title: B6MSM_01-cell_DEP_01_067_03


title: B6MSM_01-cell_DEP_01_067_02

status: Public on Jun 24 2024

type: SRA

city: Kobe

first: Hirohisa

last: Kyogoku

state: Hyogo

address: 1-1, Rokkodai-chou

department: Agricultural Science

country: Japan

institute: Kobe university

description:
B6MSM_01cell_log2med.txt.gz
B6MSM_01cell_binary.txt.gz
B6MSM_01cell_B6_haplotype_log2med.txt.gz
B6MSM_01cell_MSM_haplotype_log2med.txt.gz
B6MSM_01cell_B6_haplotype_binary.txt.gz
B6MSM_01cell_MSM_haplotype_binary.txt.gz

library_source: genomic

data_processing:
Two-step adapter trimming was performed to first remove the Illumina adapter and the SEQXE adapter.
Trimmed fastq files were aligned to mm9 or a constructed B6/MSM specific diploid genome (Takahashi et al., 2019) for non-haplotype or haplotype-resolved analysis, respectively.
Genome coordinates of allele-specific uniquely mapped reads (MAPQ >16) were converted to mm9 by liftOver tool (UCSC Genome Browser). Duplicated reads were filtered out.
For quality control of scRepli-seq data, we applied median-absolute-deviation (MAD) score evaluation to filter out cells with problematic RT (MAD scores = 0 or >1.0).
For generating log2[(mappability-corrected S-phase reads)/median] scores (log2median RT score) to obtain single-cell RT profiles using cells that passed MAD score evaluation, we counted the reads in sliding windows of 1-Mb at 200-kb intervals, 200-kb at 40-kb intervals, or 1-Mb at 200-kb intervals (haplotype-resolved analysis for B6MSM)  after normalizing S-phase data with AneuFinder’s correctMappability command based on G1 control without karyotype defects in each strain. (Miura et al., 2020).
The binarization for each 80-kb (non-haplotype) or 400-kb (haplotype-resolved analysis for B6MSM) was performing find CNVs command in AneuFinder (Miura et al., 2020). For 4-cell, we applied 1-somy mode for early S-phase, and 2-somy mode for mid/late S-phase. Other stages including 1-, 2-cell, we applied 2-somy mode for binarization. Repliscore as a percentage of replicated bins in the total number of replicated and unreplicated bins was calculated from binarized scRepli-seq data without X chromosome (Miura et al., 2020).
Assembly: mm9
Supplementary files format and content: log2median RT score (log2med.txt)
Supplementary files format and content: Binary data (binary.txt)
Library strategy: Single-cell Repli-seq

molecule: genomic DNA

organism: Mus musculus

source_name: embryo

growth_protocol: Developmental conditions for embryos, (1) in vitro: Embryos were cultured in Chatot, Ziomek, and Bavister medium (CZB). (2) in vivo: In vivo development zygotes and embryos were collected from the oviducts of pregnant mice that had been induced to superovulate and mated with male mice. Embryos within 1 to 2 hours after cytokinesis were classified as G1.

extract_protocol:
Single-cell isolation: Collection of single blastomeres was performed using micromanipulation. Embryos were transferred into M2 medium supplemented with 5 μg/ml cytochalasin B (Sigma-Aldrich) for 10 min. Then, the zona pellucida was cut by the LYKOS laser system (Hamilton Thorne) in a micromanipulation chamber, which was put on a warmed stage (37°C) in an inverted microscope (Olympus Co.). After cutting the zona pellucida, a fire-polished injection pipette (inner dia. 30 µm) was inserted through the hole of the zona pellucida, single blastomere was isolated. For late 8-cell and 16-cell stage embryos, embryos were treated with TrypLE Express (gibco) for 5 min before single-cell isolation. TE and ICM cells were isolated described previously (Xu et al., 2013) and microsurgical isolation to single cell was performed by micromanipulator.  After the single-cell isolation, sample preparations were performed as described (Miura et al., 2020).
DNA samples were subject to whole-genome amplification (WGA) with a SeqPlex kit (Sigma, SEQXE). NGS libraries were constructed WGA DNA with an NGS LTP Library Preparation Kit (KAPA, KK8232) according to the manufacturer’s instructions

treatment_protocol: Treatments for embryos, (1) IVF or ICSI: For IVF was performed according to the manufacturer's instructions using CARD MEDIUM (Cosmo Bio). To limit the time of fertilization, the insemination time was 1 hour. ICSI with sperm heads was carried out as described previously (Kyogoku et al., 2018). (2) SCNT: SCNT was performed as described previously (Kyogoku et al., 2018). (3) EdU labeling: in-vitro developed embryos were treated with 20 µM EdU for 30 min and tripsynized into single-cells. Cells were fixed in 3.7% paraformaldehyde in phosphate-buffered saline (PBS) for 30 min. EdU staining was performed using Click-iT Plus EdU Alexa Flour 594 Imaging Kit. Each labeled single-cell was collected by mouth pipette under the microscopy.

tag: strain

tag: tissue

value: embryo

tag: developmental stage

tag: developmental condition

value: in vitro

tag: treatment

value: IVF or ICSI


title: B6MSM_01-cell_DEP_01_066_61


title: B6MSM_01-cell_DEP_01_066_63


title: B6MSM_01-cell_DEP_01_066_62


title: B6MSM_01-cell_DEP_01_066_60


title: B6MSM_01-cell_DEP_01_066_58


title: B6MSM_01-cell_DEP_01_066_59


title: Coronary sinus blood sample [PBHF02_007]

type: RNA

city: Nantes

first: Marja

last: Steenman

address: 8 quai Moncousu

country: France

institute: L'institut du thorax

description: Gene expression before placement of CRT-D

hyb_protocol: 600 ng of Cy3-labeled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent Hi-RPM hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human Gene Expression microarrays (G4851B) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent). Next, microarrays were washed 30 seconds in acetonitrile and 30 seconds in Stabilization and Drying Solution.

scan_protocol: Slides were scanned immediately after washing on the Agilent G2565CA Microarray Scanner using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1-107_Sep09 and Grid: 039494_D_F_20120628) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Data were normalized using R statistical software. Raw values of all probes on all arrays were normalized against a virtual median chip (median raw intensity per row) using a locally weighted scattered plot smoother analysis (LOWESS). Values for replicate probes were averaged. The data were filtered to remove probes with low intensity values.

molecule: total RNA

organism: Homo sapiens

source_name: Coronary sinus blood

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from100 ng RNA using the Low Input QuickAmp Labeling Kit One-Color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: The LeukoLOCKTM Fractionation & Stabilization Kit (ThermoFisher) was used to isolate leukocytes and stabilize RNA. Total RNA was isolated using the LeukoLOCKTM Alternative Protocol following manufacturer's instructions. RNA quality was assessed using either an Agilent 2100 Bioanalyzer or an Agilent TapeStation System

value: Whole blood

tag: gender

value: Female

tag: age

tag: cardiopathy

value: ischemic

tag: cardiac rhythm at start of the study

value: Sinus rhythm

tag: cardiac rhythm after 1 year follow-up


title: B6MSM_01-cell_DEP_01_066_64


title: Coronary sinus blood sample [PBHF01_145]

value: Male


title: B6MSM_01-cell_DEP_01_066_57


title: Coronary sinus blood sample [PBHF01_143]

value: non ischemic


title: Coronary sinus blood sample [PBHF03_001a]


title: Coronary sinus blood sample, replicate [PBHF03_001b]


title: Coronary sinus blood sample [PBHF02_014]


title: Coronary sinus blood sample [PBHF01_141a]


title: Coronary sinus blood sample [PBHF01_142]


title: Coronary sinus blood sample, replicate [PBHF01_139b]


title: Coronary sinus blood sample, replicate [PBHF01_141b]


title: B6MSM_01-cell_DEP_01_066_56


title: Coronary sinus blood sample [PBHF02_010]


title: Coronary sinus blood sample [PBHF01_136]


title: Coronary sinus blood sample [PBHF02_013]


title: B6MSM_01-cell_DEP_01_066_55


title: Coronary sinus blood sample [PBHF01_137]


title: Coronary sinus blood sample [PBHF01_135]


title: Coronary sinus blood sample [PBHF01_139a]


title: B6MSM_01-cell_DEP_01_066_54


title: B6MSM_01-cell_DEP_01_066_53


title: B6MSM_01-cell_DEP_01_066_52


title: B6MSM_01-cell_DEP_01_066_50


title: B6MSM_01-cell_DEP_01_066_49


title: B6MSM_01-cell_DEP_01_066_51


title: B6MSM_01-cell_DEP_01_066_48


title: Coronary sinus blood sample, replicate [PBHF01_130b]


title: B6MSM_01-cell_DEP_01_066_47


title: B6MSM_01-cell_DEP_01_066_46


title: Coronary sinus blood sample [PBHF01_131]


title: B6MSM_01-cell_DEP_01_066_45


title: B6MSM_01-cell_DEP_01_066_44


title: Coronary sinus blood sample [PBHF01_123]

value: Atrial fibrillation


title: Coronary sinus blood sample [PBHF01_125]


title: B6MSM_01-cell_DEP_01_066_42


title: Coronary sinus blood sample [PBHF01_116]


title: B6MSM_01-cell_DEP_01_066_43


title: B6MSM_01-cell_DEP_01_066_41


title: B6MSM_01-cell_DEP_01_066_40


title: Coronary sinus blood sample [PBHF01_113]


title: Coronary sinus blood sample [PBHF01_122]


title: Coronary sinus blood sample [PBHF01_115]


title: Coronary sinus blood sample [PBHF01_119]

value: mixed


title: B6MSM_01-cell_DEP_01_066_39


title: Coronary sinus blood sample [PBHF01_120]


title: B6MSM_01-cell_DEP_01_066_37


title: B6MSM_01-cell_DEP_01_066_38


title: B6MSM_01-cell_DEP_01_066_36


title: B6MSM_01-cell_DEP_01_066_35


title: Coronary sinus blood sample [PBHF01_105]


title: B6MSM_01-cell_DEP_01_066_34


title: Coronary sinus blood sample [PBHF01_111]


title: B6MSM_01-cell_DEP_01_066_32


title: Coronary sinus blood sample, replicate [PBHF01_103b]


title: Coronary sinus blood sample [PBHF01_108a]


title: B6MSM_01-cell_DEP_01_066_33


title: Coronary sinus blood sample [PBHF01_109]


title: Coronary sinus blood sample, replicate [PBHF01_108b]


title: Coronary sinus blood sample [PBHF01_102]


title: Coronary sinus blood sample [PBHF01_101]


title: Coronary sinus blood sample, replicate [PBHF01_099b]


title: Coronary sinus blood sample [PBHF01_103a]


title: B6MSM_01-cell_DEP_01_066_30


title: Coronary sinus blood sample [PBHF01_099a]


title: B6MSM_01-cell_DEP_01_066_31


title: B6MSM_01-cell_DEP_01_066_29


title: Coronary sinus blood sample [PBHF01_094]


title: B6MSM_01-cell_DEP_01_066_28


title: Coronary sinus blood sample [PBHF01_092]


title: B6MSM_01-cell_DEP_01_066_27


title: B6MSM_01-cell_DEP_01_066_26


title: Coronary sinus blood sample [PBHF01_089b]


title: B6MSM_01-cell_DEP_01_066_25


title: Coronary sinus blood sample [PBHF01_089a]


title: Coronary sinus blood sample [PBHF01_087]


title: B6MSM_01-cell_DEP_01_066_24


title: B6MSM_01-cell_DEP_01_066_23


title: Coronary sinus blood sample [PBHF01_082]


title: B6MSM_01-cell_DEP_01_066_22


title: Coronary sinus blood sample [PBHF01_130a]


title: Coronary sinus blood sample [PBHF01_091]


title: B6MSM_01-cell_DEP_01_066_21


title: B6MSM_01-cell_DEP_01_066_19


title: B6MSM_01-cell_DEP_01_066_20


title: Coronary sinus blood sample [PBHF01_077]


title: B6MSM_01-cell_DEP_01_066_18


title: B6MSM_01-cell_DEP_01_066_16


title: Coronary sinus blood sample [PBHF01_078]


title: Coronary sinus blood sample [PBHF01_076]


title: B6MSM_01-cell_DEP_01_066_17


title: Coronary sinus blood sample [PBHF01_080]


title: Coronary sinus blood sample [PBHF01_071]


title: B6MSM_01-cell_DEP_01_066_14


title: B6MSM_01-cell_DEP_01_066_12


title: B6MSM_01-cell_DEP_01_066_13


title: Coronary sinus blood sample [PBHF01_074]


title: Coronary sinus blood sample [PBHF01_084]


title: B6MSM_01-cell_DEP_01_066_11


title: Coronary sinus blood sample [PBHF01_088]


title: B6MSM_01-cell_DEP_01_066_10


title: B6MSM_01-cell_DEP_01_066_09


title: B6MSM_01-cell_DEP_01_066_15


title: Coronary sinus blood sample [PBHF01_075]


title: Coronary sinus blood sample [PBHF01_068]


title: Coronary sinus blood sample [PBHF01_070]


title: B6MSM_01-cell_DEP_01_066_08


title: Coronary sinus blood sample [PBHF01_065]


title: Coronary sinus blood sample [PBHF01_066]


title: B6MSM_01-cell_DEP_01_066_06


title: B6MSM_01-cell_DEP_01_066_02


title: BDF1_in-vitro_TE_DEP_01_065_82

description:
BDF1_in-vitro_TE_log2med.txt.gz
BDF1_in-vitro_TE_binary.txt.gz

value: TE


title: B6MSM_01-cell_DEP_01_066_04


title: B6MSM_01-cell_DEP_01_066_07


title: B6MSM_01-cell_DEP_01_066_01


title: B6MSM_01-cell_DEP_01_066_05


title: Coronary sinus blood sample [PBHF01_061]


title: 4260, GEX (sorted, spike AIM positive CD4 memory T cells) biol rep 3, tech rep 2

city: La Jolla

first: Shane

last: Crotty

state: CA

address: 9420 Athena Circle

country: USA

institute: La Jolla Institute for Immunology

description:
4260_S_CD4_3_GEX2_barcodes.tsv.gz
4260_S_CD4_3_GEX2_features.tsv.gz
4260_S_CD4_3_GEX2_matrix.mtx.gz

library_source: transcriptomic

data_processing:
CellRanger v6.0 or higher mkfastq and count were used for GEX/CSP to generate a single set of processed files per paired GEX/CSP samples. CellRanger v6.0 or higher vdj used for TCR and BCR sequencing to  annotate contigs and call cells.
Filtered CellRanger output files for GEX/CSP were used for Seurat v4.0 (or higher) analysis to determine cell counts, cluster cells by identity, etc.
BCR and TCR sequence analysis was performed using Immcantation or Platypus (TCR), with the cell barcodes used to assign BCR and TCR sequences to cells present in the Seurat object made from the GEX/CSP data.
Assembly: GRCh38
Supplementary files format and content: CellRanger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz for GEX/CSP; feature_reference.csv lists CSP features (CITE-seq Ab for samples labeled with TBNK Ab, HTO for hashtag Ab labeled samples, ADT for probe-labeled samples)
Supplementary files format and content: CellRanger output files: filtered_contig_annotations.csv, filtered_contig.fasta for TCR and BCR sequencing
Library strategy: CITE-seq

source_name: PBMC

extract_protocol:
NP single cell suspensions were subjected to column-based dead cell removal (Miltenyi) then stained with CITE-seq Ab +/- probes before single cells were encapsulated in gel-beads-in emulsion (GEMs) using the 10x controller with a Chromium single cell 5' GEM libray and gel bead kit (v2). Sorted probe-positive memory B cells or AIM+ memory T cells underwent the same 10x processing.
CITE-seq per manufacturer's protocol
scRNA-seq, CITE-seq, scTCR-seq, scBCR-seq

value: PBMC

tag: library type

value: mRNA


title: Coronary sinus blood sample [PBHF01_067]


title: Coronary sinus blood sample [PBHF01_060]


title: Coronary sinus blood sample [PBHF01_052]


title: 4260, scTCRseq (sorted, spike AIM positive CD4 memory T cells) biol rep 3, tech rep 2

data_processing:
CellRanger v6.0 or higher mkfastq and count were used for GEX/CSP to generate a single set of processed files per paired GEX/CSP samples. CellRanger v6.0 or higher vdj used for TCR and BCR sequencing to  annotate contigs and call cells.
Filtered CellRanger output files for GEX/CSP were used for Seurat v4.0 (or higher) analysis to determine cell counts, cluster cells by identity, etc.
BCR and TCR sequence analysis was performed using Immcantation or Platypus (TCR), with the cell barcodes used to assign BCR and TCR sequences to cells present in the Seurat object made from the GEX/CSP data.
Assembly: GRCh38
Supplementary files format and content: CellRanger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz for GEX/CSP; feature_reference.csv lists CSP features (CITE-seq Ab for samples labeled with TBNK Ab, HTO for hashtag Ab labeled samples, ADT for probe-labeled samples)
Supplementary files format and content: CellRanger output files: filtered_contig_annotations.csv, filtered_contig.fasta for TCR and BCR sequencing

value: TCR


title: Coronary sinus blood sample [PBHF01_062]


title: Coronary sinus blood sample [PBHF01_055]


title: Coronary sinus blood sample [PBHF01_054]


title: Coronary sinus blood sample [PBHF01_064]


title: BDF1_in-vitro_TE_DEP_01_065_81


title: 4260, scTCRseq (sorted, spike AIM positive CD4 memory T cells) biol rep 3, tech rep 1


title: N2, control, rep2

city: Helsinki

first: Olli

last: Matilainen

address: Viikinkaari 9C

country: Finland

institute: University of Helsinki

data_processing:
Original image data file from Illumina platform was transformed to Raw Reads by CASAVA base recognition (Base Calling).
Paired-end clean reads were mapped to the reference genome using HISAT2 software.
FeatureCounts was used to count the read numbers mapped on each gene.
Data processing was done by Novogene.
Assembly: ncbi_caenorhabditis_elegans_gcf_000002985_6_wbcel235
Supplementary files format and content: gene_count.txt, content: read counts
Supplementary files format and content: gene_fpkm.txt, content: FPKM values
Supplementary files format and content: gene_id gene_name A1_C A2_C A3_C G1_AJO2 G2_AJO2 G3_AJO2

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: Wild-type C. elegans (N2) was synchronized by bleaching and plated as L1 larvae on OP50 plates supplemented with Protein powder 2 (AJO2-samples) or H2O (control, C-samples). Plates were kept at 20 degrees Celcius. At L4 larval stage, animals were transferred to plates containing 5-fluorouracil. Animals were collected at day 2 of adulthood (three biological replicates for both strains) and freezed in liquid nitrogen.

extract_protocol:
Total RNA was extracted with TRIzol Reagent (ThermoFisher Scientific) and purified with GeneJET RNA Purification Kit (ThermoFisher Scientific)
Messenger RNA was purified from total RNA 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. Library construction and sequencing were done by Novogene.

value: whole animal

tag: cell line

value: day 2 adult on OP50

tag: culture condition

value: 20 degrees Celcius

tag: genotype

value: N2 (wild-type)

value: control (H2O)


title: N2, Protein powder 2, rep3

value: Protein powder 2


title: N2, control, rep1


title: N2, control, rep3


title: N2, Protein powder 2, rep1


title: N2, Protein powder 2, rep2


title: 4260, HTO (sorted, spike AIM positive CD4 memory T cells) biol rep 3, tech rep 2

library_source: other

molecule: protein

value: HTO

tag: csp


title: BDF1_in-vitro_TE_DEP_01_065_78

value: embryo

value: in vitro


title: B6MSM_01-cell_DEP_01_066_03

value: IVF or ICSI


title: 4260, HTO (sorted, spike AIM positive CD4 memory T cells) biol rep 3, tech rep 1

description:
4260_S_CD4_3_GEX_barcodes.tsv.gz
4260_S_CD4_3_GEX_features.tsv.gz
4260_S_CD4_3_GEX_matrix.mtx.gz


title: BDF1_in-vitro_TE_DEP_01_065_70


title: BDF1_in-vitro_TE_DEP_01_065_76


title: BDF1_in-vitro_TE_DEP_01_065_61


title: 4260, GEX (sorted, spike AIM positive CD4 memory T cells) biol rep 3, tech rep 1


title: BDF1_in-vitro_TE_DEP_01_065_75


title: BDF1_in-vitro_TE_DEP_01_065_67


title: BDF1_in-vitro_TE_DEP_01_065_63


title: 4260, scTCRseq (sorted, spike AIM positive CD4 memory T cells) biol rep 2, tech rep 2


title: 4260, HTO (sorted, spike AIM positive CD4 memory T cells) biol rep 2, tech rep 2

description:
4260_S_CD4_2_GEX2_barcodes.tsv.gz
4260_S_CD4_2_GEX2_features.tsv.gz
4260_S_CD4_2_GEX2_matrix.mtx.gz


title: 4260, GEX (sorted, spike AIM positive CD4 memory T cells) biol rep 2, tech rep 2


title: 4260, HTO (sorted, spike AIM positive CD4 memory T cells) biol rep 2, tech rep 1

description:
4260_S_CD4_2_GEX_barcodes.tsv.gz
4260_S_CD4_2_GEX_features.tsv.gz
4260_S_CD4_2_GEX_matrix.mtx.gz


title: 4260, GEX (sorted, spike AIM positive CD4 memory T cells) biol rep 2, tech rep 1


title: BDF1_in-vitro_TE_DEP_01_065_53


title: 4260, scTCRseq (sorted, spike AIM positive CD4 memory T cells) biol rep 1, tech rep 2


title: BDF1_in-vitro_TE_DEP_01_065_48


title: BDF1_in-vitro_TE_DEP_01_065_52


title: BDF1_in-vitro_TE_DEP_01_065_55


title: 4260, HTO (sorted, spike AIM positive CD4 memory T cells) biol rep 1, tech rep 1

description:
4260_S_CD4_1_GEX_barcodes.tsv.gz
4260_S_CD4_1_GEX_features.tsv.gz
4260_S_CD4_1_GEX_matrix.mtx.gz


title: 4260, scTCRseq (sorted, spike AIM positive CD4 memory T cells) biol rep 2, tech rep 1


title: BDF1_in-vitro_TE_DEP_01_065_58


title: 4260, GEX (sorted, spike AIM positive CD4 memory T cells) biol rep 1, tech rep 1


title: 4260, GEX (sorted, spike AIM positive CD4 memory T cells) biol rep 1, tech rep 2

description:
4260_S_CD4_1_GEX2_barcodes.tsv.gz
4260_S_CD4_1_GEX2_features.tsv.gz
4260_S_CD4_1_GEX2_matrix.mtx.gz


title: 4260, scTCRseq (sorted, spike AIM positive CD4 memory T cells) biol rep 1, tech rep 1


title: BDF1_in-vitro_TE_DEP_01_065_36


title: BDF1_in-vitro_TE_DEP_01_065_37


title: 4093, scTCRseq (sorted, spike AIM positive CD4 memory T cells) tech rep 2


title: BDF1_in-vitro_TE_DEP_01_065_47


title: BDF1_in-vitro_TE_DEP_01_065_33


title: BDF1_in-vitro_TE_DEP_01_065_32


title: BDF1_in-vitro_TE_DEP_01_065_28


title: BDF1_in-vitro_TE_DEP_01_065_23


title: 4093, scTCRseq (sorted, spike AIM positive CD4 memory T cells) tech rep 1


title: 4093, HTO (sorted, spike AIM positive CD4 memory T cells) tech rep 1

description:
4093_S_CD4_GEX_barcodes.tsv.gz
4093_S_CD4_GEX_features.tsv.gz
4093_S_CD4_GEX_matrix.mtx.gz


title: BDF1_in-vitro_TE_DEP_01_065_54


title: BDF1_in-vitro_TE_DEP_01_065_27


title: 4260, HTO (sorted, spike AIM positive CD4 memory T cells) biol rep 1, tech rep 2


title: 4093, GEX (sorted, spike AIM positive CD4 memory T cells) tech rep 1


title: BDF1_in-vitro_TE_DEP_01_065_13


title: BDF1_in-vitro_TE_DEP_01_065_16


title: BDF1_in-vitro_TE_DEP_01_064_76


title: 3864, scTCRseq (sorted, spike AIM positive CD4 memory T cells) tech rep 2


title: 3864, GEX (sorted, spike AIM positive CD4 memory T cells) tech rep 2

description:
3864_S_CD4_GEX2_barcodes.tsv.gz
3864_S_CD4_GEX2_features.tsv.gz
3864_S_CD4_GEX2_matrix.mtx.gz


title: 3864, HTO (sorted, spike AIM positive CD4 memory T cells) tech rep 2


title: BDF1_in-vitro_TE_DEP_01_064_74


title: 3864, scTCRseq (sorted, spike AIM positive CD4 memory T cells) tech rep 1


title: 4093, HTO (sorted, spike AIM positive CD4 memory T cells) tech rep 2

description:
4093_S_CD4_GEX2_barcodes.tsv.gz
4093_S_CD4_GEX2_features.tsv.gz
4093_S_CD4_GEX2_matrix.mtx.gz


title: BDF1_in-vitro_TE_DEP_01_064_72


title: 4093, GEX (sorted, spike AIM positive CD4 memory T cells) tech rep 2


title: BDF1_in-vitro_TE_DEP_01_064_65


title: BDF1_in-vitro_TE_DEP_01_064_64


title: 3864, HTO (sorted, spike AIM positive CD4 memory T cells) tech rep 1

description:
3864_S_CD4_GEX_barcodes.tsv.gz
3864_S_CD4_GEX_features.tsv.gz
3864_S_CD4_GEX_matrix.mtx.gz


title: 3864, GEX (sorted, spike AIM positive CD4 memory T cells) tech rep 1


title: BDF1_in-vitro_ICM_DEP_01_064_48

description:
BDF1_in-vitro_ICM_log2med.txt.gz
BDF1_in-vitro_ICM_binary.txt.gz

value: ICM


title: BDF1_in-vitro_TE_DEP_01_064_59


title: BDF1_in-vitro_TE_DEP_01_064_62


title: 4206, 4301, scTCRseq (sorted, spike AIM positive CD8 memory T cells) tech rep 1


title: 4206, 4301, scTCRseq (sorted, spike AIM positive CD8 memory T cells) tech rep 2


title: BDF1_in-vitro_TE_DEP_01_064_61


title: 4206, 4301, HTO (sorted, spike AIM positive CD8 memory T cells) tech rep 2

description:
20240223_CD8_GEX2_barcodes.tsv.gz
20240223_CD8_GEX2_features.tsv.gz
20240223_CD8_GEX2_matrix.mtx.gz


title: 4206, 4301, GEX (sorted, spike AIM positive CD8 memory T cells) tech rep 2


title: 4206, 4301, GEX (sorted, spike AIM positive CD8 memory T cells) tech rep 1

description:
20240223_CD8_GEX_barcodes.tsv.gz
20240223_CD8_GEX_features.tsv.gz
20240223_CD8_GEX_matrix.mtx.gz


title: 4206, 4301, HTO (sorted, spike AIM positive CD8 memory T cells) tech rep 1


title: BDF1_in-vitro_ICM_DEP_01_064_40


title: BDF1_in-vitro_ICM_DEP_01_064_31


title: 4206, 4255, 4301, HTO (sorted, spike and non-S AIM positive CD4 memory T cells) tech rep 2

description:
20240223_CD4_GEX2_barcodes.tsv.gz
20240223_CD4_GEX2_features.tsv.gz
20240223_CD4_GEX2_matrix.mtx.gz


title: 4206, 4255, 4301, scTCRseq (sorted, spike and non-S AIM positive CD4 memory T cells) tech rep 2


title: BDF1_in-vitro_ICM_DEP_01_064_27


title: BDF1_in-vitro_ICM_DEP_01_064_23


title: 4206, 4255, 4301, GEX (sorted, spike and non-S AIM positive CD4 memory T cells) tech rep 2


title: BDF1_in-vitro_ICM_DEP_01_064_28


title: 4206, 4255, 4301, scTCRseq (sorted, spike and non-S AIM positive CD4 memory T cells) tech rep 1


title: BDF1_in-vitro_ICM_DEP_01_064_21


title: 4206, 4255, 4301, HTO (sorted, spike and non-S AIM positive CD4 memory T cells) tech rep 1

description:
20240223_CD4_GEX_barcodes.tsv.gz
20240223_CD4_GEX_features.tsv.gz
20240223_CD4_GEX_matrix.mtx.gz


title: 4206, 4255, 4301, GEX (sorted, spike and non-S AIM positive CD4 memory T cells) tech rep 1


title: 3864, 4093, 4260, scTCRseq (sorted, spike AIM positive CD8 memory T cells) tech rep 2


title: BDF1_in-vitro_16-cell_DEP_01_034-48

description:
BDF1_in-vitro_16cell_log2med.txt.gz
BDF1_in-vitro_16cell_binary.txt.gz


title: 3864, 4093, 4260, GEX (sorted, spike AIM positive CD8 memory T cells) tech rep 2

description:
20240221_CD8_GEX2_barcodes.tsv.gz
20240221_CD8_GEX2_features.tsv.gz
20240221_CD8_GEX2_matrix.mtx.gz


title: BDF1_in-vitro_16-cell_DEP_01_034-46


title: BDF1_in-vitro_16-cell_DEP_01_034-45


title: BDF1_in-vitro_ICM_DEP_01_064_44


title: 3864, 4093, 4260, HTO (sorted, spike AIM positive CD8 memory T cells) tech rep 2


title: BDF1_in-vitro_16-cell_DEP_01_034-47


title: 3864, 4093, 4260, scTCRseq (sorted, spike AIM positive CD8 memory T cells) tech rep 1


title: BDF1_in-vitro_16-cell_DEP_01_034-44


title: BDF1_in-vitro_16-cell_DEP_01_034-43


title: 4447, scTCRseq (sorted, spike AIM positive CD8 memory T cells)


title: BDF1_in-vitro_ICM_DEP_01_064_13


title: BDF1_in-vitro_16-cell_DEP_01_034-42

description:
filtered by MAD score
BDF1_in-vitro_16cell_log2med.txt.gz
BDF1_in-vitro_16cell_binary.txt.gz


title: 4447, HTO (sorted, spike AIM positive CD8 memory T cells)

description:
4447_S_CD8_GEX_barcodes.tsv.gz
4447_S_CD8_GEX_features.tsv.gz
4447_S_CD8_GEX_matrix.mtx.gz


title: BDF1_in-vitro_16-cell_DEP_01_034-40


title: BDF1_in-vitro_16-cell_DEP_01_034-39


title: 4447, scTCRseq (sorted, spike AIM positive CD4 memory T cells)


title: 4447, GEX (sorted, spike AIM positive CD8 memory T cells)


title: BDF1_in-vitro_16-cell_DEP_01_034-49


title: 4447, HTO (sorted, spike AIM positive CD4 memory T cells)

description:
4447_S_CD4_GEX_barcodes.tsv.gz
4447_S_CD4_GEX_features.tsv.gz
4447_S_CD4_GEX_matrix.mtx.gz


title: BDF1_in-vitro_16-cell_DEP_01_034-38


title: BDF1_in-vitro_16-cell_DEP_01_034-37


title: 4258, scTCRseq (sorted, spike AIM positive CD8 memory T cells)


title: BDF1_in-vitro_16-cell_DEP_01_034-36


title: 4447, GEX (sorted, spike AIM positive CD4 memory T cells)


title: 4258, GEX (sorted, spike AIM positive CD8 memory T cells)

description:
4258_S_CD8_GEX_barcodes.tsv.gz
4258_S_CD8_GEX_features.tsv.gz
4258_S_CD8_GEX_matrix.mtx.gz


title: 3864, 4093, 4260, HTO (sorted, spike AIM positive CD8 memory T cells) tech rep 1

description:
20240221_CD8_GEX_barcodes.tsv.gz
20240221_CD8_GEX_features.tsv.gz
20240221_CD8_GEX_matrix.mtx.gz


title: 4258, HTO (sorted, spike AIM positive CD8 memory T cells)


title: BDF1_in-vitro_16-cell_DEP_01_034-35


title: BDF1_in-vitro_16-cell_DEP_01_034-33


title: 3864, 4093, 4260, GEX (sorted, spike AIM positive CD8 memory T cells) tech rep 1


title: BDF1_in-vitro_16-cell_DEP_01_034-31


title: 4258, HTO (sorted, spike AIM positive CD4 memory T cells)

description:
4258_S_CD4_GEX_barcodes.tsv.gz
4258_S_CD4_GEX_features.tsv.gz
4258_S_CD4_GEX_matrix.mtx.gz


title: 4041, scTCRseq (sorted, spike AIM positive CD8 memory T cells)


title: BDF1_in-vitro_16-cell_DEP_01_034-32


title: BDF1_in-vitro_16-cell_DEP_01_034-41


title: 4258, GEX (sorted, spike AIM positive CD4 memory T cells)


title: BDF1_in-vitro_16-cell_DEP_01_034-30


title: 4041, HTO (sorted, spike AIM positive CD8 memory T cells)

description:
4041_S_CD8_GEX_barcodes.tsv.gz
4041_S_CD8_GEX_features.tsv.gz
4041_S_CD8_GEX_matrix.mtx.gz


title: BDF1_in-vitro_16-cell_DEP_01_034-29


title: BDF1_in-vitro_16-cell_DEP_01_034-27


title: 4041, GEX (sorted, spike AIM positive CD8 memory T cells)


title: BDF1_in-vitro_16-cell_DEP_01_034-26


title: 4041, GEX (sorted, spike AIM positive CD4 memory T cells)

description:
4041_S_CD4_GEX_barcodes.tsv.gz
4041_S_CD4_GEX_features.tsv.gz
4041_S_CD4_GEX_matrix.mtx.gz


title: 4041, HTO (sorted, spike AIM positive CD4 memory T cells)


title: 4041, scTCRseq (sorted, spike AIM positive CD4 memory T cells)


title: 3853, scTCRseq (sorted, spike AIM positive CD8 memory T cells)


title: BDF1_in-vitro_16-cell_DEP_01_034-34


title: BDF1_in-vitro_16-cell_DEP_01_034-24


title: 4258, scTCRseq (sorted, spike AIM positive CD4 memory T cells)


title: BDF1_in-vitro_16-cell_DEP_01_034-23


title: BDF1_in-vitro_16-cell_DEP_01_034-22


title: 3853, GEX (sorted, spike AIM positive CD8 memory T cells)

description:
3853_S_CD8_GEX_barcodes.tsv.gz
3853_S_CD8_GEX_features.tsv.gz
3853_S_CD8_GEX_matrix.mtx.gz


title: 3853, HTO (sorted, spike AIM positive CD4 memory T cells)

description:
3853_S_CD4_GEX_barcodes.tsv.gz
3853_S_CD4_GEX_features.tsv.gz
3853_S_CD4_GEX_matrix.mtx.gz


title: 3853, scTCRseq (sorted, spike AIM positive CD4 memory T cells)


title: BDF1_in-vitro_16-cell_DEP_01_034-21


title: BDF1_in-vitro_16-cell_DEP_01_034-20


title: 3853, 4447, scTCRseq (sorted, non-S AIM positive CD8 memory T cells)


title: 3853, GEX (sorted, spike AIM positive CD4 memory T cells)


title: BDF1_in-vitro_08-cell_DEP_01_048-90

description:
BDF1_in-vitro_08cell_log2med.txt.gz
BDF1_in-vitro_08cell_binary.txt.gz


title: BDF1_in-vitro_16-cell_DEP_01_034-28


title: BDF1_in-vitro_16-cell_DEP_01_034-19


title: 3853, 4447, GEX (sorted, non-S AIM positive CD8 memory T cells)

description:
0126_CD8RE_GEX_barcodes.tsv.gz
0126_CD8RE_GEX_features.tsv.gz
0126_CD8RE_GEX_matrix.mtx.gz


title: BDF1_in-vitro_08-cell_DEP_01_048-89


title: 3853, 4447, HTO (sorted, non-S AIM positive CD8 memory T cells)


title: BDF1_in-vitro_16-cell_DEP_01_034-25


title: BDF1_in-vitro_08-cell_DEP_01_048-88


title: 3853, HTO (sorted, spike AIM positive CD8 memory T cells)


title: BDF1_in-vitro_08-cell_DEP_01_048-87


title: 3853, 4447, scTCRseq (sorted, non-S AIM positive CD4 memory T cells)


title: 3853, 4447, HTO (sorted, non-S AIM positive CD4 memory T cells)

description:
0126_CD4RE_GEX_barcodes.tsv.gz
0126_CD4RE_GEX_features.tsv.gz
0126_CD4RE_GEX_matrix.mtx.gz


title: BDF1_in-vitro_08-cell_DEP_01_048-85


title: BDF1_in-vitro_08-cell_DEP_01_048-86


title: 3853, 4447, GEX (sorted, non-S AIM positive CD4 memory T cells)


title: 4041, 4258, scTCRseq (sorted, non-S AIM positive CD8 memory T cells)


title: 4041, 4258, HTO (sorted, non-S AIM positive CD8 memory T cells)

description:
0124_CD8RE_GEX_barcodes.tsv.gz
0124_CD8RE_GEX_features.tsv.gz
0124_CD8RE_GEX_matrix.mtx.gz


title: BDF1_in-vitro_08-cell_DEP_01_048-84


title: 4041, 4258, GEX (sorted, non-S AIM positive CD8 memory T cells)


title: BDF1_in-vitro_08-cell_DEP_01_048-81


title: 4041, 4258, scTCRseq (sorted, non-S AIM positive CD4 memory T cells)


title: BDF1_in-vitro_08-cell_DEP_01_048-82


title: BDF1_in-vitro_08-cell_DEP_01_048-83


title: BDF1_in-vitro_08-cell_DEP_01_048-80


title: BDF1_in-vitro_08-cell_DEP_01_048-79

description:
no R2 fastq data
BDF1_in-vitro_08cell_log2med.txt.gz
BDF1_in-vitro_08cell_binary.txt.gz


title: 4041, 4258, GEX (sorted, non-S AIM positive CD4 memory T cells)

description:
0124_CD4RE_GEX_barcodes.tsv.gz
0124_CD4RE_GEX_features.tsv.gz
0124_CD4RE_GEX_matrix.mtx.gz


title: BDF1_in-vitro_08-cell_DEP_01_048-78


title: BDF1_in-vitro_08-cell_DEP_01_048-77


title: 4219, 4236, scTCRseq (sorted AIM positive CD8 memory T cells) biol rep 1


title: Ctrl, mock, midguts, day 9, replicate B

city: Paris

first: Hugo

last: Varet

address: 28 rue du Docteur Roux

institute: Institut Pasteur

data_processing:
Raw RNA-sequencing reads were cleaned of adapter sequences and low-quality sequences using cutadapt version 2.10 with options "-m 25 -q 30 -O 6 --trim-n --max-n 1".
Gene expression quantification was performed using salmon version 1.9.0. First, the Aedes aegypti reference transcriptome (downloaded from VectorBase 66) was indexed along with its corresponding genome using the "--decoys" option.
Transcript expression was then quantified for each sample using the "-l A" option and summarized at the gene level using the "--geneMap" parameter.
Gene expression data was imported into R version 4.3.2 using the tximport package. The normalization and dispersion estimation were performed with DESeq2 using the default parameters and statistical tests for differential expression were performed applying the independent filtering algorithm.
A generalized linear model was set in order to test for the infection effect on the gene expression, separately for WT and Vago mosquitoes. Raw p-values were adjusted for multiple testing according to the Benjamini and Hochberg (BH) procedure.
Assembly: AaegyptiLVP_AGWG from VectorBase 66 (https://vectorbase.org/common/downloads/release-66/AaegyptiLVP_AGWG/fasta/data/)
Supplementary files format and content: Text file containing gene-level expression generated by the salmon software.
Supplementary files format and content: Excel file containing the results of the differential analysis performed with DESeq2 (VLG-1 vs Ctrl).

organism: Aedes aegypti

source_name: midguts

extract_protocol:
Total RNA extracts from pools of 10 tissues were isolated with TRIzol (Invitrogen) and treated with DNA-free kit (Invitrogen, AM1906) following the manufacturer’s instructions. The quality of the samples was assessed using a BioAnalyzer RNA Nano kit (Agilent Technologies).
RNA libraries were built using an Illumina Stranded mRNA library Preparation Kit following the manufacturer’s protocol depending on the insert size required. All the samples were eluted for 2 minutes at 80°C after polyA capture to obtain 300-bp inserts.
Sequencing was performed on two lanes 10B300 of NovaSeqX (Illumina) by Novogen.

value: midguts

value: Ctrl

tag: days post_infection

tag: infection

value: mock

tag: replicate

value: B


title: VLG-1, mock, midguts, day 9, replicate A

tag: tissue

value: A


title: VLG-1, mock, midguts, day 9, replicate C

value: C


title: Ctrl, mock, midguts, day 9, replicate C


title: 4219, 4236, HTO (sorted AIM positive CD8 memory T cells) biol rep 2

description:
GEX_CD8_2_barcodes.tsv.gz
GEX_CD8_2_features.tsv.gz
GEX_CD8_2_matrix.mtx.gz

value: PBMC


title: 4041, 4258, HTO (sorted, non-S AIM positive CD4 memory T cells)


title: 4219, 4236, HTO (sorted AIM positive CD8 memory T cells) biol rep 1

description:
GEX_CD8_1_barcodes.tsv.gz
GEX_CD8_1_features.tsv.gz
GEX_CD8_1_matrix.mtx.gz


title: Ctrl, mock, midguts, day 9, replicate A


title: VLG-1, DENV1, midguts, day 9, replicate B


title: VLG-1, DENV1, midguts, day 9, replicate C


title: BDF1_in-vitro_08-cell_DEP_01_048-74

tag: strain

tag: developmental stage


title: Ctrl, DENV1, midguts, day 9, replicate B


title: VLG-1, mock, midguts, day 9, replicate B


title: BDF1_in-vitro_08-cell_DEP_01_048-73

tag: developmental condition

tag: treatment


title: Ctrl, DENV1, midguts, day 9, replicate A


title: 4219, 4236, scTCRseq (sorted AIM positive CD8 memory T cells) biol rep 2

value: TCR


title: VLG-1, mock, midguts, day 5, replicate C


title: BDF1_in-vitro_08-cell_DEP_01_048-72


title: 4219, 4236, GEX (sorted AIM positive CD8 memory T cells) biol rep 2

value: mRNA


title: 4219, 4236, GEX (sorted AIM positive CD8 memory T cells) biol rep 1


title: VLG-1, mock, midguts, day 5, replicate A


title: VLG-1, mock, midguts, day 5, replicate B


title: 4219, 4236, scTCRseq (sorted AIM positive CD4 memory T cells)


title: BDF1_in-vitro_08-cell_DEP_01_048-76


title: BDF1_in-vitro_08-cell_DEP_01_048-71


title: Ctrl, mock, midguts, day 5, replicate C


title: Ctrl, mock, midguts, day 5, replicate B


title: BDF1_in-vitro_08-cell_DEP_01_048-70


title: 4219, 4236, GEX (sorted AIM positive CD4 memory T cells)

description:
GEX_CD4_barcodes.tsv.gz
GEX_CD4_features.tsv.gz
GEX_CD4_matrix.mtx.gz


title: BDF1_in-vitro_08-cell_DEP_01_048-75


title: Ctrl, mock, midguts, day 5, replicate A


title: 4379, scBCRseq (sorted probe positive memory B cells)

value: BCR


title: VLG-1, DENV1, midguts, day 9, replicate A


title: BDF1_in-vitro_08-cell_DEP_01_048-69


title: VLG-1, DENV1, midguts, day 5, replicate C


title: BDF1_in-vitro_08-cell_DEP_01_048-68


title: 4379, probe hashtags

description:
2_4379_MBC_GEX_barcodes.tsv.gz
2_4379_MBC_GEX_features.tsv.gz
2_4379_MBC_GEX_matrix.mtx.gz

value: spike, RBD, N probes


title: 4219, 4236, HTO (sorted AIM positive CD4 memory T cells)


title: Ctrl, DENV1, midguts, day 9, replicate C


title: VLG-1, DENV1, midguts, day 5, replicate A


title: 4379, GEX (sorted probe positive memory B cells)


title: VLG-1, DENV1, midguts, day 5, replicate B


title: Ctrl, DENV1, midguts, day 5, replicate C


title: VLG-1, mock, midguts, day 2, replicate B


title: Ctrl, DENV1, midguts, day 5, replicate A


title: 4809, scBCRseq (sorted probe positive memory B cells)


title: BDF1_in-vitro_08-cell_DEP_01_048-67


title: Ctrl, DENV1, midguts, day 5, replicate B


title: 4809, probe hashtags tech rep 2

description:
3_4809_MBC_GEX_barcodes.tsv.gz
3_4809_MBC_GEX_features.tsv.gz
3_4809_MBC_GEX_matrix.mtx.gz


title: BDF1_in-vitro_08-cell_DEP_01_048-66


title: VLG-1, mock, midguts, day 2, replicate C


title: Ctrl, mock, midguts, day 2, replicate C


title: BDF1_in-vitro_08-cell_DEP_01_048-65


title: 4809, probe hashtags tech rep 1


title: BDF1_in-vitro_08-cell_DEP_01_048-64


title: VLG-1, mock, midguts, day 2, replicate A


title: Ctrl, mock, midguts, day 2, replicate A


title: 4809, GEX (sorted probe positive memory B cells)


title: Ctrl, mock, midguts, day 2, replicate B


title: VLG-1, DENV1, midguts, day 2, replicate C


title: BDF1_in-vitro_08-cell_DEP_01_048-63


title: VLG-1, DENV1, midguts, day 2, replicate B


title: BDF1_in-vitro_08-cell_DEP_01_048-62


title: VLG-1, DENV1, midguts, day 2, replicate A


title: Ctrl, DENV1, midguts, day 2, replicate B


title: Ctrl, DENV1, midguts, day 2, replicate C


title: BDF1_in-vitro_08-cell_DEP_01_048-61


title: 8302 (aka 4202), scBCRseq (sorted probe positive memory B cells)


title: Ctrl, DENV1, midguts, day 2, replicate A


title: 8302 (aka 4202), probe hashtags tech rep 2

description:
1_4202_MBC_GEX_barcodes.tsv.gz
1_4202_MBC_GEX_features.tsv.gz
1_4202_MBC_GEX_matrix.mtx.gz


title: VLG-1, mock, bodies, day 9, replicate C

source_name: bodies

value: bodies


title: 8302 (aka 4202), probe hashtags tech rep 1

value: HTO


title: BDF1_in-vitro_08-cell_DEP_01_048-60

value: embryo


title: VLG-1, mock, bodies, day 9, replicate B


title: BDF1_in-vitro_08-cell_DEP_01_048-59

value: in vitro


title: VLG-1, mock, bodies, day 9, replicate A


title: 8302 (aka 4202), GEX (sorted probe positive memory B cells) tech rep 2


title: Ctrl, mock, bodies, day 9, replicate C


title: BDF1_in-vitro_08-cell_DEP_01_048-58


title: Ctrl, mock, bodies, day 9, replicate A


title: 4379 NP cells, scBCRseq biol rep 2

source_name: nasopharynx

value: nasopharynx


title: BDF1_in-vitro_08-cell_DEP_01_048-57


title: VLG-1, DENV1, bodies, day 9, replicate C


title: Ctrl, mock, bodies, day 9, replicate B


title: 8302 (aka 4202), GEX (sorted probe positive memory B cells) tech rep 1


title: VLG-1, DENV1, bodies, day 9, replicate B


title: VLG-1, DENV1, bodies, day 9, replicate A


title: BDF1_in-vitro_08-cell_DEP_01_048-56


title: 4379 NP cells, scBCRseq biol rep 1


title: Ctrl, DENV1, bodies, day 9, replicate C


title: Ctrl, DENV1, bodies, day 9, replicate B


title: Ctrl, DENV1, bodies, day 9, replicate A


title: 4379 NP cells, scTCRseq biol rep 2


title: BDF1_in-vitro_08-cell_DEP_01_048-55


title: 4379 NP cells, scTCRseq biol rep 1


title: VLG-1, mock, bodies, day 5, replicate C


title: VLG-1, mock, bodies, day 5, replicate B


title: BDF1_in-vitro_08-cell_DEP_01_048-54


title: 4379 NP cells, CITE-seq biol rep 2

description:
Swab_4379_GEX_2_barcodes.tsv.gz
Swab_4379_GEX_2_features.tsv.gz
Swab_4379_GEX_2_matrix.mtx.gz

value: ADT

value: TotalSeq-C TBNK


title: VLG-1, mock, bodies, day 5, replicate A


title: BDF1_in-vitro_08-cell_DEP_01_048-53


title: Ctrl, mock, bodies, day 5, replicate A

value: Ctrl


title: Ctrl, mock, bodies, day 5, replicate B

value: mock


title: 4379 NP cells, GEX biol rep 2


title: BDF1_in-vitro_08-cell_DEP_01_048-51


title: Ctrl, mock, bodies, day 5, replicate C


title: BDF1_in-vitro_08-cell_DEP_01_048-50


title: Ctrl, DENV1, bodies, day 5, replicate C


title: 4379 NP cells, GEX biol rep 1

description:
Swab_4379_GEX_1_barcodes.tsv.gz
Swab_4379_GEX_1_features.tsv.gz
Swab_4379_GEX_1_matrix.mtx.gz


title: Ctrl, DENV1, bodies, day 5, replicate A


title: VLG-1, DENV1, bodies, day 5, replicate B

value: B


title: 4809 NP cells, scBCRseq biol rep 1


title: Ctrl, DENV1, bodies, day 5, replicate B


title: BDF1_in-vitro_08-cell_DEP_01_048-49


title: 4809 NP cells, scTCRseq biol rep 1


title: VLG-1, mock, bodies, day 2, replicate C


title: VLG-1, mock, bodies, day 2, replicate B


title: BDF1_in-vitro_08-cell_DEP_01_048-48


title: Ctrl, mock, bodies, day 2, replicate B


title: 4809 NP cells, GEX biol rep 1

description:
GEX_swab4809_barcodes.tsv.gz
GEX_swab4809_features.tsv.gz
GEX_swab4809_matrix.mtx.gz


title: BDF1_in-vitro_08-cell_DEP_01_048-47


title: 4379 NP cells, CITE-seq biol rep 1


title: VLG-1, mock, bodies, day 2, replicate A

value: A


title: 4809 NP cells, CITE-seq biol rep 1


title: BDF1_in-vitro_08-cell_DEP_01_048-52


title: Ctrl, mock, bodies, day 2, replicate C

value: C


title: VLG-1, DENV1, bodies, day 5, replicate C


title: BDF1_in-vitro_08-cell_DEP_01_048-46


title: VLG-1, DENV1, bodies, day 5, replicate A


title: Ctrl, mock, bodies, day 2, replicate A


title: 4202 NP cells, scBCRseq biol rep 1


title: BDF1_in-vitro_08-cell_DEP_01_048-45


title: VLG-1, DENV1, bodies, day 2, replicate C


title: VLG-1, DENV1, bodies, day 2, replicate A


title: 4202 NP cells, scTCRseq biol rep 1


title: Ctrl, DENV1, bodies, day 2, replicate C


title: 4202 NP cells, CITE-seq biol rep 1

description:
GEX_swab4202_barcodes.tsv.gz
GEX_swab4202_features.tsv.gz
GEX_swab4202_matrix.mtx.gz


title: VLG-1, DENV1, bodies, day 2, replicate B


title: BDF1_in-vitro_08-cell_DEP_01_048-43


title: Ctrl, DENV1, bodies, day 2, replicate B


title: 4202 NP cells, GEX biol rep 1


title: Ctrl, DENV1, bodies, day 2, replicate A


title: Optimization;Plasmid_AsCas12a

city: Frederick

first: Thomas

last: Gonatopoulos-Pournatzis

address: 1050 Boyles Street

institute: NCI/NIH

data_processing:
demultiplexing
mapping to library with bowtie 1 and extract read count for each gRNA in the library
Assembly: hg18
Supplementary files format and content: read counts of the mapped sequencing data in the format of txt.
Library strategy: CRISPR

molecule: other

organism: unidentified plasmid

source_name: plasmid

extract_protocol:
Genomic DNA was extracted from the cell pellets collected at the start (T0) and end time points using the Wizard Genomic DNA Purification Kit (Promega #A1120).
First, the lentiviral integrated hgRNA expression cassettes were amplified from genomic (g)DNA equivalent of ~ 100-fold library coverage using NEBNext Ultra II Q5 Master Mix (New England Biolabs #M0544X). Individual 50 µL PCR reactions containing 3.5 μg gDNA were performed using PCR1_Hybrid_Outer_F2 and PCR1_Hybrid_Outer_R1 primers for the optimization and exon deletion screens and primers A265 and PCR1_BE_Rev for the base editor screens, respectively (see Table S3). After pooling the individual PCR-1 reactions, a fraction was purified using a PCR purification column and used as template for PCR-2, in which each sample was barcoded with unique i5 and i7 index primer combinations. The resulting PCR-2  products were resolved on a 2% agarose gel using SYBR Safe DNA stain (ThermoFisher Scientific #S33102). The desired band was excised and subjected to gel extraction (ThermoFisher Scientific #K0691). Quantification of the extracted libraries was conducted using the Qubit dsDNA HS assay (ThermoFisher Scientific #Q32851) and Tape Station (Agilent #5067-5582 and #5067-5583). The quantified and validated sequencing libraries were pooled, and paired-end sequencing was performed on either an Illumina NextSeq 500 or a NovaSeq 6000 platform.

value: plasmid


title: Optimization;Plasmid_LbCas12a


title: BDF1_in-vitro_08-cell_DEP_01_048-42


title: Base editor; BE_plasmid


title: Optimization2; Plasmid


title: BDF1_in-vitro_08-cell_DEP_01_048-41


title: 4236 NP cells, scBCRseq biol rep 1


title: 4236 NP cells, scTCRseq biol rep 1

value: TCR


title: VPS29 hgRNA

data_processing:
demultiplexing, trimming, remove PCR duplicates
mapping to genome
Assembly: hg38
Supplementary files format and content: mapped output file

growth_protocol: RPE1 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) with high glucose and pyruvate (Gibco #11995073) supplemented with 10% heat-inactivated fetal bovine serum (HI-FBS) (Gibco #16140071) and 1% penicillin-streptomycin (Gibco #15140122). All cells were grown at 37°C in a humidified atmosphere with 5% CO2. Cells were routinely passaged using 0.25% trypsin-EDTA (Gibco #25200056) and seeded at appropriate densities in tissue culture-treated plates or flasks for experimental purposes. Medium was changed every 2-3 days, and cells were monitored for confluency using EVOS™ M5000 Imaging System (Invitrogen). Cell viability was assessed using Vi-Cell BLU Cell Viability Analyzer (Beckman Coulter).

extract_protocol:
Genomic DNA was extracted from the cell pellets collected with GeneJET Gel Extraction Kit (Thermo Scientific#K0692).
The GUIDE-seq experiment was conducted following an established protocol with minor modifications (PMID: 34773119). In brief, double-stranded dsODN was generated by annealing two modified oligonucleotides as described in a previous study (PMID: 30654827). 40, 000 RPE1 cells stably expressing both Cas9 and Cas12a nucleases were nucleofected with 1 μL of dsODN (100 μM) in 20 μl Solution P3 (Lonza#V4XP-3032) using program EA-114 on a Lonza 4D-Nucleofector Transfection System (Lonza), following the manufacturer’s instructions and then seeded into a 6-well plate. After a 1.5-hour incubation at 37 °C with 5% CO2, cells were transduced with lentivirus carrying specific hgRNA targeting genomic loci. Twenty-four hours later, puromycin (2 μg/mL) was added to select virus-infected cells, which were then cultured for an additional 48 hours before harvesting for gDNA extraction using the GeneJET Gel Extraction Kit (Thermo Scientific#K0692). A starting material of 300 ng gDNA was sheared to an average size of 500 nt using the M220 Focused-ultrasonicator (Covaris#500295) with the following settings: duty factor 20%, peak 50, cycles 200, duration 45 seconds, and temperature 20 oC. The fragmented gDNA were then purified and enriched with SPRIselect (Beckman#B23318) followed by library preparation following the same procedure as previously described (PMID: 34773119), except for using SPRIselect (Beckman#B23318) for purification. The final library was purified using SPRIselect double-sided selection (ratios 0.8-0.61), retaining fragments of 230-660 nt. Library quality and concentration were assessed using the High Sensitivity D1000 ScreenTape (Agilent#5067-5584) with High Sensitivity D1000 Reagents (Agilent#5067-5585) on a 4150 TapeStation System (Agilent#G2992AA). Finally, libraries were pooled, spiked-in with 15% Phix, and sequenced on a NextSeq 1000/2000 platform (Illumina) using NextSeq 1000/2000 P2 Reagents (200 Cycles) v3 (Illumina#20046812).
Customized library preparation and Illumina high-throughput sequencing.

treatment_protocol: None.


title: 4236 NP cells, CITE-seq biol rep 1

description:
12_GEX_4236_CR-NS_1_barcodes.tsv.gz
12_GEX_4236_CR-NS_1_features.tsv.gz
12_GEX_4236_CR-NS_1_matrix.mtx.gz


title: 4236 NP cells, GEX biol rep 1

value: mRNA


title: TAF5 hgRNA


title: BIN1 hgRNA


title: BDF1_in-vitro_08-cell_DEP_01_048-38

description:
BDF1_in-vitro_08cell_log2med.txt.gz
BDF1_in-vitro_08cell_binary.txt.gz


title: BDF1_in-vitro_08-cell_DEP_01_048-44


title: BDF1_in-vitro_08-cell_DEP_01_048-40


title: BDF1_in-vitro_08-cell_DEP_01_048-39


title: 4219 NP cells, scBCRseq biol rep 1

value: BCR


title: Optimization;RPE1;opCas12a_Ultra;T21C

source_name: cell line

value: cell line

tag: cell type

value: retinal pigment epithelial cells

value: lenti virus infected


title: intergenic2 control hgRNA


title: intergenic3 control hgRNA


title: 4219 NP cells, scTCRseq biol rep 1


title: Optimization;RPE1;opCas12a_Ultra;T21B


title: Optimization;RPE1;opCas12a_Ultra;T21A


title: BDF1_in-vitro_08-cell_DEP_01_048-37

value: embryo


title: BDF1_in-vitro_08-cell_DEP_01_048-36

value: in vitro


title: Optimization;RPE1;opCas12a;T21C


title: 4219 NP cells, CITE-seq biol rep 1

description:
9_GEX_4219_CR-NS_1_barcodes.tsv.gz
9_GEX_4219_CR-NS_1_features.tsv.gz
9_GEX_4219_CR-NS_1_matrix.mtx.gz

value: nasopharynx


title: BDF1_in-vitro_08-cell_DEP_01_048-35


title: 4219 NP cells, GEX biol rep 1


title: Optimization;RPE1;opCas12a;T21B


title: intergenic4 control hgRNA


title: Optimization;RPE1;opCas12a;T21A


title: Optimization;RPE1;enCas12a;T21B


title: Optimization;RPE1;enCas12a;T21C


title: BDF1_in-vitro_08-cell_DEP_01_048-34

description:
filtered by MAD score
BDF1_in-vitro_08cell_log2med.txt.gz
BDF1_in-vitro_08cell_binary.txt.gz


title: Optimization;RPE1;enCas12a;T21A


title: Optimization;RPE1;LbCas12a_8NLS;T21C


title: Optimization;RPE1;LbCas12a_8NLS;T21A


title: BDF1_in-vitro_08-cell_DEP_01_048-32


title: BDF1_in-vitro_08-cell_DEP_01_048-33


title: Optimization;RPE1;LbCas12a_2NLS;T21C


title: BDF1_in-vitro_08-cell_DEP_01_048-31


title: BDF1_in-vitro_08-cell_DEP_01_048-30


title: Optimization;RPE1;LbCas12a_2NLS;T21B


title: 3853 NP cells, scTCRseq biol rep 1


title: 3853 NP cells, CITE-seq biol rep 1

description:
8_GEX_3853_CR-NS_1_barcodes.tsv.gz
8_GEX_3853_CR-NS_1_features.tsv.gz
8_GEX_3853_CR-NS_1_matrix.mtx.gz

value: ADT


title: 3853 NP cells, GEX biol rep 1


title: Optimization;RPE1;LbCas12a_2NLS;T21A


title: Optimization;RPE1;opCas12a_Ultra;T0


title: 4258 NP cells, scBCRseq biol rep 1


title: Optimization;RPE1;opCas12a;T0


title: Optimization;RPE1;enCas12a;T0


title: 3853 NP cells, scBCRseq biol rep 1


title: 4258 NP cells, scTCRseq biol rep 1


title: BDF1_in-vitro_08-cell_DEP_01_048-28


title: Optimization;RPE1;LbCas12a_8NLS;T21B


title: Optimization;RPE1;LbCas12a_2NLS;T0


title: 4258 NP cells, CITE-seq biol rep 1

description:
7_GEX_4258_CR-NS_1_barcodes.tsv.gz
7_GEX_4258_CR-NS_1_features.tsv.gz
7_GEX_4258_CR-NS_1_matrix.mtx.gz

value: TotalSeq-C TBNK


title: BDF1_in-vitro_08-cell_DEP_01_048-27


title: Optimization;HAP1;opCas12a_Ultra;T15C

value: chronic myelogenous leukemia (CML) cell line KBM-29

value: wild type


title: Optimization;HAP1;opCas12a_Ultra;T15B

value: chronic myelogenous leukemia (CML) cell line KBM-28


title: 4258 NP cells, GEX biol rep 1


title: Optimization;HAP1;opCas12a;T15C

value: chronic myelogenous leukemia (CML) cell line KBM-26


title: BDF1_in-vitro_08-cell_DEP_01_048-26


title: Optimization;HAP1;opCas12a_Ultra;T15A

value: chronic myelogenous leukemia (CML) cell line KBM-27


title: Optimization;HAP1;opCas12a;T15B

value: chronic myelogenous leukemia (CML) cell line KBM-25


title: 3864 NP cells, scBCRseq biol rep 2


title: BDF1_in-vitro_08-cell_DEP_01_048-25


title: BDF1_in-vitro_08-cell_DEP_01_048-29


title: Optimization;HAP1;opCas12a;T15A

value: chronic myelogenous leukemia (CML) cell line KBM-24


title: Optimization;HAP1;enCas12a;T15C

value: chronic myelogenous leukemia (CML) cell line KBM-23


title: Optimization;RPE1;LbCas12a_8NLS;T0


title: BDF1_in-vitro_08-cell_DEP_01_048-24


title: BDF1_in-vitro_08-cell_DEP_01_048-23


title: Optimization;HAP1;LbCas12a_8NLS;T15C

value: chronic myelogenous leukemia (CML) cell line KBM-20


title: 3864 NP cells, scTCRseq biol rep 2

value: TCR


title: Optimization;HAP1;enCas12a;T15B

value: cell line

value: chronic myelogenous leukemia (CML) cell line KBM-22


title: Optimization;HAP1;enCas12a;T15A

value: chronic myelogenous leukemia (CML) cell line KBM-21

value: lenti virus infected


title: Optimization;HAP1;LbCas12a_8NLS;T15B

value: chronic myelogenous leukemia (CML) cell line KBM-19


title: 3864 NP cells, scBCRseq biol rep 1

value: nasopharynx

value: BCR


title: 3864 NP cells, scTCRseq biol rep 1


title: BDF1_in-vitro_08-cell_DEP_01_048-22

value: embryo

value: in vitro


title: Optimization;HAP1;LbCas12a_8NLS;T15A

value: chronic myelogenous leukemia (CML) cell line KBM-18

value: wild type


title: BDF1_in-vitro_08-cell_DEP_01_048-21


title: Optimization;HAP1;LbCas12a_2NLS;T15C

value: chronic myelogenous leukemia (CML) cell line KBM-17


title: Optimization;HAP1;LbCas12a_2NLS;T15A

value: chronic myelogenous leukemia (CML) cell line KBM-15


title: 3864 NP cells, CITE-seq biol rep 2

description:
7_GEX_3864_CR_NS_2_barcodes.tsv.gz
7_GEX_3864_CR_NS_2_features.tsv.gz
7_GEX_3864_CR_NS_2_matrix.mtx.gz

value: ADT

value: TotalSeq-C TBNK


title: 3864 NP cells, CITE-seq biol rep 1

description:
7_GEX_3864_CR_NS_1_barcodes.tsv.gz
7_GEX_3864_CR_NS_1_features.tsv.gz
7_GEX_3864_CR_NS_1_matrix.mtx.gz


title: Optimization;HAP1;opCas12a_Ultra;T0

value: chronic myelogenous leukemia (CML) cell line KBM-14


title: BDF1_in-vitro_08-cell_DEP_01_048-19


title: Optimization;HAP1;opCas12a;T0

value: chronic myelogenous leukemia (CML) cell line KBM-13


title: BDF1_in-vitro_08-cell_DEP_01_048-20


title: 3864 NP cells, GEX biol rep 1

value: mRNA


title: Optimization;HAP1;LbCas12a_8NLS;T0

value: cell line

value: chronic myelogenous leukemia (CML) cell line KBM-11


title: 3864 NP cells, GEX biol rep 2


title: BDF1_in-vitro_08-cell_DEP_01_048-18


title: Optimization;HAP1;LbCas12a_2NLS;T0

value: chronic myelogenous leukemia (CML) cell line KBM-10

value: lenti virus infected


title: BDF1_in-vitro_08-cell_DEP_01_048-17


title: BDF1_in-vitro_08-cell_DEP_01_048-16


title: Optimization;HAP1;LbCas12a_2NLS;T15B

value: chronic myelogenous leukemia (CML) cell line KBM-16


title: BDF1_in-vitro_08-cell_DEP_01_048-15


title: 4447 NP cells, scBCRseq biol rep 2

value: nasopharynx

value: BCR


title: 4447 NP cells, scTCRseq biol rep 1

value: TCR


title: 4447 NP cells, scTCRseq biol rep 2


title: BDF1_in-vitro_08-cell_DEP_01_048-14

value: embryo

value: in vitro


title: 4447 NP cells, CITE-seq biol rep 2

description:
6_GEX_4447_CR-NS_2_barcodes.tsv.gz
6_GEX_4447_CR-NS_2_features.tsv.gz
6_GEX_4447_CR-NS_2_matrix.mtx.gz


title: SCC0104_pool2_KO_Multiseq

city: Würzburg

first: Alexander

middle: M.

last: Leipold

address: Josef-Schneider-Str. 2

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
KO_raw_feature_bc_matrix.tar.gz
KO_raw_molecule_info.h5

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression, ADT and HTO barcode counts) was performed using the 10x genomics Cell Ranger pipeline where ADT and HTO sequences were concatenated and treated as Custom library with default settings (v3.0.2) and aligning to the mm10 genome build and Ensembl 93 annotations.
Further processing was done with Seurat v3.1.1 (cell and gene filtering, clustering, differential gene expression analysis).
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: MULTI-seq

source_name: Aorta

extract_protocol:
Mice (n=4 per genotype) were killed, perfused with cold PBS and whole aortas were dissected and harvested free of fat and connective tissue. Aortas were longitudinally dissected, and endothelial cells were removed manually using a cotton bud. Then, adventitial layers were manually removed after 10 min incubation in Collagenase Type IV (1mg/ml) and porcine pancreatic elastase (1 U/ml) in DMEM. Medial cell layers were then fully digested for 60 minutes at 37°C in Collagenase Type IV (2.5 mg/mL) collagenase IV and porcine pancreatic elastase (2.5 U/mL) in sterile DMEM. Aortic cell suspensions were labeled with CMO tags (10x Genomics) according to the manufacturer’s instructions (Sm22Cre-Wnk1lox/lox aortas: CMO 4, 5, 6, 7; Sm22Cre+Wnk1lox/lox aortas: CMO 8, 9, 10, 11), washed and counted with viability assessed using Trypan blue (Sm22Cre-Wnk1lox/lox cells: 1000 cells/µl, 61% viability; Sm22Cre+Wnk1lox/lox cells: 837 cells/µl, 87% viability). Cells were loaded in the 10x Genomics Chromium with the aim to capture 10,000 cells per library using volumes according to 10x Genomics recommendations. Libraries were generated with the Chromium Single Cell 3’ Reagents Kit v3 (10x Genomics) according to the manufacturer’s instruction. Libraries were sequenced using Illumina NextSeq2000 with a P3 flow cell.
Single cells were encapsulated into droplets with the Chromium™ Controller (10x Genomics). Transcripts captured in all cells encapsulated with a bead were uniquely barcoded using a combination of a 16 bp 10x Barcode and a 12 bp unique molecular identifier (UMI). cDNA libraries were generated using the Chromium™ Single Cell 3’ Library & Gel Bead Kit v3 (10x Genomics) following the detailed protocol provided by the manufacturer.
MULTI-seq library: amplification was performed at 95°C for 5’ followed by nine cycles at 98°C for 15’’; 60°C for 30’’; 72°C for 30’’ and final elongation 72°C for 1’ with 5’-CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA-3’ Small RNA RPI1 and RPI2 primer as i7 primer (Illumina).
The following 5’- AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3’ SI-PCR primer as i5 primer (Illumina) was used for MULTI-seq library amplification.
Following the final bead purification, both libraries were pooled as 90% mRNA library, 10%  MULTI-seq library before sequencing.

value: Aorta

value: Total viable cells

value: various


title: Optimization;HAP1;enCas12a;T0

value: chronic myelogenous leukemia (CML) cell line KBM-12

value: wild type


title: SCC0104_pool2_KO

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
KO_raw_feature_bc_matrix.tar.gz
KO_raw_molecule_info.h5

molecule: polyA RNA


title: 4447 NP cells, CITE-seq biol rep 1

description:
6_GEX_4447_CR-NS_1_barcodes.tsv.gz
6_GEX_4447_CR-NS_1_features.tsv.gz
6_GEX_4447_CR-NS_1_matrix.mtx.gz

value: ADT

value: TotalSeq-C TBNK


title: BDF1_in-vitro_08-cell_DEP_01_048-12


title: SCC0104_pool1_WT_Multiseq

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
WT_raw_feature_bc_matrix.tar.gz
WT_raw_molcule_info.h5


title: SCC0104_pool1_WT

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
WT_raw_feature_bc_matrix.tar.gz
WT_raw_molcule_info.h5


title: 4447 NP cells, GEX biol rep 2

value: mRNA


title: 4447 NP cells, scBCRseq biol rep 1


title: VEGF/LysM, scRNAseq

city: Zurich

first: Zheng

last: Fan

address: Winterthurerstrasse 190

department: Anatomy Institute

country: Switzerland

institute: University of Zurich

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The 10x Genomics scRNA-seq data was processed using cellranger-7.0.1 with the mouse refdata-gex-mm10-2020-A. Based on filtered gene-cell count matrix by CellRanger’s default cell calling algorithm, we performed the Seurat workflow.
Assembly: mm10
Supplementary files format and content: tsv.gz and mtx.gz

source_name: Adrenal gland

extract_protocol:
Mice were euthanized and adrenal glands from both kidneys were immediately dissected and placed in a Petri dish on ice. Adrenal glands were finely minced with a scalpel until a homogeneous paste-like mash was formed. Thereafter, the mashed tissue was enzymatically digested in digestion buffer containing 10 mg/ml Bacillus Licheniformis protease (P5380, Sigma-Aldrich), 1 mg/ml DNAse I (Roche, 04716728001), 5 mM CaCl2 and 2% BSA in HBSS at 5°C for 10 min, with gentle pipetting every 3 min. The reaction was stopped by immediately adding an equal volume of ice cold HBSS containing 20% FBS and the suspension was passed through a 70-μm cell strainer (#431751, Corning, New York, USA) then 40-μm cell strainer (#431750, Corning, New York, USA) to remove tissue debris. Cell suspension was centrifuged at 500 g for 5 min at 4 ̊C, then the pellet was washed with ice cold HBSS (+20% FBS) followed by a centrifugation at 400 g for 5 min in 4 ̊C. Next, the cell pellet was re-suspended in antibody medium (EGM2 CC-3162, Lonza, Basel, Switzerland) with anti-mouse CD31 PE antibody (1:400) (553373, BD Biosciences, Basel, Switzerland) and anti-mouse CD45 PerCP antibody (1:400) (557235 BD Biosciences, Basel, Switzerland) and placed on ice for 20 min in the dark. Before sorting, the cell suspension was washed in FACS buffer (1xPBS+1%BSA) and centrifuged at 400 g for 5 min, 4 ̊C, then the washed cell pellet was re-suspended in FACS buffer containing cell viability dye, SYTOXTM blue (1:1000) (S34857, Thermo Fischer Scientific, Zurich, Switzerland). Viable endothelial cells (CD31+, CD45-, SYTOXTM blue-) were sorted by a FACS Aria III (BD Bioscience) sorter. For single cell RNA-seq, adrenal gland ECs were directly sorted (130 μm nozzle) into ice cold collecting medium (EGM2). The collected ECs were placed on ice (no more than 30 min) until loading into10x genomics chromium.
Single-cell RNA-seq libraries were obtained following the 10x Genomics recommended protocol, using the reagents included in the Chromium Single Cell 3′v3.1 Reagent Kit Libraries.

value: Adrenal gland

value: endothelial cells

value: VEGF/LysM


title: WT, scRNAseq

description: 10x Genomics

value: wild type (WT)


title: 4447 NP cells, GEX biol rep 1

value: nasopharynx


title: SAMR1 mouse brain after TCQA treatment_rep1

city: Tsukuba

first: Yu Jia

last: Chen

state: Ibaraki

address: 1 Chome-1-1 Tennodai

institute: University of Tsukuba

description: Gene expression data from SAMR1 mice brain cortex after oral administration of TCQA for 1 month

hyb_protocol: The cartridge array hybridization was performed using the Clariom cartridge array (Clariom S array, Mouse; ThermoFisher Scientific).

scan_protocol: Scanning was performed using GeneChip Scanner (ThermoFisher Scientific).

data_processing:
The raw data were normalized following the signal space transformation robust multi-chip analysis (SST-RMA) algorithm. Further, gene-level analysis was performed using the Limma Bioconductor package. For differential expression analysis, a One-Way ANOVA followed by an empirical Bayes correction was performed. The detected above background (DABG) cutoff was set to 0.05. The positive vs negative area under the curve (AUC) value was set at greater than or equal to 0.7.
SST-RMA

label: biotin

label_protocol: Biotinylated cRNA were prepared according to the standard WT PLUS Reagent Kit protocol (ThermoFisher Scientific) from 100 ng/ uL total RNA.

growth_protocol: 7-month-old male SAMR1 mice were housed individually in cages at the Gene research center at the University of Tsukuba for 4 months.

extract_protocol: Total RNA was extracted using ISOGEN (Nippon Gene Co., Ltd, Tokyo, Japan) following the manufacture’s instruction.

treatment_protocol: The 11 month old mice received 5 mg/kg daily oral administration of TCQA for 1 month. MilliQ water was administered for control groups.

value: Brain cortex


title: SAMP8 mouse brain control_rep2

description: Gene expression data from SAMP8 mice brain cortex after oral administration of MilliQ water for 1 month

growth_protocol: 7-month-old male SAMP8 mice were housed individually in cages at the Gene research center at the University of Tsukuba for 4 months.


title: multiplexed mitochondria library: DepSeq-L5

city: Philadelphia

first: Junhyong

last: Kim

state: PA

address: 433 S University Avenue

department: Biology

institute: University of Pennsylvania

data_processing:
Reads from each single sequencing run was first demultiplexed into individual libraries using bcl2fastq (v2.20.0.422). Then for each library, reads from different mitochondria were demultiplexed by the mito-barcode (M1-10, for sequences see mito_annotation.csv.gz, column "barcode seq").  Sequencing adapters and low-quality bases were trimmed from the raw reads, and processed reads were mapped by STAR (v2.7.2d) against the mouse mm10 mito-genome.
The uniquely mapped reads were further demultiplexed into each of the 12 SNV regions. Only reads inside each SNV region were used for base pileup analysis using samtools (v1.13, subcommand `mpileup`). In case of memory exhaustion, for each mitochondrion for each SNV region we downsampled BAM to 500,000 reads if the actual read count exceeded the threshold.
To eliminate sequencing errors, SNVs were called from bases with Phred scores >=30. For statistical confidence, SNV calling was further limited to genomic sites where (1) read depth is ≥ 50, (2) variant allele frequency (VAF) is ≥ 5%. To reduce false positive SNVs caused by STAR misalignment, another alignment tool BWA (0.7.17-r1188) was employed and SNV calling was performed with the same parameters. Only SNV sites that were supported by both STAR and BWA were retained.
Finally, a more stringent SNV list was constructed using SNVs shared by >= 3 different mitos and herein referred to as the "common SNVs".
Assembly: mm10
Supplementary files format and content: inherited_vaf_snv_by_mito.csv, comma-separated table containing variant allele frequency (%) of inherited SNVs (rows) in single-mitochondrion samples including controls (columns).
Supplementary files format and content: somatic_vaf_snv_by_mito.csv, comma-separated table containing variant allele frequency (%) of somatic SNVs (rows) in single-mitochondrion samples including controls (columns).
Supplementary files format and content: mito_annotation.csv, common-separated table, each row containing a mitochondrion or control sample's metadata.

source_name: brain cortex

growth_protocol: Primary neuron cells or astrocytes were plated from mouse (C57BL/6J) pup’s cortex on the coverslips of a 35mm dish. The experiments used neuron or astrocytes at day 3 or day 7.

extract_protocol:
A single neuron or astrocyte was harvested using a micropipette from a coverslip of the Mitotracker labeled neuron cells under the microscope (40x magnification, Olympus IX70), and then was placed in the 1.7 mL Eppendorf Tube with 4 μl of lysis buffer (20 mM Tris, 150 mM NaCl, 1 mM EDTA, 2% CHAPS, PH 8, and freshly added Proteinase inhibitor cocotail). After spinning down briefly, the Eppendorf Tube was incubated on ice for 10 minutes. Then 15 μl of mitochondrial buffer (220 mM sucrose, 68 mM mannitol, 10 mM KCl, 5 mM KH2PO4, 2 mM MgCl2, 0.5 mM EGTA, PH 7.2; 0.01% BSA and 1X Proteinase inhibitors cocktail) was added into the Eppendorf Tube. The isolated mitochondria from single neuron or astrocyte were now ready for the flow cytometry sorting preparation.
Single mitochondria were sorted in each of the wells of a 96-well plate containing 4 uL of lysis buffer (1x TE, 0.1M NaCl, 2mM CaCl2). 1 uL of 0.25 ug/uL Proteinase K was added to each well and incubated at 55 °C for 30 mins. The Proteinase K inactivation was performed by incubation at 95 °C for 10 mins. The plates were rested on ice until the next step. Nuclease free water and 2.5 uL reaction buffer (10X) was added to each well followed by incubation at 70 °C for 3 mins. The plates were immediately rested on ice for at least 2 mins to complete denaturation. After addition of the random primers (40 ng/uL), the plate was incubated at 25 °C for 50 minutes. Bovine serum albumin (0.1 mg/mL), dNTPs (2mM), DTT (10mM) and Phi 29 DNA (5U) polymerase was added to each well. The 25 uL reaction mixture was incubated at 30 °C for 28 hours. Another 5U of Phi 29 DNA polymerase was added to the reaction mixture at 20 hours to continue the reaction. The reaction was stopped after 32 hours by incubation at 65 °C for 10 mins. The RCA product was stored at -20 °C until the next step.
Each single mitochondrion was then amplified with 12 different SNVs using the same Non-Seq Barcode Mx (x=1-10) in front of its genomic forward primer. The amplification reaction on each single mitochondrion was set up as follows in a 25 μl Volume:  1μl of mtDNA amplified by Rolling Circle Amplification (RCA) from single cell, 1μl of 24 oligos pool for 12 SNVs amplification (1.25μM), 23 μl Platinum PCR SuperMix (Invitrogen, 12532-016).  The amplification was performed on a T100 thermal cycler (BioRad) using the following program: 94℃ 2 min for the 1st cycle, followed by 25 cycles of 94℃ 30s, 49℃ 30 s, 68℃ 30 s, and then added another 15 μl Platinum PCR SuperMix for another 20 cycles using the same PCR program as the previous 25 cycles, and finally hold at 4℃. After the amplification, each single mitochondrion was analyzed on the Agilent Type Station 4150 using an Agilent High Sense DNA kit. Then the 10 single mitochondria (M1 through M10) were pooled together and cleaned up by 1.5X AMpure XP beads (A63881, Beckman Coulter). The 50 ng of the pool was input into a library construction using TruSeq Nano DNA kit (Illumina, 20015964) per the manufacturer’s instructions. Libraries were combined into a sequencing pool and then run on Illumina NextSeq 500 with 150bp single-end reads.

treatment_protocol: Neuron cells or astrocytes were labeled with the 100 nM of Mitotracker Deep Red (Invitrogen, M22426) at 37℃ for 20 minutes in an incubator (5% CO2, 37 °C). The cell medium with Mitotracker was exchanged for fresh medium and incubated for another 20 minutes.

value: brain cortex

value: mixed

tag: multiplexing barcodes


title: SAMR1 mouse brain control_rep1

description: Gene expression data from SAMR1 mice brain cortex after oral administration of MilliQ water for 1 month


title: SAMP8 mouse brain after TCQA treatment_rep1

description: Gene expression data from SAMP8 mice brain cortex after oral administration of TCQA  for 1 month


title: SAMP8 mouse brain control_rep1

description: Gene expression data from SAMP8 mice brain cortex after oral administration of MilliQ water  for 1 month


title: SAMR1 mouse brain after TCQA treatment_rep2

source_name: SAMR1 mice brain cortex after oral administration of TCQA


title: BDF1_in-vitro_08-cell_DEP_01_048-10

description:
BDF1_in-vitro_08cell_log2med.txt.gz
BDF1_in-vitro_08cell_binary.txt.gz

value: embryo

value: in vitro


title: multiplexed mitochondria library: DepSeq-L4


title: 4206 NP cells, scBCRseq biol rep 2

value: BCR


title: SAMP8 mouse brain after TCQA treatment_rep2

source_name: SAMP8 mice brain cortex after oral administration of TCQA


title: BDF1_in-vitro_08-cell_DEP_01_048-13

description:
filtered by MAD score
BDF1_in-vitro_08cell_log2med.txt.gz
BDF1_in-vitro_08cell_binary.txt.gz


title: SAMR1 mouse brain control_rep2

source_name: SAMR1 mice brain cortex after oral administration of MilliQ water


title: BDF1_in-vitro_08-cell_DEP_01_048-09


title: BDF1_in-vitro_08-cell_DEP_01_048-11


title: 4206 NP cells, scBCRseq biol rep 1


title: multiplexed mitochondria library: DepSeq-L3

value: Astrocyte


title: BDF1_in-vitro_08-cell_DEP_01_048-08


title: 4206 NP cells, scTCRseq biol rep 2

value: TCR


title: BDF1_in-vitro_08-cell_DEP_01_048-07


title: multiplexed mitochondria library: DepSeq-L1

value: Neuron


title: BDF1_in-vitro_08-cell_DEP_01_048-06


title: multiplexed mitochondria library: L19R61P2


title: 4206 NP cells, CITE-seq biol rep 2

description:
6_GEX_4206_CR_NS_2_barcodes.tsv.gz
6_GEX_4206_CR_NS_2_features.tsv.gz
6_GEX_4206_CR_NS_2_matrix.mtx.gz

value: ADT


title: multiplexed mitochondria library: L18R61P2


title: BDF1_in-vitro_08-cell_DEP_01_048-05


title: multiplexed mitochondria library: L16R61P2


title: BDF1_in-vitro_08-cell_DEP_01_048-03


title: 4206 NP cells, GEX biol rep 2


title: 4206 NP cells, GEX biol rep 1

description:
6_GEX_4206_CR_NS_1_barcodes.tsv.gz
6_GEX_4206_CR_NS_1_features.tsv.gz
6_GEX_4206_CR_NS_1_matrix.mtx.gz


title: multiplexed mitochondria library: DepSeq-L2


title: multiplexed mitochondria library: L15R61P2


title: BDF1_in-vitro_08-cell_DEP_01_048-02


title: 4301 NP cells, scBCRseq biol rep 2


title: 4206 NP cells, scTCRseq biol rep 1


title: BDF1_in-vitro_08-cell_DEP_01_048-01


title: multiplexed mitochondria library: L13R61P2


title: M-07e

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

description: Gene expression data from cultured acute myeloid leukemia cell line.

hyb_protocol: Following fragmentation, 12.5 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix Genechip Scanner 3000.

data_processing: Data were normalized by Robust Multichip Average (RMA) using R 3.3.1, Bioconductor Affy package ver 1.5

label: Biotin

source_name: AMKL_cultured AML cell line

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from 200ng total RNA

extract_protocol: Total RNA was extracted by Qiagen RNEasy kit according to the manufacturer's instructions.

value: Cultured AML cell line

tag: cell subtype

value: AMKL


title: OCI-AML5

source_name: non-AMKL_cultured AML cell line

value: non-AMKL


title: 4301 NP cells, scBCRseq biol rep 1


title: NB-4


title: MOLM-16


title: multiplexed mitochondria library: L12R61P2


title: AML-193


title: Kasumi-3


title: AP-1060


title: BDF1_in-vitro_04-cell_DEP_01_123_80

description:
BDF1_in-vitro_04cell_log2med.txt.gz
BDF1_in-vitro_04cell_binary.txt.gz

source_name: embryo


title: BDF1_in-vitro_08-cell_DEP_01_048-04


title: 4206 NP cells, CITE-seq biol rep 1

value: TotalSeq-C TBNK


title: 4301 NP cells, scTCRseq biol rep 2


title: multiplexed mitochondria library: L17R61P2


title: multiplexed mitochondria library: L11R61P2


title: BDF1_in-vitro_04-cell_DEP_01_123_79


title: BDF1_in-vitro_04-cell_DEP_01_123_78


title: MEG-O1


title: multiplexed mitochondria library: L10R61P12


title: MM6


title: 4301 NP cells, CITE-seq biol rep 2

description:
4_GEX_4301_CR-NS_2_barcodes.tsv.gz
4_GEX_4301_CR-NS_2_features.tsv.gz
4_GEX_4301_CR-NS_2_matrix.mtx.gz


title: SKNO-1


title: 4301 NP cells, CITE-seq biol rep 1

description:
4_GEX_4301_CR-NS_1_barcodes.tsv.gz
4_GEX_4301_CR-NS_1_features.tsv.gz
4_GEX_4301_CR-NS_1_matrix.mtx.gz


title: BDF1_in-vitro_04-cell_DEP_01_123_76


title: 4301 NP cells, GEX biol rep 2

value: mRNA


title: BDF1_in-vitro_04-cell_DEP_01_123_75


title: 4301 NP cells, scTCRseq biol rep 1


title: 4301 NP cells, GEX biol rep 1


title: BDF1_in-vitro_04-cell_DEP_01_123_74


title: 4260 NP cells, scBCRseq biol rep 2


title: CMK-11-5


title: multiplexed mitochondria library: L6R61P1


title: Kasumi-6


title: multiplexed mitochondria library: L7R61P1


title: BDF1_in-vitro_04-cell_DEP_01_123_72


title: multiplexed mitochondria library: L9R61P1


title: multiplexed mitochondria library: L3R61P1


title: 4260 NP cells, scBCRseq biol rep 1


title: 4260 NP cells, scTCRseq biol rep 2


title: HL60


title: BDF1_in-vitro_04-cell_DEP_01_123_71


title: BDF1_in-vitro_04-cell_DEP_01_123_77


title: multiplexed mitochondria library: L8R61P1


title: HEL

value: HEL


title: BDF1_in-vitro_04-cell_DEP_01_123_73


title: multiplexed mitochondria library: L5R61P1


title: KG1a


title: 4260 NP cells, scTCRseq biol rep 1

value: nasopharynx


title: F36-P


title: 4260 NP cells, CITE-seq biol rep 2

description:
3_GEX_4260_CR_NS_2_barcodes.tsv.gz
3_GEX_4260_CR_NS_2_features.tsv.gz
3_GEX_4260_CR_NS_2_matrix.mtx.gz


title: BDF1_in-vitro_04-cell_DEP_01_123_69


title: multiplexed mitochondria library: L1R61P1


title: BDF1_in-vitro_04-cell_DEP_01_123_70


title: multiplexed mitochondria library: L4R61P1


title: 4260 NP cells, CITE-seq biol rep 1

description:
3_GEX_4260_CR_NS_1_barcodes.tsv.gz
3_GEX_4260_CR_NS_1_features.tsv.gz
3_GEX_4260_CR_NS_1_matrix.mtx.gz


title: CMK86


title: BDF1_in-vitro_04-cell_DEP_01_123_68


title: TF-1


title: 4260 NP cells, GEX biol rep 1


title: BDF1_in-vitro_04-cell_DEP_01_123_67


title: 4260 NP cells, GEX biol rep 2


title: HL60/MX2


title: BDF1_in-vitro_04-cell_DEP_01_123_66


title: multiplexed mitochondria library: L6R46P1


title: multiplexed mitochondria library: L7R46P1


title: multiplexed mitochondria library: L5R46P1


title: 4093 NP cells, scBCRseq biol rep 1


title: 4093 NP cells, scBCRseq biol rep 2


title: UT-7


title: multiplexed mitochondria library: L2R61P1


title: multiplexed mitochondria library: L4R46P1


title: NOMO-1


title: BDF1_in-vitro_04-cell_DEP_01_123_65


title: Kasumi-1


title: multiplexed mitochondria library: L3R46P1


title: BDF1_in-vitro_04-cell_DEP_01_123_64


title: BDF1_in-vitro_04-cell_DEP_01_123_63


title: 4093 NP cells, scTCRseq biol rep 2


title: TF-1a


title: multiplexed mitochondria library: L8R46P1


title: MM1


title: MEG-A2


title: 4093 NP cells, scTCRseq biol rep 1


title: multiplexed mitochondria library: L2R46P1


title: multiplexed mitochondria library: L1R46P1


title: 4093 NP cells, CITE-seq biol rep 2

description:
2_GEX_4093_CR_NS_2_barcodes.tsv.gz
2_GEX_4093_CR_NS_2_features.tsv.gz
2_GEX_4093_CR_NS_2_matrix.mtx.gz


title: BDF1_in-vitro_04-cell_DEP_01_123_61


title: BDF1_in-vitro_04-cell_DEP_01_123_62


title: 4093 NP cells, CITE-seq biol rep 1

description:
2_GEX_4093_CR_NS_1_barcodes.tsv.gz
2_GEX_4093_CR_NS_1_features.tsv.gz
2_GEX_4093_CR_NS_1_matrix.mtx.gz


title: multiplexed mitochondria library: L9R48P1


title: BDF1_in-vitro_04-cell_DEP_01_123_60


title: multiplexed mitochondria library: L8R48P1


title: BDF1_in-vitro_04-cell_DEP_01_123_58


title: GDM-1


title: 4093 NP cells, GEX biol rep 1


title: 4093 NP cells, GEX biol rep 2


title: multiplexed mitochondria library: L7R48P1


title: K562


title: BDF1_in-vitro_04-cell_DEP_01_123_59


title: TUR

value: TUR


title: multiplexed mitochondria library: L6R48P1

value: brain cortex


title: MV4;11


title: multiplexed mitochondria library: L5R48P1


title: MOLM14


title: BDF1_in-vitro_04-cell_DEP_01_123_56


title: 4255 NP cells, scBCRseq biol rep 2


title: 4255 NP cells, scBCRseq biol rep 1


title: 4255 NP cells, scTCRseq biol rep 2


title: HL60/MX1


title: KU812


title: BDF1_in-vitro_04-cell_DEP_01_123_55


title: multiplexed mitochondria library: L3R48P1

value: mixed


title: BDF1_in-vitro_04-cell_DEP_01_123_54

value: embryo


title: 4255 NP cells, scTCRseq biol rep 1


title: 4255 NP cells, CITE-seq biol rep 2

description:
1_GEX_4255_CR_NS_2_barcodes.tsv.gz
1_GEX_4255_CR_NS_2_features.tsv.gz
1_GEX_4255_CR_NS_2_matrix.mtx.gz


title: THP-1


title: 4255 NP cells, CITE-seq biol rep 1

description:
1_GEX_4255_CR_NS_1_barcodes.tsv.gz
1_GEX_4255_CR_NS_1_features.tsv.gz
1_GEX_4255_CR_NS_1_matrix.mtx.gz


title: multiplexed mitochondria library: L2R48P1


title: multiplexed mitochondria library: L1R48P1


title: BDF1_in-vitro_04-cell_DEP_01_123_57

value: in vitro


title: BDF1_in-vitro_04-cell_DEP_01_123_52


title: multiplexed mitochondria library: L4R48P1


title: KG-1


title: 4255 NP cells, GEX biol rep 2


title: BDF1_in-vitro_04-cell_DEP_01_123_51


title: 4255 NP cells, GEX biol rep 1


title: MG-S

value: MG-S


title: multiplexed mitochondria library: L8R53P1_b


title: U937


title: 4041 NP cells, scBCRseq biol rep 2

value: BCR


title: BDF1_in-vitro_04-cell_DEP_01_123_50


title: BDF1_in-vitro_04-cell_DEP_01_123_49


title: HNT-34


title: multiplexed mitochondria library: L6R53P1_b


title: 4041 NP cells, scBCRseq biol rep 1


title: EOL-1


title: BDF1_in-vitro_04-cell_DEP_01_123_48


title: 4041 NP cells, scTCRseq biol rep 2

value: TCR


title: multiplexed mitochondria library: L5R53P1_b

value: Neuron


title: BDF1_in-vitro_04-cell_DEP_01_123_53


title: BDF1_in-vitro_04-cell_DEP_01_123_47


title: multiplexed mitochondria library: L4R53P1_b


title: 4041 NP cells, CITE-seq biol rep 2

description:
1_GEX_4041_CR-NS_2_barcodes.tsv.gz
1_GEX_4041_CR-NS_2_features.tsv.gz
1_GEX_4041_CR-NS_2_matrix.mtx.gz

value: ADT


title: BDF1_in-vitro_04-cell_DEP_01_123_46


title: SIG-M5

value: Cultured AML cell line


title: multiplexed mitochondria library: L3R53P1_b

value: Astrocyte


title: BDF1_in-vitro_04-cell_DEP_01_123_45


title: MOLM-13

value: non-AMKL


title: multiplexed mitochondria library: L7R53P1_b


title: PLB-985


title: 4041 NP cells, CITE-seq biol rep 1

description:
1_GEX_4041_CR-NS_1_barcodes.tsv.gz
1_GEX_4041_CR-NS_1_features.tsv.gz
1_GEX_4041_CR-NS_1_matrix.mtx.gz

value: TotalSeq-C TBNK


title: multiplexed mitochondria library: L2R53P1_b


title: SKM-1


title: BDF1_in-vitro_04-cell_DEP_01_123_44


title: 4041 NP cells, GEX biol rep 2

value: mRNA


title: OCI-M2


title: multiplexed mitochondria library: L1R53P1_b


title: BDF1_in-vitro_04-cell_DEP_01_123_43


title: 4041 NP cells, GEX biol rep 1


title: multiplexed mitochondria library: L19R53P1_2_b


title: OCI-M1


title: multiplexed mitochondria library: L9R53P1_b


title: multiplexed mitochondria library: L18R53P2_b


title: Untreated, old processing, rep 8

city: Utrecht

first: Niels

last: Aerts

state: Utrecht

address: Padualaan 8

country: Netherlands

institute: Utrecht University

data_processing:
Reads were aligned to the Arabidopsis genome (TAIR v10) using TOPHAT v2.0.4 with the settings ‘transcriptome-mismatches 3’, ‘N 3’, ‘bowtie1’, ‘no-novel-juncs’, ‘genome-read-mismatches 3’, ‘p 6’, ‘read-mismatches 3’, ‘G’, ‘min-intron-length 40’, ‘max-intron-length 2000’. Reads were assigned to annotated gene models of TAIR v10 using HTSeq-count v0.6.1 with default settings except ‘-s no’. Normalization was done using the medium count ratio, following the principle applied in the DESeq2 R package.
Assembly: TAIR v10
Supplementary files format and content: Rows: genes, columns: samples

organism: Arabidopsis thaliana

source_name: Leaf 6 of rosette

extract_protocol:
Rneasy plant mini kit (Qiagen) according to the manufacturer's instructions. Included on-column DNAse step.
TruSeq mRNA Sample Prep Kit (Illumina), according to the manufacturer's instructions.

value: Leaf 6 of rosette

value: Untreated

tag: timepoint


title: 4041 NP cells, scTCRseq biol rep 1

value: nasopharynx

tag: library type


title: multiplexed mitochondria library: L17R53P2_b

value: brain cortex


title: BDF1_in-vitro_04-cell_DEP_01_123_42


title: Donor2_PMA/Ionomycin_Rep1_Bulk RNAseq

city: Foster City

first: Ruidong

last: Li

address: 324 Lakeside Drive

department: Research Data Sciences

institute: Gilead Sciences, Inc.

data_processing:
A custom Nextflow workflow was used to perform quality control (QC) and primary analysis of RNAseq data. FastQC (v0.11.8) was first adopted to assess the quality of sequencing data. Reads were then mapped to human reference genome GRCh38 using STAR (v2.7.6a) and gene expression count matrix was generated using featureCounts (Subread v2.0.1).
We also performed an additional QC analysis using RNASeQC2 (v2.4.2) to ensure high data quality and generated a MultiQC report by using MultiQC (v1.10.1) software.
Assembly: GRCh38
Supplementary files format and content: tab-delimited TXT file includes raw counts for all the samples

source_name: PBMC

extract_protocol:
PBMCs from healthy donors were isolated by SepMateTM tubes (STEMCELL Technologies, Catalog#85450), following manufacturer’s instruction, and resuspended in RPMI 1640 medium (Gibco, Catalog#11875093) containing 5% human serum (Sigma, Catalog# H3667-100ML) and 1% penicillin-streptomycin and cultured in 6-well plates (3 mL/well). After overnight culture, the PBMC was resuspended and cultured at 5 × 106 cells/ml in 48-well plate and treated immediately with DMSO or phorbol-12-myristate-13-acetate (PMA) plus ionomycin (PMA/Ionomycin) cocktail (Cell stimulation cocktail, eBioscience, Catalog#00-4970) for 3 h. Then, PBMC was stained with APC mouse anti-human CD4 (SK3, BD Biosciences, Catalog#340443) and Alexa Fluor 488 mouse anti-human CD3 (UCHT1, BioLegend, Catalog#300454) before sorting. The dead cells were gated out after staining with viability dye eFluor 780 (Invitrogen, Catalog#65-0865-14). The CD4+ T-cells were sorted into 15-ml centrifuge tubes with collection buffer (PBS with 1% BSA). Qiagen RNeasy Mini Kit was used for RNA extraction.
RNA-seq libraries were generated using the TruSeq Stranded mRNA Kit

value: PBMC

value: CD4+ T cells

tag: donor id

value: Donor 2

value: Replicate 1

tag: disease

value: Healthy

value: PMA/Ionomycin


title: BDF1_in-vitro_04-cell_DEP_01_123_41

value: embryo

value: in vitro


title: Untreated, old processing, rep 7

tag: genotype


title: BDF1_in-vitro_04-cell_DEP_01_123_40


title: Donor2_DMSO_Rep2_Bulk RNAseq

value: Replicate 2

value: DMSO


title: BDF1_in-vitro_04-cell_DEP_01_123_39


title: Donor2_DMSO_Rep1_Bulk RNAseq


title: multiplexed mitochondria library: L16R53P2_b

value: mixed


title: OCI-AML3

tag: cell line

value: Cultured AML cell line

value: non-AMKL


title: OCI-AML2


title: BDF1_in-vitro_04-cell_DEP_01_123_38


title: Donor1_PMA/Ionomycin_Rep2_Bulk RNAseq

value: Donor 1


title: multiplexed mitochondria library: L15R53P2_b

value: Astrocyte


title: Untreated, old processing, rep 5

value: Leaf 6 of rosette

value: Untreated


title: BDF1_in-vitro_04-cell_DEP_01_123_37


title: CMK

value: CMK

value: AMKL


title: multiplexed mitochondria library: L14R53P2_b

value: brain cortex


title: Donor2_PMA/Ionomycin_Rep2_Bulk RNAseq

value: PBMC

value: CD4+ T cells

value: Donor 2


title: multiplexed mitochondria library: L13R53P2_b

value: Neuron


title: BDF1_in-vitro_04-cell_DEP_01_123_36

value: embryo

value: in vitro


title: Untreated, old processing, rep 6


title: Untreated, old processing, rep 3


title: Donor1_PMA/Ionomycin_Rep1_Bulk RNAseq

value: Replicate 1

value: Healthy

value: PMA/Ionomycin


title: ML-2

value: Cultured AML cell line

value: non-AMKL


title: Donor1_DMSO_Rep2_Bulk RNAseq

value: Donor 1

value: Replicate 2

value: DMSO


title: multiplexed mitochondria library: L12R53P2_b


title: BDF1_in-vitro_04-cell_DEP_01_123_35


title: Donor1_DMSO_Rep1_Bulk RNAseq


title: Untreated, old processing, rep 2

value: Leaf 6 of rosette

value: Untreated


title: Untreated, old processing, rep 1


title: BDF1_in-vitro_04-cell_DEP_01_123_34


title: multiplexed mitochondria library: L11R53P2_b

value: brain cortex

value: mixed


title: BDF1_in-vitro_04-cell_DEP_01_123_33


title: multiplexed mitochondria library: L10R53P2_b

value: Astrocyte


title: WGBS_Human_PrimedESCs_Rep2

city: Beijing

first: Fan

last: Guo

state: Beijing

address: 1 Beichen West Road, Chaoyang District

department: The State Key Laboratory of Stem Cell and Reproductive Biology

country: China

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
Raw 150 bp paired-end reads were trimmed using TrimGalore (v0.6.6) with the following parameters: --quality 20 --stringency 3 --length 50 --clip_R1 9 --clip_R2 9 --paired --trim1 --phred33. Adapters and low-quality reads were filtered out. The remaining reads were aligned to the reference genome (UCSC version hg19) using Bismark (v0.23.1). The alignment process was carried out in paired-end mode initially, followed by two independent rounds of alignment in single-end mode for unmapped Read1 and Read2. The deduplication of the resulting reads was performed using sambamba markup (v0.8.2), and the function filter_non_conversion in Bismark was utilized to filter out reads with three consecutive nonconversion sites. The remaining reads were then subjected to downstream analysis. MethylDackel (v0.5.0) was used to extract and count cytosines in the CpG sequence context.
Assembly: hg19
Supplementary files format and content: bedGraph, CpGs methylation levels. Column 4 for unmethylated C (T), Column 5 for methylated C (C), Column 6 for CpG methylation level, which is defined as C/(C + T).

source_name: Human embryonic stem cells

extract_protocol:
Genomic DNA (gDNA) was extracted from hESCs by using DNeasy Blood & Tissue Kits (Qiagen, Cat# 69504) according to the manufacturer’s protocol.
200 ng of purified gDNA of hESC was subjected to bisulfite conversion and purification by using the EZ-96 DNA Methylation-Direct MagPrep kit (Zymo Research, Cat# D5045) according to the manufacturer’s protocol. Then, WGBS libraries were constructed via our recently published TAILS method. In brief, P5-N6-oligo1 (5’-CTACACGACG-CTCTTCCGATCTN6-3’) was used for the first round of random priming in the presence of the Klenow exo(-) fragment. The remaining oligos and dNTPs were removed by Exo-SAP IT Express, and the dC tailing step was performed with the TdT enzyme. Then, a second round of priming was conducted by using P7-G6-oligo2 (5’-AGACGTGTGCTCTTCCGATCTG6HN-3’) in the presence of the Klenow exo(-) fragment. After one round of purification with AMPure XP beads, libraries were constructed by PCR amplification. Next, the libraries were purified, and the size distribution was checked on the fragment analyzer. Finally, the WGBS libraries were sequenced on a NovaSeq 6000 sequencer with a 150 bp paired-end sequencing strategy.

value: Human embryonic stem cells


title: Mock, 16 h, rep 4

value: Mock

value: 16 h after treatment


title: Untreated, old processing, rep 4


title: BDF1_in-vitro_04-cell_DEP_01_123_32

value: embryo

value: in vitro


title: Mock, 16 h, rep 3


title: multiplexed mitochondria library: L23R45P3


title: BDF1_in-vitro_04-cell_DEP_01_123_31


title: multiplexed mitochondria library: L22R45P3

value: Neuron


title: CUTTag_hESC_OE_OTX2_Rep2

data_processing:
Adaptors were trimmed from raw sequences using Trim Galore (v0.6.6). The trimmed reads were aligned to the human reference genome (hg19) using bowtie2 with parameters: --local --verysensitive --no-mixed --no-discordant --phred33 -I 10 -X 700. PCR duplicates were identified and removed using sambamba (v0.8.2). Unmapped reads were further excluded using samtools (v1.17). Read pairs that were on the same chromosome and fragment length less than 1000 bp were used for the downstream analysis. Peak calling was performed using SEACR (v1.3). The enriched regions in OTX2-overexpressed hESC were called using the wildtype hESC as control track.
Assembly: hg19
Supplementary files format and content: bigWig, OTX2 binding signals; bed, SEACR called peaks
Library strategy: CUT&Tag

extract_protocol:
Human ES cells were cultured in Essential-8 medium (Thermo Fisher, Cat# A1517001) containing Matrigel (Corning, Cat# 354277). Cells were dissociated using Versene Solution (Gibco, Cat# 15040066)
Hyperactive Universal CUT&Tag Assay Kit (Vazyme, Cat# TD904) was used to construct the CUT&Tag libraries of OTX2-overexpressed hESCs according to the manufacturer’s protocol. hESCs that were not transfected with OTX2-overexpression plasmid were used as the negative control. Briefly, 100,000 EGFP-positive OTX2-overexpressed hESCs or control hESCs were washed and resuspended in 100 μL wash buffer before 10 µL of activated Concanavalin A coated magnetic beads were added to each sample and incubated at room temperature (RT) for 10 mins. After that, cells were incubated with 4 µg of anti-flag antibody (Sigma, Cat# F7425) on a rotating platform for 2 hrs at RT. Then, Anti-rabbit IgG antibody (Abcam, Cat# ab6702) was added and incubated at RT for 60 mins. Next, cells were washed three times with Dig-Wash buffer to remove unbound antibodies. After that, pA/G-Tnp incubation was performed on a rotating platform for 1 hr at RT. Similarly, cells were washed three times with Dig-300 buffer to remove unbound pA/G-Tnp protein and resuspended in tagmentation buffer and incubated at 37ºC for 1 hr. Tagmentation was stopped by adding of 10% SDS and incubating at 55 ºC for 10 mins. Then cells were plated on a magnet rack, supernatant was transferred into a new PCR tube and DNA was extracted by using DNA Extract Beads Pro. Finally, libraries were constructed using TruePrep Index Kit V2 for Illumina (Vazyme, Cat# TD202). All CUT&Tag libraries were sequenced using the Illumina NovaSeq 6000 platform with PE150 sequencing strategy.

tag: chip antibody

value: anti-flag antibody (Sigma, Cat# F7425)

value: OE OTX2


title: multiplexed mitochondria library: L21R45P3


title: Mock, 16 h, rep 2


title: CUTTag_hESC_OE_OTX2_Rep1


title: Mock, 16 h, rep 1


title: BDF1_in-vitro_04-cell_DEP_01_123_30

data_processing:
Two-step adapter trimming was performed to first remove the Illumina adapter and the SEQXE adapter.
Trimmed fastq files were aligned to mm9 or a constructed B6/MSM specific diploid genome (Takahashi et al., 2019) for non-haplotype or haplotype-resolved analysis, respectively.
Genome coordinates of allele-specific uniquely mapped reads (MAPQ >16) were converted to mm9 by liftOver tool (UCSC Genome Browser). Duplicated reads were filtered out.
For quality control of scRepli-seq data, we applied median-absolute-deviation (MAD) score evaluation to filter out cells with problematic RT (MAD scores = 0 or >1.0).
For generating log2[(mappability-corrected S-phase reads)/median] scores (log2median RT score) to obtain single-cell RT profiles using cells that passed MAD score evaluation, we counted the reads in sliding windows of 1-Mb at 200-kb intervals, 200-kb at 40-kb intervals, or 1-Mb at 200-kb intervals (haplotype-resolved analysis for B6MSM)  after normalizing S-phase data with AneuFinder’s correctMappability command based on G1 control without karyotype defects in each strain. (Miura et al., 2020).
The binarization for each 80-kb (non-haplotype) or 400-kb (haplotype-resolved analysis for B6MSM) was performing find CNVs command in AneuFinder (Miura et al., 2020). For 4-cell, we applied 1-somy mode for early S-phase, and 2-somy mode for mid/late S-phase. Other stages including 1-, 2-cell, we applied 2-somy mode for binarization. Repliscore as a percentage of replicated bins in the total number of replicated and unreplicated bins was calculated from binarized scRepli-seq data without X chromosome (Miura et al., 2020).
Assembly: mm9
Supplementary files format and content: log2median RT score (log2med.txt)
Supplementary files format and content: Binary data (binary.txt)
Library strategy: Single-cell Repli-seq


title: BDF1_in-vitro_04-cell_DEP_01_123_29


title: multiplexed mitochondria library: L20R45P3


title: CUTTag_hESC_control_input

value: WT


title: Mock, 12 h, rep 4

value: 12 h after treatment


title: ACE_Human_PrimedESCs

data_processing:
Raw 150 bp paired-end reads were trimmed using TrimGalore (v0.6.6) with the following parameters: --quality 20 --stringency 3 --length 50 --clip_R1 9 --clip_R2 9 --paired --trim1 --phred33. Adapters and low-quality reads were filtered out. The remaining reads were aligned to the reference genome (UCSC version hg19) using Bismark (v0.23.1). The alignment process was carried out in paired-end mode initially, followed by two independent rounds of alignment in single-end mode for unmapped Read1 and Read2. The deduplication of the resulting reads was performed using sambamba markup (v0.8.2), and the function filter_non_conversion in Bismark was utilized to filter out reads with three consecutive nonconversion sites. The remaining reads were then subjected to downstream analysis. MethylDackel (v0.5.0) was used to extract and count cytosines in the CpG sequence context.
Assembly: hg19
Supplementary files format and content: bedGraph, 5hmC levels on CpGs. Column 4 for unmethylated C (T), Column 5 for methylated C (C), Column 6 for CpG 5hmC level, which is defined as C/(C + T).
Library strategy: ACE-seq

extract_protocol:
Genomic DNA (gDNA) was extracted from human embryonic stem cells by using DNeasy Blood & Tissue Kits (Qiagen, Cat# 69504) according to the manufacturer’s protocol.
200 ng of gDNA was then subjected to the optimized ACE-seq protocol. The genomic DNA was first fragmented and then subjected to the ACE-seq library construction protocol with modifications. Briefly, fragmented gDNA was glycosylated by using UDP-glucose and T4 Phage β-glucosyltransferase (New England Biolabs, Cat# M0357) at 37°C for 1 hr. Afterwards, 0.1 M NaOH was added for denaturation at 55°C for 10 mins. The APOBEC enzyme (New England Biolabs, Cat# E7125) was used to deaminate gDNA at 37°C for 3 hrs. After deamination, gDNA was purified once using AMPure XP beads (Beckman coulter, Cat# A63882) before library construction following to the TAILS procedure. Fragment Analyzer (Agilent 5200) was used to check the size distribution of the final libraries. Finally, the ACE-seq libraries were sequenced on a NovaSeq 6000 sequencer by a 150 bp paired-end sequencing strategy. Additionally, in vitro CpG-methylated lambda DNA (Thermo Fisher Scientific, Cat# SD0021) was used as a spike-in to estimate the deamination rate in the 5mCpG context and unmodified CH context (H=A, C, T). In addition, we incorporated fully hydroxymethylated DNA to assess the protection rate of 5hmC by glycosylation in individual samples.