title: RNA-seq,Trp53_KO,Rep1

description:
Trp53_KO.Neg.Abs.bw
Trp53_KO.Pos.Abs.bw


title: Sample_H_FRE

status: Public on Mar 26 2024

type: SRA

city: Charlestown

first: Mahesh Chandra

last: Kodali

state: MA

department: Neurology

country: USA

institute: Massachusetts General Hospital / Harvard Medical School

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Reads were aligned to reference 2020-A (Ensembl 98) transcriptome 156 and quantified using Cell Ranger v6.0.2 multipipeline.
Assembly: reference 2020-A (Ensembl 98) transcriptome
Supplementary files format and content: 10X Cell Ranger Outputs

molecule: total RNA

organism: Homo sapiens

source_name: Cerebrospinal Fluid Cells

extract_protocol:
Fresh or thawed cryopreserved CSF mixed with 10x 5’ v2 RT Reagent Master Mix were immediately processed with the 10x Genomics Chromium Next GEM Single Cell 5’ v2 kit (10x Genomics, Pleasanton, CA), cDNA amplified, and library constructed per the manufacturer’s protocol. Library quality control (QC) was based on Agilent Tapestation 4200 HS D1000 screentapes (Agilent Technologies, Waldbronn, Germany). Multiplexed library pool QC was based on Agilent Tapestation 4200 HS D1000 and Kapa Library Quantification Kit for Illumina platforms (Kapa BioSystems, Boston, MA) and sequenced at shallow depths on Illumina’s iSeq 100 v2 flow cell for 26x10x10x90 cycles for estimated reads per cell. After demultiplexing,  libraries were rebalanced based on reads per cell. Normalized pool QC was based on Agilent Tapestation 4200 HS D1000 and Kapa Library Quantification Kit for Illumina platforms and high depth sequenced on Illumina’s NovaSeq 6000 S4 v1.5 flow cell for 26x10x10x90 cycles, to obtain a sequencing depth of 50K reads/cell (whole transcriptome libraries). Reads were aligned to reference 2020-A (Ensembl 98) transcriptome and quantified using Cell Ranger v6.0.2 multipipeline.
Fresh or thawed cryopreserved CSF mixed with 10x 5’ v2 RT Reagent Master Mix were immediately processed with the 10x Genomics Chromium Next GEM Single Cell 5’ v2 kit (10x Genomics, Pleasanton, CA), cDNA amplified, and library constructed per the manufacturer’s protocol. Library quality control (QC) was based on Agilent Tapestation 4200 HS D1000 screentapes (Agilent Technologies, Waldbronn, Germany). Multiplexed library pool QC was based on Agilent Tapestation 4200 HS D1000 and Kapa Library Quantification Kit for Illumina platforms (Kapa BioSystems, Boston, MA) and sequenced at shallow depths on Illumina’s iSeq 100 v2 flow cell for 26x10x10x90 cycles for estimated reads per cell. After demultiplexing,  libraries were rebalanced based on reads per cell. Normalized pool QC was based on Agilent Tapestation 4200 HS D1000 and Kapa Library Quantification Kit for Illumina platforms and high depth sequenced on Illumina’s NovaSeq 6000 S4 v1.5 flow cell for 26x10x10x90 cycles, to obtain a sequencing depth of 50K reads/cell (whole transcriptome libraries). Reads were aligned to reference 2020-A (Ensembl 98) transcriptome and quantified using Cell Ranger v6.0.2 multipipeline.
Fresh or thawed cryopreserved CSF mixed with 10x 5’ v2 RT Reagent Master Mix were immediately processed with the 10x Genomics Chromium Next GEM Single Cell 5’ v2 kit (10x Genomics, Pleasanton, CA), cDNA amplified, and library constructed per the manufacturer’s protocol. Library quality control (QC) was based on Agilent Tapestation 4200 HS D1000 screentapes (Agilent Technologies, Waldbronn, Germany). Multiplexed library pool QC was based on Agilent Tapestation 4200 HS D1000 and Kapa Library Quantification Kit for Illumina platforms (Kapa BioSystems, Boston, MA) and sequenced at shallow depths on Illumina’s iSeq 100 v2 flow cell for 26x10x10x90 cycles for estimated reads per cell. After demultiplexing,  libraries were rebalanced based on reads per cell. Normalized pool QC was based on Agilent Tapestation 4200 HS D1000 and Kapa Library Quantification Kit for Illumina platforms and high depth sequenced on Illumina’s NovaSeq 6000 S4 v1.5 flow cell for 26x10x10x90 cycles, to obtain a sequencing depth of 50K reads/cell (whole transcriptome libraries). Reads were aligned to reference 2020-A (Ensembl 98) transcriptome and quantified using Cell Ranger v6.0.2 multipipeline.

tag: tissue

value: Cerebrospinal Fluid Cells

tag: cell line

tag: cell type

value: Primary

tag: protocol

value: FRE


title: Sample_G_REC

description: 10x Genomics

value: REC


title: RNA-seq,Trp53_KO,Rep2

city: Toronto

first: Sajid

middle: A

last: Marhon

state: ON

address: 101 College Street

country: Canada

institute: Princess Margaret Cancer Centre

description:
Trp53_KO.Neg.Abs.bw
Trp53_KO.Pos.Abs.bw

library_source: transcriptomic

data_processing:
Raw reads were trimmed to remove adapters and low quality bases. Trimmed reads were aligned to the mouse genome mm10 using the STAR pipeline. Read counts were calculated for genes and repeat elements using featureCount tool. Differential analysis was performed using edgeR tool.
Assembly: mm10
Supplementary files format and content: Bigwig files include genome track signal of the normalized reads.

organism: Mus musculus

source_name: ovarian surface epithelium

growth_protocol: Asynchronous growth

extract_protocol:
total RNA isolation and DNaseI treatment was performed using RNeasy Mini Kit (Qiagen) as per manufacturer’s protocol
TruSeq® Stranded Total RNA Library Prep Gold (96 Samples) kit (Illumina, 20020599)

tag: strain

value: ovarian surface epithelium

value: epithelial

tag: genotype

tag: treatment

value: immortalized, untreated

tag: time


title: nrt1.1, Root, 21C, rep3

city: La Jolla

first: Ling

last: Zhang

state: CA

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

data_processing:
Sequenced reads were trimmed for adaptors and masked for low-quality sequence
RNA-Seq read were mapped to A. thaliana reference genome (TAIR10) using STAR 2.7.0a
Differentially expressed genes were detected by edgeR (version 3.36.0)
Assembly: TAIR10
Supplementary files format and content: Tab-delimited text files include FPKM values for all Samples
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Arabidopsis

source_name: Root

extract_protocol:
The root total RNA was isolated from around 50 roots (as a pool for one biological replicate) by using RNeasy Plant Mini Kit (Qiagen, Cat. 74904).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Root


title: nrt1.1, Root, 28C, rep2


title: nrt1.1, Root, 28C, rep1


title: nrt1.1, Root, 21C, rep2


title: nrt1.1, Root, 28C, rep3


title: Sample_I_FBS_3

description: 10x Genomics

value: FBS


title: Sample_G_FBS

description: 10x Genomics


title: TAC 8W_Sema_4W_3

city: Wuhan

first: Yu-lan

last: Ma

state: None Selected

address: No. 9 Zhangzhidong Road, Wuchang District, Wuhan City, Hubei Province, China号

country: China

institute: The First Clinical College of Wuhan University

data_processing:
The adapter and low-quality reads were filtered out through cutadapt (version 1.11)
These genes were subjected to alignment against public protein databases;NR(RefSeq non-redundant proteins). Featurecount(v1.6.0) was used for transcript abundance estimation and normalization of expression values as FPKM (Fragments per kilobase of transcript per million fragments mapped)
Differentially expressed genes were identified with edgeR with a filter threshold of FDR<0.05 and |log2FoldChange| > 1. ClusterProfiler (http://www.bioconductor.org/packages/release/ bioc/html/clusterProfiler.html) in R package  was employed to perform GO
yoto Encyclopedia of Genes and Genomes, http://www.genome.jp/kegg/) enrichment analysis. The GO and KEGG enrichment analysis were calculated using hypergeometric distribution with a q value cutoff of 0.05
Assembly: mm10
Supplementary files format and content: All_sample_counts.xlsx

source_name: heart

extract_protocol:
RNA-seq were performed by Wuhan IGENEBOOK Biotechnology Co.,Ltd (http://www.igenebook.com) . Briefly ,total RNA was extracted using the RNAprep Pure Kit DP432 (TIANGEN Biotech Co.,Ltd., Beijing, China), following the manufacturer’s instructions.
All the RNA samples were assessed for their integrity using Qsep1 instrument. To construct RNA libraries with the VAHTS mRNA-seq V3 Library Prep Kit for Illumina, 1 μg of total RNA was used

value: heart

value: Mouse cardiomyocytes

value: WT

value: TAC+sema


title: Sample_F_REC

description: 10x Genomics


title: nrt1.1, Root, 21C, rep1


title: TAC 8W_Sema_4W_2


title: hy5, Root, 28C, rep3


title: Sample_G_DNA

description: 10x Genomics

value: DNA


title: Sample_F_FBS

description: 10x Genomics


title: TAC 8W_Sema_4W_1


title: hy5, Root, 28C, rep2


title: hy5, Root, 21C, rep3


title: hy5, Root, 28C, rep1


title: hy5, Root, 21C, rep2


title: Sham_Sema 4W_3

value: sema treatment


title: Sample_F_DNA

description: 10x Genomics


title: Col0, Root, 28C, rep3


title: hy5, Root, 21C, rep1


title: Sample_E_REC

description: 10x Genomics


title: Col0, Root, 21C, rep3


title: Sham_Sema 4W_2


title: Sham_6

value: vehicle


title: Sample_E_FBS

description: 10x Genomics


title: Sample_E_FRE

description: 10x Genomics


title: Sham_Sema 4W_1


title: nrt1.1, Shoot, 28C, rep2

source_name: Shoot

value: Shoot


title: Col0, Root, 21C, rep1


title: Sham_5


title: nrt1.1, Shoot, 28C, rep3


title: Sample_D_REC

description: 10x Genomics

value: Cerebrospinal Fluid Cells


title: nrt1.1, Shoot, 28C, rep1


title: nrt1.1, Shoot, 21C, rep3


title: Sample_D_FBS

description: 10x Genomics

value: Primary


title: Sham_4


title: Sample_D_DNA

description: 10x Genomics


title: Col0, Root, 21C, rep2


title: nrt1.1, Shoot, 21C, rep2


title: TAC 8W_Sema 8W_3


title: nrt1.1, Shoot, 21C, rep1


title: hy5, Shoot, 28C, rep3


title: Col0, Root, 28C, rep2


title: Col0, Root, 28C, rep1


title: TAC 8W_Sema 8W_2


title: hy5, Shoot, 28C, rep2


title: TAC 8W_Sema 8W_1


title: hy5, Shoot, 28C, rep1


title: Sample_C_FRE

description: 10x Genomics

value: FRE


title: hy5, Shoot, 21C, rep3


title: hy5, Shoot, 21C, rep2


title: Sample_C_FBS

description: 10x Genomics


title: TAC 8W_3

value: TAC+vehicle


title: Col0, Shoot, 28C, rep3


title: TAC 8W_2


title: hy5, Shoot, 21C, rep1


title: Col0, Shoot, 28C, rep2


title: Sample_C_DNA

description: 10x Genomics


title: Col0, Shoot, 28C, rep1


title: Col0, Shoot, 21C, rep3


title: Col0, Shoot, 21C, rep1


title: Sample_B_FBS

description: 10x Genomics


title: Col0, Shoot, 21C, rep2


title: Sham_Sema_3


title: Sample_B_REC

description: 10x Genomics

value: REC


title: Sample_B_FRE

description: 10x Genomics


title: S12, healthy donor, ADT, source: PB, donor: I, sorting: CD34p

city: Milano

first: Guido

last: Pacini

address: Via Olgettina 60

department: Pathogenesis and therapy of primary immunodeficiencies

country: Italy

institute: San Raffaele Telethon Institute for Gene Therapy

description:
Antibody-derived oligonucleotide (ADT)
ADT: index1 file contains library index; read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag (ADT) reads
S12_adt

library_source: other

data_processing:
Sequenced libraries were processed and de-multiplexed by Cell Ranger Single-Cell Software Suite (version 4.0.0, 10X Genomics) by “cellranger mkfastq” function. We generated a genes-barcode matrix of UMI counts for each of the samples separately and aligned the reads to the GRCh38 human reference genome using STAR v.2.5.1b. We used the “cellranger count” function to generate a UMI count matrix for both GEX and ADT libraries.
After importing UMI counts matrix, gene and cell barcode lists, we generated a Seurat object (Seurat R package v.3.0) including every sequenced cell. Cells with a percentage of mitochondrial reads higher than 20%, as well as those with <200 or >8,000 expressed genes, were removed from the dataset. The filtered UMI count matrix was then log-normalized with the “NormalizeData” function in Seurat, and the top 20% most variable genes were selected for downstream analysis through the “FindVariableFeatures” function in Seurat, which relies on the “vst” method. The cell cycle phase of each cell was inferred by the expression levels of specific cell cycle marker genes (Regev list) with the “CellCycleScore” function in Seurat. Following this we computed the difference between the S and G2M scores, which indicates if the cell is actively cycling (G2M/S) or rather in a quiescent state (G1). Each single-cell UMI count was regressed for the following covariates: cell cycle difference, total number of UMIs and percentage of mitochondrial UMI counts. Where the above scaling procedure was performed through the “ScaleData” function in Seurat. Furthermore, between-donor variability was accounted for using the Harmony data integration procedure (harmony R package v.0.1), with the “RunHarmony” function in harmony.
UMAP dimensionality reduction and cell clustering were performed with default parameters using the first 80 Harmony components and setting the cluster’s resolution parameter to 0.6, respectively using the “RunUMAP” and “FindClusters” functions in Seurat. Differentially expressed genes across clusters were identified with the “FindAllMarkers” function in Seurat. The above test was performed separately for each cluster, restricting the analysis to the subset of genes expressed by at least 10% of cells in either of the two groups being compared (min.pct = 0.1). Cluster-specific marker genes were identified as the most significant genes (Bonferroni’s adjusted p < 0.05) whose expression was enriched in the cluster of interest (logFC > 0). Cell type annotation was inferred (SingleR R package v.1.8.1) based on the expression of specific lineage marker genes and published HSPC gene signatures. Each cluster was classified by inspecting the expression of curated marker genes and published gene signatures, respectively using the “FeaturePlot” and “AddModuleScore” functions in Seurat. A custom gating strategy was defined by first converting sequencing data into “.fcs” files to be explored manually with FlowJo software v.10.5.3 (BD Biosciences) through the flowcore R package v.2.8.0. Gates were manually set based on comparison with conventional flow cytometry analysis performed on the same sample prior to single-cell library preparation. For samples enriched for primitive CD38- HSPC fraction, the proportions of ADT-detected HSPC subsets were normalized according to FACS immunophenotyping performed prior to single-cell library preparation.
For each cluster under investigation, the “FindMarkers” function in Seurat was used to identify differentially expressed genes between PB and BM cells. Where the above function performs, gene-wise Wilcoxon signed-rank tests between cells isolated by PB and BM samples, separately for each cell cluster. Notably the above tests were performed setting the logFC threshold parameter (logfc.threshold) to 0, in order to obtain unfiltered gene lists for all tested conditions. Furthermore, only intra-cluster comparisons between groups with at least 5 cells were considered for differential gene expression analysis. We then performed Gene Set Enrichment Analysis using the “GSEA” function of ClusterProfiler R package v.3.16 17 aiming to identify enriched Gene Ontology (GO) sets, focusing mainly on the Biological Process (GO-BP) terms. This procedure results in a list of statistically significant (adjusted p < 0.05) GO-BP terms. These can be further divided into enriched and depleted terms based on their normalized enrichment score (NES) value, NES>0 (NESpos) and NES<0 (NESneg) respectively. Where positive NES values indicate gene sets with higher expression in the PB samples, conversely negative NES values indicate gene sets whose expression is enriched in the BM samples. To perform transcriptional analyses on lymphoid cells, we investigated the expression of TSP1 gene signature19 on lymphoid clusters (namely, clusters 4 and 15). Cells were first clustered into K=3 groups by K-means clustering algorithm based on the percentage of expressed (UMI > 0) TSP1-associated genes. Specifically, TSP-high cells express more than 75% of the TSP1 genes, while TSP-low genes express less than 45% of these genes. Similarly to the previous section, a putative set of genes regulating the TSP1 signature was identified performing gene-wise differential expression analyses through Wilcoxon signed-rank tests. This procedure was used to identify the genes which significantly (adjusted p < 0.05) drive the expression of the TSP1 signature (PB-TSPhigh vs PB-TSPlow, BM-TSPhigh vs BM-TSPlow), and the ones which differentially modulate its expression across RNA sources (BM-TSPhigh vs PB-TSPhigh).
Assembly: GRCh38
Supplementary files format and content: 10x Genomics output files: {SampleID}_features.tsv.gz, {SampleID}_barcodes.tsv.gz, {SampleID}_matrix.mtx.gz
Supplementary files format and content: scRNA-Seq UMI count matrices (scRNA_CountMatrix.rds): matrix of counts quantifying the expression of each GRCh38 annotated gene (rows) across all single cells (columns)
Supplementary files format and content: ADT count matrix (ADT_CountMatrix.rds): matrix of counts quantifying the expression of each ADT under investigation (rows) across all single cells (columns)
Supplementary files format and content: Seurat metadata object (Metadata.rds): matrix storing the features (columns) associated to each single cell (rows)
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

molecule: protein

source_name: Peripheral Blood

extract_protocol:
PB and BM mononuclear cells (MNC) from healthy donors (HD) were isolated using Lympholyte human cell separation medium (Euroclone). PB CD34+ cells were purified from PBMC using positive selection with immunomagnetic beads according to the manufacturer’s specifications (Miltenyi Biotec). HD-derived BM CD34+ cells were purchased from Stem Cell Technologies or purified from BM MNC using positive selection with immunomagnetic beads according to the manufacturer’s specifications (Miltenyi Biotec). Both mononuclear cells and purified PB and BM CD34+ cell fractions were frozen in liquid nitrogen until use. Upon thawing, adult HD-derived BM or PB purified CD34+ or PBMC samples were labeled with a mix composed by both fluorescent antibodies against lineage markers (LIN, anti-CD3/CD14/ CD16/CD19/CD20/CD56), CD15, CD38, CD34 (Biolegend) for FACS immunophenotyping, and  TotalSeq-A antibodies against CD90, CD45RA, CD7, CD10, CD71, CD41 (Biolegend) for ADT barcoding through scRNAseq. Staining for ADT barcoding was applied only on the following HD-derived samples: BM C, BM D, BM E, PB D, PB H, PB I. Staining with TotalSeq-A antibodies and reagents was performed according to the manufacturer’s specifications, and TotalSeq-A antibodies were used at concentrations defined by titration of corresponding fluorescent antibodies. After surface marking, cells were incubated with PI (Biolegend) to label dead cells. We applied three different FACS sorting strategies for sample preparation prior to scRNAseq processing: 1) isolation of both bulk HSPC (live LIN- CD34+) and primitive HSPC (live LIN- CD34+ CD38-) fractions starting from purified CD34+ cells (BM A, BM B, PB F, PB G); 2) isolation of both primitive (live LIN- CD34+ CD38-) and progenitor (live LIN- CD34+ CD38+) HSPC fractions starting from purified CD34+ cells (BM C, BM D, PB H) or PBMC (PB D); 3) isolation of bulk HSPC (live LIN- CD34+) starting from purified CD34+ cells (BME, PB I).  Sorted BM and PB samples were counted with trypan blue for vitality when FACS cell recovery was >10,000 cells.
3’ gene expression (GEX) libraries and ADT libraries constructions were performed following Chromium 10x 3’ Gene Expression protocol v2 or v3 chemistry and TotalSeq™-A Antibodies and Cell Hashing with 10x Single Cell 3' Reagent Kit v3 Protocol. Chromium 10x 3’ GEX libraries were sequenced on Illumina NovaSeq S1 platform, while ADT libraries were sequenced together with GEX libraries or independently on Illumina NextSeq platform following manufacturer’s indications.

tag: facs sorting

value: HSPCs

value: Peripheral Blood

tag: donor

value: I

tag: Sex

value: Male

tag: library type

value: ADT

tag: adt

value: Anti-CD10/TotSeq-A, Anti-CD127/TotSeq-A, Anti-CD38/TotSeq-A, Anti-CD41/TotSeq-A, Anti-CD45RA/TotSeq-A, Anti-CD7/TotSeq-A, Anti-CD71/TotSeq-A, Anti-CD90/TotSeq-A, Anti-CXCR4/TotSeq-A


title: Sample_C_REC

description: 10x Genomics


title: Sham_Sema_2

value: heart

value: Mouse cardiomyocytes

value: WT


title: S11, healthy donor, ADT, source: BM, donor: E, sorting: CD34p

description:
Antibody-derived oligonucleotide (ADT)
ADT: index1 file contains library index; read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag (ADT) reads
S11_adt

source_name: Bone Marrow

value: Bone Marrow

value: E


title: S10, healthy donor, ADT, source: PB, donor: H, sorting: CD34pCD38p

description:
Antibody-derived oligonucleotide (ADT)
ADT: index1 file contains library index; read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag (ADT) reads
S10_adt

value: Progenitor HSPCs

value: H

value: Female


title: Sample_A_REC_2

description: 10x Genomics

value: Cerebrospinal Fluid Cells

value: Primary


title: Sham_Sema_1

value: sema treatment


title: S9, healthy donor, ADT, source: PB, donor: H, sorting: CD34pCD38n

description:
Antibody-derived oligonucleotide (ADT)
ADT: index1 file contains library index; read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag (ADT) reads
S9_adt

value: Primitive HSPCs


title: Sample_A_REC_1

description: 10x Genomics

value: REC


title: S7, healthy donor, ADT, source: PB, donor: D, sorting: CD34pCD38n

description:
Antibody-derived oligonucleotide (ADT)
ADT: index1 file contains library index; read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag (ADT) reads
S7_adt

value: Peripheral Blood

value: D


title: Sham_3

value: vehicle


title: TAC 8W_1

value: TAC+vehicle


title: S6, healthy donor, ADT, source: BM, donor: D, sorting: CD34pCD38p

description:
Antibody-derived oligonucleotide (ADT)
ADT: index1 file contains library index; read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag (ADT) reads
S6_adt

value: Male

value: ADT

value: Anti-CD10/TotSeq-A, Anti-CD127/TotSeq-A, Anti-CD38/TotSeq-A, Anti-CD41/TotSeq-A, Anti-CD45RA/TotSeq-A, Anti-CD7/TotSeq-A, Anti-CD71/TotSeq-A, Anti-CD90/TotSeq-A, Anti-CXCR4/TotSeq-A


title: Sample_A_FRE_3

description: 10x Genomics

value: FRE


title: Sham_2

value: heart

value: Mouse cardiomyocytes

value: WT


title: S5, healthy donor, ADT, source: BM, donor: D, sorting: CD34pCD38n

description:
Antibody-derived oligonucleotide (ADT)
ADT: index1 file contains library index; read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag (ADT) reads
S5_adt

value: Bone Marrow


title: Sample_A_FRE_2

description: 10x Genomics

value: Cerebrospinal Fluid Cells


title: Sham_1


title: S4, healthy donor, ADT, source: BM, donor: C, sorting: CD34pCD38p

description:
Antibody-derived oligonucleotide (ADT)
ADT: index1 file contains library index; read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag (ADT) reads
S4_adt

value: Progenitor HSPCs

value: C

value: Female


title: S3, healthy donor, ADT, source: BM, donor: C, sorting: CD34pCD38n

description:
Antibody-derived oligonucleotide (ADT)
ADT: index1 file contains library index; read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag (ADT) reads
S3_adt

value: Primitive HSPCs


title: S2, healthy donor, ADT, source: PB, donor: D, sorting: CD34pCD38p

description:
Antibody-derived oligonucleotide (ADT)
ADT: index1 file contains library index; read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag (ADT) reads
S2_adt

value: Peripheral Blood


title: S1, healthy donor, ADT, source: PB, donor: D, sorting: CD34pCD38n

description:
Antibody-derived oligonucleotide (ADT)
ADT: index1 file contains library index; read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag (ADT) reads
S1_adt

value: D


title: Sample_A_FRE_1

description: 10x Genomics

value: Primary


title: LV3833-LV3688_DNMT1_MORC2_CRISPRi_H3K4me3_rep1

city: Lund

first: Ninoslav

last: Pandiloski

address: Sölvegatan 17

country: Sweden

institute: Lund University

library_source: genomic

data_processing:
Paired-end reads (2x75)  were aligned to the hg38 genome using bowtie2 v2.3.4.2 (--local–very-sensitive-local --no-unal –no-mixed –no-discordant –phred33 -I 10 -X 700)
SAM files were converted to bam files with SAMtools v1.9. The BAM files were filtered according to alignment quality (MAPQ>10) using samtools (samtools view -bq 10 {BAM} > {FILTERED_BAM}).
Normalized bigwig coverage tracks were made with bamCoverage v2.4.3, with RPKM normalization.
GRCh38
Assembly: Bigwigs of filtered alignments for genome browser visualization, normalized with RPKM
Library strategy: CUT&RUN

molecule: genomic DNA

growth_protocol: An embryo-derived human neural epithelial-like stem cell (hNSC) line, Sai2, was used (Tailor et al 2013). The hNSCs were cultured according to standard protocol (Falk et al 2012). Briefly, the cells were kept in DMEM/F12 (Thermo Fisher Scientific) supplemented with Glutamine (2mM, Sigma), Penicillin/Streptomycin (1x, Gibco), N2 (1x, Thermo Fisher Scientific), B27 (0.05x, Thermo Fisher Scientific), EGF and FGF2 (both 10ng/ml, Thermo Fisher Scientific). 10 mM Y27632 Rock inhibitor (Miltenyi) was also used. Cells were grown on Nunc multidishes or T25 flasks pre-coated with Poly L-Ornithine (15μg/ml, Sigma) and Laminin (2μg/ml, Sigma). Cells were passaged 1:3 every 2-3 days using TryplLETM Express enzyme (GIBCO) and Trypsin Inhibitor (GIBCO).

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

treatment_protocol:
To silence the transcription of MORC2 and TASOR, we used the catalytically inactive Cas9 (deadCas9) fused to the transcriptional repressor KRAB (Johansson et al 2022). Single guide sequences were designed to recognize DNA regions just down-stream of the transcription start site (TSS) according to the GPP Portal (Broad Institute). The following lentiviral backbone was used: pLV hU6-sgRNA hUbC-dCas9-KRAB-T2a-GFP. Lentiviruses were produced as described below yielding titers of 108-109 TU/ml, which was determined using qRT–PCR. Control virus with a gRNA sequence not present in the human genome (LacZ) was also produced and used in all experiments. GFP cells were FACS isolated (FACSAria, BD sciences) on day 10 at 10°C (reanalysis showed > 97% purity) and pelleted at 400 g for 5 min, snap frozen on dry ice and stored at −80°C until RNA isolation.
To do the DNMT1 knock out, we used a CRISPR cut approach. LV.gRNA.CAS9-GFP vectors were used to target DNMT1 (Liao et al 2015) or LacZ (control) as described in (Jönsson et al 2019). Lentiviral vectors were produced as described previously and had a titer of 108-109 TU/ml which was determined using qRT-PCR. hNSCs were transduced with a MOI of 10–15 and allowed to expand 10 days and were FACS sorted as described previously.

value: human neuroepithelial-like stem cells

tag: cutandrun antibody


title: S8, healthy donor, ADT, source: PB, donor: D, sorting: CD34pCD38p

description:
Antibody-derived oligonucleotide (ADT)
ADT: index1 file contains library index; read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag (ADT) reads
S8_adt

value: Male


title: wild-type atRA+PKCi HFSCs 1, RNA-seq

city: New York

first: Matthew

middle: T

last: Tierney

state: NY

address: 1230 York Ave, Box 300

institute: Rockefeller University

data_processing:
Transcript abundance was quantified using Salmon (v.1.4.0) with a reference genome sequence fetched from BSGenome.Mmusculus.UCSC.mm10 package. Gene level counts and transcripts per million (TPM) were calculated using Tximport (v.1.12.3) package.
Assembly: mm10
Supplementary files format and content: Tab-delineated text files or comma separated value files contain raw counts.

source_name: Telogen (P55) skin mouse 1

extract_protocol:
To resuspend HFSCs, 3D cultures were washed with sterile PBS, dissociated into single cell suspensions using TrpLE-Express (Gibco) for 15min at 37°C. After filtering, total RNA was collected in Trizol and purified using the Direct-zol RNA MiniPrep kit (Zymo Research) according to the manufacturer's instructions. DNase treatment was performed to remove genomic DNA (RNase-Free DNase Set, Qiagen). Sample quality was determined using an Agilent 2100 Bioanalyzer; all samples for sequencing had RNA integrity (RIN) numbers >8.
cDNA library construction was performed by the Rockefeller University (RU) Genomic Core facility.

value: Telogen (P55) skin mouse 1

value: Hair follicle stem cells

value: wild-type

value: atRA+PKCi


title: wild-type FBS HFSCs 1, RNA-seq

value: FBS


title: wild-type atRA+PKCi HFSCs 2, RNA-seq

source_name: Telogen (P55) skin mouse 2

value: Telogen (P55) skin mouse 2


title: wild-type FBS HFSCs 2, RNA-seq


title: CR153_LV3800_DNMT1_CRISPRi_H3K4me3_rep2


title: Sample_A_FBS_1

description: 10x Genomics


title: imMKCL 300mm s-1-off day3-3

city: Chiba

first: Naoya

last: Takayama

state: Chiba

address: 1-8-1 Inohana, Chuo-ku

department: Graduate School of Medicine

country: Japan

institute: Chiba University

data_processing:
TopHat (version 2.1.1; with default parameters) was used to map to the reference genome (UCSC/hg19) with annotation data from iGenomes (Illumina).
Levels of gene expression were quantified using Cuffdiff (Cufflinks version 2.2.1; with default parameters).
Assembly: hg19
Supplementary files format and content: .xlsx and FPKM values for each sample

source_name: imMKCL clone 7

extract_protocol:
Total RNA from imMKCL 150mm s-1-off day3,5 or imMKCL 300mm s-1-off day3,5 was isolated using an RNeasy Micro Kit (QIAGEN)
~10 ng total RNA was used as input for cDNA conversion using a SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (cat. #634890, Clontech, Takara). cDNA was fragmented using an S220 Focused-ultrasonicator (Covaris). The cDNA library was then amplified using a NEBNext® Ultra™ DNA Library Prep Kit for Illumina (cat. #E7370L, New England Biolabs).

value: imMKCL clone 7

value: iPSC-derived megakaryocyte cell line


title: CR153_LV3800_DNMT1_CRISPRi_H3K4me3_rep1


title: Sample_A_DNA_2

description: 10x Genomics

value: Cerebrospinal Fluid Cells

value: DNA


title: CR153_LV3599_Control_H3K4me3_rep1


title: Sample_A_DNA_1

description: 10x Genomics


title: Rxra cKO atRA+PKCi HFSCs 2, RNA-seq

value: Rxra cKO


title: NCI-H226, Xenograft, Vehice 5d-5

city: Boston

first: Eric

last: Muise

address: 33 Ave. Louis Pasteur

department: GPGX

institute: Merck

data_processing:
Reads potentially derived from mouse were removed from fastq files with BBSplit (BBMap 7 v39.01)[1] with parameters ‘maxindel=200k ambiguous2=best’, with all other parameters at their default values. Briefly, reads were aligned to both human genome GRCh38 and mouse genome mm10 with the BBMap aligner, and the species of origin of the reads were determined based on the relative goodness of alignment to either genome. Reads confidently assigned to human were collected and used for downstream analysis (cleaned fastq files). OmicSoft OSA aligner (version 11.7) was used to align human reads against the Human.B38_Ensembl.R108.gmodel3 model and generate gene-level counts.
Gene level raw counts, and FPKM, were determined by the OSA algorithm as implemented in Omicsoft Array Studio and using Ensembl.R108 gene models.
Assembly: Human.B38
Supplementary files format and content: Tab-delimited text files include raw counts and FPKM values for each sample. Each column corresponds to one sample (barcode).

growth_protocol: All cell lines were cultured in RPMI1640 (Gibco) with 10% Fetal Bovine Serum (FBS) (Corning Inc) in a 37 °C, 5% CO2 cell culture incubator.

extract_protocol:
For the cell samples, Total RNA was extracted using Qiagen RNeasy Mini kit with DNase Digestion protocol following manufacturer’s instructions (Qiagen, Hilden, Germany). For the tissue samples, Total RNA was extracted using Qiagen RNeasy Plus Universal kit following manufacturer’s instructions (Qiagen, Hilden, Germany).
TruSeq Stranded Total RNA Ribozero

treatment_protocol: For in vitro studies, NCI-H226 or MSTO-211H cells were plated into T25 plates at 135,000 cells/plate in 4 mL of complete media, 18 hours later 400 μL of test compound or DMSO was added to each plate to a final concentration of 300 nM and cells were cultured for 6 or 48 more hours.  At harvest cells were washed twice with PBS before lysis in 350 microliters RLT + Beta-mercaptoethanol buffer. For in vivo studies, NSG mice were injected sub-cutaneous on the right flank with 5x10e6 cells in 100 μL of a 50:50 PBS:growth factor reduced-phenol red free Matrigel solution (Corning). Mice were randomized to treatment group when average tumor size was 150 mm3 and dosed orally with MRK-A at 30 mg/kg (twice daily). Mice were euthanized following IACUC approved protocol using CO2 followed by secondary cervical dislocation. Tumors were rapidly excised and collected into cryovials and snap frozen in liquid nitrogen for RNA processing.

value: mesothelioma


title: imMKCL 300mm s-1-off day5-3


title: LV3833-LV3688_DNMT1_MORC2_CRISPRi_H3K4me3_rep2


title: imMKCL 300mm s-1-off day5-2


title: Sample_A_FBS_2

description: 10x Genomics


title: Rxra cKO atRA+PKCi HFSCs 1, RNA-seq


title: CR153_LV3599_Control_H3K4me3_rep2


title: imMKCL 300mm s-1-off day3-2


title: NCI-H226, Xenograft, Vehice 5d-4


title: imMKCL 150mm s-1-off day3-3


title: Rxra cKO FBS HFSCs 2, RNA-seq


title: NCI-H226, Xenograft, Vehice 5d-3


title: imMKCL 150mm s-1-off day3-2


title: Rxra cKO FBS HFSCs 1, RNA-seq


title: imMKCL 150mm s-1-off day5-2


title: NCI-H226, Xenograft, Vehice 5d-2


title: imMKCL 150mm s-1-off day5-3


title: Development_K

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

data_processing:
Fastqs were generated using CellRanger v7.2 mkfastq
Reads were aligned to the Flex probeset v1.0.1 reference
Assembly: N/A (probe set v.1.0.1)
Supplementary files format and content: For development libraries, a summary of the metrics from the CellRanger count call
Supplementary files format and content: For the PERFF-seq libraries, h5 files representing probe gene expression counts
Library strategy: 10x Genomics Flex

molecule: other

source_name: peripherial blood mononculear cells

extract_protocol:
cDNA was extracted according to the 10x Genomics Flex scRNA-seq workflow
Libraries were constructed according to 10x Genomics Flex workflow; R1 is technical barcode sequence; R2 is the probe barcode sequences

value: peripherial blood mononculear cells

tag: flowfish probes

value: immune


title: NCI-H226, Xenograft, Vehice 20d-5


title: NCI-H226, Xenograft, Vehice 5d-1


title: wild-type atRA+PKCi HFSCs 1, ATAC-seq

description: ATAC-seq

data_processing:
50 bp paired-end FASTQs were aligned to the mouse genome (mm10) using the Bowtie (v.1.1.2). Aligned reads were de-duplicated with Picard (v.2.3.0; Broad Institute, 2019) and shifted to correct for Tn5 insertion bias. Peaks were called using MACS2 (v.2.1.1), concatenated to a union peak set, and the read coverage of each sample at these peaks was calculated with Bedtools (v.2.25).
Assembly: mm10
Supplementary files format and content: Bedfiles of peaks called using MACS2 (v.2.1.1).

extract_protocol:
To resuspend HFSCs, 3D cultures were washed with sterile PBS, dissociated into single cell suspensions using TrpLE-Express (Gibco) for 15min at 37°C. After filtering, cells were pelleted, lysed, and processed as described in Buenrostro et al., 2013.
Libraries were prepared according to the manufacturer’s guidelines (Illumina). Briefly cells were transposed with Tn5 transposase for 30 min and samples were barcoded.


title: Development_L


title: Development_G


title: wild-type FBS HFSCs 1, ATAC-seq

description: ATAC-seq


title: Development_E


title: NCI-H226, Xenograft, Vehice 20d-4


title: Development_H


title: Pilot_Flex


title: Development_I


title: wild-type FBS HFSCs 2, ATAC-seq

description: ATAC-seq


title: wild-type atRA+PKCi HFSCs 2, ATAC-seq

description: ATAC-seq


title: Development_D


title: NCI-H226, Xenograft, Vehice 20d-3


title: Development_C


title: Development_F


title: NCI-H226, Xenograft, Vehice 20d-2


title: Rxra cKO atRA+PKCi HFSCs 2, ATAC-seq

description: ATAC-seq


title: Rxra cKO atRA+PKCi HFSCs 1, ATAC-seq

description: ATAC-seq


title: Development_B


title: NCI-H226, Xenograft, Vehice 20d-1


title: Rxra cKO FBS HFSCs 2, ATAC-seq

description: ATAC-seq


title: NCI-H226, Xenograft, MRK-A, 30mpk 5d-5

value: MRK-A


title: Development_A


title: CR137_LV3800_DNMT1_CRISPRi_midXL_IgG

data_processing:
Paired-end reads (2x75 for CR136&CR137 and 2x150 for the rest of the sequencing runs)  were aligned to the hg38 genome using bowtie2 v2.3.4.2 (--local–very-sensitive-local --no-unal –no-mixed –no-discordant –phred33 -I 10 -X 700)
SAM files were converted to bam files with SAMtools v1.9. The BAM files were filtered according to alignment quality (MAPQ>10) using samtools (samtools view -bq 10 {BAM} > {FILTERED_BAM}).
Normalized bigwig coverage tracks were made with bamCoverage v2.4.3, with RPKM normalization.
GRCh38
Assembly: Bigwigs of filtered alignments for genome browser visualization, normalized with RPKM
Library strategy: CUT&RUN-Seq

value: human neuroepithelial-like stem cells

value: IgG


title: CR137_LV3800_DNMT1_CRISPRi_midXL_MORC2


title: Rxra cKO FBS HFSCs 1, ATAC-seq

description: ATAC-seq

value: Telogen (P55) skin mouse 1


title: NCI-H226, Xenograft, MRK-A, 30mpk 5d-4


title: CR137_LV3599_Control_midXL_IgG


title: Development_J


title: W4, multiplex

city: Chapel Hill

first: Li

last: Qian

state: North Carolina

address: 111 Mason Farm Road, MBRB

department: Department of Pathology

institute: UNC

description:
4Wbarcodes.tsv.gz
4Wfeatures.tsv.gz
4Wmatrix.mtx.gz

data_processing:
After sequencing, bcl2fastq ver 2.20.0 was used to create fastq files.
CellRanger multi was then used to identify cells specific to each condition and create gene expression matrices using the CellPlex CMOs (GFP(301 and 302) and SEG(303 and 304))
Data was further processed and analyzed using Seurat
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

growth_protocol: EGM2 Media

extract_protocol:
10x Genomics
Cells were detached from cell culture plates with trypsin.  Then labeled with CellPlex Oligos (GFP(#301 and #302) and SEG(#303 and #304)) following CellPlex standard protocol).  Libraries of cellplex labeled cells were then constructed using standard 10X Genomics 3' Reagent Kit v3.1

value: heart

value: iEC


title: NCI-H226, Xenograft, MRK-A, 30mpk 5d-3


title: CR136_Sai2_untransduced_midXL_IgG


title: NCI-H226, Xenograft, MRK-A, 30mpk 5d-2


title: CR136_Sai2_untransduced_midXL_MORC2


title: W2, multiplex

description:
2Wbarcodes.tsv.gz
2Wfeatures.tsv.gz
2Wmatrix.mtx.gz


title: CR114_LV3367_DNMT1_CRISPRcut_H3K9me3_rep2


title: NCI-H226, Xenograft, MRK-A, 30mpk 5d-1


title: CR137_LV3599_Control_midXL_MORC2


title: W2, gene, expression


title: NCI-H226, Xenograft, MRK-A, 30mpk 46d-5


title: ME49_IAA-48h_rep2

city: Indianapolis

first: Michael

middle: James

last: Holmes

state: IN

address: 635 Barnhill Drive

department: Pharmacology & Toxicology

institute: Indiana University School of Medicine

data_processing:
map fastq with hisat2 using default settings
count reads with htseq-count
differential gene expression with DESeq2
Assembly: ME49 genome v54, available at toxodb.org
Supplementary files format and content: tab delimited file with gene counts

molecule: polyA RNA

organism: Toxoplasma gondii

source_name: ME49-TIR1 eIF4E1mAID-HA

growth_protocol: parasites innoculated at MOI 2:1, grown in confluent human foreskin fibroblasts in DMEM+10%FBS (no antibiotic) for 16h prior to addition of 0.5% DMSO (vehicle) or 500uM IAA

extract_protocol:
infected monolayer was scraped & syringe lysed. Parasites  washed once with PBS. Pellet resuspended in TRIzol
RNA libraries were prepared for sequencing using standard Illumina protocols
paired end 2x150bp RNAseq

treatment_protocol: treatment with 500 uM 3-indole acetic acid (IAA) for 24h or 48h

value: ME49-TIR1 eIF4E1mAID-HA

value: 500uM IAA, 48h


title: CR114_LV3367_DNMT1_CRISPRcut_H3K4me3_rep1


title: CR114_LV3367_DNMT1_CRISPRcut_IgG_rep2


title: D7, multiplex

description:
D7barcodes.tsv.gz
D7features.tsv.gz
D7matrix.mtx.gz


title: NCI-H226, Xenograft, MRK-A, 30mpk 46d-4


title: ME49_IAA-48h_rep1


title: CR114_LV3367_DNMT1_CRISPRcut_IgG_rep1


title: NCI-H226, Xenograft, MRK-A, 30mpk 46d-3


title: D3, mulitplex

description:
D3barcodes.tsv.gz
D3features.tsv.gz
D3matrix.mtx.gz


title: ME49_IAA-24h_rep3

value: 500uM IAA, 24h


title: W4, gene, expression


title: NCI-H226, Xenograft, MRK-A, 30mpk 46d-2


title: D3, gene, expression


title: ME49_IAA-24h_rep2


title: ME49_IAA-24h_rep1


title: CR114_LV3393_Control_H3K4me3_rep1


title: CR114_LV3367_DNMT1_CRISPRcut_H3K4me3_rep2


title: NCI-H226, Xenograft, MRK-A, 30mpk 46d-1


title: ME49_DMSO_rep3

value: DMSO


title: NCI-H226, Xenograft, MRK-A, 30mpk 25d-5


title: CR114_LV3393_Control_H3K9me3_rep2


title: DARID_F_0h_cohort1_1

city: London

first: Leticia

last: Perez Sisques

address: Great Maze Pond

department: Centre for Craniofacial and Regenerative Biology

country: United Kingdom

institute: King's College London

data_processing:
Reads were aligned to the mouse genome (GRCm38.p6) using RNA STAR(v2.7.8a)
Unnormalized gene counts were obtained using GenomicAlignments and gRanges
Assembly: GRCm38.p6
Supplementary files format and content: Text file containing read counts for all samples assigned to features (genes)

source_name: Hippocampus

extract_protocol:
Total RNA was extracted from hippocampal samples with 1ml TRIzol (Thermo Fisher Scientific) and further purified with the Monarch Total RNA miniprep kit (New England Biolabs) following the manufacturer’s recommendations (including DNAse treatment step). mRNA quality was analysed using Agilent Total RNA 6000 Pico on a Bioanalyser (Agilent, 2100). Single-end sequencing (150bp read length) was performed on the Illumina Novaseq 6000 platform.
Library prep was performed by Novogene (Cambridge, United Kingdom): Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: Experiments include baseline samples (homecage mice)

value: Hippocampus

value: Baseline

value: Female


title: ME49_IAA-48h_rep3


title: CR114_LV3393_Control_H3K9me3_rep1


title: CR114_LV3367_DNMT1_CRISPRcut_H3K9me3_rep1


title: DARID_F_0h_cohort1_2


title: DARID_M_0h_cohort1_2

value: Male


title: ME49_DMSO_rep2


title: NCI-H226, Xenograft, MRK-A, 30mpk 25d-4

value: mesothelioma


title: CR114_LV3393_Control_IgG_rep2


title: NCI-H226, Xenograft, MRK-A, 30mpk 25d-3


title: D7, gene, expression


title: ME49_DMSO_rep1


title: NCI-H226, Xenograft, MRK-A, 30mpk 25d-2


title: CR114_LV3393_Control_H3K4me3_rep2


title: WT_F_0h_cohort1_2

value: Wild-type


title: NCI-H226, Xenograft, MRK-A, 30mpk 25d-1


title: RH_IAA-48h_rep2

source_name: RH-TIR1 eIF4E1mAID-HA

value: RH-TIR1 eIF4E1mAID-HA


title: NCI-H226, MRK-A 6h-3

value: MRK-A


title: CR117_LV3691_TASOR_CRISPRi_H3K4me3_rep1

value: human neuroepithelial-like stem cells


title: WT_F_0h_cohort1_1


title: WT_M_0h_cohort1_2


title: NCI-H226, MRK-A 6h-2


title: RH_IAA-48h_rep1


title: RH_IAA-24h_rep3


title: WT_M_0h_cohort1_1


title: RH_IAA-24h_rep2


title: NCI-H226, MRK-A 6h-1


title: CR117_LV3688_MORC2_CRISPRi_H3K4me3_rep2


title: DARID_F_3h_cohort2_3

data_processing:
Reads were aligned to the mouse genome (mm10) usingRNA STAR(v2.7.8a)
Reads were counted using FeatureCounts (v2.0.1)
Assembly: mm10
Supplementary files format and content: Text file containing read counts for all samples assigned to features (genes)

source_name: Dorsal hippocampus

extract_protocol:
Total RNA was extracted from hippocampal samples with 1ml TRIzol (Thermo Fisher Scientific) and further purified with the Monarch Total RNA miniprep kit (New England Biolabs) following the manufacturer’s recommendations (including DNAse treatment step). mRNA quality was analysed using Agilent Total RNA 6000 Pico on a Bioanalyser (Agilent, 2100). Pair-end sequencing (150bp read length) was performed on the Illumina Novaseq 6000 platform.
Library prep was performed by Novogene (Cambridge, United Kingdom): Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: Experiments include baseline samples, and samples collected 1h or 3h after a fear conditioning protocol: mice were placed inside the chamber and left to freely explore it. After 148 seconds, three electric shocks (0.7mA, 2sec each, 30 seconds apart) were administered. The animals were then removed from the testing chamber after 30 additional seconds

value: Dorsal hippocampus

value: 3h post-US


title: CR117_LV3688_MORC2_CRISPRi_H3K4me3_rep1


title: CR114_LV3393_Control_IgG_rep1

value: IgG


title: RH_IAA-24h_rep1


title: DARID_F_3h_cohort2_2


title: NCI-H226, MRK-A 48h-3


title: RH_IAA-48h_rep3


title: NCI-H226, MRK-A 48h-2


title: DARID_M_0h_cohort1_1


title: CR112_LV3688_MORC2_CRISPRi_H3K9me3_rep2


title: RH_DMSO_rep3


title: DARID_F_3h_cohort2_1


title: NCI-H226, MRK-A 48h-1


title: CR117_LV3691_TASOR_CRISPRi_H3K4me3_rep2


title: RH_DMSO_rep2


title: CR117_LV3691_TASOR_CRISPRi_H3K9me3_rep2


title: DARID_M_3h_cohort2_3


title: DARID_M_3h_cohort2_2


title: NCI-H226, DMSO 6h-3


title: NCI-H226, DMSO 6h-2


title: CR117_LV3691_TASOR_CRISPRi_IgG_rep1


title: CR117_LV3691_TASOR_CRISPRi_H3K9me3_rep1


title: ONT_cDNAseq_LV3367_DNMT1_CRISPRcut

description: ONT cDNA sequencing

data_processing:
Long read DNA sequencing data were aligned to the human genome (GRCh38) using minimap2 (-k15 -w5 -uf -x splice -O6,24).
SAM files were converted to bam files with SAMtools v1.9. The BAM files were filtered according to alignment quality (MAPQ>10) using samtools (samtools view -bq 10 {BAM} > {FILTERED_BAM}).
Normalized bigwig coverage tracks were made with bamCoverage v2.4.3, with RPKM normalization.
Assembly: GRCh38

extract_protocol: 1.5 μg total RNA was isolated as above for each of the four samples tested (Control, MORC2-CRISPRi, TASOR-CRISPRi and DNMT1-KO hNPCs, 10 days post-transduction in each case). Ribosomal RNA was depleted using the RiboMinus Eukaryote System v2 (ThermoFisher). 5 ng of the resulting RNA was used to make barcoded cDNA libraries (2 barcodes per sample) using the cDNA-PCR kit SQK-PCB-111-24 (Oxford Nanopore Technologies), which incorporates a strand-switching step to enrich for full-length transcripts. Fifteen PCR cycles were used with 7 min extension time. Inspection of the final cDNA product by capillary electrophoresis confirmed a peak at around 2-2.5 kb, approximately the size of an average human mRNA. The libraries were sequenced with a FLO-PRO002 PromethION Flow Cell R9 Version on a PromethION (Oxford Nanopore Technologies) at SciLifeLab

treatment_protocol: To silence the transcription of DNMT1 we used the catalytically inactive Cas9 (deadCas9) fused to the transcriptional repressor KRAB (Johansson et al 2022). Single guide sequences were designed to recognize DNA regions just down-stream of the transcription start site (TSS) according to the GPP Portal (Broad Institute). The following lentiviral backbone was used: pLV hU6-sgRNA hUbC-dCas9-KRAB-T2a-GFP. Lentiviruses were produced as described below yielding titers of 108-109 TU/ml, which was determined using qRT–PCR. Control virus with a gRNA sequence not present in the human genome (LacZ) was also produced and used in all experiments. GFP cells were FACS isolated (FACSAria, BD sciences) on day 10 at 10°C (reanalysis showed > 97% purity) and pelleted at 400 g for 5 min, snap frozen on dry ice and stored at −80°C.

value: DNMT1 CRISPRcut

value: CRISPR cut


title: NCI-H226, DMSO 6h-1


title: ONT_cDNAseq_LV3691_TASOR_CRISPRi

description: ONT cDNA sequencing

value: TASOR CRISPRi

value: CRISPR interference


title: WT_F_3h_cohort2_3


title: RH_DMSO_rep1

value: DMSO


title: CR117_LV3599_Control_H3K4me3_rep2


title: ONT_cDNAseq_LV3688_MORC2_CRISPRi

description: ONT cDNA sequencing

value: MORC2 CRISPRi


title: NCI-H226, DMSO 48h-2


title: CR117_LV3599_Control_H3K4me3_rep1


title: CR117_LV3599_Control_H3K9me3_rep3


title: ONT_DNAseq_LV3688_MORC2_CRISPRi_WG_MethCalls

description: ONT whole genome DNA

data_processing:
Long read DNA sequencing data were aligned to the human genome (GRCh38) using minimap2 (-a -x map-ont) and 5mC base modifications were detected using the nanopolish tool.
To detect the modifications, we indexed the fast5 files using nanopolish (nanopolish index -d fast5_files/ reads.fasta)
Assembly: GRCh38

extract_protocol: High molecular weight DNA was extracted from frozen pellets (1 million cells) using the Nanobind HMW DNA Extraction kit (PacBio) following the manufacturer’s instructions. The final product was eluted in 100 μL. DNA concentration and quality were measured using Nanodrop and Qubit from the top, middle, and bottom of each tube, and by agarose gel electrophoresis. Whole genome sequencing was done using SQK-LSK109 Ligation Sequencing kit (Oxford Nanopore Technologies) and FLO-PRO002 PromethION Flow Cell R9 Version and was sequenced on a PromethION (Oxford Nanopore Technologies) at SciLifeLab.

value: Control


title: NCI-H226, DMSO 48h-1


title: CR112_LV3688_MORC2_CRISPRi_H3K9me3_rep1


title: CR112_LV3599_Control_H3K9me3_rep2


title: MSTO-211H, MRK-A 6h-3


title: CR112_LV3599_Control_H3K9me3_rep1


title: NCI-H226, DMSO 48h-3


title: WT_M_3h_cohort2_3


title: MSTO-211H, MRK-A 6h-2


title: ONT_cDNAseq_LV3599_Control

description: ONT cDNA sequencing


title: DARID_M_3h_cohort2_1


title: MSTO-211H, MRK-A 6h-1


title: CR112_LV3599_Control_IgG_rep3


title: WT_M_3h_cohort2_2


title: CR112_LV3688_MORC2_CRISPRi_IgG_rep1


title: WT_F_3h_cohort2_1

value: Female


title: BY4742, 30C, 6h, biol rep 6

city: Umea

first: ALEXANDER

last: VERGARA

address: Historiegrand 9, 1002

department: Physics

institute: Umea University

data_processing:
StringTie and nfcore/rnaseq best-practice analysis pipeline at National Genomics Infrastructure (NGI), Uppsala, Sweden (https://github.com/nf-core/rnaseq).
STAR
featureCounts
Assembly: Saccharomyces_cerevisiae.R64-1-1.106.gtf
Supplementary files format and content: Two tab delimited txt files for each sample containing counts over exons and whole gene respectively.

organism: Saccharomyces cerevisiae

growth_protocol: BY4742 cells were inoculated YPD medium, precultivated in YPD at  30 C, diluted in fresh YPD to an OD600nm of 0.1 to 0.15 and cultivated for 2 h at 30 ºC after which the first (0h) samples  were harvested.

extract_protocol:
RNeasy Mini Kit (Qiagen) Purification of total RNA from yeast by enzymatic lysis
Library including polyA selection, were prepared from 500 ng of total RNA using the TruSeq stranded mRNA library preparation kit, Illumina Inc

treatment_protocol: Continued growth for 2 h, 4 h and 6 h after the 0 h time point

value: Wt

value: 6 h


title: DARID_F_1h_cohort2_3

value: 1h post-US


title: BY4742, 30C, 6h, biol rep 5


title: CR117_LV3599_Control_IgG_rep2


title: WT_F_3h_cohort2_2

value: Wild-type


title: CR117_LV3599_Control_IgG_rep1


title: MSTO-211H, MRK-A 48h-3

value: mesothelioma

value: MRK-A


title: MSTO-211H, MRK-A 48h-2


title: DARID_F_1h_cohort2_2

value: Dorsal hippocampus


title: MSTO-211H, MRK-A 48h-1


title: DARID_F_1h_cohort2_1


title: proQ++, 24 min, biol rep 6 (Sample 132)

city: Würzburg

first: Laura

last: Jenniches

address: Josef-Schneider-Straße 2/D15

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research

data_processing:
Adapters were removed with Cutadapt v4.1
Alignment: STAR 2.6.0a (Dobin et al., 2013)
Quantification: htseq-count 2.0.2
Assembly: FQ312003.1, HE654724.1, HE654725.1 and HE654726.1
Supplementary files format and content: counts
Library strategy: RIF-seq

organism: Salmonella enterica subsp. enterica serovar Typhimurium

growth_protocol: Overnight growth from single colonies at 37 °C in LB medium

extract_protocol:
Hot phenol extraction followed by DNase treatment.
RNA-seq libraries were prepared by Vertis AG (Freising-Weihenstephan, Germany). The ribodepleted RNA samples were fragmented using ultrasound (4 pulses of 30 s each at 4 C). Subsequently, an oligonucleotide adapter was ligated to the 3' end of the RNA molecules. First-strand cDNA synthesis was performed using M-MLV reverse transcriptase and the 3' adapter as primer. The first-strand cDNA was purified and the 5' Illumina TruSeq sequencing adapter was ligated to the 3' end of the antisense cDNA. The resulting cDNA was PCR-amplified to about 10-20 ng/ul using a high fidelity DNA polymerase. cDNA was purified with the Agencourt AMPure XP kit (Beckman Coulter Genomics).

treatment_protocol: The cultures were treated with 500µl/ml of rifampicin (stock solution 50mg/ml resuspended in DMSO)

value: proQ++

value: 24 min after rif. treatment


title: proQ++, 12 min, biol rep 6 (Sample 131)

value: 12 min after rif. treatment


title: DARID_M_1h_cohort2_3

value: Male


title: MSTO-211H, DMSO 6h-3


title: BY4742, 30C, 6h, biol rep 2


title: WT_M_3h_cohort2_1

value: 3h post-US


title: BY4742, 30C, 6h, biol rep 1


title: MSTO-211H, DMSO 6h-2


title: proQ++, 3 min, biol rep 6 (Sample 129)

value: 3 min after rif. treatment


title: DARID_M_1h_cohort2_1


title: DARID_M_1h_cohort2_2


title: proQ++, 6 min, biol rep 6 (Sample 130)

value: 6 min after rif. treatment


title: BY4742, 30C, 4h, biol rep 6

value: 4 h


title: BY4742, 30C, 4h, biol rep 5


title: MSTO-211H, DMSO 6h-1

value: DMSO


title: MSTO-211H, DMSO 48h-3


title: WT_F_1h_cohort2_2

value: Female


title: ΔproQ, 24 min, biol rep 6 (Sample 127)

value: {delta}proQ


title: proQ++, 0 min, biol rep 6 (Sample 128)

value: 0 min after rif. treatment


title: BY4742, 30C, 6h, biol rep 4

value: Wt

value: 6 h


title: ΔproQ, 12 min, biol rep 6 (Sample 126)


title: MSTO-211H, DMSO 48h-2

value: mesothelioma


title: WT_F_1h_cohort2_3

value: Wild-type

value: 1h post-US


title: ONT_DNAseq_LV3599_Control_WG_MethCalls

description: ONT whole genome DNA

value: human neuroepithelial-like stem cells

value: Control

value: CRISPR interference


title: BY4742, 30C, 4h, biol rep 3


title: BY4742, 30C, 6h, biol rep 3


title: WT_F_1h_cohort2_1

value: Dorsal hippocampus


title: ΔproQ, 6 min, biol rep 6 (Sample 125)


title: WT_M_1h_cohort2_3

value: Male


title: BY4742, 30C, 4h, biol rep 2


title: DNMT1_CRISPRi_rep4

data_processing:
Paired-end reads (2x150) were aligned to the hg38 genome using STAR v2.6.0c. Both unique (--outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.03) and multimapping (--outFilterMultimapNmax 100 --winAnchorMultimapNmax 200) steps were performed
SAM files were converted to BAM and further sorted and indexed using SAMtools v1.9.
Coverage tracks were made with bamCoverage v2.4.3 normalizing with a reads per kilobase million factor (RPKM)
Read count over genes and transposable elements was performed using FeatureCounts v1.6.3 taking into consideration the strandedness of the genomic element
Assembly: GRCh38
Supplementary files format and content: BigWig file format normalized according to RPKM for each sample. The BigWig files were created from the BAMs containing reads with a MAPQ>=10

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (Quiagen) with on column DNAse treatment following the manufacturer’s instructions.
Libraries for RNA sequencing were generated using Illumina TruSeq Stranded mRNA library prep kit (poly-A selection), optimized for long fragments, and sequenced on a Novaseq6000 (paired end, ~ 250 bp).

treatment_protocol:
To silence the transcription of MORC2, TASOR and DNMT1, we used the catalytically inactive Cas9 (deadCas9) fused to the transcriptional repressor KRAB (Johansson et al 2022). Single guide sequences were designed to recognize DNA regions just down-stream of the transcription start site (TSS) according to the GPP Portal (Broad Institute). The following lentiviral backbone was used: pLV hU6-sgRNA hUbC-dCas9-KRAB-T2a-GFP. Lentiviruses were produced as described below yielding titers of 108-109 TU/ml, which was determined using qRT–PCR. Control virus with a gRNA sequence not present in the human genome (LacZ) was also produced and used in all experiments. GFP cells were FACS isolated (FACSAria, BD sciences) on day 10 at 10°C (reanalysis showed > 97% purity) and pelleted at 400 g for 5 min, snap frozen on dry ice and stored at −80°C until RNA isolation.
To do a double KD of DNMT1 and MORC2 we did a double transduction method. To knock down MORC2 we transduced with the previously mentioned deadCas9-KRAB-T2A-GFP lentiviral containing the dead Cas9 protein and a GFP. At the same time, to knock down DNMT1 the cells were transduced with lentivirus containing the pLV.U6BsmBI.EFS-NS.H2b-RFPW lentiviral backbone, that had the gRNA for DNMT1 and mCherry as a marker but lacked deadCas9. Double (mCherry and GFP) positive cells were FACS sorted as previously described and stored at -80 until RNA extraction.

value: DNMT1 knockdown

value: 10 days after transduction


title: BY4742, 30C, 4h, biol rep 1

value: 4 h


title: WT_M_1h_cohort2_2


title: ΔproQ, 3 min, biol rep 6 (Sample 124)

value: 3 min after rif. treatment


title: DNMT1_CRISPRi_rep3


title: BY4742, 30C, 2h, biol rep 6

value: 2 h


title: DNMT1_CRISPRi_rep2


title: BY4742, 30C, 2h, biol rep 5


title: WT_M_1h_cohort2_1


title: ΔproQ, 0 min, biol rep 6 (Sample 123)

value: {delta}proQ


title: DARID_F_0h_cohort2_3

value: Baseline

value: Female


title: DNMT1_CRISPRi_rep1


title: BY4742, 30C, 4h, biol rep 4

value: Wt


title: WT, 24 min, biol rep 6 (Sample 122)

value: WT

value: 24 min after rif. treatment


title: WT, 12 min, biol rep 6 (Sample 121)

value: 12 min after rif. treatment


title: BY4742, 30C, 2h, biol rep 3


title: BY4742, 30C, 2h, biol rep 4


title: WT, 6 min, biol rep 6 (Sample 120)

value: 6 min after rif. treatment


title: DARID_F_0h_cohort2_2


title: MSTO-211H, DMSO 48h-1

value: mesothelioma

value: DMSO


title: WT, 3 min, biol rep 6 (Sample 119)


title: DNMT1i_CRISPRi_control_rep4

value: human neuroepithelial-like stem cells

value: Control

value: CRISPR interference


title: DARID_F_0h_cohort2_1

value: Dorsal hippocampus


title: DNMT1i_CRISPRi_control_rep3

value: 10 days after transduction


title: DARID_M_0h_cohort2_3

value: Male


title: BY4742, 30C, 2h, biol rep 1

value: 2 h


title: DNMT1_CRISPRi_control_rep2


title: WT, 0 min, biol rep 6 (Sample 118)

value: 0 min after rif. treatment


title: DARID_M_0h_cohort2_2

value: Baseline


title: DNMT1_CRISPRi_control_rep1


title: BY4742, 30C, 0h, biol rep 24

value: 0 h


title: DARID_M_0h_cohort2_1


title: proQ++, 24 min, biol rep 5 (Sample 117)

value: proQ++


title: DNMT1_and_MORC2_doubleCRISPRi_rep4

value: DNMT1 and MORC2 double knockdown


title: BY4742, 30C, 0h, biol rep 23

value: Wt


title: WT_F_0h_cohort2_3

value: Wild-type

value: Female


title: DNMT1_and_MORC2_doubleCRISPRi_rep3


title: proQ++, 6 min, biol rep 5 (Sample 115)

value: 6 min after rif. treatment


title: BY4742, 30C, 0h, biol rep 22


title: DNMT1_and_MORC2_doubleCRISPRi_rep2


title: WT_F_0h_cohort2_2


title: proQ++, 12 min, biol rep 5 (Sample 116)

value: 12 min after rif. treatment


title: DNMT1_and_MORC2_doubleCRISPRi_rep1

value: human neuroepithelial-like stem cells


title: BY4742, 30C, 0h, biol rep 21


title: WT_F_0h_cohort2_1


title: BY4742, 30C, 2h, biol rep 2


title: proQ++, 3 min, biol rep 5 (Sample 114)

value: 3 min after rif. treatment


title: BY4742, 30C, 0h, biol rep 20


title: ΔproQ, 24 min, biol rep 5 (Sample 112)

value: {delta}proQ

value: 24 min after rif. treatment


title: WT_M_0h_cohort2_2

value: Dorsal hippocampus


title: DNMT1_and_MORC2_doubleCRISPRi_control_rep4

value: Control

value: CRISPR interference

value: 10 days after transduction


title: WT_M_0h_cohort2_3

value: Baseline

value: Male


title: BY4742, 30C, 0h, biol rep 19

value: 0 h


title: BY4742, 30C, 0h, biol rep 18


title: DNMT1_and_MORC2_doubleCRISPRi_control_rep2


title: BY4742, 30C, 0h, biol rep 17


title: ΔproQ, 6 min, biol rep 5 (Sample 110)


title: ΔproQ, 12 min, biol rep 5 (Sample 111)


title: proQ++, 0 min, biol rep 5 (Sample 113)

value: proQ++

value: 0 min after rif. treatment


title: Cultured HFSCs mouse 2, HTO

description:
10x Genomics
hashtag_barcode_sample.csv

data_processing:
Sample and cell demultiplexing, alignment, filtering, barcode counting, and sample aggregation were performed using the Cell Ranger software v7.0.1.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: HTO

source_name: AnaVI back skin

extract_protocol:
To isolate cells from mouse back skin, samples were dissected and digested in 0.25% collagenase (Sigma) in HBSS for 35 min before 0.25% trypsin-EDTA for an additional 15 min. Single cell suspensions were obtained by scraping the epidermal side gently using a blunt scalpel. After washing with FACS buffer (5% FBS in PBS), cells were filtered through 70- and 45-μm strainers, pelleted, washed with FACS buffer, and incubated with published antibodies for 20 min on ice. To resuspend autologous hair follicle stem cells (HFSCs), 3D cultures were washed with sterile PBS, dissociated into single cell suspensions using TrpLE-Express (Gibco) for 15min at 37°C. After filtering, cells were pelleting, washed with Cell Staining Buffer, and incubated with TotalSeq-B hashtag antibodies for 20 min on ice.
Libraries were constructed according to the manufacter’s instructions (3' Gene Expression V3, 10x Genomics).

value: Hair follicle stem cells mouse 2

value: Hair follicle stem cells

value: wild-type

tag: culture condition

value: mixed samples


title: BY4742, 30C, 0h, biol rep 16

value: Wt


title: ΔproQ, 3 min, biol rep 5 (Sample 109)

value: 3 min after rif. treatment


title: DNMT1_and_MORC2_doubleCRISPRi_control_rep1

value: human neuroepithelial-like stem cells


title: Cultured HFSCs mouse 2, scRNA-seq

description:
10x Genomics
hashtag_barcode_sample.csv

data_processing:
Sample and cell demultiplexing, alignment, filtering, barcode counting, and sample aggregation were performed using the Cell Ranger software v7.0.1.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files


title: TASOR_CRISPRi_rep4

value: TASOR knockdown


title: ΔproQ, 0 min, biol rep 5 (Sample 108)

value: {delta}proQ


title: Cultured HFSCs mouse 1, HTO

description:
10x Genomics
hashtag_barcode_sample.csv

value: Hair follicle stem cells mouse 1


title: BY4742, 30C, 0h, biol rep 15


title: BY4742, 30C, 0h, biol rep 14


title: DNMT1_and_MORC2_doubleCRISPRi_control_rep3

value: Control

value: CRISPR interference


title: WT, 24 min, biol rep 5 (Sample 107)

value: WT

value: 24 min after rif. treatment


title: TASOR_CRISPRi_rep3

value: 10 days after transduction


title: TASOR_CRISPRi_rep2


title: WT, 6 min, biol rep 5 (Sample 105)

value: 6 min after rif. treatment


title: AnaVI (P32) skin mouse 2, scRNA-seq

description: 10x Genomics

value: AnaVI (P32) skin mouse 2

value: Skin and hair follicle cells


title: WT, 12 min, biol rep 5 (Sample 106)

value: 12 min after rif. treatment


title: BY4742, 30C, 0h, biol rep 13

value: 0 h


title: BY4742, 30C, 0h, biol rep 12


title: TASOR_CRISPRi_rep1


title: WT_M_0h_cohort2_1

value: Dorsal hippocampus

value: Wild-type

value: Baseline

value: Male


title: WT, 3 min, biol rep 5 (Sample 104)

value: 3 min after rif. treatment


title: AnaVI (P32) skin mouse 1, scRNA-seq

description: 10x Genomics

value: AnaVI (P32) skin mouse 1

value: wild-type


title: BY4742, 30C, 0h, biol rep 11

value: Wt


title: BY4742, 30C, 0h, biol rep 10


title: WT, 0 min, biol rep 5 (Sample 103)

value: 0 min after rif. treatment


title: BY4742, 30C, 0h, biol rep 9


title: MORC2_CRISPRi_rep1

value: human neuroepithelial-like stem cells

value: MORC2 knockdown

value: CRISPR interference


title: MORC2_CRISPRi_rep2

value: 10 days after transduction


title: proQ++, 24 min, biol rep 4 (Sample 102)

value: proQ++

value: 24 min after rif. treatment


title: MORC2_and_TASOR_CRISPRi_control_rep4

value: Control


title: proQ++, 12 min, biol rep 4 (Sample 101)

value: 12 min after rif. treatment


title: BY4742, 30C, 0h, biol rep 8

value: 0 h


title: MORC2_and_TASOR_CRISPRi_control_rep3


title: Cultured HFSCs mouse 1, scRNA-seq

description:
10x Genomics
hashtag_barcode_sample.csv

value: Hair follicle stem cells mouse 1

value: Hair follicle stem cells

value: mixed samples


title: BY4742, 30C, 0h, biol rep 7


title: MORC2_CRISPRi_rep3


title: BY4742, 30C, 0h, biol rep 6


title: MORC2_and_TASOR_CRISPRi_control_rep2


title: proQ++, 6 min, biol rep 4 (Sample 100)

value: 6 min after rif. treatment


title: proQ++, 3 min, biol rep 4 (Sample 99)

value: 3 min after rif. treatment


title: MORC2_and_TASOR_CRISPRi_control_rep1


title: H9P_ctrl_3

city: Hangzhou

first: Qianyu

last: Liu

address: YuhangTang Road

institute: Zhejiang University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Supplementary files format and content: excel file include FPKM and count values for each Sample .

source_name: H9 hESC

growth_protocol: PXGL naïve hESC was cultured in N2B27 medium supplemented with 1 mM PD0325901, 2 mM XAV939 , 2 mM Go¨ 6983  and 10 ng/mL human LIF on the MEF layer.

extract_protocol:
Total RNA was extracted usingTrizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: H9 hESC

value: Human embryonic stem cell

value: WT

value: treated with primed medium


title: BY4742, 30C, 0h, biol rep 4

value: Wt


title: BY4742, 30C, 0h, biol rep 5


title: H9P_ctrl_2


title: H9P_shOGA_3

value: OGA knockdown


title: H9P_ctrl_1


title: ΔproQ, 24 min, biol rep 4 (Sample 97)

value: {delta}proQ


title: BY4742, 30C, 0h, biol rep 2


title: ΔproQ, 6 min, biol rep 4 (Sample 95)


title: BY4742, 30C, 0h, biol rep 1


title: ΔproQ, 3 min, biol rep 4 (Sample 94)


title: BY4742, 30C, 0h, biol rep 3


title: proQ++, 0 min, biol rep 4 (Sample 98)

value: proQ++

value: 0 min after rif. treatment


title: H9P_shOGA_2


title: ΔproQ, 0 min, biol rep 4 (Sample 93)


title: PXGL_ctrl_reprime3


title: ΔproQ, 12 min, biol rep 4 (Sample 96)


title: WT, 12 min, biol rep 4 (Sample 91)


title: Control_Med1_4h and Med15_4h

description: Control for Med1_4h and Med15_4h

data_processing:
Reads were mapped using Bowtie2 to the sacCer3 reference genome. After mapping of reads, we called narrow peaks at an average fragment size of 300 bp and an FDR value < 0.05
ChIP-seq using an untagged wild type strain was used as control for peak calling and enrichment analyses
Assembly: sacCer3
Supplementary files format and content: bigwig files (narrow peaks)

growth_protocol: For experiments using cells at different growth phases, single colonies of Saccharomyces cerevisiae BY4742 cells were inoculated into 10 ml of YPD medium (1% yeast extract, 2% bacto-peptone and 2% glucose), precultivated in YPD at 30 ◦C, diluted in fresh YPD to an OD600nm of 0.1 to 0.15 and cultivated for 2 h at 30 ºC after which the first samples (labelled 0 h in the figures) were harvested. Subsequent samples were harvested at 2 h, 4 h and 6 h after the 0 h point

extract_protocol:
Cell lysis and separation of chromatin fractions were performed using the standard protocol Svejstrup et al., (2003), except that we used ammonium sulfate to 0.5 M final concentration instead of 1 M to release chromatin-associated proteins, as we have described previously
DNA fragments were then cleaned using the ChIP DNA clean & concentratorTM kit (ZYMO RESEARCH). Aliquots of 1 to 2 ng of DNA from each sample were tested for proper shearing using a fragment analyzer (Agilent 2100 Bioanalyzer G2938C), and then sent for library preparation using the SMARTer ThruPLEX kit and subsequent pair-ended sequencing using Illumina NovaSeq S4-200 cycle flow cells in individual lanes.

tag: chip antibody

value: IgG

tag: time (hrs)


title: WT, 24 min, biol rep 4 (Sample 92)

value: 24 min after rif. treatment


title: Med15_4h

description: Wt Med15-Ab ChIP 4 hours


title: PXGL_ctrl_reprime2

tag: cell line


title: Lsm3-TAP R2_2h

description: Lsm3-TAP IgG-Ab 2h Rep2

value: Lsm3-TAP R2


title: WT, 6 min, biol rep 4 (Sample 90)


title: PXGL_ctrl_reprime1

tag: cell type


title: Lsm3-TAP R1_2h

description: Lsm3-TAP IgG-Ab 2h Rep1

value: Lsm3-TAP R1


title: WT, 3 min, biol rep 4 (Sample 89)


title: PXGL_shOGA_reprime3


title: WT, 0 min, biol rep 4 (Sample 88)


title: Control  Lsm3-TAP R1_2h, Lsm3-TAP R2_2h, Med1_2h, Med15_2h

description: Control for  Med1_2h, Med15_2h, Lsm3_R1 and Lsm3_R2


title: Med15_0h

description: Wt Med15-Ab ChIP 0 hours


title: PXGL_ctrl_3


title: proQ++, 12 min, biol rep 3 (Sample 86)

value: 12 min after rif. treatment


title: Med1_0h

description: Wt Med1-Ab ChIP 0 hours


title: PXGL_shOGA_reprime2


title: proQ++, 24 min, biol rep 3 (Sample 87)


title: proQ++, 6 min, biol rep 3 (Sample 85)


title: PXGL_shOGA_reprime1


title: PXGL_ctrl_2


title: proQ++, 3 min, biol rep 3 (Sample 84)


title: Control_Med1_0h and Med15_0h

description: Control for Med1_0h and Med15_0h


title: Med1_4h

description: Wt Med1-Ab ChIP 4 hours


title: PXGL_ctrl_1


title: H9P_shOGA_1


title: Ciprofloxacin (12 ng/mL) 75 min post-treatment; BR 3

city: Trondheim

first: Amanda

middle: Holstad

last: Singleton

address: Erling Skjalgsons gate 1

department: Department of Clinical and Molecular Medicine

country: Norway

institute: Norwegian University of Science and Technology

data_processing:
FASTQ files were generated using bcl2fastq2 Conversion Software v 2.20.0.422. Processing of the sequence data was done with the ProkSeq v 2.0 program using Docker, with the  E. coli K-12 substr. MG1655 reference genome ASM584v2 (RefSeq: GCF_000005845.2) and corresponding reference transcriptome. ProkSeq is a docker based, full RNA-Seq pipeline for prokaryotes, which includes quality assessment, alignment, gene counting, and analysis. The count tables countFile.csv, countFileNucleotideAvgCount.csv and countFile_TPM_CPM.tsv were exported from ProkSeq and used for further analysis.
The sample counts were were analyzed in R using the quasi-likelihood test in EdgeR v 3.36.0 from Bioconductor. Poorly expressed genes were filtered out, and library size was normalized using trimmed mean of M-value (TMM). Differentially expressed genes were defined with FDR < 0.05 and presented as LFC compared to the control.
Assembly: ASM584v2 (RefSeq: GCF_000005845.2)
Supplementary files format and content: The processed data file (countFile.csv) contains the count for each sample of each identified gene.

organism: Escherichia coli str. K-12 substr. MG1655

growth_protocol: The E. coli pre-culture was diluted to OD600 = 0.0125. E. coli was grown in cation-adjusted Mueller-Hinton broth in 1 1L Applikon bioreactors as batch culitvation. Stirring was adjusted between 200 and 600 rpm to maintain a dissolved oxygen concentration above 40%. The aeration rate was kept at 500 mL min-1. pH 7 was maintained by automatic titration of 3 M HCl and 4 M NaOH.

extract_protocol:
Transcriptomics was sampled according to the protocol provided with RNeasy Mini kit (Qiagen). The sample volume was based on OD600 at each sampling timepoint to ensure 3.35 x 10^8 cells per sample. The sample was immediately added to 2 volumes of RNA protect and vortexed. After minimum 5 min, the samples were centrifuged (10 min, max rcf). The supernatant was discarded, and the pellet was frozen in N2 (l). RNA was isolated using RNeasy Mini Kit (Qiagen), according to manufacturer's protocol 4 (Enzymatic lysis and Proteinase K digestion of bacteria) and protocol 7 (Purification of total RNA) with on-column Dnase (Qiagen) digestion. The RNA concentration in each sample was measured using NanoDrop-1000 spectrophotometer. Isolated RNA was sent to the Genomics Core Facility at NTNU for further processing and sequencing.
RNA sequencing libraries were prepared using the QIAseq FastSelect 5S/16S/23S kit (Qiagen) for rRNA removal and the QIAseq stranded RNA Lib kit (Qiagen) for library construction, according to the manufacturer's instructions.  Briefly, 500 ng total RNA was used as starting material. Removal of ribosomal RNA (rRNA) was conducted by a combined heat fragmentation (89°C for 7 min) and FastSelect hybridization protocol (75-4°C ramping process) where the FastSelect reagent inhibited reverse transcription of bacterial rRNA. Next, purification was conducted using QIAseq Beads followed by a first-strand synthesis using a RNase H- Reverse Transcriptase (RT) in combination with random primers, a second-strand synthesis, end-repair, A-addition, and adapter ligation. The second-strand synthesis was performed using 5’phosphorylated random primers which enable subsequent strand-specific ligation. DNA fragments were further enriched by CleanStart library amplification (15 cycles of PCR reaction). Finally, the libraries were purified using the QIAseq Beads, quantitated by qPCR using Collibri Library Quantification Kit (Thermo Fisher Scientific), and validated using Perkin Elmer DNA 1K/12K/Hi Sensitivity Assay LabChip on a Labchip GX instrument (Perkin Elmer, USA). The size range of the DNA fragments were measured to be in the range of 270 to 570 bp and peaked around 355 bp. Prior to sequencing, libraries were normalized and pooled to 2.3 pM and subjected to clustering on three NextSeq 500 HO flowcells (Illumina, USA).

treatment_protocol: At OD600 = 0.2, E. coli was treated with 12 ng/mL ciprofloxacin.

value: Ciprofloxacin 12 ng/mL


title: Ciprofloxacin (12 ng/mL) 120 min post-treatment; BR 3


title: PXGL_shOGA_3


title: Ciprofloxacin (12 ng/mL) 50 min post-treatment; BR 3


title: proQ++, 0 min, biol rep 3 (Sample 83)


title: ΔproQ, 24 min, biol rep 3 (Sample 82)


title: ΔproQ, 12 min, biol rep 3 (Sample 81)


title: PXGL_shOGA_2


title: Ciprofloxacin (12 ng/mL) 10 min post-treatment; BR 3


title: Ciprofloxacin (12 ng/mL) 25 min post-treatment; BR 3


title: HKI-2-AR-2-Cut and tag

city: Tianjin

first: Yuyang

state: Tianjin

address: 94 Weijin Road

department: cell and genetic department

institute: Nankai university

data_processing:
library strategy: CUT&TAG
Clean reeas of RNA-seq were mapped to hg38 using STAR.RNA-seq datasets were performed using the TOPMed RNA-seq pipeline . Differentially expressed genes were identified using DESeq2 according to default parameters .Genes with an absolute log2 fold change > 1 and an adjusted P-value < 0.05 were considered as differentially expressed ones
Clean reads of ChIRP-seq were mapped to hg38 using STAR. Normalized bigwigs of even, odd, and merged files were generated using the ChIRP-seq processing scripts . Peaks of merged bigwig were called using MACS2, and called peaks were filtered to exclude blacklist regions from ENCODE. Peaks with correlation of even and odd > 0.8, FDR < 0.05, and read coverage > 2-fold of the input were kept as confident HOTAIR target regions.
Clean reads of ChIP-seq and Cut and tag were mapped to hg38 using STAR.Biological replicates that showed a good correlation (Pearson correlation coefficient > 0.8) were merged for downstream analysis, including peak calling and plots.  Peaks for histone modifications were called using MACS2 , peaks for transcription factors were called using SPP.Genomic annotation for called peaks was performed using Homer  with default parameters. Normalized coverage track (bigWig) files were generated using bamCoverage from deepTools.
Assembly: hg38
Supplementary files format and content: xlsx file  include genes counts values and bw files include ChIP, ChIRP, Cut and tag signal peaks for each Sample

source_name: 22Rv1_Cell line

growth_protocol: 22Rv1 cell line was cultured in 1640 medium supplemented with 10% fetal bovine serum (FBS)

extract_protocol:
RNA-seq:Total RNA was extracted using TRIzol according to the manufacturer’s instruction. Then, ribosomal RNA was deleted from 5 μg of total extracted RNA using the Ribo-Zero Gold Kit, using Illumina novaseq 6000. ChIRP-seq: Cells were fixed with glutaraldehyde  for 10 min and nucleus was isolated and sheared to 100-500 bp fragments by sonication, then hybridized with DNA probes. Libraries were prepared using the NEBNext DNA library kit according to the manufacturer's instructions (New England BioLabs), using Illumina novaseq 6000. ChIP-sq:Cells were fixed with formaldehyde  for 10 min and nucleus was isolated and sheared to 200-500 bp DNA fragments by sonication, then immunoprecipitated with the corresponding antibodies. Libraries were prepared using the NEBNext DNA library kit according to the manufacturer's instructions (New England BioLabs), using Illumina novaseq 6000. Cut and tag: The experiments were performed using Hyperactive Universal  CUT & Tag Assay Kit (Vazyme, TD901). Briefly, Cells were incubated with Concanavalin A- Coated beads and then incubated with antibody. DNA sequencing library was built by pA-Tn5 transpose, then sequenced by Illumina novaseq 6000.
RNA-seq, ChIRP-seq , ChIP-seq and Cut and tag  libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HKI cell lines were acquired by Crispr/Cas9 mediated HOTAIR poly-A knock in .

value: HOTAIR Poly-A knock in

tag: antibody


title: ΔproQ, 6 min, biol rep 3 (Sample 80)

tag: strain

value: 6 min after rif. treatment


title: Ciprofloxacin (12 ng/mL) 1 min post-treatment; BR 3

tag: genotype


title: ΔproQ, 0 min, biol rep 3 (Sample 78)

tag: treatment


title: Untreated control 120 min post-treatment; BR 3

value: Untreated control


title: HKI-2-AR-1-Cut and tag


title: HKI-1-AR-2-Cut and tag


title: Ciprofloxacin (12 ng/mL) 1 min pre-treatment; BR 3


title: WT, 24 min, biol rep 3 (Sample 77)


title: Untreated control 75 min post-treatment; BR 3


title: PFA 33980 | 012 | Full ROI - WTA

city: Woodland

first: Sonny

middle: Ramirez

last: Elizaldi

address: County Road 98 and, Hutchison Dr

department: Immunology

institute: University of California Davis

description: FFPE Spatial Transcriptome sequencing

data_processing:
Raw sequencing data was processed using Nanostring's GeoMx DSP Control Center
Assembly: N/A, sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform
Supplementary files format and content: Digital Count Conversion (DCC) file format outputted from GeoMx NGS Pipeline, contains software versions, scan attributes, GeoMx NGS pipeline parameters and output metrics, Q30 scores, and list of deduplicated counts per RTS_ID (probe barcode)
Library strategy: Spatial Transcriptomics

organism: Macaca mulatta

source_name: Brain - Hippocampus

extract_protocol:
5um sections were cut from Paraformaldehyde-Fixed Paraffin-Embedded slides.  Samples were incubated with either DNA-oligo barcoded RNA-ISH probes or antibodies which were conjugated with a UV-photocleavable linker following standard ISH protocols, along with fluorescently labeled antibodies for visualization of morphological structures. Regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x)
Spatial transcriptome sequencing libraries were prepared with Nanostring reagents according to manufacturer's specifications

treatment_protocol: Rhesus macaques were intravenously inoculated with SIVCL757

tag: tissue

value: Brain - Hippocampus

value: N/A - healthy

tag: panel

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA


title: 22Rv1-WT-AR-2-Cut and tag


title: WT, 12 min, biol rep 3 (Sample 76)

value: WT


title: Untreated control 50 min post-treatment; BR 3


title: PFA 33980 | 011 | Full ROI - WTA

description: FFPE Spatial Transcriptome sequencing


title: PFA 33980 | 009 | Full ROI - WTA

description: FFPE Spatial Transcriptome sequencing


title: PFA 33980 | 010 | Full ROI - WTA

description: FFPE Spatial Transcriptome sequencing


title: PFA 33980 | 007 | Full ROI - WTA

description: FFPE Spatial Transcriptome sequencing


title: PFA 33980 | 008 | Full ROI - WTA

description: FFPE Spatial Transcriptome sequencing


title: PFA 33980 | 006 | Full ROI - WTA

description: FFPE Spatial Transcriptome sequencing


title: WT, 6 min, biol rep 3 (Sample 75)


title: PXGL_shOGA_1

value: H9 hESC

value: Human embryonic stem cell

value: OGA knockdown


title: Untreated control 25 min post-treatment; BR 3


title: ΔproQ, 3 min, biol rep 3 (Sample 79)

value: {delta}proQ

value: 3 min after rif. treatment


title: WT, 3 min, biol rep 3 (Sample 74)


title: HKI-2-Pol2s2-ChIP-seq

data_processing:
Clean reeas of RNA-seq were mapped to hg38 using STAR.RNA-seq datasets were performed using the TOPMed RNA-seq pipeline . Differentially expressed genes were identified using DESeq2 according to default parameters .Genes with an absolute log2 fold change > 1 and an adjusted P-value < 0.05 were considered as differentially expressed ones
Clean reads of ChIRP-seq were mapped to hg38 using STAR. Normalized bigwigs of even, odd, and merged files were generated using the ChIRP-seq processing scripts . Peaks of merged bigwig were called using MACS2, and called peaks were filtered to exclude blacklist regions from ENCODE. Peaks with correlation of even and odd > 0.8, FDR < 0.05, and read coverage > 2-fold of the input were kept as confident HOTAIR target regions.
Clean reads of ChIP-seq and Cut and tag were mapped to hg38 using STAR.Biological replicates that showed a good correlation (Pearson correlation coefficient > 0.8) were merged for downstream analysis, including peak calling and plots.  Peaks for histone modifications were called using MACS2 , peaks for transcription factors were called using SPP.Genomic annotation for called peaks was performed using Homer  with default parameters. Normalized coverage track (bigWig) files were generated using bamCoverage from deepTools.
Assembly: hg38
Supplementary files format and content: xlsx file  include genes counts values and bw files include ChIP, ChIRP, Cut and tag signal peaks for each Sample


title: PFA 33980 | 005 | Full ROI - WTA

description: FFPE Spatial Transcriptome sequencing


title: WT, 0 min, biol rep 3 (Sample 73)

value: 0 min after rif. treatment


title: HKI-1-Pol2s2-ChIP-seq


title: Untreated control 1 min post-treatment; BR 3


title: HKI-1-AR-1-Cut and tag


title: proQ++, 24 min, biol rep 2 (Sample 72)

value: proQ++

value: 24 min after rif. treatment


title: Untreated control 10 min post-treatment; BR 3


title: PFA 33980 | 004 | Full ROI - WTA

description: FFPE Spatial Transcriptome sequencing


title: Untreated control 1 min pre-treatment; BR 3


title: HKI-2-Pol2s5-ChIP-seq


title: Ciprofloxacin (12 ng/mL) 120 min post-treatment; BR 2


title: 22Rv1-WT-Pol2s2-ChIP-seq


title: 22Rv1-WT-AR-1-Cut and tag


title: PFA 33980 | 001 | Full ROI - WTA

description: FFPE Spatial Transcriptome sequencing


title: HKI-1-Pol2s5-ChIP-seq


title: proQ++, 3 min, biol rep 2 (Sample 69)


title: PFA 33980 | 002 | Full ROI - WTA

description: FFPE Spatial Transcriptome sequencing


title: Ciprofloxacin (12 ng/mL) 50 min post-treatment; BR 2


title: 22Rv1-WT-Pol2s5-ChIP-seq


title: HKI-2-BRD4-ChIP-seq


title: Ciprofloxacin (12 ng/mL) 25 min post-treatment; BR 2


title: proQ++, 0 min, biol rep 2 (Sample 68)


title: PFA 35595 | 012 | Full ROI - WTA

description: FFPE Spatial Transcriptome sequencing

value: Chronic SIV CL757 infection


title: PFA 35595 | 011 | Full ROI - WTA

description: FFPE Spatial Transcriptome sequencing


title: ΔproQ, 24 min, biol rep 2 (Sample 67)


title: HKI-1-BRD4-ChIP-seq


title: Ciprofloxacin (12 ng/mL) 10 min post-treatment; BR 2

value: Ciprofloxacin 12 ng/mL


title: PFA 35595 | 010 | Full ROI - WTA

description: FFPE Spatial Transcriptome sequencing


title: ΔproQ, 12 min, biol rep 2 (Sample 66)

value: 12 min after rif. treatment


title: PFA 33980 | 003 | Full ROI - WTA

description: FFPE Spatial Transcriptome sequencing


title: 22Rv1-WT-BRD4-ChIP-seq


title: proQ++, 12 min, biol rep 2 (Sample 71)


title: Ciprofloxacin (12 ng/mL) 1 min post-treatment; BR 2


title: ΔproQ, 6 min, biol rep 2 (Sample 65)

value: 6 min after rif. treatment


title: HKI-2-H3K4me1-ChIP-seq

value: HOTAIR Poly-A knock in


title: proQ++, 6 min, biol rep 2 (Sample 70)


title: PFA 35595 | 008 | Full ROI - WTA

description: FFPE Spatial Transcriptome sequencing

value: Brain - Hippocampus


title: Ciprofloxacin (12 ng/mL) 75 min post-treatment; BR 2


title: Untreated control 120 min post-treatment; BR 2

value: Untreated control


title: HKI-1-H3K4me1-ChIP-seq


title: Untreated control 75 min post-treatment; BR 2


title: PFA 35595 | 007 | Full ROI - WTA

description: FFPE Spatial Transcriptome sequencing

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA


title: ΔproQ, 3 min, biol rep 2 (Sample 64)


title: WT, 24 min, biol rep 2 (Sample 62)

value: WT


title: ΔproQ, 0 min, biol rep 2 (Sample 63)


title: PFA 35595 | 006 | Full ROI - WTA

description: FFPE Spatial Transcriptome sequencing


title: HKI-2-H3K27me3-ChIP-seq


title: Untreated control 25 min post-treatment; BR 2


title: HKI-1-H3K27me3-ChIP-seq


title: Untreated control 50 min post-treatment; BR 2


title: PFA 35595 | 005 | Full ROI - WTA

description: FFPE Spatial Transcriptome sequencing


title: PFA 35595 | 004 | Full ROI - WTA

description: FFPE Spatial Transcriptome sequencing


title: WT, 6 min, biol rep 2 (Sample 60)


title: 22Rv1-WT-H3K27me3-ChIP-seq


title: Untreated control 10 min post-treatment; BR 2


title: Ciprofloxacin (12 ng/mL) 1 min pre-treatment; BR 2


title: PFA 35595 | 003 | Full ROI - WTA

description: FFPE Spatial Transcriptome sequencing


title: PFA 35595 | 009 | Full ROI - WTA

description: FFPE Spatial Transcriptome sequencing


title: Untreated control 1 min post-treatment; BR 2


title: WT, 0 min, biol rep 2 (Sample 58)


title: HKI-2-H3K27ac-ChIP-seq


title: WT, 3 min, biol rep 2 (Sample 59)


title: 22Rv1-WT-H3K4me1-ChIP-seq


title: HKI-1-H3K27ac-ChIP-seq


title: PFA 35595 | 001 | Full ROI - WTA

description: FFPE Spatial Transcriptome sequencing


title: proQ++, 24 min, biol rep 1 (Sample 57)


title: 22Rv1-WT-H3k27ac-ChIP-seq


title: Untreated control 75 min post-treatment; BR 1


title: PFA 33980 | 012 | Full ROI

description: FFPE Spatial Transcriptome sequencing

value: N/A - healthy

value: (v1.0) Human NGS Glial Cell Subtyping Protein, (v1.0) Human NGS Autophagy Protein, (v1.0) Human NGS Parkinson's Pathology Protein, (v1.0) Human NGS Alzheimer's Pathology Extended Protein, (v1.0) Human NGS Alzheimer's Pathology Protein, (v1.0) Human NGS Cell Death Protein, (v1.0) Human NGS Neural Cell Typing Protein, (v1.0) Human NGS Immune Cell Profiling Protein Core, (v1.0) Human NGS Pan-Tumor Protein Module, (v1.0) Human NGS MAPK Signaling Protein, (v1.0) Human NGS Immune Cell Typing Protein Module, (v1.0) Human NGS Immune Activation Status Protein Module, (v1.1) Human NGS IO Drug Target Protein Module, (v1.1) Human NGS Myeloid Module, (v1.0) Human NGS PI3K/AKT Signaling Protein


title: PFA 33980 | 011 | Full ROI

description: FFPE Spatial Transcriptome sequencing

value: (v1.0) Human NGS Immune Cell Profiling Protein Core, (v1.0) Human NGS Glial Cell Subtyping Protein, (v1.0) Human NGS Autophagy Protein, (v1.0) Human NGS Parkinson's Pathology Protein, (v1.0) Human NGS Alzheimer's Pathology Extended Protein, (v1.0) Human NGS Alzheimer's Pathology Protein, (v1.0) Human NGS Cell Death Protein, (v1.0) Human NGS Neural Cell Typing Protein, (v1.0) Human NGS PI3K/AKT Signaling Protein, (v1.0) Human NGS Pan-Tumor Protein Module, (v1.0) Human NGS MAPK Signaling Protein, (v1.0) Human NGS Immune Cell Typing Protein Module, (v1.0) Human NGS Immune Activation Status Protein Module, (v1.1) Human NGS IO Drug Target Protein Module, (v1.1) Human NGS Myeloid Module


title: Untreated control 120 min post-treatment; BR 1


title: 22Rv1-WT-HOTAIR-even-ChIRP-seq

data_processing:
library strategy: ChIRP-seq
Clean reeas of RNA-seq were mapped to hg38 using STAR.RNA-seq datasets were performed using the TOPMed RNA-seq pipeline . Differentially expressed genes were identified using DESeq2 according to default parameters .Genes with an absolute log2 fold change > 1 and an adjusted P-value < 0.05 were considered as differentially expressed ones
Clean reads of ChIRP-seq were mapped to hg38 using STAR. Normalized bigwigs of even, odd, and merged files were generated using the ChIRP-seq processing scripts . Peaks of merged bigwig were called using MACS2, and called peaks were filtered to exclude blacklist regions from ENCODE. Peaks with correlation of even and odd > 0.8, FDR < 0.05, and read coverage > 2-fold of the input were kept as confident HOTAIR target regions.
Clean reads of ChIP-seq and Cut and tag were mapped to hg38 using STAR.Biological replicates that showed a good correlation (Pearson correlation coefficient > 0.8) were merged for downstream analysis, including peak calling and plots.  Peaks for histone modifications were called using MACS2 , peaks for transcription factors were called using SPP.Genomic annotation for called peaks was performed using Homer  with default parameters. Normalized coverage track (bigWig) files were generated using bamCoverage from deepTools.
Assembly: hg38
Supplementary files format and content: xlsx file  include genes counts values and bw files include ChIP, ChIRP, Cut and tag signal peaks for each Sample


title: WT, 12 min, biol rep 2 (Sample 61)


title: proQ++, 6 min, biol rep 1 (Sample 55)


title: PFA 33980 | 010 | Full ROI

description: FFPE Spatial Transcriptome sequencing


title: HKI-2-RNA-seq

description: 22Rv1 WT vs HKI RNA-seq


title: 22Rv1-WT-HOTAIR-odd-ChIRP-seq


title: proQ++, 3 min, biol rep 1 (Sample 54)


title: Untreated control 25 min post-treatment; BR 1


title: PFA 35595 | 002 | Full ROI - WTA

description: FFPE Spatial Transcriptome sequencing


title: Untreated control 10 min post-treatment; BR 1


title: proQ++, 0 min, biol rep 1 (Sample 53)


title: Untreated control 1 min pre-treatment; BR 2


title: PFA 33980 | 007 | Full ROI

description: FFPE Spatial Transcriptome sequencing


title: PFA 33980 | 008 | Full ROI

description: FFPE Spatial Transcriptome sequencing


title: HKI-1-RNA-seq

description: 22Rv1 WT vs HKI RNA-seq


title: ΔproQ, 6 min, biol rep 1 (Sample 50)

value: {delta}proQ


title: Untreated control 1 min post-treatment; BR 1


title: ΔproQ, 24 min, biol rep 1 (Sample 52)


title: ΔproQ, 12 min, biol rep 1 (Sample 51)


title: proQ++, 12 min, biol rep 1 (Sample 56)


title: PFA 33980 | 006 | Full ROI

description: FFPE Spatial Transcriptome sequencing


title: Untreated control 1 min pre-treatment; BR 1


title: Ciprofloxacin (12 ng/mL) 120 min post-treatment; BR 1


title: ΔproQ, 3 min, biol rep 1 (Sample 49)

value: 3 min after rif. treatment


title: Ciprofloxacin (12 ng/mL) 75 min post-treatment; BR 1


title: PFA 33980 | 005 | Full ROI

description: FFPE Spatial Transcriptome sequencing


title: WT, 24 min, biol rep 1 (Sample 47)


title: PFA 33980 | 004 | Full ROI

description: FFPE Spatial Transcriptome sequencing