title: K562, Cas9 enrichment, HS2

city: Cambridge

first: Heejin

last: Roh

state: MA

address: 12 Oxford St

institute: Harvard

description: Library name: Cas9_enrichment

data_processing:
For DddA11-WGS or MGYFPDa829-WGS, nanopore sequencing data were aligned using Minimap2. Duplicate reads were removed, and base-specific mutation counts were extracted using Samtools mpileup. Mutation rates at each cytosine were calculated, saved as a bedGraph file, and converted to a BigWig file. The distribution of cytosine deamination fractions was analyzed and plotted using computeMatrix and plotProfile from deepTools
For TDAC-seq, Nanopore sequencing data were aligned using the mappy. Reads with larger than 500 bp unaligned regions compared to the full amplicon on either end of the read were removed. Single base mutations and indels were extracted using the cs tag after alignment. CpG sites were masked from mutation calling to prevent bias introduced by endogenous CpG methylation. Only C-to-T and G-to-A mutations were recorded as potential DddA edits. Reads with more C-to-T than G-to-A mutations were assigned to the top strand of the template and vice versa.
Assembly: hg38
Supplementary files format and content: XXX_sort_rmdups_coverage_mutationrate.bw: The first three columns represent the chromosome, start, end, and the last column contains the DddA mutation rate (C>T or G>A) per base.
Supplementary files format and content: XXX_DddA_edit_coo_mtx.tsv: Tab delimited file storing the read-by-position matrix M of DddA edits in a sparse IJV (COO matrix) format. Contains 3 columns corresponding to the row (read index), column (single base pair position in the target locus), and value of each non-zero element. If a the i^th read and j^th position is edited by DddA, then M[i, j] = 1, otherwise M[i, j] = 0.
Supplementary files format and content: XXX_ABE_edit_coo_mtx.tsv: Tab delimited file storing the read-by-position matrix M of ABE edits in a sparse IJV (COO matrix) format. Contains 3 columns corresponding to the row (read index), column (single base pair position in the target locus), and value of each non-zero element. If a the i^th read and j^th position is edited by ABE, then M[i, j] = 1, otherwise M[i, j] = 0. Row order is the same as the corresponding XXX_DddA_edit_coo_mtx.tsv
Supplementary files format and content: XXX_del_coo_mtx.tsv: Tab delimited file storing the read-by-position matrix M of deletions in a sparse IJV (COO matrix) format. Contains 3 columns corresponding to the row (read index), column (single base pair position in the target locus), and value of each non-zero element. If a the i^th read and j^th position overlaps with a deletion, then M[i, j] = 1, otherwise M[i, j] = 0. Row order is the same as the corresponding XXX_DddA_edit_coo_mtx.tsv
Supplementary files format and content: XXX_read_strands.tsv: Tab delimited file storing the strand of each read. 0 corresponds to C-to-T strand and 1 corresponds to G-to-A strand. Row order is the same as the corresponding XXX_DddA_edit_coo_mtx.tsv

source_name: Blood

growth_protocol: K562 and MOLM-13 were cultured in RPMI-1640 supplemented with 10%, and GM12878 were cultured in RPMI-1640 supplemented with 15% FBS.  CD34+ HSPCs were cultured in hematopoietic stem cell expansion media consisting of StemSpan SFEM II supplemented CC100 cytokine cocktail, 50 ng/mL human TPO, 1% L-Glutamine, 1% penicillin/streptomycin, and 35 nM UM171.

extract_protocol:
Genomic DNA was isolated using a Zymo genomic DNA extraction kit.
Cells were washed with PBS and permeabilized by incubation in lysis buffer for 10 minutes at room temperature, followed by an additional incubation at 4°C for 5 minutes. After washing once with wash buffer, the cell pellet was resuspended in activation buffer supplemented with purified DddA11-MBP or MGYFPDa829 to achieve a final enzyme concentration of 3-10 µM. The reaction mixture was incubated at 37°C for 2 hours or 3 minutes with shaking at 300 rpm. The reaction was quenched by adding SDS to a final concentration of 0.5%. Proteinase K was then added, and the sample was incubated at 56°C for 10 minutes. Genomic DNA was isolated using a Zymo genomic DNA extraction kit. For naked DNA data, gDNA was extracted from K562 cells using the QIAamp DNA Blood Kit to obtain deproteinized DNA, followed by the DddA reaction.For TDAC-seq, nested PCR was performed using target-specific primers with KOD One PCR Master Mix, and libraries were prepared following the Ligation Sequencing V14 – PCR Barcoding Kit protocol from Oxford Nanopore. For DddA11-Whole genome sequencing, gDNA was fragmented to 10 kbp, and libraries were prepared using the same ligation sequencing kit.

treatment_protocol: Cells were transduced with lentiviral particles carrying the sgRNA plasmid. K562 and MOLM-13 cells were and selected with puromycin and subsequently electroporated with Cas9 or purified ABE. For CD34+ cells, after transduction with lentiviral particles carrying the sgRNA plasmid, Cas9 was electroporated, and cells were selected with puromycin two days after electroporation. When erythroid differentiation was required, it was initiated two days after electroporation by switching to EDM media supplemented with puromycin.

value: Blood

tag: cell type

value: CML Lymphoblast Cells

value: WT


title: Circulating_D-1

status: Public on Jul 04 2025

type: SRA

city: chiba city

first: Masahiro

last: Kiuchi

state: chiba

address: cyuoku inohana1-8-1

country: Japan

institute: Chiba univercity

description: Library name: Circulating_D-1

library_source: transcriptomic

data_processing:
Sequencing reads were aligned to the mouse reference genome (GRCm38) using Bowtie 2 and TopHat (v1.3.2) for RNA-seq, and Hisat2 (v2.2.1) for ChIP-seq and ATAC-seq.
For RNA-seq, transcript abundance was quantified as FPKM using Cufflinks (v2.0.2). For ChIP-seq and ATAC-seq, peaks were called using MACS2 with optimized parameters (ChIP-seq: window_size = 300; ATAC-seq: window_size = 100; FDR = 0.01).
Differentially expressed genes (DEGs) in RNA-seq were identified using DESeq2 (v1.10.1) on pseudobulk data, with thresholds of log2(fold change) > 1 or < –1 and p-value < 0.01. For ATAC-seq, differentially accessible regions (DARs) were detected using HOMER's getDifferentialPeaks.
ChIP-seq and ATAC-seq peaks were annotated using HOMER (annotatePeaks.pl). Overlapping peaks between assays were identified using mergePeaks, and motifs were enriched using findMotifsGenome.pl with a 200-bp window.
Co-expression networks for RNA-seq were constructed using Simpson's coefficient and visualized with Cytoscape (v3.7.1). Signal intensity tracks (BigWig) were generated using SAMtools, BEDtools, and deepTools, and visualized in the Integrative Genomics Viewer (IGV).
Assembly: Mouse genome GRCm38 (mm10).
Supplementary files format and content: Processed RNA-seq data are provided as gene-level FPKM tables. ChIP-seq and ATAC-seq data include peak BigWig signal tracks.

molecule: total RNA

organism: Mus musculus

source_name: Lung

extract_protocol:
For RNA-seq, total RNA was extracted using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions. For ChIP-seq, chromatin was extracted from paraformaldehyde-fixed cells lysed with SDS lysis buffer, followed by sonication. For ATAC-seq, nuclei were isolated by cell lysis and immediately subjected to transposition.
RNA-seq libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina) following the manufacturer’s protocol. ChIP-seq libraries were constructed using the NEBNext Ultra II DNA Library Prep Kit for Illumina, including adapter ligation and PCR amplification. ATAC-seq libraries were prepared from transposed DNA fragments using PCR amplification (11–12 cycles) prior to sequencing. All libraries were sequenced on an Illumina NextSeq500 system.

tag: tissue

value: Lung

tag: treatment

value: Asp-Ag

tag: term

tag: hlf

value: negative

tag: iv staining

value: positive


title: NoDddA, HS2

country: USA

description: Library name: NoDddA HS2

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell line

tag: genotype


title: AKO_1

status: Public on Jul 05 2025

city: Chongqing

first: Ting

last: Zeng

address: No. 1 Medical College Road

country: China

institute: Chongqing medical university

data_processing:
Data Trimming，mRNA Annotation，Gene Quantification
Sequence reads were trimmed for adaptor sequence/low-quanlity sequence using SQAPnuke
The trimmed sequence were mapped to GrCM38/mm10 using HISAT2
mRNA expression level of genes was calculated by RSEM (v1.3.1)
Assembly: mmu10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes RPKM for each sample

source_name: iWAT

extract_protocol:
Total RNA was harvested using Trizol (Invitrogen). 200ng of total RNA was used for the construction of sequencing libraries.
Sample QC, mRNA Isolation, mRNA Fragmentation,  cDNA Synthesis,  End Repair, Add A and Adaptor Ligation, PCR, Library QC, Circularization, Sequencing

value: iWAT

value: adipocyte-specific Celf1 knockout

value: cold stimulation at 4℃ for 6 hours


title: Unmethylated naked DNA, DddA11, HOXA

description: Library name: naked DNA unmethylated

source_name: Colon

value: Colon

value: HCT116 DKO

value: Colorectal Carcinoma cell

value: Knockouts of  DNMT1 (-/-) and DNMT3b (-/-)


title: NoDddA, HOXA

description: Library name: NoDddA HOXA


title: Methylated naked DNA, DddA11, HOXA

description: Library name: naked DNA metyhylated


title: K562, MGYFPDa829-WGS, replicate 2

description: Library name: MGYFPDa829_WGS_2


title: K562, MGYFPDa829-WGS, replicate 1

description: Library name: MGYFPDa829_WGS_1


title: CD34+, Cas9 screen, rep1

description: Library name: TDAC_CD34_Cas9_rep1

value: CD34+ HSPC

value: Hematopoietic stem and progenitor cells

value: Deletions at GFI1B enhancer

value: sgRNA transduction, Cas9 electroportaion

tag: time

value: Day 6 after electroporation


title: CD34+, Cas9 screen, rep2

description: Library name: TDAC_CD34_Cas9_rep2

value: Blood


title: Hlfnegative_TRM_D-3

description: Library name: Hlfnegative_TRM_D-3

value: Lung


title: K562, MGYFPDa829 3uM, 3min, UGI -, replicate 2

description: Library name: TDAC_UGI_rep2_7

value: CML Lymphoblast Cells

value: WT


title: K562,  DddA11 10uM, 120min, UGI +, replicate 2

description: Library name: TDAC_UGI_rep2_6


title: Hlfpositive_TRM_C-2

description: Library name: Hlfpositive_TRM_C-2

value: Asp-Ag

value: positive

value: negative


title: K562,  DddA11 10uM, 30min, UGI -, replicate 2

description: Library name: TDAC_UGI_rep2_2


title: K562,  DddA11 10uM, 10min, UGI +, replicate 2

description: Library name: TDAC_UGI_rep2_4


title: K562,  DddA11 10uM, 120min, UGI -, replicate 2

description: Library name: TDAC_UGI_rep2_3


title: K562,  DddA11 10uM, 30min, UGI +, replicate 1

description: Library name: TDAC_UGI_rep1_5


title: K562,  DddA11 10uM, 10min, UGI +, replicate 1

description: Library name: TDAC_UGI_rep1_4


title: K562,  DddA11 10uM, 120min, UGI +, replicate 1

description: Library name: TDAC_UGI_rep1_6


title: K562,  DddA11 10uM, 30min, UGI -, replicate 1

description: Library name: TDAC_UGI_rep1_2


title: K562,  DddA11 10uM, 10min, UGI -, replicate 1

description: Library name: TDAC_UGI_rep1_1


title: Circulating_C-1

description: Library name: Circulating_C-1


title: K562, DddA11 1uM, 120min, replicate 2

description: Library name: TDAC_titration_rep2_3


title: K562,  DddA11 10uM, 120min, UGI -, replicate 1

description: Library name: TDAC_UGI_rep1_3


title: K562, DddA11 1uM, 30min, replicate 2

description: Library name: TDAC_titration_rep2_2


title: K562, DddA11 3uM, 30min, replicate 1

description: Library name: TDAC_titration_rep1_5


title: K562, DddA11 3uM, 30min, replicate 2

description: Library name: TDAC_titration_rep2_5


title: K562, DddA11 3uM, 10min, replicate 2

description: Library name: TDAC_titration_rep2_4


title: K562, DddA11 3uM, 10min, replicate 1

description: Library name: TDAC_titration_rep1_4


title: K562, DddA11 1uM, 30min, replicate 1

description: Library name: TDAC_titration_rep1_2


title: K562, DddA11 3uM, 120min, replicate 1

description: Library name: TDAC_titration_rep1_6


title: K562, DddA11 1uM, 10min, replicate 1

description: Library name: TDAC_titration_rep1_1


title: K562, TDAC-seq, region2, MGYFPDa829, replicate 2

description: Library name: TDAC_K562_ MGYFPDa829_region2_rep2


title: K562, DddA11 1uM, 10min, replicate 2

description: Library name: TDAC_titration_rep2_1


title: K562, TDAC-seq, GFI1B enhancer, MGYFPDa829, replicate 2

description: Library name: TDAC_K562_GFI1B_4


title: K562, TDAC-seq, region1, MGYFPDa829, replicate 2

description: Library name: TDAC_K562_ MGYFPDa829_region1_rep2


title: K562, TDAC-seq, region2, MGYFPDa829, replicate 1

description: Library name: TDAC_K562_ MGYFPDa829_region2_rep1


title: K562, TDAC-seq, GFI1B enhancer, MGYFPDa829, replicate 1

description: Library name: TDAC_K562_GFI1B_3


title: K562,  DddA11 10uM, 30min, UGI +, replicate 2

description: Library name: TDAC_UGI_rep2_5


title: K562, TDAC-seq, GFI1B enhancer, DddA11, replicate 2

description: Library name: TDAC_K562_GFI1B_2


title: MOLM13, HOXA7/9, sgRNA4, replicate 2

description: Library name: TDAC_MOML13_Cas9_rep2_4

value: Human-derived acute myeloid leukemia cells

value: CTCF motif deletion


title: K562, DddA11 1uM, 120min, replicate 1

description: Library name: TDAC_titration_rep1_3


title: MOLM13, HOXA7/9, sgRNA3, replicate 2

description: Library name: TDAC_MOML13_Cas9_rep2_3


title: MOLM13, HOXA7/9, sgRNA2, replicate 2

description: Library name: TDAC_MOML13_Cas9_rep2_2


title: MOLM13, HOXA7/9, sgRNA4, replicate 1

description: Library name: TDAC_MOML13_Cas9_rep1_4


title: MOLM13, HOXA7/9, sgRNA3, replicate 1

description: Library name: TDAC_MOML13_Cas9_rep1_3


title: MOLM13, HOXA7/9, sgRNA2, replicate 1

description: Library name: TDAC_MOML13_Cas9_rep1_2


title: CD34+, D9, HBB/HBD, MGYFPDa829, replicate 2

description: Library name: TDAC_CD34_D9_4

value: Erythroid differentiation

value: Day 9 after differentiation induction


title: MOLM13, HOXA7/9, sgRNA1, replicate 2

description: Library name: TDAC_MOML13_Cas9_rep2_1


title: K562, MGYFPDa829 3uM, 3min, UGI -, replicate 1

description: Library name: TDAC_UGI_rep1_7


title: CD34+, D13,HBB/HBD, MGYFPDa829, replicate 2

description: Library name: TDAC_CD34_D13_4

value: Day 13 after differentiation induction


title: CD34+, D5, HBB/HBD, MGYFPDa829, replicate 2

description: Library name: TDAC_CD34_D5_4

value: CD34+ HSPC

value: Day 5 after differentiation induction


title: CD34+, D5, HBB/HBD, MGYFPDa829, replicate 1

description: Library name: TDAC_CD34_D5_3

value: Hematopoietic stem and progenitor cells


title: CD34+, D9, HBB/HBD, DddA11, replicate 2

description: Library name: TDAC_CD34_D9_2


title: CD34+, D13,HBB/HBD, MGYFPDa829, replicate 1

description: Library name: TDAC_CD34_D13_3


title: CD34+, D5, HBB/HBD, DddA11, replicate 2

description: Library name: TDAC_CD34_D5_2


title: K562, TDAC-seq, region1, MGYFPDa829, replicate 1

description: Library name: TDAC_K562_ MGYFPDa829_region1_rep1


title: CD34+, D13,HBB/HBD, DddA11, replicate 2

description: Library name: TDAC_CD34_D13_2


title: K562, dCas9-with sgRNA, HEK3, replicate  2

description: Library name: TDAC_K562_dCas9_sgRNA_2

value: dCas9, sgRNA transduction


title: K562, dCas9-no sgRNA, HEK3, replicate  2

description: Library name: TDAC_K562_dCas9_nosgRNA_2

value: dCas9 transduction


title: K562, TDAC-seq region12, replicate 2

description: Library name: TDAC_K562_2_12

value: Blood


title: K562, TDAC-seq region11, replicate 2

description: Library name: TDAC_K562_2_11


title: K562, TDAC-seq region14, replicate 2

description: Library name: TDAC_K562_2_14


title: K562, TDAC-seq region10, replicate 2

description: Library name: TDAC_K562_2_10


title: K562, TDAC-seq, GFI1B enhancer, DddA11, replicate 1

description: Library name: TDAC_K562_GFI1B_1


title: K562, TDAC-seq region13, replicate 2

description: Library name: TDAC_K562_2_13


title: K562, TDAC-seq region7, replicate 2

description: Library name: TDAC_K562_2_7


title: K562, TDAC-seq region9, replicate 2

description: Library name: TDAC_K562_2_9


title: K562, TDAC-seq region8, replicate 2

description: Library name: TDAC_K562_2_8


title: K562, TDAC-seq region6, replicate 2

description: Library name: TDAC_K562_2_6


title: CD34+, D9, HBB/HBD, MGYFPDa829, replicate 1

description: Library name: TDAC_CD34_D9_3


title: K562, TDAC-seq region4, replicate 2

description: Library name: TDAC_K562_2_4


title: K562, TDAC-seq region5, replicate 2

description: Library name: TDAC_K562_2_5


title: K562, TDAC-seq region2, replicate 2

description: Library name: TDAC_K562_2_2


title: K562, DddA-WGS, replicate 2

description: Library name: DddA_WGS_2


title: K562, TDAC-seq region1, replicate 2

description: Library name: TDAC_K562_2_1


title: K562, TDAC-seq region3, replicate 2

description: Library name: TDAC_K562_2_3


title: CD34+, nc, NoDddA

description: Library name: TDAC_CD34_nc_NoDddA

data_processing:
For DddA11-WGS, nanopore sequencing data were aligned using Minimap2. Duplicate reads were removed, and base-specific mutation counts were extracted using Samtools mpileup. Mutation rates at each cytosine were calculated, saved as a bedGraph file, and converted to a BigWig file. The distribution of cytosine deamination fractions was analyzed and plotted using computeMatrix and plotProfile from deepTools
For TDAC-seq, Nanopore sequencing data were aligned using the mappy. Reads with larger than 500 bp unaligned regions compared to the full amplicon on either end of the read were removed. Single base mutations and indels were extracted using the cs tag after alignment. CpG sites were masked from mutation calling to prevent bias introduced by endogenous CpG methylation. Only C-to-T and G-to-A mutations were recorded as potential DddA edits. Reads with more C-to-T than G-to-A mutations were assigned to the top strand of the template and vice versa.
Assembly: hg38
Supplementary files format and content: HJR253_4_sort_rmdups_coverage_mutationrate.bw: The first three columns represent the chromosome, start, end, and the last column contains the DddA mutation rate (C>T or G>A) per base.
Supplementary files format and content: XXX_DddA_edit_coo_mtx.tsv: Tab delimited file storing the read-by-position matrix M of DddA edits in a sparse IJV (COO matrix) format. Contains 3 columns corresponding to the row (read index), column (single base pair position in the target locus), and value of each non-zero element. If a the i^th read and j^th position is edited by DddA, then M[i, j] = 1, otherwise M[i, j] = 0.
Supplementary files format and content: XXX_ABE_edit_coo_mtx.tsv: Tab delimited file storing the read-by-position matrix M of ABE edits in a sparse IJV (COO matrix) format. Contains 3 columns corresponding to the row (read index), column (single base pair position in the target locus), and value of each non-zero element. If a the i^th read and j^th position is edited by ABE, then M[i, j] = 1, otherwise M[i, j] = 0. Row order is the same as the corresponding XXX_DddA_edit_coo_mtx.tsv
Supplementary files format and content: XXX_del_coo_mtx.tsv: Tab delimited file storing the read-by-position matrix M of deletions in a sparse IJV (COO matrix) format. Contains 3 columns corresponding to the row (read index), column (single base pair position in the target locus), and value of each non-zero element. If a the i^th read and j^th position overlaps with a deletion, then M[i, j] = 1, otherwise M[i, j] = 0. Row order is the same as the corresponding XXX_DddA_edit_coo_mtx.tsv
Supplementary files format and content: XXX_read_strands.tsv: Tab delimited file storing the strand of each read. 0 corresponds to C-to-T strand and 1 corresponds to G-to-A strand. Row order is the same as the corresponding XXX_DddA_edit_coo_mtx.tsv

extract_protocol:
Genomic DNA was isolated using a Zymo genomic DNA extraction kit.
Cells were washed with PBS and permeabilized by incubation in lysis buffer for 10 minutes at room temperature, followed by an additional incubation at 4°C for 5 minutes. After washing once with wash buffer, the cell pellet was resuspended in activation buffer supplemented with purified DddA11-MBP to achieve a final enzyme concentration of 10 µM. The reaction mixture was incubated at 37°C for 2 hours with shaking at 300 rpm. The reaction was quenched by adding SDS to a final concentration of 0.5%. Proteinase K was then added, and the sample was incubated at 56°C for 10 minutes. Genomic DNA was isolated using a Zymo genomic DNA extraction kit. For naked DNA data, gDNA was extracted from K562 cells using the QIAamp DNA Blood Kit to obtain deproteinized DNA, followed by the DddA reaction.For TDAC-seq, nested PCR was performed using target-specific primers with KOD One PCR Master Mix, and libraries were prepared following the Ligation Sequencing V14 – PCR Barcoding Kit protocol from Oxford Nanopore. For DddA11-Whole genome sequencing, gDNA was fragmented to 10 kbp, and libraries were prepared using the same ligation sequencing kit.

treatment_protocol: Cells were transduced with lentiviral particles carrying the sgRNA plasmid and selected with puromycin. Subsequently, K562 or MOLM-13 were electroporated with Cas9 or purified ABE. For CD34+ cells, erythroid differentiation was initiated 2 days after electroporation by switching to EDM media.

value: sgRNA transduction, Cas9 electroportaion, erythroid differentiation


title: CD34+, sgRNA68, rep1

description: Library name: TDAC_CD34_sgRNA68_rep1

value: sgRNA-68 HBG deletion


title: CD34+, nc, rep1

description: Library name: TDAC_CD34_nc_rep1

value: WT


title: CD34+, sgRNA68, NoDddA

description: Library name: TDAC_CD34_sgRNA68_NoDddA


title: CD34+, sgRNA68, rep2

description: Library name: TDAC_CD34_sgRNA68_rep2


title: CD34+, nc, rep2

description: Library name: TDAC_CD34_nc_rep2


title: K562, HS2, ABE rep1

description: Library name: TDAC_K562_HS2_ABE_rep1

value: CML Lymphoblast Cells

value: ABE edits at HS2

value: sgRNA transduction, ABE electroportaion

value: Day 6 after electroporation


title: K562, HS2, Cas9 rep1

description: Library name: TDAC_K562_HS2_Cas9_rep1

value: Deletions at HS2

value: sgRNA transduction, Cas9 electroportaion


title: MOLM13, HOXA7/9, sgRNA1, replicate 1

data_processing:
For DddA11-WGS or MGYFPDa829-WGS, nanopore sequencing data were aligned using Minimap2. Duplicate reads were removed, and base-specific mutation counts were extracted using Samtools mpileup. Mutation rates at each cytosine were calculated, saved as a bedGraph file, and converted to a BigWig file. The distribution of cytosine deamination fractions was analyzed and plotted using computeMatrix and plotProfile from deepTools
For TDAC-seq, Nanopore sequencing data were aligned using the mappy. Reads with larger than 500 bp unaligned regions compared to the full amplicon on either end of the read were removed. Single base mutations and indels were extracted using the cs tag after alignment. CpG sites were masked from mutation calling to prevent bias introduced by endogenous CpG methylation. Only C-to-T and G-to-A mutations were recorded as potential DddA edits. Reads with more C-to-T than G-to-A mutations were assigned to the top strand of the template and vice versa.
genome build/assembly: hg38
processed data files format and content: XXX_sort_rmdups_coverage_mutationrate.bw: The first three columns represent the chromosome, start, end, and the last column contains the DddA mutation rate (C>T or G>A) per base.
processed data files format and content: XXX_DddA_edit_coo_mtx.tsv: Tab delimited file storing the read-by-position matrix M of DddA edits in a sparse IJV (COO matrix) format. Contains 3 columns corresponding to the row (read index), column (single base pair position in the target locus), and value of each non-zero element. If a the i^th read and j^th position is edited by DddA, then M[i, j] = 1, otherwise M[i, j] = 0.
processed data files format and content: XXX_ABE_edit_coo_mtx.tsv: Tab delimited file storing the read-by-position matrix M of ABE edits in a sparse IJV (COO matrix) format. Contains 3 columns corresponding to the row (read index), column (single base pair position in the target locus), and value of each non-zero element. If a the i^th read and j^th position is edited by ABE, then M[i, j] = 1, otherwise M[i, j] = 0. Row order is the same as the corresponding XXX_DddA_edit_coo_mtx.tsv
processed data files format and content: XXX_del_coo_mtx.tsv: Tab delimited file storing the read-by-position matrix M of deletions in a sparse IJV (COO matrix) format. Contains 3 columns corresponding to the row (read index), column (single base pair position in the target locus), and value of each non-zero element. If a the i^th read and j^th position overlaps with a deletion, then M[i, j] = 1, otherwise M[i, j] = 0. Row order is the same as the corresponding XXX_DddA_edit_coo_mtx.tsv
processed data files format and content: XXX_read_strands.tsv: Tab delimited file storing the strand of each read. 0 corresponds to C-to-T strand and 1 corresponds to G-to-A strand. Row order is the same as the corresponding XXX_DddA_edit_coo_mtx.tsv

value: Human-derived acute myeloid leukemia cells

value: CTCF motif deletion


title: K562, dCas9-with sgRNA, HEK3, replicate  1


title: CD34+, D9, HBB/HBD, DddA11, replicate 1

value: CD34+ HSPC

value: Erythroid differentiation

value: Day 9 after differentiation induction


title: K562, HS2, ABE rep2

description: Library name: TDAC_K562_HS2_ABE_rep2


title: K562, dCas9-no sgRNA, HEK3, replicate  1


title: K562, TDAC-seq region14, replicate 1


title: CD34+, D13,HBB/HBD, DddA11, replicate 1

value: Hematopoietic stem and progenitor cells

value: Day 13 after differentiation induction


title: K562, TDAC-seq region13, replicate 1

value: Blood


title: K562, DddA11 3uM, 120min, replicate 2

description: Library name: TDAC_titration_rep2_6


title: K562, TDAC-seq region10, replicate 1


title: K562, TDAC-seq region11, replicate 1


title: GM12878, TDAC-seq region1, replicate 2

description: Library name: TDAC_GM12878_2

value: Lymphoblastoid Cells


title: K562, TDAC-seq region12, replicate 1


title: K562, TDAC-seq region9, replicate 1


title: K562, TDAC-seq region4, replicate 1


title: K562, TDAC-seq region5, replicate 1


title: K562, TDAC-seq region3, replicate 1


title: K562, HS2, Cas9 rep2

description: Library name: TDAC_K562_HS2_Cas9_rep2


title: K562, TDAC-seq region1, replicate 1


title: GM12878, TDAC-seq region1, replicate 1


title: CD34+, D5, HBB/HBD, DddA11, replicate 1

value: Day 5 after differentiation induction


title: K562, DddA-WGS, replicate 1

value: WT


title: ino80-5_input_rep2, ChIP-seq

city: Shanghai

first: Xiaolong

last: Wu

state: Shanghai

address: 2005 Songhu Road, Shanghai

institute: Fudan University

description:
Library name: ino80-5_input_rep2
replicate2

data_processing:
Raw reads were trimmed to remove the adapters and take out the reads with low sequencing quality score using TrimGalore/Cutadapt.
Clean reads were aligned to the Arabidopsis thaliana reference genome (TAIR10) using Bowtie2.
Reads mapped to the chromosome genome were preserved and tools of SAMtools were used to obtain high quality alignments.
Sequencing signals were normalized by the bamCoverage tool in deepTools. To obtain the enrichment signal around the gene body, TSS and TTS, computeMatrix tool in deepTools was employed.
Assembly: TAIR10
Supplementary files format and content: BIGWIG

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Arabidopsis thaliana seedlings were grown on MS medium under 16-h light/8-h dark conditions at 22°C for 14 days.

extract_protocol:
Seedlings were harvested and fixed with the buffer containing 0.4 M sucrose, 10 mM Tris-HCl (pH 8.0), 1 mM EDTA, 1% formaldehyde, and 1 mM PMSF. Chromatin was sonicated into DNA fragments around 200~500-bp in size using lysis buffer containing 50 mM HEPES (pH 7.5), 150 mM NaCl, 1 mM EDTA, 1 mM PMSF, 1% SDS, 0.1% Na deoxycholate, 1% Triton X-100 and Protease Inhibitor cocktail.
ChIP-seq libraries were constructed by following the manufacturer’s instructions of VAHTSTM Universal DNA Library Prep Kit (Vazyme).

value: seedlings

tag: ecotype

value: no treatment


title: ino80-5_input_rep1, ChIP-seq

description:
Library name: ino80-5_input_rep1
replicate1


title: K562, naked DNA

description: Library name: DddA_naked_DNA

value: CML Lymphoblast Cells


title: ino80-5_H3K27me3_rep2, ChIP-seq

description:
Library name: ino80-5_H3K27me3_rep2
replicate2


title: ino80-5_H3_rep2, ChIP-seq

description:
Library name: ino80-5_H3_rep2
replicate2


title: ino80-5_H3K27me3_rep1, ChIP-seq

description:
Library name: ino80-5_H3K27me3_rep1
replicate1


title: ino80-5_H3_rep1, ChIP-seq

description:
Library name: ino80-5_H3_rep1
replicate1


title: ino80-5_H3K4me3_rep2, ChIP-seq

description:
Library name: ino80-5_H3K4me3_rep2
replicate2


title: ino80-5_H2AZ_rep2, ChIP-seq

description:
Library name: ino80-5_H2AZ_rep2
replicate2


title: ino80-5_H2AZ_rep1, ChIP-seq

description:
Library name: ino80-5_H2AZ_rep1
replicate1


title: elf6-126_input_rep2, ChIP-seq

description:
Library name: elf6-126_input_rep2
replicate2


title: elf6-126_input_rep1, ChIP-seq

description:
Library name: elf6-126_input_rep1
replicate1


title: K562, TDAC-seq region7, replicate 1


title: K562, TDAC-seq region6, replicate 1


title: elf6-126_ino80-5_input_rep2, ChIP-seq

description:
Library name: elf6-126_ino80-5_input_rep2
replicate2


title: elf6-126_ino80-5_H3K27me3_rep2, ChIP-seq

description:
Library name: elf6-126_ino80-5_H3K27me3_rep2
replicate2


title: elf6-126_ino80-5_input_rep1, ChIP-seq

description:
Library name: elf6-126_ino80-5_input_rep1
replicate1


title: elf6-126_ino80-5_H3K4me3_rep2, ChIP-seq

description:
Library name: elf6-126_ino80-5_H3K4me3_rep2
replicate2


title: elf6-126_ino80-5_H3K27me3_rep1, ChIP-seq

description:
Library name: elf6-126_ino80-5_H3K27me3_rep1
replicate1


title: K562, TDAC-seq region2, replicate 1


title: elf6-126_ino80-5_H3_rep2, ChIP-seq

description:
Library name: elf6-126_ino80-5_H3_rep2
replicate2


title: elf6-126_ino80-5_H3K4me3_rep1, ChIP-seq

description:
Library name: elf6-126_ino80-5_H3K4me3_rep1
replicate1


title: elf6-126_ino80-5_H3_rep1, ChIP-seq

description:
Library name: elf6-126_ino80-5_H3_rep1
replicate1


title: elf6-126_ino80-5_H2AZ_rep2, ChIP-seq

description:
Library name: elf6-126_ino80-5_H2AZ_rep2
replicate2


title: elf6-126_ino80-5_H2AZ_rep1, ChIP-seq

description:
Library name: elf6-126_ino80-5_H2AZ_rep1
replicate1


title: elf6-126_H3K27me3_rep2, ChIP-seq

description:
Library name: elf6-126_H3K27me3_rep2
replicate2


title: elf6-126_H3K27me3_rep1, ChIP-seq

description:
Library name: elf6-126_H3K27me3_rep1
replicate1


title: ino80-5_H3K4me3_rep1, ChIP-seq

description:
Library name: ino80-5_H3K4me3_rep1
replicate1


title: elf6-126_H3K4me3_rep1, ChIP-seq

description:
Library name: elf6-126_H3K4me3_rep1
replicate1


title: elf6-126_H3_rep2, ChIP-seq

description:
Library name: elf6-126_H3_rep2
replicate2


title: elf6-126_H3_rep1, ChIP-seq

description:
Library name: elf6-126_H3_rep1
replicate1


title: elf6-126_H2AZ_rep2, ChIP-seq

description:
Library name: elf6-126_H2AZ_rep2
replicate2


title: elf6-126_H2AZ_rep1, ChIP-seq

description:
Library name: elf6-126_H2AZ_rep1
replicate1


title: Col-0_input_rep2, ChIP-seq

description:
Library name: Col-0_input_rep2
replicate2

value: wild-type


title: Col-0_input_rep1, ChIP-seq

description:
Library name: Col-0_input_rep1
replicate1


title: Col-0_H3K27me3_rep2, ChIP-seq

description:
Library name: Col-0_H3K27me3_rep2
replicate2


title: Col-0_H3K27me3_rep1, ChIP-seq

description:
Library name: Col-0_H3K27me3_rep1
replicate1


title: Col-0_H3K4me3_rep2, ChIP-seq

description:
Library name: Col-0_H3K4me3_rep2
replicate2


title: Col-0_H3_rep2, ChIP-seq

description:
Library name: Col-0_H3_rep2
replicate2


title: Col-0_H2AZ_rep1, ChIP-seq

description:
Library name: Col-0_H2AZ_rep1
replicate1


title: Col-0_H2AZ_rep2, ChIP-seq

description:
Library name: Col-0_H2AZ_rep2
replicate2


title: Col-0_H3_rep1, ChIP-seq

description:
Library name: Col-0_H3_rep1
replicate1


title: Col-0_H3K4me3_rep1, ChIP-seq

description:
Library name: Col-0_H3K4me3_rep1
replicate1


title: clf-29_H3K27me3_rep2, ChIP-seq

description:
Library name: clf-29_H3K27me3_rep2
replicate2


title: clf-29_H3K27me3_rep1, ChIP-seq

description:
Library name: clf-29_H3K27me3_rep1
replicate1


title: clf-29_input_rep2, ChIP-seq

description:
Library name: clf-29_input_rep2
replicate2


title: clf-29_input_rep1, ChIP-seq

description:
Library name: clf-29_input_rep1
replicate1


title: 27°C_mannitol_rep1

city: Beijing

first: Xiaoyi

last: Li

address: west beichen

department: Chinese Academy of Sciences

institute: Institute of Genetics and Developmental Biology

description: Library name: 27C_mannitol_rep1

data_processing:
Adapter trimming was performed and low quality reads were filtered with fastp version 0.20.1
Reads were aligned to the Arabidopsis genome (TAIR10) using Hisat2 version 2.1.10
Transcripts per million (TPM) values were generated using R
Differential gene expression analysis was performed using DESeq2 version 1.26.0
Genes were considered as differentially expressed if they exhibited a fold change greater than two and a P adjust value < 0.05
Assembly: TAIR10
Supplementary files format and content: *.txt: TPM values for all samples

source_name: Seedlings

growth_protocol: Plants were germinated and grown under short day conditions (8h light/16h dark) at 21°C until day 7

extract_protocol:
Total RNA was extracted with Eastep Super Total RNA Extraction Kit (Promega, LS1040)
Sequencing libraries were prepared with the NEBNext Ultra RNA library prep kit for Illumina (NEB, 7530L) according to the manufacturer’s instruction

treatment_protocol: 7-day-old seedlings grown at 21°C were shifted to 27°C or kept at 21°C with or without mannitol treatment at ZT1, and seedlings were collected at ZT13.

value: Seedlings

value: Wild type Columbia


title: 27°C_mannitol_rep2

description: Library name: 27C_mannitol_rep2


title: 27°C_mannitol_rep3

description: Library name: 27C_mannitol_rep3


title: 27°C_rep2

description: Library name: 27C_rep2


title: elf6-126_H3K4me3_rep2, ChIP-seq

description:
Library name: elf6-126_H3K4me3_rep2
replicate2


title: 27°C_rep1

description: Library name: 27C_rep1


title: 21°C_mannitol_rep2

description: Library name: 21C_mannitol_rep2


title: 21°C_mannitol_rep1

description: Library name: 21C_mannitol_rep1


title: 21°C_rep2

description: Library name: 21C_rep2


title: 21°C_rep3

description: Library name: 21C_rep3


title: 21°C_rep1

description: Library name: 21C_rep1


title: K562, TDAC-seq region8, replicate 1


title: elf6-126_rep2, mRNA-seq

description:
Library name: elf6-126_rep2
replicate2

data_processing:
Raw reads were cleaned by Cutadapt v3.5 to remove low quality bases and sequencing adapters.
Then trimmed reads were mapped to Arabidopsis thaliana reference genome TAIR10 using HISAT2 v2.1.0.
Samtools v1.17 was used to remove the low mapping quality (MAPQ<20) reads and then featureCounts v2.0.1 was used to count the number of reads that were aligned to exons.
Assembly: TAIR10
Supplementary files format and content: Binary bw files (bigwig)

molecule: polyA RNA

source_name: 14-day-old seedlings

extract_protocol:
RNA was extracted using an RNAprep pure Plant Kit (Tiangen Biotech).
The strand-specific RNA-seq libraries were constructed by following the KAPA stranded mRNA-seq Kit instructions (Illumina® Platforms, KR0960-v5.17), according to the manufacturer’s instructions.

value: 14-day-old seedlings


title: ino80-5_rep2, mRNA-seq

description:
Library name: ino80-5_rep2
replicate2


title: elf6-126_rep3, mRNA-seq

description:
Library name: elf6-126_rep3
replicate3


title: ino80-5_rep1, mRNA-seq

description:
Library name: ino80-5_rep1
replicate1


title: ino80-5_rep3, mRNA-seq

description:
Library name: ino80-5_rep3
replicate3


title: elf6-126_ino80-5_rep3, mRNA-seq

description:
Library name: elf6-126_ino80-5_rep3
replicate3


title: elf6-126_rep1, mRNA-seq

description:
Library name: elf6-126_rep1
replicate1


title: elf6-126_ino80-5_rep1, mRNA-seq

description:
Library name: elf6-126_ino80-5_rep1
replicate1


title: Col-0_rep3, mRNA-seq

description:
Library name: Col-0_rep3
replicate3

value: wild-type (Col-0)


title: Col-0_rep2, mRNA-seq

description:
Library name: Col-0_rep2
replicate2


title: 27°C_rep3

description: Library name: 27C_rep3


title: phot2 camta2, 20C, ZT24, rep3

city: La Jolla

first: Adam

last: Seluzicki

state: CA

address: 10010 N. Torrey Pines Rd.

department: Plant Biology Laboratory

institute: HHMI, Salk Institute for Biological Studies

data_processing:
Samples were split and sequenced on two lanes, resulting in four files for each sample: two for each strand. Data were demultiplexed using bcl2fastq Conversion Software (Illumina, San Diego, CA). Fastq filesfor each strand were merged prior to alignment.
alignment to TAIR10 genome: STAR-2.7.10a, alignIntronMax 2000, outFilterMismatchNmax 2
HTSeq-count:  MODE: intersect_strict Used Araport11 gene/transposon list
edgeR-3.36.0 only included genes with cumulative CPM>1 across all samples
Note: Sample 25 (Col0, 15C, ZT12, rep1) was omitted from final analysis due to evidence of pathogen infection, and is not included in the normCPM_H1.csv data sheet. The raw counts file is labeled "REMOVED" to indicate this.
Assembly: TAIR10
Supplementary files format and content: tab delimited text file with raw counts for nuclear genes
Supplementary files format and content: tab-delimited text file with normalized Counts per million reads (CPM) for all samples – one column per sample

source_name: 10-day-old Shoot (above-ground)

growth_protocol: seeds germinated on 1/2x Linsmaier & Skoog medium, grown for two days, transplanted to soil and moved to chambers with light intensity ~100umol m-2 s-1 at noted growth temperature. Above-ground (shoot) tissue from six plants per sample were harvested at the indicated time.

extract_protocol:
RNA was extracted using the RNeasy Plant Mini Kit (Qiagen)
Truseq Stranded mRNA kit with Truseq UDI RNA index (IDT Truseq UDI #20022371), 500ng input

value: 10-day-old Shoot (above-ground)

value: phot2 camta2

value: full day time course,  16h light, 8h dark, 20C

tag: time (zeitgeber_time-zt)


title: phot2, 20C, ZT24, rep3


title: Col0, 20C, ZT24, rep3

value: Col0 (wt)


title: camta2, 20C, ZT24, rep3


title: camta2, 15C, ZT24, rep3

value: full day time course,  16h light, 8h dark, 15C


title: 21°C_mannitol_rep3

description: Library name: 21C_mannitol_rep3


title: phot2, 15C, ZT24, rep3


title: phot2 camta2, 15C, ZT24, rep3


title: Col0, 15C, ZT24, rep3

value: full day time course, 16h light, 8h dark, 15C


title: phot2 camta2, 20C, ZT20, rep3


title: camta2, 20C, ZT20, rep3


title: Col0, 20C, ZT20, rep3


title: phot2, 20C, ZT20, rep3


title: phot2 camta2, 15C, ZT20, rep3


title: camta2, 15C, ZT20, rep3


title: phot2, 15C, ZT20, rep3


title: Col0, 15C, ZT20, rep3


title: elf6-126_ino80-5_rep2, mRNA-seq

description:
Library name: elf6-126_ino80-5_rep2
replicate2


title: phot2, 20C, ZT16, rep3


title: phot2 camta2, 15C, ZT16, rep3


title: Col-0_rep1, mRNA-seq

description:
Library name: Col-0_rep1
replicate1


title: camta2, 15C, ZT16, rep3


title: phot2 camta2, 20C, ZT16, rep3


title: Col0, 15C, ZT16, rep3


title: camta2, 20C, ZT16, rep3


title: phot2 camta2, 20C, ZT12, rep3


title: phot2, 20C, ZT12, rep3


title: phot2 camta2, 15C, ZT12, rep3


title: Col0, 20C, ZT12, rep3


title: camta2, 20C, ZT12, rep3


title: phot2 camta2, 20C, ZT8, rep3


title: phot2 camta2, 15C, ZT8, rep3


title: phot2, 20C, ZT8, rep3


title: Col0, 15C, ZT12, rep3


title: camta2, 20C, ZT8, rep3


title: phot2, 15C, ZT12, rep3


title: camta2, 15C, ZT8, rep3


title: phot2, 15C, ZT8, rep3


title: Col0, 15C, ZT8, rep3


title: camta2, 20C, ZT4, rep3


title: phot2, 20C, ZT4, rep3


title: Col0, 20C, ZT16, rep3


title: phot2 camta2, 20C, ZT4, rep3


title: phot2 camta2, 15C, ZT4, rep3


title: phot2, 15C, ZT16, rep3


title: Col0, 20C, ZT8, rep3


title: camta2, 15C, ZT4, rep3


title: phot2 camta2, 20C, ZT0, rep3


title: Col0, 20C, ZT0, rep3


title: phot2, 20C, ZT0, rep3


title: camta2, 20C, ZT0, rep3


title: camta2, 15C, ZT12, rep3


title: phot2 camta2, 15C, ZT0, rep3


title: phot2, 15C, ZT0, rep3


title: phot2 camta2, 20C, ZT24, rep2


title: Col0, 20C, ZT24, rep2


title: camta2, 20C, ZT24, rep2


title: camta2, 15C, ZT0, rep3


title: phot2, 15C, ZT24, rep2


title: phot2, 20C, ZT24, rep2


title: camta2, 15C, ZT24, rep2


title: Col0, 20C, ZT4, rep3


title: Col0, 15C, ZT24, rep2


title: phot2, 20C, ZT20, rep2


title: camta2, 20C, ZT20, rep2


title: phot2 camta2, 20C, ZT20, rep2


title: phot2 camta2, 15C, ZT20, rep2


title: phot2, 15C, ZT4, rep3


title: Col0, 20C, ZT20, rep2


title: camta2, 15C, ZT20, rep2


title: phot2, 15C, ZT20, rep2


title: Col0, 15C, ZT20, rep2


title: camta2, 20C, ZT16, rep2


title: phot2, 20C, ZT16, rep2


title: phot2 camta2, 20C, ZT16, rep2


title: Col0, 20C, ZT16, rep2


title: camta2, 15C, ZT16, rep2


title: Col0, 15C, ZT0, rep3


title: phot2, 15C, ZT16, rep2


title: phot2 camta2, 15C, ZT24, rep2


title: Col0, 15C, ZT16, rep2


title: V4

city: Bethesda

first: Peng

last: Jiang

state: Maryland

address: 41 Center Drive

department: Center for Cancer Research

institute: National Cancer Institute

description:
Library name: V4
CD8 T cells isolated from mouse splenocytes were pre-treated with ethanol control and then activated by anti-CD3/28 beads in the presence of 10% glycerol PBS
RSEM.TPM.processed.gz
MiXCR.Repertoire
AOAH.DESeq

data_processing:
Raw fastq files were processed using the RNA-seq data-processing pipeline described in our publication.
Only the UMI deduped fastq files were uploaded.
The DESeq2 analysis needs a group column to include the batch, as all biological replicates are paired.
Assembly: mm39
Supplementary files format and content: RSEM TPM values, tab delimited gzip file
Supplementary files format and content: DESeq2, Tab delimited text file
Supplementary files format and content: MiXCR summary, Tab delimited text file

source_name: CD8 T cells

growth_protocol: TexMACS Medium (Miltenyi)+ 10% heat-inactivated fetal bovin serum (Quality Biological)+ 50 µM 2-Mercaptoethanol (Gibco) with or without 100 IU/mL recombinant human IL-2 (R&D Systems)

extract_protocol:
Total RNA was extracted using Qiagen Rneasy Plus Mini kit following manufacturer's instructions (Qiagen, Hilden, Germany). RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA). ERCC RNA Spike-In Mix (Cat: #4456740) from ThermoFisher Scientific, was added to normalized total RNA prior to library preparation following manufacturer's protocol.
RNA sequencing libraries were prepared using the NEBNext B88Ultra II RNA Library Prep Kit for Illumina using manufacturer's instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized using primers which included random priming sites and Unique Molecular Identifiers (UMIs). UMI sequences were incorporated in the resultant cDNA. cDNA fragments were end repaired and adenylated at 3'ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA,USA).  The sequencing libraries were clustered on a flowcell. After clustering, the flowcell was loaded on the Illumina NovaSeq instrument according to manufacturer's instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the Control software. Raw sequence data (.bcl files) generated by the sequencer were converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.

treatment_protocol: The mouse CD8+ T cells were first isolated from splenocytes of C57BL/6 mice using EasySep™ Mouse CD8+ T Cell Isolation Kit (Stem cell technologies), and pre-treated in T-cell medium (Miltenyi) with either 10 µg/mL rhAOAH-His (Wuxi Biologics) + ethanol control, or equal volume of 10% glycerol PBS + ethanol control, or  10% glycerol PBS + 60 µM PC16:0-20:4 (Avanti Lipids) for 22 hours. Next, the pre-treated CD8+ T cells were activated by 1 µg/mL plate-bound anti-mouse CD3 antibody (Cytek Biosciences) and 0.5 µg/mL anti-mouse CD28 antibody (Cytek Biosciences) for 24 hours.

value: CD8 T cells

value: Ethanol control -> Protein buffer control

tag: batch


title: V3

description:
Library name: V3
CD8 T cells isolated from mouse splenocytes were pre-treated with ethanol control and then activated by anti-CD3/28 beads in the presence of 10% glycerol PBS
RSEM.TPM.processed.gz
MiXCR.Repertoire
AOAH.DESeq
PC.DESeq


title: phot2 camta2, 20C, ZT12, rep2


title: V2

description:
Library name: V2
CD8 T cells isolated from mouse splenocytes were pre-treated with ethanol control and then activated by anti-CD3/28 beads in the presence of 10% glycerol PBS
RSEM.TPM.processed.gz
MiXCR.Repertoire
AOAH.DESeq
PC.DESeq


title: camta2, 20C, ZT12, rep2


title: V1

description:
Library name: V1
CD8 T cells isolated from mouse splenocytes were pre-treated with ethanol control and then activated by anti-CD3/28 beads in the presence of 10% glycerol PBS
RSEM.TPM.processed.gz
MiXCR.Repertoire
AOAH.DESeq
PC.DESeq


title: phot2, 20C, ZT12, rep2


title: PC16-3

description:
Library name: PC16-3
CD8 T cells isolated from mouse splenocytes were pre-treated with 60 µM PC16:0-20:4 and then activated by anti-CD3/28 beads in the presence of 10% glycerol PBS
RSEM.TPM.processed.gz
MiXCR.Repertoire
PC.DESeq

value: PC(16:0_20:4) -> Protein buffer control


title: Col0, 20C, ZT12, rep2


title: A4

description:
Library name: A4
CD8 T cells isolated from mouse splenocytes were pre-treated with ethanol control and then activated by anti-CD3/28 beads in the presence of 10 µg/mL recombinant human AOAH
RSEM.TPM.processed.gz
MiXCR.Repertoire
AOAH.DESeq

value: Ethanol control -> AOAH-His


title: camta2, 15C, ZT12, rep2


title: PC16-2

description:
Library name: PC16-2
CD8 T cells isolated from mouse splenocytes were pre-treated with 60 µM PC16:0-20:4 and then activated by anti-CD3/28 beads in the presence of 10% glycerol PBS
RSEM.TPM.processed.gz
MiXCR.Repertoire
PC.DESeq


title: phot2, 15C, ZT12, rep2


title: PC16-1

description:
Library name: PC16-1
CD8 T cells isolated from mouse splenocytes were pre-treated with 60 µM PC16:0-20:4 and then activated by anti-CD3/28 beads in the presence of 10% glycerol PBS
RSEM.TPM.processed.gz
MiXCR.Repertoire
PC.DESeq


title: Col0, 15C, ZT12, rep2


title: A2

description:
Library name: A2
CD8 T cells isolated from mouse splenocytes were pre-treated with ethanol control and then activated by anti-CD3/28 beads in the presence of 10 µg/mL recombinant human AOAH
RSEM.TPM.processed.gz
MiXCR.Repertoire
AOAH.DESeq


title: phot2 camta2, 20C, ZT8, rep2


title: A1

description:
Library name: A1
CD8 T cells isolated from mouse splenocytes were pre-treated with ethanol control and then activated by anti-CD3/28 beads in the presence of 10 µg/mL recombinant human AOAH
RSEM.TPM.processed.gz
MiXCR.Repertoire
AOAH.DESeq


title: Con-spleno-24hrs-3

description:
Library name: Con-spleno-24hrs-3
Mouse splenocytes pretreated with protein buffer control and then co-cultured with hgp100 pulsed splenocytes
RSEM.TPM.processed.gz
MiXCR.Repertoire
Splenocyte.DESeq

data_processing:
Raw fastq files were processed using the RNA-seq data-processing pipeline described in our publication.
Only the UMI deduped fastq files were uploaded.
The DESeq2 analysis needs a group column to include the biological replicate, as all samples are paired.
Assembly: mm39
Supplementary files format and content: RSEM TPM values, tab delimited gzip file
Supplementary files format and content: DESeq2, Tab delimited text file
Supplementary files format and content: MiXCR summary, Tab delimited text file

source_name: Splenocyte

extract_protocol:
Total RNA was extracted using Qiagen Rneasy Plus Mini kit following manufacturer's instructions (Qiagen, Hilden, Germany). RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA). ERCC RNA Spike-In Mix (Cat: #4456740) from ThermoFisher Scientific, was added to normalized total RNA prior to library preparation following manufacturer's protocol.
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer's instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized using primers which included random priming sites and Unique Molecular Identifiers (UMIs). UMI sequences were incorporated in the resultant cDNA. cDNA fragments were end repaired and adenylated at 3'ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA,USA).  The sequencing libraries were clustered on a flowcell. After clustering, the flowcell was loaded on the Illumina NovaSeq instrument according to manufacturer's instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the Control software. Raw sequence data (.bcl files) generated by the sequencer were converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.

treatment_protocol: The splenocytes were first isolated from the spleens of pmel mice, and pre-treated in T-cell medium (Miltenyi) with either 10 µg/mL rhAOAH-His (Wuxi Biologics) or buffer (PBS + 10%glycerol) for 22 hours. Next, the splenocytes from C57BL/6 mice were pulsed with 100 nM hgp100 antigens (GeneScript) in RPMI-1640 iat 37 °C for 2 hours and  mixed with the pre-treated pmel splenocytes at the 3:1 ratio in T-cell medium (Miltenyi) + 100 IU/mL recombinant human IL-2 (R&D Systems) with either 10 µg/mL rhAOAH-His (Wuxi Biologics) or vehicle for 24 hours.

value: Splenocyte

value: Buffer (Phosphate-buffered saline + 10% glycerol)

tag: duration (hour)

tag: biologica replicate


title: camta2, 20C, ZT8, rep2


title: phot2 camta2, 15C, ZT16, rep2


title: phot2, 20C, ZT8, rep2


title: phot2 camta2, 15C, ZT8, rep2


title: camta2, 15C, ZT8, rep2


title: Donor-03-BM-LymphDepleted_GEX

city: New York

first: Maria

last: Sirenko

state: NY

address: 550 1st Avenue

institute: NYU Langone

description:
Library name: Donor-03-BM-LymphDepleted_GEX
scRNAseq

library_source: transcriptomic single cell

data_processing:
FASTQs were aligned to GRCh38 and cell by gene count matrices were generated using CellRanger 5.0.1 with default parameters. CellRanger quality control metrics are provided in Table S1. Gene expression analysis was conducted using Seurat v4 in R4.2.2.
Assembly: GRCh38 - default CellRanger reference
Supplementary files format and content: cellranger filtered barcode matrices provided
Supplementary files format and content: seurat object in rds format

source_name: Bone Marrow

extract_protocol:
Samples from AML-01, AML-02, AML-03, AML-04, AML-05, AML-06, CH-01, CH-02 were processed as follows. Frozen bone marrow and peripheral blood samples were thawed under standard procedures and prepared for sorting by flow cytometry. Briefly, cryopreserved samples were thawed and transferred to 15 ml conical tubes containing 10 ml of RPMI media with 10% fetal bovine serum (FBS) and 0.1mL of a 1 mg/mL DNAse I solution. Cells were centrifuged at 300 x g for 4 minutes at 4°C, and supernatant was removed. Cells were resuspended in FACS buffer and incubated with Fc blocker for 15 minutes. Next, cells were stained with PE-conjugated CD45, and FITC-conjugated CD3, CD19, and CD56 to enable lymphoid-depleted sorting. Cells were stained for 15 minutes and resuspended in FACS-DAPI to enable enrichment for live cells. Cells were then sorted for DAPI-, CD3-/CD19-/CD56- cells using the BD Influx at the Weill Cornell Medicine flow cytometry core.
Sorted cells were processed using the 10X Genomics Chromium controller with the Single Cell Gene Expression 5’ V1 protocol (except sample CH-05 which was processed on 5’ V2 after V1 was discontinued). The 5’ kit was selected to maximize genotyping efficiency because most mutations, including IDH1, IDH2, NRAS, and SRSF2, were closer to the 5’ end of the mRNA. Single cell gene expression libraries were sequenced on a Nova-seq 6000 with R1:R2:I1 27:176:8bp paired end format where R1 contains the 10X barcode and UMI, R2 contains the transcript sequence, and I1 the sample index. Single cell genotyping was applied to 13 patients/donors (AML-01, AML-02, AML-03, AML-04, AML-05, AML-06, AML-16, AML-17, AML-18, AML-19, AML-20, CH-01, CH-02). Somatic mutations detected by clinical targeted DNA sequencing informed the design of multiplexed single cell genotyping using Genotyping of Transcriptomes (GoT).25 GoT targets were prioritized to capture mutations representative of distinct subclones with greater than 5% VAF in targeted DNA sequencing and sufficient gene expression in 10X data. Cells were profiled using the 5’ 10X Genomics kit to maximize GoT efficiency, as most mutations were within 1000bp of the 5’ end (IDH1/2, NRAS, NPM1, and SRSF2) (Figures S4B and S4C). GoT libraries were prepared for IDH1, IDH2, NRAS, NPM1, FLT3 and SRSF2 as described in Nam et al.25 We did not genotype DNMT3A which is often clonal and co-occurring within the same cells as IDH mutations, due to technical limitations of low gene expression (Average expression in single cell data: 0.19; comparable to IDH1 0.15) and >2000 base pair mutation distance from 5’ end. Primers used for GoT are provided in Table S1. GoT Libraries were pooled and sequenced on Illumina MiniSeq 300 cycle mid-output kit in 147:8:147 paired end configuration or spiked in at 1-2% of gene expression library sequencing runs on NovaSeqX Plus with configuration as described above.

value: Bone Marrow

value: LymphDepleted

value: GEX Library


title: Donor-04-BM-LymphDepleted_GEX

description:
Library name: Donor-04-BM-LymphDepleted_GEX
scRNAseq


title: phot2, 15C, ZT8, rep2


title: Donor-02-PB-Live_GEX

description:
Library name: Donor-02-PB-Live_GEX
scRNAseq

source_name: Peripheral Blood

value: Peripheral Blood

value: Live


title: Con-spleno-24hrs-1

description:
Library name: Con-spleno-24hrs-1
Mouse splenocytes pretreated with protein buffer control and then co-cultured with hgp100 pulsed splenocytes
RSEM.TPM.processed.gz
MiXCR.Repertoire
Splenocyte.DESeq


title: Con-spleno-24hrs-2

description:
Library name: Con-spleno-24hrs-2
Mouse splenocytes pretreated with protein buffer control and then co-cultured with hgp100 pulsed splenocytes
RSEM.TPM.processed.gz
MiXCR.Repertoire
Splenocyte.DESeq


title: A-spleno-24hrs-4

description:
Library name: A-spleno-24hrs-4
Mouse splenocytes pretreated with AOAH protein and then co-cultured with hgp100 pulsed splenocytes
RSEM.TPM.processed.gz
MiXCR.Repertoire
Splenocyte.DESeq

value: Human recombinant AOAH-His-tag in buffer

tag: dose (ug/ml)


title: phot2 camta2, 20C, ZT4, rep2

value: 10-day-old Shoot (above-ground)

value: phot2 camta2


title: Donor-01-PB-LymphDepleted-02_GEX

description:
Library name: Donor-01-PB-LymphDepleted-02_GEX
scRNAseq


title: camta2, 20C, ZT4, rep2

value: full day time course,  16h light, 8h dark, 20C


title: phot2 camta2, 15C, ZT12, rep2

value: full day time course,  16h light, 8h dark, 15C


title: Col0, 15C, ZT8, rep2

value: Col0 (wt)

value: full day time course, 16h light, 8h dark, 15C


title: A3

description:
Library name: A3
CD8 T cells isolated from mouse splenocytes were pre-treated with ethanol control and then activated by anti-CD3/28 beads in the presence of 10 µg/mL recombinant human AOAH
RSEM.TPM.processed.gz
MiXCR.Repertoire
AOAH.DESeq

value: CD8 T cells


title: A-spleno-24hrs-3

description:
Library name: A-spleno-24hrs-3
Mouse splenocytes pretreated with AOAH protein and then co-cultured with hgp100 pulsed splenocytes
RSEM.TPM.processed.gz
MiXCR.Repertoire
Splenocyte.DESeq


title: Col0, 20C, ZT4, rep2


title: A-spleno-24hrs-2

description:
Library name: A-spleno-24hrs-2
Mouse splenocytes pretreated with AOAH protein and then co-cultured with hgp100 pulsed splenocytes
RSEM.TPM.processed.gz
MiXCR.Repertoire
Splenocyte.DESeq


title: phot2, 20C, ZT4, rep2


title: phot2 camta2, 15C, ZT4, rep2


title: Donor-01-PB-Live_GEX

description:
Library name: Donor-01-PB-Live_GEX
scRNAseq


title: camta2, 15C, ZT4, rep2


title: phot2, 15C, ZT4, rep2


title: A-spleno-24hrs-1

description:
Library name: A-spleno-24hrs-1
Mouse splenocytes pretreated with AOAH protein and then co-cultured with hgp100 pulsed splenocytes
RSEM.TPM.processed.gz
MiXCR.Repertoire
Splenocyte.DESeq


title: Col0, 15C, ZT4, rep2


title: Col0, 20C, ZT8, rep2


title: phot2 camta2, 20C, ZT0, rep2


title: AML-06-Dx-LymphDepleted_GEX

description:
Library name: AML-06-Dx-LymphDepleted_GEX
scRNAseq

value: Dx

value: Diagnosis


title: camta2, 20C, ZT0, rep2


title: AML-05-postTx-Live_GEX

description:
Library name: AML-05-postTx-Live_GEX
scRNAseq

value: postTx

value: Post-Treatment


title: Col0, 20C, ZT0, rep2


title: camta2, 15C, ZT0, rep2


title: AML-05-Dx-LymphDepleted_GEX

description:
Library name: AML-05-Dx-LymphDepleted_GEX
scRNAseq


title: phot2, 15C, ZT0, rep2


title: phot2 camta2, 15C, ZT0, rep2


title: B16mhgp100-Vector-3

description:
Library name: B16-Vec-3
B16mghp100 tumor 7 with vector over-expression
RSEM.TPM.processed.gz
MiXCR.Repertoire
B16mhgp100.DESeq

data_processing:
Raw fastq files were processed using the RNA-seq data-processing pipeline described in our publication.
Assembly: mm39
Supplementary files format and content: RSEM TPM values, tab delimited gzip file
Supplementary files format and content: DESeq2, Tab delimited text file
Supplementary files format and content: MiXCR summary, Tab delimited text file

source_name: Subcutaneous implanted tumor

extract_protocol:
Total RNA was extracted using Qiagen Rneasy Plus Mini kit following manufacturer's instructions (Qiagen, Hilden, Germany). RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA). ERCC RNA Spike-In Mix (Cat: #4456740) from ThermoFisher Scientific, was added to normalized total RNA prior to library preparation following manufacturer's protocol.
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer's instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized using primers which included random priming sites. cDNA fragments were end repaired and adenylated at 3'ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA,USA).  The sequencing libraries were clustered on a flowcell. After clustering, the flowcell was loaded on the Illumina NovaSeq instrument according to manufacturer's instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the Control software. Raw sequence data (.bcl files) generated by the sequencer were converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.

treatment_protocol: 10 days (6 days for B16F10 cells) after the inoculation of tumor cells, anti-PD1 (BioXCell, #BE0146, 200 μg/dose) or  anti-PD1+ anti-CTLA4 (BioXcell, #BE0131, 200 μg/dose) was given to the tumor-bearing mice twice per week for a total of 4 doses. One day after the last dose, tumor samples were harvested from the mice and used to RNA extraction.

value: Subcutaneous implanted tumor

value: bulk tumor


title: B16mhgp100-Vector-4

description:
Library name: B16-Vec-4
B16mghp100 tumor 8 with vector over-expression
RSEM.TPM.processed.gz
MiXCR.Repertoire
B16mhgp100.DESeq


title: AML-04-postTxD84-Live_GEX

description:
Library name: AML-04-postTxD84-Live_GEX
scRNAseq

value: GEX Library


title: Col0, 15C, ZT0, rep2


title: Donor-01-PB-LymphDepleted-01_GEX

description:
Library name: Donor-01-PB-LymphDepleted-01_GEX
scRNAseq

value: Peripheral Blood


title: phot2 camta2, 20C, ZT24, rep1


title: AML-04-postTxD28-LymphDepleted_GEX

description:
Library name: AML-04-postTxD28-LymphDepleted_GEX
scRNAseq

value: LymphDepleted


title: AML-06-postTx-Live_GEX

description:
Library name: AML-06-postTx-Live_GEX
scRNAseq

value: Live


title: B16mhgp100-Vector-2

description:
Library name: B16-Vec-2
B16mghp100 tumor 6 with vector over-expression
RSEM.TPM.processed.gz
MiXCR.Repertoire
B16mhgp100.DESeq


title: phot2, 20C, ZT24, rep1

value: 10-day-old Shoot (above-ground)


title: AML-04-postTxD28-Live_GEX

description:
Library name: AML-04-postTxD28-Live_GEX
scRNAseq


title: B16F10-Vector-2

description:
Library name: B16-Vec-6
B16F10 tumor 4 with vector over-expression
RSEM.TPM.processed.gz
MiXCR.Repertoire
B16F10.DESeq


title: B16mhgp100-Vector-1

description:
Library name: B16-Vec-1
B16mghp100 tumor 5 with vector over-expression
RSEM.TPM.processed.gz
MiXCR.Repertoire
B16mhgp100.DESeq


title: B16F10-Aoah-2

description:
Library name: B16-A-6
B16F10 tumor 2 with Aoah over-expression
RSEM.TPM.processed.gz
MiXCR.Repertoire
B16F10.DESeq


title: phot2 camta2, 15C, ZT24, rep1

value: phot2 camta2


title: Col0, 20C, ZT24, rep1

value: full day time course,  16h light, 8h dark, 20C


title: camta2, 20C, ZT24, rep1


title: B16F10-Vector-1

description:
Library name: B16-Vec-5
B16F10 tumor 3 with vector over-expression
RSEM.TPM.processed.gz
MiXCR.Repertoire
B16F10.DESeq


title: B16F10-Aoah-1

description:
Library name: B16-A-5
B16F10 tumor 1 with Aoah over-expression
RSEM.TPM.processed.gz
MiXCR.Repertoire
B16F10.DESeq


title: AML-04-Dx-LymphDepleted_GEX

description:
Library name: AML-04-Dx-LymphDepleted_GEX
scRNAseq


title: camta2, 15C, ZT24, rep1

value: full day time course,  16h light, 8h dark, 15C


title: phot2, 20C, ZT0, rep2


title: AML-03-postTx-LymphDepleted_GEX

description:
Library name: AML-03-postTx-LymphDepleted_GEX
scRNAseq

value: Bone Marrow


title: phot2, 15C, ZT24, rep1


title: Col0, 15C, ZT24, rep1

value: Col0 (wt)

value: full day time course, 16h light, 8h dark, 15C


title: phot2 camta2, 20C, ZT20, rep1


title: B16mhgp100-Aoah-4

description:
Library name: B16-A-4
B16mghp100 tumor 4 with Aoah over-expression
RSEM.TPM.processed.gz
MiXCR.Repertoire
B16mhgp100.DESeq


title: B16mhgp100-Aoah-3

description:
Library name: B16-A-3
B16mghp100 tumor 3 with Aoah over-expression
RSEM.TPM.processed.gz
MiXCR.Repertoire
B16mhgp100.DESeq


title: AML-03-Dx-LymphDepleted_GEX

description:
Library name: AML-03-Dx-LymphDepleted_GEX
scRNAseq

value: Dx


title: AML-02-postTx-LymphDepleted_GEX

description:
Library name: AML-02-postTx-LymphDepleted_GEX
scRNAseq


title: phot2, 20C, ZT20, rep1


title: Col0, 20C, ZT20, rep1


title: phot2 camta2, 15C, ZT20, rep1


title: camta2, 15C, ZT20, rep1


title: B16mhgp100-Aoah-2

description:
Library name: B16-A-2
B16mghp100 tumor 2 with Aoah over-expression
RSEM.TPM.processed.gz
MiXCR.Repertoire
B16mhgp100.DESeq


title: B16mhgp100-Aoah-1

description:
Library name: B16-A-1
B16mghp100 tumor 1 with Aoah over-expression
RSEM.TPM.processed.gz
MiXCR.Repertoire
B16mhgp100.DESeq


title: phot2, 15C, ZT20, rep1


title: AML-02-Dx-LymphDepleted_GEX

description:
Library name: AML-02-Dx-LymphDepleted_GEX
scRNAseq

value: Diagnosis


title: AML-02-Dx-Blasts_GEX

description:
Library name: AML-02-Dx-Blasts_GEX
scRNAseq

value: Blasts


title: Col0, 15C, ZT20, rep1


title: B2905-M4-Vec-4

description:
Library name: B2905-M4-Vec-4
M4 tumor 9 with vector over-expression

data_processing:
Raw fastq files were processed using the RNA-seq data-processing pipeline described in our publication.
Only the UMI deduped fastq files were uploaded.
Assembly: mm39
Supplementary files format and content: RSEM TPM values, tab delimited gzip file
Supplementary files format and content: DESeq2, Tab delimited text file
Supplementary files format and content: MiXCR summary, Tab delimited text file

treatment_protocol: This experiment did not involve immunotherapy treatment for two reasons. First, B2905-M4 tumors with the vector over-expression grow extremely slowly, and immunotherapy treatment may remove the tumors, thus no sufficient samples are available for sequencing. Second, tumors in Adamts7 and vector control over-expression groups achieved significant size difference without any treatments.

tag: tissue type

tag: host strain

value: M4 tumor with vector over-expression


title: phot2, 20C, ZT16, rep1


title: AML-01-postTx-LymphDepleted_GEX

description:
Library name: AML-01-postTx-LymphDepleted_GEX
scRNAseq

value: postTx

tag: cell type

value: Post-Treatment


title: camta2, 20C, ZT16, rep1

tag: tissue


title: AML-01-Dx-LymphDepleted_GEX

description:
Library name: AML-01-Dx-LymphDepleted_GEX
scRNAseq

tag: treatment

value: GEX Library


title: Col0, 20C, ZT16, rep1


title: B2905-M4-Vec-3

description:
Library name: B2905-M4-Vec-3
M4 tumor 8 with vector over-expression

value: Subcutaneous implanted tumor

value: bulk tumor


title: camta2, 20C, ZT20, rep1


title: B2905-M4-Vec-2

description:
Library name: B2905-M4-Vec-2
M4 tumor 7 with vector over-expression


title: CH-02_GEX

description:
Library name: CH-02_GEX
scRNAseq

value: Peripheral Blood


title: AML-01-Dx-Blasts_GEX

description:
Library name: AML-01-Dx-Blasts_GEX
scRNAseq


title: Col0, 15C, ZT16, rep1

value: 10-day-old Shoot (above-ground)


title: phot2, 15C, ZT16, rep1


title: B2905-M4-Vec-1

description:
Library name: B2905-M4-Vec-1
M4 tumor 6 with vector over-expression


title: phot2 camta2, 15C, ZT16, rep1

value: phot2 camta2


title: phot2 camta2, 20C, ZT12, rep1

value: full day time course,  16h light, 8h dark, 20C


title: B2905-M4-Vec-5

description:
Library name: B2905-M4-Vec-5
M4 tumor 10 with vector over-expression


title: camta2, 20C, ZT12, rep1


title: phot2, 20C, ZT12, rep1


title: B2905-M4-Adamts7-5

description:
Library name: B2905-M4-Adamts7-5
M4 tumor 5 with Adamts7 over-expression

value: M4 tumor with Adamts7 over-expression


title: CH-01_01_GEX

description:
Library name: CH-01_01_GEX
scRNAseq


title: B2905-M4-Adamts7-4

description:
Library name: B2905-M4-Adamts7-4
M4 tumor 4 with Adamts7 over-expression


title: Col0, 20C, ZT12, rep1


title: camta2, 15C, ZT12, rep1

value: full day time course,  16h light, 8h dark, 15C


title: ECRS_PBMC_5

description: Library name: CD45_ECRS_PBMC_GEX

data_processing:
Basecalls and mapping performed using Cell Ranger ver v4.3.2 and 7.0.1
Assembly: mm10, GRCh38
Supplementary files format and content: Matrix.h5 including barcodes, features and matrix tsv files

extract_protocol:
Single-cell suspensions were prepared from mouse lung tissues by isolating CD4(iv)-negative tissue-resident and CD4(iv)-positive circulating CD4⁺ T cells via FACS (BD FACS Aria III), with 10,000 viable cells (>98% viability) collected per subset; human nasal polyps were finely minced and enzymatically digested in RPMI 1640 containing collagenase III, hyaluronidase, and DNase I, followed by mononuclear cell isolation through Percoll density gradient centrifugation and 70-μm nylon mesh filtration, while peripheral blood mononuclear cells were isolated using Ficoll-Paque Plus and similarly filtered to ensure high-quality single-cell suspensions.
Single-cell RNA-seq libraries for both mouse and human (nasal polyps and PBMCs) samples were generated using the Chromium Single Cell 3’ Reagent Kits v3.1 with dual indexing (10x Genomics), and single-cell ATAC-seq libraries for mouse samples were prepared using the Chromium Next GEM Single Cell ATAC Reagent Kits v1.1 (10x Genomics), followed by sequencing on a NovaSeq 6000 system (Illumina) with appropriate read settings and achieving a minimum depth of 20,000–25,000 read pairs per cell or nucleus according to assay type.

treatment_protocol: Mouse models were sensitized by intranasal administration of Aspergillus fumigatus antigen (Greer, Lenoir, NC, USA) over a 7-week period using a modified protocol: 50 μg of antigen was delivered once weekly for the initial 3 weeks, followed by 20 μg twice weekly for the remaining 4 weeks; assays were typically conducted 24 hours after the final antigen exposure, though in some experiments, mice were analyzed at specific time points—days 0, 8, 22, and 36 during sensitization, or 7 weeks post-final antigen administration.

tag: disease

value: ECRS


title: phot2 camta2, 20C, ZT16, rep1


title: B2905-M4-Adamts7-3

description:
Library name: B2905-M4-Adamts7-3
M4 tumor 3 with Adamts7 over-expression


title: phot2 camta2, 15C, ZT12, rep1


title: phot2, 15C, ZT12, rep1


title: ECRS_Polyp_5

description: Library name: CD45_ECRS_Polyp_GEX

source_name: PBMC

value: PBMC


title: Col0, 15C, ZT12, rep1

value: Col0 (wt)

value: full day time course, 16h light, 8h dark, 15C


title: B2905-M4-Adamts7-2

description:
Library name: B2905-M4-Adamts7-2
M4 tumor 2 with Adamts7 over-expression


title: phot2 camta2, 20C, ZT8, rep1


title: ECRS_Polyp_4

description: Library name: 191127_ECRS_Polyp_GEX

source_name: Polyp

value: Polyp


title: camta2, 20C, ZT8, rep1


title: ECRS_PBMC_4

description: Library name: 191127_ECRS_PBMC_GEX


title: phot2, 20C, ZT8, rep1


title: Col0, 20C, ZT8, rep1


title: 3'END CEA10_42°C_4

city: Jena

first: Matthew

middle: George

last: Blango

address: Adolf-Reichwein-Str. 23

department: Junior Resaerch Group RNA Biology of Fungal Infections

country: Germany

institute: Leibniz Institute for Natural Product Research and Infection Biology

description:
Library name: B4
150-bp paired-end read sequencing

data_processing:
The quality of raw reads was assessed with FastQC (v0.12.0). Unique molecular identifiers (UMIs were removed with umi_tools (v0.5.5; with the setting –bc-pattern=NNNNNNNNNN for recognition of UMIs). Remaining adaptor sequences were removed with Trimgalore (v0.5.0). 3’ End-Seq reads were further treated with fastp (v0.22.0). Resulting fastq files were again checked for quality with FastQC and then aligned to the A. fumigatus CEA10 strain genome (Aspergillus_fumigatusa1163.ASM15014v1) with HiSat (v2.2.1), allowing for a maximum intron length of 5000 nt. The resulting bam files were converted to wig files using bam2wig (v1.6; dependent on samtools v1.14). Both read strands were then combined into a single file. To scale and transform the files into the bedgraph format, wiggletools (v1.2.11) was used with default parameters.
Peak calling was performed according to https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3002724 followed by manual curation to assess quality of end sites.
Assembly: Aspergillus fumigatus A1163 ASM15014v1
Supplementary files format and content: A single .xlsx file (3_end_list.xlsx) contains the 3' poly(A)-enriched RNA end sites identified at high confidence (3), medium confidence (2), and low confidence (1).

organism: Aspergillus fumigatus

source_name: mycelium

growth_protocol: A. fumigatus was grown on Aspergillus minimal medium (AMM) agar plates (70 mM NaNO3, 11.2 mM KH2PO4, 7 mM KCl, 2 mM MgSO4, 1% (w/v) glucose and 1 μl/ml trace element solution (pH 6.5)). The trace element solution was composed of 1 g FeSO4 • 7 H2O, 8.8 g ZnSO4 • 7 H2O, 0.4 g CuSO4 • 5 H2O, 0.15 g MnSO4 • H2O, 0.1 g NaB4O7 • 10 H2O, 0.05 g (NH4)6Mo7O24 • 4 H2O, and ultra-filtrated water to 1000 ml. Spores were harvested after 5 days with 10 ml of sterile distilled water using a T-shaped inoculation spreader and spore suspensions were filtered through a 30-µm cell strainer (MACS, Miltenyi Biotec GmbH, Germany) to exclude mycelium. After counting, 50-mL liquid AMM cultures were inoculated with 1x10^8 freshly harvested spores and incubated at 37°C/42°C and 200 rpm.

extract_protocol:
Fungal mycelium was collected from liquid culture using Miracloth (Millipore) and disrupted in liquid nitrogen using a precooled mortar and pestle. Roughly 0.5 g of homogenized mycelium was transferred into a 2-mL Eppendorf tube. An amount of 800 µL TRIzol was added to the ground mycelia and vortexed vigorously. Tubes were frozen briefly for 5 sec in liquid nitrogen and allowed to thaw on ice. An amount of 160 µL of chloroform was added to the thawed mixture, vortexed, and centrifugated for 5 min at 4°C at full speed. The aqueous upper phase was transferred to a fresh 2-mL tube without disturbing the interphase. RNA extraction from aqueous phase was done with one volume of phenol/chloroform/isoamyl alcohol (25:24:1, v/v). Brief vortexing preceded centrifugation for 5 min at 4°C. Extraction was repeated until no more interphase was observable, and this was followed by another extraction with 400 µL of chloroform. RNA was precipitated using 400 µL of isopropanol for 20 min, followed by pelleting by centrifugation for 20 min at 4°C. The pellet was washed with 700 µL of 70% ethanol and air dried for 5 min at 37°C prior to resuspension in RNase-free water. Total RNA was DNase-treated according to the manufacturer’s recommendation (ThermoFisher, RNase-free DNase) and DNase treated RNA was purified using the RNA Clean and Concentrator™ kit (Zymo Research, USA) after the manufacturer’s recommendations.
Libraries were constructed with 3'RNA-End sequencing from Eclipse Bioinnovations according to the manufacturers recommendations

value: mycelium

tag: growth condition

value: Aspergillus minimal media liquid culture + doxcycline

value: wild type

value: 24 h at 42°C


title: camta2, 15C, ZT16, rep1


title: ECRS_Polyp_3

description: Library name: 191114_ECRS_Polyp_GEX


title: B2905-M4-Adamts7-1

description:
Library name: B2905-M4-Adamts7-1
M4 tumor 1 with Adamts7 over-expression

value: Subcutaneous implanted tumor


title: camta2, 15C, ZT8, rep1


title: 3'END CEA10_42°C_3

description:
Library name: B3
150-bp paired-end read sequencing


title: phot2 camta2, 15C, ZT8, rep1


title: Col0, 15C, ZT8, rep1


title: Col0, 15C, ZT4, rep3


title: phot2 camta2, 20C, ZT4, rep1


title: camta2, 20C, ZT4, rep1


title: phot2, 15C, ZT8, rep1


title: ECRS_PBMC_3

description: Library name: 191114_ECRS_PBMC_GEX


title: ECRS_Polyp_2

description: Library name: 191023_ECRS_Polyp_GEX


title: ECRS_PBMC_2

description: Library name: 191023_ECRS_PBMC_GEX


title: 3'END CEA10_37°C_4

description:
Library name: A4
150-bp paired-end read sequencing

value: 24 h at 37°C


title: 3'END CEA10_42°C_1

description:
Library name: B1
150-bp paired-end read sequencing


title: phot2 camta2, 15C, ZT4, rep1


title: phot2, 20C, ZT4, rep1


title: 3'END CEA10_42°C_2

description:
Library name: B2
150-bp paired-end read sequencing


title: 3'END CEA10_37°C_3

description:
Library name: A3
150-bp paired-end read sequencing

value: Aspergillus minimal media liquid culture


title: ECRS_PBMC_1

description: Library name: 190918_ECRS_PBMC_GEX


title: phot2, 15C, ZT4, rep1

value: 10-day-old Shoot (above-ground)


title: Col0, 15C, ZT4, rep1


title: phot2 camta2, 20C, ZT0, rep1

value: phot2 camta2


title: K562, sgRNA-11, rep2

description: Library name: HS2_11_r2

data_processing:
After removing adapters using NGmerge, the ATAC-seq data was aligned using bowtie2, and duplicates were removed by using picard MarkDuplicates.
Bam files were converted into fragments files by using bedtools bamtobed.
The genomic region of interest was divided into 1 bp bins and the number of Tn5 fragment ends overlapping with each bin was quantified as the Tn5 insertion density. Then the insertion density track was smoothed by a 250 bp window to obtain the final coverage track. The coverage tracks were exported to bigwig format and visualize in IGV
Assembly: hg38
Supplementary files format and content: XXX.frags.gz: ATAC fragments files. Containing 5 columns corresponding to the chromosome, start, end, sample ID, and count of each fragment.

growth_protocol: K562 cells were cultured in RPMI-1640 supplemented with 10%. CD34+ HSPCs were cultured in hematopoietic stem cell expansion media consisting of StemSpan SFEM II supplemented CC100 cytokine cocktail, 50 ng/mL human TPO, 1% L-Glutamine, 1% penicillin/streptomycin, and 35 nM UM171.

extract_protocol:
DNA was purified with the Qiagen MinElute PCR Purification Kit
Cells were washed twice with PBS and resuspended in PBS. 10, 000 cells in 5 µL PBS were mixed 42.5 µL of transposition buffer. The reaction was incubated at room temperature for 10 minutes, followed by the addition of 2.5 µL of assembled Tn5 transposase, and then incubated at 37 °C for 30 minutes in a Thermomixer set to 300 rpm. DNA was subsequently purified with the Qiagen MinElute PCR Purification Kit and minimally amplified for sequencing. Final libraries were purified again with the MinElute PCR Purification Kit.

treatment_protocol: Cells were transduced with lentiviral particles carrying the sgRNA plasmid and selected with puromycin. Subsequently, cells were electroporated with Cas9. For CD34+ cells, erythroid differentiation was initiated 2 days after electroporation by switching to EDM media.

value: Blood

value: CML Lymphoblast Cells

value: sgRNA-11 HS2 deletion

value: sgRNA transduction, Cas9 electroportaion

value: Day 6 after electroporation


title: 3'END CEA10_37°C_1

description:
Library name: A1
150-bp paired-end read sequencing


title: K562, sgRNA-11, rep1

description: Library name: HS2_11_r1


title: Col0, 20C, ZT0, rep1

value: Col0 (wt)

value: full day time course,  16h light, 8h dark, 20C


title: Col0, 20C, ZT4, rep1


title: 5'END CEA10_42°C_3

data_processing:
The quality of raw reads was assessed with FastQC (v0.12.0). Unique molecular identifiers (UMIs were removed with umi_tools (v0.5.5; with the setting –bc-pattern=NNNNNNNNNN for recognition of UMIs). Remaining adaptor sequences were removed with Trimgalore (v0.5.0). 5’ End-Seq reads were further treated with fastp (v0.22.0). Resulting fastq files were again checked for quality with FastQC and then aligned to the A. fumigatus CEA10 strain genome (Aspergillus_fumigatusa1163.ASM15014v1) with HiSat (v2.2.1), allowing for a maximum intron length of 5000 nt. The resulting bam files were converted to wig files using bam2wig (v1.6; dependent on samtools v1.14). Both read strands were then combined into a single file. To scale and transform the files into the bedgraph format, wiggletools (v1.2.11) was used with default parameters.
Peak calling was performed according to https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3002724 followed by manual curation to assess quality of end sites.
Assembly: Aspergillus fumigatus A1163 ASM15014v1
Supplementary files format and content: A single .xlsx file (5_end_list.xlsx) contains the 5' poly(A)-enriched RNA end sites identified at high confidence (3), medium confidence (2), and low confidence (1).

extract_protocol:
Fungal mycelium was collected from liquid culture using Miracloth (Millipore) and disrupted in liquid nitrogen using a precooled mortar and pestle. Roughly 0.5 g of homogenized mycelium was transferred into a 2-mL Eppendorf tube. An amount of 800 µL TRIzol was added to the ground mycelia and vortexed vigorously. Tubes were frozen briefly for 5 sec in liquid nitrogen and allowed to thaw on ice. An amount of 160 µL of chloroform was added to the thawed mixture, vortexed, and centrifugated for 5 min at 4°C at full speed. The aqueous upper phase was transferred to a fresh 2-mL tube without disturbing the interphase. RNA extraction from aqueous phase was done with one volume of phenol/chloroform/isoamyl alcohol (25:24:1, v/v). Brief vortexing preceded centrifugation for 5 min at 4°C. Extraction was repeated until no more interphase was observable, and this was followed by another extraction with 400 µL of chloroform. RNA was precipitated using 400 µL of isopropanol for 20 min, followed by pelleting by centrifugation for 20 min at 4°C. The pellet was washed with 700 µL of 70% ethanol and air dried for 5 min at 37°C prior to resuspension in RNase-free water. Total RNA was DNase-treated according to the manufacturer’s recommendation (ThermoFisher, RNase-free DNase) and DNase treated RNA was purified using the RNA Clean and Concentrator™ kit (Zymo Research, USA) after the manufacturer’s recommendations.
Libraries were constructed with 5'RNA-End sequencing from Eclipse Bioinnovations according to the manufacturers recommendations


title: phot2 camta2, 15C, ZT0, rep1

value: full day time course,  16h light, 8h dark, 15C


title: K562, sgRNA-1, rep2

description: Library name: HS2_1_r2

value: sgRNA-1 HS2 deletion


title: phot2, 15C, ZT0, rep1


title: Col0, 15C, ZT0, rep1

value: full day time course, 16h light, 8h dark, 15C


title: camta2, 15C, ZT0, rep1


title: 5'END CEA10_42°C_2

value: mycelium

value: Aspergillus minimal media liquid culture + doxcycline

value: wild type


title: K562, sgRNA-1, rep1

description: Library name: HS2_1_r1


title: F4-OCIAML3-RMC7977-24h-R4

city: San Francisco

first: Catherine

last: Smith

address: 513 Parnassus Ave.

department: Medicine, Hematology/Oncology

institute: UCSF

description: Library name: F4

data_processing:
Raw FASTQ files were processed through a Snakemake pipeline (v9.3.1), which incorporated quality control assessments using MultiQC (v1.28). Adapter sequences and low-quality bases were removed using Trimmomatic (v0.36).
Cleaned reads were aligned to the human reference genome (hg38) using STAR (v2.7.8a) and quantified with RSEM (v1.3.3). Normalization of aligned read counts was performed using the trimmed mean of M-values (TMM) method implemented in the EdgeR package (v3.24.3), followed by log2 transformation of the counts.
The mean-variance relationship was modeled using the VOOM function from the limma package (v3.38.3) to assign precision weights and perform differential expression analysis.
Genes were annotated using the packages STRING (v.12.0.0) and panther (v. 1.0.12) databases on R. Gene set enrichment analysis (GSEA v4.3.3) and clusterProfiler (v4.16) were subsequently employed to identify significantly enriched functional gene sets.
Replicate F3 was considered an outlier and removed from the analysis.
Assembly: GRCh38
Supplementary files format and content: processed_data.csv
Supplementary files format and content: Table containing normalized counts (Log_CPM)

source_name: myeloid cells

growth_protocol: Cells were grown in RPMI (Gibco) supplemented with 10% FBS and 1% pen-strep-glutamine (PSG) at 37C, 5% CO2

extract_protocol:
Qiagen RNAeasy; Messenger RNA (mRNA) was purified from total RNA using poly-T oligoattached magnetic beads
Library preparation included end repair, A-tailing, adapter ligation, size selection, amplification, and purification. Libraries were quantified using Qubit and real-time PCR, and fragment size distribution was assessed using a Bioanalyzer.

treatment_protocol: 5 million cells/condition were treated with either DMSO or RMC-7977 (25 nM, for 2 or 24 hours).

value: myeloid cells

value: Human AML cell line

value: NRAS Q61L


title: ECRS_Polyp_1

description: Library name: 190918_ECRS_Polyp_GEX

value: Polyp

value: ECRS


title: K562, Non-targeting sgRNA, rep2

description: Library name: HS2_nc_r2

source_name: Blood

value: Blood

value: CML Lymphoblast Cells

value: WT


title: camta2, 15C, ZT4, rep1

value: 10-day-old Shoot (above-ground)


title: F2-OCIAML3-RMC7977-24h-R2

description: Library name: F2


title: 5'END CEA10_37°C_3

value: Aspergillus minimal media liquid culture

value: 24 h at 37°C


title: F3-OCIAML3-RMC7977-24h-R3

description: Library name: F3


title: K562, Non-targeting sgRNA, rep1

description: Library name: HS2_nc_r1

value: sgRNA transduction, Cas9 electroportaion

value: Day 6 after electroporation


title: 5'END CEA10_37°C_2

description:
Library name: A2
150-bp paired-end read sequencing


title: 3'END CEA10_37°C_2


title: F1-OCIAML3-RMC7977-24h-R1

description: Library name: F1


title: E4-OCIAML3-RMC7977-2h-R4

description: Library name: E4


title: camta2, 20C, ZT0, rep1

value: full day time course,  16h light, 8h dark, 20C


title: phot2, 20C, ZT0, rep1


title: MDA-MB-231_PdB_Rec_24h_REP3

city: Rome

first: Marco

last: Pieraccioli

address: Largo Francesco Vito 1

country: Italy

institute: Catholic University of the Sacred Heart rome

data_processing:
Raw pairend-ends reads fastq files were preprocessed with fastp v0.23.2 to remove lower quality bases and adapters.
Trimmed reads were mapped to hg38 using STAR v2.7.9a.
Statistics on strandness reads, genebody coverage, reads distribuition and insert size estimation were performed using RSeQC v.4.0.0 and picard CollectRnaSeqMetrics v.2.26.10.
The uniquely mapped reads from biological replicates were kept and counted with featureCounts v.2.0.3.
Differential gene expression on read counts matrix were performed using DESeq2 v.1.30.0.
Assembly: hg38
Supplementary files format and content: tab-delimited text files with raw read counts for each sample.

growth_protocol: MDA-MB-231 cells were maintained in RPMI 1640 (Euroclone) supplemented with 10% fetal bovine serum (GIBCO), 4500 mg/L glucose (Sigma-Aldrich), 10 mM Hepes (Eurocolone), 1mM sodium pyruvate (Euroclone), 100 U/mL penicillin (Euroclone) and 100 μg/mL streptomycin (Euroclone).

extract_protocol:
RNA was isolated and DNase digested using the RNAeasy Mini Kit (Qiagen) according to manufacturer’s instruction.
RNA libraries for RNA-seq were prepared with Universal Plus mRNA-Seq with NuQuant following manufacturer's instructions.

treatment_protocol: Cells were treated with 10 nM Pladienolide B for 16 hours or DMSO. Cells were also collected after 24 hours of recovery from Pladienolide B. Cells were lysed and total RNA was extracted.

value: breast cancer TNBC cells

value: Recovery PdB 24 hours


title: E2-OCIAML3-RMC7977-2h-R2

description: Library name: E2


title: MDA-MB-231_PdB_Rec_24h_REP2


title: 5'END CEA10_42°C_1

value: mycelium

value: Aspergillus minimal media liquid culture + doxcycline

value: wild type

value: 24 h at 42°C


title: 5'END CEA10_37°C_1


title: E1-OCIAML3-RMC7977-2h-R1

description: Library name: E1

value: myeloid cells

value: Human AML cell line

value: NRAS Q61L


title: CEA10_42°C_4

data_processing:
The quality of raw reads was assessed with FastQC (v0.12.0). Unique molecular identifiers (UMIs were removed with umi_tools (v0.5.5; with the setting –bc-pattern=NNNNNNNNNN for recognition of UMIs). Remaining adaptor sequences were removed with Trimgalore (v0.5.0). 5’ End-Seq reads were further treated with fastp (v0.22.0). Resulting fastq files were again checked for quality with FastQC and then aligned to the A. fumigatus CEA10 strain genome (Aspergillus_fumigatusa1163.ASM15014v1) with HiSat (v2.2.1), allowing for a maximum intron length of 5000 nt. The resulting bam files were converted to wig files using bam2wig (v1.6; dependent on samtools v1.14). Both read strands were then combined into a single file. To scale and transform the files into the bedgraph format, wiggletools (v1.2.11) was used with default parameters.
Assembly: Aspergillus fumigatus A1163 ASM15014v1
Supplementary files format and content: Two .csv files (deseq2results.csv; htseqcountresults.csv) contain raw read counts for all samples and DEseq2 output.

extract_protocol:
Fungal mycelium was collected from liquid culture using Miracloth (Millipore) and disrupted in liquid nitrogen using a precooled mortar and pestle. Roughly 0.5 g of homogenized mycelium was transferred into a 2-mL Eppendorf tube. An amount of 800 µL TRIzol was added to the ground mycelia and vortexed vigorously. Tubes were frozen briefly for 5 sec in liquid nitrogen and allowed to thaw on ice. An amount of 160 µL of chloroform was added to the thawed mixture, vortexed, and centrifugated for 5 min at 4°C at full speed. The aqueous upper phase was transferred to a fresh 2-mL tube without disturbing the interphase. RNA extraction from aqueous phase was done with one volume of phenol/chloroform/isoamyl alcohol (25:24:1, v/v). Brief vortexing preceded centrifugation for 5 min at 4°C. Extraction was repeated until no more interphase was observable, and this was followed by another extraction with 400 µL of chloroform. RNA was precipitated using 400 µL of isopropanol for 20 min, followed by pelleting by centrifugation for 20 min at 4°C. The pellet was washed with 700 µL of 70% ethanol and air dried for 5 min at 37°C prior to resuspension in RNase-free water. Total RNA was DNase-treated according to the manufacturer’s recommendation (ThermoFisher, RNase-free DNase) and DNase treated RNA was purified using the RNA Clean and Concentrator™ kit (Zymo Research, USA) after the manufacturer’s recommendations.
For poly(A)-RNA-Seq, library preparation was performed by NovoGene, UK according to standard protocols. Briefly, mRNA was purified from total RNA using poly-(T) oligo-attached magnetic beads. Following fragmentation, first strand cDNA was synthesized using random hexamer primers. The second strand cDNA was synthesized using dUTP. The directional library was considered complete after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and finally purification. The library was then checked by Qubit and real-time PCR for quantification and by bioanalyzer for size distribution, prior to pooling for Illumina sequencing using an Illumina Novaseq 6000.


title: D2-OCIAML3-DMSO-R2

description: Library name: D2

value: DMSO


title: D3-OCIAML3-DMSO-R3

description: Library name: D3


title: CEA10_42°C_3


title: D4-OCIAML3-DMSO-R4

description: Library name: D4


title: MDA-MB-231_PdB_10nM_16h_REP3

value: PdB 10 nM 16 hours


title: MDA-MB-231_PdB_10nM_16h_REP2


title: C3-Molm14-RMC7977-24h-R3

description: Library name: C3


title: CEA10_42°C_1


title: D1-OCIAML3-DMSO-R1

description: Library name: D1


title: CEA10_42°C_2


title: MDA-MB-231_PdB_10nM_16h_REP1


title: C4-Molm14-RMC7977-24h-R4

description: Library name: C4


title: CEA10_37°C_4


title: C2-Molm14-RMC7977-24h-R2

description: Library name: C2


title: C1-Molm14-RMC7977-24h-R1

description: Library name: C1


title: MDA-MB-231_DMSO_REP3


title: B4-Molm14-RMC7977-2h-R4

description: Library name: B4


title: E3-OCIAML3-RMC7977-2h-R3

description: Library name: E3


title: B2-Molm14-RMC7977-2h-R2

description: Library name: B2


title: MDA-MB-231_PdB_Rec_24h_REP1


title: CEA10_37°C_3


title: CEA10_37°C_2


title: MDA-MB-231_DMSO_REP1


title: MDA-MB-231_DMSO_REP2


title: CEA10_37°C_1


title: A3-Molm14-DMSO-R3

description: Library name: A3


title: T0 pellet

city: Hamilton

first: Sheila

middle: K

last: Singh

state: ON

address: 1280 Main St. West

department: Surgery

country: Canada

institute: McMaster University

data_processing:
Demultiplexed samples were then input into Galaxy to make use of Cutadapt and Trimgalore features
20 nucleotide sequences corresponding to sgRNA detected in each sample were aligned to an index file of all sgRNA and corresponding target genes contained within the Calabrese A library
Aligned reads from each sample were combined into a read matrix file in R and normalized to 1 million reads per sample
Normalized reads were then utilized to determine sgRNA abundance in the lungs and brains
Assembly: Human Calabrese libaray A index file
Supplementary files format and content: each processed data file type consists of the 20 nucleotide sgRNA sequences amplified from each mouse lung or brain.  These will need to be aligned to the library index file in order to obtain raw sgRNA counts.

source_name: cell line

growth_protocol: 2x10^6 CRUK0748-GLD cells transduced with the Calabrese "A" library were inoculated into the lung of an NSG mice.  This was repeated for 29 other mice.  At endpoint, lungs and brains were extracted and sequenced for sgRNA abundance

extract_protocol:
Genomic DNA was extracted from each tissue using the Gentra Puregene tissue kit (Qiagen #158689) and DNA pellets were resuspended in nuclease-free water.  DNA was phenol:chloroform extracted and ethanol precipitated before proceeding
sgRNA were amplified from DNA extracts from lung or brain tissue.  Amplicons were then amplified with a mix p5 (including stagger for diversity) and uniquely barcoded p7 primers to add illumina adapters to each sample
amplicon sequencing

treatment_protocol: No treatment was used in this experiment

value: cell line

value: Lung adenocarcinoma cell line modified to express dCas9, GFP and luciferase


title: HLF_ATAC_rep2_ivpos

description: Library name: HLF_ATAC_rep2_ivpos

data_processing:
Sequencing reads were aligned to the mouse reference genome (GRCm38) using Bowtie 2 and TopHat (v1.3.2) for RNA-seq, and Hisat2 (v2.2.1) for ChIP-seq and ATAC-seq.
For RNA-seq, transcript abundance was quantified as FPKM using Cufflinks (v2.0.2). For ChIP-seq and ATAC-seq, peaks were called using MACS2 with optimized parameters (ChIP-seq: window_size = 300; ATAC-seq: window_size = 100; FDR = 0.01).
Differentially expressed genes (DEGs) in RNA-seq were identified using DESeq2 (v1.10.1) on pseudobulk data, with thresholds of log2(fold change) > 1 or < –1 and p-value < 0.01. For ATAC-seq, differentially accessible regions (DARs) were detected using HOMER's getDifferentialPeaks.
ChIP-seq and ATAC-seq peaks were annotated using HOMER (annotatePeaks.pl). Overlapping peaks between assays were identified using mergePeaks, and motifs were enriched using findMotifsGenome.pl with a 200-bp window.
Co-expression networks for RNA-seq were constructed using Simpson's coefficient and visualized with Cytoscape (v3.7.1). Signal intensity tracks (BigWig) were generated using SAMtools, BEDtools, and deepTools, and visualized in the Integrative Genomics Viewer (IGV).
Assembly: Mouse genome GRCm38 (mm10).
Supplementary files format and content: Processed RNA-seq data are provided as gene-level FPKM tables. ChIP-seq and ATAC-seq data include peak BigWig signal tracks.

source_name: Lung

extract_protocol:
For RNA-seq, total RNA was extracted using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions. For ChIP-seq, chromatin was extracted from paraformaldehyde-fixed cells lysed with SDS lysis buffer, followed by sonication. For ATAC-seq, nuclei were isolated by cell lysis and immediately subjected to transposition.
RNA-seq libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina) following the manufacturer’s protocol. ChIP-seq libraries were constructed using the NEBNext Ultra II DNA Library Prep Kit for Illumina, including adapter ligation and PCR amplification. ATAC-seq libraries were prepared from transposed DNA fragments using PCR amplification (11–12 cycles) prior to sequencing. All libraries were sequenced on an Illumina NextSeq500 system.

value: Lung

value: Asp-Ag

tag: term

tag: hlf

value: negative

tag: iv staining

value: positive


title: A1-Molm14-DMSO-R1

description: Library name: A1

tag: cell line

tag: genotype


title: HLF_ATAC_rep2_ivnega_HLFposi

description: Library name: HLF_ATAC_rep2_ivnega_HLFposi


title: individual MA_24339, lithium-treated

city: Montreal

first: Guy

last: Rouleau

state: Quebec

address: 3801 Rue University

department: Neurology

institute: McGill University

data_processing:
Trimmomatic 0.39: Sequence reads were trimmed for adaptor sequence/low-quality sequence. Parameters: ILLUMINACLIP:TruSeq2-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:30 MINLEN:36
star 2.7.9a: Trimmed sequence reads were mapped to GRCh38 with default parameters
rsem 1.3.3: read count extraction was performed using default parameters
edgeR 3.34.1: read count normalization was done with a cutoff of >1CPM in >80% of samples. Values are log2(CPM)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include log2(CPM) values for each Sample

source_name: iPSC-derived neurons, 4 weeks old

growth_protocol: see section " iPSC line generation and neuronal differentiation" in Method of the manuscript

extract_protocol:
Total RNA was extracted from ~3x106 cells for each condition using miRNeasy kit (Qiagen, USA) according to the manufacturer’s instructions. RNA was resuspended in RNAse-free water
Library preparation was done using the TruSeq Stranded Total RNA Kit (Ilumina) with Ribo-Zero depletion. Sequencing was done on the NovaSeq 6000 at 150bp paired end reads with a total of 113M reads (~17Gb/sample).

treatment_protocol: Li treatment 1.5mM (Sigma)

value: iPSC-derived neurons, 4 weeks old

value: wildtype

tag: phenotype

value: Lithium


title: individual NS0539C, lithium-treated


title: A4-Molm14-DMSO-R4

description: Library name: A4

tag: batch


title: HLF_ATAC_rep2_ivnega_HLFnega

description: Library name: HLF_ATAC_rep2_ivnega_HLFnega


title: individual MA_24339, untreated

value: untreated


title: B3-Molm14-RMC7977-2h-R3

description: Library name: B3


title: HLF_ATAC_rep1_ivpos

description: Library name: HLF_ATAC_rep1_ivpos


title: individual NS0539C, untreated


title: HLF_ATAC_rep1_ivnega_HLFposi

description: Library name: HLF_ATAC_rep1_ivnega_HLFposi


title: B1-Molm14-RMC7977-2h-R1

description: Library name: B1


title: individual MA_14501, lithium-treated


title: HLF_ATAC_rep1_ivnega_HLFnega

description: Library name: HLF_ATAC_rep1_ivnega_HLFnega


title: CH-01_02_GEX

description:
Library name: CH-01_02_GEX
scRNAseq

value: Peripheral Blood

value: GEX Library