

description:
Methylation data from brain tumor sample.
206842050081_R06C01


title: A7_Plate 8B

description:
Library name: BSSE-QGF-131307
Smart-seq2


title: Young3_10X

description:
Library name: Sample 5
10X Genomics


title: MMR77

description:
Methylation data from brain tumor sample.
206522890082_R05C01


title: RNA_lib2_Col_rep1


title: B7_Plate 8B

description:
Library name: BSSE-QGF-131308
Smart-seq2


title: Young2_10X

description:
Library name: Sample 3
10X Genomics


title: MMR76_3

description:
Methylation data from brain tumor sample.
205841310088_R06C01


title: RNA_lib1_mbd567_rep3


title: RNA_lib1_mbd567_rep2


title: MMR76_1

description:
Methylation data from brain tumor sample.
205841310088_R05C01


title: C7_Plate 8B

description:
Library name: BSSE-QGF-131309
Smart-seq2


title: D7_Plate 8B

description:
Library name: BSSE-QGF-131310
Smart-seq2


title: Aged2_10X

description:
Library name: Sample 9
10X Genomics


title: RNA_lib2_mbd7_rep3


title: Young1_10X

description:
Library name: Sample 1
10X Genomics


title: MMR72

description:
Methylation data from brain tumor sample.
206842050081_R05C01


title: RNA_lib1_mbd567_rep1


title: E7_Plate 8B

description:
Library name: BSSE-QGF-131311
Smart-seq2


title: MMR68

description:
Methylation data from brain tumor sample.
206966330105_R06C01


title: CARD11C49Y/C49Y MZ, anti-IgM, 24hrs, Rep 3

city: Baltimore

first: Joel

last: Pomerantz

address: 733 N. Broadway

department: Biological Chemistry

institute: Johns Hopkins University School of Medicine

description: Library name: M36

data_processing:
Raw reads of fastq format were cleaned by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data using Perl scripts.
Paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
FPKM (Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: Mus Musculus(GRCm38/mm10)
Supplementary files format and content: gene_count.xls tab-delimited xls file contains raw counts for each gene in each sample.
Supplementary files format and content: gene_fpkm.xls tab delimited xls file contains FPKM for each gene in each sample.

source_name: Marginal Zone B cells

extract_protocol:
Total RNA was extracted using a Qiagen RNeasy Mini Kit with on-column DNase digestion according to the manufacturer’s instructions.
mRNA was purified from total RNA via polyA enrichment using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis. Sequencing libraries were generated using NEBNext UltraRNA Library Prep Kit for Illumina (NEB) following the manufacturer’s recommendation.

treatment_protocol: Follicular (FO) and Marginal Zone (MZ) B cells were harvested from the spleen using the Miltenyi MZ and FO B Cell Isolation Kit (Mouse) according to the manufacturer's instructions. Cells were either left unstimulated or treated for 24hrs with 4µg/mL anti-IgM.

value: Marginal Zone B cells

value: 4μg/mL anti-IgM, 24hrs


title: CARD11C49Y/C49Y MZ, anti-IgM, 24hrs, Rep 2

description: Library name: M35


title: F7_Plate 8B

description:
Library name: BSSE-QGF-131312
Smart-seq2

extract_protocol:
Dorsal pancreatic tissue (E12.5) was dissected from Tg(Prox1-EGFP), Tg(Nkx2.5-Cre;mTmG) and Tg(Nkx3.2-Cre;mTmG) transgenic mice and dissociated into single-cell suspensions. GFP+ cells were FACS-sorted at 4°C using an Aria II or Aria III flow cytometer (BD) into 96-well plates containing cell lysis buffer. Plates containing FACS-sorted cells were then frozen and kept at -80°C until shipment to the Genomic Facility for library preparation and sequencing.
Libraries were prepared for sequencing using Nextera XT DNA library preparation kit (Illumina) protocols.


title: RNA_lib1_mbd56_rep2


title: MMR67

description:
Methylation data from brain tumor sample.
206842050081_R02C01


title: CARD11C49Y/C49Y MZ, anti-IgM, 24hrs, Rep 1

description: Library name: M34


title: RNA_lib1_mbd56_rep1


title: MMR65

description:
Methylation data from brain tumor sample.
207108790013_R07C01


title: CARD11C49Y/C49Y MZ, Unstim, Rep 3

description: Library name: M33

value: Unstim


title: H7_Plate 8B

description:
Library name: BSSE-QGF-131314
Smart-seq2

value: Dorsal Pancreas


title: MMR64

description:
Methylation data from brain tumor sample.
207108790072_R05C01


title: RNA_lib1_mbd7_rep3


title: A8_Plate 8B

description:
Library name: BSSE-QGF-131315
Smart-seq2


title: MMR63

description:
Methylation data from brain tumor sample.
207108790013_R04C01


title: CARD11C49Y/C49Y MZ, Unstim, Rep 2

description: Library name: M32


title: B8_Plate 8B

description:
Library name: BSSE-QGF-131316
Smart-seq2


title: CARD11C49Y/C49Y MZ, Unstim, Rep 1

description: Library name: M31


title: MMR59

description:
Methylation data from brain tumor sample.
204234720056_R04C01


title: CARD11+/C49Y MZ, anti-IgM, 24hrs, Rep 3

description: Library name: M30


title: RNA_lib1_mbd56_rep3


title: MMR62

description:
Methylation data from brain tumor sample.
205841310088_R03C01


title: C8_Plate 8B

description:
Library name: BSSE-QGF-131317
Smart-seq2


title: CARD11+/C49Y MZ, anti-IgM, 24hrs, Rep 2

description: Library name: M29


title: RNA_lib1_Col_rep3


title: MMR58

description:
Methylation data from brain tumor sample.
206601460194_R04C01


title: RNA_lib1_Col_rep2


title: D8_Plate 8B

description:
Library name: BSSE-QGF-131318
Smart-seq2


title: CARD11+/C49Y MZ, anti-IgM, 24hrs, Rep 1

description: Library name: M28


title: RNA_lib1_Col_rep1


title: MMR56

description:
Methylation data from brain tumor sample.
206966330105_R07C01


title: G7_Plate 8B

description:
Library name: BSSE-QGF-131313
Smart-seq2


title: CARD11+/C49Y MZ, Unstim, Rep 3

description: Library name: M27


title: MMR55

description:
Methylation data from brain tumor sample.
205715830011_R03C01


title: G8_Plate 8B

description:
Library name: BSSE-QGF-131321
Smart-seq2


title: CARD11+/C49Y MZ, Unstim, Rep 2

description: Library name: M26


title: MMR54

description:
Methylation data from brain tumor sample.
204234720085_R08C01


title: RNA_lib1_mbd7_rep2


title: BS_lib5_mbd56SWAP_rep3

data_processing:
Reads were trimmed for low quality sequences and adapter contamination using TrimGalore (Babraham Institute) and mapped to the TAIR10 genome with Bismark. Bismark was also used to obtain the methylation percentages for each cytosine and to generate the per-position DNA methylation tracks.
Assembly: TAIR10
Supplementary files format and content: BED-like files containing six fields: chromosome, start, end (0-based end exclusive, same as BED), number of reads overlapping this position with an unmethylated cytosine, number of reads overlapping this position with a methylated cytosine, and the resulting % methylation, equal to 100*(# methyl / (# methyl + # unmethyl)). The three sequence contexts CG, CHG and CHH are in separate files. Each position in the file should correspond to a cytosine in the respective context in the TAIR10 genome sequence.

extract_protocol:
Pollen extraction was performed following protocol in Ichino et al. 2022. Briefly, ~500 uL of open flowers were harvested into 1.7 mL epp tubes, then 700 uL of Galbraith buffer (45 mM MgCl2, 30 mM C6H5Na3O7.2H2O [Trisodium citrate dihydrate], 20 mM MOPS, 0.1% [v/v] Triton X-100, pH 7, 5 l per ml of 14.3M Beta-mercaptoethanol [CAS-60-24-2, Fisher Scientific]) was added and samples were vortexed at max strength 2 min at 4C to release pollen from anthers. The suspension was filtered with an 80 um nylon mesh into a new 1.5 ml tube. The procedure was repeated one more time with the same flowers to increase the yield of pollen. The two aliquots of filtered pollen suspension were combined and centrifuged for 5 min at 500 g, 4°C. The pollen pellet was frozen in liquid nitrogen and stored at -80C. DNA extraction from pollen pellets was performed with the cetyl trimethylammonium bromide (CTAB) method and treated with RNase A (Qiagen).
40-100 ng of DNA per sample were sheared with the Covaris S2 instrument to an average fragment size of 200bp (Duty Cycle = 10%, Intensity = 5, Cycles per Burst = 200, Treatment Time = 120 seconds). The sheared DNA was used as input for BS-seq library preparation using the Nugen Ultralow Methyl-Seq kit, following manufacturer’s instructions except for the bisulfite conversion, which was done with the EpiTect Bisulfite Kit (Qiagen, 59104) instead of the TrueMethyl oxBS. The bisulfite conversion reaction in the thermocycler was performed twice (overnight) to increase the efficiency. Final libraries were sequenced on Novaseq 6000 machines.

value: mbd5 mbd6 TDNA  + MBD6(SWAP) transgene


title: BS_lib5_mbd56SWAP_rep2


title: CARD11+/C49Y MZ, Unstim, Rep 1

description: Library name: M25


title: BS_lib5_mbd56SWAP_rep1


title: RNA_lib1_mbd7_rep1


title: H8_Plate 8B

description:
Library name: BSSE-QGF-131322
Smart-seq2


title: E8_Plate 8B

description:
Library name: BSSE-QGF-131319
Smart-seq2


title: MMR52

description:
Methylation data from brain tumor sample.
206966330105_R02C01


title: CARD11+/+ MZ, anti-IgM, 24hrs, Rep 2

description: Library name: M23


title: MMR51_T2

description:
Methylation data from brain tumor sample.
207108790072_R03C01


title: C9_Plate 8B

description:
Library name: BSSE-QGF-131325
Smart-seq2


title: BS_lib5_mbd56_rep3

value: mbd5 mbd6 TDNA


title: CARD11+/+ MZ, anti-IgM, 24hrs, Rep 1

description: Library name: M22


title: MMR50

description:
Methylation data from brain tumor sample.
206522880071_R06C01


title: MMR49_T1

description:
Methylation data from brain tumor sample.
206522890082_R07C01


title: B9_Plate 8B

description:
Library name: BSSE-QGF-131324
Smart-seq2


title: D9_Plate 8B

description:
Library name: BSSE-QGF-131326
Smart-seq2


title: CARD11+/+ MZ, Unstim, Rep 3

description: Library name: M21


title: CARD11+/+ MZ, anti-IgM, 24hrs, Rep 3

description: Library name: M24


title: BS_lib5_ColSWAP_rep3

value: wild-type + MBD6(SWAP) transgene


title: F8_Plate 8B

description:
Library name: BSSE-QGF-131320
Smart-seq2


title: BS_lib5_mbd56_rep4


title: CARD11+/+ MZ, Unstim, Rep 2

description: Library name: M20


title: F9_Plate 8B

description:
Library name: BSSE-QGF-131328
Smart-seq2


title: MMR45

description:
Methylation data from brain tumor sample.
207108790072_R01C01


title: E9_Plate 8B

description:
Library name: BSSE-QGF-131327
Smart-seq2


title: CARD11C49Y/C49Y FO, anti-IgM, 24hrs, Rep 3

description: Library name: F18

source_name: Follicular B cells

value: Follicular B cells


title: A9_Plate 8B

description:
Library name: BSSE-QGF-131323
Smart-seq2


title: BS_lib5_mbd56_rep1


title: CARD11+/+ MZ, Unstim, Rep 1

description: Library name: M19


title: G9_Plate 8B

description:
Library name: BSSE-QGF-131329
Smart-seq2


title: BS_lib5_ColSWAP_rep1


title: MMR44

description:
Methylation data from brain tumor sample.
207108790072_R02C01


title: CARD11C49Y/C49Y FO, anti-IgM, 24hrs, Rep 1

description: Library name: F16


title: BS_lib5_Col_rep3

value: wild-type


title: A10_Plate 8B

description:
Library name: BSSE-QGF-131331
Smart-seq2


title: BS_lib5_Col_rep2


title: MMR42

description:
Methylation data from brain tumor sample.
207108790013_R08C01


title: MMR47

description:
Methylation data from brain tumor sample.
206522890082_R08C01


title: BS_lib5_Col_rep1


title: MMR46

description:
Methylation data from brain tumor sample.
207108790072_R06C01


title: C10_Plate 8B

description:
Library name: BSSE-QGF-131333
Smart-seq2


title: BS_lib4_YJ_lil_rep1


title: BS_lib5_ColSWAP_rep2


title: CARD11C49Y/C49Y FO, Unstim, Rep 2

description: Library name: F14


title: D10_Plate 8B

description:
Library name: BSSE-QGF-131334
Smart-seq2


title: MMR41

description:
Methylation data from brain tumor sample.
206522880071_R02C01


title: BS_lib4_YJ_ctrl_rep1


title: CARD11C49Y/C49Y FO, Unstim, Rep 1

description: Library name: F13


title: BS_lib4_mbd7_rep2

value: YJ


title: MMR39

description:
Methylation data from brain tumor sample.
204234720085_R05C01


title: MMR38

description:
Methylation data from brain tumor sample.
200991630136_R05C01


title: CARD11+/C49Y FO, anti-IgM, 24hrs, Rep 3

description: Library name: F12


title: E10_Plate 8B

description:
Library name: BSSE-QGF-131335
Smart-seq2


title: F10_Plate 8B

description:
Library name: BSSE-QGF-131336
Smart-seq2


title: MMR43

description:
Methylation data from brain tumor sample.
206522880071_R03C01


title: H9_Plate 8B

description:
Library name: BSSE-QGF-131330
Smart-seq2


title: CARD11C49Y/C49Y FO, anti-IgM, 24hrs, Rep 2

description: Library name: F17


title: BS_lib4_Col_rep2

value: mature pollen


title: CARD11+/C49Y FO, anti-IgM, 24hrs, Rep 2

description: Library name: F11


title: MMR35

description:
Methylation data from brain tumor sample.
200991630102_R05C01


title: BS_lib4_mbd7_rep1


title: G10_Plate 8B

description:
Library name: BSSE-QGF-131337
Smart-seq2


title: CARD11+/C49Y FO, anti-IgM, 24hrs, Rep 1

description: Library name: F10


title: CARD11C49Y/C49Y FO, Unstim, Rep 3

description: Library name: F15


title: BS_lib4_Col_rep1


title: MMR34

description:
Methylation data from brain tumor sample.
200992300032_R08C01


title: H10_Plate 8B

description:
Library name: BSSE-QGF-131338
Smart-seq2


title: MMR40

description:
Methylation data from brain tumor sample.
200991630136_R06C01


title: B10_Plate 8B

description:
Library name: BSSE-QGF-131332
Smart-seq2


title: CARD11+/C49Y FO, Unstim, Rep 3

description: Library name: F9


title: BS_lib3_mbd567_rep2

value: mbd5 mbd6 CRISPR1


title: A11_Plate 8B

description:
Library name: BSSE-QGF-131339
Smart-seq2


title: BS_lib3_mbd567_rep1


title: CARD11+/C49Y FO, Unstim, Rep 2

description: Library name: F8


title: MMR31

description:
Methylation data from brain tumor sample.
200992300032_R06C01

value: Primary MMRD Glioma


title: C11_Plate 8B

description:
Library name: BSSE-QGF-131341
Smart-seq2


title: CARD11+/C49Y FO, Unstim, Rep 1

description: Library name: F7


title: MMR29

description:
Methylation data from brain tumor sample.
200991630136_R02C01


title: MMR32

description:
Methylation data from brain tumor sample.
200992300032_R07C01


title: BS_lib3_mbd56_rep1


title: CARD11+/+ FO, anti-IgM, 24hrs, Rep 3

description: Library name: F6


title: B11_Plate 8B

description:
Library name: BSSE-QGF-131340
Smart-seq2


title: E11_Plate 8B

description:
Library name: BSSE-QGF-131343
Smart-seq2


title: CARD11+/+ FO, Unstim, Rep 3

description: Library name: F3


title: CARD11+/+ FO, anti-IgM, 24hrs, Rep 1

description: Library name: F4


title: F11_Plate 8B

description:
Library name: BSSE-QGF-131344
Smart-seq2


title: BS_lib3_Col_rep1


title: MMR33

description:
Methylation data from brain tumor sample.
200991630102_R08C01


title: BS_lib1_sln_rep2

value: mbd5 mbd6 mbd7


title: BS_lib1_sln_rep1


title: MMR26

description:
Methylation data from brain tumor sample.
200992300002_R07C01


title: CARD11+/+ FO, anti-IgM, 24hrs, Rep 2

description: Library name: F5


title: D11_Plate 8B

description:
Library name: BSSE-QGF-131342
Smart-seq2


title: BS_lib1_Col_rep2

value: sln


title: MMR28

description:
Methylation data from brain tumor sample.
205567990086_R08C01


title: MMR27_T2

description:
Methylation data from brain tumor sample.
201492570127_R08C01


title: MMR27_T1

description:
Methylation data from brain tumor sample.
200991630102_R04C01


title: BS_lib2_mbd56_rep1