title: BDF1_in-vitro_04-cell_DEP_01_123_28

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


title: Mock, 12 h, rep 3

status: Public on Jun 24 2024

type: SRA

city: Utrecht

first: Niels

last: Aerts

state: Utrecht

address: Padualaan 8

department: Biology

country: Netherlands

institute: Utrecht University

library_source: transcriptomic

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

molecule: total RNA

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.

tag: tissue

value: Leaf 6 of rosette

tag: genotype

tag: treatment

value: Mock

tag: timepoint

value: 12 h after treatment


title: BDF1_in-vitro_04-cell_DEP_01_123_27

city: Kobe

first: Hirohisa

last: Kyogoku

state: Hyogo

address: 1-1, Rokkodai-chou

department: Agricultural Science

country: Japan

institute: Kobe university

description:
BDF1_in-vitro_04cell_log2med.txt.gz
BDF1_in-vitro_04cell_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.

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

value: embryo

tag: developmental stage

tag: developmental condition

value: in vitro


title: multiplexed mitochondria library: L18R45P2

city: Philadelphia

first: Junhyong

last: Kim

state: PA

address: 433 S University Avenue

country: USA

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

tag: cell type

value: mixed

tag: multiplexing barcodes


title: RNA_hESC_OE OTX2_Rep3

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 reads were retrieved from published datasets. Alignment was performed using STAR (v2.7.10b). The UCSC version hg19 and mm9 genome sequences were used for Homo sapiens and Mus musculus, respectively. Raw counts for gene expression were quantified using featureCounts (v2.0.4). Annotations were retrieved from UCSC genome browsers and TEtranscripts.
Assembly: hg19
Supplementary files format and content: csv, expression counts

molecule: polyA RNA

organism: Homo sapiens

source_name: Human embryonic stem cells

extract_protocol:
Nearly 100 EGFP-positive hESCs were collected as one biological replicate for RNA-seq library construction.
Cells were picked and transferred to lysis buffer, and poly(A)+ RNA was captured by oligo(dT) primers. First-strand cDNA was synthesized by reverse transcription and then amplified, purified and fragmented. Fragmented cDNA was processed to construct an RNA-seq library by using the NEBNext UltraII DNA Library Prep Kit (New England Biolabs, Cat# E7645L) according to the manufacturer’s protocol for sequencing on an Illumina NovaSeq 6000 sequencer with a 150 bp paired-end sequencing strategy.

tag: cell line

value: Human embryonic stem cells

value: OE OTX2


title: multiplexed mitochondria library: L17R45P2


title: WGBS_Human_PrimedESCs_Rep1

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).

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.


title: BDF1_in-vitro_04-cell_DEP_01_123_26


title: Mock, 12 h, rep 1


title: RNA_hESC_OE OTX2_Rep1


title: multiplexed mitochondria library: L16R45P2

value: Astrocyte


title: BDF1_in-vitro_04-cell_DEP_01_123_25


title: Mock, 10 h, rep 4

value: 10 h after treatment


title: RNA_hESC_control_Rep2

value: WT


title: Mock, 10 h, rep 3


title: BDF1_in-vitro_04-cell_DEP_01_123_24


title: RNA_hESC_control_Rep1


title: BDF1_in-vitro_04-cell_DEP_01_123_23


title: Mock, 10 h, rep 2


title: multiplexed mitochondria library: L13R45P2


title: BDF1_in-vitro_04-cell_DEP_01_123_22


title: multiplexed mitochondria library: L19R45P3

value: Neuron


title: multiplexed mitochondria library: L12R45P2


title: BDF1_in-vitro_04-cell_DEP_01_123_21


title: Mock, 8 h, rep 4

value: 8 h after treatment


title: RNA_hESC_OE OTX2_Rep2


title: multiplexed mitochondria library: L11R45P2


title: Mock, 12 h, rep 2


title: BDF1_in-vitro_04-cell_DEP_01_123_20


title: Mock, 8 h, rep 3


title: multiplexed mitochondria library: L10R45P2


title: multiplexed mitochondria library: L9R45P1


title: multiplexed mitochondria library: L15R45P2


title: BDF1_in-vitro_04-cell_DEP_01_123_18


title: Mock, 8 h, rep 2


title: multiplexed mitochondria library: L8R45P1


title: Mock, 8 h, rep 1


title: Mock, 7 h, rep 4

value: 7 h after treatment


title: BDF1_in-vitro_04-cell_DEP_01_123_16


title: Mock, 7 h, rep 3


title: BDF1_in-vitro_04-cell_DEP_01_123_17


title: multiplexed mitochondria library: L14R45P2


title: BDF1_in-vitro_04-cell_DEP_01_123_15


title: Mock, 10 h, rep 1


title: multiplexed mitochondria library: L6R45P1


title: Mock, 7 h, rep 2


title: BDF1_in-vitro_04-cell_DEP_01_123_14


title: multiplexed mitochondria library: L5R45P1


title: Mock, 7 h, rep 1


title: BDF1_in-vitro_04-cell_DEP_01_123_13


title: multiplexed mitochondria library: L4R45P1


title: multiplexed mitochondria library: L3R45P1


title: BDF1_in-vitro_04-cell_DEP_01_123_12


title: BDF1_in-vitro_04-cell_DEP_01_123_19


title: Mock, 6 h, rep 3

value: 6 h after treatment


title: multiplexed mitochondria library: L2R45P1


title: BDF1_in-vitro_04-cell_DEP_01_123_11


title: BDF1_in-vitro_04-cell_DEP_01_123_10


title: Mock, 6 h, rep 1


title: multiplexed mitochondria library: L1R45P1


title: multiplexed mitochondria library: L7R45P1


title: Mock, 5 h, rep 4

value: 5 h after treatment


title: multiplexed mitochondria library: L15R30P2B


title: BDF1_in-vitro_04-cell_DEP_01_123_08


title: BDF1_in-vitro_04-cell_DEP_01_123_09


title: multiplexed mitochondria library: L14R30P2B


title: Mock, 5 h, rep 2

value: Leaf 6 of rosette


title: multiplexed mitochondria library: L13R30P2B


title: BDF1_in-vitro_04-cell_DEP_01_123_07


title: Mock, 5 h, rep 3

value: Mock


title: Mock, 5 h, rep 1


title: Mock, 6 h, rep 4


title: multiplexed mitochondria library: L10R30P2B


title: BDF1_in-vitro_04-cell_DEP_01_123_06


title: Mock, 4 h, rep 4

value: 4 h after treatment


title: Mock, 4 h, rep 2


title: Mock, 4 h, rep 3


title: BDF1_in-vitro_04-cell_DEP_01_123_05

value: embryo


title: multiplexed mitochondria library: L12R30P2B


title: multiplexed mitochondria library: L11R30P2B


title: multiplexed mitochondria library: L9R30P2B


title: BDF1_in-vitro_04-cell_DEP_01_123_03

value: in vitro


title: Mock, 4 h, rep 1


title: multiplexed mitochondria library: L16R30P2B

value: brain cortex


title: BDF1_in-vitro_04-cell_DEP_01_123_02


title: Mock, 3 h, rep 4

value: 3 h after treatment


title: multiplexed mitochondria library: L6R30P1B


title: BDF1_in-vitro_04-cell_DEP_01_123_01


title: multiplexed mitochondria library: L5R30P1B


title: BDF1_in-vitro_04-cell_DEP_01_122_79


title: multiplexed mitochondria library: L4R30P1B


title: BDF1_in-vitro_04-cell_DEP_01_122_78


title: Mock, 3 h, rep 1


title: SK-N-BE(2), FOSL2, ChIP, rep2

city: Suzhou

first: Zimu

last: Zhang

state: Jiangsu

address: Zhongnan Street

institute: Children’s Hospital of Soochow University

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output. CUT&Tag reads were trimmed using Fastp v0.23.2 with default settings, and were aligned to the UCSC hg38 genome using Bowtie2 version v2.4.4 with parameter --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700.
Peaks were identified using MACS3 (v3.0.0a6) with the significance cut-off FDR<0.01
bigWig files were generated using bedGraphToBigWig tool. narrowPeak files were generated using MACS v3 with default settings.
Assembly: hg38
Supplementary files format and content: bigwig files
Library strategy: CUT&Tag

extract_protocol:
CUT&Tag was performed with Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme) according to the manufacturer’s protocol.
Library construction was performed using TruePrep® DNA Library Prep Kit V2 for Illumina (Vazyme) and TruePrep® Index Kit V2 for Illumina (Vazyme).

value: neuroblastoma

tag: chip antibody

value: FOSL2(Abclonal, #A2729)


title: BDF1_in-vitro_04-cell_DEP_01_122_77


title: SK-N-BE(2), FOSL2, ChIP, rep1


title: BDF1_in-vitro_04-cell_DEP_01_123_04


title: Mock, 2 h, rep 3

value: 2 h after treatment


title: multiplexed mitochondria library: L3R30P1B

value: Astrocyte


title: multiplexed mitochondria library: L8R30P1B


title: BDF1_in-vitro_04-cell_DEP_01_122_76


title: SK-N-BE(2), c-Jun, ChIP, rep2


title: BDF1_in-vitro_04-cell_DEP_01_122_75


title: SK-N-BE(2), c-Jun, ChIP, rep1


title: Mock, 2 h, rep 2


title: multiplexed mitochondria library: L7R30P1B


title: BDF1_in-vitro_04-cell_DEP_01_122_73


title: Mock, 1.5 h, rep 4

value: 1.5 h after treatment


title: multiplexed mitochondria library: L1R30P1B


title: multiplexed mitochondria library: L2R30P1B


title: Mock, 3 h, rep 3


title: SK-N-BE(2), SOX11, ChIP

value: SOX11(Sigma, #ABN105)


title: Mock, 2 h, rep 1


title: Mock, 3 h, rep 2


title: SK-N-BE(2), MYCN, ChIP, rep2


title: BDF1_in-vitro_04-cell_DEP_01_122_72


title: Mock, 2 h, rep 4


title: multiplexed mitochondria library: L1R29P1B


title: BDF1_in-vitro_04-cell_DEP_01_122_71


title: multiplexed mitochondria library: CTRR29P1B


title: Mock, 1.5 h, rep 3


title: Mock, 1.5 h, rep 2


title: SK-N-BE(2), IRF2BP2, ChIP, rep2

value: IRF2BP2(Sigma, #HPA027815)


title: BDF1_in-vitro_04-cell_DEP_01_122_70


title: multiplexed mitochondria library: L25R29P3B


title: Mock, 1.5 h, rep 1


title: BDF1_in-vitro_04-cell_DEP_01_122_74


title: multiplexed mitochondria library: L24R29P3B


title: Mock, 1 h, rep 4

value: 1 h after treatment


title: BDF1_in-vitro_04-cell_DEP_01_122_67


title: multiplexed mitochondria library: L21R29P3B


title: BDF1_in-vitro_04-cell_DEP_01_122_68


title: SK-N-BE(2), sh-IRF2BP2, ATAC, rep2

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output. ATAC-seq reads were trimmed using Fastp v0.23.2 with default settings, and were aligned to the UCSC hg38 genome using Bowtie2 version v2.4.4 with parameter --very-sensitive -X 2000.
Peaks were identified using MACS3 (v3.0.0a6) with the significance cut-off FDR<0.01
bigWig files were generated using bedGraphToBigWig tool. narrowPeak files were generated using MACS v3 with default settings.
Assembly: hg38
Supplementary files format and content: bigwig files

extract_protocol:
ATAC-seq was performed with Hyperactive ATAC-Seq Library Prep Kit for Illumina (Vazyme, China) according to the manufacturer’s protocol.
Library construction was performed using TruePrep® DNA Library Prep Kit V2 for Illumina (Vazyme) and TruePrep® Index Kit V2 for Illumina (Vazyme).


title: Mock, 1 h, rep 3


title: SK-N-BE(2), sh-NC, ATAC, rep1

value: sh-NC


title: Mock, 1 h, rep 2


title: multiplexed mitochondria library: L22R29P3B


title: Mock, 1 h, rep 1


title: SK-N-BE(2), MYCN, ChIP, rep1


title: BDF1_in-vitro_04-cell_DEP_01_122_65


title: BDF1_in-vitro_04-cell_DEP_01_122_66


title: SK-N-BE(2), sh-IRF2BP2, ATAC, rep1


title: multiplexed mitochondria library: L18R29P2B


title: multiplexed mitochondria library: L17R29P2B


title: ChIP_RNAPolII_siTAF5+TAF5-∆E8_Replicate2

city: Frederick

first: Thomas

last: Gonatopoulos-Pournatzis

state: MD

address: Building 560

institute: National Cancer Institute

data_processing:
Demultiplexing was performed using Bcl2fastq 2.20
Adatpter and quality trimming was performed by Cutadapt 1.18 to select bases with quality score  ≥ 30
Processed ChIP-seq reads were mapped to the human genome hg38 using the Software Bowtie2 (version 2.3.4.1)
bigWig files were generated for samples TBP, RNAPol II and IgG normalized to the Input samples. For this Deeptools (version 3.5.2) bamCompare was used with the options "--binSize 50 --smoothLength 500 --effectiveGenomeSize 2913022398
bigwig for Input were generated by Deeptools (version 3.5.2) bamCoverage. Selected options were: --binSize 50 --smoothLength 500 --effectiveGenomeSize 2913022398
Assembly: hg38
Supplementary files format and content: bigWig

source_name: Hek293 FLP-in

growth_protocol: HEK293 Flp-In 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.

extract_protocol:
Cells were fixed with 1% formaldehyde (Pierce #PI28908) for 10 minutes and the fixation was stopped with 125 mM of glycine (Sigma #G8898) for 7 minutes. The cell pellets were resuspended in 45 mL of Farnham lysis buffer (5 mM PIPES pH 8.0_85 mM KCl and 0.5% NP-40) and incubated at 4°C for 20 minutes with gentle shaking. The supernatant was discarded by centrifugation_and the pellets were again resuspended in 25 mL of Farnham lysis buffer and incubated at 4°C for 15 minutes with gentle shaking. The purified nuclei pellets were subsequently resuspended in 0.8 mL of CHIP lysis buffer (50 mM HEPES-KOH pH7.5_140 mM NaCl_1 mM EDTA pH8.0_1% Triton X-100_0.1% Sodium Deoxycholate_0.1% SDS and protease inhibitors cocktail) and sonicated using a BioruptorPlus (Diagenode) at high power for 15 cycles (30 seconds on and 30 seconds off). The sheared chromatin was centrifuged at 18,500 rcf for 5 minutes_and the supernatant was collected. For each immunoprecipitation_50 μg of sheared chromatin_6 μg of the antibodies [rabbit IgG (Proteintech #30000-0-AP)_TBP (Proteintech #22006-1-AP)_and RNA polymerase II (ThermoFisher Scientific #A300653A)]_and 40 μL of Dyna-Protein G beads were used. The immunoprecipitations were performed at 4°C overnight using RIPA buffer. 10% of the sheared chromatin was kept aside as input. The beads were then washed twice with low salt (0.1% SDS_1% Triton X-100_2 mM EDTA_20 mM Tris-HCl pH 8.0 and 150 mM NaCl)_high salt (0.1% SDS_1% Triton X-100_2 mM EDTA_20 mM Tris-HCl pH 8.0 and 500 mM NaCl)_and LiCl wash buffers (0.25 M LiCl_1% NP-40_1% Sodium Deoxycholate_1 mM EDTA and 10 mM Tris-HCl pH 8.0). The chromatin was eluted using 100 μL of elution buffer (1% SDS and 100 mM NaHCO3) by incubating for 1 hour at room temperature and 15 minutes at 65°C. The eluted samples and input DNA were subjected to overnight decrosslinking followed by RNaseA (Invitrogen #12091021_0.2 mg/ml final concentration) and Proteinase-K (ThermoFisher Scientific #EO0492_0.4 mg/ml final concentration) treatment for 1 hour and purified using a QIAquick PCR Purification Kit (Qiagen #28104).
The sequencing library was prepared from 11.5 ng of purified DNA using the Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences # 21096)

treatment_protocol: HEK293 Flp-In cells were depleted of endogenous TAF5 by transfecting TAF5 siRNA (Dharmacon #J-012357-07) using Lipofectamine RNAiMax . After 24 hours_the cells were induced with doxycycline (10-5 µg/mL for TAF5-FL and 10-4 µg/mL for TAF5-ΔEx8_Sigma #D9891) for 48 hours to rescue with siRNA-resistant TAF5-FL (Addgene #209053/209055) or TAF5-ΔEx8 (Addgene #209054/209056) proteins_prior cell lysis for chromatin extraction.

value: Hek293 FLP-in

value: Human embryonic kidney

value: siRNA+dox


title: BDF1_in-vitro_04-cell_DEP_01_122_64


title: SK-N-BE(2), IRF2BP2, ChIP, rep1


title: Mock, 30 min, rep 3

value: Leaf 6 of rosette

value: Mock

value: 30 min after treatment


title: ChIP_RNAPolII_siTAF5+TAF5-FL_Replicate2

value: RNA polymerase II (ThermoFisher Scientific #A300653A)


title: multiplexed mitochondria library: L16R29P2B

value: brain cortex


title: BDF1_in-vitro_04-cell_DEP_01_122_63

value: embryo

value: in vitro


title: BDF1_in-vitro_04-cell_DEP_01_122_69


title: ChIP_RNAPolII_siTAF5_Replicate2


title: Mock, 30 min, rep 2


title: multiplexed mitochondria library: L23R29P3B


title: multiplexed mitochondria library: L15R29P2B


title: SK-N-BE(2), sh-NC, ATAC, rep2

value: neuroblastoma


title: Mock, 30 min, rep 1


title: ChIP_RNAPolII_siNT_Replicate2


title: Mock, 15 min, rep 4

value: 15 min after treatment


title: multiplexed mitochondria library: L14R29P2B

value: Astrocyte


title: BDF1_in-vitro_04-cell_DEP_01_122_61


title: multiplexed mitochondria library: L19R29P2B


title: BDF1_in-vitro_04-cell_DEP_01_122_60


title: Mock, 15 min, rep 3


title: Mock, 30 min, rep 4


title: ChIP_RNAPolII_siTAF5+TAF5-FL_Replicate1


title: ChIP_RNAPolII_siTAF5+TAF5-∆E8_Replicate1


title: Mock, 15 min, rep 2


title: BDF1_in-vitro_04-cell_DEP_01_122_59


title: multiplexed mitochondria library: L13R29P2B


title: multiplexed mitochondria library: L12R29P1B


title: Mock, 15 min, rep 1


title: ChIP_RNAPolII_siNT_Replicate1


title: ChIP_RNAPolII_siTAF5_Replicate1


title: BDF1_in-vitro_04-cell_DEP_01_122_57


title: BDF1_in-vitro_04-cell_DEP_01_122_62


title: BDF1_in-vitro_04-cell_DEP_01_122_56


title: ChIP_TBP_siTAF5+TAF5-∆E8_Replicate2

value: TBP (Proteintech #22006-1-AP)


title: BDF1_in-vitro_04-cell_DEP_01_122_55


title: multiplexed mitochondria library: L8R29P1B


title: multiplexed mitochondria library: L7R29P1B


title: ChIP_TBP_siTAF5+TAF5-FL_Replicate2


title: BDF1_in-vitro_04-cell_DEP_01_122_53


title: multiplexed mitochondria library: L9R29P1B


title: ChIP_TBP_siNT_Replicate2


title: ChIP_TBP_siTAF5_Replicate2


title: multiplexed mitochondria library: L6R29P1B


title: ChIP_TBP_siTAF5+TAF5-∆E8_Replicate1


title: BDF1_in-vitro_04-cell_DEP_01_122_52


title: multiplexed mitochondria library: L5R29P1B


title: multiplexed mitochondria library: L4R29P1B


title: multiplexed mitochondria library: L11R29P1B


title: BDF1_in-vitro_04-cell_DEP_01_122_58


title: ChIP_TBP_siTAF5_Replicate1


title: ChIP_TBP_siTAF5+TAF5-FL_Replicate1


title: multiplexed mitochondria library: L3R29P1B


title: BDF1_in-vitro_04-cell_DEP_01_122_50


title: BDF1_in-vitro_04-cell_DEP_01_122_51


title: multiplexed mitochondria library: L2R29P1B


title: ChIP_TBP_siNT_Replicate1


title: BDF1_in-vitro_04-cell_DEP_01_122_49


title: I8,Conv,Blood

city: New York

last: Connors

state: New York

address: 3595 Broadway CHN 10-24

institute: Columbia University Medical Center

data_processing:
Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mis-match was allowed for index sequence identification.
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Homo sapiens reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Assembly: GRCh39
Supplementary files format and content: comma-delimited CSV file combined for all Samples

source_name: Blood

extract_protocol:
Total RNA was extracted from cells sorted in RLT lysis buffer (Qiagen) using RNeasy Plus Mini Kit (Qiagen, Germantown, MD, USA). RNA was quantified using Qubit Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked with TapeStation (Agilent Technologies, Palo Alto, CA, USA).
SMART-Seq v4 Ultra Low Input Kit for Sequencing was used for full-length cDNA synthesis and amplification (Clontech, Mountain View, CA), and Illumina Nextera XT library was used for sequencing library preparation. Briefly, cDNA was fragmented, and adaptor was added using Transposase, followed by limited-cycle PCR to enrich and add index to the cDNA fragments. The final library was assessed with Agilent TapeStation.

value: Blood

value: primary

value: Conv

value: WT

tag: age

value: Infant


title: M397 cells,DMSO,216 hours

city: SEATTLE

first: Wei

last: Wei

state: Washington

address: 401 Terry Ave N

institute: Institute For Systems Biology

data_processing:
Reads were aligned against the human genome (hg19) using STAR (v2.7.3a). Read counts were quantified using htseq-count with known gene annotations from UCSC.The gene expression level was calculated from Fragments Per Kilobase per Million reads (FPKM) normalized expression values
Assembly: hg19
Supplementary files format and content: tab-delimited txt file includes FPKM values for each samples

growth_protocol: Cells were cultured in a water-saturated incubator at 37 °C with 5% CO2 in RPMI 1640 with L-glutamine (Life Technologies), supplemented with 10% fetal bovine serum (ATCC), and 0.2% antibiotics (MycoZapTM Plus-CL from Lonza).

extract_protocol:
Total RNA was extracted from the cell pellets using AllPrep DNA/RNA kit (Qiagen)
mRNA library was constructed with TruSeq RNA Sample Preparation Kit and sequenced on the Illumina Hiseq 2500 with pair-end 150bp reads following the manufacturer's recommendations by Novogene.

treatment_protocol: Cells were treated with 3 μM  BRAF inhibitor (vemurafenib, S1267),which is from SelleckChemicals LLC,at the selected time points.

value: melanoma cancer cell line

value: DMSO


title: M397 cells,DMSO,72 hours


title: HD73_2

type: RNA

first: Qi

last: PENG

address: No.2 Yuan Ming Yuan West Road

institute: IPPCAAS

description: Gene expression when OD600 reached to 0.7

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings，Dye channel: Green ,Scan resolution=5μm, PMT 100%，10% ，16bit.

data_processing: The scanned images were analyzed with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: Bacillus thuringiensis

source_name: Bt HD73

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color  (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s  instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH,  Germany).

growth_protocol: Bt HD73 strain was cultured in LB at 30 °C and 220 rpm.

extract_protocol: Total RNA was extracted using the Qiagen Easy RNA kit (Hilden, Germany) . Qualified total RNA was  further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNeasy  micro kit (Cat#74004, QIAGEN, GmBH, Germany)and RNase-Free DNase Set (Cat#79254,  QIAGEN, GmBH, Germany).

treatment_protocol: NaOH was added at a concentration of 28 mM to the cultures when the OD600 reached 0.7. After 10 minutes of incubation, total RNA was extracted

value: serovar kurstaki str. HD73


title: I8,Treg,Blood

value: Treg


title: ChIP_IgG_siTAF5+TAF5-∆E8_Replicate2

value: rabbit IgG (Proteintech #30000-0-AP)

value: Hek293 FLP-in

value: Human embryonic kidney

value: siRNA+dox


title: BDF1_in-vitro_04-cell_DEP_01_122_54

value: embryo

value: in vitro


title: HD73_3


title: multiplexed mitochondria library: L20R29P2B

value: brain cortex

value: Astrocyte


title: BDF1_in-vitro_04-cell_DEP_01_122_48


title: HD73_1


title: ChIP_IgG_siTAF5+TAF5-FL_Replicate2


title: multiplexed mitochondria library: L10R29P1B


title: BDF1_in-vitro_04-cell_DEP_01_122_47


title: BDF1_in-vitro_04-cell_DEP_01_122_46


title: ChIP_IgG_siTAF5_Replicate2


title: I8,Conv,Tonsil

source_name: Tonsil

value: Tonsil


title: HD73_alkaline_1

description: Gene expression after treated with NaOH for 10 min

source_name: Bt HD73, treat with NaOH


title: I8,Treg,Tonsil

value: primary


title: multiplexed mitochondria library: L7R25P1B

value: Neuron


title: HD73_alkaline_3


title: HD73_alkaline_2


title: multiplexed mitochondria library: L6R25P1B


title: BDF1_in-vitro_04-cell_DEP_01_122_45


title: I7,Conv,Blood

value: Blood

value: Conv

value: WT


title: ChIP_IgG_siTAF5+TAF5-∆E8_Replicate1


title: ChIP_IgG_siNT_Replicate2


title: BDF1_in-vitro_04-cell_DEP_01_122_44


title: ChIP_IgG_siTAF5+TAF5-FL_Replicate1


title: I7,Treg,Blood

value: Infant


title: multiplexed mitochondria library: L5R25P1B


title: BDF1_in-vitro_04-cell_DEP_01_122_43


title: multiplexed mitochondria library: L4R25P1B


title: BDF1_in-vitro_04-cell_DEP_01_122_42


title: ChIP_IgG_siTAF5_Replicate1


title: I7,Treg,Tonsil


title: ChIP_IgG_siNT_Replicate1


title: I6,Conv,Blood


title: multiplexed mitochondria library: CTRR25P1B


title: I7,Conv,Tonsil


title: multiplexed mitochondria library: L8R25P1B


title: BDF1_in-vitro_04-cell_DEP_01_122_41


title: multiplexed mitochondria library: L9R25R30B

value: mixed


title: BDF1_in-vitro_04-cell_DEP_01_122_40


title: I6,Treg,Blood

value: Treg


title: Input_siTAF5+TAF5-FL_Replicate2


title: multiplexed mitochondria library: L3R25P1B


title: multiplexed mitochondria library: L2R25P1B


title: Input_siTAF5_Replicate2


title: I6,Conv,Tonsil


title: BDF1_in-vitro_04-cell_DEP_01_122_39


title: BDF1_in-vitro_04-cell_DEP_01_122_38


title: BDF1_in-vitro_04-cell_DEP_01_122_37


title: multiplexed mitochondria library: L1R25P1B


title: I6,Treg,Tonsil


title: Input_siNT_Replicate2


title: I5,Conv,Blood


title: Input_siTAF5+TAF5-∆E8_Replicate1


title: multiplexed mitochondria library: L16R24P3C


title: Input_siTAF5+TAF5-FL_Replicate1


title: I5,Conv,Tonsil


title: multiplexed mitochondria library: L15R24P2C


title: Input_siTAF5_Replicate1


title: I5,Treg,Blood


title: multiplexed mitochondria library: L10R24P2C


title: BDF1_in-vitro_04-cell_DEP_01_122_34


title: BDF1_in-vitro_04-cell_DEP_01_122_36


title: I5,Treg,Tonsil


title: Input_siTAF5+TAF5-∆E8_Replicate2


title: Input_siNT_Replicate1


title: multiplexed mitochondria library: L26R29P3B


title: BDF1_in-vitro_04-cell_DEP_01_122_33


title: mRNA-seq of Hek293 FLP-in cells with siTAF5+TAF5-DE8, Replicate3

data_processing:
Raw sequencing reads were trimmed for adapters and low-quality bases using Cutadapt 1.18, and processed reads were aligned to the human reference genome (hg38) and annotated transcripts using the STAR 2.7.0f alignment tool. Raw counts for individual samples were calculated, gene expression levels were quantified from read normalized counts, and differential gene expression analysis was performed using the Deseq2 pipeline in Partek Flow software (version 10.0.23.0531).
Assembly: hg38
Supplementary files format and content: Tab-delimited text file including raw counts for each sample

extract_protocol:
Total RNA was extracted from HEK293 Flp-In cells of TAF5 isoform rescue experiments (see above) using the RNeasy Plus Mini Kit (Qiagen #74136).
The library was prepared using the Illumina® Stranded mRNA Prep kit

treatment_protocol: HEK293 Flp-In cells were depleted of endogenous TAF5 by transfecting TAF5 siRNA (Dharmacon #J-012357-07) using Lipofectamine RNAiMax . After 24 hours, the cells were induced with doxycycline (10-5 µg/mL for TAF5-FL and 10-4 µg/mL for TAF5-ΔEx8, Sigma #D9891) for 48 hours to rescue with siRNA-resistant TAF5-FL (Addgene #209053/209055) or TAF5-ΔEx8 (Addgene #209054/209056) proteins, prior cell lysis for RNA extraction.


title: multiplexed mitochondria library: L20R24P3C


title: A3,Conv,Tonsil

value: Adult


title: BDF1_in-vitro_04-cell_DEP_01_122_32


title: mRNA-seq of Hek293 FLP-in cells with siTAF5+TAF5-FL, Replicate3

value: Hek293 FLP-in


title: A3,Treg,Tonsil


title: multiplexed mitochondria library: L19R24P3C


title: A2,Conv,Tonsil


title: multiplexed mitochondria library: L18R24P3C


title: mRNA-seq of Hek293 FLP-in cells with siTAF5, Replicate3

value: Human embryonic kidney


title: BDF1_in-vitro_04-cell_DEP_01_122_31


title: A2,Treg,Tonsil


title: mRNA-seq of Hek293 FLP-in cells with siNT, Replicate3

value: siRNA+dox


title: multiplexed mitochondria library: L17R24P3C


title: BDF1_in-vitro_04-cell_DEP_01_122_35

value: embryo


title: BDF1_in-vitro_04-cell_DEP_01_122_29

value: in vitro


title: A1,Conv,Tonsil


title: mRNA-seq of Hek293 FLP-in cells with siTAF5+TAF5-DE8, Replicate2


title: multiplexed mitochondria library: L9R24P1C

value: brain cortex


title: multiplexed mitochondria library: L6R24P1C


title: BDF1_in-vitro_04-cell_DEP_01_122_27


title: mRNA-seq of Hek293 FLP-in cells with siTAF5+TAF5-FL, Replicate2


title: mRNA-seq of Hek293 FLP-in cells with siTAF5, Replicate2


title: multiplexed mitochondria library: L5R24P1C


title: BDF1_in-vitro_04-cell_DEP_01_122_28


title: I4,Treg,Blood


title: A1,Treg,Tonsil


title: I4,Conv,Blood


title: i3,Treg,Blood


title: mRNA-seq of Hek293 FLP-in cells with siTAF5+TAF5-DE8, Replicate1


title: mRNA-seq of Hek293 FLP-in cells with siNT, Replicate2


title: multiplexed mitochondria library: L3R24P1C


title: BDF1_in-vitro_04-cell_DEP_01_122_25


title: I3,Conv,Blood


title: BDF1_in-vitro_04-cell_DEP_01_122_26


title: multiplexed mitochondria library: L2R24P1C


title: mRNA-seq of Hek293 FLP-in cells with siTAF5+TAF5-FL, Replicate1


title: BDF1_in-vitro_04-cell_DEP_01_122_23


title: mRNA-seq of Hek293 FLP-in cells with siTAF5, Replicate1


title: BDF1_in-vitro_04-cell_DEP_01_122_24


title: I2,Treg,Blood


title: BDF1_in-vitro_04-cell_DEP_01_122_30


title: multiplexed mitochondria library: L8R24P1C


title: BDF1_in-vitro_04-cell_DEP_01_122_22


title: I2,Conv,Blood


title: multiplexed mitochondria library: L1R24P1C


title: mRNA-seq of Hek293 FLP-in cells with siNT, Replicate1


title: BDF1_in-vitro_04-cell_DEP_01_122_21


title: I1,Treg,Blood


title: RPE1 cells; RNAseq; Rep2

address: 1050 Boyles Street

institute: NCI/NIH

data_processing:
Demultiplexing
Sequencing reads were mapped to human hg18 genome using STAR.
Whippet was used to estimate percent splice in (PSI)
Assembly: hg18
Supplementary files format and content: PSI value of each splicing event was estimated using Whippet.

source_name: cell line

growth_protocol: HAP1 cells and 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:
Total RNA was extracted from HAP1 and RPE1 cells using the RNeasy Plus Mini Kit (Qiagen #74136).
The library was prepared using the Illumina® Stranded mRNA Prep kit followed by RNAseq on Illumina NovaSeq platform.

treatment_protocol: None.

value: cell line

value: retinal pigment epithelial cells


title: multiplexed mitochondria library: CTRR23P2B


title: BDF1_in-vitro_04-cell_DEP_01_122_20


title: multiplexed mitochondria library: CTRR23P1B


title: multiplexed mitochondria library: L4R24P1C


title: BDF1_in-vitro_04-cell_DEP_01_122_19


title: I1,Conv,Blood

value: primary


title: RPE1 cells; RNAseq; Rep1


title: HAP1 cells; RNAseq; Rep2

value: chronic myelogenous leukemia (CML) cell line KBM-8

value: wild type


title: A7,Treg,Blood

value: Blood


title: multiplexed mitochondria library: L4R23P2B

value: Neuron


title: HAP1 cells; RNAseq; Rep1

value: chronic myelogenous leukemia (CML) cell line KBM-7


title: multiplexed mitochondria library: L3R23P2B


title: A6,Conv,Blood

value: Conv

value: WT


title: BDF1_in-vitro_04-cell_DEP_01_122_17


title: multiplexed mitochondria library: L2R23P2B


title: Exon deletion; RPE1; T21B

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

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: lenti virus infected


title: A6,Treg,Blood

value: Treg

value: Adult


title: BDF1_in-vitro_04-cell_DEP_01_122_15


title: multiplexed mitochondria library: L1R23P2B


title: A5,Conv,Blood


title: Exon deletion; RPE1; T21A


title: multiplexed mitochondria library: L14R23P1C


title: BDF1_in-vitro_04-cell_DEP_01_122_14


title: A5,Treg,Blood


title: Exon deletion; RPE1; T0


title: A7,Conv,Blood


title: A4,Conv,Blood


title: multiplexed mitochondria library: L6R23P2B


title: multiplexed mitochondria library: L7R23P2B


title: Exon deletion; HAP1; T18C

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


title: A4,Treg,Blood


title: BDF1_in-vitro_04-cell_DEP_01_122_12

value: embryo


title: multiplexed mitochondria library: L5R23P2B


title: BDF1_in-vitro_04-cell_DEP_01_122_18

value: in vitro


title: Exon deletion; RPE1; T21C


title: BDF1_in-vitro_04-cell_DEP_01_122_16


title: Exon deletion; HAP1; T18B

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


title: HBC, 50nM PMA-treated, 12 hours, rep3

city: Boston

first: Camila

last: Barrios-Camacho

state: MA

address: 136 Harrison Avenue

institute: Tufts University

data_processing:
Novogene Inc trimmed raw reads
aligned to the rat genome with STAR version 2.7.5b with setting —quantMode GeneCounts
raw counts were normalized with DESeq2
Assembly: rn6
Supplementary files format and content: text files which include unnormalized gene counts from STAR for each sample

organism: Rattus norvegicus

source_name: olfactory epithelium

growth_protocol: HBCs were cultured using our established primary culture HBC culture system (Peterson et al., 2019)  with slight modifications to the antibiotic regimen. Instead of utilizing Penicillin-Streptomycin, we used Primocin (100 μg/ml final concentration) and anti-mycotic/anti-biotic (1X final concentration, Gibco Catalogue #15240062).

extract_protocol:
RNA was extracted using the PureLink RNA MiniKit and residual DNA was removed with the PureLink DNAse kit
libraries were prepared by Novagene. Inc

value: olfactory epithelium

value: primary dissociation

value: horizontal basal cell

value: SD

tag: time

tag: passage

value: 50nM Phorbol 12-myristate 13-acetate treated


title: Exon deletion; HAP1; T18A

value: cell line

value: chronic myelogenous leukemia (CML) cell line KBM-9

value: wild type


title: BDF1_in-vitro_04-cell_DEP_01_122_11


title: multiplexed mitochondria library: L12R23P1C

value: brain cortex

value: Neuron


title: multiplexed mitochondria library: L13R23P1C


title: SK-N-BE2 shIRF2BP2_rep2

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.2.0 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al.. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include readcount values for each Sample.

extract_protocol:
Cells were harvested, and total RNA was extracted with TRIzol (Invitrogen) according to the manufacturer's protocol. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Neuroblastoma cells


title: BDF1_in-vitro_04-cell_DEP_01_122_09


title: Exon deletion; HAP1; T0

value: chronic myelogenous leukemia (CML) cell line KBM-8

value: lenti virus infected


title: BDF1_in-vitro_04-cell_DEP_01_122_08


title: multiplexed mitochondria library: L11R23P1C


title: BDF1_in-vitro_04-cell_DEP_01_122_13


title: HBC, 50nM PMA-treated, 6 hours, rep3


title: HBC, 50nM PMA-treated, 6 hours, rep2


title: multiplexed mitochondria library: L10R23P1C


title: SK-N-BE2 shScb_rep2

value: scramble shRNA (sh-Scb)


title: SK-N-BE2 shIRF2BP2_rep1


title: multiplexed mitochondria library: L9R23P1C


title: BDF1_in-vitro_04-cell_DEP_01_122_07

value: embryo


title: SK-N-BE2 shScb_rep1


title: BDF1_in-vitro_04-cell_DEP_01_122_06

value: in vitro


title: BDF1_in-vitro_04-cell_DEP_01_122_10


title: HBC, 50nM PMA-treated, 6 hours, rep1


title: BDF1_in-vitro_04-cell_DEP_01_122_05


title: HBC, vehicle-treated, rep3

value: vehicle-treated (0.1percent DMSO)


title: HBC, 50nM PMA-treated, 12 hours, rep2

value: olfactory epithelium


title: multiplexed mitochondria library: L8R23P1C


title: BDF1_in-vitro_04-cell_DEP_01_122_03


title: BM_HSPC_Aged_70F [snRNA-seq]

city: Toronto

first: Andy

last: Zeng

state: ON

address: 101 College Street

country: Canada

institute: University of Toronto

description: 10x Genomics Multiome, snRNA-seq profiles

library_source: transcriptomic single cell

data_processing:
Raw sequencing data was processed with Cell Ranger ARC version 2.0.0
Assembly: GRCh38
Supplementary files format and content: 10x output from Cell Ranger ARC v2 with features, matrix, and barcodes

molecule: nuclear RNA

source_name: Bone Marrow

extract_protocol:
Nuclei were extracted following the low-input version of the Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing Protocol from 10x Genomics. We used a 3 minute lysis times for these samples.
Library construction was performed following the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression user guide.

value: Bone Marrow

value: Hematopoietic Stem and Progenitor Cells

tag: Sex

value: F


title: BDF1_in-vitro_04-cell_DEP_01_122_04

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


title: HBC, vehicle-treated, rep1

value: primary dissociation

value: horizontal basal cell

value: SD


title: HBC, 50nM PMA-treated, 12 hours, rep1

value: 50nM Phorbol 12-myristate 13-acetate treated


title: multiplexed mitochondria library: L15R23P1C

value: brain cortex


title: BM_HSPC_Aged_77F [snRNA-seq]


title: BDF1_in-vitro_04-cell_DEP_01_122_02


title: BM_HSPC_Young_26F [snRNA-seq]


title: multiplexed mitochondria library: L9R22P2B

value: Neuron


title: HBC, vehicle-treated, rep2


title: BM_HSPC_Young_24M [snRNA-seq]

value: M


title: multiplexed mitochondria library: L8R22P2B


title: BDF1_in-vitro_04-cell_DEP_01_122_01


title: multiplexed mitochondria library: L7R22P2B

value: mixed


title: multiplexed mitochondria library: L6R22P2B


title: CTC 1

city: Woolloongabba

first: Haotian

last: Yang

state: QLD

address: 37 Kent Street

department: Frazer Institute

country: Australia

institute: The University of Queensland

data_processing:
Illumina adapter and reads with a quality score less than 20 were removed.
The sequence reads were then aligned against the Homo sapiens genome (hg38) using STAR aligner (v2.5.3a).
Gene counts were generated using the FeatureCounts (v1.5.3).
Assembly: hg38
Supplementary files format and content: tab-delimited text file of the raw count matrix for each sample

extract_protocol:
RNA from TSCs, PCs and CTCs was extracted and purified using RNeasy Plus Micro Kit (Qiagen, USA). Quality control of the extracted RNA was assessed by RNA integrity using Bioanalyzer 2100 system (Agilent, USA). Ribosomal RNA was depleted using Ribo-Zero Plus rRNA Depletion kit (Illumina, USA).
DNA library was prepared by 3' adenylation of DNA fragments and ligation of the adapter sequences. Individual libraries were quantified by qPCR and all libraries were normalised to 2 nM. Libraries were pooled and clustered through the Illumina cBot system using TruSeq PE Cluster Kit v3 reagents

value: Blood

value: Human colorectal cancer cell line

tag: cell subtype

value: CTC


title: CTC 2


title: Atlantic salmon, fin, 60h post sea lice exposure

city: Midlothian

first: Sarah

last: Salisbury

address: Easter Bush Campus

country: United Kingdom

institute: The Roslin Institute, University of Edinburgh

description: Sample 42

data_processing:
Genome indexing and library mapping was performed with STAR (version 2.7.10a).
Assembly: We appended the mitochondrial genome from the ENSEMBL V2 Atlantic salmon genome (Salmo_salar.ICSASG_v2.dna_rm.toplevel.fa.gz, v2, release 105, masked genome, assembly ID: GCA_000233375.4) to the ENSEMBL V3 Atlantic salmon genome (Salmo_salar.Ssal_v3.1.dna_rm.toplevel.fa.gz, v3.1, release 106, masked genome, assembly ID: GCA_905237065.2) for both the .gff and .fna files prior to indexing. For coho salmon, we appended this species’ mitochondrial genome (version NC_009263.1, NCBI) to the ENSEMBL V2 coho salmon genome (Oncorhynchus_kisutch.Okis_V2.dna_rm.toplevel.fa.gz, v2, release 106, masked genome, assembly ID: GCA_002021735.2) for both the .gff and .fna files prior to indexing.
Supplementary files format and content: Tab-separated values file for barcodes
Supplementary files format and content: Tab-separated values file for features
Supplementary files format and content: Matrix file

organism: Salmo salar

source_name: pelvic fin

extract_protocol:
Nuclei were extracted in accordance with Ruiz Daniels et al. (2023) (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10484441/). In brief, approximately 45 mg tissue samples were cut with scissors in 1 mL of TST buffer for 10 minutes on ice before being filtered through a 40 µm Falcon™ cell strainer (Thermo Fisher Scientific, catalog no. 08-771-2). A further 1 mL of TST and 3 mL of 1X PBS + BSA buffer were added to each sample before centrifuging at 4°C for 5 minutes at 500 g. Samples were resuspended in 1 mL 1X ST buffer filtered again through a 40 µm cell strainer, stained with Hoechst 33342 Solution (Thermo Fisher Scientific, catalog no. 62249) and then nuclei integrity was visually assessed using a fluorescent microscope. A disposable flow haemocytometer (C-Chip Neubauer Improved (100 µm depth), NanoEnTek, catalog no. DHC-N01) was then used to estimate nuclei counts.
Samples were processed with Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index) (10X Genomics) using the protocol outlined in the User Guide (CG000315 Rev C). Samples were diluted with nuclease-free water to a target concentration that would recover approximately 7000 nuclei in the final library. Samples were then loaded on the Chromium Controller for nuclei droplet formation. After subsequent nuclei and UMI barcoding and reverse transcription, resulting cDNA was then amplified, fragmented, and indexed with Truseq adapters and Illumina sample indexes.

value: pelvic fin

value: 60h post sea lice exposure


title: multiplexed mitochondria library: L4R22P1B

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.

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.


title: multiplexed mitochondria library: L5R22P2B


title: PC 3

source_name: Primary tumour

value: Primary tumour

value: PC


title: PC 2


title: Atlantic salmon, fin, 48h post sea lice exposure

description: Sample 13

value: 48h post sea lice exposure


title: multiplexed mitochondria library: L3R22P1B


title: Atlantic salmon, fin, 36h post sea lice exposure

description: Sample 8

value: 36h post sea lice exposure


title: multiplexed mitochondria library: L2R22P1B


title: Atlantic salmon, fin, 24h post sea lice exposure

description: Sample 7

value: 24h post sea lice exposure


title: Atlantic salmon, fin, 12h post sea lice exposure

description: Sample 17

value: 12h post sea lice exposure


title: TSC 3

value: TSC


title: PC 1


title: TSC 1


title: Atlantic salmon, skin, 60h post sea lice exposure

description: Sample 22

source_name: skin

value: skin


title: TSC 2


title: multiplexed mitochondria library: LB2R20P2B

value: brain cortex


title: Donor 4, after booster vaccination, TCR-seq

city: Würzburg 97074

first: Chunguang

last: Liang

state: Bayern

address: Bioinformatik, Biozentrum, Uni Würzburg, Am Hubland

department: Bioinformatics

country: Germany

institute: Biozentrum

description: 10x Genomics

data_processing:
counted by cellranger
processed by Seurat 4
batch effect removing by CCA
normalized by LogNormalize
Assembly: Cellranger preprocessed refdata-gex-GRCh38-2020-A and refdata-cellranger-vdj-GRCm38-alts-ensembl-5.0.0
Supplementary files format and content: csv contains GEX normalized count and ADT normalized counts
Supplementary files format and content: meta data contains cluster_id and sample description
Library strategy: TCR-seq

source_name: PBMC

extract_protocol:
Freshly sorted human TFH cells were loaded on the Chromium Single Cell Controller (10x Genomics) using the Single Cell 5′ Library & Gel Bead Kit v1.1 (10x Genomics #PN-1000165). cDNAs were amplified using 13-14 cycles of PCR.
ScRNAseq libraries were constructed using 14-15 cycles of PCR and scCITEseq libraries were constructed using 9 cycles of PCR. ScTCRseq libraries were generated from the same cDNAs using the Single Cell V(D)J Enrichment Kit, Human T Cell (10x Genomics) (10 cycles of PCR)

value: PBMC

value: after booster vaccination

tag: antibodies/tags


title: multiplexed mitochondria library: L1R22P1B

tag: tissue

value: Neuron


title: SWNT-SHP1i, B9100

city: SHANGHAI

first: Fudi

last: Wang

state: SHANGHAI

address: 320, YUEYANG ROAD

institute: Stanford University

data_processing:
TrimGalore was employed for the trimming of sequence reads.
The RNA-seq reads were aligned to the pig genome (Sscrofa11.1) using the STAR.
Raw read counts were subjected to variance stabilizing transformation (VST) using the DESeq2.
Assembly: Sscrofa11.1
Supplementary files format and content: tab-delimited text files includes raw counts for each sample

organism: Sus scrofa

source_name: carotid artery

growth_protocol: Pigs were then transitioned to a high fat/high calorie Western diet and randomized to SWNT control and SWNT-SHP1i experimental treatment groups. Pigs were maintained on the high fat diet for 12 weeks.

extract_protocol:
RNA was extracted using Trizol reagent (Life Technologies, 15596018)
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. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: Each week, pigs were placed under general anesthesia and 400 nM of SWNT or SWNT-SHP1i was infused intravenously for approximately 15-30 minutes with close monitoring of vitals and body temperature.

value: carotid artery

value: 400nM of SWNT-SHP1i


title: multiplexed mitochondria library: L3R20R23B


title: Atlantic salmon, skin, 48h post sea lice exposure

description: Sample 26


title: multiplexed mitochondria library: LB1R20P1B


title: Atlantic salmon, skin, 36h post sea lice exposure

description: Sample 36


title: Donor 4, Before booster vaccination, TCR-seq

description: 10x Genomics

value: Before booster vaccination


title: Donor 3, after booster vaccination, TCR-seq

description: 10x Genomics


title: Atlantic salmon, skin, 24h post sea lice exposure

description: Sample 31


title: Sulfo3_12h

city: Rehovot

first: Danielle

last: Algranati

address: 234 Herzl Street

department: Department of Immunology & Regenerative Biology

country: Israel

institute: Weizmann Institute of Science

description:
DESeq2_12h.xlsx
Sulfo3_12h

data_processing:
Bcl files were converted into fastq by bcl2fastq. Demultiplexing is done using the sample barcode found on R2, the UMI found on R2 is inserted in the read name (in R1 fastq).  R1 Fastq data submitted.
MARS-seq analysis was done using the UTAP transcriptome analysis pipeline (Kohen et al., 2019). Reads were trimmed using Cutadapt (parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a “A{10}” –times 2 -u 3 -u -3 -q 20 -m 25) and mapped to hg38 genome using STAR v2.4.2a (parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic, –alignSoftClipAtReferenceEnds No).
The pipeline quantifies the 3’ of Gencode annotated genes (The 3’ region contains 1,000 bases upstream of the 3’ end and 100 bases downstream). Counting was done using htseq-count (union mode). Genes having minimum 5 UMI-corrected reads in at least one sample, were considered. Normalization of the counts and differential expression analysis was performed using DESeq2 package. Differentially expressed genes were defined as genes that had a significant adjusted p value of less than 0.05 and at least 2-fold change.
Assembly: hg38
Supplementary files format and content: Excel file include raw counts, normalized abundance measurements and DESeq2 analysis

source_name: MARS-seq on SU-DIPG13 treated with Sulfopin for 12h

growth_protocol: DIPG derived cells SU-DIPG-13 (H3.3-K27M, female) were generated in the lab of Dr. Michelle Monje, Stanford University (Grasso et al., 2015). Cells were maintained at 37°C with 5% CO2 and were cultured in Tumor Stem Media (TSM) consisting of a 1:1 mixture of DMEM/F12 (Invitrogen, 31330038) and Neurobasal (-A) (Invitrogen, 10888022), with addition of HEPES Buffer Solution (1M) (Invitrogen 15630-080), MEM Sodium Pyruvate Solution 100mM (100X), liquid (Invitrogen, 11360-070) MEM Non-Essential Amino Acids Solution 10mM (100X), Invitrogen, 11140-050), GlutaMAX-I (Invitrogen, 35050-061) Antibiotic-Antimycotic (100X) (Invitrogen,15240-096) B27(-A) (Invitrogen, 12587010), human-bFGF (20 ng/mL) (Shenandoah Biotechnology, 100-146), human-EGF (20 ng/mL) (Shenandoah Biotechnology, 100-26), human PDGF-AA (20 ng/mL) (Shenandoah Biotechnology, 100-16), human PDGF-BB (20 ng/mL, 100-18) (Shenandoah Biotechnology) and heparin (10 ng/mL) (Stemcell Technologies, 07980).

extract_protocol:
RNA was isolated from SU-DIPG13 cells using the NucleoSpin kit (Macherey Nagel, 740955)
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Cells were plated at a density of 2500 cells per well in 96-well plates in at least triplicates and subjected to drug treatment for 3 days (1uM Vorinostat),  12 hours/8 days (10uM Sulfopin), Vorinostat+Sulfopin (72h,1uM+8,10uM) or DMSO. When treated for 8 days one pulse were given at day 4. Cell viability was measured by CelltiterGlo assay (G7571, Promega) according to the manufacturer’s instructions. Luminescence was measured by Cytation 5 plate reader and viability was compared to DMSO treated control cells.

value: Glioma

value: Sulfopin

tag: genotype


title: SWNT-SHP1i, B3891

tag: treatment


title: Donor 3, Before booster vaccination, TCR-seq

description: 10x Genomics


title: Sulfo2_12h

description:
DESeq2_12h.xlsx
Sulfo2_12h


title: Sulfo1_12h

description:
DESeq2_12h.xlsx
Sulfo1_12h


title: DMSO3_12h

description:
DESeq2_12h.xlsx
DMSO3_12h

source_name: MARS-seq on SU-DIPG13 treated with DMSO for 12h

value: DMSO


title: Tonsil3, TCR-seq

description: 10x Genomics

value: Tonsil


title: SWNT-SHP1i, B9131


title: SWNT-SHP1i, B9174


title: SWNT-SHP1i, B9128


title: DMSO2_12h

description:
DESeq2_12h.xlsx
DMSO2_12h


title: Atlantic salmon, skin, control

description: Sample 11

value: control


title: Tonsil1, TCR-seq

description: 10x Genomics


title: Tonsil2, TCR-seq

description: 10x Genomics


title: Hi-C of E.coli :MG1655 + DPAG 50 uM (30 min) Paris

city: Paris

first: Justine

middle: Rozenn

last: Groseille

address: 28 rue du Dr Roux

country: France

institute: Institut Pasteur

data_processing:
Reads were aligned with bowtie2 v2.4.4 and Hi-C contact maps were generated using hicstuff v3.0.3 (https://github.com/koszullab/hicstuff) with default parameters and using HpaII enzyme to digest. Contacts were filtered as described in42, and PCR duplicates (defined as paired reads mapping at exactly the same position) were discarded.
Matrices were binned 4kb. Balanced normalizations were performed using ICE algorithm43. For all comparative analyses, matrices were downsampled to the same number of contacts. The Hi-C signal was computed as the contacts between adjacent 5kb bins as described in Lioyet al. (2018)44. In order to compare this signal with other genomics tracks, we binned it at the desired resolution
Assembly: hicstuff v3.0.3
Supplementary files format and content: raw files and cool files

organism: Escherichia coli

growth_protocol: E. coliMG1655 carrying plasmids pFR85 (PtetariAB) and pFD250 (PPhlFocr), or the pFR66 (sfGFP) + pFD245 (PhlF sfGFP) control plasmids were diluted 1:100 from an overnight culture in LB + kanamycin 50 μg/ml + chloramphenicol 20 μg/ml and grown until OD600 = 0.3.

extract_protocol:
Cell fixation was performed with 4% formaldehyde (Sigma-Aldrich, Cat. F8775) as described in Cockram et al. (2021)41. Quenching of formaldehyde with 300 mM glycine was performed at 4°C for 20 min. Hi-C experiments were performed with the Arima kit. Samples were sonicated using Covaris (DNA 300bp).
Preparation of the samples for paired-end sequencing was performed using Invitrogen TM Colibri TM PS DNA Library Prep Kit for Illumina according to manufacturer instructions. The detailed protocol is available in Cockram et al. (2021)

treatment_protocol: DAPG 50 μM was then added, followed by incubation for 15 and 30min. To compare the effect of PARIS activation with that of treatment with chloramphenicol,E. coliMG1655 harboring pFR66 were diluted 1:100 from an overnight culture in LB + kanamycin 50 μg/ml until OD600= 0.3, followed by addition of chloramphenicol 20 μg/ml and incubation for 15 and 30min

value: bacteria

value: MG1655 pFR85 (PARIS-2) + pFD250 (PhlF ocr)

value: DAPG 30 min


title: Atlantic salmon, fin, control

description: Sample 12

value: pelvic fin


title: Hi-C of E.coli :MG1655 + cm 20 µg/ml Contrôle (15min)

value: MG1655 pFR66 (sfGFP) + pBAD18 Cm20 ug/ml

value: Cm 15 min


title: SWNT, B9123

value: 400nM of SWNT


title: Donor 2, After CsA treatment, TCR-seq

description: 10x Genomics

value: PBMC

value: After CsA treatment


title: Vorino2

description:
DESeq2_Drugs.xlsx
Vorino2

source_name: MARS-seq on SU-DIPG13 treated with Vorinostat for 72h

value: Vorinostat

value: 72 hours


title: SWNT, B3866

value: carotid artery


title: Donor 2, During CsA treatment, TCR-seq

description: 10x Genomics

value: During CsA treatment


title: SWNT-SHP1i, B3889

description:
Died before harvest
B3889C

value: 400nM of SWNT-SHP1i


title: Atlantic salmon, skin, 12h post sea lice exposure

description: Sample 21

value: skin

value: 12h post sea lice exposure


title: Vorino1

description:
DESeq2_Drugs.xlsx
Vorino1

value: Glioma


title: Donor 1, After CsA treatment, TCR-seq

description: 10x Genomics


title: Hi-C of E.coli :MG1655 + DPAG 50 uM (30 min) WT

value: bacteria

value: MG1655 pFR66 (sfGFP) + pFD245 (PhlF sfGFP)


title: SulfoVorino3

description:
DESeq2_Drugs.xlsx
SulfoVorino3

source_name: MARS-seq on SU-DIPG13 treated with Vorinostat for 72h+Sulfopin for 8d

value: Sulfopin+Vorinostat

value: 8 days/72 hours


title: Hi-C of E.coli: MG1655 + DPAG 50 uM (15 min) WT

value: DAPG 15 min


title: Hi-C of E.coli :MG1655 + cm 20 µg/ml Contrôle (30min)

value: MG1655 pFR66 (sfGFP) + pBAD18 Cm20 ug/ml

value: Cm 15 min


title: Donor 1, During CsA treatment, TCR-seq

description: 10x Genomics

value: PBMC


title: SWNT, B9124

value: 400nM of SWNT


title: SWNT, B9130


title: Vorino3

description:
DESeq2_Drugs.xlsx
Vorino3

value: Vorinostat


title: SulfoVorino1

description:
DESeq2_Drugs.xlsx
SulfoVorino1


title: SulfoVorino2

description:
DESeq2_Drugs.xlsx
SulfoVorino2


title: Gentamicin, 60 min, 3'-end-seq, Δmfd

first: Jintao

last: Liu

address: Haidian District

institute: Tsinghua University

data_processing:
For 3’ -end-seq, firstly, sequencing raw data was subjected to FastQC (v0.11.9) for quality control and cutadapt (2.10) for adaptor trimming. In detail, fastqc was used with default parameters, cutadapt command was used with parameters -q 10,10 --minimum-length 100:100 --max-n 3 --pair-filter=any -o. The data was then demultiplexed by cutadapt based on the unique RNA adaptors. Paired-end reads were aligned to E. coli reference genome (NC_000913.3) by bowtie2 (2.4.1) with parameters -X 1000 -I 18 --no-mixed --no-discordant. The mapped reads were converted to bam files by samtools (1.10). To minimize the effect of sequencing depth on further analysis, we subsampled every bam file to the equal number of 4.5 million paired-end reads. Reads were counted for bam files using R (4.0.2) method summarizeOverlaps from GenomicAlignments package (v1.26.0) in a strand specific manner, with the following options “mode = "Union", ignore.strand = FALSE, singleEnd = FALSE, preprocess.reads = invertStrand”.
For RNA-seq data, data processing was similar to our previous report (Wang et al., Environmental Microbiology 2022). Adaptor trimming, alignment to genome and gene read count table were all the same with 3’-end-seq as shown above.
Assembly: NC000913.3
Supplementary files format and content: comma-delimited text file for expression matrix
Supplementary files format and content: xlsx file for 3' -end-seq CPM of PRSEs

organism: Escherichia coli BW25113

growth_protocol: In all experiments, E. coli K12 BW25113 was used (originally from CICC, 23872) as the wildtype strain. Single colony was picked up from a stock LB agar plate and was grown aerobically with shaking at 220 rpm in Luria-Bertani (LB) broth (10 g/L tryptone (Oxoid, LP0042), 10 g/L NaCl (Macklin, S805275), 5 g/L yeast extract (Oxoid, LP0021)) medium overnight (typically 12 h) as the seed culture. All cultures were carried out at 37 °C with shaking at 200 rpm.

extract_protocol:
For RNA exactraction, bacteria lysate was prepared using lysozyme and proteinase K. Total RNA was then purified by RNAClean XP beads (Beckman, A63987). For genomic DNA, TIANamp Bacteria DNA kit (TIANGEN, DP302) were used. See decrisption in our paper for details.
3' -end-seq library preparation method was adopted from a previous multiplexed RNA-seq library preparation method reported by Avraham et al. Systematic modifications were introduced to repurpose it to keep 3’ end information of bacterial transcripts. To prepare RNA-seq library, here we did not follow routine RNA-seq library construction method, in order to minimize the batch effect introduced when applying different library preparation protocols.

treatment_protocol: Overnight seed cultures were diluted by 1:350 into 700 μL of fresh medium and grown in a 48-well plate in a microplate reader (Tecan, Spark). When the cultures grew to OD600 ~ 0.2, we carried out another dilution of 1:50 into fresh medium and cultivated with the same condition. When subcultures reached an OD600 of ~ 0.25, 10 μL gentamicin (Selleck, S4030) was supplemented to make a final concentration of 6 mg/L.

value: deleted mfd

value: 6 mg/L, gentamicin

tag: seq method

value: 3' -end-seq


title: Donor 4, Before booster vaccination, ADT

description: 10x Genomics

library_source: other

data_processing:
counted by cellranger
processed by Seurat 4
batch effect removing by CCA
normalized by LogNormalize
Assembly: Cellranger preprocessed refdata-gex-GRCh38-2020-A and refdata-cellranger-vdj-GRCm38-alts-ensembl-5.0.0
Supplementary files format and content: csv contains GEX normalized count and ADT normalized counts
Supplementary files format and content: meta data contains cluster_id and sample description
Library strategy: CITE-seq

molecule: protein

value: Before booster vaccination

value: CXCR3, PD-1, CD25, CCR6


title: Sulfo3

description:
DESeq2_Drugs.xlsx
Sulfo3

source_name: MARS-seq on SU-DIPG13 treated with Sulfopin for 8d

value: Sulfopin

value: 8 days


title: Hi-C of E.coli :MG1655 + DPAG 50 uM (15min) Paris

value: bacteria

value: MG1655 pFR85 (PARIS-2) + pFD250 (PhlF ocr)


title: Donor 3, after booster vaccination, ADT

description: 10x Genomics

value: after booster vaccination


title: 0 min, 3'-end-seq, Δmfd

tag: strain


title: Donor 3, Before booster vaccination, ADT

description: 10x Genomics


title: Gentamicin, 110 min, 3'-end-seq, wildtype

value: wildtype


title: Sulfo1

description:
DESeq2_Drugs.xlsx
Sulfo1

value: Glioma


title: SWNT, B9099

value: carotid artery


title: Sulfo2

description:
DESeq2_Drugs.xlsx
Sulfo2


title: Gentamicin, 74 min, 3'-end-seq, wildype


title: BV2_PNU+HSV_3

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression from BV2 cells treated with PNU-282987 before HSV-1 infection

scan_protocol: RNA expression was quantified on the nCounter Digital AnalyzerTM.

data_processing: All data were adjusted utilizing the manufacturer’s positive and negative experimental control probes, as well as five highly correlated HK genes (Aars, Cnot10, Csnk2a2, Lars, and Tada2b).

label: biotin

source_name: BV2 cells treated with PNU-282987 before HSV-1 infection Rep 3

label_protocol: 100 ng of each total RNA sample was prepared as per the manufacturer’s instructions.

growth_protocol: BV2 cells were cultured in high glucose DMEM medium supplmented with 5% fetal bovine serum (FBS). The α7 nicotinic receptor agonist, PNU-282987, was diluted in the culture medium and treated the cells for 1 hour before HSV-1 infection. Cells were collected at 8 hours after infection, and subjected to NanoString analysis.

extract_protocol: Total RNA were isolated using Maxwell RSC miRNA kit

treatment_protocol: BV2 cells were treated with PNU-282987 (30 uM) for 1 hour. After treatment, BV2 cells were infected with HSV-1 (MOI=0.1) for I hour, and the medium were added back to the cells. The cells were collected at 8 hours after infection.


title: Tonsil3, ADT

description: 10x Genomics

value: Tonsil


title: Gentamicin, 60 min, 3'-end-seq, wildtype


title: Tonsil2, ADT

description: 10x Genomics


title: Gentamicin, 110 min, 3'-end-seq, Δmfd


title: DMSO3

description:
DESeq2_Drugs.xlsx
DMSO3

source_name: MARS-seq on SU-DIPG13 treated with DMSO for 8d

value: DMSO


title: Donor 4, after booster vaccination, ADT

description: 10x Genomics

value: PBMC


title: BV2_PNU+HSV_1

source_name: BV2 cells treated with PNU-282987 before HSV-1 infection Rep 1


title: BV2_HSV_3

description: Gene expression from BV2 cells infected with HSV-1, no choline treatment

source_name: BV2 cells infected with HSV-1, no choline treatment Rep 3


title: Tonsil1, ADT

description: 10x Genomics

source_name: Tonsil


title: Gentamicin, 40 min, 3'-end-seq, wildtype


title: BV2_PNU+HSV_2

source_name: BV2 cells treated with PNU-282987 before HSV-1 infection Rep 2


title: Gentamicin, 20 min, 3'-end-seq, wildtype


title: BV2_HSV_1

source_name: BV2 cells infected with HSV-1, no choline treatment Rep 1


title: BV2_HSV_2

source_name: BV2 cells infected with HSV-1, no choline treatment Rep 2


title: DMSO1

description:
DESeq2_Drugs.xlsx
DMSO1


title: DMSO2

description:
DESeq2_Drugs.xlsx
DMSO2


title: Donor 2, After CsA treatment, ADT

description: 10x Genomics

value: After CsA treatment


title: BV2_PNU_3

description: Gene expression from BV2 cells treated with PNU0282987 no virus

source_name: BV2 cells treated with PNU0282987 no virus Rep 3


title: Gentamicin, 13 min, 3'-end-seq, wildtype


title: Donor 2, During CsA treatment, ADT

description: 10x Genomics

value: During CsA treatment


title: Cut& Run on SU-DIPG13 treated with Sulfopin+Vorinostat using H3K27me3 ab

data_processing:
Paiered-end reads were preprocessed with cutadapt to remove adapters and low-quality bases (parameters: --times 2 -q 30 -m 20). Reads were mapped to human genome (hg38, UCSC) using Bowtie version 2.3.5.1 (--local --very-sensitive-local --no-unal --no-mixed --no-discordant -I 10 -X 700 --dovetail ).
Nucleosome fragments at the length >120bp were selected from the remaining unique reads using picard-tools, and broad peaks were called using MACS2 against the corresponding HRP samples as background control (parameters: -f BAMPE --SPMR --nomodel --extsize 100 --keep-dup auto -q 0.05).  Bigwig files were constructed from BAM alignments using deepTools2 suite with bamCoverage, using RPKM-normalization in 10bp bins.
Assembly: hg38
Supplementary files format and content: Bigwig files were constructed from BAM alignments using deepTools2 suite with bamCoverage, using RPKM-normalization in 10bp bins.
Supplementary files format and content: Peaks files were constructed using MACS2 against HRP samples as background control.
Library strategy: CUT&RUN

extract_protocol:
Cut&Run assay was done as described in (Meers et al., 2019; Skene and Henikoff, 2017) with slight modifications as follows: Cells were harvested and counted, with 200,000 cells taken per reaction. Permeabilized cells, bound to Concanavalin A-coated beads (Bangs Laboratories, BP531), were mixed with individual primary antibody (Table S1) and incubated overnight at 4°C while rotating. Secondary antibody, anti-rabbit HRP (Table S1), was used as a negative control. pAG-MNase enzyme (generated in the Department of Life Sciences Core Facilities, WIS, using Addgene plasmid 123461) was added to each sample followed by incubation step of 1 h at 4°C. Targeted digestion was done by 15 min incubation on ice block (0°C) under low salt conditions. DNA purification was done using Nucleospin gel and PCR clean-up kit (Machery-Nagel, 740609).
Libraries were prepared from 1-20ng of DNA as previously described (Blecher-Gonen et al., 2013). Briefly, DNA Fragments were repaired by T4 DNA polymerase (NEB, M0203), and T4 polynucleotide kinase (T4 PNK, NEB, M0201) was used to add a phosphate group at the 5′ ends. An adenosine base was then added by Klenow fragments (NEB, M0212) to allow efficient ligation, using T4 quick ligase (NEB, M2200), of sequencing adapters, which contain a T-overhang. DNA fragments were amplified by PCR reaction (Pfu Ultra II fusion, Agilent Technologies, 600670), which also introduced the Illumina-P5 adapter at one end of the molecule. SPRI beads were used to purify proper sized DNA fragments after each enzymatic step. Libraries were quantified by Qubit (ThermoFisher Scientific) and proper fragment range (200-400bp) was verified by TapeStation (Agilent). Sequencing was done on a Next-Seq 500 instrument (Illumina, #20024904) using a V2 150 cycles mid output kit (paired end sequencing).

treatment_protocol: Cells were plated at a density of 2500 cells per well in 96-well plates in at least triplicates and subjected to drug treatment for 3 days (1uM Vorinostat),  8 days (10uM Sulfopin), Vorinostat+Sulfopin (72h,1uM+8,10uM) or DMSO. When treated for 8 days one pulse were given at day 4. Cell viability was measured by CelltiterGlo assay (G7571, Promega) according to the manufacturer’s instructions. Luminescence was measured by Cytation 5 plate reader and viability was compared to DMSO treated control cells.

value: Sulfopin+Vorinostat

value: 8 days/72 hours

tag: antibody

value: anti-histone H3K27me3


title: Donor 1, After CsA treatment, ADT

description: 10x Genomics

value: CXCR3, PD-1, CD25, CCR6


title: Gentamicin, 6 min, 3'-end-seq, wildtype

value: 6 mg/L, gentamicin

value: 3' -end-seq


title: Donor 1, During CsA treatment, ADT

description: 10x Genomics


title: 0 min, replicate 2, 3'-end-seq, wildtype


title: Cut& Run on SU-DIPG13 treated with Vorinostat using H3K27me3 ab

value: Vorinostat

value: 72 hours


title: BV2_PNU_1

source_name: BV2 cells treated with PNU0282987 no virus Rep 1


title: 0 min, replicate 1, 3'-end-seq, wildtype


title: BV2_control_2

description: Gene expression from non-treated BV2 cells

source_name: non-treated BV2 cells Rep 2


title: BV2_control_3

source_name: non-treated BV2 cells Rep 3


title: Donor 4, after booster vaccination, Gene expression

description: 10x Genomics

data_processing:
counted by cellranger
processed by Seurat 4
batch effect removing by CCA
normalized by LogNormalize
Assembly: Cellranger preprocessed refdata-gex-GRCh38-2020-A and refdata-cellranger-vdj-GRCm38-alts-ensembl-5.0.0
Supplementary files format and content: csv contains GEX normalized count and ADT normalized counts
Supplementary files format and content: meta data contains cluster_id and sample description

source_name: PBMC

value: after booster vaccination


title: Cut& Run on SU-DIPG13 treated with Vorinostat using H3K27ac ab

value: anti-histone H3K27ac


title: Donor 4, Before booster vaccination, Gene expression

description: 10x Genomics

value: Before booster vaccination


title: Gentamicin, 60 min, RNA-seq, Δmfd

value: deleted mfd

value: RNA-seq


title: Cut& Run on SU-DIPG13 treated with Sulfopin using H3K27me3 ab

value: Glioma

value: Sulfopin

value: 8 days


title: Cut& Run on SU-DIPG13 using HRP ab

value: NT

value: Secondary antibody anti-rabbit HRP


title: BV2_control_1

source_name: non-treated BV2 cells Rep 1


title: Donor 3, after booster vaccination, Gene expression

description: 10x Genomics

value: PBMC


title: Gentamicin, 110 min, RNA-seq, Δmfd


title: Donor 3, Before booster vaccination, Gene expression

description: 10x Genomics


title: BV2_PNU_2

source_name: BV2 cells treated with PNU0282987 no virus Rep 2


title: 0 min, RNA-seq, Δmfd


title: Gentamicin, 110 min, RNA-seq, wildtype

value: wildtype


title: Cut& Run on SU-DIPG13 treated with DMSO using H3K27me3 ab

value: DMSO

value: anti-histone H3K27me3


title: BV2 choline+HSV 3

description: Gene expression from BV2 cells treated with choline before HSV-1 infection

data_processing: Data were adjusted utilizing the manufacturer’s positive and negative experimental control probes, as well as all 10 HK genes.

source_name: BV2 cells treated with choline before HSV-1 infection Rep 3

label_protocol: 50 ng of each total RNA sample was processed as per the manufacturer’s instructions.

growth_protocol: BV2 cells were cultured in high glucose DMEM medium supplmented with 5% fetal bovine serum (FBS). The α7 nicotinic receptor agonist, choline, was diluted in the culture medium and treated the cells for 1 hour before HSV-1 infection. Cells were collected at 8 hours after infection, and subjected to NanoString analysis.

treatment_protocol: BV2 cells were treated with choline (30 mM) for 1 hour. After treatment, BV2 cells were infected with HSV-1 (MOI=0.1) for I hour, and the medium were added back to the cells. The cells were collected at 8 hours after infection.


title: Cut& Run on SU-DIPG13 treated with Sulfopin+Vorinostat using H3K27ac ab

value: Sulfopin+Vorinostat

value: 8 days/72 hours


title: Gentamicin, 74 min, RNA-seq, wildype

value: 6 mg/L, gentamicin


title: Tonsil3, Gene expression

description: 10x Genomics

value: Tonsil


title: BV2 choline+HSV 2

source_name: BV2 cells treated with choline before HSV-1 infection Rep 2


title: Tonsil2, Gene expression

description: 10x Genomics


title: Cut& Run on SU-DIPG13 treated with DMSO using H3K27ac ab

value: anti-histone H3K27ac


title: BV2 HSV 3


title: Gentamicin, 60 min, RNA-seq, wildtype


title: Day9_Treatment_Rep2

city: Baltimore

first: Dong Won

middle: Thomas

last: Kim

state: Maryland

address: 733 N.Broadway, MRB building (Rm 332)

department: Neuroscience

institute: Johns Hopkins University

description: snRNA-Seq

data_processing:
Bulk RNA-Seq (human): Illumina adapters of libraries after sequencing were removed using Cutadapt (v1.18)  with default parameters. Libraries were then aligned to GRPRA8 using STAR (v2.42a)  with –twopassMode Basic. RSEM (v1.3.1)  was used for transcript quantification, with rsem-calculate-expression (--forwad-prob 0.5). TPM value from RSEM was used to plot white, beige, or brown adipocytes-enriched markers using ggplot (v3.32).
scRNA-Seq: Sequencing results were processed through the Cell Ranger pipeline (10x Genomics) with default parameters. Seurat V3 was used to perform downstream analysis following the standard pipeline.
Genome_build: Human:  GRCh38
Supplementary_files_format_and_content: count matrix

extract_protocol:
scRNA-Seq following 10x V2.0 or V3.0 guideline
10x Genomics V2.0

tag: time point

value: Fibroblast


title: Donor 2, After CsA treatment, Gene expression

description: 10x Genomics

value: After CsA treatment


title: Gentamicin, 40 min, RNA-seq, wildtype

value: RNA-seq


title: Tonsil1, Gene expression

description: 10x Genomics


title: Day5_Treatment

description: snRNA-Seq


title: Cut& Run on SU-DIPG13 treated with Sulfopin using H3K27ac ab

tag: cell type

value: Glioma


title: Day9_Treatment_Rep1

description: snRNA-Seq


title: BV2 HSV 1


title: BV2 choline+HSV 1

source_name: BV2 cells treated with choline before HSV-1 infection Rep 1


title: Donor 1, After CsA treatment, Gene expression

description: 10x Genomics


title: BV2 choline 3

description: Gene expression from BV2 cells treated with choine no virus

source_name: BV2 cells treated with choine no virus Rep 3


title: Day0_Treatment

description: snRNA-Seq


title: Gentamicin, 13 min, RNA-seq, wildtype


title: Donor 2, During CsA treatment, Gene expression

description: 10x Genomics

value: During CsA treatment


title: Gentamicin, 20 min, RNA-seq, wildtype


title: Donor 1, During CsA treatment, Gene expression

description: 10x Genomics


title: Gentamicin, 6 min, RNA-seq, wildtype


title: GDfat001

description: bulk RNA-Seq

extract_protocol: Human orbital fat was obtained using using a protocol approved by the Institutional Review Board. RNA was extracted from each fat depot using Trizol and RNeasy mini kits. RNA sequencing performed using Illumina Nextseq500.

value: Orbital fat

value: 51 years old

value: Female

value: orbital fat


title: BV2 cholline 1

source_name: BV2 cells treated with choine no virus Rep 1


title: BV2 choline 2

source_name: BV2 cells treated with choine no virus Rep 2


title: GDfat005

description: bulk RNA-Seq

value: Male


title: 0 min, replicate 2, RNA-seq, wildtype

value: wildtype


title: BV2 control 3


title: BV2 HSV 2


title: Fat003

description: bulk RNA-Seq

value: 37 years old


title: 0 min, replicate 1, RNA-seq, wildtype


title: Day21_Treatment_Rep2

description: snRNA-Seq

extract_protocol:
scRNA-Seq following 10x V2.0 or V3.0 guideline
10x Genomics V3.1


title: Day21_Treatment_Rep1

description: snRNA-Seq


title: Fat010

description: bulk RNA-Seq

value: 58 years old


title: BV2 control 2


title: BV2 control 1


title: mRNA_Tumor_T1_3

status: Public on Jun 23 2024

city: Hangzhou

first: Shiqun

state: Zhejiang Province

address: No. 150, Fucheng Road, Hangzhou Economic and Technological Development Zone

institute: Institute of Cancer and Basic Medicine, Chinese Academy of Sciences (CAS)

description: 10X Genomics single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1
Assembly: Mus_musculus (GRCm39)
Supplementary files format and content: Results from Illumina sequencing offline were converted to FASTQ format using bcl2fastq software (version 5.0.1).
Supplementary files format and content: Tab-separated values files and matrix files

source_name: KPC shUbed3-1 tumor tissues

extract_protocol:
The obtained tissues were transferred to a Petri dish (Petri dish was placed on wet ice) pre-spiked with 1×PBS (without RNase and Ca, Mg ions) and washed with 1XPBS to remove blood stains, grease and other adherents from the tissue surface. The tissue was then cut into 0.5 mm2 pieces and washed again with 1×PBS. The washed pieces were added with dissociation solvent (0.35% collagenase IV5, 2 mg/ml papain, 120 Units/ml DNase I) and reacted for 20 min at 37°C in a water bath shaker (100 rpm). PBS (containing 10% fetal bovine serum) was used to terminate the dissociation. The cells were repeatedly puffed 5-10 times with a pipette gun (gentle handling to prevent cell death due to shear force). The cell suspension was filtered through a 70-30um cell sieve and subsequently centrifuged at 300g for 5 min at 4°C. After centrifugation, the cell sediment was collected and the cells were resuspended by adding 100ul of 1× PBS(0.04% BSA)solution. To remove erythrocytes, 1 ml of 1X erythrocyte lysis solution (MACS 130-094-183, 10×) was added and reacted at room temperature or on wet ice for 2-10 min. After lysis, the cells were centrifuged at 300g for 5 min at 4°C, and the cell precipitate was collected after centrifugation. Add 100μl of Dead Cell Removal MicroBeads (MACS 130-090-101), mix well and incubate for 15min at room temperature. At the end of incubation, Binding Buffer was added, after MS Columns (130-042-201) to remove reagents, and dead cells.Cell precipitates were collected by centrifugation at 300g for 5min at 4°C. Subsequently 1×PBS (0.04% BSA) was used to resuspend the cell precipitate and centrifuged at 4°C 300g for 5min (repeated twice). The candidate cells were obtained after tissue dissociation, lysis of erythrocytes and removal of dead cells, and 100 μl of 1×PBS (0.04% BSA) was added to form a cell suspension. The cell activity was detected by trypan blue staining method, and the cell activity was required to be >85%. The number of cells was counted using a hemocytometer or Countess II Automated Cell Counter, and the cell concentration was 700-1200 cells/μ.
Chromium 10x Genomics library and sequencing
For the mRNA library, cDNA was fragmented to 200-300 base pairs, with sequencing adapters and primers added as per traditional library preparation methods, concluding with PCR amplification. For the immune repertoire library, nested PCR targeting the constant region of TCR/BCR enriched TCR sequences. Following fragmentation and controlled interruption for full V(D)J cDNA sequence coverage, the fragments were prepared with A-tailing and adapter ligation, creating a V(D)J library equipped with P5 and P7 adapters.

value: KPC shUbed3-1 tumor tissues

value: FCM-sorted tumor-inflitrating CD8+ T cells