title: SCRB_MM_D0_ctrl_3

source_name: Optmization SCBR-seq TCL

extract_protocol:
the single-cell transcriptomes are generated with a modified version of the SCRB-seq protocol using Qiagen TCL buffer supplemented with Î²-mercaptoethanol
[Purification of mouse and human PBMCs]  Mouse and human lymphocytes were isolated from a mouse spleen and human blood with the use of Lympholyte M (Cedarlane) and Ficoll-Paque PLUS (GE Healthcare) density gradient media respectively. Cells were washed with media and sorted on BD FACS Fusion (100-micron nozzle  standard operation settings  single-cell purity)  where individual cells meeting the gating strategy were sorted in a tube containing media and used immediately for generating Drop-seq single-cell transcriptomes.
[Purification of naive P14 T cells]  Single cell splenocyte suspensions were obtained by mashing total spleens through a 100 Î¼m nylon cell strainer (BD Falcon) and lysing red blood cells with a hypotonic ACK buffer. NaÃ¯ve transgenic P14 CD8 T-cells were isolated using the mouse CD8+ T-cell enrichment kit (Miltenyi Biotech  Bergisch-Gladbach  Germany). Surface staining was performed for 40 min at 4Â°C in supplemented DMEM media (Gibco  ThermoFisher Scientific) using the following antibodies: anti-CD8a (53-6.7  eBioscience)  CD4 (RM4-4  Biolegend)  and VÎ±2 (V20.1  eBioscience). Cells were washed twice with media and sorted on BD FACS Fusion (100-micron nozzle  standard operation settings  single-cell purity). Individual cells meeting the gating strategy were sorted in tube containing media (Drop-seq) and used immediately or directly in lysis buffer into individual wells of a low-binding PCR plate (SCRB-seq)  which was subsequently spun down  snap-frozen on dry ice and stored at -80oC until use. All data were analyzed using FlowJo (TreeStar).
[Purification of activated P14 T cells]  Single cell splenocyte suspensions were obtained by mashing total spleens through a 100 Î¼m nylon cell strainer (BD Falcon) and red blood cells were lysed with a hypotonic ACK buffer. NaÃ¯ve transgenic P14 CD8 T-cells were isolated using the mouse CD8+ T-cell enrichment kit (Miltenyi Biotech  Bergisch-Gladbach  Germany). 2x103 CD45.1+ P14 TCRÎ±Î² were transferred into naÃ¯ve CD45.2+ C57BL/6 mice  followed by their infection. On the day of the sort  single cell splenocyte suspensions were obtained as described above. Activated transgenic P14 CD8 T-cells were isolated using anti-CD45.1 biotin/anti-biotin conjugated microbeads and magnetic MACS cell separation (Miltenyi Biotech  Bergisch-Gladbach  Germany). Surface staining was performed for 40 min at 4Â°C in supplemented DMEM media (Gibco  ThermoFisher Scientific) using the following antibodies: anti-CD8a (53-6.7  eBbioscience)  CD4 (RM4-4  Biolegend)  CD45.1 (A20  eBioscience) and CD45.2 (104  eBioscience). Cells were washed twice with media and sorted on BD FACS Fusion (100-micron nozzle  standard operation settings  single-cell purity). Individual cells meeting the gating strategy were sorted in tube containing media (Drop-seq) and used immediately or directly in lysis buffer into individual wells of a low-binding PCR plate (SCRB-seq)  which was subsequently spun down  snap-frozen on dry ice and stored at -80oC until use. All data were analyzed using FlowJo (TreeStar).
[Drop-seq library construction protocol]  The original Drop-seq protocol was performed as described by Macosko and colleagues16. All runs were performed at 3000 Âµl/hour cell and bead rates with the use of Drop-seq PDMS device (Nanoshift). The following reagents were used for the Drop-seq modification described in this article: Lithium dodecyl sulfate (L9781  Sigma-Aldrich)  Lithium chloride (62476  SigmalAldrich)  Igepal (I8896-50ML  Sigma-Aldrich)  NaCl (S3014  Sigma-Aldrich)  3âLNA(G)TSO (IDT)  Maxima H Minus RT (EP0753  ThermoFisher)  SuperScript IV RT (18090010  ThermoFisher)  SMARTScribe RT (639536  Takara Bio) and Ficoll PM 400 (GE17-0300-10  GE Healthcare). After RNA purification and reverse transcription  the generated single-cell cDNA was amplified for 18 cycles. The barcoded single-cell amplicons were purified with the use of (0.6x) Agencourt AMPure XP beads. 1 ng of the resulting amplified cDNA were used for library preparation with the Illumina Nextera XT DNA Library reagents (FC-131-1024  Illumina). After PCR amplification of the fragmented libraries  the samples were purified with (0.6x) Agencourt AMPure XP beads and eluted in 10 Âµl of molecular grade water. The quality of the resulting library was assessed with the use of Agilent High Sensitivity DNA Kit (5067-4626  Agilent). The library quantification was performed based on the Illumina recommendations (SY-930-1010  Illumina) with the use of KAPA SYBR FAST qPCR Master Mix (KK4600  Kapa Biosystems). The samples were sequenced on Illumina HiSeq 2500 system at the following conditions - rapid run  paired-end  20 bp read 1  45 bp read 2  single-indexed sequencing resulting in 0.5 million reads per single-cell.
[SCRB-seq library construction protocol]  The original SCRB-seq protocol was performed as described by Soumillon and colleagues17. To allow profiling of T cells  we introduced a step of RNA purification before reverse transcription with the use of RNAClean XP (A63987  Beckman Coulter). This was used for all modifications assessed in this paper. The following reagents were used for the SCRB-seq modification described in this article: Triton X-100 (T9284-100ML  Sigma-Aldrich)  Buffer TCL (1031576  Qiagen)  2-Mercaptoethanol (M3148-25ML  Sigma-Aldrich)  3âLNA(G)TSO (IDT) and Betaine solution (B0300-1VL  Sigma-Aldrich). After reverse transcription  the single-cell transcriptomes were amplified without pooling for 20 cycles. The barcoded single-cell amplicons were purified with the use of (0.6x) Agencourt AMPure XP beads and libraries were generated as for Drop-seq. The samples were sequenced on Illumina HiSeq 2500 system at the following conditions - rapid run  paired-end  16 bp read 1  49 bp read 2  single-indexed sequencing resulting in 0.5 million reads per single-cell.


title: A549 5k-RNA

status: Public on Dec 13 2020

type: SRA

city: San Francisco

first: Matthew

middle: Gregory

last: Jones

state: CA

country: USA

institute: UCSF

description: RNA library of M5k

library_source: transcriptomic

data_processing:
Library strategy: scRNA-seq
10x cellranger v2.0.1
Target Site analysis with Cassiopeia
Phylogenetic inference with Cassiopeia
Genome_build: "dummy" build, hg19, and GRCh38
Supplementary_files_format_and_content: Target-Site FASTQs were processed with 10X cell ranger v2.0.1. using a "dummy" transcriptome build. Cassiopeia preprocess pipeline was then applied to the resulting possorted_genome_bam to produce allele tables for each mouse, containing Target-Site information for each cell in the Target-Site library. Cassiopeia was then used to create character matrices and phylogenetic trees for each clonal population; trees are stored in newick format. RNA-seq FASTQs were processed with 10X cell ranger v2.0.1.; samples corresponding to M10K and M100k used the hg19 genome build, while M5k and M30k used the GRCh38 genome build. Sparse expression matrices of raw counts, gene names, and cell barcodes are provided as processed files resulting from the 10X processing.

molecule: total RNA

organism: Homo sapiens

source_name: A549 lung adenocarcinoma cell line

growth_protocol: A549 cells (human lung adenocarcinoma line, ATCC CCL-185) were maintained in Dulbecco’s modified eagle medium (DMEM, Gibco) supplemented with 10% FBS (VWR Life Science Seradigm), 2 mM glutamine, 100 units/mL penicillin, and 100 µg/mL streptomycin. Cells were transplanted in a matrigel plug into the left lung of immunodeficient mice and grown as xenografts for ~2 months.

extract_protocol:
Cells were washed with PBS with 0.04% w/v bovine serum albumin (BSA, New England Biolabs), filtered through 40 µm FlowMi filter tips filter tips (Bel-Art), and counted according to the 10x Genomics protocol. Approximately 14,000 cells per sample were loaded into the 10x Genomics Chromium Single Cell 3' Library and Gel Bead Kit v2 or v3 kit, and cDNA was reverse-transcribed, amplified, and purified according to the manufacturer's protocol. Resulting cDNA libraries were quantified by BioAnalyzer, yielidng the expected size distribution described in the manufacturer's protocol.
To prepare the Target Site amplicon sequencing library, resulting amplified cDNA libraries were further amplified with custom, Target Site-specific primers containing P5/P7 Illumina adapters and sample indices. PCR amplification was performed using Kapa HiFi HotStart ReadyMix according to the following program: melting at 95C for 3 minutes, then 14 cycles at 98C for 15 seconds and 70C for 20 seconds. Approximately 12 fmol of template cDNA were used per reaction; amplification was performed in quadruplicate to avoid PCR-induced library biases, such as jack-potting. PCR products were re-pooled and purified by SPRI bead selection at 0.9x ratio and quantified by BioAnalyzer.

treatment_protocol: To construct the lineage tracing-competent cell line, A549 cells were transduced by serial lentiviral infection with the three lineage tracing components: (1) Cas9, (2) Target Site, and (3) triple-sgRNAs. First, A549 cells were transduced by Cas9 (mCherry) lentivirus and mCherry+ cells were selected to purity by fluorescenceactivated cell sorting on the BD FACS Aria II. Second, A549-Cas9 cells were transduced by concentrated Target Site (GFP) lentivirus and GFP+ cells were selected by FACS; after sorting, Target Site infection and sorting were repeated two more times for a total of three serial lentiviral transfections, sorting for cells with progressively higher GFP signal after each infection. This strategy of serial transfection with concentrated lentivirus yielded cells with high copy numbers of the Target Site, which were confirmed by quantitative PCR. Third, A549 cells with Cas9 and Target Site were transduced by titered triple-sgRNA (BFP-PuroR) lentivirus and selected

tag: cell line

tag: cell type

value: lung adenocarcinoma

tag: plate


title: A549 10k-TS

description: TargetSite library of M10k

source_name: A549 lu+C31ng adenocarcinoma cell line


title: SCRB_MM_D0_ctrl_1

city: Freising

first: Patrick

last: Roelli

address: Weihenstephaner Berg 3

department: Tierphysiologie & Immunologie

country: Germany

institute: TUM

data_processing:
dropSeqPipe 0.4. The pipeline includes filtering mapping and cell/UMI demultiplexing. Each protocols has it's own supplementary configuration file describing all the paramters used.
Filtering is done by cutadapt
Mapping is done by STAR
Demultiplexing is done by drop-seq tools v2
Supplementary_files_format_and_content: custom_adapter.fa - Adapters used in the protocols. Used to trim data in the pipeline
gtf_biotypes.yaml - List of biotypes used for mapping with STAR.
DS_config.yaml - Drop-seq configuration file with all the parameters used in the pipeline
SCRB_config.yaml - scrb-seq configuration file with all the parameters used in the pipeline
SCRB_barcodes csv - List of cell barcodes in the SCRB-seq protocols used in the pipeline
barcodes.tsv.gz - Cell barcodes with prefix
features.tsv.gz - Genes
matrix.mtx.gz - MTX matrix of UMI counts

organism: Mus musculus

source_name: Basic SCBR-seq naÃ¯ve P14s

extract_protocol:
the single-cell transcriptomes are generated with the baseline SCRB-seq
[Purification of mouse and human PBMCs]  Mouse and human lymphocytes were isolated from a mouse spleen and human blood with the use of Lympholyte M (Cedarlane) and Ficoll-Paque PLUS (GE Healthcare) density gradient media respectively. Cells were washed with media and sorted on BD FACS Fusion (100-micron nozzle  standard operation settings  single-cell purity)  where individual cells meeting the gating strategy were sorted in a tube containing media and used immediately for generating Drop-seq single-cell transcriptomes.
[Purification of naive P14 T cells]  Single cell splenocyte suspensions were obtained by mashing total spleens through a 100 Î¼m nylon cell strainer (BD Falcon) and lysing red blood cells with a hypotonic ACK buffer. NaÃ¯ve transgenic P14 CD8 T-cells were isolated using the mouse CD8+ T-cell enrichment kit (Miltenyi Biotech  Bergisch-Gladbach  Germany). Surface staining was performed for 40 min at 4Â°C in supplemented DMEM media (Gibco  ThermoFisher Scientific) using the following antibodies: anti-CD8a (53-6.7  eBioscience)  CD4 (RM4-4  Biolegend)  and VÎ±2 (V20.1  eBioscience). Cells were washed twice with media and sorted on BD FACS Fusion (100-micron nozzle  standard operation settings  single-cell purity). Individual cells meeting the gating strategy were sorted in tube containing media (Drop-seq) and used immediately or directly in lysis buffer into individual wells of a low-binding PCR plate (SCRB-seq)  which was subsequently spun down  snap-frozen on dry ice and stored at -80oC until use. All data were analyzed using FlowJo (TreeStar).
[Purification of activated P14 T cells]  Single cell splenocyte suspensions were obtained by mashing total spleens through a 100 Î¼m nylon cell strainer (BD Falcon) and red blood cells were lysed with a hypotonic ACK buffer. NaÃ¯ve transgenic P14 CD8 T-cells were isolated using the mouse CD8+ T-cell enrichment kit (Miltenyi Biotech  Bergisch-Gladbach  Germany). 2x103 CD45.1+ P14 TCRÎ±Î² were transferred into naÃ¯ve CD45.2+ C57BL/6 mice  followed by their infection. On the day of the sort  single cell splenocyte suspensions were obtained as described above. Activated transgenic P14 CD8 T-cells were isolated using anti-CD45.1 biotin/anti-biotin conjugated microbeads and magnetic MACS cell separation (Miltenyi Biotech  Bergisch-Gladbach  Germany). Surface staining was performed for 40 min at 4Â°C in supplemented DMEM media (Gibco  ThermoFisher Scientific) using the following antibodies: anti-CD8a (53-6.7  eBbioscience)  CD4 (RM4-4  Biolegend)  CD45.1 (A20  eBioscience) and CD45.2 (104  eBioscience). Cells were washed twice with media and sorted on BD FACS Fusion (100-micron nozzle  standard operation settings  single-cell purity). Individual cells meeting the gating strategy were sorted in tube containing media (Drop-seq) and used immediately or directly in lysis buffer into individual wells of a low-binding PCR plate (SCRB-seq)  which was subsequently spun down  snap-frozen on dry ice and stored at -80oC until use. All data were analyzed using FlowJo (TreeStar).
[Drop-seq library construction protocol]  The original Drop-seq protocol was performed as described by Macosko and colleagues16. All runs were performed at 3000 Âµl/hour cell and bead rates with the use of Drop-seq PDMS device (Nanoshift). The following reagents were used for the Drop-seq modification described in this article: Lithium dodecyl sulfate (L9781  Sigma-Aldrich)  Lithium chloride (62476  SigmalAldrich)  Igepal (I8896-50ML  Sigma-Aldrich)  NaCl (S3014  Sigma-Aldrich)  3âLNA(G)TSO (IDT)  Maxima H Minus RT (EP0753  ThermoFisher)  SuperScript IV RT (18090010  ThermoFisher)  SMARTScribe RT (639536  Takara Bio) and Ficoll PM 400 (GE17-0300-10  GE Healthcare). After RNA purification and reverse transcription  the generated single-cell cDNA was amplified for 18 cycles. The barcoded single-cell amplicons were purified with the use of (0.6x) Agencourt AMPure XP beads. 1 ng of the resulting amplified cDNA were used for library preparation with the Illumina Nextera XT DNA Library reagents (FC-131-1024  Illumina). After PCR amplification of the fragmented libraries  the samples were purified with (0.6x) Agencourt AMPure XP beads and eluted in 10 Âµl of molecular grade water. The quality of the resulting library was assessed with the use of Agilent High Sensitivity DNA Kit (5067-4626  Agilent). The library quantification was performed based on the Illumina recommendations (SY-930-1010  Illumina) with the use of KAPA SYBR FAST qPCR Master Mix (KK4600  Kapa Biosystems). The samples were sequenced on Illumina HiSeq 2500 system at the following conditions - rapid run  paired-end  20 bp read 1  45 bp read 2  single-indexed sequencing resulting in 0.5 million reads per single-cell.
[SCRB-seq library construction protocol]  The original SCRB-seq protocol was performed as described by Soumillon and colleagues17. To allow profiling of T cells  we introduced a step of RNA purification before reverse transcription with the use of RNAClean XP (A63987  Beckman Coulter). This was used for all modifications assessed in this paper. The following reagents were used for the SCRB-seq modification described in this article: Triton X-100 (T9284-100ML  Sigma-Aldrich)  Buffer TCL (1031576  Qiagen)  2-Mercaptoethanol (M3148-25ML  Sigma-Aldrich)  3âLNA(G)TSO (IDT) and Betaine solution (B0300-1VL  Sigma-Aldrich). After reverse transcription  the single-cell transcriptomes were amplified without pooling for 20 cycles. The barcoded single-cell amplicons were purified with the use of (0.6x) Agencourt AMPure XP beads and libraries were generated as for Drop-seq. The samples were sequenced on Illumina HiSeq 2500 system at the following conditions - rapid run  paired-end  16 bp read 1  49 bp read 2  single-indexed sequencing resulting in 0.5 million reads per single-cell.

tag: tissue

value: spleen

value: gp33-specific T cell receptor transgenic P14 CD8 T cells

tag: time

tag: infection

value: non-infected

tag: sample group

value: naive P14 T cells

tag: replicate


title: FFPE tissue SK11

city: Nagoya

first: Motoki

last: Nakamura

state: Aichi

address: 1-Kawasumi, Mizuho-ku, Mizuho-cho

department: Department of Geriatric and Environmental Dermatology

country: Japan

institute: Nagoya City University Graduate School of Medical Sciences

description:
SK11
groupA_vs_groupB.deseq.res.csv
MCPyV_Negative_vs_Positive.deseq.res.csv
Metastasis_early_vs_advance.deseq.res.csv
Regression_control_vs_regression.deseq.res.csv
PDL1_low_vs_high.deseq.res.csv

data_processing:
Basecalls performed in the MiniSeq system (Illumina)
FASTQ files were up-loaded and analyzed on the cloud-based software application BaseSpace Sequence Hub (Illumina).
Genome_build: hg19
Supplementary_files_format_and_content: 1 csv file and 2 deseq files for each analyses

source_name: FFPE tissue

extract_protocol:
Total RNA was refined using AllPrep DNA/RNA FFPE Kit (Qiagen) according to the supplier’s instruction.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: lesion

value: primary

tag: tumor stage

tag: mcpyv

value: negative


title: FFPE tissue SK10

description:
SK10
groupA_vs_groupB.deseq.res.csv
MCPyV_Negative_vs_Positive.deseq.res.csv
Metastasis_early_vs_advance.deseq.res.csv
Regression_control_vs_regression.deseq.res.csv
PDL1_low_vs_high.deseq.res.csv

value: positive


title: SCRB_MM_D0_ctrl_2

source_name: Optmization SCBR-seq TCL + LNA

extract_protocol:
the single-cell transcriptomes are generated with a modified version of the SCRB-seq protocol using Qiagen TCL buffer supplemented with Î²-mercaptoethanol for cell lysis and a template switching oligo with locked nucleic acid
[Purification of mouse and human PBMCs]  Mouse and human lymphocytes were isolated from a mouse spleen and human blood with the use of Lympholyte M (Cedarlane) and Ficoll-Paque PLUS (GE Healthcare) density gradient media respectively. Cells were washed with media and sorted on BD FACS Fusion (100-micron nozzle  standard operation settings  single-cell purity)  where individual cells meeting the gating strategy were sorted in a tube containing media and used immediately for generating Drop-seq single-cell transcriptomes.
[Purification of naive P14 T cells]  Single cell splenocyte suspensions were obtained by mashing total spleens through a 100 Î¼m nylon cell strainer (BD Falcon) and lysing red blood cells with a hypotonic ACK buffer. NaÃ¯ve transgenic P14 CD8 T-cells were isolated using the mouse CD8+ T-cell enrichment kit (Miltenyi Biotech  Bergisch-Gladbach  Germany). Surface staining was performed for 40 min at 4Â°C in supplemented DMEM media (Gibco  ThermoFisher Scientific) using the following antibodies: anti-CD8a (53-6.7  eBioscience)  CD4 (RM4-4  Biolegend)  and VÎ±2 (V20.1  eBioscience). Cells were washed twice with media and sorted on BD FACS Fusion (100-micron nozzle  standard operation settings  single-cell purity). Individual cells meeting the gating strategy were sorted in tube containing media (Drop-seq) and used immediately or directly in lysis buffer into individual wells of a low-binding PCR plate (SCRB-seq)  which was subsequently spun down  snap-frozen on dry ice and stored at -80oC until use. All data were analyzed using FlowJo (TreeStar).
[Purification of activated P14 T cells]  Single cell splenocyte suspensions were obtained by mashing total spleens through a 100 Î¼m nylon cell strainer (BD Falcon) and red blood cells were lysed with a hypotonic ACK buffer. NaÃ¯ve transgenic P14 CD8 T-cells were isolated using the mouse CD8+ T-cell enrichment kit (Miltenyi Biotech  Bergisch-Gladbach  Germany). 2x103 CD45.1+ P14 TCRÎ±Î² were transferred into naÃ¯ve CD45.2+ C57BL/6 mice  followed by their infection. On the day of the sort  single cell splenocyte suspensions were obtained as described above. Activated transgenic P14 CD8 T-cells were isolated using anti-CD45.1 biotin/anti-biotin conjugated microbeads and magnetic MACS cell separation (Miltenyi Biotech  Bergisch-Gladbach  Germany). Surface staining was performed for 40 min at 4Â°C in supplemented DMEM media (Gibco  ThermoFisher Scientific) using the following antibodies: anti-CD8a (53-6.7  eBbioscience)  CD4 (RM4-4  Biolegend)  CD45.1 (A20  eBioscience) and CD45.2 (104  eBioscience). Cells were washed twice with media and sorted on BD FACS Fusion (100-micron nozzle  standard operation settings  single-cell purity). Individual cells meeting the gating strategy were sorted in tube containing media (Drop-seq) and used immediately or directly in lysis buffer into individual wells of a low-binding PCR plate (SCRB-seq)  which was subsequently spun down  snap-frozen on dry ice and stored at -80oC until use. All data were analyzed using FlowJo (TreeStar).
[Drop-seq library construction protocol]  The original Drop-seq protocol was performed as described by Macosko and colleagues16. All runs were performed at 3000 Âµl/hour cell and bead rates with the use of Drop-seq PDMS device (Nanoshift). The following reagents were used for the Drop-seq modification described in this article: Lithium dodecyl sulfate (L9781  Sigma-Aldrich)  Lithium chloride (62476  SigmalAldrich)  Igepal (I8896-50ML  Sigma-Aldrich)  NaCl (S3014  Sigma-Aldrich)  3âLNA(G)TSO (IDT)  Maxima H Minus RT (EP0753  ThermoFisher)  SuperScript IV RT (18090010  ThermoFisher)  SMARTScribe RT (639536  Takara Bio) and Ficoll PM 400 (GE17-0300-10  GE Healthcare). After RNA purification and reverse transcription  the generated single-cell cDNA was amplified for 18 cycles. The barcoded single-cell amplicons were purified with the use of (0.6x) Agencourt AMPure XP beads. 1 ng of the resulting amplified cDNA were used for library preparation with the Illumina Nextera XT DNA Library reagents (FC-131-1024  Illumina). After PCR amplification of the fragmented libraries  the samples were purified with (0.6x) Agencourt AMPure XP beads and eluted in 10 Âµl of molecular grade water. The quality of the resulting library was assessed with the use of Agilent High Sensitivity DNA Kit (5067-4626  Agilent). The library quantification was performed based on the Illumina recommendations (SY-930-1010  Illumina) with the use of KAPA SYBR FAST qPCR Master Mix (KK4600  Kapa Biosystems). The samples were sequenced on Illumina HiSeq 2500 system at the following conditions - rapid run  paired-end  20 bp read 1  45 bp read 2  single-indexed sequencing resulting in 0.5 million reads per single-cell.
[SCRB-seq library construction protocol]  The original SCRB-seq protocol was performed as described by Soumillon and colleagues17. To allow profiling of T cells  we introduced a step of RNA purification before reverse transcription with the use of RNAClean XP (A63987  Beckman Coulter). This was used for all modifications assessed in this paper. The following reagents were used for the SCRB-seq modification described in this article: Triton X-100 (T9284-100ML  Sigma-Aldrich)  Buffer TCL (1031576  Qiagen)  2-Mercaptoethanol (M3148-25ML  Sigma-Aldrich)  3âLNA(G)TSO (IDT) and Betaine solution (B0300-1VL  Sigma-Aldrich). After reverse transcription  the single-cell transcriptomes were amplified without pooling for 20 cycles. The barcoded single-cell amplicons were purified with the use of (0.6x) Agencourt AMPure XP beads and libraries were generated as for Drop-seq. The samples were sequenced on Illumina HiSeq 2500 system at the following conditions - rapid run  paired-end  16 bp read 1  49 bp read 2  single-indexed sequencing resulting in 0.5 million reads per single-cell.


title: FFPE tissue SK4

description:
SK4
groupA_vs_groupB.deseq.res.csv
MCPyV_Negative_vs_Positive.deseq.res.csv
Metastasis_early_vs_advance.deseq.res.csv
Regression_control_vs_regression.deseq.res.csv


title: tDS_MM_D0_arm_2

source_name: tDrop-seq P14s from day 8 acute infection 2

extract_protocol:
the single-cell transcriptomes are generated with a T-cell tailored version of the Drop-seq protocol using Igepal CA-630 for cell lysis  increase to 0.5Ð NaCl during hybridization and a template switching oligo with locked nucleic acid.
[Purification of mouse and human PBMCs]  Mouse and human lymphocytes were isolated from a mouse spleen and human blood with the use of Lympholyte M (Cedarlane) and Ficoll-Paque PLUS (GE Healthcare) density gradient media respectively. Cells were washed with media and sorted on BD FACS Fusion (100-micron nozzle  standard operation settings  single-cell purity)  where individual cells meeting the gating strategy were sorted in a tube containing media and used immediately for generating Drop-seq single-cell transcriptomes.
[Purification of naive P14 T cells]  Single cell splenocyte suspensions were obtained by mashing total spleens through a 100 Î¼m nylon cell strainer (BD Falcon) and lysing red blood cells with a hypotonic ACK buffer. NaÃ¯ve transgenic P14 CD8 T-cells were isolated using the mouse CD8+ T-cell enrichment kit (Miltenyi Biotech  Bergisch-Gladbach  Germany). Surface staining was performed for 40 min at 4Â°C in supplemented DMEM media (Gibco  ThermoFisher Scientific) using the following antibodies: anti-CD8a (53-6.7  eBioscience)  CD4 (RM4-4  Biolegend)  and VÎ±2 (V20.1  eBioscience). Cells were washed twice with media and sorted on BD FACS Fusion (100-micron nozzle  standard operation settings  single-cell purity). Individual cells meeting the gating strategy were sorted in tube containing media (Drop-seq) and used immediately or directly in lysis buffer into individual wells of a low-binding PCR plate (SCRB-seq)  which was subsequently spun down  snap-frozen on dry ice and stored at -80oC until use. All data were analyzed using FlowJo (TreeStar).
[Purification of activated P14 T cells]  Single cell splenocyte suspensions were obtained by mashing total spleens through a 100 Î¼m nylon cell strainer (BD Falcon) and red blood cells were lysed with a hypotonic ACK buffer. NaÃ¯ve transgenic P14 CD8 T-cells were isolated using the mouse CD8+ T-cell enrichment kit (Miltenyi Biotech  Bergisch-Gladbach  Germany). 2x103 CD45.1+ P14 TCRÎ±Î² were transferred into naÃ¯ve CD45.2+ C57BL/6 mice  followed by their infection. On the day of the sort  single cell splenocyte suspensions were obtained as described above. Activated transgenic P14 CD8 T-cells were isolated using anti-CD45.1 biotin/anti-biotin conjugated microbeads and magnetic MACS cell separation (Miltenyi Biotech  Bergisch-Gladbach  Germany). Surface staining was performed for 40 min at 4Â°C in supplemented DMEM media (Gibco  ThermoFisher Scientific) using the following antibodies: anti-CD8a (53-6.7  eBbioscience)  CD4 (RM4-4  Biolegend)  CD45.1 (A20  eBioscience) and CD45.2 (104  eBioscience). Cells were washed twice with media and sorted on BD FACS Fusion (100-micron nozzle  standard operation settings  single-cell purity). Individual cells meeting the gating strategy were sorted in tube containing media (Drop-seq) and used immediately or directly in lysis buffer into individual wells of a low-binding PCR plate (SCRB-seq)  which was subsequently spun down  snap-frozen on dry ice and stored at -80oC until use. All data were analyzed using FlowJo (TreeStar).
[Drop-seq library construction protocol]  The original Drop-seq protocol was performed as described by Macosko and colleagues16. All runs were performed at 3000 Âµl/hour cell and bead rates with the use of Drop-seq PDMS device (Nanoshift). The following reagents were used for the Drop-seq modification described in this article: Lithium dodecyl sulfate (L9781  Sigma-Aldrich)  Lithium chloride (62476  SigmalAldrich)  Igepal (I8896-50ML  Sigma-Aldrich)  NaCl (S3014  Sigma-Aldrich)  3âLNA(G)TSO (IDT)  Maxima H Minus RT (EP0753  ThermoFisher)  SuperScript IV RT (18090010  ThermoFisher)  SMARTScribe RT (639536  Takara Bio) and Ficoll PM 400 (GE17-0300-10  GE Healthcare). After RNA purification and reverse transcription  the generated single-cell cDNA was amplified for 18 cycles. The barcoded single-cell amplicons were purified with the use of (0.6x) Agencourt AMPure XP beads. 1 ng of the resulting amplified cDNA were used for library preparation with the Illumina Nextera XT DNA Library reagents (FC-131-1024  Illumina). After PCR amplification of the fragmented libraries  the samples were purified with (0.6x) Agencourt AMPure XP beads and eluted in 10 Âµl of molecular grade water. The quality of the resulting library was assessed with the use of Agilent High Sensitivity DNA Kit (5067-4626  Agilent). The library quantification was performed based on the Illumina recommendations (SY-930-1010  Illumina) with the use of KAPA SYBR FAST qPCR Master Mix (KK4600  Kapa Biosystems). The samples were sequenced on Illumina HiSeq 2500 system at the following conditions - rapid run  paired-end  20 bp read 1  45 bp read 2  single-indexed sequencing resulting in 0.5 million reads per single-cell.
[SCRB-seq library construction protocol]  The original SCRB-seq protocol was performed as described by Soumillon and colleagues17. To allow profiling of T cells  we introduced a step of RNA purification before reverse transcription with the use of RNAClean XP (A63987  Beckman Coulter). This was used for all modifications assessed in this paper. The following reagents were used for the SCRB-seq modification described in this article: Triton X-100 (T9284-100ML  Sigma-Aldrich)  Buffer TCL (1031576  Qiagen)  2-Mercaptoethanol (M3148-25ML  Sigma-Aldrich)  3âLNA(G)TSO (IDT) and Betaine solution (B0300-1VL  Sigma-Aldrich). After reverse transcription  the single-cell transcriptomes were amplified without pooling for 20 cycles. The barcoded single-cell amplicons were purified with the use of (0.6x) Agencourt AMPure XP beads and libraries were generated as for Drop-seq. The samples were sequenced on Illumina HiSeq 2500 system at the following conditions - rapid run  paired-end  16 bp read 1  49 bp read 2  single-indexed sequencing resulting in 0.5 million reads per single-cell.

value: acute LCMV Armstrong infection

value: activated P14 T cells


title: CMK_STAG2mutant_clone1_replicate1_Wnt3a4hr

city: Dunedin

first: Jisha

last: Antony

state: Otago

address: 58 Hanover Street

department: Pathology

country: New Zealand

institute: University of Otago

description:
CMK_STAG2mutant_clone1_replicate_1_Wnt3a4hr
CRISPR-Cas9 edited

data_processing:
Reads were adaptor and quality trimmed (Q20) using fastq-mcf.version v1.5.3.
Reads were aligned to the human genome GRCh37 (hg19) version using HISAT2 version 2.0.5 with gene annotation from Ensembl version 75.
Read counts were retrieved by exon and summarized by gene using featureCount version v1.5.3 and mapQ >10.
Genome_build: Human hg19
Supplementary_files_format_and_content: count

source_name: CMK cell line

growth_protocol: MCF10A and its cohesin-deficient derivatives were maintained in Dulbecco’s modified Eagle medium (DMEM) (Life Technologies) supplemented with 5% horse serum (Life Technologies), 20 ng/mL of epidermal growth factor (EGF) (Peprotech), 0.5 mg/mL of hydrocortisone, 100 ng/mL of cholera toxin and 10 μg/mL of insulin (Actrapid). CMK cells were maintained in RPMI 1640 media containing 10% fetal bovine serum.

extract_protocol:
Total RNA was extracted using the NucleoSpin RNA kit (MACHEREY-NAGEL)
MCF10A mRNA libraries were prepared using the NEBNext® Ultra™ RNA Library Prep Kit (Illumina®). CMK mRNA libraries were prepared using the TruSeq mRNA library kit (Illumina®)

treatment_protocol: For Wnt3a stimulation CMK cells were treated with 200 ng/ml of recombinant human Wnt3a protein ( 5036-WN; R&D systems)

tag: genotype

value: STAG2 R614*

tag: agent

value: CMK


title: CMK_STAG2mutant_clone1_replicate3_Wnt3a4hr

description:
CMK_STAG2mutant_clone1_replicate_3_Wnt3a4hr
CRISPR-Cas9 edited


title: tDS_MM_D0_arm_1

source_name: tDrop-seq P14s from day 8 acute infection 1


title: A549 30k-RNA

description: RNA library of M30k


title: FFPE tissue o6

description:
o6
groupA_vs_groupB.deseq.res.csv
MCPyV_Negative_vs_Positive.deseq.res.csv
Metastasis_early_vs_advance.deseq.res.csv
Regression_control_vs_regression.deseq.res.csv
PDL1_low_vs_high.deseq.res.csv


title: FFPE tissue o8

description:
o8
groupA_vs_groupB.deseq.res.csv
MCPyV_Negative_vs_Positive.deseq.res.csv
Metastasis_early_vs_advance.deseq.res.csv
Regression_control_vs_regression.deseq.res.csv
PDL1_low_vs_high.deseq.res.csv


title: FFPE tissue SK12

description:
SK12
regression after biopsy
groupA_vs_groupB.deseq.res.csv
MCPyV_Negative_vs_Positive.deseq.res.csv
Metastasis_early_vs_advance.deseq.res.csv
Regression_control_vs_regression.deseq.res.csv
PDL1_low_vs_high.deseq.res.csv


title: FFPE tissue o9

description:
o9
groupA_vs_groupB.deseq.res.csv
MCPyV_Negative_vs_Positive.deseq.res.csv
Metastasis_early_vs_advance.deseq.res.csv
Regression_control_vs_regression.deseq.res.csv
PDL1_low_vs_high.deseq.res.csv


title: FFPE tissue SK7

description:
SK7
groupA_vs_groupB.deseq.res.csv
MCPyV_Negative_vs_Positive.deseq.res.csv
Metastasis_early_vs_advance.deseq.res.csv
Regression_control_vs_regression.deseq.res.csv
PDL1_low_vs_high.deseq.res.csv


title: FFPE tissue o4

description:
o4
groupA_vs_groupB.deseq.res.csv
MCPyV_Negative_vs_Positive.deseq.res.csv
Metastasis_early_vs_advance.deseq.res.csv
Regression_control_vs_regression.deseq.res.csv
PDL1_low_vs_high.deseq.res.csv


title: FFPE tissue G10

description:
G10
groupA_vs_groupB.deseq.res.csv
MCPyV_Negative_vs_Positive.deseq.res.csv
Metastasis_early_vs_advance.deseq.res.csv
Regression_control_vs_regression.deseq.res.csv


title: DS_MM_D0_ctrl_4

source_name: Optimization Drop-seq Igepal CA-630

extract_protocol:
the single-cell transcriptomes are generated with a modified version of the Drop-seq protocol using Igepal CA-630 for cell lysis
[Purification of mouse and human PBMCs]  Mouse and human lymphocytes were isolated from a mouse spleen and human blood with the use of Lympholyte M (Cedarlane) and Ficoll-Paque PLUS (GE Healthcare) density gradient media respectively. Cells were washed with media and sorted on BD FACS Fusion (100-micron nozzle  standard operation settings  single-cell purity)  where individual cells meeting the gating strategy were sorted in a tube containing media and used immediately for generating Drop-seq single-cell transcriptomes.
[Purification of naive P14 T cells]  Single cell splenocyte suspensions were obtained by mashing total spleens through a 100 Î¼m nylon cell strainer (BD Falcon) and lysing red blood cells with a hypotonic ACK buffer. NaÃ¯ve transgenic P14 CD8 T-cells were isolated using the mouse CD8+ T-cell enrichment kit (Miltenyi Biotech  Bergisch-Gladbach  Germany). Surface staining was performed for 40 min at 4Â°C in supplemented DMEM media (Gibco  ThermoFisher Scientific) using the following antibodies: anti-CD8a (53-6.7  eBioscience)  CD4 (RM4-4  Biolegend)  and VÎ±2 (V20.1  eBioscience). Cells were washed twice with media and sorted on BD FACS Fusion (100-micron nozzle  standard operation settings  single-cell purity). Individual cells meeting the gating strategy were sorted in tube containing media (Drop-seq) and used immediately or directly in lysis buffer into individual wells of a low-binding PCR plate (SCRB-seq)  which was subsequently spun down  snap-frozen on dry ice and stored at -80oC until use. All data were analyzed using FlowJo (TreeStar).
[Purification of activated P14 T cells]  Single cell splenocyte suspensions were obtained by mashing total spleens through a 100 Î¼m nylon cell strainer (BD Falcon) and red blood cells were lysed with a hypotonic ACK buffer. NaÃ¯ve transgenic P14 CD8 T-cells were isolated using the mouse CD8+ T-cell enrichment kit (Miltenyi Biotech  Bergisch-Gladbach  Germany). 2x103 CD45.1+ P14 TCRÎ±Î² were transferred into naÃ¯ve CD45.2+ C57BL/6 mice  followed by their infection. On the day of the sort  single cell splenocyte suspensions were obtained as described above. Activated transgenic P14 CD8 T-cells were isolated using anti-CD45.1 biotin/anti-biotin conjugated microbeads and magnetic MACS cell separation (Miltenyi Biotech  Bergisch-Gladbach  Germany). Surface staining was performed for 40 min at 4Â°C in supplemented DMEM media (Gibco  ThermoFisher Scientific) using the following antibodies: anti-CD8a (53-6.7  eBbioscience)  CD4 (RM4-4  Biolegend)  CD45.1 (A20  eBioscience) and CD45.2 (104  eBioscience). Cells were washed twice with media and sorted on BD FACS Fusion (100-micron nozzle  standard operation settings  single-cell purity). Individual cells meeting the gating strategy were sorted in tube containing media (Drop-seq) and used immediately or directly in lysis buffer into individual wells of a low-binding PCR plate (SCRB-seq)  which was subsequently spun down  snap-frozen on dry ice and stored at -80oC until use. All data were analyzed using FlowJo (TreeStar).
[Drop-seq library construction protocol]  The original Drop-seq protocol was performed as described by Macosko and colleagues16. All runs were performed at 3000 Âµl/hour cell and bead rates with the use of Drop-seq PDMS device (Nanoshift). The following reagents were used for the Drop-seq modification described in this article: Lithium dodecyl sulfate (L9781  Sigma-Aldrich)  Lithium chloride (62476  SigmalAldrich)  Igepal (I8896-50ML  Sigma-Aldrich)  NaCl (S3014  Sigma-Aldrich)  3âLNA(G)TSO (IDT)  Maxima H Minus RT (EP0753  ThermoFisher)  SuperScript IV RT (18090010  ThermoFisher)  SMARTScribe RT (639536  Takara Bio) and Ficoll PM 400 (GE17-0300-10  GE Healthcare). After RNA purification and reverse transcription  the generated single-cell cDNA was amplified for 18 cycles. The barcoded single-cell amplicons were purified with the use of (0.6x) Agencourt AMPure XP beads. 1 ng of the resulting amplified cDNA were used for library preparation with the Illumina Nextera XT DNA Library reagents (FC-131-1024  Illumina). After PCR amplification of the fragmented libraries  the samples were purified with (0.6x) Agencourt AMPure XP beads and eluted in 10 Âµl of molecular grade water. The quality of the resulting library was assessed with the use of Agilent High Sensitivity DNA Kit (5067-4626  Agilent). The library quantification was performed based on the Illumina recommendations (SY-930-1010  Illumina) with the use of KAPA SYBR FAST qPCR Master Mix (KK4600  Kapa Biosystems). The samples were sequenced on Illumina HiSeq 2500 system at the following conditions - rapid run  paired-end  20 bp read 1  45 bp read 2  single-indexed sequencing resulting in 0.5 million reads per single-cell.
[SCRB-seq library construction protocol]  The original SCRB-seq protocol was performed as described by Soumillon and colleagues17. To allow profiling of T cells  we introduced a step of RNA purification before reverse transcription with the use of RNAClean XP (A63987  Beckman Coulter). This was used for all modifications assessed in this paper. The following reagents were used for the SCRB-seq modification described in this article: Triton X-100 (T9284-100ML  Sigma-Aldrich)  Buffer TCL (1031576  Qiagen)  2-Mercaptoethanol (M3148-25ML  Sigma-Aldrich)  3âLNA(G)TSO (IDT) and Betaine solution (B0300-1VL  Sigma-Aldrich). After reverse transcription  the single-cell transcriptomes were amplified without pooling for 20 cycles. The barcoded single-cell amplicons were purified with the use of (0.6x) Agencourt AMPure XP beads and libraries were generated as for Drop-seq. The samples were sequenced on Illumina HiSeq 2500 system at the following conditions - rapid run  paired-end  16 bp read 1  49 bp read 2  single-indexed sequencing resulting in 0.5 million reads per single-cell.


title: FFPE tissue SK6

description:
SK6
groupA_vs_groupB.deseq.res.csv
MCPyV_Negative_vs_Positive.deseq.res.csv
Metastasis_early_vs_advance.deseq.res.csv
Regression_control_vs_regression.deseq.res.csv


title: DS_MM_D0_ctrl_3

source_name: Optimization Drop-seq increased NaCl

extract_protocol:
the single-cell transcriptomes are generated with a modified version of the Drop-seq protocol using increase to 0.5Ð NaCl during hybridization
[Purification of mouse and human PBMCs]  Mouse and human lymphocytes were isolated from a mouse spleen and human blood with the use of Lympholyte M (Cedarlane) and Ficoll-Paque PLUS (GE Healthcare) density gradient media respectively. Cells were washed with media and sorted on BD FACS Fusion (100-micron nozzle  standard operation settings  single-cell purity)  where individual cells meeting the gating strategy were sorted in a tube containing media and used immediately for generating Drop-seq single-cell transcriptomes.
[Purification of naive P14 T cells]  Single cell splenocyte suspensions were obtained by mashing total spleens through a 100 Î¼m nylon cell strainer (BD Falcon) and lysing red blood cells with a hypotonic ACK buffer. NaÃ¯ve transgenic P14 CD8 T-cells were isolated using the mouse CD8+ T-cell enrichment kit (Miltenyi Biotech  Bergisch-Gladbach  Germany). Surface staining was performed for 40 min at 4Â°C in supplemented DMEM media (Gibco  ThermoFisher Scientific) using the following antibodies: anti-CD8a (53-6.7  eBioscience)  CD4 (RM4-4  Biolegend)  and VÎ±2 (V20.1  eBioscience). Cells were washed twice with media and sorted on BD FACS Fusion (100-micron nozzle  standard operation settings  single-cell purity). Individual cells meeting the gating strategy were sorted in tube containing media (Drop-seq) and used immediately or directly in lysis buffer into individual wells of a low-binding PCR plate (SCRB-seq)  which was subsequently spun down  snap-frozen on dry ice and stored at -80oC until use. All data were analyzed using FlowJo (TreeStar).
[Purification of activated P14 T cells]  Single cell splenocyte suspensions were obtained by mashing total spleens through a 100 Î¼m nylon cell strainer (BD Falcon) and red blood cells were lysed with a hypotonic ACK buffer. NaÃ¯ve transgenic P14 CD8 T-cells were isolated using the mouse CD8+ T-cell enrichment kit (Miltenyi Biotech  Bergisch-Gladbach  Germany). 2x103 CD45.1+ P14 TCRÎ±Î² were transferred into naÃ¯ve CD45.2+ C57BL/6 mice  followed by their infection. On the day of the sort  single cell splenocyte suspensions were obtained as described above. Activated transgenic P14 CD8 T-cells were isolated using anti-CD45.1 biotin/anti-biotin conjugated microbeads and magnetic MACS cell separation (Miltenyi Biotech  Bergisch-Gladbach  Germany). Surface staining was performed for 40 min at 4Â°C in supplemented DMEM media (Gibco  ThermoFisher Scientific) using the following antibodies: anti-CD8a (53-6.7  eBbioscience)  CD4 (RM4-4  Biolegend)  CD45.1 (A20  eBioscience) and CD45.2 (104  eBioscience). Cells were washed twice with media and sorted on BD FACS Fusion (100-micron nozzle  standard operation settings  single-cell purity). Individual cells meeting the gating strategy were sorted in tube containing media (Drop-seq) and used immediately or directly in lysis buffer into individual wells of a low-binding PCR plate (SCRB-seq)  which was subsequently spun down  snap-frozen on dry ice and stored at -80oC until use. All data were analyzed using FlowJo (TreeStar).
[Drop-seq library construction protocol]  The original Drop-seq protocol was performed as described by Macosko and colleagues16. All runs were performed at 3000 Âµl/hour cell and bead rates with the use of Drop-seq PDMS device (Nanoshift). The following reagents were used for the Drop-seq modification described in this article: Lithium dodecyl sulfate (L9781  Sigma-Aldrich)  Lithium chloride (62476  SigmalAldrich)  Igepal (I8896-50ML  Sigma-Aldrich)  NaCl (S3014  Sigma-Aldrich)  3âLNA(G)TSO (IDT)  Maxima H Minus RT (EP0753  ThermoFisher)  SuperScript IV RT (18090010  ThermoFisher)  SMARTScribe RT (639536  Takara Bio) and Ficoll PM 400 (GE17-0300-10  GE Healthcare). After RNA purification and reverse transcription  the generated single-cell cDNA was amplified for 18 cycles. The barcoded single-cell amplicons were purified with the use of (0.6x) Agencourt AMPure XP beads. 1 ng of the resulting amplified cDNA were used for library preparation with the Illumina Nextera XT DNA Library reagents (FC-131-1024  Illumina). After PCR amplification of the fragmented libraries  the samples were purified with (0.6x) Agencourt AMPure XP beads and eluted in 10 Âµl of molecular grade water. The quality of the resulting library was assessed with the use of Agilent High Sensitivity DNA Kit (5067-4626  Agilent). The library quantification was performed based on the Illumina recommendations (SY-930-1010  Illumina) with the use of KAPA SYBR FAST qPCR Master Mix (KK4600  Kapa Biosystems). The samples were sequenced on Illumina HiSeq 2500 system at the following conditions - rapid run  paired-end  20 bp read 1  45 bp read 2  single-indexed sequencing resulting in 0.5 million reads per single-cell.
[SCRB-seq library construction protocol]  The original SCRB-seq protocol was performed as described by Soumillon and colleagues17. To allow profiling of T cells  we introduced a step of RNA purification before reverse transcription with the use of RNAClean XP (A63987  Beckman Coulter). This was used for all modifications assessed in this paper. The following reagents were used for the SCRB-seq modification described in this article: Triton X-100 (T9284-100ML  Sigma-Aldrich)  Buffer TCL (1031576  Qiagen)  2-Mercaptoethanol (M3148-25ML  Sigma-Aldrich)  3âLNA(G)TSO (IDT) and Betaine solution (B0300-1VL  Sigma-Aldrich). After reverse transcription  the single-cell transcriptomes were amplified without pooling for 20 cycles. The barcoded single-cell amplicons were purified with the use of (0.6x) Agencourt AMPure XP beads and libraries were generated as for Drop-seq. The samples were sequenced on Illumina HiSeq 2500 system at the following conditions - rapid run  paired-end  16 bp read 1  49 bp read 2  single-indexed sequencing resulting in 0.5 million reads per single-cell.


title: FFPE tissue G9

description:
G9
groupA_vs_groupB.deseq.res.csv
MCPyV_Negative_vs_Positive.deseq.res.csv
Metastasis_early_vs_advance.deseq.res.csv
Regression_control_vs_regression.deseq.res.csv
PDL1_low_vs_high.deseq.res.csv


title: CMK_STAG2mutant_clone1_replicate2_con

description:
CMK_STAG2mutant_clone1_replicate_2_con
CRISPR-Cas9 edited


title: CMK_STAG2mutant_clone1_replicate1_con

description:
CMK_STAG2mutant_clone1_replicate_1_con
CRISPR-Cas9 edited


title: CMK_WT_replicate3_Wnt3a4hr

description:
CMK_WT_replicate3_Wnt3a4hr
original CMK

value: parental


title: FFPE tissue SMU4

description:
SMU4
groupA_vs_groupB.deseq.res.csv
MCPyV_Negative_vs_Positive.deseq.res.csv
Metastasis_early_vs_advance.deseq.res.csv
Regression_control_vs_regression.deseq.res.csv
PDL1_low_vs_high.deseq.res.csv


title: FFPE tissue yoko6

description:
yoko6
groupA_vs_groupB.deseq.res.csv
MCPyV_Negative_vs_Positive.deseq.res.csv
Metastasis_early_vs_advance.deseq.res.csv
PDL1_low_vs_high.deseq.res.csv

value: skin metastasis


title: DS_MM_D0_ctrl_2

source_name: Optimization Drop-seq LNA TSO

extract_protocol:
the single-cell transcriptomes are generated with a modified version of the Drop-seq protocol using a template switching oligo with locked nucleic acid
[Purification of mouse and human PBMCs]  Mouse and human lymphocytes were isolated from a mouse spleen and human blood with the use of Lympholyte M (Cedarlane) and Ficoll-Paque PLUS (GE Healthcare) density gradient media respectively. Cells were washed with media and sorted on BD FACS Fusion (100-micron nozzle  standard operation settings  single-cell purity)  where individual cells meeting the gating strategy were sorted in a tube containing media and used immediately for generating Drop-seq single-cell transcriptomes.
[Purification of naive P14 T cells]  Single cell splenocyte suspensions were obtained by mashing total spleens through a 100 Î¼m nylon cell strainer (BD Falcon) and lysing red blood cells with a hypotonic ACK buffer. NaÃ¯ve transgenic P14 CD8 T-cells were isolated using the mouse CD8+ T-cell enrichment kit (Miltenyi Biotech  Bergisch-Gladbach  Germany). Surface staining was performed for 40 min at 4Â°C in supplemented DMEM media (Gibco  ThermoFisher Scientific) using the following antibodies: anti-CD8a (53-6.7  eBioscience)  CD4 (RM4-4  Biolegend)  and VÎ±2 (V20.1  eBioscience). Cells were washed twice with media and sorted on BD FACS Fusion (100-micron nozzle  standard operation settings  single-cell purity). Individual cells meeting the gating strategy were sorted in tube containing media (Drop-seq) and used immediately or directly in lysis buffer into individual wells of a low-binding PCR plate (SCRB-seq)  which was subsequently spun down  snap-frozen on dry ice and stored at -80oC until use. All data were analyzed using FlowJo (TreeStar).
[Purification of activated P14 T cells]  Single cell splenocyte suspensions were obtained by mashing total spleens through a 100 Î¼m nylon cell strainer (BD Falcon) and red blood cells were lysed with a hypotonic ACK buffer. NaÃ¯ve transgenic P14 CD8 T-cells were isolated using the mouse CD8+ T-cell enrichment kit (Miltenyi Biotech  Bergisch-Gladbach  Germany). 2x103 CD45.1+ P14 TCRÎ±Î² were transferred into naÃ¯ve CD45.2+ C57BL/6 mice  followed by their infection. On the day of the sort  single cell splenocyte suspensions were obtained as described above. Activated transgenic P14 CD8 T-cells were isolated using anti-CD45.1 biotin/anti-biotin conjugated microbeads and magnetic MACS cell separation (Miltenyi Biotech  Bergisch-Gladbach  Germany). Surface staining was performed for 40 min at 4Â°C in supplemented DMEM media (Gibco  ThermoFisher Scientific) using the following antibodies: anti-CD8a (53-6.7  eBbioscience)  CD4 (RM4-4  Biolegend)  CD45.1 (A20  eBioscience) and CD45.2 (104  eBioscience). Cells were washed twice with media and sorted on BD FACS Fusion (100-micron nozzle  standard operation settings  single-cell purity). Individual cells meeting the gating strategy were sorted in tube containing media (Drop-seq) and used immediately or directly in lysis buffer into individual wells of a low-binding PCR plate (SCRB-seq)  which was subsequently spun down  snap-frozen on dry ice and stored at -80oC until use. All data were analyzed using FlowJo (TreeStar).
[Drop-seq library construction protocol]  The original Drop-seq protocol was performed as described by Macosko and colleagues16. All runs were performed at 3000 Âµl/hour cell and bead rates with the use of Drop-seq PDMS device (Nanoshift). The following reagents were used for the Drop-seq modification described in this article: Lithium dodecyl sulfate (L9781  Sigma-Aldrich)  Lithium chloride (62476  SigmalAldrich)  Igepal (I8896-50ML  Sigma-Aldrich)  NaCl (S3014  Sigma-Aldrich)  3âLNA(G)TSO (IDT)  Maxima H Minus RT (EP0753  ThermoFisher)  SuperScript IV RT (18090010  ThermoFisher)  SMARTScribe RT (639536  Takara Bio) and Ficoll PM 400 (GE17-0300-10  GE Healthcare). After RNA purification and reverse transcription  the generated single-cell cDNA was amplified for 18 cycles. The barcoded single-cell amplicons were purified with the use of (0.6x) Agencourt AMPure XP beads. 1 ng of the resulting amplified cDNA were used for library preparation with the Illumina Nextera XT DNA Library reagents (FC-131-1024  Illumina). After PCR amplification of the fragmented libraries  the samples were purified with (0.6x) Agencourt AMPure XP beads and eluted in 10 Âµl of molecular grade water. The quality of the resulting library was assessed with the use of Agilent High Sensitivity DNA Kit (5067-4626  Agilent). The library quantification was performed based on the Illumina recommendations (SY-930-1010  Illumina) with the use of KAPA SYBR FAST qPCR Master Mix (KK4600  Kapa Biosystems). The samples were sequenced on Illumina HiSeq 2500 system at the following conditions - rapid run  paired-end  20 bp read 1  45 bp read 2  single-indexed sequencing resulting in 0.5 million reads per single-cell.
[SCRB-seq library construction protocol]  The original SCRB-seq protocol was performed as described by Soumillon and colleagues17. To allow profiling of T cells  we introduced a step of RNA purification before reverse transcription with the use of RNAClean XP (A63987  Beckman Coulter). This was used for all modifications assessed in this paper. The following reagents were used for the SCRB-seq modification described in this article: Triton X-100 (T9284-100ML  Sigma-Aldrich)  Buffer TCL (1031576  Qiagen)  2-Mercaptoethanol (M3148-25ML  Sigma-Aldrich)  3âLNA(G)TSO (IDT) and Betaine solution (B0300-1VL  Sigma-Aldrich). After reverse transcription  the single-cell transcriptomes were amplified without pooling for 20 cycles. The barcoded single-cell amplicons were purified with the use of (0.6x) Agencourt AMPure XP beads and libraries were generated as for Drop-seq. The samples were sequenced on Illumina HiSeq 2500 system at the following conditions - rapid run  paired-end  16 bp read 1  49 bp read 2  single-indexed sequencing resulting in 0.5 million reads per single-cell.


title: FFPE tissue SMU3-2

description:
SMU3-2
groupA_vs_groupB.deseq.res.csv
PDL1_low_vs_high.deseq.res.csv


title: FFPE tissue SMU3-1

description:
SMU3-1
groupA_vs_groupB.deseq.res.csv
MCPyV_Negative_vs_Positive.deseq.res.csv
Metastasis_early_vs_advance.deseq.res.csv
Regression_control_vs_regression.deseq.res.csv
PDL1_low_vs_high.deseq.res.csv


title: FFPE tissue N5-1

description:
N5-1
groupA_vs_groupB.deseq.res.csv
MCPyV_Negative_vs_Positive.deseq.res.csv
Metastasis_early_vs_advance.deseq.res.csv
Regression_control_vs_regression.deseq.res.csv


title: CMK_STAG2mutant_clone1_replicate3_con

description:
CMK_STAG2mutant_clone1_replicate_3_con
CRISPR-Cas9 edited


title: FFPE tissue N4

description:
N4
groupA_vs_groupB.deseq.res.csv
MCPyV_Negative_vs_Positive.deseq.res.csv
Metastasis_early_vs_advance.deseq.res.csv
Regression_control_vs_regression.deseq.res.csv
PDL1_low_vs_high.deseq.res.csv


title: FFPE tissue N2

description:
N2
groupA_vs_groupB.deseq.res.csv
MCPyV_Negative_vs_Positive.deseq.res.csv
Metastasis_early_vs_advance.deseq.res.csv
Regression_control_vs_regression.deseq.res.csv
PDL1_low_vs_high.deseq.res.csv


title: FFPE tissue kin4

description:
kin4
groupA_vs_groupB.deseq.res.csv
MCPyV_Negative_vs_Positive.deseq.res.csv
Metastasis_early_vs_advance.deseq.res.csv
Regression_control_vs_regression.deseq.res.csv


title: CMK_WT_replicate2_con

description:
CMK_WT_replicate2_con
original CMK


title: DS_MM_D0_ctrl_1

source_name: Original Drop-seq naÃ¯ve P14s

extract_protocol:
the single-cell transcriptomes are generated with the baseline Drop-seq
[Purification of mouse and human PBMCs]  Mouse and human lymphocytes were isolated from a mouse spleen and human blood with the use of Lympholyte M (Cedarlane) and Ficoll-Paque PLUS (GE Healthcare) density gradient media respectively. Cells were washed with media and sorted on BD FACS Fusion (100-micron nozzle  standard operation settings  single-cell purity)  where individual cells meeting the gating strategy were sorted in a tube containing media and used immediately for generating Drop-seq single-cell transcriptomes.
[Purification of naive P14 T cells]  Single cell splenocyte suspensions were obtained by mashing total spleens through a 100 Î¼m nylon cell strainer (BD Falcon) and lysing red blood cells with a hypotonic ACK buffer. NaÃ¯ve transgenic P14 CD8 T-cells were isolated using the mouse CD8+ T-cell enrichment kit (Miltenyi Biotech  Bergisch-Gladbach  Germany). Surface staining was performed for 40 min at 4Â°C in supplemented DMEM media (Gibco  ThermoFisher Scientific) using the following antibodies: anti-CD8a (53-6.7  eBioscience)  CD4 (RM4-4  Biolegend)  and VÎ±2 (V20.1  eBioscience). Cells were washed twice with media and sorted on BD FACS Fusion (100-micron nozzle  standard operation settings  single-cell purity). Individual cells meeting the gating strategy were sorted in tube containing media (Drop-seq) and used immediately or directly in lysis buffer into individual wells of a low-binding PCR plate (SCRB-seq)  which was subsequently spun down  snap-frozen on dry ice and stored at -80oC until use. All data were analyzed using FlowJo (TreeStar).
[Purification of activated P14 T cells]  Single cell splenocyte suspensions were obtained by mashing total spleens through a 100 Î¼m nylon cell strainer (BD Falcon) and red blood cells were lysed with a hypotonic ACK buffer. NaÃ¯ve transgenic P14 CD8 T-cells were isolated using the mouse CD8+ T-cell enrichment kit (Miltenyi Biotech  Bergisch-Gladbach  Germany). 2x103 CD45.1+ P14 TCRÎ±Î² were transferred into naÃ¯ve CD45.2+ C57BL/6 mice  followed by their infection. On the day of the sort  single cell splenocyte suspensions were obtained as described above. Activated transgenic P14 CD8 T-cells were isolated using anti-CD45.1 biotin/anti-biotin conjugated microbeads and magnetic MACS cell separation (Miltenyi Biotech  Bergisch-Gladbach  Germany). Surface staining was performed for 40 min at 4Â°C in supplemented DMEM media (Gibco  ThermoFisher Scientific) using the following antibodies: anti-CD8a (53-6.7  eBbioscience)  CD4 (RM4-4  Biolegend)  CD45.1 (A20  eBioscience) and CD45.2 (104  eBioscience). Cells were washed twice with media and sorted on BD FACS Fusion (100-micron nozzle  standard operation settings  single-cell purity). Individual cells meeting the gating strategy were sorted in tube containing media (Drop-seq) and used immediately or directly in lysis buffer into individual wells of a low-binding PCR plate (SCRB-seq)  which was subsequently spun down  snap-frozen on dry ice and stored at -80oC until use. All data were analyzed using FlowJo (TreeStar).
[Drop-seq library construction protocol]  The original Drop-seq protocol was performed as described by Macosko and colleagues16. All runs were performed at 3000 Âµl/hour cell and bead rates with the use of Drop-seq PDMS device (Nanoshift). The following reagents were used for the Drop-seq modification described in this article: Lithium dodecyl sulfate (L9781  Sigma-Aldrich)  Lithium chloride (62476  SigmalAldrich)  Igepal (I8896-50ML  Sigma-Aldrich)  NaCl (S3014  Sigma-Aldrich)  3âLNA(G)TSO (IDT)  Maxima H Minus RT (EP0753  ThermoFisher)  SuperScript IV RT (18090010  ThermoFisher)  SMARTScribe RT (639536  Takara Bio) and Ficoll PM 400 (GE17-0300-10  GE Healthcare). After RNA purification and reverse transcription  the generated single-cell cDNA was amplified for 18 cycles. The barcoded single-cell amplicons were purified with the use of (0.6x) Agencourt AMPure XP beads. 1 ng of the resulting amplified cDNA were used for library preparation with the Illumina Nextera XT DNA Library reagents (FC-131-1024  Illumina). After PCR amplification of the fragmented libraries  the samples were purified with (0.6x) Agencourt AMPure XP beads and eluted in 10 Âµl of molecular grade water. The quality of the resulting library was assessed with the use of Agilent High Sensitivity DNA Kit (5067-4626  Agilent). The library quantification was performed based on the Illumina recommendations (SY-930-1010  Illumina) with the use of KAPA SYBR FAST qPCR Master Mix (KK4600  Kapa Biosystems). The samples were sequenced on Illumina HiSeq 2500 system at the following conditions - rapid run  paired-end  20 bp read 1  45 bp read 2  single-indexed sequencing resulting in 0.5 million reads per single-cell.
[SCRB-seq library construction protocol]  The original SCRB-seq protocol was performed as described by Soumillon and colleagues17. To allow profiling of T cells  we introduced a step of RNA purification before reverse transcription with the use of RNAClean XP (A63987  Beckman Coulter). This was used for all modifications assessed in this paper. The following reagents were used for the SCRB-seq modification described in this article: Triton X-100 (T9284-100ML  Sigma-Aldrich)  Buffer TCL (1031576  Qiagen)  2-Mercaptoethanol (M3148-25ML  Sigma-Aldrich)  3âLNA(G)TSO (IDT) and Betaine solution (B0300-1VL  Sigma-Aldrich). After reverse transcription  the single-cell transcriptomes were amplified without pooling for 20 cycles. The barcoded single-cell amplicons were purified with the use of (0.6x) Agencourt AMPure XP beads and libraries were generated as for Drop-seq. The samples were sequenced on Illumina HiSeq 2500 system at the following conditions - rapid run  paired-end  16 bp read 1  49 bp read 2  single-indexed sequencing resulting in 0.5 million reads per single-cell.

value: gp33-specific  T cell receptor transgenic P14 CD8 T cells


title: CMK_WT_replicate2_Wnt3a4hr

description:
CMK_WT_replicate2_Wnt3a4hr
original CMK


title: MCF10A_STAG2mutant_replicate1

description:
MCF10A_STAG2mutant_replicate1
CRISPR-Cas9 edited

source_name: MCF10A cell line

value: STAG2 mutant


title: FFPE tissue N3

description:
N3
groupA_vs_groupB.deseq.res.csv
MCPyV_Negative_vs_Positive.deseq.res.csv
Metastasis_early_vs_advance.deseq.res.csv
Regression_control_vs_regression.deseq.res.csv


title: MCF10A_STAG2mutant_replicate2

description:
MCF10A_STAG2mutant_replicate2
CRISPR-Cas9 edited


title: FFPE tissue kin3-2

description:
kin3-2
groupA_vs_groupB.deseq.res.csv
PDL1_low_vs_high.deseq.res.csv


title: CMK_WT_replicate3_con

description:
CMK_WT_replicate3_con
original CMK


title: CMK_WT_replicate1_Wnt3a4hr

description:
CMK_WT_replicate1_Wnt3a4hr
original CMK


title: FFPE tissue N1

description:
N1
groupA_vs_groupB.deseq.res.csv
MCPyV_Negative_vs_Positive.deseq.res.csv
Metastasis_early_vs_advance.deseq.res.csv
Regression_control_vs_regression.deseq.res.csv
PDL1_low_vs_high.deseq.res.csv


title: MCF10A_SMC3mutant_replicate3

description:
MCF10A_SMC3mutant_replicate3
CRISPR-Cas9 edited

value: SMC3 mutant


title: FFPE tissue gi1

description:
gi1
regression after biopsy
groupA_vs_groupB.deseq.res.csv
MCPyV_Negative_vs_Positive.deseq.res.csv
Metastasis_early_vs_advance.deseq.res.csv
Regression_control_vs_regression.deseq.res.csv


title: MCF10A_SMC3mutant_replicate2

description:
MCF10A_SMC3mutant_replicate2
CRISPR-Cas9 edited


title: CMK_WT_replicate1_con

description:
CMK_WT_replicate1_con
original CMK


title: MCF10A_STAG2mutant_replicate3

description:
MCF10A_STAG2mutant_replicate3
CRISPR-Cas9 edited


title: CMK_STAG2mutant_clone1_replicate2_Wnt3a4hr

description:
CMK_STAG2mutant_clone1_replicate_2_Wnt3a4hr
CRISPR-Cas9 edited


title: PECT1d16-1

city: Seoul

first: Zeeshan

last: Nasim

address: Anam-ro 145, Seongbuk-Gu

department: School of Life Sciences and Biotechnology

country: South Korea

institute: Korea University

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and differentially expressed genes were identified using CLC Genomics Workbench 11.0.1
Genome_build: TAIR 10
Supplementary_files_format_and_content: RPM values for each sample, in excel file

organism: Arabidopsis thaliana

source_name: Shoot apex

growth_protocol: Plant was growed at 23°C short day condition on 1/2 MS plate

extract_protocol:
Total RNA was extracted using trizol reagent
mRNA libraries were prepared using NEBnext ultra II Directional RNA-seq kit, according to the manufacturer's instruction.

tag: age

value: ZT 8

value: pFD::amiR-PECT1 knockdown


title: PECT1d16-2


title: FFPE tissue 17

description:
17
groupA_vs_groupB.deseq.res.csv
MCPyV_Negative_vs_Positive.deseq.res.csv
Metastasis_early_vs_advance.deseq.res.csv
Regression_control_vs_regression.deseq.res.csv


title: FFPE tissue SMU1-1

description:
SMU1-1
groupA_vs_groupB.deseq.res.csv
MCPyV_Negative_vs_Positive.deseq.res.csv
Metastasis_early_vs_advance.deseq.res.csv
Regression_control_vs_regression.deseq.res.csv
PDL1_low_vs_high.deseq.res.csv


title: FFPE tissue 18

description:
18
regression after biopsy
groupA_vs_groupB.deseq.res.csv
MCPyV_Negative_vs_Positive.deseq.res.csv
Metastasis_early_vs_advance.deseq.res.csv
Regression_control_vs_regression.deseq.res.csv
PDL1_low_vs_high.deseq.res.csv


title: MCF10A_RAD21mutant_replicate3

description:
MCF10A_RAD21mutant_replicate3
CRISPR-Cas9 edited

value: RAD21 mutant


title: MCF10A_SMC3mutant_replicate1

description:
MCF10A_SMC3mutant_replicate1
CRISPR-Cas9 edited


title: FFPE tissue 16

description:
16
groupA_vs_groupB.deseq.res.csv
PDL1_low_vs_high.deseq.res.csv


title: FFPE tissue 15

description:
15
groupA_vs_groupB.deseq.res.csv
MCPyV_Negative_vs_Positive.deseq.res.csv
Metastasis_early_vs_advance.deseq.res.csv
Regression_control_vs_regression.deseq.res.csv
PDL1_low_vs_high.deseq.res.csv


title: PECT1d10-2


title: FFPE tissue 14

description:
14
groupA_vs_groupB.deseq.res.csv
PDL1_low_vs_high.deseq.res.csv


title: MCF10A_RAD21mutant_replicate2

description:
MCF10A_RAD21mutant_replicate2
CRISPR-Cas9 edited


title: FFPE tissue 11

description:
11
groupA_vs_groupB.deseq.res.csv
PDL1_low_vs_high.deseq.res.csv


title: MCF10A_RAD21mutant_replicate1

description:
MCF10A_RAD21mutant_replicate1
CRISPR-Cas9 edited


title: PECT1d10-1


title: FFPE tissue 6

description:
6
groupA_vs_groupB.deseq.res.csv
PDL1_low_vs_high.deseq.res.csv


title: FFPE tissue 21

description:
21
groupA_vs_groupB.deseq.res.csv
MCPyV_Negative_vs_Positive.deseq.res.csv
Metastasis_early_vs_advance.deseq.res.csv
Regression_control_vs_regression.deseq.res.csv


title: FFPE tissue 8

description:
8
groupA_vs_groupB.deseq.res.csv
MCPyV_Negative_vs_Positive.deseq.res.csv
Metastasis_early_vs_advance.deseq.res.csv
Regression_control_vs_regression.deseq.res.csv
PDL1_low_vs_high.deseq.res.csv


title: MCF10A_WT_replicate3

description:
MCF10A_WT_replicate3
original MCF10A


title: FFPE tissue 20

description:
20
regression after biopsy
groupA_vs_groupB.deseq.res.csv
MCPyV_Negative_vs_Positive.deseq.res.csv
Metastasis_early_vs_advance.deseq.res.csv
Regression_control_vs_regression.deseq.res.csv


title: WTd16-2

value: wild type


title: WTd16-1


title: WTd10-2


title: MCF10A_WT_replicate1

description:
MCF10A_WT_replicate1
original MCF10A


title: FFPE tissue 2

description:
2
groupA_vs_groupB.deseq.res.csv
MCPyV_Negative_vs_Positive.deseq.res.csv
Metastasis_early_vs_advance.deseq.res.csv
Regression_control_vs_regression.deseq.res.csv
PDL1_low_vs_high.deseq.res.csv


title: MCF10A_WT_replicate2

description:
MCF10A_WT_replicate2
original MCF10A


title: FFPE tissue 1

description:
1
groupA_vs_groupB.deseq.res.csv
MCPyV_Negative_vs_Positive.deseq.res.csv
Metastasis_early_vs_advance.deseq.res.csv
Regression_control_vs_regression.deseq.res.csv


title: FFPE tissue 4

description:
4
groupA_vs_groupB.deseq.res.csv
PDL1_low_vs_high.deseq.res.csv


title: bmp7_CHX_rep2

status: Public on Dec 12 2020

city: Philadelphia

first: Hannah

last: Greenfeld

state: PA

address: 421 Curie Blvd

department: Cell and Developmental Biology

institute: University of Pennsylvania

data_processing:
Reads were aligned to the zebrafish genome (danRer11) and transcript expression quantified using RUM (version rum-2.0.5_06) (Grant et al Bioinformatics 2011 PMID: 21775302).
Differential expression call were performed using edgeR (Robinson et al) with an FDR cutoff of 10%.
Genome_build: zebrafish reference genome GRCz11
Supplementary_files_format_and_content: Matrix table with raw gene counts and normalized abundance measurements generated by edgeR for every gene and every sample …

organism: Danio rerio

source_name: whole embryo

extract_protocol:
Embryos were dechorionated and flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent.
Libraries were prepared from total RNA using the Illumina truSeq high-throughput stranded polyA kit.

treatment_protocol: Dechorionated embryos were treated with 10 ug/ml of cycloheximide (CHX) (Sigma #C4859) at 4 hours post fertilization (hpf) for 30 minutes and injected with 3 nl of hBMP2-hBMP7 heterodimer (120nM) (R&D Systems 2339-BM).

value: whole embryo

tag: developmental stage

value: 4 hpf

tag: treatment

value: CHX


title: bmp7_CHX_rep3


title: bmp7_CHX_BMPinj_rep1

value: CHX + BMP2/7


title: bmp7_CHX_BMPinj_rep2


title: bmp7_CHX_BMPinj_rep3


title: bmp7_6hpf_rep1

value: 6 hpf

value: untreated


title: bmp7_6hpf_rep2


title: bmp7_8hpf_rep2

value: 8 hpf


title: WT_8hpf_rep1

value: wild-type


title: WT_6hpf_rep2


title: WT_8hpf_rep2


title: NTT_2c rep1

city: Yangling

first: Lei

last: Zhang

state: Shaanxi

address: taicheng road

country: China

institute: NWAFU

data_processing:
Illumina CASAVA v1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Seqtk.
Mapped to UMD3.1 whole genome using the spliced mapping algorithm of Hisat2 (version:2.0.4)
FPKM values were derived through fragments counting by Stringtie (version:1.3.0), normalization by TMM (trimmed mean of M values) and calculation by perl.
Genome_build: UMD3.1
Supplementary_files_format_and_content: gene_expression_anno.xls including FPKM values and read count for each sample.

organism: Bos taurus

source_name: early embryo

growth_protocol: Preimplantation embryos were cultured in G1.5/G2.5 sequential media (Vitrolife AB, Gothenburg, Sweden) in a humidified atmosphere of 5% CO2

extract_protocol:
Embryos were fully washed in RNase free polyvinyl alcohol-phosphate-buffered saline (PVA- PBS). Ten embryos in each fertilized or cloned group were collected in lysis buffer containing Triton X-100 and RNase-out in water. The samples were then immediately preserved in an ultralow-temperature freezer.
Samples were first amplified according to instructions of SMARTer Ultra Low Input RNA for Illumina Kit. cDNA libraries were prepared for sequencing using standard Illumina protocols,including fragmentation, terminal repair, 3' end plus A, ligation linker, enrichment and other steps.

treatment_protocol: Before the reconstruction of cloned embryos, donor cells were treated with vitamin C (0.15 mM) for 3 days

value: early embryo

value: 2-cell embryo

tag: method

value: SCNT

tag: donor cell

value: Vc-treated donor cell


title: NTT_2c rep2


title: NTT_bl rep1

value: blastocyst


title: NTT_bl rep2


title: FFPE tissue 3

description:
3
groupA_vs_groupB.deseq.res.csv
MCPyV_Negative_vs_Positive.deseq.res.csv
Metastasis_early_vs_advance.deseq.res.csv
Regression_control_vs_regression.deseq.res.csv

value: primary

value: negative


title: NTC_bl rep2

value: normal donor cell


title: NTC_bl rep1


title: NTC_2c rep1


title: IVF_bl rep2

value: IVF

value: not applicable


title: bmp7_CHX_rep1

value: whole embryo

value: 4 hpf


title: IVF_bl rep1


title: IVF_2c rep2


title: IVF_2c rep1


title: MII rep1

source_name: oocyte

value: oocyte

value: maturated oocyte


title: FFPE tissue 12

description:
12
groupA_vs_groupB.deseq.res.csv
MCPyV_Negative_vs_Positive.deseq.res.csv
Metastasis_early_vs_advance.deseq.res.csv
Regression_control_vs_regression.deseq.res.csv
PDL1_low_vs_high.deseq.res.csv

value: positive


title: MII rep2


title: WT_6hpf_rep1

value: 6 hpf

value: untreated


title: 90_M1_BTS_1

city: Los Angeles

first: Robert

middle: D.

last: Cooper

address: 612 Charles E. Young Drive East

institute: UCLA

description: muscle.exon.csv

data_processing:
Raw sequences were trimmed for adapter sequence and low quality bases using Trimmomatic
Quality and repetitive regions were assessed across all samples using FASTQC
Reads were mapped to the recently published Mexican Axolotl (Ambystoma mexicanum) genome using STAR
Mapped reads were counted for differential expression analysis using HTSeq-count with exons as the target feature
Genome_build: Reads were mapped to the recently published Mexican Axolotl (Ambystoma mexicanum) genome (Nowoshilow et al., 2018)

molecule: polyA RNA

organism: Ambystoma californiense

source_name: Muscle Tissue (Leg)

extract_protocol:
Samples were extracted using a modified Purelink RNA Mini Kit- TRIzol spin column protocol
Libraries were prepared using Kapa mRNA Stranded Library Prep kits and standard protocols.
RNA-Seq: Libraries were pooled then split across six lanes of 100bp single-end reads on an Illumina HiSeq4000 at the QB3 Genomics Sequencing Laboratory in Berkeley, CA.

treatment_protocol: Individuals in the treatment group were exposed to acute thermal stress until they failed to right themselves for 30 seconds after being placed on their dorsum. (loss of righting response)

value: Muscle Tissue (Leg)

tag: Sex

value: Male

value: Treatment

value: BTS


title: 91_M1_F1_1

description: muscle.exon.csv

value: Female


title: bmp7_8hpf_rep1

value: 8 hpf


title: 87_M1_F1_1

description: muscle.exon.csv


title: 84_M1_F1_1

description: muscle.exon.csv

value: CTSbc


title: 86_M1_F1_1

description: muscle.exon.csv


title: 76_M1_BTS_1

description: muscle.exon.csv

value: CTS


title: 83_M1_CTS_0

description: muscle.exon.csv

value: Control


title: 75_M1_BTS_1

description: muscle.exon.csv


title: 78_M1_BTS_1

description: muscle.exon.csv


title: 74_M1_BTS_0

description: muscle.exon.csv


title: 80_M1_BTS_0

description: muscle.exon.csv


title: FFPE tissue 10

description:
10
groupA_vs_groupB.deseq.res.csv
MCPyV_Negative_vs_Positive.deseq.res.csv
Metastasis_early_vs_advance.deseq.res.csv
Regression_control_vs_regression.deseq.res.csv

value: primary


title: 73_M1_F1_0

description: muscle.exon.csv


title: 72_M1_F1_0

description: muscle.exon.csv


title: 71_M1_BTS_0

description: muscle.exon.csv


title: 68_M1_BTS_0

description: muscle.exon.csv


title: 67_M1_F1_1

description: muscle.exon.csv


title: 64_M1_F1_1

description: muscle.exon.csv


title: 66_M1_CTS_0

description: muscle.exon.csv


title: 63_M1_CTS_0

description: muscle.exon.csv


title: 77_M1_CTS_0

description: muscle.exon.csv


title: 60_M1_BTS_0

description: muscle.exon.csv


title: 57_M1_CTS_0

description: muscle.exon.csv


title: MDA-MB-231 Cells GNE140 Replicate1

type: RNA

city: Tallahassee

first: Elizabeth

middle: A

last: Mazzio

state: Florida

address: 1515 MLK Blvd

department: College of Pharmacy & Pharmaceutical Science

institute: Florida Agricultural & Mechanical University

description: Gene expression data from MDA-MB-232 cells grown under variable experimental treatment

hyb_protocol: Hybrization was conducted according to manufacturer's instructions as per the GeneChipTM WT PLUS Reagent Manual for Whole Transcript (WT) Expression Arrays. (Affymetrix, ThermoFisher Scientific).

scan_protocol: Arrays were scanned with GeneAtlas Imaging station scanner  (Affymetrix, ThermoFisher Scientific)

data_processing: The data was processed using Affymetrix expression console and evaluated by Affymetrix transcription console software (Affymetrix, ThermoFisher Scientific)

label: Biotin

source_name: MDA-MB-231 ATCC® HTB-26™ cells -GNE-140 50 uM

label_protocol: cDNA was labeled using according to manufacturer's instructions as per the GeneChipTM WT PLUS Reagent Manual for Whole Transcript (WT) Expression Arrays. (Affymetrix, ThermoFisher Scientific).

growth_protocol: MDA-MB-231 cells were cultured in Dulbecco’s Modified Eagle’s Medium - high glucose with 4500 mg/L glucose, L-glutamine, sodium pyruvate, and sodium bicarbonate, supplemented with 10% FBS and 100 U/ml penicillin G sodium /100 μg/ml streptomycin sulfate. Cells were grown at 37°C with 95% air and 5% CO2 and sub-cultured every three to five days.

extract_protocol: After treatment, cells were washed three times in HBSS, rapidly frozen and stored at -80 C. Total RNA was isolated/ purified using the TRIzol/chloroform method, quality was assessed and concentration was equalized to 82ng/ul in nuclease free water

treatment_protocol: GM-453, GNE-140 and Paclitaxel were dissolved in DMSO [20mg/mL] prior to dilution in culture media. For whole transcriptome microarray studies, we first established a GL50 (growth inhibition curve)  in fully viable cells using GM-453 and Paclitaxel over a 7 day experimental period and inhibition of lactic acid production by GNE140. A single concentration for microarray analysis was determined for  compounds at non-toxic , fully effective biologically effective concentrations, established at 1ug/mL Paclitaxel, 5 ug/ml GM453 and 50uM of GNE-140.  Cells were treated for 36 hours and , then rapidly washed in HBSS 3x, spun and frozen at -80C.

value: mammary gland/breast; derived from metastatic site:pleural effusion

tag: cell line


title: 53_M1_BTS_1

description: muscle.exon.csv

tag: tissue


title: MDA-MB-231 Cells GNE140 Replicate3

description: Gene expression data from MDA-MB-234 cells grown under variable experimental treatment


title: MDA-MB-231 Cells GNE140 Replicate2

description: Gene expression data from MDA-MB-233 cells grown under variable experimental treatment


title: 49_M1_F1_0

description: muscle.exon.csv


title: 45_M1_F1_0

description: muscle.exon.csv


title: MDA-MB-231 Cells GM453 Replicate3

description: Gene expression data from MDA-MB-231 cells grown under variable experimental treatment

source_name: MDA-MB-231 ATCC® HTB-26™ cells -GM-453 5ug/ml


title: 59As9 PLEKHA5 siRNA #1

city: TOKYO

first: Hideki

last: Yamaguchi

address: 2-2, KANDASURUGADAI, CHIYODA-KU

department: Cancer Cell Research

institute: Sasaki Institute

description: Gene expression data from 58As9 transfected with siRNA against PLEKHA5 #1.

hyb_protocol: Approximately 5.5 microgram of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45 degrees Celsius for 16 hour.

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: Array data export processing and analysis was performed using Affymetrix GeneChip Command Console Software (AGCC).

label: biotin

source_name: 58As9 transfected with PLEKHA5 siRNA #1

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit.

growth_protocol: 58As9 cells were cultured in RPMI-1640 medium supplemented with 10 % fetal bovine serum and antibiotics at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol: Total RNA was purified using an RNeasy Mini kit (Qiagen), according to the manufacturer’s instructions.

treatment_protocol: 58As9 cells were transfected with control or PLEKHA5 siRNA at 20 nM and were harvested 1 day after transfection for RNA extraction.

value: stomach


title: WTd10-1

tag: time

value: ZT 8

value: wild type


title: 59As9 control siRNA

description: Gene expression data from 58As9 transfected with control siRNA.

source_name: 58As9 transfected with control siRNA


title: MDA-MB-231 Cells Paclitaxel Replicate1

source_name: MDA-MB-231 ATCC® HTB-26™ cells -Paclitaxel 1ug/ml

value: Paclitaxel


title: MDA-MB-231 Cells GM453 Replicate2


title: 59As9 PLEKHA5 siRNA #2

description: Gene expression data from 58As9 transfected with siRNA against PLEKHA5 #2.

source_name: 58As9 transfected with PLEKHA5 siRNA #2


title: 38_M1_BTS_1

description: muscle.exon.csv


title: 30_M1_F1_1

description: muscle.exon.csv

value: BTSbc


title: 44_M1_F1_1

description: muscle.exon.csv


title: 52_M1_F1_0

description: muscle.exon.csv


title: tms2_zh043

city: Moscow

first: Alexey

middle: Igorevich

last: Kalinkin

state: Russia

address: Moskvorechie st., 1

department: Epigenetics

country: Russia

institute: RCMG

library_source: genomic

data_processing:
Basecalls performed using Ion Torrent Suite 4.0
XmaI-RRBS reads were aligned to the hg19 genome assembly using Bismark v0.12.2 with bowtie2 v2.2.3 with settings --non_directional -L 24 --rdg 0,3 --rfg 0,3.
Data were filtered to remove artificial methylation using custom script
Methylation state called using bismark_methylation_extractor
Genome_build: hg19
Supplementary_files_format_and_content: .cov files were generated using bismark_methylation_extractor. Column headers are: Chromosome, Start position, End Position, Methylation percentage, Count of methylated cytosines and Count of unmethylated cytosines.

molecule: genomic DNA

source_name: Breast

extract_protocol:
Phenol:chloroform protocol after proteinase K treatment
XmaI-RRBS protocol as in: Tanas AS, Borisova ME, Kuznetsova EB et al. Rapid and affordable genome-wide bisulfite DNA sequencing by XmaI-reduced representation bisulfite sequencing. Epigenomics. 9 (6), 833-847 (2017).

value: LumB Breast Cancer


title: tms2_s088


title: MDA-MB-231 Cells GM453 Replicate1


title: MDA-MB-231 Cells Control  Replicate3

source_name: MDA-MB-231 ATCC® HTB-26™ cells - No treatment


title: MDA-MB-231 Cells Paclitaxel Replicate2


title: tms2_k104


title: 23_M1_F1_0

description: muscle.exon.csv

value: Muscle Tissue (Leg)


title: 25_M1_F1_0

description: muscle.exon.csv


title: 24_M1_F1_0

description: muscle.exon.csv


title: MDA-MB-231 Cells Control  Replicate2


title: 22_M1_F1_1

description: muscle.exon.csv


title: MDA-MB-231 Cells Control  Replicate4

source_name: MDA-MB-231 ATCC® HTB-27™ cells - No treatment


title: tms2_k069


title: tms2_v077


title: MDA-MB-231 Cells Control  Replicate1


title: 26_M1_BTS_0

description: muscle.exon.csv


title: NTC_2c rep2

value: early embryo

value: 2-cell embryo

value: SCNT

value: normal donor cell


title: 20_M1_BTS_1

description: muscle.exon.csv

value: Female

value: Treatment

value: BTS


title: tms2_s059


title: tms2_c063


title: tms2_d071


title: 16_M1_F1_1

description: muscle.exon.csv


title: 19_M1_F1_0

description: muscle.exon.csv

value: Control


title: 17_M1_F1_1

description: muscle.exon.csv


title: tms2_b112


title: 14_M1_CTS_1

description: muscle.exon.csv

value: Male

value: CTS


title: 13_M1_CTS_1

description: muscle.exon.csv


title: tms2_aUNKN1


title: tms2_k078


title: tms2_b070


title: tms044_resequenced

description: sample re-sequenced to achieve better read quality


title: WJF_LSY2

city: Guangzhou

first: Jufang

last: Wang

address: Guangzhou Higher Education Mega Center, Panyu District, Guangzhou

department: School of Bioscience and Bioengineering

institute: South China University of Technology

data_processing:
Illumina Casava software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using fastx, then mapped to R20291 whole genome using FANSe2.
The readcounts were calculated, and differential expression analysis for RNA-seq data was performed using edgeR.
Genome_build: FN545816.1
Supplementary_files_format_and_content: Excel files include Genome annotation (Gene ID, Gene Name), Raw Counts (con,cys), CPM (con,cys), Statistics (cys/con) for samples from 4 h, 8 h or 12 h indepedenely.

organism: Clostridioides difficile R20291

source_name: Clostridioides difficile R20291

growth_protocol: 37 °C,anaerobic atmosphere (10% H2, 5% CO2, and 85% N2)

extract_protocol:
Total RNA was extracted from the collected cell pellets using the RNAprep Pure Cell/Bacteria Kit (TIANGEN),rRNA was removed from total RNA using the Ribo-Zero rRNA Removal kit (Gram-Postive Bacteria)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Overnight cultured Clostridium difficile R20291 cells were inoculated into TY broth or TY broth supplied with 5mM cysteine. After cultured for 4 hours,8 hours and 12 hours, the C. difficile cells were harvested by centrifugation at 4000 g for 10 min at 4 °C.

tag: strain

tag: culture conditions

value: treated with cysteine for 12h


title: WJF_LSC1

value: untreated with cysteine for 12h


title: tms031_resequenced


title: 12_M1_BTS_1

description: muscle.exon.csv


title: WJF_MSY1

value: wild type

value: treated with cysteine for 8h


title: WJF_MSC2

value: untreated with cysteine for 8h


title: 11_M1_F1_1

description: muscle.exon.csv


title: tms022

value: LumB Breast Cancer


title: WJF_MSC1


title: WJF_MSY2


title: WJF_ISY2

value: treated with cysteine for 4h


title: 09_M1_F1_0

description: muscle.exon.csv

value: Muscle Tissue (Leg)


title: WJF_ISY1


title: tms096


title: WJF_ISC1

value: untreated with cysteine for 4h


title: WJF_LSY1


title: 08_M1_F1_0

description: muscle.exon.csv


title: 07_M1_CTS_1

description: muscle.exon.csv


title: tms090


title: 06_M1_F1_1

description: muscle.exon.csv


title: WJF_ISC2


title: 05_M1_F1_0

description: muscle.exon.csv


title: tms089


title: WJF_LSC2


title: tms080


title: 02_M1_F1_1

description: muscle.exon.csv


title: HepG2_siPVT1-1

city: Jinan

first: Jupeng

last: Yuan

state: Shandong

address: Jiyan road 440#

department: Cancer Research Center

institute: Shandong Cancer Hospital Affiliated to Shandong University

hyb_protocol: HOA v7.1 arrays were pre-heat at 60℃ for 10 mins, rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, 5 µg Cy5-labeled aRNA was hybridize on HOA in the presentation of the Phalanx OneArray hybridization buffer in duplication.

scan_protocol: The arrays were scanned by Agilent Scanner G2505C 0.1 XDR protocol and quantify the fluoresence intensity.

data_processing: Data processing was performed and calculated by Rosetta Resolver® (Rosetta Biosoftware). The probes that ﬂag <0 in all samples were filtered out, then normalized by median scaling method between technical replicates. Pair-wise comparisons between samples were calculated by Rosetta error model and presented by log2 ratio and p-value.

label_protocol: 1 µg of total RNA was reverse-transcribed and amplified using MessageAmpTM aRNA Amplification Kit (Ambion).  Indirect labeling the aa-UTP whereon by NHS-CyDye (Cy5, Amershan).

growth_protocol: Human HepG2 cells were cultured in RPMI-1640 media supplied with 10% fetal bovine serum (Hyclone) at 37°C with 5% CO2.

extract_protocol: RNA extraction by Trizol Reagent (Invitrogen). RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, A260/A230≧1.5, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧6).

treatment_protocol: miRNA-214 mimics and small interfering RNA (siRNA) duplexes (siPVT1-1, siPVT1-2) were products of Genepharma (Shanghai, China). The negative control RNA duplex (NC) for miRNA mimics, miRNA inhibitors or siRNAs (Genepharma, Shanghai, China) was nonhomologous to any human genome sequence. All small RNAs were transfected into HepG2 cells with INTERFERin® (Polyplus).

tag: miRNA transfection


title: tms088


title: HepG2_siPVT1-2


title: 04_M1_CTS_1

description: muscle.exon.csv


title: tms053


title: HepG2_miR214-mimic

value: miR214 mimics


title: HepG2_siNC

value: NC control


title: 87_B1_F1_1

description: brain.exon.csv

source_name: Whole Brain Tissue

value: Whole Brain Tissue


title: 03_M1_F1_0

description: muscle.exon.csv

value: Female


title: K562 30min TBP CUT&RUN

city: Ithaca

first: Charles

middle: G

last: Danko

address: Hungerford Hill Rd

institute: Baker Institute

description: i7 index: GATCAG

data_processing:
Library strategy: CUT&RUN
Data from each experiment was aligned to genome assemblies as following:
i.) MNase ChIP-seq reads were aligned to hg19 merged to D.iulia assembly (Lewis et al., 2019). All positions with sequence similarity between the two genomes were masked using bedtools maskfasta;
ii.) ChRO-seq data was aligned to hg19 merged to the D.melanogaster dm3 genome assembly. All positions with sequence similarity between the two genomes were masked using bedtools maskfasta;
iii.) CUT&RUN was aligned to hg19 merged to S.cerevisiae SacCer1;
iv.) ATAC-seq was only aligned to hg19.
Masking hg19 was performed with BedTools maskfasta (Quinlan and Hall, 2010). All sequencing data was aligned using bowtie2 version 2.3.5.1 (Langmead and Salzberg, 2012) with parameters: --no-discordant --no-dovetail --no-unal --no-mixed. Reads mapping multiple times were removed with samtools view (Li et al., 2009), parameter: -F 256. The remaining reads were converted to paired-end BigWig files using BedTools and visualized in the WashU genome browser version 46.2 (Li et al., 2019; Zhou et al., 2011).
Supplementary_files_format_and_content: We only provide BigWig files for untreated samples due to normalization, which was performed from BAM files to preserve the identity of each read pair. In our experiments, both the human and spike-in samples were mixed and treated with MNase together, before the antibody incubation. To correct IP signals for biases in MNase cutting efficiency, handling, and other errors, we used the spike adjusted procedure (SAP) method (Bonhoure et al., 2014). We assume that ChIP-seq data reflects a linear combination of three factors: signal from the mark of interest, background which may be partially correlated with the mark, and random noise. SAP assumes that the background signals should be the same in treated and untreated samples and enforces this assumption by subtracting the expected background read count observed in the input.

source_name: Human K562 cells

growth_protocol: K562 cells (ATCC, CCL-243) were cultured at 37oC, 5% CO2  at a density between 0.3-1 x 106cells/mL in RPMI medium (VWR 45000-396) topped up with 10% Fetal Bovine Serum (Genesee Scientific, cat: #25-514).  Cells were split at a consistent interval of 3 days, when the cells reach 106 cells/mL.

extract_protocol: Library prep was performed using the NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645S). The barcodes used were purchased from NEB:NEBNext Multiplex Oligos for Illumina (E6440S).

treatment_protocol: 24h prior to Triptolide treatment, K562 cells were resuspended in fresh (RPMI) medium at a density of 0.6 x 106 cells/mL. On the day of the experiment, cells were recounted, aliquoted in equal cell numbers to 6 T-100 ThermoFisher Tissue Culture Flasks (each flask corresponding to one time point) and treated with Triptolide (Sigma-Aldrich, T3652-1MG) to a final concentration of 500 nM Triptolide. The Triptolide treatment was performed for 0 min, 15 min, 30 min, 1h, and respectively 4h.

value: Triptolide treated

tag: time point

tag: replicate


title: K562 0h TBP CUT&RUN

description: i7 index: CAGATC

value: untreated


title: FAM_3: shRNA for FAM83H-AS1

city: CDMX

first: Alberto

last: Cedro-Tanda

state: CMDX

address: Periferico sur #4809

country: Mexico

institute: INMEGEN

description: SST-RMA expression value derived from Expression Console software 3.0 (Affymetrix)

hyb_protocol: Samples were hybridized with GeneChip Human Transcriptome Array 2.0 Arrays (Affymetrix)

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix). GeneChips were scanned using The Genechip Scanner 3000 7G (Affymetrix , Santa Clara, USA).

data_processing: Array signal intensitive were analyzed with the Affymetrix Expression Console using Signal Space Transformation-Robust Multichip Analysis (SST-RMA) for the background correction.

source_name: Treatment

label_protocol: WT Plus Reagent Kit were used to generate the biotinylated cRNA starting from 100ng of total RNA according to the manufacturer (Manual Target preparation for GeneChip Whole transcript (WT) expression arrays, Affymetrix).

growth_protocol: The MCF7 cell line was grown in DMEM + 10% fetal bovine serum prior to treatment with shRNAs

extract_protocol: Trizol method was used to extract the total RNA

treatment_protocol: MCF7 cell line was transfected with 3ug of plasmid to silence FAM83H-AS1. As negative control (NC) a shRNA directed to GFP was transfected.

tag: genotype/variation

value: FAM83H-AS1 knockdown


title: K562 15min TBP CUT&RUN

description: i7 index: ACTTGA


title: tms094


title: tms077


title: NC_1: Negative Control shRNA_1

source_name: Negative Control

value: control


title: tms078


title: K562 0h ChRO-seq

description: i7 index: TCCGCGAA

data_processing:
Library strategy: ChRO-seq
Data from each experiment was aligned to genome assemblies as following:
i.) MNase ChIP-seq reads were aligned to hg19 merged to D.iulia assembly (Lewis et al., 2019). All positions with sequence similarity between the two genomes were masked using bedtools maskfasta;
ii.) ChRO-seq data was aligned to hg19 merged to the D.melanogaster dm3 genome assembly. All positions with sequence similarity between the two genomes were masked using bedtools maskfasta;
iii.) CUT&RUN was aligned to hg19 merged to S.cerevisiae SacCer1;
iv.) ATAC-seq was only aligned to hg19.
Masking hg19 was performed with BedTools maskfasta (Quinlan and Hall, 2010). All sequencing data was aligned using bowtie2 version 2.3.5.1 (Langmead and Salzberg, 2012) with parameters: --no-discordant --no-dovetail --no-unal --no-mixed. Reads mapping multiple times were removed with samtools view (Li et al., 2009), parameter: -F 256. The remaining reads were converted to paired-end BigWig files using BedTools and visualized in the WashU genome browser version 46.2 (Li et al., 2019; Zhou et al., 2011).
Supplementary_files_format_and_content: We only provide BigWig files for untreated samples due to normalization, which was performed from BAM files to preserve the identity of each read pair. In our experiments, both the human and spike-in samples were mixed and treated with MNase together, before the antibody incubation. To correct IP signals for biases in MNase cutting efficiency, handling, and other errors, we used the spike adjusted procedure (SAP) method (Bonhoure et al., 2014). We assume that ChIP-seq data reflects a linear combination of three factors: signal from the mark of interest, background which may be partially correlated with the mark, and random noise. SAP assumes that the background signals should be the same in treated and untreated samples and enforces this assumption by subtracting the expected background read count observed in the input.


title: 91_B1_F1_1

description: brain.exon.csv

value: Treatment

tag: genotype


title: K562 1h ChRO-seq

description: i7 index: TCTCGCGC


title: K562 4h ChRO-seq

description: i7 index: AGCGATAG


title: 86_B1_F1_1

description: brain.exon.csv


title: tms047


title: FAM_2: shRNA for FAM83H-AS1


title: FAM_1: shRNA for FAM83H-AS1


title: tms050


title: K562 0h H3 CUT&RUN replicate 3

description: i7 index: TruSeq 10


title: NC_2: Negative Control shRNA_2


title: NC_3: Negative Control shRNA_3


title: 90_B1_BTS_1

description: brain.exon.csv

value: Male

value: BTS


title: K562 4h H3 CUT&RUN replicate 2

description: i7 index: TruSeq 8


title: 83_B1_CTS_0

description: brain.exon.csv

value: Control

value: CTS


title: K562 4h H3 CUT&RUN replicate 3

description: i7 index: TruSeq 12


title: K562 0h H3 CUT&RUN replicate 2

description: i7 index: TruSeq 6


title: 84_B1_F1_1

description: brain.exon.csv

value: CTSbc


title: tms042

value: LumB Breast Cancer


title: K562 1h H3 CUT&RUN replicate 3

description: i7 index: TruSeq 11


title: tms048


title: K562 1h ATAC replicate 1

description: i7 index: CATGCC

data_processing:
Data from each experiment was aligned to genome assemblies as following:
i.) MNase ChIP-seq reads were aligned to hg19 merged to D.iulia assembly (Lewis et al., 2019). All positions with sequence similarity between the two genomes were masked using bedtools maskfasta;
ii.) ChRO-seq data was aligned to hg19 merged to the D.melanogaster dm3 genome assembly. All positions with sequence similarity between the two genomes were masked using bedtools maskfasta;
iii.) CUT&RUN was aligned to hg19 merged to S.cerevisiae SacCer1;
iv.) ATAC-seq was only aligned to hg19.
Masking hg19 was performed with BedTools maskfasta (Quinlan and Hall, 2010). All sequencing data was aligned using bowtie2 version 2.3.5.1 (Langmead and Salzberg, 2012) with parameters: --no-discordant --no-dovetail --no-unal --no-mixed. Reads mapping multiple times were removed with samtools view (Li et al., 2009), parameter: -F 256. The remaining reads were converted to paired-end BigWig files using BedTools and visualized in the WashU genome browser version 46.2 (Li et al., 2019; Zhou et al., 2011).
Supplementary_files_format_and_content: We only provide BigWig files for untreated samples due to normalization, which was performed from BAM files to preserve the identity of each read pair. In our experiments, both the human and spike-in samples were mixed and treated with MNase together, before the antibody incubation. To correct IP signals for biases in MNase cutting efficiency, handling, and other errors, we used the spike adjusted procedure (SAP) method (Bonhoure et al., 2014). We assume that ChIP-seq data reflects a linear combination of three factors: signal from the mark of interest, background which may be partially correlated with the mark, and random noise. SAP assumes that the background signals should be the same in treated and untreated samples and enforces this assumption by subtracting the expected background read count observed in the input.


title: K562 4h ATAC replicate 1

description: i7 index: CCTCTC


title: K562 1h H3 CUT&RUN replicate 2

description: i7 index: TruSeq 7


title: tms046


title: K562 1h H3 CUT&RUN replicate 1

description: i7 index: AGTTCC


title: 77_B1_CTS_0

description: brain.exon.csv


title: K562 0h ATAC replicate 1

description: i7 index: TTCTGC


title: tms044


title: K562 0h H3 CUT&RUN replicate 1

description: i7 index: TAGCTT


title: 75_B1_BTS_1

description: brain.exon.csv


title: K562 4h H3 CUT&RUN replicate 1

description: i7 index: CCGTCC


title: tms035


title: tms033


title: 78_B1_BTS_1

description: brain.exon.csv


title: K562 1h Input replicate 2 resequence

description:
i7 index: GTCAGTCA
i5 index: TAATGCCG


title: K562 1h Input replicate 1 resequence

description:
i7 index: GACGAACT
i5 index: TCGCATTG


title: K562 4h Input replicate 2 resequence

description:
i7 index: CCTTCCAT
i5 index: ATTGCGTG


title: K562 0h Input replicate 1 resequence

description:
i7 index: CCGCTTAA
i5 index: ACGATGAC


title: 73_B1_F1_0

description: brain.exon.csv


title: 76_B1_BTS_1

description: brain.exon.csv


title: K562 0h Input replicate 2 resequence

description:
i7 index: AACCAGAG
i5 index: AACCGAAG


title: K562 4h Input replicate 1 resequence

description:
i7 index: TCCACGTT
i5 index: GTTCAACC


title: tms032