title: Hela cells transduced with ID2-S5D at time 10h [SA126]

city: New York

first: Anna

last: Lasorella

state: New York

address: 1130 St Nicholas Ave

department: Irving Cancer Research Center

institute: Columbia University

description:
SA126
RawCounts.txt

data_processing:
We use RTA (Illumina) for base calling and bcl2fastq2 (version 2.20) for converting BCL to fastq format, coupled with adaptor trimming.
We performed a pseudoalignment to a kallisto index created from transcriptomes (GRCh38) using kallisto.
We computed the estimated counts for each gene using tximport R package (v.1.20.0).
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: RawCounts.txt: Tab-delimited text file includes estimated counts for each sample and gene.

source_name: HeLa cells

extract_protocol:
Total RNA was purified with TRIZOL (ThermoFisher, #155960026).
Total RNA was poly9A)-selected and sequencing libraries were constructed using the TruSeq Stranded mRNA Library Prep (lllumina, # 20020594) and Seq RNA CD Index Plate (Illumina, 20019792). Libraries were sequenced on a NovaSeq 6000 System (Illumina). We multiplex samples in each lane, which yields targeted number of paired-end 100bp reads for each sample.

value: HeLa

tag: condition

tag: time point

tag: replicate


title: 786-M1A-sgHNF1B_8_REP_3

status: Public on Mar 11 2022

type: SRA

city: Helsinki

first: Sakari

last: Vanharanta

address: Haartmaninkatu 8

department: Translational Cancer Medicine Program

country: Finland

institute: University of Helsinki

library_source: transcriptomic

data_processing:
Fastq files were mapped to the human transcriptome using Bowtie2.
Relative gene expression was determined using RSEM.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: *.genes.results.txt: Gene-level RSEM output files.

molecule: total RNA

organism: Homo sapiens

source_name: ccRCC cell line

growth_protocol: Cells grown under standard tissue culture conditions in RPMI + 10% FBS.

extract_protocol:
RNA was extracted from 80% confluent cells using the RNeasy Mini Kit (Qiagen 74104) following the manufacturer’s recommendations. RNA quality was assessed with the RNA Nano 6000 kit (Agilent 5067-1511) and Agilent Bioanalyzer 2100 instrument.
Purified RNA (1µg) was used to prepare Illumina multiplexed sequencing libraries. Libraries were prepared following the KAPA Stranded mRNA-seq Kit (KR0960) Illumina platforms sample preparation protocol (v3.15). Briefly, poly(A) RNA was captured with magnetic oligo-dT beads and heat fragmented (94°C) to a size of 200-300bp. Fragmented RNA was used for 1st strand cDNA synthesis, generating cDNA-RNA hybrids which were used for 2nd strand synthesis and marking to obtain dscNDA marked with dUTP. Newly synthesized fragments were end-repaired and A-tailed to add dAMP to the 3’-end of dscDNA fragments. These 3’-dA-tailed library fragments were then ligated with 3’-dTMP adapters. After adapter ligation, libraries were cleaned up using the Agencourt AMPure XP reagent (A63880) according to manufacturer’s recommendations. Purified, adapter-ligated DNA was amplified for 15 cycles. PCR libraries were pooled in equimolar concentrations and sequenced.

tag: cell line

tag: construct


title: Hela cells transduced with ID2-S5D at time 8h [SA124]

country: USA

description:
SA124
RawCounts.txt


title: Hela cells transduced with ID2-S5D at time 10h [SA125]

description:
SA125
RawCounts.txt


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-025

city: Seattle

first: Chengxiang

last: Qiu

state: WA

address: William H. Foege Hall, 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

description:
sci-RNA-seq3 with mouse embryo atlas (deeper sequencing)
sci-RNA-seq3 library

data_processing:
Base calls were converted to fastq format using Illumina’s bcl2fastq/v2.20 and demultiplexed based on PCR i5 and i7 barcodes using maximum likelihood demultiplexing package deML (Renaud et al. 2015) with default settings. Downstream sequence processing and single cell digital expression matrix generation were similar to sci-RNA-seq (Cao et al. 2017) except that RT index was combined with hairpin adaptor index, and thus the mapped reads were split into constituent cellular indices by demultiplexing reads using both the RT index and ligation index (Levenshtein edit distance (ED) < 2, including insertions and deletions).
Briefly, demultiplexed reads were filtered based on RT index and ligation index (ED < 2, including insertions and deletions) and adaptor-clipped using trim_galore/v0.6.5 with default settings. Trimmed reads were mapped to the mouse reference genome (mm10) for mouse embryo nuclei, using STAR/v2.6.1d (Dobin et al. 2013) with default settings and gene annotations (GENCODE VM12 for mouse). Uniquely mapping reads were extracted, and duplicates were removed using the unique molecular identifier (UMI) sequence (ED < 2, including insertions and deletions), reverse transcription (RT) index, hairpin ligation adaptor index and read 2 end-coordinate (i.e. reads with UMI sequence less than 2 edit distance, RT index, ligation adaptor index and tagmentation site were considered duplicates).
Finally, mapped reads were split into constituent cellular indices by further demultiplexing reads using the RT index and ligation hairpin (ED < 2, including insertions and deletions). To generate digital expression matrices, we calculated the number of strand-specific UMIs for each cell mapping to the exonic and intronic regions of each gene with python/v2.7.13 HTseq package (Anders, Pyl, and Huber 2015). For multi-mapped reads, reads were assigned to the closest gene, except in cases where another intersected gene fell within 100 bp to the end of the closest gene, in which case the read was discarded. For most analyses we included both expected-strand intronic and exonic UMIs in per-gene single-cell expression matrices.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files include a cell annotation csv  file, gene annotation csv file, and a gene count sparse matrix file (using scanpy.read_loom to open)

molecule: polyA RNA

organism: Mus musculus

source_name: mouse embryos

growth_protocol: The C57BL/6 mice were obtained from The Jackson Laboratory (Bar Harbor, ME) and plug matings were set up. Noon on the day of the vaginal plug was considered as embryonic day (E) 0.5. Dissections were done as previously described76 and all embryos were immediately snap frozen in liquid nitrogen. All animal procedures were in accordance with institutional, state, and government regulations (IACUC protocol 4378-01).

extract_protocol:
Mouse embryos from different development stages were processed together to reduce batch effect. Each mouse embryo was minced into small pieces by blade in 1 mL ice-cold cell lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630 from77, modified to also include 1% SUPERase In and 1% BSA) and transferred to the top of a 40um cell strainer (Falcon). Tissues were homogenized with the rubber tip of a syringe plunger (5ml, BD) in 4ml cell lysis buffer. The filtered nuclei were then transferred to a new 15ml tube (Falcon) and pelleted by centrifuge at 500xg for 5min and washed once with 1ml cell lysis buffer. The nuclei were fixed in 4ml ice cold 4% paraformaldehyde (EMS) for 15min on ice. After fixation, the nuclei were washed twice in 1ml nuclei wash buffer (cell lysis buffer without IGEPAL), and re-suspended in 500ul nuclei wash buffer.
The samples were split to two tubes with 250ul in each tube and flash frozen in liquid nitrogen. We estimated the nuclei extraction efficiency based on extracted nuclei number vs. expected total nuclei number in each embryo and the nuclei extraction efficiency range from 60% to 85%. Thawed nuclei are permeabilized with 0.2% tritonX-100 (in nuclei wash buffer) for 3 minutes on ice, and briefly sonicated (Diagenode, 12s on low power mode) to reduce nuclei clumping. The nuclei were then washed once with nuclei wash buffer and filtered through 1ml Flowmi cell strainer (Flowmi).
Filtered nuclei were spun down at 500xg for 5min and resuspended in nuclei wash buffer. Nuclei from each mouse embryo were then distributed into several individual wells in four 96-well plates. The links between well id and mouse embryo were recorded for downstream data processing. For each well, 80,000 nuclei (16 µL) were mixed with 8 µl of 25 µM anchored oligo-dT primer (5′- /5Phos/CAGAGCNNNNNNNN[10bp barcode]TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT-3′, where “N” is any base; IDT) and 2 µL 10 mM dNTP mix (Thermo), denatured at 55°C for 5 min and immediately placed on ice. 14 µL of first-strand reaction mix, containing 8 µL 5X Superscript IV First-Strand Buffer (Invitrogen), 2 µl 100 mM DTT (Invitrogen), 2 µl SuperScript IV reverse transcriptase (200 U/μl, Invitrogen), 2 μL RNaseOUT Recombinant Ribonuclease Inhibitor (Invitrogen), was then added to each well.
Reverse transcription was carried out by incubating plates by gradient temperature (4°C 2 minutes, 10°C 2 minutes, 20°C 2 minutes, 30°C 2 minutes, 40°C 2 minutes, 50°C 2 minutes and 55°C 10 minutes). After ligation reaction, 60µL nuclei dilution buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 1% BSA) was added into each well. Nuclei from all wells were pooled together and spun down at 500xg for 10min. Nuclei were then resuspended in nuclei wash buffer and redistributed into another four 96-well plates with each well including 4µL T4 ligation buffer (NEB), 2µL T4 DNA ligase (NEB), 4µL Betaine solution (5M, Sigma-Aldrich), 6µL nuclei in nuclei wash buffer, 8µL barcoded ligation adaptor (100uM, 5’- GCTCTG[9bp or 10bp barcode A]/ideoxyU/ACGACGCTCTTCCGATCT[reverse complement of barcode A]-3’) and 16µL 40% PEG 8000 (Sigma-Aldrich). The ligation reaction was done at 16°C for 3 hours.
After RT reaction, 60µL nuclei dilution buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 1% BSA) was added into each well. Nuclei from all wells were pooled together and spun down at 600xg for 10min. Nuclei were washed once with nuclei wash buffer and filtered with 1ml Flowmi cell strainer (Flowmi) twice, counted and redistributed into eight 96-well plates with each well including 2,500 nuclei in 5µL nuclei wash buffer and 5µL elution buffer (Qiagen).
1.33 μl mRNA Second Strand Synthesis buffer (NEB) and 0.66 μl mRNA Second Strand Synthesis enzyme (NEB) were then added to each well, and second strand synthesis was carried out at 16°C for 180 min. For tagmentation, each well was mixed with 11 μL Nextera TD buffer (Illumina) and 1 μL i7 only TDE1 enyzme (62.5nM, Illumina), and then incubated at 55°C for 5 min to carry out tagmentation. The reaction was then stopped by adding 24 μL DNA binding buffer (Zymo) per well and incubating at room temperature for 5 min. Each well was then purified using 1.5x AMPure XP beads (Beckman Coulter).
In the elution step, each well was added with 8µL nuclease free water, 1µL 10X USER buffer (NEB), 1µL USER enzyme (NEB) and incubated at 37°C for 15 min. Another 6.5µL elution buffer was added into each well. The AMPure XP beads were removed by magnetic stand and the elution product was transferred into a new 96-well plate. For PCR amplification, each well (16µL product) was mixed with 2μL of 10 μM indexed P5 primer (5′-AATGATACGGCGACCACCGAGATCTACAC[i5]ACACTCTTTCCCTACACGACGCTCTTCCGATCT-3′; IDT), 2 μL of 10 μM P7 primer (5′-CAAGCAGAAGACGGCATACGAGAT[i7]GTCTCGTGGGCTCGG-3′, IDT), and 20 μL NEBNext High-Fidelity 2X PCR Master Mix (NEB). Amplification was carried out using the following program: 72°C for 5 min, 98°C for 30 sec, 12-14 cycles of (98°C for 10 sec, 66°C for 30 sec, 72°C for 1 min) and a final 72°C for 5 min.

tag: developmental stage

tag: strain


title: 786-M1A-sgHNF1B_8_REP_2


title: ATAC-seq_RCCJF_Rep1

library_source: genomic

data_processing:
Pre-processing fastq files: Cutadapt (version 2.10) was used to remove adapter contaminations identified by FastQC (version 0.11.9), trim low quality bases from read ends (<20) and discard reads shorter than 10 bases.
Mapping to human genome: Reads were mapped to hg38 using BWA (version 0.7.17).
File formatting: The output SAM files were converted to bigwig format using samtools (version 1.9) (SAM -> BAM). Reads which mapped to blacklisted regions and reads which did not map to chr1-22, X and Y were removed. Reads with low mapping quality (MAPQ<20) were also removed. Reads were corrected for the Tn5 offset (+ve strand: +4bp, -ve strand: -5bp). DeepTools (version 3.5.0) was used to convert BAM into bigwig.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files

molecule: genomic DNA

extract_protocol:
Cells at 75% confluency were trypsinised, counted and 50,000 cells were subjected to ATAC-seq protocol directly as previously described (Buenrostro et al., 2013).
Libraries were prepared using the Illumina Nextera DNA library preparation kit (FC-121-1030) and purified using the minElute PCR purification kit (Qiagen 28004). Following purification, library fragments were amplified using NEBNext PCR master mix and custom Nextera PCR primers. Libraries were amplified for a total of 8-12 cycles and cleaned-up using the Agencourt AMPureXP reagent (A63880) according to manufacturer's recommendations, and pooled in equimolar concentrations prior to sequencing.

treatment_protocol: 1μg/ml doxycycline for 10 days to induce the expression of shRNA constructs.

value: RCC-JF


title: Hela cells transduced with ID2-S5D at time 8h [SA123]

description:
SA123
RawCounts.txt


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-026


title: N_rep_2

city: Waltham

first: Sebastian

last: Kadener

state: MA

address: 415 South Street

institute: Brandeis University

description:
RNA-seq polyA+
transfected HEK293T
N_2_all_S2_
CovidProteinCounts_normalized_L1

data_processing:
Alignment to the human genome (hg38) using STAR
CircRNA expression anlysis using find_circ.py (Memczak S et al 2013)
Counting number of reads for each gene using ESAT for polyA data and featureCounts for total RNA data
Genome_build: hg38
Supplementary_files_format_and_content: Table with reads counts for each gene.
Supplementary_files_format_and_content: Table with  back-spliced reads and linear spliced reads for total RNA data

growth_protocol: HEK293T cells were a kind gift from Dr. Marr at Brandeis University. HEK293T were maintained in Dulbecco's Modified Eagle's Medium (Genesee Scientific, 25-500), supplemented with 10% serum (FetalPlex, Gemini Bio/Fisher, # 100-602), and 1X Penicillin-Streptomycin (Penicillin-Streptomycin 100x, Genesee Scientific, 25-512).

extract_protocol:
Total RNA was extracted using Trizol reagent (Sigma) and treated with DNase I (NEB) following the manufacturer's protocol.
For 3' RNA sequencing libraries, 75ng of RNA were used as input  following CelSeq2(Hashimshony et al., 2016) protocol, changing the UMI to 6 bases. Sequencing was performed on Illumina NextSeq 500. For total RNA libraries 40ng of rRNA depleted RNA was used as a starting material for library preparation. NEBNext rRNA Depletion kit( NEB #E7405) was used to deplete ribosomal RNA. Libraries were prepared using the NEXTFLEX® Rapid Directional RNA-Seq Kit 2.0 by PerkinElmer, following the manufacturer’s instructions. The samples were sequenced by Novogene (Novogene Corporation Inc. 8801 Folsom BLVD, Suite 290, Sacramento, CA 95826) with Hiseq-4000.
3' RNA sequencing libraries stranded, CelSeq2 based. For total RNA libraries, stranded  ligation-based.

treatment_protocol:
Plasmids pLVX-EF1alpha-SARS-CoV-2-proteins-2xStrep-IRES-Puro proteins are a gift from Nevan Krogan (Addgene)(Gordon et al., 2020). The day before transfection, 0.35*106 cells per well were plated in 12 well-plates. Then, cells were transfected with PEI (Polyethylenimine 25kD linear from Polysciences, cat# 23966-2). Briefly, 1500ng of total DNA (1200 ng of pLVX-EF1alpha-SARS-CoV-2-proteins-2xStrep-IRES-Pur + 300ng of pLVX-EF1alpha-eGFP-2xStrep-IRES-Puro ) were incubated at RT for 20 min with PEI, with a ratio 3 1=PEI
DNA in 100ul of serum free medium, and the mixture was added to the cells.  RNA extraction was performed at the indicated timepoint after transfection, or at 48h if not indicated.

tag: transfection

tag: timepoint

value: 48h post transfection

tag: treatment

value: no treatment


title: 786-M1A-sgHNF1B_2_REP_4


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-023


title: N_rep_1

description:
RNA-seq polyA+
transfected HEK293T
N_1_all_S1_
CovidProteinCounts_normalized_L1


title: Hela cells transduced with ID2-S5D at time 8h [SA122]

description:
SA122
RawCounts.txt


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-024


title: Hela cells transduced with ID2-S5D at time 0h [SA121]

description:
SA121
RawCounts.txt


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-022


title: 786-M1A-sgHNF1B_8_REP_1


title: 786-M1A-sgHNF1B_2_REP_3


title: Hela cells transduced with ID2-S5D at time 10h [SA127]

description:
SA127
RawCounts.txt


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-028


title: 786-M1A-sgHNF1B_2_REP_2


title: ccRCC_D0_sample_3_2

description: Tumours formed in mice on doxycycline diet after which doxycycline was removed. Samples collected at different time points after doxycycline removal.

data_processing:
Non-mouse reads were identified by exluding all reads that map to the mouse trasncriptome (mm10) using Bowtie2. The remaining reads were then mapped to human transcriptome (hg38) using Bowtie2. Relative expression of human transcripts was determined using RSEM.
Genome_build: hg38
Supplementary_files_format_and_content: Gene level RSEM output files.

source_name: ccRCC xenograft

growth_protocol: Xenograft tumours formed by human cancer cells in immunocompromised athymic mice.

extract_protocol:
RNA was extracted from fresh frozen tumours using the RNeasy Mini Kit (Qiagen 74104) following the manufacturer’s recommendations. RNA quality was assessed with the RNA Nano 6000 kit (Agilent 5067-1511) and Agilent Bionalyzer 2100 instrument.
Purified RNA (1µg) was used to prepare Illumina multiplexed sequencing libraries. Libraries were prepared following the KAPA Stranded mRNA-seq Kit (KR0960) Illumina platforms sample preparation protocol (v3.15). Briefly, poly(A) RNA was captured with magnetic oligo-dT beads and heat fragmented (94°C) to a size of 200-300bp. Fragmented RNA was used for 1st strand cDNA synthesis, generating cDNA-RNA hybrids which were used for 2nd strand synthesis and marking to obtain dscNDA marked with dUTP. Newly synthesized fragments were end-repaired and A-tailed to add dAMP to the 3’-end of dscDNA fragments. These 3’-dA-tailed library fragments were then ligated with 3’-dTMP adapters. After adapter ligation, libraries were cleaned up using the Agencourt AMPure XP reagent (A63880) according to manufacturer’s recommendations. Purified, adapter-ligated DNA was amplified for 15 cycles. PCR libraries were pooled in equimolar concentrations and sequenced.

tag: cell type

value: renal carcinoma

value: HIF2A knock-out clone derived from 786-M1A cells

tag: transgene

value: doxycycline-dependent HIF2A contruct

tag: mouse dox status

value: on dox


title: BM sample donor2

city: Verona

first: Francisco

middle: Miguel Angel

last: Bianchetto-Aguilera

state: VR

address: Strade le Grazie, 8

department: Department of Medicine

country: Italy

institute: University of Verona

description:
BD Single-Cell multiplexing Kit SampleTag08_hs
BD Single-Cell multiplexing Kit SampleTag09_hs
BD Single-Cell multiplexing Kit SampleTag10_hs
BD Single-Cell multiplexing Kit SampleTag11_hs
BD Single-Cell multiplexing Kit SampleTag12_hs

data_processing:
Basecalls performed using bcl2fastq version 2.20.0.422
FASTQ files obtained from sequencing were provided to the BD Rhapsody WTA Analysis Pipeline Targeted Multiplex Rhapsody Pipeline v1.0 with default settings
The quality-filtered R1 reads were analyzed to identify the cell label sequence (CL), Molecular Identifier sequence (UMI), and poly-dT tail sequence. Putative cells information were combined together with RSEC-adjusted molecules to generate a single-cell expression matrix.
Raw gene expression matrices were read into R (version ) separately and converted to Seurat objects using the Seurat R package (3.2.2)
Genome_build: hg38
Supplementary_files_format_and_content: Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every single cell

extract_protocol:
The different cell populations (NCP1s, NCP2s, NCP3s, NCP4s and cMoPs) were sorted from BM by using a Becton Dickinson FACS Aria Fusion (BD Biosciences) and then labelled with the BD Single-Cell Multiplexing Kit (BD Biosciences), strictly following the manufacturer's protocol. Both cell viability and counts were then evaluated by the BD Rhapsody scanner, and only samples with high viability (> 85 %) were used for sequencing. Approximately 15000 cells were pooled together and loaded in a single BD Rhapsody cartridge. The procedure described above was repeated for three different BMs
cDNA Libraries were prepared using the BD Rhapsody Whole Transcriptome Analysis (WTA) Amplification kit and BD Single-Cell Multiplexing kit (BD Biosciences) following the manufacturer's protocol

tag: subject

tag: tissue

value: bone marrow

value: mixed cells (NPs, cMoP)


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-021


title: BM sample donor3

description:
BD Single-Cell multiplexing Kit SampleTag01_hs
BD Single-Cell multiplexing Kit SampleTag02_hs
BD Single-Cell multiplexing Kit SampleTag03_hs
BD Single-Cell multiplexing Kit SampleTag04_hs
BD Single-Cell multiplexing Kit SampleTag05_hs


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-019


title: Hela cells transduced with ID2 wild type at time 10h [SA118]

description:
SA118
RawCounts.txt


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-020


title: ccRCC_D0_sample_3_1


title: Hela cells transduced with ID2 wild type at time 10h [SA117]

description:
SA117
RawCounts.txt


title: Hela cells transduced with ID2-S5D at time 0h [SA119]

description:
SA119
RawCounts.txt


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-018


title: Hela cells transduced with ID2 wild type at time 10h [SA116]

description:
SA116
RawCounts.txt


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-017


title: GC7_2

city: Edinburgh

first: Thomas

last: Tan

address: Charlotte Auerbach Road

department: Institute of Immunology and Infection Research

country: United Kingdom

institute: The University of Edinburgh

description: SIINFEKL activated and then IL-2 expanded

data_processing:
Illumina Universal Adapter (AGATCGGAAGAGC) were trimmed off in reads using Cutadapt
Pair-end reads were mapped to mouse genome (GRCm38.96) using STAR.
Gene raw counts were generated with featureCounts in Rsubread.
CPM normalisation and differential gene analysis were done with edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw gene counts for each sample

source_name: lymphocyte

growth_protocol: Cells were cultured in IMDM medium supplemented with 10% FCS, L-glutamine, 100U/ml penicillin, 100U/ml streptomycin and 50μM 2β-ME. 100nM SIINFEKL (N4) peptide were added to culture media and the cells were incubated at 37°C for 2 days. Cells were then washed off peptide, and cultured for 2 days in the culture media supplemented with 20ng/mL recombinant human IL-2 in the presence or absence of 10µM GC7.

extract_protocol:
2 million cells were harvested. Total RNA was extracted using Direct-Zol RNA Miniprep (Zymo Research)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: CD8 T cell


title: GC7_1


title: GC7_3


title: GC7_4


title: Hela cells transduced with ID2 wild type at time 8h [SA115]

description:
SA115
RawCounts.txt


title: Hela cells transduced with ID2-S5D at time 0h [SA120]

description:
SA120
RawCounts.txt


title: ccRCC_D0_sample_1


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-016


title: Mock_4


title: BM sample donor1

description:
BD Single-Cell multiplexing Kit SampleTag03_hs
BD Single-Cell multiplexing Kit SampleTag04_hs
BD Single-Cell multiplexing Kit SampleTag05_hs
BD Single-Cell multiplexing Kit SampleTag06_hs
BD Single-Cell multiplexing Kit SampleTag07_hs


title: Hela cells transduced with ID2 wild type at time 8h [SA113]

description:
SA113
RawCounts.txt


title: ccRCC_D3_sample_3

value: dox off for 72H


title: Hela cells transduced with ID2 wild type at time 8h [SA114]

description:
SA114
RawCounts.txt


title: ccRCC_D3_sample_2_1


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-015


title: Hela cells transduced with ID2 wild type at time 0h [SA112]

description:
SA112
RawCounts.txt


title: 786-M1A-sgHNF1B_2_REP_1


title: Mock_3


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-014


title: ccRCC_D0_sample_2


title: ccRCC_D3_sample_2_2


title: Hela cells transduced with ID2 wild type at time 0h [SA111]

description:
SA111
RawCounts.txt


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-013


title: Mock_1


title: S_POS_3

city: Beijing

first: Huilei

last: Zhang

address: 15, Datun road, Chaoyang District

country: China

institute: Institute of Biophysics

data_processing:
Illumina HiSeqTM2500/4000 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 version 2.1.0 with parameters --dta-cufflinks
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cuffquant following by cuffnorm
Genome_build: mm10
Supplementary_files_format_and_content: excel files include readcount values for each group

source_name: S100A4+ CD8+ TEM

growth_protocol: Murine CD8+TEM cells that isolated from the OVA-induced asthma model of S100A4WT-EGFP mice were sorted by flow cytometry into two subset populations, CD3+CD8+CD4-CD44+CD62L-EGFP- and CD3+CD8+CD4-CD44+CD62L-EGFP+.

extract_protocol:
Total RNA was extracted by commerical RNA extraction Kit
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: untreated

tag: strain background

tag: genotype/variation

value: spleen


title: Mock_2


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-011


title: Hela cells transduced with ID2 wild type at time 0h [SA110]

description:
SA110
RawCounts.txt

tag: condition


title: S_POS_1


title: ccRCC_0H_sample_5


title: Hela cells transduced with empty vector at time 10h [SA108]

description:
SA108
RawCounts.txt

value: EV

tag: time point


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-009


title: ccRCC_0H_sample_3


title: S_POS_2


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-010


title: ccRCC_0H_sample_4


title: Hela cells transduced with empty vector at time 10h [SA107]

description:
SA107
RawCounts.txt

tag: replicate


title: S_NE_2

source_name: S100A4- CD8+ TEM


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-008


title: Hela cells transduced with empty vector at time 8h [SA106]

description:
SA106
RawCounts.txt

tag: cell line


title: S_NE_1


title: ccRCC_D3_sample_1


title: Hela cells transduced with empty vector at time 8h [SA105]

description:
SA105
RawCounts.txt


title: ccRCC_32H_sample_6

value: dox off for 32H


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-007


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-012


title: ccRCC_32H_sample_5


title: Treat_3

city: Shanghai

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

institute: Shanghai Jiao Tong University

data_processing:
BBMAP used for triming reads. It can binning reads based on mapping to multiple references at once
Mapping sequencing RNA reads to align genome assembly using sofeware Hisat2
DEseq2 used to analyze the difference expression of mRNA
Supplementary_files_format_and_content: tab-delimited text files include the number of reads relative RPKM values, and P-values for control and experimental group Sample.

source_name: Female germ line stem cells

extract_protocol:
Total RNA was extracted from FGSCs using Trizol reagent (Life Technologies, CA). Next, 1000 ng of the digested RNA was used for the VAHTSTM mRNA-seqv2 Library Prep kit for Illumina1, and sequencing libraries were created according to the manufacturer's protocol.
The extracted further treated with DNase to remove genomic DNA contamination. Isolation of mRNA was performed using the Oligotex mRNA Mini Kit (Qiagen GmbH, Hilden, Germany) and the mRNA was then used for RNA-Seq library preparation with the NEB Next Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA, USA). The library was then subjected to Illumina sequencing with paired-end 2x150 as the sequencing mode.

value: C89 treated group


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-006


title: Treat_2


title: ccRCC_32H_sample_4


title: S_NE_3


title: Hela cells transduced with empty vector at time 8h [SA104]

description:
SA104
RawCounts.txt


title: Hela cells transduced with empty vector at time 10h [SA109]

description:
SA109
RawCounts.txt


title: Treat_1


title: ccRCC_0H_sample_6


title: Hela cells transduced with empty vector at time 0h [SA103]

description:
SA103
RawCounts.txt


title: ccRCC_32H_sample_2


title: DMSO_3

value: control group


title: Hela cells transduced with empty vector at time 0h [SA101]

description:
SA101
RawCounts.txt

value: HeLa


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-003


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-004


title: ccRCC_32H_sample_1


title: Hela cells transduced with empty vector at time 0h [SA102]

description:
SA102
RawCounts.txt


title: DMSO_2


title: DMSO_1


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-002


title: Nsp1014_R1_3

description:
total RNA-seq (ribo-)
transfected HEK293T
Nsp1014_3_
Nsp14_totalRNA_normalized_counts_all

value: Nsp14-SARS-CoV-2 and Nsp10 SARS-CoV-6


title: ccRCC_28H_sample_6

value: dox off for 28H


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-001


title: Nsp1014_R1_2

description:
total RNA-seq (ribo-)
transfected HEK293T
Nsp1014_2_
Nsp14_totalRNA_normalized_counts_all

value: Nsp14-SARS-CoV-2 and Nsp10 SARS-CoV-4

value: 48h post transfection

value: no treatment


title: ccRCC_28H_sample_4

value: renal carcinoma

value: HIF2A knock-out clone derived from 786-M1A cells

value: doxycycline-dependent HIF2A contruct


title: ccRCC_28H_sample_5


title: Nsp1014_R1_1

description:
total RNA-seq (ribo-)
transfected HEK293T
Nsp1014_1_
Nsp14_totalRNA_normalized_counts_all

value: Nsp14-SARS-CoV-2 and Nsp10 SARS-CoV-2


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-005


title: Cre.Pos.4OHT_S11

city: Brisbane

first: Jasmin

last: Straube

state: QLD

address: 300 Herston Rd

country: Australia

institute: QIMR Berghofer

data_processing:
Reads were trimmed for adapter sequences using Cutadapt (version 1.11) and aligned using STAR (version 2.5.2a) to the GRCM38 assembly using the gene, transcript, and exon features of Ensembl (release 67) gene model. Expression was estimated using RSEM (version 1.2.30).
Transcripts with zero read counts across all samples were removed prior analysis. Normalisation of RSEM expected read counts was performed by dividing by million reads mapped to generate counts per million (CPM), followed by the trimmed mean of M-values (TMM) method from the edgeR package.
Genome_build: GRCM38
Supplementary_files_format_and_content: tab-delimited text files include RSEM expected read count values for each sample

source_name: Mouse Embryonic Fibroblast (MEF)

growth_protocol: Primary MEFs were generated as previously described from E13.5 pregnant mouse (Shi, W et al 2013 PLoS Genetics). For immortalisation, viral media collected from pMSCV- Puromycin (Puro) SV40 large T-antigen or pMSCV- Blasticidin (Bsd) SV40 large T-antigen plasmids were transduced to the passage 1 MEFs. All MEFs were maintained in Dulbecco’s Modified Eagle’s Media (DMEM) from Life Technologies™, Carlsbad, CA, USA containing 10 % Foetal Bovine Serum (FBS) from SAFC Biosciences™, Lenexa, USA and 1 % Penicillin-Streptomycin (Life Technologies™).

extract_protocol:
RNA extraction was performed using QIAgen RNeasy® Plus Mini kit (Qiagen, 74106, Valencia, CA, USA) as per the user’s manual
Paired end seq 1 x NextSeq 150 cycle (2x75bp) High Output Run 3, 12 x TruSeq Stranded Total RNA (Ribo-Zero GOLD) Library Preparation

treatment_protocol: Immortalised RosaCreERT2+ Ssb1Flox/Flox, Ssb2 Flox/Flox and Cre negative Ssb1Flox/Flox, Ssb2 Flox/Flox Mouse Embryonic Fibroblasts treated with Ethanol or 4-OHT for 5 days

value: SV40T antigen immortalised MEF

value: E13.5 mouse embryo

value: 5 days post tamoxifen treatment

tag: genotype

value: Cre +ve; Ssb1 Fl/F; Ssb2 Fl/Fl


title: ccRCC_28H_sample_3


title: ccRCC_32H_sample_3

value: dox off for 32H


title: Cre.Neg.EtOH_S10

value: 5 days post vehicle treatment

value: Cre -ve; Ssb1 Fl/Fl; Ssb2 Fl/Fl


title: Cre.Pos.4OHT_S12


title: ccRCC_24H_sample_6

value: dox off for 24H


title: Nsp10_R1_3

description:
total RNA-seq (ribo-)
transfected HEK293T
Nsp10_3
Nsp14_totalRNA_normalized_counts_all


title: Nsp10_R1_2

description:
total RNA-seq (ribo-)
transfected HEK293T
Nsp10_2
Nsp14_totalRNA_normalized_counts_all


title: macrophages of healthy male donor 2 treated with TLC

type: RNA

city: Duesseldorf

first: Anna-Kathrin

last: Schupp

address: Moorenstr. 5

country: Germany

institute: Heinrich Heine University Duesseldorf

description: gene expression data from TLC treated cells (Donor 2)

hyb_protocol: After fragmentation labelled cRNA was hybridized to Affymetrix PrimeView Human Gene Expression Microarrays for 16 h at 45 °C, stained by streptavidin/phycoerythrin conjugate and scanned according to the manufacturer’s protocol. Fluidics Station 450 was used.

scan_protocol: Using the Affymetrix Calvin Scan Acquisition on the Affymetrix GeneChip Scanner 3000 7G with the Affymetrix GeneChip Command Console Scan Control.

data_processing: Data analyses on Affymetrix CEL files were conducted with GeneSpring GX software (Vers. 12.5; Agilent Technologies). Probes within each probe set were summarized by Rate Monotonic Analysis (RMA) after quantile normalization of probe level signal intensities across all samples to reduce inter-array variability. Input data pre-processing was concluded by baseline transformation to the median of all samples. To further improve signal-to-noise ratio, a given probe set had to be expressed above background (i.e., fluorescence signal of a probe set was detected within the 20th and 100th percentiles of the raw signal distribution of a given array) in all three replicates in at least one of two, or both conditions to be subsequently analysed in pairwise comparisons. Differential gene expression was statistically determined by moderated T-tests. If applicable, the resulting p-values were corrected for multiple testing (Benjamini-Hochberg FDR).

label: biotin labeling

source_name: Donor 2

label_protocol: Synthesis of cDNA and subsequent biotin labelling of cRNA was performed according to the manufacturer’s instructions (3′ IVT Plus Kit; Affymetrix, Inc., Karlsruhe, Germany). Briefly, 100 ng of pooled total RNA were converted to cDNA, followed by in vitro transcription and biotin labelling of cRNA.

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from human blood (healthy volunteers, male) using buffy coats obtained from the Heinrich-Heine-University of Düsseldorf, Blood Transfusion Service, by Ficoll Plaque gradient centrifugation. CD14-positive cells were separated by antibodies labelled with magnetic beads, according to the manufacturer’s instructions, using human CD14 MicroBeads, LS columns, for QuadroMACS (Miltenyi Biotec, Bergisch Gladbach, Germany) and 3 × 106 cells/well were cultured for 9 days. RPMI medium supplemented with 10% FCS, 100 U/ml penicillin, 100 mg/ml streptomycin and 25 ng/ml human M-CSF was used to differentiate these cells into macrophages. Medium volume was increased every 3rd day by 30% inclusive of freshly added M-CSF. Cells were grown at 37 °C in 5% CO2.

extract_protocol: Total RNA from cells was prepared with the ReliaPrep™ RNA Cell Miniprep System (Promega, Mannheim, Germany).

treatment_protocol: Primary human macrophages were pre-incubated for 45 min with TLC (50 μM) and then stimulated with LPS (10 ng/ml) for 3 h or left untreated.

tag: Sex

value: male

value: macrophage

value: TLC


title: macrophages of healthy male donor 3 treated with TLC

description: gene expression data from  TLC treated cells (Donor 3)

source_name: Donor 3


title: Cre.Neg.EtOH_S9

tag: strain


title: macrophages of healthy male donor 1 treated with TLC

description: gene expression data from TLC treated cells (Donor 1)

source_name: Donor 1


title: ccRCC_0H_sample_2

value: on dox


title: Nsp14_R1_3

description:
total RNA-seq (ribo-)
transfected HEK293T
Nsp14_3
Nsp14_totalRNA_normalized_counts_all

tag: transfection

value: 48h post transfection

value: no treatment


title: Cre.Pos.Uninduced_S7

value: untreated


title: Cre.Neg.4OHT_S6


title: Nsp10_R1_1

description:
total RNA-seq (ribo-)
transfected HEK293T
Nsp10_1
Nsp14_totalRNA_normalized_counts_all

tag: timepoint


title: ccRCC_24H_sample_5

value: renal carcinoma

value: HIF2A knock-out clone derived from 786-M1A cells

value: doxycycline-dependent HIF2A contruct


title: Cre.Pos.Uninduced_S8

value: SV40T antigen immortalised MEF

value: E13.5 mouse embryo


title: Nsp14_R1_2

description:
total RNA-seq (ribo-)
transfected HEK293T
Nsp14_2
Nsp14_totalRNA_normalized_counts_all

tag: treatment


title: ccRCC_0H_sample_1

tag: cell type


title: Cre.Neg.4OHT_S5

value: 5 days post tamoxifen treatment


title: ccRCC_24H_sample_4

tag: transgene


title: macrophages of healthy male donor 3 treated with LPS

description: gene expression data from LPS treated cells (Donor 3)

value: LPS


title: ccRCC_24H_sample_3

description: Tumours formed in mice on doxycycline diet after which doxycycline was removed. Samples collected at different time points after doxycycline removal.

tag: mouse dox status


title: Ctrl_R1_rep_3

description:
total RNA-seq (ribo-)
transfected HEK293T
Ctrl_3_
Nsp14_totalRNA_normalized_counts_all

value: empty vector


title: Cre.Pos.EtOH_S4

value: 5 days post vehicle treatment

value: Cre +ve; Ssb1 Fl/F; Ssb2 Fl/Fl


title: ccRCC_24H_sample_2

value: dox off for 24H


title: Cre.Pos.EtOH_S3


title: Nsp14_R1_1

description:
total RNA-seq (ribo-)
transfected HEK293T
Nsp14_1
Nsp14_totalRNA_normalized_counts_all


title: Ctrl_R1_rep_2

description:
total RNA-seq (ribo-)
transfected HEK293T
Ctrl_2_
Nsp14_totalRNA_normalized_counts_all


title: macrophages of healthy male donor 1 treated with TLC and LPS

description: gene expression data from LPS and TLC treated cells (Donor 1)

value: male

value: macrophage

value: LPS+TLC


title: macrophages of healthy male donor 2 treated with TLC and LPS

description: gene expression data from LPS and TLC treated cells (Donor 2)


title: macrophages of healthy male donor 2 treated with LPS

description: gene expression data from LPS treated cells (Donor 2)


title: ccRCC_24H_sample_1


title: Cre.Neg.Uninduced_S2

value: Cre -ve; Ssb1 Fl/Fl; Ssb2 Fl/Fl


title: ccRCC_28H_sample_2

value: dox off for 28H


title: Cre.Neg.Uninduced_S1

value: untreated


title: Ctrl_R1_rep_1

description:
total RNA-seq (ribo-)
transfected HEK293T
Ctrl_1_
Nsp14_totalRNA_normalized_counts_all

value: 48h post transfection

value: no treatment


title: ccRCC_28H_sample_1

value: renal carcinoma

value: HIF2A knock-out clone derived from 786-M1A cells

value: doxycycline-dependent HIF2A contruct


title: Control hCD34+ scRNAseq

first: Sergei

last: Doulatov

address: 1705 N.E. Pacific Street

department: Hematology

description:
LB1_C11_combined_CB_scRNAseq_cds.RDS
10x scRNAseq

data_processing:
After alignment to hg38 using the 10X genomics Cell Ranger count tool, cells with < 10 percent mitochondrial UMI reads > 50,000  and < 100 UMI reads were filtered from both datasets. The Monocle3 R package (Cao et al., 2019) was used to perform dimensional reduction, UMAP generation, clustering (resolution = 6e-4, seed = 42), and trajectory analysis. For comparison of the dataset to the Atlas of human Blood Cells (ABC) (Xie et al., 2020), the SingleR (Aran et al., 2019) reference-based scRNAseq annotation tool was used based on the annotated immunophenotypes in the ABC reference. Differential gene expression analysis was performed for each indicated cell type using regression analysis based on the dataset of origin, with a q-value (Benjamini/Hochberg) < 0.05. Gene set enrichment analysis (GSEA) was performed using pre-ranked DEGs based on fold change with q-value < 0.05, where genesets with NOM p-value of < 0.05 were considered.
cell data set (CDS) Monocle3 R object
STAR, Subread, DESeq2
BWA, Juicer, HOMER
CellRanger, Monocle 3
Genome_build: hg38
Supplementary_files_format_and_content: .csv, .bw, .bed, .hic, .rds

source_name: 12 week NSG mouse engrafted hCD34+

extract_protocol:
NOD/LtSz-scidIL2Rgnull (NSG) (Jackson Labs) mice were bred and housed at the University of Washington animal care facility. Animal experiments were performed in accordance to institutional guidelines approved by UW animal care committee. Intra-femoral transplants were performed as previously described (Notta et al., 2011). Briefly, 8 – 14 week old mice were irradiated at 275 rads 24 hrs before transplant. To ensure consistency, only female mice were used. Prior to transplantation, mice were temporarily sedated with isoflurane. A 27g needle was used to drill the right femur (injected femur), and 20-30,000 CB CD34+ cells were transplanted in a 25 μl volume using a 29.5g insulin needle.
Transplanted human CB cells were harvested from mice 14 weeks post-transplant. Cells harvested from 5 mice with equivalent engraftment for each condition were pooled and CD34+ cells isolated using the MACS selection column (Miltenyi, cat. #130-046-702). Cells were then stained with the CD34-PE antibody (BD, cat. #555822) and CD34+ cells were further purified by flow sorting on a BD FACS Aria III sorter. Single cell sequencing was performed using the 10X Chromium Next GEM Single Cell 3’ Reagents kit v.3.1 on a Chromium Controller.

value: 12 week NSG mouse engrafted hCD34+

tag: shRNA lentivirus

value: C11 Luciferase shRNA

tag: mouse strain


title: D_SNI3

status: Public on Mar 10 2022

city: Wuhan

first: Zhen

middle: Zhen

last: Xu

state: Hubei

address: 1277 Jiefang Avenue, Kong Hon District

department: Department of Anesthesiology

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

description: The tibial and common peroneal nerves were cut and ligated through SNI, while the sural nerve was preserved. Given that the common peroneal and tibial nerves are closely connected, we subsequently removed 3–5 mm of the distal nerve ends. Care was taken to avoid damaging the nearby sural nerve

data_processing: SNI transcriptomic data were obtained from Institute BGI data portal (https://biosys.bgi.com/) and the detailed sample numbers are listed in Supporting Information Tables S1. Student’s t‐test was also used for comparing the difference between SNI tissues and Sham tissues (P<0.05; |Fold change| > 2).

organism: Rattus norvegicus

source_name: DRG Tissue

growth_protocol: DRG tissue were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.

extract_protocol:
We extracted total RNA from approximately 150 mg of DRG tissue using a MirVana total RNA extraction kit (Ambion, Carlsbad, CA, United States). RNA levels were measured using the Qubit® RNA Assay Kit and a Qubit® 2.0 Fluorometer (Life Technologies, Carlsbad, CA, United States). We assessed RNA integrity using an RNA Nano 6,000 Assay Kit of the Bioanalyzer 2,100 system (Agilent Technologies, CA, United States).
We used 1.5 μg of RNA per sample as the follow-up test material for RNA sample preparation. Whole transcriptome profiling was performed using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, Ipswich, MA, United States) following the manufacturer’s instructions(Xu et al., 2021).

treatment_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

value: SD

tag: tissue

value: dorsal root ganglion (DRG)

value: SNI


title: D_sham3

description: The skin was cut to expose the sciatic nerve and its three terminal branches directly through the part formed by the biceps muscle: the lateral side, common fibular nerve, and tibial nerves. Close the skin

value: sham


title: D_sham2


title: macrophages of healthy male donor 2 treated with DMSO

description: gene expression data from DMSO treated cells (Donor 2)

value: male

value: DMSO


title: D_SNI1


title: macrophages of healthy male donor 1 treated with DMSO

description: gene expression data from DMSO treated cells (Donor 1)

value: macrophage


title: macrophages of healthy male donor 3 treated with DMSO

description: gene expression data from DMSO treated cells (Donor 3)


title: macrophages of healthy male donor 3 treated with TLC and LPS

description: gene expression data from LPS and TLC treated cells (Donor 3)

value: LPS+TLC


title: D_SNI2


title: HEK293FT_TargetSeq_Sample_497

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

institute: Fudan University

data_processing:
DNA deep sequencing read quality was evaluated by FastQC (v0.11.8) and low quality read sequences were trimmed.
BWA-MEM algorithm (0.7.17-r1188) was used to map clean reads to the targeted sequences.
Base substitution calling was performed by SAMtools (v1.9) mpileup function and indel calling was based on the CIGAR values of the SAM/BAM files.
Frequencies of base substitutions and indels are calculated according to reported CFBI (https://github.com/YangLab/CFBI, v1.0.0).
Assembly: hg19 for human samples
Supplementary files format and content: Excel for indel and base subtitution calculation results

source_name: HEK293FT cells

growth_protocol: 293FT (Thermo Fisher Scientific, R70007), U2OS (ATCC® HTB-96) and HeLa (ATCC® CCL-2™) cells were maintained in DMEM (10566, Gibco/Thermo Fisher Scientific) + 10% FBS (16000-044, Gibco/Thermo Fisher Scientific) and regularly tested to exclude mycoplasma contamination.

extract_protocol:
The genomic DNA was extracted from the cells with QuickExtractTM DNA Extraction Solution (QE09050, Epicentre) for subsequent sequencing analysis.
DNA libraries were prepared by using the NEBNext Ultra II FS DNA Library Prep Kit for Illumina. After quantitated with Qubit High-Sensitivity DNA kit (Invitrogen), PCR products with different tags were pooled together for deep sequencing by using the Illumina HiSeq X10 (2×150) or NovaSeq 6000 (2×150) at Shanghai Institute Nutrition and Health, Big Data Center Omics Core, Shanghai, China.

treatment_protocol: For prime editing with pegRNA (spegRNA or apegRNA), 293FT, U2OS or Hela cells were seeded in a 24-well plate at a density of 1×105 per well and transfected with 250 μl serum-free Opti-MEM that contained 2.6 μl LIPOFECTAMINE LTX (Life, Invitrogen), 1.3 μl LIPOFECTAMINE plus (Life, Invitrogen), 0.9 μg PE2 expression vector, 0.3 μg pegRNA (spegRNA or apegRNA) expression vector with 0.1 μg nick-sgRNA expression vector. After 24 hrs, puromycin (ant-pr-1, InvivoGen) was added to the medium at the final concentration of 4 μg/ml.

tag: type

value: DNA


title: HEK293FT_TargetSeq_Sample_495


title: HEK293FT_TargetSeq_Sample_496


title: HEK293FT_TargetSeq_Sample_490


title: HEK293FT_TargetSeq_Sample_491


title: HEK293FT_TargetSeq_Sample_494


title: HEK293FT_TargetSeq_Sample_488


title: HEK293FT_TargetSeq_Sample_489


title: HEK293FT_TargetSeq_Sample_487


title: HEK293FT_TargetSeq_Sample_493


title: HEK293FT_TargetSeq_Sample_486


title: LMNB1 KD hCD34+ scRNAseq

value: LB1 LMNB1 shRNA Sigma, TRCN0000029271

value: NOD/LtSz-scidIL2Rgnull (NSG) (Jackson Labs)


title: D_sham1


title: HEK293FT_TargetSeq_Sample_484


title: HEK293FT_TargetSeq_Sample_485


title: HEK293FT_TargetSeq_Sample_492


title: HEK293FT_TargetSeq_Sample_483


title: HEK293FT_TargetSeq_Sample_477


title: HEK293FT_TargetSeq_Sample_479


title: HEK293FT_TargetSeq_Sample_480


title: HEK293FT_TargetSeq_Sample_476


title: HEK293FT_TargetSeq_Sample_481


title: HEK293FT_TargetSeq_Sample_475


title: HEK293FT_TargetSeq_Sample_474


title: HEK293FT_TargetSeq_Sample_472


title: macrophages of healthy male donor 1 treated with LPS

description: gene expression data from LPS treated cells (Donor 1)

tag: condition

value: LPS


title: HEK293FT_TargetSeq_Sample_478


title: HEK293FT_TargetSeq_Sample_473


title: HEK293FT_TargetSeq_Sample_471


title: HEK293FT_TargetSeq_Sample_469


title: HEK293FT_TargetSeq_Sample_467


title: HEK293FT_TargetSeq_Sample_466


title: HEK293FT_TargetSeq_Sample_470


title: HEK293FT_TargetSeq_Sample_462


title: HEK293FT_TargetSeq_Sample_464


title: HEK293FT_TargetSeq_Sample_468


title: HEK293FT_TargetSeq_Sample_463


title: HEK293FT_TargetSeq_Sample_459


title: HEK293FT_TargetSeq_Sample_460


title: HEK293FT_TargetSeq_Sample_461


title: HEK293FT_TargetSeq_Sample_458


title: HEK293FT_TargetSeq_Sample_457


title: HEK293FT_TargetSeq_Sample_456


title: HEK293FT_TargetSeq_Sample_482


title: HEK293FT_TargetSeq_Sample_452


title: HEK293FT_TargetSeq_Sample_453


title: HEK293FT_TargetSeq_Sample_455


title: HEK293FT_TargetSeq_Sample_454


title: HEK293FT_TargetSeq_Sample_449


title: HEK293FT_TargetSeq_Sample_448


title: HEK293FT_TargetSeq_Sample_446


title: HEK293FT_TargetSeq_Sample_447


title: HEK293FT_TargetSeq_Sample_442


title: HEK293FT_TargetSeq_Sample_445


title: HEK293FT_TargetSeq_Sample_444


title: HEK293FT_TargetSeq_Sample_441


title: HEK293FT_TargetSeq_Sample_443


title: HEK293FT_TargetSeq_Sample_440


title: HEK293FT_TargetSeq_Sample_436


title: HEK293FT_TargetSeq_Sample_438


title: HEK293FT_TargetSeq_Sample_439


title: HEK293FT_TargetSeq_Sample_435


title: HEK293FT_TargetSeq_Sample_465


title: HEK293FT_TargetSeq_Sample_433


title: HEK293FT_TargetSeq_Sample_434


title: HEK293FT_TargetSeq_Sample_432


title: HEK293FT_TargetSeq_Sample_431


title: HEK293FT_TargetSeq_Sample_430


title: HEK293FT_TargetSeq_Sample_428


title: HEK293FT_TargetSeq_Sample_429


title: HEK293FT_TargetSeq_Sample_427


title: HEK293FT_TargetSeq_Sample_425


title: HEK293FT_TargetSeq_Sample_451


title: HEK293FT_TargetSeq_Sample_450


title: HEK293FT_TargetSeq_Sample_422


title: HEK293FT_TargetSeq_Sample_420


title: HEK293FT_TargetSeq_Sample_424


title: HEK293FT_TargetSeq_Sample_421


title: HEK293FT_TargetSeq_Sample_423


title: HEK293FT_TargetSeq_Sample_418


title: HEK293FT_TargetSeq_Sample_417


title: HEK293FT_TargetSeq_Sample_416


title: HEK293FT_TargetSeq_Sample_414


title: HEK293FT_TargetSeq_Sample_415


title: HEK293FT_TargetSeq_Sample_413


title: HEK293FT_TargetSeq_Sample_412


title: HEK293FT_TargetSeq_Sample_411


title: HEK293FT_TargetSeq_Sample_437


title: HEK293FT_TargetSeq_Sample_410


title: HEK293FT_TargetSeq_Sample_409


title: HEK293FT_TargetSeq_Sample_408


title: HEK293FT_TargetSeq_Sample_407


title: HeLa_TargetSeq_Sample_404

value: HeLa


title: HEK293FT;HeLa_TargetSeq_Sample_406

source_name: HEK293FT cells;HeLa cells


title: HEK293FT;HeLa_TargetSeq_Sample_405


title: HEK293FT;HeLa_TargetSeq_Sample_401


title: HEK293FT;HeLa_TargetSeq_Sample_403


title: HEK293FT_TargetSeq_Sample_426


title: HEK293FT;HeLa_TargetSeq_Sample_402


title: HEK293FT_TargetSeq_Sample_397


title: HEK293FT;HeLa_TargetSeq_Sample_400


title: HEK293FT_TargetSeq_Sample_398


title: HEK293FT;HeLa_TargetSeq_Sample_395


title: HEK293FT;HeLa_TargetSeq_Sample_396


title: HEK293FT;HeLa_TargetSeq_Sample_392


title: HEK293FT;HeLa_TargetSeq_Sample_393


title: HEK293FT_TargetSeq_Sample_419


title: HEK293FT;HeLa_TargetSeq_Sample_391


title: HEK293FT;HeLa_TargetSeq_Sample_389


title: HEK293FT_TargetSeq_Sample_390


title: HEK293FT_TargetSeq_Sample_387


title: HEK293FT_TargetSeq_Sample_386


title: HEK293FT;HeLa_TargetSeq_Sample_384


title: HEK293FT;HeLa_TargetSeq_Sample_382


title: HeLa_TargetSeq_Sample_383


title: HEK293FT_TargetSeq_Sample_381


title: HEK293FT;HeLa_TargetSeq_Sample_380


title: HEK293FT_TargetSeq_Sample_377


title: HEK293FT_TargetSeq_Sample_376


title: HEK293FT_TargetSeq_Sample_375


title: HEK293FT;HeLa_TargetSeq_Sample_379


title: HEK293FT_TargetSeq_Sample_374


title: HEK293FT_TargetSeq_Sample_372


title: HEK293FT_TargetSeq_Sample_373


title: HEK293FT_TargetSeq_Sample_399


title: HEK293FT_TargetSeq_Sample_370


title: HEK293FT_TargetSeq_Sample_371


title: HeLa_TargetSeq_Sample_394


title: HEK293FT_TargetSeq_Sample_365


title: HEK293FT_TargetSeq_Sample_368


title: HEK293FT_TargetSeq_Sample_369


title: HEK293FT_TargetSeq_Sample_362


title: HEK293FT_TargetSeq_Sample_361


title: HEK293FT_TargetSeq_Sample_388


title: HEK293FT_TargetSeq_Sample_363


title: HEK293FT_TargetSeq_Sample_358


title: HEK293FT_TargetSeq_Sample_366


title: HEK293FT_TargetSeq_Sample_356


title: HEK293FT_TargetSeq_Sample_364


title: HEK293FT_TargetSeq_Sample_354


title: HEK293FT_TargetSeq_Sample_352


title: HEK293FT_TargetSeq_Sample_359


title: HEK293FT_TargetSeq_Sample_349


title: HEK293FT_TargetSeq_Sample_355


title: HEK293FT;HeLa_TargetSeq_Sample_385


title: HEK293FT_TargetSeq_Sample_353


title: HEK293FT_TargetSeq_Sample_346


title: HEK293FT_TargetSeq_Sample_347


title: HEK293FT_TargetSeq_Sample_348


title: HEK293FT_TargetSeq_Sample_345


title: HEK293FT_TargetSeq_Sample_351


title: HEK293FT;HeLa_TargetSeq_Sample_378


title: HEK293FT_TargetSeq_Sample_344


title: HEK293FT_TargetSeq_Sample_350


title: HEK293FT_TargetSeq_Sample_341


title: HEK293FT_TargetSeq_Sample_343


title: HEK293FT_TargetSeq_Sample_367


title: HEK293FT_TargetSeq_Sample_339


title: HEK293FT_TargetSeq_Sample_340


title: HEK293FT_TargetSeq_Sample_338


title: HEK293FT_TargetSeq_Sample_360


title: HEK293FT_TargetSeq_Sample_335


title: HEK293FT_TargetSeq_Sample_336


title: HEK293FT_TargetSeq_Sample_337


title: HEK293FT_TargetSeq_Sample_333


title: HEK293FT_TargetSeq_Sample_334


title: HEK293FT_TargetSeq_Sample_332


title: HEK293FT_TargetSeq_Sample_331


title: HEK293FT_TargetSeq_Sample_357


title: HEK293FT_TargetSeq_Sample_330


title: HEK293FT_TargetSeq_Sample_328


title: HEK293FT_TargetSeq_Sample_326


title: HEK293FT_TargetSeq_Sample_327


title: HEK293FT_TargetSeq_Sample_325


title: HEK293FT_TargetSeq_Sample_324


title: HEK293FT_TargetSeq_Sample_323


title: HEK293FT_TargetSeq_Sample_322


title: HEK293FT_TargetSeq_Sample_321


title: HEK293FT_TargetSeq_Sample_319


title: HEK293FT_TargetSeq_Sample_320


title: HEK293FT_TargetSeq_Sample_318


title: HEK293FT_TargetSeq_Sample_317


title: HEK293FT_TargetSeq_Sample_316


title: HEK293FT_TargetSeq_Sample_314


title: HEK293FT_TargetSeq_Sample_315


title: HEK293FT_TargetSeq_Sample_342


title: HEK293FT_TargetSeq_Sample_311


title: HEK293FT_TargetSeq_Sample_310


title: HEK293FT_TargetSeq_Sample_307


title: HEK293FT_TargetSeq_Sample_309


title: HEK293FT_TargetSeq_Sample_306


title: HEK293FT_TargetSeq_Sample_304


title: HEK293FT_TargetSeq_Sample_303


title: HEK293FT_TargetSeq_Sample_301


title: HEK293FT_TargetSeq_Sample_302


title: HEK293FT_TargetSeq_Sample_300


title: HEK293FT_TargetSeq_Sample_298


title: HEK293FT_TargetSeq_Sample_299


title: HEK293FT_TargetSeq_Sample_329


title: HEK293FT_TargetSeq_Sample_312


title: HEK293FT_TargetSeq_Sample_294


title: HEK293FT_TargetSeq_Sample_296


title: HEK293FT_TargetSeq_Sample_293


title: HEK293FT_TargetSeq_Sample_291


title: HEK293FT_TargetSeq_Sample_292


title: HEK293FT_TargetSeq_Sample_295


title: HEK293FT_TargetSeq_Sample_290


title: HEK293FT_TargetSeq_Sample_288


title: HEK293FT_TargetSeq_Sample_313


title: HEK293FT_TargetSeq_Sample_283


title: HEK293FT_TargetSeq_Sample_289


title: HEK293FT_TargetSeq_Sample_287


title: HEK293FT_TargetSeq_Sample_280


title: HEK293FT_TargetSeq_Sample_286


title: HEK293FT_TargetSeq_Sample_284


title: HEK293FT_TargetSeq_Sample_285


title: HEK293FT_TargetSeq_Sample_275


title: HEK293FT_TargetSeq_Sample_308


title: HEK293FT_TargetSeq_Sample_274


title: HEK293FT_TargetSeq_Sample_273


title: HEK293FT_TargetSeq_Sample_271


title: HEK293FT_TargetSeq_Sample_282


title: HEK293FT_TargetSeq_Sample_279


title: HEK293FT_TargetSeq_Sample_272


title: HEK293FT_TargetSeq_Sample_305


title: HEK293FT_TargetSeq_Sample_278


title: HEK293FT_TargetSeq_Sample_297


title: HEK293FT_TargetSeq_Sample_276


title: HEK293FT_TargetSeq_Sample_268


title: HEK293FT_TargetSeq_Sample_269


title: HEK293FT_TargetSeq_Sample_265


title: HEK293FT_TargetSeq_Sample_264


title: HEK293FT_TargetSeq_Sample_266


title: HEK293FT_TargetSeq_Sample_261


title: HEK293FT_TargetSeq_Sample_260


title: HEK293FT_TargetSeq_Sample_263


title: HEK293FT_TargetSeq_Sample_259


title: HEK293FT_TargetSeq_Sample_256


title: HEK293FT_TargetSeq_Sample_262


title: HEK293FT_TargetSeq_Sample_258


title: HEK293FT_TargetSeq_Sample_257


title: HEK293FT_TargetSeq_Sample_255


title: HEK293FT_TargetSeq_Sample_281


title: HEK293FT_TargetSeq_Sample_277


title: HEK293FT_TargetSeq_Sample_253


title: HEK293FT_TargetSeq_Sample_254


title: HEK293FT_TargetSeq_Sample_248


title: HEK293FT_TargetSeq_Sample_251


title: HEK293FT_TargetSeq_Sample_249


title: HEK293FT_TargetSeq_Sample_247


title: HEK293FT_TargetSeq_Sample_246


title: HEK293FT_TargetSeq_Sample_245


title: HEK293FT_TargetSeq_Sample_243


title: HEK293FT_TargetSeq_Sample_244


title: HEK293FT_TargetSeq_Sample_242


title: HEK293FT_TargetSeq_Sample_241


title: HEK293FT_TargetSeq_Sample_240


title: HEK293FT_TargetSeq_Sample_250


title: HEK293FT_TargetSeq_Sample_239


title: HEK293FT_TargetSeq_Sample_270


title: HEK293FT_TargetSeq_Sample_238


title: HEK293FT_TargetSeq_Sample_237


title: HEK293FT_TargetSeq_Sample_236


title: HEK293FT_TargetSeq_Sample_235


title: HEK293FT_TargetSeq_Sample_234


title: HEK293FT_TargetSeq_Sample_232


title: HEK293FT_TargetSeq_Sample_233


title: HEK293FT_TargetSeq_Sample_231


title: HEK293FT_TargetSeq_Sample_230


title: HEK293FT_TargetSeq_Sample_229


title: HEK293FT_TargetSeq_Sample_228


title: HEK293FT_TargetSeq_Sample_227


title: HEK293FT_TargetSeq_Sample_225


title: HEK293FT_TargetSeq_Sample_226


title: HEK293FT_TargetSeq_Sample_252


title: HEK293FT_TargetSeq_Sample_222


title: HEK293FT_TargetSeq_Sample_223


title: HEK293FT_TargetSeq_Sample_224


title: HEK293FT_TargetSeq_Sample_219


title: HEK293FT_TargetSeq_Sample_216


title: HEK293FT_TargetSeq_Sample_220


title: HEK293FT_TargetSeq_Sample_221


title: HEK293FT_TargetSeq_Sample_213


title: HEK293FT_TargetSeq_Sample_215


title: HEK293FT_TargetSeq_Sample_217


title: HEK293FT_TargetSeq_Sample_214


title: HEK293FT_TargetSeq_Sample_211


title: HEK293FT_TargetSeq_Sample_210


title: HEK293FT_TargetSeq_Sample_267


title: HEK293FT_TargetSeq_Sample_218


title: HEK293FT_TargetSeq_Sample_212


title: HEK293FT_TargetSeq_Sample_206


title: HEK293FT_TargetSeq_Sample_205


title: HEK293FT_TargetSeq_Sample_209


title: HEK293FT_TargetSeq_Sample_203


title: HEK293FT_TargetSeq_Sample_208


title: HEK293FT_TargetSeq_Sample_202


title: HEK293FT_TargetSeq_Sample_199


title: HEK293FT_TargetSeq_Sample_200


title: HEK293FT_TargetSeq_Sample_201


title: HEK293FT_TargetSeq_Sample_197


title: HEK293FT_TargetSeq_Sample_195


title: HEK293FT_TargetSeq_Sample_196


title: HEK293FT_TargetSeq_Sample_194


title: HEK293FT_TargetSeq_Sample_193


title: HEK293FT_TargetSeq_Sample_191


title: HEK293FT_TargetSeq_Sample_189


title: HEK293FT_TargetSeq_Sample_184


title: HEK293FT_TargetSeq_Sample_192


title: HEK293FT_TargetSeq_Sample_185


title: HEK293FT_TargetSeq_Sample_190


title: HEK293FT_TargetSeq_Sample_188


title: HEK293FT_TargetSeq_Sample_187


title: HEK293FT_TargetSeq_Sample_183


title: HEK293FT_TargetSeq_Sample_186


title: HEK293FT_TargetSeq_Sample_179


title: HEK293FT_TargetSeq_Sample_182


title: HEK293FT_TargetSeq_Sample_181


title: HEK293FT_TargetSeq_Sample_177


title: HEK293FT_TargetSeq_Sample_180


title: HEK293FT_TargetSeq_Sample_178


title: HEK293FT_TargetSeq_Sample_174


title: HEK293FT_TargetSeq_Sample_176


title: HEK293FT_TargetSeq_Sample_173


title: HEK293FT_TargetSeq_Sample_207


title: HEK293FT_TargetSeq_Sample_204


title: HEK293FT_TargetSeq_Sample_171


title: HEK293FT_TargetSeq_Sample_172


title: HEK293FT_TargetSeq_Sample_170


title: HEK293FT_TargetSeq_Sample_198


title: HEK293FT_TargetSeq_Sample_163


title: HEK293FT_TargetSeq_Sample_166


title: HEK293FT_TargetSeq_Sample_160


title: HEK293FT_TargetSeq_Sample_158


title: HEK293FT_TargetSeq_Sample_159


title: HEK293FT_TargetSeq_Sample_169


title: HEK293FT_TargetSeq_Sample_153


title: HEK293FT_TargetSeq_Sample_154


title: HEK293FT_TargetSeq_Sample_164


title: HEK293FT_TargetSeq_Sample_150


title: HEK293FT_TargetSeq_Sample_157


title: HEK293FT_TargetSeq_Sample_167


title: HEK293FT_TargetSeq_Sample_147


title: HEK293FT_TargetSeq_Sample_156


title: HEK293FT_TargetSeq_Sample_161


title: HEK293FT_TargetSeq_Sample_162


title: HEK293FT_TargetSeq_Sample_144


title: HEK293FT_TargetSeq_Sample_168


title: HEK293FT_TargetSeq_Sample_151


title: HEK293FT_TargetSeq_Sample_141


title: HEK293FT_TargetSeq_Sample_148


title: HEK293FT_TargetSeq_Sample_152


title: HEK293FT_TargetSeq_Sample_145


title: HEK293FT_TargetSeq_Sample_149


title: HEK293FT_TargetSeq_Sample_175


title: HEK293FT_TargetSeq_Sample_155


title: HEK293FT_TargetSeq_Sample_140


title: HEK293FT_TargetSeq_Sample_138


title: HEK293FT_TargetSeq_Sample_146


title: HEK293FT_TargetSeq_Sample_165


title: HEK293FT_TargetSeq_Sample_142


title: HEK293FT_TargetSeq_Sample_134


title: HEK293FT_TargetSeq_Sample_133


title: HEK293FT_TargetSeq_Sample_143


title: HEK293FT_TargetSeq_Sample_132


title: HEK293FT_TargetSeq_Sample_139


title: HEK293FT_TargetSeq_Sample_130


title: HEK293FT_TargetSeq_Sample_124


title: HEK293FT_TargetSeq_Sample_126


title: HEK293FT_TargetSeq_Sample_123


title: HEK293FT_TargetSeq_Sample_129


title: HEK293FT_TargetSeq_Sample_121


title: HEK293FT_TargetSeq_Sample_119


title: HEK293FT_TargetSeq_Sample_136


title: HEK293FT_TargetSeq_Sample_117


title: HEK293FT_TargetSeq_Sample_114


title: HEK293FT_TargetSeq_Sample_135


title: HEK293FT_TargetSeq_Sample_112


title: HEK293FT_TargetSeq_Sample_137


title: HEK293FT_TargetSeq_Sample_131


title: HEK293FT_TargetSeq_Sample_111


title: HEK293FT_TargetSeq_Sample_110


title: HEK293FT_TargetSeq_Sample_113


title: HEK293FT_TargetSeq_Sample_127


title: HEK293FT_TargetSeq_Sample_118


title: HEK293FT_TargetSeq_Sample_104


title: HEK293FT_TargetSeq_Sample_108


title: HEK293FT_TargetSeq_Sample_103


title: HEK293FT_TargetSeq_Sample_128


title: HEK293FT_TargetSeq_Sample_116


title: HEK293FT_TargetSeq_Sample_115


title: HEK293FT_TargetSeq_Sample_106


title: HEK293FT_TargetSeq_Sample_125


title: HEK293FT_TargetSeq_Sample_109


title: HEK293FT_TargetSeq_Sample_107


title: HEK293FT_TargetSeq_Sample_99


title: HEK293FT_TargetSeq_Sample_105


title: HEK293FT_TargetSeq_Sample_98


title: HEK293FT_TargetSeq_Sample_100


title: HEK293FT_TargetSeq_Sample_96


title: HEK293FT_TargetSeq_Sample_101


title: HEK293FT_TargetSeq_Sample_95


title: HEK293FT_TargetSeq_Sample_122


title: HEK293FT_TargetSeq_Sample_120


title: HEK293FT_TargetSeq_Sample_94


title: HEK293FT_TargetSeq_Sample_93


title: HEK293FT_TargetSeq_Sample_92


title: HEK293FT;U2OS;HeLa_TargetSeq_Sample_89

source_name: HEK293FT cells;U2OS cells;HeLa cells


title: HEK293FT;U2OS;HeLa_TargetSeq_Sample_90


title: U2OS;HeLa_TargetSeq_Sample_88

source_name: U2OS cells;HeLa cells


title: HEK293FT_TargetSeq_Sample_91


title: HEK293FT;U2OS;HeLa_TargetSeq_Sample_87


title: HEK293FT;U2OS;HeLa_TargetSeq_Sample_86


title: HEK293FT_TargetSeq_Sample_84


title: HEK293FT_TargetSeq_Sample_85


title: U2OS;HeLa_TargetSeq_Sample_82


title: HEK293FT_TargetSeq_Sample_83


title: HEK293FT_TargetSeq_Sample_81


title: HEK293FT_TargetSeq_Sample_79


title: HEK293FT_TargetSeq_Sample_80


title: HEK293FT_TargetSeq_Sample_102


title: HEK293FT;U2OS_TargetSeq_Sample_78

source_name: HEK293FT cells;U2OS cells


title: HEK293FT;U2OS_TargetSeq_Sample_76


title: HEK293FT;U2OS_TargetSeq_Sample_77


title: HEK293FT;U2OS_TargetSeq_Sample_75


title: HEK293FT;U2OS_TargetSeq_Sample_73


title: HEK293FT;U2OS_TargetSeq_Sample_72


title: HEK293FT;U2OS_TargetSeq_Sample_69


title: HEK293FT;U2OS_TargetSeq_Sample_70


title: HEK293FT_TargetSeq_Sample_97


title: HEK293FT;U2OS_TargetSeq_Sample_68


title: HEK293FT;U2OS_TargetSeq_Sample_67


title: HEK293FT;U2OS_TargetSeq_Sample_66


title: HEK293FT;U2OS_TargetSeq_Sample_65


title: HEK293FT;U2OS;HeLa_TargetSeq_Sample_61


title: U2OS;HeLa_TargetSeq_Sample_62


title: HEK293FT;U2OS_TargetSeq_Sample_63


title: HEK293FT;U2OS;HeLa_TargetSeq_Sample_60


title: HEK293FT;U2OS;HeLa_TargetSeq_Sample_59


title: U2OS;HeLa_TargetSeq_Sample_58


title: HEK293FT;U2OS;HeLa_TargetSeq_Sample_55


title: U2OS;HeLa_TargetSeq_Sample_54


title: U2OS;HeLa_TargetSeq_Sample_51


title: HEK293FT;U2OS;HeLa_TargetSeq_Sample_52


title: HEK293FT;U2OS;HeLa_TargetSeq_Sample_57


title: HEK293FT_TargetSeq_Sample_47


title: HEK293FT_TargetSeq_Sample_48


title: HEK293FT;U2OS;HeLa_TargetSeq_Sample_49


title: HEK293FT;U2OS;HeLa_TargetSeq_Sample_53


title: HEK293FT_TargetSeq_Sample_46


title: HEK293FT;U2OS;HeLa_TargetSeq_Sample_50


title: HEK293FT_TargetSeq_Sample_43


title: HEK293FT_TargetSeq_Sample_40


title: HEK293FT_TargetSeq_Sample_39


title: HEK293FT_TargetSeq_Sample_42


title: HEK293FT_TargetSeq_Sample_37


title: HEK293FT;U2OS_TargetSeq_Sample_74


title: HEK293FT_TargetSeq_Sample_41


title: HEK293FT_TargetSeq_Sample_35


title: HEK293FT_TargetSeq_Sample_34


title: HEK293FT_TargetSeq_Sample_36


title: HEK293FT;U2OS;HeLa_TargetSeq_Sample_71


title: HEK293FT_TargetSeq_Sample_33


title: HEK293FT;U2OS_TargetSeq_Sample_64


title: HEK293FT_TargetSeq_Sample_32


title: HEK293FT_TargetSeq_Sample_28


title: HEK293FT;U2OS;HeLa_TargetSeq_Sample_56


title: HEK293FT_TargetSeq_Sample_27


title: HEK293FT_TargetSeq_Sample_30


title: HEK293FT_TargetSeq_Sample_45


city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description:
Cy5 vs. Cy3
Replicate 2 of PknK WT overexpression at 96 h post induction with acetamide

hyb_protocol: Cy3 and Cy5 labeled cRNA samples were mixed and hybridized on the array using the Gene Expression Hybridization kit (Part Number 5190-0404; Agilent) in Sure hybridization Chambers (Agilent) at 65º C for 16 hours. Hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327).

scan_protocol: Scanned using the Agilent Microarray Scanner G2505C at 5 micron resolution. Data extraction from Images was done using Agilent Feature Extraction software .

data_processing: Data Analysis was performed using Genespring GX Software using LOWESS normalization.(Gene based analysis was performed)

organism: Mycolicibacterium smegmatis

source_name: Logarithmic phase cells post induction with 0.2% acetamide

label_protocol: The samples were labeled using Agilent Quick Amp Kit (Part number: 5190-0444). 500ng of total RNA was reverse transcribed using Random hexamer primer tagged to T7 promoter sequence. cDNA thus obtained was converted to double stranded cDNA in the same reaction. Further the cDNA was converted to cRNA in the in-vitro transcription step using T7 RNA polymerase enzyme and Cy3/Cy5 dye was added into the reaction mix. During cRNA synthesis Cy3/Cy5 dye was incorporated into the newly synthesized strands. cRNA obtained was cleaned up using Qiagen RNeasy columns(Qiagen, Cat No: 74106). Concentration and amount of dye incorporated was determined using Nanodrop.

growth_protocol: The M. smegmatis strains LIX79 overexpressing WT PknKMtb  and LIX80 overexpressing K55M mutant PknKMtb along with LIX70 empty vector control were grown as described previously (Malhotra et al., 2012). Briefly, these strains were grown in LB broth supplemented with 0.05% Tween 80 with aeration or on LB agar plates at 37C. Acetamide was added at a final concentration of 0.2% during exponential growth in liquid medium to induce pknKMtb expression.

extract_protocol: RNA extraction was done using TRI Reagent as per manufacturers instructions.

treatment_protocol: RNA was isolated from empty vector control, Wild type PknK overexpression and phosphorylation defective Mutant PknK overexpression strains at 24 h and 96 h post induction with 0.2% acetamide.

value: acteamide

tag: time

source_name: Replicate 2, log phase cells at t=96 h post induction with 0.2% acteamide


description:
Cy3 vs. Cy5--Dye swap
Replicate 1 of PknK K55M Mutant overexpression at 24 h post induction with acetamide

source_name: Replicate 1, log phase cells at t=24 h post induction with 0.2% acteamide


description:
Cy5 vs. Cy3
Replicate 2 of PknK WT overexpression at 24 h post induction with acetamide

source_name: Replicate 2, log phase cells at t=24 h post induction with 0.2% acteamide


description:
Cy5 vs. Cy3
Replicate 2 of PknK K55M Mutant overexpression at 96 h post induction with acetamide


description:
Cy3 vs. Cy5--Dye swap
Replicate 1 of PknK K55M Mutant overexpression at 96 h post induction with acetamide


title: HEK293FT_TargetSeq_Sample_25


description:
Cy3 vs. Cy5--Dye swap
Replicate 1 of PknK WT overexpression at 96 h post induction with acetamide

source_name: Replicate 1, log phase cells at t=96 h post induction with 0.2% acteamide


title: HEK293FT_TargetSeq_Sample_44


title: HEK293FT_TargetSeq_Sample_26


title: HEK293FT_TargetSeq_Sample_24


title: HEK293FT_TargetSeq_Sample_38


title: 7006 [H11/H12-mLK CD1]

city: Berlin

first: Karsten

last: Jürchott

address: Luisenstraße

department: Rahel Hirsch Center

institute: BIH at Charité

data_processing:
Fastq-files were quality checked with FastQC (Babraham Bioinformatics)
Trimming was done with Trimmomatic (v0.36) (settings: Nextera adaptors, ILLUMINACLIP:${ADAPTER}:2:30:10, LEADING:3, TRAILING:3, SLIDINGWINDOW:3:20, MINLEN:36)
Reads were aligned to mm10 using TopHat and Bowtie 2
Counts per gene were calculated from the bam files by adding all counts mapped to the region of a corresponding gene (Rsamtools).
Raw data were filtered and normalized in R using the scater package.
Assembly: mm10
Supplementary files format and content: Raw counts - tab-deliminated file with reads summerized per gene.
Supplementary files format and content: Normalized data - tab-deliminated file with normelized and log2-transformed data

source_name: CD4+ Tcells

growth_protocol: Wild-type female C57BL/6 mice (age 8-10 weeks) were purchased from Janvier Labs (Saint-Berthevin, France). All animals were maintained under specific pathogen-free (SPF) conditions and were fed standard chow ad libidum.

extract_protocol:
Capture and processing of single CD4+ T cells was performed using the Fluidigm C1 autoprep system. Sorted CD4+ T cells (50 cells/µl) were mixed with (ratio 6/4) C1 Cell Suspension Reagent (Fluidigm) and subsequently loaded onto a 5-10-μm-diameter C1 Integrated Fluidic Circuit (IFC; Fluidigm).
Reverse transcription and cDNA preamplification were performed using the SMARTer Ultra Low RNA kit (Clontech). Sequencing libraries were prepared using Nextera XT DNA Sample Preparation kit with 96 indices (Illumina), according to the protocol supplied by Fluidigm. Size distribution in final libraries was analyzed by Bioanalyzer High Sensitivity DNA assay (Agilent) and library concentrations were quantified by Qubit High Sensitivity DNA assay (ThermoFisher).

treatment_protocol: H. polygyrus was maintained by serial passage in C57BL/6 mice (H0099/13). Mice were infected with 225 third-stage infective (L3) H. polygyrus larvae via oral gavage in 200µL drinking water. For cure of infection, mice were treated on two consecutive days during the acute stage of infection (day 14-15) with 2mg pyrantel pamoate (Sigma, St. Louis, MO, USA) in 200µL drinking water via oral gavage. On indicated days, mice were sedated via isofluorane inhalation, followed by cervical dislocation. All animal experiments were performed in accordance with the National Animal Protection Guidelines and approved by the German Animal Ethics Committee for the Protection of Animals (LAGeSO, G0176/20).

value: TH2 cells

value: mLK

value: wild type


title: 7007 [H12/E9-mLK CD1]


title: HEK293FT_TargetSeq_Sample_23


title: 7005 [H10/H11-mLK CD1]


description:
Cy3 vs. Cy5--Dye swap
Replicate 1 of PknK WT overexpression at 24 h post induction with acetamide


title: 7004 [H9/H10-mLK CD1]


title: HEK293FT_TargetSeq_Sample_22


title: HEK293FT_TargetSeq_Sample_21


title: 7003 [H8/H7-mLK CD1]


title: 7002 [H7/H4-mLK CD1]


title: HEK293FT_TargetSeq_Sample_31


title: HEK293FT_TargetSeq_Sample_20


title: HEK293FT_TargetSeq_Sample_17


title: 7001 [H6/H3-mLK CD1]


title: HEK293FT_TargetSeq_Sample_19


title: 6999 [H4/H1-mLK CD1]


description:
Cy5 vs. Cy3
Replicate 2 of PknK K55M Mutant overexpression at 24 h post induction with acetamide


title: 6998 [H3/G11-mLK CD1]


title: 6996 [H1/G7-mLK CD1]


title: HEK293FT_TargetSeq_Sample_13


title: HEK293FT_TargetSeq_Sample_14


title: HEK293FT_TargetSeq_Sample_29


title: HEK293FT_TargetSeq_Sample_18


title: HEK293FT_TargetSeq_Sample_16


title: 6995 [G12/G3-mLK CD1]


title: HEK293FT_TargetSeq_Sample_11


title: 6992 [G9/F12-mLK CD1]


title: HEK293FT_TargetSeq_Sample_15


title: 7000 [H5/H2-mLK CD1]


title: 6997 [H2/G9-mLK CD1]


title: HEK293FT_TargetSeq_Sample_6


title: 6988 [G5/F3-mLK CD1]


title: HEK293FT_TargetSeq_Sample_12


title: 6994 [G11/G2-mLK CD1]


title: HEK293FT_TargetSeq_Sample_5


title: 6987 [G4/F2-mLK CD1]


title: 6993 [G10/G1-mLK CD1]


title: HEK293FT_TargetSeq_Sample_9


title: HEK293FT_TargetSeq_Sample_8


title: HEK293FT_TargetSeq_Sample_10


title: 6986 [G3/F1-mLK CD1]


title: 6984 [G1/E11-mLK CD1]


title: Obp56hKO_F_2

city: Greenwood

first: Heather

last: Flanagan-Steet

state: SC

address: 101 Gregor Mendel circle

institute: Greenwood Genetic Center

description: Obp56h knockout

data_processing:
AfterQC, bbduk, GSNAP, samtools and Subread were used for the initial data processing and alignment steps
We normalized the raw counts using GeTMM
Genome_build: Dmel_Release_6

organism: Drosophila melanogaster

source_name: heads

growth_protocol: 3-5 day old flies grown under controlled conditions.

extract_protocol:
Flies were frozen and heads collected on dry ice. RNA extraction was done using the Direct-Zol microprep kit (ZymoResearch)
We used the NuQuant+UDI, Drosophila AnyDeplete kit (Tecan) to deplete ribosomal RNA and prepare bar-coded cDNA libraries for sequencing after 17 cycles of amplification. Pooled 3nM libraries were run on a Novaseq6000 (Illumina).

treatment_protocol: No treatment

tag: line name in manuscript

value: female

tag: age

value: 3-5 day old


title: HEK293FT_TargetSeq_Sample_3

data_processing:
DNA deep sequencing read quality was evaluated by FastQC (v0.11.8) and low quality read sequences were trimmed.
BWA-MEM algorithm (0.7.17-r1188) was used to map clean reads to the targeted sequences.
Base substitution calling was performed by SAMtools (v1.9) mpileup function and indel calling was based on the CIGAR values of the SAM/BAM files.
Base subsutitution and indels frequencies are calculated according to reported CFBI (https://github.com/YangLab/CFBI, v1.0.0).
Genome_build: hg19 for human samples
Supplementary_files_format_and_content: Excel for indel and base subtitution calculation results

treatment_protocol: For prime editing with pegRNA (spegRNA or apegRNA), 293FT, U2OS or Hela cells were seeded in a 24-well plate at a density of 1×10^5 per well and transfected with 250 μl serum-free Opti-MEM that contained 2.6 μl LIPOFECTAMINE LTX (Life, Invitrogen), 1.3 μl LIPOFECTAMINE plus (Life, Invitrogen), 0.9 μg PE2 expression vector, 0.3 μg pegRNA (spegRNA or apegRNA) expression vector with 0.1 μg nick-sgRNA expression vector. After 24 hrs, puromycin (ant-pr-1, InvivoGen) was added to the medium at the final concentration of 4 μg/ml.

tag: cell line


title: 6990 [G7/F9-mLK CD1]

tag: genotype


title: HEK293FT_TargetSeq_Sample_7


title: 6981 [F10/E5-mLK CD1]

tag: strain


title: 6982 [F11/E6-mLK CD1]


title: 6989 [G6/F8-mLK CD1]


title: 6980 [F9/E4-mLK CD1]


title: HEK293FT_TargetSeq_Sample_4


title: 6985 [G2/E12-mLK CD1]


title: Obp56hKO_M_1

description: Obp56h knockout

tag: Sex


title: CSB_F_1

description: original genotype

value: CSB


title: 6978 [F7/D11-mLK CD1]


title: 6991 [G8/F10-mLK CD1]


title: HEK293FT_TargetSeq_Sample_1


title: 6983 [F12/E7-mLK CD1]


title: HEK293FT_TargetSeq_Sample_2


title: 6979 [F8/E3-mLK CD1]


title: Obp56hKO_F_1

description: Obp56h knockout


title: Obp56hKO_M_2

description: Obp56h knockout


title: 6974 [F3/D7-mLK CD1]


title: CSB_F_2

description: original genotype


title: 6977 [F6/D10-mLK CD1]


title: AV_K_M_4

description: downstream SNP


title: 6971 [E12/C12-mLK CD1]


title: 6970 [E11/C10-mLK CD1]


title: AV_K_M_2

description: downstream SNP


title: CSB_M_2

description: original genotype


title: 6976 [F5/D9-mLK CD1]


title: AV_O_F_1

description: rare allele in 3'UTR


title: CSB_M_1

description: original genotype


title: 6975 [F4/D8-mLK CD1]


title: AV_O_M_1

description: rare allele in 3'UTR


title: 6973 [F2/D6-mLK CD1]


title: 6963 [E4/A12-mLK CD1]


title: AV_K_M_1

description: downstream SNP


title: AV_K_M_3

description: downstream SNP


title: AV_O_F_2

description: rare allele in 3'UTR


title: AV_354_M_2

description: SNP in exon 2


title: 6968 [E9/C8-mLK CD1]


title: 6967 [E8/C7-mLK CD1]


title: 6972 [F1/D2-mLK CD1]


title: 6966 [E7/C2-mLK CD1]


title: AV_O_M_2

description: rare allele in 3'UTR


title: AV_118_F_2

description: SNP in exon 1


title: 6959 [D12/A5-mLK CD1]


title: AV_118_M_2

description: SNP in exon 1


title: AV_K_F_1

description: downstream SNP


title: 6958 [D11/H12-siLPCD2_2]

value: siLP


title: 6957 [D10/H5-siLPCD2_2]


title: 6965 [E6/B7-mLK CD1]


title: AV_354_F_2

description: SNP in exon 2


title: AV_354_F_1

description: SNP in exon 2


title: 6964 [E5/B4-mLK CD1]


title: 6962 [E3/A11-mLK CD1]


title: 6956 [D9/G12-siLPCD2_2]


title: AV_K_F_2

description: downstream SNP


title: AV_354_M_1

description: SNP in exon 2

value: male


title: AV_015_F_1

description: upstream SNP


title: AV_118_F_1

description: SNP in exon 1


title: 6969 [E10/C9-mLK CD1]


title: 6954 [D7/G9-siLPCD2_2]


title: 6961 [E2/A10-mLK CD1]


title: 6951 [D4/F3-siLPCD2_2]


title: AV_015_F_2

description: upstream SNP


title: 6950 [D3/F1-siLPCD2_2]


title: AV_015_M_2

description: upstream SNP


title: 6955 [D8/G10-siLPCD2_2]


title: pDC pano ATAC

city: Melbourne

first: Izabela

last: Todorovski

state: VIC

address: 305 Grattan Street

department: Cancer Research Division

institute: Peter MacCallum Centre

data_processing:
Bcl2fastq (v2.17.1.14) was used to demultiplex sequencing files and resulting Fastq output was quality checked using FASTQC (v0.11.6).
Fastq read alignment to the mouse genome (mm10/GRCm38) was performed using Botwtie2 (v2.3.4.1).
SAM files generated were converted to BAM file format and subsequently sorted, indexed and potential PCR duplicates were removed using Samtools (v1.9) with view, sort, index and rmdup functions, respectively. Deeptools (v3.0.0) bamCoverage function was used for BAM to BigWig file conversion using the following settings (--normalizeUsing CPM --smooth length 150 -bs 50 -e 225).
BAM file peak calling was performed MACS (v2.1.1) with the following settings (-g mm -f BAM --call-summits --nomodel --extsize 100). BigWig file average read density across defined genomic intervals was performed using Deeptools (v3.0.0) computeMatrix function with the following settings (reference-point --referencePoint center --upstream 2000 --downstream 2000 -bs 50) where average read density was calculated +/- 2Kb of ATAC peak summits.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

source_name: plasmacytoid dendritic cells

extract_protocol:
Spleens were removed and dendritic cells sorted. Cells were lysed in cold ATAC-seq cell lysis buffer and exposed to Tn5 transposase (Nextera) for 30min at 37C
Transposed chromatin was amplified using customized Nextera PCR Primer 1 and Primer 2 (barcode) and HotStart KAPA ReadyMix (Roche)

value: spleen

tag: disease status

value: leukemia

value: panobinostat


title: 6948 [D1/D9-siLPCD2_2]


title: 6960 [E1/A6-mLK CD1]


title: AV_015_M_1

description: upstream SNP


title: 6946 [C11/D2-siLPCD2_2]


title: WT_Leukemia-bearing vehicle_pano_Antibody_Derived_Tag

data_processing:
10X Genomics’ Cell Ranger Software (v3.1.0) was used to align reads to the mm10/GRCm38 reference genome, demultiplex cellular barcodes and quantify unique molecular identifiers (UMIs) and antibody capture (Hashtag oligos (HTOs) and Antibody Derived Tags (ADTs))
Inter-sample doublets and intra-sample doublets were removed using Seurat’s HTODemux function and the Scrublet python package (v0.2.1), respectively.
Counts with more than one median absolute derivation (MAD) above the median Scrublet score were retained.
The Seurat R package (v3.1.0) (64) was used to process gene expression and antibody count matrices within R studio (v3.6.1). Seurat’s SCTransform function was subsequently used to sctransform normalise RNA transcript counts for barcodes identified as cells by Cell Ranger. Transformation of counts with no covariates in the sctranform model was first performed, then Seurat’s CellCycleScoring function with cell cycle gene sets of mouse homologues was used to calculate cell cycle phase scores. Cell cycle phase scores and the percent of raw RNA counts belonging to mitochondrial genes for each cell were used to rerun sctransform normalisation and regress out of the model.
Centred log ratio (CLR) transformation was performed to normalise ADT counts.
Sctransform scaled RNA expression values for genes with residual variance greater than 1.3 in the sctransform model were used for Principle component analysis (PCA). The top 10 principle components were used to calculate a shared-nearest-neighbours (SNN) network with the FingNeighbors function with a cosine distance metric and 50 k-nearest neighbors. Cell populations were subsequently identified using the SNN network and the FindClusters function with the Louvain algorithm and a resolution parameter of 0.6. The top 10 principle components were also used to calculate Uniform Manifold Approximation and Projection (UMAP) values using the RunUMAP function with a cosine distance metric and 50 nearest neighbors as parameters.
Genome_build: mm10
Supplementary_files_format_and_content: Raw Counts

source_name: dendritic cells

extract_protocol:
Spleens were removed and dendritic cells isolated. Pooled DC samples were loaded onto the 10x Chromium instrument (10x Genomics) to generate single-cell Gel Beads-in-Emulsion (GEMs) and capture/barcode cells.
10x Genomics Single Cell 3′ v3

tag: treatment

value: vehicle, panobinostat


title: 6953 [D6/G7-siLPCD2_2]

tag: cell type


title: cDC pano ATAC

source_name: conventional dendritic cells


title: 6947 [C12/D7-siLPCD2_2]


title: 6952 [D5/F11-siLPCD2_2]


title: cDC vehicle ATAC

value: vehicle


title: pDC pano_Input

data_processing:
Bcl2fastq (v2.17.1.14) was used to demultiplex sequencing files and resulting Fastq output was quality checked using FASTQC (v0.11.6)
Fastq read alignment to the mouse genome (mm10/GRCm38) was performed using Botwtie2 (v2.3.4.1).
SAM files generated were converted to BAM file format and subsequently sorted, indexed and potential PCR duplicates were removed using Samtools (v1.9) with view, sort, index and rmdup functions, respectively.
Deeptools (v3.0.0) bamCoverage function was used for BAM to BigWig file conversion using the following settings (--normalizeUsing CPM --smooth length 150 -bs 50 -e 225).
BigWig file average read density across defined genomic intervals was performed using Deeptools (v3.0.0) computeMatrix function with the following settings (reference-point --referencePoint center --upstream 2000 --downstream 2000 -bs 50 --missingDataAsZero), where average read density was calculated +/- 2Kb of ATAC peak summits and genomic regions spanning mm10 blacklist intervals (ENCODE, accession ENCFF547MET) were removed.
BAM file peak calling was performed MACS (v2.1.1) with the following settings (-f BAM -m 10 30 --broad --cutoff-analysis -g mm -c INPUT) and resulting BED files were filtered for regions spanning mm10 blacklist intervals (ENCODE, accession ENCFF547MET) and modified into GFF file format using Rstudio (v3.6.1) to meet input criteria for ROSE2 (v1.0.5).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

extract_protocol:
Spleens were removed and dendritic cells sorted. Cells were fixed with 1% formaldehyde for 6min and sonicated using the S220 Focused-ultrasonicator (Covaris) for 8min. Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with H3K27Ac antibody (Abcam Cat# ab4729). Chromatin was isolated with the True Microchip Kit (Diagenode Cat# C01010130).
Libraries were prepared using the DNA Library Prep NEB (New England Biolabs)


title: cDC vehicle_Input


title: cDC pano_Input


title: WT_Leukemia-bearing vehicle_pano_Hashtag


title: 6945 [C10/C6-siLPCD2_2]


title: 6949 [D2/E1-siLPCD2_2]


title: pDC vehicle ATAC


title: 6943 [C8/C1-siLPCD2_2]


title: pDC vehicle_Input


title: 6944 [C9/C3-siLPCD2_2]


title: cDC pano H3K27Ac


title: 6942 [C7/B7-siLPCD2_2]


title: 6941 [C6/B4-siLPCD2_2]


title: AV_118_M_1

description: SNP in exon 1


title: pDC pano H3K27Ac


title: 6940 [C5/A3-siLPCD2_2]


title: 6939 [C4/H12-siLP CD1_2]


title: pDC vehicle H3K27Ac


title: 6938 [C3/G12-siLP CD1_2]


title: cDC_pano_rep1_RNAseq

data_processing:
Sequencing files were demultiplexed (Bcl2fastq, v2.17.1.14) and QC was performed on FASTQ files using FASTQC (v0.11.6).
Sequencing reads were trimmed (cutadapt v2.1) and aligned to the mm10 mouse reference genome using HISAT2 (v2.1.0).
Read counting across genomic features was performed using FeatureCounts (Subread, v2.0.0)
Differential gene expression analysis was performed using Voom-Limma in R (v3.42.2)
Genome_build: mm10
Supplementary_files_format_and_content: Raw Counts

extract_protocol:
Spleens were removed and leukemia cells sorted, RNA was isolated using Trizol reagent and the Direct-zol RNA MicroPrep kit (Zymo Research) according to the manufacturers instructions
mRNA libraries were generated using NEBNext Single Cell/Low Input RNA Library Preparation kit.

value: conventional dendritic cells


title: 6937 [C2/G10-siLP CD1_2]


title: cDC_vehicle_rep2_RNAseq


title: cDC_pano_rep2_RNAseq


title: cDC_vehicle_rep1_RNAseq


title: pDC_pano_rep2_RNAseq

value: plasmacytoid dendritic cells


title: 6935 [B12/G7-siLP CD1_2]


title: 6934 [B11/G5-siLP CD1_2]


title: pDC_vehicle_rep2_RNAseq


title: 6931 [B8/G1-siLP CD1_2]


title: pDC_vehicle_rep1_RNAseq


title: 6932 [B9/G3-siLP CD1_2]


title: pDC_pano_rep1_RNAseq


title: 6930 [B7/F12-siLP CD1_2]


title: 6933 [B10/G4-siLP CD1_2]


title: MEP GATA1 low biorep 2, techrep 2

city: Stanford

first: Amy

last: Chen

state: CA

address: 279 Campus Drive West

institute: Stanford University

description:
MEP_countmatrix.csv
MEP GATA1 low rep 2.2

data_processing:
Adapters were trimmed using cutadapt and reads were mapped using bowtie2 with max fragment length of 2000bp to hg19 (primary bone marrow samples) or hg38 (GM12878 and K562 samples).
Reads were filtered for non-mitochondrial reads, mapq > 20, and properly paired reads. We then removed duplicates using Picard tools
Peaks were called using macs2 with the following parameters on Tn5 insertion sites: --shift -75 --extsize 150 --nomodel --call-summits --nolambda -p 0.01 -B –SPMR
Genome_build: hg19 for bone marrow samples, hg38 for K562 and GM12878

source_name: Ficoll-separated bone marrow mononuclear cells

growth_protocol: GM12878 and K562 cells were grown in RPMI 1640 with 15% FBS

extract_protocol: Transposed DNA fragments were purified using Qiagen minelute columns then PCR amplified with barcoded Nextera adapters to generate ATAC-seq libraries

treatment_protocol: Cells were fixed and stained with GATA1 antibody where applicable and sorted based on GATA1 levels. Cells were then transposed with Tn5 and reversal of crosslinks was performed at 37C overnight for fixed samples.

tag: facs sorting

value: Sorted for CD34+CD38+CD10-CD123-CD45RA-GATA1lo cells


title: cDC vehicle H3K27Ac


title: 6928 [B5/F8-siLP CD1_2]


title: MEP GATA1 low biorep 2, techrep 1

description:
MEP_countmatrix.csv
MEP GATA1 low rep 2.1

value: Ficoll-separated bone marrow mononuclear cells


title: ISC 2 month (young) SM6 WT rep3

city: Clayton

first: Monika

last: Mohenska

address: 15 Innovation Walk

institute: Monash University

data_processing:
Sample reads were aligned to the mouse genome (GENCODE GRCm38 primary assembly) using STAR version 2.4.2a.
Transcript quantification was performed using featureCounts (exonic regions of GENCODE’s vM15 annotation version), and transcripts with more than 5 sequencing reads and 1 count per million of mapped reads in at least one sample were used for further analysis, previously library-size normalized using the TMM method.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: intestinal stem cell (ISC)

extract_protocol:
The isolated small intestine was flushed with PBS and opened longitudinally. The tissue was then scraped with a glass coverslip to remove villi, cut into 5-mm pieces and washed with PBS five times (20 inversions of the tube per wash). Following incubation for 30 min at 4°C in 4mM EDTA-PBS, intestinal crypts were released from small intestinal tissue fragments by mechanically pipetting with a 10ml pipette in PBS and repeating this step twice. After centrifugation (430xg for 5 min at 4°C), the pellet was resuspended in PBS and strained using a 70-μm cell strainer (BD Biosciences). Following centrifugation (430xg for 5 min at 4°C), the collected crypts were incubated for 30 minutes at 4°C in DMEM/F12 – 10% serum (Gibco), pelleted again by centrifugation (430xg for 5 min at 4°C) and then dissociated in TrypLE Express (Invitrogen) supplemented with 10 μM Rock inhibitor (Y-27632, Abcam) and 2.5µg/ml DNAse 1 (Sigma-Aldrich) for 4 minutes at 37°C. The dissociated cells were strained using a 70-μm cell strainer and were washed twice with PBS and collected by centrifugation at 4°C at 430xg for 5 minutes. Cellularized intestinal epithelial were labelled with antibodies and ISCs isolated by FACS (SM6 strategy, CD31-/CD45-/CD24med/CD166+/CD44high/GRP78low/EPHB2high/EPCAM+).
A 3-prime biased approach was used to generate sequencing libraries (see methods in publication for further details). An 8 bp sample index and a 10 bp unique molecular identifier (UMI) were added during initial poly(A) priming and pooled samples were amplified using a template switching oligonucleotide. The Illumina P5 (5' AAT GAT ACG GCG ACC ACC GA 3') and P7 (5' CAA GCA GAA GAC GGC ATA CGA GAT 3') sequences were added by PCR and Nextera transposase, respectively. The library was designed so that the forward read (R1) utilizes a custom primer (5' GCC TGT CCG CGG AAG CAG TGG TAT CAA CGC AGA GTA C 3') to sequence directly into the index and then the 10 bp UMI. The reverse read (R2) uses the standard R2 primer to sequence the cDNA in the sense direction for transcript identification. Sequencing was performed on the NextSeq550 (Illumina), using the V2 High output kit (Illumina, #TG-160-2005) in accordance with the Illumina Protocol 15046563 v02, generating 2 reads per cluster composed of a 19 bp R1 and a 72 bp R2.

value: intestinal stem cell (ISC)

value: WT

value: 2 months

tag: developmental stage

value: young


title: MEP GATA1 high biorep 2, techrep 2

description:
MEP_countmatrix.csv
MEP GATA1 high rep 2.2

value: Sorted for CD34+CD38+CD10-CD123-CD45RA-GATA1hi cells


title: 6927 [B4/F6-siLP CD1_2]

value: TH2 cells

value: wild type


title: ISC 2 month (young) SM6 WT rep2


title: 6926 [B3/F1-siLP CD1_2]

value: siLP


title: MEP GATA1 low biorep 1, techrep 2

description:
MEP_countmatrix.csv
MEP GATA1 low rep 1.2


title: 6924 [B1/E7-siLP CD1_2]


title: 6936 [C1/G8-siLP CD1_2]


title: ISC 2 month (young) SM6 WT rep1


title: MEP GATA1 low biorep 1, techrep 1

description:
MEP_countmatrix.csv
MEP GATA1 low rep 1.1


title: 6923 [A12/E6-siLP CD1_2]


title: 6922 [A11/E2-siLP CD1_2]


title: 6921 [A10/D5-siLP CD1_2]


title: 6920 [A9/D2-siLP CD1_2]


title: ISC 22 month (old) SM6 WT rep3

value: 22 months

value: old


title: MEP GATA1 high biorep 1, techrep 2

description:
MEP_countmatrix.csv
MEP GATA1 high rep 1.2


title: 6919 [A8/C11-siLP CD1_2]


title: 6916 [A5/B8-siLP CD1_2]


title: 6917 [A6/B10-siLP CD1_2]


title: ISC 22 month (old) SM6 WT rep2


title: Bone marrow progenitor GATA1- biorep 2, techrep 2

description:
BMprogenitor_countmatrix.csv
Bone marrow progenitor GATA1- rep 2.2

value: Sorted for CD34+CD38+GATA1- cells


title: 6918 [A7/C2-siLP CD1_2]


title: 6915 [A4/B1-siLP CD1_2]


title: MEP GATA1 high biorep 1, techrep 1

description:
MEP_countmatrix.csv
MEP GATA1 high rep 1.1


title: 6929 [B6/F10-siLP CD1_2]


title: ISC 22 month (old) SM6 WT rep1


title: ISC 2 month (young) Lgr5-GFP rep2


title: ISC 2 month (young) Lgr5-GFP rep3


title: 6925 [B2/E12-siLP CD1_2]


title: 6914 [A3/A12-siLP CD1_2]


title: Bone marrow progenitor GATA1- biorep 2, techrep 1

description:
BMprogenitor_countmatrix.csv
Bone marrow progenitor GATA1- rep 2.1


title: MEP GATA1 high biorep 2, techrep 1

description:
MEP_countmatrix.csv
MEP GATA1 high rep 2.1


title: 6913 [A2/A9-siLP CD1_2]


title: 6912 [A1/A6-siLP CD1_2]


title: Bone marrow progenitor GATA1+ biorep 2, techrep 2

description:
BMprogenitor_countmatrix.csv
Bone marrow progenitor GATA1+ rep 2.2

value: Sorted for CD34+CD38+GATA1+ cells


title: 6883 [F8/H12-PEC-CD2]

value: PEC


title: Bone marrow progenitor GATA1+ biorep 2, techrep 1

description:
BMprogenitor_countmatrix.csv
Bone marrow progenitor GATA1+ rep 2.1


title: 6882 [F7/H10-PEC-CD2]


title: ISC 2 month (young) Lgr5-GFP rep1


title: ISC 22 month (old) Lgr5-GFP rep3


title: Bone marrow progenitor GATA1- biorep 1, techrep 2

description:
BMprogenitor_countmatrix.csv
Bone marrow progenitor GATA1- rep 1.2


title: 6881 [F6/H8-PEC-CD2]


title: ISC 22 month (old) Lgr5-GFP rep2


title: Bone marrow progenitor GATA1- biorep 1, techrep 1

description:
BMprogenitor_countmatrix.csv
Bone marrow progenitor GATA1- rep 1.1


title: 6879 [F4/H6-PEC-CD2]


title: ISC 22 month (old) Lgr5-GFP rep1


title: 6878 [F3/H5-PEC-CD2]


title: Bone marrow progenitor GATA1+ biorep 1, techrep 2

description:
BMprogenitor_countmatrix.csv
Bone marrow progenitor GATA1+ rep 1.2


title: 6876 [F1/H3-PEC-CD2]


title: 6877 [F2/H4-PEC-CD2]